Sample records for crystal structure particle

  1. Crystal structure of an H\\/ACA box ribonucleoprotein particle

    Microsoft Academic Search

    Ling Li; Keqiong Ye

    2006-01-01

    H\\/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. They also participate in eukaryotic ribosomal RNA processing and are a component of vertebrate telomerases. Here we report the crystal structure, at 2.3Å resolution, of an entire archaeal H\\/ACA RNP consisting of proteins Cbf5, Nop10, Gar1 and L7ae, and a single-hairpin H\\/ACA

  2. Crystal Structure and Morphology of Fine Particles of Vanadium Silicides

    Microsoft Academic Search

    Tsutomu Ishimasa; Yasushige Fukano

    1983-01-01

    In this experiment, fine particles of various vanadium silicides were made by the gas-evaporation technique. The structure and morphology of the particles were observed by electron microscope. The A15 structure was found to appear at 20.0 and 25.0 at.%Si, while the D88 and D8m structures appeared at 35.2 and 37.5 at.%Si. The particles were surrounded by crystallographic planes with low

  3. Dependence of the crystal structure on particle size in barium titanate

    Microsoft Academic Search

    Kenji Uchino; T. Hirose; E. Sadanaga

    1989-01-01

    The authors discuss the effect of the sample particle size on the crystal structure and the Curie temperature of BaTiOâ powder investigated in the particle size range 0.1 to 1.0 μm. The transformation from tetragonal to cubic symmetry occurs at a critical particle size of 0.12 μm at room temperature, and the Curie temperature drops below room temperature at the

  4. Structural changes in the 6CHBT liquid crystal doped with spherical, rodlike, and chainlike magnetic particles.

    PubMed

    Kopcanský, Peter; Tomasovicová, Natália; Koneracká, Martina; Závisová, Vlasta; Timko, Milan; Dzarová, Anezka; Sprincová, Adriana; Eber, Nándor; Fodor-Csorba, Katalin; Tóth-Katona, Tibor; Vajda, Aniko; Jadzyn, Jan

    2008-07-01

    In this work the 4-(trans- 4'-n -hexylcyclohexyl)-isothiocyanatobenzene (6CHBT) liquid crystal was doped with differently shaped magnetite nanoparticles. The structural changes were observed by capacitance measurements and showed significant influence of the shape and size of the magnetic particles on the magnetic Fréedericksz transition. For the volume concentration phi= 2 x 10(-4) of the magnetic particles, the critical magnetic field was established for the pure liquid crystal, and for liquid crystals doped with spherical, chainlike, and rodlike magnetic particles. The influence of the magnetic field depends on the type of anchoring, which is characterized by the density of anchoring energy and by the initial orientation between the liquid crystal molecules and the magnetic moment of the magnetic particles. The experimental results indicated soft anchoring in the case of spherical magnetic particles and rigid anchoring in the case of rodlike and chainlike magnetic particles, with parallel initial orientation between the magnetic moments of the magnetic particles and director. PMID:18763968

  5. Three-dimensional photonic crystal structures achieved with self-organization of colloidal particles

    Microsoft Academic Search

    J. Song; H. Sun; Y. Xu; Y. Fu; S. Matsuo; H. Misawa; G. Du

    2000-01-01

    Three-dimensional polystyrene\\/air photonic crystal structure with different particle diameters: 200, 270 and 340 nm was achieved. Strong photonic band gap effect reflected with transmission minimum down to -16 dB was observed. The central wavelengths of the valleys of spectra were well fitted with theoretical calculation. The augmentation of band gap effect versus particle diameter was attributed to an improved self-assembling

  6. Tuning the colloidal crystal structure of magnetic particles by external field.

    PubMed

    Pal, Antara; Malik, Vikash; He, Le; Erné, Ben H; Yin, Yadong; Kegel, Willem K; Petukhov, Andrei V

    2015-02-01

    Manipulation of the self-assembly of magnetic colloidal particles by an externally applied magnetic field paves a way toward developing novel stimuli responsive photonic structures. Using microradian X-ray scattering technique we have investigated the different crystal structures exhibited by self-assembly of core-shell magnetite/silica nanoparticles. An external magnetic field was employed to tune the colloidal crystallization. We find that the equilibrium structure in absence of the field is random hexagonal close-packed (RHCP) one. External field drives the self-assembly toward a body-centered tetragonal (BCT) structure. Our findings are in good agreement with simulation results on the assembly of these particles. PMID:25510837

  7. The stability of a crystal with diamond structure for patchy particles with tetrahedral symmetry

    NASA Astrophysics Data System (ADS)

    Noya, Eva G.; Vega, Carlos; Doye, Jonathan P. K.; Louis, Ard A.

    2010-06-01

    The phase diagram of model anisotropic particles with four attractive patches in a tetrahedral arrangement has been computed at two different values of the range of the potential, with the aim of investigating the conditions under which a diamond crystal can be formed. We find that the diamond phase is never stable for our longer-ranged potential. At low temperatures and pressures, the fluid freezes into a body-centered-cubic solid that can be viewed as two interpenetrating diamond lattices with a weak interaction between the two sublattices. Upon compression, an orientationally ordered face-centered-cubic crystal becomes more stable than the body-centered-cubic crystal, and at higher temperatures, a plastic face-centered-cubic phase is stabilized by the increased entropy due to orientational disorder. A similar phase diagram is found for the shorter-ranged potential, but at low temperatures and pressures, we also find a region over which the diamond phase is thermodynamically favored over the body-centered-cubic phase. The higher vibrational entropy of the diamond structure with respect to the body-centered-cubic solid explains why it is stable even though the enthalpy of the latter phase is lower. Some preliminary studies on the growth of the diamond structure starting from a crystal seed were performed. Even though the diamond phase is never thermodynamically stable for the longer-ranged model, direct coexistence simulations of the interface between the fluid and the body-centered-cubic crystal and between the fluid and the diamond crystal show that at sufficiently low pressures, it is quite probable that in both cases the solid grows into a diamond crystal, albeit involving some defects. These results highlight the importance of kinetic effects in the formation of diamond crystals in systems of patchy particles.

  8. The stability of a crystal with diamond structure for patchy particles with tetrahedral symmetry.

    PubMed

    Noya, Eva G; Vega, Carlos; Doye, Jonathan P K; Louis, Ard A

    2010-06-21

    The phase diagram of model anisotropic particles with four attractive patches in a tetrahedral arrangement has been computed at two different values of the range of the potential, with the aim of investigating the conditions under which a diamond crystal can be formed. We find that the diamond phase is never stable for our longer-ranged potential. At low temperatures and pressures, the fluid freezes into a body-centered-cubic solid that can be viewed as two interpenetrating diamond lattices with a weak interaction between the two sublattices. Upon compression, an orientationally ordered face-centered-cubic crystal becomes more stable than the body-centered-cubic crystal, and at higher temperatures, a plastic face-centered-cubic phase is stabilized by the increased entropy due to orientational disorder. A similar phase diagram is found for the shorter-ranged potential, but at low temperatures and pressures, we also find a region over which the diamond phase is thermodynamically favored over the body-centered-cubic phase. The higher vibrational entropy of the diamond structure with respect to the body-centered-cubic solid explains why it is stable even though the enthalpy of the latter phase is lower. Some preliminary studies on the growth of the diamond structure starting from a crystal seed were performed. Even though the diamond phase is never thermodynamically stable for the longer-ranged model, direct coexistence simulations of the interface between the fluid and the body-centered-cubic crystal and between the fluid and the diamond crystal show that at sufficiently low pressures, it is quite probable that in both cases the solid grows into a diamond crystal, albeit involving some defects. These results highlight the importance of kinetic effects in the formation of diamond crystals in systems of patchy particles. PMID:20572725

  9. The stability of a crystal with diamond structure for patchy particles with tetrahedral symmetry

    E-print Network

    Eva G. Noya; Carlos Vega; Jonathan P. K. Doye; Ard A. Louis

    2010-05-28

    The phase diagram of model anisotropic particles with four attractive patches in a tetrahedral arrangement has been computed at two different values for the range of the potential, with the aim of investigating the conditions under which a diamond crystal can be formed. We find that the diamond phase is never stable for our longer-ranged potential. At low temperatures and pressures, the fluid freezes into a body-centred-cubic solid that can be viewed as two interpenetrating diamond lattices with a weak interaction between the two sublattices. Upon compression, an orientationally ordered face-centred-cubic crystal becomes more stable than the body-centred-cubic crystal, and at higher temperatures a plastic face-centered-cubic phase is stabilized by the increased entropy due to orientational disorder. A similar phase diagram is found for the shorter-ranged potential, but at low temperatures and pressures, we also find a region over which the diamond phase is thermodynamically favored over the body-centred-cubic phase. The higher vibrational entropy of the diamond structure with respect to the body-centred-cubic solid explains why it is stable even though the enthalpy of the latter phase is lower. Some preliminary studies on the growth of the diamond structure starting from a crystal seed were performed. Even though the diamond phase is never thermodynamically stable for the longer-ranged model, direct coexistence simulations of the interface between the fluid and the body-centred-cubic crystal and between the fluid and the diamond crystal show that, at sufficiently low pressures, it is quite probable that in both cases the solid grows into a diamond crystal, albeit involving some defects. These results highlight the importance of kinetic effects in the formation of diamond crystals in systems of patchy particles.

  10. Crystal structures of small Al-rich Fe alloy particles formed by a gas-evaporation technique

    Microsoft Academic Search

    M. Tsuchimori; T. Ishimasa; Y. Fukano

    1992-01-01

    Crystal structures in small Al-rich Fe particles were studied by powder X-ray diffraction and transmission electron microscopy. The specimens of the small particles were made by evaporating an Al alloy material containing 5.0-33.3 at.% Fe in Xe gas at a pressure of 3.3 × 10 Pa. The small particles were 70-150 nm in diameter. In the particles, f.c.c. Al-Fe solid

  11. Crystal structures of enterovirus 71 (EV71) recombinant virus particles provide insights into vaccine design.

    PubMed

    Lyu, Ke; Wang, Guang-Chuan; He, Ya-Ling; Han, Jian-Feng; Ye, Qing; Qin, Cheng-Feng; Chen, Rong

    2015-02-01

    Hand-foot-and-mouth disease (HFMD) remains a major health concern in the Asia-Pacific regions, and its major causative agents include human enterovirus 71 (EV71) and coxsackievirus A16. A desirable vaccine against HFMD would be multivalent and able to elicit protective responses against multiple HFMD causative agents. Previously, we have demonstrated that a thermostable recombinant EV71 vaccine candidate can be produced by the insertion of a foreign peptide into the BC loop of VP1 without affecting viral replication. Here we present crystal structures of two different naturally occurring empty particles, one from a clinical C4 strain EV71 and the other from its recombinant virus containing an insertion in the VP1 BC loop. Crystal structure analysis demonstrated that the inserted foreign peptide is well exposed on the particle surface without significant structural changes in the capsid. Importantly, such insertions do not seem to affect the virus uncoating process as illustrated by the conformational similarity between an uncoating intermediate of another recombinant virus and that of EV71. Especially, at least 18 residues from the N terminus of VP1 are transiently externalized. Altogether, our study provides insights into vaccine development against HFMD. PMID:25492868

  12. Artificial silver sulfide Ag2S: Crystal structure and particle size in deposited powders

    NASA Astrophysics Data System (ADS)

    Sadovnikov, S. I.; Gusev, A. I.; Rempel, A. A.

    2015-07-01

    Chemical deposition from aqueous solutions of silver nitrate and sodium sulfide was used for synthesis of coarse-crystalline and nanocrystalline silver sulfide Ag2S powders. Sodium citrate was used as a complexing and stabilizing agent during synthesis. X-ray diffraction study shows that synthesized Ag2S powders have monoclinic (space group P21/c) ?-Ag2S acanthite type crystal structure. The unit cell of artificial monoclinic silver sulfide Ag2S contains four Ag2S formula units and has the following parameters: a = 0.42264 nm, b = 0.69282 nm, c = 0.95317 nm and ? = 125.554°. The size of silver sulfide particles in deposited powders was estimated by the X-ray diffraction and BET methods. By varying the ratio between the concentrations of reagents in the initial reaction mixture it is possible to deposit Ag2S nanoparticles with average size ranging in the interval from ?1000 to ?30 nm. Ag2S nanopowders have no deformation distortions of the crystal lattice practically because the microstrains ? in the synthesized powders do not exceed 0.15%. All the Ag2S powders with different particle size have an identical morphology.

  13. Low temperature synthesis, crystal structure and thermal stability studies of nanocrystalline VN particles

    SciTech Connect

    Gajbhiye, N.S. [Department of Chemistry, Indian Institute of Technology, Kanpur 208016, U.P. (India)]. E-mail: nsg@iitk.ac.in; Ningthoujam, R.S. [Department of Chemistry, Indian Institute of Technology, Kanpur 208016, U.P. (India); Chemistry Division, Bhabha Atomic Research Centre, Mumbai 400085 (India)

    2006-09-14

    The simultaneous thermal decomposition and nitridation of [VO(NH{sub 2}O){sub 2}Gly].H{sub 2}O complex in NH{sub 3} atmosphere at 723-973 K gives the nanocrystalline vanadium nitride (VN) having crystallite size of 8-32 nm. It shows cubic NaCl structure with lattice parameter of a = 4.137 nm. XRD pattern Rietveld analysis program for crystal structure of VN shows the space group-Fm3m. The particle sizes measured by BET and SEM techniques are in the range of 26-100 nm. The particles are spherical and distributed homogeneously and found larger than XRD crystallite size because of agglomeration of crystallites. The fundamental IR absorption of VN material is found at 995 cm{sup -1} which gives the force constant of 634.3 Nm{sup -1}. The electrical resistivity and magnetic studies show the superconducting to normal transition (T {sub c}) at 9.2 K. Thermal decomposition of VN is carried out in O{sub 2} atmosphere which goes through the formation of an oxynitride (V-N {sub p}-O {sub q}) intermediate phase up to 913 K. Finally, nanocrystalline V{sub 2}O{sub 5} is formed at 973 K. The V{sub 2}O{sub 5} has orthorhombic structure with lattice parameters of a = 11.537, b = 3.568 and c = 4.380 A and the XRD crystallite size of 10 nm.

  14. Effects of Mn on the crystal structure of ?-Al(Mn,Fe)Si particles in A356 alloys

    NASA Astrophysics Data System (ADS)

    Kim, Hyun You; Park, Tea Young; Han, Sang Won; Lee, Hyuck Mo

    2006-05-01

    In a commercial Al-7.0Si-0.38Mg cast alloy (A356) with 0.20 wt% Fe, added Mn modifies acicular ?-Al 5FeSi particles to less acicular ?-Al(Mn,Fe)Si in both crystallization and precipitation conditions. The crystal structure of ?-Al(Mn,Fe)Si changes from body-centered cubic (bcc)/ simple cubic (sc) to Pm3 structures in response to an increase in the bulk Mn content of the alloy. The ?-Al(Mn,Fe)Si particles (50-200 nm) precipitate during solution treatment and their precipitation temperature is about 485 °C in the as-cast condition.

  15. The crystal structure of the signal recognition particle in complex with its receptor.

    PubMed

    Ataide, Sandro F; Schmitz, Nikolaus; Shen, Kuang; Ke, Ailong; Shan, Shu-ou; Doudna, Jennifer A; Ban, Nenad

    2011-02-18

    Cotranslational targeting of membrane and secretory proteins is mediated by the universally conserved signal recognition particle (SRP). Together with its receptor (SR), SRP mediates the guanine triphosphate (GTP)-dependent delivery of translating ribosomes bearing signal sequences to translocons on the target membrane. Here, we present the crystal structure of the SRP:SR complex at 3.9 angstrom resolution and biochemical data revealing that the activated SRP:SR guanine triphosphatase (GTPase) complex binds the distal end of the SRP hairpin RNA where GTP hydrolysis is stimulated. Combined with previous findings, these results suggest that the SRP:SR GTPase complex initially assembles at the tetraloop end of the SRP RNA and then relocalizes to the opposite end of the RNA. This rearrangement provides a mechanism for coupling GTP hydrolysis to the handover of cargo to the translocon. PMID:21330537

  16. Research of the cirrus structure with the polarization lidar: parameters of particle orientation in crystal clouds

    Microsoft Academic Search

    Gennadii G. Matvienko; Ignaty V. Samokhvalov; Bruno V. Kaul

    2004-01-01

    The particles of upper clouds are ice crystals with various sizes and shapes. Under certain conditions they can be oriented in space. This circumstance leads to the significant anisotropy of light in cirrus clouds that should be taken into account when solving problems of radiation propagation through the atmosphere. Acquiring the information on parameters of particle orientation in ensembles of

  17. Structure of a single particle from scattering by many particles randomly oriented about an axis: toward structure solution without crystallization?

    NASA Astrophysics Data System (ADS)

    Saldin, D. K.; Shneerson, V. L.; Howells, M. R.; Marchesini, S.; Chapman, H. N.; Bogan, M.; Shapiro, D.; Kirian, R. A.; Weierstall, U.; Schmidt, K. E.; Spence, J. C. H.

    2010-03-01

    In this paper is demonstrated a complete algorithm for determining the electron density of an individual particle from diffraction patterns of many particles, randomly oriented about a single axis. The algorithm operates on angular correlations among the measured intensity distributions. We also demonstrate the ability to recover the angular correlation functions of a single particle from measured diffraction patterns.

  18. Single crystal structure analysis of a single Sm{sub 2}Fe{sub 17}N{sub 3} particle

    SciTech Connect

    Inami, Nobuhito, E-mail: nobuhito.inami@kek.jp; Takeichi, Yasuo; Saito, Kotaro; Sagayama, Ryoko; Kumai, Reiji; Ono, Kanta [High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801 (Japan); Ueno, Tetsuro [National Institute for Materials Science (NIMS), Tsukuba 305-0047 (Japan)

    2014-05-07

    We performed single crystal structure analysis of Sm{sub 2}Fe{sub 17}N{sub 3} using X-ray diffraction. A pick-up system combined with a micromanipulation tool driven by piezoelectric actuators and a microgripper was used. A single Sm{sub 2}Fe{sub 17}N{sub x} particle with the diameter of about 20??m was picked up, and X-ray diffraction was measured using an X-ray diffractometer at the synchrotron radiation beamline at the Photon Factory, KEK. Single crystal structure analysis of a Sm{sub 2}Fe{sub 17}N{sub 3} particle was performed and the structure was successfully determined from X-ray diffraction patterns. The space group and the lattice constants were determined to be R-3m (number sign166) a?=?b?=?8.7206?Å and c?=?12.6345?Å, respectively. Atomic positions of Sm and Fe atoms were accurately determined by single crystal structure analysis of only one particle.

  19. Crystal Structure and Prediction

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    The notion of structure is central to the subject of chemistry. This review traces the development of the idea of crystal structure since the time when a crystal structure could be determined from a three-dimensional diffraction pattern and assesses the feasibility of computationally predicting an unknown crystal structure of a given molecule. Crystal structure prediction is of considerable fundamental and applied importance, and its successful execution is by no means a solved problem. The ease of crystal structure determination today has resulted in the availability of large numbers of crystal structures of higher-energy polymorphs and pseudopolymorphs. These structural libraries lead to the concept of a crystal structure landscape. A crystal structure of a compound may accordingly be taken as a data point in such a landscape.

  20. The effect of V/III ratio and catalyst particle size on the crystal structure and optical properties of InP nanowires.

    PubMed

    Paiman, S; Gao, Q; Tan, H H; Jagadish, C; Pemasiri, K; Montazeri, M; Jackson, H E; Smith, L M; Yarrison-Rice, J M; Zhang, X; Zou, J

    2009-06-01

    InP nanowires were grown on 111B InP substrates by metal-organic chemical vapour deposition in the presence of colloidal gold particles as catalysts. Transmission electron microscopy and photoluminescence measurements were carried out to investigate the effects of V/III ratio and nanowire diameter on structural and optical properties. Results show that InP nanowires grow preferably in the wurtzite crystal structure than the zinc blende crystal structure with increasing V/III ratio or decreasing diameter. Additionally, time-resolved photoluminescence (TRPL) studies have revealed that wurtzite nanowires show longer recombination lifetimes of approximately 2500 ps with notably higher quantum efficiencies. PMID:19436086

  1. Crystal Lattice Structures

    NSDL National Science Digital Library

    This site provides an index of common crystal lattice structures--arrangements of atoms in a crystalline substance. The structures are indexed by Strukturbericht designation, Pearson symbol, space group, and prototype. Each structure is illustrated and accompanied by a brief description. The structure graphics can be viewed online, downloaded for external viewing, or manipulated in virtual space using a Java applet.

  2. The crystal structure of the third signal-recognition particle GTPase FlhF reveals a homodimer with bound GTP

    PubMed Central

    Bange, Gert; Petzold, Georg; Wild, Klemens; Parlitz, Richard O.; Sinning, Irmgard

    2007-01-01

    Flagella are well characterized as the organelles of locomotion and allow bacteria to react to environmental changes. The assembly of flagella is a multistep process and relies on a complex type III export machinery located in the cytoplasmic membrane. The FlhF protein is essential for the placement and assembly of polar flagella and has been classified as a signal-recognition particle (SRP)-type GTPase. SRP GTPases appeared early in evolution and form a unique subfamily within the guanine nucleotide binding proteins with only three members: the signal sequence-binding protein SRP54, the SRP receptor FtsY, and FlhF. We report the crystal structures of FlhF from Bacillus subtilis in complex with GTP and GMPPNP. FlhF shares SRP GTPase-specific features such as the presence of an N-terminal ?-helical domain and the I-box insertion. It forms a symmetric homodimer sequestering a composite active site that contains two head-to-tail arranged nucleotides similar to the heterodimeric SRP-targeting complex. However, significant differences to the GTPases of SRP and the SRP receptor include the formation of a stable homodimer with GTP as well as severe modifications and even the absence of motifs involved in regulation of the other two SRP GTPases. Our results provide insights into SRP GTPases and their roles in two fundamentally different protein-targeting routes that both rely on efficient protein delivery to a secretion channel. PMID:17699634

  3. The crystal structure of the third signal-recognition particle GTPase FlhF reveals a homodimer with bound GTP.

    PubMed

    Bange, Gert; Petzold, Georg; Wild, Klemens; Parlitz, Richard O; Sinning, Irmgard

    2007-08-21

    Flagella are well characterized as the organelles of locomotion and allow bacteria to react to environmental changes. The assembly of flagella is a multistep process and relies on a complex type III export machinery located in the cytoplasmic membrane. The FlhF protein is essential for the placement and assembly of polar flagella and has been classified as a signal-recognition particle (SRP)-type GTPase. SRP GTPases appeared early in evolution and form a unique subfamily within the guanine nucleotide binding proteins with only three members: the signal sequence-binding protein SRP54, the SRP receptor FtsY, and FlhF. We report the crystal structures of FlhF from Bacillus subtilis in complex with GTP and GMPPNP. FlhF shares SRP GTPase-specific features such as the presence of an N-terminal alpha-helical domain and the I-box insertion. It forms a symmetric homodimer sequestering a composite active site that contains two head-to-tail arranged nucleotides similar to the heterodimeric SRP-targeting complex. However, significant differences to the GTPases of SRP and the SRP receptor include the formation of a stable homodimer with GTP as well as severe modifications and even the absence of motifs involved in regulation of the other two SRP GTPases. Our results provide insights into SRP GTPases and their roles in two fundamentally different protein-targeting routes that both rely on efficient protein delivery to a secretion channel. PMID:17699634

  4. Periodic dynamics, localization metastability, and elastic interaction of colloidal particles with confining surfaces and helicoidal structure of cholesteric liquid crystals.

    PubMed

    Varney, Michael C M; Zhang, Qiaoxuan; Tasinkevych, Mykola; Silvestre, Nuno M; Bertness, Kris A; Smalyukh, Ivan I

    2014-12-01

    Nematic and cholesteric liquid crystals are three-dimensional fluids that possess long-range orientational ordering and can support both topological defects and chiral superstructures. Implications of this ordering remain unexplored even for simple dynamic processes such as the ones found in so-called "fall experiments," or motion of a spherical inclusion under the effects of gravity. Here we show that elastic and surface anchoring interactions prompt periodic dynamics of colloidal microparticles in confined cholesterics when gravity acts along the helical axis. We explore elastic interactions between colloidal microparticles and confining surfaces as well as with an aligned ground-state helical structure of cholesterics for different sizes of spheres relative to the cholesteric pitch, demonstrating unexpected departures from Stokes-like behavior at very low Reynolds numbers. We characterize metastable localization of microspheres under the effects of elastic and surface anchoring periodic potential landscapes seen by moving spheres, demonstrating the important roles played by anchoring memory, confinement, and topological defect transformation. These experimental findings are consistent with the results of numerical modeling performed through minimizing the total free energy due to colloidal inclusions at different locations along the helical axis and with respect to the confining substrates. A potential application emerging from this work is colloidal sorting based on particle shapes and sizes. PMID:25615114

  5. X-ray crystal structure of the rotavirus inner capsid particle at 3.8 Å resolution

    PubMed Central

    McClain, Brian; Settembre, Ethan; Temple, Brenda R.S.; Bellamy, A. Richard; Harrison, Stephen C.

    2010-01-01

    The rotavirus inner capsid particle, known as the “double-layered particle” (DLP), is the “payload” delivered into a cell in the process of viral infection. Its inner and outer protein layers, composed of VP2 and VP6, respectively, package the eleven segments of double-stranded RNA (dsRNA) of the viral genome, as well as about the same number of polymerase molecules (VP1) and capping-enzyme molecules (VP3). We have determined the crystal structure of the bovine rotavirus DLP. There is one full particle (outer diameter ~700 Å) in the asymmetric unit of the P212121 unit cell, of dimensions a= 740 Å, b= 1198 Å, c= 1345 Å. A three-dimensional reconstruction from electron cryomicroscopy was used as a molecular-replacement model for initial phase determination to about 18.5 Å resolution and the sixty-fold redundancy of the icosahedral particle symmetry allowed phases to be extended stepwise to the limiting resolution of the data (3.8 Å). The structure of a VP6 trimer (determined previously by others) fits the outer-layer density with very little adjustment. The T=13 triangulation number of that layer implies that there are four and one-third VP6 trimers per icosahedral asymmetric unit. The inner layer has 120 copies of VP2 and thus two per icosahedral asymmetric unit, designated VP2A and VP2B. Residues 101-880 fold into a relatively thin, principal domain, comma-like in outline, shaped such that only rather modest distortions (concentrated at two “subdomain” boundaries) allow VP2A and B to form a uniform layer with essentially no gaps at the subunit boundaries, except for a modest pore along the fivefold axis. The VP2 principal domain resembles those of the corresponding shells and homologous proteins in other dsRNA viruses: ?1 in orthoreoreoviruses, VP3 in orbiviruses. Residues 1-80 of VP2A and VP2B fold together with four other such pairs into a “fivefold hub” that projects into the DLP interior along the fivefold axis; residues 81-100 link the ten polypeptide chains emerging from a fivefold hub to the N-termini of their corresponding principal domains, clustered into a decameric assembly unit. The fivefold hub appears to have several distinct functions. One is to recruit a copy of VP1 (or of a VP1–VP3 complex), potentially along with a segment of (+)-strand RNA, as a decamer of VP2 assembles. A second is to serve as a shaft around which can coil a segment of dsRNA. A third is to guide nascent mRNA, synthesized in the DLP interior by VP1 and 5?-capped by the action of VP3, out through a fivefold exit channel. We propose a model for rotavirus particle assembly, based on known requirements for virion formation together with the structure of the DLP and that of VP1, determined earlier. PMID:20122940

  6. Anisotropic colloidal crystal particles from microfluidics.

    PubMed

    Cheng, Yao; Zhu, Cun; Xie, Zhuoying; Gu, Hongcheng; Tian, Tian; Zhao, Yuanjin; Gu, Zhongze

    2014-05-01

    Anisotropic colloidal crystal particles (CCPs) have showed their great potential in biotechnology and structural materials due to their anisotropic shapes and tunable optical property. However, their controllable generation is still a challenge. Here, a novel microfluidic approach is developed to generate anisotropic CCPs. The microfluidic device is composed of an injection capillary and a collection capillary with available size and shape. Based on the device, the anisotropic particles with non-close-packed colloidal crystal structures are achieved by photo-polymerizing droplet templates in a confined collection capillary with different shapes and sizes. Moreover, anisotropic close-packed CCPs can be made from non-close-packed CCPs through a thermal process. It is demonstrated that the anisotropic CCPs in different sizes, structural colors and shapes (rods, cuboids and disks) can be generated. These distinguishable features of resultant particles make them ideal barcodes for high-throughput bioassays. In order to prove it, DNA multiplex detection is carried out. The experimental results indicate that achieved particles have a great encoding capacity and are highly practical for multiplex coding bioassays. Therefore, we believe that the anisotropic CCPs would be highly promising barcodes in biomedical applications, including high-throughput bioassays and cell culture research where multiplexing is needed. PMID:24594033

  7. Monodispersed Ultrafine Zeolite Crystal Particles by Microwave Hydrothermal Synthesis

    SciTech Connect

    Hu, Michael Z. [ORNL; Harris, Michael Tyrone [ORNL; Khatri, Lubna [ORNL

    2008-01-01

    Microwave hydrothermal synthesis of zeolites is reviewed. Monodispersed ultrafine crystal particles of zeolite (Silicalite-1) have been synthesized in batch reactor vessels by microwave irradiation heating of aqueous basic silicate precursor solutions with tetra propyl ammonium hydroxide as the templating molecule. The effects of major process parameters (such as synthesis temperature, microwave heating rate, volume ratio (i.e., the volume of the initial synthesis solution over the total volume of the reactor vessel), and synthesis time on the zeolite particle characteristics are studied using a computer-controlled microwave reactor system that allows real-time monitoring and control of reaction medium temperature. The changes in the morphology, size and crystal structure of the particles are investigated using scanning electron microscope, dynamic light scattering, X-ray diffraction, and BET surface analysis. We have found that the synthesis temperature, volume ratio, and heating rate play a significant role in controlling the particle size, uniformity, and morphology. Microwave processing has generated new morphologies of zeolite particles (i.e., uniform block-shaped particles that contain mixed gel-nanocrystallites and agglomerated crystal particles) that could not be made by a conventional hydrothermal process. At higher synthesis temperature and lower volume ratio, irregular block-shaped particles were produced, whereas increasing the volume ratio promoted the formation of monodispersed single-crystal particles with uniform shape. Our results clearly demonstrate that faster microwave heating is advantageous to enhance the zeolite crystallization kinetics and produces larger-size crystal particles in shorter time. In addition, zeolite crystallization mechanisms, depending on the microwave heating rate, were also discussed.

  8. Structural color painting by rubbing particle powder.

    PubMed

    Park, ChooJin; Koh, Kunsuk; Jeong, Unyong

    2015-01-01

    Structural colors originate from purely physical structures. Scientists have been inspired to mimic the structures found in nature, the realization of these structures still presents a great challenge. We have recently introduced unidirectional rubbing of a dry particle powder on a rubbery surface as a quick, highly reproducible means to fabricate a single crystal monolayer assembly of particles over an unlimited area. This study extends the particle-rubbing process to a novel fine-art painting, structural color painting (SCP). SCP is based on structural coloring with varying iridescence according to the crystal orientation, as controlled by the rubbing direction. This painting technique can be applied on curved surfaces, which enriches the objects to be painted and helps the painter mimic the structures found in nature. It also allows for quick fabrication of complicated particle-assembly patterns, which enables replication of paintings. PMID:25661669

  9. Structural Color Painting by Rubbing Particle Powder

    PubMed Central

    Park, ChooJin; Koh, Kunsuk; Jeong, Unyong

    2015-01-01

    Structural colors originate from purely physical structures. Scientists have been inspired to mimic the structures found in nature, the realization of these structures still presents a great challenge. We have recently introduced unidirectional rubbing of a dry particle powder on a rubbery surface as a quick, highly reproducible means to fabricate a single crystal monolayer assembly of particles over an unlimited area. This study extends the particle-rubbing process to a novel fine-art painting, structural color painting (SCP). SCP is based on structural coloring with varying iridescence according to the crystal orientation, as controlled by the rubbing direction. This painting technique can be applied on curved surfaces, which enriches the objects to be painted and helps the painter mimic the structures found in nature. It also allows for quick fabrication of complicated particle-assembly patterns, which enables replication of paintings. PMID:25661669

  10. Structural Color Painting by Rubbing Particle Powder

    NASA Astrophysics Data System (ADS)

    Park, Choojin; Koh, Kunsuk; Jeong, Unyong

    2015-02-01

    Structural colors originate from purely physical structures. Scientists have been inspired to mimic the structures found in nature, the realization of these structures still presents a great challenge. We have recently introduced unidirectional rubbing of a dry particle powder on a rubbery surface as a quick, highly reproducible means to fabricate a single crystal monolayer assembly of particles over an unlimited area. This study extends the particle-rubbing process to a novel fine-art painting, structural color painting (SCP). SCP is based on structural coloring with varying iridescence according to the crystal orientation, as controlled by the rubbing direction. This painting technique can be applied on curved surfaces, which enriches the objects to be painted and helps the painter mimic the structures found in nature. It also allows for quick fabrication of complicated particle-assembly patterns, which enables replication of paintings.

  11. Photonic Crystal Laser Accelerator Structures

    SciTech Connect

    Cowan, Benjamin M

    2003-05-21

    Photonic crystals have great potential for use as laser-driven accelerator structures. A photonic crystal is a dielectric structure arranged in a periodic geometry. Like a crystalline solid with its electronic band structure, the modes of a photonic crystal lie in a set of allowed photonic bands. Similarly, it is possible for a photonic crystal to exhibit one or more photonic band gaps, with frequencies in the gap unable to propagate in the crystal. Thus photonic crystals can confine an optical mode in an all-dielectric structure, eliminating the need for metals and their characteristic losses at optical frequencies. We discuss several geometries of photonic crystal accelerator structures. Photonic crystal fibers (PCFs) are optical fibers which can confine a speed-of-light optical mode in vacuum. Planar structures, both two- and three-dimensional, can also confine such a mode, and have the additional advantage that they can be manufactured using common microfabrication techniques such as those used for integrated circuits. This allows for a variety of possible materials, so that dielectrics with desirable optical and radiation-hardness properties can be chosen. We discuss examples of simulated photonic crystal structures to demonstrate the scaling laws and trade-offs involved, and touch on potential fabrication processes.

  12. Crystal structure of propaquizafop

    PubMed Central

    Jeon, Youngeun; Kim, Jineun; Lee, Sangjin; Kim, Tae Ho

    2014-01-01

    The title compound, C22H22ClN3O5 {systematic name: 2-(propan-2-yl­idene­amino­oxy)ethyl (R)-2-[4-(6-chloro­quin­oxalin-2-yl­oxy)phen­oxy]propionate}, is a herbicide. The asymmetric unit comprises two independent mol­ecules in which the dihedral angles between the phenyl ring and the quinoxaline ring plane are 75.93?(7) and 82.77?(8)°. The crystal structure features C—H?O, C—H?N, and C—H?Cl hydrogen bonds, as well as weak ?–? inter­actions [ring-centroid separation = 3.782?(2) and 3.5952?(19)?Å], resulting in a three-dimensional architecture. PMID:25553037

  13. Electrorotation of colloidal particles in liquid crystals.

    PubMed

    Liao, G; Smalyukh, I I; Kelly, J R; Lavrentovich, O D; Jákli, A

    2005-09-01

    We present the first observations of dc electric-field-induced rotational motion of finite particles in liquid crystals. We show that the electrorotation is essentially identical to the well-known Quincke rotation, which in liquid crystals triggers an additional translational motion at higher fields. In the smectic phase the translational motion is confined to the two-dimensional geometry of smectic layers, in contrast to the isotropic and nematic phases, where the particles can move in all three dimensions. We demonstrate that by a proper analysis of the electrorotation, one can determine the in-plane viscosity of smectic liquid crystals. This method needs only a small amount of material, does not require uniform alignment over large areas, and enables probing rheological properties locally. PMID:16241457

  14. Three-Dimensional Photonic Crystal Laser-Driven Accelerator Structures

    SciTech Connect

    Cowan, B.; /SLAC

    2006-09-07

    We discuss simulated photonic crystal structure designs for laser-driven particle acceleration, focusing on three-dimensional planar structures based on the so-called ''woodpile'' lattice. We describe guiding of a speed-of-light accelerating mode by a defect in the photonic crystal lattice and discuss the properties of this mode, including particle beam dynamics and potential coupling methods for the structure. We also discuss possible materials and power sources for this structure and their effects on performance parameters, as well as possible manufacturing techniques and the required tolerances. In addition we describe the computational technique and possible improvements in numerical modeling that would aid development of photonic crystal structures.

  15. Dense packing crystal structures of physical tetrahedra

    E-print Network

    Kallus, Yoav

    2010-01-01

    We present a method for discovering dense packings of general convex hard particles and apply it to study the dense packing behavior of a one-parameter family of particles with tetrahedral symmetry representing a deformation of the ideal mathematical tetrahedron into a less ideal, physical, tetrahedron and all the way to the sphere. Thus, we also connect the two well studied problems of sphere packing and tetrahedron packing on a single axis. Our numerical results uncover a rich optimal-packing behavior, compared to that of other continuous families of particles previously studied. We present four structures as candidates for the optimal packing at different values of the parameter, providing an atlas of crystal structures which might be observed in systems of nano-particles with tetrahedral symmetry.

  16. Crystal structure refinement with SHELXL

    SciTech Connect

    Sheldrick, George M., E-mail: gsheldr@shelx.uni-ac.gwdg.de [Department of Structural Chemistry, Georg-August Universität Göttingen, Tammannstraße 4, Göttingen 37077 (Germany)

    2015-01-01

    New features added to the refinement program SHELXL since 2008 are described and explained. The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as ‘a CIF’) containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.

  17. Crystal structure of pseudoguainolide

    PubMed Central

    Beghidja, Noureddine; Benayache, Samir; Benayache, Fadila; Knight, David W.; Kariuki, Benson M.

    2015-01-01

    The lactone ring in the title mol­ecule, C15H22O3 (systematic name: 3,4a,8-tri­methyl­dodeca­hydro­azuleno[6,5-b]furan-2,5-dione), assumes an envelope conformation with the methine C atom adjacent to the the methine C atom carrying the methyl substituent being the flap atom. The other five-membered ring adopts a twisted conformation with the twist being about the methine–methyl­ene C—C bond. The seven-membered ring is based on a twisted boat conformation. No specific inter­actions are noted in the the crystal packing. PMID:25844227

  18. Crystal Structure of Ettringite

    Microsoft Academic Search

    A. Moore; H. F. W. TAYLOR

    1968-01-01

    ETTRINGITE (Ca6[Al(OH)6]2(SO4)3.26H2O) occurs as a natural mineral, and is technically important as a hydration product of Portland and supersulphated cements and in its use, as satin white, for coating paper. It forms hexagonal, prismatic crystals which in synthetic material are often highly elongated. Bannister, Hey and Bernal1 obtained unit-cell data (hexagonal: a 11.26, c 21.48 Å, space group P63\\/mmc, Z

  19. Effect of particle size and particle size distribution on physical characteristics, morphology and crystal structure of explosively compacted high-T(sub c) superconductors

    NASA Technical Reports Server (NTRS)

    Kotsis, I.; Enisz, M.; Oravetz, D.; Szalay, A.

    1995-01-01

    A superconductor, of composition Y(Ba,K,Na)2Cu3O(x)/F(y) and a composite of composition Y(Ba,K,Na)2Cu3O(x)/F(y) + Ag, with changing K, Na and F content but a constant silver content (Ag = 10 mass%) was prepared using a single heat treatment. the resulting material was ground in a corundum lined mill, separated to particle size fractions of 0-40 micron, 0-63 micron and 63-900 micron and explosively compacted, using an explosive pressure of 10(exp 4) MPa and a subsequent heat treatment. Best results were obtained with the 63-900 micron fraction of composition Y(Ba(1.95) K(0.01)Cu3O(x)F(0),(05)/Ag: porosity less than 0.01 cu cm/g and current density 2800 A/sq cm at 77K.

  20. Photonic crystal devices formed by a charged-particle beam

    Microsoft Academic Search

    S. Y. Lin; H. W. P. Koops

    2000-01-01

    A photonic crystal device and method are disclosed. The photonic crystal device comprises a substrate with at least one photonic crystal formed thereon by a charged-particle beam deposition method. Each photonic crystal comprises a plurality of spaced elements having a composition different from the substrate, and may further include one or more impurity elements substituted for spaced elements. Embodiments of

  1. Photonic crystal devices formed by a charged-particle beam

    Microsoft Academic Search

    Shawn-Yu Lin; Hans W. P. Koops

    2000-01-01

    A photonic crystal device and method. The photonic crystal device comprises a substrate with at least one photonic crystal formed thereon by a charged-particle beam deposition method. Each photonic crystal comprises a plurality of spaced elements having a composition different from the substrate, and may further include one or more impurity elements substituted for spaced elements. Embodiments of the present

  2. Photonic Crystal Laser-Driven Accelerator Structures

    SciTech Connect

    Cowan, Benjamin M.

    2007-08-22

    Laser-driven acceleration holds great promise for significantly improving accelerating gradient. However, scaling the conventional process of structure-based acceleration in vacuum down to optical wavelengths requires a substantially different kind of structure. We require an optical waveguide that (1) is constructed out of dielectric materials, (2) has transverse size on the order of a wavelength, and (3) supports a mode with speed-of-light phase velocity in vacuum. Photonic crystals---structures whose electromagnetic properties are spatially periodic---can meet these requirements. We discuss simulated photonic crystal accelerator structures and describe their properties. We begin with a class of two-dimensional structures which serves to illustrate the design considerations and trade-offs involved. We then present a three-dimensional structure, and describe its performance in terms of accelerating gradient and efficiency. We discuss particle beam dynamics in this structure, demonstrating a method for keeping a beam confined to the waveguide. We also discuss material and fabrication considerations. Since accelerating gradient is limited by optical damage to the structure, the damage threshold of the dielectric is a critical parameter. We experimentally measure the damage threshold of silicon for picosecond pulses in the infrared, and determine that our structure is capable of sustaining an accelerating gradient of 300 MV/m at 1550 nm. Finally, we discuss possibilities for manufacturing these structures using common microfabrication techniques.

  3. Crystal structure of difenoconazole

    PubMed Central

    Cho, Seonghwa; Kang, Gihaeng; Lee, Sangjin; Kim, Tae Ho

    2014-01-01

    In the title compound difenoconazole [systematic name: 1-({2-[2-chloro-4-(4-chloro­phen­oxy)phen­yl]-4-methyl-1,3-dioxolan-2-yl}meth­yl)-1H-1,2,4-triazole], C19H17Cl2N3O3, the dihedral angle between the planes of the 4-chloro­phenyl and 2-chloro­phenyl rings is 79.34?(9)°, while the dihedral angle between the planes of the triazole ring and the dioxolanyl group is 59.45?(19)°. In the crystal, pairs of C—H?N hydrogen bonds link adjacent mol­ecules, forming dimers with R 2 2(6) loops. In addition, the dimers are linked by C—H?O hydrogen bonds, resulting in a three-dimensional architecture. Disorder was modeled for one C atom of the dioxolanyl group over two sets of sites with an occupancy ratio of 0.566?(17):0.434?(17). PMID:25484812

  4. The flow structure in the near field of jets and its effect on cavitation inception, and, Implementation of ferroelectric liquid crystal and birefringent crystal for image shifting in particle image velocimetry

    NASA Astrophysics Data System (ADS)

    Gopalan, Shridhar

    1999-10-01

    Cavitation experiments performed in the near field of a 50-mm diameter (D) jet at ReD = 5 × 105, showed inception in the form of inclined ``cylindrical'' bubbles at axial distances (x/D) less than 0.55, with indices of 2.5. On tripping the boundary layer, cavitation inception occurred at x/D ~ 2, as distorted ``spherical'' bubbles with inception indices of 1.7. To investigate these substantial differences, the near field of the jet was measured using Particle Image Velocimetry (PIV). Data on the primary flow, the strength distribution of the ``streamwise''vortices and the velocity profiles within the initial boundary layers were obtained. The untripped case showed a direct transition to three-dimensional flow in the near field (x/D < 0.7) even before rolling up to distinct vortex rings. Strong ``streamwise'' vortices with strengths up to 25% of the jet velocity times the characteristic wavelength were seen. Cavitation inception occurred in the core of these vortices. In contrast, in the tripped jet the vortex sheet rolled up to the familiar Kelvin- Helmholtz vortex rings with weak secondary vortices. Using the measured nuclei distribution, strengths and straining of the ``streamwise'' structures, the rates of cavitation events were estimated. The estimated results match very well with the measured cavitation rates. Also, the Reynolds stresses in the near field of the jet show similar trends and magnitudes to those of Browand & Latigo (1979) and Bell & Mehta (1990) for a plane shear layer. In the second part of this essay we discuss the implementation of electro-optical image shifting to resolve directional ambiguity in PIV measurements. The technique uses a ferroelectric liquid crystal (FLC) as an electro-optic half wave plate and a birefringent crystal (calcite) as the shifter. The system can be used with non-polarized light sources and fluorescent particles. The minimum shifting time is approximately 100?s. This compact electrooptical device usually is positioned in front of the camera lens, though it has also been mounted inside the lens body. This device extensively was used to acquire data in the near field of the jet, which is discussed in Chapter 2. Sample vector maps from a turbulent multidirectional flow are also included.

  5. Crystal structure of guggulsterone Z

    SciTech Connect

    Gupta, V. K., E-mail: vivek_gupta2k2@hotmail.com; Bandhoria, P. [University of Jammu, Post Graduate Department of Physics (India); Gupta, B. D.; Gupta, K. K. [Regional Research Laboratory (India)

    2006-03-15

    The crystal structure of the title compound (4,17(20)-trans-pregnadiene-3,16-dione, C{sub 21}H{sub 28}O{sub 2}) has been determined by direct methods using single-crystal X-ray diffraction data. The compound crystallizes into the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1} with the unit cell parameters a = 7.908(2) A, b = 13.611(3) A, c = 16.309(4) A, and Z = 4. The structure has been refined to R = 0.058 for 3667 observed reflections. The bond distances and angles are in good agreement with guggulsterone E and other related steroid molecules. Ring A exists in the distorted sofa conformation, while rings B and C adopt the distorted chair conformation. Five-membered ring D is intermediate between the half-chair and envelope conformations. The A/B ring junction is quasi-trans, while ring systems B/C and C/D are trans fused about the C(8)-C(9) and C(13)-C(14) bonds, respectively. The steroid nucleus has a small twist, as shown by the C(19)-C(10)...C(13)-C(18) pseudo-torsion angle of 7.2{sup o}. The crystal structure is stabilized by intra-and intermolecular C-H...O hydrogen bonds.

  6. The Surface Structure of Ground Metal Crystals

    NASA Technical Reports Server (NTRS)

    Boas, W.; Schmid, E.

    1944-01-01

    The changes produced on metallic surfaces as a result of grinding and polishing are not as yet fully understood. Undoubtedly there is some more or less marked change in the crystal structure, at least, in the top layer. Hereby a diffusion of separated crystal particles may be involved, or, on plastic material, the formation of a layer in greatly deformed state, with possible recrystallization in certain conditions. Czochralski verified the existence of such a layer on tin micro-sections by successive observations of the texture after repeated etching; while Thomassen established, roentgenographically by means of the Debye-Scherrer method, the existence of diffused crystal fractions on the surface of ground and polished tin bars, which he had already observed after turning (on the lathe). (Thickness of this layer - 0.07 mm). Whether this layer borders direct on the undamaged base material or whether deformed intermediate layers form the transition, nothing is known. One observation ty Sachs and Shoji simply states that after the turning of an alpha-brass crystal the disturbance starting from the surface, penetrates fairly deep (approx. 1 mm) into the crystal (proof by recrystallization at 750 C).

  7. Dusty Plasma Crystals: Structure and Phase Transitions

    Microsoft Academic Search

    Martin Lampe; Glenn Joyce; Gurudas Ganguli

    2003-01-01

    Dust clouds residing above a discharge electrode are subject to ions streaming at about the ion sound speed. At high pressure, the dust grains self-organize into crystal structures. We use analytic theory and simulations to show that the basic unit of crystal structure is a rigid string of grains aligned with the ion flow, that several quite different crystal structures

  8. The crystallization processes in the aluminum particles production technology

    NASA Astrophysics Data System (ADS)

    Arkhipov, Vladimir; Bondarchuk, Sergey; Goldin, Victor; Zharova, Irina

    2015-01-01

    The physical and mathematical model of the crystallization process of liquid aluminum particles in the spray-jet of the ejection-type atomizer was proposed. The results of mathematical modeling of two-phase flow in the spray-jet and the crystallization process of fluid particles are given. The influence of the particle size, of the flow rate and the stagnation temperature gas in the ranges of industrial technology implemented for the production of powders aluminum of brands ASD, on the crystallization characteristics were investigated. The approximations of the characteristics of the crystallization process depending on the size of the aluminum particles on the basis of two approaches to the mathematical description of the process of crystallization of aluminum particles were obtained. The results allow to optimize the process parameters of ejection-type atomizer to produce aluminum particles with given morphology.

  9. American Mineralogist Crystal Structure Database

    NSDL National Science Digital Library

    R. T. Downs

    This database provides access to information on every crystal structure published in the American Mineralogist, the Canadian Mineralogist, European Journal of Mineralogy, and Physics and Chemistry of Minerals, as well as selected datasets from other journals. The data are searchable by mineral name, author, chemistry, cell parameters and symmetry, diffraction pattern, and a general search. There are also lists of minerals represented in the database and authors of publications cited.

  10. Macrofiber structure and the dynamics of sickle cell hemoglobin crystallization.

    PubMed

    Potel, M J; Wellems, T E; Vassar, R J; Deer, B; Josephs, R

    1984-08-25

    Fibers of deoxyhemoglobin S undergo spontaneous crystallization by a mechanism involving a variety of intermediate structures. These intermediate structures, in common with the fiber and crystal, consist of Wishner-Love double strands of hemoglobin S molecules arranged in different configurations. The structure of one of the key intermediates linking the fiber and crystal, called a macrofiber, has been studied by a variety of analytical procedures. The results of the analysis indicate that the intermediates involved in the fiber to crystal transition have many common structural features. Fourier analysis of electron micrographs of macrofibers confirms that they are composed of Wishner-Love double strands of hemoglobin molecules. Electron micrographs of macrofiber cross-sections reveal that the arrangement of the double strands in macrofibers resembles that seen in micrographs of the a axis projection of the crystal. This orientation provides an end-on view of the double strands which appear as paired dumb-bell-like masses. The structural detail becomes progressively less distinct towards the edge of the particle due to twisting of the double strands about the particle axis. Serial sections of macrofibers confirm that these particles do indeed rotate about their axes. The twist of the particle is right handed and its average pitch is 10,000 A. The effect of rotation on the appearance of macrofiber cross-sections 300 to 400 A thick can be simulated by a 15 degrees rotation of an a axis crystal projection. The relative polarity of the double strands in macrofibers and crystals can be determined easily by direct inspection of the micrographs. In both macrofibers and crystals they are in an anti-parallel array. On the basis of these observations we conclude that crystallization of macrofibers involves untwisting and alignment of the double strands. PMID:6481805

  11. The structural consequences of calcium crystal deposition.

    PubMed

    Durcan, Laura; Bolster, Ferdia; Kavanagh, Eoin C; McCarthy, Geraldine M

    2014-05-01

    Calcium pyrophosphate dihydrate and basic calcium phosphate (BCP) crystals are the most common calcium-containing crystals associated with rheumatic disease. Clinical manifestations of calcium crystal deposition include acute or chronic inflammatory and degenerative arthritides and certain forms of periarthritis. The intra-articular presence of BCP crystals correlates with the degree of radiographic degeneration. Calcium crystal deposition contributes directly to joint degeneration. Vascular calcification is caused by the deposition of calcium hydroxyapatite crystals in the arterial intima. These deposits may contribute to local inflammation and promote further calcification, thus aggravating the atherosclerotic process. Calcium crystal deposition results in substantial structural consequence in humans. PMID:24703349

  12. Improved synthesis of fine zinc borate particles using seed crystals

    NASA Astrophysics Data System (ADS)

    Gürhan, Deniz; Çakal, Gaye Ö.; Ero?lu, ?nci; Özkar, Saim

    2009-03-01

    Zinc borate is a flame retardant additive used in polymers, wood applications and textile products. There are different types of zinc borate having different chemical compositions and structures. In this study, the production of zinc borate having the molecular formula of 2ZnO·3B 2O 3·3.5H 2O was reexamined by studying the effects of reaction parameters on the properties of product as well as the reaction kinetics. Production of zinc borate from the reaction of boric acid and zinc oxide in the presence of seed crystals was performed in a continuously stirred, temperature-controlled batch reactor having a volume of 1.5 L. Samples taken in regular time intervals during the experiments were analyzed for the concentration of zinc oxide and boron oxide in the solid as well as for the conversion of zinc oxide to zinc borate versus time. The zinc borate production reaction was fit to the logistic model. The reaction rate, reaction completion time, composition and particle size distribution of zinc borate product were determined by varying the following parameters: the boric acid to zinc oxide ratio (H 3BO 3:ZnO=3:1, 3.5:1, 5:1 and 7:1), the particle size of zinc oxide (10 and 25 ?m), stirring rate (275, 400, 800 and 1600 rpm), temperature (75, 85 and 95 °C) and the size of seed crystals (10 and 2 ?m). The products were also analyzed for particle size distribution. The experimental results showed that the reaction rate increases with the increase in H 3BO 3:ZnO ratio, particle size of zinc oxide, stirring rate and temperature. Concomitantly, the reaction completion time is decreased by increasing the H 3BO 3:ZnO ratio, stirring rate and temperature. The average particle sizes of the zinc borate products are in the range 4.3-16.6 ?m (wet dispersion analysis).

  13. Simulations of Photonic Crystal and Dielectric Structures

    SciTech Connect

    Werner, G. R. [Center for Integrated Plasma Studies, University of Colorado, Boulder, CO 80309 (United States)

    2010-11-04

    Dielectric materials and photonic crystal structures have electromagnetic properties that could potentially offer great benefits for accelerators. Computer simulation plays a critical role in designing, understanding, and optimizing these structures, especially the non-intuitive photonic crystal structures for which there is no relevant zeroth-order analytic model.

  14. Elastic octopoles and colloidal structures in nematic liquid crystals.

    PubMed

    Chernyshuk, S B; Tovkach, O M; Lev, B I

    2014-03-01

    We propose a simple theoretical model which explains the formation of dipolar two- (2D) and three-dimensional (3D) colloidal structures in nematic liquid crystals. The colloidal particles are treated as effective hard spheres interacting via their elastic dipole, quadrupole, and octopole moments. It is shown that the octopole moment plays an important role in the formation of 2D and 3D nematic colloidal crystals. We generalize this assumption to the case of an external electric field and theoretically explain a giant electrostriction effect in 3D crystals observed recently. PMID:24730862

  15. Particle guidance in hollow-core photonic crystal fiber

    Microsoft Academic Search

    F. Benabid; J. C. Knight; P.St.J. Russell

    2002-01-01

    Among the numerous prospects opened by the development of hollow-core photonic crystal fiber (hc-pcf) is laser guidance of atoms and particles. we report the first observation of particle guidance in hollow-core photonic crystal fiber (hc-pcf). A cw argon ion laser of about 200 mW operating at 514.5 nm is focused by a 4 x objective and directed vertically on the

  16. The structure of small penta-twinned gold particles

    NASA Astrophysics Data System (ADS)

    Gao, Pei-Yu; Kunath, W.; Gleiter, H.; Weiss, K.

    1989-03-01

    The structural feathers of penta-twinned gold particles (size between 2 and 6 nm) generated by gas evaporation have been investigated by high resolution TEM. The structural characteristic of penta-twinned particles is different from that of quasi-crystals that the five coherent or incoherent twin boundaries separating the twin oriented segments do not join up along a common edge. The lattice parameter is reduced by 4 5% in comparison to that of bulk gold. The formation of the penta-twinned particles is proposed to occur by particle collision. The particles were observed to be crystalline at ambient temperature.

  17. Formation of a columnar liquid crystal in a simple one-component system of particles.

    PubMed

    Metere, Alfredo; Sarman, Sten; Oppelstrup, Tomas; Dzugutov, Mikhail

    2015-06-01

    We report a molecular dynamics simulation demonstrating that a columnar liquid crystal, commonly formed by disc-shaped molecules, can be formed by identical particles interacting via a spherically symmetric potential. Upon isochoric cooling from a low-density isotropic liquid state the simulated system underwent a weak first order phase transition which produced a liquid crystal phase composed of parallel particle columns arranged in a hexagonal pattern in the plane perpendicular to the column axis. The particles within columns formed a liquid structure and demonstrated a significant intracolumn diffusion. Further cooling resulted in another first-order transition whereby the column structure became periodically ordered in three dimensions transforming the liquid-crystal phase into a crystal. This result is the first observation of a columnar liquid crystal formation in a simple one-component system of particles. Its conceptual significance is in that it demonstrated that liquid crystals that have so far only been produced in systems of anisometric molecules can also be formed by mesoscopic soft-matter and colloidal systems of spherical particles with appropriately tuned interatomic potential. PMID:25959363

  18. Crystal structure analysis of intermetallic compounds

    NASA Technical Reports Server (NTRS)

    Conner, R. A., Jr.; Downey, J. W.; Dwight, A. E.

    1968-01-01

    Study concerns crystal structures and lattice parameters for a number of new intermetallic compounds. Crystal structure data have been collected on equiatomic compounds, formed between an element of the Sc, Ti, V, or Cr group and an element of the Co or Ni group. The data, obtained by conventional methods, are presented in an easily usable tabular form.

  19. New crystal structure maps for intermetallic compounds

    Microsoft Academic Search

    Yoshihisa Harada; Masahiko Morinaga; Jun-ichi Saito; Yasuharu Takagi

    1997-01-01

    New crystal structure maps have been proposed on the basis of the 0953-8984\\/9\\/38\\/008\\/img6 molecular orbital calculations of electronic structures. Two electronic parameters have been introduced and employed as new parameters for the classification of crystal structures. One is the bond order and the other is the d-orbital energy level of elements. Both of them change following the position of elements

  20. Defect structures in metallic photonic crystals

    SciTech Connect

    Oezbay, E.; Temelkuran, B. [Department of Physics, Bilkent University, Bilkent, Ankara 06533 (Turkey)] [Department of Physics, Bilkent University, Bilkent, Ankara 06533 (Turkey); Sigalas, M.; Tuttle, G.; Soukoulis, C.M.; Ho, K.M. [Ames Laboratory and Microelectronics Research Center, Iowa State University, Ames, Iowa 50011 (United States)] [Ames Laboratory and Microelectronics Research Center, Iowa State University, Ames, Iowa 50011 (United States)

    1996-12-01

    We have investigated metallic photonic crystals built around a layer-by-layer geometry. Two different crystal structures (face-centered-tetragonal and tetragonal) were built and their properties were compared. We obtained rejection rates of 7{endash}8 dB per layer from both metallic crystals. Defect modes created by removing rods resulted in high peak transmission (80{percent}), and high quality factors (1740). Our measurements were in good agreement with theoretical simulations. {copyright} {ital 1996 American Institute of Physics.}

  1. Crystal structure refinement from electron diffraction data

    Microsoft Academic Search

    A. P. Dudka; A. S. Avilov; G. G. Lepeshov

    2008-01-01

    A procedure of crystal structure refinement from electron diffraction data is described. The electron diffraction data on polycrystalline films are processed taking into account possible overlap of reflections and two-beam interaction. The diffraction from individual single crystals in an electron microscope equipped with a precession attachment is described using the Bloch-wave method, which takes into account multibeam scattering, and a

  2. Compact Couplers for Photonic Crystal Laser-Driven Accelerator Structures

    SciTech Connect

    Cowan, Benjamin; /Tech-X, Boulder; Lin, M.C.; /Tech-X, Boulder; Schwartz, Brian; /Tech-X, Boulder; Byer, Robert; /Stanford U., Phys. Dept.; McGuinness, Christopher; /Stanford U., Phys. Dept.; Colby, Eric; /SLAC; England, Robert; /SLAC; Noble, Robert; /SLAC; Spencer, James; /SLAC

    2012-07-02

    Photonic crystal waveguides are promising candidates for laser-driven accelerator structures because of their ability to confine a speed-of-light mode in an all-dielectric structure. Because of the difference between the group velocity of the waveguide mode and the particle bunch velocity, fields must be coupled into the accelerating waveguide at frequent intervals. Therefore efficient, compact couplers are critical to overall accelerator efficiency. We present designs and simulations of high-efficiency coupling to the accelerating mode in a three-dimensional photonic crystal waveguide from a waveguide adjoining it at 90{sup o}. We discuss details of the computation and the resulting transmission. We include some background on the accelerator structure and photonic crystal-based optical acceleration in general.

  3. crystal: growth, crystal structure perfection, piezoelectric, and acoustic properties

    NASA Astrophysics Data System (ADS)

    Roshchupkin, Dmitry; Ortega, Luc; Plotitcyna, Olga; Irzhak, Dmitry; Emelin, Evgenii; Fahrtdinov, Rashid; Alenkov, Vladimir; Buzanov, Oleg

    2014-09-01

    A five-component crystal of lanthanum-gallium silicate group La3Ga5.3Ta0.5Al0.2O14 (LGTA) was grown by the Czochralski method. The LGTA crystal possesses unique thermal properties and substitution of Al for Ga in the unit cell leads to a substantial increase of electrical resistance at high temperatures. The unit cell parameters of LGTA were determined by powder diffraction. X-ray topography was used to study the crystal structure perfection: the growth banding normal to the growth axis were visualized. The independent piezoelectric constants d 11 and d 14 were measured by X-ray diffraction in the Bragg and Laue geometries. Excitation and propagation of surface acoustic waves were studied by the double-crystal X-ray diffraction at the BESSY II synchrotron radiation source. The analysis of the diffraction spectra of acoustically modulated crystals permitted the determination of the velocity of acoustic wave propagation and the power flow angles in different acoustic cuts of the LGTA crystal.

