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Sample records for crystal structure particle

  1. Membrane protein structures without crystals, by single particle electron cryomicroscopy

    PubMed Central

    Vinothkumar, Kutti R

    2015-01-01

    It is an exciting period in membrane protein structural biology with a number of medically important protein structures determined at a rapid pace. However, two major hurdles still remain in the structural biology of membrane proteins. One is the inability to obtain large amounts of protein for crystallization and the other is the failure to get well-diffracting crystals. With single particle electron cryomicroscopy, both these problems can be overcome and high-resolution structures of membrane proteins and other labile protein complexes can be obtained with very little protein and without the need for crystals. In this review, I highlight recent advances in electron microscopy, detectors and software, which have allowed determination of medium to high-resolution structures of membrane proteins and complexes that have been difficult to study by other structural biological techniques. PMID:26435463

  2. Single crystal particles of a mesoporous mixed transition metal oxide with a wormhole structure.

    PubMed

    Lee, B; Lu, D; Kondo, J N; Domen, K

    2001-10-21

    A new type of mesoporous mixed transition metal oxide of Nb and Ta (NbTa-TIT-1) has been prepared through a two-step calcination, which consists of single crystal particles with wormhole mesoporous structure. PMID:12240191

  3. Single crystal structure analysis of a single Sm2Fe17N3 particle

    NASA Astrophysics Data System (ADS)

    Inami, Nobuhito; Takeichi, Yasuo; Ueno, Tetsuro; Saito, Kotaro; Sagayama, Ryoko; Kumai, Reiji; Ono, Kanta

    2014-05-01

    We performed single crystal structure analysis of Sm2Fe17N3 using X-ray diffraction. A pick-up system combined with a micromanipulation tool driven by piezoelectric actuators and a microgripper was used. A single Sm2Fe17Nx particle with the diameter of about 20 μm 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 Sm2Fe17N3 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 (#166) 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.

  4. Mechanism of Formation of Three Dimensional Structures of Particles Dispersed in a Liquid Crystal

    NASA Astrophysics Data System (ADS)

    West, John; Glushchenko, Anatoliy; Liao, Guangxun; Reznikov, Yuriy; Andrienko, Denis; Allen, Michael

    2002-03-01

    Recently, colloidal dispersions of small particles in a nematic liquid crystal have been reported. These particles introduce topological defects in the liquid crystal, (H. Stark, Euro. Phys. J. B 10), 311 (1999).(T. C. Lubensky, D. Pettey, N. Currier, and H. Stark, Phys. Rev. E, 57), 610 (1998). and the liquid crystal introduces additional long-range forces between the colloidal particles(B. I. Lev and P. M. Tomchuk, Phys. Rev. E., 59), 591 (1999).. Interestingly the particles form complex three-dimensional structures that affect the physical properties of the liquid crystal(P. Poulin, H. Stark, T. C. Lubensky, and D. A. Weitz, Science, 275), 1770 (1997).(P. Poulin and D. A. Weitz, Phys. Rev. E, 57), 626 (1998).(V. J. Anderson, E. M. Terentjev, S. P. Meeker, J. Crain, and W.C. K. Poon, Eur, Phys. J. 4), 11, 2001).(V. J. Anderson and E. M. Terentjev, Euro, Phys. J. 4), 21, (2001).(S. P Meeker, W. C. K. Poon, J. Crain and E. M. Terentjev, Phys. Rev. E. 61), R6083 (2000). and offer the potential of being used in a variety of applications(W. Russel, D. Saville, and W. Schowalter, Colloidal Dispersions (Cambridge University Press, Cambridge, 1989) .)We investigated the formation of the three dimensional structures formed from a random dispersion of these small particles upon cooling of the liquid crystal from the isotropic into the nematic phase. Specifically, we studied the force on a particle suspended in the isotropic phase as the front of a moving nematic-isotropic interface passed. The balance of forces explains the movement of these particles by the advancing interface. We observed different three-dimensional structures depending on the rate of cooling. Our results can be used to control the morphology and physical properties of these colloidal dispersions.

  5. Biological and immunological characteristics of hepatitis E virus-like particles based on the crystal structure

    PubMed Central

    Yamashita, Tetsuo; Mori, Yoshio; Miyazaki, Naoyuki; Cheng, R. Holland; Yoshimura, Masato; Unno, Hideaki; Shima, Ryoichi; Moriishi, Kohji; Tsukihara, Tomitake; Li, Tian Cheng; Takeda, Naokazu; Miyamura, Tatsuo; Matsuura, Yoshiharu

    2009-01-01

    Hepatitis E virus (HEV) is a causative agent of acute hepatitis. The crystal structure of HEV-like particles (HEV-LP) consisting of capsid protein was determined at 3.5-? resolution. The capsid protein exhibited a quite different folding at the protruding and middle domains from the members of the families of Caliciviridae and Tombusviridae, while the shell domain shared the common folding. Tyr-288 at the 5-fold axis plays key roles in the assembly of HEV-LP, and aromatic amino acid residues are well conserved among the structurally related viruses. Mutational analyses indicated that the protruding domain is involved in the binding to the cells susceptive to HEV infection and has some neutralization epitopes. These structural and biological findings are important for understanding the molecular mechanisms of assembly and entry of HEV and also provide clues in the development of preventive and prophylactic measures for hepatitis E. PMID:19620712

  6. Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle

    PubMed Central

    Tsunaka, Yasuo; Kajimura, Naoko; Tate, Shin-ichi; Morikawa, Kosuke

    2005-01-01

    Gene expression in eukaryotes depends upon positioning, mobility and packaging of nucleosomes; thus, we need the detailed information of the human nucleosome core particle (NCP) structure, which could clarify chromatin properties. Here, we report the 2.5 ? crystal structure of a human NCP. The overall structure is similar to those of other NCPs reported previously. However, the DNA path of human NCP is remarkably different from that taken within other NCPs with an identical DNA sequence. A comparison of the structural parameters between human and Xenopus laevis DNA reveals that the DNA path of human NCP consecutively shifts by 1 bp in the regions of superhelix axis location ?5.0 to ?2.0 and 5.0 to 7.0. This alteration of the human DNA path is caused predominantly by tight DNADNA contacts within the crystal. It is also likely that the conformational change in the human H2B tail induces the local alteration of the DNA path. In human NCP, the region with the altered DNA path lacks Mn2+ ions and the B-factors of the DNA phosphate groups are substantially high. Therefore, in contrast to the histone octamer, the nucleosomal DNA is sufficiently flexible and mobile and can undergo drastic conformational changes, depending upon the environment. PMID:15951514

  7. 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) α-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 β = 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 ε in the synthesized powders do not exceed 0.15%. All the Ag2S powders with different particle size have an identical morphology.

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

    SciTech Connect

    Inami, Nobuhito Takeichi, Yasuo; Saito, Kotaro; Sagayama, Ryoko; Kumai, Reiji; Ono, Kanta; Ueno, Tetsuro

    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 μm 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.

  9. RADCHARM++: A C++ routine to compute the electromagnetic radiation generated by relativistic charged particles in crystals and complex structures

    NASA Astrophysics Data System (ADS)

    Bandiera, Laura; Bagli, Enrico; Guidi, Vincenzo; Tikhomirov, Victor V.

    2015-07-01

    The analytical theories of coherent bremsstrahlung and channeling radiation well describe the process of radiation generation in crystals under some special cases. However, the treatment of complex situations requires the usage of a more general approach. In this report we present a C++ routine, named RADCHARM++, to compute the electromagnetic radiation emitted by electrons and positrons in crystals and complex structures. In the RADCHARM++ routine, the model for the computation of e.m. radiation generation is based on the direct integration of the quasiclassical formula of Baier and Katkov. This approach allows one taking into account real trajectories, and thereby the contribution of incoherent scattering. Such contribution can be very important in many cases, for instance for electron channeling. The generality of the Baier-Katkov operator method permits one to simulate the electromagnetic radiation emitted by electrons/positrons in very different cases, e.g., in straight, bent and periodically bent crystals, and for different beam energy ranges, from sub-GeV to TeV and above. The RADCHARM++ routine has been implemented in the Monte Carlo code DYNECHARM++, which solves the classical equation of motion of charged particles traveling through a crystal under the continuum potential approximation. The code has proved to reproduce the results of experiments performed at the MAinzer MIkrotron (MAMI) with 855 MeV electrons and has been used to predict the radiation spectrum generated by the same electron beam in a bent crystal.

  10. The structure of the multidrug resistance protein 1 (MRP1/ABCC1). crystallization and single-particle analysis.

    PubMed

    Rosenberg, M F; Mao, Q; Holzenburg, A; Ford, R C; Deeley, R G; Cole, S P

    2001-05-11

    Multidrug resistance protein 1 (MRP1/ABCC1) is an ATP-binding cassette (ABC) polytopic membrane transporter of considerable clinical importance that confers multidrug resistance on tumor cells by reducing drug accumulation by active efflux. MRP1 is also an efficient transporter of conjugated organic anions. Like other ABC proteins, including the drug resistance conferring 170-kDa P-glycoprotein (ABCB1), the 190-kDa MRP1 has a core structure consisting of two membrane-spanning domains (MSDs), each followed by a nucleotide binding domain (NBD). However, unlike P-glycoprotein and most other ABC superfamily members, MRP1 contains a third MSD with five predicted transmembrane segments with an extracytosolic NH(2) terminus. Moreover, the two nucleotide-binding domains of MRP1 are considerably more divergent than those of P-glycoprotein. In the present study, the first structural details of MRP1 purified from drug-resistant lung cancer cells have been obtained by electron microscopy of negatively stained single particles and two-dimensional crystals formed after reconstitution of purified protein with lipids. The crystals display p2 symmetry with a single dimer of MRP1 in the unit cell. The overall dimensions of the MRP1 monomer are approximately 80 x 100 A. The MRP1 monomer shows some pseudo-2-fold symmetry in projection, and in some orientations of the detergent-solubilized particles, displays a stain filled depression (putative pore) appearing toward the center of the molecule, presumably to enable transport of substrates. These data represent the first structural information of this transporter to approximately 22-A resolution and provide direct structural evidence for a dimeric association of the transporter in a reconstituted lipid bilayer. PMID:11279022

  11. Crystal structure and prediction.

    PubMed

    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. PMID:25422850

  12. Characterization of synthetic nanocrystalline mackinawite: crystal structure, particle size, and specific surface area

    PubMed Central

    Jeong, Hoon Y.; Lee, Jun H.; Hayes, Kim F.

    2010-01-01

    Iron sulfide was synthesized by reacting aqueous solutions of sodium sulfide and ferrous chloride for 3 days. By X-ray powder diffraction (XRPD), the resultant phase was determined to be primarily nanocrystalline mackinawite (space group: P4/nmm) with unit cell parameters a = b = 3.67 and c = 5.20 . Iron K-edge XAS analysis also indicated the dominance of mackinawite. Lattice expansion of synthetic mackinawite was observed along the c-axis relative to well-crystalline mackinawite. Compared with relatively short-aged phase, the mackinawite prepared here was composed of larger crystallites with less elongated lattice spacings. The direct observation of lattice fringes by HR-TEM verified the applicability of Bragg diffraction in determining the lattice parameters of nanocrystalline mackinawite from XRPD patterns. Estimated particle size and external specific surface area (SSAext) of nanocrystalline mackinawite varied significantly with the methods used. The use of Scherrer equation for measuring crystallite size based on XRPD patterns is limited by uncertainty of the Scherrer constant (K) due to the presence of polydisperse particles. The presence of polycrystalline particles may also lead to inaccurate particle size estimation by Scherrer equation, given that crystallite and particle sizes are not equivalent. The TEM observation yielded the smallest SSAext of 103 m2/g. This measurement was not representative of dispersed particles due to particle aggregation from drying during sample preparation. In contrast, EGME method and PCS measurement yielded higher SSAext (276345 m2/g by EGME and 424 130 m2/g by PCS). These were in reasonable agreement with those previously measured by the methods insensitive to particle aggregation. PMID:21085620

  13. 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

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

    NASA Astrophysics Data System (ADS)

    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.

  15. Teaching with Crystal Structures: Helping Students Recognize and Classify the Smallest Repeating Particle in a Given Substance

    ERIC Educational Resources Information Center

    Smithenry, Dennis W.

    2009-01-01

    Classifying a particle requires an understanding of the type of bonding that exists within and among the particles, which requires an understanding of atomic structure and electron configurations, which requires an understanding of the elements of periodic properties, and so on. Rather than getting tangled up in all of these concepts at the start

  16. Teaching with Crystal Structures: Helping Students Recognize and Classify the Smallest Repeating Particle in a Given Substance

    ERIC Educational Resources Information Center

    Smithenry, Dennis W.

    2009-01-01

    Classifying a particle requires an understanding of the type of bonding that exists within and among the particles, which requires an understanding of atomic structure and electron configurations, which requires an understanding of the elements of periodic properties, and so on. Rather than getting tangled up in all of these concepts at the start…

  17. 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

  18. Passive particle dosimetry. [silver halide crystal growth

    NASA Technical Reports Server (NTRS)

    Childs, C. B.

    1977-01-01

    Present methods of dosimetry are reviewed with emphasis on the processes using silver chloride crystals for ionizing particle dosimetry. Differences between the ability of various crystals to record ionizing particle paths are directly related to impurities in the range of a few ppm (parts per million). To understand the roles of these impurities in the process, a method for consistent production of high purity silver chloride, and silver bromide was developed which yields silver halides with detectable impurity content less than 1 ppm. This high purity silver chloride was used in growing crystals with controlled doping. Crystals were grown by both the Czochalski method and the Bridgman method, and the Bridgman grown crystals were used for the experiments discussed. The distribution coefficients of ten divalent cations were determined for the Bridgman crystals. The best dosimeters were made with silver chloride crystals containing 5 to 10 ppm of lead; other impurities tested did not produce proper dosimeters.

  19. Particle tracking microrheology of lyotropic liquid crystals.

    PubMed

    Alam, Mohammad Mydul; Mezzenga, Raffaele

    2011-05-17

    We present comprehensive results on the microrheological study of lyotropic liquid crystalline phases of various space groups constituted by water-monoglyceride (Dimodan) mixtures. In order to explore the viscoelastic properties of these systems, we use particle tracking of probe colloidal particles suitably dispersed in the liquid crystals and monitored by diffusing wave spectroscopy. The identification of the various liquid crystalline phases was separately carried out by small-angle X-ray scattering. The restricted motion of the particles was monitored and identified by the decay time of intensity autocorrelation function and the corresponding time-dependent mean square displacement (MSD), which revealed space group-dependent behavior. The characteristic time extracted by the intersection of the slopes of the MSD at short and long time scales, provided a characteristic time which could be directly compared with the relaxation time obtained by microrheology. Further direct comparison of microrheology and bulk rheology measurements was gained via the Laplace transform of the generalized time-dependent MSD, yielding the microrheology storage and loss moduli, G'(?) and G''(?), in the frequency domain ?. The general picture emerging from the microrheology data is that all liquid crystals exhibit viscoelastic properties in line with results from bulk rheology and the transition regime (elastic to viscous) differs according to the specific liquid crystal considered. In the case of the lamellar phase, a plastic fluid is measured by bulk rheology, while microrheology indicates viscoelastic behavior. Although we generally find good qualitative agreement between the two techniques, all liquid crystalline systems are found to relax faster when studied with microrheology. The most plausible explanation for this difference is due to the different length scales probed by the two techniques: that is, microscopical relaxation on these structured fluids, is likely to occur at shorter time scales which are more suitably probed by microrheology, whereas bulk, macroscopic relaxations occurring at longer time scales can only be probed by bulk rheology. PMID:21510686

  20. Monodispersed Ultrafine Zeolite Crystal Particles by Microwave Hydrothermal Synthesis

    SciTech Connect

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

    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.

  1. The crystallization of small particles and droplets

    NASA Technical Reports Server (NTRS)

    Weinberg, M. C.

    1985-01-01

    A general expression is derived for the volume fraction of material crystallized as a function of time for the situation where boundary effects may be important, and it is applied to a sample consisting of a monodisperse array of small particles. It is assumed that crystallization occurs via homogeneous nucleation followed by crystal growth. The crystallization rate is shown to be controlled by a single dimensionless parameter, beta. Beta exp 1/4 is a dimensionless particle radius which tends to be small when the growth rate is large or when the nucleation rate is small. When beta is large, the general expression for the volume fraction transformed reduces to the standard expression valid for bulk samples. When beta is small, it reduces to the formula used to compute the volume fraction crystallized in droplet undercooling experiments. Hence, the present results are pertinent for the interpretation of some droplet undercooling experiments as well as isothermal DSC and DTA experiments.

  2. 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

  3. 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

  4. Crystallization by Particle Attachment in Synthetic, Biogenic, and Geologic Environments

    SciTech Connect

    De Yoreo, James J.; Gilbert, Pupa U.; Sommerdijk, Nico; Penn, R. Lee; Whitelam, Stephen B.; Joester, Derk; Zhang, Hengzhong; Rimer, Jeffrey D.; Navrotsky, Alexandra; Banfield, Jillian F.; Wallace, Adam F.; Michel, F. M.; Meldrum, Fiona C.; Colfen, Helmut; Dove, Patricia M.

    2015-07-31

    Field and laboratory observations show that crystals commonly form by the addition and attachment of particles that range from multi-ion complexes to fully formed nanoparticles. These non-classical pathways to crystallization are diverse, in contrast to classical models that consider the addition of monomeric chemical species. We review progress toward understanding crystal growth by particle attachment processes and show that multiple pathways result from the interplay of free energy landscapes and reaction dynamics. Much remains unknown about the fundamental aspects; particularly the relationships between solution structure, interfacial forces, and particle motion. Developing a predictive description that connects molecular details to ensemble behavior will require revisiting long-standing interpretations of crystal formation in synthetic systems and patterns of mineralization in natural environments.

  5. Ionizing particle detection based on phononic crystals

    NASA Astrophysics Data System (ADS)

    Aly, Arafa H.; Mehaney, Ahmed; Eissa, Mostafa F.

    2015-08-01

    Most conventional radiation detectors are based on electronic or photon collections. In this work, we introduce a new and novel type of ionizing particle detector based on phonon collection. Helium ion radiation treats tumors with better precision. There are nine known isotopes of helium, but only helium-3 and helium-4 are stable. Helium-4 is formed in fusion reactor technology and in enormous quantities during Big Bang nucleo-synthesis. In this study, we introduce a technique for helium-4 ion detection (sensing) based on the innovative properties of the new composite materials known as phononic crystals (PnCs). PnCs can provide an easy and cheap technique for ion detection compared with conventional methods. PnC structures commonly consist of a periodic array of two or more materials with different elastic properties. The two materials are polymethyl-methacrylate and polyethylene polymers. The calculations showed that the energies lost to target phonons are maximized at 1 keV helium-4 ion energy. There is a correlation between the total phonon energies and the transmittance of PnC structures. The maximum transmission for phonons due to the passage of helium-4 ions was found in the case of making polyethylene as a first layer in the PnC structure. Therefore, the concept of ion detection based on PnC structure is achievable.

  6. CRYSTAL GROWTH. Crystallization by particle attachment in synthetic, biogenic, and geologic environments.

    PubMed

    De Yoreo, James J; Gilbert, Pupa U P A; Sommerdijk, Nico A J M; Penn, R Lee; Whitelam, Stephen; Joester, Derk; Zhang, Hengzhong; Rimer, Jeffrey D; Navrotsky, Alexandra; Banfield, Jillian F; Wallace, Adam F; Michel, F Marc; Meldrum, Fiona C; Clfen, Helmut; Dove, Patricia M

    2015-07-31

    Field and laboratory observations show that crystals commonly form by the addition and attachment of particles that range from multi-ion complexes to fully formed nanoparticles. The particles involved in these nonclassical pathways to crystallization are diverse, in contrast to classical models that consider only the addition of monomeric chemical species. We review progress toward understanding crystal growth by particle-attachment processes and show that multiple pathways result from the interplay of free-energy landscapes and reaction dynamics. Much remains unknown about the fundamental aspects, particularly the relationships between solution structure, interfacial forces, and particle motion. Developing a predictive description that connects molecular details to ensemble behavior will require revisiting long-standing interpretations of crystal formation in synthetic systems, biominerals, and patterns of mineralization in natural environments. PMID:26228157

  7. Inorganic Crystal Structure Database (ICSD)

    National Institute of Standards and Technology Data Gateway

    SRD 84 FIZ/NIST Inorganic Crystal Structure Database (ICSD) (PC database for purchase)   The Inorganic Crystal Structure Database (ICSD) is produced cooperatively by the Fachinformationszentrum Karlsruhe(FIZ) and the National Institute of Standards and Technology (NIST). The ICSD is a comprehensive collection of crystal structure data of inorganic compounds containing more than 140,000 entries and covering the literature from 1915 to the present.

  8. 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 CH?O, CH?N, and CH?Cl hydrogen bonds, as well as weak ?? interactions [ring-centroid separation = 3.782?(2) and 3.5952?(19)?], resulting in a three-dimensional architecture. PMID:25553037

  9. Crystal Structures of Phosphoketolase

    PubMed Central

    Suzuki, Ryuichiro; Katayama, Takane; Kim, Byung-Jun; Wakagi, Takayoshi; Shoun, Hirofumi; Ashida, Hisashi; Yamamoto, Kenji; Fushinobu, Shinya

    2010-01-01

    Thiamine diphosphate (ThDP)-dependent enzymes are ubiquitously present in all organisms and catalyze essential reactions in various metabolic pathways. ThDP-dependent phosphoketolase plays key roles in the central metabolism of heterofermentative bacteria and in the pentose catabolism of various microbes. In particular, bifidobacteria, representatives of beneficial commensal bacteria, have an effective glycolytic pathway called bifid shunt in which 2.5 mol of ATP are produced per glucose. Phosphoketolase catalyzes two steps in the bifid shunt because of its dual-substrate specificity; they are phosphorolytic cleavage of fructose 6-phosphate or xylulose 5-phosphate to produce aldose phosphate, acetyl phosphate, and H2O. The phosphoketolase reaction is different from other well studied ThDP-dependent enzymes because it involves a dehydration step. Although phosphoketolase was discovered more than 50 years ago, its three-dimensional structure remains unclear. In this study we report the crystal structures of xylulose 5-phosphate/fructose 6-phosphate phosphoketolase from Bifidobacterium breve. The structures of the two intermediates before and after dehydration (α,β-dihydroxyethyl ThDP and 2-acetyl-ThDP) and complex with inorganic phosphate give an insight into the mechanism of each step of the enzymatic reaction. PMID:20739284

  10. 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.

  11. Demonstration of Crystal Structure.

    ERIC Educational Resources Information Center

    Neville, Joseph P.

    1985-01-01

    Describes an experiment where equal parts of copper and aluminum are heated then cooled to show extremely large crystals. Suggestions are given for changing the orientation of crystals by varying cooling rates. Students are more receptive to concepts of microstructure after seeing this experiment. (DH)

  12. 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.

  13. Crystal structure determination of Efavirenz

    NASA Astrophysics Data System (ADS)

    Popeneciu, Horea; Tripon, Carmen; Borodi, Gheorghe; Pop, Mihaela Maria; Dumitru, Ristoiu

    2015-12-01

    Needle-shaped single crystals of the title compound, C14H9ClF3NO2, were obtained from a co-crystallization experiment of Efavirenz with maleic acid in a (1:1) ratio, using methanol as solvent. Crystal structure determination at room temperature revealed a significant anisotropy of the lattice expansion compared to the previously reported low-temperature structure. In both low- and room temperature structures the cyclopropylethynyl fragment in one of the asymmetric unit molecules is disordered. While at low-temperature only one C atom exhibits positional disorder, at room temperature the disorder is present for two C atoms of the cyclopropane ring.

  14. Colloidal particles in blue phase liquid crystals.

    PubMed

    Pawsey, Anne C; Clegg, Paul S

    2015-05-01

    We study the effect of disorder on the phase transitions of a system already dominated by defects. Micron-sized colloidal particles are dispersed chiral nematic liquid crystals which exhibit a blue phase (BP). The colloids are a source of disorder, disrupting the liquid crystal as the system is heated from the cholesteric to the isotropic phase through the blue phase. The colloids act as a preferential site for the growth of BPI from the cholesteric; in high chirality samples BPII also forms. In both BPI and BPII the colloids lead to localised melting to the isotropic, giving rise to faceted isotropic inclusions. This is in contrast to the behaviour of a cholesteric LC where colloids lead to system spanning defects. PMID:25698218

  15. Fabrication of Artificial Crystal Architectures by Micro-Manipulation of Spherical Particles

    NASA Astrophysics Data System (ADS)

    Takagi, Kenta; Kawasaki, Akira

    2008-02-01

    Materials with three-dimensional periodic structures have the potential to produce photonic effects such as photonic crystals. We therefore developed a fabrication technique for such structured materials through assembly of monosized spherical micro-particles. First, a three-dimensional particle array system was designed and manufactured. In this system, a robotic micro-manipulator accurately positions spherical particles onto the lattice points, and subsequently, fiber lasers micro-weld contact points between neighboring particles. One-dimensional arrays were constructed using monosized tin particles with the diameter of 400 um. Moreover, on the basis of optimized laser conditions, we successfully constructed three-dimensional crystals such as those of diamond structures. The diamond structure, in particular, is expected to evolve towards a practical photonic crystal device, since it possesses the largest photonic band gap among all the crystal structures.

  16. 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.

  17. Micropolar crystal plasticity simulation of particle strengthening

    NASA Astrophysics Data System (ADS)

    Mayeur, J. R.; McDowell, D. L.

    2015-09-01

    The yield and work hardening behavior of a small-scale initial-boundary value problem involving dislocation plasticity in an idealized particle strengthened system is investigated using micropolar single crystal plasticity and is compared with results for the same problem from dislocation dynamics simulations. A micropolar single crystal is a work-conjugate higher-order continuum that treats the lattice rotations as generalized displacements, and supports couple stresses that are work-conjugate to the lattice torsion-curvature, leading to a non-symmetric Cauchy stress. The resolved skew-symmetric component of the Cauchy stress tensor results in slip system level kinematic hardening during heterogeneous deformation that depends on gradients of lattice torsion-curvature. The scale-dependent mechanical response of the micropolar single crystal is dictated both by energetic (higher-order elastic constants) and dissipative (plastic torsion-curvature) intrinsic material length scales. We show that the micropolar model captures essential details of the average stress-strain behavior predicted by discrete dislocation dynamics and of the cumulative slip and dislocation density fields predicted by statistical dislocation dynamics.

  18. Crystal structure of oryzalin

    PubMed Central

    Kang, Gihaeng; Kim, Jineun; Jeon, Youngeun; Kim, Tae Ho

    2015-01-01

    The title compound, C12H18N4O6S (systematic name: 4-di­propyl­amino-3,5-di­nitro­benzene­sulfonamide), is a sulfonamide with herbicidal properties marketed as oryzalin. The dihedral angles between the benzene ring and the mean planes of the nitro groups are 26.15 (11) and 54.80 (9)°. The propyl arms of the di­propyl­amino substituent lie on opposite sides of this ring plane. In the crystal, N—H⋯O and C—H⋯O hydrogen bonds generate a three-dimensional network. PMID:26090208

  19. 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 100μs. 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.

  20. SSZ-13 Crystallization by Particle Attachment and Deterministic Pathways to Crystal Size Control.

    PubMed

    Kumar, Manjesh; Luo, Helen; Romn-Leshkov, Yuriy; Rimer, Jeffrey D

    2015-10-14

    Many synthetic and natural crystalline materials are either known or postulated to grow via nonclassical pathways involving the initial self-assembly of precursors that serve as putative growth units for crystallization. Elucidating the pathway(s) by which precursors attach to crystal surfaces and structurally rearrange (postattachment) to incorporate into the underlying crystalline lattice is an active and expanding area of research comprising many unanswered fundamental questions. Here, we examine the crystallization of SSZ-13, which is an aluminosilicate zeolite that possesses exceptional physicochemical properties for applications in separations and catalysis (e.g., methanol upgrading to chemicals and the environmental remediation of NO(x)). We show that SSZ-13 grows by two concerted mechanisms: nonclassical growth involving the attachment of amorphous aluminosilicate particles to crystal surfaces and classical layer-by-layer growth via the incorporation of molecules to advancing steps on the crystal surface. A facile, commercially viable method of tailoring SSZ-13 crystal size and morphology is introduced wherein growth modifiers are used to mediate precursor aggregation and attachment to crystal surfaces. We demonstrate that small quantities of polymers can be used to tune crystal size over 3 orders of magnitude (0.1-20 ?m), alter crystal shape, and introduce mesoporosity. Given the ubiquitous presence of amorphous precursors in a wide variety of microporous crystals, insight of the SSZ-13 growth mechanism may prove to be broadly applicable to other materials. Moreover, the ability to selectively tailor the physical properties of SSZ-13 crystals through molecular design offers new routes to optimize their performance in a wide range of commercial applications. PMID:26376337

  1. Crystal structure of pyriproxyfen.

    PubMed

    Kang, Gihaeng; Kim, Jineun; Park, Hyunjin; Kim, Tae Ho

    2015-08-01

    In the title compound {systematic name: 4-phen-oxy-phenyl (RS)-2-[(pyridin-2-yl)-oxy]propyl ether}, C20H19NO3, which is a juvenile hormone mimic and insecticide, the dihedral angles between the plane of the central benene ring and those of the pendant pyridine ring and phenyl ring are 78.09?(6) and 82.14?(8), respectively. The conformation of the O-C-C-O linkage is gauche [torsion angle = -75.0?(2)]. In the crystal, weak aromatic ?-? stacking inter-actions [centroid-centroid separation = 3.8436?(13)?] and C-H?? inter-actions link adjacent mol-ecules, forming a three-dimensional network. PMID:26396811

  2. Crystal structure of pyriproxyfen

    PubMed Central

    Kang, Gihaeng; Kim, Jineun; Park, Hyunjin; Kim, Tae Ho

    2015-01-01

    In the title compound {systematic name: 4-phenoxyphenyl (RS)-2-[(pyridin-2-yl)oxy]propyl ether}, C20H19NO3, which is a juvenile hormone mimic and insecticide, the dihedral angles between the plane of the central benene ring and those of the pendant pyridine ring and phenyl ring are 78.09?(6) and 82.14?(8), respectively. The conformation of the OCCO linkage is gauche [torsion angle = ?75.0?(2)]. In the crystal, weak aromatic ?? stacking interactions [centroidcentroid separation = 3.8436?(13)?] and CH?? interactions link adjacent molecules, forming a three-dimensional network. PMID:26396811

  3. Crystal structure of mandipropamid

    PubMed Central

    Park, Hyunjin; Kim, Jineun; Kang, Gihaeng; Kim, Tae Ho

    2015-01-01

    In the title compound, C23H22ClNO4 (systematic name: (RS)-2-(4-chlorophenyl)-N-{2-[3-methoxy-4-(prop-2-yn-1-yloxy)phenyl]ethyl}-2-(prop-2-ynyloxy)acetamide), an amide fungicide, the dihedral angle between the chlorobenzene and benzene rings is 65.36?(6). In the crystal, NH?O hydrogen bonds lead to zigzag supramolecular chains along the c axis (glide symmetry). These are connected into layers by CH?O and CH?? interactions; the layers stack along the a axis with no specific intermolecular interactions between them. PMID:26594445

  4. Crystal structure of mandipropamid.

    PubMed

    Park, Hyunjin; Kim, Jineun; Kang, Gihaeng; Kim, Tae Ho

    2015-10-01

    In the title compound, C23H22ClNO4 (systematic name: (RS)-2-(4-chloro-phen-yl)-N-{2-[3-meth-oxy-4-(prop-2-yn-1-yl-oxy)phen-yl]eth-yl}-2-(prop-2-yn-yloxy)acetamide), an amide fungicide, the dihedral angle between the chloro-benzene and benzene rings is 65.36?(6). In the crystal, N-H?O hydrogen bonds lead to zigzag supra-molecular chains along the c axis (glide symmetry). These are connected into layers by C-H?O and C-H?? inter-actions; the layers stack along the a axis with no specific inter-molecular inter-actions between them. PMID:26594445

  5. Crystal structure of cyproconazole

    PubMed Central

    Kang, Gihaeng; Kim, Jineun; Kwon, Eunjin; Kim, Tae Ho

    2015-01-01

    The title compound [systematic name: 2-(4-chlorophenyl)-3-cyclopropyl-1-(1H-1,2,4-triazol-1-yl)butan-2-ol], C15H18ClN3O, is a conazole fungicide. The asymmetric unit comprises two enantiomeric pairs (molecules A and B) in which the dihedral angles between the chlorophenyl and triazole rings are 46.54?(9) (molecule A) and 67.03?(8) (molecule B). In the crystal, CH?O, OH?N and CH?Cl hydrogen bonds and weak CH?? interactions [3.473?(2)?] link adjacent molecules, forming columns along the a axis. PMID:26870467

  6. Crystal structure refinement with SHELXL.

    PubMed

    Sheldrick, George M

    2015-01-01

    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 MacOSX operating systems, and is particularly suitable for multiple-core processors. PMID:25567568

  7. Crystal structure refinement with SHELXL

    PubMed Central

    Sheldrick, George M.

    2015-01-01

    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 MacOSX operating systems, and is particularly suitable for multiple-core processors. PMID:25567568

  8. Crystal structure refinement with SHELXL

    SciTech Connect

    Sheldrick, George M.

    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.