  4. Efficient transportation of nano-sized particles along slotted photonic crystal waveguide.

    PubMed

    Lin, Pin-Tso; Lee, Po-Tsung

    2012-01-30

    We design a slotted photonic crystal waveguide (S-PhCW) and numerically propose that it can efficiently transport polystyrene particle with diameter as small as 50 nm in a 100 nm slot. Excellent optical confinement and slow light effect provided by the photonic crystal structure greatly enhance the optical force exerted on the particle. The S-PhCW can thus transport the particle with optical propulsion force as strong as 5.3 pN/W, which is over 10 times stronger than that generated by the slotted strip waveguide (S-SW). In addition, the vertical optical attraction force induced in the S-PhCW is over 2 times stronger than that of the S-SW. Therefore, the S-PhCW transports particles not only efficiently but also stably. We anticipate this waveguide structure will be beneficial for the future lab-on-chip development. PMID:22330556

  5. Melting of Dust Crystals by Single Particles

    SciTech Connect

    Ivanov, Yuriy; Melzer, Andre [Institut fuer Physik, Ernst-Moritz-Arndt-Universitaet Greifswald, 17489 Greifswald (Germany)

    2005-10-31

    The melting transition of 2D finite dust clusters has been investigated. Therefore, a single dust particle was placed in a plane below the actual cluster plane. With reducing the gas pressure and with increase of the plasma power an instability due to the non-reciprocal attraction of the lower dust particle was excited that heats the cluster layer. The novel method of singular value decomposition (SVD) has been applied for the analysis of the cluster dynamics during melting.

  6. Crystal structure of meteoritic schreibersites: determination of absolute structure

    NASA Astrophysics Data System (ADS)

    Skála, Roman; Císa?ová, Ivana

    Minerals of the schreibersite nickelphosphide series (Fe,Ni)3P crystallize in the non-centrosymmetric space group Ibar 4. As a consequence, they can possess two different spatial arrangements of the constituting atoms within the unit cell, related by the inversion symmetry operation. Here, we present the crystal structure refinements from single crystal X-ray diffraction data for schreibersite grains from iron meteorites Acuña, Carlton, Hex River Mts. (three different crystals), Odessa (two different crystals), Sikhote Alin, and Toluca aiming for the determination of the absolute structure of the examined crystals. The crystals studied cover the composition range from 58 mol% to 80 mol% Fe3P end-member. Unit-cell parameter a and volume of the unit cell V, as well as certain topological structural parameters tightly correlate with Fe3P content. Unit-cell parameter c, on the other hand, does not show such strong correlation. Eight of the nine crystal structure refinements allowed unambiguous absolute structure assignment. The single crystal extracted from Toluca is, however, of poor quality and consequently the structure refinement did not provide as good results as the rest of the materials. Also, this crystal has only weak inversion distinguishing power to provide unequivocal absolute structure determination. Six of the eight unambiguous absolute structure determinations indicated inverted atomic arrangement compared to that reported in earlier structure refinements (here called standard). Only two grains, one taken from Odessa iron and the other from the Hex River Mts. meteorite, reveal the dominance of standard crystal structure setting.

  7. Crystal Structure and Orientation in Thin Films

    Microsoft Academic Search

    G. I. Finch; A. G. Quarrell

    1933-01-01

    IN crystal growth, the well-known phenomenon of pseudomorphism extends to all three dimensions. Recently we have found that thin films of aluminium on platinum, of zinc oxide on zinc and of magnesium oxide on magnesium possess abnormal crystal structures. For example, aluminium, normally of face-centred cubic structure (a = 4.05 A.), when deposited as a sufficiently thin layer on face-centred

  8. Design of a Highly Focused Photonic Crystal Lens Using Boolean Particle Swarm Optimization

    Microsoft Academic Search

    Alireza Marandi; Farzaneh Afshinmanesh; Poman P. M. So

    2008-01-01

    The Boolean particle swarm optimization technique in conjunction with the scattering matrix method is proposed to design two dimensional photonic crystal based structures. The potential of this approach is illustrated in a lens design problem. The resulting lens has a superb F-number of 0.39. Furthermore, the effectiveness of this method in comparison with a genetic algorithm based optimization procedure is

  9. Metal oxide superconducting powder comprised of flake-like single crystal particles

    DOEpatents

    Capone, Donald W. (Bolingbrook, IL); Dusek, Joseph (Downers Grove, IL)

    1994-01-01

    Powder of a ceramic superconducting material is synthesized such that each particle of the powder is a single crystal having a flake-like, nonsymmetric morphology such that the c-axis is aligned parallel to the short dimension of the flake. Nonflake powder is synthesized by the normal methods and is pressed into pellets or other shapes and fired for excessive times to produce a coarse grained structure. The fired products are then crushed and ground producing the flake-like powder particles which exhibit superconducting characteristics when aligned with the crystal lattice.

  10. Sticky quartz crystal microbalance as a particle monitor

    NASA Astrophysics Data System (ADS)

    Uy, O. Manuel; Cain, Russell P.; Carkhuff, Bliss G.; Lennon, Andrew M.

    1999-10-01

    Quartz crystal microbalances (QCM) have been used for over twenty years as contamination monitors in space satellites to measure film deposition on sensitive surfaces such optical mirrors, thermal radiators and solar arrays. However, it is only recently that miniature quartz crystal microbalances were used as particle monitors after the QCMs were coated with low outgassing grease to trap and measure the mass of particles impinging on the quartz surfaces. Results of these experiments utilizing 'sticky' QCMs are described for a series of wind- tunnel missile tests.

  11. The structure of small, vapor-deposited particles. II - Experimental study of particles with hexagonal profile

    NASA Technical Reports Server (NTRS)

    Yacaman, M. J.; Heinemann, K.; Yang, C. Y.; Poppa, H.

    1979-01-01

    'Multiply-twinned' gold particles with hexagonal bright field TEM profile were determined to be icosahedra composed of 20 identical and twin-related tetrahedral building units that do not have an fcc structure. The crystal structure of these slightly deformed tetrahedra is rhombohedral. Experimental evidence supporting this particle model was obtained by selected-zone dark field and weak beam dark field electron microscopy. In conjunction with the results of part I, it has been concluded that multiply-twinned gold particles of pentagonal or hexagonal profile that are found during the early stages of the vapor deposition growth process on alkali halide surfaces do not have an fcc crystal structure, which is in obvious contrast to the structure of bulk gold.

  12. Photonic crystals of shape-anisotropic colloidal particles

    NASA Astrophysics Data System (ADS)

    Velikov, Krassimir P.; van Dillen, Teun; Polman, Albert; van Blaaderen, Alfons

    2002-07-01

    Spherical silica (SiO2), zinc sulfide (ZnS), and core-shell particles of these materials undergo substantial anisotropic plastic deformation under high-energy ion irradiation. Individual particles can be turned into oblate or prolate ellipsoids with exact control over the aspect ratio. In this letter, we report on the fabrication and optical characterization of thin three-dimensional photonic crystals of spherical particles, which have been anisotropically deformed into spheroidal oblates by means of ion irradiation. As a result of the collective deformation process, both the unit cell symmetry and the particle form factor have been changed leading to appreciable tunability in the optical properties of the photonic crystal.

  13. Structures of cyano-biphenyl liquid crystals

    NASA Technical Reports Server (NTRS)

    Chu, Yuan-Chao; Tsang, Tung; Rahimzadeh, E.; Yin, L.

    1989-01-01

    The structures of p-alkyl- p'-cyano- bicyclohexanes, C(n)H(2n+1) (C6H10)(C6H10) CN (n-CCH), and p-alkyl- p'-cyano- biphenyls, C(n)H(2n+1) (C6H4)(C6H4) CN (n-CBP), were studied. It is convenient to use an x ray image intensification device to search for symmetric x ray diffraction patterns. Despite the similarities in molecular structures of these compounds, very different crystal structures were found. For the smectic phase of 2CCH, the structure is close to rhombohedral with threefold symmetry. In contrast, the structure is close to hexagonal close-packed with two molecules per unit cell for 4CCH. Since intermolecular forces may be quite weak for these liquid crystals systems, it appears that crystal structures change considerably when the alkyl chain length is slightly altered. Different structures were also found in the crystalline phase of n-CBP for n = 6 to 9. For n = 7 to 9, the structures are close to monclinic. The structures are reminiscent of the smectic-A liquid crystal structures with the linear molecules slightly tilted away from the c-axis. In contrast, the structure is quite different for n = 6 with the molecules nearly perpendicular to the c-axis.

  14. Surface structure of potassium dichromate (KBC) crystals

    NASA Astrophysics Data System (ADS)

    Reedijk, M. F.; Arsic, J.; Kaminski, D.; van Enckevort, W. J. P.; Vlieg, E.

    2003-02-01

    We present a surface X-ray diffraction study of the {0 0 1} faces of potassium dichromate crystals in a humid environment. An etch-resistant layer develops in such an environment, which prevents the crystal from etching in a low-solubility solution. This layer is shown to be amorphous and is likely to be permeable for water molecules. The interface between the crystal and the amorphous layer is atomically flat. The crystal surface is not reconstructed, showing a potassium termination. The atomic structure of the surface is influenced by the relative humidity (RH), at 40% RH the top layer of molecules is expanded while at 100% RH these molecules are compressed. A first indication is given of a structural difference between the (0 0 1) and ( 0 0 1¯) faces, which is relevant for understanding the hypomorphism exhibited by this system.

  15. Crystal structure refinement from electron diffraction data

    Microsoft Academic Search

    A. P. Dudka; A. S. Avilov; G. G. Lepeshov

    2008-01-01

    A procedure of crystal structure refinement from electron diffraction data is described. The electron diffraction data on\\u000a polycrystalline films are processed taking into account possible overlap of reflections and two-beam interaction. The diffraction\\u000a from individual single crystals in an electron microscope equipped with a precession attachment is described using the Bloch-wave\\u000a method, which takes into account multibeam scattering, and a

  16. Specific features of quartz crystals lamellar structure

    Microsoft Academic Search

    N. M. Bauer; A. P. Pogrebnyak; S. N. Abdrafikov; N. A. Mamaev; B. V. Shulgin

    1995-01-01

    This report gives results of experimental investigations of the structural Al distribution in quartz crystals grown on seeds making desired angles with the face {101¯0} (nonsingular faces (NF) of the zone [0001]). It has previously been shown that regeneration growth pyramids of these crystals possess a stepped growth surface formed by faces {1¯120} and {101¯0}. Moreover, certain relationships between the

  17. Preliminary analysis of two and three dimensional crystals of vault ribonucleoprotein particles.

    PubMed

    Querol-Audí, Jordi; Perez-Luque, Rosa; Fita, Ignacio; Lopéz-Iglesias, Carmen; Castón, José R; Carrascosa, José L; Verdaguer, Nuria

    2005-07-01

    Vaults are large ribonucleoprotein particles found in a wide variety of eukaryotes. When imaged by electron-microscopy vaults present a strikingly conserved barrel-shaped structure with an invaginated waist and two protruding caps. In this work, we present two dimensional (2D) and three dimensional (3D) crystals of naturally produced vaults in murine and monkey cells, respectively. The 2D-crystals presented a hexagonal packing with the lattice parameter defined by the diameter of the vault barrel. Fourier transforms from images of the negatively stained 2D-crystals showed spots till about 45 A resolution. The 3D-crystals reached about 0.15 x 0.15 x 0.02 mm3 in size and presented a flat triangular morphology with well-developed faces. The preliminary characterization of these 3D-crystals, which diffract very weakly to approximately 10 A resolution, suggests a trigonal packing with the R32 space group symmetry. The 3D-crystals appear to be formed by adding layers of vaults, which retain the hexagonal organization seen in the 2D-crystals, with relative shifts that maximize the interdigitation of particles in adjacent layers. Accurate crystal symmetry in the 2D- and 3D-crystals requires neighbor particles interacting according to a 6-fold and a 3-fold dihedral symmetry, respectively. Compatibility with the reported 8-fold symmetry would imply multiples of 24-fold rotational symmetry, in agreement with the recently proposed 48-fold dihedral symmetry for reconstituted recombinant vaults. PMID:15964767

  18. Control of crystal habit and particle morphology of calcium sulfite hemihydrate crystals

    NASA Astrophysics Data System (ADS)

    Chen, Pao-Chi; Tai, Clifford Y.; Shih, Shin-Min

    1992-09-01

    Using a pH-stat apparatus, we produced crystals of calcium sulfite hemihydrate in a semibatch crystallizer by reacting Ca(OH) 2 with NaHSO 3 under various operational conditions. The habits of calcium sulfite hemihydrate obtained in this study were acicular, long-platelet, platelet and tabular. Each of them was prone to form agglomerates, depending on the pH value, solution composition and concentration of additives. At low pH and high concentration of sodium bisulfite the agglomerate of acicular crystal would form. In contrast, platelet and tabular crystals and their agglomerates were obtained at high pH and low levels of sodium bisulfite concentration. The particle morphology was not significantly altered by the addition of EDTA and DMA, but the crystal habit was tabular at low EDTA concentration and became platelet as the EDTA concentration increased.

  19. Photonic crystal structures in sensing technology

    NASA Astrophysics Data System (ADS)

    Bjarklev, Anders; Jensen, Jesper B.; Riishede, Jesper; Broeng, Jes; Laegsgaard, J.; Tanggaard Larsen, T.; Sorensen, Thorkild; Hougaard, Kristian; Bang, Ole

    2004-06-01

    Photonic crystal materials and waveguides have since their appearance in 1987 attracted very much attention from the scientific community. From being a more academia discipline, new components and functionalities have emerged, and photonic crystals have today started to enter the field of commercial devices. Especially the photonic crystal fiber (PCF) with its lattice of air holes running along the length of the fiber has matured, and the technology provides a large variety of novel optical properties and improvements compared to standard optical fibers. With respect to optical sensors, the photonic crystal structures have several important properties. First of all the wavelength-scale periodically-arranged material structures provide completely new means of fabricating tailored optical properties either using modified total internal reflection or the photonic bandgap effect. Secondly, the new materials with numerous micro- or even nano-scale structures and voids allow for superior mode control, use of polarization properties, and even more a the potential of close interaction between optical field and the material under test. The present paper will be using the example of the relatively mature photonic crystal fiber to discuss the fundamental optical properties of the photonic crystals, and recent examples of their use as optical sensors will be reviewed.

  20. Interaction between two spherical particles in a nematic liquid crystal

    NASA Astrophysics Data System (ADS)

    Fukuda, Jun-Ichi; Stark, Holger; Yoneya, Makoto; Yokoyama, Hiroshi

    2004-04-01

    We numerically investigate the interaction between two spherical particles in a nematic liquid crystal mediated by elastic distortions in the orientational order. We pay attention to the cases where two particles with equal radii R0 impose rigid normal anchoring on their surfaces and carry a pointlike topological defect referred to as a hyperbolic hedgehog. To describe the geometry of our system, we use bispherical coordinates, which prove useful in the implementation of boundary conditions at the particle surfaces and at infinity. We adopt the Landau de Gennes continuum theory in terms of a second-rank tensor order parameter Qij for the description of the orientational order of a nematic liquid crystal. We also utilize an adaptive mesh refinement scheme that has proven to be an efficient way of dealing with topological defects whose core size is much smaller than the particle size. When the two “dipoles,” composed of a particle and a hyperbolic hedgehog, are in parallel directions, the two-particle interaction potential is attractive for large interparticle distances D and proportional to D-3 as expected from the form of the dipole-dipole interaction, until the well-defined potential minimum at D?2.46 R0 is reached. For the antiparallel configuration with no hedgehogs between the two particles, the interaction potential is repulsive and behaves as D-2 for D?10 R0 , which is stronger than the dipole-dipole repulsion ( ˜ D-3 ) expected theoretically as an asymptotic behavior for large D .

  1. Data mining chemistry and crystal structure

    NASA Astrophysics Data System (ADS)

    Yang, Lusann W.

    The availability of large amounts of data generated by high-throughput computing and experimentation has generated interest in the application of machine learning techniques to materials science. Machine learning of materials behavior requires the use of feature vectors that capture compositional or structural information influence a target property. We present methods for assessing the similarity of compositions, substructures, and crystal structures. Similarity measures are important for the classification and clustering of data points, allowing for the organization of data and the prediction of materials properties. The similarity functions between ions, compositions, substructures and crystal structure are based upon a data-mined probability with which two ions will substitute for each other within the same structure prototype. The composition similarity is validated via the prediction of crystal structure prototypes for oxides from the Inorganic Crystal Structure Database. It performs particularly well on the quaternary oxides, predicting the correct prototype within 5 guesses 90% of the time. The sustructural similarity is validated via the prediction of Li insertion sites in the oxides; it finds all of the Li sites with less than 8 incorrect guesses 90% of the time.

  2. Crystal structure of anagyrine perchlorate.

    PubMed

    Turgunov, Kambarali K; Rakhimov, Shukhrat B; Vinogradova, Valentina I; Tashkhodjaev, Bakhodir

    2015-05-01

    The title mol-ecular salt, C15H21N2O(+)·ClO4 (-), crystallizes with four cations (A, B, C and D) and four anions in the chiral unit cell (space group P21). The alkaloid was isolated from the aerial parts of Genista Hispanica collected in the Samarkand region of Uzbekistan. Each cation is protonated at the N atom that bridges the alkaloid rings C and D. In each cation, ring A is almost planar and ring B adops a sofa conformation with the methyl-ene group bridging to the C ring as the flap. Rings C and D adopt chair conformations with a cis ring junction in all four cations. In the crystal, A+B and C+D dimeric pairs linked by pairs of N-H?O hydrogen bonds are observed, which generate R 2 (2)(16) loops in each case. The dimers are consolidated by weak aromatic ?-? stacking inter-actions between the A rings [centroid-centroid distances = 3.913?(3) and 3.915?(3)?Å]. PMID:25995939

  3. Crystal structure and chirality of natural floridoside.

    PubMed

    Simon-Colin, Christelle; Michaud, François; Léger, Jean-Michel; Deslandes, Eric

    2003-10-31

    The crystal structure and absolute configuration of natural floridoside (2-O-alpha-D-galactopyranosylglycerol) were determined by single-crystal X-ray diffraction analysis. The space group is orthorhombic P2(1)2(1)2(1) with Z=4, a=4.885(1), b=9.734(1), c=23.886(2) A at 296 +/- 2 K. The structure was solved by a direct method and refined to R=0.0351 from 1914 reflections of Cu Kalpha radiation. PMID:14572727

  4. Computing stoichiometric molecular composition from crystal structures

    PubMed Central

    Gražulis, Saulius; Merkys, Andrius; Vaitkus, Antanas; Okuli?-Kazarinas, Mykolas

    2015-01-01

    Crystallographic investigations deliver high-accuracy information about positions of atoms in crystal unit cells. For chemists, however, the structure of a molecule is most often of interest. The structure must thus be reconstructed from crystallographic files using symmetry information and chemical properties of atoms. Most existing algorithms faithfully reconstruct separate molecules but not the overall stoichiometry of the complex present in a crystal. Here, an algorithm that can reconstruct stoichiometrically correct multimolecular ensembles is described. This algorithm uses only the crystal symmetry information for determining molecule numbers and their stoichiometric ratios. The algorithm can be used by chemists and crystallographers as a standalone implementation for investigating above-molecular ensembles or as a function implemented in graphical crystal analysis software. The greatest envisaged benefit of the algorithm, however, is for the users of large crystallographic and chemical databases, since it will permit database maintainers to generate stoichiometrically correct chemical representations of crystal structures automatically and to match them against chemical databases, enabling multidisciplinary searches across multiple databases.

  5. Solitons and domain structure in elastic crystals with a microstructure

    Microsoft Academic Search

    G. A. Maugin

    Elastic crystals with a microstructure include ferroelectric crystals, ferromagnetic crystals and crystals with internal mechanical degrees of freedom. In recent works concerning the discrete or continuum modelling of the behavior of such elastic crystals, we have been able to delineate general descriptive framework in which,using the concepts of solitary waves and solitons, the dynamics of simple structures in domains and

  6. Crystal structure of 9-methacryloylanthracene

    PubMed Central

    Agrahari, Aditya; Wagers, Patrick O.; Schildcrout, Steven M.; Masnovi, John; Youngs, Wiley J.

    2015-01-01

    In the title compound, C18H14O, with systematic name 1-(anthracen-9-yl)-2-methyl­prop-2-en-1-one, the ketonic C atom lies 0.2030?(16)?Å out of the anthryl-ring-system plane. The dihedral angle between the planes of the anthryl and methacryloyl moieties is 88.30?(3)° and the stereochemistry about the Csp 2—Csp 2 bond in the side chain is transoid. In the crystal, the end rings of the anthryl units in adjacent mol­ecules associate in parallel–planar orientations [shortest centroid–centroid distance = 3.6320?(7)?Å]. A weak hydrogen bond is observed between an aromatic H atom and the O atom of a mol­ecule displaced by translation in the a-axis direction, forming sheets of parallel-planar anthryl groups packing in this direction.

  7. The Systems Dynamics of the Structured Particles

    E-print Network

    V. M. Somsikov

    2010-06-16

    Dynamics of the structured particles consisting of potentially interacting material points is considered in the framework of classical mechanics. Equations of interaction and motion of structured particles have been derived. The expression for friction force has been obtained. It has been shown that irreversibility of dynamics of structured particles is caused by increase of their internal energy due to the energy of motion. It has been shown also that the dynamics of the structured particles is determined by two types of symmetry: the symmetry of the space and the internal symmetry of the structured particles. Possibility of theoretical substantiation of the laws of thermodynamics has been considered.

  8. Requirements for structure determination of aperiodic crystals

    SciTech Connect

    Li, X.; Stern, E.A.; Ma, Y. (Department of Physics, FM-15, University of Washington, Seattle, Washington 98195 (US))

    1991-01-15

    Using computer simulation, we compared the Patterson functions of one-dimensional (1D) randomly packed and quasiperiodic Fibonacci lattices with or without disorder, and a 2D Penrose lattice and random packing of pentagons (icosahedral glass model). Based on these comparisons, we derived some empirical guidelines for distinguishing ideal quasicrystals from aperiodic crystals with disorder using diffraction data. In contrast to periodic crystals, it is essential to include the background to obtain correct Patterson functions of the average structure since the background contains unresolved peaks. In particular, a Bragg peak scattering measurement {ital cannot}, in general, determine the structure of aperiodic crystals. Instead, a diffuse scattering measurement is required, which determines the absolute value of the diffraction background, in addition to the Bragg peaks. We further estimate that, dependent upon the disorder present, it is necessary to include up to 75% of the total diffracted intensity in any analysis.

  9. Strategies for crystallizing a chromatin protein in complex with the nucleosome core particle.

    PubMed

    Makde, Ravindra D; Tan, Song

    2013-11-15

    The molecular details of how chromatin factors and enzymes interact with the nucleosome are critical to understanding fundamental genetic processes including cell division and gene regulation. A structural understanding of such processes has been hindered by the difficulty in producing diffraction-quality crystals of chromatin proteins in complex with the nucleosome. We describe here the steps used to grow crystals of the 300-kDa RCC1 chromatin factor/nucleosome core particle complex that diffract to 2.9-Å resolution. These steps include both pre- and postcrystallization strategies potentially useful to other complexes. We screened multiple variant RCC1/nucleosome core particle complexes assembled using different RCC1 homologs and deletion variants, and nucleosomes containing nucleosomal DNA with different sequences and lengths, as well as histone deletion variants. We found that using RCC1 from different species produced different crystal forms of the RCC1/nucleosome complex consistent with key crystal packing interactions mediated by RCC1. Optimization of postcrystallization soaks to dehydrate the crystals dramatically improved the diffraction quality of the RCC1/nucleosome crystal from 5.0- to 2.9-Å resolution. PMID:23928047

  10. Flying particle sensors in hollow-core photonic crystal fibre

    NASA Astrophysics Data System (ADS)

    Bykov, D. S.; Schmidt, O. A.; Euser, T. G.; Russell, P. St. J.

    2015-07-01

    Optical fibre sensors make use of diverse physical effects to measure parameters such as strain, temperature and electric field. Here we introduce a new class of reconfigurable fibre sensor, based on a ‘flying-particle’ optically trapped inside a hollow-core photonic crystal fibre and illustrate its use in electric field and temperature sensing with high spatial resolution. The electric field distribution near the surface of a multi-element electrode is measured with a resolution of ?100??m by monitoring changes in the transmitted light signal due to the transverse displacement of a charged silica microparticle trapped within the hollow core. Doppler-based velocity measurements are used to map the gas viscosity, and thus the temperature, along a hollow-core photonic crystal fibre. The flying-particle approach represents a new paradigm in fibre sensors, potentially allowing multiple physical quantities to be mapped with high positional accuracy over kilometre-scale distances.

  11. Surface-induced structures in nematic liquid crystal colloids.

    PubMed

    Chernyshuk, S B; Tovkach, O M; Lev, B I

    2014-08-01

    We predict theoretically the existence of a class of colloidal structures in nematic liquid crystal (NLC) cells, which are induced by surface patterns on the plates of the cell (like cells with UV-irradiated polyamide surfaces using micron sized masks in front of the cell). These bulk structures arise from nonuniform boundary conditions for the director distortions at the confining surfaces. In particular, we demonstrate that quadrupole spherical particles (like spheres with boojums or Saturn-ring director configurations) form a square lattice inside a planar NLC cell, which has checkerboard patterns on both its plates. PMID:25215675

  12. Crystal structure of methane oxidation enzyme determined

    SciTech Connect

    Baum, R.

    1994-01-10

    A team of chemists has determined to 2.2-[angstrom] resolution the crystal structure of the hydroxylase protein of methane monooxygenase, the enzyme system responsible for the biological oxidation of methane. The hydroxylase, at a molecular weight of 251,000 daltons, if by far the largest component of methane monooxygenase. Although the crystal structure of the hydroxylase did not reveal any startling surprises about the enzyme-many features of the hydroxylase had been inferred previously from modeling and spectroscopic studies -- obtaining it is a significant achievement. For one thing, the crystal structure unambiguously confirms aspects of the enzyme structure that been at least somewhat speculative. The three-dimensional structure of the enzyme, the chemist say, also provides important insight into biological methane oxidation, including how methane, a relatively inert gas, might diffuse to and bind near the active site of the enzyme. The structure points to particular amino acid residues that are likely to participate in catalysis, and clarifies the structure of the dinuclear iron core of the enzyme.

  13. Crystal structure of the anthrax lethal factor

    Microsoft Academic Search

    Andrew D. Pannifer; Thiang Yian Wong; Robert Schwarzenbacher; Martin Renatus; Carlo Petosa; Jadwiga Bienkowska; D. Borden Lacy; R. John Collier; Stephen H. Leppla; Philip Hanna; Robert C. Liddington

    2001-01-01

    Lethal factor (LF) is a protein (relative molecular mass 90,000) that is critical in the pathogenesis of anthrax. It is a highly specific protease that cleaves members of the mitogen-activated protein kinase kinase (MAPKK) family near to their amino termini, leading to the inhibition of one or more signalling pathways. Here we describe the crystal structure of LF and its

  14. Phononic crystals of spherical particles: A tight binding approach

    SciTech Connect

    Mattarelli, M., E-mail: maurizio.mattarelli@fisica.unipg.it [NiPS Laboratory, Dipartimento di Fisica, Università di Perugia, Via Pascoli, 06100 Perugia (Italy); Secchi, M. [CMM - Fondazione Bruno Kessler, Via Sommarive 18, 38123 Trento (Italy) [CMM - Fondazione Bruno Kessler, Via Sommarive 18, 38123 Trento (Italy); Dipartimento di Fisica, Università di Trento, Via Sommarive 14, 38123 Trento (Italy); Montagna, M. [Dipartimento di Fisica, Università di Trento, Via Sommarive 14, 38123 Trento (Italy)] [Dipartimento di Fisica, Università di Trento, Via Sommarive 14, 38123 Trento (Italy)

    2013-11-07

    The vibrational dynamics of a fcc phononic crystal of spheres is studied and compared with that of a single free sphere, modelled either by a continuous homogeneous medium or by a finite cluster of atoms. For weak interaction among the spheres, the vibrational dynamics of the phononic crystal is described by shallow bands, with low degree of dispersion, corresponding to the acoustic spheroidal and torsional modes of the single sphere. The phonon displacements are therefore related to the vibrations of a sphere, as the electron wave functions in a crystal are related to the atomic wave functions in a tight binding model. Important dispersion is found for the two lowest phonon bands, which correspond to zero frequency free translation and rotation of a free sphere. Brillouin scattering spectra are calculated at some values of the exchanged wavevectors of the light, and compared with those of a single sphere. With weak interaction between particles, given the high acoustic impedance mismatch in dry systems, the density of phonon states consist of sharp bands separated by large gaps, which can be well accounted for by a single particle model. Based on the width of the frequency gaps, tunable with the particle size, and on the small number of dispersive acoustic phonons, such systems may provide excellent materials for application as sound or heat filters.

  15. Phononic crystals of spherical particles: A tight binding approach

    NASA Astrophysics Data System (ADS)

    Mattarelli, M.; Secchi, M.; Montagna, M.

    2013-11-01

    The vibrational dynamics of a fcc phononic crystal of spheres is studied and compared with that of a single free sphere, modelled either by a continuous homogeneous medium or by a finite cluster of atoms. For weak interaction among the spheres, the vibrational dynamics of the phononic crystal is described by shallow bands, with low degree of dispersion, corresponding to the acoustic spheroidal and torsional modes of the single sphere. The phonon displacements are therefore related to the vibrations of a sphere, as the electron wave functions in a crystal are related to the atomic wave functions in a tight binding model. Important dispersion is found for the two lowest phonon bands, which correspond to zero frequency free translation and rotation of a free sphere. Brillouin scattering spectra are calculated at some values of the exchanged wavevectors of the light, and compared with those of a single sphere. With weak interaction between particles, given the high acoustic impedance mismatch in dry systems, the density of phonon states consist of sharp bands separated by large gaps, which can be well accounted for by a single particle model. Based on the width of the frequency gaps, tunable with the particle size, and on the small number of dispersive acoustic phonons, such systems may provide excellent materials for application as sound or heat filters.

  16. Crystallization and order-disorder transition of colloidal particles in a drying suspension: a phase field crystal approach

    E-print Network

    Nirmalendu Ganai; Arnab Saha; Surajit Sengupta

    2012-09-05

    Using a phase field crystal model we study the structure and dynamics of a drop of colloidal suspension during evaporation of the solvent. We model an experimental system where contact line pinning of the drop on the substrate is non-existent. Under such carefully controlled conditions, evaporation of the drop produces an ordered or disordered arrangement of the colloidal residue depending on the initial average density of solute and the drying rate. We obtain a non-equilibrium phase boundary showing amorphous and crystalline phases of single component and binary mixtures of colloidal particles in the density- drying rate plane. While single component colloids order in the two dimensional triangular lattice, a symmetric binary mixture of mutually repulsive particles orders in a three sub-lattice order where two of the sub-lattices of the triangular lattice are occupied by the two species of particles with the third sub-lattice vacant.

  17. Crystal structure of a plectonemic RNA supercoil

    SciTech Connect

    Stagno, Jason R.; Ma, Buyong; Li, Jess; Altieri, Amanda S.; Byrd, R. Andrew; Ji, Xinhua (NCI); (Maryland)

    2012-12-14

    Genome packaging is an essential housekeeping process in virtually all organisms for proper storage and maintenance of genetic information. Although the extent and mechanisms of packaging vary, the process involves the formation of nucleic-acid superstructures. Crystal structures of DNA coiled coils indicate that their geometries can vary according to sequence and/or the presence of stabilizers such as proteins or small molecules. However, such superstructures have not been revealed for RNA. Here we report the crystal structure of an RNA supercoil, which displays one level higher molecular organization than previously reported structures of DNA coiled coils. In the presence of an RNA-binding protein, two interlocking RNA coiled coils of double-stranded RNA, a 'coil of coiled coils', form a plectonemic supercoil. Molecular dynamics simulations suggest that protein-RNA interaction is required for the stability of the supercoiled RNA. This study provides structural insight into higher order packaging mechanisms of nucleic acids.

  18. Crystal structures of monohalogenated benzoic acids

    Microsoft Academic Search

    Olga V. Grineva; Petr M. Zorky; Evgenij S. Rostov

    2007-01-01

    Crystal structures resulting from a combination of different types of specific intermolecular interactions have been analysed\\u000a using examples of 12 monohalogenated benzoic acids (HBA). These have been compared with structures known for corresponding\\u000a monofunctional compounds, namely benzoic acid, fluorobenzene, chlorobenzene and iodobenzene. It is found that common for carboxylic\\u000a acids centrosymmetric hydrogen-bonded dimers exist in all HBA, and at the same

  19. Genesis of crystal structures of superconducting oxides

    SciTech Connect

    Dmitriev, V.P. [Rostov State Univ., Rostov-na-Donu (Russian Federation); Toledano, P. [Universite de Pikardie, Amiens (France)

    1995-05-01

    Using a phenomenological approach, we show that various structural types of HTSC oxides can be derived from the general latent body-centered structure. The parameters, describing ordering mechanisms and ion displacements that lead to the real crystal structures of HTSC oxides belong to the same {Gamma}-{Delta}-{Zeta} direction in the Brillouin zone of the cubic latent phase. New families of HTSC compounds, differing from the known ones by the presence of low-dimensional structural elements, are proposed. 14 refs., 2 tabs.

  20. Transfer-Printing and Host?Guest Properties of 3D Supramolecular Particle Structures

    Microsoft Academic Search

    Xing Yi Ling; In Yee Phang; David N. Reinhoudt; G. Julius Vancso; Jurriaan Huskens

    2009-01-01

    Mechanically robust and crystalline supramolecular particle structures have been constructed by decoupling nanoparticle assembly and supramolecular glue infiltration into a sequential process. First, ?-cyclodextrin (CD)-functionalized polystyrene particles (d 500 nm) were assembled on a CD-functionalized surface via convective assembly to form highly ordered, but mechanically unstable, particle crystals. Subsequently, the crystals were infiltrated by a solution of adamantyl-functionalized dendrimers, functioning

  1. 5.841 Crystal Structure Refinement, Fall 2006

    E-print Network

    Mueller, Peter

    This course in crystal structure refinement examines the practical aspects of crystal structure determination from data collection strategies to data reduction and basic and advanced refinement problems of organic and ...

  2. 5.067 Crystal Structure Refinement, Fall 2007

    E-print Network

    Mueller, Peter

    This course in crystal structure refinement examines the practical aspects of crystal structure determination from data collection strategies to data reduction and basic and advanced refinement problems of organic and ...

  3. 'Weird' crystal structures of elements at high pressure

    Microsoft Academic Search

    Tat'yana N Kolobyanina

    2002-01-01

    New crystal structures, in particular incommensurate composite crystals, discovered in the high-pressure phases of Group I, II, IV, and V elements are described, and their intermetallic and other binary structural analogs are discussed.

  4. Crystal structure refinement from electron diffraction data

    NASA Astrophysics Data System (ADS)

    Dudka, A. P.; Avilov, A. S.; Lepeshov, G. G.

    2008-05-01

    A procedure of crystal structure refinement from electron diffraction data is described. The electron diffraction data on polycrystalline films are processed taking into account possible overlap of reflections and two-beam interaction. The diffraction from individual single crystals in an electron microscope equipped with a precession attachment is described using the Bloch-wave method, which takes into account multibeam scattering, and a special approach taking into consideration the specific features of the diffraction geometry in the precession technique. Investigations were performed on LiF, NaF, CaF2, and Si crystals. A method for reducing experimental data, which allows joint electron and X-ray diffraction study, is proposed.

  5. Crystal structure refinement from electron diffraction data

    SciTech Connect

    Dudka, A. P., E-mail: dudka@ns.crys.ras.ru; Avilov, A. S.; Lepeshov, G. G. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2008-05-15

    A procedure of crystal structure refinement from electron diffraction data is described. The electron diffraction data on polycrystalline films are processed taking into account possible overlap of reflections and two-beam interaction. The diffraction from individual single crystals in an electron microscope equipped with a precession attachment is described using the Bloch-wave method, which takes into account multibeam scattering, and a special approach taking into consideration the specific features of the diffraction geometry in the precession technique. Investigations were performed on LiF, NaF, CaF{sub 2}, and Si crystals. A method for reducing experimental data, which allows joint electron and X-ray diffraction study, is proposed.

  6. STRUCTURE NOTE Crystal Structure of Stilbene Synthase From Arachis

    E-print Network

    Suh, Dae-Yeon

    .3.1.95] and chalcone synthase (CHS; EC 2.3.1.74) are members of the type III polyketide synthases (PKSs) and plantSTRUCTURE NOTE Crystal Structure of Stilbene Synthase From Arachis hypogaea Yasuhito Shomura,1 Institute/SPring-8, Hyogo, Japan Introduction. Stilbene synthase [STS; Enzyme Commis- sion (EC) 2

  7. Crystal Structures Classifier for an Evolutionary Algorithm Structure Predictor

    E-print Network

    Oganov, Artem R.

    Crystal Structures Classifier for an Evolutionary Algorithm Structure Predictor Mario Valle Data expertise. The use of the classifier has already accelerated the analysis of US- PEX output by at least one]: Design Methodology--Classifier design and evaluation 1 INTRODUCTION USPEX [20] is a computational method

  8. Soviet research on crystal channeling of charged particle beams

    NASA Astrophysics Data System (ADS)

    Kassel, S.

    1985-03-01

    This report presents an overview of Soviet research in charged particle beam channeling in crystals from 1972 to the present, and the resulting electromagnetic emission, including Soviet proposals for channeling emission lasers in the X-ray region of the spectrum. It analyzes Soviet attitudes toward crystal channeling of charged particles as a subject of research, describes performers of the research, and indicates the level of effort involved. It presents a brief history of crystal channeling research, the differences between channeling and other kinds of electromagnetic radiation, the definition of the main research issues, and estimates of the potential capabilities of channeling radiation, all based on the Soviet viewpoint. It then describes Soviet proposals for laser systems utilizing the channeling radiation mechanism, and analyzes Soviet experimental work involving the observation and measurement of channeling radiation. The author concludes that the outstanding feature of Soviet research in this area is the optimistic belief of Soviet specialists in the technological potential of this research, but finds that the role of the laser proposals in Soviet planning is ambiguous.

  9. Fourier Analysis and Structure Determination--Part III: X-ray Crystal Structure Analysis.

    ERIC Educational Resources Information Center

    Chesick, John P.

    1989-01-01

    Discussed is single crystal X-ray crystal structure analysis. A common link between the NMR imaging and the traditional X-ray crystal structure analysis is reported. Claims that comparisons aid in the understanding of both techniques. (MVL)

  10. Reflection of multidomain structured cholesteric liquid crystals

    Microsoft Academic Search

    Christian Bohley; Toralf Scharf; Rolf Klappert; Joachim Grupp

    2001-01-01

    The simulation of polymer-dispersed cholesteric liquid crystals is carried out using a model, which takes into account the domain structure of the layer. The model is based on the 4x4 matrix calculation method of Berreman. One considers different orientations of the helical axis in multi- and single-domain configurations. The distribution of the helical axis orientations in the multi-domain model allows

  11. Observations on the crystal structures of lueshite

    NASA Astrophysics Data System (ADS)

    Mitchell, Roger H.; Burns, Peter C.; Knight, Kevin S.; Howard, Christopher J.; Chakhmouradian, Anton R.

    2014-06-01

    Laboratory powder XRD patterns of the perovskite-group mineral lueshite from the type locality (Lueshe, Kivu, DRC) and pure NaNbO3 demonstrate that lueshite does not adopt the same space group ( Pbma; #57) as the synthetic compound. The crystal structures of lueshite (2 samples) from Lueshe, Mont Saint-Hilaire (Quebec, Canada) and Sallanlatvi (Kola, Russia) have been determined by single-crystal CCD X-ray diffraction. These room temperature X-ray data for all single-crystal samples can be satisfactorily refined in the orthorhombic space group Pbnm (#62). Cell dimensions, atomic coordinates of the atoms, bond lengths and octahedron tilt angles are given for four crystals. Conventional neutron diffraction patterns for Lueshe lueshite recorded over the temperature range 11-1,000 K confirm that lueshite does not adopt space group Pbma within these temperatures. Neutron diffraction indicates no phase changes on cooling from room temperature to 11 K. None of these neutron diffraction data give satisfactorily refinements but suggest that this is the space group Pbnm. Time-of-flight neutron diffraction patterns for Lueshe lueshite recorded from room temperature to 700 °C demonstrate phase transitions above 550 °C from Cmcm through P4 /mbm to above 650 °C. Cell dimensions and atomic coordinates of the atoms are given for the three high-temperature phases. The room temperature to 400 °C structures cannot be satisfactorily resolved, and it is suggested that the lueshite at room temperature consists of domains of pinned metastable phases with orthorhombic and/or monoclinic structures. However, the sequence of high-temperature phase transitions observed is similar to those determined for synthetic NaTaO3, suggesting that the equilibrated room temperature structure of lueshite is orthorhombic Pbnm.

  12. Structure and Elasticity of Nematic and Isotropic Liquid Crystals

    E-print Network

    liquid crystals consisting of soft­ellipsoidal particles. (2) The correla­ tion functions in the bulk calculations. We model the nematic liquid crystals molecules as soft­ellipsoidal particles interacting through in spherical harmonics, taking the dependence of these functions on the orientation of the director

  13. Structure and Elasticity of Nematic and Isotropic Liquid Crystals

    E-print Network

    liquid crystals consisting of soft-ellipsoidal particles. (2) The correla- tion functions in the bulk calculations. We model the nematic liquid crystals molecules as soft-ellipsoidal particles interacting through correlation function. We expand all these functions in spherical harmonics, taking the dependence

  14. Crystallization and preliminary X-ray diffraction analysis of recombinant hepatitis E virus-like particle

    SciTech Connect

    Wang, Che-Yen [Molecular and Cellular Biology, University of California, Davis, CA 95616 (United States); Karolinska Institute Structural Virology, F68 Karolinska University Hospital, SE-14186 Stockholm (Sweden); Institute of Public Health, National Yang-Ming University, 112 Taipei,Taiwan (China); Miyazaki, Naoyuki [Molecular and Cellular Biology, University of California, Davis, CA 95616 (United States); Karolinska Institute Structural Virology, F68 Karolinska University Hospital, SE-14186 Stockholm (Sweden); Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Yamashita, Tetsuo [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Institute for Microbial Diseases, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Higashiura, Akifumi; Nakagawa, Atsushi [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Li, Tian-Cheng; Takeda, Naokazu [Department of Virology II, National Institute of Infectious Diseases, Tokyo (Japan); Xing, Li [Molecular and Cellular Biology, University of California, Davis, CA 95616 (United States); Karolinska Institute Structural Virology, F68 Karolinska University Hospital, SE-14186 Stockholm (Sweden); Hjalmarsson, Erik; Friberg, Claes [Crystal Research AB, 22370 Lund (Sweden); Liou, Der-Ming [Institute of Public Health, National Yang-Ming University, 112 Taipei,Taiwan (China); Sung, Yen-Jen [Institute of Public Health, National Yang-Ming University, 112 Taipei,Taiwan (China); Institute of Anatomy and Cell Biology, National Yang-Ming University, 112 Taipei,Taiwan (China); Tsukihara, Tomitake [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Matsuura, Yoshiharu [Institute for Microbial Diseases, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Miyamura, Tatsuo [Department of Virology II, National Institute of Infectious Diseases, Tokyo (Japan); Cheng, R. Holland, E-mail: rhch@ucdavis.edu [Molecular and Cellular Biology, University of California, Davis, CA 95616 (United States); Karolinska Institute Structural Virology, F68 Karolinska University Hospital, SE-14186 Stockholm (Sweden)

    2008-04-01

    A recombinant virus-like particle that is a potential oral hepatitis E vaccine was crystallized. Diffraction data were collected to 8.3 Å resolution and the X-ray structure was phased with the aid of a low-resolution density map determined using cryo-electron microscopy data. Hepatitis E virus (HEV) accounts for the majority of enterically transmitted hepatitis infections worldwide. Currently, there is no specific treatment for or vaccine against HEV. The major structural protein is derived from open reading frame (ORF) 2 of the viral genome. A potential oral vaccine is provided by the virus-like particles formed by a protein construct of partial ORF3 protein (residue 70–123) fused to the N-terminus of the ORF2 protein (residues 112–608). Single crystals obtained by the hanging-drop vapour-diffusion method at 293 K diffract X-rays to 8.3 Å resolution. The crystals belong to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 337, b = 343, c = 346 Å, ? = ? = ? = 90°, and contain one particle per asymmetric unit.

  15. Geometry of crystal structure with defects. I. Euclidean picture

    SciTech Connect

    Trzesowski, A.

    1987-04-01

    Continuously distributed defects of crystal structure are considered. The starting point is the Euclidean geometry of the ideal crystal lattice and the topological description of the distortion of the crystal structure. It is shown how the non-Euclidean geometry of distorted crystal structure, as well as the basic assumptions of the phenomenological plasticity theory concerning the deformation of a continuum, are related to those theories. A form for an affine connection describing continuously distributed dislocations is proposed.

  16. Nonviscous motion of a slow particle in a dust crystal under microgravity conditions.

    PubMed

    Zhukhovitskii, D I; Fortov, V E; Molotkov, V I; Lipaev, A M; Naumkin, V N; Thomas, H M; Ivlev, A V; Schwabe, M; Morfill, G E

    2012-07-01

    Subsonic motion of a large particle moving through the bulk of a dust crystal formed by negatively charged small particles is investigated using the PK-3 Plus laboratory onboard the International Space Station. Tracing the particle trajectories shows that the large particle moves almost freely through the bulk of the plasma crystal, while dust particles move along characteristic ?-shaped pathways near the large particle. In the hydrodynamic approximation, we develop a theory of nonviscous dust particle motion about a large particle and calculate particle trajectories. Good agreement with experiment validates our approach. PMID:23005544

  17. Crystal structure and interaction dependence of the crystal-melt interfacial free energy

    E-print Network

    Davidchack, R. L.; Laird, Brian Bostian

    2005-03-01

    We examine via molecular simulation the dependence of the crystal-melt interfacial free energy gamma on molecular interaction and crystal structure (fcc vs bcc) for systems interacting with inverse-power repulsive potentials, u...

  18. Cloud structure and crystal growth in nimbostratus clouds. Mengistu Wolde*

    E-print Network

    Vali, Gabor

    1 Cloud structure and crystal growth in nimbostratus clouds. Mengistu Wolde* , Gabor Vali-mail: mengistu.wolde@nrc.ca. #12;2 Abstract Cloud structure and crystal growth in two nimbostratus were examined made available by large scale lifting was taken up by depositional growth of the ice crystals

  19. PROTEIN STRUCTURE REPORT Crystal structure of the Yersinia type III

    E-print Network

    Yersinia pestis utilizes a contact-dependent (type III) secretion system (T3SS) to transport virulence of oligomerization is discussed. Keywords: Yersinia pestis; plague; type III secretion; YscE; crystal structure Yersinia pestis, the causative agent of plague, utilizes a type III secretion system (T3SS) to inject

  20. Crystal structure of MboIIA methyltransferase

    PubMed Central

    Osipiuk, Jerzy; Walsh, Martin A.; Joachimiak, Andrzej

    2003-01-01

    DNA methyltransferases (MTases) are sequence-specific enzymes which transfer a methyl group from S-adenosyl-l-methionine (AdoMet) to the amino group of either cytosine or adenine within a recognized DNA sequence. Methylation of a base in a specific DNA sequence protects DNA from nucleolytic cleavage by restriction enzymes recognizing the same DNA sequence. We have determined at 1.74 ? resolution the crystal structure of a ?-class DNA MTase MboIIA (M·MboIIA) from the bacterium Moraxella bovis, the smallest DNA MTase determined to date. M·MboIIA methylates the 3? adenine of the pentanucleotide sequence 5?-GAAGA-3?. The protein crystallizes with two molecules in the asymmetric unit which we propose to resemble the dimer when M·MboIIA is not bound to DNA. The overall structure of the enzyme closely resembles that of M·RsrI. However, the cofactor-binding pocket in M·MboIIA forms a closed structure which is in contrast to the open-form structures of other known MTases. PMID:12954781

  1. Crystal structure of MboIIA methyltransferase.

    PubMed

    Osipiuk, Jerzy; Walsh, Martin A; Joachimiak, Andrzej

    2003-09-15

    DNA methyltransferases (MTases) are sequence-specific enzymes which transfer a methyl group from S-adenosyl-L-methionine (AdoMet) to the amino group of either cytosine or adenine within a recognized DNA sequence. Methylation of a base in a specific DNA sequence protects DNA from nucleolytic cleavage by restriction enzymes recognizing the same DNA sequence. We have determined at 1.74 A resolution the crystal structure of a beta-class DNA MTase MboIIA (M.MboIIA) from the bacterium Moraxella bovis, the smallest DNA MTase determined to date. M.MboIIA methylates the 3' adenine of the pentanucleotide sequence 5'-GAAGA-3'. The protein crystallizes with two molecules in the asymmetric unit which we propose to resemble the dimer when M.MboIIA is not bound to DNA. The overall structure of the enzyme closely resembles that of M.RsrI. However, the cofactor-binding pocket in M.MboIIA forms a closed structure which is in contrast to the open-form structures of other known MTases. PMID:12954781

  2. Large-area optoelastic manipulation of colloidal particles in liquid crystals using photoresponsive molecular surface monolayers

    PubMed Central

    Martinez, Angel; Mireles, Hector C.; Smalyukh, Ivan I.

    2011-01-01

    Noncontact optical trapping and manipulation of micrometer- and nanometer-sized particles are typically achieved by use of forces and torques exerted by tightly focused high-intensity laser beams. Although they were instrumental for many scientific breakthroughs, these approaches find few technological applications mainly because of the small-area manipulation capabilities, the need for using high laser powers, limited application to anisotropic fluids and low-refractive-index particles, as well as complexity of implementation. To overcome these limitations, recent research efforts have been directed toward extending the scope of noncontact optical control through the use of optically-guided electrokinetic forces, vortex laser beams, plasmonics, and optofluidics. Here we demonstrate manipulation of colloidal particles and self-assembled structures in nematic liquid crystals by means of single-molecule-thick, light-controlled surface monolayers. Using polarized light of intensity from 1,000 to 100,000 times smaller than that in conventional optical tweezers, we rotate, translate, localize, and assemble spherical and complex-shaped particles of various sizes and compositions. By controlling boundary conditions through the monolayer, we manipulate the liquid crystal director field and the landscape of ensuing elastic forces exerted on colloids by the host medium. This permits the centimeter-scale, massively parallel manipulation of particles and complex colloidal structures that can be dynamically controlled by changing illumination or assembled into stationary stable configurations dictated by the “memorized” optoelastic potential landscape due to the last illumination pattern. We characterize the strength of optically guided elastic forces and discuss the potential uses of this noncontact manipulation in fabrication of novel optically- and electrically-tunable composites from liquid crystals and colloids. PMID:22160673

  3. Electron Cryomicroscopy of Membrane Proteins: Specimen Preparation for Two-Dimensional Crystals and Single Particles

    PubMed Central

    Schmidt-Krey, Ingeborg; Rubinstein, John L.

    2010-01-01

    Membrane protein structure and function can be studied by two powerful and highly complementary electron cryomicroscopy (cryo-EM) methods: electron crystallography of two-dimensional (2D) crystals and single particle analysis of detergent-solubilized protein complexes. To obtain the highest-possible resolution data from membrane proteins, whether prepared as 2D crystals or single particles, cryo-EM samples must be vitrified with great care. Grid preparation for cryo-EM of 2D crystals is possible by back-injection, the carbon sandwich technique, drying in sugars before cooling in the electron microscope, or plunge-freezing. Specimen grids for single particle cryo-EM studies of membrane proteins are usually produced by plunge-freezing protein solutions, supported either by perforated or a continuous carbon film substrate. This review outlines the different techniques available and the suitability of each method for particular samples and studies. Experimental considerations in sample preparation and preservation include the protein itself and the presence of lipid or detergent. The appearance of cryo-EM samples in different conditions is also discussed. PMID:20678942

  4. Crystal structure of plant photosystem I

    NASA Astrophysics Data System (ADS)

    Ben-Shem, Adam; Frolow, Felix; Nelson, Nathan

    2003-12-01

    Oxygenic photosynthesis is the principal producer of both oxygen and organic matter on Earth. The conversion of sunlight into chemical energy is driven by two multisubunit membrane protein complexes named photosystem I and II. We determined the crystal structure of the complete photosystem I (PSI) from a higher plant (Pisum sativum var. alaska) to 4.4Å resolution. Its intricate structure shows 12 core subunits, 4 different light-harvesting membrane proteins (LHCI) assembled in a half-moon shape on one side of the core, 45 transmembrane helices, 167 chlorophylls, 3 Fe-S clusters and 2 phylloquinones. About 20 chlorophylls are positioned in strategic locations in the cleft between LHCI and the core. This structure provides a framework for exploration not only of energy and electron transfer but also of the evolutionary forces that shaped the photosynthetic apparatus of terrestrial plants after the divergence of chloroplasts from marine cyanobacteria one billion years ago.

  5. Portlandite crystal: Bulk, bilayer, and monolayer structures

    NASA Astrophysics Data System (ADS)

    Aierken, Y.; Sahin, H.; Iyikanat, F.; Horzum, S.; Suslu, A.; Chen, B.; Senger, R. T.; Tongay, S.; Peeters, F. M.

    2015-06-01

    Ca(OH)2 crystals, well known as portlandite, are grown in layered form, and we found that they can be exfoliated on different substrates. We performed first principles calculations to investigate the structural, electronic, vibrational, and mechanical properties of bulk, bilayer, and monolayer structures of this material. Different from other lamellar structures such as graphite and transition-metal dichalcogenides, intralayer bonding in Ca(OH)2 is mainly ionic, while the interlayer interaction remains a weak dispersion-type force. Unlike well-known transition-metal dichalcogenides that exhibit an indirect-to-direct band gap crossover when going from bulk to a single layer, Ca(OH)2 is a direct band gap semiconductor independent of the number layers. The in-plane Young's modulus and the in-plane shear modulus of monolayer Ca(OH)2 are predicted to be quite low while the in-plane Poisson ratio is larger in comparison to those in the monolayer of ionic crystal BN. We measured the Raman spectrum of bulk Ca(OH)2 and identified the high-frequency OH stretching mode A1 g at 3620 cm-1 . In this study, bilayer and monolayer portlandite [Ca(OH)2 ] are predicted to be stable and their characteristics are analyzed in detail. Our results can guide further research on ultrathin hydroxites.

  6. Crystal structure of rasvumite, KFerS

    Microsoft Academic Search

    R. Crem

    1980-01-01

    Rasvumite, KFerSr, isostructural with BaFerS, described by Hong and Steinfink (1972), is orthorhombic, Cmcm, a :9.M9(6), D : I1.019(7), c : 5.431()A, V : 541.543, Z: 4, density (calc) : 3.O29 g cm-3. Least-squares refinement of 332 single-crystal hkl redue,ed the conven- tional residual to 0.081. The structure contains double edge-sharing chains of Fe-S tetra- hedra parallel to c and

  7. Particle Size Distribution and Magnetic Structure of Colloidal Ferrite Particles.

    NASA Astrophysics Data System (ADS)

    Yu, Zhong Chen

    A colloidal suspension of very fine magnetic particles is called a ferromagnetic liquid, or "ferrofluid". The colloidal particles are extremely small (~ 10 nm, or 100 angstrom) and are found to be very different in their magnetic properties from the bulk material. The size of such particles, defined by images observed by electron microscopy of a sample and called the physical size, usually ranges from 50 to 300 angstrom in diameter. Magnetic domain theory predicts that if the size of a particle is smaller than the critical value it will likely become single domain particle. The size of such a domain is called the magnetic moment size, or simply 'magnetic size', which is defined as the cube root of magnetic moment of a particle divided by 4pi/3 times the saturated magnetization of the bulk material (for a spherical particle). The first goal in this investigation is to determine the physical size and the magnetic size of particles in given samples. The second goal is to answer the question: if the magnetic size of a particle is smaller than the critical value, is the particle necessarily a single domain particle? If the particle magnetic size is smaller than its physical size, what is the magnetization distribution within the particle and the 'magnetic structure' of the particle?. The sample of colloidal particles used in this investigation is a water based Fe_3O _4 ferrofluid designated EMG805 made by Ferrofluidics Corp. In order to determine the dependence of various quantities on particle size, the sample was fractionationed using chromatographic techniques. The original sample was also diluted into different dilutions, which were used to obtain information about the effects of interparticle interactions. A colloid of CoFe_2O _4 suspended in kerosene obtained from G. E. Corp. was also investigated. Fractionation was not performed as kerosene is not compatible with the available gel. Its magnetic, physical and crystallite size distributions were also determined. Experiments employed electron microscopy, small angle neutron scattering with and without polarized neutrons, magnetization measurement and X-ray powder diffraction. It has been found that the independent domain model of colloidal particles should be replaced by a mixture model. (Abstract shortened with permission of author.).

  8. Soft-core particles freezing to form a quasicrystal and a crystal-liquid phase

    E-print Network

    A. J. Archer; A. M. Rucklidge; E. Knobloch

    2015-07-07

    Systems of soft-core particles interacting via a two-scale potential are studied. The potential is responsible for peaks in the structure factor of the liquid state at two different but comparable length scales, and a similar bimodal structure is evident in the dispersion relation. Dynamical density functional theory in two dimensions is used to identify two novel states of this system, the crystal-liquid state, in which the majority of the particles are located on lattice sites but a minority remains free and so behaves like a liquid, and a 12-fold quasicrystalline state. Both are present even for deeply quenched liquids and are found in a regime in which the liquid is unstable with respect to modulations on the smaller scale only. As a result the system initially evolves towards a small scale crystal state; this state is not a minimum of the free energy, however, and so the system subsequently attempts to reorganize to generate the lower energy larger scale crystals. This dynamical process generates a disordered state with quasicrystalline domains, and takes place even when this large scale is linearly stable, i.e., it is a nonlinear process. With controlled initial conditions a perfect quasicrystal can form. The results are corroborated using Brownian dynamics simulations.

  9. Structural evolution of colloidal crystal films in the process of melting revealed by bragg peak analysis.

    PubMed

    Sulyanova, Elena A; Shabalin, Anatoly; Zozulya, Alexey V; Meijer, Janne-Mieke; Dzhigaev, Dmitry; Gorobtsov, Oleg; Kurta, Ruslan P; Lazarev, Sergey; Lorenz, Ulf; Singer, Andrej; Yefanov, Oleksandr; Zaluzhnyy, Ivan; Besedin, Ilya; Sprung, Michael; Petukhov, Andrei V; Vartanyants, Ivan A

    2015-05-19

    In situ X-ray diffraction studies of structural evolution of colloidal crystal films formed by polystyrene spherical particles upon incremental heating are reported. The Bragg peak parameters, such as peak position, integrated intensity, and radial and azimuthal widths were analyzed as a function of temperature. A quantitative study of colloidal crystal lattice distortions and mosaic spread as a function of temperature was carried out using Williamson-Hall plots based on mosaic block model. The temperature dependence of the diameter of polystyrene particles was obtained from the analysis of Bragg peaks, and the form factor contribution extracted from the diffraction patterns. Four stages of structural evolution in a colloidal crystal upon heating were identified. Based on this analysis, a model of the heating and melting process in the colloidal crystal film is suggested. PMID:25594683

  10. Exciton dynamics in alpha-particle tracks in organic crystals: Magnetic field study of the scintillation in tetracene crystals

    Microsoft Academic Search

    Nicholas E. Geacintov; Michael Binder; Charles E. Swenberg; Martin Pope

    1975-01-01

    The mechanisms of scintillation of organic crystals bombarded by alpha particles are discussed in terms of the current knowledge of exciton dynamics, which has been derived from a study of the photofluorescence of crystals such as anthracene and tetracene. The scintillation of tetracene excited by 4.4-MeV alpha particles incident in a direction perpendicular to the ab plane has been studied

  11. Crystal structure of yeast Sco1

    SciTech Connect

    Abajian, Carnie; Rosenzweig, Amy C. (NWU)

    2010-03-05

    The Sco family of proteins are involved in the assembly of the dinuclear CuA site in cytochrome c oxidase (COX), the terminal enzyme in aerobic respiration. These proteins, which are found in both eukaryotes and prokaryotes, are characterized by a conserved CXXXC sequence motif that binds copper ions and that has also been proposed to perform a thiol:disulfide oxidoreductase function. The crystal structures of Saccharomyces cerevisiae apo Sco1 (apo-ySco1) and Sco1 in the presence of copper ions (Cu-ySco1) were determined to 1.8- and 2.3-{angstrom} resolutions, respectively. Yeast Sco1 exhibits a thioredoxin-like fold, similar to that observed for human Sco1 and a homolog from Bacillus subtilis. The Cu-ySco1 structure, obtained by soaking apo-ySco1 crystals in copper ions, reveals an unexpected copper-binding site involving Cys181 and Cys216, cysteine residues present in ySco1 but not in other homologs. The conserved CXXXC cysteines, Cys148 and Cys152, can undergo redox chemistry in the crystal. An essential histidine residue, His239, is located on a highly flexible loop, denoted the Sco loop, and can adopt positions proximal to both pairs of cysteines. Interactions between ySco1 and its partner proteins yeast Cox17 and yeast COX2 are likely to occur via complementary electrostatic surfaces. This high-resolution model of a eukaryotic Sco protein provides new insight into Sco copper binding and function.

  12. Crystal structure of human cathepsin V.

    PubMed

    Somoza, J R; Zhan, H; Bowman, K K; Yu, L; Mortara, K D; Palmer, J T; Clark, J M; McGrath, M E

    2000-10-17

    Cathepsin V is a lysosomal cysteine protease that is expressed in the thymus, testis and corneal epithelium. We have determined the 1.6 A resolution crystal structure of human cathepsin V associated with an irreversible vinyl sulfone inhibitor. The fold of this enzyme is similar to the fold adopted by other members of the papain superfamily of cysteine proteases. This study provides a framework for understanding the structural basis for cathepsin V's activity and will aid in the design of inhibitors of this enzyme. A comparison of cathepsin V's active site with the active sites of related proteases revealed a number of differences, especially in the S2 and S3 subsites, that could be exploited in identifying specific cathepsin V inhibitors or in identifying inhibitors of other cysteine proteases that would be selective against cathepsin V. PMID:11027133

  13. Some Lower Valence Vanadium Fluorides: Their Crystal Distortions, Domain Structures, Modulated Structures, Ferrimagnetism, and Composition Dependence.

    ERIC Educational Resources Information Center

    Hong, Y. S.; And Others

    1980-01-01

    Describes some contemporary concepts unique to the structure of advanced solids, i.e., their crystal distortions, domain structures, modulated structures, ferrimagnetism, and composition dependence. (Author/CS)

  14. Aggregate Structure and Free Energy Changes in Chromonic Liquid Crystals

    E-print Network

    Collings, Peter

    Aggregate Structure and Free Energy Changes in Chromonic Liquid Crystals Alexandra J. Dickinson, Swarthmore College, Swarthmore, PA, USA Past and recent x-ray and absorption data on chromonic liquid crystal phase forms at higher concentrations. Keywords: aggregation; chromonic; liquid crystals

  15. Crystal structure of human nicotinic acid phosphoribosyltransferase

    PubMed Central

    Marletta, Ada Serena; Massarotti, Alberto; Orsomando, Giuseppe; Magni, Giulio; Rizzi, Menico; Garavaglia, Silvia

    2015-01-01

    Nicotinic acid phosphoribosyltransferase (EC 2.4.2.11) (NaPRTase) is the rate-limiting enzyme in the three-step Preiss–Handler pathway for the biosynthesis of NAD. The enzyme catalyzes the conversion of nicotinic acid (Na) and 5-phosphoribosyl-1-pyrophosphate (PRPP) to nicotinic acid mononucleotide (NaMN) and pyrophosphate (PPi). Several studies have underlined the importance of NaPRTase for NAD homeostasis in mammals, but no crystallographic data are available for this enzyme from higher eukaryotes. Here, we report the crystal structure of human NaPRTase that was solved by molecular replacement at a resolution of 2.9 Å in its ligand-free form. Our structural data allow the assignment of human NaPRTase to the type II phosphoribosyltransferase subfamily and reveal that the enzyme consists of two domains and functions as a dimer with the active site located at the interface of the monomers. The substrate-binding mode was analyzed by molecular docking simulation and provides hints into the catalytic mechanism. Moreover, structural comparison of human NaPRTase with the other two human type II phosphoribosyltransferases involved in NAD biosynthesis, quinolinate phosphoribosyltransferase and nicotinamide phosphoribosyltransferase, reveals that while the three enzymes share a conserved overall structure, a few distinctive structural traits can be identified. In particular, we show that NaPRTase lacks a tunnel that, in nicotinamide phosphoribosiltransferase, represents the binding site of its potent and selective inhibitor FK866, currently used in clinical trials as an antitumoral agent.

  16. Effect of polymer matrix on structure of Se particles formed in aqueous solutions during redox process

    NASA Astrophysics Data System (ADS)

    Suvorova, E. I.; Klechkovskaya, V. V.

    2010-12-01

    Transmission electron microscopy and X-ray energy dispersive microanalysis study of the structure of particles formed during the reduction of Se(IV) to Se(0) in aqueous solutions in the presence of amphiphilic polymers showed the formation of Se/polymer composite particles. The content of carbon inside the particles can be as large as 80 at %. Polymers deeply influence the structure of particles. Depending on polymers, the composite particles may be unstable with time and they spontaneously evolve from Se/polymer composite particles to crystalline particles of monoclinic Se. For the stable ones, addition of bacterial cellulose Acetobacter xylinum gel-film can induce crystallization in the particles which expel the polymeric material. The Se/polymer composite particles and Se crystalline particles exhibit different sensitivity to electron irradiation and stiffness.

  17. Dynamic self-assembly and control of microfluidic particle crystals

    PubMed Central

    Lee, Wonhee; Amini, Hamed; Stone, Howard A.; Di Carlo, Dino

    2010-01-01

    Engineered two-phase microfluidic systems have recently shown promise for computation, encryption, and biological processing. For many of these systems, complex control of dispersed-phase frequency and switching is enabled by nonlinearities associated with interfacial stresses. Introducing nonlinearity associated with fluid inertia has recently been identified as an easy to implement strategy to control two-phase (solid-liquid) microscale flows. By taking advantage of inertial effects we demonstrate controllable self-assembling particle systems, uncover dynamics suggesting a unique mechanism of dynamic self-assembly, and establish a framework for engineering microfluidic structures with the possibility of spatial frequency filtering. Focusing on the dynamics of the particle–particle interactions reveals a mechanism for the dynamic self-assembly process; inertial lift forces and a parabolic flow field act together to stabilize interparticle spacings that otherwise would diverge to infinity due to viscous disturbance flows. The interplay of the repulsive viscous interaction and inertial lift also allow us to design and implement microfluidic structures that irreversibly change interparticle spacing, similar to a low-pass filter. Although often not considered at the microscale, nonlinearity due to inertia can provide a platform for high-throughput passive control of particle positions in all directions, which will be useful for applications in flow cytometry, tissue engineering, and metamaterial synthesis. PMID:21149674

  18. Particle Mass Measurements and Strong Interaction Studies with Exotic Atoms using X-ray Crystal Spectrometer

    E-print Network

    Titov, Anatoly

    with crystal spectrometer are discussed which aim to improve particle masses and to study hyperon- nucleus Deexcitation and Isotope Exchange of Excited Mesic Hydrogen A. V. Kravtsov, A. I. Mikhailov Àííîòàöèÿ ÏðîöåññûParticle Mass Measurements and Strong Interaction Studies with Exotic Atoms using X-ray Crystal

  19. Behavior of colloidal particles at an air/nematic liquid crystal interface

    E-print Network

    M. A. Gharbi; M. Nobili; M. In; G. Prévot; P. Galatola; J. B. Fournier; Ch. Blanc

    2010-07-04

    We examine the behavior of spherical silica particles trapped at an air-nematic liquid crystal interface. When a strong normal anchoring is imposed, the beads spontaneously form various structures depending on their area density and the nematic thickness. Using optical tweezers, we determine the pair potential and explain the formation of these patterns. The energy profile is discussed in terms of capillary and elastic interactions. Finally, we detail the mechanisms that control the formation of an hexagonal lattice and analyze the role of gravity for curved interfaces.

  20. About mechanics of the structured particles

    E-print Network

    V. M. Somsikov

    2011-03-15

    The principles of creation of the mechanics of structured particles in the frame of the Newton's laws are considered. The explanation how this mechanics leads to the account of dissipative forces is offered. Why the motions of the system determine by two type of symmetry: symmetry of the system and symmetry of space and how it leads to two types of energy and forces accordingly are discussed. How the mechanics of the structured particles leads to thermodynamics, statistical physics and kinetics are explained.

  1. Crystal structure of Junin virus nucleoprotein.

    PubMed

    Zhang, Yinjie; Li, Le; Liu, Xiang; Dong, Shishang; Wang, Wenming; Huo, Tong; Guo, Yu; Rao, Zihe; Yang, Cheng

    2013-10-01

    Junin virus (JUNV) has been identified as the aetiological agent of Argentine haemorrhagic fever (AHF), which is a serious public health problem with approximately 5 million people at risk. It is treated as a potential bioterrorism agent because of its rapid transmission by aerosols. JUNV is a negative-sense ssRNA virus that belongs to the genus Arenavirus within the family Arenaviridae, and its genomic RNA contains two segments encoding four proteins. Among these, the nucleoprotein (NP) has essential roles in viral RNA synthesis and immune suppression, but the molecular mechanisms of its actions are only partially understood. Here, we determined a 2.2 Å crystal structure of the C-terminal domain of JUNV NP. This structure showed high similarity to the Lassa fever virus (LASV) NP C-terminal domain. However, both the structure and function of JUNV NP showed differences compared with LASV NP. This study extends our structural insight into the negative-sense ssRNA virus NPs. PMID:23884367

  2. Crystal structures of the human adiponectin receptors.

    PubMed

    Tanabe, Hiroaki; Fujii, Yoshifumi; Okada-Iwabu, Miki; Iwabu, Masato; Nakamura, Yoshihiro; Hosaka, Toshiaki; Motoyama, Kanna; Ikeda, Mariko; Wakiyama, Motoaki; Terada, Takaho; Ohsawa, Noboru; Hato, Masakatsu; Ogasawara, Satoshi; Hino, Tomoya; Murata, Takeshi; Iwata, So; Hirata, Kunio; Kawano, Yoshiaki; Yamamoto, Masaki; Kimura-Someya, Tomomi; Shirouzu, Mikako; Yamauchi, Toshimasa; Kadowaki, Takashi; Yokoyama, Shigeyuki

    2015-04-16

    Adiponectin stimulation of its receptors, AdipoR1 and AdipoR2, increases the activities of 5' AMP-activated protein kinase (AMPK) and peroxisome proliferator-activated receptor (PPAR), respectively, thereby contributing to healthy longevity as key anti-diabetic molecules. AdipoR1 and AdipoR2 were predicted to contain seven transmembrane helices with the opposite topology to G-protein-coupled receptors. Here we report the crystal structures of human AdipoR1 and AdipoR2 at 2.9 and 2.4 Å resolution, respectively, which represent a novel class of receptor structure. The seven-transmembrane helices, conformationally distinct from those of G-protein-coupled receptors, enclose a large cavity where three conserved histidine residues coordinate a zinc ion. The zinc-binding structure may have a role in the adiponectin-stimulated AMPK phosphorylation and UCP2 upregulation. Adiponectin may broadly interact with the extracellular face, rather than the carboxy-terminal tail, of the receptors. The present information will facilitate the understanding of novel structure-function relationships and the development and optimization of AdipoR agonists for the treatment of obesity-related diseases, such as type 2 diabetes. PMID:25855295

  3. Crystal Structures of Respiratory Pathogen Neuraminidases

    SciTech Connect

    Hsiao, Y.; Parker, D; Ratner, A; Prince, A; Tong, L

    2009-01-01

    Currently there is pressing need to develop novel therapeutic agents for the treatment of infections by the human respiratory pathogens Pseudomonas aeruginosa and Streptococcus pneumoniae. The neuraminidases of these pathogens are important for host colonization in animal models of infection and are attractive targets for drug discovery. To aid in the development of inhibitors against these neuraminidases, we have determined the crystal structures of the P. aeruginosa enzyme NanPs and S. pneumoniae enzyme NanA at 1.6 and 1.7 {angstrom} resolution, respectively. In situ proteolysis with trypsin was essential for the crystallization of our recombinant NanA. The active site regions of the two enzymes are strikingly different. NanA contains a deep pocket that is similar to that in canonical neuraminidases, while the NanPs active site is much more open. The comparative studies suggest that NanPs may not be a classical neuraminidase, and may have distinct natural substrates and physiological functions. This work represents an important step in the development of drugs to prevent respiratory tract colonization by these two pathogens.

  4. Structural ordering and glass forming of soft spherical particles with harmonic repulsions

    SciTech Connect

    Sun, Bin [School of Materials and Chemical Engineering, Zhongyuan University of Technology, Zhengzhou 450007 (China)] [School of Materials and Chemical Engineering, Zhongyuan University of Technology, Zhengzhou 450007 (China); Sun, Zhiwei; Ouyang, Wenze, E-mail: oywz@imech.ac.cn; Xu, Shenghua, E-mail: xush@imech.ac.cn [Key Laboratory of Microgravity (National Microgravity Laboratory), Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190 (China)] [Key Laboratory of Microgravity (National Microgravity Laboratory), Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190 (China)

    2014-04-07

    We carry out dissipative particle dynamics simulations to investigate the dynamic process of phase transformation in the system with harmonic repulsion particles. Just below the melting point, the system undergoes liquid state, face-centered cubic crystallization, body-centered cubic crystallization, and reentrant melting phase transition upon compression, which is in good agreement with the phase diagram constructed previously via thermodynamic integration. However, when the temperature is decreased sufficiently, the system is trapped into an amorphous and frustrated glass state in the region of intermediate density, where the solid phase and crystal structure should be thermodynamically most stable.

  5. Crystallization and X-ray diffraction of virus-like particles from a piscine betanodavirus.

    PubMed

    Luo, Yu-Chun; Wang, Chun-Hsiung; Wu, Yi-Min; Liu, Wangta; Lu, Ming-Wei; Lin, Chan-Shing

    2014-08-01

    Dragon grouper nervous necrosis virus (DGNNV), a member of the genus Betanodavirus, causes high mortality of larvae and juveniles of the grouper fish Epinephelus lanceolatus. Currently, there is no reported crystal structure of a fish nodavirus. The DGNNV virion capsid is derived from a single open reading frame that encodes a 338-amino-acid protein of approximately 37?kDa. The capsid protein of DGNNV was expressed to form virus-like particles (VLPs) in Escherichia coli. The VLP shape is T = 3 quasi-symmetric with a diameter of ?38?nm in cryo-electron microscopy images and is highly similar to the native virion. In this report, crystals of DGNNV VLPs were grown to a size of 0.27?mm within two weeks by the hanging-drop vapour-diffusion method at 283?K and diffracted X-rays to ?7.5?Å resolution. In-house X-ray diffraction data of the DGNNV VLP crystals showed that the crystals belonged to space group R32, with unit-cell parameters a = b = 353.00, c = 800.40?Å, ? = ? = 90, ? = 120°. 23?268 unique reflections were acquired with an overall Rmerge of 18.2% and a completeness of 93.2%. Self-rotation function maps confirmed the fivefold, threefold and twofold symmetries of the icosahedron of DGNNV VLPs. PMID:25084387

  6. Creation of giant two-dimensional crystal of zinc oxide nanodisk by method of single-particle layer of organo-modified inorganic fine particles.

    PubMed

    Meng, Qi; Honda, Nanami; Uchida, Saki; Hashimoto, Kazuaki; Shibata, Hirobumi; Fujimori, Atsuhiro

    2015-09-01

    In this study, the formation and structure of a single-particle layer of organo-zinc oxide are investigated using surface-pressure-area (?-A) isotherms, out-of-plane X-ray diffraction (XRD) analysis, and atomic force microscopy (AFM). Further, techniques for achieving the solubilization of inorganic fine particles in general solvents have been proposed, and a single-particle layer has been formed using such an inorganic solution as a "spreading solution" for an interfacial film. Surface modification of ZnO is performed using a long-chain carboxylic acid. Accordingly, a regular arrangement of ZnO can be easily achieved in order to overcome the relatively weak van der Walls interactions between inorganic materials. A condensed Langmuir monolayer of these particles is also formed. A multiparticle layered structure is constructed by the Langmuir-Blodgett (LB) technique. Out-of-plane XRD measurement results for a single-particle layer of organo-ZnO clearly show a sharp peak at 42Å. This peak is attributed to the distance between ZnO layers. The AFM image of this single-particle layer of organo-ZnO shows a particle assembly with a uniform height of 60nm. These aggregated particles form large two-dimensional crystals. In other words, a regular periodic structure along the c-axis and a condensed single-particle layer had been fabricated using Langmuir and LB techniques. PMID:25978556

  7. Structure dependent hydrogen induced etching features of graphene crystals

    NASA Astrophysics Data System (ADS)

    Thangaraja, Amutha; Shinde, Sachin M.; Kalita, Golap; Papon, Remi; Sharma, Subash; Vishwakarma, Riteshkumar; Sharma, Kamal P.; Tanemura, Masaki

    2015-06-01

    H2 induced etching of graphene is of significant interest to understand graphene growth process as well as to fabricate nanoribbons and various other structures. Here, we demonstrate the structure dependent H2 induced etching behavior of graphene crystals. We synthesized graphene crystals on electro-polished Cu foil by an atmospheric pressure chemical vapor deposition process, where some of the crystals showed hexagonal shaped snowflake-dendritic morphology. Significant differences in H2 induced etching behavior were observed for the snowflake-dendritic and regular graphene crystals by annealing in a gas mixture of H2 and Ar. The regular graphene crystals were etched anisotropically creating hexagonal holes with pronounced edges, while etching of all the dendritic crystals occurred from the branches of lobs creating symmetrical fractal structures. The etching behavior provides important clue of graphene nucleation and growth as well as their selective etching to fabricate well-defined structures for nanoelectronics.

  8. Crystal structure of ruthenocenecarbo­nitrile

    PubMed Central

    Strehler, Frank; Korb, Marcus; Lang, Heinrich

    2015-01-01

    The mol­ecular structure of ruthenocenecarbo­nitrile, [Ru(?5-C5H4C N)(?5-C5H5)], exhibits point group symmetry m, with the mirror plane bis­ecting the mol­ecule through the C N substituent. The RuII atom is slightly shifted from the ?5-C5H4 centroid towards the C N substituent. In the crystal, mol­ecules are arranged in columns parallel to [100]. One-dimensional inter­molecular ?–? inter­actions [3.363?(3)?Å] between the C N carbon atom and one carbon of the cyclo­penta­dienyl ring of the overlaying mol­ecule are present.

  9. Water structure in cubic insulin crystals.

    PubMed Central

    Badger, J; Caspar, D L

    1991-01-01

    The electron density distribution of the solvent in the cubic insulin crystal structure, which occupies 65% of the volume, has been mapped from 1.7-A resolution diffraction data by an iterative difference Fourier method, using the previously determined protein structure as the refinement restraint. Starting with phases from the protein and a flat solvent model, the difference map calculated from the data was added outside the protein envelope, and the modified map was then used to recalculate phases for the iterative refinement. Tests of the method with model data, with the experimental data and a variant protein model, and by carrying out a partial refinement of the solvent map demonstrate that the refinement algorithm produces reliable values for the solvent density within the noise level of the data. Fluctuations in density are observed throughout the solvent space, demonstrating that nonrandom arrangements of the water molecules extend several layers from the well-ordered hydration shell in contact with the protein surface. Such ordering may account for the hydration force opposing close approach of hydrophilic surfaces and other long-range water-dependent interactions in living structures. Images PMID:1988957

  10. A structural analysis of small vapor-deposited 'multiply twinned' gold particles

    NASA Technical Reports Server (NTRS)

    Yang, C. Y.; Heinemann, K.; Yacaman, M. J.; Poppa, H.

    1979-01-01

    High resolution selected zone dark field, Bragg reflection imaging and weak beam dark field techniques of transmission electron microscopy were used to determine the structure of small gold particles vapor deposited on NaCl substrates. Attention was focused on the analysis of those particles in the 50-150 A range that have pentagonal or hexagonal bright field profiles. These particles have been previously described as multiply twinned crystallites composed of face-centered cubic tetrahedra. The experimental evidence of the present studies can be interpreted on the assumption that the particle structure is a regular icosahedron or decahedron for the hexagonal or the pentagonal particles respectively. The icosahedron is a multiply twinned rhombohedral crystal and the decahedron is a multiply twinned body-centered orthorhombic crystal, each of which constitutes a slight distortion from the face-centered cubic structure.

  11. Polymorphic crystal structures of an all-AT DNA dodecamer.

    PubMed

    Acosta-Reyes, Francisco J; Subirana, Juan A; Pous, Joan; Sánchez-Giraldo, Raquel; Condom, Núria; Baldini, Roberto; Malinina, Lucy; Campos, J Lourdes

    2015-03-01

    In this work, we explore the influence of different solvents and ions on the crystallization behavior of an all-AT dodecamer d(AATAAATTTATT)2 In all cases, the oligonucleotides are found as continuous columns of stacked duplexes. The spatial organization of such columns is variable; consequently we have obtained seven different crystal forms. The duplexes can be made to crystallize in either parallel or crossed columns. Such versatility in the formation of a variety of crystal forms is characteristic for this sequence. It had not been previously reported for any other sequence. In all cases, the oligonucleotide duplexes have been found to crystallize in the B form. The crystallization conditions determine the organization of the crystal, although no clear local interactions have been detected. Mg(2+) and Ni(2+) can be used in order to obtain compact crossed structures. DNA-DNA interactions in the crystals of our all-AT duplexes present crossovers which are different from those previously reported for mixed sequence oligonucleotides. Our results demonstrate that changes in the ionic atmosphere and the crystallization solvent have a strong influence on the DNA-DNA interactions. Similar ionic changes will certainly influence the biological activity of DNA. Modulation of the crystal structure by ions should also be explored in DNA crystal engineering. Liquid crystals with a peculiar macroscopic shape have also been observed. © 2014 Wiley Periodicals, Inc. Biopolymers 103: 123-133, 2015. PMID:25257185

  12. Predicting crystal structure by merging data mining with quantum mechanics

    Microsoft Academic Search

    Christopher C. Fischer; Kevin J. Tibbetts; Dane Morgan; Gerbrand Ceder

    2006-01-01

    Modern methods of quantum mechanics have proved to be effective tools to understand and even predict materials properties. An essential element of the materials design process, relevant to both new materials and the optimization of existing ones, is knowing which crystal structures will form in an alloy system. Crystal structure can only be predicted effectively with quantum mechanics if an

  13. Undergraduates Improve upon Published Crystal Structure in Class Assignment

    ERIC Educational Resources Information Center

    Horowitz, Scott; Koldewey, Philipp; Bardwell, James C.

    2014-01-01

    Recently, 57 undergraduate students at the University of Michigan were assigned the task of solving a crystal structure, given only the electron density map of a 1.3 Å crystal structure from the electron density server, and the position of the N-terminal amino acid. To test their knowledge of amino acid chemistry, the students were not given the…

  14. Hierarchical structuring of liquid crystal polymer-Laponite hybrid materials.

    PubMed

    Tritschler, Ulrich; Zlotnikov, Igor; Zaslansky, Paul; Aichmayer, Barbara; Fratzl, Peter; Schlaad, Helmut; Cölfen, Helmut

    2013-09-01

    Biomimetic organic-inorganic composite materials were fabricated via one-step self-organization on three hierarchical levels. The organic component was a polyoxazoline with pendent cholesteryl and carboxyl (N-Boc-protected amino acid) side chains that was able to form a chiral nematic lyotropic phase and bind to positively charged inorganic faces of Laponite. The Laponite particles formed a mesocrystalline arrangement within the liquid-crystal (LC) polymer phase upon shearing a viscous dispersion of Laponite nanoparticles and LC polymer in DMF. Complementary analytical and mechanical characterization techniques (AUC, POM, TEM, SEM, SAXS, ?CT, and nanoindentation) covering the millimeter, micrometer, and nanometer length scales reveal the hierarchical structures and properties of the composite materials consisting of different ratios of Laponite nanoparticles and liquid-crystalline polymer. PMID:23790152

  15. Correlation-crystal-field analysis of Nd3+(4f3) energy-level structures in various crystal hosts

    Microsoft Academic Search

    E Rukmini; C K Jayasankar; M F Reid

    1994-01-01

    We have performed an in-depth correlation-crystal-field (CCF) analysis of the energy-level structures in 10 Nd3+(4f3) crystal systems: NdF3, Nd2Te4O11, NdVO4, NdPO4, Nd3+:LiYF4, Nd3+:LaVO4, Nd3+:LaCl3, Nd3+:BaY2F8, Nd3+:YAlO3 and Nd3+:LuA1O3. A model Hamiltonian employing 20 free-ion parameters, appropriate one-electron crystal-field interaction parameters and also selected two-particle CCF interaction parameters was diagonalized within the complete 364 SLJMJ basis set of the 4f3 electronic

  16. Fabrication of large binary colloidal crystals with a NaCl structure

    PubMed Central

    Vermolen, E. C. M.; Kuijk, A.; Filion, L. C.; Hermes, M.; Thijssen, J. H. J.; Dijkstra, M.; van Blaaderen, A.

    2009-01-01

    Binary colloidal crystals offer great potential for tuning material properties for applications in, for example, photonics, semiconductors and spintronics, because they allow the positioning of particles with quite different characteristics on one lattice. For micrometer-sized colloids, it is believed that gravity and slow crystallization rates hinder the formation of high-quality binary crystals. Here, we present methods for growing binary colloidal crystals with a NaCl structure from relatively heavy, hard-sphere-like, micrometer-sized silica particles by exploring the following external fields: electric, gravitational, and dielectrophoretic fields and a structured surface (colloidal epitaxy). Our simulations show that the free-energy difference between the NaCl and NiAs structures, which differ in their stacking of the hexagonal planes of the larger spheres, is very small (?0.002 kBT). However, we demonstrate that the fcc stacking of the large spheres, which is crucial for obtaining the pure NaCl structure, can be favored by using a combination of the above-mentioned external fields. In this way, we have successfully fabricated large, 3D, oriented single crystals having a NaCl structure without stacking disorder. PMID:19805259

  17. Hybrid photonic crystal and conventional waveguide structures

    NASA Astrophysics Data System (ADS)

    Kim, Seunghyun

    Higher levels of integration are required in planar lightwave circuits (PLCs) to lower costs and increase functionality in smaller footprint. Many different approaches using conventional waveguides (CWGs) and photonic crystal (PhC) structures have been proposed to meet such demands. CWGs are attractive due to low propagation loss, low coupling loss to and from fiber, and low dispersion. However the large radius of curvature required for high efficiency bends limits the possible level of integration in PLCs. Alternatively, PhCs have received much attention due to their capability to manipulate light propagation in a compact region. However, high propagation loss and coupling loss from and to fiber are problematic issues for PhC structures. In this dissertation, I examine the combination of PhCs and CWGs in hybrid structures that leverage the advantages of each approach. Hybrid structures consist of CWGs for the low loss transport of light integrated with PhC regions of very limited spatial extent to dramatically reduce the size of waveguide devices. This preserves the traditional advantages of CWGs while advantageously using the attractive properties of PhCs. Ultracompact high efficiency 90 degree bends, splitters, and a polarizing beam splitter using hybrid PhC and CWG structures are numerically designed and analyzed. Wave vector diagrams have been used to understand hybrid PhC and CWG structures. For some cases, diffraction at the periodic boundary surface of PhC limits the maximum 90 degree bend efficiencies. A micro genetic algorithm (muGA) combined with 2-D finite difference time domain (FDTD) method is used to effectively suppress undesired diffraction by manipulating parameters of the PhC region and the periodic boundary layer which in turn maximizes the bend efficiency. A compact Mach-Zender interferometer and ring resonators are designed by combining ultracompact high efficiency hybrid PhC and CWG 90 degree bend and splitter structures. The proposed Mach-Zender interferometer and ring resonator show attractive performance characteristics and design flexibilities.

  18. Multiresponsive hydrogel photonic crystal microparticles with inverse-opal structure.

    PubMed

    Wang, Jianying; Hu, Yuandu; Deng, Renhua; Liang, Ruijing; Li, Weikun; Liu, Shanqin; Zhu, Jintao

    2013-07-16

    Hydrogel photonic crystal microparticles (HPCMs) with inverse-opal structure are generated through a combination of microfluidic and templating technique. Temperature and pH responsive HPCMs have firstly been prepared by copolymerizing functional monomers, for example, N-isopropylacrylamide (NIPAm) and methacrylic acid (MAA). HPCMs not only show tunable color variation almost covering the entire wavelength of visible light (above 150 nm of stop-band shift) by simply tailoring temperature or pH value of the solution, but also display rapid response (less than 1 min) due to the small volume and well-ordered porous structure. Importantly, the temperature sensing window of the HPCMs can be enlarged by controlling the transition temperature of the hydrogel matrix, and the HPCMs also exhibit good reversibility and reproducibility for pH response. Moreover, functional species or particles (such as azobenzene derivative or magnetic nanoparticles) can be further introduced into the hydrogel matrix by using post-treatment process. These functionalized HPCMs can respond to the UV/visible light without significantly influencing the temperature and pH response, and thus, multiresponsive capability within one single particle can be realized. The presence of magnetic nanoparticles may facilitate secondary assembly, which has potential applications in advanced optical devices. PMID:23768084

  19. Tensor Product Structures, Entanglement, and Particle Scattering

    E-print Network

    N. L. Harshman; S. Wickramsekara

    2006-12-28

    Particle systems admit a variety of tensor product structures (TPSs) depending on the complete system of commuting observables chosen for the analysis. Different notions of entanglement are associated with these different TPSs. Global symmetry transformations and dynamical transformations factor into products of local unitary operators with respect to certain TPSs and not with respect to others. Symmetry-invariant and dynamical-invariant TPSs and corresponding measures of entanglement are defined for particle scattering systems.

  20. Structural studies of large nucleoprotein particles, vaults

    PubMed Central

    TANAKA, Hideaki; TSUKIHARA, Tomitake

    2012-01-01

    Vault is the largest nonicosahedral cytosolic nucleoprotein particle ever described. The widespread presence and evolutionary conservation of vaults suggest important biologic roles, although their functions have not been fully elucidated. X-ray structure of vault from rat liver was determined at 3.5 Å resolution. It exhibits an ovoid shape with a size of 40 × 40 × 67 nm3. The cage structure of vault consists of a dimer of half-vaults, with each half-vault comprising 39 identical major vault protein (MVP) chains. Each MVP monomer folds into 12 domains: nine structural repeat domains, a shoulder domain, a cap-helix domain and a cap-ring domain. Interactions between the 42-turn-long cap-helix domains are key to stabilizing the particle. The other components of vaults, telomerase-associated proteins, poly(ADP-ribose) polymerases and small RNAs, are in location in the vault particle by electron microscopy. PMID:23060231

  1. Single-crystal CVD diamond detector for high-resolution particle spectrometry

    NASA Astrophysics Data System (ADS)

    Sato, Y.; Murakami, H.; Shimaoka, T.; Tsubota, M.; Kaneko, J. H.

    2014-11-01

    The performance of a single-crystal diamond detector, grown by chemical vapour deposition, as an energy spectrometer for charged particles was studied. The detector was able to identify four different energies of 241\\text{Am} ? -particles (5.389, 5.443, 5.486, and 5.545 MeV) thanks to a superior intrinsic energy resolution of ˜0.4{%} (full width at half maximum). The electrode configuration, specifically the electric field configuration inside the diamond crystal, and the electrode materials, strongly affect the energy resolution for charged particles. The charge collection efficiency inside the diamond crystal was ˜97{%} for both electrons and holes.

  2. Growth of Sillenite-Structure Single Crystals

    Microsoft Academic Search

    V. M. Skorikov; Yu. F. Kargin; A. V. Egorysheva; V. V. Volkov; M. Gospodinov

    2005-01-01

    The main processes for preparing bulk single crystals and films of photorefractive and piezoelectric Bi12MxO20±? (M = Group II–VIII elements) sillenite compounds are considered. Experimental data are summarized on the crystal growth of\\u000a Bi12MxO20±? from the melt and under hydrothermal conditions, and the key morphological features of sillenites are analyzed. Various types\\u000a of macroscopic growth defects in sillenite-type crystals are

  3. Polypropylene/Layered Double Hydroxide (LDH) Nanocomposites: Influence of LDH Particle Size on the Crystallization Behavior of Polypropylene.

    PubMed

    Nagendra, Baku; Mohan, Kiran; Bhoje Gowd, E

    2015-06-17

    Highly dispersed isotactic polypropylene (iPP) nanocomposites were prepared by incorporating two different sized Mg-Al LDH nanoparticles with different loadings from 1 to 10 wt % using a modified solvent mixing method. Larger sized LDH nanoparticles (?3-4 ?m) were prepared from the gel form of Mg-Al LDH, and the smaller sized nanoparticles (?50-200 nm) were prepared by sonication of as-synthesized LDH particles. Such obtained LDH nanoparticles were carefully characterized using wide-angle X-ray diffraction (WAXD), transmission electron microscopy, and scanning electron microscopy. WAXD and atomic force microscopy results indicate that the LDH nanoparticles were highly dispersed in the iPP matrix. The influence of LDH nanoparticles size and concentration on the thermal stability, spherulitic morphology, melting behavior, isothermal crystallization kinetics, and lamellar structure of iPP were investigated. Incorporation of low loadings of sonicated LDH particles (e.g., 1-2.5 wt %) show substantial effect on thermal stability, spherulite size, crystallinity, and crystallization half-time and lamellar morphology of iPP compared to the pure iPP and that of nanocomposites with larger LDH particles with same loadings. The better nucleation ability of iPP in the presence of sonicated LDH can be attributed to the high surface area of LDH nanoparticles along with its better dispersibility within the polymer matrix. The incorporation of LDH nanoparticles does not change the crystallization growth mechanism and crystal structure of iPP. PMID:25741910

  4. Evolutionary Crystal Structure Prediction and Novel High-Pressure Phases

    Microsoft Academic Search

    Artem R. Oganov; Yanming Ma; Andriy O. Lyakhov; Mario Valle; Carlo Gatti

    2010-01-01

    \\u000a Prediction of stable crystal structures at given pressure-temperature conditions, based only on the knowledge of the chemical\\u000a composition, is a central problem of condensed matter physics. This extremely challenging problem is often termed “crystal\\u000a structure prediction problem”, and recently developed evolutionary algorithm USPEX (Universal Structure Predictor: Evolutionary\\u000a Xtallography) made an important progress in solving it, enabling efficient and reliable prediction

  5. In vivo protein crystallization opens new routes in structural biology

    PubMed Central

    Koopmann, Rudolf; Cupelli, Karolina; Redecke, Lars; Nass, Karol; DePonte, Daniel P; White, Thomas A; Stellato, Francesco; Rehders, Dirk; Liang, Mengning; Andreasson, Jakob; Aquila, Andrew; Bajt, Sasa; Barthelmess, Miriam; Barty, Anton; Bogan, Michael J; Bostedt, Christoph; Boutet, Sébastien; Bozek, John D; Caleman, Carl; Coppola, Nicola; Davidsson, Jan; Doak, R Bruce; Ekeberg, Tomas; Epp, Sascha W; Erk, Benjamin; Fleckenstein, Holger; Foucar, Lutz; Graafsma, Heinz; Gumprecht, Lars; Hajdu, Janos; Hampton, Christina Y; Hartmann, Andreas; Hartmann, Robert; Hauser, Günter; Hirsemann, Helmut; Holl, Peter; Hunter, Mark S; Kassemeyer, Stephan; Kirian, Richard A; Lomb, Lukas; Maia, Filipe R N C; Kimmel, Nils; Martin, Andrew V; Messerschmidt, Marc; Reich, Christian; Rolles, Daniel; Rudek, Benedikt; Rudenko, Artem; Schlichting, Ilme; Schulz, Joachim; Seibert, M Marvin; Shoeman, Robert L; Sierra, Raymond G; Soltau, Heike; Stern, Stephan; Strüder, Lothar; Timneanu, Nicusor; Ullrich, Joachim; Wang, Xiaoyu; Weidenspointner, Georg; Weierstall, Uwe; Williams, Garth J; Wunderer, Cornelia B; Fromme, Petra; Spence, John C H; Stehle, Thilo; Chapman, Henry N; Betzel, Christian; Duszenko, Michael

    2012-01-01

    Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo–grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology. PMID:22286384

  6. In vivo protein crystallization opens new routes in structural biology.

    PubMed

    Koopmann, Rudolf; Cupelli, Karolina; Redecke, Lars; Nass, Karol; Deponte, Daniel P; White, Thomas A; Stellato, Francesco; Rehders, Dirk; Liang, Mengning; Andreasson, Jakob; Aquila, Andrew; Bajt, Sasa; Barthelmess, Miriam; Barty, Anton; Bogan, Michael J; Bostedt, Christoph; Boutet, Sébastien; Bozek, John D; Caleman, Carl; Coppola, Nicola; Davidsson, Jan; Doak, R Bruce; Ekeberg, Tomas; Epp, Sascha W; Erk, Benjamin; Fleckenstein, Holger; Foucar, Lutz; Graafsma, Heinz; Gumprecht, Lars; Hajdu, Janos; Hampton, Christina Y; Hartmann, Andreas; Hartmann, Robert; Hauser, Günter; Hirsemann, Helmut; Holl, Peter; Hunter, Mark S; Kassemeyer, Stephan; Kirian, Richard A; Lomb, Lukas; Maia, Filipe R N C; Kimmel, Nils; Martin, Andrew V; Messerschmidt, Marc; Reich, Christian; Rolles, Daniel; Rudek, Benedikt; Rudenko, Artem; Schlichting, Ilme; Schulz, Joachim; Seibert, M Marvin; Shoeman, Robert L; Sierra, Raymond G; Soltau, Heike; Stern, Stephan; Strüder, Lothar; Timneanu, Nicusor; Ullrich, Joachim; Wang, Xiaoyu; Weidenspointner, Georg; Weierstall, Uwe; Williams, Garth J; Wunderer, Cornelia B; Fromme, Petra; Spence, John C H; Stehle, Thilo; Chapman, Henry N; Betzel, Christian; Duszenko, Michael

    2012-03-01

    Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo-grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology. PMID:22286384

  7. Crystal structures of histone Sin mutant nucleosomes reveal altered protein–DNA interactions

    Microsoft Academic Search

    Uma M Muthurajan; Yunhe Bao; Lawrence J Forsberg; Rajeswari S Edayathumangalam; Pamela N Dyer; Cindy L White; Karolin Luger

    2004-01-01

    Here we describe 11 crystal structures of nucleosome core particles containing individual point mutations in the structured regions of histones H3 and H4. The mutated residues are located at the two protein-DNA interfaces flanking the nucleosomal dyad. Five of the mutations partially restore the in vivo effects of SWI\\/SNF inactivation in yeast. We find that even nonconservative mutations of these

  8. Electronic Structure of Point Defects in Crystals

    Microsoft Academic Search

    M. H. L. Pryce

    1962-01-01

    Impurity ions in insulating crystals can be regarded as isolated electronic systems. Their paramagnetic resonance is determined by their ground state characteristics, which can be derived from application of Hund's rules, together with simple applications of ligand-field theory and consideration of spin-orbit interaction. The paramagnetic resonance is characteristic of the ion and its coordination in the crystal, and furnishes a

  9. Enabling tablet product development of 5-fluorocytosine through integrated crystal and particle engineering.

    PubMed

    Perumalla, Sathyanarayana Reddy; Sun, Changquan Calvin

    2014-04-01

    The antifungal drug, 5-fluorocytosine (FC), is marketed as a capsule (250 or 500 mg strength) instead of the preferred tablet dosage form. Through systematic characterization of solid-state properties, including mechanical properties, we identify tabletability and poor physical stability of FC as the problems that likely have prevented the successful development of a FC tablet product. We then design an FC oxalate 2:1 salt (FCOXA21), based on established relationship between crystal structure and properties, to address these deficient properties. FCOXA21 is subsequently used to develop a direct compression tablet product using predictive and material-sparing powder characterization tools, that is, ring shear cell for powder flowability and compaction simulator for powder tabletability. The initial tablet formulation, which contains 84.5% (wt %) FCOXA21, exhibits excellent tabletability but inadequate flowability. We solve the powder flowability problem through controlling the particle size of FCOXA21. A batch of FCOXA21 tablets (500 mg FC equivalent dose) is then prepared. Finally, systematic evaluation on tablet weight variation, content uniformity, friability, and dissolution using standard methods confirms the commercial manufacturability of FC tablets. Through this work, we have demonstrated the potential of integrated crystal and particle engineering in expediting the development of tablet products of challenging drugs using the economical direct compression process. PMID:24515970

  10. Ultrastructure of Calcareous Dinophytes (Thoracosphaeraceae, Peridiniales) with a Focus on Vacuolar Crystal-Like Particles

    PubMed Central

    Zinssmeister, Carmen; Keupp, Helmut; Tischendorf, Gilbert; Kaulbars, Freya; Gottschling, Marc

    2013-01-01

    Biomineralization in calcareous dinophytes (Thoracosphaeracaea, Peridiniales) takes place in coccoid cells and is presently poorly understood. Vacuolar crystal-like particles as well as collection sites within the prospective calcareous shell may play a crucial role during this process at the ultrastructural level. Using transmission electron microscopy, we investigated the ultrastructure of coccoid cells at an early developmental stage in fourteen calcareous dinophyte strains (corresponding to at least ten species of Calciodinellum, Calcigonellum, Leonella, Pernambugia, Scrippsiella, and Thoracosphaera). The shell of the coccoid cells consisted either of one (Leonella, Thoracosphaera) or two matrices (Scrippsiella and its relatives) of unknown element composition, whereas calcite is deposited in the only or the outer layer, respectively. We observed crystal-like particles in cytoplasmic vacuoles in cells of nine of the strains investigated and assume that they are widespread among calcareous dinophytes. However, similar structures are also found outside the Thoracosphaeraceae, and we postulate an evolutionarily old physiological pathway (possibly involved in detoxification) that later was specialized for calcification. We aim to contribute to a deeper knowledge of the biomineralization process in calcareous dinophytes. PMID:23320120

  11. Diffraction phenomena in spontaneous and stimulated radiation by relativistic particles in crystals (Review)

    SciTech Connect

    Baryshevsky, V.G. (Inst. of Nuclear Problems, Minsk (Belarus)); Dubovskaya, I.Ya. (Lawrence Berkeley Lab., CA (United States))

    1991-12-01

    This report discusses: the dispersion characteristics of parametric x-ray radiation (PXR) and diffraction radiation of oscillator; cooperative effects in x-radiation by charged particles in crystals; and diffraction x-radiation by relativistic oscillator.

  12. Population structure and particle swarm performance

    Microsoft Academic Search

    James Kennedy; Rui Mendes

    2002-01-01

    The effects of various population topologies on the particle swarm algorithm were systematically investigated. Random graphs were generated to specifications, and their performance on several criteria was compared. What makes a good population structure? We discovered that previous assumptions may not have been correct

  13. Multiscale models of colloidal dispersion of particles in nematic liquid crystals.

    PubMed

    Bennett, T P; D'Alessandro, G; Daly, K R

    2014-12-01

    We use homogenization theory to develop a multiscale model of colloidal dispersion of particles in nematic liquid crystals under weak-anchoring conditions. We validate the model by comparing it with simulations by using the Landau-de Gennes free energy and show that the agreement is excellent. We then use the multiscale model to study the effect that particle anisotropy has on the liquid crystal: spherically symmetric particles always reduce the effective elastic constant. Asymmetric particles introduce an effective alignment field that can increase the Fredericks threshold and decrease the switch-off time. PMID:25615117

  14. Determination of particle size distribution of salt crystals in aqueous slurries. [From reprocessing of fuel elements

    Microsoft Academic Search

    1977-01-01

    A method for determining particle size distribution of water-soluble crystals in aqueous slurries is described. The salt slurries, containing sodium salts of predominantly nitrate, but also nitrite, sulfate, phosphate, aluminates, carbonate, and hydroxide, occur in radioactive, concentrated chemical waste from the reprocessing of nuclear fuel elements. The method involves separating the crystals from the aqueous phase, drying them, and then

  15. Electronic structure of Cr{sup 3+} in forsterite crystals

    SciTech Connect

    Avanesov, A.G.; Zhorin, V.V.; Pisarenko, V.F. [Kuban` State Univ., Krasnodar (Russian Federation)

    1994-11-01

    Specific properties of silicate crystals that make them promising in applications as active media for IR tunable lasers are discussed. The energy level structure of Cr{sup 3+} ions in a forsterite crystal field is analyzed. 4 refs., 3 tabs.

  16. Band structures of bilayer radial phononic crystal plate with crystal gliding

    NASA Astrophysics Data System (ADS)

    Ma, Ting; Chen, Tianning; Wang, Xiaopeng; Li, Yinggang; Wang, Peng

    2014-09-01

    Lamb wave propagation in bilayer radial phononic crystal plate with crystal gliding is investigated. Axial symmetric model in cylindrical coordinate is applied to the bilayer radial phononic crystal plate for band structure calculation and transmission spectra. Gliding in radial direction and direction vertical to plate thickness is analyzed to modulate band gaps. Physical mechanism of gliding effects on radial phononic crystal plate is also studied with displacement fields of super cells. Numerical results show that crystal gliding both in radial direction and direction vertical to plate thickness can significantly tune omnidirectional band gaps. New lower band gaps occur and attenuation areas in transmission spectra are in good agreement with gaps of band structure calculation. Band structure evolution together with eigenmodes indicate that gliding effect converts lamb wave modes resulting in separations or interactions of adjacent bands to open new gaps or close the original ones. In addition, band gaps' sensitivity to crystal gliding is also investigated. Higher gaps are more sensitive to crystal gliding in thickness direction, and lowest gap extends in the map. Crystal gliding in radial direction can open new lowest order gap and open or close another two higher gaps, while the fourth gap is insensitive to it. The omnidirectional band gaps properties have potential application in acoustic device with isotropic gap characters.

  17. Novel photonic crystal cavities and related structures.

    SciTech Connect

    Luk, Ting Shan

    2007-11-01

    The key accomplishment of this project is to achieve a much more in-depth understanding of the thermal emission physics of metallic photonic crystal through theoretical modeling and experimental measurements. An improved transfer matrix technique was developed to enable incorporation of complex dielectric function. Together with microscopic theory describing emitter radiative and non-radiative relaxation dynamics, a non-equilibrium thermal emission model is developed. Finally, experimental methodology was developed to measure absolute emissivity of photonic crystal at high temperatures with accuracy of +/-2%. Accurate emissivity measurements allow us to validate the procedure to treat the effect of the photonic crystal substrate.

  18. Crystal structure-crystal chemistry relationships in the zeolites erionite and offretite

    Microsoft Academic Search

    A. GUALTIERI; G. ARTIOLI; E. PASSAGLIA; S. BIGI; A. VIANI; J. C. HANSON

    This study clarifies the crystal structure variations and relationships in the zeolites eri- onite and offretite. The crystal structure analyses used Rietveld analysis of X-ray powder diffraction data, obtained both by synchrotron radiation and conventional X-ray sources, and on diffraction patterns obtained by transmission electron microscopy. The framework Al atoms in erionite are preferentially located in the single six-membered ring

  19. Synthesis, characterization, crystal structure determination, computational study, and thermal decomposition into NiO nano-particles of a new NiIIL2 Schiff base complex (L = 2-{(E)-[2-chloroethyl)imino]methylphenolate)

    NASA Astrophysics Data System (ADS)

    Grivani, Gholamhossein; Vakili, Mohammad; Khalaji, Aliakbar Dehno; Bruno, Giuseppe; Rudbari, Hadi Amiri; Taghavi, Maedeh; Tahmasebi, Vida

    2014-08-01

    The Nickel (II) Schiff base complex of NiL2, (L = 2-{(E)-[2-chloroethyl) imino]methylphenolate) have been synthesized and characterized by elemental (CHN) analysis, UV-vis and FT-IR spectroscopy. The molecular structure of [NiL2] was determined by single crystal X-ray diffraction technique. The Schiff base ligand HL acts as a chelating ligand and coordinates via one nitrogen atom and one oxygen atom to the metal center. The nickel (II) center is coordinated by two nitrogen and two oxygen atoms from two Schiff base ligands in an approximately square planar trans-[MN2O2] coordination geometry. Thermogravimetric analysis of NiL2 showed that it decomposed in three stages. In addition, complex NiL2 thermally decomposed in air at 660 °C and the XRD pattern of the obtained solid showed the formation of NiO nanoparticles with an average size of 43 nm. In addition, the conformational analysis and molecular structures of NiL2 were investigated by means of density functional theory (DFT) calculations at B3LYP/6-311G* level and the calculated geometrical parameters were compared with the experimental results.

  20. Optically Generated Reconfigurable Photonic Structures of Elastic Quasiparticles in Frustrated Cholesteric Liquid Crystals

    SciTech Connect

    Smalyukh,, I. I.; Kaputa, D.; Kachynski, A. V.; Kuzmin, A. N.; Ackerman, P. J.; Twombly, C. W.; Lee, T.; Trivedi, R. P.; Prasad, P. N.

    2012-03-26

    We describe laser-induced two-dimensional periodic photonic structures formed by localized particle-like excitations in an untwisted confined cholesteric liquid crystal. The individual particle-like excitations (dubbed 'Torons') contain three-dimensional twist of the liquid crystal director matched to the uniform background director field by topological point defects. Using both single-beam-steering and holographic pattern generation approaches, the periodic crystal lattices are tailored by tuning their periodicity, reorienting their crystallographic axes, and introducing defects. Moreover, these lattices can be dynamically reconfigurable: generated, modified, erased and then recreated, depending on the needs of a particular photonic application. This robust control is performed by tightly focused laser beams of power 10-100 mW and by low-frequency electric fields at voltages {approx}10 V applied to the transparent electrodes.

  1. Crystal Structure of Human Plasma Platelet-Activating Factor Acetylhydrolase

    SciTech Connect

    Samanta, U.; Bahnson, B

    2008-01-01

    Human plasma platelet-activating factor (PAF) acetylhydrolase functions by reducing PAF levels as a general anti-inflammatory scavenger and is linked to anaphylactic shock, asthma, and allergic reactions. The enzyme has also been implicated in hydrolytic activities of other pro-inflammatory agents, such as sn-2 oxidatively fragmented phospholipids. This plasma enzyme is tightly bound to low and high density lipoprotein particles and is also referred to as lipoprotein-associated phospholipase A{sub 2}. The crystal structure of this enzyme has been solved from x-ray diffraction data collected to a resolution of 1.5{angstrom}. It has a classic lipase {alpha}/{beta}-hydrolase fold, and it contains a catalytic triad of Ser{sup 273}, His{sup 351}, and Asp{sup 296}. Two clusters of hydrophobic residues define the probable interface-binding region, and a prediction is given of how the enzyme is bound to lipoproteins. Additionally, an acidic patch of 10 carboxylate residues and a neighboring basic patch of three residues are suggested to play a role in high density lipoprotein/low density lipoprotein partitioning. A crystal structure is also presented of PAF acetylhydrolase reacted with the organophosphate compound paraoxon via its active site Ser{sup 273}. The resulting diethyl phosphoryl complex was used to model the tetrahedral intermediate of the substrate PAF to the active site. The model of interface binding begins to explain the known specificity of lipoprotein-bound substrates and how the active site can be both close to the hydrophobic-hydrophilic interface and at the same time be accessible to the aqueous phase.

  2. Flash Nanoprecipitation: Particle Structure and Stability

    PubMed Central

    Pustulka, Kevin M.; Wohl, Adam R.; Lee, Han Seung; Michel, Andrew R.; Han, Jing; Hoye, Thomas R.; McCormick, Alon V.; Panyam, Jayanth; Macosko, Christopher W.

    2013-01-01

    Flash nanoprecipitation (FNP) is a process that, through rapid mixing, stabilizes an insoluble low molecular weight compound in a nano-sized, polymer-stabilized delivery vehicle. The polymeric components are typically amphiphilic diblock copolymers (BCPs). In order to fully exploit the potential of FNP, factors affecting particle structure, size, and stability must be understood. Here we show that polymer type, hydrophobicity and crystallinity of the small molecule, and small molecule loading levels all affect particle size and stability. Of the four block copolymers (BCP) that we have studied here, poly(ethylene glycol)-b-poly(lactic-co-glycolic acid) (PEG-b-PLGA) was most suitable for potential drug delivery applications due to its ability to give rise to stable nanoparticles, its biocompatibility, and its degradability. We found little difference in particle size when using PLGA block sizes over the range of 5 to 15kDa. The choice of hydrophobic small molecule was important, as molecules with a calculated water-octanol partition coefficient (clogP) below 6 gave rise to particles that were unstable and underwent rapid Ostwald ripening. Studies probing the internal structure of nanoparticles were also performed. Analysis of differential scanning calorimetry (DSC), cryogenic transmission electron microscopy (cryo-TEM), and 1H-NMR experiments support a three-layer core-shell-corona nanoparticle structure. PMID:24053447

  3. Crystal Structure and Pair Potentials: A Molecular-Dynamics Study

    Microsoft Academic Search

    M. Parrinello; A. Rahman

    1980-01-01

    With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.

  4. Broadband super-collimation in a hybrid photonic crystal structure

    E-print Network

    Hamam, Rafif E.

    We propose a two dimensional (2D) photonic crystal (PhC) structure that supports super-collimation over a large frequency range (over 4 times that of a traditional square lattice of holes). We theoretically and numerically ...

  5. The interaction of colloidal particles with weak homeotropic anchoring energy in homogeneous nematic liquid crystal cells.

    PubMed

    Kim, Sung-Jo; Kim, Jong-Hyun

    2014-04-21

    We have investigated interactions of colloidal particles with weak homeotropic anchoring energy in homogeneous nematic liquid crystal cells. Particle-wall and inter-particle interactions were observed experimentally and analyzed using typical dipole-dipole and quadrupole-quadrupole interactions, including substrate effects as the image charges. Both experimental results matched well with the calculated results for the effective particle radius reflecting the weak anchoring. The effective radius is reduced by the amount of extrapolation length than the actual particle radius. The effective radii of polyethylene micro-particles were reduced to a coefficient ? (0.78 ? ? ? 0.52) times the actual radius with anchoring coefficients in the range of 3.8 × 10(-6) to 1.4 × 10(-6) J m(-2). The anchoring energy of the particles is, therefore, a key component for explaining liquid crystal colloidal systems. PMID:24647470

  6. Teaching Mineralogy with Crystal Structure Databases and Visualization Software

    NSDL National Science Digital Library

    Kent Ratajeski

    2002-01-01

    This resource collection provides information on how to incorporate crystal structure databases and 3-D visualization software into undergraduate mineralogy courses. Features include background information for teachers on how to teach with data, models, and visualizations; commentary on the benefits of physical versus virtual models; and a set of links to online crystal structure databases. There are also links to visualization software, tutorials, and example exercises and activities.

  7. Allophycocyanin and phycocyanin crystal structures reveal facets of phycobilisome assembly.

    PubMed

    Marx, Ailie; Adir, Noam

    2013-03-01

    X-ray crystal structures of the isolated phycobiliprotein components of the phycobilisome have provided high resolution details to the description of this light harvesting complex at different levels of complexity and detail. The linker-independent assembly of trimers into hexamers in crystal lattices of previously determined structures has been observed in almost all of the phycocyanin (PC) and allophycocyanin (APC) structures available in the Protein Data Bank. In this paper we describe the X-ray crystal structures of PC and APC from Synechococcus elongatus sp. PCC 7942, PC from Synechocystis sp. PCC 6803 and PC from Thermosynechococcus vulcanus crystallized in the presence of urea. All five structures are highly similar to other PC and APC structures on the levels of subunits, monomers and trimers. The Synechococcus APC forms a unique loose hexamer that may show the structural requirements for core assembly and rod attachment. While the Synechococcus PC assembles into the canonical hexamer, it does not further assemble into rods. Unlike most PC structures, the Synechocystis PC fails to form hexamers. Addition of low concentrations of urea to T. vulcanus PC inhibits this proteins propensity to form hexamers, resulting in a crystal lattice composed of trimers. The molecular source of these differences in assembly and their relevance to the phycobilisome structure is discussed. PMID:23201474

  8. Genome structure of incomplete particles of adenovirus.

    PubMed Central

    Daniell, E

    1976-01-01

    Incomplete particles arising during productive growth of adenovirus were separated from infectious particles by density gradient centrifugation. The DNA contained in particles of low density was characterized by restriction enzyme analysis and by electron microscopy and heteroduplexing techniques. The DNA is heterogeneous in length, ranging in size from 15% of the normal genome to full length. Many individual molecules contain long, inverted terminal repetitions, which consist of the sequences extending from the normal left-hand end of the viral genome inward; the normal right end sequences appear to be missing from these molecules. The region of the genome reiterated in these molecules is that which has been implicated in transformation of rat cells by adenovirus (Gallimore, Sharp, and Sambrook, 1974; Graham, van der Eb, and Heijneker, 1974). A model for adenovirus replication is presented that accounts for the aberrant structures observed. Images PMID:957486

  9. Quantitative crystal structure descriptors from multiplicative congruential generators.

    PubMed

    Hornfeck, Wolfgang

    2012-03-01

    Special types of number-theoretic relations, termed multiplicative congruential generators (MCGs), exhibit an intrinsic sublattice structure. This has considerable implications within the crystallographic realm, namely for the coordinate description of crystal structures for which MCGs allow for a concise way of encoding the numerical structural information. Thus, a conceptual framework is established, with some focus on layered superstructures, which proposes the use of MCGs as a tool for the quantitative description of crystal structures. The multiplicative congruential method eventually affords an algorithmic generation of three-dimensional crystal structures with a near-uniform distribution of atoms, whereas a linearization procedure facilitates their combinatorial enumeration and classification. The outlook for homometric structures and dual-space crystallography is given. Some generalizations and extensions are formulated in addition, revealing the connections of MCGs with geometric algebra, discrete dynamical systems (iterative maps), as well as certain quasicrystal approximants. PMID:22338652

  10. Non Linear Compton Scattering of Strong Laser Radiation on Channeled Particles in a Crystal

    E-print Network

    A. K. Avetissian; K. Z. Hatsagortsian; G. F. Mkrtchian; Kh. V. Sedrakian

    2001-08-31

    A version for intense $\\gamma $-ray radiation based on the multiphoton scattering of strong laser radiation on relativistic particle beam channeled in a crystal is proposed. The scheme is considered when the incident laser beam and charged paricles beam are counter-propagating and the laser radiation is resonant to the energy levels of transversal motion of channeled particles.

  11. Rapid and continuous hydrothermal crystallization of metal oxide particles in supercritical water

    Microsoft Academic Search

    Tadafumi Adschiri; Katsuhito Kanazawa; Kunio Arai

    1992-01-01

    This paper reports on hydrolysis of 10 metal salt aqueous solutions of 6 metal oxides that was conducted in supercritical water. Continuous and rapid production of metal oxide fine particles was achieved by mixing a metal salt aqueous solution with preheated water fed from another line. The reaction time required was less than 2 min. Particle size, morphology, and crystal

  12. Particle levitation and guidance in hollow-core photonic crystal fiber

    Microsoft Academic Search

    Fetah Benabid; J. C. Knight; P. St. J. Russell

    2002-01-01

    We report the guidance of dry micron-sized dielectric particles in hollow core photonic crystal fiber. The particles were levitated in air and then coupled to the air-core of the fiber using an Argon ion laser beam operating at a wavelength of 514 nm. The diameter of the hollow core of the fiber is 20 m . A laser power of

  13. Grain size, chemistry, and structure of fine and ultrafine particles in stainless steel welding fumes

    Microsoft Academic Search

    B. Moroni; C. Viti

    2009-01-01

    A combined SEM–TEM study was performed on samples of metal inert gas (MIG) stainless steel (SS) arc welding fumes to characterize fine and ultrafine particle fractions in terms of size distributions, crystal structures, and chemistry. Overall observations indicate that welding fumes consist of a complex mixture of magnetite-like nanocrystals and non-spinel particles in different phases, with distinguishing grain size distributions

  14. Coarsening of extracellularly biosynthesized cadmium crystal particles induced by thioacetamide in solution.

    PubMed

    Chen, Gui-Qiu; Zou, Zheng-Jun; Zeng, Guang-Ming; Yan, Ming; Fan, Jia-Qi; Chen, An-Wei; Yang, Fan; Zhang, Wen-Juan; Wang, Liang

    2011-05-01

    A novel coarsening route for extracellularly biosynthesized cadmium nanocrystals was investigated for the first time. In this process, the white rot fungus Coriolus versicolor was employed to take up cadmium ions and synthesize extracellular cadmium crystal particles. The coarsening of the particles was induced by thioacetamide under certain conditions. Scanning electron microscopy showed that the formed cadmium crystal particles were coarsened from about 100nm to 2-3?m. The corresponding energy-dispersive X-ray spectra confirmed the presence of proteins in the particles. The maximum removal efficiency of Cd(II) increased from 17% to 87%, and the corresponding sorption capacity of biomass increased from 4 to 24mgg(-1) with the completion of the coarsening process. The properties of the coarsened particles were also examined using X-ray diffraction (XRD) and transmission electron microscopy (TEM). XRD analysis of fungal mycelial pellets embedded with the coarsened particles confirmed the formation of cubic crystalline cadmium sulfide particles. The TEM results suggest that the coarsened particles were composed of clusters of several smaller particles. The changes in the functional groups on the biomass surface were studied through Fourier transform infrared spectroscopy. Based on the results above, a possible mechanism for the formation and coarsening of cadmium crystal particle is also discussed. PMID:21489598

  15. Structures and phase transitions of a vertically confined plasma crystal

    Microsoft Academic Search

    K. Qiao; T. W. Hyde

    2004-01-01

    Dusty plasmas consist of an ionized gas containing small (usually negatively charged) particles. Dusty plasmas are of interest in both astrophysics and space physics as well as in research in plasma processing and nanofabrication. In this work, the formation of plasma crystals confined in an external one-dimensional parabolic potential well is simulated for a normal experimental environment employing a computer

  16. Particle levitation and guidance in hollow-core photonic crystal fiber.

    PubMed

    Benabid, Fetah; Knight, J; Russell, P

    2002-10-21

    We report the guidance of dry micron-sized dielectric particles in hollow core photonic crystal fiber. The particles were levitated in air and then coupled to the air-core of the fiber using an Argon ion laser beam operating at a wavelength of 514 nm. The diameter of the hollow core of the fiber is 20 m . A laser power of 80 mW was sufficient to levitate a 5 m diameter polystyrene sphere and guide it through a ~150 mm long hollow-core crystal photonic fiber. The speed of the guided particle was measured to be around 1 cm/s. PMID:19451980

  17. Formation of classical crystals of dipolar particles in a helical geometry

    E-print Network

    J. K. Pedersen; D. V. Fedorov; A. S. Jensen; N. T. Zinner

    2014-08-11

    We consider crystal formation of particles with dipole-dipole interactions that are confined to move in a one-dimensional helical geometry with their dipole moments oriented along the symmetry axis of the confining helix. The stable classical lowest energy configurations are found to be chain structures for a large range of pitch-to-radius ratios for relatively low density of dipoles and a moderate total number of particles. The classical normal mode spectra support the chain interpretation both through structure and the distinct degeneracies depending discretely on the number of dipoles per revolution. A larger total number of dipoles leads to a clusterization where the dipolar chains move closer to each other. This implies a change in the local density and the emergence of two length scales, one for the cluster size and one for the inter-cluster distance along the helix. Starting from three dipoles per revolution, this implies a breaking of the initial periodicity to form a cluster of two chains close together and a third chain removed from the cluster. This is driven by the competition between in-chain and out-of-chain interactions, or alternatively the side-by-side repulsion and the head-to-tail attraction in the system. The speed of sound propagates along the chains. It is independent of the number of chains although depending on geometry.

  18. Application of multispectral data processing techniques to cholesteric liquid crystal tracer particles

    E-print Network

    Wilcox, Neal Allen

    1985-01-01

    -overlapping particle images versus the number of particles in the tank. . . . . . . . . . 33 9 Positions of the lights and tank relative to the camera. 10 Diagram of digitizer system. 11 Coordinate prediction model calibration fixture. 12 Examples of the two... calibration of liquid crystals. Color Temperature ( C) SR 31. 1 31. 6 SB 32. 2 30 Figure 6. Color print of the tracer particles being heated in the stirred tank. 31 Aluminum wall Black wall section Inner tank To camera Outer tank Figure 7...

  19. Wear particles of single-crystal silicon carbide in vacuum

    NASA Technical Reports Server (NTRS)

    Miyoshi, K.; Buckley, D. H.

    1980-01-01

    Sliding friction experiments, conducted in vacuum with silicon carbide /000/ surface in contact with iron based binary alloys are described. Multiangular and spherical wear particles of silicon carbide are observed as a result of multipass sliding. The multiangular particles are produced by primary and secondary cracking of cleavage planes /000/, /10(-1)0/, and /11(-2)0/ under the Hertzian stress field or local inelastic deformation zone. The spherical particles may be produced by two mechanisms: (1) a penny shaped fracture along the circular stress trajectories under the local inelastic deformation zone, and (2) attrition of wear particles.

  20. The Mechanics of the Systems of Structured Particles

    E-print Network

    V. M. Somsikov

    2012-10-02

    The mechanics of the structured particles develops. The substantiation of applicability of such mechanics for the description of processes of evolution in open nonequilibrium systems is offered. The consequences following from the equations of dynamics of structured particles are analyzed.

  1. Crystal and quasicrystal structures in Al-Mn-Si alloys

    Microsoft Academic Search

    Veit Elser; C. L. Henley

    1985-01-01

    It is shown that the alpha-(AlMnSi) crystal structure is closely (and systematically) related to that of the icosahedral Al-Mn-Si alloys. Using a modification of the 'projection' method of generating icosahedral structures from six-dimensional lattices, a simple description of the alpha-(AlMnSi) structure is found. This structure, and (it is conjectured) the icosahedral one, can also be described as a packing of

  2. On the composite structure of elementary particles

    NASA Astrophysics Data System (ADS)

    Tata, X. R.