  9. Crystal structure of pyrazoxyfen.

    PubMed

    Kwon, Eunjin; Kim, Jineun; Kang, Gihaeng; Kim, Tae Ho

    2015-12-01

    The title compound, C20H16Cl2N2O3 (systematic name: 2-{[4-(2,4-di-chloro-benzo-yl)-1,3-di-methyl-pyrazol-5-yl}-oxy}-1-phenyl-ethan-1-one), is the benzoyl-pyrazole herbicide pyrazoxyfen. The asymmetric unit comprises two independent mol-ecules, A and B, in which the pyrazole ring makes dihedral angles of 80.29?(10) and 61.70?(10) and 87.60?(10) and 63.92?(8), respectively, with the di-chloro-phenyl and phenyl rings. In the crystal, C-H?O and C-H?N hydrogen bonds, and C-H?? and ?-? [3.646?(2)?] inter-actions link adjacent mol-ecules, forming a two-dimensional network parellel to (011). In addition, the networks are linked by weak inter-molecular C-Cl?? [3.356?(2), 3.950?(2), 3.250?(2) and 3.575?(2)?] inter-actions, resulting in a three-dimensional architecture. PMID:26870483

  10. 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 CH?N hydrogen bonds link adjacent molecules, forming dimers with R 2 2(6) loops. In addition, the dimers are linked by CH?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

  11. Crystal structure of chlorfluazuron

    PubMed Central

    Cho, Seonghwa; Kim, Jineun; Lee, Sangjin; Kim, Tae Ho

    2015-01-01

    The title compound (systematic name: 1-{3,5-dichloro-4-[3-chloro-5-(trifluoromethyl)pyridin-2-yloxy]phenyl}-3-(2,6-difluorobenzoyl)urea), C20H9Cl3F5N3O3, is a benzoylphenylurea insecticide. The dihedral angles between the planes of the central dichlorophenyl and the terminal difluorophenyl and chloropyridyl rings are 79.51?(6) and 78.84 6), respectively. In the crystal, pairs of NH?O hydrogen bonds link adjacent molecules, forming R 2 2(8) inversion dimers. In addition, the dimers are linked by short F?Cl [3.1060?(16)?] and Cl?Cl [3.2837?(7)?] contacts, as well as weak intermolecular ?? interactions [ring centroid separation = 3.6100?(11) and 3.7764?(13)?], resulting in a two-dimensional architecture parallel to (111). PMID:25705506

  12. Crystal structure of pyrazoxyfen

    PubMed Central

    Kwon, Eunjin; Kim, Jineun; Kang, Gihaeng; Kim, Tae Ho

    2015-01-01

    The title compound, C20H16Cl2N2O3 (systematic name: 2-{[4-(2,4-di­chloro­benzo­yl)-1,3-di­methyl­pyrazol-5-yl}­oxy}-1-phenyl­ethan-1-one), is the benzoyl­pyrazole herbicide pyrazoxyfen. The asymmetric unit comprises two independent mol­ecules, A and B, in which the pyrazole ring makes dihedral angles of 80.29 (10) and 61.70 (10)° and 87.60 (10) and 63.92 (8)°, respectively, with the di­chloro­phenyl and phenyl rings. In the crystal, C—H⋯O and C—H⋯N hydrogen bonds, and C—H⋯π and π–π [3.646 (2) Å] inter­actions link adjacent mol­ecules, forming a two-dimensional network parellel to (011). In addition, the networks are linked by weak inter­molecular C—Cl⋯π [3.356 (2), 3.950 (2), 3.250 (2) and 3.575 (2) Å] inter­actions, resulting in a three-dimensional architecture. PMID:26870483

  13. 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.

  14. Reversible switching of liquid crystal micro-particles in a nematic liquid crystal.

    PubMed

    Imamura, Koki; Yoshida, Hiroyuki; Ozaki, Masanori

    2016-01-21

    Liquid crystal micro-particles are functional materials possessing optical and dielectric anisotropies originating from the arrangement of rod-like molecules within the particles. Although they can be switched by an electric field, particles dispersed in isotropic hosts usually cannot return to their original state, because there is no restoration force acting on the particles. Here, we describe reversible switching of liquid crystal micro-particles by dispersing them in a nematic liquid crystal host. We fabricate square micro-particles with unidirectional molecular alignment and investigate their static and dynamic electro-optic properties by applying an in-plane electric field. The behavior of the micro-particles is well-described by the theoretical model we construct, making this study potentially useful for the development of liquid crystal-liquid crystal particle composites with engineered properties. PMID:26514389

  15. 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.

  16. Crystal structure of guggulsterone Z

    SciTech Connect

    Gupta, V. K. Bandhoria, P.; Gupta, B. D.; Gupta, K. K.

    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.

  17. Reduction of glycine particle size by impinging jet crystallization.

    PubMed

    Tari, Tmea; Fekete, Zoltn; Szab-Rvsz, Piroska; Aigner, Zoltn

    2015-01-15

    The parameters of crystallization processes determine the habit and particle size distribution of the products. A narrow particle size distribution and a small average particle size are crucial for the bioavailability of poorly water-soluble pharmacons. Thus, particle size reduction is often required during crystallization processes. Impinging jet crystallization is a method that results in a product with a reduced particle size due to the homogeneous and high degree of supersaturation at the impingement point. In this work, the applicability of the impinging jet technique as a new approach in crystallization was investigated for the antisolvent crystallization of glycine. A factorial design was applied to choose the relevant crystallization factors. The results were analysed by means of a statistical program. The particle size distribution of the crystallized products was investigated with a laser diffraction particle size analyser. The roundness and morphology were determined with the use of a light microscopic image analysis system and a scanning electron microscope. Polymorphism was characterized by differential scanning calorimetry and powder X-ray diffraction. Headspace gas chromatography was utilized to determine the residual solvent content. Impinging jet crystallization proved to reduce the particle size of glycine. The particle size distribution was appropriate, and the average particle size was an order of magnitude smaller (d(0.5)=8-35?m) than that achieved with conventional crystallization (d(0.5)=82-680?m). The polymorphic forms of the products were influenced by the solvent ratio. The quantity of residual solvent in the crystallized products was in compliance with the requirements of the International Conference on Harmonization. PMID:25448571

  18. Diamond-structured photonic crystals.

    PubMed

    Maldovan, Martin; Thomas, Edwin L

    2004-09-01

    Certain periodic dielectric structures can prohibit the propagation of light for all directions within a frequency range. These 'photonic crystals' allow researchers to modify the interaction between electromagnetic fields and dielectric media from radio to optical wavelengths. Their technological potential, such as the inhibition of spontaneous emission, enhancement of semiconductor lasers, and integration and miniaturization of optical components, makes the search for an easy-to-craft photonic crystal with a large bandgap a major field of study. This progress article surveys a collection of robust complete three-dimensional dielectric photonic-bandgap structures for the visible and near-infrared regimes based on the diamond morphology together with their specific fabrication techniques. The basic origin of the complete photonic bandgap for the 'champion' diamond morphology is described in terms of dielectric modulations along principal directions. Progress in three-dimensional interference lithography for fabrication of near-champion diamond-based structures is also discussed. PMID:15343291

  19. 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).

  20. Crystal Structures of Yeast-Produced Enterovirus 71 and Enterovirus 71/Coxsackievirus A16 Chimeric Virus-Like Particles Provide the Structural Basis for Novel Vaccine Design against Hand-Foot-and-Mouth Disease

    PubMed Central

    Lyu, Ke; He, Ya-Ling; Li, Hao-Yang

    2015-01-01

    ABSTRACT Human enterovirus 71 (EV71) and coxsackievirus A16 (CVA16) are the two major causative agents for hand-foot-and-mouth disease (HFMD). Previously, we demonstrated that a virus-like particle (VLP) for EV71 produced from Saccharomyces cerevisiae is a potential vaccine candidate against EV71 infection, and an EV71/CVA16 chimeric VLP can elicit protective immune responses against both virus infections. Here, we presented the crystal structures of both VLPs, showing that both the linear and conformational neutralization epitopes identified in EV71 are mostly preserved on both VLPs. The replacement of only 4 residues in the VP1 GH loop converted strongly negatively charged surface patches formed by portions of the SP70 epitope in EV71 VLP into a relatively neutral surface in the chimeric VLP, which likely accounted for the additional neutralization capability of the chimeric VLP against CVA16 infection. Such local variations in the amino acid sequences and the surface charge potential are also present in different types of polioviruses. In comparison to EV71 VLP, the chimeric VLP exhibits structural changes at the local site of amino acid replacement and the surface loops of all capsid proteins. This is consistent with the observation that the VP1 GH loop located near the pseudo-3-fold junction is involved in extensive interactions with other capsid regions. Furthermore, portions of VP0 and VP1 in EV71 VLP are at least transiently exposed, revealing the structural flexibility of the VLP. Together, our structural analysis provided insights into the structural basis of enterovirus neutralization and novel vaccine design against HFMD and other enterovirus-associated diseases. IMPORTANCE Our previous studies demonstrated that the enterovirus 71 (EV71) virus-like particle (VLP) produced from yeast is a vaccine candidate against EV71 infection and that a chimeric EV71/coxsackievirus A16 (CVA16) VLP with the replacement of 4 amino acids in the VP1 GH loop can confer protection against both EV71 and CVA16 infections. This study reported the crystal structures of both the EV71 VLP and the chimeric EV71/CVA16 VLP and revealed that the major neutralization epitopes of EV71 are mostly preserved in both VLPs. In addition, the mutated VP1 GH loop in the chimeric VLP is well exposed on the particle surface and exhibits a surface charge potential different from that contributed by the original VP1 GH loop in EV71 VLP. Together, this study provided insights into the structural basis of enterovirus neutralization and evidence that the yeast-produced VLPs can be developed into novel vaccines against hand-foot-and-mouth disease (HFMD) and other enterovirus-associated diseases. PMID:25833050

  1. Structural Dynamics of the Vault Ribonucleoprotein Particle

    NASA Astrophysics Data System (ADS)

    Casaas, Arnau; Querol, Jordi; Fita, Ignasi; Verdaguer, Nria

    Vaults are ubiquitous, highly conserved, 13 MDa ribonucleoprotein particles, involved in a diversity of cellular processes, including multidrug resistance, transport mechanisms and signal transmission. There are between 104 and 106 vault particles per mammalian cell and they do not trigger autoimmunity. The vault particle shows a hollow barrel-shaped structure organized in two identical moieties, each consisting of 39 copies of the major vault protein (MVP). Other data indicated that vault halves can dissociate at acidic pH. The high resolution, crystal structure of the of the seven N-terminal domains (R1-R7) of MVP, forming the central vault barrel, together with that of the native vault particle (solved at 8 resolution), revealed the interactions governing vault association and suggested a pH-dependent mechanism for a reversible dissociation induced by low pH. Vault particles posses many features making them very promising vehicles for the delivery of therapeutic agents including self-assembly, 100 nm size range, emerging atomic-level structural information, natural presence in humans ensuring biocompability, recombinant production system, existing features for targeting species to the large lumen and a dynamic structure that may be controlled for manipulation of drug release kinetics. All these attributes provide vaults with enormous potential as a drug/gene delivery platform.

  2. Crystal structures and freezing of dipolar fluids.

    PubMed

    Groh, B; Dietrich, S

    2001-02-01

    We investigate the crystal structure of classical systems of spherical particles with an embedded point dipole at T=0. The ferroelectric ground state energy is calculated using generalizations of the Ewald summation technique. Due to the reduced symmetry compared to the nonpolar case the crystals are never strictly cubic. For the Stockmayer (i.e., Lennard-Jones plus dipolar) interaction three phases are found upon increasing the dipole moment: hexagonal, body-centered orthorhombic, and body-centered tetragonal. An even richer phase diagram arises for dipolar soft spheres with a purely repulsive inverse power law potential approximately r(-n). A crossover between qualitatively different sequences of phases occurs near the exponent n=12. The results are applicable to electro- and magnetorheological fluids. In addition to the exact ground state analysis we study freezing of the Stockmayer fluid by density-functional theory. PMID:11308482

  3. Crystallization of Brownian Particles from Walls Induced by a Uniform External Force

    NASA Astrophysics Data System (ADS)

    Sato, Masahide; Katsuno, Hiroyasu; Suzuki, Yoshihisa

    2013-08-01

    Keeping the formation of colloidal crystal under a centrifugal force in mind, we study the ordering of Brownian particles induced by a uniform external force. When the uniform external force is added, the particles move in the direction of the external force and the density of particles near walls becomes high. The ordering of particles starts on the walls, and successive ordering in bulk occurs near the walls. In bulk, both domains of the face-centered cubic structure and hexagonal close-packed structure appear. By controlling the direction and the strength of the external force, the number of ordered particles and distribution of cluster size are changed.

  4. Crystal structure of lignin peroxidase

    SciTech Connect

    Edwards, S.L. National Institutes of Health, Bethesda, MD ); Raag, R. ); Wariishi, Hiroyuki; Gold, M.H. ); Poulos, T.L. Univ. of California, Irvine )

    1993-01-15

    The crystal structure of lignin peroxidase (LiP) from the basidiomycete Phanerochaete chrysosporium has been determined to 2.6 [Angstrom] resolution by using multiple isomorphous replacement methods and simulated annealing refinement. Of the 343 residues, residues 3-335 have been accounted for in the electron density map, including four disulfide bonds. The overall three-dimensional structure is very similar to the only other peroxidase in this group for which a high-resolution crystal structure is available, cytochrome c peroxidase, despite the fact that the sequence identity is only [approx]20%, LiP has four disulfide bonds, while cytochrome c peroxidase has none, and Lip is larger (343 vs. 294 residues). The basic helical fold and connectivity defined by 11 helical segments with the heme sandwiched between the distal and proximal helices found in cytochrome c peroxidase is maintained in LiP. Both enzymes have a histidine as a proximal heme ligand, which is hydrogen bonded to a buried aspartic acid side chain. The distal or peroxide binding pocket also is similar, including the distal arginine and histidine. The most striking difference is that, whereas cytochrome c peroxidase has tryptophans contacting the distal and proximal heme surfaces, LiP has phenylalanines. This in part explains why, in the reaction with peroxides, cytochrome c peroxidase forms an amino acid-centered free radical, whereas LiP forms a porphyrin [pi] cation radical. 42 refs., 4 figs., 2 tabs.

  5. Crystal structure of lignin peroxidase.

    PubMed Central

    Edwards, S L; Raag, R; Wariishi, H; Gold, M H; Poulos, T L

    1993-01-01

    The crystal structure of lignin peroxidase (LiP) from the basidiomycete Phanerochaete chrysosporium has been determined to 2.6 A resolution by usine multiple isomorphous replacement methods and simulated annealing refinement. Of the 343 residues, residues 3-335 have been accounted for in the electron density map, including four disulfide bonds. The overall three-dimensional structure is very similar to the only other peroxidase in this group for which a high-resolution crystal structure is available, cytochrome c peroxidase, despite the fact that the sequence identity is only approximately 20%, LiP has four disulfide bonds, while cytochrome c peroxidase has none, and LiP is larger (343 vs. 294 residues). The basic helical fold and connectivity defined by 11 helical segments with the heme sandwiched between the distal and proximal helices found in cytochrome c peroxidase is maintained in LiP. Both enzymes have a histidine as a proximal heme ligand, which is hydrogen bonded to a buried aspartic acid side chain. The distal or peroxide binding pocket also is similar, including the distal arginine and histidine. The most striking difference is that, whereas cytochrome c peroxidase has tryptophans contacting the distal and proximal heme surfaces, LiP has phenylalanines. This in part explains why, in the reaction with peroxides, cytochrome c peroxidase forms an amino acid-centered free radical, whereas LiP forms a porphyrin pi cation radical. Images PMID:11607355

  6. Local crystal structure of iron oxide nanoparticles synthesized from Ferritin

    NASA Astrophysics Data System (ADS)

    Krispin, Michael; Preisinger, Marcus; Pfalzer, Peter; Horn, Siegfried; Strongin, Daniel

    2007-03-01

    We have investigated the size dependence of the local crystal structure of nanosized iron oxide by extended x-ray absorption fine structure (EXAFS) at the iron K-edge. Hematite (?-Fe2O3) nanoparticles of different diameters were produced by thermal treatment of horse spleen ferritin molecules and remineralized apo-ferritin molecules, respectively. The structure of these particles was compared to ?-Fe2O3 and ?-Fe2O3 nanopowder references. The Fourier transformed EXAFS spectra of the nanoparticles differ significantly from hematite and maghemite reference spectra and change systematically as a function of particle diameter, signalling a corresponding evolution of the structure. We show that the Fe--O bond length decreases with decreasing diameter of the particles and with decreasing particle density. This is explained by a core-shell model, in which the fraction of a ?-Fe2O3 like particle shell increases while the hematite core decreases with decreasing particle size.

  7. Old and New Particle Structure

    NASA Astrophysics Data System (ADS)

    Wolff, Milo

    2002-05-01

    This discussion will compare the old concept of the structure of matter with Nature. How did the ancient model affect scientific thinking leading science down blind pathways producing paradoxes? What instead is the simple logic and surprising consequences of Nature's choice, the Wave Structure of Matter? The old concept due to the Greek Democritus was a discrete particle like a grain of sand. It has survived almost unchanged. Even today, we prefer to regard mathematical entities, the 'photon' and quarks, as tiny grains. Only recently has the wave structure of particles been determined. Human emotions prefer explanations that agree with personal experience. We know that atomic sizes are much smaller than our senses can reveal, but most people, including scientists, prefer to imagine the electron like a baseball or a bullet. It is not. The quantum Wave Structure of Matter reveals the origin of the Natural laws, and opens a door to research in chemistry, biology, energy, and micro-electronics. Why had this not been found before? Because the Democritus particle agreed with emotions. Few people looked elsewhere. Modern structure is at www.QuantumMatter.com

  8. Isomorph invariance of the structure and dynamics of classical crystals

    NASA Astrophysics Data System (ADS)

    Albrechtsen, Dan E.; Olsen, Andreas E.; Pedersen, Ulf R.; Schrder, Thomas B.; Dyre, Jeppe C.

    2014-09-01

    This paper shows by computer simulations that some crystalline systems have curves in their thermodynamic phase diagrams, so-called isomorphs, along which structure and dynamics in reduced units are invariant to a good approximation. The crystals are studied in a classical-mechanical framework, which is generally a good description except significantly below melting. The existence of isomorphs for crystals is validated by simulations of particles interacting via the Lennard-Jones pair potential arranged into a face-centered cubic (fcc) crystalline structure; the slow vacancy-jump dynamics of a defective fcc crystal is also shown to be isomorph invariant. In contrast, a NaCl crystal model does not exhibit isomorph invariances. Other systems simulated, though in less detail, are the Wahnstrm binary Lennard-Jones crystal with the MgZn2 Laves crystal structure, monatomic fcc crystals of particles interacting via the Buckingham pair potential and via a purely repulsive pair potential diverging at a finite separation, an ortho-terphenyl molecular model crystal, and SPC/E hexagonal ice. Except for NaCl and ice, the crystals simulated all have isomorphs. Based on previous simulations of liquid models, we conjecture that crystalline solids with isomorphs include most or all formed by atoms or molecules interacting via metallic or van der Waals forces, whereas covalently bonded or hydrogen-bonded crystals are not expected to have isomorphs; crystals of ions or dipolar molecules constitute a limiting case for which isomorphs are only expected when the Coulomb interactions are relatively weak. We briefly discuss the consequences of the findings for theories of melting and crystallization.

  9. Dependence of crystallization of Brownian particles by sedimentation on the force direction

    NASA Astrophysics Data System (ADS)

    Sato, Masahide; Yusuf Hakim Widianto, Muhammad; Kanatsu, Youhei

    2015-11-01

    The formation of a large close-packed colloidal crystal with the fcc structure was observed during the sedimentation of colloidal particles in an inverted pyramidal pit [S. Matsuo et al., Appl. Phys. Lett. 82, 4285 (2003)]. Carrying out Brownian dynamics simulations, we confirmed that large grains with the fcc structure are formed when the apex angle of the inverted pyramidal container is suitable and the force direction is parallel to the the center axis [Y. Kanatsu and M. Sato, J. Phys. Soc. Jpn. 84, 044601 (2015)]. To form a high-quality colloidal crystal without defects, it is important to investigate in detail how the quality of a colloidal crystal is affected by the force direction and container shape. In this paper, we focus on the effect of the force direction on crystal quality and investigate how the ratio of the number of the hcp structured particles, Nhcp, to that of fcc structured particles, Nfcc, is affected by the force direction. In our simulation, the ratio of Nfcc to Nhcp is hardly changed when the force direction deviates from the central axis: Nfcc is much larger than Nhcp irrespective of the force direction. Thus, our results show that the crystal structure is insensitive to the force direction in forming a colloidal crystal by sedimentation in an inverted pyramidal container.

  10. Process to make structured particles

    DOEpatents

    Knapp, Angela Michelle; Richard, Monique N; Luhrs, Claudia; Blada, Timothy; Phillips, Jonathan

    2014-02-04

    Disclosed is a process for making a composite material that contains structured particles. The process includes providing a first precursor in the form of a dry precursor powder, a precursor liquid, a precursor vapor of a liquid and/or a precursor gas. The process also includes providing a plasma that has a high field zone and passing the first precursor through the high field zone of the plasma. As the first precursor passes through the high field zone of the plasma, at least part of the first precursor is decomposed. An aerosol having a second precursor is provided downstream of the high field zone of the plasma and the decomposed first material is allowed to condense onto the second precursor to from structured particles.

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

    DOEpatents

    Lin, Shawn-Yu (Albuquerque, NM); Koops, Hans W. P. (Ober-Ramstadt, DE)

    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 invention may be provided as electromagnetic wave filters, polarizers, resonators, sources, mirrors, beam directors and antennas for use at wavelengths in the range from about 0.2 to 200 microns or longer. Additionally, photonic crystal devices may be provided with one or more electromagnetic waveguides adjacent to a photonic crystal for forming integrated electromagnetic circuits for use at optical, infrared, or millimeter-wave frequencies.

  12. Simulations of Photonic Crystal and Dielectric Structures

    SciTech Connect

    Werner, G. R.

    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.

  13. Dexterous acoustic trapping and patterning of particles assisted by phononic crystal plate

    NASA Astrophysics Data System (ADS)

    Wang, Tian; Ke, Manzhu; Xu, Shengjun; Feng, Junheng; Qiu, Chunyin; Liu, Zhengyou

    2015-04-01

    In this letter, we present experimental demonstration of multi-particles trapping and patterning by the artificially engineered acoustic field of phononic crystal plate. Polystyrene particles are precisely trapped and patterned in two dimensional arrays, for example, the square, triangular, or quasi-periodic arrays, depending on the structures of the phononic crystal plates with varying sub-wavelength holes array. Analysis shows that the enhanced acoustic radiation force, induced by the resonant transmission field highly localized near the sub-wavelength apertures, accounts for the particles self-organizing. It can be envisaged that this kind of simple design of phononic crystal plates would pave an alternative route for self-assembly of particles and may be utilized in the lab-on-a-chip devices.

  14. Dexterous acoustic trapping and patterning of particles assisted by phononic crystal plate

    SciTech Connect

    Wang, Tian; Ke, Manzhu Xu, Shengjun; Feng, Junheng; Qiu, Chunyin; Liu, Zhengyou

    2015-04-20

    In this letter, we present experimental demonstration of multi-particles trapping and patterning by the artificially engineered acoustic field of phononic crystal plate. Polystyrene particles are precisely trapped and patterned in two dimensional arrays, for example, the square, triangular, or quasi-periodic arrays, depending on the structures of the phononic crystal plates with varying sub-wavelength holes array. Analysis shows that the enhanced acoustic radiation force, induced by the resonant transmission field highly localized near the sub-wavelength apertures, accounts for the particles self-organizing. It can be envisaged that this kind of simple design of phononic crystal plates would pave an alternative route for self-assembly of particles and may be utilized in the lab-on-a-chip devices.

  15. Experimental modelling of single-particle dynamic processes in crystallization by controlled colloidal assembly.

    PubMed

    Zhang, Tian Hui; Liu, Xiang Yang

    2014-04-01

    In the last few decades, the controlled colloidal assembly was adopted as a new modelling technology for the study of the crystallization mechanism. In colloidal systems, the movement of particles is slow enough to follow and the particle dynamics can be monitored at the single-particle level using normal optical microscopes. So far, the studies of colloidal crystallization have produced a number of insights, which have significantly improved our understanding of crystallization. In this review, we summarize the recent advances in understanding the mechanism of crystallization, which were achieved using colloidal model systems, i.e., the kinetics of nucleation, growth and defect formation. Such model systems allow us to not only visualize some "atomic" details of nucleation and surface processes of crystallization, but also quantify previous models to such an extent that has never been achieved before by other approaches. In the case of nucleation, the quantitative observation of the kinetic process was made at the single-particle level; the results include the ideal case and the deviations from classical theories. The deviations include multi-step crystallization, supersaturation-driven structural mismatch nucleation, defect creation and migration kinetics, surface roughening, etc. It can be foreseen that this approach will become a powerful tool to study the fundamental process of crystallization and other phase transitions. PMID:24435291

  16. 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

  17. 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.

  18. Analysis of the structure and morphology of fenoxycarb crystals.

    PubMed

    Zeglinski, Jacek; Svrd, Michael; Karpinska, Jolanta; Kuhs, Manuel; Rasmuson, ke C

    2014-09-01

    In this paper, we have explored the relationship between surface structure and crystal growth and morphology of fenoxycarb (FC). Experimental vs. predicted morphologies/face indices of fenoxycarb crystals are presented. Atomic-scale surface structures of the crystalline particles, derived from experimentally indexed single crystals, are also modelled. Single crystals of fenoxycarb exhibit a platelet-like morphology which closely matches predicted morphologies. The solvent choice does not significantly influence either morphology or crystal habit. The crystal morphology is dominated by the {001} faces, featuring weakly interacting aliphatic or aromatic groups at their surfaces. Two distinct modes of interaction of a FC molecule in the crystal can be observed, which appear to be principal factors governing the microscopic shape of the crystal: the relatively strong collateral and the much weaker perpendicular bonding. Both forcefield-based and quantum-chemical calculations predict that the aromatic and aliphatic terminated {001} faces have comparably high stability as a consequence of weak intermolecular bonding. Thus we predict that the most developed {001} surfaces of fenoxycarb crystals should be terminated randomly, favouring neither aliphatic nor aromatic termination. PMID:25089714

  19. 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.

  20. Crystallization and preliminary X-ray diffraction analysis of apolipoprotein E-containing lipoprotein particles

    SciTech Connect

    Newhouse, Yvonne; Peters-Libeu, Clare; Weisgraber, Karl H.

    2005-11-01

    Further understanding of the structure and function of plasma apolipoproteins requires the determination of their high-resolution structures when complexed with lipids. In these studies, the production of homogeneous, biologically active lipoprotein particles of apolipoprotein E complexed with dipalmitoylphosphatidylcholine and their crystallization and X-ray diffraction are demonstrated. High-resolution structural information is available for several soluble plasma apolipoproteins (apos) in a lipid-free state. However, this information provides limited insight into structurefunction relationships, as this class of proteins primarily performs its functions of lipid transport and modulation of lipid metabolism in a lipid-bound state on lipoprotein particles. Here, the possibility of generating homogeneous lipoprotein particles that could be crystallized was explored, opening the possibility of obtaining high-resolution structural information by X-ray crystallography. To test this possibility, apoE4 complexed with the phospholipid dipalmitoylphosphatidylcholine was chosen. Uniform particles containing 50% lipid and 50% apoE4 were obtained and crystallized using the hanging-drop method. Two crystal forms diffract to beyond 8 resolution.

  1. Dynamic interaction between suspended particles and defects in a nematic liquid crystal

    NASA Astrophysics Data System (ADS)

    Grollau, S.; Abbott, N. L.; de Pablo, J. J.

    2003-05-01

    Insertion of spherical particles into a uniform nematic liquid crystal gives rise to the formation of topological defects. In the present work, we investigate how a spherical particle accompanied by its topological defects interacts with neighboring disclination lines. We perform two- and three-dimensional dynamic simulations to analyze the effect of a particle on the annihilation process of two disclination lines. The dynamics of the liquid crystal is described by a time-dependent evolution equation on the symmetric traceless order parameter that includes some of the salient features of liquid crystalline materials: excluded volume effects, or equivalently, short-range order elasticity and long-range order elasticity. At the surface of the particle, the liquid crystal is assumed to exhibit strong homeotropic anchoring. The particle is located between two disclination lines of topological charges +1/2 and -1/2. Two-dimensional simulations indicate that the topological defects bound to the particle mediate an interaction between the two disclination lines which increases the attraction between them. This result is confirmed by three-dimensional simulations that provide a complete description of the director field and of the order parameter around the particle. These simulations indicate that a spherical particle between two disclination lines can be surrounded by a Saturn ring, and suggest that the dynamic behavior of disclination lines could be used to report the structure of a defect around the particle.

  2. Crystal structure of benzimidazolium salicylate.

    PubMed

    Amudha, M; Kumar, P Praveen; Chakkaravarthi, G

    2015-10-01

    In the anion of the title mol-ecular salt, C7H7N2 (+)C7H5O3 (-) (systematic name: 1H-benzimidazol-3-ium 2-hy-droxy-ben-zo-ate), there is an intra-molecular O-H?O hydrogen bond that generates an S(6) ring motif. The CO2 group makes a dihedral angle of 5.33?(15) with its attached ring. In the crystal, the dihedral angle between the benzimidazolium ring and the anion benzene ring is 75.88?(5). Two cations bridge two anions via two pairs of N-H?O hydrogen bonds, enclosing an R (4) 4(16) ring motif, forming a four-membered centrosymmetric arrangement. These units are linked via C-H?O hydrogen bonds, forming chains propagating along the b-axis direction. The chains are linked by C-H?? and ?-? inter-actions [inter-centroid distances = 3.4156?(7) and 3.8196?(8)?], forming a three-dimensional structure. PMID:26594483

  3. Crystal growth, spectral, structural and optical studies of ?-conjugated stilbazolium crystal: 4-bromobenzaldehyde-4'-N'-methylstilbazolium tosylate.

    PubMed

    Krishna Kumar, M; Sudhahar, S; Bhagavannarayana, G; Mohan Kumar, R

    2014-05-01

    Nonlinear optical (NLO) organic compound, 4-bromobenzaldehyde-4'-N'-methylstilbazolium tosylate was synthesized by reflux method. The formation of molecular complex was confirmed from (1)H NMR, FT-IR and FT-Raman spectral analyses. The single crystals were grown by slow evaporation solution growth method and the crystal structure and atomic packing of grown crystal was identified. The morphology and growth axis of grown crystal were determined. The crystal perfection was analyzed using high resolution X-ray diffraction study on (001) plane. Thermal stability, decomposition stages and melting point of the grown crystal were analyzed. The optical absorption coefficient (?) and energy band gap (E(g)) of the crystal were determined using UV-visible absorption studies. Second harmonic generation efficiency of the grown crystal was examined by Kurtz powder method with different particle size using 1064 nm laser. Laser induced damage threshold study was carried out for the grown crystal using Nd:YAG laser. PMID:24531108

  4. Crystal growth, spectral, structural and optical studies of ?-conjugated stilbazolium crystal: 4-Bromobenzaldehyde-4?-N?-methylstilbazolium tosylate

    NASA Astrophysics Data System (ADS)

    Krishna Kumar, M.; Sudhahar, S.; Bhagavannarayana, G.; Mohan Kumar, R.

    Nonlinear optical (NLO) organic compound, 4-bromobenzaldehyde-4?-N?-methylstilbazolium tosylate was synthesized by reflux method. The formation of molecular complex was confirmed from 1H NMR, FT-IR and FT-Raman spectral analyses. The single crystals were grown by slow evaporation solution growth method and the crystal structure and atomic packing of grown crystal was identified. The morphology and growth axis of grown crystal were determined. The crystal perfection was analyzed using high resolution X-ray diffraction study on (0 0 1) plane. Thermal stability, decomposition stages and melting point of the grown crystal were analyzed. The optical absorption coefficient (?) and energy band gap (Eg) of the crystal were determined using UV-visible absorption studies. Second harmonic generation efficiency of the grown crystal was examined by Kurtz powder method with different particle size using 1064 nm laser. Laser induced damage threshold study was carried out for the grown crystal using Nd:YAG laser.

  5. A novel approach to identifying the elemental composition of individual residue particles retained in single snow crystals.

    PubMed

    Ma, Chang-Jin; Hwang, Kyung-Chul; Kim, Ki-Hyun

    2013-01-01

    This study was carried out to describe the chemical characteristics of individual residual particles in hexagonal snow crystals, which can provide a clue to the aerosol removal mechanism during snowfall. In the present study, to collect snow crystal individually and to identify the elemental composition of individual residues retained in a hexagonal crystal, an orchestration of the replication technique and micro-particle induced X-ray emission (micro-PIXE) analysis was carried out. Information concerning the elemental compositions and their abundance in the snow crystals showed a severe crystal-to-crystal fluctuation. The residues retained in the hexagonal snow crystals were dominated primarily by mineral components, such as silica and calcium. Based on the elemental mask and the spectrum of micro-PIXE, it was possible to presume the chemical inner-structure as well as the elemental mixing state in and/or on the individual residues retained in single snow crystals. PMID:23934568

  6. Application of channeling in bent crystals to charged particle beams

    SciTech Connect

    Carrigan, Jr., Richard A.

    1986-03-01

    The process of channeling of charged particle beams in bent crystals is described, including the effects of angular acceptance, spatial acceptance, normal dechanneling, bending dechanneling, and surface acceptance. Some bending applications that have been tried and future possibilities are reviewed. 29 refs., 30 figs. (LEW)

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

    DOEpatents

    Capone, D.W.; Dusek, J.

    1994-10-18

    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. 3 figs.

  8. 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.

  9. Budded baculovirus particle structure revisited.

    PubMed

    Wang, Qiushi; Bosch, Berend-Jan; Vlak, Just M; van Oers, Monique M; Rottier, Peter J; van Lent, Jan W M

    2016-02-01

    Baculoviruses are a group of enveloped, double-stranded DNA insect viruses with budded (BV) and occlusion-derived (ODV) virions produced during their infection cycle. BVs are commonly described as rod shaped particles with a high apical density of protein extensions (spikes) on the lipid envelope surface. However, due to the fragility of BVs the conventional purification and electron microscopy (EM) staining methods considerably distort the native viral structure. Here, we use cryo-EM analysis to reveal the near-native morphology of two intensively studied baculoviruses, Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) and Spodoptera exigua MNPV (SeMNPV), as models for BVs carrying GP64 and F as envelope fusion protein on the surface. The now well-preserved AcMNPV and SeMNPV BV particles have a remarkable elongated, ovoid shape leaving a large, lateral space between nucleocapsid (NC) and envelope. Consistent with previous findings the NC has a distinctive cap and base structure interacting tightly with the envelope. This tight interaction may explain the partial retaining of the envelope on both ends of the NC and the disappearance of the remainder of the BV envelope in the negative-staining EM images. Cryo-EM also reveals that the viral envelope contains two layers with a total thickness of ?6-7nm, which is significantly thicker than a usual biological membrane (<4nm) as measured by X-ray scanning. Most spikes are densely clustered at the two apical ends of the virion although some envelope proteins are also found more sparsely on the lateral regions. The spikes on the surface of AcMNPV BVs appear distinctly different from those of SeMNPV. Based on our observations we propose a new near-native structural model of baculovirus BVs. PMID:26743500

  10. Defect structures in metallic photonic crystals

    SciTech Connect

    Oezbay, E.; Temelkuran, B.; Sigalas, M.; Tuttle, G.; Soukoulis, C.M.; Ho, K.M.