    It is shown that the recombination model associated with modified Kuti-Wiesskopf structure functions provides, within the framework of the quark-parton model, a consistent description of low p sub T particle production in the fragmentation domain of colliding hadrons. The parameters needed to specify the structure functions of the hadrons are all determined from the inclusive single meson production data. The compositeness of particles is then studied from the more fundamental field theoretic point of view. The sense in which a Yakama type interaction may be regarded as equivalent to a four point interaction, with the intermediate boson of the Yakawa theory being regarded as a composite particle, is examined. Irrespective of the bosonic or fermionic nature of the constituents of the four point interaction, the compositeness conditions do not by themselves, ensure the identity of the two theories. It is further shown that the Yukawa interaction may be made to undergo a transmutation into a four point interaction provided certain spectral contributions that occur in the Yukawa theory are explicity omitted. In view of this, it is suggested that all proofs of the equilvalence of the four fermion theory with the corresponding Yukawa theory need to be reexamined.

  3. Crystal structure refinement of aluminian lizardite-2H2

    Microsoft Academic Search

    MARIA FRANCA BRIGATTI; E RMANNO GALLI; L UCA MEDICI; LUCIANO POPPI

    1997-01-01

    Well-crystallized euhedral crystals of aluminian lizardite-2 H2 2.35 0.06 0.07 0.52 were found near Schio (Vicenza, Italy). To gain insight into the role (Si Al )O (OH) 1.41 0.59 5.00 4.00 of a high Al content lizardite, chemical analyses and single-crystal X-ray data collection were conducted. Structure refinement, completed in space groupP63 (agreement factor R 5 0.034), gives mean T-O

  4. Band structure engineering of two-dimensional magnonic vortex crystals

    NASA Astrophysics Data System (ADS)

    Behncke, Carolin; Hänze, Max; Adolff, Christian F.; Weigand, Markus; Meier, Guido

    2015-06-01

    Magnonic vortex crystals are studied via scanning transmission x-ray microscopy and ferromagnetic-resonance spectroscopy. We investigate a two-dimensional vortex crystal by imprinting waves with tunable wave vectors. The dispersion relation ? (k ) is determined via ferromagnetic-resonance spectroscopy with a tunable frequency and wave vector for two vortex core polarization patterns that are adjusted by self-organized state formation prior to the measurement. We demonstrate that the band structure of the crystal is reprogrammed by tuning the vortex polarizations.

  5. Ice nucleation: elemental identification of particles in snow crystals.

    PubMed

    Parungo, F P; Pueschel, R F

    1973-06-01

    A scanning field-emission electron microscope combined with an x-ray analyzer is used to locate the ice nucleus within a three-dimensional image of a snow crystal and determine the chemical composition of the nucleus. This makes it possible to better understand the effect of nuclei in cloud seeding. PMID:17806581

  6. Phase Change Materials: from crystal structures to kinetics

    Microsoft Academic Search

    R. Detemple; H. Dieker; J. Kalb; M. Luo; F. Spaepen; C. Steimer; D. Wamwangi; H. W. Wöltgens; S. Ziegler; M. Wuttig

    Phase change materials are characterized by a structural transition that is accompanied by a pronounced change of properties. We have recently focused our efforts to understand and identify suitable phase change materials onto the identification of suitable structures and the detailed study of crystallization kinetics. For a large number of samples it could be shown that only those samples with

  7. Nitric Oxide Myoglobin: Crystal Structure and Analysis of Ligand Geometry

    E-print Network

    Phillips, George N. Jr.

    Nitric Oxide Myoglobin: Crystal Structure and Analysis of Ligand Geometry Eric Allen Brucker,1 John School of Medicine, Cleveland, Ohio ABSTRACT The structure of the ferrous nitric oxide form of native, the rate of nitric oxide dissociation from myoglobin increases tenfold. Proteins 30:352­356, 1998. 1998

  8. Hexagonal structures for two-dimensional photonic crystals

    Microsoft Academic Search

    D. Cassagne; C. Jouanin; D. Bertho

    1996-01-01

    Periodic dielectric structures have been recently proposed to inhibit spontaneous emission in semiconductors. From this suggestion, the new concepts of photonic band gap and photonic crystal have been developed. Zero-threshold lasers, waveguides, antenna substrates, filters and polarizers are promising applications. We propose a new class of two-dimensional periodic dielectric structures with hexagonal symmetry. We study the gap opening according to

  9. Protein Structures Total Chemical Synthesis and X-ray Crystal

    E-print Network

    Bang, Duhee

    in Scheme 1b. Data for the synthesis of native ubiquitin are shown in Figure 1. The C-terminal peptide and the peptide-a thioesters were prepared by solid-phase peptide synthesis by using manual stepwise BocProtein Structures Total Chemical Synthesis and X-ray Crystal Structure of a Protein Diastereomer

  10. Predicting crystal structure by merging data mining with quantum mechanics

    E-print Network

    Ceder, Gerbrand

    ARTICLES Predicting crystal structure by merging data mining with quantum mechanics CHRISTOPHER C@mit.edu Published online: 9 July 2006; doi:10.1038/nmat1691 Modern methods of quantum mechanics have proved with quantum mechanics if an algorithm to direct the search through the large space of possible structures

  11. Photonic crystal and photonic wire device structures

    Microsoft Academic Search

    Richard De La Rue; Marc Sorel; Nigel Johnson; Faiz Rahman; Charles Ironside; Lee Cronin; Ian Watson; Robert Martin; Chongjun Jin; Pierre Pottier; Harold Chong; Marco Gnan; Aju Jugessur; Edilson Camargo; Grant Erwin; Iraklis Ntakis; Lois Hobbs; Hua Zhang; Mario Armenise; Caterina Ciminelli; Dominique Coquillat

    2005-01-01

    Photonic devices that exploit photonic crystal (PhC) principles in a planar environment continue to provide a fertile field of research. 2D PhC based channel waveguides can provide both strong confinement and controlled dispersion behaviour. In conjunction with, for instance, various electro-optic, thermo-optic and other effects, a range of device functionality is accessible in very compact PhC channel-guide devices that offer

  12. Cambridge Structural Database as a tool for studies of general structural features of organic molecular crystals

    NASA Astrophysics Data System (ADS)

    Kuleshova, Lyudmila N.; Antipin, Mikhail Yu

    1999-01-01

    The review surveys and generalises data on the use of the Cambridge Structural Database (CSD) for studying and revealing general structural features of organic molecular crystals. It is demonstrated that software and facilities of the CSD allow one to test the applicability of a number of known concepts of organic crystal chemistry (the principle of close packing, the frequency of occurrence of space groups, the preferred formation of centrosymmetrical molecular crystals, etc.) on the basis of abundant statistical data. Examples of the use of the Cambridge Structural Database in engineering of molecular crystals and in the systematic search for compounds with specified properties are given. The bibliography includes 122 references.

  13. Some new results on the frequency characteristics on quartz crystals irradiated by ionizing and particle radiations

    NASA Astrophysics Data System (ADS)

    Bahadur, H.; Parshad, R.

    1981-03-01

    The frequency behavior of AT-cut quartz crystals irradiated by X -, gamma rays and fast neutrons. Initial instability in frequency for gamma and neutron irradiated crystals was found. All the different radiations first give a negative frequency shift at lower doses which are followed by positive frequency shift for increased doses. Results are explained in terms of the fundamental crystal structure. Applications of the frequency results for radiation hardening are proposed.

  14. Rotational analysis of birefringent crystal particles based on modified theory in optical tweezers

    NASA Astrophysics Data System (ADS)

    Wei, Yong; Zhu, Yanying; Yao, Wenying; Pei, Huan

    2015-04-01

    In order to achieve high-precision, controllable rotation of uniaxial birefringent crystal particles, we study the principle of optical rotation due to the transfer of spin angular momentum from light to birefringent crystal particles. The interaction process between the beam and particles is affected by various factors existed actually, for instance: the reflection of beam on the crystal surface, laser power, the set of angle between the crystal optical axis and surface, radius, phase difference between the ordinary ray and extraordinary ray. According to the analysis of these factors, the theoretical model of optical rotation is reconstructed. The theoretical curves of calcium carbonate and silicon particles chosen as experimental material between the rotational frequency and the radius are simulated and calculated. The result shows that the rotation frequency is inversely proportional to the cube of radius, and compared the performance of modified model with traditional model. The birefringent particles are rotated by optical tweezers in the experiment, and rotation frequency is measured with the same laser power. According to the experimental results of optical rotation, the modified Friese theoretical model is proved to be the reasonably and excellence, in addition, the result shows the maximum frequency of calcium carbonate is 19.1Hz, and the maximum frequency of silicon particles is 11.5Hz. The rationality of our experiment is testified by compared with theoretical analysis. Our study has great directive significance to the design of optical driven micro-mechanical motor and the material selection of rotor.

  15. Direct Deposition of Aerosol Particles on an ATR Crystal for FTIR Spectroscopy Using an Electrostatic Precipitator

    Microsoft Academic Search

    J. Ofner; H.-U. Krüger; C. Zetzsch; H. Grothe

    2009-01-01

    An electrostatic precipitator (ESP) has been developed for collecting aerosol samples for attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) from an aerosol chamber. The ESP deposits the aerosol particles directly onto the ATR crystal with high efficiency. The ESP-ATR spectra are observed to agree well with the spectrum of a filter sample, transferred by impression. ZnSe ATR crystals have

  16. Pressure induced structural transitions in nanometer size particles of PbS

    Microsoft Academic Search

    S. B. Qadri; J. Yang; B. R. Ratna; E. F. Skelton; J. Z. Hu

    1996-01-01

    At elevated pressure, PbS undergoes a first order phase transition from the NaCl or B1 structure to an orthorhombic structure. The effects of particle sizes in the nanometer range on this transition have been investigated using energy-dispersive x-ray diffraction of synchrotron produced wiggler radiation. Relative to the bulk crystals, the onset of transition pressure showed a significant increase with decreasing

  17. Ytterbium- and neodymium-doped vanadate laser hose crystals having the apatite crystal structure

    DOEpatents

    Payne, S.A.; Kway, W.L.; DeLoach, L.D.; Krupke, W.F.; Chai, B.H.T.

    1994-08-23

    Yb[sup 3+] and Nd[sup 3+] doped Sr[sub 5](VO[sub 4])[sub 3]F crystals serve as useful infrared laser media that exhibit low thresholds of oscillation and high slope efficiencies, and can be grown with high optical quality. These laser media possess unusually high absorption and emission cross sections, which provide the crystals with the ability to generate greater gain for a given amount of pump power. Many related crystals such as Sr[sub 5](VO[sub 4])[sub 3]F crystals doped with other rare earths, transition metals, or actinides, as well as the many structural analogs of Sr[sub 5](VO[sub 4])[sub 3]F, where the Sr[sup 2+] and F[sup [minus

  18. Ytterbium- and neodymium-doped vanadate laser hose crystals having the apatite crystal structure

    DOEpatents

    Payne, Stephen A. (Castro Valley, CA); Kway, Wayne L. (Fremont, CA); DeLoach, Laura D. (Manteca, CA); Krupke, William F. (Pleasanton, CA); Chai, Bruce H. T. (Oviedo, FL)

    1994-01-01

    Yb.sup.3+ and Nd.sup.3+ doped Sr.sub.5 (VO.sub.4).sub.3 F crystals serve as useful infrared laser media that exhibit low thresholds of oscillation and high slope efficiencies, and can be grown with high optical quality. These laser media possess unusually high absorption and emission cross sections, which provide the crystals with the ability to generate greater gain for a given amount of pump power. Many related crystals such as Sr.sub.5 (VO.sub.4).sub.3 F crystals doped with other rare earths, transition metals, or actinides, as well as the many structural analogs of Sr.sub.5 (VO.sub.4).sub.3 F, where the Sr.sup.2+ and F.sup.- ions are replaced by related chemical species, have similar properties.

  19. Effect of Complex Inclusion Particles on the Solidification Structure of Fe-Ni-Mn-Mo Alloy

    NASA Astrophysics Data System (ADS)

    Park, Jun Seok; Lee, Changhee; Park, Joo Hyun

    2012-12-01

    The effect of combinations of several deoxidizers, i.e., Mg-Al, Mg-Ti, Al-Ti, and Ce-Al, on the solidification structure of Fe-2 mass pct Ni-1 mass pct Mn-1 mass pct Mo alloy melt was investigated using a melt sampling and quenching method. Using this method, we evaluated the catalytic potency of several complex inclusion particles by taking the inclusion evolution process into account. Fine equiaxed crystals were obtained in the Mg-Ti-deoxidized steel wherein the MgO(MgAl2O4)-TiN complex compounds formed. However, the longer the holding time at high temperatures, the larger the fraction of Ti2O3, and very fine TiN formed because of microsegregation during solidification, resulting in poor equiaxed crystals. When the steel was deoxidized with Mg-Al, the initial structure was dominantly columnar. However, the longer the holding time, the larger the fraction of MgAl2O4 spinel, resulting in the formation of fine equiaxed crystals. Ce-Al complex deoxidation provided a relatively small portion of equiaxed crystals, whereas Ti-Al deoxidation produced the fewest equiaxed crystals because of the formation of alumina. The effectiveness of each inoculant particle for the crystallization of the primary ?-iron was explained well by the lattice disregistry concept.

  20. Crystal structure of cis-diamminebis(nitrito-?N)platinum(II)

    PubMed Central

    Kahlenberg, Volker; Gelbrich, Thomas; Tessadri, Richard; Klauser, Frederik

    2015-01-01

    Single crystals of cis-[Pt(NO2)2(NH3)2], were obtained by means of hyper­saturation directly out of a plating electrolyte. The square-planar coordination environment of the divalent PtII atom is formed by four N atoms belonging to two ammine and two monodentate nitrite ligands. The ligands adopt a cis configuration. The crystal structure contains stacks of close-packed mol­ecules which run parallel to [001]. There are nine crystallographically independent inter­molecular N—H?O hydrogen bonds, resulting in a hydrogen-bonded hxl-type framework in which each mol­ecule serves as an eight-connected node. Four of the nine distinct hydrogen bonds connect complexes which belong to the same close-packed column parallel to [001]. In contrast to the previously reported crystal structure of the trans isomer, the title structure does not display intra­molecular hydrogen bonding. PMID:26029392

  1. Synchronization of particle motion induced by mode coupling in a two-dimensional plasma crystal.

    PubMed

    Couëdel, L; Zhdanov, S; Nosenko, V; Ivlev, A V; Thomas, H M; Morfill, G E

    2014-05-01

    The kinematics of dust particles during the early stage of mode-coupling induced melting of a two-dimensional plasma crystal is explored. It is found that the formation of the hybrid mode causes the particle vibrations to partially synchronize at the hybrid frequency. Phase- and frequency-locked hybrid particle motion in both vertical and horizontal directions (hybrid mode) is observed. The system self-organizes in a rhythmic pattern of alternating in-phase and antiphase oscillating chains of particles. The spatial orientation of the synchronization pattern correlates well with the directions of the maximal increment of the shear-free hybrid mode. PMID:25353905

  2. Crystallization and X-ray analysis of the T = 4 particle of hepatitis B capsid protein with an N-terminal extension

    SciTech Connect

    Tan, Wen Siang [Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor (Malaysia); McNae, Iain W.; Ho, Kok Lian; Walkinshaw, Malcolm D., E-mail: m.walkinshaw@ed.ac.uk [Institute of Structural and Molecular Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, King’s Buildings, Mayfield Road, Edinburgh EH9 3JR,Scotland (United Kingdom); Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor (Malaysia)

    2007-08-01

    Hepatitis B virus capsids have significant potential as carriers for immunogenic peptides. The crystal structure of the T = 4 particle of hepatitis B core protein containing an N-terminal extension reveals that the fusion peptide is exposed on the exterior of the particle. Hepatitis B core (HBc) particles have been extensively exploited as carriers for foreign immunological epitopes in the development of multicomponent vaccines and diagnostic reagents. Crystals of the T = 4 HBc particle were grown in PEG 20 000, ammonium sulfate and various types of alcohols. A temperature jump from 277 or 283 to 290 K was found to enhance crystal growth. A crystal grown using MPD as a cryoprotectant diffracted X-rays to 7.7 Å resolution and data were collected to 99.6% completeness at 8.9 Å. The crystal belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 352.3, b = 465.5, c = 645.0 Å. The electron-density map reveals a protrusion that is consistent with the N-terminus extending out from the surface of the capsid. The structure presented here supports the idea that N-terminal insertions can be exploited in the development of diagnostic reagents, multicomponent vaccines and delivery vehicles into mammalian cells.

  3. Liquid Crystal Phase Behaviour of Attractive Disc-Like Particles

    PubMed Central

    Wu, Liang; Jackson, George; Müller, Erich A.

    2013-01-01

    We employ a generalized van der Waals-Onsager perturbation theory to construct a free energy functional capable of describing the thermodynamic properties and orientational order of the isotropic and nematic phases of attractive disc particles. The model mesogen is a hard (purely repulsive) cylindrical disc particle decorated with an anisotropic square-well attractive potential placed at the centre of mass. Even for isotropic attractive interactions, the resulting overall inter-particle potential is anisotropic, due to the orientation-dependent excluded volume of the underlying hard core. An algebraic equation of state for attractive disc particles is developed by adopting the Onsager trial function to characterize the orientational order in the nematic phase. The theory is then used to represent the fluid-phase behaviour (vapour-liquid, isotropic-nematic, and nematic-nematic) of the oblate attractive particles for varying values of the molecular aspect ratio and parameters of the attractive potential. When compared to the phase diagram of their athermal analogues, it is seen that the addition of an attractive interaction facilitates the formation of orientationally-ordered phases. Most interestingly, for certain aspect ratios, a coexistence between two anisotropic nematic phases is exhibited by the attractive disc-like fluids. PMID:23965962

  4. Model solution for volume reflection of relativistic particles in a bent crystal

    SciTech Connect

    Bondarenco, M. V. [Kharkov Institute of Physics and Technology, 1 Academic St., 61108 Kharkov (Ukraine)

    2010-10-15

    For volume reflection process in a bent crystal, exact analytic expressions for positively- and negatively-charged particle trajectories are obtained within a model of parabolic continuous potential in each interplanar interval, with the neglect of incoherent multiple scattering. In the limit of the crystal bending radius greatly exceeding the critical value, asymptotic formulas are obtained for the particle mean deflection angle in units of Lindhard's critical angle, and for the final beam profile. Volume reflection of negatively charged particles is shown to contain effects of rainbow scattering and orbiting, whereas with positively charged particles none of these effects arise within the given model. The model predictions are compared with experimental results and numerical simulations. Estimates of the volume reflection mean angle and the final beam profile robustness under multiple scattering are performed.

  5. Voids and yolk-shells from crystals that coat particles.

    PubMed

    Sindoro, Melinda; Granick, Steve

    2014-10-01

    We investigate curvature-driven core-shell morphology that emerges when polycrystalline shells of ZIF-8 (zeolitic imidazolate framework coordination polymer) grow on colloid-sized particles. In early growth stages, the shell is continuous, but it transforms to yolk-shell, with neither sacrificial template nor core etching, because of geometrical frustration. A design rule is developed regarding how local surface curvature matters. Comparing shells grown on cubic, rod-like, and peanut-shaped hematite core particles, we validate the argument. PMID:25243973

  6. Structurally Coloured Secondary Particles Composed of Black and White Colloidal Particles

    PubMed Central

    Takeoka, Yukikazu; Yoshioka, Shinya; Teshima, Midori; Takano, Atsushi; Harun-Ur-Rashid, Mohammad; Seki, Takahiro

    2013-01-01

    This study investigated the colourful secondary particles formed by controlling the aggregation states of colloidal silica particles and the enhancement of the structural colouration of the secondary particles caused by adding black particles. We obtained glossy, partially structurally coloured secondary particles in the absence of NaCl, but matte, whitish secondary particles were obtained in the presence of NaCl. When a small amount of carbon black was incorporated into both types of secondary particles, the incoherent multiple scattering of light from the amorphous region was considerably reduced. However, the peak intensities in the reflection spectra, caused by Bragg reflection and by coherent single wavelength scattering, were only slightly decreased. Consequently, a brighter structural colour of these secondary particles was observed with the naked eye. Furthermore, when magnetite was added as a black particle, the coloured secondary particles could be moved and collected by applying an external magnetic field. PMID:23917891

  7. Solitons and domain structure in elastic crystals with a microstructure: Mathematical aspects

    Microsoft Academic Search

    G. A. Maugin

    1986-01-01

    Elastic crystals with a microstructure include ferroelectric crystals, ferromagnetic crystals and crystals with internal mechanical degrees of freedom. In recent works concerning the discrete or continuum modelling of the behavior of such elastic crystals, we have been able to delineate a general descriptive framework in which,using the concepts of solitary waves and solitons, the dynamics of simple structures in domains

  8. CRYSTAL STRUCTURE ANALYSIS OF A PUTATIVE OXIDOREDUCTASE FROM KLEBSIELLA PNEUMONIAE

    SciTech Connect

    Baig, M.; Brown, A.; Eswaramoorthy, S.; Swaminathan, S.

    2009-01-01

    Klebsiella pneumoniae, a gram-negative enteric bacterium, is found in nosocomial infections which are acquired during hospital stays for about 10% of hospital patients in the United States. The crystal structure of a putative oxidoreductase from K. pneumoniae has been determined. The structural information of this K. pneumoniae protein was used to understand its function. Crystals of the putative oxidoreductase enzyme were obtained by the sitting drop vapor diffusion method using Polyethylene glycol (PEG) 3350, Bis-Tris buffer, pH 5.5 as precipitant. These crystals were used to collect X-ray data at beam line X12C of the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory (BNL). The crystal structure was determined using the SHELX program and refi ned with CNS 1.1. This protein, which is involved in the catalysis of an oxidation-reduction (redox) reaction, has an alpha/beta structure. It utilizes nicotinamide adenine dinucleotide phosphate (NADP) or nicotine adenine dinucleotide (NAD) to perform its function. This structure could be used to determine the active and co-factor binding sites of the protein, information that could help pharmaceutical companies in drug design and in determining the protein’s relationship to disease treatment such as that for pneumonia and other related pathologies.

  9. Toxicity of TiO2 nanoparticles to Escherichia coli: effects of particle size, crystal phase and water chemistry.

    PubMed

    Lin, Xiuchun; Li, Jingyi; Ma, Si; Liu, Gesheng; Yang, Kun; Tong, Meiping; Lin, Daohui

    2014-01-01

    Controversial and inconsistent results on the eco-toxicity of TiO2 nanoparticles (NPs) are commonly found in recorded studies and more experimental works are therefore warranted to elucidate the nanotoxicity and its underlying precise mechanisms. Toxicities of five types of TiO2 NPs with different particle sizes (10?50 nm) and crystal phases were investigated using Escherichia coli as a test organism. The effect of water chemistry on the nanotoxicity was also examined. The antibacterial effects of TiO2 NPs as revealed by dose-effect experiments decreased with increasing particle size and rutile content of the TiO2 NPs. More bacteria could survive at higher solution pH (5.0-10.0) and ionic strength (50-200 mg L(-1) NaCl) as affected by the anatase TiO2 NPs. The TiO2 NPs with anatase crystal structure and smaller particle size produced higher content of intracellular reactive oxygen species and malondialdehyde, in line with their greater antibacterial effect. Transmission electron microscopic observations showed the concentration buildup of the anatase TiO2 NPs especially those with smaller particle sizes on the cell surfaces, leading to membrane damage and internalization. These research results will shed new light on the understanding of ecological effects of TiO2 NPs. PMID:25310452

  10. Crystal Structure of the 30 S Ribosomal Subunit from Thermus thermophilus: Purification, Crystallization

    E-print Network

    Ramakrishnan, Venki

    of a detailed atomic-resolution model. # 2001 Academic Press Keywords: 30 S; ribosome; crystallography are referred to as 50 S and 30 S, respectively, according to their rate of sedi- mentation. The ribosome hasCrystal Structure of the 30 S Ribosomal Subunit from Thermus thermophilus: Purification

  11. Role of Surface Area, Primary Particle Size, and Crystal Phase on Titanium Dioxide Nanoparticle Dispersion Properties

    Microsoft Academic Search

    Komkrit Suttiponparnit; Jingkun Jiang; Manoranjan Sahu; Sirikalaya Suvachittanont; Tawatchai Charinpanitkul; Pratim Biswas

    2011-01-01

    Characterizing nanoparticle dispersions and understanding the effect of parameters that alter dispersion properties are important for both environmental applications and toxicity investigations. The role of particle surface area, primary particle size, and crystal phase on TiO2 nanoparticle dispersion properties is reported. Hydrodynamic size, zeta potential, and isoelectric point (IEP) of ten laboratory synthesized TiO2 samples, and one commercial Degussa TiO2

  12. Volume Reflection and Volume Refraction of Relativistic Particles in a Uniformly Bent Crystal

    E-print Network

    Gennady V. Kovalev

    2014-10-12

    The scattering of fast charged particles in a bent crystal has been analyzed in the framework of relativistic classical mechanics. The expressions obtained for the deflection function are in satisfactory agreement with the experimental data for the volume reflection of relativistic protons obtained in [1,2,3]. The features of the scattering of the particles on ring potentials are considered in a wide range of impact parameters

  13. Structure and mechanical properties of biogenic single calcite crystals

    NASA Astrophysics Data System (ADS)

    Aizenberg, Joanna; Weiner, Steve; Addadi, Lia

    2000-03-01

    Composite materials, in which the organic host is stiffened by guest crystalline particles, are widely used in nature (bones, teeth, mollusk shells) and are produced synthetically by man (fiber-reinforced composites). Organisms also produce a different type of composite in which the host is a single crystal and the guests are macromolecules occluded in an orderly fashion within the crystal. The best-studied examples, to date, are skeletal elements composed of a single calcite crystal. These skeletons have unique mechanical properties, and fracture with a glassy conchoidal surface, which is quite different from the smooth planar cleavage of pure calcite. The specific positions of macromolecules in calcite crystals were identified by in vitro crystallization experiments and synchrotron X-ray studies. We show that the occluded macromolecules introduced specifically along crystallographic planes that are oblique to the cleavage planes of calcite strengthen the material against failure by both absorbing and deviating the advancing cracks. These novel, "reverse" fiber-reinforced, composites may be just one example of strategies used in nature for producing materials with improved properties.

  14. Crystal structures of carbonates up to Mbar pressures determined by single crystal synchrotron radiation diffraction

    NASA Astrophysics Data System (ADS)

    Merlini, M.

    2013-12-01

    The recent improvements at synchrotron beamlines, currently allow single crystal diffraction experiments at extreme pressures and temperatures [1,2] on very small single crystal domains. We successfully applied such technique to determine the crystal structure adopted by carbonates at mantle pressures. The knowledge of carbon-bearing phases is in fact fundamental for any quantitative modelling of global carbon cycle. The major technical difficulty arises after first order transitions or decomposition reactions, since original crystal (apx. 10x10x5 ?m3) is transformed in much smaller crystalline domains often with random orientation. The use of 3D reciprocal space visualization software and the improved resolution of new generation flat panel detectors, however, allow both identification and integration of each single crystal domain, with suitable accuracy for ab-initio structure solution, performed with direct and charge-flipping methods and successive structure refinements. The results obtained on carbonates, indicate two major crystal-chemistry trends established at high pressures. The CO32- units, planar and parallel in ambient pressure calcite and dolomite structures, becomes non parallel in calcite- and dolomite-II and III phases, allowing more flexibility in the structures with possibility to accommodate strain arising from different cation sizes (Ca and Mg in particular). Dolomite-III is therefore also observed to be thermodynamically stable at lower mantle pressures and temperatures, differently from dolomite, which undergoes decomposition into pure end-members in upper mantle. At higher pressure, towards Mbar (lowermost mantle and D'' region) in agreement with theoretical calculations [3,4] and other experimental results [5], carbon coordination transform into 4-fold CO4 units, with different polymerisation in the structure depending on carbonate composition. The second important crystal chemistry feature detected is related to Fe2+ in Fe-bearing magnesite, which spontaneously oxidises at HP/HT, forming Fe3+ carbonates, Fe3+ oxides and reduced carbon (diamonds). Single crystal diffraction approach allowed full structure determination of these phases, yielding to the discovery of few unpredicted structures, such as Mg2Fe2C4O13 and Fe13O19, which can be well reproduced in different experiments. Mg2Fe2C4O13 carbonate present truncated chain C4O13 groups, and Fe13O19 oxide, whose stoichiometry is intermediate between magnetite and hematite, is a one-layer structure, with features encountered in superconducting materials. The results fully support the ideas of unexpected complexities in the mineralogy of the lowermost mantle, and single crystal technique, once properly optimized in ad-hoc synchrotron beamlines, is fundamental for extracting accurate structural information, otherwise rarely accessible with other experimental techniques. References: [1] Merlini M., Hanfland M. (2013). Single crystal diffraction at Mbar conditions by synchrotron radiation. High Pressure Research, in press. [2] Dubrovinsky et al., (2010). High Pressure Research, 30, 620-633. [3] Arapan et al. (1997). Phys. Rev. Lett., 98, 268501. [4] Oganov et al. (2008) EPSL, 273, 38-47. [5] Boulard et al. (2011) PNAS, 108, 5184-5187.

  15. Crystallization of interleukin-18 for structure-based inhibitor design.

    PubMed

    Krumm, Brian; Meng, Xiangzhi; Xiang, Yan; Deng, Junpeng

    2015-06-01

    Interleukin-18 (IL-18) is a pleiotropic pro-inflammatory cytokine belonging to the IL-1 superfamily. IL-18 plays an important role in host innate and acquired immune defense, with its activity being modulated in vivo by its naturally occurring antagonist IL-18 binding protein (IL-18BP). Recent crystal structures of human IL-18 (hIL-18) in complex with its antagonist or cognate receptor(s) have revealed a conserved binding interface on hIL-18 representing a promising drug target. An important step in this process is obtaining crystals of apo hIL-18 or hIL-18 in complex with small-molecule inhibitors, preferably under low ionic strength conditions. In this study, surface-entropy reduction (SER) and rational protein design were employed to facilitate the crystallization of hIL-18. The results provide an excellent platform for structure-based drug design. PMID:26057800

  16. Crystal Structure Representations for Machine Learning Models of Formation Energies

    E-print Network

    Faber, Felix; von Lilienfeld, O Anatole; Armiento, Rickard

    2015-01-01

    We introduce and evaluate a set of feature vector representations of crystal structures for machine learning (ML) models of formation energies of solids. ML models of atomization energies of organic molecules have been successful using a Coulomb matrix representation of the molecule. We consider three ways to generalize such representations to periodic systems: (i) a matrix where each element is related to the Ewald sum of the electrostatic interaction between two different atoms in the unit cell repeated over the lattice; (ii) an extended Coulomb-like matrix that takes into account a number of neighboring unit cells; and (iii) an Ansatz that mimics the periodicity and the basic features of the elements in the Ewald sum matrix by using a sine function of the crystal coordinates of the atoms. The representations are compared for a Laplacian kernel with Manhattan norm, trained to reproduce formation energies using a data set of 3938 crystal structures obtained from the Materials Project. For training sets consi...

  17. Crystal structure of Sb 2 MoO 6

    Microsoft Academic Search

    Ahmed Laarif; François R. Theobald; Hervé Vivier; Alan W. Hewat

    1984-01-01

    Crystal structureISb2Mo06 Abstract.The molybdenum antimony oxide Sb2Mo06 crystallizes in the triclinic space group Pl. Cell parameters measured on an X-ray dif- fractometer CAD4 were a=7.481(2)A; b=7.504(1)A; c=10.120(2)A; 1X=70.43(2t; f3=70.91(2t; y=83.35(2t. From neutron diffraction the following parameters were obtained a=7.4774(2) A; b=7.5017(2)*; c=10.1259(2)*; a=70.374(1t; f3=70.889(lt; y=83.246(lt. The structure determination is based on a single crystal X-ray diffraction studyand a powder neutron

  18. Spontaneous pairing and cooperative movements of micro-particles in a two dimensional plasma crystal

    NASA Astrophysics Data System (ADS)

    Zhdanov, S. K.; Couëdel, L.; Nosenko, V.; Thomas, H. M.; Morfill, G. E.

    2015-05-01

    In an argon plasma of 20 W rf discharge at a pressure of 1.38 Pa, a stable highly ordered monolayer of microparticles is suspended. We observe spontaneous particle pairing when suddenly reducing the gas pressure. Special types of dynamical activity, in particular, entanglement and cooperative movements of coupled particles have been registered. In the course of the experiment first appeared single vertical pairs of particles, in further they gradually accumulated causing melting of the entire crystal. To record pairing events, the particle suspension is side-view imaged using a vertically extended laser sheet. The long-lasting pre-melting phase assured the credible recording and identification of isolated particle pairs. The high monolayer charge density is crucial to explain the spontaneous pairing events observed in our experiments as the mutual repulsion between the particles comprising the monolayer make its vertical extend thicker.

  19. Effect of Particle Size on Dissolution Rates of Nanometer-Scale Talc Crystals

    Microsoft Academic Search

    T. Diedrich; J. Schott; E. Oelkers

    2010-01-01

    Reactivity of nanoparticles can differ markedly from their bulk analogs; however, the relationship between particle size, surface area, and reactivity at the nano-scale is poorly understood. Experiments are currently underway to measure dissolution rates of talc from the macoscopic to nanoscopic scale. Multiple samples of talc crystals, ranging in size from approximately 10 to 100 nanometers, have been synthesized from

  20. Peculiarities of particle ejection in scattering and sputtering of single crystals

    Microsoft Academic Search

    V. E. Yurasova; V. I. Shulga; I. G. Bunin; B. M. Mamaev; L. N. Nevzorova; A. S. Petrov

    1976-01-01

    This paper deals with experimental and computer studies of sputtering : nd scattering of ions with energies of several keV from Cu and InSb single crystals. A substantial importance of the ejected particle channelling for the formation of some peaks in the patterns of spatial distribution of scattered ions and sputtered atoms has been shown.

  1. Possibility of Observing Spiral Scattering of Relativistic Particles in a Bent Crystal

    E-print Network

    Gennady V. Kovalev

    2014-09-25

    The peak position, impact-parameter range, and optimal conditions for observing spiral scattering of relativistic particles in a uniformly bent crystal are estimated. The existence of spiral scattering with a square-root singularity is pointed out. In this case, the secondary process of volume capture to the channeling mode is absent and the conditions for observing this effect are most favorable.

  2. Optical Properties of Cholesteric Liquid Crystals with Functional Structural Defects

    Microsoft Academic Search

    Hiroyuki Yoshida; Chee Heng Lee; Yusuke Miura; Kazuki Tokuoka; Satoshi Suzuki; Akihiko Fujii; Masanori Ozaki

    2008-01-01

    The authors numerically investigate the optical transmission properties of cholesteric liquid crystals with a local modulation of pitch and refractive indices. The transmittance spectra of structures with various defect thickness, refractive indices and pitch are calculated using the 4 × 4 matrix method. Calculation results showed that single or multiple transmittance peaks arise in the selective reflection band for light incidence with

  3. Materials research at Stanford University. [composite materials, crystal structure, acoustics

    NASA Technical Reports Server (NTRS)

    1975-01-01

    Research activity related to the science of materials is described. The following areas are included: elastic and thermal properties of composite materials, acoustic waves and devices, amorphous materials, crystal structure, synthesis of metal-metal bonds, interactions of solids with solutions, electrochemistry, fatigue damage, superconductivity and molecular physics and phase transition kinetics.

  4. Crystal structure transformers in inorganic nitrites, nitrates, and carbonates

    Microsoft Academic Search

    C. N. R. Rao; B. Prakash; M. Natarajan

    1975-01-01

    A critical survey of the data describing crystal structure transformations in inorganic nitrites, nitrates and carbonates is compiled. Data on crystallographic, thermodynamic, spectroscopic, electrical, dielectric and other properties are given for each solid. Experimental techniques used to obtain the data are given and comments on the data are included in the tables. The literature is surveyed up to June 1973.

  5. Birefringence induced by irregular structure in photonic crystal fiber

    Microsoft Academic Search

    In-Kag Hwang; Yong-Jae Lee; Yong-Hee Lee

    2003-01-01

    The unintentional birefringence induced by the irregular structure in photonic crystal fibers is analyzed numerically using the plane wave expansion method. The statistical correlations between the birefringence and the various irregularities are obtained. The birefringence is found to be largely dependent on the fiber design parameters as well as the degree of the irregularity. And the large pitch and the

  6. The structure and vibrational frequencies of nitric acid hydrates crystals

    Microsoft Academic Search

    R. Escribano; D. Fernández; V. J. Herrero; B. Maté; A. Medialdea; M. A. Moreno; I. K. Ortega

    2003-01-01

    The relevance of nitric acid hydrates in stratospheric processes has prompted a large number of investigations on the structure and physicochemical properties of these species. We are carrying out in our lab a study on the spectroscopy of crystals of nitric acid and the mono-, di- and trihydrates, NAM, NAD and NAT, respectively, as a first step to addressing more

  7. Hopping and microscopic dynamics of ultrasoft particles in cluster crystals

    E-print Network

    Daniele Coslovich; Lukas Strauss; Gerhard Kahl

    2010-12-09

    We have investigated the slow dynamics of ultrasoft particles in crystalline cluster phases, where point particles interact through the generalized exponential potential u(r) = \\epsilon \\exp[-(r/\\sigma)^n], focusing on the cluster fcc phase of this model with n=4. In an effort to elucidate how the mechanisms of mass transport depend on the microscopic dynamics and in order to mimic a realistic scenario in a related experiment we have performed molecular dynamics, Brownian dynamics, and Monte Carlo simulations. In molecular dynamics simulations the diffusion of particles proceeds through long-range jumps, guided by strong correlations in the momentum direction. In Monte Carlo and Brownian dynamics simulations jump events are short-ranged, reflecting the purely configurational nature of the dynamics. In contrast to what was found in models of glass-forming liquids, the effect of Newtonian and stochastic microscopic dynamics on the long-time relaxation cannot be accounted for by a temperature-independent rescaling of the time units. From the obvious qualitative discrepancies in the short time behavior between the three simulation methods and the non-trivial difference in jump length distributions, long time relaxation, and dynamic heterogeneity, we learn that a more complex modeling of the dynamics in realistic systems of ultrasoft colloids is required.

  8. Crystal Structure of the Bacillus subtilis Superoxide Dismutase

    SciTech Connect

    Liu, Ping; Ewis, H.E.; Huang, Y.-J; Lu, C.-D.; Tai, P.C.; Weber, Irene T. (GSU)

    2008-06-01

    The sodA gene of Bacillus subtilis was expressed in Escherichia coli, purified and crystallized. The crystal structure of MnSOD was solved by molecular replacement with four dimers per asymmetric unit and refined to an R factor of 21.1% at 1.8 {angstrom} resolution. The dimer structure is very similar to that of the related enzyme from B. anthracis. Larger structural differences were observed with the human MnSOD, which has one less helix in the helical domain and a longer loop between two -strands and also showed differences in three amino acids at the intersubunit interface in the dimer compared with the two bacterial MnSODs. These structural differences can be exploited in the design of drugs that selectively target the Bacillus enzymes.

  9. Domain Structures in Nematic Liquid Crystals on a Polycarbonate Surface

    PubMed Central

    Parshin, Alexander M.; Gunyakov, Vladimir A.; Zyryanov, Victor Y.; Shabanov, Vasily F.

    2013-01-01

    Alignment of nematic liquid crystals on polycarbonate films obtained with the use of solvents with different solvations is studied. Domain structures occurring during the growth on the polymer surface against the background of the initial thread-like or schlieren texture are demonstrated. It is established by optical methods that the domains are stable formations visualizing the polymer surface structures. In nematic droplets, the temperature-induced transition from the domain structure with two extinction bands to the structure with four bands is observed. This transition is shown to be caused by reorientation of the nematic director in the liquid crystal volume from the planar alignment to the homeotropic state with the pronounced radial configuration of nematic molecules on the surface. The observed textures are compared with different combinations of the volume LC orientations and the radial distribution of the director field and the disclination lines at the polycarbonate surface. PMID:23965955

  10. VO{sub 2} (A): Reinvestigation of crystal structure, phase transition and crystal growth mechanisms

    SciTech Connect

    Rao Popuri, Srinivasa [ICMCB, CNRS, UPR 9048, F-33608 Pessac (France); University of Bordeaux, ICMCB, UPR 9048, F-33608 Pessac (France); National Institute for Research and Development in Electrochemistry and Condensed Matter, Timisoara, Plautius Andronescu Str. No. 1, 300224 Timisoara (Romania); Artemenko, Alla [ICMCB, CNRS, UPR 9048, F-33608 Pessac (France); University of Bordeaux, ICMCB, UPR 9048, F-33608 Pessac (France); Labrugere, Christine [CeCaMA, University of Bordeaux 1, ICMCB, 87 Avenue du Dr. A. Schweitzer, F-33608 Pessac (France); Miclau, Marinela [National Institute for Research and Development in Electrochemistry and Condensed Matter, Timisoara, Plautius Andronescu Str. No. 1, 300224 Timisoara (Romania); Villesuzanne, Antoine [ICMCB, CNRS, UPR 9048, F-33608 Pessac (France); University of Bordeaux, ICMCB, UPR 9048, F-33608 Pessac (France); Pollet, Michaël, E-mail: pollet@icmcb-bordeaux.cnrs.fr [ICMCB, CNRS, UPR 9048, F-33608 Pessac (France); University of Bordeaux, ICMCB, UPR 9048, F-33608 Pessac (France)

    2014-05-01

    Well crystallized VO{sub 2} (A) microrods were grown via a single step hydrothermal reaction in the presence of V{sub 2}O{sub 5} and oxalic acid. With the advantage of high crystalline samples, we propose P4/ncc as an appropriate space group at room temperature. From morphological studies, we found that the oriented attachment and layer by layer growth mechanisms are responsible for the formation of VO{sub 2} (A) micro rods. The structural and electronic transitions in VO{sub 2} (A) are strongly first order in nature, and a marked difference between the structural transition temperatures and electronic transitions temperature was evidenced. The reversible intra- (LTP-A to HTP-A) and irreversible inter- (HTP-A to VO{sub 2} (M1)) structural phase transformations were studied by in-situ powder X-ray diffraction. Attempts to increase the size of the VO{sub 2} (A) microrods are presented and the possible formation steps for the flower-like morphologies of VO{sub 2} (M1) are described. - Graphical abstract: Using a single step and template free hydrothermal synthesis, well crystallized VO{sub 2} (A) microrods were prepared and the P4/ncc space group was assigned to the room temperature crystal structure. Reversible and irreversible phase transitions among different VO{sub 2} polymorphs were identified and their progressive nature was highlighted. Attempts to increase the microrods size, involving layer by layer formation mechanisms, are presented. - Highlights: • Highly crystallized VO{sub 2} (A) microrods were grown via a single step hydrothermal process. • The P4/ncc space group was determined for VO{sub 2} (A) at room temperature. • The electronic structure and progressive nature of the structural phase transition were investigated. • A weak coupling between structural and electronic phase transitions was identified. • Different crystallite morphologies were discussed in relation with growth mechanisms.

  11. Analysis of wave curvature experiments for monomodal explosives with different crystal quality and particle size characteristics

    SciTech Connect

    Sutherland, G. T. [Technology Development Department, Naval Surface Warfare Center, Indian Head, MD 20640 (United States); Lemar, E. R.; Marcus, M. H. [Energetics Technology Department, Naval Surface Warfare Center, Indian Head, MD 20640 (United States)

    2007-12-12

    Wood-Kirkwood theory reaction zone thickness determinations and computer simulations of wave curvature experiments of two sets of explosives are presented. One set included explosives composed of RDX with different crystal quality characteristics. The other set of explosives was composed of monomodal explosives made from fine, coarse and very coarse sieved RDX and bimodal explosives made from combining the fine and very coarse RDX. The calculated reaction zone thickness was found to be greater for explosives with higher RDX crystal quality and for those of higher mean particle size. A simplified two-term ignition and growth reactive model parameterized by embedded gauge experiments was used in CTH hydrocode simulations of the wave curvature experiments for the explosives where crystal quality was varied. The simulations under-predicted the axial position lag seen in experiment and predicted as seen in experiment, that the explosive containing the higher quality crystals had a greater axial position lag.

  12. Reflection chromaticity of multilayered structures incorporating cholesteric liquid crystals

    Microsoft Academic Search

    E. M. Nascimento; I. N. de Oliveira; M. L. Lyra

    2008-01-01

    We investigate the chromaticity of the light reflected by multilayered structures containing cholesteric liquid crystals (ChLCs). We considered a single-pitched ChLC multilayered system with quasiperiodic Fibonaccian phase defects as well as an alternate sequence of single-pitched ChLC and isotropic dielectric layers. Using the Berreman 4×4 matrix formalism, we numerically obtain the reflection spectrum and the chromaticity diagram of these structures.

  13. Crystal structure of the Clostridium limosum C3 exoenzyme

    Microsoft Academic Search

    Martin Vogelsgesang; Benjamin Stieglitz; Christian Herrmann; Alex Pautsch; Klaus Aktories

    2008-01-01

    C3-like toxins ADP-ribosylate and inactivate Rho GTPases. Seven C3-like ADP-ribosyltransferases produced by Clostridium botulinum, Clostridium limosum, Bacillus cereus and Staphylococcus aureus were identified and two representatives – C3bot from C. botulinum and C3stau2 from S. aureus – were crystallized. Here we present the 1.8Å structure of C. limosum C3 transferase C3lim and compare it to the structures of other family

  14. Crystal structure of Bi4Ti3O12

    Microsoft Academic Search

    J. F. Dorrian; R. E. Newnham; D. K. Smith; M. I. Kay

    1972-01-01

    The crystal structure of Bi4Ti3O12 has been determined from x-ray and neutron diffraction patterns. Physical properties indicate monoclinic symmetry, but the diffraction data are consistent with a polar orthorhombic structure, space group B2cb, with a = 5.448(2), b = 5.411(2), c = 32,83(1) Å, and Z = 4. Integrated intensities of 2500 x-ray reflections were measured using an automated diffractometer,

  15. Single Crystal Structure Determination of Alumina to 1 Mbar

    NASA Astrophysics Data System (ADS)

    Dong, H.; Zhang, L.; Prakapenka, V.; Mao, H.

    2014-12-01

    Aluminum oxide (Al2O3) is an important ceramic material and a major oxide in the earth. Additionally, alumina is a widely used pressure standard in static high-pressure experiments (Cr3+-bearing corundum, ruby). The changes of its crystal structure with pressure (P) and temperature (T) are important for its applications and understanding its physical properties in the deep Earth. There have been numerous reports on the high P-T polymorphs of alumina. Previous theoretical calculations and experiments suggest that the crystal structure of Al2O3 evolves greatly at high P-T. In this study, we used the newly developed multigrain crystallography method combined with single-crystal x-ray diffraction analysis technique for the structure determination of alumina at high P-T to provide single-crystal structure refinement for high-pressure phases of Al2O3. Alumina powder was mixed with ~10% Pt and Ne was used as both pressure transmitting media and thermal insulating layers during laser-heating. Coarse-grained aggregates of Al2O3 were synthesized in a laser-heated diamond anvil cell. The structure change of Al2O3 was monitored by in situ x-ray diffraction at ~1 Mbar and 2700 K. The results allow us to distinguish the structural differences between the Rh2O3 (II) structure (space group Pbcn) and perovskite structure (space group Pbnm) for the first high-pressure phase of Al2O3. More detailed results will be discussed in the later work.

  16. Structural long-period gratings in photonic crystal fibers

    Microsoft Academic Search

    G. Kakarantzas; T. A. Birks; P. St. J. Russell

    2002-01-01

    We report what is believed to be the first example of structural long-period gratings written in pure silica photonic crystal fibers (PCFs). The gratings are realized by periodic collapse of the holes of the PCF by heat treatment with a CO2 laser. The resulting periodic hole-size perturbation produces core-to-cladding-mode conversion. These results can lead to a new family of structural

  17. Structural long-period gratings in photonic crystal fibers.

    PubMed

    Kakarantzas, G; Birks, T A; Russell, P St J

    2002-06-15

    We report what is believed to be the first example of structural long-period gratings written in pure silica photonic crystal fibers (PCFs). The gratings are realized by periodic collapse of the holes of the PCF by heat treatment with a CO(2) laser. The resulting periodic hole-size perturbation produces core-to-cladding-mode conversion. These results can lead to a new family of structural all-fiber devices that use the unique properties of PCFs. PMID:18026349

  18. Decagonal and hexagonal structures in small gold particles

    NASA Astrophysics Data System (ADS)

    José-Yacamán, M.; Herrera, R.; Gómez, A.; Tehuacanero, S.; Schabes-Retchkiman, P.

    1990-11-01

    In the present work we report the study of gold particles using HREM and image processing. Particles which are not conventional fcc are discussed as well as penta-twinned particles which show twin boundaries that do not join along a common point. It is shown that there are particles with an hcp structure. This structure is probably due to repeated faulting and excess vacancies.

  19. Crystal structure of GnsA from Escherichia coli.

    PubMed

    Wei, Yong; Zhan, Lihong; Gao, Zengqiang; Privé, Gilbert G; Dong, Yuhui

    2015-06-19

    Escherichia Coli GnsA is a regulator of phosphatidylethanolamine synthesis and functions as a suppressor of both a secG null mutation and fabA6 mutations. GnsA may also be a toxin with the cognate antitoxin YmcE. Here we report the crystal structure of GnsA to 1.8 Å. GnsA forms a V shaped hairpin structure that is tightly associated into a homodimer. Our comprehensive structural study suggests that GnsA is structurally similar to an outer membrane protein, suggesting a function of protein binding. PMID:25839658

  20. Intermetallic crystal structures as foams. Beyond Frank-Kasper.

    PubMed

    Bonneau, Charlotte; O'Keeffe, Michael

    2015-02-01

    In many intermetallic structures, the atoms and bonds divide space into tilings by tetrahedra. The well-known Frank-Kasper phases are examples. The dual tilings divide space into a tiling by polyhedra that is topologically a foam. The number of faces of the dual polyhedron corresponds to the atom coordination number in the direct structure, and face sharing by adjacent polyhedra corresponds to bonds in the direct structure. A number of commonly occurring intermetallic crystal structures are shown as their duals. A major advantage of this alternative mode of depiction is that coordination of all of the atoms can be seen simultaneously. PMID:25247234

  1. Crystal structure of interleukin 8: Symbiosis of NMR and crystallography

    SciTech Connect

    Baldwin, E.T.; Weber, I.T.; St. Charles, R.; Xuan, Jiancheng; Matsushima, Kouji; Wlodawer, A. (National Cancer Inst., Frederick, MD (United States)); Appella, E.; Clore, G.M.; Gronenborn, A.M. (National Inst. of Health, Bethesda, MD (United States)); Yamada, Masaki (Dainippon Pharmaceutical Co., Ltd., Osaka (Japan)); Edwards, B.F.P. (Wayne State Univ. School of Medicine, Detroit, MI (United States))

    1991-01-15

    The crystal structure of a host defense system chemotactic factor, interleukin 8, has been solved by molecular replacement using as a model the solution structure derived from nuclear magnetic resonance experiments. The structure was refined with 2 {angstrom} x-ray data to an R factor of 0.817. A comparison indicates some potential differences between the structure in solution and in the crystalline state. The analysis also predicts that residues 4 through 9 on the amino terminus and the {beta}-bend, which includes His-33, may be important for receptor binding.

  2. Synthesis, crystal structure and EPR spectra of tetraaquabis(methylisonicotinate) copper(II) disaccharinate single crystal

    NASA Astrophysics Data System (ADS)

    Çelik, Yunus; Bozkurt, Esat; Uçar, ?brahim; Karabulut, Bünyamin

    2011-10-01

    The crystal structure of the [Cu(mein)2(H2O)4]·(sac)2 complex (mein: methylisonicotinate, sac: saccharine) was investigated by single crystal X-ray diffraction technique. The vibrational spectrum was also discussed in relation with the other compounds containing methylisonicotinate and saccharinate complexes. The EPR spectra of [Cu(mein)2(H2O)4]·(sac)2 single crystal have been studied in the temperature range between 113 and 300 K in three mutually perpendicular planes and exhibit two sets of four hyperfine lines of Cu2+ ion. The ground state wave function of the Cu2+ ion is an admixture of dx2-y2 and dz2 states.

  3. Single crystal growth, crystal structure characterization and magnetic properties of UCo0.5Sb2

    SciTech Connect

    Bukowski, Z. [W. Trzebiatowski Institute of Low Temperature and Structure Research, Polish Academy of Sciences, P.O. Box 1410, 50-950 Wroclaw (Poland)]. E-mail: bukowski@int.pan.wroc.pl; Tran, V.H. [W. Trzebiatowski Institute of Low Temperature and Structure Research, Polish Academy of Sciences, P.O. Box 1410, 50-950 Wroclaw (Poland); Stepien-Damm, J. [W. Trzebiatowski Institute of Low Temperature and Structure Research, Polish Academy of Sciences, P.O. Box 1410, 50-950 Wroclaw (Poland); Troc, R. [W. Trzebiatowski Institute of Low Temperature and Structure Research, Polish Academy of Sciences, P.O. Box 1410, 50-950 Wroclaw (Poland)

    2004-11-01

    Single crystals of uranium intermetallic compound UCo0.5Sb2 were grown by means of the antimony-flux technique. The characterization of the samples has been carried out utilizing single crystal X-ray diffraction and magnetization measurements. UCo0.5Sb2 is found to crystallize in the tetragonal HfCuSi2-type structure, space group P4/nmm with Z=2 formula units per cell, and the lattice parameters a=0.4300(1) and c=0.8958(2)nm. The refinement of the occupancy parameters and the energy dispersive X-ray analysis have indicated a distinct deficiency on the cobalt sites. The results of magnetization measurements showed that UCo0.5Sb2 orders ferromagnetically below 65K with a huge magnetocrystalline anisotropy with the c direction being the easy magnetization axis.

  4. Crystal structures of Ziegler-Natta catalyst supports.

    PubMed

    Malizia, Federica; Fait, Anna; Cruciani, Giuseppe

    2011-12-01

    The crystal structures of three MgCl(2)·nEtOH complexes with n=1.5, 2.8, and 3.3 have been fully determined. Such complexes are the fundamental precursors for Ziegler-Natta polymerization catalysts used to produce polyolefins on a multimillion-ton scale worldwide. The ab initio structure solution showed that the structure of MgCl(2)·nEtOH complexes with n=1.5 and 2.8 are based on ribbons of metal-centered octahedra, whereas for n=3.3 this chainlike arrangement breaks into a threadlike structure of isolated octahedra linked by hydrogen bonds. A clear correlation between catalyst performance and the crystal structure of precursors has been found, and reveals the fundamental role of the latter in determining catalyst properties. The direct knowledge of building blocks in the precursor structures will help to develop more accurate models for activated catalysts. These models will not require the arbitrary and oversimplified assumption of locating the catalyst active sites on selected cut surfaces of the ?-MgCl(2) crystal lattice. PMID:22052708

  5. Crystal Structure of Triosephosphate Isomerase from Trypanosoma cruzi in Hexane

    NASA Astrophysics Data System (ADS)

    Gao, Xiu-Gong; Maldonado, Ernesto; Perez-Montfort, Ruy; Garza-Ramos, Georgina; Tuena de Gomez-Puyou, Marietta; Gomez-Puyou, Armando; Rodriguez-Romero, Adela

    1999-08-01

    To gain insight into the mechanisms of enzyme catalysis in organic solvents, the x-ray structure of some monomeric enzymes in organic solvents was determined. However, it remained to be explored whether the structure of oligomeric proteins is also amenable to such analysis. The field acquired new perspectives when it was proposed that the x-ray structure of enzymes in nonaqueous media could reveal binding sites for organic solvents that in principle could represent the starting point for drug design. Here, a crystal of the dimeric enzyme triosephosphate isomerase from the pathogenic parasite Trypanosoma cruzi was soaked and diffracted in hexane and its structure solved at 2- angstrom resolution. Its overall structure and the dimer interface were not altered by hexane. However, there were differences in the orientation of the side chains of several amino acids, including that of the catalytic Glu-168 in one of the monomers. No hexane molecules were detected in the active site or in the dimer interface. However, three hexane molecules were identified on the surface of the protein at sites, which in the native crystal did not have water molecules. The number of water molecules in the hexane structure was higher than in the native crystal. Two hexanes localized at <4 angstrom from residues that form the dimer interface; they were in close proximity to a site that has been considered a potential target for drug design.

  6. Crystal structure of the Escherichia coli

    E-print Network

    of the HIV-1 Nef gene, sharing 45% amino acid sequence identity with it. The structure of the E. coli,16. Surprisingly, the human enzyme was found to bind to, and be activated by, the product of the HIV Nef gene diagram showing an overview of the tertiary architecture of TEII. The -helices are magenta

  7. Crystal structure of thioredoxin-2 from Anabaena

    Microsoft Academic Search

    Markku Saarinen; Florence K Gleason; Hans Eklund

    1995-01-01

    Background: Thioredoxins are ubiquitous proteins that serve as reducing agents and general protein disulfide reductases. The structures of thioredoxins from a number of species, including man and Escherichia coli, are known. Cyanobacteria, such as Anabaena, contain two thioredoxins that exhibit very different activities with target enzymes and share little sequence similarity. Thioredoxin-2 (Trx-2) from Anabaena resembles chloroplast type-f thioredoxin in

  8. Crystal structure of tin(IV) chloride octa-hydrate.

    PubMed

    Hennings, Erik; Schmidt, Horst; Voigt, Wolfgang

    2014-12-01

    The title compound, [SnCl4(H2O)2]·6H2O, was crystallized according to the solid-liquid phase diagram at lower temperatures. It is built-up of SnCl4(H2O)2 octa-hedral units (point group symmetry 2) and lattice water mol-ecules. An intricate three-dimensional network of O-H?O and O-H?Cl hydrogen bonds between the complex molecules and the lattice water molecules is formed in the crystal structure. PMID:25552971

  9. On calculating the equilibrium structure of molecular crystals.

    SciTech Connect

    Mattsson, Ann Elisabet; Wixom, Ryan R.; Mattsson, Thomas Kjell Rene

    2010-03-01

    The difficulty of calculating the ambient properties of molecular crystals, such as the explosive PETN, has long hampered much needed computational investigations of these materials. One reason for the shortcomings is that the exchange-correlation functionals available for Density Functional Theory (DFT) based calculations do not correctly describe the weak intermolecular van der Waals' forces present in molecular crystals. However, this weak interaction also poses other challenges for the computational schemes used. We will discuss these issues in the context of calculations of lattice constants and structure of PETN with a number of different functionals, and also discuss if these limitations can be circumvented for studies at non-ambient conditions.

  10. Crystal structure of tin(IV) chloride octa­hydrate

    PubMed Central

    Hennings, Erik; Schmidt, Horst; Voigt, Wolfgang

    2014-01-01

    The title compound, [SnCl4(H2O)2]·6H2O, was crystallized according to the solid–liquid phase diagram at lower temperatures. It is built-up of SnCl4(H2O)2 octa­hedral units (point group symmetry 2) and lattice water mol­ecules. An intricate three-dimensional network of O—H?O and O—H?Cl hydrogen bonds between the complex molecules and the lattice water molecules is formed in the crystal structure. PMID:25552971

  11. Synthesis, crystal structure and characterization of alkali metal hydroxoantimonates

    Microsoft Academic Search

    Alexey A. Mikhaylov; Elena A. Mel’nik; Andrei V. Churakov; Vladimir M. Novotortsev; Judith A. K. Howard; Sergey Sladkevich; Jenny Gun; Subramanian Bharathi; Ovadia Lev; Petr V. Prikhodchenko

    2011-01-01

    Several alkali metal hydroxoantimonates, K2[Sb(O)(OH)5], Na[Sb(OH)6], Cs[Sb(OH)6] and Cs2[Sb2(?-O)2(OH)8] were isolated from aqueous solutions and characterized by single crystal and powder X-ray diffraction studies and by FTIR and thermal analysis. Crystal structures involving [Sb(O)(OH)5]2? were never anticipated before, and this is also the first disclosure of a dinuclear antimonate [Sb2(?-O)2(OH)8]2?. Aqueous antimonate solutions of different pH were studied by high

  12. Electronic structures of lead iodide based low-dimensional crystals

    NASA Astrophysics Data System (ADS)

    Umebayashi, T.; Asai, K.; Kondo, T.; Nakao, A.

    2003-04-01

    The electronic structures of three-dimensional and two-dimensional lead-halide-based crystals CH3NH3PbI3 and (C4H9NH3)2PbI4 are investigated by photoelectron spectroscopy and band calculations using the linear combination of atomic orbitals within the density-functional theory. For both crystals, the top of the valence band is found to consist mainly of the ?-antibonding states of Pb 6s and I 5p orbitals, and the bottom of the conduction band to be composed primarily of the ?-antibonding states of Pb 6p and I 5s orbitals. Photoelectron spectra of the valence-band region indicate that the electronic structures change depending on the dimensionality of the crystals. Based on the calculation results, the differences observed in the spectra are rationalized in terms of narrowing bandwidth as the dimensionality decreases from three to two dimensions. It is shown that the bandwidth narrowing of the two-dimensional crystal is due to zero dispersion in the vertical direction and the Jahn-Teller effect in the layered structure. These effects lead to a wideband gap and high exciton stability in (C4H9NH3)2PbI4.

  13. Crystal structure of tannase from Lactobacillus plantarum.

    PubMed

    Ren, Bin; Wu, Mingbo; Wang, Qin; Peng, Xiaohong; Wen, Hua; McKinstry, William J; Chen, Qianming

    2013-08-01

    Tannins are water-soluble polyphenolic compounds in plants. Hydrolyzable tannins are derivatives of gallic acid (3,4,5-trihydroxybenzoic acid) or its meta-depsidic forms that are esterified to polyol, catechin, or triterpenoid units. Tannases are a family of esterases that catalyze the hydrolysis of the galloyl ester bond in hydrolyzable tannins to release gallic acid. The enzymes have found wide applications in food, feed, beverage, pharmaceutical, and chemical industries since their discovery more than a century ago, although little is known about them at the molecular level, including the details of the catalytic and substrate binding sites. Here, we report the first three-dimensional structure of a tannase from Lactobacillus plantarum. The enzyme displays an ?/? structure, featured by a large cap domain inserted into the classical serine hydrolase fold. A catalytic triad was identified in the structure, which is composed of Ser163, His451, and Asp419. During the binding of gallic acid, the carboxyl group of the molecule forges hydrogen-bonding interactions with the catalytic triad of the enzyme while the three hydroxyl groups make contacts with Asp421, Lys343, and Glu357 to form another hydrogen-bonding network. Mutagenesis studies demonstrated that these residues are indispensable for the activity of the enzyme. Structural studies of the enzyme in complex with a number of substrates indicated that the interactions at the galloyl binding site are the determinant force for the binding of substrates. The single galloyl binding site is responsible for the esterase and depsidase activities of the enzyme. PMID:23648840

  14. Crystal structure of mammalian purple acid phosphatase

    Microsoft Academic Search

    Luke W Guddat; Alan S McAlpine; David Hume; Susan Hamilton; John de Jersey; Jennifer L Martin

    1999-01-01

    Background: Mammalian purple acid phosphatases are highly conserved binuclear metal-containing enzymes produced by osteoclasts, the cells that resorb bone. The enzyme is a target for drug design because there is strong evidence that it is involved in bone resorption.Results: The 1.55Å resolution structure of pig purple acid phosphatase has been solved by multiple isomorphous replacement. The enzyme comprises two sandwiched?

  15. The Mechanics of the Systems of Structured Particles and Irreversibility

    E-print Network

    V. M. Somsikov

    2009-08-21

    Dynamics of systems of structured particles consisting of potentially interacting material points is considered in the framework of classical mechanics. Equations of interaction and motion of structured particles have been derived. The expression for friction force has been obtained. It has been shown that irreversibility of dynamics of structured particles is caused by increase of their internal energy due to the energy of motion. Possibility of theoretical substantiation of the laws of thermodynamics has been considered.

  16. Crystal structure of Li2FeS2

    NASA Astrophysics Data System (ADS)

    Batchelor, R. J.; Einstein, F. W. B.; Jones, C. H. W.; Fong, Rosamaria; Dahn, J. R.

    1988-03-01

    The crystal structure of Li2FeS2 has space group P3¯m1 with a=3.902(1) Å, c=6.294(2) Å, U=83.00 Aṧ, and Z=1. The structure refinement gives a final residual Rf=0.043 for 283 observations and nine variables (from single-crystal data using Mo K? radiation ?=0.710 69 Å). The structure consists of hexagonally-close-packed layers of sulfur with iron and lithium, equally and randomly, filling all of the tetrahedral interstices between the more separated pairs of sulfur layers. The remaining lithium atoms fill the octahedral interstices between the alternate, closer sulfur layers. To our knowledge this is the first ternary compound to have Fe(II) coordinated by sulfur atoms.

  17. The crystal structure of Ba 3V 4O 13

    NASA Astrophysics Data System (ADS)

    Gatehouse, B. M.; Guddat, L. W.; Roth, R. S.

    1987-12-01

    Ba 3V 4O 13 crystallizes in the monoclinic system with unit-cell dimensions (from single-crystal data) a = 16.100(3), b = 8.947(3), c = 10.173(3) Å, ? = 114.39(2)°, and space group {C2}/{c}, z = 4 . The structure was solved using Patterson and Fourier techniques. The structure was refined by full-matrix least-squares methods, using 1604 ( I ? 3 ?( I) unique countermeasured reflections, to a conventional R of 0.028 ( Rw 0.041). The structure comprises Ba 2+ and [V 4O 13] 6- ions. The [V 4O 13] 6- polyanion consists of four corner-shared vanadium tetrahedra in a U-shaped arrangement for which the torsion angle between the vanadium atoms is 56.07(6)°. Other known E4O n- 13 anions ( E = Al, Si, P, or Cr) comprising corner-shared tetrahedra all have torsion angles that are >172°.

  18. Crystal structure of the TSP-1 type 1 repeats

    PubMed Central

    Tan, Kemin; Duquette, Mark; Liu, Jin-huan; Dong, Yicheng; Zhang, Rongguang; Joachimiak, Andrzej; Lawler, Jack; Wang, Jia-huai

    2002-01-01

    Thrombospondin-1 (TSP-1) contains three type 1 repeats (TSRs), which mediate cell attachment, glycosaminoglycan binding, inhibition of angiogenesis, activation of TGF?, and inhibition of matrix metalloproteinases. The crystal structure of the TSRs reported in this article reveals a novel, antiparallel, three-stranded fold that consists of alternating stacked layers of tryptophan and arginine residues from respective strands, capped by disulfide bonds on each end. The front face of the TSR contains a right-handed spiral, positively charged groove that might be the “recognition” face, mediating interactions with various ligands. This is the first high-resolution crystal structure of a TSR domain that provides a prototypic architecture for structural and functional exploration of the diverse members of the TSR superfamily. PMID:12391027

  19. GPCR crystal structures: Medicinal chemistry in the pocket.

    PubMed

    Shonberg, Jeremy; Kling, Ralf C; Gmeiner, Peter; Löber, Stefan

    2015-07-15

    Recent breakthroughs in GPCR structural biology have significantly increased our understanding of drug action at these therapeutically relevant receptors, and this will undoubtedly lead to the design of better therapeutics. In recent years, crystal structures of GPCRs from classes A, B, C and F have been solved, unveiling a precise snapshot of ligand-receptor interactions. Furthermore, some receptors have been crystallized in different functional states in complex with antagonists, partial agonists, full agonists, biased agonists and allosteric modulators, providing further insight into the mechanisms of ligand-induced GPCR activation. It is now obvious that there is enormous diversity in the size, shape and position of the ligand binding pockets in GPCRs. In this review, we summarise the current state of solved GPCR structures, with a particular focus on ligand-receptor interactions in the binding pocket, and how this can contribute to the design of GPCR ligands with better affinity, subtype selectivity or efficacy. PMID:25638496

  20. Use of Pom Pons To Illustrate Cubic Crystal Structures

    NASA Astrophysics Data System (ADS)

    Cady, Susan G.

    1997-07-01

    In general chemistry classes, students are introduced to the ways in which atoms are arranged in cubic crystal structures. Transposing the textbook illustrations into three dimensional structures is difficult for some students. This transitions is easier if a three dimensional model is available for examination. Several 3D models are cited. A quick to assemble, inexpensive, colorful, and durable alternative to these models and styrofoam balls is the use of olefin pom pons. Different sized pom pons can be used to demonstrate how the atomic radius will vary when comparing the different types of cubic crystal unit cells. Being made of a coarse material, pom pons can be stacked to illustrate different packing arrangements such as hexagonal close-packed and cubic close-packed structures. Pom pons make great atoms.

  1. Trapping of topological-structural defects in Coulomb crystals.

    PubMed

    Mielenz, M; Brox, J; Kahra, S; Leschhorn, G; Albert, M; Schaetz, T; Landa, H; Reznik, B

    2013-03-29

    We study experimentally and theoretically structural defects which are formed during the transition from a laser cooled cloud to a Coulomb crystal, consisting of tens of ions in a linear radio frequency trap. We demonstrate the creation of predicted topological defects ("kinks") in purely two-dimensional crystals and also find kinks which show novel dynamical features in a regime of parameters not considered before. The kinks are always observed at the center of the trap, showing a large nonlinear localized excitation, and the probability of their occurrence saturates at ?0.5. Simulations reveal a strong anharmonicity of the kink's internal mode of vibration, due to the kink's extension into three dimensions. As a consequence, the periodic Peierls-Nabarro potential experienced by a discrete kink becomes a globally confining potential, capable of trapping one cooled defect at the center of the crystal. PMID:23581315

  2. Synthesis and Crystallization of Nano-Ceria Particles by Solvothermal Routes

    NASA Astrophysics Data System (ADS)

    Fu, Cong; Li, Ruixing; Zhang, Yue

    Cerium oxides (CeO2) were synthesized by two steps solvothermal routes. First, a precursor was precipitated using solutions of cerium (III) nitrate and ammonia, and then this precursor was treated via solvothermal techniques in an autoclave. Narrow distribution of CeO2 particle size, between 10 to 15 nm, was achieved in different solvents. Hard agglomerates of nano-CeO2 were mitigated in an ethanol solvent. Most of crystal particles were in the shape of a quadrangle for the precursor. Morphology of CeO2 particles gradually changed after the precursor was treated by solvothermal techniques. There were both quadrangular and symmetrically hexagonal particles at an alkaline pH value. Alternatively, the quadrangular particles disappeared, instead of geometrically unsymmetrical hexagon with decreasing pH to a more acid value. The evolution mechanism of the morphology was discussed. These results have important implications for recognizing and controlling the crystalline shape by solvothermal techniques.

  3. Lidar Inelastic Multiple-Scattering Parameters of Cirrus Particle Ensembles Determined with Geometrical-Optics Crystal Phase Functions

    Microsoft Academic Search

    Jens Reichardt; Michael Hess; Andreas Macke

    2000-01-01

    Multiple-scattering correction factors for cirrus particle extinction coefficients measured with Raman and high spectral resolution lidars are calculated with a radiative-transfer model. Cirrus particle-ensemble phase functions are computed from single-crystal phase functions derived in a geometrical-optics approximation. Seven crystal types are considered. In cirrus clouds with height-independent particle extinction coefficients the general pattern of the multiple-scattering parameters has a steep

  4. Crystal and molecular structure of N-methylpiperidine betaine hydrochloride

    NASA Astrophysics Data System (ADS)

    Dega-Szafran, Z.; Szafran, M.; Dulewicz, E.; Addlagatta, A.; Jaskólski, M.

    2003-06-01

    A 1:1 complex between N-methylpiperidine betaine and hydrochloric acid, MPBH·Cl, has been characterized by single crystal X-ray analysis, FTIR spectroscopy, and DFT calculations. The crystals are monoclinic, space group P2 1/ n, with a=6.0644(3), b=13.0220(6), c=12.7653(7) Å, ?=101.925(5)°. The piperidine ring adopts a chair conformation with the -CH 2COOH group in an axial and the-CH 3 group in an equatorial position. In the crystal, the Cl -anion is engaged in a medium-strong hydrogen bond with the COOH group (O-H⋯Cl -=2.9503(7) Å), in several C-H⋯Cl - contacts and, additionally, in three N +⋯Cl -intermolecular interactions. Four conformations (axial and equatorial, both protonated and unprotonated) of MPBHCl were examined by the B3LYP/6-31G(d,p) method. The calculated structure of MPBH·Cl(ax) is very similar to that in the crystal, except the N(1)-C(8)-C(9)-O(1) and N(1)-C(8)-C(9)-O(2) units, which are planar in the crystal but nonplanar in the isolated molecule. Powder FTIR spectra of MPBH·Cl and its deuterated analogue (MPBD·Cl) were measured and assignments of the observed bands to vibrations of the hydrogen bond and to internal vibrations are proposed.

  5. Structural diversity and the role of particle shape and dense fluid behavior in assemblies of hard polyhedra

    E-print Network

    Pablo F. Damasceno; Michael Engel; Sharon C. Glotzer

    2012-02-10

    A fundamental characteristic of matter is its ability to form ordered structures under the right thermodynamic conditions. Predicting these structures - and their properties - from the attributes of a material's building blocks is the holy grail of materials science. Here, we investigate the self-assembly of 145 hard convex polyhedra whose thermodynamic behavior arises solely from their anisotropic shape. Our results extend previous works on entropy-driven crystallization by demonstrating a remarkably high propensity for self-assembly and an unprecedented structural diversity, including some of the most complex crystalline phases yet observed in a non-atomic system. In addition to 22 Bravais and non-Bravais crystals, we report 66 plastic crystals (both Bravais and topologically close-packed), 21 liquid crystals (nematic, smectic, and columnar), and 44 glasses. We show that from simple measures of particle shape and local order in the disordered fluid, the class of ordered structure can be predicted.

  6. Geometry-guided colloidal interactions and self-tiling of elastic dipoles formed by truncated pyramid particles in liquid crystals.

    PubMed

    Senyuk, Bohdan; Liu, Qingkun; Bililign, Ephraim; Nystrom, Philip D; Smalyukh, Ivan I

    2015-04-01

    The progress of realizing colloidal structures mimicking natural forms of organization in condensed matter is inherently limited by the availability of suitable colloidal building blocks. To enable new forms of crystalline and quasicrystalline self-organization of colloids, we develop truncated pyramidal particles that form nematic elastic dipoles with long-range electrostaticlike and geometry-guided low-symmetry short-range interactions. Using a combination of nonlinear optical imaging, laser tweezers, and video microscopy, we characterize colloidal pair interactions and demonstrate unusual forms of self-tiling of these particles into crystalline, quasicrystalline, and other arrays. Our findings are explained using an electrostatics analogy along with liquid crystal elasticity and symmetry breaking considerations, potentially expanding photonic and electro-optic applications of colloids. PMID:25974426

  7. Crystal structure of four-stranded Oxytricha telomeric DNA

    NASA Technical Reports Server (NTRS)

    Kang, C.; Zhang, X.; Ratliff, R.; Moyzis, R.; Rich, A.

    1992-01-01

    The sequence d(GGGGTTTTGGGG) from the 3' overhang of the Oxytricha telomere has been crystallized and its three-dimensional structure solved to 2.5 A resolution. The oligonucleotide forms hairpins, two of which join to make a four-stranded helical structure with the loops containing four thymine residues at either end. The guanine residues are held together by cyclic hydrogen bonding and an ion is located in the centre. The four guanine residues in each segment have a glycosyl conformation that alternates between anti and syn. There are two four-stranded molecules in the asymmetric unit showing that the structure has some intrinsic flexibility.

  8. Ultra-high resolution crystal structure of recombinant caprine ?-lactoglobulin.

    PubMed

    Crowther, Jennifer M; Lassé, Moritz; Suzuki, Hironori; Kessans, Sarah A; Loo, Trevor S; Norris, Gillian E; Hodgkinson, Alison J; Jameson, Geoffrey B; Dobson, Renwick C J

    2014-11-01

    ?-Lactoglobulin (?lg) is the most abundant whey protein in the milks of ruminant animals. While bovine ?lg has been subjected to a vast array of studies, little is known about the caprine ortholog. We present an ultra-high resolution crystal structure of caprine ?lg complemented by analytical ultracentrifugation and small-angle X-ray scattering data. In both solution and crystalline states caprine ?lg is dimeric (K(D)<5 ?M); however, our data suggest a flexible quaternary arrangement of subunits within the dimer. These structural findings will provide insight into relationships among structural, processing, nutritional and immunological characteristics that distinguish cow's and goat's milk. PMID:25241165

  9. Crystal structure of inactive form of Rab3B

    SciTech Connect

    Zhang, Wei; Shen, Yang; Jiao, Ronghong; Liu, Yanli; Deng, Lingfu; Qi, Chao (Hebei); (Toronto); (Huazhong)

    2012-06-28

    Rab proteins are the largest family of ras-related GTPases in eukaryotic cells. They act as directional molecular switches at membrane trafficking, including vesicle budding, cargo sorting, transport, tethering, and fusion. Here, we generated and crystallized the Rab3B:GDP complex. The structure of the complex was solved to 1.9 {angstrom} resolution and the structural base comparison with other Rab3 members provides a structural basis for the GDP/GTP switch in controlling the activity of small GTPase. The comparison of charge distribution among the members of Rab3 also indicates their different roles in vesicular trafficking.

  10. Multiplication constant of knocked-on atoms in passage of high-energy particles in crystals

    SciTech Connect

    Entinzon, I.R.; Shevchenko, G.L.

    1992-07-01

    The multiplication coefficient of knocked-on atoms of a crystal in a cascade of atom-atom movements was calculated. A more realistic (in comparison to the generally used) probability function W(T) of formation of a separate Frenkel pair as a function of the energy T obtained by an atom in elastic collision with a fast particle was used. The multiplication constant for a silicon crystal was significantly lower (by almost one order of magnitude) than the constant determined by the existing Kinchin-Pease formula. 15 refs., 4 figs.

  11. Crystal structure of the ?-racemate of methohexital

    PubMed Central

    Gelbrich, Thomas; Griesser, Ulrich J.

    2015-01-01

    Mol­ecules of the title compound, C14H18N2O3 [systematic name: 5-allyl-5-(hex-3-yn-2-yl)-1-methylpyrimidine-2,4,6(1H,3H,5H)-trione in the (RbSh)/(SbRh) racemic form], are connected by mutual N—H?O=C hydrogen bonds in which the carbonyl group at the 2-position of the pyrimidine­trione ring is employed. These inter­actions result in an inversion dimer which displays a central R 2 2(8) ring motif. This dimer is topologically distinct from that of the previously reported (SbRh) form, which is, however, also based on an R 2 2(8) motif. The methyl group at the 1-position of the pyrimidine­trione ring in the title structure is disordered over two sets of sites in a 0.57?(2):0.43?(2) ratio. PMID:25878820

  12. Improved synthesis of fine zinc borate particles using seed crystals

    Microsoft Academic Search

    Deniz Gürhan; Gaye Ö. Çakal; Inci Eroglu; Saim Özkar

    2009-01-01

    Zinc borate is a flame retardant additive used in polymers, wood applications and textile products. There are different types of zinc borate having different chemical compositions and structures. In this study, the production of zinc borate having the molecular formula of 2ZnO·3B2O3·3.5H2O was reexamined by studying the effects of reaction parameters on the properties of product as well as the

  13. Disclination loops, standing alone and around solid particles, in nematic liquid crystals

    NASA Astrophysics Data System (ADS)

    Terentjev, E. M.

    1995-02-01

    A suspended particle with specific director anchoring on its surface introduces a complex distortion field in a nematic liquid crystal matrix. Topological defects-disclination loops, boojums, and hedgehogs, are needed to match the director near the particle surface with that at the far distance, which is determined by boundary conditions on the sample. This paper analyzes the elastic energy and stability of a singular loop of wedge disclination and the first-order transition of the radial hedgehog into a wide singular loop, driven by an external magnetic field. The far field of distortions, created by a ``Saturn ring'' of disclination around the spherical radial particle, allows one to calculate the potential of interaction between such particles and with the surface of the liquid crystal. Particles are repelled from each other and from the rigidly anchored surface with the potential U~1/r3. If the sample surface has soft anchoring, the particle is attracted to it at close distances and is repelled, if beyond the anchoring coherence length ?w. Several experiments to test these conclusions are suggested.

  14. EVO—Evolutionary algorithm for crystal structure prediction

    NASA Astrophysics Data System (ADS)

    Bahmann, Silvia; Kortus, Jens

    2013-06-01

    We present EVO—an evolution strategy designed for crystal structure search and prediction. The concept and main features of biological evolution such as creation of diversity and survival of the fittest have been transferred to crystal structure prediction. EVO successfully demonstrates its applicability to find crystal structures of the elements of the 3rd main group with their different spacegroups. For this we used the number of atoms in the conventional cell and multiples of it. Running EVO with different numbers of carbon atoms per unit cell yields graphite as the lowest energy structure as well as a diamond-like structure, both in one run. Our implementation also supports the search for 2D structures and was able to find a boron sheet with structural features so far not considered in literature. Program summaryProgram title: EVO Catalogue identifier: AEOZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOZ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 23488 No. of bytes in distributed program, including test data, etc.: 1830122 Distribution format: tar.gz Programming language: Python. Computer: No limitations known. Operating system: Linux. RAM: Negligible compared to the requirements of the electronic structure programs used Classification: 7.8. External routines: Quantum ESPRESSO (http://www.quantum-espresso.org/), GULP (https://projects.ivec.org/gulp/) Nature of problem: Crystal structure search is a global optimisation problem in 3N+3 dimensions where N is the number of atoms in the unit cell. The high dimensional search space is accompanied by an unknown energy landscape. Solution method: Evolutionary algorithms transfer the main features of biological evolution to use them in global searches. The combination of the "survival of the fittest" (deterministic) and the randomised choice of the parents and normally distributed mutation steps (non-deterministic) provides a thorough search. Restrictions: The algorithm is in principle only restricted by a huge search space and simultaneously increasing calculation time (memory, etc.), which is not a problem for our piece of code but for the used electronic structure programs. Running time: The simplest provided case runs serially and takes 30 minutes to one hour. All other calculations run for significantly longer time depending on the parameters like the number and sort of atoms and the electronic structure program in use as well as the level of parallelism included.

  15. Drying dissipative structures of lycopodium spore particles in aqueous dispersion

    Microsoft Academic Search

    Tsuneo Okubo; Etsuo Kokufuta; Masaharu Nakamuro; Kohji Yoshinaga; Masashi Mizutani; Akira Tsuchida

    2010-01-01

    Drying dissipative structures of aqueous dispersions of lycopodium particles (31?m in average diameter) from the spores of Lycopodium clavatum were studied as a function of the particle concentrations in the presence and the absence of sodium chloride. The drying patterns formed on a cover glass, a watch glass and a Petri glass dish were observed macroscopically and microscopically. Lycopodium particles

  16. Designing smart particles for the assembly of complex macroscopic structures.

    PubMed

    Garcia-Tunon, Esther; Barg, Suelen; Bell, Robert; Weaver, Jonathan V M; Walter, Claudia; Goyos, Lidia; Saiz, Eduardo

    2013-07-22

    Particle get-together: Surface functionalization with a branched copolymer surfactant is used to create responsive inorganic particles that can self-assemble in complex structures. The assembly process is triggered by a pH switch that reversibly activates multiple hydrogen bonds between ceramic particles (see picture; yellow) and soft templates (n-decane; green). PMID:23780923

  17. English Verb-particle Constructions: Two Types, Two Structures

    E-print Network

    Zoerner, Ed

    1996-01-01

    This paper proposes that resultative verb-particle constructions (VPCs) have an underlyingly different structure from idiomatic VPCs; both structures differ from the Small Clause analysis of Kayne (1985) et al and the ...

  18. Crystal structure of bis(pyridine betaine) hydrochloride monohydrate

    NASA Astrophysics Data System (ADS)

    Xiao-Ming, Chen; Mak, Thomas C. W.

    1990-04-01

    Bis(pyridine betaine) hydrochloride monohydrate, 2C 5H 5NCH 2COO·HCl·H 2O, crystallizes in space group Pnna (No. 52), with a=15.623(3), b=19.707(3), c=5.069(1) Å, and Z=4. The structure has been refined to RF=0.067 for 1207 observed (| F0|>6?| F0|) Mo K? data. The carboxylate groups of a pair of pyridine betaine molecules are bridged by a proton to form a centrosymmetric dimer featuring a very strong hydrogen bond of length 2.436(6) Å. The crystal structure comprises a packing of such [(C 5H 5NCH 2COO) 2H] + moieties and hydrogen-bonded (Cl -{dH 2O} ?) zigzag chains running parallel to the c axis.

  19. Crystal structure of BIS(Betaine) hydrochloride monohydrate

    NASA Astrophysics Data System (ADS)

    Chen, Xiao-Ming; Mak, Thomas C. W.

    1990-11-01

    Bis(betaine) hydrochloride monohydrate, 2Me 3NCH 2COO·HCI·H 2O, crystallizes in space group Pnma (No. 62), with a=11.904(1), b=22.454(5), c=5.624(1) Å, and Z=4. The structure has been refined to RinF=0.046 for 863 observed (| Fo||>6?| Fo|) Mo K? data. the carboxylate groups of a pair of betaine molecules are bridged by a proton to form a centrosymmetric dimer featuring a very strong hydrogen bond of length 2.454(4) Å. The crystal structure comprises a packing of such [(Me 3NCH 2COO) 2H] + moieties and hydrogen-bonded (Cl -·H 2O) ? zigzag chains running parallel to the c axis.

  20. Synthesis and crystal structure of EuBi{sub 2}

    SciTech Connect

    Sun Zhongming [State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou City, Fujian Province 350002 (China); Mao Jianggao [State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou City, Fujian Province 350002 (China)]. E-mail: mjg@ms.fjirsm.ac.cn

    2004-10-01

    The new hypervalent binary phase EuBi{sub 2} was obtained from high temperature solid-state reactions of the pure metal elements in welded Ta tubes under argon atmosphere. Its structure was established by single-crystal X-ray diffraction. The title compound crystallizes in the tetragonal space group I4{sub 1}/amd (No. 141) with cell parameters of a=4.726(1),c=34.221(9)A,V=764.3(3)A3, and Z=8. The structure of EuBi{sub 2} is isotypic with HfGa{sub 2} and features 1D Bi{sup -} zigzag anionic chains along both a- and b-axes and 2D Bi{sup -} square sheets normal to c-axis. It can be formulated as Eu{sup 2+}(Bi){sub chain}{sup -}(Bi){sub square}{sup -}.

  1. Crystal structure of laser-induced subsurface modifications in Si

    NASA Astrophysics Data System (ADS)

    Verburg, P. C.; Smillie, L. A.; Römer, G. R. B. E.; Haberl, B.; Bradby, J. E.; Williams, J. S.; Huis in't Veld, A. J.

    2015-06-01

    Laser-induced subsurface modification of dielectric materials is a well-known technology. Applications include the production of optical components and selective etching. In addition to dielectric materials, the subsurface modification technology can be applied to silicon, by employing near to mid-infrared radiation. An application of subsurface modifications in silicon is laser-induced subsurface separation, which is a method to separate wafers into individual dies. Other applications for which proofs of concept exist are the formation of waveguides and resistivity tuning. However, limited knowledge is available about the crystal structure of subsurface modifications in silicon. In this work, we investigate the geometry and crystal structure of laser-induced subsurface modifications in monocrystalline silicon wafers. In addition to the generation of lattice defects, we found that transformations to amorphous silicon and Siuc(-iii)/Siuc(-xii) occur as a result of the laser irradiation.

  2. Crystal Structures of Aedes Aegypt Alanine Glyoxylate Aminotransferase

    SciTech Connect

    Han,Q.; Robinson, H.; Gao, Y.; Vogelaar, N.; Wilson, S.; Rizzi, M.; Li, J.

    2006-01-01

    Mosquitoes are unique in having evolved two alanine glyoxylate aminotransferases (AGTs). One is 3-hydroxykynurenine transaminase (HKT), which is primarily responsible for catalyzing the transamination of 3-hydroxykynurenine (3-HK) to xanthurenic acid (XA). Interestingly, XA is used by malaria parasites as a chemical trigger for their development within the mosquito. This 3-HK to XA conversion is considered the major mechanism mosquitoes use to detoxify the chemically reactive and potentially toxic 3-HK. The other AGT is a typical dipteran insect AGT and is specific for converting glyoxylic acid to glycine. Here we report the 1.75{angstrom} high-resolution three-dimensional crystal structure of AGT from the mosquito Aedes aegypti (AeAGT) and structures of its complexes with reactants glyoxylic acid and alanine at 1.75 and 2.1{angstrom} resolution, respectively. This is the first time that the three-dimensional crystal structures of an AGT with its amino acceptor, glyoxylic acid, and amino donor, alanine, have been determined. The protein is dimeric and adopts the type I-fold of pyridoxal 5-phosphate (PLP)-dependent aminotransferases. The PLP co-factor is covalently bound to the active site in the crystal structure, and its binding site is similar to those of other AGTs. The comparison of the AeAGT-glyoxylic acid structure with other AGT structures revealed that these glyoxylic acid binding residues are conserved in most AGTs. Comparison of the AeAGT-alanine structure with that of the Anopheles HKT-inhibitor complex suggests that a Ser-Asn-Phe motif in the latter may be responsible for the substrate specificity of HKT enzymes for 3-HK.

  3. Crystal structure of the sodium–potassium pump

    Microsoft Academic Search

    J. Preben Morth; Bjørn P. Pedersen; Mads S. Toustrup-Jensen; Thomas L.-M. Sørensen; Janne Petersen; Jens Peter Andersen; Bente Vilsen; Poul Nissen

    2007-01-01

    The Na+,K+-ATPase generates electrochemical gradients for sodium and potassium that are vital to animal cells, exchanging three sodium ions for two potassium ions across the plasma membrane during each cycle of ATP hydrolysis. Here we present the X-ray crystal structure at 3.5Å resolution of the pig renal Na+,K+-ATPase with two rubidium ions bound (as potassium congeners) in an occluded state

  4. Crystal structure of the PB1 domain of NBR1

    Microsoft Academic Search

    Simone Müller; Inari Kursula; Peijian Zou; Matthias Wilmanns

    2006-01-01

    The scaffold protein NBR1 is involved in signal transmission downstream of the serine\\/protein kinase from the giant muscle protein titin. Its N-terminal Phox and Bem1p (PB1) domain plays a critical role in mediating protein–protein interactions with both titin kinase and with another scaffold protein, p62. We have determined the crystal structure of the PB1 domain of NBR1 at 1.55Å resolution.

  5. Crystal structure of the human laminin receptor precursor.

    PubMed

    Jamieson, Kelly V; Wu, Jinhua; Hubbard, Stevan R; Meruelo, Daniel

    2008-02-01

    The human laminin receptor (LamR) interacts with many ligands, including laminin, prions, Sindbis virus, and the polyphenol (-)-epigallocatechin-3-gallate (EGCG), and has been implicated in a number of diseases. LamR is overexpressed on tumor cells, and targeting LamR elicits anti-cancer effects. Here, we report the crystal structure of human LamR, which provides insights into its function and should facilitate the design of novel therapeutics targeting LamR. PMID:18063583

  6. A diffusion model of Frenkel defects formation during high-energy particle passage in crystals

    NASA Astrophysics Data System (ADS)

    Entinzon, I. P.; Shevchenko, G. L.; Chujko, A. A.

    The cross-section ?( E) of Frenkel defect formation resulted from fast energy E particle elastic scattering by a crystal atom is calculated, taking into account the real dependence of the defect formation probability W( T) on the transferred energy value T essentially differing from a step-like probability. Thus obtained ?( E) is in agreement with experimental dependences for Si and Ge exposed to fast E ? 1 MeV electron irradiation. The multiplication factor k(T) of the crystal atoms knocked-out in a cascade of atom-atom displacements is estimated with allowance for a more realistic probability function W(T). The resulted multiplication factor for a silicon crystal proved to be almost by an order of magnitude smaller than that determined by the known Kinchin-Pease relation. So, the suggested consideration predicts an essentially lower efficiency of radiation defect insertion approaching the estimated and experimental values.

  7. Structural contribution to the roughness of supersmooth crystal surface

    SciTech Connect

    Butashin, A. V.; Muslimov, A. E., E-mail: amuslimov@mail.ru; Kanevsky, V. M.; Deryabin, A. N.; Pavlov, V. A.; Asadchikov, V. E. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2013-05-15

    Technological advances in processing crystals (Si, sapphire {alpha}-Al{sub 2}O{sub 3}, SiC, GaN, LiNbO{sub 3}, SrTiO{sub 3}, etc.) of substrate materials and X-ray optics elements make it possible to obtain supersmooth surfaces with a periodicity characteristic of the crystal structure. These periodic structures are formed by atomically smooth terraces and steps of nano- and subnanometer sizes, respectively. A model surface with such nanostructures is proposed, and the relations between its roughness parameters and the height of atomic steps are determined. The roughness parameters calculated from these relations almost coincide with the experimental atomic force microscopy (AFM) data obtained from 1 Multiplication-Sign 1 and 10 Multiplication-Sign 10 {mu}m areas on the surface of sapphire plates with steps. The minimum roughness parameters for vicinal crystal surfaces, which are due to the structural contribution, are calculated based on the approach proposed. A comparative analysis of the relief and roughness parameters of sapphire plate surfaces with different degrees of polishing is performed. A size effect is established: the relief height distribution changes from stochastic to regular with a decrease in the surface roughness.

  8. Crystal structure of lead(II) tartrate: a redetermination.

    PubMed

    Weil, Matthias

    2015-01-01

    Single crystals of poly[?4-tartrato-?(6) O (1),O (3):O (1'):O (2),O (4):O (4')-lead], [Pb(C4H4O6)] n , were grown in a gel medium. In comparison with the previous structure determination of this compound from laboratory powder X-ray diffraction data [De Ridder et al. (2002 ?). Acta Cryst. C58, m596-m598], the redetermination on the basis of single-crystal data reveals the absolute structure, all atoms with anisotropic displacement parameters and a much higher accuracy in terms of bond lengths and angles. It could be shown that a different space group or incorporation of water as reported for similarly gel-grown lead tartrate crystals is incorrect. In the structure, each Pb(2+) cation is bonded to eight O atoms of five tartrate anions, while each tartrate anion links four Pb(2+) cations. The resulting three-dimensional framework is stabilized by O-H?O hydrogen bonds between the OH groups of one tartrate anion and the carboxyl-ate O atoms of adjacent anions. PMID:25705458

  9. Crystal structure of lead(II) tartrate: a redetermination

    PubMed Central

    Weil, Matthias

    2015-01-01

    Single crystals of poly[?4-tartrato-?6 O 1,O 3:O 1?:O 2,O 4:O 4?-lead], [Pb(C4H4O6)]n, were grown in a gel medium. In comparison with the previous structure determination of this compound from laboratory powder X-ray diffraction data [De Ridder et al. (2002 ?). Acta Cryst. C58, m596–m598], the redetermination on the basis of single-crystal data reveals the absolute structure, all atoms with anisotropic displacement parameters and a much higher accuracy in terms of bond lengths and angles. It could be shown that a different space group or incorporation of water as reported for similarly gel-grown lead tartrate crystals is incorrect. In the structure, each Pb2+ cation is bonded to eight O atoms of five tartrate anions, while each tartrate anion links four Pb2+ cations. The resulting three-dimensional framework is stabilized by O—H?O hydrogen bonds between the OH groups of one tartrate anion and the carboxyl­ate O atoms of adjacent anions. PMID:25705458

  10. Liquid Crystal-Based Emulsions for Synthesis and Non-Spherical Particles with Chemical Patches

    PubMed Central

    Mondiot, Frédéric; Wang, Xiaoguang; de Pablo, Juan J.; Abbott, Nicholas L.

    2013-01-01

    We report the use of liquid crystal (LC)-in-water emulsions for the synthesis of either spherical or non-spherical particles with chemically-distinct domains located at the poles of the particles. The approach involves the localization of solid colloids at topological defects that form predictably at surfaces of water-dispersed LC droplets. By polymerizing the LC droplets displaying the colloids at their surface defects, we demonstrate formation of both spherical and, upon extraction of the mesogen, anisotropic composite particles with colloids located at either one or both of the poles. Because the colloids protrude from the surfaces of the particles, they also define organized, chemical patches with functionality controlled by the colloid surface. PMID:23600692

  11. Optofluidic immobility of particles trapped in liquid-filled hollow-core photonic crystal fiber.

    PubMed

    Garbos, M K; Euser, T G; Russell, P St J

    2011-09-26

    We study the conditions under which a particle, laser-guided in a vertically-oriented hollow-core photonic crystal fiber filled with liquid, can be kept stationary against a microfluidic counter-flow. An immobility parameter-the fluid flow rate required to immobilize a particle against the radiation force produced by unit guided optical power-is introduced to quantify the conditions under which this occurs, including radiation, viscous and gravity forces. Measurements show that this parameter depends strongly on the ratio of particle radius a to core radius R, peaking at an intermediate value of a/R. The results follow fairly well the theoretical estimates of the optical (calculated approximately using a ray optics approach) and numerically simulated drag forces. We suggest that the system has potential applications in, e.g., measurement of the diameter, refractive index and density of particles, synthesis and biomedical research. PMID:21996905

  12. Metrology of laser-guided particles in air-filled hollow-core photonic crystal fiber.

    PubMed

    Schmidt, O A; Garbos, M K; Euser, T G; Russell, P St J

    2012-01-01

    Micrometer-sized particles are trapped in front of an air-filled hollow-core photonic crystal fiber using a novel dual-beam trap. A backward guided mode produces a divergent beam that diffracts out of the core, and simultaneously a focused laser beam launches a forward-propagating mode into the core. By changing the backward/forward power balance, a trapped particle can be selectively launched into the hollow core. Once inside, particles can be optically propelled along several meters of fiber with mobilities as high as 19 cm·s(-1) W(-1) (precisely measured using in-fiber Doppler velocimetry). The results are in excellent agreement with theory. The system allows determination of fiber loss as well as the mass density and refractive index of single particles. PMID:22212801

  13. Crystal structure of a COG4313 outer membrane channel.

    PubMed

    Berg, Bert van den; Bhamidimarri, Satya Prathyusha; Winterhalter, Mathias

    2015-01-01

    COG4313 proteins form a large and widespread family of outer membrane channels and have been implicated in the uptake of a variety of hydrophobic molecules. Structure-function studies of this protein family have so far been hampered by a lack of structural information. Here we present the X-ray crystal structure of Pput2725 from the biodegrader Pseudomonas putida F1, a COG4313 channel of unknown function, using data to 2.3?Å resolution. The structure shows a 12-stranded barrel with an N-terminal segment preceding the first ?-strand occluding the lumen of the barrel. Single channel electrophysiology and liposome swelling experiments suggest that while the narrow channel visible in the crystal structure does allow passage of ions and certain small molecules in vitro, Pput2725 is unlikely to function as a channel for hydrophilic molecules. Instead, the presence of bound detergent molecules inside the barrel suggests that Pput2725 mediates uptake of hydrophobic molecules. Sequence alignments and the locations of highly conserved residues suggest the presence of a dynamic lateral opening through which hydrophobic molecules might gain entry into the cell. Our results provide the basis for structure-function studies of COG4313 family members with known function, such as the SphA sphingosine uptake channel of Pseudomonas aeruginosa. PMID:26149193

  14. SHELXT – Integrated space-group and crystal-structure determination

    SciTech Connect

    Sheldrick, George M., E-mail: gsheldr@shelx.uni-ac.gwdg.de [Georg-August Universität Göttingen, Tammannstrasse 4, Göttingen, 37077 (Germany)

    2015-01-01

    SHELXT automates routine small-molecule structure determination starting from single-crystal reflection data, the Laue group and a reasonable guess as to which elements might be present. The new computer program SHELXT employs a novel dual-space algorithm to solve the phase problem for single-crystal reflection data expanded to the space group P1. Missing data are taken into account and the resolution extended if necessary. All space groups in the specified Laue group are tested to find which are consistent with the P1 phases. After applying the resulting origin shifts and space-group symmetry, the solutions are subject to further dual-space recycling followed by a peak search and summation of the electron density around each peak. Elements are assigned to give the best fit to the integrated peak densities and if necessary additional elements are considered. An isotropic refinement is followed for non-centrosymmetric space groups by the calculation of a Flack parameter and, if appropriate, inversion of the structure. The structure is assembled to maximize its connectivity and centred optimally in the unit cell. SHELXT has already solved many thousand structures with a high success rate, and is optimized for multiprocessor computers. It is, however, unsuitable for severely disordered and twinned structures because it is based on the assumption that the structure consists of atoms.

  15. Crystal structure of a COG4313 outer membrane channel

    PubMed Central

    Berg, Bert van den; Bhamidimarri, Satya Prathyusha; Winterhalter, Mathias

    2015-01-01

    COG4313 proteins form a large and widespread family of outer membrane channels and have been implicated in the uptake of a variety of hydrophobic molecules. Structure-function studies of this protein family have so far been hampered by a lack of structural information. Here we present the X-ray crystal structure of Pput2725 from the biodegrader Pseudomonas putida F1, a COG4313 channel of unknown function, using data to 2.3?Å resolution. The structure shows a 12-stranded barrel with an N-terminal segment preceding the first ?-strand occluding the lumen of the barrel. Single channel electrophysiology and liposome swelling experiments suggest that while the narrow channel visible in the crystal structure does allow passage of ions and certain small molecules in vitro, Pput2725 is unlikely to function as a channel for hydrophilic molecules. Instead, the presence of bound detergent molecules inside the barrel suggests that Pput2725 mediates uptake of hydrophobic molecules. Sequence alignments and the locations of highly conserved residues suggest the presence of a dynamic lateral opening through which hydrophobic molecules might gain entry into the cell. Our results provide the basis for structure-function studies of COG4313 family members with known function, such as the SphA sphingosine uptake channel of Pseudomonas aeruginosa. PMID:26149193

  16. Effect of Crystal Growth Direction on Domain Structure of Mn-Doped (Na,K)NbO3 Crystal

    NASA Astrophysics Data System (ADS)

    Tsuchida, Kohei; Kakimoto, Ken-ichi; Kagomiya, Isao

    2013-09-01

    Single crystals of (Na0.55K0.45)(Nb0.995Mn0.005)O3 have been grown by a floating zone method in N2 and decompression atmosphere to avoid alkaline metal volatilization on the SrTiO3 material base. The variation of their ferroelectric domain structure and the chemical composition of the grown crystal in the growth direction were evaluated. In the crystal grown in N2 atmosphere, the Na and K are not distributed homogeneously. In addition, the phase transition temperature TC and TO-T showed different values between the grown crystal and raw material. By using laser scanning confocal microscope, the domain structures of the grown crystal revealed random patterns in the initial growth stage and lamellar patterns in the progressing crystal growth. In decompression atmosphere, the TC and TO-T values of the grown crystal were similar to those of the raw material and the domain structures showed a constant domain size. The electrical property of the crystal became stable and the domain structure was easily switched against applied electrical field because the oriented lamellar domain was created during cooling of the crystal.

  17. Ab initio molecular crystal structures, spectra, and phase diagrams.

    PubMed

    Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

    2014-09-16

    Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling illustrations of their unprecedented power in addressing some of the outstanding problems of solid-state chemistry, high-pressure chemistry, or geochemistry. They are the structure and spectra of ice Ih, in particular, the origin of two peaks in the hydrogen-bond-stretching region of its inelastic neutron scattering spectra, a solid-solid phase transition from CO2-I to elusive, metastable CO2-III, pressure tuning of Fermi resonance in solid CO2, and the structure and spectra of solid formic acid, all at the level of second-order Møller-Plesset perturbation theory or higher. PMID:24754304

  18. Equilibrium state of a cylindrical particle with flat ends in nematic liquid crystals

    NASA Astrophysics Data System (ADS)

    Hashemi, S. Masoomeh; Ejtehadi, Mohammad Reza

    2015-01-01

    A continuum theory is employed to numerically study the equilibrium orientation and defect structures of a circular cylindrical particle with flat ends under a homeotropic anchoring condition in a uniform nematic medium. Different aspect ratios of this colloidal geometry from thin discotic to long rodlike shapes and several colloidal length scales ranging from mesoscale to nanoscale are investigated. We show that the equilibrium state of this colloidal geometry is sensitive to the two geometrical parameters: aspect ratio and length scale of the particle. For a large enough mesoscopic particle, there is a specific asymptotic equilibrium angle associated to each aspect ratio. Upon reducing the particle size to nanoscale, the equilibrium angle follows a descending or ascending trend in such a way that the equilibrium angle of a particle with the aspect ratio bigger than 1:1 (a discotic particle) goes to a parallel alignment with respect to the far-field nematic, whereas the equilibrium angle for a particle with the aspect ratio 1:1 and smaller (a rodlike particle) tends toward a perpendicular alignment to the uniform nematic direction. The discrepancy between the equilibrium angles of the mesoscopic and nanoscopic particles originates from the significant differences between their defect structures. The possible defect structures related to mesoscopic and nanoscopic colloidal particles of this geometry are also introduced.

  19. Equilibrium state of a cylindrical particle with flat ends in nematic liquid crystals

    E-print Network

    S. Masoomeh Hashemi; Mohammad Reza Ejtehadi

    2015-01-25

    A continuum theory is employed to numerically study the equilibrium orientation and defect structures of a circular cylindrical particle with flat ends under a homeotropic anchoring condition in a uniform nematic medium. Different aspect ratios of this colloidal geometry from thin discotic to long rod-like shapes and several colloidal length scales ranging from mesoscale to nanoscale are investigated. We show that the equilibrium state of this colloidal geometry is sensitive to the two geometrical parameters: aspect ratio and length scale of the particle. For a large enough mesoscopic particle, there is a specific asymptotic equilibrium angle associated to each aspect ratio. Upon reducing the particle size to nanoscale, the equilibrium angle follows a descending or ascending trend in such a way that the equilibrium angle of a particle with the aspect ratio bigger than 1:1 (a discotic particle) goes to a parallel alignment with respect to the far field nematic, whereas the equilibrium angle for a particle with the aspect ratio 1:1 and smaller (a rod-like particle) tends toward a perpendicular alignment to the uniform nematic direction. The discrepancy between the equilibrium angles of the mesoscopic and nanoscopic particles originates from the significant differences between their defect structures. The possible defect structures related to mesoscopic and nanoscopic colloidal particles of this geometry are also introduced.

  20. Gyroid cuticular structures in butterfly wing scales: biological photonic crystals.

    PubMed

    Michielsen, K; Stavenga, D G

    2008-01-01

    We present a systematic study of the cuticular structure in the butterfly wing scales of some papilionids (Parides sesostris and Teinopalpus imperialis) and lycaenids (Callophrys rubi, Cyanophrys remus, Mitoura gryneus and Callophrys dumetorum). Using published scanning and transmission electron microscopy (TEM) images, analytical modelling and computer-generated TEM micrographs, we find that the three-dimensional cuticular structures can be modelled by gyroid structures with various filling fractions and lattice parameters. We give a brief discussion of the formation of cubic gyroid membranes from the smooth endoplasmic reticulum in the scale's cell, which dry and harden to leave the cuticular structure behind when the cell dies. The scales of C. rubi are a potentially attractive biotemplate for producing three-dimensional optical photonic crystals since for these scales the cuticle-filling fraction is nearly optimal for obtaining the largest photonic band gap in a gyroid structure. PMID:17567555

  1. Crystal structure of a soluble cleaved HIV-1 envelope trimer

    PubMed Central

    Julien, Jean-Philippe; Cupo, Albert; Sok, Devin; Stanfield, Robyn L.; Lyumkis, Dmitry; Deller, Marc C.; Klasse, Per-Johan; Burton, Dennis R.; Sanders, Rogier W.; Moore, John P.; Ward, Andrew B.; Wilson, Ian A.

    2013-01-01

    HIV-1 entry into CD4+ target cells is mediated by cleaved envelope glycoprotein (Env) trimers that have been challenging to characterize structurally. Here, we describe the crystal structure at 4.7 Å of an antigenically near-native, cleaved, stabilized, soluble Env trimer (termed BG505 SOSIP.664 gp140) in complex with a potent broadly neutralizing antibody, PGT122. The structure shows a pre-fusion state of gp41, the interaction between the component gp120 and gp41 subunits, and how a close association between the gp120 V1/V2/V3 loops stabilizes the trimer apex around the three-fold axis. The complete epitope of PGT122 on the trimer involves gp120 V1, V3 and several surrounding glycans. This trimer structure advances our understanding of how Env functions and is presented to the immune system, and provides a blueprint for structure-based vaccine design. PMID:24179159

  2. Crystal structure of a soluble cleaved HIV-1 envelope trimer.

    PubMed

    Julien, Jean-Philippe; Cupo, Albert; Sok, Devin; Stanfield, Robyn L; Lyumkis, Dmitry; Deller, Marc C; Klasse, Per-Johan; Burton, Dennis R; Sanders, Rogier W; Moore, John P; Ward, Andrew B; Wilson, Ian A

    2013-12-20

    HIV-1 entry into CD4(+) target cells is mediated by cleaved envelope glycoprotein (Env) trimers that have been challenging to characterize structurally. Here, we describe the crystal structure at 4.7 angstroms of a soluble, cleaved Env trimer that is stabilized and antigenically near-native (termed the BG505 SOSIP.664 gp140 trimer) in complex with a potent broadly neutralizing antibody, PGT122. The structure shows a prefusion state of gp41, the interaction between the component gp120 and gp41 subunits, and how a close association between the gp120 V1/V2/V3 loops stabilizes the trimer apex around the threefold axis. The complete epitope of PGT122 on the trimer involves gp120 V1, V3, and several surrounding glycans. This trimer structure advances our understanding of how Env functions and is presented to the immune system, and provides a blueprint for structure-based vaccine design. PMID:24179159

  3. Hydrothermal synthesis of nanostructured SnO particles through crystal growth in the presence of gelatin

    NASA Astrophysics Data System (ADS)

    Uchiyama, Hiroaki; Nakanishi, Shunsuke; Kozuka, Hiromitsu

    2014-09-01

    Crystalline SnO particles were obtained from Sn6O4(OH)4 by the hydrothermal treatment in aqueous solutions containing gelatin at 150 °C for 24 h, where the morphologies of the SnO products changed from blocks to layered disks, stacked plates and unshaped aggregates with increasing amount of gelatin in the solutions. Such morphological changes of SnO particles were thought to be attributed to the suppression of the growth of SnO crystals by the adsorbed gelatin.

  4. Synthesis, crystal growth, structural, thermal, optical and mechanical properties of solution grown 4-methylpyridinium 4-hydroxybenzoate single crystal.

    PubMed

    Sudhahar, S; Krishna Kumar, M; Sornamurthy, B M; Mohan Kumar, R

    2014-01-24

    Organic nonlinear optical material, 4-methylpyridinium 4-hydroxybenzoate (4MPHB) was synthesized and single crystal was grown by slow evaporation solution growth method. Single crystal and powder X-ray diffraction analyses confirm the structure and crystalline perfection of 4MPHB crystal. Infrared, Raman and NMR spectroscopy techniques were used to elucidate the functional groups present in the compound. TG-DTA analysis was carried out in nitrogen atmosphere to study the decomposition stages, endothermic and exothermic reactions. UV-visible and Photoluminescence spectra were recorded for the grown crystal to estimate the transmittance and band gap energy respectively. Linear refractive index, birefringence, and SHG efficiency of the grown crystal were studied. Laser induced surface damage threshold and mechanical properties of grown crystal were studied to assess the suitability of the grown crystals for device applications. PMID:24184578

  5. Fractal Particles: Titan's Thermal Structure and IR Opacity

    NASA Technical Reports Server (NTRS)

    McKay, C. P.; Rannou, P.; Guez, L.; Young, E. F.; DeVincenzi, Donald (Technical Monitor)

    1998-01-01

    Titan's haze particles are the principle opacity at solar wavelengths. Most past work in modeling these particles has assumed spherical particles. However, observational evidence strongly favors fractal shapes for the haze particles. We consider the implications of fractal particles for the thermal structure and near infrared opacity of Titan's atmosphere. We find that assuming fractal particles with the optical properties based on laboratory tholin material and with a production rate that allows for a match to the geometric albedo results in warmer troposphere and surface temperatures compared to spherical particles. In the near infrared (1-3 microns) the predicted opacity of the fractal particles is up to a factor of two less than for spherical particles. This has implications for the ability of Cassini to image Titan's surface at 1 micron.

  6. Rattle-type colloidal crystals composed of spherical hollow particles containing an anisotropic, movable core.

    PubMed

    Watanabe, Kanako; Nagao, Daisuke; Ishii, Haruyuki; Konno, Mikio

    2015-05-19

    Controls over the position and orientation of anisotropic particles in their assemblies are intriguing issues for functional colloidal crystals that are switchable with external fields such as electric and magnetic fields. We propose a novel approach for the fabrication of rattle-type colloidal crystals containing an anisotropic, movable core surrounded by a void space that allows rearrangement of the anisotropic core in the assembly. In the fabrication, multilayered core-shell particles composed of a titania core, polystyrene shell, and silica shell were prepared and then heated at 500 °C for 4 h to selectively remove the middle layer of polystyrene. The heating treatment induced deformation of spherical titania cores in the compartment of silica shells, while the void space required for the orientation and relocation of anisotropic core was generated. The rattle particles fabricated were self-assembled by a simple dip-coating to form an arrangement of the spherical yolk/shell particles incorporating an anisotropic core. Brownian motion of the anisotropic cores observed with an optical microscope showed that the assembly of rattle-type particles had the potential to control location and orientation of the anisotropic cores in the shell compartment by application of external fields. PMID:25918953

  7. Crystal Structure of Uronate Dehydrogenase from Agrobacterium tumefaciens*

    PubMed Central

    Parkkinen, Tarja; Boer, Harry; Jänis, Janne; Andberg, Martina; Penttilä, Merja; Koivula, Anu; Rouvinen, Juha

    2011-01-01

    Uronate dehydrogenase from Agrobacterium tumefaciens (AtUdh) belongs to the short-chain dehydrogenase/reductase superfamily and catalyzes the oxidation of d-galacturonic acid and d-glucuronic acid with NAD+ as a cofactor. We have determined the crystal structures of an apo-form of AtUdh, a ternary form in complex with NADH and product (substrate-soaked structure), and an inactive Y136A mutant in complex with NAD+. The crystal structures suggest AtUdh to be a homohexamer, which has also been observed to be the major form in solution. The monomer contains a Rossmann fold, essential for nucleotide binding and a common feature of the short-chain dehydrogenase/reductase family enzymes. The ternary complex structure reveals a product, d-galactaro-1,5-lactone, which is bound above the nicotinamide ring. This product rearranges in solution to d-galactaro-1,4-lactone as verified by mass spectrometry analysis, which agrees with our previous NMR study. The crystal structure of the mutant with the catalytic residue Tyr-136 substituted with alanine shows changes in the position of Ile-74 and Ser-75. This probably altered the binding of the nicotinamide end of NAD+, which was not visible in the electron density map. The structures presented provide novel insights into cofactor and substrate binding and the reaction mechanism of AtUdh. This information can be applied to the design of efficient microbial conversion of d-galacturonic acid-based waste materials. PMID:21676870

  8. Effect of the polydispersion in the crystallization and micro-structure of the high charged colloids

    NASA Astrophysics Data System (ADS)

    Urrutia-Bañuelos, Efraín; Aranda-Espinosa, Helim; Chasvez-Paez, Martin

    2008-03-01

    In this work we investigate the effect of the polydipersion in the crystallization and micro-structure of the high charged colloids particles with tow and three different types and different concentrations of that types. This results were obtained by computer simulation, the particles interaction was modeled by a screened Coulomb potential. We used 4000 particles in our simulation cell to let them evolution from an initial random configuration, periodic boundary conditions was imposed to simulate the bulk. The temporal evolutions of the configuration show long-ranged self-ordering and a crystalline transition, the crystalline nucleation depend of the concentrations of different kinds as well as of types of particle. The common neighbor analysis (CNA) exhibit the competition of two micro-structures, icosahedral and bcc, in the equilibrium bcc crystalline order is dominant with relative abundance over the other micro-structures. 1.- U. Gasser, Eric R. Weeks et al, Science, 292 (258), 2001. 2.- Stefan Auer, Daan Frenkel, Letter of Nature, 409 (1020), 2001. 3.- J.P. Hoogenboom, et al , Phys. Rev. Leeters, 89 (256104), 2002. 4.- M. Ch'avez-P'aez, E. Urrutia-Bañuelos and M. Medina --Noyola, Phys. Rev. E, 58 (681),1998 5.- Andrew S. Clarke and Hannes J'onsson, Phys. Rev. E, 47 (3975), 1993.

  9. Crystallization of acicular platelet particles of W-type hexagonal strontium ferrite for magnetic recording applications

    Microsoft Academic Search

    Shanker Ram

    1990-01-01

    Acicular platelets of the W-type hexagonal strontium ferrite (SrFe18O27) have been crystallized from the borate glass system with the aid of ~ 1 mol% SiO2 and Bi2O3. It was found that particle size and morphology of the system can be effectively altered by proper use of the additives and the thermal treatment of the samples. Addition of SiO2 induces growth

  10. Physicochemical properties and plastic crystal structures of phosphonium fluorohydrogenate salts.

    PubMed

    Enomoto, Takeshi; Kanematsu, Shunsuke; Tsunashima, Katsuhiko; Matsumoto, Kazuhiko; Hagiwara, Rika

    2011-07-21

    Fluorohydrogenate salts of quaternary phosphonium cations with alkyl and methoxy groups (tetraethylphosphonium (P(2222)(+)), triethyl-n-pentylphosphonium (P(2225)(+)), triethyl-n-octylphosphonium (P(2228)(+)), and triethylmethoxymethylphosphonium (P(222(101))(+))) have been synthesized by the metatheses of anhydrous hydrogen fluoride and the corresponding phosphonium bromide or chloride precursors. The three salts with asymmetric cations, P(222m)(FH)(2.1)F (m = 5, 8, and 101), are room temperature ionic liquids (ILs) and are characterized by differential scanning calorimetry, density, viscosity, and conductivity measurements. Linear sweep voltammetry using a glassy carbon working electrode shows these phosphonium fluorohydrogenate ILs have wide electrochemical windows (>4.9 V) with the lowest viscosity and highest conductivity in the known phosphonium-based ILs. Thermogravimetry shows their thermal stabilities are also improved compared to previously reported alkylammonium cation-based fluorohydrogenate salts. Differential scanning calorimetry and X-ray diffraction revealed that tetraethylphosphonium fluorohydrogenate salt, P(2222)(FH)(2)F, exhibits two plastic crystal phases. The high temperature phase has a hexagonal lattice, which is the first example of a plastic crystal phase with an inverse nickel arsenide-type structure, and the low-temperature phase has an orthorhombic lattice. The high-temperature plastic crystal phase exhibits a conductivity of 5 mS cm(-1) at 50 °C, which is the highest value for the neat plastic crystals. PMID:21666902

  11. Crystal structure of the PB1 domain of NBR1.

    PubMed

    Müller, Simone; Kursula, Inari; Zou, Peijian; Wilmanns, Matthias

    2006-01-01

    The scaffold protein NBR1 is involved in signal transmission downstream of the serine/protein kinase from the giant muscle protein titin. Its N-terminal Phox and Bem1p (PB1) domain plays a critical role in mediating protein-protein interactions with both titin kinase and with another scaffold protein, p62. We have determined the crystal structure of the PB1 domain of NBR1 at 1.55A resolution. It reveals a type-A PB1 domain with two negatively charged residue clusters. We provide a structural perspective on the involvement of NBR1 in the titin kinase signalling pathway. PMID:16376336

  12. Crystal structure of catena-O , O ?-diethylphosphonoacetatotriphenyltin

    Microsoft Academic Search

    Seik Weng; V. G. Kumar Das

    1994-01-01

    Triphenyltin diethylphosphonoacetate, which crystallizes in the monoclinc space groupP21\\/c (a=15.154(4),b=9.159(3),c=17.685(4) Å, ß=91.410(8)°), adopts a polymeric structure in which planar triphenyltin cations (?C—Sn—C=357.3(6)°) are axially linked by the diethylphosphonoacetato anions (Sn-Oesteryl=2.129(3), Sn?Ophosphoryl=2.420(3) Å; O-Sn?O=171.9(1)° into chains that propagate by translations along theb-axis. The structure has been erfined toR=0.037 for 3384I=3s(I) reflections.

  13. 3D Structural Fluctuation of IgG1 Antibody Revealed by Individual Particle Electron Tomography.

    PubMed

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J; Zhang, Shengli; Ren, Gang

    2015-01-01

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1-3?nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions. PMID:25940394

  14. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    DOE PAGESBeta

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

    2015-05-05

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, wemore »derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.« less

  15. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    DOE PAGESBeta

    Zhang, Xing [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Xi'an Jiaotong Univ., Xi'an, Shaanxi (China); Zhang, Lei [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Tong, Huimin [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Peng, Bo [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Rames, Matthew J. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Zhang, Shengli [Xi'an Jiaotong Univ., Xi'an, Shaanxi (China); Ren, Gang [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2015-05-05

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.

  16. The crystal structure of human GDP-L-fucose synthase.

    PubMed

    Zhou, Huan; Sun, Lihua; Li, Jian; Xu, Chunyan; Yu, Feng; Liu, Yahui; Ji, Chaoneng; He, Jianhua

    2013-09-01

    Human GDP-l-fucose synthase, also known as FX protein, synthesizes GDP-l-fucose from its substrate GDP-4-keto-6-deoxy-d-mannose. The reaction involves epimerization at both C-3 and C-5 followed by an NADPH-dependent reduction of the carbonyl at C-4. In this paper, the first crystal structure of human FX protein was determined at 2.37 Å resolution. The asymmetric unit of the crystal structure contains four molecules which form two homodimers. Each molecule consists of two domains, a Rossmann-fold NADPH-binding motif and a carboxyl terminal domain. Compared with the Escherichia coli GDP-l-fucose synthase, the overall structures of these two enzymes have four major differences. There are four loops in the structure of human FX protein corresponding to two ?-helices and two ?-sheets in that of the E. coli enzyme. Besides, there are seven different amino acid residues binding with NAPDH comparing human FX protein with that from E. coli. The structure of human FX reveals the key catalytic residues and could be useful for the design of drugs for the treatment of inflammation, auto-immune diseases, and possibly certain types of cancer. PMID:23774504

  17. Crystal structure of the gramicidin/potassium thiocyanate complex.

    PubMed

    Doyle, D A; Wallace, B A

    1997-03-14

    The hydrophobic channel-forming polypeptide gramicidin adopts a left-handed antiparallel double helix conformation with 6.4 residues per turn when in complex with monovalent cation salts in a methanol environment. The crystal structure of the gramicidin/potassium thiocyanate complex (a = 32.06 A, b = 51.80 A, and c = 31.04 A; space group P2(1)2(1)2(1)) has been solved to 2.5 A with an R-factor of 0.193. In the structure, binding sites for the cations are formed by the polypeptide backbone carbonyl groups tilting away from the helix axis toward the ions located in the central lumen. The polypeptide backbone conformations and the side-chain orientations in this potassium complex are significantly different from those in the previously solved gramicidin/caesium chloride crystal complex, due to the requirements for interactions with the smaller sized potassium cation. The locations and numbers of potassium binding sites also differ considerably from the locations and numbers of caesium binding sites in the other structure. Combining information from all the cation binding sites in the two gramicidin/ion complexes produces different views of the three-dimensional structures of a cation as it is transported along a transmembrane pore, and provides an experimental structural basis for modeling the dynamics of peptide-ion binding and ion transport. PMID:9086274

  18. Monomer structure of a hyperthermophilic ?-glucosidase mutant forming a dodecameric structure in the crystal form

    PubMed Central

    Nakabayashi, Makoto; Kataoka, Misumi; Watanabe, Masahiro; Ishikawa, Kazuhiko

    2014-01-01

    One of the ?-glucosidases from Pyrococcus furiosus (BGLPf) is found to be a hyperthermophilic tetrameric enzyme that can degrade cellooligosaccharides. Recently, the crystal structures of the tetrameric and dimeric forms were solved. Here, a new monomeric form of BGLPf was constructed by removing the C-terminal region of the enzyme and its crystal structure was solved at a resolution of 2.8?Å in space group P1. It was discovered that the mutant enzyme forms a unique dodecameric structure consisting of two hexameric rings in the asymmetric unit of the crystal. Under biological conditions, the mutant enzyme forms a monomer. This result helps explain how BGLPf has attained its oligomeric structure and thermostability. PMID:25005077

  19. Crystal structure of the Fe-member of usovite.

    PubMed

    Weil, Matthias

    2015-06-01

    Crystals of the title compound, with the idealized composition Ba2CaFeAl2F14, dibarium calcium iron(II) dialuminium tetra-deca-fluoride, were obtained serendipitously by reacting a mixture of the binary fluorides BaF2, CaF2 and AlF3 in a leaky steel reactor. The compound crystallizes in the usovite structure type (Ba2CaMgAl2F14), with Fe(2+) cations replacing the Mg(2+) cations. The principal building units are distorted [CaF8] square-anti-prisms (point group symmetry 2), [FeF6] octa-hedra (point group symmetry -1) and [AlF6] octa-hedra that are condensed into undulating (2) ?[CaFeAl2F14](4-) layers parallel (100). The Ba(2+) cations separate the layers and exhibit a coordination number of 12. Two crystal structure models with a different treatment of the disordered Fe site [mixed Fe/Ca occupation, model (I), versus underoccupation of Fe, model (II)], are discussed, leading to different refined formulae Ba2Ca1.310?(15)Fe0.690?(15)Al2F14 [model (I)] and Ba2CaFe0.90?(1)Al2F14 [model (II)]. PMID:26090139

  20. Crystal structure of the Fe-member of usovite

    PubMed Central

    Weil, Matthias

    2015-01-01

    Crystals of the title compound, with the idealized composition Ba2CaFeAl2F14, dibarium calcium iron(II) dialuminium tetra­deca­fluoride, were obtained serendipitously by reacting a mixture of the binary fluorides BaF2, CaF2 and AlF3 in a leaky steel reactor. The compound crystallizes in the usovite structure type (Ba2CaMgAl2F14), with Fe2+ cations replacing the Mg2+ cations. The principal building units are distorted [CaF8] square-anti­prisms (point group symmetry 2), [FeF6] octa­hedra (point group symmetry -1) and [AlF6] octa­hedra that are condensed into undulating 2 ?[CaFeAl2F14]4? layers parallel (100). The Ba2+ cations separate the layers and exhibit a coordination number of 12. Two crystal structure models with a different treatment of the disordered Fe site [mixed Fe/Ca occupation, model (I), versus underoccupation of Fe, model (II)], are discussed, leading to different refined formulae Ba2Ca1.310?(15)Fe0.690?(15)Al2F14 [model (I)] and Ba2CaFe0.90?(1)Al2F14 [model (II)].