    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.}

  11. 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 .

  12. Crystal structures of MBP fusion proteins.

    PubMed

    Waugh, David S

    2016-03-01

    Although chaperone-assisted protein crystallization remains a comparatively rare undertaking, the number of crystal structures of polypeptides fused to maltose-binding protein (MBP) that have been deposited in the Protein Data Bank (PDB) has grown dramatically during the past decade. Altogether, 102 fusion protein structures were detected by Basic Local Alignment Search Tool (BLAST) analysis. Collectively, these structures comprise a range of sizes, space groups, and resolutions that are typical of the PDB as a whole. While most of these MBP fusion proteins were equipped with short inter-domain linkers to increase their rigidity, fusion proteins with long linkers have also been crystallized. In some cases, surface entropy reduction mutations in MBP appear to have facilitated the formation of crystals. A comparison of the structures of fused and unfused proteins, where both are available, reveals that MBP-mediated structural distortions are very rare. PMID:26682969

  13. Crystal structure and morphology of syndiotactic polypropylene single crystals

    SciTech Connect

    Bu, J.Z.; Cheng, S.Z.D.

    1996-12-31

    In the past several years there have been an increased interest in the crystal structure and morphology of s-PP due to the new development of homogeneous metallocene catalysts which can produce s-PP having a high stereoregularity. In this research, the crystal structure and morphology of s-PP single crystals grown from the melt were investigated. A series of ten fractions of s-PP was studied with different molecular weights ranging from 10,300 to 234,000 (g/mol). These fractions all possess narrow molecular weight distributions (around 1.1-1.2) and high syndiotacticities ([r]{approximately}95%). The main techniques employed including transmission electron microscopy (TEM), atomic force microscopy (AFM), wide-angle X-ray diffraction (WAXD), and small-angle X-ray scattering (SAXS).

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

    SciTech Connect

    Cowan, Benjamin; Lin, M.C.; Schwartz, Brian; Byer, Robert; McGuinness, Christopher; Colby, Eric; England, Robert; Noble, Robert; 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.

  15. Hydrodynamic Effects of Particle Motions in Colloidal Crystal

    NASA Astrophysics Data System (ADS)

    Ueno, T.; Yamazaki, K.; Nishio, I.

    2006-05-01

    We analyzed the particle motion in colloidal crystals by digital video microscopy, and obtained the dispersion relation of amplitude and relaxation time for the normal cooperative relaxation mode of particle dynamics. These results were found to be differ from the prediction of simple overdamped bead-spring lattice (OBS) model which predicts relaxation time to be proportional to |q|-2 for small q region. These discrepancies are believed to be the results of hydrodynamic coupling between particles. We found that relaxation mode in which large number of particles move to the same direction, i.e. small q, has much shorter relaxation time compared to the simple theory. So we introduce a simple power law dependence to dispersion relation of the q-dependent viscous drag coefficient and lattice factor. The results of modified OBS model were in good agreement with the experimental results.

  16. 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.

  17. Resistive cooling circuits for charged particle traps using crystal resonators.

    PubMed

    Kaltenbacher, T; Caspers, F; Doser, M; Kellerbauer, A; Pribyl, W

    2011-11-01

    The paper addresses a novel method to couple a signal from charged particles in a Penning trap to a high Q resonant circuit using a crystal resonator. Traditionally, the trap capacity is converted into a resonator by means of an inductance. The tuned circuit's Q factor is directly linked to the input impedance "seen" by the trapped particles at resonance frequency. This parallel resonance impedance is a measure of the efficiency of resistive cooling and thus it should be optimized. We propose here a commercially available crystal resonator since it exhibits a very high Q value and a parallel resonance impedance of several MΩ. The possibility to tune the parallel resonance frequency of the quartz results in filter behavior that allows covering a range of some tens of its 3dB bandwidth by means of tuning. PMID:22128997

  18. 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.

  19. Formation of the structure of gold nanoclusters during crystallization

    SciTech Connect

    Gafner, Yu. Ya. Goloven'ko, Zh. V.; Gafner, S. L.

    2013-02-15

    The structure formation in gold nanoparticles 1.6-5.0 nm in diameter is studied by molecular dynamics simulation using a tight-binding potential. The simulation shows that the initial fcc phase in small Au clusters transforms into other structural modifications as temperature changes. As the cluster size increases, the transition temperature shifts toward the melting temperature of the cluster. The effect of various crystallization conditions on the formation of the internal structure of gold nanoclusters is studied in terms of microcanonical and canonical ensembles. The stability boundaries of various crystalline isomers are analyzed. The obtained dependences are compared with the corresponding data obtained for copper and nickel nanoparticles. The structure formation during crystallization is found to be characterized by a clear effect of the particle size on the stability of a certain isomer modification. Nickel and copper clusters are shown to exhibit common features in the formation of their structural properties, whereas gold clusters demonstrate much more complex behavior.

  20. Liquid crystal light valve structures

    NASA Technical Reports Server (NTRS)

    Koda, N. J. (inventor)

    1985-01-01

    An improved photosensor film and liquid crystal light valves embodying said film is provided. The photosensor film and liquid crystal light valve is characterized by a significant lower image retention time while maintaining acceptable photosensitivity. The photosensor film is produced by sputter depositing CdS onto an ITO substrate in an atmosphere of argon/H2S gas while maintaining the substrate at a temperature in the range of about 130 C to about 200 C and while introducing nitrogen gas into the system to the extent of not more than about 1% of plasma mixture. Following sputter deposition of the CdS, the film is annealed in an inert gas at temperatures ranging from about 300 C to about 425 C.

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

    SciTech Connect

    Mattarelli, M.; Secchi, M.; Dipartimento di Fisica, Università di Trento, Via Sommarive 14, 38123 Trento ; Montagna, M.

    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.

  2. Particle tracking from image sequences of complex plasma crystals

    SciTech Connect

    Hadziavdic, Vedad; Melandsoe, Frank; Hanssen, Alfred

    2006-05-15

    In order to gather information about the physics of the complex plasma crystals from the experimental data, particles have to be tracked through a sequence of images. An application of the Kalman filter for that purpose is presented, using a one-dimensional approximation of the particle dynamics as a model for the filter. It is shown that Kalman filter is capable of tracking dust particles even with high levels of measurement noise. An inherent part of the Kalman filter, the innovation process, can be used to estimate values of the physical system parameters from the experimental data. The method is shown to be able to estimate the characteristic oscillation frequency from noisy data.

  3. Crystal Structure Studies of Organic Superconductors

    NASA Astrophysics Data System (ADS)

    Thorup, N.; Rindorf, G.; Soling, H.

    1982-06-01

    X-ray crystal structure determinations have been carried out on (TMTSF)2X, where TMTSF = tetramethyltetraselenafulvalene and X = PF6-, ClO4-, ReO4-. These solids exhibit superconductivity at low temperature (~ 1 K); for PF6- and ReO4- hydrostatic pressure of the order 10 kbar is also required. This paper deals with a description and a comparison of the crystal structures, which have been determined at ambient temperature and pressure. Possible relationships between structural features and physical properties are discussed.

  4. SINGLE CRYSTAL NIOBIUM TUBES FOR PARTICLE COLLIDERS ACCELERATOR CAVITIES

    SciTech Connect

    MURPHY, JAMES E

    2013-02-28

    The objective of this research project is to produce single crystal niobium (Nb) tubes for use as particle accelerator cavities for the Fermi laboratorys International Linear Collider project. Single crystal Nb tubes may have superior performance compared to a polycrystalline tubes because the absence of grain boundaries may permit the use of higher accelerating voltages. In addition, Nb tubes that are subjected to the high temperature, high vacuum crystallization process are very pure and well annealed. Any impurity with a significantly higher vapor pressure than Nb should be decreased by the relatively long exposure at high temperature to the high vacuum environment. After application of the single crystal process, the surfaces of the Nb tubes are bright and shiny, and the tube resembles an electro polished Nb tube. For these reasons, there is interest in single crystal Nb tubes and in a process that will produce single crystal tubes. To convert a polycrystalline niobium tube into a single crystal, the tube is heated to within a few hundred ?C of the melting temperature of niobium, which is 2477 ?C. RF heating is used to rapidly heat the tube in a narrow zone and after reaching the operating temperature, the hot zone is slowly passed along the length of the tube. For crystallization tests with Nb tubes, the traverse rate was in the range of 1-10 cm per hour. All the crystallization tests in this study were performed in a water-cooled, stainless steel chamber under a vacuum of 5 x10-6 torr or better. In earliest tests of the single crystal growth process, the Nb tubes had an OD of 1.9 cm and a wall thickness of 0.15 mm. With these relatively small Nb tubes, the single crystal process was always successful in producing single crystal tubes. In these early tests, the operating temperature was normally maintained at 2200 ?C, and the traverse rate was 5 cm per hour. In the next test series, the Nb tube size was increased to 3.8 cm OD and the wall thickness was increased 0.18 mm and eventually to 0.21 mm. Again, with these larger tubes, single crystal tubes were usually produced by the crystallization process. The power supply was generally operated at full output during these tests, and the traverse rate was 5 cm per hour. In a few tests, the traverse rate was increased to 10 cm per hour, and at the faster traverse rate, single crystal growth was not achieved. In these tests with a faster traverse rate, it was thought that the tube was not heated to a high enough temperature to achieve single crystal growth. In the next series of tests, the tube OD was unchanged at 3.8 cm and the wall thickness was increased to 0.30 mm. The increased wall thickness made it difficult to reach an operating temperature above 2,000 ?C, and although the single crystal process caused a large increase in the crystal grains, no single crystal tubes were produced. It was assumed that the operating temperature in these tests was not high enough to achieve single crystal growth. In FY 2012, a larger power supply was purchased and installed. With the new power supply, temperatures above the melting point of Nb were easily obtained regardless of the tube thickness. A series of crystallization tests was initiated to determine if indeed the operating temperature of the previous tests was too low to achieve single crystal growth. For these tests, the Nb tube OD remained at 3.8 cm and the wall thickness was 0.30 mm. The first test had an operating temperature of 2,000 ?C. and the operating temperature was increased by 50 ?C increments for each successive test. The final test was very near the Nb melting temperature, and indeed, the Nb tube eventually melted in the center of the tube. These tests showed that higher temperatures did yield larger grain sizes if the traverse rate was held constant at 5 cm per hour, but no single crystal tubes were produced even at the highest operating temperature. In addition, slowing the traverse rate to as low as 1 cm per hour did not yield a single crystal tube regardless of operating temperature. At this time, it appears that the wall thickness of the Nb tube rather than the operating temperature is the most important parameter to achieving single crystal growth. Single crystal growth was easily obtained with thinner wall tubes, but with thicker tubes, it was not achieved under varied growth conditions.

  5. Particle beam and crabbing and deflecting structure

    DOEpatents

    Delayen, Jean

    2011-02-08

    A new type of structure for the deflection and crabbing of particle bunches in particle accelerators comprising a number of parallel transverse electromagnetic (TEM)-resonant) lines operating in opposite phase from each other. Such a structure is significantly more compact than conventional crabbing cavities operating the transverse magnetic TM mode, thus allowing low frequency designs.

  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)? 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 2Csp 2 bond in the side chain is transoid. In the crystal, the end rings of the anthryl units in adjacent molecules associate in parallelplanar orientations [shortest centroidcentroid distance = 3.6320?(7)?]. 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. PMID:26029389

  7. Slip Flow through Colloidal Crystals of Varying Particle Diameter

    PubMed Central

    Rogers, Benjamin J.; Wirth, Mary J.

    2012-01-01

    Slip flow of water through silica colloidal crystals was investigated experimentally for 8 different particle diameters, which have hydraulic channel radii ranging from 15 nm to 800 nm. The particle surfaces were silylated to be low in energy, with a water contact angle of 83, as determined for a silylated flat surface. Flow rates through centimeter lengths of colloidal crystal were measured using a commercial liquid chromatograph for accurate comparisons of water and toluene flow rates using pressure gradients as high as 1010 Pa/m. Toluene exhibited no-slip Hagen-Poiseuille flow for all hydraulic channel radii. For water, the slip flow enhancement as a function of hydraulic channel radius was described well by the expected slip flow correction for Hagen-Poiseuille flow, and the data revealed a constant slip length of 633 nm. A flow enhancement of 202 was observed for the smallest hydraulic channel radius of 15 nm. The amount of slip flow was found to be independent of shear rate over a range of fluid velocities from 0.7 to 5.8 mm/s. The results support the applicability of the slip flow correction for channel radii as small as 15 nm. The work demonstrates that packed beds of submicrometer particles enable slip flow to be employed for high volume flow rates. PMID:23237590

  8. 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.

  9. Crystal structure and chirality of natural floridoside.

    PubMed

    Simon-Colin, Christelle; Michaud, Franois; Lger, 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

  10. Crystal structure of potassium sodium tartrate trihydrate

    SciTech Connect

    Egorova, A. E. Ivanov, V. A.; Somov, N. V.; Portnov, V. N.; Chuprunov, E. V.

    2011-11-15

    Crystals of potassium sodium tartrate trihydrate (dl-KNaC{sub 4}H{sub 4}O{sub 6} {center_dot} 3H{sub 2}O) were obtained from an aqueous solution. The crystal shape was described. The atomic structure of the compound was determined and compared with the known structures of dl-KNaC{sub 4}H{sub 4}O{sub 6} {center_dot} 4H{sub 2}O and l-KNaC{sub 4}H{sub 4}O{sub 6} {center_dot} 4H{sub 2}O.

  11. Faceting and Commensurability in Crystal Structures of Colloidal Thin Films

    NASA Astrophysics Data System (ADS)

    Ramiro-Manzano, F.; Meseguer, F.; Bonet, E.; Rodriguez, I.

    2006-07-01

    This Letter investigates the influence of finite size effects on the particle arrangement of thin film colloidal crystals. A rich variety of crystallographic faceting with large single domain microcrystallites is shown. Optical reflectance experiments together with scanning electron microscopy permit the identification of the crystal symmetry and the facet orientation, as well as the exact number of monolayers. When the cell thickness is not commensurable with a high symmetry layering, particles arrange themselves in a periodic distribution of (111)- and (100)-orientated face centered cubic (fcc) microcrystallites separated by planar defects. These structures can be described as a fcc ordering orientated along a vicinal surface, modified by a periodic distribution of fcc (111) stacking faults.

  12. Faceting and commensurability in crystal structures of colloidal thin films.

    PubMed

    Ramiro-Manzano, F; Meseguer, F; Bonet, E; Rodriguez, I

    2006-07-14

    This Letter investigates the influence of finite size effects on the particle arrangement of thin film colloidal crystals. A rich variety of crystallographic faceting with large single domain microcrystallites is shown. Optical reflectance experiments together with scanning electron microscopy permit the identification of the crystal symmetry and the facet orientation, as well as the exact number of monolayers. When the cell thickness is not commensurable with a high symmetry layering, particles arrange themselves in a periodic distribution of (111)- and (100)-orientated face centered cubic (fcc) microcrystallites separated by planar defects. These structures can be described as a fcc ordering orientated along a vicinal surface, modified by a periodic distribution of fcc (111) stacking faults. PMID:16907485

  13. The crystal structure and crystal chemistry of fernandinite and corvusite

    USGS Publications Warehouse

    Evans, H.T., Jr.; Post, J.E.; Ross, D.R.; Nelen, J.A.

    1994-01-01

    Using type material of fernandinite from Minasragra, Peru, and corvusite from the Jack Claim, La Sal Mountains, Utah, the properties and crystal chemistry of these minerals have been determined by Rietveld analysis of the powder X-ray-diffraction patterns. The crystal structure of both species is isotypic with the V2O5 -type layer first found for ??-Ag0.68V2O5; it consists of chains of VO6 octahedra linked by opposite corners (parallel to b) condensed by edge-sharing to form the layer. The vanadium has average valence 4.8, and the resulting layer-charge is balanced by varying amounts of Ca, Na, and K in the interlayer region accompanied by labile water. This study has confirmed the validity of fernandinite as a unique mineral species. It is closely related to corvusite, from which it is distinguished on the basis of the dominant interlayer cation: Ca for fernandinite, Na for curvusite. -Authors

  14. Computing stoichiometric molecular composition from crystal structures

    PubMed Central

    Graulis, 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. PMID:26089747

  15. Crystal structure of Arabidopsis thaliana cytokinin dehydrogenase

    SciTech Connect

    Bae, Euiyoung; Bingman, Craig A.; Bitto, Eduard; Aceti, David J.; Phillips, Jr., George N.

    2008-08-13

    Since first discovered in Zea mays, cytokinin dehydrogenase (CKX) genes have been identified in many plants including rice and Arabidopsis thaliana, which possesses CKX homologues (AtCKX1-AtCKX7). So far, the three-dimensional structure of only Z. mays CKX (ZmCKX1) has been determined. The crystal structures of ZmCKX1 have been solved in the native state and in complex with reaction products and a slowly reacting substrate. The structures revealed four glycosylated asparagine residues and a histidine residue covalently linked to FAD. Combined with the structural information, recent biochemical analyses of ZmCKX1 concluded that the final products of the reaction, adenine and a side chain aldehyde, are formed by nonenzymatic hydrolytic cleavage of cytokinin imine products resulting directly from CKX catalysis. Here, we report the crystal structure of AtCKX7 (gene locus At5g21482.1, UniProt code Q9FUJ1).

  16. Structure-property evolution during polymer crystallization

    NASA Astrophysics Data System (ADS)

    Arora, Deepak

    The main theme of this research is to understand the structure-property evolution during crystallization of a semicrystalline thermoplastic polymer. A combination of techniques including rheology, small angle light scattering, differential scanning calorimetry and optical microscopy are applied to follow the mechanical and optical properties along with crystallinity and the morphology. Isothermal crystallization experiments on isotactic poly-1-butene at early stages of spherulite growth provide quantitative information about nucleation density, volume fraction of spherulites and their crystallinity, and the mechanism of connecting into a sample spanning structure. Optical microscopy near the fluid-to-solid transition suggests that the transition, as determined by time-resolved mechanical spectroscopy, is not caused by packing/jamming of spherulites but by the formation of a percolating network structure. The effect of strain, Weissenberg number (We ) and specific mechanical work (w) on rate of crystallization (nucleation followed by growth) and on growth of anisotropy was studied for shear-induced crystallization of isotactic poly-1-butene. The samples were sheared for a finite strain at the beginning of the experiment and then crystallized without further flow (Janeschitz-Kriegl protocol). Strain requirements to attain steady state/leveling off of the rate of crystallization were found to be much larger than the strain needed to achieve steady state of flow. The large strain and We>1 criteria were also observed for morphological transition from spherulitic growth to oriented growth. An apparatus for small angle light scattering (SALS) and light transmission measurements under shear was built and tested at the University of Massachusetts Amherst. As a new development, the polarization direction can be rotated by a liquid crystal polarization rotator (LCPR) with a short response time of 20 ms. The experiments were controlled and analyzed with a LabVIEW(TM) based code (LabVIEW(TM) 7.1) in real time. The SALS apparatus was custom built for ExxonMobil Research in Clinton NJ.

  17. Crystal structures and morphologies of fractionated milk fat in nanoemulsions.

    PubMed

    Truong, Tuyen; Morgan, Garry P; Bansal, Nidhi; Palmer, Martin; Bhandari, Bhesh

    2015-03-15

    The triacylglycerol (TAG) crystal structures and morphologies of fractionated milk lipids in nanoemulsions were investigated at 4C. Droplet size (0.17 versus 1.20 ?m), lipid composition (stearin versus olein) and cooling rate (1 versus 10C min(-1)) had an influence on the structural properties. Five crystal polymorphs (?, ?'1, ?'2, ?1, and ?2) were formed with either triple and/or double chain length structures in the solid phases of the emulsified systems. X-ray scattering peak intensities were reduced with the nanoemulsion particles. The internal structure of TAG exhibited stacking of individual lamellar layers (3.8-4.2 nm). Various anisometric shapes of fat nanoparticles were formed due to a highly sharp curvature of the nano-size droplets. The shape of olein nanoparticles was more polyhedral compared to the stearin. TAG crystals arranged in a planar-layered organisation at the slower cooling rate. These differences imply that the nanometric confinement of oil droplets modifies the fat crystal habit. PMID:25308656

  18. Requirements for structure determination of aperiodic crystals

    SciTech Connect

    Li, X.; Stern, E.A.; Ma, Y. )

    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.

  19. Shear induced structures in crystallizing cocoa butter

    NASA Astrophysics Data System (ADS)

    Mazzanti, Gianfranco; Guthrie, Sarah E.; Sirota, Eric B.; Marangoni, Alejandro G.; Idziak, Stefan H. J.

    2004-03-01

    Cocoa butter is the main structural component of chocolate and many cosmetics. It crystallizes in several polymorphs, called phases I to VI. We used Synchrotron X-ray diffraction to study the effect of shear on its crystallization. A previously unreported phase (phase X) was found and a crystallization path through phase IV under shear was observed. Samples were crystallized under shear from the melt in temperature controlled Couette cells, at final crystallization temperatures of 17.5^oC, 20^oC and 22.5^oC in Beamline X10A of NSLS. The formation of phase X was observed at low shear rates (90 s-1) and low crystallization temperature (17.5^oC), but was absent at high shear (720 s-1) and high temperature (20^oC). The d-spacing and melting point suggest that this new phase is a mixture rich on two of the three major components of cocoa butter. We also found that, contrary to previous reports, the transition from phase II to phase V can happen through the intermediate phase IV, at high shear rates and temperature.

  20. Defect structure around two colloids in a liquid crystal.

    PubMed

    Guzmán, O; Kim, E B; Grollau, S; Abbott, N L; de Pablo, J J

    2003-12-01

    This Letter investigates the defect structures that arise between two colloidal spheres immersed in a nematic liquid crystal. Molecular simulations and a dynamic field theory are employed to arrive at molecular-level and mesoscopic descriptions of the systems of interest. At large separations, each sphere is surrounded by a Saturn ring defect. However, at short separations both theory and simulation predict that a third disclination ring appears in between the spheres, in a plane normal to the Saturn rings. This feature gives rise to an effective binding of the particles. The structures predicted by field theory and molecular simulations are consistent with each other. PMID:14683198

  1. 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

  2. Architecture of crystal structures from square planes.

    PubMed

    Hauck, J; Mika, K

    2000-10-01

    The crystal structures of ordered b.c.c. (body-centered cubic), f.c. c. (face-centered cubic) or primitive cubic alloys AxBy and related NaCl, ZnS or CaF(2) derivative structures are characterized by the self-coordination numbers T(1), T(2) of the A atoms with A atoms. Structures with identical T(1) and T(2) values for all A atoms are at the corners of T(1) and T(2) structure maps, and can be analyzed for attractive or repulsive interactions of A atoms. Most observed structures are at the borders of the structure map and can be obtained by approximately 10 different combinations of structural units. The different combination mechanisms explain e.g. the shear structures of CuAu II or Nb(2)O(5) and the occurrence of vacancies in NaCl-related structures like NbO. PMID:11006550

  3. Structure analysis on synthetic emerald crystals

    NASA Astrophysics Data System (ADS)

    Lee, Pei-Lun; Lee, Jiann-Shing; Huang, Eugene; Liao, Ju-Hsiou

    2013-05-01

    Single crystals of emerald synthesized by means of the flux method were adopted for crystallographic analyses. Emerald crystals with a wide range of Cr3+-doping content up to 3.16 wt% Cr2O3 were examined by X-ray single crystal diffraction refinement method. The crystal structures of the emerald crystals were refined to R 1 (all data) of 0.019-0.024 and w R 2 (all data) of 0.061-0.073. When Cr3+ substitutes for Al3+, the main adjustment takes place in the Al-octahedron and Be-tetrahedron. The effect of substitution of Cr3+ for Al3+ in the beryl structure results in progressively lengthening of the Al-O distance, while the length of the other bonds remains nearly unchanged. The substitution of Cr3+ for Al3+ may have caused the expansion of a axis, while keeping the c axis unchanged in the emerald lattice. As a consequence, the Al-O-Si and Al-O-Be bonding angles are found to decrease, while the angle of Si-O-Be increases as the Al-O distance increases during the Cr replacement.

  4. Crystal structure of a plectonemic RNA supercoil

    SciTech Connect

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

    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.

  5. Crystal Structure of Human Enterovirus 71

    SciTech Connect

    Plevka, Pavel; Perera, Rushika; Cardosa, Jane; Kuhn, Richard J.; Rossmann, Michael G.

    2013-04-08

    Enterovirus 71 is a picornavirus associated with fatal neurological illness in infants and young children. Here, we report the crystal structure of enterovirus 71 and show that, unlike in other enteroviruses, the 'pocket factor,' a small molecule that stabilizes the virus, is partly exposed on the floor of the 'canyon.' Thus, the structure of antiviral compounds may require a hydrophilic head group designed to interact with residues at the entrance of the pocket.

  6. Crystal structure of zwitterionic bisimidazolium sulfonates

    NASA Astrophysics Data System (ADS)

    Kohmoto, Shigeo; Okuyama, Shinpei; Yokota, Nobuyuki; Takahashi, Masahiro; Kishikawa, Keiki; Masu, Hyuma; Azumaya, Isao

    2012-05-01

    Crystal structures of three zwitterionic bisimidazolium salts 1-3 in which imidazolium sulfonate moieties were connected with aromatic linkers, p-xylylene, 4,4'-dimethylenebiphenyl, and phenylene, respectively, were examined. The latter two were obtained as hydrates. An S-shaped molecular structure in which the sulfonate moiety was placed on the imidazolium ring was observed for 1. A helical array of hydrated water molecules was obtained for 2 while a linear array of hydrated water molecules was observed for 3.

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

    SciTech Connect

    Wang, Che-Yen; Miyazaki, Naoyuki; Yamashita, Tetsuo; Higashiura, Akifumi; Nakagawa, Atsushi; Li, Tian-Cheng; Takeda, Naokazu; Xing, Li; Hjalmarsson, Erik; Friberg, Claes; Liou, Der-Ming; Sung, Yen-Jen; Tsukihara, Tomitake; Matsuura, Yoshiharu; Miyamura, Tatsuo; Cheng, R. Holland

    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, α = β = γ = 90°, and contain one particle per asymmetric unit.

  8. Optically driven translational and rotational motions of micro-rod particles in a nematic liquid crystal

    NASA Astrophysics Data System (ADS)

    Stannarius, Ralf; Eremin, Alexey; Nadasi, Hajnalka; Takezoe, Hideo; Hirankittiwong, Pemika; Chattham, Nattaporn; Haba, Osamu; Yonetake, Koichiro

    2015-03-01

    Liquid crystals are self-organized mesomorphic materials with various symmetries and structures. Their unique features can be exploited for smart multifunctional materials. Colloidal dispersions of micro- and nano-particles in LCs have been widely studied. We demonstrate controlled light-driven translational and rotational motions of micro-rods in a nematic matrix. A small amount of azo-dendrimer molecules dissolved in a liquid crystal drives translation and rotation under non-polarized UV light irradiation. This is initiated by a light-induced trans-to-cis conformational change of the dendrimer adsorbed at the rod surface and the associated director reorientation. This system represents an optically driven molecular microactuator, which exploits molecular reorientation on a particle surface and transforms it into a mechanical torque.

  9. Crystal structure of riboflavin synthase

    SciTech Connect

    Liao, D.-I.; Wawrzak, Z.; Calabrese, J.C.; Viitanen, P.V.; Jordan, D.B.

    2010-03-05

    Riboflavin synthase catalyzes the dismutation of two molecules of 6,7-dimethyl-8-(1'-D-ribityl)-lumazine to yield riboflavin and 4-ribitylamino-5-amino-2,6-dihydroxypyrimidine. The homotrimer of 23 kDa subunits has no cofactor requirements for catalysis. The enzyme is nonexistent in humans and is an attractive target for antimicrobial agents of organisms whose pathogenicity depends on their ability to biosynthesize riboflavin. The first three-dimensional structure of the enzyme was determined at 2.0 {angstrom} resolution using the multiwavelength anomalous diffraction (MAD) method on the Escherichia coli protein containing selenomethionine residues. The homotrimer consists of an asymmetric assembly of monomers, each of which comprises two similar {beta} barrels and a C-terminal {alpha} helix. The similar {beta} barrels within the monomer confirm a prediction of pseudo two-fold symmetry that is inferred from the sequence similarity between the two halves of the protein. The {beta} barrels closely resemble folds found in phthalate dioxygenase reductase and other flavoproteins. The three active sites of the trimer are proposed to lie between pairs of monomers in which residues conserved among species reside, including two Asp-His-Ser triads and dyads of Cys-Ser and His-Thr. The proposed active sites are located where FMN (an analog of riboflavin) is modeled from an overlay of the {beta} barrels of phthalate dioxygenase reductase and riboflavin synthase. In the trimer, one active site is formed, and the other two active sites are wide open and exposed to solvent. The nature of the trimer configuration suggests that only one active site can be formed and be catalytically competent at a time.

  10. Crystal structure control in Au-free self-seeded InSb wire growth.

    PubMed

    Mandl, Bernhard; Dick, Kimberly A; Kriegner, Dominik; Keplinger, Mario; Bauer, Gnther; Stangl, Julian; Deppert, Knut

    2011-04-01

    In this work we demonstrate experimentally the dependence of InSb crystal structure on the ratio of Sb to In atoms at the growth front. Epitaxial InSb wires are grown by a self-seeded particle assisted growth technique on several different III-V substrates. Detailed investigations of growth parameters and post-growth energy dispersive x-ray spectroscopy indicate that the seed particles initially consist of In and incorporate up to 20at.% Sb during growth. By applying this technique we demonstrate the formation of zinc-blende, 4H and wurtzite structure in the InSb wires (identified by transmission electron microscopy and synchrotron x-ray diffraction), and correlate this sequential change in crystal structure to the increasing Sb/In ratio at the particle-wire interface. The low ionicity of InSb and the large diameter of the wire structures studied in this work are entirely outside the parameters for which polytype formation is predicted by current models of particle seeded wire growth, suggesting that the V/III ratio at the interface determines crystal structure in a manner well beyond current understanding. These results therefore provide important insight into the relationship between the particle composition and the crystal structure, and demonstrate the potential to selectively tune the crystal structure in other III-V compound materials as well. PMID:21346304

  11. Impacts of Crystallization on Protein Structural Dynamics

    NASA Astrophysics Data System (ADS)

    Kelemen, Lorand; Nie, Beining; Xie, Aihua; Anderson, Spencer; Philip, Andrew; Hoff, Wouter D.

    2005-10-01

    X-ray crystallographic technique is a powerful technique for structural determination of steady state proteins. Now this technique has been further developed to determine the structures of transient states of proteins during their functional processes. Can a protein function in the crystalline state? It is often assumed but untested that the functionally important structural dynamics of a protein are preserved in the crystalline state. This lack of test is largely due to the fact that major structural determination techniques, x-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, can only be applied to either crystalline state or solution state, not both. Here we report our direct study on the impacts of protein crystallization on the structural dynamics of a blue light photoreceptor protein using time-resolved Fourier transform infrared (FTIR) difference spectroscopic techniques. We found that proteins in crystalline state experience suppressed conformational changes, accelerated kinetics, and altered proton transfer pathway upon light activation. Furthermore, we show that crystallization salt itself has profound impacts on structural dynamics and proton transfer pathway. These results strongly demonstrate that it is necessary and crucial to test and determine whether transient/cold-trapped x-ray crystallography can resolve the protein structures of intermediate states that reflect the natural protein structural dynamics.

  12. Stability and dynamics of crystals and glasses of motorized particles

    PubMed Central

    Shen, Tongye; Wolynes, Peter G.

    2004-01-01

    Many of the large structures of the cell, such as the cytoskeleton, are assembled and maintained far from equilibrium. We study the stabilities of various structures for a simple model of such a far-from-equilibrium organized assembly in which spherical particles move under the influence of attached motors. From the variational solutions of the many-body master equation for Brownian motion with motorized kicking we obtain a closed equation for the order parameter of localization. Thus, we obtain the transition criterion for localization and stability limits for the crystalline phase and frozen amorphous structures of motorized particles. The theory also allows an estimate of nonequilibrium effective temperatures characterizing the response and fluctuations of motorized asemblies. PMID:15173584

  13. Coagulation factor XII protease domain crystal structure

    PubMed Central

    Pathak, M; Wilmann, P; Awford, J; Li, C; Hamad, BK; Fischer, PM; Dreveny, I; Dekker, LV; Emsley, J

    2015-01-01

    Background Coagulation factor XII is a serine protease that is important for kinin generation and blood coagulation, cleaving the substrates plasma kallikrein and FXI. Objective To investigate FXII zymogen activation and substrate recognition by determining the crystal structure of the FXII protease domain. Methods and results A series of recombinant FXII protease constructs were characterized by measurement of cleavage of chromogenic peptide and plasma kallikrein protein substrates. This revealed that the FXII protease construct spanning the light chain has unexpectedly weak proteolytic activity compared to β-FXIIa, which has an additional nine amino acid remnant of the heavy chain present. Consistent with these data, the crystal structure of the light chain protease reveals a zymogen conformation for active site residues Gly193 and Ser195, where the oxyanion hole is absent. The Asp194 side chain salt bridge to Arg73 constitutes an atypical conformation of the 70-loop. In one crystal form, the S1 pocket loops are partially flexible, which is typical of a zymogen. In a second crystal form of the deglycosylated light chain, the S1 pocket loops are ordered, and a short α-helix in the 180-loop of the structure results in an enlarged and distorted S1 pocket with a buried conformation of Asp189, which is critical for P1 Arg substrate recognition. The FXII structures define patches of negative charge surrounding the active site cleft that may be critical for interactions with inhibitors and substrates. Conclusions These data provide the first structural basis for understanding FXII substrate recognition and zymogen activation. PMID:25604127

  14. Crystal structures of two orthorhombic zirconias

    SciTech Connect

    Howard, C.J. ); Kisi, E.H. ); Ohtaka, O. )

    1991-09-01

    The crystal structures of orthorhombic zirconias formed by cooling magnesia-partially-stabilized zirconia (Mg-PSZ) (space group Pbc2{sub 1}) and by quenching zirconia powder from 600{degrees} C and 6 GPa (space group Pbca) are compared and contrasted. It is demonstrated that the two structures are easily distinguished by the neutron powder diffraction techniques used to establish them. The occurrence of two distinct phases is hence proved. Structural relationships between these two phases and also with the in situ high-pressure structure proposed from x-ray diffraction (XRD) are discussed. In this paper the three structures are virtually indistinguishable by XRD and so the structure of the high-pressure form in situ is considered to remain unknown.

  15. Moisture-induced surface crystallization of spray-dried amorphous lactose particles studied by atomic force microscopy.

    PubMed

    Mahlin, Denny; Berggren, Jonas; Alderborn, Göran; Engström, Sven

    2004-01-01

    The aim of this study was to show that atomic force microscopy (AFM) can be used to obtain mechanistic and kinetic information about the process of moisture-induced surface crystallization of single particles of amorphous lactose. Completely amorphous lactose particles were prepared by spray-drying a solution of alpha-lactose monohydrate, and moisture-induced crystallization was monitored for a bed of particles by microcalorimetry and for single particles by AFM. From the AFM images it was found that crystallization of the surface of single particles can be described in terms of a sequence of three events: an initial smoothening of the surface, formation of crystalline nanostructures dispersed in amorphous material, and growth of these structures to a complete crystalline surface. The surface roughness parameter rugosity was used to estimate the fraction crystalline surface, and the growth kinetics were found to obey the JMAK equation. The fraction crystalline surface at different times could also be estimated by determining the growth rate of individual crystals. It was concluded that AFM offers a unique means of visualizing the process of moisture-induced surface crystallization of amorphous particles and enables mechanistic and kinetic information about the process to be extracted. PMID:14648633

  16. 3D photonic crystals with a hierarchical pore structure

    NASA Astrophysics Data System (ADS)

    Stovpyaga, E. Yu.; Eurov, D. A.; Kurdyukov, D. A.; Yakovlev, S. A.; Kukushkina, Yu. A.; Golubev, V. G.

    2014-03-01

    Perfect 3D film photonic crystals are synthesized from submicron spherical silica particles consisting of a nonporous core and a mesoporous shell. The obtained photonic crystals with a hierarchical pore arrangementtransport macropores between particles and mesopores inside the shellare promising for application in optical gas sensors.

  17. Structural phase transitions in layered perovskitelike crystals

    SciTech Connect

    Aleksandrov, K.S.

    1995-03-01

    Possible symmetry changes due to small tilts of octahedra are considered for layered perovskite-like crystals containing slabs of several ({ell}) layers of comer-sharing octahedra. In the crystals with {ell} > 1, four types of distortions are possible; as a rule, these distortions correspond to the librational modes of the parent lattice. Condensation of these soft modes is the reason for structural phase transitions or sequences of phase transitions. The results obtained are compared with the known experimental data for a number of layered ferroelectric and ferroelastic perovskite-like compounds. An application of the results to the initial stage of determining unknown structures is discussed with particular attention paid to high-temperature superconductors. 76 refs., 9 figs., 7 tabs.

  18. Crystal structure of sodium cyclodinitridoimidodisulfophosphate dihydrate

    SciTech Connect

    Sokol, V.I.; Porai-Koshits, M.A.; Kop'eva, M.A.; Rozanov, I.A.; Beresnev, E.N.

    1987-04-01

    An x-ray structural investigation of the sodium salt with a heterocyclic anion containing P, N, and S atoms Na3HN3S2PO6 x 2H2O has been carried out (lambdaMo, 2485 reflections, anisotropic least-squares method to R = 0.043). The crystals are monoclinic: a = 7.832(2), b = 9.954(3), c = 13.281(4) A, US = 91.06, Z = 4, space group P21/n. The structure is built up from cyclic (H3S2PO4)T anions, Na cations, and molecules of water of crystallization. The heterocycle has a chair conformation and exists in the dinitridoimido tautomeric form, and the proton is located at a nitrogen atom positioned between a sulfur atom and the phosphorus atom.

  19. Amine free crystal structure: The crystal structure of d(CGCGCG){sub 2} and methylamine complex crystal

    SciTech Connect

    Ohishi, Hirofumi . E-mail: ohishi@gly.oups.ac.jp; Tsukamoto, Koji; Hiyama, Yoichi; Maezaki, Naoyoshi; Tanaka, Tetsuaki; Ishida, Toshimasa

    2006-09-29

    We succeeded in the crystallization of d(CGCGCG){sub 2} and methylamine Complex. The crystal was clear and of sufficient size to collect the X-ray crystallographic data up to 1.0 A resolution using synchrotron radiation. As a result of X-ray crystallographic analysis of 2F {sub o} - F {sub c} map was much clear and easily traced. It is First time monoamine co-crystallizes with d(CGCGCG){sub 2}. However, methylamine was not found from the complex crystal of d(CGCGCG){sub 2} and methylamine. Five Mg ions were found around d(CGCGCG){sub 2} molecules. These Mg ions neutralized the anion of 10 values of the phosphate group of DNA with five Mg{sup 2+}. DNA stabilized only by a metallic ion and there is no example of analyzing the X-ray crystal structure like this. Mg ion stabilizes the conformation of Z-DNA. To use monoamine for crystallization of DNA, we found that we can get only d(CGCGCG){sub 2} and Mg cation crystal. Only Mg cation can stabilize the conformation of Z-DNA. The method of using the monoamine for the crystallization of DNA can be applied to the crystallization of DNA of long chain of length in the future like this.

  20. 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.

  1. Crystal Structures of New Ammonium 5-Aminotetrazolates

    PubMed Central

    Lampl, Martin; Salchner, Robert; Laus, Gerhard; Braun, Doris E.; Kahlenberg, Volker; Wurst, Klaus; Fuhrmann, Gerda; Schottenberger, Herwig; Huppertz, Hubert

    2015-01-01

    The crystal structures of three salts of anionic 5-aminotetrazole are described. The tetramethylammonium salt (P1?) forms hydrogen-bonded ribbons of anions which accept weak CH?N contacts from the cations. The cystamine salt (C2/c) shows wave-shaped ribbons of anions linked by hydrogen bonds to screw-shaped dications. The tetramethylguanidine salt (P21/c) exhibits layers of anions hydrogen-bonded to the cations. PMID:26753100

  2. Predicting polymeric crystal structures by evolutionary algorithms

    NASA Astrophysics Data System (ADS)

    Zhu, Qiang; Sharma, Vinit; Oganov, Artem R.; Ramprasad, Ramamurthy

    2014-10-01

    The recently developed evolutionary algorithm USPEX proved to be a tool that enables accurate and reliable prediction of structures. Here we extend this method to predict the crystal structure of polymers by constrained evolutionary search, where each monomeric unit is treated as a building block with fixed connectivity. This greatly reduces the search space and allows the initial structure generation with different sequences and packings of these blocks. The new constrained evolutionary algorithm is successfully tested and validated on a diverse range of experimentally known polymers, namely, polyethylene, polyacetylene, poly(glycolic acid), poly(vinyl chloride), poly(oxymethylene), poly(phenylene oxide), and poly (p-phenylene sulfide). By fixing the orientation of polymeric chains, this method can be further extended to predict the structures of complex linear polymers, such as all polymorphs of poly(vinylidene fluoride), nylon-6 and cellulose. The excellent agreement between predicted crystal structures and experimentally known structures assures a major role of this approach in the efficient design of the future polymeric materials.

  3. Lagrangian coherent structures and inertial particle dynamics

    NASA Astrophysics Data System (ADS)

    Sudharsan, M.; Brunton, Steven L.; Riley, James J.

    2016-03-01

    In this work we investigate the dynamics of inertial particles using finite-time Lyapunov exponents (FTLE). In particular, we characterize the attractor and repeller structures underlying preferential concentration of inertial particles in terms of FTLE fields of the underlying carrier fluid. Inertial particles that are heavier than the ambient fluid (aerosols) attract onto ridges of the negative-time fluid FTLE. This negative-time FTLE ridge becomes a repeller for particles that are lighter than the carrier fluid (bubbles). We also examine the inertial FTLE (iFTLE) determined by the trajectories of inertial particles evolved using the Maxey-Riley equations with nonzero Stokes number and density ratio. Finally, we explore the low-pass filtering effect of Stokes number. These ideas are demonstrated on two-dimensional numerical simulations of the unsteady double-gyre flow.

  4. ORTEP2. Crystal Structure Illustration Plots

    SciTech Connect

    Johnson, C.K.

    1982-02-17

    ORTEP2 draws crystal structure illustrations using a CalComp plotter. Ball and stick type illustrations of publication quality are produced with either spheres or thermal motion probability ellipsoids on the atomic sites. The program can produce stereoscopic pairs of illustrations which aid in the visualization of complex packing arrangements of atoms and thermal motion patterns. Interatomic distances, bond angles, and principal axes of thermal motion are calculated also as part of the structural study. ORTEP2 includes a hidden line algorithm to eliminate those portions of atoms or bonds behind other atoms or bonds.

  5. Crystal structure and DFT calculations of andrographiside

    NASA Astrophysics Data System (ADS)

    Seth, Saikat Kumar; Banerjee, Sukdeb; Kar, Tanusree

    2010-02-01

    Crystal and molecular structure of a labdane diterpenoid glucoside, andrographiside ( 1) is determined from 2D-NMR and X-ray diffraction data. The 2D-NMR study indicates that the carbohydrate moiety is in ?-linkage and the sugar moiety is linked to C-19 of the aglycon. These observations are further confirmed from the X-ray diffraction studies. Both the six-membered rings are in chair conformation whereas the glucose ring adopts a twist-boat conformation. The molecular geometries and electronic structure of ( 1) were calculated at the DFT level using the hybrid exchange-correlation functional, BLYP, PW91 and PBE.

  6. 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)

  7. Bio-Inspired Approaches to Crystals with Composite Structures

    NASA Astrophysics Data System (ADS)

    Meldrum, Fiona

    2013-03-01

    Advances in technology demand an ever-increasing degree of control over material structure, properties and function. As the properties of monolithic materials are necessary limited, one route to extending them is to create a composite by combining contrasting materials. The potential of this approach is beautifully illustrated by the formation of biominerals where organic macromolecules are combined with brittle minerals such as calcite to create crystals with considerable fracture toughness. This talk will discuss how bio-inspired approaches can be used to generate single crystals with composite crystals through a simple one-pot method. By precipitating calcite crystals in the presence of ``occlusion species'' ranging from latex particles, to organic and inorganic nanoparticles and finally small molecules we demonstrate that high amounts of foreign species can be incorporated through control over the additive surface chemistry, and that this can lead to an enhancement of the mechanical properties of the calcite. Occlusion of 20 nm anionic diblock copolymer micelles was achieved at levels of over 13 wt%, and the properties of the resuktant composite calcite crystals were measured using a range of techniques including IR spectroscopy, high resolution powder XRD and high resolution TEM. Incorporation of these macromolecules leads to crystals with structures and mechanical properties similar to those of biominerals. With sizes in the range of some intracrystalline proteins, the micelles act as ``pseudo-proteins'', thereby providing an excellent model system for investigation of the mechanism of macromolecule insertion within biominerals. Extension of these studies to the incorporation of small molecules (amino acids) again demonstrated high levels of incorporation without any change in the crystal morphology. Further, occlusion of these small molecules within the calcite lattice again resulted in a significant increase in the hardness of the calcite, a result which appears to derive from an increase in lattice strain on molecular occlusion. Finally, the generality of this strategy is demonstrated by its extension to the incorporation of inorganic particles such as magnetite and gold within calcite, leading to the formation of inorganic-inorganic composites. I would like to acknowledge the EPSRC for funding under grants EP/G00868X/1, EP/E037364/1 and EP/K006304/1

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

    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 unusual states of this system: a 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. Crystal structure of the eukaryotic ribosome.

    PubMed

    Ben-Shem, Adam; Jenner, Lasse; Yusupova, Gulnara; Yusupov, Marat

    2010-11-26

    Crystal structures of prokaryotic ribosomes have described in detail the universally conserved core of the translation mechanism. However, many facets of the translation process in eukaryotes are not shared with prokaryotes. The crystal structure of the yeast 80S ribosome determined at 4.15 angstrom resolution reveals the higher complexity of eukaryotic ribosomes, which are 40% larger than their bacterial counterparts. Our model shows how eukaryote-specific elements considerably expand the network of interactions within the ribosome and provides insights into eukaryote-specific features of protein synthesis. Our crystals capture the ribosome in the ratcheted state, which is essential for translocation of mRNA and transfer RNA (tRNA), and in which the small ribosomal subunit has rotated with respect to the large subunit. We describe the conformational changes in both ribosomal subunits that are involved in ratcheting and their implications in coordination between the two associated subunits and in mRNA and tRNA translocation. PMID:21109664

  10. Method of using triaxial magnetic fields for making particle structures

    DOEpatents

    Martin, James E.; Anderson, Robert A.; Williamson, Rodney L.

    2005-01-18

    A method of producing three-dimensional particle structures with enhanced magnetic susceptibility in three dimensions by applying a triaxial energetic field to a magnetic particle suspension and subsequently stabilizing said particle structure. Combinations of direct current and alternating current fields in three dimensions produce particle gel structures, honeycomb structures, and foam-like structures.

  11. Continuous flow structuring of anisotropic biopolymer particles.

    PubMed

    Erni, Philipp; Cramer, Carsten; Marti, Irene; Windhab, Erich J; Fischer, Peter

    2009-08-30

    We review concepts and provide examples for the controlled structuring of biopolymer particles in hydrodynamic flow fields. The structuring concepts are grouped by the physical mechanisms governing drop deformation and shaping: (i) capillary structuring, (ii) shear and elongational structuring and (iii) confined flow methods. Non-spherical drops can be permanently structured if a solidification process, such as gelation or glass formation in the bulk or at the interface, is superimposed to the flow field. The physical and engineering properties of these processes critically depend on an elaborate balance between capillary phenomena, rheology, gel or glass formation kinetics, and bulk heat, mass and momentum transfer in multiphase fluids. This overview is motivated by the potential of non-spherical suspension particles, in particular those formed from 'natural' and 'sustainable' biopolymers, as rheology modifiers in food materials, consumer products, cosmetics or pharmaceuticals. PMID:19481192

  12. Revealing Structural Transformations during Crystallization of DNA-Nanoparticle Assemblies

    NASA Astrophysics Data System (ADS)

    Zhang, Yugang; Lu, Fang; van der Lelie, Daniel; Gang, Oleg

    2013-03-01

    Nanoparticle assembly via sequence-specific DNA recognition emerges as a powerful strategy for the fabrication of nanoparticle (NP)-based crystalline materials. Generally, a delicate thermal annealing is essential for the crystallization of NPs from kinetically trapped disordered states. Due to the complex coupling between interactions, entropic and chain effects in these systems, the crystallization pathway remains an intricate and open question. Herein, we present an experimental study of the crystallization process for DNA-directed nanoparticle assembly systems using synchrotron-based small angle x-ray scattering (SAXS). We demonstrated the effects of two crystallization-dominant factors, namely, temperature and volume fraction, on the structural transformation and order development. By combining a single component and binary systems we uncovered the evolution of global and local particle arrangements, such as correlation length, compositional disorder and coordination number, during the phase transformation. Research was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, under Contract No. DE-AC02-98CH10886.

  13. When and Why Like-Sized, Oppositely Charged Particles Assemble into Diamond-like Crystals.

    PubMed

    Bishop, Kyle J M; Chevalier, Nicolas R; Grzybowski, Bartosz A

    2013-05-01

    Like-sized, oppositely charged nanoparticles are known to assemble into large crystals with diamond-like (ZnS) ordering, in sharp contrast to analogous molecular ions and micrometer-scale colloids, which invariably favor more closely packed structures (NaCl or CsCl). Here, we show that these experimental observations can be understood as a consequence of ionic screening and the slight asymmetry in surface charge present on the assembling particles. With this asymmetry taken into account, free-energy calculations predict that the diamond-like ZnS lattice is more favorable than other 1:1 ionic structures, namely, NaCl or CsCl, when the Debye screening length is considerably larger than the particle size. A thermodynamic model describes how the presence of neutralizing counterions within the interstitial regions of the crystal acts to bias the formation of low-volume-fraction structures. The results provide general insights into the self-assembly of non-close-packed structures via electrostatic interactions. PMID:26282306

  14. Crystal structure of MboIIA methyltransferase.

    SciTech Connect

    Osipiuk, J.; Walsh, M. A.; Joachimiak, A.; Biosciences Division; Univ. of Gdansk; Medical Research Council France

    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 {angstrom} resolution the crystal structure of a {beta}-class DNA MTase MboIIA (M {center_dot} MboIIA) from the bacterium Moraxella bovis, the smallest DNA MTase determined to date. M {center_dot} 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 {center_dot} MboIIA is not bound to DNA. The overall structure of the enzyme closely resembles that of M {center_dot} RsrI. However, the cofactor-binding pocket in M {center_dot} MboIIA forms a closed structure which is in contrast to the open-form structures of other known MTases.

  15. The First Mammalian Aldehyde Oxidase Crystal Structure

    PubMed Central

    Coelho, Catarina; Mahro, Martin; Trinco, Jos; Carvalho, Alexandra T. P.; Ramos, Maria Joo; Terao, Mineko; Garattini, Enrico; Leimkhler, Silke; Romo, Maria Joo

    2012-01-01

    Aldehyde oxidases (AOXs) are homodimeric proteins belonging to the xanthine oxidase family of molybdenum-containing enzymes. Each 150-kDa monomer contains a FAD redox cofactor, two spectroscopically distinct [2Fe-2S] clusters, and a molybdenum cofactor located within the protein active site. AOXs are characterized by broad range substrate specificity, oxidizing different aldehydes and aromatic N-heterocycles. Despite increasing recognition of its role in the metabolism of drugs and xenobiotics, the physiological function of the protein is still largely unknown. We have crystallized and solved the crystal structure of mouse liver aldehyde oxidase 3 to 2.9 ?. This is the first mammalian AOX whose structure has been solved. The structure provides important insights into the protein active center and further evidence on the catalytic differences characterizing AOX and xanthine oxidoreductase. The mouse liver aldehyde oxidase 3 three-dimensional structure combined with kinetic, mutagenesis data, molecular docking, and molecular dynamics studies make a decisive contribution to understand the molecular basis of its rather broad substrate specificity. PMID:23019336

  16. Crystal Structure of the Human Primase*

    PubMed Central

    Baranovskiy, Andrey G.; Zhang, Yinbo; Suwa, Yoshiaki; Babayeva, Nigar D.; Gu, Jianyou; Pavlov, Youri I.; Tahirov, Tahir H.

    2015-01-01

    DNA replication in bacteria and eukaryotes requires the activity of DNA primase, a DNA-dependent RNA polymerase that lays short RNA primers for DNA polymerases. Eukaryotic and archaeal primases are heterodimers consisting of small catalytic and large accessory subunits, both of which are necessary for RNA primer synthesis. Understanding of RNA synthesis priming in eukaryotes is currently limited due to the lack of crystal structures of the full-length primase and its complexes with substrates in initiation and elongation states. Here we report the crystal structure of the full-length human primase, revealing the precise overall organization of the enzyme, the relative positions of its functional domains, and the mode of its interaction with modeled DNA and RNA. The structure indicates that the dramatic conformational changes in primase are necessary to accomplish the initiation and then elongation of RNA synthesis. The presence of a long linker between the N- and C-terminal domains of p58 provides the structural basis for the bulk of enzyme's conformational flexibility. Deletion of most of this linker affected the initiation and elongation steps of the primer synthesis. PMID:25550159

  17. Crystal Structure of the 30S Ribosomal Subunit from Thermus Thermophilus. Purification, Crystallization and Structure Determination

    SciTech Connect

    Clemons, William M.; Brodersen, Ditlev E.; McCutcheonn, John P.; May, Joanna L.C.; Carter, Andrew P.; Morgan-Warren, Robert J.; Wimberly, Brian T.; Ramakrishnan, Venki

    2009-10-07

    We describe the crystallization and structure determination of the 30 S ribosomal subunit from Thermus thermophilus. Previous reports of crystals that diffracted to 10 {angstrom} resolution were used as a starting point to improve the quality of the diffraction. Eventually, ideas such as the addition of substrates or factors to eliminate conformational heterogeneity proved less important than attention to detail in yielding crystals that diffracted beyond 3 {angstrom} resolution. Despite improvements in technology and methodology in the last decade, the structure determination of the 30 S subunit presented some very challenging technical problems because of the size of the asymmetric unit, crystal variability and sensitivity to radiation damage. Some steps that were useful for determination of the atomic structure were: the use of anomalous scattering from the LIII edges of osmium and lutetium to obtain the necessary phasing signal; the use of tunable, third-generation synchrotron sources to obtain data of reasonable quality at high resolution; collection of derivative data precisely about a mirror plane to preserve small anomalous differences between Bijvoet mates despite extensive radiation damage and multi-crystal scaling; the pre-screening of crystals to ensure quality, isomorphism and the efficient use of scarce third-generation synchrotron time; pre-incubation of crystals in cobalt hexaammine to ensure isomorphism with other derivatives; and finally, the placement of proteins whose structures had been previously solved in isolation, in conjunction with biochemical data on protein-RNA interactions, to map out the architecture of the 30 S subunit prior to the construction of a detailed atomic-resolution model.

  18. Crystal structure of the dynein motor domain.

    PubMed

    Carter, Andrew P; Cho, Carol; Jin, Lan; Vale, Ronald D

    2011-03-01

    Dyneins are microtubule-based motor proteins that power ciliary beating, transport intracellular cargos, and help to construct the mitotic spindle. Evolved from ring-shaped hexameric AAA-family adenosine triphosphatases (ATPases), dynein's large size and complexity have posed challenges for understanding its structure and mechanism. Here, we present a 6 angstrom crystal structure of a functional dimer of two ~300-kilodalton motor domains of yeast cytoplasmic dynein. The structure reveals an unusual asymmetric arrangement of ATPase domains in the ring-shaped motor domain, the manner in which the mechanical element interacts with the ATPase ring, and an unexpected interaction between two coiled coils that create a base for the microtubule binding domain. The arrangement of these elements provides clues as to how adenosine triphosphate-driven conformational changes might be transmitted across the motor domain. PMID:21330489

  19. 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 4.4 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.

  20. The Crystal Structures of Potentially Tautomeric Compounds

    NASA Astrophysics Data System (ADS)

    Furmanova, Nina G.

    1981-08-01

    Data on the structures of potentially proto-, metallo-, and carbono-tropic compounds, obtained mainly by X-ray diffraction, are surveyed. The results of neutron and electron diffraction studies have also been partly used. It is shown that a characteristic feature of all the systems considered is the formation of hydrogen or secondary bonds ensuring the contribution of both possible tautomeric forms to the structure. Systematic consideration of the experimental data leads to the conclusion that there is a close relation between the crystal structure and the dynamic behaviour of the molecules in solution and that secondary and hydrogen bonds play a significant role in the tautomeric transition. The bibliography includes 152 references.

  1. Track-Structure Simulations for Charged Particles

    PubMed Central

    Dingfelder, Michael

    2013-01-01

    Monte-Carlo track-structure simulations provide a detailed and accurate picture of radiation transport of charged particles through condensed matter of biological interest. Liquid water serves as surrogate for soft tissue and is used in most Monte-Carlo track-structure codes. Basic theories of radiation transport and track-structure simulations are discussed and differences to condensed history codes highlighted. Interaction cross sections for electrons, protons, alpha particles, light and heavy ions are required input data for track-structure simulations. Different calculation methods, including the plane-wave Born approximation, the dielectric theory, and semi-empirical approaches are presented using liquid water as a target. Low-energy electron transport and light ion transport are discussed as areas of special interest. PMID:23032889

  2. Crystal structure prediction from first principles: The crystal structures of glycine

    NASA Astrophysics Data System (ADS)

    Lund, Albert M.; Pagola, Gabriel I.; Orendt, Anita M.; Ferraro, Marta B.; Facelli, Julio C.

    2015-04-01

    Here we present the results of our unbiased searches of glycine polymorphs obtained using the genetic algorithms search implemented in MGAC, modified genetic algorithm for crystals, coupled with the local optimization and energy evaluation provided by Quantum Espresso. We demonstrate that it is possible to predict the crystal structures of a biomedical molecule using solely first principles calculations. We were able to find all the ambient pressure stable glycine polymorphs, which are found in the same energetic ordering as observed experimentally and the agreement between the experimental and predicted structures is of such accuracy that the two are visually almost indistinguishable.

  3. 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 (π-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 42 Å. 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 60 nm. 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

  4. 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.

  5. Crystal structure of a DNA catalyst.

    PubMed

    Ponce-Salvatierra, Almudena; Wawrzyniak-Turek, Katarzyna; Steuerwald, Ulrich; Hbartner, Claudia; Pena, Vladimir

    2016-01-14

    Catalysis in biology is restricted to RNA (ribozymes) and protein enzymes, but synthetic biomolecular catalysts can also be made of DNA (deoxyribozymes) or synthetic genetic polymers. In vitro selection from synthetic random DNA libraries identified DNA catalysts for various chemical reactions beyond RNA backbone cleavage. DNA-catalysed reactions include RNA and DNA ligation in various topologies, hydrolytic cleavage and photorepair of DNA, as well as reactions of peptides and small molecules. In spite of comprehensive biochemical studies of DNA catalysts for two decades, fundamental mechanistic understanding of their function is lacking in the absence of three-dimensional models at atomic resolution. Early attempts to solve the crystal structure of an RNA-cleaving deoxyribozyme resulted in a catalytically irrelevant nucleic acid fold. Here we report the crystal structure of the RNA-ligating deoxyribozyme 9DB1 (ref. 14) at 2.8? resolution. The structure captures the ligation reaction in the post-catalytic state, revealing a compact folding unit stabilized by numerous tertiary interactions, and an unanticipated organization of the catalytic centre. Structure-guided mutagenesis provided insights into the basis for regioselectivity of the ligation reaction and allowed remarkable manipulation of substrate recognition and reaction rate. Moreover, the structure highlights how the specific properties of deoxyribose are reflected in the backbone conformation of the DNA catalyst, in support of its intricate three-dimensional organization. The structural principles underlying the catalytic ability of DNA elucidate differences and similarities in DNA versus RNA catalysts, which is relevant for comprehending the privileged position of folded RNA in the prebiotic world and in current organisms. PMID:26735012

  6. Temperature dependent spin structures in Hexaferrite crystal

    NASA Astrophysics Data System (ADS)

    Chao, Y. C.; Lin, J. G.; Chun, S. H.; Kim, K. H.

    2016-01-01

    In this work, the Hexaferrite Ba0.5Sr1.5Zn2Fe12O22 (BSZFO) is studied due to its interesting characteristics of long-wavelength spin structure. Ferromagnetic resonance (FMR) is used to probe the magnetic states of BSZFO single crystal and its temperature dependence behavior is analyzed by decomposing the multiple lines of FMR spectra into various phases. Distinguished phase transition is observed at 110 K for one line, which is assigned to the ferro(ferri)-magnetic transition from non-collinear to collinear spin state.

  7. Elasticity of some mantle crystal structures. II.

    NASA Technical Reports Server (NTRS)

    Wang, H.; Simmons, G.

    1973-01-01

    The single-crystal elastic constants are determined as a function of pressure and temperature for rutile structure germanium dioxide (GeO2). The data are qualitatively similar to those of rutile TiO2 measured by Manghnani (1969). The compressibility in the c direction is less than one-half that in the a direction, the pressure derivative of the shear constant is negative, and the pressure derivative of the bulk modulus has a relatively high value of about 6.2. According to an elastic strain energy theory, the negative shear modulus derivative implies that the kinetic barrier to diffusion decreases with increasing pressure.

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

    SciTech Connect

    Sun, Bin; Sun, Zhiwei; Ouyang, Wenze Xu, Shenghua

    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.

  9. Structure and magnetic properties of Nd-Fe-B fine particles produced by spark erosion

    SciTech Connect

    Wan, H.; Berkowitz, A.E.

    1995-06-01

    Nd-Fe-B particles have been fabricated by spark erosion in different dielectric media, the best results have been obtained in liquid Ar, with the product consisting of crystalline 2:14:1 and amorphous Nd-Fe-B phases. The average particle size and volume percent of amorphous component are affected by power supply parameters, with higher discharge current pulses producing smaller average size and a higher ratio of amorphous component. Mixtures of soft and hard magnetic phases exists in as-made particles. The small particles (<5 {mu}m), which have the amorphous structure, are magnetically soft. To further obtain single domain particles of Nd{sub 2}Fe{sub 14}B, crystallization of submicron size particles is required. Since the crystallization temperature is about 600 C, it is crucial to prevent oxidation and sintering of such small particles during annealing. This latter work is in progress.

  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. Crystal structure of yeast Sco1.

    PubMed

    Abajian, Carnie; Rosenzweig, Amy C

    2006-06-01

    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-A 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. PMID:16570183

  12. Crystal structure of yeast Sco1

    SciTech Connect

    Abajian, Carnie; Rosenzweig, Amy C.

    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.

  13. Continuous synthesis of polymer-coated drug particles by porous hollow fiber membrane-based antisolvent crystallization.

    PubMed

    Chen, Dengyue; Singh, Dhananjay; Sirkar, Kamalesh K; Pfeffer, Robert

    2015-01-13

    Using porous hollow fiber membranes, this study illustrates a novel technique to continuously synthesize polymer-coated drug crystals by antisolvent crystallization. The synthesized polymer-coated drug crystals involve crystals of the drug Griseofulvin (GF) coated by a thin layer of the polymer Eudragit RL100. The process feed, an acetone solution of the drug GF containing the dissolved polymer, was passed through the shell side of a membrane module containing many porous hollow fibers of Nylon-6. Through the lumen of the hollow fibers, the antisolvent water was passed at a higher pressure to inject water jets through every pore in the fiber wall into the shell-side acetone feed solution, creating an extremely high level of supersaturation and immediate crystallization. It appears that the GF crystals are formed first and serve as nuclei for the precipitation of the polymer Eudragit, which forms a thin coating around the GF crystals. The polymer-coated drug crystals were collected by a filtration device at the shell-side outlet of the membrane module, and the surface morphology, particle size distribution, and the polymer coating thickness were then characterized by scanning electron microscopy (SEM), scanning transmission electron microscopy (STEM), laser diffraction spectroscopy (LDS), and thermogravimetric analysis (TGA). To study the properties of the coated drug crystals, X-ray diffraction (XRD), Raman spectroscopy, and dissolution tests were implemented. These results indicate that a polymer-coated, free-flowing product was successfully developed under appropriate conditions in this novel porous hollow fiber antisolvent crystallization (PHFAC) method. The coated drug particles can be potentially used for controlled release. The molecular and the crystal structures of GF were not affected by the PHFAC method, which may be easily scaled up. PMID:25552289

  14. 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

  15. The Crystal Structure of Human Argonaute2

    SciTech Connect

    Schirle, Nicole T.; MacRae, Ian J.

    2012-07-18

    Argonaute proteins form the functional core of the RNA-induced silencing complexes that mediate RNA silencing in eukaryotes. The 2.3 angstrom resolution crystal structure of human Argonaute2 (Ago2) reveals a bilobed molecule with a central cleft for binding guide and target RNAs. Nucleotides 2 to 6 of a heterogeneous mixture of guide RNAs are positioned in an A-form conformation for base pairing with target messenger RNAs. Between nucleotides 6 and 7, there is a kink that may function in microRNA target recognition or release of sliced RNA products. Tandem tryptophan-binding pockets in the PIWI domain define a likely interaction surface for recruitment of glycine-tryptophan-182 (GW182) or other tryptophan-rich cofactors. These results will enable structure-based approaches for harnessing the untapped therapeutic potential of RNA silencing in humans.

  16. Crystal Structure of Human Nicotinamide Riboside Kinase

    SciTech Connect

    Khan,J.; Xiang, S.; Tong, L.

    2007-01-01

    Nicotinamide riboside kinase (NRK) has an important role in the biosynthesis of NAD{sup +} as well as the activation of tiazofurin and other NR analogs for anticancer therapy. NRK belongs to the deoxynucleoside kinase and nucleoside monophosphate (NMP) kinase superfamily, although the degree of sequence conservation is very low. We report here the crystal structures of human NRK1 in a binary complex with the reaction product nicotinamide mononucleotide (NMN) at 1.5 {angstrom} resolution and in a ternary complex with ADP and tiazofurin at 2.7 {angstrom} resolution. The active site is located in a groove between the central parallel {beta} sheet core and the LID and NMP-binding domains. The hydroxyl groups on the ribose of NR are recognized by Asp56 and Arg129, and Asp36 is the general base of the enzyme. Mutation of residues in the active site can abolish the catalytic activity of the enzyme, confirming the structural observations.