  1. Multiple solvent crystal structures: probing binding sites, plasticity and hydration.

    PubMed

    Mattos, Carla; Bellamacina, Cornelia R; Peisach, Ezra; Pereira, Antonio; Vitkup, Dennis; Petsko, Gregory A; Ringe, Dagmar

    2006-04-14

    Multiple solvent crystal structures (MSCS) of porcine pancreatic elastase were used to map the binding surface the enzyme. Crystal structures of elastase in neat acetonitrile, 95% acetone, 55% dimethylformamide, 80% 5-hexene-1,2-diol, 80% isopropanol, 80% ethanol and 40% trifluoroethanol showed that the organic solvent molecules clustered in the active site, were found mostly unclustered in crystal contacts and in general did not bind elsewhere on the surface of elastase. Mixtures of 40% benzene or 40% cyclohexane in 50% isopropanol and 10% water showed no bound benzene or cyclohexane molecules, but did reveal bound isopropanol. The clusters of organic solvent probe molecules coincide with pockets occupied by known inhibitors. MSCS also reveal the areas of plasticity within the elastase binding site and allow for the visualization of a nearly complete first hydration shell. The pattern of organic solvent clusters determined by MSCS for elastase is consistent with patterns for hot spots in protein-ligand interactions determined from database analysis in general. The MSCS method allows probing of hot spots, plasticity and hydration simultaneously, providing a powerful complementary strategy to guide computational methods currently in development for binding site determination, ligand docking and design. PMID:16488429

  2. Crystal Structure of a Fructokinase Homolog from Halothermothrix orenii

    SciTech Connect

    Khiang, C.; Seetharaman, J; Kasprzak, J; Cherlyn, N; Patel, B; Love, C; Bujnicki, J; Sivaraman, J

    2010-01-01

    Fructokinase (FRK; EC 2.7.1.4) catalyzes the phosphorylation of D-fructose to D-fructose 6-phosphate (F6P). This irreversible and near rate-limiting step is a central and regulatory process in plants and bacteria, which channels fructose into a metabolically active state for glycolysis. Towards understanding the mechanism of FRK, here we report the crystal structure of a FRK homolog from a thermohalophilic bacterium Halothermothrix orenii (Hore{_}18220 in sequence databases). The structure of the Hore{_}18220 protein reveals a catalytic domain with a Rossmann-like fold and a b-sheet 'lid' for dimerization. Based on comparison of Hore{_}18220 to structures of related proteins, we propose its mechanism of action, in which the lid serves to regulate access to the substrate binding sites. Close relationship of Hore{_}18220 and plant FRK enzymes allows us to propose a model for the structure and function of FRKs.

  3. Crystal structure of homoserine O-acetyltransferase from Leptospira interrogans

    SciTech Connect

    Wang Mingzhu [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101 (China); School of Life Sciences, IBP-USTC Joint Laboratory for Protein Sciences, University of Science and Technology of China, Hefei, Anhui 230026 (China); Graduate University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049 (China); Liu Lin; Wang Yanli; Wei Zhiyi; Zhang Ping; Li Yikun; Jiang Xiaohua [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101 (China); School of Life Sciences, IBP-USTC Joint Laboratory for Protein Sciences, University of Science and Technology of China, Hefei, Anhui 230026 (China); Xu Hang [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101 (China)], E-mail: hxu@moon.ibp.ac.cn; Gong Weimin [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101 (China); School of Life Sciences, IBP-USTC Joint Laboratory for Protein Sciences, University of Science and Technology of China, Hefei, Anhui 230026 (China)], E-mail: wgong@ibp.ac.cn

    2007-11-30

    Homoserine O-acetyltransferase (HTA, EC 2.3.1.31) initiates methionine biosynthesis pathway by catalyzing the transfer of acetyl group from acetyl-CoA to homoserine. This study reports the crystal structure of HTA from Leptospira interrogans determined at 2.2 A resolution using selenomethionyl single-wavelength anomalous diffraction method. HTA is modular and consists of two structurally distinct domains-a core {alpha}/{beta} domain containing the catalytic site and a helical bundle called the lid domain. Overall, the structure fold belongs to {alpha}/{beta} hydrolase superfamily with the characteristic 'catalytic triad' residues in the active site. Detailed structure analysis showed that the catalytic histidine and serine are both present in two conformations, which may be involved in the catalytic mechanism for acetyl transfer.

  4. Dipole Parallel Alignment in the Crystal Structure of a Polar Biphenyl: 4-Acetyl-4-Methoxybiphenyl (AMB)

    E-print Network

    Glaser, Rainer

    Dipole Parallel Alignment in the Crystal Structure of a Polar Biphenyl: 4-Acetyl-4-Methoxybiphenyl, and the crystals are noncentrosymmetric, space group Pna21. The crystal structure of AMB features parallel. The lattice architecture of AMB is compared to the motives realized in the only two other parallel

  5. Discovery of ordered and quasi-ordered photonic crystal structures in the scales of the

    E-print Network

    Discovery of ordered and quasi-ordered photonic crystal structures in the scales of the beetle in the yellow elytral bands comprise highly ordered 3D photonic crystal structures, whereas the scales crystals. References and links 1. J. D. Joannopoulos, S. G. Johnson, J. N. Winn, and R. D. Meade, Photonic

  6. PROTEIN STRUCTURE REPORT Crystal structure of the protease-resistant core

    E-print Network

    PROTEIN STRUCTURE REPORT Crystal structure of the protease-resistant core domain of Yersinia pestis; ACCEPTED March 28, 2005) Abstract Yersinia pestis, the causative agent of the plague, employs a type III that YopR may play a role in the regulation of type III secretion. Keywords: Yersinia pestis; plague; type

  7. Structural, mechanical, optical, dielectric and SHG studies of undoped and urea-doped ?-glycine crystals

    Microsoft Academic Search

    P. Selvarajan; J. Glorium Arulraj; S. Perumal

    2010-01-01

    Single crystals of undoped and urea-doped ?-glycine (gamma-glycine) were grown from aqueous solutions by slow evaporation technique. Morphological changes were noticed in ?-glycine crystals when urea was added as dopant. Single crystal X-ray diffraction (XRD) studies were carried out to find crystal structure and lattice parameters of the grown crystals. UV-Visible transmittance spectra were recorded for the samples to analyze

  8. On calculating the equilibrium structure of molecular crystals

    NASA Astrophysics Data System (ADS)

    Mattsson, Ann E.; Wixom, Ryan R.; Mattsson, Thomas R.

    2010-03-01

    The difficulty of calculating the ambient properties of molecular crystals, such as the explosive PETN, has long hampered much needed computational investigations of these materials. One reason for the shortcomings is that the exchange-correlation functionals available for Density Functional Theory (DFT) based calculations do not correctly describe the weak intermolecular van der Waals' forces present in molecular crystals. However, this weak interaction also poses other challenges for the computational schemes used. We will discuss these issues in the context of calculations of lattice constants and structure of PETN with a number of different functionals, and also discuss if these limitations can be circumvented for studies at non-ambient conditions. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  9. Models for the aggregate structure of soot particles

    SciTech Connect

    Patterson, Robert I.A.; Kraft, Markus [Department of Chemical Engineering, University of Cambridge, New Museums Site, Pembroke Street, Cambridge CB2 3RA (United Kingdom)

    2007-10-15

    New bivariate models for soot particle structure are introduced to qualitatively replicate observed particle shapes and are found to offer quantitative improvements over older single-variable models. Models for the development of particle shape during surface growth and for particle collision diameters are described and implemented along with two models taken from other published work. Using a stochastic approach, bivariate soot particle distributions are calculated for the first time. Distributions calculated for the new models are found to be insensitive to the collision diameter model used for coagulation. The total mass of soot produced in a laminar premixed flame is found to vary by no more than 20% as the model for the geometric effects of chemical reactions on the surface of particles is changed. Histories of individual particles are analyzed and show the limitations of collector particle techniques for predicting the evolution of aggregate shape descriptors. (author)

  10. Pitfalls in the interpretation of structural changes in mutant proteins from crystal structures

    PubMed Central

    Pokkuluri, P. R.; Yang, X.; Londer, Y. Y.; Schiffer, M.

    2014-01-01

    PpcA is a small protein with 71 residues that contains three covalently bound hemes. The structures of single mutants at residue 58 have shown larger deviations in another part of the protein molecule than at the site of the mutation. Closer examination of the crystal packing has revealed the origin of this unexpected structural change. The site of mutation is within Van der Waals distance from another protein molecule related by a crystallographic twofold axis within the crystal. The structural changes occurred at or near the mutation site have led to a slight adjustment of the surface residues in contact. The observed deviations between the native and the mutant molecular structures are derived from the new crystal packing even though the two crystals are essentially isomorphous. Without careful consideration of the crystal lattice a non-expert looking at only the coordinates deposited in the Protein Data Bank could draw erroneous conclusion that mutation in one part of the molecule affected the structure of the protein in a distant part of the molecule. PMID:23099666

  11. Crystal Structure of Cruxrhodopsin-3 from Haloarcula vallismortis

    PubMed Central

    Chan, Siu Kit; Kitajima-Ihara, Tomomi; Fujii, Ryudoh; Gotoh, Toshiaki; Murakami, Midori; Ihara, Kunio; Kouyama, Tsutomu

    2014-01-01

    Cruxrhodopsin-3 (cR3), a retinylidene protein found in the claret membrane of Haloarcula vallismortis, functions as a light-driven proton pump. In this study, the membrane fusion method was applied to crystallize cR3 into a crystal belonging to space group P321. Diffraction data at 2.1 Å resolution show that cR3 forms a trimeric assembly with bacterioruberin bound to the crevice between neighboring subunits. Although the structure of the proton-release pathway is conserved among proton-pumping archaeal rhodopsins, cR3 possesses the following peculiar structural features: 1) The DE loop is long enough to interact with a neighboring subunit, strengthening the trimeric assembly; 2) Three positive charges are distributed at the cytoplasmic end of helix F, affecting the higher order structure of cR3; 3) The cytoplasmic vicinity of retinal is more rigid in cR3 than in bacteriorhodopsin, affecting the early reaction step in the proton-pumping cycle; 4) the cytoplasmic part of helix E is greatly bent, influencing the proton uptake process. Meanwhile, it was observed that the photobleaching of retinal, which scarcely occurred in the membrane state, became significant when the trimeric assembly of cR3 was dissociated into monomers in the presence of an excess amount of detergent. On the basis of these observations, we discuss structural factors affecting the photostabilities of ion-pumping rhodopsins. PMID:25268964

  12. Crystal Structure of the Japanese Encephalitis Virus Envelope Protein

    SciTech Connect

    Luca, Vincent C.; AbiMansour, Jad; Nelson, Christopher A.; Fremont, Daved H. (WU-MED)

    2012-03-13

    Japanese encephalitis virus (JEV) is the leading global cause of viral encephalitis. The JEV envelope protein (E) facilitates cellular attachment and membrane fusion and is the primary target of neutralizing antibodies. We have determined the 2.1-{angstrom} resolution crystal structure of the JEV E ectodomain refolded from bacterial inclusion bodies. The E protein possesses the three domains characteristic of flavivirus envelopes and epitope mapping of neutralizing antibodies onto the structure reveals determinants that correspond to the domain I lateral ridge, fusion loop, domain III lateral ridge, and domain I-II hinge. While monomeric in solution, JEV E assembles as an antiparallel dimer in the crystal lattice organized in a highly similar fashion as seen in cryo-electron microscopy models of mature flavivirus virions. The dimer interface, however, is remarkably small and lacks many of the domain II contacts observed in other flavivirus E homodimers. In addition, uniquely conserved histidines within the JEV serocomplex suggest that pH-mediated structural transitions may be aided by lateral interactions outside the dimer interface in the icosahedral virion. Our results suggest that variation in dimer structure and stability may significantly influence the assembly, receptor interaction, and uncoating of virions.

  13. Crystal structure of Cruxrhodopsin-3 from Haloarcula vallismortis.

    PubMed

    Chan, Siu Kit; Kitajima-Ihara, Tomomi; Fujii, Ryudoh; Gotoh, Toshiaki; Murakami, Midori; Ihara, Kunio; Kouyama, Tsutomu

    2014-01-01

    Cruxrhodopsin-3 (cR3), a retinylidene protein found in the claret membrane of Haloarcula vallismortis, functions as a light-driven proton pump. In this study, the membrane fusion method was applied to crystallize cR3 into a crystal belonging to space group P321. Diffraction data at 2.1 Å resolution show that cR3 forms a trimeric assembly with bacterioruberin bound to the crevice between neighboring subunits. Although the structure of the proton-release pathway is conserved among proton-pumping archaeal rhodopsins, cR3 possesses the following peculiar structural features: 1) The DE loop is long enough to interact with a neighboring subunit, strengthening the trimeric assembly; 2) Three positive charges are distributed at the cytoplasmic end of helix F, affecting the higher order structure of cR3; 3) The cytoplasmic vicinity of retinal is more rigid in cR3 than in bacteriorhodopsin, affecting the early reaction step in the proton-pumping cycle; 4) the cytoplasmic part of helix E is greatly bent, influencing the proton uptake process. Meanwhile, it was observed that the photobleaching of retinal, which scarcely occurred in the membrane state, became significant when the trimeric assembly of cR3 was dissociated into monomers in the presence of an excess amount of detergent. On the basis of these observations, we discuss structural factors affecting the photostabilities of ion-pumping rhodopsins. PMID:25268964

  14. Lithium-cation conductivity and crystal structure of lithium diphosphate

    SciTech Connect

    Voronin, V.I., E-mail: voronin@imp.uran.ru [Institute of Metal Physics Urals Branch RAS, S.Kovalevskoy Street 18, 620041 Ekaterinburg (Russian Federation); Sherstobitova, E.A. [Institute of Metal Physics Urals Branch RAS, S.Kovalevskoy Street 18, 620041 Ekaterinburg (Russian Federation); Blatov, V.A., E-mail: blatov@samsu.ru [Samara Center for Theoretical Materials Science (SCTMS), Samara State University, Ac.Pavlov Street 1, 443011 Samara (Russian Federation); Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589 (Saudi Arabia); Shekhtman, G.Sh., E-mail: shekhtman@ihte.uran.ru [Institute of High Temperature Electrochemistry Urals Branch RAS, Akademicheskaya 20, 620990 Ekaterinburg (Russian Federation)

    2014-03-15

    The electrical conductivity of lithium diphosphate Li{sub 4}P{sub 2}O{sub 7} has been measured and jump-like increasing of ionic conductivity at 913 K has been found. The crystal structure of Li{sub 4}P{sub 2}O{sub 7} has been refined using high temperature neutron diffraction at 300–1050 K. At 913 K low temperature triclinic form of Li{sub 4}P{sub 2}O{sub 7} transforms into high temperature monoclinic one, space group P2{sub 1}/n, a=8.8261(4) Å, b=5.2028(4) Å, c=13.3119(2) Å, ?=104.372(6)°. The migration maps of Li{sup +} cations based on experimental data implemented into program package TOPOS have been explored. It was found that lithium cations in both low- and high temperature forms of Li{sub 4}P{sub 2}O{sub 7} migrate in three dimensions. Cross sections of the migrations channels extend as the temperature rises, but at the phase transition point have a sharp growth showing a strong “crystal structure – ion conductivity” correlation. -- Graphical abstract: Crystal structure of Li{sub 4}P{sub 2}O{sub 7} at 950 K. Red balls represent oxygen atoms; black lines show Li{sup +} ion migration channels in the layers perpendicular to [001] direction. Highlights: • Structure of Li{sub 4}P{sub 2}O{sub 7} has been refined using high temperature neutron diffraction. • At 913 K triclinic form of Li{sub 4}P{sub 2}O{sub 7} transforms into high temperature monoclinic one. • The migration maps of Li{sup +} implemented into program package TOPOS have been explored. • Cross sections of the migrations channels at the phase transition have a sharp growth.

  15. Crystal structure of the BIR1 domain of XIAP In two crystal forms

    PubMed Central

    Lin, Su-Chang; Huang, Yihua; Lo, Yu-Chih; Lu, Miao; Wu, Hao

    2007-01-01

    X-linked inhibitor of apoptosis (XIAP) is a potent negative regulator of apoptosis. It also plays a role in BMP signaling, TGF-? signaling, and copper homeostasis. Previous structural studies have shown that the BIR2 and BIR3 domains of XIAP interact with the IAP-binding-motifs (IBM) in several apoptosis proteins such as Smac and caspase-9 via the conserved IBM-binding groove. Here, we report the crystal structure in two crystal forms of the BIR1 domain of XIAP, which does not possess this IBM-binding groove and cannot interact with Smac or caspase-9. Instead, the BIR1 domain forms a conserved dimer through the region corresponding to the IBM-binding groove. Structural and sequence analyses suggest that this dimerization of BIR1 in XIAP may be conserved in other IAP family members such as cIAP1 and cIAP2 and may be important for the action of XIAP in TGF? and BMP signaling and the action of cIAP1 and cIAP2 in TNF receptor signaling. PMID:17698078

  16. Crystal structure and characterization of a novel organic crystal: 4-Dimethylaminobenzophenone

    SciTech Connect

    Anandha babu, G. [Centre for Crystal Growth, SSN College of Engineering, Kalavakkam 603110 (India); Ramasamy, P., E-mail: ramasamyp@ssn.edu.in [Centre for Crystal Growth, SSN College of Engineering, Kalavakkam 603110 (India); Ravikumar, K.; Sridhar, B. [X-Ray Division, Indian Institute of Chemical Technology, Hyderabad 500007 (India)

    2009-06-03

    Single crystals of a novel organic material, dimethylaminobenzophenone were grown from aqueous solution employing the technique of controlled evaporation. Dimethylaminobenzophenone belongs to the monoclinic system, with a = 12.5755(7) A, b = 7.9749(4) A, c = 13.0946(7) A, {alpha} = 90{sup o}, {beta} = 111.6380(10){sup o} and {gamma} = 90{sup o}. Fourier transform infrared study has been performed to identify the functional groups. The transmittance of dimethylaminobenzophenone has been used to calculate the refractive index n; the extinction coefficient K and both the real {epsilon}{sub r} and imaginary {epsilon}{sub i} components of the dielectric constant as functions of photon energy. The optical band gap of dimethylaminobenzophenone is 2.9 eV. The structural prefection of the grown crystals has been analyzed by high-resolution X-ray diffraction rocking curve measurements. Thermo gravimetric analysis and differential thermal analysis have also been carried out, and the thermal behavior of dimethylaminobenzophenone crystal has been studied. The dielectric properties and mechanical properties have been investigated.

  17. Structure, Hydrodynamics, and Phase Transition of Freely Suspended Liquid Crystals

    NASA Technical Reports Server (NTRS)

    Clark, Noel A.

    2000-01-01

    Smectic liquid crystals are phases of rod shaped molecules organized into one dimensionally (1D) periodic arrays of layers, each layer being between one and two molecular lengths thick. In the least ordered smectic phases, the smectics A and C, each layer is a two dimensional (2D) liquid. Additionally there are a variety of more ordered smectic phases having hexatic short range translational order or 2D crystalline quasi long range translational order within the layers. The inherent fluid-layer structure and low vapor pressure of smectic liquid crystals enable the long term stabilization of freely suspended, single component, layered fluid films as thin as 30A, a single molecular layer. The layering forces the films to be an integral number of smectic layers thick, quantizing their thickness in layer units and forcing a film of a particular number of layers to be physically homogeneous with respect to its layer structure over its entire area. Optical reflectivity enables the precise determination of the number of layers. These ultrathin freely suspended liquid crystal films are structures of fundamental interest in condensed matter and fluid physics. They are the thinnest known stable condensed phase fluid structures and have the largest surface-to-volume ratio of any stable fluid preparation, making them ideal for the study of the effects of reduced dimensionality on phase behavior and on fluctuation and interface phenomena. Their low vapor pressure and quantized thickness enable the effective use of microgravity to extend the study of basic capillary phenomena to ultrathin fluid films. Freely suspended films have been a wellspring of new liquid crystal physics. They have been used to provide unique experimental conditions for the study of condensed phase transitions in two dimensions. They are the only system in which the hexatic has been unambiguously identified as a phase of matter, and the only physical system in which fluctuations of a 2D XY system and Kosterlitz Thouless phase transition has been observed and 2D XY quasi long range order verified. Smectic films have enabled the precise determination of smectic layer electron density and positional fluctuation profile and have been used to show that the interlayer interactions in anti-ferroelectric tilted smectics do not extend significantly beyond nearest neighbors. The interactions which are operative in liquid crystals are generally weak in comparison to those in crystalline phases, leading to the facile manipulation of the order in liquid crystals by external agents such as applied fields and surfaces. Effects arising from weak ordering are significantly enhanced in ultrathin free films and filaments wherein the intermolecular coupling is effectively reduced by loss of neighbors. Over the past four years this research, which we now detail, has produced a host of exciting new discoveries and unexpected results, maintaining the position of the study of freely suspended liquid crystal structures as one of most exciting and fruitful areas of complex fluid physics. In addition, several potentially interesting microgravity free film experiments have been identified.

  18. The optical Tamm states in a photonic-crystal Structure based on the cholesteric liquid crystal

    E-print Network

    Vetrov, Stepan Ya; Timofeev, Ivan V

    2015-01-01

    We investigate the localized surface modes in a structure consisting of the cholesteric liquid crystal layer, a phase plate, and a metal layer. These modes are analogous to the optical Tamm states. The anisotropy of transmission of light propagating the forward and backward directions is established. It is demonstrated that the transmission spectrum can be controlled by external fields acting on the cholesteric and by varying the plane of polarization of the incident light. [The text is presented both in English (pp 1-10) and in Russian (pp 11-20)

  19. Crystal structure and phase transitions in Sr3WO6.

    PubMed

    King, Graham; Abakumov, Artem M; Hadermann, J; Alekseeva, Anastasiya M; Rozova, Marina G; Perkisas, Tyche; Woodward, Patrick M; Van Tendeloo, Gustaaf; Antipov, Evgeny V

    2010-07-01

    The crystal structures of the beta and gamma polymorphs of Sr(3)WO(6) and the gamma<-->beta phase transition have been investigated using electron diffraction, synchrotron X-ray powder diffraction, and neutron powder diffraction. The gamma-Sr(3)WO(6) polymorph is stable above T(c) approximately 470 K and adopts a monoclinically distorted double perovskite A(2)BB'O(6) = Sr(2)SrWO(6) structure (space group Cc, a = 10.2363(1)A, b = 17.9007(1)A, c = 11.9717(1)A, beta = 125.585(1)(o) at T = 1373 K, Z = 12, corresponding to a = a(p) + 1/2b(p) - 1/2c(p), b = 3/2b(p) + 3/2c(p), c = -b(p) + c(p), a(p),b(p), c(p), lattice vectors of the parent Fm3m double perovskite structure). Upon cooling it undergoes a continuous phase transition into the triclinically distorted beta-Sr(3)WO(6) phase (space group C1, a = 10.09497(3)A, b = 17.64748(5)A, c = 11.81400(3)A, alpha = 89.5470(2)(o), beta = 125.4529(2)(o), gamma = 90.2889(2)(o) at T = 300 K). Both crystal structures of Sr(3)WO(6) belong to a family of double perovskites with broken corner sharing connectivity of the octahedral framework. A remarkable feature of the gamma-Sr(3)WO(6) structure is a non-cooperative rotation of the WO(6) octahedra. One third of the WO(6) octahedra are rotated by approximately 45 degrees about either the b(p) or the c(p) axis of the parent double perovskite structure. As a result, the WO(6) octahedra do not share corners but instead share edges with the coordination polyhedra of the Sr cations at the B positions increasing their coordination number from 6 to 7 or 8. The crystal structure of the beta-phase is very close to the structure of the gamma-phase; decreasing symmetry upon the gamma-->beta transformation occurs because of unequal octahedral rotation angles about the b(p) and c(p) axes and increasing distortions of the WO(6) octahedra. PMID:20527961

  20. Effect of Plastic Deformation on the Crystal Structure and Crystallization Activation Energy of Ni-W-P Alloy Coating

    NASA Astrophysics Data System (ADS)

    Wang, Yuehua; Yu, Meiqi; Qiao, Qi; You, Fei; Li, Cailing; Xu, Zhefeng; Matsugi, Kazuhiro; Yu, Jinku

    2015-05-01

    Jet electrodeposition method was used to prepare Ni-W-P amorphous alloy coating and effects of plastic deformation on the crystal structure and crystallization kinetics were investigated. Based on the results of differential scanning calorimeter, x-ray diffractometer and transmission electron microscope, it can be seen that when the plastic deformation is up to 20%, the Ni-W-P amorphous alloy coating begins to crystallize. An increase of plastic deformation will lead to a decrease of crystallization temperature as well as a decrease of crystallization activation energy calculated by Kissinger equation. The effective activation energy is reduced from 268.63 kJ/mol in the as-deposited state to 246.63 kJ/mol in the cold deformation up to 40%. Analyses were presented to discuss the possible mechanism for the effect of plastic deformation on the crystallization kinetics of the Ni-W-P amorphous alloy coatings.

  1. Surface and zeta-potentials of silver halide single crystals: pH-dependence in comparison to particle systems.

    PubMed

    Selmani, Atiða; Lützenkirchen, Johannes; Kallay, Nikola; Preo?anin, Tajana

    2014-06-18

    We have carried out surface and zeta-potential measurements on AgCl and AgBr single crystals. As for particle systems we find that, surprisingly and previously unnoted, the zeta-potential exhibits pH-dependence, while the surface potential does not. A possible interpretation of these observations is the involvement of water ions in the interfacial equilibria and in particular, stronger affinity of the hydroxide ion compared to the proton. The pH-dependence of the zeta-potential can be suppressed at sufficiently high silver concentrations, which agrees with previous measurements in particle systems where no pH-dependence was found at high halide ion concentrations. The results suggest a subtle interplay between the surface potential determining the halide and silver ion concentrations, and the water ions. Whenever the charge due to the halide and silver ions is sufficiently high, the influence of the proton/hydroxide ion on the zeta-potential vanishes. This might be related to the water structuring at the relevant interfaces which should be strongly affected by the surface potential. Another interesting observation is accentuation of the assumed water ion effect on the zeta-potential at the flat single crystal surfaces compared to the corresponding silver halide colloids. Previous generic MD simulations have indeed predicted that hydroxide ion adsorption is accentuated on flat/rigid surfaces. A thermodynamic model for AgI single crystals was developed to describe the combined effects of iodide, silver and water ions, based on two independently previously published models for AgI (that only consider constituent and background electrolyte ions) and inert surfaces (that only consider water and background electrolyte ions). The combined model correctly predicts all the experimentally observed trends. PMID:24863080

  2. Forming Nanocrystalline Structures in Metal Particle Impact

    NASA Astrophysics Data System (ADS)

    Lemiale, Vincent; Estrin, Yuri; Kim, Hyoung Seop; O'Donnell, Robert

    2011-10-01

    Grain refinement by plastic deformation is becoming increasingly popular as a way of producing metals with improved properties, such as higher mechanical strength. Surface treatment techniques in which a metallic substrate is bombarded with metallic particles can generate nanocrystalline layers in the impact zone. Understanding the physical mechanisms underlying this grain refinement is crucial for achieving an improvement of existing experimental processes. In this article, we propose a numerical framework combining finite element (FE) simulations with a dislocation-based material model to predict the evolution of the microstructure under particle impact. A single particle normally impacting on a metallic substrate was simulated at different initial velocities. The simulations were compared with previously reported numerical and experimental data. The results indicate that our model accurately captures the grain refinement in the impact zone for a broad range of velocities. This approach provides valuable information on the formation of nanocrystalline layers in both the substrate and the impacting particle. Its potential applications include processes involving surface treatment by high velocity particles, such as shot peening, surface mechanical attrition treatment, kinetic metallization, cold spray, etc.

  3. Low Temperature Crystal Structure and Magnetic Properties of RAl2

    SciTech Connect

    Pathak, Arjun K. [Ames Laboratory; Paudyal, Durga [Ames Laboratory; Gschneidner, Karl A. [Ames Laboratory; Pecharsky, Vitalij K. [Ames Laboratory

    2014-01-08

    Low temperature crystal structure and magnetic properties of RAl2 (R?=?Pr and Nd) have been studied using temperature dependent powder x-ray diffraction, magnetization, and heat capacity measurements. Unlike PrAl2, NdAl2 retains cubic MgCu2-type structure from room temperature down to 5?K, which is also confirmed from first principles electronic structure calculations. The magnetization measurements show both PrAl2 and NdAl2 order ferromagnetically at TC?=?32?K and 77?K, respectively. However, the magnetization measurements show the former is a hard ferromagnet compared to the latter which is a soft ferromagnetic material. The magnetic entropy change obtained from heat capacity measurements at ?H?=?30 kOe for PrAl2 and NdAl2 are 3.15?J?mol?1 K?1 and 1.18?J?mol?1 K?1, respectively.

  4. Crystal Structure of Antagonist Bound Human Lysophosphatidic Acid Receptor 1.

    PubMed

    Chrencik, Jill E; Roth, Christopher B; Terakado, Masahiko; Kurata, Haruto; Omi, Rie; Kihara, Yasuyuki; Warshaviak, Dora; Nakade, Shinji; Asmar-Rovira, Guillermo; Mileni, Mauro; Mizuno, Hirotaka; Griffith, Mark T; Rodgers, Caroline; Han, Gye Won; Velasquez, Jeffrey; Chun, Jerold; Stevens, Raymond C; Hanson, Michael A

    2015-06-18

    Lipid biology continues to emerge as an area of significant therapeutic interest, particularly as the result of an enhanced understanding of the wealth of signaling molecules with diverse physiological properties. This growth in knowledge is epitomized by lysophosphatidic acid (LPA), which functions through interactions with at least six cognate G protein-coupled receptors. Herein, we present three crystal structures of LPA1 in complex with antagonist tool compounds selected and designed through structural and stability analyses. Structural analysis combined with molecular dynamics identified a basis for ligand access to the LPA1 binding pocket from the extracellular space contrasting with the proposed access for the sphingosine 1-phosphate receptor. Characteristics of the LPA1 binding pocket raise the possibility of promiscuous ligand recognition of phosphorylated endocannabinoids. Cell-based assays confirmed this hypothesis, linking the distinct receptor systems through metabolically related ligands with potential functional and therapeutic implications for treatment of disease. PMID:26091040

  5. Modulated structures of flexoelectric origin in nematic liquid crystals.

    PubMed

    Barbero, G; Lelidis, I

    2003-06-01

    A structural instability of flexoelectric origin is predicted in a homeotropic cell, of insulating nematic liquid crystal, by the action of an electric field applied in the direction of the initially nonperturbed nematic director. The instability gives rise to a two-dimensional periodic structure. The critical field to observe the predicted modulated structure as well as the wavelength at the threshold are evaluated. Both vary as the inverse square root of the cell thickness. The role of the dielectric anisotropy on the phenomenon is investigated. Our analysis is performed in the limit of weak anchoring energy strength, where the extrapolation length is large with respect to the thickness of the nematic sample. PMID:16241245

  6. Crystal structure of deglycosylated human IgG4-Fc

    PubMed Central

    Davies, Anna M.; Jefferis, Roy; Sutton, Brian J.

    2014-01-01

    The Fc region of IgG antibodies, important for effector functions such as antibody-dependent cell-mediated cytotoxicity, antibody-dependent cellular phagocytosis and complement activation, contains an oligosaccharide moiety covalently attached to each CH2 domain. The oligosaccharide not only orients the CH2 domains but plays an important role in influencing IgG effector function, and engineering the IgG-Fc oligosaccharide moiety is an important aspect in the design of therapeutic monoclonal IgG antibodies. Recently we reported the crystal structure of glycosylated IgG4-Fc, revealing structural features that could explain the anti-inflammatory biological properties of IgG4 compared with IgG1. We now report the crystal structure of enzymatically deglycosylated IgG4-Fc, derived from human serum, at 2.7 ? resolution. Intermolecular CH2-CH2 domain interactions partially bury the CH2 domain surface that would otherwise be exposed by the absence of oligosaccharide, and two Fc molecules are interlocked in a symmetric, open conformation. The conformation of the CH2 domain DE loop, to which oligosaccharide is attached, is altered in the absence of carbohydrate. Furthermore, the CH2 domain FG loop, important for Fc? receptor and C1q binding, adopts two different conformations. One loop conformation is unique to IgG4 and would disrupt binding, consistent with IgG4's anti-inflammatory properties. The second is similar to the conserved conformation found in IgG1, suggesting that in contrast to IgG1, the IgG4 CH2 FG loop is dynamic. Finally, crystal packing reveals a hexameric arrangement of IgG4-Fc molecules, providing further clues about the interaction between C1q and IgG. PMID:24956411

  7. Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus.

    PubMed

    Tahirov, T H; Oki, H; Tsukihara, T; Ogasahara, K; Yutani, K; Ogata, K; Izu, Y; Tsunasawa, S; Kato, I

    1998-11-20

    The structure of methionine aminopeptidase from hyperthermophile Pyrococcus furiosus (PfMAP) with an optimal growth temperature of 100 degreesC was determined by the multiple isomorphous replacement method and refined in three different crystal forms, one monoclinic and two hexagonal, at resolutions of 2.8, 2.9, and 3.5 A. The resolution of the monoclinic crystal form was extended to 1.75 A by water-mediated transformation to a low-humidity form, and the obtained diffraction data used for high-resolution structure refinement. This is the first description of a eukaryotic type methionine aminopeptidase structure. The PfMAP molecule is composed of two domains, a catalytic domain and an insertion domain, connected via two antiparallel beta-strands. The catalytic domain, which possesses an internal 2-fold symmetry and contains two cobalt ions in the active site, resembles the structure of a prokaryotic type MAP from Escherichia coli (EcMAP), while the structure of the insertion domain containing three helices has a novel fold and accounts for a major difference between the eukaryotic and prokaryotic types of methionine aminopeptidase. Analysis of the PfMAP structure in comparison with EcMAP and other mesophile proteins reveals several factors which may contribute to the hyperthermostability of PfMAP: (1) a significantly high number of hydrogen bonds and ion-pairs between side-chains of oppositely charged residues involved in the stabilization of helices; (2) an increased number of hydrogen bonds between the positively charged side-chain and neutral oxygen; (3) a larger number of buried water molecules involved in crosslinking the backbone atoms of sequentially separate segments; (4) stabilization of two antiparallel beta-strands connecting the two domains of the molecule by proline residues; (5) shortening of N and C-terminal tails and stabilization of the loop c3E by deletion of three residues. PMID:9811545

  8. Refinement of the crystal structure of lithium-bearing uvite

    SciTech Connect

    Rozhdestvenskaya, I. V., E-mail: ivrozhdestvenska@mail.ru; Frank-Kamenetskaya, O. V. [St. Petersburg State University, Department of Crystallography (Russian Federation); Kuznetsova, L. G. [Russian Academy of Sciences, Vinogradov Institute of Geochemistry, Siberian Division (Russian Federation); Bannova, I. I.; Bronzova, Yu. M. [St. Petersburg State University, Department of Crystallography (Russian Federation)

    2007-03-15

    The crystal structure of a natural calcium tourmaline, i.e., uvite with a high lithium content (0.51 au per formula (aupf) at the Y site, is refined to R = 0.019, R{sub w} = 0.020, and S = 1.11. It is shown that, in nature, there exist uvites in which the charge balance in the case where the Z site is occupied by trivalent cations is provided by the replacement of part of the divalent magnesium cations at the Y site by univalent cations, divalent calcium cations at the X site by sodium cations, and univalent anions at the W site by oxygen anions. The W site is found to be split into two sites, namely, the W1 and W11 sites (the W1-W11 distance is 0.14 A), which are partially occupied by the fluorine and oxygen anions, respectively. An analysis of the results obtained in this study and the data available in the literature on the crystal structure of uvites allows the conclusion that uvite can be considered a superspecies and that the nomenclature of this mineral group needs refinement with the use of structural data.

  9. Crystal Structure of the Monomeric Porin OmpG

    SciTech Connect

    Subbarao,G.; van den Berg, B.

    2006-01-01

    The outer membrane (OM) of Gram-negative bacteria contains a large number of channel proteins that mediate the uptake of ions and nutrients necessary for growth and functioning of the cell. An important group of OM channel proteins are the porins, which mediate the non-specific, diffusion-based passage of small (<600 Da) polar molecules. All porins of Gram-negative bacteria that have been crystallized to date form stable trimers, with each monomer composed of a 16-stranded {beta}-barrel with a relatively narrow central pore. In contrast, the OmpG porin is unique, as it appears to function as a monomer. We have determined the X-ray crystal structure of OmpG from Escherichia coli to a resolution of 2.3 Angstroms. The structure shows a 14-stranded {beta}{beta}-barrel with a relatively simple architecture. Due to the absence of loops that fold back into the channel, OmpG has a large ({approx}13 Angstroms) central pore that is considerably wider than those of other E. coli porins, and very similar in size to that of the toxin a-hemolysin. The architecture of the channel, together with previous biochemical and other data, suggests that OmpG may form a non-specific channel for the transport of larger oligosaccharides. The structure of OmpG provides the starting point for engineering studies aiming to generate selective channels and for the development of biosensors.

  10. Crystal structure of bovine coronavirus spike protein lectin domain.

    PubMed

    Peng, Guiqing; Xu, Liqing; Lin, Yi-Lun; Chen, Lang; Pasquarella, Joseph R; Holmes, Kathryn V; Li, Fang

    2012-12-01

    The spike protein N-terminal domains (NTDs) of bovine coronavirus (BCoV) and mouse hepatitis coronavirus (MHV) recognize sugar and protein receptors, respectively, despite their significant sequence homology. We recently determined the crystal structure of MHV NTD complexed with its protein receptor murine carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1), which surprisingly revealed a human galectin (galactose-binding lectin) fold in MHV NTD. Here, we have determined at 1.55 ? resolution the crystal structure of BCoV NTD, which also has the human galectin fold. Using mutagenesis, we have located the sugar-binding site in BCoV NTD, which overlaps with the galactose-binding site in human galectins. Using a glycan array screen, we have identified 5-N-acetyl-9-O-acetylneuraminic acid as the preferred sugar substrate for BCoV NTD. Subtle structural differences between BCoV and MHV NTDs, primarily involving different conformations of receptor-binding loops, explain why BCoV NTD does not bind CEACAM1 and why MHV NTD does not bind sugar. These results suggest a successful viral evolution strategy in which coronaviruses stole a galectin from hosts, incorporated it into their spike protein, and evolved it into viral receptor-binding domains with altered sugar specificity in contemporary BCoV or novel protein specificity in contemporary MHV. PMID:23091051

  11. Refinement of the mangan-neptunite crystal structure

    NASA Astrophysics Data System (ADS)

    Zolotarev, A. A.; Krivovichev, S. V.; Yakovenchuk, V. N.

    2007-12-01

    The crystal structure of mangan-neptunite, a manganese analogue of neptunite, has been refined in two space groups ( Cc and C2/ c). The mineral is monoclinic, with the correct space group Cc; the unit-cell dimensions are: a = 16.4821(6), b = 12.5195(4), c = 10.0292(3) Å, ? = 115.474(1)°, and V = 1868.31 Å3. The crystal structure has been refined to R 1 = 0.0307 ( wR 2 = 0.0901) on the basis of 4892 observed reflections with | F hkl | ? 4?| F hkl |. The most plausible acentric model is caused by the Ti- and (Fe, Mn, Mg)-ordering in the structure. Ti-octahedrons are strongly distorted and consist of short bond Ti-O (1.7 Å), one long bond (2.2 Å), and four equal bonds (2.0 Å). Fe-octahedrons are regularly shaped, with all Fe-O bonds being approximately identical.

  12. Crystal structure and spectroscopic investigations of an organic monophosphate

    SciTech Connect

    Dhaouadi, H. [Laboratoire de Chimie des Materiaux, Faculte des Sciences, 7021 Zarzouna, Bizerte (Tunisia); Marouani, H. [Laboratoire de Chimie des Materiaux, Faculte des Sciences, 7021 Zarzouna, Bizerte (Tunisia)], E-mail: houda.marouani@fsb.rnu.tn; Rzaigui, M. [Laboratoire de Chimie des Materiaux, Faculte des Sciences, 7021 Zarzouna, Bizerte (Tunisia); Madani, A. [Laboratoire de Physique des Materiaux, Faculte des Sciences, 7021 Zarzouna, Bizerte (Tunisia)

    2008-12-01

    Single crystals of (p-ClC{sub 6}H{sub 4}NH{sub 3})H{sub 2}PO{sub 4} are synthesized in water by interaction of H{sub 3}PO{sub 4} and (p-ClC{sub 6}H{sub 4}NH{sub 2}). This compound crystallizes in the orthorhombic system with the Pbca space group. Its unit-cell parameters are a = 9.724(3), b = 7.861(1), c = 25.078(6) A, V = 1917.1(6) A{sup 3} and Z = 8. The crystal structure has been solved and refined to R = 0.039, using 4298 independent reflections. The atomic arrangement can be described by inorganic layers parallel to ab plane, between which the organic cations are located. This compound exhibits a reversible phase transition at 403 K. The electrical conductivity measurements show that the (p-ClC{sub 6}H{sub 4}NH{sub 3})H{sub 2}PO{sub 4} has a conductivity value which goes from {sigma} = 0.88 x 10{sup -6} {omega}{sup -1} cm{sup -1} at room temperature (293 K) to 3.31 x 10{sup -4} {omega}{sup -1} cm{sup -1} at 433 K. Its characterisation by TA, NMR and IR is reported too.

  13. Phase-field-crystal methodology for modeling of structural transformations

    NASA Astrophysics Data System (ADS)

    Greenwood, Michael; Rottler, Jörg; Provatas, Nikolas

    2011-03-01

    We introduce and characterize free-energy functionals for modeling of solids with different crystallographic symmetries within the phase-field-crystal methodology. The excess free energy responsible for the emergence of periodic phases is inspired by classical density-functional theory, but uses only a minimal description for the modes of the direct correlation function to preserve computational efficiency. We provide a detailed prescription for controlling the crystal structure and introduce parameters for changing temperature and surface energies, so that phase transformations between body-centered-cubic (bcc), face-centered-cubic (fcc), hexagonal-close-packed (hcp), and simple-cubic (sc) lattices can be studied. To illustrate the versatility of our free-energy functional, we compute the phase diagram for fcc-bcc-liquid coexistence in the temperature-density plane. We also demonstrate that our model can be extended to include hcp symmetry by dynamically simulating hcp-liquid coexistence from a seeded crystal nucleus. We further quantify the dependence of the elastic constants on the model control parameters in two and three dimensions, showing how the degree of elastic anisotropy can be tuned from the shape of the direct correlation functions.

  14. Natural pseudowollastonite: Crystal structure, associated minerals, and geological context

    NASA Astrophysics Data System (ADS)

    Seryotkin, Yurii V.; Sokol, Ella V.; Kokh, Svetlana N.

    2012-03-01

    Pseudowollastonite, an extremely rare constituent of ultrahigh-temperature combustion metamorphic and igneous rocks, has been found as a rock-forming mineral in Ca-rich paralava veins of Nabi Musa fossil mud volcano (Dead Sea area). Pseudowollastonite-bearing paralavas are the products of combustion metamorphism associated with spontaneous burning of methane. The melt began to crystallize at 1480-1500 °C about the ambient pressure. Pseudowollastonite enters two mineral assemblages: (1) rankinite, larnite, nagelschmidtite, wollastonite (1T), gehlenite-rich melilite, Ti-rich andradite, cuspidine, and fluorapatite; (2) parawollastonite (2M), wollastonite (1T), gehlenite-rich melilite, Ti-rich andradite, fluorellestadite. In this study we present the first single-crystal structure determination of natural pseudowollastonite. Pseudowollastonite from Nabi Musa dome is stoichiometric CaSiO3 and belongs to the most widespread four-layer polytype: a = 6.83556(10) Å, b = 11.86962(18) Å, c = 19.6255(3) Å, ? = 90.6805(13)°, V = 1592.21(4) Å3, space group C2/c. We argue that pseudowollastonite is so scarce in nature because its formation requires joint action of several uncommon factors: availability of hot melts of T > 1200 °C that bear free calcium but are poor in Mg and Fe (mostly as Fe3 +) and their crystallization in the shallow crust followed by quenching.

  15. Crystal structure of S,N-dibenzyl-d-penicillamine monohydrate

    PubMed Central

    Yoshinari, Nobuto; Konno, Takumi

    2014-01-01

    In the asymmetric unit of the title compound, C19H23NO2S·H2O, there are two independent organic mol­ecules and two water mol­ecules. Both organic mol­ecules exist as the zwitterionic form. The dihedral angles between the planes of the rings in the organic mol­ecules are 86.84?(10) and 88.77?(11)°. An intramolecular N—H?S hydrogen bond occurs. In the crystal, organic and water mol­ecules are linked by N—H?O and O—H?O hydrogen bonds, generating a tape structure running along the b-axis direction. PMID:25484833

  16. A neutron diffraction study of the crystal structure of ferrocene

    E-print Network

    Takusagawa, Fusao; Koetzle, Thomas F.

    1979-05-01

    . E. (1968) . Acta Chem. Scand. 22, 2 6 5 3 - 2 6 7 0 . HOLM, C. H. & IBERS, J. A . (1959) . J. Chem. Phys. 30, 885-888. HYAMS, I. J. & RON, A . (1973) . J. Chem. Phys. 59, 3027- 3030. JOHNSON, C . K. (1965) . ORTEP. Report ORNL-3794. Oak Ridge..., in agree-ment with the results of earlier electron diffraction studies [Bohn & Haaland (1966). J. Organomet. Chem. 5, 470-476; Haaland & Nilsson (1968). Acta Chem. Scand. 22, 2653-2670]. The crystal structure is dis- * Research carried out at Brookhaven...

  17. Crystal structure of hexa-aqua-dichlorido-ytterbium(III) chloride.

    PubMed

    Knopf, Kevin M; Crundwell, Guy; Westcott, Barry L

    2015-06-01

    The crystal structure of the title compound, [YbCl2(H2O)6]Cl, was determined at 110?K. Samples were obtained from evaporated aceto-nitrile solutions containing the title compound, which consists of a [YbCl2(H2O)6](+) cation and a Cl(-) anion. The cations in the title compound sit on a twofold axis and form O-H?Cl hydrogen bonds with the nearby Cl(-) anion. The coordination geometry around the metal centre forms a distorted square anti-prism. The ytterbium complex is isotypic with the europium complex [Tambrornino et al. (2014 ?). Acta Cryst. E70, i27]. PMID:26090164

  18. Crystal structure of hexa­aqua­dichlorido­ytterbium(III) chloride

    PubMed Central

    Knopf, Kevin M.; Crundwell, Guy; Westcott, Barry L.

    2015-01-01

    The crystal structure of the title compound, [YbCl2(H2O)6]Cl, was determined at 110?K. Samples were obtained from evaporated aceto­nitrile solutions containing the title compound, which consists of a [YbCl2(H2O)6]+ cation and a Cl? anion. The cations in the title compound sit on a twofold axis and form O—H?Cl hydrogen bonds with the nearby Cl? anion. The coordination geometry around the metal centre forms a distorted square anti­prism. The ytterbium complex is isotypic with the europium complex [Tambrornino et al. (2014 ?). Acta Cryst. E70, i27]. PMID:26090164

  19. Crystal Structure of the Pseudomonas aeruginosa Virulence Factor Regulator ?†

    PubMed Central

    Cordes, Timothy J.; Worzalla, Gregory A.; Ginster, Aaron M.; Forest, Katrina T.

    2011-01-01

    Virulence factor regulator (Vfr) enhances Pseudomonas aeruginosa pathogenicity through its role as a global transcriptional regulator. The crystal structure of Vfr shows that it is a winged-helix DNA-binding protein like its homologue cyclic AMP receptor protein (CRP). In addition to an expected primary cyclic AMP-binding site, a second ligand-binding site is nestled between the N-terminal domain and the C-terminal helix-turn-helix domain. Unlike CRP, Vfr is a symmetric dimer in the absence of DNA. Removal of seven disordered N-terminal residues of Vfr prevents the growth of P. aeruginosa. PMID:21665969

  20. Structural, mechanical and light yield characterisation of heat treated LYSO:Ce single crystals for medical imaging applications

    NASA Astrophysics Data System (ADS)

    Mengucci, P.; André, G.; Auffray, E.; Barucca, G.; Cecchi, C.; Chipaux, R.; Cousson, A.; Davì, F.; Di Vara, N.; Rinaldi, D.; Santecchia, E.

    2015-06-01

    Five single crystals of cerium-doped lutetium yttrium oxyorthosilicate (LYSO:Ce) grown by the Czochralski method were submitted to structural characterisation by X-ray (XRD) and neutron (ND) diffraction, scanning (SEM) and transmission (TEM) electron microscopy and energy dispersive microanalysis (EDS). The Ultimate Tensile Strength (UTS), the Young Modulus (YM) and the Light Yield (LY) of the samples were also measured in order to correlate the mechanical and the optical behaviour of the crystals with the characteristics of their microstructure. Two of the samples analysed were also heat treated at 300 °C for 10 h to evidence possible variations induced by the temperature in the optical and mechanical response of the crystals. Results showed that the mean compositional variations evidenced by the structural analyses do not affect the mechanical and optical behaviour of the samples. On the contrary, the thermal treatment could induce the formation of coherent spherical particles (size 10 to 15 nm), not uniformly distributed inside the sample, that strongly reduce the UTS and YM values, but it does not affect the optical response of the crystal. This latter result was attributed to the low value of the heating temperature (300 °C) that is not sufficiently high to induce annealing of the oxygen vacancies traps that are responsible of the deterioration of the scintillation properties of the LYSO:Ce crystals. This study was carried out in the framework of the Crystal Clear Collaboration (CCC).

  1. Structure and Dynamics of Freely Suspended Liquid Crystals

    NASA Technical Reports Server (NTRS)

    Clark, Noel A.

    2004-01-01

    Smectic liquid crystals are phases of rod shaped molecules organized into one dimensionally (1 D) periodic arrays of layers, each layer being between one and two molecular lengths thick. In the least ordered smectic phases, the smectics A and C, each layer is a two dimensional (2D) liquid. Additionally there are a variety of more ordered smectic phases having hexatic short range translational order or 2D crystalline or quasi long range translational order within the layers. The inherent fluid-layer structure and low vapor pressure of smectic liquid crystals enables the long term stabilization of freely suspended, single component, layered fluid films as thin as 30A, a single molecular layer. The layering forces the films to be an integral number of smectic layers thick, quantizing their thickness in layer units and forcing a film of a particular number of layers to be physically homogeneous with respect to its layer structure over its entire area. Optical reflectivity enables the precise determination of the number of layers. These ultrathin freely suspended liquid crystal films are structures of fundamental interest in condensed matter and fluid physics. They are the thinnest known stable fluid structures and have the largest surface-to-volume ratio of any stable fluid preparation, making them ideal for the study of the effects of reduced dimensionality on phase behavior and on fluctuation and interface phenomena. Their low vapor pressure and quantized thickness enable the effective use of microgravity to extend the study of basic capillary phenomena to ultrathin fluid films. Freely suspended films have been a wellspring of new LC physics. They have been used to provide unique experimental conditions for the study of condensed phase transitions in two dimensions. They are the only system in which the hexatic has been unambiguously identified as a phase of matter, and the only physical system in which fluctuations of a 2D XY system and Kosterlitz Thouless phase transition has been observed and 2D XY quasi long range order verified. Smectic films have enabled the precise determination of smectic layer electron density and positional fluctuation profiles and have been used to show that the interlayer interactions in antiferroelectric tilted smectics do not extend significantly beyond nearest neighbors. Freely suspended films played a pivotal role in the recent discovery of macroscopic chiral-polar ordering in fluids of achiral molecules. The interactions which are operative in liquid crystals are generally weak in comparison to those in crystalline phases, leading to the facile manipulation of the order in liquid crystals by external agents such as applied fields and surfaces. Effects arising from weak ordering are significantly enhanced in ultrathin free films and filaments, in which the intermolecular coupling is effectively further reduced by loss of neighbors. Over the past four years this research, which we now detail, has produced a host of exciting new discoveries and unexpected results, maintaining the study of freely suspended liquid crystal structures as one of most exciting and fruitful areas of complex fluid physics. In addition, a class of experiments on the behavior of 1D interfaces in 2D films have been pursued with results that point to potentially quite interesting effects in microgravity.

  2. Probing the molecular structure of interfacial films and crystals

    NASA Astrophysics Data System (ADS)

    Wang, Anfeng

    The properties of outside surfaces were found to play an important role in the nucleation and crystallization processes. Thus controlling the surface properties would provide an effective means for crystal engineering. Hydrophobic surface is prepared by self-assembled monolayer (SAM) formation of octadecyltrichlorosilane (OTS) on silicon surface, with the hydrophobicity adjusted by the monolayer coverage. Silicon wafer treated by RCA method is hydrophilic, so are SAMs formed by two amine-terminated organosilanes on silicon. However these three hydrophilic surfaces are unstable, due to contamination of the amine-terminated SAMs and hydrolysis of RCA treated silicon. Polymethine dyes, BDH+Cl- and BDH +ClO4-, are synthesized and characterized by UV spectra and crystal morphology. They have identical UV spectrum in dilute solutions due to the same chromophore, and J-aggregation happens at much higher concentrations. IR spectra are analyzed to monitor the crystallization process of BDH+Cl- OTS SAM surface and the crystallization process of BDH+Cl- on substrates with varying hydrophobicity was monitored by optical microscopy and compared. Due to the extreme flexibility of polysiloxane, silicone surfactants can arrange themselves at the interfaces quickly to adopt configurations with minimum free energy. Polysiloxane is hydrophobic but not oleophilic, which makes them effective emulsifiers and stabilizers in aqueous and nonaqueous media. The interaction between an AFM Si3N4 tip and a hydrophobic surface in silicone polyether (SPE) solution in the presence of ethanol was investigated by Atomic Force Microscopy (AFM) force measurement. ABA triblock type and comb-type SPE surfactants, adsorbed at the liquid-solid interface, provide steric barriers, even with significant addition of ethanol. On the contrary, conventional low-molecular weight and polymeric alkyl surfactants display no steric barrier even in the presence of moderate amount of ethanol. This unique property makes SPEs to be used as emulsion-stabilizers in products or processes involving alcohols or other organic solvents. Formation of polymer brush structure at the interface is essential to the existence of steric barrier. ABA-type SPEs adopt buoy-anchor-buoy configuration to fulfill this requirement, and comb-type SPEs attach to hydrophobic surface with siloxane backbone with many polyether buoys. Both configurations contribute to the formation of polymer brush structure. As a general trend, increase of ethanol content leads to smaller force maximum and critical barrier thickness. ABA-type SPEs display better alcohol tolerance than comb-type ones. The incorporation of propylene oxide (PO) segments in the polyether chain was found to improve the alcohol tolerance. Two competing factors are involved upon ethanol content increase: extension of the polyether chain and reduction of adsorption density of the surfactants at the interface.

  3. Optical switching of near infrared light transmission in metamaterial-liquid crystal cell structure.

    PubMed

    Kang, Boyoung; Woo, J H; Choi, E; Lee, Hyun-Hee; Kim, E S; Kim, J; Hwang, Tae-Jong; Park, Young-Soon; Kim, D H; Wu, J W

    2010-08-01

    A metamaterial-liquid crystal cell structure is fabricated with the metamaterial as one of the liquid crystal alignment layers. Nano-sized double-split ring resonator in the metamaterial accommodates two distinct resonances in the near infrared regime. By adopting an azo-nematic liquid crystal in a twisted nematic liquid crystal cell structure, a photo-isomerization process is utilized to achieve an optical switching of light transmissions between two resonances. A single device of the metamaterial-liquid crystal cell structure has a potential application in the photonic switching in optical fiber telecommunications. PMID:20721037

  4. Designing ‘Smart’ Particles for the Assembly of Complex Macroscopic Structures**

    PubMed Central

    Barg, S.; Bell, R.; Weaver, J.; Walter, C.; Goyos, L.; Saiz, E.

    2013-01-01

    Surface functionalization with a branched copolymer surfactant is used to create responsive inorganic particles that can self-assemble in complex structures. The assembly process is triggered by a pH switch that reversibly activates multiple hydrogen bonds between ceramic particles and soft templates. PMID:23780923

  5. Evolving the Structure of the Particle Swarm Optimization Algorithms

    Microsoft Academic Search

    Laura Diosan; Mihai Oltean

    2006-01-01

    A new model for evolving the structure of a Particle Swarm Optimization (PSO) algorithm is proposed in this paper. The model is a hybrid technique that combines a Genetic Algorithm (GA) and a PSO algorithm. Each GA chromosome is an array encoding a meaning for updating the particles of the PSO algorithm. The evolved PSO algo- rithm is compared to

  6. Self-Assembly of Colloidal Particles on Template Structures

    NASA Technical Reports Server (NTRS)

    Yodh, Arjun G.

    2002-01-01

    I will discuss recent experiments from my lab, which use surface templates to induce ordered colloidal structures. Particle assembly driven by entropic depletion, fluid convection, and sedimentation will be described. Confocal microscopy was used to visualize most of these samples.

  7. Optical Crystals

    ERIC Educational Resources Information Center

    Bergsten, Ronald

    1974-01-01

    Discusses the production and structure of a sequence of optical crystals which can serve as one-, two-, and three-dimensional diffraction plates to illustrate diffraction patterns by using light rather than x-rays or particles. Applications to qualitative presentations of Laue theory at the secondary and college levels are recommended. (CC)

  8. Influence of colloidal particle transfer on the quality of self-assembling colloidal photonic crystal under confined condition

    NASA Astrophysics Data System (ADS)

    Zhao, Yong-Qiang; Li, Juan; Liu, Qiu-Yan; Dong, Wen-Jun; Chen, Ben-Yong; Li, Chao-Rong

    2015-02-01

    The relationship between colloidal particle transfer and the quality of colloidal photonic crystal (CPC) is investigated by comparing colloidal particle self-assembling under the vertical channel (VC) and horizontal channel (HC) conditions. Both the theoretical analyses and the experimental measurements indicate that crystal quality depends on the stability of mass transfer. For the VC, colloidal particle transfer takes place in a stable laminar flow, which is conducive to forming high-quality crystal. In contrast, it happens in an unstable turbulent flow for the HC. Crystals with cracks and an uneven surface formed under the HC condition can be seen from the images of a field emission scanning electron microscope (SEM) and a three-dimensional (3D) laser scanning microscope (LSM), respectively. Project supported by the National Natural Science Foundation of China (Grant Nos. 91122022 and 51172209) and the Program for Changjiang Scholars and Innovative Research Team in University (PCSIRT), China (Grant No. IRT13097).

  9. The crystal structure of {pi}-ErBO{sub 3}: New single-crystal data for an old problem

    SciTech Connect

    Pitscheider, Almut [Institut fuer Allgemeine, Anorganische und Theoretische Chemie, Leopold-Franzens-Universitaet Innsbruck, Innrain 52a, A-6020 Innsbruck (Austria); Kaindl, Reinhard [Institut fuer Mineralogie und Petrographie, Leopold-Franzens-Universitaet Innsbruck, Innrain 52, A-6020 Innsbruck (Austria); Oeckler, Oliver [Department Chemie, Ludwig-Maximilians-Universitaet Muenchen, Butenandtstrasse 5-13, D-81377 Muenchen (Germany); Huppertz, Hubert, E-mail: Hubert.Huppertz@uibk.ac.a [Institut fuer Allgemeine, Anorganische und Theoretische Chemie, Leopold-Franzens-Universitaet Innsbruck, Innrain 52a, A-6020 Innsbruck (Austria)

    2011-01-15

    Single crystals of the orthoborate {pi}-ErBO{sub 3} were synthesized from Er{sub 2}O{sub 3} and B{sub 2}O{sub 3} under high-pressure/high-temperature conditions of 2 GPa and 800 {sup o}C in a Walker-type multianvil apparatus. The crystal structure was determined on the basis of single-crystal X-ray diffraction data, collected at room temperature. The title compound crystallizes in the monoclinic pseudowollastonite-type structure, space group C2/c, with the lattice parameters a=1128.4(2) pm, b=652.6(2) pm, c=954.0(2) pm, and {beta}=112.8(1){sup o} (R{sub 1}=0.0124 and wR{sub 2}=0.0404 for all data). -- graphical abstract: The first satisfying single-crystal structure determination of {pi}-ErBO{sub 3} sheds light on the extensively discussed structure of {pi}-orthoborates. The application of light pressure during the solid state synthesis yielded in high-quality crystals, due to pressure-induced crystallization. Research highlights: {yields} High-quality single crystals of {pi}-ErBO{sub 3} were prepared via high-pressure-induced crystallization. {yields} At least five different space groups for the rare-earth {pi}-orthoborates are reported. {yields} {pi}-ErBO{sub 3} is isotypic to the pseudowollastonite-type CaSiO{sub 3}. {yields} Remaining ambiguities regarding the structure of the rare-earth {pi}-orthoborates are resolved.