  17. Crystal structure of glucokinase regulatory protein.

    PubMed

    Pautsch, Alexander; Stadler, Nadja; Lhle, Adelheid; Rist, Wolfgang; Berg, Adina; Glocker, Lucia; Nar, Herbert; Reinert, Dirk; Lenter, Martin; Heckel, Armin; Schnapp, Gisela; Kauschke, Stefan G

    2013-05-21

    Glucokinase (GK) plays a major role in the regulation of blood glucose homeostasis in both the liver and the pancreas. In the liver, GK is controlled by the GK regulatory protein (GKRP). GKRP in turn is activated by fructose 6-phosphate (F6P) and inactivated by fructose 1-phosphate (F1P). Disrupting the GK-GKRP complex increases the activity of GK in the cytosol and is considered an attractive concept for the regulation of blood glucose. We have determined the crystal structure of GKRP in its inactive F1P-bound form. The binding site for F1P is located deeply buried at a domain interface, and H-D exchange experiments confirmed that F1P and F6P compete for this site. The structure of the inactive GKRP-F1P complex provides a starting point for understanding the mechanism of fructose phosphate-dependent GK regulation at an atomic level. PMID:23621087

  18. Crystal structure of human nicotinamide riboside kinase.

    PubMed

    Khan, Javed A; Xiang, Song; Tong, Liang

    2007-08-01

    Nicotinamide riboside kinase (NRK) has an important role in the biosynthesis of NAD(+) as well as the activation of tiazofurin and other NR analogs for anticancer therapy. NRK belongs to the deoxynucleoside kinase and nucleoside monophosphate (NMP) kinase superfamily, although the degree of sequence conservation is very low. We report here the crystal structures of human NRK1 in a binary complex with the reaction product nicotinamide mononucleotide (NMN) at 1.5 A resolution and in a ternary complex with ADP and tiazofurin at 2.7 A resolution. The active site is located in a groove between the central parallel beta sheet core and the LID and NMP-binding domains. The hydroxyl groups on the ribose of NR are recognized by Asp56 and Arg129, and Asp36 is the general base of the enzyme. Mutation of residues in the active site can abolish the catalytic activity of the enzyme, confirming the structural observations. PMID:17698003

  19. Photoresponsive Release from Azobenzene-Modified Single Cubic Crystal NaCl/Silica Particles

    DOE PAGESBeta

    Jiang, Xingmao; Liu, Nanguo; Assink, Roger A.; Jiang, Yingbing; Brinker, C. Jeffrey

    2011-01-01

    Azobenzene ligands were uniformly anchored to the pore surfaces of nanoporous silica particles with single crystal NaCl using 4-(3-triethoxysilylpropylureido)azobenzene (TSUA). The functionalization delayed the release of NaCl significantly. The modified particles demonstrated a photocontrolled release by trans/cis isomerization of azobenzene moieties. The addition of amphiphilic solvents, propylene glycol (PG), propylene glycol propyl ether (PGPE), and dipropylene glycol propyl ether (DPGPE) delayed the release in water, although the wetting behavior was improved and the delay is the most for the block molecules with the longest carbon chain. The speedup by UV irradiation suggests a strong dependence of diffusion on the switchablemore » pore size. TGA, XRD, FTIR, and NMR techniques were used to characterize the structures.« less

  20. Crystal structure of bacterioferritin from Rhodobacter sphaeroides

    SciTech Connect

    Nam, Ki Hyun; Xu, Yongbin; Piao, Shunfu; Priyadarshi, Amit; Lee, Eun Hye; Kim, Hye-Yeon; Jeon, Young Ho; Ha, Nam-Chul; Hwang, Kwang Yeon

    2010-01-01

    Iron is essential for the survival of organisms, but either excess or deficient levels of iron induce oxidative stress, thereby causing cell damage. As a result, iron regulation is essential for proper cell growth and proliferation in most organisms. Bacterioferritin is a ferritin-like family protein that contains a heme molecule and a ferroxidase site at the di-iron center. This protein plays a primary role in intracellular iron storage for iron homeostasis, as well as in the maintenance of iron in a soluble and non-toxic form. Although several bacterioferritin structures have been determined, no structural studies have successfully elucidated the molecular function of the heme molecule and the ferroxidase center. Here, we report the crystal structure of bacterioferritin from Rhodobacter sphaeroides. This protein exists in a roughly spherical configuration via the assembly of 24 subunits. We describe the oligomeric arrangement, ferroxidase center and heme-binding site based on this structure. The protein contains a single iron-binding configuration in the ferroxidase center, which allows for the release of iron by His130 when the protein is in the intermediate state. The heme molecule in RsBfr is stabilized by shifting of the van der Waals interaction center between the porphyrin of the heme and Trp26. We anticipate that further structural analysis will provide a more complete understanding of the molecular mechanisms of members of the ferritin-like family.

  1. Chemical and structural studies of 'Brownlee' particles. [extraterrestrial dust in upper atmosphere

    NASA Technical Reports Server (NTRS)

    Flynn, G. J.; Fraundorf, P.; Shirck, J.; Walker, R. M.

    1978-01-01

    Several techniques were applied to the study of small particles (around 10 microns) collected in the upper atmosphere by U-2 aircraft. The major element chemistry of roughly 1/3 of the particles is similar to that of chondritic meteorites, although considerable variation of element ratios is observed from particle to particle, and even within a given particle. All particles of 'chondritic' composition are polycrystalline aggregates. About half have fully re-entrant structures; the remaining ones have more compact structures ranging from platey to spherical morphologies. Micro-crystallites with various internal structures are observed in the size range from less than 100 A to several microns. Although tracks are clearly observed in transmission electron microscope examination of terrestrial analog crystals, no tracks of solar flare origin have yet been identified in the U-2 particles. Induced fission track analysis of one aggregate shows that the U concentration is less than 15 ppbm, lending support to the extraterrestrial origin hypothesis.

  2. 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

  3. Crystal structure of strontium dinickel iron orthophosphate.

    PubMed

    Ouaatta, Said; Assani, Abderrazzak; Saadi, Mohamed; El Ammari, Lahcen

    2015-10-01

    The title compound, SrNi2Fe(PO4)3, synthesized by solid-state reaction, crystallizes in an ordered variant of the ?-CrPO4 structure. In the asymmetric unit, two O atoms are in general positions, whereas all others atoms are in special positions of the space group Imma: the Sr cation and one P atom occupy the Wyckoff position 4e (mm2), Fe is on 4b (2/m), Ni and the other P atom are on 8g (2), one O atom is on 8h (m) and the other on 8i (m). The three-dimensional framework of the crystal structure is built up by [PO4] tetra-hedra, [FeO6] octa-hedra and [Ni2O10] dimers of edge-sharing octa-hedra, linked through common corners or edges. This structure comprises two types of layers stacked alternately along the [100] direction. The first layer is formed by edge-sharing octa-hedra ([Ni2O10] dimer) linked to [PO4] tetra-hedra via common edges while the second layer is built up from a strontium row followed by infinite chains of alternating [PO4] tetra-hedra and FeO6 octa-hedra sharing apices. The layers are held together through vertices of [PO4] tetra-hedra and [FeO6] octa-hedra, leading to the appearance of two types of tunnels parallel to the a- and b-axis directions in which the Sr cations are located. Each Sr cation is surrounded by eight O atoms. PMID:26594419

  4. Crystal structures of five 6-mercaptopurine derivatives.

    PubMed

    Gomes, Lígia R; Low, John Nicolson; Magalhães E Silva, Diogo; Cagide, Fernando; Borges, Fernanda

    2016-03-01

    The crystal structures of five 6-mercaptopurine derivatives, viz. 2-[(9-acetyl-9H-purin-6-yl)sulfan-yl]-1-(3-meth-oxy-phen-yl)ethan-1-one (1), C16H14N4O3S, 2-[(9-acetyl-9H-purin-6-yl)sulfan-yl]-1-(4-meth-oxy-phen-yl)ethan-1-one (2), C16H14N4O3S, 2-[(9-acetyl-9H-purin-6-yl)sulfan-yl]-1-(4-chloro-phen-yl)ethan-1-one (3), C15H11ClN4O2S, 2-[(9-acetyl-9H-purin-6-yl)sulfan-yl]-1-(4-bromo-phen-yl)ethan-1-one (4), C15H11BrN4O2S, and 1-(3-meth-oxy-phen-yl)-2-[(9H-purin-6-yl)sulfan-yl]ethan-1-one (5), C14H12N4O2S. Compounds (2), (3) and (4) are isomorphous and accordingly their mol-ecular and supra-molecular structures are similar. An analysis of the dihedral angles between the purine and exocyclic phenyl rings show that the mol-ecules of (1) and (5) are essentially planar but that in the case of the three isomorphous compounds (2), (3) and (4), these rings are twisted by a dihedral angle of approximately 38°. With the exception of (1) all mol-ecules are linked by weak C-H⋯O hydrogen bonds in their crystals. There is π-π stacking in all compounds. A Cambridge Structural Database search revealed the existence of 11 deposited compounds containing the 1-phenyl-2-sulfanyl-ethanone scaffold; of these, only eight have a cyclic ring as substituent, the majority of these being heterocycles. PMID:27006794

  5. Crystal structure of strontium dinickel iron orthophosphate

    PubMed Central

    Ouaatta, Said; Assani, Abderrazzak; Saadi, Mohamed; El Ammari, Lahcen

    2015-01-01

    The title compound, SrNi2Fe(PO4)3, synthesized by solid-state reaction, crystallizes in an ordered variant of the α-CrPO4 structure. In the asymmetric unit, two O atoms are in general positions, whereas all others atoms are in special positions of the space group Imma: the Sr cation and one P atom occupy the Wyckoff position 4e (mm2), Fe is on 4b (2/m), Ni and the other P atom are on 8g (2), one O atom is on 8h (m) and the other on 8i (m). The three-dimensional framework of the crystal structure is built up by [PO4] tetra­hedra, [FeO6] octa­hedra and [Ni2O10] dimers of edge-sharing octa­hedra, linked through common corners or edges. This structure comprises two types of layers stacked alternately along the [100] direction. The first layer is formed by edge-sharing octa­hedra ([Ni2O10] dimer) linked to [PO4] tetra­hedra via common edges while the second layer is built up from a strontium row followed by infinite chains of alternating [PO4] tetra­hedra and FeO6 octa­hedra sharing apices. The layers are held together through vertices of [PO4] tetra­hedra and [FeO6] octa­hedra, leading to the appearance of two types of tunnels parallel to the a- and b-axis directions in which the Sr cations are located. Each Sr cation is surrounded by eight O atoms. PMID:26594419

  6. Crystal structures of the human adiponectin receptors

    PubMed Central

    Tanabe, Hiroaki; Fujii, Yoshifumi; 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

    2015-01-01

    Adiponectin stimulation of its receptors, AdipoR1 and AdipoR2, increases AMPK and PPAR activities, 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 receptor (GPCR)s. Here we report the crystal structures of human AdipoR1 and AdipoR2 at 2.9- and 2.4- resolution, respectively, which represent a novel class of receptor structure. The seven-transmembrane helices, conformationally distinct from those of GPCRs, enclose a large cavity where three conserved histidine residues coordinate a zinc ion. The zinc-binding structure may play a role in the adiponectin-stimulated AMPK phosphorylation and UCP2 upregulation. Adiponectin may broadly interact with the extracellular face, rather than the C-terminal flexible 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

  7. 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 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 thanthe 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

  8. 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} α -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.

  9. Crystal structures of respiratory pathogen neuraminidases

    PubMed Central

    Hsiao, Yu-Shan; Parker, Dane; Ratner, Adam J.; Prince, Alice; Tong, Liang

    2013-01-01

    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 Å 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. PMID:19284989

  10. 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.

  11. Crystal structure of natural phaeosphaeride A

    PubMed Central

    Abzianidze, Victoria V.; Poluektova, Ekaterina V.; Bolshakova, Ksenia P.; Panikorovskii, Taras L.; Bogachenkov, Alexander S.; Berestetskiy, Alexander O.

    2015-01-01

    The asymmetric unit of the title compound, C15H23NO5, contains two independent mol­ecules. Phaeosphaeride A contains two primary sections, an alkyl chain consisting of five C atoms and a cyclic system consisting of fused five- and six-membered rings with attached substituents. In the crystal, the mol­ecules form layered structures. Nearly planar sheets, parallel to the (001) plane, form bilayers of two-dimensional hydrogen-bonded networks with the hy­droxy groups located on the inter­ior of the bilayer sheets. The network is constructed primarily of four O—H⋯O hydrogen bonds, which form a zigzag pattern in the (001) plane. The butyl chains inter­digitate with the butyl chains on adjacent sheets. The crystal was twinned by a twofold rotation about the c axis, with refined major–minor occupancy fractions of 0.718 (6):0.282 (6). PMID:26396831

  12. Crystal structure of ruthenocenecarbonitrile

    PubMed Central

    Strehler, Frank; Korb, Marcus; Lang, Heinrich

    2015-01-01

    The molecular structure of ruthenocenecarbonitrile, [Ru(?5-C5H4CN)(?5-C5H5)], exhibits point group symmetry m, with the mirror plane bisecting the molecule through the CN substituent. The RuII atom is slightly shifted from the ?5-C5H4 centroid towards the CN substituent. In the crystal, molecules are arranged in columns parallel to [100]. One-dimensional intermolecular ?? interactions [3.363?(3)?] between the CN carbon atom and one carbon of the cyclopentadienyl ring of the overlaying molecule are present. PMID:26029400

  13. Crystal structure of morpholin-4-ium cinnamate

    PubMed Central

    Smith, Graham

    2015-01-01

    In the anhydrous salt formed from the reaction of morpholine with cinnamic acid, C4H10NO+C9H7O2 ?, the acid side chain in the trans-cinnamate anion is significantly rotated out of the benzene plane [CCC C torsion angle = 158.54?(17)]. In the crystal, one of the the aminium H atoms is involved in an asymmetric three-centre cationanion NH?(O,O?) R 1 2(4) hydrogen-bonding interaction with the two carboxylate O-atom acceptors of the anion. The second aminium-H atom forms an inter-species NH?Ocarboxylate hydrogen bond. The result of the hydrogen bonding is the formation of a chain structure extending along [100]. Chains are linked by CH?O interactions, forming a supramolecular layer parallel to (01-1). PMID:26594560

  14. Exploring structural phase transitions of ion crystals.

    PubMed

    Yan, L L; Wan, W; Chen, L; Zhou, F; Gong, S J; Tong, X; Feng, M

    2016-01-01

    Phase transitions have been a research focus in many-body physics over past decades. Cold ions, under strong Coulomb repulsion, provide a repealing paradigm of exploring phase transitions in stable confinement by electromagnetic field. We demonstrate various conformations of up to sixteen laser-cooled (40)Ca(+) ion crystals in a home-built surface-electrode trap, where besides the usually mentioned structural phase transition from the linear to the zigzag, two additional phase transitions to more complicated two-dimensional configurations are identified. The experimental observation agrees well with the numerical simulation. Heating due to micromotion of the ions is analysed by comparison of the numerical simulation with the experimental observation. Our investigation implies very rich and complicated many-body behaviour in the trapped-ion systems and provides effective mechanism for further exploring quantum phase transitions and quantum information processing with ultracold trapped ions. PMID:26865229

  15. Crystal structure of oligoacenes under high pressure

    SciTech Connect

    Oehzelt, M.; Aichholzer, A.; Resel, R.; Heimel, G.; Venuti, E.; Della Valle, R. G.

    2006-09-01

    We report crystal structures of anthracene, tetracene, and pentacene under pressure. Energy dispersive x-ray diffraction experiments up to 9 GPa were performed. Quasiharmonic lattice dynamics calculations are compared to the experimental results and show excellent agreement. The results are discussed with particular emphasis on the pressure dependence of the unit cell dimensions and the rearrangement of the molecules. The high pressure data also allow an analysis of the equation of state of these substances as a function of molecular length. We report the bulk modulus of tetracene and pentacene (B{sub 0}=9.0 and 9.6 GPa, respectively) and its pressure derivative (B{sub 0}{sup '}=7.9 and 6.4, respectively). We find that the unit-cell volume and bulk modulus at ambient pressure follow a linear relationship with the molecular length.

  16. Crystal structure of morpholin-4-ium cinnamate.

    PubMed

    Smith, Graham

    2015-11-01

    In the anhydrous salt formed from the reaction of morpholine with cinnamic acid, C4H10NO(+)C9H7O2 (-), the acid side chain in the trans-cinnamate anion is significantly rotated out of the benzene plane [C-C-C- C torsion angle = 158.54?(17)]. In the crystal, one of the the aminium H atoms is involved in an asymmetric three-centre cation-anion N-H?(O,O') R 1 (2)(4) hydrogen-bonding inter-action with the two carboxyl-ate O-atom acceptors of the anion. The second aminium-H atom forms an inter-species N-H?Ocarboxyl-ate hydrogen bond. The result of the hydrogen bonding is the formation of a chain structure extending along [100]. Chains are linked by C-H?O inter-actions, forming a supra-molecular layer parallel to (01-1). PMID:26594560

  17. Crystal structure of betulinic acid methanol monosolvate.

    PubMed

    Tang, Wei; Chen, Neng-Hua; Li, Guo-Qiang; Wang, Guo-Cai; Li, Yao-Lan

    2014-12-01

    The title compound [systematic name: 3β-hy-droxy-lup-20(29)-en-28-oic acid methanol monosolvate], C30H48O3·CH3OH, is a solvent pseudopolymorph of a naturally occurring plant-derived lupane-type penta-cyclic triterpenoid, which was isolated from the traditional Chinese medicinal plant Syzygium jambos (L.) Alston. The dihedral angle between the planes of the carb-oxy-lic acid group and the olefinic group is 12.17 (18)°. The A/B, B/C, C/D and D/E ring junctions are all trans-fused. In the crystal, O-H⋯O hydrogen bonds involving the hy-droxy and carb-oxy-lic acid groups and the methanol solvent mol-ecule give rise to a two-dimensional network structure lying parallel to (001). PMID:25553022

  18. Exploring structural phase transitions of ion crystals

    PubMed Central

    Yan, L. L.; Wan, W.; Chen, L.; Zhou, F.; Gong, S. J.; Tong, X.; Feng, M.

    2016-01-01

    Phase transitions have been a research focus in many-body physics over past decades. Cold ions, under strong Coulomb repulsion, provide a repealing paradigm of exploring phase transitions in stable confinement by electromagnetic field. We demonstrate various conformations of up to sixteen laser-cooled 40Ca+ ion crystals in a home-built surface-electrode trap, where besides the usually mentioned structural phase transition from the linear to the zigzag, two additional phase transitions to more complicated two-dimensional configurations are identified. The experimental observation agrees well with the numerical simulation. Heating due to micromotion of the ions is analysed by comparison of the numerical simulation with the experimental observation. Our investigation implies very rich and complicated many-body behaviour in the trapped-ion systems and provides effective mechanism for further exploring quantum phase transitions and quantum information processing with ultracold trapped ions. PMID:26865229

  19. Crystal structure of a snake venom cardiotoxin

    SciTech Connect

    Rees, B.; Samama, J.P.; Thierry, J.C.; Gilibert, M.; Fischer, J.; Schweitz, H.; Lazdunski, M.; Moras, D.

    1987-05-01

    Cardiotoxin V/sup II/4 from Naja mossambica crystallizes in space group P6/sub 1/ (a = b = 73.9 A; c = 59.0 A) with two molecules of toxin (molecular mass = 6715 Da) in the asymmetric unit. The structure was solved by using a combination of multiple isomorphous replacement and density modification methods. Model building and least-squares refinement led to an agreement factor of 27% for a data set to 3-A resolution prior to any inclusion of solvent molecules. The topology of the molecule is similar to that found in short and long snake neurotoxins, which block the nicotinic acetylcholine receptor. Major differences occur in the conformation of the central loop, resulting in a change in the concavity of the molecule. Hydrophobic residues are clustered in two distinct areas. The existence of stable dimeric entities in the crystalline state, with the formation of a six-stranded antiparallel ..beta.. sheet, may be functionally relevant.

  20. 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)

  1. Synthesis and textural evolution of alumina particles with mesoporous structures

    SciTech Connect

    Liu Xun; Peng Tianyou; Yao Jinchun; Lv Hongjin; Huang Cheng

    2010-06-15

    Alumina particles with mesostructures were synthesized through a chemical precipitation method by using different inorganic aluminum salts followed by a heterogeneous azeotropic distillation and calcination process. The obtained mesoporous {gamma}-alumina particles were systematically characterized by the X-ray diffraction, transmission electron microscopy and nitrogen adsorption-desorption measurement. Effects of the aluminum salt counter anion, pH value and the azeotropic distillation process on the structural or textural evolution of alumina particles were investigated. It is found that Cl{sup -} in the reaction solution can restrain the textural evolution of the resultant precipitates into two-dimensional crystallized pseudoboehmite lamellae during the heterogeneous azeotropic distillation, and then transformed into {gamma}-Al{sub 2}O{sub 3} particles with mesostructures after further calcination at 1173 K, whereas coexisting SO{sub 4}{sup 2-} can promote above morphology evolution and then transformed into {gamma}-Al{sub 2}O{sub 3} nanofibers after calcination at 1173 K. Moreover nearly all materials retain relatively high specific surface areas larger than 100 m{sup 2} g{sup -1} even after calcinations at 1173 K. - Graphical abstract: Co-existing Cl{sup -} is beneficial for the formation of {gamma}-alumina nanoparticles with mesostructures during the precipitation process. Interparticle and intraparticle mesopores can be derived from acidic solution and near neutral solution, respectively.

  2. Crystal structure of human GDF11.

    PubMed

    Padyana, Anil K; Vaidialingam, Bhamini; Hayes, David B; Gupta, Priyanka; Franti, Michael; Farrow, Neil A

    2016-03-01

    Members of the TGF-? family of proteins are believed to play critical roles in cellular signaling processes such as those involved in muscle differentiation. The extent to which individual family members have been characterized and linked to biological function varies greatly. The role of myostatin, also known as growth differentiation factor 8 (GDF8), as an inhibitor of muscle differentiation is well understood through genetic linkages. In contrast, the role of growth differentiation factor 11 (GDF11) is much less well understood. In humans, the mature forms of GDF11 and myostatin are over 94% identical. In order to understand the role that the small differences in sequence may play in the differential signaling of these molecules, the crystal structure of GDF11 was determined to a resolution of 1.50?. A comparison of the GDF11 structure with those of other family members reveals that the canonical TGF-? domain fold is conserved. A detailed structural comparison of GDF11 and myostatin shows that several of the differences between these proteins are likely to be localized at interfaces that are critical for the interaction with downstream receptors and inhibitors. PMID:26919518

  3. The crystal structure of a nonstoichiometric nasicon

    SciTech Connect

    Rudolf, F.; Clearfield, A.; Jorgensen, J.D.; Subramanian, M.A.

    1985-06-01

    The crystal structure of a nonstoichiometric NASICON prepared from a hydrothermally synthesized precursor phase was solved by means of Xray powder and neutron powder diffraction methods. The NASICON phase is monoclinic with unit cell parameters, from Rietveld refinement of the neutron data, of a = 15.6209(8), b = 9.0326(5), c = 9.2172(5)A, ..beta.. = 123.67(1)A, V = 1082.5A/sup 3/. The space group is C2/c with Z = 4. The structure is essentially that proposed earlier by Hong, but the nonstoichiometry results from replacement of part of the Zr/sup 4 +/ by Na/sup +/. Refinement of site occupancies coupled with the requirement of overall charge balance yields the formula Na /sub 2.88/ (Na /sub 0.32/ Zr /sub 1.68/ )Si /sub 1.84/ P /sub 1.16/ O /sub 11.54/ which also agrees well with analytical data. Only 20% of the Na1 sites are occupied, but 80% of the Na3 sites are filled. This structure provides a framework from which to rationalize the many reports in the literature that NASICON can only be prepared with difficulty by high temperature solid state reactions.

  4. 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

  5. Polymer induced changes of the crystallization scenario in suspensions of hard sphere like microgel particles

    NASA Astrophysics Data System (ADS)

    Beyer, Richard; Iacopini, Sara; Palberg, Thomas; Schpe, Hans Joachim

    2012-06-01

    We investigated the crystallization scenario of highly cross linked polystyrene particles dispersed in the good solvent 2-ethylnaphtalene and their mixtures with non-adsorbing low molecular weight polysterene polymer using time resolved static light scattering. The samples were prepared slightly below the melting volume fraction of the polymer free system. For the polymer free samples, we obtained polycrystalline solids via crystallization scenario known from hard sphere suspensions with little competition of wall crystal formation. Addition of non-adsorbing low molecular weight polystyrene polymer leads to a considerably slowing down of the bulk crystallization kinetics. We observed a delay of the precursor to crystal conversion for the bulk crystallization while the induction times for the wall nucleation are reduced. The increased polymer concentration thus shifts the balance between the two competing crystallization pathways giving the possibility to tune the relative amount of wall based crystals.

  6. Crystal Structure of Homo Sapiens Kynureninase

    PubMed Central

    Lima, Santiago; Kristoforov, Roman; Momany, Cory; Phillips, Robert S.

    2008-01-01

    Kynureninase is a member of a large family of catalytically diverse but structurally homologous pyridoxal-5?-phosphate dependent enzymes known as the aspartate aminotransferase superfamily or ?-family. The Homo sapiens and other eukaryotic constitutive kynureninases preferentially catalyze the hydrolytic cleavage of 3-hydroxy-L-kynurenine to produce 3-hydroxyanthranilate and L-alanine, while L-kynurenine is the substrate of many prokaryotic inducible kynureninases. The human enzyme was cloned with an N-terminal hexahistidine tag, expressed, and purified from a bacterial expression system using Ni-metal ion affinity chromatography. Kinetic characterization of the recombinant enzyme reveals classic Michaelis-Menten behavior, with a Km= 28.3 1.9 ?M, and a specific activity of 1.75 ?mol min-1 mg-1 for 3-hydroxy-DL-kynurenine. Crystals of recombinant kynureninase were obtained that diffracted to 2.0 , and the atomic structure of the PLP-bound holoenzyme was solved by molecular replacement using the Pseudomonas fluorescens kynureninase structure (PDB accession 1qz9) as the phasing model. A structural superposition with the P. fluorescens kynureninase revealed that these two structures resemble the open and closed conformations of aspartate aminotransferase. The comparison illustrates the dynamic nature of these proteins small domains and reveals a role for Arg-434 similar to that in other AAT ?-family members. Docking of 3-hydroxy-L-kynurenine into the human kynureninase active site suggests that Asn-333 and His-102 are involved in substrate binding and molecular discrimination between inducible and constitutive kynureninase substrates. PMID:17300176

  7. Crystal Structure of Human Spermine Synthase

    PubMed Central

    Wu, Hong; Min, Jinrong; Zeng, Hong; McCloskey, Diane E.; Ikeguchi, Yoshihiko; Loppnau, Peter; Michael, Anthony J.; Pegg, Anthony E.; Plotnikov, Alexander N.

    2008-01-01

    The crystal structures of two ternary complexes of human spermine synthase (EC 2.5.1.22), one with 5′-methylthioadenosine and spermidine and the other with 5′-methylthioadenosine and spermine, have been solved. They show that the enzyme is a dimer of two identical subunits. Each monomer has three domains: a C-terminal domain, which contains the active site and is similar in structure to spermidine synthase; a central domain made up of four β-strands; and an N-terminal domain with remarkable structural similarity to S-adenosylmethionine decarboxylase, the enzyme that forms the aminopropyl donor substrate. Dimerization occurs mainly through interactions between the N-terminal domains. Deletion of the N-terminal domain led to a complete loss of spermine synthase activity, suggesting that dimerization may be required for activity. The structures provide an outline of the active site and a plausible model for catalysis. The active site is similar to those of spermidine synthases but has a larger substrate-binding pocket able to accommodate longer substrates. Two residues (Asp201 and Asp276) that are conserved in aminopropyltransferases appear to play a key part in the catalytic mechanism, and this role was supported by the results of site-directed mutagenesis. The spermine synthase·5′-methylthioadenosine structure provides a plausible explanation for the potent inhibition of the reaction by this product and the stronger inhibition of spermine synthase compared with spermidine synthase. An analysis to trace possible evolutionary origins of spermine synthase is also described. PMID:18367445

  8. 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 PreissHandler 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 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. PMID:26042198

  9. Crystal structure of human nicotinic acid phosphoribosyltransferase.

    PubMed

    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 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. PMID:26042198

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

    SciTech Connect

    Baryshevsky, V.G. ); Dubovskaya, I.Ya. )

    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.

  11. Liquid-crystal patterns of rectangular particles in a square nanocavity.

    PubMed

    Gonzlez-Pinto, Miguel; Martnez-Ratn, Yuri; Velasco, Enrique

    2013-09-01

    Using density-functional theory in the restricted-orientation approximation, we analyze the liquid-crystal patterns and phase behavior of a fluid of hard rectangular particles confined in a two-dimensional square nanocavity of side length H composed of hard inner walls. Patterning in the cavity is governed by surface-induced order as well as capillary and frustration effects and depends on the relative values of the particle aspect ratio ??L/?, with L the length and ? the width of the rectangles (L??), and cavity size H. Ordering may be very different from bulk (H??) behavior when H is a few times the particle length L (nanocavity). Bulk and confinement properties are obtained for the cases ?=1, 3, and 6. In bulk the isotropic phase is always stable at low packing fractions ?=L??_{0} (with ?_{0} the average density) and nematic, smectic, columnar, and crystal phases can be stabilized at higher ? depending on ?: For increasing ? the sequence of isotropic to columnar is obtained for ?=1 and 3, whereas for ?=6 we obtain isotropic to nematic to smectic (the crystal being unstable in all three cases for the density range explored). In the confined fluid surface-induced frustration leads to fourfold symmetry breaking in all phases (which become twofold symmetric). Since no director distortion can arise in our model by construction, frustration in the director orientation is relaxed by the creation of domain walls (where the director changes by 90^{?}); this configuration is necessary to stabilize periodic phases. For ?=1 the crystal becomes stable with commensurate transitions taking place as H is varied. These transitions involve structures with different number of peaks in the local density. In the case ?=3 the commensurate transitions involve columnar phases with different number of columns. In the case ?=6 the high-density region of the phase diagram is dominated by commensurate transitions between smectic structures; at lower densities there is a symmetry-breaking isotropic to nematic transition exhibiting nonmonotonic behavior with cavity size. Apart from the present application in a confinement setup, our model could be used to explore the bulk region near close packing in order to elucidate the possible existence of disordered phases at close packing. PMID:24125284

  12. Crystal and electronic structure of copper sulfides

    NASA Astrophysics Data System (ADS)

    Lukashev, Pavel

    Copper sulfides with different copper concentration exist in mineral form ranging from CuS to Cu2S. Among these, chalcosite Cu 2S, and digenite Cu1.8S were the subject of extensive research for decades mainly because of their use as the absorber in photovoltaic cells. Yet; their electronic structure is poorly understood because their crystal structure is complex. Most of the results published so far report the semiconducting nature of these compounds with the energy band gap being in the range of 0.84 to 1.9 eV. The crystal structure consists of a close-packed lattice of S with mobile Cu occupying various types of interstitial sites with a statistical distribution depending on temperature. In this thesis we present the first computational study of their electronic band structure. Initially, we investigated the simpler antifluorite structure. Both local density approximation (LDA) and self-consistent quasiparticle GW calculations with the full-potential linearized muffin-tin orbital method give a semimetallic band structure. Inspection of the nature of the bands shows that the lowest conduction band is mainly Cu-s-like except right near the center of the Brillouin zone where a Cu-s-like state lies about 1 eV below the valence band maximum. Significantly, in GW calculations, this state shifts up by several 0.1 eV but not sufficiently to open a gap. A random distortion of the Cu atoms from the perfect antifluorite positions is found to break the degeneracy of the d state at the Gamma-point and thus opens up a small gap of about 0.1 eV in LDA. As our next step we constructed supercell models for the cubic and hexagonal phases with the Cu positions determined by a weighted random number generator. The low temperature monoclinic phase was also studied. The computed total energies of these structures follow the same order as the reported phases with increasing temperatures. All these models gave similar small band gaps of order 0.1-0.2 eV. However, their conduction band is now mainly s-like and addition of an expected Cu-s level shift opens the gap to about 0.5 eV. Some simpler hexagonal model structures gave slightly larger band gap but were found to be unrealistic. The optical absorption data all show a strong intraband absorption with a minimum in absorption at about 1 eV. Our calculations suggest a significantly lower gap of order 0.5 eV with low absorption cross section, the true nature of which is masked by the free carrier absorption. As part of our study of the related Cu-compounds, we analyzed the quasiparticle effects beyond LDA obtained from a GW calculation on the effective masses and Kohn-Luttinger hamiltonian parameters for CuBr.

  13. 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

  14. A facile method for the structure control of TiO2 particles at low temperature

    NASA Astrophysics Data System (ADS)

    Li, Zhaoqing; Zhu, Yun; Wang, Lianwen; Wang, Jiatai; Guo, Qian; Li, Jiangong

    2015-11-01

    Crystalline and amorphous TiO2 particles have important potential applications in photocatalysis, structural ceramics, solar batteries and nanoglasses. Hence controlling the structure of TiO2 particles is of practical importance. Crystalline TiO2 particles are usually prepared by calcination of their amorphous precursor. Here a facile method was developed to control the structure of TiO2 particles at a low temperature. TiO2 particles were prepared by sol-gel method; and it was found that during the washing process, the TiO2 particles washed with water are crystalline whereas the TiO2 particles washed with ethanol are amorphous. Further analyses indicate that ethanol washing may introduce an organic cover layer on the TiO2 particles which hinders the crystallization of amorphous TiO2 particles. Therefore, the structure of TiO2 particles, amorphous or crystalline (anatase), can be controlled just by changing the washing medium, water or ethanol. This method seems a common method for controlling the (amorphous or crystalline) structure of metal oxides and hydroxides and was verified in the preparation of ZrO2, FeO(OH), and Al(OH)3 particles.

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

    PubMed

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

    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

  16. Crystal structures of five 6-mercaptopurine derivatives

    PubMed Central

    Gomes, Lígia R.; Low, John Nicolson; Magalhães e Silva, Diogo; Cagide, Fernando; Borges, Fernanda

    2016-01-01

    The crystal structures of five 6-mercaptopurine derivatives, viz. 2-[(9-acetyl-9H-purin-6-yl)sulfan­yl]-1-(3-meth­oxy­phen­yl)ethan-1-one (1), C16H14N4O3S, 2-[(9-acetyl-9H-purin-6-yl)sulfan­yl]-1-(4-meth­oxy­phen­yl)ethan-1-one (2), C16H14N4O3S, 2-[(9-acetyl-9H-purin-6-yl)sulfan­yl]-1-(4-chloro­phen­yl)ethan-1-one (3), C15H11ClN4O2S, 2-[(9-acetyl-9H-purin-6-yl)sulfan­yl]-1-(4-bromo­phen­yl)ethan-1-one (4), C15H11BrN4O2S, and 1-(3-meth­oxy­phen­yl)-2-[(9H-purin-6-yl)sulfan­yl]ethan-1-one (5), C14H12N4O2S. Compounds (2), (3) and (4) are isomorphous and accordingly their mol­ecular and supra­molecular structures are similar. An analysis of the dihedral angles between the purine and exocyclic phenyl rings show that the mol­ecules of (1) and (5) are essentially planar but that in the case of the three isomorphous compounds (2), (3) and (4), these rings are twisted by a dihedral angle of approximately 38°. With the exception of (1) all mol­ecules are linked by weak C—H⋯O hydrogen bonds in their crystals. There is π–π stacking in all compounds. A Cambridge Structural Database search revealed the existence of 11 deposited compounds containing the 1-phenyl-2-sulfanyl­ethanone scaffold; of these, only eight have a cyclic ring as substituent, the majority of these being heterocycles. PMID:27006794

  17. 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.

  18. Crystal structure of the dynamin tetramer.

    PubMed

    Reubold, Thomas F; Faelber, Katja; Plattner, Nuria; Posor, York; Ketel, Katharina; Curth, Ute; Schlegel, Jeanette; Anand, Roopsee; Manstein, Dietmar J; No, Frank; Haucke, Volker; Daumke, Oliver; Eschenburg, Susanne

    2015-09-17

    The mechanochemical protein dynamin is the prototype of the dynamin superfamily of large GTPases, which shape and remodel membranes in diverse cellular processes. Dynamin forms predominantly tetramers in the cytosol, which oligomerize at the neck of clathrin-coated vesicles to mediate constriction and subsequent scission of the membrane. Previous studies have described the architecture of dynamin dimers, but the molecular determinants for dynamin assembly and its regulation have remained unclear. Here we present the crystal structure of the human dynamin tetramer in the nucleotide-free state. Combining structural data with mutational studies, oligomerization measurements and Markov state models of molecular dynamics simulations, we suggest a mechanism by which oligomerization of dynamin is linked to the release of intramolecular autoinhibitory interactions. We elucidate how mutations that interfere with tetramer formation and autoinhibition can lead to the congenital muscle disorders Charcot-Marie-Tooth neuropathy and centronuclear myopathy, respectively. Notably, the bent shape of the tetramer explains how dynamin assembles into a right-handed helical oligomer of defined diameter, which has direct implications for its function in membrane constriction. PMID:26302298

  19. Crystal Structure of Human Kynurenine Aminotransferase ll*

    SciTech Connect

    Han,Q.; Robinson, H.; Li, J.

    2008-01-01

    Human kynurenine aminotransferase II (hKAT-II) efficiently catalyzes the transamination of knunrenine to kynurenic acid (KYNA). KYNA is the only known endogenous antagonist of N-methyl-d-aspartate (NMDA) receptors and is also an antagonist of 7-nicotinic acetylcholine receptors. Abnormal concentrations of brain KYNA have been implicated in the pathogenesis and development of several neurological and psychiatric diseases in humans. Consequently, enzymes involved in the production of brain KYNA have been considered potential regulatory targets. In this article, we report a 2.16 Angstroms crystal structure of hKAT-II and a 1.95 Angstroms structure of its complex with kynurenine. The protein architecture of hKAT-II reveals that it belongs to the fold-type I pyridoxal 5-phosphate (PLP)-dependent enzymes. In comparison with all subclasses of fold-type I-PLP-dependent enzymes, we propose that hKAT-II represents a novel subclass in the fold-type I enzymes because of the unique folding of its first 65 N-terminal residues. This study provides a molecular basis for future effort in maintaining physiological concentrations of KYNA through molecular and biochemical regulation of hKAT-II.

  20. Electric field generation of Skyrmion-like structures in a nematic liquid crystal.

    PubMed

    Cattaneo, Laura; Kos, iga; Savoini, Matteo; Kouwer, Paul; Rowan, Alan; Ravnik, Miha; Muevi?, Igor; Rasing, Theo

    2016-01-21

    Skyrmions are particle-like topological objects that are increasingly drawing attention in condensed matter physics, where they are connected to inversion symmetry breaking and chirality. Here we report the generation of stable Skyrmion-like structures in a thin nematic liquid crystal film on chemically patterned patchy surfaces. Using the interplay of material elasticity and surface boundary conditions, we use a strong electric field to quench the nematic liquid crystal from a fully aligned phase to vortex-like nematic liquid crystal structures, centered on patterned patches, which carry two different sorts of topological defects. Numerical calculations reveal that these are Skyrmion-like structures, seeded from the surface boojum topological defects and swirling towards the second confining surface. These observations, supported by numerical methods, demonstrate the possibility to generate, manipulate and study Skyrmion-like objects in nematic liquid crystals on patterned surfaces. PMID:26549212

  1. Crystallization and Structure Determination of Superantigens and Immune Receptor Complexes.

    PubMed

    Rdstrm, Karin E J; Lindkvist-Petersson, Karin

    2016-01-01

    Structure determination of superantigens and the complexes they form with immune receptors have over the years provided insight in their modes of action. This technique requires growing large and highly ordered crystals of the superantigen or receptor-superantigen complex, followed by exposure to X-ray radiation and data collection. Here, we describe methods for crystallizing superantigens and superantigen-receptor complexes using the vapor diffusion technique, how the crystals may be optimized, and lastly data collection and structure determination. PMID:26676036

  2. Large scale structures in liquid crystal/clay colloids

    NASA Astrophysics Data System (ADS)

    van Duijneveldt, Jeroen S.; Klein, Susanne; Leach, Edward; Pizzey, Claire; Richardson, Robert M.

    2005-04-01

    Suspensions of three different clays in K15, a thermotropic liquid crystal, have been studied by optical microscopy and small angle x-ray scattering. The three clays were claytone AF, a surface treated natural montmorillonite, laponite RD, a synthetic hectorite, and mined sepiolite. The claytone and laponite were sterically stabilized whereas sepiolite formed a relatively stable suspension in K15 without any surface treatment. Micrographs of the different suspensions revealed that all three suspensions contained large scale structures. The nature of these aggregates was investigated using small angle x-ray scattering. For the clays with sheet-like particles, claytone and laponite, the flocs contain a mixture of stacked and single platelets. The basal spacing in the stacks was independent of particle concentration in the suspension and the phase of the solvent. The number of platelets in the stack and their percentage in the suspension varied with concentration and the aspect ratio of the platelets. The lath shaped sepiolite did not show any tendency to organize into ordered structures. Here the aggregates are networks of randomly oriented single rods.

  3. Monodispersepoly[BMA-co-(COPS-I)] Particles by Soap-Free Emulsion Copolymerization and Its Optical Properties as Photonic Crystals.

    PubMed

    Lee, Ki Chang; Choo, Hun Seung

    2015-10-01

    In order to study the surfactant-free emulsion copolymerization of benzyl methacrylate (BMA) with sodium 1-allyloxy-2-hydroxypropane sulfonate (COPS-I) and the resulting optical properties, a series of experiments was carried out at various reaction conditions such as the changes of BMA concentration, COPS-I concentration, BMA concentration under a fixed COPS-I amount, initiator and divinyl benzene (DVB) concentration. All the latices showed highly monodispersed spherical particles in the size range of 144~435 nm and the respective shiny structural colors from their colloidal photonic crystals. It is found that the changes in such polymerization factors greatly affect the number of particles and particle diameter, polymerization rate, molecular weight, zeta-potential, and refractive indices. The increase of number of particles led to the increased rate of polymerization and zeta-potential of the latices, on the other hand, to the decreased molecular weight. Refractive indices and the reflectivity increased with COPS-I concentration, on the other hand, and decreased with DVB concentration. Especially, refractive indices of the resulting poly[BMA-co-(COPS-I)] colloidal photonic crystals showed much higher values of 1.65~2.21 than that of polystyrene, due to the formation of core-shell shaped morphology. Monodisperse and high refractive index of poly[BMA-co-(COPS-I)] particles prepared in this work could be used for the study in photonic crystals and electrophoretic display. PMID:26726393

  4. 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…

  5. 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 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

  6. Use of Pom Pons to Illustrate Cubic Crystal Structures.

    ERIC Educational Resources Information Center

    Cady, Susan G.

    1997-01-01

    Describes a method that uses olefin pom pons to illustrate cubic crystal structure. Facilitates hands-on examination of different packing arrangements such as hexagonal close-packed and cubic close-packed structures. (JRH)

  7. Orientational defects near colloidal particles in a nematic liquid crystal.

    PubMed

    Feng, James J; Zhou, Chixing

    2004-01-01

    We study the interaction between a surface-anchoring colloidal particle and a liquid-crystalline host, and in particular the formation of orientational defects near the particle. A mean-field theory based on the nonlocal Marrucci-Greco nematic potential is used to represent molecular interactions in an inhomogeneous orientational field. An evolution equation for the molecular configuration tensor is solved numerically whose steady state minimizes the total free energy of the system. With strong homeotropic anchoring on the particle surface, three types of solutions may appear depending on initial conditions and particle size: Saturn rings, satellite point defects, and polar rings. The Saturn ring remains stable on micrometer-sized particles, contrary to previous calculations but consistent with experiments. A phase diagram is constructed for the three regimes. Based on the free energy, the most stable state is the Saturn ring for smaller particles and the satellite defect for larger ones. PMID:14651897

  8. Simulation studies of crystal-photodetector assemblies for the Turkish accelerator center particle factory electromagnetic calorimeter

    NASA Astrophysics Data System (ADS)

    Kocak, F.

    2015-07-01

    The Turkish Accelerator Center Particle Factory detector will be constructed for the detection of the produced particles from the collision of a 1 GeV electron beam against a 3.6 GeV positron beam. PbWO4 and CsI(Tl) crystals are considered for the construction of the electromagnetic calorimeter part of the detector. The generated optical photons in these crystals are detected by avalanche or PIN photodiodes. Geant4 simulation code has been used to estimate the energy resolution of the calorimeter for these crystal-photodiode assemblies.

  9. 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.

  10. Spontaneous formation and spin of particle pairs in a single-layer complex plasma crystal

    NASA Astrophysics Data System (ADS)

    Nosenko, V.; Zhdanov, S. K.; Thomas, H. M.; Carmona-Reyes, J.; Hyde, T. W.

    2015-11-01

    In an experiment with a single-layer plasma crystal, spontaneous pairing of particles was observed upon a sudden reduction of the discharge power. The pairs were oriented vertically with the upper particle above the crystal layer and the lower particle beneath it, the pair size was about 0.2 mm. The pairs were spinning around their vertical axis with the upper particle leading and the lower one following it; the rotation speed was 1013 Hz. Spinning particle pairs disturbed the plasma crystal through interaction with their neighbors. Upon further reduction of the discharge power, the spinning pairs proliferated in the plasma crystal and eventually it melted. The experiment was performed with micron-size polymer particles suspended in the radio-frequency (rf) argon plasma at a pressure of 157 mtorr. We propose a theoretical model of a spinning particle pair based on the plasma wake effect. Spinning particle pairs can be used as a diagnostic tool for plasma wakes or as a generic model of a 2D system of vortices.

  11. Crystal structure of the Varkud satellite ribozyme.

    PubMed

    Suslov, Nikolai B; DasGupta, Saurja; Huang, Hao; Fuller, James R; Lilley, David M J; Rice, Phoebe A; Piccirilli, Joseph A

    2015-11-01

    The Varkud satellite (VS) ribozyme mediates rolling-circle replication of a plasmid found in the Neurospora mitochondrion. We report crystal structures of this ribozyme from Neurospora intermedia at 3.1 resolution, which revealed an intertwined dimer formed by an exchange of substrate helices. In each protomer, an arrangement of three-way helical junctions organizes seven helices into a global fold that creates a docking site for the substrate helix of the other protomer, resulting in the formation of two active sites in trans. This mode of RNA-RNA association resembles the process of domain swapping in proteins and has implications for RNA regulation and evolution. Within each active site, adenine and guanine nucleobases abut the scissile phosphate, poised to serve direct roles in catalysis. Similarities to the active sites of the hairpin and hammerhead ribozymes highlight the functional importance of active-site features, underscore the ability of RNA to access functional architectures from distant regions of sequence space, and suggest convergent evolution. PMID:26414446

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

    PubMed

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

    2009-09-22

    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 (approximately 0.002 k(B)T). 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

  13. Programmably structured plasma waveguide for development of table-top photon and particle sources

    SciTech Connect

    Hung, T.-S.; Ho, Y.-C.; Wong, S.-J.; Chen, S.-Y.; Chang, Y.-L.; Chu, H.-H.; Lin, J.-Y.; Wang, J.

    2012-06-15

    Programmable fabrication of longitudinal spatial structures in an optically preformed plasma waveguide in a gas jet was achieved, by using laser machining with a liquid-crystal spatial light modulator as the pattern mask. Fabrication of periodic structures with a minimal period of 200 {mu}m and density-ramp structures with a minimal slope length of 100 {mu}m was attained. The technique is useful for the optimization of various laser-plasma-based photon and particle sources.

  14. Spectroscopic, thermal and structural studies on manganous malate crystals

    SciTech Connect

    Thomas, J. Lincy, A. Mahalakshmi, V.; Saban, K. V.

    2013-01-15

    Prismatic crystals of manganous malate have been prepared by controlled ionic diffusion in hydrosilica gel. The structure was elucidated using single crystal X-ray diffraction. The crystals are orthorhombic with space group Pbca. Vibrations of the functional groups were identified by the FTIR spectrum. Thermogravimetric and differential thermal analyses (TG-DTA) were carried out to explore the thermal decomposition pattern of the material. Structural information derived from FTIR and TG-DTA studies is in conformity with the single crystal XRD data.

  15. Preparation of iridescent colloidal crystal coatings with variable structural colors.

    PubMed

    Cong, Hailin; Yu, Bing; Wang, Shaopeng; Qi, Limin; Wang, Jilei; Ma, Yurong

    2013-07-29

    Iridescent colloidal crystal coatings with variable structural colors were fabricated by incorporating carbon black nanoparticles (CB-NPs) into the voids of polystyrene (PS) colloidal crystals. The structural color of the colloid crystal coatings was not only greatly enhanced after the composition but also varied with observation angles. By changing the diameter of monodisperse PS colloids in the composites, colloidal crystal coatings with three primary colors for additive or subtractive combination were obtained. After incorporation of the PS/CB-NPs hybrid coatings into polydimethylsiloxane (PDMS) matrix, manmade opal jewelry with variable iridescent colors was made facilely. PMID:23938656

  16. Infrared response from metallic particles embedded in a single-crystal Si matrix - The layered internal photoemission sensor

    NASA Technical Reports Server (NTRS)

    Fathauer, R. W.; Iannelli, J. M.; Nieh, C. W.; Hashimoto, Shin

    1990-01-01

    Infrared radiation at wavelengths of 1-2 microns has been detected in a new device labeled the layered internal photoemission sensor. The device structure, which is grown by molecular beam epitaxy, incorporates epitaxial CoSi2 particles with dimensions of 10-50 nm. Radiation absorbed by these particles photoexcites carriers into a surrounding single-crystal silicon matrix. A peak quantum efficiency of 1.3 percent is measured, which is approximately six times higher than in planar CoSi2 Schottky diodes with 5-nm silicide thickness.

  17. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-08-01

    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.

  19. Photonic crystal structures with tunable structure color as colorimetric sensors.

    PubMed

    Wang, Hui; Zhang, Ke-Qin

    2013-01-01

    Colorimetric sensing, which transduces environmental changes into visible color changes, provides a simple yet powerful detection mechanism that is well-suited to the development of low-cost and low-power sensors. A new approach in colorimetric sensing exploits the structural color of photonic crystals (PCs) to create environmentally-influenced color-changeable materials. PCs are composed of periodic dielectrics or metallo-dielectric nanostructures that affect the propagation of electromagnetic waves (EM) by defining the allowed and forbidden photonic bands. Simultaneously, an amazing variety of naturally occurring biological systems exhibit iridescent color due to the presence of PC structures throughout multi-dimensional space. In particular, some kinds of the structural colors in living organisms can be reversibly changed in reaction to external stimuli. Based on the lessons learned from natural photonic structures, some specific examples of PCs-based colorimetric sensors are presented in detail to demonstrate their unprecedented potential in practical applications, such as the detections of temperature, pH, ionic species, solvents, vapor, humidity, pressure and biomolecules. The combination of the nanofabrication technique, useful design methodologies inspired by biological systems and colorimetric sensing will lead to substantial developments in low-cost, miniaturized and widely deployable optical sensors. PMID:23539027

  20. Photonic Crystal Structures with Tunable Structure Color as Colorimetric Sensors

    PubMed Central

    Wang, Hui; Zhang, Ke-Qin

    2013-01-01

    Colorimetric sensing, which transduces environmental changes into visible color changes, provides a simple yet powerful detection mechanism that is well-suited to the development of low-cost and low-power sensors. A new approach in colorimetric sensing exploits the structural color of photonic crystals (PCs) to create environmentally-influenced color-changeable materials. PCs are composed of periodic dielectrics or metallo-dielectric nanostructures that affect the propagation of electromagnetic waves (EM) by defining the allowed and forbidden photonic bands. Simultaneously, an amazing variety of naturally occurring biological systems exhibit iridescent color due to the presence of PC structures throughout multi-dimensional space. In particular, some kinds of the structural colors in living organisms can be reversibly changed in reaction to external stimuli. Based on the lessons learned from natural photonic structures, some specific examples of PCs-based colorimetric sensors are presented in detail to demonstrate their unprecedented potential in practical applications, such as the detections of temperature, pH, ionic species, solvents, vapor, humidity, pressure and biomolecules. The combination of the nanofabrication technique, useful design methodologies inspired by biological systems and colorimetric sensing will lead to substantial developments in low-cost, miniaturized and widely deployable optical sensors. PMID:23539027

  1. 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.

  2. Crystal structure, spectral, thermal and dielectric studies of a new zinc benzoate single crystal

    NASA Astrophysics Data System (ADS)

    Bijini, B. R.; Prasanna, S.; Deepa, M.; Nair, C. M. K.; Rajendra Babu, K.

    2012-11-01

    Single crystals of zinc benzoate with a novel structure were grown in gel media. Sodium metasilicate of gel density 1.04 g/cc at pH 6 was employed to yield transparent single crystals. The crystal structure of the compound was ascertained by single crystal X-ray diffractometry. It was noted that the crystal belongs to monoclinic system with space group P21/c with unit cell parameters a = 10.669(1) , b = 12.995(5) , c = 19.119(3) , and ? = 94.926(3). The crystal was seen to possess a linear polymeric structure along b-axis; with no presence of coordinated or lattice water. CHN analysis established the stoichiometric composition of the crystal. The existence of functional groups present in the single crystal system was confirmed by FT-IR studies. The thermal characteristic of the sample was analysed by TGA-DTA techniques, and the sample was found to be thermally stable up to 280 C. The kinetic and thermodynamic parameters were also determined. UV-Vis spectroscopy corroborated the transparency of the crystal and revealed the optical band gap to be 4 eV. Dielectric studies showed decrease in the dielectric constant of the sample with increase in frequency.

  3. Monodisperse spherical mesoporous silica particles: fast synthesis procedure and fabrication of photonic-crystal films

    NASA Astrophysics Data System (ADS)

    Trofimova, E. Yu; Kurdyukov, D. A.; Yakovlev, S. A.; Kirilenko, D. A.; Kukushkina, Yu A.; Nashchekin, A. V.; Sitnikova, A. A.; Yagovkina, M. A.; Golubev, V. G.

    2013-04-01

    A procedure for the synthesis of monodisperse spherical mesoporous silica particles (MSMSPs) via the controlled coagulation of silica/surfactant clusters into spherical aggregates with mean diameters of 250-1500 nm has been developed. The synthesis is fast (taking less than 1 h) because identical clusters are simultaneously formed in the reaction mixture. The results of microscopic, x-ray diffraction, adsorption and optical measurements allowed us to conclude that the clusters are 15 nm in size and have hexagonally packed cylindrical pore channels. The channel diameters in MSMSPs obtained with cethyltrimethylammonium bromide and decyltrimethylammonium bromide as structure-directing agents were 3.1 0.15 and 2.3 0.12 nm, respectively. The specific surface area and the pore volume of MSMSP were, depending on synthesis conditions, 480-1095 m2 g-1 and 0.50-0.65 cm3 g-1. The MSMSP were used to grow opal-like photonic-crystal films possessing a hierarchical macro-mesoporous structure, with pores within and between the particles. A selective filling of mesopore channels with glycerol, based on the difference between the capillary pressures in macro- and mesopores, was demonstrated. It is shown that this approach makes it possible to control the photonic bandgap position in mesoporous opal films by varying the degree of mesopore filling with glycerol.

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

    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 a relatively low density of dipoles and a moderate total number of particles. The classical normal mode spectra support the chain interpretation through both structure and 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 by 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 it does depend on the geometry.

  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. Dependence of the Apex Angle of an Inverted Pyramidal-Shaped Container on Crystallization of Brownian Particles

    NASA Astrophysics Data System (ADS)

    Kanatsu, Youhei; Sato, Masahide

    2015-11-01

    Large grains of a close-packed colloidal crystal have been experimentally shown to form in an inverted pyramidal pit by sedimentation [S. Matsuo et al., Appl. Phys. Lett. 82, 4285 (2003)]. Keeping this experiment in mind, we study the crystallization of Brownian particles. We carry out Brownian dynamics simulations in an inverted pyramidal-shaped container. The Brownian particles settle out toward the apex of the container by a uniform external force. If the apex angle is suitable, large grains with the face-centered cubic (fcc) structure are formed [Y. Kanatsu and M. Sato, J. Phys. Soc. Jpn. 84, 044601 (2015)]. When the apex angle deviates from a suitable value, the number of hexagonal close-packed (hcp) structured particles, Nhcp, increases with increasing angle deviation. The formation of the hcp structure is induced by disordered particles remaining in the center region of the container.

  7. Magnetic-Directed Assembly from Janus Building Blocks to Multiplex Molecular-Analogue Photonic Crystal Structures.

    PubMed

    Yin, Su-Na; Yang, Shengyang; Wang, Cai-Feng; Chen, Su

    2016-01-20

    The predictable assembly of colloidal particles into a programmable superstructure is a challenging and vital task in chemistry and materials science. In this work, we develop an available magnetic-directed assembly strategy to construct a series of molecular-analogue photonic crystal cluster particles involving dot, line, triangle, tetrahedron, and triangular bipyramid configurations from solid-liquid Janus building blocks. These versatile multiplex molecular-analogue structural clusters containing photonic band gap, fluorescent, and magnetic information can open a new promising access to a variety of robust hierarchical microstructural particle materials. PMID:26708560

  8. Slow light performance enhancement of Bragg slot photonic crystal waveguide with particle swarm optimization algorithm

    NASA Astrophysics Data System (ADS)

    Abedi, Kambiz; Mirjalili, Seyed Mohammad

    2015-03-01

    Recently, majority of current research in the field of designing Phonic Crystal Waveguides (PCW) focus in extracting the relations between output slow light properties of PCW and structural parameters through a huge number of tedious non-systematic simulations in order to introduce better designs. This paper proposes a novel systematic approach which can be considered as a shortcut to alleviate the difficulties and human involvements in designing PCWs. In the proposed method, the problem of PCW design is first formulated as an optimization problem. Then, an optimizer is employed in order to automatically find the optimum design for the formulated PCWs. Meanwhile, different constraints are also considered during optimization with the purpose of applying physical limitations to the final optimum structure. As a case study, the structure of a Bragg-like Corrugation Slotted PCWs (BCSPCW) is optimized by using the proposed method. One of the most computationally powerful techniques in Computational Intelligence (CI) called Particle Swarm Optimization (PSO) is employed as an optimizer to automatically find the optimum structure for BCSPCW. The optimization process is done by considering five constraints to guarantee the feasibility of the final optimized structures and avoid band mixing. Numerical results demonstrate that the proposed method is able to find an optimum structure for BCSPCW with 172% and 100% substantial improvements in the bandwidth and Normalized Delay-Bandwidth Product (NDBP) respectively compared to the best current structure in the literature. Moreover, there is a time domain analysis at the end of the paper which verifies the performance of the optimized structure and proves that this structure has low distortion and attenuation simultaneously.

  9. Transport of particles by a thermally induced gradient of the order parameter in nematic liquid crystals

    NASA Astrophysics Data System (ADS)

    Škarabot, M.; Lokar, Ž.; Muševič, I.

    2013-06-01

    We demonstrate manipulation and transport of microparticles and even fluorescent molecules by the thermally induced gradient of the order parameter in the nematic liquid crystal. We use IR light absorption of the tightly focused beam of laser tweezers to heat locally a thin layer of the nematic liquid crystal by several degrees. This creates a spatial gradient of temperature of the nematic liquid crystal over separations of several tens of micrometers. We show that a dipolar colloidal particle is attracted into the hot spot of the laser tweezers. The depth of the trapping potential scales linearly with particle radius, indicating that the trapping mechanism is due to elastic self-energy of the distorted nematic liquid crystal around the particle and softening of the elasticity with increased temperature of the liquid crystal. We also demonstrate that this thermal trapping mechanism is efficient down to the nanoscale, as fluorescent molecules are also transported into hotter regions of the liquid crystal. This effect is absent in the isotropic phase, which calls into question particle transport due to the Soret effect.

  10. Synthesis, crystal structure and thermal analysis of a new stilbazolium salt crystal

    NASA Astrophysics Data System (ADS)

    Teng, Bing; Kong, Weijin; Feng, Ke; You, Fei; Cao, Lifeng; Zhong, Degao; Hao, Lun; Sun, Qing; van Smaalen, Sander; Gong, Wenhui

    2015-04-01

    A new organic crystal of 4-N, N-dimethylamino-4'-N'-methyl-stilbazolium benzene sulfonate (DASBS) was synthesized and characterized for the first time. It is a derivative of 4-N, N-dimethylamino-4'-N'-methyl-stilbazolium tosylate (DAST) with the benzene sulfonate replacing p-toluenesulfonate. Single crystal XRD demonstrated that the crystal structure of DASBSH2O was triclinic. The thermal analysis of this new crystal was also conducted, and the melting point was obtained to be 232C.

  11. 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.

  12. 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

  13. Crystal packing of a bacteriophage MS2 coat protein mutant corresponds to octahedral particles

    PubMed Central

    Plevka, Pavel; Tars, Kaspars; Liljas, Lars

    2008-01-01

    A covalent dimer of the bacteriophage MS2 coat protein was created by performing genetic fusion of two copies of the gene while removing the stop codon of the first gene. The dimer was crystallized in the cubic F432 space group. The organization of the asymmetric unit together with the F432 symmetry results in an arrangement of subunits that corresponds to T = 3 octahedral particles. The octahedral particles are probably artifacts created by the particular crystal packing. When it is not crystallized in the F cubic crystal form, the coat protein dimer appears to assemble into T = 3 icosahedral particles indistinguishable from the wild-type particles. To form an octahedral particle with closed surface, the dimer subunits interact at sharper angles than in the icosahedral arrangement. The fold of the covalent dimer is almost identical to the wild-type dimer with differences located in loops and in the covalent linker region. The main differences in the subunit packing between the octahedral and icosahedral arrangements are located close to the fourfold and fivefold symmetry axes where different sets of loops mediate the contacts. The volume of the wild-type virions is 7 times bigger than that of the octahedral particles. PMID:18662904

  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. Hydroflux synthesis and crystal structure of new lanthanide tungstate oxyhydroxides

    NASA Astrophysics Data System (ADS)

    Latshaw, Allison M.; Smith, Mark D.; Chance, W. Michael; zur Loye, Hans-Conrad

    2015-04-01

    Single crystals of Na5Ln(OH)6WO4 where Ln = Er, Tm, and Yb were grown out of a NaOH hydroflux. The crystals were characterized by single crystal X-ray diffraction and were found to crystallize in the monoclinic space group I2/a. The lattice parameter ranges for the three structures are a = 11.2024(7) Å-11.2412(6) Å, b = 16.1850(10) Å-16.2220(10) Å, and c = 11.9913(7) Å-12.0323(7) Å while the β angle range is 101.999(2)°-102.025(2)°.

  16. Size dependences of crystal structure and magnetic properties of DyMnO3 nanoparticles

    NASA Astrophysics Data System (ADS)

    Tajiri, T.; Terashita, N.; Hamamoto, K.; Deguchi, H.; Mito, M.; Morimoto, Y.; Konishi, K.; Kohno, A.

    2013-11-01

    We synthesized DyMnO3 nanoparticles with particle sizes of about 7.5-15.3 nm in the pores of mesoporous silica and investigated their crystal structure and magnetic properties. As the particle size decreased, the lattice constants of the DyMnO3 nanoparticles deviated from those of the bulk crystal, and the Jahn-Teller distortion in the nanoparticle systems decreased. In addition, the estimated lattice strain increased with decreasing particle size. The DyMnO3 nanoparticles showed superparamagnetic behavior. The blocking temperature and the coercive field increased with decreasing particle size, and this behavior was contrary to the usual magnetic size effects. It is deduced that these unique size dependences of the magnetic properties for the DyMnO3 nanoparticles were derived from the changes in lattice constants and lattice strain. The anisotropic lattice deformation in the crystal structure of the nanoparticles induces an enhancement of the magnetic anisotropy, which results in the increase in blocking temperature and coercive field with decreasing particle size.

  17. 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.

  18. DNA variability in five crystal structures of d(CGCAATTGCG).

    PubMed

    Valls, Nria; Wright, Glenford; Steiner, Roberto A; Murshudov, Garib N; Subirana, Juan A

    2004-04-01

    The deoxyoligonucleotide d(CGCAATTGCG) has previously been crystallized in four different space groups. The crystals diffract to moderate resolution (2.3-2.9 A). Here, a fifth crystal form that diffracts to higher resolution (1.6 A) is presented which was obtained thanks to the use of Co2+ and cryogenic temperatures. The availability of five different crystal structures allows a thorough analysis of the conformational variability of this DNA sequence. It is concluded that the central hexamer sequence CAATTG has a practically constant conformation under all conditions, whilst the terminal base pairs at both ends vary considerably as a result of differing interactions in the crystals. The new crystal structure presented here is stabilized by guanine-Co2+-guanine interactions and the formation of C1+ -G8.C3 triplexes between neighbouring duplexes. As a result of the higher resolution of the crystal structure, a more regular structure was obtained and a clear definition of the spine of hydration was observed which was not visible in the four previous structures. PMID:15039556

  19. Crystal structure engineering for improved performance of emerging nanoscale devices

    NASA Astrophysics Data System (ADS)

    Chimalgi, Vinay Uday

    Recent advances in growth techniques and increasing number of experimental studies have made nanostructures grown along different crystallographic directions a reality. These new structures could not only benefit the electronic devices used in mainstream information technology but also show great promise for applications in lasers, solid-state lighting, near-field photolithography, free-space quantum cryptography, consumer displays, quantum computation, as well as diagnostic medicine and imaging. However, only few theoretical investigations have been performed on these structures due to the complex nature of the interplay of atomicity, structural fields, polarization, and quantum size-quantization, all strong function of the crystallographic direction. The objective of this work is mainly four-fold: (1) Integrate a computational framework employing a combination of fully atomistic valence force-field molecular mechanics and 20-band sp3s*d5-SO tight-binding based electronic bandstructure models, and numerically investigate the effects of internal fields on the electronic and optical properties of zincblende InAs/GaAs quantum dots grown on (100), (110), and (111) orientated substrates. (2) Augment/extend the open source NEMO 3-D bandstructure simulator by incorporating a recently proposed first principles based model to gauge the importance of nonlinear piezoelectricity on the single-particle electronic states and interband optical transitions in emerging In(Ga)N/GaN disk-in-wire LED structures having c-plane and m-plane wurtzite crystal symmetry. (3) Coupling the NEMO 3-D software toolkit with a commercial TCAD simulator to determine the terminal electrical and optical characteristics of InGaN/GaN disk-in-wire LEDs; and (4) Finding an optimum crystallographic device for InGaN/GaN disk-in-wire LEDs to achieve improved internal quantum efficiency (IQE).

  20. Magnetization Reversal Process of Single Crystal α-Fe Containing a Nonmagnetic Particle

    SciTech Connect

    Li, Yi; Xu, Ben; Hu, Shenyang Y.; Li, Yulan; Li, Qiu-Lin; Liu, Wei

    2015-09-25

    The magnetization reversal process and hysteresis loops in a single crystal α-iron with nonmagnetic particles are simulated in this work based on the Landau-Lifshitz–Gilbert equation. The evolutions of the magnetic domain morphology are studied, and our analyses show that the magnetization reversal process is affected by the interaction between the moving domain wall and the existing nonmagnetic particles. This interaction strongly depends on the size of the particles, and it is found that particles with a particular size contribute the most to magnetic hardening.

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

    NASA Astrophysics Data System (ADS)

    Coudel, 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.

  2. Strain-responsive structural colored elastomers by fixing colloidal crystal assembly.

    PubMed

    Ito, Tatsunori; Katsura, Chihiro; Sugimoto, Hideki; Nakanishi, Eiji; Inomata, Katsuhiro

    2013-11-12

    Colloidal crystal assembly film was prepared by using monodispersed colloidal particles of cross-linked random copolymer of methyl methacrylate and ethyl acrylate prepared by soap-free emulsion polymerization. The colloidal crystal film exhibited structural color when swollen with ethyl acrylate monomer. The structural color was maintained even after polymerization of the swelling monomer and cross-linker, suggesting the colloidal crystalline order was successfully fixed and embedded in the matrix of poly(ethyl acrylate) elastomer. Stretching deformation of the structural colored elastomer induced a sensitive change to shorter wavelength color. Peak wavelength of the UV-vis absorption spectrum of the stretched elastomer revealed an excellent proportional relationship with film thickness. In the swollen colloidal crystal film, ethyl acrylate was absorbed in the colloidal particle; therefore, poly(ethyl acrylate) chain should be penetrating into the colloidal particle after the polymerization of the matrix elastomer. This interpenetrated polymer network structure was considered to be effective for the rubber-like elasticity and sensitive strain-responsive color-changing phenomena of the structural colored elastomer. PMID:24099483

  3. Determination of channeling perspectives for complex crystal structures

    SciTech Connect

    Allen, W.R.