  10. Phase behavior of lyotropic rigid-chain polymer liquid crystal studied by dissipative particle dynamics.

    PubMed

    Zhao, Tongyang; Wang, Xiaogong

    2011-12-28

    The phase behavior of lyotropic rigid-chain liquid crystal polymer was studied by dissipative particle dynamics (DPD) with variations of the solution concentration and temperature. A chain of fused DPD particles was used to represent each mesogenic polymer backbone surrounded with the strongly interacted solvent molecules. The free solvent molecules were modeled as independent DPD particles, where each particle includes a lump of solvent molecules with the volume roughly equal to the solvated polymer segment. The simulation shows that smectic-B (S(B)), smectic-A (S(A)), nematic (N), and isotropic (I) phases exist within certain regions in the temperature and concentration parameter space. The temperature-dependent S(B)?S(A), S(A)?N, and N?I phase transitions occur in the high concentration range. In the intermediate concentration range, the simulation shows coexistence of the anisotropic phases and isotropic phase, where the anisotropic phases can be the S(B), S(A), or N phases. Mole fraction and compositions of the coexisted phases are determined from the simulation, which indicates that concentration of rigid rods in isotropic phase increases as the temperature increases. By fitting the orientational distribution function of the systems, the biphasic coexistence is further confirmed. From the parameter ? obtained for the simulation, the distribution of the rigid rods in the two coexistence phases is quantitatively evaluated. By using model and simulation methods developed in this work, the phase diagrams of the lyotropic rigid-chain polymer liquid crystal are obtained. Incorporating the solvent particles in the DPD simulation is critical to predict the phase coexistence and obtain the phase diagrams. PMID:22225183

  11. Azimuthal structures of produced particles in heavy-ion interactions

    SciTech Connect

    Vokal, S., E-mail: vokal@sunhe.jinr.ru; Orlova, G. I. [VBLHEP, JINR (Russian Federation); Lehocka, S. [University of P. J. Safarik (Slovakia)

    2009-02-15

    The angular structures of particles produced in {sup 208}Pb at 158 A GeV/c and {sup 197}Au at 11.6 A GeV/c induced interactions with Ag(Br) nuclei in emulsion detector have been investigated. Nonstatistical well-ordered ring-like structures of produced particles in azimuthal plane of a collision have been found, and their parameters have been determined.

  12. Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: Photoconversion and signal transduction

    SciTech Connect

    Yang, Xiaojing; Kuk, Jane; Moffat, Keith (UC)

    2008-11-12

    Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria via reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here we report the crystal structure at 2.9 {angstrom} resolution of a bacteriophytochrome from Pseudomonas aeruginosa with an intact, fully photoactive photosensory core domain in its dark-adapted Pfr state. This structure reveals how unusual interdomain interactions, including a knot and an 'arm' structure near the chromophore site, bring together the PAS (Per-ARNT-Sim), GAF (cGMP phosphodiesterase/adenyl cyclase/FhlA), and PHY (phytochrome) domains to achieve Pr/Pfr photoconversion. The PAS, GAF, and PHY domains have topologic elements in common and may have a single evolutionary origin. We identify key interactions that stabilize the chromophore in the Pfr state and provide structural and mutational evidence to support the essential role of the PHY domain in efficient Pr/Pfr photoconversion. We also identify a pair of conserved residues that may undergo concerted conformational changes during photoconversion. Modeling of the full-length bacteriophytochrome structure, including its output histidine kinase domain, suggests how local structural changes originating in the photosensory domain modulate interactions between long, cross-domain signaling helices at the dimer interface and are transmitted to the spatially distant effector domain, thereby regulating its histidine kinase activity.

  13. Role of the Range in the Fluid-Crystal Coexistence for a Patchy Particle Model Flavio Romano,*,

    E-print Network

    Sciortino, Francesco

    Role of the Range in the Fluid-Crystal Coexistence for a Patchy Particle Model Flavio Romano.; Frenkel, D. J. Chem. Phys. 2003, 118, 9882.], a model representative of particles interacting via short-range orientational interactions, for several values of the interaction range. Similar to what has been found

  14. The introduction of structure types into the Inorganic Crystal Structure Database ICSD

    PubMed Central

    Allmann, Rudolf; Hinek, Roland

    2007-01-01

    Both the approach used and the progress made in the assignment of structure types to the crystal structures contained in the ICSD database are reported. Extending earlier work, an hierarchical set of criteria for the separation of isopointal structures into isoconfigurational structure types is used. It is shown how these criteria, which include the space group (number), Wyckoff sequence and Pearson symbol, c/a ratio, ? ranges, ANX formulae and, in certain cases, the necessary elements and forbidden elements, may be used to uniquely identify the representative structure types of the compounds contained in the ICSD database. PMID:17703075

  15. The crystal structure of NlpI A prokaryotic tetratricopeptide repeat protein with a globular fold

    E-print Network

    Mochrie, Simon

    The crystal structure of NlpI A prokaryotic tetratricopeptide repeat protein with a globular fold-dimensional structure of a globular protein. The NlpI struc- ture is also the first TPR structure from a prokaryote

  16. Structure of cleaved (001) USb2 single crystal

    SciTech Connect

    Chen, Shao-ping [Los Alamos National Laboratory; Hawley, Marilyn [Los Alamos National Laboratory; Bauer, Eric D [Los Alamos National Laboratory; Stockum, Phil B [STANFORD UNIV.; Manoharan, Hari C [STANFORD UNIV

    2009-01-01

    We have achieved what we believe to be the first atomic resolution STM images for a uranium compound taken at room temperature. The a, b, and c lattice parameters in the images confirm that the USb{sub 2} crystals cleave on the (001) basal plane as expected. The a and b dimensions were equal, with the atoms arranged in a cubic pattern. Our calculations indicate a symmetric cut between Sb planes to be the most favorable cleavage plane and U atoms to be responsible for most of the DOS measured by STM. Some strange features observed in the STM will be discussed in conjunction with ab initio calculations. The purpose of this work is to demonstrate the power of scanning tunneling microscopy (STM) techniques combined with a theoretical underpinning to determine the surface atomic structure and properties of actinide materials, such as the quasi 2-dimensional uranium dipnictide USb{sub 2} single crystal, thereby contributing to the understanding of their surface structural and electronic properties. The members of this interesting UX{sub 2} (X=P, As, Sb, Bi) series of compounds display dual localized and itinerant 5f electron behavior within the same compound due to the hybridization of the 5f orbitals with the conduction band. With the exception of UO{sub 2}, which has to be studied at elevated temperature to generate enough carriers for STM imaging, STM techniques have not been applied successfully to the characterization of the surface atomic structure of any other single crystal actinide compound, to the best of our knowledge. However, STM has been used to a limited extent for the study of some cerium compounds. STM probes electronic properties at the atomic level and can directly provide information about the local density of filled and empty states (LDOS) states simultaneously. A STM topograph provides the local atomic arrangement and spacing of the atoms on the surface, local defect structures (e.g. steps, vacancies, and kink sites) and the presence of contaminants, all of which are averaged over when probed in photoemission studies. The quasi two-dimensional USb{sub 2} has a layered tetragonal structure that is easily cleaved and has been extensively studied by a number of different techniques, such as resistivity, Hall effect measurements, photoemission and angle-resolved photoemission spectroscopy, de Haas-van Alphen, neutron diffraction, nuclear magnetic resonance, and U{sup 238} Mossbauer spectroscopy techniques. Here, we provide local information about the surfaces of this interesting compound, which we find to contain a high density of defects.

  17. Crystal structure of K[Hg(SCN)3] - a redetermination.

    PubMed

    Weil, Matthias; Häusler, Thomas

    2014-09-01

    The crystal structure of the room-temperature modification of K[Hg(SCN)3], potassium tri-thio-cyanato-mercurate(II), was redetermined based on modern CCD data. In comparison with the previous report [Zhdanov & Sanadze (1952 ?). Zh. Fiz. Khim. 26, 469-478], reliability factors, standard deviations of lattice parameters and atomic coordinates, as well as anisotropic displacement parameters, were revealed for all atoms. The higher precision and accuracy of the model is, for example, reflected by the Hg-S bond lengths of 2.3954?(11), 2.4481?(8) and 2.7653?(6)?Å in comparison with values of 2.24, 2.43 and 2.77?Å. All atoms in the crystal structure are located on mirror planes. The Hg(2+) cation is surrounded by four S atoms in a seesaw shape [S-Hg-S angles range from 94.65?(2) to 154.06?(3)°]. The HgS4 polyhedra share a common S atom, building up chains extending parallel to [010]. All S atoms of the resulting (1) ?[HgS2/1S2/2] chains are also part of SCN(-) anions that link these chains with the K(+) cations into a three-dimensional network. The K-N bond lengths of the distorted KN7 polyhedra lie between 2.926?(2) and 3.051?(3)?Å. PMID:25309170

  18. Crystal structures of superconducting sodium intercalates of hafnium nitride chloride

    SciTech Connect

    Oro-Sole, J. [Institut de Ciencia de Materials de Barcelona (CSIC), Campus UAB, 08193 Bellaterra (Spain); Frontera, C. [Institut de Ciencia de Materials de Barcelona (CSIC), Campus UAB, 08193 Bellaterra (Spain); Beltran-Porter, D. [Institut de Ciencia de Materials de la Universitat de Valencia, PO Box 2085, Poligono 'La Coma' s/n, 46980 Paterna (Spain); Lebedev, O.I. [EMAT, RUCA, Groenenborgerlaan 171, Antwerp 2020 (Belgium); Van Tendeloo, G. [EMAT, RUCA, Groenenborgerlaan 171, Antwerp 2020 (Belgium); Fuertes, A. [Institut de Ciencia de Materials de Barcelona (CSIC), Campus UAB, 08193 Bellaterra (Spain)]. E-mail: amparo.fuertes@icmab.es

    2006-05-25

    Sodium intercalation compounds of HfNCl have been prepared at room temperature in naphtyl sodium solutions in tetrahydrofuran and their crystal structure has been investigated by Rietveld refinement using X-ray powder diffraction data and high-resolution electron microscopy. The structure of two intercalates with space group R3-bar m and lattice parameters a=3.58131(6)A, c=57.752(6)A, and a=3.58791(8)A, c=29.6785(17)A is reported, corresponding to the stages 2 and 1, respectively, of Na{sub x}HfNCl. For the stage 2 phase an ordered model is presented, showing two crystallographically independent [HfNCl] units with an alternation of the Hf-Hf interlayer distance along the c-axis, according with the occupation by sodium atoms of one out of two van der Waals gaps. Both stages 1 and 2 phases are superconducting with critical temperatures between 20 and 24K, they coexist in different samples with proportions depending on the synthesis conditions, and show a variation in c spacing that can be correlated with the sodium stoichiometry. High-resolution electron microscopy images of the host and intercalated samples show bending of the HfNCl bilayers as well as stacking faults in some regions, which coexist in the same crystal with ordered domains.

  19. Crystal Structure of 3S-hydroxy-7 Melleine

    NASA Astrophysics Data System (ADS)

    Liu, Xiao-hong; Xu, Fang; Zhang, Yi; Liu, Li-hong; Huang, Hua-rong; She, Zhi-gang; Lin, Yong-cheng; Chan, Winglai

    2006-10-01

    A new compound, 3S-hydroxy-7 melleine was isolated from the endophytic fungus Xylariasp No.2508 from the mangrove tree on the South China Sea coast. It was the first time that this kind of compound was isolated from marine fungus. The structure was elucidated by NMR data, infrared spectrum (IR) and mass spectrometry (MS). In addition, its structure was determined by the single-crystal X-ray diffraction analysis. It crystallized in monoclinic, space group P21 with a=10.8884(19) Å, b=7.2284(13) Å, c=13.398(2) Å, ?=104.217(3)°, C10H10O4·H2O, Mr=212.20, V=1022.2(3) Å3, Z=4, Dc=1.379 mg/m3, F(000)=448, ?=0.112 mm-1, the final R=0.0498, ?R=0.101 for 2407 observed reflections (I>2?(I)). The molecular backbone of the compound includes a benzopyran ring. By comparing with the melting point and the optical rotation of the known 3R-hydroxy-7 melleine in literature, the absolute configuration of the compound was determined as 3S. It didn't exhibit antibacterial activity against Gram-positive bacterium Staphylococcus aureus at 200 ?g/disk in the preliminary test.

  20. Protein structure. Crystal structures of translocator protein (TSPO) and mutant mimic of a human polymorphism.

    PubMed

    Li, Fei; Liu, Jian; Zheng, Yi; Garavito, R Michael; Ferguson-Miller, Shelagh

    2015-01-30

    The 18-kilodalton translocator protein (TSPO), proposed to be a key player in cholesterol transport into mitochondria, is highly expressed in steroidogenic tissues, metastatic cancer, and inflammatory and neurological diseases such as Alzheimer's and Parkinson's. TSPO ligands, including benzodiazepine drugs, are implicated in regulating apoptosis and are extensively used in diagnostic imaging. We report crystal structures (at 1.8, 2.4, and 2.5 angstrom resolution) of TSPO from Rhodobacter sphaeroides and a mutant that mimics the human Ala(147)?Thr(147) polymorphism associated with psychiatric disorders and reduced pregnenolone production. Crystals obtained in the lipidic cubic phase reveal the binding site of an endogenous porphyrin ligand and conformational effects of the mutation. The three crystal structures show the same tightly interacting dimer and provide insights into the controversial physiological role of TSPO and how the mutation affects cholesterol binding. PMID:25635101

  1. Crystal structure of a phosphorylation-coupled saccharide transporter

    PubMed Central

    Cao, Yu; Jin, Xiangshu; Levin, Elena J.; Huang, Hua; Zong, Yinong; Quick, Matthias; Weng, Jun; Pan, Yaping; Love, James; Punta, Marco; Rost, Burkhard; Hendrickson, Wayne A.; Javitch, Jonathan A.; Rajashankar, Kanagalaghatta R.; Zhou, Ming

    2011-01-01

    Saccharides play a central role in the nutrition of all living organisms. Whereas several saccharide uptake systems are shared between the different phylogenetic kingdoms, the phosphoenolpyruvate-dependent phosphotransferase system exists almost exclusively in bacteria. This multi-component system includes an integral membrane protein EIIC that transports saccharides and assists in their phosphorylation. Here we present the crystal structure of an EIIC from Bacillus cereus that transports diacetylchitobiose. The EIIC is a homodimer, with an expansive interface formed between the N-terminal halves of the two protomers. The C-terminal half of each protomer has a large binding pocket that contains a diacetylchitobiose, which is occluded from both sides of the membrane with its site of phosphorylation near the conserved His250 and Glu334 residues. The structure shows the architecture of this important class of transporters, identifies the determinants of substrate binding and phosphorylation, and provides a framework for understanding the mechanism of sugar translocation. PMID:21471968

  2. Crystal Structure of a Phosphorylation-coupled Saccharide Transporter

    SciTech Connect

    Y Cao; X Jin; E Levin; H Huang; Y Zong; W Hendrickson; J Javitch; K Rajashankar; M Zhou; et al.

    2011-12-31

    Saccharides have a central role in the nutrition of all living organisms. Whereas several saccharide uptake systems are shared between the different phylogenetic kingdoms, the phosphoenolpyruvate-dependent phosphotransferase system exists almost exclusively in bacteria. This multi-component system includes an integral membrane protein EIIC that transports saccharides and assists in their phosphorylation. Here we present the crystal structure of an EIIC from Bacillus cereus that transports diacetylchitobiose. The EIIC is a homodimer, with an expansive interface formed between the amino-terminal halves of the two protomers. The carboxy-terminal half of each protomer has a large binding pocket that contains a diacetylchitobiose, which is occluded from both sides of the membrane with its site of phosphorylation near the conserved His250 and Glu334 residues. The structure shows the architecture of this important class of transporters, identifies the determinants of substrate binding and phosphorylation, and provides a framework for understanding the mechanism of sugar translocation.

  3. Crystal structure of the multifunctional G?5–RGS9 complex

    PubMed Central

    Cheever, Matthew L; Snyder, Jason T; Gershburg, Svetlana; Siderovski, David P; Harden, T Kendall; Sondek, John

    2009-01-01

    Regulators of G-protein signaling (RGS) proteins enhance the intrinsic GTPase activity of G protein ? (G?) subunits and are vital for proper signaling kinetics downstream of G protein–coupled receptors (GPCRs). R7 subfamily RGS proteins specifically and obligately dimerize with the atypical G protein ?5 (G?5) subunit through an internal G protein ? (G?)-subunit–like (GGL) domain. Here we present the 1.95-Å crystal structure of the G?5–RGS9 complex, which is essential for normal visual and neuronal signal transduction. This structure reveals a canonical RGS domain that is functionally integrated within a molecular complex that is poised for integration of multiple steps during G-protein activation and deactivation. PMID:18204463

  4. Crystals

    NSDL National Science Digital Library

    Lawrence Hall of Science

    2009-01-01

    In this earth science/math/art activity, learners use simple ingredients to grow crystals and examine the repeating geometric shapes and patterns. Learners compare the growth of crystals from four types of crystal-starters (table salt, Borax, sand, and Epsom salt) to see which starter grows the most crystals in 14 days. Learners report their results online and find out what other learners discovered. Afterward, learners can use the crystals they grew to create works of art.

  5. Automated High Throughput Protein Crystallization Screening at Nanoliter Scale and Protein Structural Study on Lactate Dehydrogenase

    SciTech Connect

    Fenglei Li

    2006-08-09

    The purposes of our research were: (1) To develop an economical, easy to use, automated, high throughput system for large scale protein crystallization screening. (2) To develop a new protein crystallization method with high screening efficiency, low protein consumption and complete compatibility with high throughput screening system. (3) To determine the structure of lactate dehydrogenase complexed with NADH by x-ray protein crystallography to study its inherent structural properties. Firstly, we demonstrated large scale protein crystallization screening can be performed in a high throughput manner with low cost, easy operation. The overall system integrates liquid dispensing, crystallization and detection and serves as a whole solution to protein crystallization screening. The system can dispense protein and multiple different precipitants in nanoliter scale and in parallel. A new detection scheme, native fluorescence, has been developed in this system to form a two-detector system with a visible light detector for detecting protein crystallization screening results. This detection scheme has capability of eliminating common false positives by distinguishing protein crystals from inorganic crystals in a high throughput and non-destructive manner. The entire system from liquid dispensing, crystallization to crystal detection is essentially parallel, high throughput and compatible with automation. The system was successfully demonstrated by lysozyme crystallization screening. Secondly, we developed a new crystallization method with high screening efficiency, low protein consumption and compatibility with automation and high throughput. In this crystallization method, a gas permeable membrane is employed to achieve the gentle evaporation required by protein crystallization. Protein consumption is significantly reduced to nanoliter scale for each condition and thus permits exploring more conditions in a phase diagram for given amount of protein. In addition, evaporation rate can be controlled or adjusted in this method during the crystallization process to favor either nucleation or growing processes for optimizing crystallization process. The protein crystals gotten by this method were experimentally proven to possess high x-ray diffraction qualities. Finally, we crystallized human lactate dehydrogenase 1 (H4) complexed with NADH and determined its structure by x-ray crystallography. The structure of LDH/NADH displays a significantly different structural feature, compared with LDH/NADH/inhibitor ternary complex structure, that subunits in LDH/NADH complex show open conformation or two conformations on the active site while the subunits in LDH/NADH/inhibitor are all in close conformation. Multiple LDH/NADH crystals were obtained and used for x-ray diffraction experiments. Difference in subunit conformation was observed among the structures independently solved from multiple individual LDH/NADH crystals. Structural differences observed among crystals suggest the existence of multiple conformers in solution.

  6. Crystal Structure and Inhibition Studies of Transglutaminase from Streptomyces mobaraense*

    PubMed Central

    Yang, Ming-Te; Chang, Cheng-Hsiang; Wang, Jiou Ming; Wu, Tung Kung; Wang, Yu-Kuo; Chang, Chin-Yuan; Li, TienHsiung Thomas

    2011-01-01

    The crystal structure of the microbial transglutaminase (MTGase) zymogen from Streptomyces mobaraense has been determined at 1.9-? resolution using the molecular replacement method based on the crystal structure of the mature MTGase. The overall structure of this zymogen is similar to that of the mature form, consisting of a single disk-like domain with a deep active cleft at the edge of the molecule. A major portion of the prosequence (45 additional amino acid residues at the N terminus of the mature transglutaminase) folds into an L-shaped structure, consisting of an extended N-terminal segment linked with a one-turn short helix and a long ?-helix. Two key residues in the short helix of the prosequence, Tyr-12 and Tyr-16, are located on top of the catalytic triad (Cys-110, Asp-301, and His-320) to block access of the substrate acyl donors and acceptors. Biochemical characterization of the mature MTGase, using N-?-benzyloxycarbonyl-l-glutaminylglycine as a substrate, revealed apparent Km and kcat/Km values of 52.66 mm and 40.42 mm?1 min?1, respectively. Inhibition studies using the partial prosequence SYAETYR and homologous sequence SQAETYR showed a noncompetitive inhibition mechanism with IC50 values of 0.75 and 0.65 mm, respectively, but no cross-linking product formation. Nevertheless, the prosequence homologous oligopeptide SQAETQR, with Tyr-12 and Tyr-16 each replaced with Gln, exhibited inhibitory activity with the formation of the SQAETQR-monodansylcadaverine fluorophore cross-linking product (SQAETQR-C-DNS). MALDI-TOF tandem MS analysis of SQAETQR-C-DNS revealed molecular masses corresponding to those of NSQAETQC-C-DNS and C-DNS-NQRC sequences, suggesting the incorporation of C-DNS onto the C-terminal Gln residue of the prosequence homologous oligopeptide. These results support the putative functional roles of both Tyr residues in substrate binding and inhibition. PMID:21193394

  7. Drying dissipative structures of lycopodium spore particles in aqueous dispersion.

    PubMed

    Okubo, Tsuneo; Kokufuta, Etsuo; Nakamuro, Masaharu; Yoshinaga, Kohji; Mizutani, Masashi; Tsuchida, Akira

    2010-10-15

    Drying dissipative structures of aqueous dispersions of lycopodium particles (31 microm in average diameter) from the spores of Lycopodium clavatum were studied as a function of the particle concentrations in the presence and the absence of sodium chloride. The drying patterns formed on a cover glass, a watch glass and a Petri glass dish were observed macroscopically and microscopically. Lycopodium particles were the combination of hemisphere and tetrahedron in their shape and possessed the weakly acidic groups on their surfaces. The vague broad ring structure was observed even for the very large colloidal particles, and their size on a cover glass decreased as particle concentration decreased. Microscopic drying patterns almost disappeared except the short chain-like patterns. These observations support that the convectional contribution on the dissipative drying pattern formation is still effective in the lycopodium suspensions, though the convectional forces in the suspension are very weak compared with the sedimentation forces. PMID:20598865

  8. Classification of HIV-1 Protease Crystal Structures Using Random Forest, Linear Discriminant Analysis and Logistic Regression

    E-print Network

    Kumar, Sunil

    Classification of HIV-1 Protease Crystal Structures Using Random Forest, Linear Discriminant of 70 HIV-1 protease crystal structures in terms of their structural descriptors to their complexed HIV on their complexed ligands. The selected descriptors would play a crucial role in understanding the HIV-1 protease

  9. Band gap widening by photonic crystal heterostructures composed of two dimensional holes and diamond structure

    NASA Astrophysics Data System (ADS)

    Chen, Shibin; Li, Dichen; Zhi-Hui, Yuan

    2013-06-01

    A new kind of heterostructures containing 3D diamond and 2D holes structures, and diamond-structure photonic crystals and 2D holes-structure photonic crystals fabricated by stereolithography and gel-casting with alumina were studied at microwave range, respectively. The heterostructures were designed by 2D holes structure embedded in 3D diamond structure, in which the lattice of three kinds of structures was equivalent. It was found that the band gaps of photonic crystal heterostructure were broadened by 124.6% and 150% comparing to that of diamond-structure crystal and 2D aerial holes structure. Experimental results showed the band gap broadened was not connected with a linear superposition of the band gap of 2D and 3D photonic crystals, which was the superposition of partial overlap.

  10. Thin colloidal crystals : a series of structural transitions (*) B. Pansu, P. Pieranski and L. Strzelecki

    E-print Network

    Paris-Sud XI, Université de

    531 Thin colloidal crystals : a series of structural transitions (*) B. Pansu, P. Pieranski and L les couches. Abstract. 2014 We study thin layers of colloidal crystals made of polystyrene balls (1.1 03BCm diameter) in aqueous suspension. These thin layers are produced by confining colloidal crystals

  11. Database guided conformation selection in crystal structure prediction of Timothy G. Cooper,a

    E-print Network

    de Gispert, Adrià

    of developing reliable computational methods for flexible molecules and, specifically, to study the crystal crystals, but are nonionised for the isolated molecules. The quantum mechanically optimised structure of the isolated molecule is therefore a poor starting point for computationally generating putative crystal

  12. Crystal Structure of the BARD1 BRCT Domains

    SciTech Connect

    Birrane,G.; Varma, A.; Soni, A.; Ladias, J.

    2007-01-01

    The interaction of the breast tumor suppressor BRCA1 with the protein BARD1 results in the formation of a heterodimeric complex that has ubiquitin ligase activity and plays central roles in cell cycle checkpoint control and DNA repair. Both BRCA1 and BARD1 possess a pair of tandem BRCT domains that interact in a phosphorylation-dependent manner with target proteins. We determined the crystal structure of the human BARD1 BRCT repeats (residues 568-777) at 1.9 {angstrom} resolution. The composition and structure of the BARD1 phosphoserine-binding pocket P{sub 1} are strikingly similar to those of the BRCA1 and MDC1 BRCT domains, suggesting a similar mode of interaction with the phosphate group of the ligand. By contrast, the BARD1 BRCT selectivity pocket P{sub 2} exhibits distinct structural features, including two prominent histidine residues, His685 and His686, which may be important for ligand binding. The protonation state of these histidines has a marked effect on the calculated electrostatic potential in the vicinity of P{sub 2}, raising the possibility that ligand recognition may be regulated by changes in pH. Importantly, the BARD1 BRCT structure provides insights into the mechanisms by which the cancer-associated missense mutations C645R, V695L, and S761N may adversely affect the structure and function of BARD1.

  13. Crystal structure of the human glucose transporter GLUT1

    NASA Astrophysics Data System (ADS)

    Deng, Dong; Xu, Chao; Sun, Pengcheng; Wu, Jianping; Yan, Chuangye; Hu, Mingxu; Yan, Nieng

    2014-06-01

    The glucose transporter GLUT1 catalyses facilitative diffusion of glucose into erythrocytes and is responsible for glucose supply to the brain and other organs. Dysfunctional mutations may lead to GLUT1 deficiency syndrome, whereas overexpression of GLUT1 is a prognostic indicator for cancer. Despite decades of investigation, the structure of GLUT1 remains unknown. Here we report the crystal structure of human GLUT1 at 3.2 Å resolution. The full-length protein, which has a canonical major facilitator superfamily fold, is captured in an inward-open conformation. This structure allows accurate mapping and potential mechanistic interpretation of disease-associated mutations in GLUT1. Structure-based analysis of these mutations provides an insight into the alternating access mechanism of GLUT1 and other members of the sugar porter subfamily. Structural comparison of the uniporter GLUT1 with its bacterial homologue XylE, a proton-coupled xylose symporter, allows examination of the transport mechanisms of both passive facilitators and active transporters.

  14. SHELXT - integrated space-group and crystal-structure determination.

    PubMed

    Sheldrick, George M

    2015-01-01

    The new computer program SHELXT employs a novel dual-space algorithm to solve the phase problem for single-crystal reflection data expanded to the space group P1. Missing data are taken into account and the resolution extended if necessary. All space groups in the specified Laue group are tested to find which are consistent with the P1 phases. After applying the resulting origin shifts and space-group symmetry, the solutions are subject to further dual-space recycling followed by a peak search and summation of the electron density around each peak. Elements are assigned to give the best fit to the integrated peak densities and if necessary additional elements are considered. An isotropic refinement is followed for non-centrosymmetric space groups by the calculation of a Flack parameter and, if appropriate, inversion of the structure. The structure is assembled to maximize its connectivity and centred optimally in the unit cell. SHELXT has already solved many thousand structures with a high success rate, and is optimized for multiprocessor computers. It is, however, unsuitable for severely disordered and twinned structures because it is based on the assumption that the structure consists of atoms. PMID:25537383

  15. Studies on synthesis, growth, structural, optical properties of organic 8-hydroxyquinolinium succinate single crystals

    NASA Astrophysics Data System (ADS)

    Thirumurugan, R.; Anitha, K.

    2014-04-01

    8-hydroxyquinolinium succinate (8HQSU), an organic material has been synthesized and single crystals were grown by employing the technique of slow evaporation. The structure of the grown crystal was elucidated by using single crystal X-ray diffraction analysis. 8HQSU crystal belongs to the monoclinic crystallographic system with non-centro symmetric space group of P21. FT-IR spectral investigation has been carried out to identify the various functional groups present in the grown crystal. UV-vis spectral studies reveal that 8HQSU crystals are transparent in the entire visible region and the cut-off wavelength has been found to be 220nm.

  16. Single Crystal Diffraction Studies of Structure I, II and H Hydrates: Structure, Cage Occupancy and Composition

    Microsoft Academic Search

    Konstantin A Udachin; Christopher I Ratcliffe; John A Ripmeester

    2002-01-01

    Recent advances in single crystal X-ray diffraction have allowed this technique to be used as a valuable tool for the analysis of hydrate structure and composition. With detailed analysis of guest disorder, not only are the guest positions clearly defined, but by using the cage occupancy as a free parameter it becomes possible to obtain estimates of hydrate composition from

  17. Structure of RCC1 chromatin factor bound to the nucleosome core particle

    PubMed Central

    Makde, Ravindra D.; England, Joseph R.; Yennawar, Hemant P.; Tan, Song

    2011-01-01

    The small GTPase Ran enzyme regulates critical eukaryotic cellular functions including nuclear transport and mitosis through the creation of a RanGTP gradient around the chromosomes. This concentration gradient is created by the chromatin bound RCC1 (regulator of chromosome condensation) protein which recruits Ran to nucleosomes and activates Ran’s nucleotide exchange activity. While RCC1 has been shown to bind directly with the nucleosome, the molecular details of this interaction were not known. We have determined the crystal structure of the RCC1-nucleosome core particle complex at 2.9 Å resolution, providing the first atomic view of how a chromatin protein interacts with the histone and DNA components of the nucleosome. Our structure also suggests that the Widom 601 DNA positioning sequence present in our nucleosomes forms a 145 bp and not the expected canonical 147 bp nucleosome core particle. PMID:20739938

  18. Manufacturing, structure and properties of recycled polyethylene terephthalate /liquid crystal polymer/montmorillonite clay nanocomposites

    NASA Astrophysics Data System (ADS)

    Japins, Guntis; Berzina, Rita; Zicans, Janis; Merijs Meri, Remo; Ivanova, Tatjana; Kalkis, Valdis; Reinholds, Ingars

    2013-12-01

    Polyethylene terephthalate (PET)/liquid crystal polymer (LCP)/monthmorillonite clay (MMT) compositions were obtained by melt mixing. Their mechanical, structural, rheological and thermal properties were investigated.

  19. Crystal Structures of Aged Phosphonylated Acetylcholinesterase: Nerve Agent Reaction Products at the Atomic Level,

    E-print Network

    Sussman, Joel L.

    Crystal Structures of Aged Phosphonylated Acetylcholinesterase: Nerve Agent Reaction ProductsVised Manuscript ReceiVed March 26, 1999 ABSTRACT: Organophosphorus acid anhydride (OP) nerve agents are potent

  20. Silicon crystals: Process for manufacturing wafer-like silicon crystals with a columnar structure

    NASA Technical Reports Server (NTRS)

    Authier, B.

    1978-01-01

    Wafer-like crystals suitable for making solar cells are formed by pouring molten Si containing suitable dopants into a mold of the desired shape and allowing it to solidify in a temperature gradient, whereby the large surface of the melt in contact with the mold is kept at less than 200 D and the free surface is kept at a temperature of 200-1000 D higher, but below the melting point of Si. The mold can also be made in the form of a slit, whereby the 2 sides of the mold are kept at different temperatures. A mold was milled in the surface of a cylindrical graphite block 200 mm in diameter. The granite block was induction heated and the bottom of the mold was cooled by means of a water-cooled Cu plate, so that the surface of the mold in contact with one of the largest surfaces of the melt was held at approximately 800 D. The free surface of the melt was subjected to thermal radiation from a graphite plate located 2 mm from the surface and heated to 1500 D. The Si crystal formed after slow cooling to room temperature had a columnar structure and was cut with a diamond saw into wafers approximately 500 mm thick. Solar cells prepared from these wafers had efficiencies of 10 to 11%.

  1. Crystal and molecular structure of dihydroxynaphthalene isomers. Effect of structure on ice-forming properties

    Microsoft Academic Search

    V. K. Bel'skii; E. V. Kharchenko; A. N. Sobolev; V. E. Zavodnik; N. A. Kolomiets; G. S. Prober; L. P. Oleksenko

    1991-01-01

    X-ray diffraction structural analysis established the structures of three dihydroxynaphthalene isomers: 1,5-dihydroxynaphthalene (space group P21\\/n, Z = 2(r), R = 0.035), 2,5-dihydroxynaphthalene (space group P21\\/a , Z --- 4(12), R = 0.058), and 2,3-dihydroxynaphthalene (space group Pcab, Z = 16(12), R = 0.032). The molecules of the dihydroxynaphthalene isomers in the crystals are connected by hydrogen bond systems. The existence

  2. Synthesis and crystal structure of tetramethylammonium fluoride octadecasil

    SciTech Connect

    Yang Xiaobo [Institute of Physical Chemistry and Electrochemistry, University of Hanover, D-30167 Hanover (Germany)]. E-mail: Xiaobo.Yang@pci.uni-hannover.de

    2006-01-05

    Octadecasil, a clathrate-type inclusion compound, has been synthesized hydrothermally at 453 K with a gel having the composition 1.0SiO{sub 2}:0.53tetramethylammonium (TMA{sup +}):0.54fluoride:86H{sub 2}O. The crystal structure has been determined based on powder X-ray diffraction data taken at 298 K, and has been refined using Rietveld method. The result confirms the AST-type, all-silica framework model developed by Caullet et al. [P. Caullet, J.L. Guth, J. Hazm, J.M. Lamblin, H. Gies, Eur. J. Solid State Inorg. Chem. 28 (1991) 345]. Furthermore, by using a rigid body model the position and orientation of the occluded TMA{sup +} cation in the rhombododecahedral [4{sup 6}6{sup 12}] cage can be determined; F{sup -} anion has been located in the hexahedral [4{sup 6}] cage. The unit cell parameters, in the tetragonal space group I4/m, have been refined as: a = b = 9.07 A, c = 13.44 A, cell volume = 1104.97 A{sup 3}. The refined unit cell composition is |[N(CH{sub 3}){sub 4} {sup +}]{sub 2.0}F{sup -} {sub 1.9}|[Si{sub 20}O{sub 40}], i.e., both TMA{sup +} and F{sup -} ions possess near full occupancies, and compensate each other's electronic charges. The crystallization of the AST framework structure is the result of a cooperative structure-directing effect of both ions.

  3. Crystal structure of adenosine 5'-phosphosulfate kinase from Penicillium chrysogenum.

    PubMed

    MacRae, I J; Segel, I H; Fisher, A J

    2000-02-22

    Adenosine 5'-phosphosulfate (APS) kinase catalyzes the second reaction in the two-step conversion of inorganic sulfate to 3'-phosphoadenosine 5'-phosphosulfate (PAPS). This report presents the 2.0 A resolution crystal structure of ligand-free APS kinase from the filamentous fungus, Penicillium chrysogenum. The enzyme crystallized as a homodimer with each subunit folded into a classic kinase motif consisting of a twisted, parallel beta-sheet sandwiched between two alpha-helical bundles. The Walker A motif, (32)GLSASGKS(39), formed the predicted P-loop structure. Superposition of the APS kinase active site region onto several other P-loop-containing proteins revealed that the conserved aspartate residue that usually interacts with the Mg(2+) coordination sphere of MgATP is absent in APS kinase. However, upon MgATP binding, a different aspartate, Asp 61, could shift and bind to the Mg(2+). The sequence (156)KAREGVIKEFT(166), which has been suggested to be a (P)APS motif, is located in a highly protease-susceptible loop that is disordered in both subunits of the free enzyme. MgATP or MgADP protects against proteolysis; APS alone has no effect but augments the protection provided by MgADP. The results suggest that the loop lacks a fixed structure until MgATP or MgADP is bound. The subsequent conformational change together with the potential change promoted by the interaction of MgATP with Asp 61 may define the APS binding site. This model is consistent with the obligatory ordered substrate binding sequence (MgATP or MgADP before APS) as established from steady state kinetics and equilibrium binding studies. PMID:10677210

  4. Structure of apo acyl carrier protein and a proposal to engineer protein crystallization through metal ions

    SciTech Connect

    Qiu, Xiayang; Janson, Cheryl A. (GSK)

    2010-11-16

    A topic of current interest is engineering surface mutations in order to improve the success rate of protein crystallization. This report explores the possibility of using metal-ion-mediated crystal-packing interactions to facilitate rational design. Escherichia coli apo acyl carrier protein was chosen as a test case because of its high content of negatively charged carboxylates suitable for metal binding with moderate affinity. The protein was successfully crystallized in the presence of zinc ions. The crystal structure was determined to 1.1 {angstrom} resolution with MAD phasing using anomalous signals from the co-crystallized Zn{sup 2+} ions. The case study suggested an integrated strategy for crystallization and structure solution of proteins via engineering surface Asp and Glu mutants, crystallizing them in the presence of metal ions such as Zn{sup 2+} and solving the structures using anomalous signals.

  5. Self-assembly and electrostriction of arrays and chains of hopfion particles in chiral liquid crystals

    NASA Astrophysics Data System (ADS)

    Ackerman, Paul J.; van de Lagemaat, Jao; Smalyukh, Ivan I.

    2015-01-01

    Some of the most exotic condensed matter phases, such as twist grain boundary and blue phases in liquid crystals and Abrikosov phases in superconductors, contain arrays of topological defects in their ground state. Comprised of a triangular lattice of double-twist tubes of magnetization, the so-called ‘A-phase’ in chiral magnets is an example of a thermodynamically stable phase with topologically nontrivial solitonic field configurations referred to as two-dimensional skyrmions, or baby-skyrmions. Here we report that three-dimensional skyrmions in the form of double-twist tori called ‘hopfions’, or ‘torons’ when accompanied by additional self-compensating defects, self-assemble into periodic arrays and linear chains that exhibit electrostriction. In confined chiral nematic liquid crystals, this self-assembly is similar to that of liquid crystal colloids and originates from long-range elastic interactions between particle-like skyrmionic torus knots of molecular alignment field, which can be tuned from isotropic repulsive to weakly or highly anisotropic attractive by low-voltage electric fields.

  6. Self-assembly and electrostriction of arrays and chains of hopfion particles in chiral liquid crystals

    PubMed Central

    Ackerman, Paul J.; van de Lagemaat, Jao; Smalyukh, Ivan I.

    2015-01-01

    Some of the most exotic condensed matter phases, such as twist grain boundary and blue phases in liquid crystals and Abrikosov phases in superconductors, contain arrays of topological defects in their ground state. Comprised of a triangular lattice of double-twist tubes of magnetization, the so-called ‘A-phase’ in chiral magnets is an example of a thermodynamically stable phase with topologically nontrivial solitonic field configurations referred to as two-dimensional skyrmions, or baby-skyrmions. Here we report that three-dimensional skyrmions in the form of double-twist tori called ‘hopfions’, or ‘torons’ when accompanied by additional self-compensating defects, self-assemble into periodic arrays and linear chains that exhibit electrostriction. In confined chiral nematic liquid crystals, this self-assembly is similar to that of liquid crystal colloids and originates from long-range elastic interactions between particle-like skyrmionic torus knots of molecular alignment field, which can be tuned from isotropic repulsive to weakly or highly anisotropic attractive by low-voltage electric fields. PMID:25607778

  7. Self-assembly and electrostriction of arrays and chains of hopfion particles in chiral liquid crystals.

    PubMed

    Ackerman, Paul J; van de Lagemaat, Jao; Smalyukh, Ivan I

    2015-01-01

    Some of the most exotic condensed matter phases, such as twist grain boundary and blue phases in liquid crystals and Abrikosov phases in superconductors, contain arrays of topological defects in their ground state. Comprised of a triangular lattice of double-twist tubes of magnetization, the so-called 'A-phase' in chiral magnets is an example of a thermodynamically stable phase with topologically nontrivial solitonic field configurations referred to as two-dimensional skyrmions, or baby-skyrmions. Here we report that three-dimensional skyrmions in the form of double-twist tori called 'hopfions', or 'torons' when accompanied by additional self-compensating defects, self-assemble into periodic arrays and linear chains that exhibit electrostriction. In confined chiral nematic liquid crystals, this self-assembly is similar to that of liquid crystal colloids and originates from long-range elastic interactions between particle-like skyrmionic torus knots of molecular alignment field, which can be tuned from isotropic repulsive to weakly or highly anisotropic attractive by low-voltage electric fields. PMID:25607778

  8. Crystal growth, crystal structure, and magnetic properties of a new lithium cobalt diphosphate

    SciTech Connect

    Sanz, F.; Parada, C.; Ruiz-Valero, C.

    2000-03-01

    Single crystals of the new lithium cobalt diphosphate Li{sub 6}Co{sub 5}(P{sub 2}O{sub 7}){sub 4} have been grown, and their structure has been determined by X-ray diffraction techniques. This compound crystallizes in the triclinic space group P1 with a = 6.3009(7), b = 8.413(1), and c = 9.937(1) {angstrom}{alpha} = 107.894(2), {beta} = 90.247(2), and {gamma} = 92.782(2){degree}, V = 500.6(1) {angstrom}{sup 3}, and Z = 1. The structure of Li{sub 6}Co{sub 5}(P{sub 2}O{sub 7}){sub 4} is characterized by the arrangement of CoO{sub 6} octahedra, CoO{sub 5} trigonal bipyramids, and diphosphate groups. The CoO{sub 6} octahedra share edges forming infinite zigzag chains [Co{sub 3}O{sub 14}] running along the b direction. Laterally, such chains share octahedra corners with CoO{sub 5} trigonal bipyramids and P{sub 2}O{sub 7} diphosphate groups connecting with another symmetrically equivalent chain. The connection between these polyhedra defines tunnels along the [100], [001], and [011] directions, where the Li cations are located. The tunnel intersection gives rise to a three-dimensional channel system. Magnetic measurements reveal the presence of antiferromagnetic interactions in the Co{sup 2+} sublattice at about 11 K. The field dependence of magnetization shows that this compound exhibits a metamagnetic transition.

  9. Charge Structure and Counterion Distribution in Hexagonal DNA Liquid Crystal

    PubMed Central

    Dai, Liang; Mu, Yuguang; Nordenskiöld, Lars; Lapp, Alain; van der Maarel, Johan R. C.

    2007-01-01

    A hexagonal liquid crystal of DNA fragments (double-stranded, 150 basepairs) with tetramethylammonium (TMA) counterions was investigated with small angle neutron scattering (SANS). We obtained the structure factors pertaining to the DNA and counterion density correlations with contrast matching in the water. Molecular dynamics (MD) computer simulation of a hexagonal assembly of nine DNA molecules showed that the inter-DNA distance fluctuates with a correlation time around 2 ns and a standard deviation of 8.5% of the interaxial spacing. The MD simulation also showed a minimal effect of the fluctuations in inter-DNA distance on the radial counterion density profile and significant penetration of the grooves by TMA. The radial density profile of the counterions was also obtained from a Monte Carlo (MC) computer simulation of a hexagonal array of charged rods with fixed interaxial spacing. Strong ordering of the counterions between the DNA molecules and the absence of charge fluctuations at longer wavelengths was shown by the SANS number and charge structure factors. The DNA-counterion and counterion structure factors are interpreted with the correlation functions derived from the Poisson-Boltzmann equation, MD, and MC simulation. Best agreement is observed between the experimental structure factors and the prediction based on the Poisson-Boltzmann equation and/or MC simulation. The SANS results show that TMA is too large to penetrate the grooves to a significant extent, in contrast to what is shown by MD simulation. PMID:17098791

  10. Structural properties of composites of polyvinylidene fluoride and mechanically activated BaTiO3 particles

    NASA Astrophysics Data System (ADS)

    Pavlovi?, V. P.; Pavlovi?, V. B.; Vlahovi?, B.; Božani?, D. K.; Pajovi?, J. D.; Doj?ilovi?, R.; Djokovi?, V.

    2013-11-01

    Nanocomposites of electroactive ceramics and ferroelectric polymers exploit favorable features of the matrix polymer and the nanostructured filler to produce new functional materials for pressure and IR sensors. In this study, the influence of mechanical activation of barium titanate (BaTiO3) particles on the structural properties of BaTiO3/polyvinylidene fluoride (PVDF) nanocomposites was investigated. Nanocomposite films were prepared by the solution casting method and characterized by scanning electron microscopy, x-ray diffraction and Raman spectroscopy. It was found that mechanically activated fillers promote the formation of a ferroelectric ?-phase during crystallization of PVDF.

  11. Crystallization, crystal-structure refinement, and IR spectroscopy of a synthetic hexahydroborite analog

    SciTech Connect

    Yamnova, N. A., E-mail: natalia-yamnova@yandex.ru; Borovikova, E. Yu.; Dimitrova, O. V. [Moscow State University, Faculty of Geology (Russian Federation)

    2011-11-15

    The crystal structure of the hexahydroborite analog Ca[B(OH){sub 4}]{sub 2} {center_dot} 2H{sub 2}O (a = 7.9941(3) Angstrom-Sign , b = 6.6321(2) Angstrom-Sign , c = 7.9871(3) Angstrom-Sign , {beta} = 104.166(4) Degree-Sign , V = 410.58(3) Angstrom-Sign {sup 3}, sp. gr. P2/c, Z = 2, {rho}{sub calc} = 1.891 g/cm{sup 3}; Xcalibur S CCD automated diffractometer, 1196 reflections with I > 2{sigma}(I), {lambda}MoK{sub {alpha}}), which was synthesized by the hydrothermal method via the recrystallization of calciborite CaB{sub 2}O{sub 4} (M) in the M - B{sub 2}O{sub 3} - H{sub 2}O system (t = 250 Degree-Sign C and P = 70-80 atm), was refined by the least-squares method with anisotropic displacement parameters (H atoms were located; R{sub 1} = 0.0260). The structure of synthetic hexahydroborite consists of infinite columns running along the c axis. The columns are formed by Ca polyhedra linked together and to [B(OH){sub 4}] orthotetrahedra by sharing edges. Along the two other axes, the translationally equivalent columns are linked only by hydrogen bonds. The presence of a stronger bond between the discrete (Ca-B-O) columns along the shortest (b = 6.6 Angstrom-Sign ) axis accounts for the possibility of the shift of the columns by 1/2T{sub b} and the formation of the second modification of Ca[B(OH){sub 4}]{sub 2} {center_dot} 2H{sub 2}O. The crystals of synthetic hexahydroborite were studied by IR spectroscopy. A crystal-chemical analysis was performed for a series of natural metaborates with the general formula CaB{sub 2}O{sub 4} {center_dot} nH{sub 2}O (CaO: B{sub 2}O{sub 3} = 1: 1, n = 0-6), including calciborite CaB{sub 2}O{sub 4} and hexahydroborite CaB{sub 2}O{sub 4} {center_dot} 6H{sub 2}O as the end members.

  12. VO2 (A): Reinvestigation of crystal structure, phase transition and crystal growth mechanisms

    NASA Astrophysics Data System (ADS)

    Rao Popuri, Srinivasa; Artemenko, Alla; Labrugere, Christine; Miclau, Marinela; Villesuzanne, Antoine; Pollet, Michaël

    2014-05-01

    Well crystallized VO2 (A) microrods were grown via a single step hydrothermal reaction in the presence of V2O5 and oxalic acid. With the advantage of high crystalline samples, we propose P4/ncc as an appropriate space group at room temperature. From morphological studies, we found that the oriented attachment and layer by layer growth mechanisms are responsible for the formation of VO2 (A) micro rods. The structural and electronic transitions in VO2 (A) are strongly first order in nature, and a marked difference between the structural transition temperatures and electronic transitions temperature was evidenced. The reversible intra- (LTP-A to HTP-A) and irreversible inter- (HTP-A to VO2 (M1)) structural phase transformations were studied by in-situ powder X-ray diffraction. Attempts to increase the size of the VO2 (A) microrods are presented and the possible formation steps for the flower-like morphologies of VO2 (M1) are described.

  13. Interface induced crystal structures of dioctyl-terthiophene thin films.

    PubMed

    Werzer, Oliver; Boucher, Nicolas; de Silva, Johann P; Gbabode, Gabin; Geerts, Yves H; Konovalov, Oleg; Moser, Armin; Novak, Jiri; Resel, Roland; Sferrazza, Michele

    2012-06-01

    Temperature dependent structural and morphological investigations on semiconducting dioctyl-terthiophene (DOTT) thin films prepared on silica surfaces reveals the coexistence of surface induce order and distinct crystalline/liquid crystalline bulk polymorphs. X-ray diffraction and scanning force microscopy measurements indicate that at room temperature two polymorphs are present: the surface induced phase grows directly on the silica interface and the bulk phase on top. At elevated temperatures the long-range order gradually decreases, and the crystal G (340 K), smectic F (348 K), and smectic C (360 K) phases are observed. Indexation of diffraction peaks reveals that an up-right standing conformation of DOTT molecules is present within all phases. A temperature stable interfacial layer close to the silica-DOTT interface acts as template for the formation of the different phases. Rapid cooling of the DOTT sample from the smectic C phase to room temperature results in freezing into a metastable crystalline state with an intermediated unit cell between the room temperature crystalline phase and the smectic C phase. The understanding of such interfacial induced phases in thin semiconducting liquid crystal films allows tuning of crystallographic and therefore physical properties within organic thin films. PMID:22578151

  14. Chemical characterization of individual particles and residuals of cloud droplets and ice crystals collected on board research aircraft in the ISDAC 2008 study

    NASA Astrophysics Data System (ADS)

    Hiranuma, N.; Brooks, S. D.; Moffet, R. C.; Glen, A.; Laskin, A.; Gilles, M. K.; Liu, P.; MacDonald, A. M.; Strapp, J. W.; McFarquhar, G. M.

    2013-06-01

    Ambient particles and the dry residuals of mixed-phase cloud droplets and ice crystals were collected during the Indirect and Semi-Direct Aerosol Campaign (ISDAC) near Barrow, Alaska, in spring of 2008. The collected particles were analyzed using Computer Controlled Scanning Electron Microscopy with Energy Dispersive X-ray analysis and Scanning Transmission X-ray Microscopy coupled with Near Edge X-ray Absorption Fine Structure spectroscopy to identify physico-chemical properties that differentiate cloud-nucleating particles from the total aerosol population. A wide range of individually mixed components was identified in the ambient particles and residuals including organic carbon compounds, inorganics, carbonates, and black carbon. Our results show that cloud droplet residuals differ from the ambient particles in both size and composition, suggesting that both properties may impact the cloud-nucleating ability of aerosols in mixed-phase clouds. The percentage of residual particles which contained carbonates (47%) was almost four times higher than those in ambient samples. Residual populations were also enhanced in sea salt and black carbon and reduced in organic compounds relative to the ambient particles. Further, our measurements suggest that chemical processing of aerosols may improve their cloud-nucleating ability. Comparison of results for various time periods within ISDAC suggests that the number and composition of cloud-nucleating particles over Alaska can be influenced by episodic events bringing aerosols from both the local vicinity and as far away as Siberia.

  15. Orientational glass in mixtures of elliptic and circular particles: Structural heterogeneities, rotational dynamics, and rheology

    NASA Astrophysics Data System (ADS)

    Takae, Kyohei; Onuki, Akira

    2014-02-01

    Using molecular dynamics simulation with an angle-dependent Lennard-Jones potential, we study orientational glass with quadrupolar symmetry in mixtures of elliptic particles and circular impurities in two dimensions. With a mild aspect ratio (=1.23) and a mild size ratio (=1.2), we realize a plastic crystal at relatively high temperature T. With further lowering T, we find a structural phase transition for very small impurity concentration c and pinned disordered orientations for not small c. The ellipses are anchored by the impurities in the planar alignment. With increasing c, the orientation domains composed of isosceles triangles gradually become smaller, resulting in orientational glass with crystal order. In our simulation, the impurity distribution becomes heterogeneous during quenching from liquid, which then produces rotational dynamic heterogeneities. We also examine rheology in orientational glass to predict a shape memory effect and a superelasticity effect, where a large fraction of the strain is due to collective orientation changes.

  16. Structure of below-barrier and above-barrier energy bands and wave functions of a particle in the periodic potential of crystalline lattice

    NASA Astrophysics Data System (ADS)

    Babakhanyan, Erine A.

    2012-05-01

    The knowledge of energy spectrum structure allows us to find the Bloch state wave functions. During the interaction of charged particles moving in a crystal, the wave functions represent the superposition of Bloch functions. The population of every Bloch state is characterized by Fourier-component squared. The analytical results received in the given work for periodic potential of a crystal lattice in the model of modified Pöschl-Teller's potential make a basis for studying the phenomena in a channeling mode of particles in crystals (the behaviour of particles at different depths of penetration into crystal, angular distributions of particles, both inside the crystal, and at its exited, etc.). The account of the zone structure of energetic spectrum of channeled electrons results in qualitative change of angular distributions of X-ray radiation under the Bragg angles. Therefore it is interesting within the framework of our approach to study the radiation, as well as an output of the nuclear reactions appearing in case of interaction of charged particles moving in a crystal.

  17. crystals

    NASA Astrophysics Data System (ADS)

    Badalyan, A.; Hovsepyan, R.; Mantashyan, P.; Mekhitaryan, V.; Drampyan, R.

    2014-07-01

    A novel combined interferometric-mask method for the formation of micro- and nanometric scale three-dimensional (3D) rotational symmetry quasi-crystalline refractive lattice structures in photorefractive materials is demonstrated experimentally. The method is based on micrometric scale spatial modulation of the light by amplitude mask in the radial directions and along the azimuthal angle and the use of counter-propagating beam geometry building up Gaussian standing wave, which defines the light modulation in the axial direction with half-wavelength periodicity. 3D intensity pattern can be represented as numerous mask-generated 2D quasi-periodic structures located in each anti-node of the standing wave. The formed 3D intensity distributions of the optical beams can be imparted into the photorefractive medium thus creating the micro- and sub-micrometric scale 3D refractive index volume lattices. The used optical scheme allows also the formation of 2D lattices by removing the back-reflecting mirror. 2D and 3D refractive lattices were recorded with the use of 532 nm laser beam and rotational symmetry mask in doped lithium niobate crystals and were tested by the probe beam far-field diffraction pattern imaging and direct observation by phase microscope. The formed rotational symmetry 3D refractive structures have the periods of 20-60 ?m in the radial directions, 60 ?m along the azimuthal angle and half-wavelength 266 nm in the axial direction.

  18. Crystal Structure of Hyperthermophilic Endo-?-1,4-glucanase

    PubMed Central

    Zheng, Baisong; Yang, Wen; Zhao, Xinyu; Wang, Yuguo; Lou, Zhiyong; Rao, Zihe; Feng, Yan

    2012-01-01

    Endo-?-1,4-glucanase from thermophilic Fervidobacterium nodosum Rt17-B1 (FnCel5A), a new member of glycosyl hydrolase family 5, is highly thermostable and exhibits the highest activity on carboxymethylcellulose among the reported homologues. To understand the structural basis for the thermostability and catalytic mechanism, we report here the crystal structures of FnCel5A and the complex with glucose at atomic resolution. FnCel5A exhibited a (?/?)8-barrel structure typical of clan GH-A of the glycoside hydrolase families with a large and deep catalytic pocket located in the C-terminal end of the ?-strands that may permit substrate access. A comparison of the structure of FnCel5A with related structures from thermopile Clostridium thermocellum, mesophile Clostridium cellulolyticum, and psychrophile Pseudoalteromonas haloplanktis showed significant differences in intramolecular interactions (salt bridges and hydrogen bonds) that may account for the difference in their thermostabilities. The substrate complex structure in combination with a mutagenesis analysis of the catalytic residues implicates a distinctive catalytic module Glu167-His226-Glu283, which suggests that the histidine may function as an intermediate for the electron transfer network between the typical Glu-Glu catalytic module. Further investigation suggested that the aromatic residues Trp61, Trp204, Phe231, and Trp240 as well as polar residues Asn51, His127, Tyr228, and His235 in the active site not only participated in substrate binding but also provided a unique microenvironment suitable for catalysis. These results provide substantial insight into the unique characteristics of FnCel5A for catalysis and adaptation to extreme temperature. PMID:22128157

  19. Crystal structure of Fe 2P 2O 7

    NASA Astrophysics Data System (ADS)

    Hoggins, J. T.; Swinnea, J. S.; Steinfink, H.

    1983-05-01

    Fe 2P 2O 7 crystallizes in the C overline1 space group with lattice parameters a = 6.649(2)Å, b = 8.484(2)Å, c = 4.488(1)Å, ? = 90.04°, ? = 103.89(3)°, ? = 92.82(3)°, and ?cal = 3.86 g/cc. It is essentially isostructural with ?-Zn 2P 2O 7. As in the Zn compound, the bridging oxygen atom in the P 2O 7 group shows a high anisotropic thermal motion. It appears that the P-O-P bond angle is linear as a result of extensive ? bonding with the p orbitals on the bridging oxygen atom. The high thermal motion is vibration of the atom into cavities in the structure.

  20. Crystal structure of a potassium ion transporter TrkH

    PubMed Central

    Cao, Yu; Jin, Xiangshu; Huang, Hua; Derebe, Mehabaw Getahun; Levin, Elena J.; Kabaleeswaran, Venkataraman; Pan, Yaping; Punta, Marco; Love, James; Weng, Jun; Quick, Matthias; Ye, Sheng; Kloss, Brian; Bruni, Renato; Martinez-Hackert, Erik; Hendrickson, Wayne A.; Rost, Burkhard; Javitch, Jonathan A.; Rajashankar, Kanagalaghatta R.; Jiang, Youxing; Zhou, Ming

    2010-01-01

    The TrkH/TrkG/KtrB proteins mediate K+ uptake in bacteria and likely evolved from simple K+ channels by multiple gene duplications or fusions. Here we present the crystal structure of a TrkH from Vibrio parahaemolyticus. TrkH is a homodimer, and each protomer contains an ion permeation pathway. A selectivity filter, similar in architecture to those of K+ channels but significantly shorter, is lined by backbone and side chain oxygen atoms. Functional studies showed that the TrkH allows permeation of K+ and Rb+ but not smaller ions such as Na+ or Li+. Immediately intracellular to the selectivity filter are an intramembrane loop and an arginine residue, both highly conserved, which constrict the permeation pathway. Substituting the arginine with an alanine significantly increases the rate of K+ flux. These results reveal the molecular basis of K+ selectivity and suggest a novel gating mechanism by this large and important family of membrane transport proteins. PMID:21317882

  1. Crystal structure of the mammalian Grb2 adaptor.

    PubMed

    Maignan, S; Guilloteau, J P; Fromage, N; Arnoux, B; Becquart, J; Ducruix, A

    1995-04-14

    The mammalian growth factor receptor-binding protein Grb2 is an adaptor that mediates activation of guanine nucleotide exchange on Ras. Grb2 binds to the receptor through its SH2 domain and to the carboxyl-terminal domain of Son of sevenless through its two SH3 domains. It is thus a key element in the signal transduction pathway. The crystal structure of Grb2 was determined to 3.1 angstrom resolution. The asymmetric unit is composed of an embedded dimer. The interlaced junctions between the SH2 and SH3 domains bring the two adjacent faces of the SH3 domains in van der Waals contact but leave room for the binding of proline-rich peptides. PMID:7716522

  2. Structural conditionality of the piezoelectric properties of langasite family crystals

    NASA Astrophysics Data System (ADS)

    Dudka, A. P.; Simonov, V. I.

    2011-11-01

    The atomic displacements upon isomorphic substitutions in crystals of the langasite family have been analyzed. The thermal parameters are determined and the probability density function of atoms is analyzed. Local potential energy minima are found which can be occupied by atoms under external effects. The contributions of cations in all four independent crystallographic positions and anions in all three such positions to the piezoelectric properties are established. One specific structural feature is the constant (at isomorphic substitutions) or possible (under external effects) but always opposite displacements of two cations along symmetry axis 2. Large cations in eight-vertex polyhedra make the main contribution to the piezoelectric properties. The cations in the tetrahedra on symmetry axis 2 weaken these properties. The cations in the octahedra in the origin of coordinates and in the tetrahedra on symmetry axes 3 only slightly affect the piezoelectricity.

  3. Crystal structure of the rabies virus nucleoprotein-RNA complex.

    PubMed

    Albertini, Aurélie A V; Wernimont, Amy K; Muziol, Tadeusz; Ravelli, Raimond B G; Clapier, Cedric R; Schoehn, Guy; Weissenhorn, Winfried; Ruigrok, Rob W H

    2006-07-21

    Negative-strand RNA viruses condense their genome into a helical nucleoprotein-RNA complex, the nucleocapsid, which is packed into virions and serves as a template for the RNA-dependent RNA polymerase complex. The crystal structure of a recombinant rabies virus nucleoprotein-RNA complex, organized in an undecameric ring, has been determined at 3.5 angstrom resolution. Polymerization of the nucleoprotein is achieved by domain exchange between protomers, with flexible hinges allowing nucleocapsid formation. The two core domains of the nucleoprotein clamp around the RNA at their interface and shield it from the environment. RNA sequestering by nucleoproteins is likely a common mechanism used by negative-strand RNA viruses to protect their genomes from the innate immune response directed against viral RNA in human host cells at certain stages of an infectious cycle. PMID:16778023

  4. Structural conditionality of the piezoelectric properties of langasite family crystals

    SciTech Connect

    Dudka, A. P., E-mail: dudka@ns.crys.ras.ru; Simonov, V. I. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2011-11-15

    The atomic displacements upon isomorphic substitutions in crystals of the langasite family have been analyzed. The thermal parameters are determined and the probability density function of atoms is analyzed. Local potential energy minima are found which can be occupied by atoms under external effects. The contributions of cations in all four independent crystallographic positions and anions in all three such positions to the piezoelectric properties are established. One specific structural feature is the constant (at isomorphic substitutions) or possible (under external effects) but always opposite displacements of two cations along symmetry axis 2. Large cations in eight-vertex polyhedra make the main contribution to the piezoelectric properties. The cations in the tetrahedra on symmetry axis 2 weaken these properties. The cations in the octahedra in the origin of coordinates and in the tetrahedra on symmetry axes 3 only slightly affect the piezoelectricity.

  5. Likelihood-based modification of experimental crystal structure electron density maps

    DOEpatents

    Terwilliger, Thomas C. (Sante Fe, NM)

    2005-04-16

    A maximum-likelihood method for improves an electron density map of an experimental crystal structure. A likelihood of a set of structure factors {F.sub.h } is formed for the experimental crystal structure as (1) the likelihood of having obtained an observed set of structure factors {F.sub.h.sup.OBS } if structure factor set {F.sub.h } was correct, and (2) the likelihood that an electron density map resulting from {F.sub.h } is consistent with selected prior knowledge about the experimental crystal structure. The set of structure factors {F.sub.h } is then adjusted to maximize the likelihood of {F.sub.h } for the experimental crystal structure. An improved electron density map is constructed with the maximized structure factors.