    1993-03-01

    Specification of the atomic arrangement for axes and planes of high symmetry is essential for crystal alignment using Rutherford backscattering and for studies of the lattice location of impurities in single crystals. By rotation of an inscribed orthogonal coordinate system, a visual image for a given perspective of a crystal structure can be specified. Knowledge of the atomic arrangement permits qualitative channeling perspectives to be visualized and calculation of continuum potentials for channeling. Channeling angular-yield profiles can then be analytically modeled and, subsequently, shadowing by host atoms of positions within the unit cell predicted. Software to calculate transformed atom positions for a channeling perspective in a single crystal are described and illustrated for the spinel crystal structure.

  4. Design rule for colloidal crystals of DNA-functionalized particles.

    PubMed

    Martinez-Veracoechea, Francisco J; Mladek, Bianca M; Tkachenko, Alexei V; Frenkel, Daan

    2011-07-22

    We report a Monte Carlo simulation study of the phase behavior of colloids coated with long, flexible DNA chains. We find that an important change occurs in the phase diagram when the number of DNAs per colloid is decreased below a critical value. In this case, the triple point disappears and the condensed phase that coexists with the vapor is always liquid. Our simulations thus explain why, in the dilute solutions typically used in experiments, colloids coated with a small number of DNA strands cannot crystallize. We understand this behavior in terms of the discrete nature of DNA binding. PMID:21867023

  5. Crystal structure of a methimazole-based ionic liquid

    PubMed Central

    Gaitor, Jamie C.; Zayas, Manuel Sanchez; Myrthil, Darrel J.; White, Frankie; Hendrich, Jeffrey M.; Sykora, Richard E.; O’Brien, Richard A.; Reilly, John T.; Mirjafari, Arsalan

    2015-01-01

    The structure of 1-methyl-2-(prop-2-en-1-ylsulfan­yl)-1H-imidazol-3-ium bromide, C7H11N2S+·Br−, has monoclinic (P21/c) symmetry. In the crystal, the components are linked by N—H⋯Br and C—H⋯Br hydrogen bonds. The crystal structure of the title compound undeniably proves that methimazole reacts through the thione tautomer, rather than the thiol tautomer in this system. PMID:26870468

  6. Crystal structure of a methimazole-based ionic liquid.

    PubMed

    Gaitor, Jamie C; Zayas, Manuel Sanchez; Myrthil, Darrel J; White, Frankie; Hendrich, Jeffrey M; Sykora, Richard E; O'Brien, Richard A; Reilly, John T; Mirjafari, Arsalan

    2015-12-01

    The structure of 1-methyl-2-(prop-2-en-1-ylsulfan-yl)-1H-imidazol-3-ium bromide, C7H11N2S(+)Br(-), has monoclinic (P21/c) symmetry. In the crystal, the components are linked by N-H?Br and C-H?Br hydrogen bonds. The crystal structure of the title compound undeniably proves that methimazole reacts through the thione tautomer, rather than the thiol tautomer in this system. PMID:26870468

  7. The Crystal and Molecular Structure of Dianhydrogossypol

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dianhydrogossypol (4,4'-dihydroxy-5,5'-diisopropyl-7,7'-dimethyl-bis(3H-naphtho[1,8-bc]furan-3-one)) was made by refluxing gossypol in m-xylene. Proton NMR confirmed that complete conversion was achieved over several hours. Single crystals were obtained by slow evaporation of the product from dichl...

  8. Band structure mapping of photonic crystal intersubband detectors

    NASA Astrophysics Data System (ADS)

    Schartner, S.; Golka, S.; Pflgl, C.; Schrenk, W.; Andrews, A. M.; Roch, T.; Strasser, G.

    2006-10-01

    The authors report on a quantum well infrared detector embedded in a surface-plasmon waveguide and processed into a deeply etched photonic crystal structure. The device was characterized by collecting the polarization dependent response spectra at different angles of incidence. With this method it is possible to map the photonic band structure by directly detecting the modes of the photonic crystal. It therefore represents a new and direct characterization procedure for photonic crystals. The device shows a strong mixing between TE and TM polarized modes, which is caused by the asymmetric vertical waveguide design.

  9. Phase separations in mixtures of a liquid crystal and a nanocolloidal particle.

    PubMed

    Matsuyama, Akihiko

    2009-11-28

    We present a mean field theory to describe phase separations in mixtures of a liquid crystal and a nanocolloidal particle. By taking into account a nematic, a smectic A ordering of the liquid crystal, and a crystalline ordering of the nanoparticle, we calculate the phase diagrams on the temperature-concentration plane. We predict various phase separations, such as a smectic A-crystal phase separation and a smectic A-isotropic-crystal triple point, etc., depending on the interactions between the liquid crystal and the colloidal surface. Inside binodal curves, we find new unstable and metastable regions, which are important in the phase ordering dynamics. We also find a crystalline ordering of the nanoparticles dispersed in a smectic A phase and a nematic phase. The cooperative phenomena between liquid-crystalline ordering and crystalline ordering induce a variety of phase diagrams. PMID:19947706

  10. Crystal structure of a actinide metals at high compression

    SciTech Connect

    Fast, L.; Soederlind, P.

    1996-05-01

    The crystal structures of some light actinide metals are studied theoretically as a function of applied pressure. The first principles electronic structure theory is formulated in the framework of density functional theory, with the gradient corrected local density approximation of the exchange-correlation functional. The light actinide metals are shown to be well described as itinerant (metallic) f-electron metals and generally, they display a crystal structure which have, in agreement with previous theoretical suggestions, increasing degree of symmetry and closed-packing upon compression. The theoretical calculations agree well with available experimental data. At very high compression, the theory predicts closed-packed structures such as the fcc or the hcp structures or the nearly closed-packed bcc structure for the light actinide metals. A simple canonical band picture is presented to explain in which particular closed-packed form these metals will crystallize at ultra-high pressure. {copyright} {ital 1996 American Institute of Physics.}

  11. Effects of dust particle internal structure on light scattering

    NASA Astrophysics Data System (ADS)

    Kemppinen, O.; Nousiainen, T.; Jeong, G. Y.

    2015-10-01

    There is a large variety of internal structures inside atmospheric dust particles, making them inherently inhomogeneous. Such structures may have a large effect on ground-level and atmospheric radiation. So far, dust particle internal structures and their effect on the light scattering properties have proved to be hard to quantify, in part due to challenges in obtaining information about these structures. Recently, internal structures of individual dust particles were revealed through focused ion beam milling and analyzed. Here, we perform a sensitivity study to evaluate the optical impacts of some of the typical internal structures revealed. To obtain suitable model particles, the first step is to generate inhomogeneous particles with varying internal structures by using an algorithm that is based on three-dimensional Voronoi tessellation. The parameters for the particle generation are obtained from studies of real-world Asian dust particles. The second step is to generate homogeneous versions of the generated particles by using an effective-medium approximation, for comparison. Third, light scattering by both versions of these particles is simulated with discrete dipole approximation code. This allows us to see how different internal structures affect light scattering, and how important it is to account for these structures explicitly. Further, this allows us to estimate the potential inaccuracies caused by using only homogeneous model particles for atmospheric studies and remote-sensing measurements. The results show that the effects vary greatly between different kinds of internal structures and single-scattering quantity considered, but for most structure types the effects are overall notable. Most significantly, hematite inclusions in particles impact light scattering heavily. Furthermore, internal pores and hematite-rich coating both affect some form of light scattering noticeably. Based on this work, it seems that it is exceedingly important that the effects of dust particle internal structures on light scattering are accounted for in a wide variety of applications.

  12. Homodiselenacalix[4]arenes: Molecules with Unique Channelled Crystal Structures.

    PubMed

    Thomas, Joice; Dobrza?ska, Liliana; Van Meervelt, Luc; Quevedo, Mario Alfredo; Wo?niak, Krzysztof; Stachowicz, Marcin; Smet, Mario; Maes, Wouter; Dehaen, Wim

    2016-01-01

    A synthetic route towards homodiselenacalix[4]arene macrocycles is presented, based on the dynamic covalent chemistry of diselenides. The calixarene inner rim is decorated with either alkoxy or tert-butyl ester groups. Single-crystal X-ray analysis of two THF solvates with methoxy and ethoxy substituents reveals the high similarity of their molecular structures and alterations on the supramolecular level. In both crystal structures, solvent channels are present and differ in both shape and capacity. Furthermore, the methoxy-substituted macrocycle undergoes a single-crystal-to-single-crystal transformation during which the molecular structure changes its conformation from 1,3-alternate (loaded with THF/water) to 1,2-alternate (apohost form). Molecular modelling techniques were applied to explore the conformational and energetic behaviour of the macrocycles. PMID:26639087

  13. Crystal structure of ?-d,l-fructose.

    PubMed

    Ishii, Tomohiko; Senoo, Tatsuya; Yoshihara, Akihide; Fukada, Kazuhiro; Sakane, Genta

    2015-10-01

    The title compound, C6H12O6, was crystallized from an aqueous solution of equimolar mixture of d- and l-fructose (1,3,4,5,6-penta-hydroxy-hexan-2-one, arabino-hexulose or levu-lose), and it was confirmed that d-fructose (or l-fructose) formed ?-pyran-ose with a (2) C 5 (or (5) C 2) conformation. In the crystal, two O-H?O hydrogen bonds between the hy-droxy groups at the C-1 and C-3 positions, and at the C-4 and C-5 positions connect homochiral mol-ecules into a column along the a axis. The columns are linked by other O-H?O hydrogen bonds between d- and l-fructose mol-ecules, forming a three-dimensional network. PMID:26594441

  14. Modes of surface premelting in colloidal crystals composed of attractive particles.

    PubMed

    Li, Bo; Wang, Feng; Zhou, Di; Peng, Yi; Ni, Ran; Han, Yilong

    2016-03-24

    Crystal surfaces typically melt into a thin liquid layer at temperatures slightly below the melting point of the crystal. Such surface premelting is prevalent in all classes of solids and is important in a variety of metallurgical, geological and meteorological phenomena. Premelting has been studied using X-ray diffraction and differential scanning calorimetry, but the lack of single-particle resolution makes it hard to elucidate the underlying mechanisms. Colloids are good model systems for studying phase transitions because the thermal motions of individual micrometre-sized particles can be tracked directly using optical microscopy. Here we use colloidal spheres with tunable attractions to form equilibrium crystal-vapour interfaces, and study their surface premelting behaviour at the single-particle level. We find that monolayer colloidal crystals exhibit incomplete premelting at their perimeter, with a constant liquid-layer thickness. In contrast, two- and three-layer crystals exhibit conventional complete melting, with the thickness of the surface liquid diverging as the melting point is approached. The microstructures of the surface liquids differ in certain aspects from what would be predicted by conventional premelting theories. Incomplete premelting in the monolayer crystals is triggered by a bulk isostructural solid-solid transition and truncated by a mechanical instability that separately induces homogeneous melting within the bulk. This finding is in contrast to the conventional assumption that two-dimensional crystals melt heterogeneously from their free surfaces (that is, at the solid-vapour interface). The unexpected bulk melting that we observe for the monolayer crystals is accompanied by the formation of grain boundaries, which supports a previously proposed grain-boundary-mediated two-dimensional melting theory. The observed interplay between surface premelting, bulk melting and solid-solid transitions challenges existing theories of surface premelting and two-dimensional melting. PMID:26976448

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

    SciTech Connect

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

    2015-05-15

    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.

  16. Crystal structure transfer in core/shell nanowires.

    PubMed

    Algra, Rienk E; Hocevar, Mora; Verheijen, Marcel A; Zardo, Ilaria; Immink, George G W; van Enckevort, Willem J P; Abstreiter, Gerhard; Kouwenhoven, Leo P; Vlieg, Elias; Bakkers, Erik P A M

    2011-04-13

    Structure engineering is an emerging tool to control opto-electronic properties of semiconductors. Recently, control of crystal structure and the formation of a twinning superlattice have been shown for III-V nanowires. This level of control has not been obtained for Si nanowires, the most relevant material for the semiconductor industry. Here, we present an approach, in which a designed twinning superlattice with the zinc blende crystal structure or the wurtzite crystal structure is transferred from a gallium phosphide core wire to an epitaxially grown silicon shell. These materials have a difference in lattice constants of only 0.4%, which allows for structure transfer without introducing extra defects. The twinning superlattices, periodicity, and shell thickness can be tuned with great precision. Arrays of free-standing Si nanotubes are obtained by a selective wet-chemical etch of the core wire. PMID:21417242

  17. The influence of PVP incorporation on moisture-induced surface crystallization of amorphous spray-dried lactose particles.

    PubMed

    Mahlin, Denny; Berggren, Jonas; Gelius, Ulrik; Engström, Sven; Alderborn, Göran

    2006-09-14

    We have recently shown that atomic force microscopy (AFM) may be an appropriate method for characterisation of the re-crystallization of amorphous particles. In this study, spray-dried composite particles consisting of lactose and polyvinyl pyrrolidon (PVP) were characterised by AFM and electron spectroscopy for chemical analysis (ESCA), and their response on increasing the relative humidity (RH) was investigated. The PVP content in the particles used was 0, 5 or 25 wt.% of either PVP K17 or PVP K90. All composite particles were found to be enriched with PVP at the surface. The incorporation of PVP in the particles influenced the way the particles responded to an increase in RH. The specific RH interval in which the surface of the particles smoothened and the RH where crystallization could be detected, increased with an increase in the amount and molecular weight of the PVP in the particles. The crystallization kinetics of single particles was analysed with AFM and by utilising the JMAK equation. The rate constant for this transformation increased in an exponential manner with increasing RH. Furthermore, above the RH needed for the crystallization to occur, the exponential increase in the crystallization rate was larger for particles with higher polymer content which indicates that the stabilising effect decreases as the water content in the particles becomes higher. In this study we report a method for determination of crystallization kinetics on single composite particles, which is valuable when evaluating the effect of stabilisers in amorphous powders. PMID:16822629

  18. Raman Studies of Particle Structure and Graphitization in Carbon Blacks.

    NASA Astrophysics Data System (ADS)

    Gruber, Tyler Charles

    Raman spectroscopy is used to probe the in-plane layer dimensions (L_{rm a} ) of graphitic nanocrystalline regions within several carbon blacks. The empirical relationship of Tuinstra and Koenig is used to relate integrated peak intensities to L_{rm a}. These data are compared to those derived from Raman spectra calculated using a theoretical phonon-confinement model developed by Richter and coworkers in their studies on silicon and not previously applied to measurements of L_ {rm a} in graphitic materials. These Raman measurements yield L_{rm a} values which correlate very well with measurements performed using an accepted x-ray diffraction-based method. Graphitization was investigated in terms of the dependence of L_{rm a} on furnace, continuous wave laser, and pulsed laser heat -treatment. Nanocrystal environment and heat transfer in carbon black particles were identified as strong influences on the final state of graphitization. Graphitic crystal planes grow substantially on the microsecond time scale, and graphitization is completed within seconds. In addition, surface activity decreased dramatically in graphitized carbon blacks, indicating surface homogenization and removal of active surface sites through increases in L _{rm a} at the particle boundary. These results give new insight to the energetic processes which govern graphitic nanolayer realignment. Three-dimensional transmission electron microscope investigations of structure in graphitized carbon blacks demonstrate that aggregates are more or less flat entities, which may be contrasted with the expected isotropic structure. Anisotropy is quantified and discussed in terms of its potential effects on the reinforcement of elastomers by carbon black. These discoveries should contribute to the development of improved carbon blacks through new production technologies.

  19. Crystal structure of the co-crystal butyl­paraben–isonicotinamide (1/1)

    PubMed Central

    Bhardwaj, Rajni M.; Yang, Huaiyu; Florence, Alastair J.

    2016-01-01

    The title 1:1 co-crystal, C11H14O3·C6H6N2O [systematic name: butyl 4-hy­droxy­benzoate–isonicotinamide (1/1)], crystallizes with one mol­ecule of butyl­paraben (BPN) and one mol­ecule of isonicotinamide (ISN) in the asymmetric unit. In the crystal, BPN and ISN mol­ecules form hydrogen-bonded (O—H⋯N and N—H⋯O) dimers of paired BPN and ISN mol­ecules. These dimers are further connected to each other via N—H⋯O=C hydrogen bonds, creating ribbons in [011] which further stack along the a axis to form a layered structure with short C⋯C contacts of 3.285 (3) Å. Packing inter­actions within the crystal structure were assessed using PIXEL calculations. PMID:26870584

  20. Crystal structure of a nematode-infecting virus.

    PubMed

    Guo, Yusong R; Hryc, Corey F; Jakana, Joanita; Jiang, Hongbing; Wang, David; Chiu, Wah; Zhong, Weiwei; Tao, Yizhi J

    2014-09-01

    Orsay, the first virus discovered to naturally infect Caenorhabditis elegans or any nematode, has a bipartite, positive-sense RNA genome. Sequence analyses show that Orsay is related to nodaviruses, but molecular characterizations of Orsay reveal several unique features, such as the expression of a capsid-? fusion protein and the use of an ATG-independent mechanism for translation initiation. Here we report the crystal structure of an Orsay virus-like particle assembled from recombinant capsid protein (CP). Orsay capsid has a T = 3 icosahedral symmetry with 60 trimeric surface spikes. Each CP can be divided into three regions: an N-terminal arm that forms an extended protein interaction network at the capsid interior, an S domain with a jelly-roll, ?-barrel fold forming the continuous capsid, and a P domain that forms surface spike projections. The structure of the Orsay S domain is best aligned to T = 3 plant RNA viruses but exhibits substantial differences compared with the insect-infecting alphanodaviruses, which also lack the P domain in their CPs. The Orsay P domain is remotely related to the P1 domain in calicivirus and hepatitis E virus, suggesting a possible evolutionary relationship. Removing the N-terminal arm produced a slightly expanded capsid with fewer nucleic acids packaged, suggesting that the arm is important for capsid stability and genome packaging. Because C. elegans-Orsay serves as a highly tractable model for studying viral pathogenesis, our results should provide a valuable structural framework for further studies of Orsay replication and infection. PMID:25136116

  1. Toxicity of TiO2 Nanoparticles to Escherichia coli: Effects of Particle Size, Crystal Phase and Water Chemistry

    PubMed Central

    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

  2. Datamining protein structure databanks for crystallization patterns of proteins.

    PubMed

    Valafar, Homayoun; Prestegard, James H; Valafar, Faramarz

    2002-12-01

    A study of 345 protein structures selected among 1,500 structures determined by nuclear magnetic resonance (NMR) methods, revealed useful correlations between crystallization properties and several parameters for the studied proteins. NMR methods of structure determination do not require the growth of protein crystals, and hence allow comparison of properties of proteins that have or have not been the subject of crystallographic approaches. One- and two-dimensional statistical analyses of the data confirmed a hypothesized relation between the size of the molecule and its crystallization potential. Furthermore, two-dimensional Bayesian analysis revealed a significant relationship between relative ratio of different secondary structures and the likelihood of success for crystallization trials. The most immediate result is an apparent correlation of crystallization potential with protein size. Further analysis of the data revealed a relationship between the unstructured fraction of proteins and the success of its crystallization. Utilization of Bayesian analysis on the latter correlation resulted in a prediction performance of about 64%, whereas a two-dimensional Bayesian analysis succeeded with a performance of about 75%. PMID:12594078

  3. Influence of particles on the functional properties of single crystals of high-strength ferromagnetic alloys

    NASA Astrophysics Data System (ADS)

    Kretinina, I. V.; Kuts, O. A.; Kuksgauzen, D. A.; Poklonov, V. V.; Pobedennaya, Z. V.; Platonova, Yu N.

    2015-01-01

    Single crystals of the ordered ferromagnetic Co49Ni21Ga30 (at.%) alloy with B2-L10 martensitic transformation and of the disordered iron-based Fe41Ni28Co17Al11.5X2.5 (X=Ta, Ti) (at.%) alloys, which undergo thermoelastic γ-a' martensitic transformations, were studied in terms of the influence of chemical composition, size and volume fraction of the dispersed γ'- phase particles on functional properties - shape memory effect and superelasticity. Single crystals of Co49Ni21Ga30 alloy showed that the precipitation of nanometric γ'-phase particles changes the martensitic transformation characteristic temperature, reduces the value of the shape memory effect and superelasticity, increases thermal and stress hysteresis, and leads to hardening of the high temperature phase, which promotes superelasticity at a wide temperature range and at high temperatures at T>373K compared with the crystals without particles. Single crystals of FeNiCoAlX (X=Ta, Ti) alloys have experimentally demonstrated that the precipitation of ordered γ'-phase particles at a size of d=5-10 nm during aging at T=973 K, 3 h, leads to the occurrence of the shape memory effect and superelasticity.

  4. Lactose particle engineering: Influence of ultrasound and anti-solvent on crystal habit and particle size

    NASA Astrophysics Data System (ADS)

    Kougoulos, E.; Marziano, I.; Miller, P. R.

    2010-11-01

    This study focuses on ultrasound-assisted anti-solvent crystallization of lactose, expanding on previous studies and presenting, for the first time, the results of large scale implementation of sonocrystallization for lactose. The results further clarify the interplay between solution chemistry - namely the role of ?-lactose - and crystallization, representing a step forward in the fine tuning of lactose properties for pharmaceutical manufacturing applications. Batches manufactured at laboratory and pilot scales were extensively characterised, including an approach for the quantification of ?-lactose in ?-lactose based on powder X-ray diffraction (PXRD), which is described here.

  5. 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; McNae, Iain W.; Ho, Kok Lian; Walkinshaw, Malcolm D.

    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.

  6. Crystal structure of benzobi­cyclon

    PubMed Central

    Kang, Gihaeng; Kim, Jineun; Lim, Hansu; Kim, Tae Ho

    2015-01-01

    In the title compound, C22H19ClO4S2 [systematic name: 3-(2-chloro-4-mesylbenzo­yl)-4-(phenyl­sulfan­yl)bi­cyclo­[3.2.1]oct-3-en-2-one], which is an unclassified herbicide, the dihedral angle between the plane of the phenyl and chloro­benzene rings is 19.9 (2)°. In the crystal, C—H⋯O hydrogen bonds link adjacent mol­ecules, generating two-dimensional networks extending parellel to (011). PMID:26870484

  7. Colloidal crystal beads composed of core-shell particles for multiplex bioassay.

    PubMed

    Xu, Hua; Zhu, Cun; Zhao, Yuanjin; Zhao, Xiangwei; Hu, Jing; Gu, Zhongze

    2009-04-01

    A convenient method was developed to fabricate colloidal crystal beads (CCBs) with tough mechanical strength, which was used as encoded carriers for multiplex bioassay. The latex particles used for the construction of the CCBs were designed with a rigid core PS and a elastomeric shell poly(MMA/EA/MAA), and were prepared via one-step soap-free emulsion polymerization. The as-above-prepared CCBs were thermo-treated to drive the elastomeric shells of adjacent latex particles joining together. It was found that the coalescence of latex particles can greatly improve the mechanical strength of the CCBs for multiplex bioassay. PMID:19438006

  8. Single-Crystal Structure of a Covalent Organic Framework

    SciTech Connect

    Zhang, YB; Su, J; Furukawa, H; Yun, YF; Gandara, F; Duong, A; Zou, XD; Yaghi, OM

    2013-11-06

    The crystal structure of a new covalent organic framework, termed COF-320, is determined by single-crystal 3D electron diffraction using the rotation electron diffraction (RED) method for data collection. The COF crystals are prepared by an imine condensation of tetra-(4-anilyl)methane and 4,4'-biphenyldialdehyde in 1,4-dioxane at 120 degrees C to produce a highly porous 9-fold interwoven diamond net. COF-320 exhibits permanent porosity with a Langmuir surface area of 2400 m(2)/g and a methane total uptake of 15.0 wt % (176 cm(3)/cm(3)) at 25 degrees C and 80 bar. The successful determination of the structure of COF-320 directly from single-crystal samples is an important advance in the development of COF chemistry.

  9. Mechanisms of crystal formation in gout-a structural approach.

    PubMed

    Pascual, Eliseo; Addadi, Lia; Andrés, Mariano; Sivera, Francisca

    2015-12-01

    The mechanisms and sites of monosodium urate monohydrate (MSU) crystal deposition in gout have received little attention from the scientific community to date. Formalin fixation of tissues leads to the dissolution of MSU crystals, resulting in their absence from routinely processed pathological samples and hence neglect. However, modern imaging techniques-especially ultrasonography but also conventional CT and dual-energy CT-reveal that MSU crystals form at the cartilage surface as well as inside tendons and ligaments, often at insertion sites. Tophi comprise round white formations of different sizes surrounded by inflammatory tissue. Studies of fibres recovered from gouty synovial fluid indicate that these fibres are likely to be a primary site of crystal formation by templated nucleation, with crystals deposited parallel to the fibres forming transverse bands. In tophi, two areas can be distinguished: one where crystals are formed on cellular tissues and another consisting predominantly of crystals, where secondary nucleation seems to take place; this organization could explain how tophi can grow rapidly. From these observations based on a crystallographic approach, it seems that initial templated nucleation on structural fibres-probably collagen-followed at some sites by secondary nucleation could explain MSU crystal deposition in gout. PMID:26369610

  10. 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.

  11. The different conformations and crystal structures of dihydroergocristine

    NASA Astrophysics Data System (ADS)

    Mönch, B.; Kraus, W.; Köppen, R.; Emmerling, F.

    2016-02-01

    The identification of different forms of dihydroergocristine (DHEC) was carried out by crystallization from different organic solvents. DHEC was identified as potential template for molecularly imprinted polymers (MIPs) for the epimeric specific analysis of ergot alkaloids (EAs) in food. DHEC was crystallized from different solvents in order to mimic the typical MIP synthesis conditions. Four new solvatomorphs of DHEC were obtained. All solvatomorphs contain a water molecule in the crystal structure, whereas three compounds contain an additional solvent molecule. Based on the conformation of DHEC a comparison with typical EA molecules was possible. The analysis showed that DHEC is a suitable template for MIPs for EAs.

  12. Crystal structure of a theta-class glutathione transferase.

    PubMed Central

    Wilce, M C; Board, P G; Feil, S C; Parker, M W

    1995-01-01

    Glutathione S-transferases (GSTs) are a family of enzymes involved in the cellular detoxification of xenotoxins. Cytosolic GSTs have been grouped into four evolutionary classes for which there are representative crystal structures of three of them. Here we report the first crystal structure of a theta-class GST. So far, all available GST crystal structures suggest that a strictly conserved tyrosine near the N-terminus plays a critical role in the reaction mechanism and such a role has been convincingly demonstrated by site-directed mutagenesis. Surprisingly, the equivalent residue in the theta-class structure is not in the active site, but its role appears to have been replaced by either a nearby serine or by another tyrosine residue located in the C-terminal domain of the enzyme. Images PMID:7774571

  13. Crystal field and magnetic structure of UO2

    NASA Astrophysics Data System (ADS)

    Zhou, Fei; Ozoli?, Vidvuds

    2011-02-01

    The properties of UO2 result from rich f-electron physics, including electronic Coulomb interactions, spin-orbit and crystal-field effects, as well as interionic multipolar coupling. We present a comprehensive theoretical study of the electronic structure of UO2 using a combined application of self-consistent DFT+U calculations and a model Hamiltonian. The ?5 ground state of U4+ and the energies of crystal-field excitations ?5??3,4,1 are reproduced in very good agreement with experiment. We also investigate competing noncollinear magnetic structures and confirm 3k as the T=0 K ground-state magnetic structure of UO2.

  14. Nanoscale structural features determined by AFM for single virus particles

    NASA Astrophysics Data System (ADS)

    Chen, Shu-Wen W.; Odorico, Michael; Meillan, Matthieu; Vellutini, Luc; Teulon, Jean-Marie; Parot, Pierre; Bennetau, Bernard; Pellequer, Jean-Luc

    2013-10-01

    In this work, we propose ``single-image analysis'', as opposed to multi-image averaging, for extracting valuable information from AFM images of single bio-particles. This approach allows us to study molecular systems imaged by AFM under general circumstances without restrictions on their structural forms. As feature exhibition is a resolution correlation, we have performed AFM imaging on surfaces of tobacco mosaic virus (TMV) to demonstrate variations of structural patterns with probing resolution. Two AFM images were acquired with the same tip at different probing resolutions in terms of pixel width, i.e., 1.95 and 0.49 nm per pixel. For assessment, we have constructed an in silico topograph based on the three-dimensional crystal structure of TMV as a reference. The prominent artifacts observed in the AFM-determined shape of TMV were attributed to tip convolutions. The width of TMV rod was systematically overestimated by ~10 nm at both probing resolutions of AFM. Nevertheless, the effects of tip convolution were less severe in vertical orientation so that the estimated height of TMV by AFM imaging was in close agreement with the in silico X-ray topograph. Using dedicated image processing algorithms, we found that at low resolution (i.e., 1.95 nm per pixel), the extracted surface features of TMV can be interpreted as a partial or full helical repeat (three complete turns with ~7.0 nm in length), while individual protein subunits (~2.5 nm) were perceivable only at high resolution. The present study shows that the scales of revealed structural features in AFM images are subject to both probing resolution and processing algorithms for image analysis.

  15. Structure of Blue Phase III of Cholesteric Liquid Crystals

    NASA Astrophysics Data System (ADS)

    Henrich, O.; Stratford, K.; Cates, M. E.; Marenduzzo, D.

    2011-03-01

    We report large scale simulations of the blue phases of cholesteric liquid crystals. Our results suggest a structure for blue phase III, the blue fog, which has been the subject of a long debate in liquid crystal physics. We propose that blue phase III is an amorphous network of disclination lines, which is thermodynamically and kinetically stabilized over crystalline blue phases at intermediate chiralities. This amorphous network becomes ordered under an applied electric field, as seen in experiments.

  16. Boron-oxygen polyanion in the crystal structure of tunellite

    USGS Publications Warehouse

    Clark, J.R.

    1963-01-01

    The crystal structure of tunellite, SrO??3B2O 3??4H2O, with infinite sheets of composition n[B6O9(OH)2]2-, has cations and water molecules in the spaces within the sheets. Adjacent sheets are held together by hydrogen bonding through the water molecules. The boron-oxygen polyanions provide the first example in hydrated borate crystals of one oxygen linked to three borons.

  17. Structure of ice crystallized from supercooled water

    PubMed Central

    Malkin, Tamsin L.; Murray, Benjamin J.; Brukhno, Andrey V.; Anwar, Jamshed; Salzmann, Christoph G.

    2012-01-01

    The freezing of water to ice is fundamentally important to fields as diverse as cloud formation to cryopreservation. At ambient conditions, ice is considered to exist in two crystalline forms: stable hexagonal ice and metastable cubic ice. Using X-ray diffraction data and Monte Carlo simulations, we show that ice that crystallizes homogeneously 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. Stacking disorder and stacking faults have been reported earlier for metastable ice I, but only for ice crystallizing in mesopores and in samples recrystallized from high-pressure ice phases rather than in water droplets. 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. These findings highlight the need to reevaluate the physical and thermodynamic properties of this metastable ice as a function of the nature and extent of stacking disorder using well-characterized samples. PMID:22232652

  18. Magnetically responsive gourd-shaped colloidal particles in cholesteric liquid crystals.

    PubMed

    Senyuk, Bohdan; Varney, Michael C M; Lopez, Javier A; Wang, Sijia; Wu, Ning; Smalyukh, Ivan I

    2014-08-28

    Particle shape and medium chirality are two key features recently used to control anisotropic colloidal self-assembly and dynamics in liquid crystals. Here, we study magnetically responsive gourd-shaped colloidal particles dispersed in cholesteric liquid crystals with periodicity comparable or smaller than the particle's dimensions. Using magnetic manipulation and optical tweezers, which allow one to position colloids near the confining walls, we measured the elastic repulsive interactions of these particles with confining surfaces and found that separation-dependent particle-wall interaction force is a non-monotonic function of separation and shows oscillatory behavior. We show that gourd-shaped particles in cholesterics reside not on a single sedimentation level, but on multiple long-lived metastable levels separated by a distance comparable to cholesteric periodicity. Finally, we demonstrate three-dimensional laser tweezers assisted assembly of gourd-shaped particles taking advantage of both orientational order and twist periodicity of cholesterics, potentially allowing new forms of orientationally and positionally ordered colloidal organization in these media. PMID:24994521

  19. Dynamical phases of attractive particles sliding on a structured surface

    NASA Astrophysics Data System (ADS)

    Hasnain, J.; Jungblut, S.; Dellago, C.

    2015-05-01

    Inspired by experiments on quartz crystal microbalance setups, we study the mobility of a monolayer of Lennard-Jones particles driven over a hexagonal external potential. We pay special attention to the changes in the dynamical phases that arise when the lattice constant of the external substrate potential and the Lennard-Jones interaction are mismatched. We find that if the average particle separation is such that the particles repel each other, or interact harmonically, the qualitative behavior of the system is akin to that of a monolayer of purely repulsive Yukawa particles. On the other hand, if the particles typically attract each other, the ensuing dynamical states are determined entirely by the relative strength of the Lennard-Jones interaction with respect to that of the external potential.

  20. Artificially Structured Boundary as a Charged Particle Beam Deflector Shield

    NASA Astrophysics Data System (ADS)

    Hedlof, R. M.; Ordonez, C. A.

    The possibility of using a planar artificially structured boundary as a charged particle beam deflector shield is studied via classical trajectory Monte Carlo simulation. The artificially structured boundary (ASB) is formed by a planar array of permanent disk magnets with like poles facing out and creates a spatially periodic magnetostatic field. A mono-energetic beam of charged particles is incident on the ASB, and the conditions under which particles penetrate through the array are determined.

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

    SciTech Connect

    Sutherland, G. T.; Lemar, E. R.; Marcus, M. H.

    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.

  2. Crystal engineering with thioureas: A structure-based inquiry

    NASA Astrophysics Data System (ADS)

    Paisner, Kathryn A.