  6. Nematic-Field Driven Positioning of Particles in Liquid Crystal Droplets

    PubMed Central

    Whitmer, Jonathan K.; Wang, Xiaoguang; Mondiot, Frederic; Miller, Daniel S.; Abbott, Nicholas L.; de Pablo, Juan J.

    2015-01-01

    Common nematic oils, such as 5CB, experience planar anchoring at aqueous interfaces. When these oils are emulsified, this anchoring preference and the resulting topological constraints lead to formation of droplets that exhibit one or two point defects within the nematic phase. Here, we explore the interactions of adsorbed particles at the aqueous interface through a combination of experiments and coarse-grained modeling, and demonstrate that surface-active particles, driven by elastic forces in the droplet, readily localize to these defect regions in a programmable manner. When droplets include two nanoparticles, these preferentially segregate to the two poles, thereby forming highly regular dipolar structures that could serve for hierarchical assembly of functional structures. Addition of sufficient concentrations of surfactant changes the interior morphology of the droplet, but pins defects to the interface, resulting in aggregation of the two particles. PMID:24329470

  7. Evaluation of Melt-Grown, ZnO Single Crystals for Use as Alpha-Particle Detectors

    Microsoft Academic Search

    John S. Neal; Nancy C. Giles; Xiaocheng Yang; R. Andrew Wall; K. Burak Ucer; Richard T. Williams; Dariusz J. Wisniewski; Lynn A. Boatner; Varatharajan Rengarajan; Jeff E Nause; Bill Nemeth

    2008-01-01

    As part of an ongoing investigation of the scintillation properties of zinc-oxide-(ZnO)-based scintillators, several melt-grown, ZnO single crystals have been characterized using alpha-particle excitation, infrared reflectance, and room temperature photoluminescence. The crystals, grown by Cermet, Inc., using an oxygen-pressurized melt-growth process, were doped with Group 1 elements (Li), Group 2 elements (Mg), Group 3 elements (Ga, In) and lanthanides (Gd,

  8. Atomic structure of amorphous particles produced by spark erosion

    Microsoft Academic Search

    S. Aur; T. Egami; A. E. Berkowitz; J. L. Walter

    1982-01-01

    The atomic structure of amorphous particles of composition Fe75Si15B10 produced by spark erosion was studied by the energy-dispersive x-ray diffraction technique and was compared to that of the amorphous ribbon of the same composition produced by melt spinning. It was found that the nearest-neighbor Fe-Fe correlation is almost identical for the ribbon and the particles of different sizes, whereas the

  9. Crystal structure of the Nogo-receptor-2.

    PubMed

    Semavina, Mariya; Saha, Nayanendu; Kolev, Momchil V; Goldgur, Yehuda; Giger, Roman J; Himanen, Juha P; Nikolov, Dimitar B

    2011-04-01

    The inhibition of axon regeneration upon mechanical injury is dependent on interactions between Nogo receptors (NgRs) and their myelin-derived ligands. NgRs are composed of a leucine-rich repeat (LRR) region, thought to be structurally similar among the different isoforms of the receptor, and a divergent "stalk" region. It has been shown by others that the LRR and stalk regions of NgR1 and NgR2 have distinct roles in conferring binding affinity to the myelin associated glycoprotein (MAG) in vivo. Here, we show that purified recombinant full length NgR1 and NgR2 maintain significantly higher binding affinity for purified MAG as compared to the isolated LRR region of either NgR1 or NgR2. We also present the crystal structure of the LRR and part of the stalk regions of NgR2 and compare it to the previously reported NgR1 structure with respect to the distinct signaling properties of the two receptor isoforms. PMID:21308849

  10. Crystal structure of a eukaryotic group II intron lariat.

    PubMed

    Robart, Aaron R; Chan, Russell T; Peters, Jessica K; Rajashankar, Kanagalaghatta R; Toor, Navtej

    2014-10-01

    The formation of branched lariat RNA is an evolutionarily conserved feature of splicing reactions for both group II and spliceosomal introns. The lariat is important for the fidelity of 5' splice-site selection and consists of a 2'-5' phosphodiester bond between a bulged adenosine and the 5' end of the intron. To gain insight into this ubiquitous intramolecular linkage, we determined the crystal structure of a eukaryotic group IIB intron in the lariat form at 3.7 Å. This revealed that two tandem tetraloop-receptor interactions, ?-?' and ?-?', place domain VI in the core to position the lariat bond in the post-catalytic state. On the basis of structural and biochemical data, we propose that ?-?' is a dynamic interaction that mediates the transition between the two steps of splicing, with ?-?' serving an ancillary role. The structure also reveals a four-magnesium-ion cluster involved in both catalysis and positioning of the 5' end. Given the evolutionary relationship between group II and nuclear introns, it is likely that this active site configuration exists in the spliceosome as well. PMID:25252982

  11. Inhibitor Bound Crystal Structures of Bacterial Nitric Oxide Synthase.

    PubMed

    Holden, Jeffrey K; Dejam, Dillon; Lewis, Matthew C; Huang, He; Kang, Soosung; Jing, Qing; Xue, Fengtian; Silverman, Richard B; Poulos, Thomas L

    2015-07-01

    Nitric oxide generated by bacterial nitric oxide synthase (NOS) increases the susceptibility of Gram-positive pathogens Staphylococcus aureus and Bacillus anthracis to oxidative stress, including antibiotic-induced oxidative stress. Not surprisingly, NOS inhibitors also improve the effectiveness of antimicrobials. Development of potent and selective bacterial NOS inhibitors is complicated by the high active site sequence and structural conservation shared with the mammalian NOS isoforms. To exploit bacterial NOS for the development of new therapeutics, recognition of alternative NOS surfaces and pharmacophores suitable for drug binding is required. Here, we report on a wide number of inhibitor-bound bacterial NOS crystal structures to identify several compounds that interact with surfaces unique to the bacterial NOS. Although binding studies indicate that these inhibitors weakly interact with the NOS active site, many of the inhibitors reported here provide a revised structural framework for the development of new antimicrobials that target bacterial NOS. In addition, mutagenesis studies reveal several key residues that unlock access to bacterial NOS surfaces that could provide the selectivity required to develop potent bacterial NOS inhibitors. PMID:26062720

  12. Crystal structure of Bacillus anthracis transpeptidase enzyme CapD.

    SciTech Connect

    Wu, R.; Richter, S.; Zhang, R.; Anderson, V. J.; Missiakas, D.; Joachimiak, A.; Biosciences Division; Univ. of Chicago

    2009-09-04

    Bacillus anthracis elaborates a poly-{gamma}-d-glutamic acid capsule that protects bacilli from phagocytic killing during infection. The enzyme CapD generates amide bonds with peptidoglycan cross-bridges to anchor capsular material within the cell wall envelope of B. anthracis. The capsular biosynthetic pathway is essential for virulence during anthrax infections and can be targeted for anti-infective inhibition with small molecules. Here, we present the crystal structures of the {gamma}-glutamyltranspeptidase CapD with and without {alpha}-l-Glu-l-Glu dipeptide, a non-hydrolyzable analog of poly-{gamma}-d-glutamic acid, in the active site. Purified CapD displays transpeptidation activity in vitro, and its structure reveals an active site broadly accessible for poly-{gamma}-glutamate binding and processing. Using structural and biochemical information, we derive a mechanistic model for CapD catalysis whereby Pro{sup 427}, Gly{sup 428}, and Gly{sup 429} activate the catalytic residue of the enzyme, Thr{sup 352}, and stabilize an oxyanion hole via main chain amide hydrogen bonds.

  13. Crystal structure of the death effector domains of caspase-8.

    PubMed

    Shen, Chen; Yue, Hong; Pei, Jianwen; Guo, Xiaomin; Wang, Tao; Quan, Jun-Min

    2015-07-31

    Caspase-8 is a key mediator in various biological processes such as apoptosis, necroptosis, inflammation, T/B cells activation, and cell motility. Caspase-8 is characterized by the N-terminal tandem death effector domains (DEDs) and the C-terminal catalytic protease domain. The DEDs mediate diverse functions of caspase-8 through homotypic interactions of the DEDs between caspase-8 and its partner proteins. Here, we report the first crystal structure of the DEDs of caspase-8. The overall structure of the DEDs of caspase-8 is similar to that of the DEDs of vFLIP MC159, which is composed of two tandem death effector domains that closely associate with each other in a head-to-tail manner. Structural analysis reveals distinct differences in the region connecting helices ?2b and ?4b in the second DED of the DEDs between caspase-8 and MC159, in which the helix ?3b in MC159 is replaced by a loop in caspase-8. Moreover, the different amino acids in this region might confer the distinct features of solubility and aggregation for the DEDs of caspase-8 and MC159. PMID:26003730

  14. Crystal structure of complex natural aluminum magnesium calcium iron oxide

    NASA Astrophysics Data System (ADS)

    Rastsvetaeva, R. K.; Aksenov, S. M.; Verin, I. A.

    2010-07-01

    The structure of a new natural oxide found near the Tashelga River (Eastern Siberia) was studied by X-ray diffraction. The pseudo-orthorhombic unit cell parameters are a = 5.6973(1) Å, b = 17.1823(4) Å, c = 23.5718(5) Å, ? = 90°, sp. gr. Pc. The structure was refined to R = 0.0516 based on 4773 reflections with | F| > 7?( F) taking into account the twin plane perpendicular to the z axis (the twin components are 0.47 and 0.53). The crystal-chemical formula ( Z = 4) is Ca2Mg{2/IV}Fe{2/(2+)IV}[Al{14/VI}O31(OH)][Al{2/IV}O][AlIV]ALIV(OH)], where the Roman numerals designate the coordination of the atoms. The structure of the mineral is based on wide ribbons of edge-sharing Al octahedra (an integral part of the spinel layer). The ribbons run along the shortest x axis and are inclined to the y and z axes. The adjacent ribbons are shifted with respect to each other along the y axis, resulting in the formation of step-like layers in which the two-ribbon thickness alternates with the three-ribbon thickness. Additional Al octahedra and Mg and Fe2+ tetrahedra are located between the ribbons. The layers are linked together to form a three-dimensional framework by Al tetrahedra, Ca polyhedra, and hydrogen bonds with the participation of OH groups.

  15. Crystal structures of designed armadillo repeat proteins: implications of construct design and crystallization conditions on overall structure.

    PubMed

    Reichen, Christian; Madhurantakam, Chaithanya; Plückthun, Andreas; Mittl, Peer R E

    2014-11-01

    Designed armadillo repeat proteins (dArmRP) are promising modular proteins for the engineering of binding molecules that recognize extended polypeptide chains. We determined the structure of a dArmRP containing five internal repeats and 3rd generation capping repeats in three different states by X-ray crystallography: without N-terminal His6 -tag and in the presence of calcium (YM5 A/Ca(2+) ), without N-terminal His6 -tag and in the absence of calcium (YM5 A), and with N-terminal His6 -tag and in the presence of calcium (His-YM5 A/Ca(2+)). All structures show different quaternary structures and superhelical parameters. His-YM5 A/Ca(2+) forms a crystallographic dimer, which is bridged by the His6 -tag, YM5 A/Ca(2+) forms a domain-swapped tetramer, and only in the absence of calcium and the His6 -tag, YM5 A forms a monomer. The changes of superhelical parameters are a consequence of calcium binding, because calcium ions interact with negatively charged residues, which can also participate in the modulation of helix dipole moments between adjacent repeats. These observations are important for further optimizations of dArmRPs and provide a general illustration of how construct design and crystallization conditions can influence the exact structure of the investigated protein. PMID:25132085

  16. Crystal structure of silver clusters formed on a Si(100)?2×1 surface

    Microsoft Academic Search

    M. V. Gomoyunova; I. I. Pronin; N. S. Faradzhev

    1998-01-01

    The crystal structure of silver clusters formed on the surface of a Si(100)?21 single crystal by annealing of a thin Ag film\\u000a deposited on a slightly heated crystal was studied by diffraction of quasielastically scattered medium-energy electrons. Simulation\\u000a of the diffraction pattern obtained at 2 keV showed that the silver islands formed on silicon have an ordered structure corresponding\\u000a to

  17. Fundamental Particle Structure in the Cosmological Dark Matter

    NASA Astrophysics Data System (ADS)

    Khlopov, Maxim

    2013-11-01

    The nonbaryonic dark matter of the universe is assumed to consist of new stable forms of matter. Their stability reflects symmetry of micro-world and mechanisms of its symmetry breaking. Particle candidates for cosmological dark matter are lightest particles that bear new conserved quantum numbers. Dark matter particles may represent ideal gas of noninteracting particles. Self-interacting dark matter weakly or superweakly coupled to ordinary matter is also possible, reflecting nontrivial pattern of particle symmetry in the hidden sector of particle theory. In the early universe the structure of particle symmetry breaking gives rise to cosmological phase transitions, from which macroscopic cosmological defects or primordial nonlinear structures can be originated. Primordial black holes (PBHs) can be not only a candidate for dark matter, but also represent a universal probe for superhigh energy physics in the early universe. Evaporating PBHs turn to be a source of even superweakly interacting particles, while clouds of massive PBHs can serve as nonlinear seeds for galaxy formation. The observed broken symmetry of the three known families may provide a simultaneous solution for the problems of the mass of neutrino and strong CP-violation in the unique framework of models of horizontal unification. Dark matter candidates can also appear in the new families of quarks and leptons and the existence of new stable charged leptons and quarks is possible, hidden in elusive "dark atoms." Such possibility, strongly restricted by the constraints on anomalous isotopes of light elements, is not excluded in scenarios that predict stable double charged particles. The excessive -2 charged particles are bound in these scenarios with primordial helium in O-helium "atoms," maintaining specific nuclear-interacting form of the dark matter, which may provide an interesting solution for the puzzles of the direct dark matter searches. In the context of cosmoparticle physics, studying fundamental relationship of micro- and macro-worlds, the problem of cosmological dark matter implies cross disciplinary theoretical, experimental and observational studies for its solution.

  18. Atomic structure of amorphous particles produced by spark erosion

    NASA Astrophysics Data System (ADS)

    Aur, S.; Egami, T.; Berkowitz, A. E.; Walter, J. L.

    1982-12-01

    The atomic structure of amorphous particles of composition Fe75Si15B10 produced by spark erosion was studied by the energy-dispersive x-ray diffraction technique and was compared to that of the amorphous ribbon of the same composition produced by melt spinning. It was found that the nearest-neighbor Fe-Fe correlation is almost identical for the ribbon and the particles of different sizes, whereas the second peak of the radial distribution function shows considerable differences among the samples. The result is consistent with decreased metal-metalloid compositional short-range order in the particles compared to that in the ribbon sample.

  19. Hierarchical structures of ZnO spherical particles synthesized solvothermally

    NASA Astrophysics Data System (ADS)

    Saito, Noriko; Haneda, Hajime

    2011-12-01

    We review the solvothermal synthesis, using a mixture of ethylene glycol (EG) and water as the solvent, of zinc oxide (ZnO) particles having spherical and flower-like shapes and hierarchical nanostructures. The preparation conditions of the ZnO particles and the microscopic characterization of the morphology are summarized. We found the following three effects of the ratio of EG to water on the formation of hierarchical structures: (i) EG restricts the growth of ZnO microcrystals, (ii) EG promotes the self-assembly of small crystallites into spheroidal particles and (iii) the high water content of EG results in hollow spheres.

  20. Multiple solvent crystal structures of ribonuclease A: An assessment of the method

    SciTech Connect

    Dechene, Michelle; Wink, Glenna; Smith, Mychal; Swartz, Paul; Mattos, Carla; (NCSU)

    2010-11-12

    The multiple solvent crystal structures (MSCS) method uses organic solvents to map the surfaces of proteins. It identifies binding sites and allows for a more thorough examination of protein plasticity and hydration than could be achieved by a single structure. The crystal structures of bovine pancreatic ribonuclease A (RNAse A) soaked in the following organic solvents are presented: 50% dioxane, 50% dimethylformamide, 70% dimethylsulfoxide, 70% 1,6-hexanediol, 70% isopropanol, 50% R,S,R-bisfuran alcohol, 70% t-butanol, 50% trifluoroethanol, or 1.0M trimethylamine-N-oxide. This set of structures is compared with four sets of crystal structures of RNAse A from the protein data bank (PDB) and with the solution NMR structure to assess the validity of previously untested assumptions associated with MSCS analysis. Plasticity from MSCS is the same as from PDB structures obtained in the same crystal form and deviates only at crystal contacts when compared to structures from a diverse set of crystal environments. Furthermore, there is a good correlation between plasticity as observed by MSCS and the dynamic regions seen by NMR. Conserved water binding sites are identified by MSCS to be those that are conserved in the sets of structures taken from the PDB. Comparison of the MSCS structures with inhibitor-bound crystal structures of RNAse A reveals that the organic solvent molecules identify key interactions made by inhibitor molecules, highlighting ligand binding hot-spots in the active site. The present work firmly establishes the relevance of information obtained by MSCS.

  1. ASSOCIATION OF SUPRATHERMAL PARTICLES WITH COHERENT STRUCTURES AND SHOCKS

    SciTech Connect

    Tessein, J. A.; Matthaeus, W. H.; Wan, M. [Department of Physics and Astronomy, University of Delaware, Newark, DE 19716 (United States)] [Department of Physics and Astronomy, University of Delaware, Newark, DE 19716 (United States); Osman, K. T. [Centre for Fusion, Space and Astrophysics, University of Warwick, Coventry CV4 7AL (United Kingdom)] [Centre for Fusion, Space and Astrophysics, University of Warwick, Coventry CV4 7AL (United Kingdom); Ruffolo, D. [Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400 (Thailand)] [Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400 (Thailand); Giacalone, J. [Department of Planetary Sciences and Lunar and Planetary Laboratory, University of Arizona, 1629 East University Boulevard, Tucson, AZ 85721 (United States)] [Department of Planetary Sciences and Lunar and Planetary Laboratory, University of Arizona, 1629 East University Boulevard, Tucson, AZ 85721 (United States)

    2013-10-10

    Various mechanisms have been proposed to explain observed suprathermal particle populations in the solar wind, including direct acceleration at flares, stochastic acceleration, shock acceleration, and acceleration by random compression or reconnection sites. Using magnetic field and suprathermal particle data from the Advanced Composition Explorer (ACE), we identify coherent structures and interplanetary shocks, and analyze the temporal association of energetic particle fluxes with these coherent structures. Coherent structures having a range of intensities are identified using the magnetic Partial Variance of Increments statistic, essentially a normalized vector increment. A stronger association of energetic particle flux in the 0.047-4.75 MeV range is found with intense magnetic discontinuities than is found with shocks. Nevertheless, the average profile of suprathermals near shocks is quite consistent with standard models of diffusive shock acceleration, while a significant amount of the energetic particles measured and strong discontinuities are found by ACE within six hours of a shock. This evidence supports the view that multiple mechanisms contribute to the acceleration and transport of interplanetary suprathermal particles.

  2. Fluoride Inhibition of Enolase: Crystal Structure and Thermodynamics?†

    PubMed Central

    Qin, Jie; Chai, Geqing; Brewer, John M.; Lovelace, Leslie L.; Lebioda, Lukasz

    2008-01-01

    Enolase is a dimeric metal-activated metalloenzyme, which uses two magnesium ions per subunit: the strongly bound conformational ion and the catalytic ion that binds to the enzyme-substrate complex inducing catalysis. The crystal structure of the human neuronal enolase-Mg2F2Pi complex (enolase fluoride/phosphate inhibitory complex, EFPIC) determined at 1.36 Å resolution shows that the combination of anions effectively mimics an intermediate state in catalysis. The phosphate ion binds in the same site as the phosphate group of the substrate/product, 2-phospho-D-glycerate/phosphoenolpyruvate, and induces binding of catalytic Mg2+ ion. One fluoride ion bridges the structural and catalytic magnesium ions while the other interacts with the structural magnesium ion and the ammonio groups of Lys 342 and Lys 393. These fluoride ion positions correspond closely to the positions of the oxygen atoms of the substrate's carboxylate moiety. To relate structural changes resulting from fluoride, phosphate and magnesium ions binding to those that are induced by phosphate and magnesium ions alone, we also determined the structure of the human neuronal enolase-Mg2Pi complex (enolase phosphate inhibitory complex, EPIC) at 1.92 Å resolution. It shows the closed conformation in one subunit and a mixture of open and semi-closed conformations in the other. The EPFIC dimer is essentially symmetric while EPIC dimer is asymmetric. Isothermal titration calorimetry data confirmed binding of four fluoride ions per dimer and yielded Kb values of 7.5 × 105 ± 1.3 × 105, 1.2 × 105 ± 0.2 × 105, 8.6 × 104 ± 1.6 × 104, 1.6 × 104 ± 0.7 × 104 M?1. The different binding constants indicate negative cooperativity between the subunits; the asymmetry of EPIC supports such an interpretation. PMID:16411755

  3. Gas-flow-induced reorientation to centimeter-sized two-dimensional colloidal single crystal of polystyrene particle.

    PubMed

    Meng, Xiaohui; Qiu, Dong

    2014-03-25

    Centimeter-sized two-dimensional (2D) colloidal single crystals of polystyrene (PS) particles were fabricated at the water/air interface by capillary-modulated self-assembly. Different from previous reports, in this work, emulsifier was used to facilitate the stress release during 2D colloidal crystal formation by adjusting the interparticle lateral interactions. With the assistance of compressed nitrogen flow, 2D hexagonal colloidal single crystals of centimeter size were obtained under appropriate emulsifier concentrations. A new method was also developed to transfer the 2D colloidal crystals from the air/water interface to the desired substrate without obvious disturbance. This new transferring method was proven not to be sensitive to surface wettability nor curvature, thus 2D colloidal single crystals with large areas could be obtained on different kinds of substrate. PMID:24588268

  4. Slow encounters of particle pairs in branched structures.

    PubMed

    Agliari, Elena; Blumen, Alexander; Cassi, Davide

    2014-05-01

    On infinite homogeneous structures, two random walkers meet with certainty if and only if the structure is recurrent; i.e., a single random walker returns to its starting point with probability 1. However, on general inhomogeneous structures this property does not hold, and, although a single random walker will certainly return to its starting point, two moving particles may never meet. This striking property has been shown to hold, for instance, on infinite combs. Due to the huge variety of natural phenomena which can be modeled in terms of encounters between two (or more) particles diffusing in comblike structures, it is fundamental to investigate if and, if so, to what extent similar effects may take place in finite structures. By means of numerical simulations we provide evidence that, indeed, even on finite structures, the topological inhomogeneity can qualitatively affect the two-particle problem. In particular, the mean encounter time can be polynomially larger than the time expected from the related one-particle problem. PMID:25353779

  5. Relationships between crystal structure and magnetic properties in Nd 2 Fe 14 B

    Microsoft Academic Search

    Jan F. Herbst; John J. Croat; Frederick E. Pinkerton

    1984-01-01

    Determination of the crystal structure of Nd2Fe14B, a new ternary phase, is reported. It has recently been demonstrated that permanent magnets having large co? ercivities and energy products can be formed from this phase, underscoring its potential technological impor? tance. We relate the crystal structure and intrinsic mag? netic properties by considering analogies with previously known rareearthtransitionmetal materials.

  6. The crystal structure and growth direction of nanowire arraysCu fabricated on a copper surface

    E-print Network

    Wang, Zhong L.

    The crystal structure and growth direction of nanowire arraysCu 2 S fabricated on a copper surface We examine the crystal structure and growth direction of nanowire arrays grown from copper surfaces10 On this line, we have recently discovered that by exposing a surfactant-treated copper surface

  7. Crystal Structure of Venus, a Yellow Fluorescent Protein with Improved Maturation and Reduced Environmental Sensitivity*

    E-print Network

    Ikura, Mitsuhiko

    Crystal Structure of Venus, a Yellow Fluorescent Protein with Improved Maturation and Reduced necessitated further mutagenesis studies of these proteins. Venus, a new variant with improved maturation the crystal structure of Venus at 2.2 Å resolution, which enabled us to correlate its novel features

  8. Crystal structure of rabbit muscle creatine kinase J.K. Mohana RaoY

    E-print Network

    Crystal structure of rabbit muscle creatine kinase J.K. Mohana RaoY *, Grzegorz BujaczY , Alexander Abstract The crystal structure of rabbit muscle creatine kinase, solved at 2.35 Aî resolution by X of arginine residues. The putative binding site of creatine, which is occupied by a sulfate group

  9. Crystal structure of mouse coronavirus receptor-binding domain complexed with its murine receptor

    E-print Network

    Li, Fang

    expansion. Mouse hepatitis coronavirus (MHV) uses the N-terminal domain (NTD) of its spike protein as itsCrystal structure of mouse coronavirus receptor- binding domain complexed with its murine receptor receptor- binding domain. Here we present the crystal structure of MHV NTD complexed with its receptor

  10. Advanced piezoelectric crystal Ca3TaGa3Si2O14: growth, crystal structure perfection, and acoustic properties

    NASA Astrophysics Data System (ADS)

    Roshchupkin, Dmitry; Ortega, Luc; Plotitcyna, Olga; Erko, Alexei; Zizak, Ivo; Irzhak, Dmitry; Fahrtdinov, Rashid; Buzanov, Oleg

    2014-03-01

    A five-component crystal of the lanthanum-gallium silicate family Ca3TaGa3Si2O14 (CTGS) was grown by the Czochralski method. The CTGS crystal, like the langasite crystal (La3Ga5SiO14, LGS), possesses unique temperature properties and the fewer number of the Ga atoms in the unit cell makes the density much lower and, consequently, increases the velocity of acoustic wave propagation. The unit-cell parameters were determined by the powder diffraction technique. The defects in the CTGS crystal structure were studied by X-ray topography, which enables the visualization of growth banding characteristics of crystals grown by the Czochralski method. Surface acoustic wave (SAW) propagation in the CTGS crystal was investigated by the high-resolution X-ray diffraction method on the BESSY II synchrotron radiation source. The velocities of propagation and power flow angles of SAWs in the Y- and X-cuts of the CTGS crystal were determined from the X-ray diffraction spectra.

  11. Protein crystal growth on board Shenzhou 3: a concerted effort improves crystal diffraction quality and facilitates structure determination.

    PubMed

    Han, Y; Cang, H-X; Zhou, J-X; Wang, Y-P; Bi, R-C; Colelesage, J; Delbaere, L T J; Nahoum, V; Shi, R; Zhou, M; Zhu, D-W; Lin, S-X

    2004-11-19

    The crystallization of 16 proteins was carried out using 60 wells on board Shenzhou 3 in 2002. Although the mission was only 7 days, careful and concerted planning at all stages made it possible to obtain crystals of improved quality compared to their ground controls for some of the proteins. Significantly improved resolutions were obtained from diffracted crystals of 4 proteins. A complete data set from a space crystal of the PEP carboxykinase yielded significantly higher resolution (1.46A vs. 1.87A), I/sigma (22.4 vs. 15.5), and a lower average temperature factor (29.2A(2) vs. 42.9A(2)) than the best ground-based control crystal. The 3-D structure of the enzyme is well improved with significant ligand density. It has been postulated that the reduced convection and absence of macromolecule sedimentation under microgravity have advantages/benefits for protein crystal growth. Improvements in experimental design for protein crystal growth in microgravity are ongoing. PMID:15485665

  12. Structure of a tractable stochastic mimic of soft particles.

    PubMed

    Craven, Galen T; Popov, Alexander V; Hernandez, Rigoberto

    2014-08-01

    The structure and assembly of soft particles is difficult to characterize because their interpenetrability allows them to be packed at ever higher density albeit with an increasing penalty in energy and/or pressure. Alternatively, the use of impenetrable particles (such as hard spheres) as a reference model for soft particles can fail because the packing densities are limited by the impossibility of complete space filling. We recently introduced the stochastic penetration algorithm (SPA) so as to allow for the computationally efficient integration of hard sphere models while including overlaps seen in soft interactions [Craven et al., J. Chem. Phys., 2013, 138, 244901]. Moving beyond the initial one-dimensional case studied earlier, we now consider the spatial properties of systems of stochastically penetrable spheres in dimensions d? 3 through the use of molecular dynamics simulations and analytic methods. The stochastic potential allows spheres to either interpenetrate with a probability ? or collide elastically otherwise. For ? > 0 the particles interpenetrate (overlap), reducing the effective volume occupied by the particles in the system. We find that the occupied volume can be accurately predicted using analytic expressions derived from mean field arguments for the particle overlap probabilities with the exception of an observed clustering regime. This anomalous clustering behavior occurs at high densities and small ?. We find that this regime is coincident with that observed in deterministic penetrable models. The behavior of the stochastic penetrable particles also indicates that soft particles would be characterizable through a single reduced parameter that captures their overlap probability. PMID:24935651

  13. Particle-Free Extraction by Using Microchannel Structures

    NASA Astrophysics Data System (ADS)

    Leu, Tzong-Shyng; Pai, Ching-Yi

    Modern separation methods of particles are usually prepared by large equipments. In this study, microfluidic chips with backward-facing-step (BFS) microchannel structures and centrifugal force are used to extract particle-free fluid from physical samples at the branch. Numerical simulation and experimental studies were performed to investigate the effects of inlet Reynolds number (Re0), as well as the particle-free fluid outlet Reynolds number (Re1), on the minimum radius of particles (R) that can be excluded from the particle-free fluid outlet channel. The fraction of the volumetric flow rate of particle-free extraction ? (=extraction flow rate/inlet flow rate) was also obtained to evaluate the efficiency of particle-free extraction. Based on the numerical and experimental results, it is found that the design with 90° elbow inlet channel has a better performance than straight inlet channel. In this experiment, 1.0 ?m radius of particles can be successfully separated from the fluid, and the volumetric fraction of the extraction flow rate was approximately 1.8% when inlet and outlet Reynolds numbers are 90 and 3.0 respectively.

  14. Normal-Coordinate Structural Decomposition of Heme Conformations in Protein Crystal Structures

    NASA Astrophysics Data System (ADS)

    Zhang, Jun; Zhang, Jun; Jia, Songling; Ma, Jianguo; Shelnutt, John A.

    1998-03-01

    All hemes from X-ray crystal structures in the Protein Data Bank have been analyzed using normal-coordinate structural decomposition(NSD). Complicated nonplanar heme distortions are caused by the asymmetric protein environment. NSD characterizes the out-of-plane and in-plane distortions of each heme by giving equivalent displacements along the normal coordinates of the D4h-symmetric porphyrin macrocycle. Even for highly distorted porphyrins, the macrocyclic structure can be accurately represented by displacements along only the lowest-frequency normal coordinates. The simplification of the structural description given by NSD reveals heme structural motifs for the proteins. These often conserved structural motifs were previously hidden in the complicated distortions of the hemes. The functional significance of the heme deformations is discussed. (Supported by US DOE Contract DE-AC04-94AL85000.)

  15. Synthesis, growth, crystal structure and characterization of a new organic NLO crystal: L-Lysine 4-nitrophenolate monohydrate (LLPNP)

    NASA Astrophysics Data System (ADS)

    Mahadevan, M.; Magesh, M.; Ramachandran, K.; Anandan, P.; Arivanandhan, M.; Hayakawa, Y.

    2014-09-01

    L-Lysine 4-nitrophenolate monohydrate (LLPNP) has been synthesized and grown by solution growth method at room temperature using deionised water as a solvent. The crystal structure of the materials was solved by single crystal X-ray diffraction analysis and it was found that the material has orthorhombic system. The crystallinity of the grown crystals was studied by the powder X-ray diffraction analysis. Molecular structure of the grown crystal was investigated by 1H NMR spectroscopy. The various functional groups of the sample were identified by Fourier transform infrared and Fourier transform-Raman spectroscopic analyses. Thermal stability of the grown crystal has been studied by Thermogravimetric and Differential thermal (TG&DTA) analysis. The optical absorption of the grown crystals has been ascertained by UV-Vis-NIR absorption studies. Second harmonic generation (SHG) efficiency of the material has been determined by Kurtz and Perry technique and the efficiency was found to be 4.45 and 1.4 times greater than that of standard KDP and urea samples, respectively.

  16. Synthesis, growth, structural, thermal and optical studies of pyrrolidinium-2-carboxylate-4-nitrophenol single crystals

    NASA Astrophysics Data System (ADS)

    Swarna Sowmya, N.; Sampathkrishnan, S.; Vidyalakshmi, Y.; Sudhahar, S.; Mohan Kumar, R.

    2015-06-01

    Organic nonlinear optical material, pyrrolidinium-2-carboxylate-4-nitrophenol (PCN) was synthesized and single crystals were grown by slow evaporation solution growth method. Single crystal X-ray diffraction analysis confirmed the structure and lattice parameters of PCN crystals. Infrared, Raman and NMR spectral analyses were used to elucidate the functional groups present in the compound. The thermal behavior of synthesized compound was studied by thermogravimetric and differential scanning calorimetry (TG-DSC) analyses. The photoluminescence property was studied by exciting the crystal at 360 nm. The relative second harmonic generation (SHG) efficiency of grown crystal was estimated by using Nd:YAG laser with fundamental wavelength of 1064 nm.

  17. Refinement of the crystal structure ?-Al 9FeMg 3Si 5

    Microsoft Academic Search

    R Krendelsberger; P Rogl; A Leithe-Jasper; C. J Simensen

    1998-01-01

    The crystal structure of the quaternary so-called ?-phase, which was originally solved from photographic single crystal data, has been refined from single crystal automatic four circle counter data. Single crystals were obtained from the residue of a slowly cooled melt of nominal composition (in at%) Al74.1Fe0.5Mg8.4Si17.0, which was dissolved in butanol. The composition of the ?-phase crystal was Al9Fe1Mg3.5Si5.0. The

  18. A microfluidic device for kinetic optimization of protein crystallization and in situ structure determination.

    PubMed

    Hansen, Carl L; Classen, Scott; Berger, James M; Quake, Stephen R

    2006-03-15

    The unprecedented economies of scale and unique mass transport properties of microfluidic devices made them viable nano-volume protein crystallization screening platforms. However, realizing the full potential of microfluidic crystallization requires complementary technologies for crystal optimization and harvesting. In this paper, we report a microfluidic device which provides a link between chip-based nanoliter volume crystallization screening and structure analysis through "kinetic optimization" of crystallization reactions and in situ structure determination. Kinetic optimization through systematic variation of reactor geometry and actuation of micromechanical valves is used to screen a large ensemble of kinetic trajectories that are not practical with conventional techniques. Using this device, we demonstrate control over crystal quality, reliable scale-up from nanoliter volume reactions, facile harvesting and cryoprotectant screening, and protein structure determination at atomic resolution from data collected in-chip. PMID:16522084

  19. CARS polarized microscopy of three-dimensional director structures in liquid crystals

    E-print Network

    A. V. Kachynski; A. N. Kuzmin; P. N. Prasad; I. I. Smalyukh

    2007-10-18

    We demonstrate three-dimensional vibrational imaging of director structures in liquid crystals using coherent anti-Stokes Raman scattering (CARS) polarized microscopy. Spatial mapping of the structures is based on sensitivity of a polarized CARS signal to orientation of anisotropic molecules in liquid crystals. As an example, we study structures in a smectic material and demonstrate that single-scan CARS and two-photon fluorescence images of molecular orientation patterns are consistent with each other and with the structure model.

  20. The structure of ice crystallized from supercooled water

    NASA Astrophysics Data System (ADS)

    Murray, Benjamin

    2013-03-01

    The freezing of water to ice is fundamentally important to fields as diverse as cloud formation to cryopreservation. Traditionally ice was thought to exist in two well-crystalline forms: stable hexagonal ice and metastable cubic ice. It has recently been shown, using X-ray diffraction data, that ice which crystallizes homogeneously and heterogeneously from supercooled water is neither of these phases. The resulting ice is disordered in one dimension and therefore possesses neither cubic nor hexagonal symmetry and is instead composed of randomly stacked layers of cubic and hexagonal sequences. We refer to this ice as stacking-disordered ice I (ice Isd) . This result is consistent with a number of computational studies of the crystallization of water. Review of the literature reveals that almost all ice that has been identified as cubic ice in previous diffraction studies and generated in a variety of ways was most likely stacking-disordered ice I with varying degrees of stacking disorder, which raises the question of whether cubic ice exists. New data will be presented which shows significant stacking disorder (or stacking faults on the order of 1 in every 100 layers of ice Ih) in droplets which froze heterogeneously as warm as 257 K. The identification of stacking-disordered ice from heterogeneous ice nucleation supports the hypothesis that the structure of ice that initially crystallises from supercooled water is stacking-disordered ice I, independent of nucleation mechanism, but this ice can relax to the stable hexagonal phase subject to the kinetics of recrystallization. The formation and persistence of stacking disordered ice in the Earth's atmosphere will also be discussed. The freezing of water to ice is fundamentally important to fields as diverse as cloud formation to cryopreservation. Traditionally ice was thought to exist in two well-crystalline forms: stable hexagonal ice and metastable cubic ice. It has recently been shown, using X-ray diffraction data, that ice which crystallizes homogeneously and heterogeneously from supercooled water is neither of these phases. The resulting ice is disordered in one dimension and therefore possesses neither cubic nor hexagonal symmetry and is instead composed of randomly stacked layers of cubic and hexagonal sequences. We refer to this ice as stacking-disordered ice I (ice Isd) . This result is consistent with a number of computational studies of the crystallization of water. Review of the literature reveals that almost all ice that has been identified as cubic ice in previous diffraction studies and generated in a variety of ways was most likely stacking-disordered ice I with varying degrees of stacking disorder, which raises the question of whether cubic ice exists. New data will be presented which shows significant stacking disorder (or stacking faults on the order of 1 in every 100 layers of ice Ih) in droplets which froze heterogeneously as warm as 257 K. The identification of stacking-disordered ice from heterogeneous ice nucleation supports the hypothesis that the structure of ice that initially crystallises from supercooled water is stacking-disordered ice I, independent of nucleation mechanism, but this ice can relax to the stable hexagonal phase subject to the kinetics of recrystallization. The formation and persistence of stacking disordered ice in the Earth's atmosphere will also be discussed. Funded by the European Research Council (FP7, 240449 ICE)

  1. Dynamics of supramolecular structures induced in liquid crystals

    NASA Astrophysics Data System (ADS)

    Kapustina, O. A.

    2015-01-01

    A theory is experimentally validated for the first time, which describes (within nonequilibrium hydrodynamics) the properties of supramolecular spatially periodic structures in a planar layer of a cholesteric liquid crystal at ultrasound intensities exceeding the threshold of their formation in a frequency range where the wavelength is larger than the cholesteric helix pitch. Distortions in the layer texture in planar and wedgeshaped capillaries with planar boundary conditions at normal incidence of longitudinal waves have been observed for the frequency range of 1-4 MHz. The domain periods at the threshold of the effect and above it are determined for layers 20-100 ?m thick at helix pitch values of 2-10 ?m. The dependences of the domain period on the ultrasound intensity and the preliminary layer extension have been established. A model constructed with allowance for structural relaxation processes and nonlinear relaxation phenomena is tested. It is shown that a complete description of the effect, which is consistent with the experimental data, can be obtained only using approach.

  2. Crystal Structure of a Full-Length [beta]-Catenin

    SciTech Connect

    Xing, Yi; Takemaru, Ken-Ichi; Liu, Jing; Berndt, Jason D.; Zheng, Jie J.; Moon, Randall T.; Xu, Wenqing (UW-MED); (SJCH)

    2008-08-19

    {beta}-catenin plays essential roles in cell adhesion and Wnt signaling, while deregulation of {beta}-catenin is associated with multiple diseases including cancers. Here, we report the crystal structures of full-length zebrafish {beta}-catenin and a human {beta}-catenin fragment that contains both the armadillo repeat and the C-terminal domains. Our structures reveal that the N-terminal region of the C-terminal domain, a key component of the C-terminal transactivation domain, forms a long {alpha} helix that packs on the C-terminal end of the armadillo repeat domain, and thus forms part of the {beta}-catenin superhelical core. The existence of this helix redefines our view of interactions of {beta}-catenin with some of its critical partners, including ICAT and Chibby, which may form extensive interactions with this C-terminal domain {alpha} helix. Our crystallographic and NMR studies also suggest that the unstructured N-terminal and C-terminal tails interact with the ordered armadillo repeat domain in a dynamic and variable manner.

  3. Modulated structures in electroconvection in nematic liquid crystals.

    PubMed

    Komineas, S; Zhao, H; Kramer, L

    2003-03-01

    Motivated by experiments in electroconvection in nematic liquid crystals with homeotropic alignment we study the coupled amplitude equations describing the formation of a stationary roll pattern in the presence of a weakly damped mode that breaks isotropy. The equations can be generalized to describe the planarly aligned case if the orienting effect of the boundaries is small, which can be achieved by a destabilizing magnetic field. The slow mode represents the in-plane director at the center of the cell. The simplest uniform states are normal rolls, which may undergo a pitchfork bifurcation to abnormal rolls with a misaligned in-plane director. We present a new class of defect-free solutions with spatial modulations perpendicular to the rolls. In a parameter range where the zigzag instability is not relevant these solutions are stable attractors, as observed in experiments. We also present two-dimensionally modulated states with and without defects which result from the destabilization of the one-dimensionally modulated structures. Finally, for no (or very small) damping, and away from the rotationally symmetric case, we find static chevrons made up of a periodic arrangement of defect chains (or bands of defects) separating homogeneous regions of oblique rolls with very small amplitude. These states may provide a model for a class of poorly understood stationary structures observed in various highly conducting materials ("prechevrons" or "broad domains"). PMID:12689082

  4. Crystal structure of isopentenyl diphosphate:dimethylallyl diphosphate isomerase

    PubMed Central

    Durbecq, Virginie; Sainz, Germaine; Oudjama, Yamina; Clantin, Bernard; Bompard-Gilles, Coralie; Tricot, Catherine; Caillet, Joël; Stalon, Victor; Droogmans, Louis; Villeret, Vincent

    2001-01-01

    Isopentenyl diphosphate:dimethylallyl diphosphate (IPP:DMAPP) isomerase catalyses a crucial activation step in the isoprenoid biosynthesis pathway. This enzyme is responsible for the isomerization of the carbon–carbon double bond of IPP to create the potent electrophile DMAPP. DMAPP then alkylates other molecules, including IPP, to initiate the extraordinary variety of isoprenoid compounds found in nature. The crystal structures of free and metal-bound Escherichia coli IPP isomerase reveal critical active site features underlying its catalytic mechanism. The enzyme requires one Mn2+ or Mg2+ ion to fold in its active conformation, forming a distorted octahedral metal coordination site composed of three histidines and two glutamates and located in the active site. Two critical residues, C67 and E116, face each other within the active site, close to the metal-binding site. The structures are compatible with a mechanism in which the cysteine initiates the reaction by protonating the carbon–carbon double bond, with the antarafacial rearrangement ultimately achieved by one of the glutamates involved in the metal coordination sphere. W161 may stabilize the highly reactive carbocation generated during the reaction through quadrupole– charge interaction. PMID:11285217

  5. Expression, characterization and crystal structure of thioredoxin from Schistosoma japonicum.

    PubMed

    Li, Yongdong; Li, Pan; Peng, Yun; Wu, Qunfeng; Huang, Fuyan; Liu, Xiang; Li, Xun; Zhou, Hui; Guo, Daoyi; Shi, Dashuang; Zhou, Xiao-Nong; Fan, Xiaolin

    2015-07-01

    Schistosoma japonicum, a human blood fluke, causes a parasitic disease affecting millions of people in Asia. Thioredoxin-glutathione system of S. japonicum plays a critical role in maintaining the redox balance in parasite, which is a potential target for development of novel antischistosomal agents. Here we cloned the gene of S. japonicum thioredoxin (SjTrx), expressed and purified the recombinant SjTrx in Escherichia coli. Functional assay shows that SjTrx catalyses the dithiothreitol (DTT) reduction of insulin disulphide bonds. The coupling assay of SjTrx with its endogenous reductase, thioredoxin glutathione reductase from S. japonicum (SjTGR), supports its biological function to maintain the redox homeostasis in the cell. Furthermore, the crystal structure of SjTrx in the oxidized state was determined at 2·0 Å resolution, revealing a typical architecture of thioredoxin fold. The structural information of SjTrx provides us important clues for understanding the maintenance function of redox homeostasis in S. japonicum and pathogenesis of this chronic disease. PMID:25810021

  6. Structure and dissolution of L-leucine-coated salbutamol sulphate aerosol particles.

    PubMed

    Raula, Janne; Seppälä, Jukka; Malm, Jari; Karppinen, Maarit; Kauppinen, Esko I

    2012-06-01

    L-Leucine formed different crystalline coatings on salbutamol sulphate aerosol particles depending on the saturation conditions of L-leucine. The work emphasizes a careful characterization of powders where structural compartments such as crystal size and particle coating may affect the performance of drug when administered. The sublimation of L-leucine from the aerosol particles took place 90°C lower temperature than the bulk L-leucine which was attributed to result from the sublimation of L-leucine from nano-sized crystalline domains. The dissolution slowed down and initial dissolution rate decreased with increasing L-leucine content. Decreasing crystalline domains to nano-scale improve heat and mass transfer which was observed as the lowered decomposition temperature of the drug salbutamol sulphate and the sublimation temperature of surface material L-leucine as well as the altered dissolution characteristics of the drug. The structure of the coated drug particles was studied by means of thermal analysis techniques (DSC and TG), and the dissolution of salbutamol sulphate was studied as an on-line measurement in a diffusion cell. PMID:22562614

  7. A model of whisker crystal growth from a pentagonal small particle

    NASA Astrophysics Data System (ADS)

    Romanov, A. E.; Dorogin, L. M.; Kolesnikova, A. L.; Kink, I.; Yasnikov, I. S.; Vikarchuk, A. A.

    2014-02-01

    We present a physical model of growth of whisker crystals from metal pentagonal small particles (PSPs). The model is based upon the notions of nucleation and slippage of prismatic dislocation loops in the elastic field of disclination defects that are inherent in PSPs. In the framework of this model, the escape of interstitial dislocation loops at the PSP surface leads to an increase in the whisker length relative to the base, while incorporation of the vacancy-type loops is accompanied by their accumulation on the internal surface. The model is illustrated by calculations that show a gain in the total PSP energy as a result of the formation of a pair of prismatic dislocation loops with opposite signs.

  8. Structure and biodegradation mechanism of milled Bombyx mori silk particles.

    PubMed

    Rajkhowa, Rangam; Hu, Xiao; Tsuzuki, Takuya; Kaplan, David L; Wang, Xungai

    2012-08-13

    The aim of this study was to understand the structure and biodegradation relationships of silk particles intended for targeted biomedical applications. Such a study is also useful in understanding structural remodelling of silk debris that may be generated from silk-based implants. Ultrafine silk particles were prepared using a combination of efficient wet-milling and spray-drying processes with no addition of chemicals other than those used in degumming. Milling reduced the intermolecular stacking forces within the ?-sheet crystallites without changing the intramolecular binding energy. Because of the rough morphology and the ultrafine size of the particles, degradation of silk particles by protease XIV was increased by about 3-fold compared to silk fibers. Upon biodegradation, the thermal degradation temperature of silk increased, which was attributed to the formation of tight aggregates by the hydrolyzed residual macromolecules. A model of the biodegradation mechanism of silk particles was developed based on the experimental data. The model explains the process of disintegration of ?-sheets, supported by quantitative secondary structural analysis and microscopic images. PMID:22746375

  9. Chirality Effects on the Morphology and Structure of Synthetic Chiral Main-chain Liquid Crystal Polyesters

    NASA Astrophysics Data System (ADS)

    Weng, X.; Li, C. Y.; Zhang, J. Z.; Bai, F.; Jin, S.; Harris, F. W.; Cheng, S. Z. D.

    2002-03-01

    The main-chain liquid crystal chiral polyesters are synthesized via an A-B type condensation polymerization from (R)-(-)-4'-w-[2-(p-hydroxy-o-nitrophenyloxy)-1-propyloxy]-1-alkyloxy-4- biphenyl carboxylic acid. The resulting polymers, abbreviated as PET(R*-10,11), exhibit multiple chiral liquid crystal phases, including chiral Smectic A* and C* phases, at different temperatures as identified by polarized optical microscopy, differential scanning calorimetry and wide angle X-ray diffraction (WAXD). For PET(R*-11), flat and helical single lamellar crystals have been obtained in the melt crystallization and solvent evaporation. All helical crystals show a right-handed twist with pitch lengths on a micrometer size as observed by transmission electron microscopy and atomic force microscopy. The crystal structures of the flat and helical crystals are determined to be identical (orthorhombic with a=1.03 nm, b=0.47 nm, c=6.43 nm) by electron diffraction and WAXD fiber pattern experiments. Rotation twin crystals in flat geometry are also observed by melt crystallization. Surprisingly, the helical crystals of PET(R*-10) prepared from the similar process are all left-handed. The structure of the flat crystal of PET(R*-10) can be explained as “micro-twin” based on the results of electron diffraction.

  10. Lagrangian coherent structures and the dynamics of inertial particles

    NASA Astrophysics Data System (ADS)

    Madhavan, Sudharsan

    Dynamics of inertial particles in two-dimensional planar flow have been investigated by evaluating finite-time Lyapunov exponents (FTLE). The first part of our work deals with inertial particle dynamics. The Maxey-Riley equations have been employed to track particles. Patterns formed by inertial particles are reported along with their dependance on Strokes number and density of particles relative to the carrier-fluid density. Our results distinguish patterns formed by particles denser than the fluid (aerosols) from those formed by particles lighter than the fluid (bubbles). Preferential concentration of these particles at specific regions of the flow have been observed. The attenuating, low-pass filter effect of Stokes drag on bubbles are reported for the first time. The results from this part of the work motivated further investigations into the underlying organizing structures of the flow, namely the Lagrangian coherent structures (LCS). LCS is traditionally evaluated using FTLE. In the next part of the work, our objective was to interpret the dynamics of inertial particles by evaluating finite-time Lyapunov exponents on their trajectories. A main result is that aerosols were found to be attracted and preferentially concentrated along ridges of negative finite-time Lyapunov exponents (nFTLE) of the underlying flow. On the other hand bubbles were found to be repelled from these structures and were therefore observed preferentially concentrating away from these zones. These results, being reported for the first time, supplement the existing literature on preferential concentration of inertial particles. Despite having an effect on particle trajectories, increasing the Stokes number had very little effect on inertial finite-time Lyapunov exponents (iFTLE). Furthermore, increasing Stokes number resulted in an increase in the ridges of iFTLE contours for aerosols, whereas for bubbles the opposite was observed. These findings indicate that optimum mixing occurs at different Stokes numbers for aerosols and bubbles. The last part of the work focussed on comparing well-known dispersion measures with inertial finite-time Lyapunov exponents. We qualitatively show that two-point dispersion contours share dominant ridges with those from inertial finite-time Lyapunov exponents. This result numerically shows that material surfaces identified by inertial finite-time Lyapunov exponents are maximally dispersed in the flow. Applications and future directions based on our work are suggested.

  11. Nonlinear optics determination of the symmetry group of a crystal using structured light

    E-print Network

    Jauregui, Rocio

    2015-01-01

    We put forward a technique to unveil to which symmetry group a nonlinear crystal belongs, making use of nonlinear optics with structured light. We consider as example the process of spontaneous parametric down-conversion. The crystal, which is illuminated with a special type of Bessel beam, is characterized by a nonlinear susceptibility tensor whose structure is dictated by the symmetry group of the crystal. The observation of the spatial angular dependence of the lower-frequency generated light provides direct information about the symmetry group of the crystal.

  12. STRUCTURAL VIROLOGY. X-ray crystal structures of native HIV-1 capsid protein reveal conformational variability.

    PubMed

    Gres, Anna T; Kirby, Karen A; KewalRamani, Vineet N; Tanner, John J; Pornillos, Owen; Sarafianos, Stefan G

    2015-07-01

    The detailed molecular interactions between native HIV-1 capsid protein (CA) hexamers that shield the viral genome and proteins have been elusive. We report crystal structures describing interactions between CA monomers related by sixfold symmetry within hexamers (intrahexamer) and threefold and twofold symmetry between neighboring hexamers (interhexamer). The structures describe how CA builds hexagonal lattices, the foundation of mature capsids. Lattice structure depends on an adaptable hydration layer modulating interactions among CA molecules. Disruption of this layer alters interhexamer interfaces, highlighting an inherent structural variability. A CA-targeting antiviral affects capsid stability by binding across CA molecules and subtly altering interhexamer interfaces remote to the ligand-binding site. Inherent structural plasticity, hydration layer rearrangement, and effector binding affect capsid stability and have functional implications for the retroviral life cycle. PMID:26044298

  13. Single crystal growth, crystal structure and characterization of a novel crystal: L-arginine 4-nitrophenolate 4-nitrophenol dehydrate (LAPP)

    NASA Astrophysics Data System (ADS)

    Wang, L. N.; Wang, X. Q.; Zhang, G. H.; Liu, X. T.; Sun, Z. H.; Sun, G. H.; Wang, L.; Yu, W. T.; Xu, D.

    2011-07-01

    A novel organic crystal, L-arginine 4-nitrophenolate 4-nitrophenol dehydrate (LAPP), synthesized and grown from aqueous solution, is presented. X-ray single diffraction shows that LAPP belongs to the monoclinic crystallographic system with space group P2 1. FT-IR and UV/vis/NIR transmission spectra have been employed to characterize the crystal. The computational calculation based on the density functional theory at the B3LYP/6-31G (d, p) level has been used to compute the first-order hyperpolarizability of LAPP relating to different molecular models. The morphology, nonlinear characteristic and thermal stability of the crystal have also been investigated.

  14. Crystal structure of complex natural aluminum magnesium calcium iron oxide

    SciTech Connect

    Rastsvetaeva, R. K., E-mail: rast@ns.crys.ras.ru; Aksenov, S. M.; Verin, I. A. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2010-07-15

    The structure of a new natural oxide found near the Tashelga River (Eastern Siberia) was studied by X-ray diffraction. The pseudo-orthorhombic unit cell parameters are a = 5.6973(1) A, b = 17.1823(4) A, c = 23.5718(5) A, {beta} = 90{sup o}, sp. gr. Pc. The structure was refined to R = 0.0516 based on 4773 reflections with vertical bar F vertical bar > 7{sigma}(F) taking into account the twin plane perpendicular to the z axis (the twin components are 0.47 and 0.53). The crystal-chemical formula (Z = 4) is Ca{sub 2}Mg{sub 2}{sup IV}Fe{sub 2}{sup (2+)IV}[Al{sub 14}{sup VI}O{sub 31}(OH)][Al{sub 2}{sup IV}O][Al{sup IV}]AL{sup IV}(OH)], where the Roman numerals designate the coordination of the atoms. The structure of the mineral is based on wide ribbons of edge-sharing Al octahedra (an integral part of the spinel layer). The ribbons run along the shortest x axis and are inclined to the y and z axes. The adjacent ribbons are shifted with respect to each other along the y axis, resulting in the formation of step-like layers in which the two-ribbon thickness alternates with the three-ribbon thickness. Additional Al octahedra and Mg and Fe{sup 2+} tetrahedra are located between the ribbons. The layers are linked together to form a three-dimensional framework by Al tetrahedra, Ca polyhedra, and hydrogen bonds with the participation of OH groups.

  15. The Crystal Structure of Toxoplasma gondii Pyruvate Kinase 1

    SciTech Connect

    Bakszt, R.; Wernimont, A; Allali-Hassani, A; Mok, M; Hills, T; Hui, R; Pizarro, J

    2010-01-01

    Pyruvate kinase (PK), which catalyzes the final step in glycolysis converting phosphoenolpyruvate to pyruvate, is a central metabolic regulator in most organisms. Consequently PK represents an attractive therapeutic target in cancer and human pathogens, like Apicomplexans. The phylum Aplicomplexa, a group of exclusively parasitic organisms, includes the genera Plasmodium, Cryptosporidium and Toxoplasma, the etiological agents of malaria, cryptosporidiosis and toxoplasmosis respectively. Toxoplasma gondii infection causes a mild illness and is a very common infection affecting nearly one third of the world's population. We have determined the crystal structure of the PK1 enzyme from T. gondii, with the B domain in the open and closed conformations. We have also characterized its enzymatic activity and confirmed glucose-6-phosphate as its allosteric activator. This is the first description of a PK enzyme in a closed inactive conformation without any bound substrate. Comparison of the two tetrameric TgPK1 structures indicates a reorientation of the monomers with a concomitant change in the buried surface among adjacent monomers. The change in the buried surface was associated with significant B domain movements in one of the interacting monomers. We hypothesize that a loop in the interface between the A and B domains plays an important role linking the position of the B domain to the buried surface among monomers through two {alpha}-helices. The proposed model links the catalytic cycle of the enzyme with its domain movements and highlights the contribution of the interface between adjacent subunits. In addition, an unusual ordered conformation was observed in one of the allosteric binding domains and it is related to a specific apicomplexan insertion. The sequence and structural particularity would explain the atypical activation by a mono-phosphorylated sugar. The sum of peculiarities raises this enzyme as an emerging target for drug discovery.

  16. Crystal structure of the entire respiratory complex I.

    PubMed

    Baradaran, Rozbeh; Berrisford, John M; Minhas, Gurdeep S; Sazanov, Leonid A

    2013-02-28

    Complex I is the first and largest enzyme of the respiratory chain and has a central role in cellular energy production through the coupling of NADH:ubiquinone electron transfer to proton translocation. It is also implicated in many common human neurodegenerative diseases. Here, we report the first crystal structure of the entire, intact complex I (from Thermus thermophilus) at 3.3?Å resolution. The structure of the 536-kDa complex comprises 16 different subunits, with a total of 64 transmembrane helices and 9 iron-sulphur clusters. The core fold of subunit Nqo8 (ND1 in humans) is, unexpectedly, similar to a half-channel of the antiporter-like subunits. Small subunits nearby form a linked second half-channel, which completes the fourth proton-translocation pathway (present in addition to the channels in three antiporter-like subunits). The quinone-binding site is unusually long, narrow and enclosed. The quinone headgroup binds at the deep end of this chamber, near iron-sulphur cluster N2. Notably, the chamber is linked to the fourth channel by a 'funnel' of charged residues. The link continues over the entire membrane domain as a flexible central axis of charged and polar residues, and probably has a leading role in the propagation of conformational changes, aided by coupling elements. The structure suggests that a unique, out-of-the-membrane quinone-reaction chamber enables the redox energy to drive concerted long-range conformational changes in the four antiporter-like domains, resulting in translocation of four protons per cycle. PMID:23417064

  17. Crystal structure of D-serine dehydratase from Escherichia coli.

    PubMed

    Urusova, Darya V; Isupov, Michail N; Antonyuk, Svetlana; Kachalova, Galina S; Obmolova, Galina; Vagin, Alexei A; Lebedev, Andrey A; Burenkov, Gleb P; Dauter, Zbigniew; Bartunik, Hans D; Lamzin, Victor S; Melik-Adamyan, William R; Mueller, Thomas D; Schnackerz, Klaus D

    2012-03-01

    D-Serine dehydratase from Escherichia coli is a member of the ?-family (fold-type II) of the pyridoxal 5'-phosphate-dependent enzymes, catalyzing the conversion of D-serine to pyruvate and ammonia. The crystal structure of monomeric D-serine dehydratase has been solved to 1.97Å-resolution for an orthorhombic data set by molecular replacement. In addition, the structure was refined in a monoclinic data set to 1.55Å resolution. The structure of DSD reveals a larger pyridoxal 5'-phosphate-binding domain and a smaller domain. The active site of DSD is very similar to those of the other members of the ?-family. Lys118 forms the Schiff base to PLP, the cofactor phosphate group is liganded to a tetraglycine cluster Gly279-Gly283, and the 3-hydroxyl group of PLP is liganded to Asn170 and N1 to Thr424, respectively. In the closed conformation the movement of the small domain blocks the entrance to active site of DSD. The domain movement plays an important role in the formation of the substrate recognition site and the catalysis of the enzyme. Modeling of D-serine into the active site of DSD suggests that the hydroxyl group of D-serine is coordinated to the carboxyl group of Asp238. The carboxyl oxygen of D-serine is coordinated to the hydroxyl group of Ser167 and the amide group of Leu171 (O1), whereas the O2 of the carboxyl group of D-serine is hydrogen-bonded to the hydroxyl group of Ser167 and the amide group of Thr168. A catalytic mechanism very similar to that proposed for L-serine dehydratase is discussed. PMID:22197591

  18. Structure analysis of inorganic crystals by energy-filtered precession electron diffraction.

    PubMed

    Kim, Jin-Gyu; Song, Kyung; Kwon, Kihyun; Hong, Kimin; Kim, Youn-Joong

    2010-01-01

    We performed structure analysis of Si single crystal and CaMoO(4) inorganic crystal by energy-filtered precession electron diffraction (PED). Structure analysis was performed using conventional selected area electron diffraction, PED and energy-filtered PED (EF-PED). The EF-PED method proved to be advantageous in determining the crystal structures and accurate cell parameters of inorganic crystals due to resolution enhancement by sharpening the peak shapes and reducing inelastic scattering. Among the EF-PED methods, zero-loss PED was most useful for structure analysis by minimizing inelastic scattering intensities, while plasmon-loss PED could be used effectively to determine crystal symmetry by closely observing the conditions of forbidden reflections. PMID:20339015

  19. Sixty years from discovery to solution: crystal structure of bovine liver catalase form III

    SciTech Connect

    Foroughi, Leila M.; Kang, You-Na; Matzger, Adam J. (Michigan)

    2012-03-27

    The crystallization and structural characterization of bovine liver catalase (BLC) has been intensively studied for decades. Forms I and II of BLC have previously been fully characterized using single-crystal X-ray diffraction. Form III has previously been analyzed by electron microscopy, but owing to the thinness of this crystal form an X-ray crystal structure had not been determined. Here, the crystal structure of form III of BLC is presented in space group P212121, with unit-cell parameters a = 68.7, b = 173.7, c = 186.3 {angstrom}. The asymmetric unit is composed of the biological tetramer, which is packed in a tetrahedron motif with three other BLC tetramers. This higher resolution structure has allowed an assessment of the previously published electron-microscopy studies.

  20. Neutron structure of monoclinic lysozyme crystals produced in microgravity

    Microsoft Academic Search

    Joseph X Ho; Jean-Paul Declercq; Dean A. A Myles; Brenda S Wright; John R Ruble; Daniel C Carter

    2001-01-01

    Crystals of the monoclinic form of lysozyme (space group P21 with a=28.00Å, b=62.88Å, c=60.30Å, ?=90.68°) were grown under microgravity conditions on the Mir station and brought back to earth on the US Space Shuttle. Counter-diffusion methods developed specifically for application in microgravity have been utilized to produce several examples of macroscopic crystals. Large crystals are of great importance for neutron