    2011-12-01

    Structural trends applicable to crystal engineering were studied in three classes of thiourea-based compounds. The aim of the study was to identify, predict, and ultimately design reliable single-molecule structural features, which could then be used to engineer crystals with desirable properties. In one class of compounds, this goal was achieved: N-alkyl and N-aryl derivatives of N,N'-bis(3-thioureidopropyl)piperazine adopted an identical conformation in the solid state, which resulted in near-identical crystal packing. A second class of closely related compounds, N-substituted tris(2-thioureidoethyl)amines, showed no such reliability in the solid state, likely because the parent structure lacked hydrogen-bonding functionalities sufficient to control intramolecular structure. In the third class of compounds that we studied, 1-benzoyl-3-(2-pyridyl)thioureas, substitution patterns were often predictive of molecular conformation; however, these intramolecular trends did not lead to recognizable crystal packing motifs. Nevertheless, certain physical properties observed in this last class of compounds---color, solubility, and often crystallinity---were conformer-specific, interestingly without any apparent relevance to crystal lattice structure. Solution-state and solid-state conformational trends in these 1-benzoyl-3-(2-pyridyl)thioureas have been documented, and speculations as to the source of color in one of the two observed conformations have been noted.

  3. Crystal structure of ammonia dihydrate II

    NASA Astrophysics Data System (ADS)

    Griffiths, Gareth I. G.; Fortes, A. Dominic; Pickard, Chris J.; Needs, R. J.

    2012-05-01

    We have used density-functional-theory (DFT) methods together with a structure searching algorithm to make an experimentally constrained prediction of the structure of ammonia dihydrate II (ADH-II). The DFT structure is in good agreement with neutron diffraction data and verifies the prediction. The structure consists of the same basic structural elements as ADH-I, with a modest alteration to the packing, but a considerable reduction in volume. The phase diagram of the known ADH and ammonia monohydrate + water-ice structures is calculated with the Perdew-Burke-Ernzerhof density functional, and the effects of a semi-empirical dispersion corrected functional are investigated. The results of our DFT calculations of the finite-pressure elastic constants of ADH-II are compared with the available experimental data for the elastic strain coefficients.

  4. Ice crystallization in ultrafine water-salt aerosols: nucleation, ice-solution equilibrium, and internal structure.

    PubMed

    Hudait, Arpa; Molinero, Valeria

    2014-06-01

    Atmospheric aerosols have a strong influence on Earth's climate. Elucidating the physical state and internal structure of atmospheric aqueous aerosols is essential to predict their gas and water uptake, and the locus and rate of atmospherically important heterogeneous reactions. Ultrafine aerosols with sizes between 3 and 15 nm have been detected in large numbers in the troposphere and tropopause. Nanoscopic aerosols arising from bubble bursting of natural and artificial seawater have been identified in laboratory and field experiments. The internal structure and phase state of these aerosols, however, cannot yet be determined in experiments. Here we use molecular simulations to investigate the phase behavior and internal structure of liquid, vitrified, and crystallized water-salt ultrafine aerosols with radii from 2.5 to 9.5 nm and with up to 10% moles of ions. We find that both ice crystallization and vitrification of the nanodroplets lead to demixing of pure water from the solutions. Vitrification of aqueous nanodroplets yields nanodomains of pure low-density amorphous ice in coexistence with vitrified solute rich aqueous glass. The melting temperature of ice in the aerosols decreases monotonically with an increase of solute fraction and decrease of radius. The simulations reveal that nucleation of ice occurs homogeneously at the subsurface of the water-salt nanoparticles. Subsequent ice growth yields phase-segregated, internally mixed, aerosols with two phases in equilibrium: a concentrated water-salt amorphous mixture and a spherical cap-like ice nanophase. The surface of the crystallized aerosols is heterogeneous, with ice and solution exposed to the vapor. Free energy calculations indicate that as the concentration of salt in the particles, the advance of the crystallization, or the size of the particles increase, the stability of the spherical cap structure increases with respect to the alternative structure in which a core of ice is fully surrounded by solution. We predict that micrometer-sized particles and nanoparticles have the same equilibrium internal structure. The variation of liquid-vapor surface tension with solute concentration is a key factor in determining whether a solution-embedded ice core or vapor-exposed ice cap is the equilibrium structure of the aerosols. In agreement with experiments, we predict that the structure of mixed-phase HNO3-water particles, representative of polar stratospheric clouds, consists of an ice core surrounded by freeze-concentrated solution. The results of this work are important to determine the phase state and internal structure of sea spray ultrafine aerosols and other mixed-phase particles under atmospherically relevant conditions. PMID:24820354

  5. Crystal structure and characterization of a novel organic optical crystal: 2-Aminopyridinium trichloroacetate

    SciTech Connect

    Dhanaraj, P.V.; Rajesh, N.P.; Vinitha, G.; Bhagavannarayana, G.

    2011-05-15

    Research highlights: {yields} Good quality crystals of 2-aminopyridinium trichloroacetate were grown for first time. {yields} 2-Aminopyridinium trichloroacetate crystal belongs to monoclinic crystal system with space group P21/c. {yields} 2-Aminopyridinium trichloroacetate crystal exhibits third order nonlinear optical properties. {yields} 2-Aminopyridinium trichloroacetate is a low dielectric constant material. -- Abstract: 2-Aminopyridinium trichloroacetate, a novel organic optical material has been synthesized and crystals were grown from aqueous solution employing the technique of controlled evaporation. 2-Aminopyridinium trichloroacetate crystallizes in monoclinic system with space group P2{sub 1}/c and the lattice parameters are a = 8.598(5) A, b = 11.336(2) A, c = 11.023(2) A, {beta} = 102.83(1){sup o} and volume = 1047.5(3) A{sup 3}. High-resolution X-ray diffraction measurements were performed to analyze the structural perfection of the grown crystals. Thermal analysis shows a sharp endothermic peak at 124 {sup o}C due to melting reaction of 2-aminopyridinium trichloroacetate. UV-vis-NIR studies reveal that 2-aminopyridinium trichloroacetate has UV cutoff wavelength at 354 nm. Dielectric studies show that dielectric constant and dielectric loss decreases with increasing frequency and finally it becomes almost a constant at higher frequencies for all temperatures. The negative nonlinear optical parameters of 2-aminopyridinium trichloroacetate were derived by the Z-scan technique.

  6. Combined crystal structure prediction and high-pressure crystallization in rational pharmaceutical polymorph screening

    NASA Astrophysics Data System (ADS)

    Neumann, M. A.; van de Streek, J.; Fabbiani, F. P. A.; Hidber, P.; Grassmann, O.

    2015-07-01

    Organic molecules, such as pharmaceuticals, agro-chemicals and pigments, frequently form several crystal polymorphs with different physicochemical properties. Finding polymorphs has long been a purely experimental game of trial-and-error. Here we utilize in silico polymorph screening in combination with rationally planned crystallization experiments to study the polymorphism of the pharmaceutical compound Dalcetrapib, with 10 torsional degrees of freedom one of the most flexible molecules ever studied computationally. The experimental crystal polymorphs are found at the bottom of the calculated lattice energy landscape, and two predicted structures are identified as candidates for a missing, thermodynamically more stable polymorph. Pressure-dependent stability calculations suggested high pressure as a means to bring these polymorphs into existence. Subsequently, one of them could indeed be crystallized in the 0.02 to 0.50 GPa pressure range and was found to be metastable at ambient pressure, effectively derisking the appearance of a more stable polymorph during late-stage development of Dalcetrapib.

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

    DOEpatents

    Payne, Stephen A.; Kway, Wayne L.; DeLoach, Laura D.; Krupke, William F.; Chai, Bruce H. T.

    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.

  8. 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

  9. Spontaneous Formation of Eutectic Crystal Structures in Binary and Ternary Charged Colloids due to Depletion Attraction

    PubMed Central

    Toyotama, Akiko; Okuzono, Tohru; Yamanaka, Junpei

    2016-01-01

    Crystallization of colloids has extensively been studied for past few decades as models to study phase transition in general. Recently, complex crystal structures in multi-component colloids, including alloy and eutectic structures, have attracted considerable attention. However, the fabrication of 2D area-filling colloidal eutectics has not been reported till date. Here, we report formation of eutectic structures in binary and ternary aqueous colloids due to depletion attraction. We used charged particles + linear polyelectrolyte systems, in which the interparticle interaction could be represented as a sum of the electrostatic, depletion, and van der Waals forces. The interaction was tunable at a lengthscale accessible to direct observation by optical microscopy. The eutectic structures were formed because of interplay of crystallization of constituent components and accompanying fractionation. An observed binary phase diagram, defined by a mixing ratio and inverse area fraction of the particles, was analogous to that for atomic and molecular eutectic systems. This new method also allows the adjustment of both the number and wavelengths of Bragg diffraction peaks. Furthermore, these eutectic structures could be immobilized in polymer gel to produce self-standing materials. The present findings will be useful in the design of the optical properties of colloidal crystals. PMID:26984298

  10. Spontaneous Formation of Eutectic Crystal Structures in Binary and Ternary Charged Colloids due to Depletion Attraction.

    PubMed

    Toyotama, Akiko; Okuzono, Tohru; Yamanaka, Junpei

    2016-01-01

    Crystallization of colloids has extensively been studied for past few decades as models to study phase transition in general. Recently, complex crystal structures in multi-component colloids, including alloy and eutectic structures, have attracted considerable attention. However, the fabrication of 2D area-filling colloidal eutectics has not been reported till date. Here, we report formation of eutectic structures in binary and ternary aqueous colloids due to depletion attraction. We used charged particles + linear polyelectrolyte systems, in which the interparticle interaction could be represented as a sum of the electrostatic, depletion, and van der Waals forces. The interaction was tunable at a lengthscale accessible to direct observation by optical microscopy. The eutectic structures were formed because of interplay of crystallization of constituent components and accompanying fractionation. An observed binary phase diagram, defined by a mixing ratio and inverse area fraction of the particles, was analogous to that for atomic and molecular eutectic systems. This new method also allows the adjustment of both the number and wavelengths of Bragg diffraction peaks. Furthermore, these eutectic structures could be immobilized in polymer gel to produce self-standing materials. The present findings will be useful in the design of the optical properties of colloidal crystals. PMID:26984298

  11. Free-Standing Photonic Crystal Films with Gradient Structural Colors.

    PubMed

    Ding, Haibo; Liu, Cihui; Ye, Baofen; Fu, Fanfan; Wang, Huan; Zhao, Yuanjin; Gu, Zhongze

    2016-03-23

    Hydrogel colloidal crystal composite materials have a demonstrated value in responsive photonic crystals (PhCs) via controllable stimuli. Although they have been successfully exploited to generate a gradient of color distribution, the soft hydrogels have limitations in terms of stability and storage caused by dependence on environment. Here, we present a practical strategy to fabricate free-standing PhC films with a stable gradient of structural colors using binary polymer networks. A colloidal crystal hydrogel film was prepared for this purpose, with continuously varying photonic band gaps corresponding to the gradient of the press. Then, a second polymer network was used to lock the inside non-close-packed PhC structures and color distribution of the hydrogel film. It was demonstrated that our strategy could bring about a solution to the angle-dependent structural colors of the PhC films by coating the surface with special microstructures. PMID:26962967

  12. Crystal structures of gold, silver, and sodium chalcogenides: Sphenoidal interpretation

    SciTech Connect

    Bakakin, V. V.

    2011-11-15

    The crystal structures of 13 chalcogenides of Na, Au(I), and Ag(I) in the Na{sub 2-n}(Au,Ag){sub n}(S,Se,Te) series, where 0 {<=} n {<=} 2, are interpreted from unified positions based on the sphenoidal representation. Its essence is in the consideration of the entire crystal space (with packing X atoms in the framework of close-packing, body-centered, or hybrid schemes) as a set of elementary space units (sphenoids). Unified one-dimensional associates of sphenoids, the so-called basic rods, with sets of possible atomic positions in them are selected for all structures. The mutual effect of the dimensional and stoichiometric ratios of all components on the features of filling rod positions is analyzed. New possibilities in the crystallochemical and crystal-geometry analysis of inorganic compounds whose structures are characterized by a relatively uniform distribution of atoms are demonstrated by the example of chalcogenides.

  13. Yolk spherocrystal: the structure, composition and liquid crystal template.

    PubMed

    Tong, Hua; Wan, Peng; Ma, Wentao; Zhong, Guirong; Cao, Lianxin; Hu, Jiming

    2008-07-01

    The structure and composition of the yolk spherocrystal, a biomineral developed in the egg yolk sac during the incubation of a chicken embryo, were investigated through various modern analytical methods. Additionally, inside the yolk sac, yolk liquid crystal, a liquid crystalline phase of lipid developed during the incubation of the embryo, was found and investigated. The spherocrystal was found to be a composite composed of calcium carbonate (vaterite and calcite, primarily the former) and the yolk liquid crystal, which is believed to act as an organic template for spherocrystals mineralization, in a concentric multi-layered sphere structure. Moreover, the yolk liquid crystal was found to have a concentric multi-layered spherical structure and a composition consistent with lecithin. We believed that the spherocrystals function as a reservoir for the storage of calcium in the egg yolk sac during the development of the embryo. PMID:18485735

  14. Crystal structure tuning in GaAs nanowires using HCl.

    PubMed

    Jacobsson, Daniel; Lehmann, Sebastian; Dick, Kimberly A

    2014-07-21

    The use of HCl during growth of nanowires presents new possibilities for controlling the growth dynamics and resulting nanowire properties. In this paper, we investigate the effects of in situ HCl on the growth of Au-seeded GaAs nanowires in a growth regime where both wurtzite and zinc blende crystal structures are possible to achieve. We find that HCl changes the crystal structure of the nanowires from pure wurtzite to defect-free zinc blende. By comparing the growth of wurtzite-zinc blende heterostructures with and without the addition of HCl, it is deduced that HCl mainly interacts with Ga species prior incorporation, reducing the amount of Ga available to contribute to the growth. We conclude that the change in crystal structure is related to the reduction of Ga adatoms, and demonstrate the realization of wurtzite-zinc blende heterostructures with atomically sharp interfaces achieved only by adding HCl. PMID:24931099

  15. Crystal structure tuning in GaAs nanowires using HCl

    NASA Astrophysics Data System (ADS)

    Jacobsson, Daniel; Lehmann, Sebastian; Dick, Kimberly A.

    2014-06-01

    The use of HCl during growth of nanowires presents new possibilities for controlling the growth dynamics and resulting nanowire properties. In this paper, we investigate the effects of in situ HCl on the growth of Au-seeded GaAs nanowires in a growth regime where both wurtzite and zinc blende crystal structures are possible to achieve. We find that HCl changes the crystal structure of the nanowires from pure wurtzite to defect-free zinc blende. By comparing the growth of wurtzite-zinc blende heterostructures with and without the addition of HCl, it is deduced that HCl mainly interacts with Ga species prior incorporation, reducing the amount of Ga available to contribute to the growth. We conclude that the change in crystal structure is related to the reduction of Ga adatoms, and demonstrate the realization of wurtzite-zinc blende heterostructures with atomically sharp interfaces achieved only by adding HCl.

  16. Crystal structure of simple metals at high pressures

    SciTech Connect

    Degtyareva, Olga

    2010-10-22

    The effects of pressure on the crystal structure of simple (or sp-) elements are analysed in terms of changes in coordination number, packing density, and interatomic distances, and general rules are established. In the polyvalent elements from groups 14-17, the covalently bonded structures tend to transform to metallic phases with a gradual increase in coordination number and packing density, a behaviour normally expected under pressure. Group 1 and 2 metallic elements, however, show a reverse trend towards structures with low packing density due to intricate changes in their electronic structure. Complex crystal structures such as host-guest and incommensurately modulated structures found in these elements are given special attention in this review in an attempt to determine their role in the observed phase-transition sequences.

  17. Dislocations and domain structures in layer crystals

    NASA Astrophysics Data System (ADS)

    Manolikas, C.; Amelinckx, S.

    1980-01-01

    The domain configurations in the transition metal dichalcogenides, NbTe 2, ?-MoTe 2, ReSe 2 and ReSe 2 with a deformed cadmium iodide or cadmium chloride structure, are analysed by electron diffraction and imaging techniques. Structural models are proposed for the different types of boundaries. The dislocation fine structure is analysed in detail, in particular in NbTe 2. The peculiar behaviour of dislocations in ?-MoTe 2 is also discussed. The interaction between the dislocation multiribbons and the domain boundaries is studied.

  18. 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.

  19. Microscopic characterization of defect structure in RDX crystals.

    PubMed

    Bouma, R H B; Duvalois, W; Van der Heijden, A E D M

    2013-12-01

    Three batches of the commercial energetic material RDX, as received from various production locations and differing in sensitivity towards shock initiation, have been characterized with different microscopic techniques in order to visualize the defect content in these crystals. The RDX crystals are embedded in an epoxy matrix and cross-sectioned. By a treatment of grinding and polishing of the crystals, the internal defect structure of a multitude of energetic crystals can be visualized using optical microscopy, scanning electron microscopy and confocal scanning laser microscopy. Earlier optical micrographs of the same crystals immersed in a refractive index matched liquid could visualize internal defects, only not in the required detail. The combination of different microscopic techniques allows for a better characterization of the internal defects, down to inclusions of approximately 0.5 μm in size. The defect structure can be correlated to the sensitivity towards a high-amplitude shock wave of the RDX crystals embedded in a polymer bonded explosive. The obtained experimental results comprise details on the size, type and quantity of the defects. These details should provide modellers with relevant and realistic information for modelling defects in energetic materials and their effect on the initiation and propagation of shock waves in PBX formulations. PMID:24117989

  20. The Crystal Structure of GXGD Membrane Protease FlaK

    SciTech Connect

    J Hu; Y Xue; S Lee; Y Ha

    2011-12-31

    The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. Representative members of the family include preflagellin peptidase, type 4 prepilin peptidase, presenilin and signal peptide peptidase. Many GXGD proteases are important in medicine. For example, type 4 prepilin peptidase may contribute to bacterial pathogenesis, and mutations in presenilin are associated with Alzheimer's disease. As yet, there is no atomic-resolution structure in this protease family. Here we report the crystal structure of FlaK, a preflagellin peptidase from Methanococcus maripaludis, solved at 3.6 {angstrom} resolution. The structure contains six transmembrane helices. The GXGD motif and a short transmembrane helix, helix 4, are positioned at the centre, surrounded by other transmembrane helices. The crystal structure indicates that the protease must undergo conformational changes to bring the GXGD motif and a second essential aspartyl residue from transmembrane helix 1 into close proximity for catalysis. A comparison of the crystal structure with models of presenilin derived from biochemical analysis reveals three common transmembrane segments that are similarly arranged around the active site. This observation reinforces the idea that the prokaryotic and human proteases are evolutionarily related. The crystal structure presented here provides a framework for understanding the mechanism of the GXGD proteases, and may facilitate the rational design of inhibitors that target specific members of the family.

  1. The crystal structure of GXGD membrane protease FlaK

    SciTech Connect

    Hu, Jian; Xue, Yi; Lee, Sangwon; Ha, Ya

    2011-09-20

    The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. Representative members of the family include preflagellin peptidase, type 4 prepilin peptidase, presenilin and signal peptide peptidase. Many GXGD proteases are important in medicine. For example, type 4 prepilin peptidase may contribute to bacterial pathogenesis, and mutations in presenilin are associated with Alzheimer's disease. As yet, there is no atomic-resolution structure in this protease family. Here we report the crystal structure of FlaK, a preflagellin peptidase from Methanococcus maripaludis, solved at 3.6 {angstrom} resolution. The structure contains six transmembrane helices. The GXGD motif and a short transmembrane helix, helix 4, are positioned at the centre, surrounded by other transmembrane helices. The crystal structure indicates that the protease must undergo conformational changes to bring the GXGD motif and a second essential aspartyl residue from transmembrane helix 1 into close proximity for catalysis. A comparison of the crystal structure with models of presenilin derived from biochemical analysis reveals three common transmembrane segments that are similarly arranged around the active site. This observation reinforces the idea that the prokaryotic and human proteases are evolutionarily related. The crystal structure presented here provides a framework for understanding the mechanism of the GXGD proteases, and may facilitate the rational design of inhibitors that target specific members of the family.

  2. Utilization of Protein Crystal Structures in Industry

    NASA Astrophysics Data System (ADS)

    Ishikawa, Kohki

    In industry, protein crystallography is used in mainly two technologies. One is structure-based drug design, and the other is structure-based enzyme engineering. Some successful cases together with recent advances are presented in this article. The cases include the development of an anti-influenza drug, and the introduction of engineered acid phosphatase to the manufacturing process of nucleotides used as umami seasoning.

  3. Crystal chemistry and structure refinement of five hydrated calcium borates

    USGS Publications Warehouse

    Clark, J.R.; Appleman, D.E.; Christ, C.L.

    1964-01-01

    The crystal structures of the five known members of the series Ca2B6O11??xH2O (x = 1, 5, 5, 7, 9, and 13) have been refined by full-matrix least-squares techniques, yielding bond distances and angles with standard errors of less than 0??01 A?? and 0??5??, respectively. The results illustrate the crystal chemical principles that govern the structures of hydrated borate compounds. The importance of hydrogen bonding in the ferroelectric transition of colemanite is confirmed by more accurate proton assignments. ?? 1964.

  4. Mechanically switchable photonic crystal structures based on coupled photonic crystal slabs

    NASA Astrophysics Data System (ADS)

    Suh, Wonjoo; Yanik, Mehmet F.; Solgaard, Olav; Fan, Shanhui

    2004-07-01

    Using both analytic theory, and first-principles finite-difference time-domain simulations, we introduce several novel mechanically tunable photonic crystal structures consisting of coupled photonic crystal slabs. These structures exploit guided resonance effects which give rise to strong variation of transmission for normally incident light. First, when the two slabs are separated apart by a few wavelengths, such a coupled slab structure behaves as a miniaturized Fabry-Perot cavity with two photonic crystal slabs acting as highly reflecting mirrors. Therefore, the transmission through the structure is highly sensitive to the spacing between the slabs. Second, when the two slabs are in proximity to each other, the evanescent tails of the resonance start to overlap. Exploiting the evanescent tunneling, we introduce a new type of optical all-pass filter. The filter exhibits near complete transmission for both on and off resonant frequencies, and yet generates large resonant group delay. Thus, we expect the coupled photonic crystal slab structures to play important roles in micro-mechanically tunable optical sensors and filters.

  5. Structures of dynamic particle accumulation in Marangoni convection in half-zone liquid bridge

    NASA Astrophysics Data System (ADS)

    Tanaka, S.; Ueno, I.; Kawamura, H.

    Thermocapillary convection is induced by the temperature difference T between two cylindrical rods sustaining liquid bridge. It is well known that the induced flow exhibits a transition from 2-D steady to 3-D time-dependent oscillatory flows with the increasing T. These convections can be visualized by using fine particles as tracers. In a certain flow condition, the particles were found to get accumulated. This is called PAS, particle accumulation structure, after Schwabe et al. (Microgravity, sci. technol. 1996). The authors group (Ueno et al, Proc. TSFP-2, 2001) categorized the induced flow fields into several regimes by the particle motion, structures and the surface temperature variation. Two sets of pulsating and rotating flows appeared. It was observed clearly that the particle gathered along a closed single path. This kind of structure was named as TL-PAS, Twisted-loop particle accumulation structure, (Tanaka et al, J. Japan Soc. Microgravity Appl, 2000). Special attention was paid for this kind of PAS in this study. The TL-PAS exhibited several types of closed path lines. Its detailed structure changed even in the same regime with a slight change of T and aspect ratio. The experimental setup consisted of the transparent crystal top and aluminum bottom rods. Flow fields were observed from top and side through two CCD cameras. A laser-light-sheet was employed in order to grasp the 3-D structures of TL-PAS. The liquid bridge of Silicone oil of 2 cSt was formed between rods of 5mm in diameter. Several kinds of particles were tested as tracer. The surface temperature variation was measured simultaneously by use of a 25?m thermocouple up to 50Hz, or 2.5?m CCT probe (constant current thermometry) up to 100Hz. By use of this apparatus, 3-D structure of TL-PAS and motions of individual particles were captured.

  6. In situ observations of aerosol particles remaining from evaporated cirrus crystals: Comparing clean and polluted air masses

    NASA Astrophysics Data System (ADS)

    Seifert, M.; Strm, J.; Krejci, R.; Minikin, A.; Petzold, A.; Gayet, J.-F.; Schumann, U.; Ovarlez, J.

    2002-10-01

    In situ observations of aerosol particles contained in cirrus crystals are presented and compared to interstitial aerosol size distributions (non-activated particles in between the cirrus crystals). The observations were conducted in cirrus clouds in the Southern and Northern Hemisphere mid-latitudes during the INCA project. The first campaign in March and April 2000 was performed from Punta Arenas, Chile (54 S) in pristine air. The second campaign in September and October 2000 was performed from Prestwick, Scotland (53 N) in the vicinity of the North Atlantic flight corridor. Size distribution measurements of crystal residuals (particles remaining after evaporation of the crystals) show that small aerosol particles (Dp < 0.1m) dominate the number density of residuals. The crystal residual size distributions were significantly different in the two campaigns. On average the residual size distributions were shifted towards larger sizes in the Southern Hemisphere. For a given integral residual number density, the calculated particle volume was on average three times larger in the Southern Hemisphere. This may be of significance to the vertical redistribution of aerosol mass by clouds in the tropopause region. In both campaigns the mean residual size increased with increasing crystal number density. The observations of ambient aerosol particles were consistent with the expected higher pollution level in the Northern Hemisphere. The fraction of residual particles only contributes to approximately a percent or less of the total number of particles, which is the sum of the residual and interstitial particles.

  7. Dengue Virus Non-structural Protein 1 Modulates Infectious Particle Production via Interaction with the Structural Proteins

    PubMed Central

    Scaturro, Pietro; Cortese, Mirko; Chatel-Chaix, Laurent; Fischl, Wolfgang; Bartenschlager, Ralf

    2015-01-01

    Non-structural protein 1 (NS1) is one of the most enigmatic proteins of the Dengue virus (DENV), playing distinct functions in immune evasion, pathogenesis and viral replication. The recently reported crystal structure of DENV NS1 revealed its peculiar three-dimensional fold; however, detailed information on NS1 function at different steps of the viral replication cycle is still missing. By using the recently reported crystal structure, as well as amino acid sequence conservation, as a guide for a comprehensive site-directed mutagenesis study, we discovered that in addition to being essential for RNA replication, DENV NS1 is also critically required for the production of infectious virus particles. Taking advantage of a trans-complementation approach based on fully functional epitope-tagged NS1 variants, we identified previously unreported interactions between NS1 and the structural proteins Envelope (E) and precursor Membrane (prM). Interestingly, coimmunoprecipitation revealed an additional association with capsid, arguing that NS1 interacts via the structural glycoproteins with DENV particles. Results obtained with mutations residing either in the NS1 Wing domain or in the β-ladder domain suggest that NS1 might have two distinct functions in the assembly of DENV particles. By using a trans-complementation approach with a C-terminally KDEL-tagged ER-resident NS1, we demonstrate that the secretion of NS1 is dispensable for both RNA replication and infectious particle production. In conclusion, our results provide an extensive genetic map of NS1 determinants essential for viral RNA replication and identify a novel role of NS1 in virion production that is mediated via interaction with the structural proteins. These studies extend the list of NS1 functions and argue for a central role in coordinating replication and assembly/release of infectious DENV particles. PMID:26562291

  8. Crystal Structures of Monomeric Actin Bound to Cytochalasin D

    PubMed Central

    Nair, Usha B.; Joel, Peteranne B.; Wan, Qun; Lowey, Susan; Rould, Mark A.; Trybus, Kathleen M.

    2008-01-01

    The fungal toxin cytochalasin D (CD) interferes with the normal dynamics of the actin cytoskeleton by binding to the barbed end of actin filaments. Despite its widespread use as a tool for studying actin-mediated processes, the exact location and nature of its binding to actin has not been previously determined. Here we describe two crystal structures of an expressed monomeric actin in complex with CD, one obtained by soaking preformed actin crystals with CD, and the other by co-crystallization. The binding site for CD, in the hydrophobic cleft between actin subdomains 1 and 3, is the same in the two structures. Polar and hydrophobic contacts play an equally important role in CD binding, and six hydrogen bonds stabilize the actin-CD complex. Many unrelated actin-binding proteins and marine toxins target this cleft, and the hydrophobic pocket at the front end of the cleft (viewing actin with subdomain 2 in the upper right corner). CD differs in that it binds to the back half of the cleft. The ability of CD to induce actin dimer formation and actin-catalyzed ATP hydrolysis may be related to its unique binding site, and the necessity to fit its bulky macrocycle into this cleft. Contacts with residues lining this cleft appear to be crucial to capping and/or severing. The co-crystallized actin-CD structure also revealed changes in actin conformation. A rotation of ~6° of the smaller actin domain (subdomains 1 and 2) with respect to the larger domain (subdomains 3 and 4) results in small changes in crystal packing that allow the D-loop to adopt an extended loop structure, instead of being disordered as it is in most crystal structures of actin. We speculate that these changes represent a potential conformation that the actin monomer can adopt on the pathway to polymerization or in the filament. PMID:18938176

  9. Layered periodic disperse structures of spherical alumina particles: Coherent transmittance and reflectance spectra

    NASA Astrophysics Data System (ADS)

    Miskevich, Alexander A.; Loiko, Valery A.

    2014-03-01

    Coherent transmittance and reflectance spectra of multilayers consisting of plane-parallel monolayers of spherical monodisperse alumina particles are investigated. In the quasicrystalline approximation (QCA) of the statistical theory of multiple scattering of waves the coherent transmission and reflection coefficients of constituent monolayers are computed. Using the coefficients obtained, the transmittance and reflectance of the multilayers are calculated using the transfer matrix method (TMM) within the wavelength range of 0.3-2.0 μm. Multilayers consisting of close-to-regularly-packed monolayers (planar photonic crystals with nonideal lattice) and partially-ordered monolayers of particles are investigated. Three types of coherent transmittance minima caused by the wave interference are singled out. The spectral positions and values of these minima are determined by optical constants, size, concentration, and the arrangement of particles in a monolayer, as well as by the spacing between the monolayer and their thicknesses. The results are in good agreement with the known theoretical and experimental data. They can be used to solve the problem of a lattice quality control in photonic crystals. Coherent transmittance and reflectance spectra of a system consisting of a glass plate coated with monolayers of spherical alumina particles are analyzed. Monolayer parameters for creating antireflection coatings, diffuse light scattering structures, and filters of transmitted and reflected light are considered. The approach developed can be applied to disperse structures of isotropic particles of other materials.

  10. 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.

  11. The crystal structure of aluminum doped ?-rhombohedral boron

    NASA Astrophysics Data System (ADS)

    Bykova, Elena; Parakhonskiy, Gleb; Dubrovinskaia, Natalia; Chernyshov, Dmitry; Dubrovinsky, Leonid

    2012-10-01

    A crystal structure of aluminum doped ?-rhombohedral boron was studied by single-crystal X-ray diffraction at 80 K. The crystals were synthesized using high-pressure high temperature technique at 3 GPa and 2100 K. The structure is based on three-dimensional framework made of B12 icosahedra with voids occupied by the B28-B-B28 units, it has the R-3m space group with a=10.9014(3), c=23.7225(7) lattice dimensions in hexagonal setting. Aluminum atoms are located in A1 and D special positions of the ?-B structure with occupancies of 82.7(6)% and 11.3(4)%, respectively. Additional boron atoms are located near the D-site. Their possible distribution is discussed. Finally we have found two appropriate structural models whose refinement suggests two possible chemical compositions, AlB44.8(5) and AlB37.8(5), which are in a good agreement with the chemical analysis data obtained from EDX. The crystal structure of AlB44.8(5) is described in detail.

  12. 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

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

    NASA Astrophysics Data System (ADS)

    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.

  14. Crystal structure of HINT from Helicobacter pylori.

    PubMed

    Tarique, K F; Devi, S; Abdul Rehman, S A; Gourinath, S

    2016-01-01

    Proteins belonging to the histidine triad (HIT) superfamily bind nucleotides and use the histidine triad motif to carry out dinucleotidyl hydrolase, nucleotidyltransferase and phosphoramidite hydrolase activities. Five different branches of this superfamily are known to exist. Defects in these proteins in humans are linked to many diseases such as ataxia, diseases of RNA metabolism and cell-cycle regulation, and various types of cancer. The histidine triad nucleotide protein (HINT) is nearly identical to proteins that have been classified as protein kinase C-interacting proteins (PKCIs), which also have the ability to bind and inhibit protein kinase C. The structure of HINT, which exists as a homodimer, is highly conserved from humans to bacteria and shares homology with the product of fragile histidine triad protein (FHit), a tumour suppressor gene of this superfamily. Here, the structure of HINT from Helicobacter pylori (HpHINT) in complex with AMP is reported at a resolution of 3?. The final model has R and Rfree values of 26 and 28%, respectively, with good electron density. Structural comparison with previously reported homologues and phylogenetic analysis shows H. pylori HINT to be the smallest among them, and suggests that it branched out separately during the course of evolution. Overall, this structure has contributed to a better understanding of this protein across the animal kingdom. PMID:26750483

  15. 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

  16. 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

  17. Contact efflorescence as a pathway for crystallization of atmospherically relevant particles.

    PubMed

    Davis, Ryan D; Lance, Sara; Gordon, Joshua A; Ushijima, Shuichi B; Tolbert, Margaret A

    2015-12-29

    Inadequate knowledge of the phase state of atmospheric particles represents a source of uncertainty in global climate and air quality models. Hygroscopic aqueous inorganic particles are often assumed to remain liquid throughout their atmospheric lifetime or only (re)crystallize at low relative humidity (RH) due to the kinetic limitations of efflorescence (salt crystal nucleation and growth from an aqueous solution). Here we present experimental observations of a previously unexplored heterogeneous nucleation pathway that we have termed "contact efflorescence," which describes efflorescence initiated by an externally located solid particle coming into contact with the surface of a metastable aqueous microdroplet. This study demonstrates that upon a single collision, contact efflorescence is a pathway for crystallization of atmospherically relevant aqueous particles at high ambient RH (?80%). Soluble inorganic crystalline particles were used as contact nuclei to induce efflorescence of aqueous ammonium sulfate [(NH4)2SO4], sodium chloride (NaCl), and ammonium nitrate (NH4NO3), with efflorescence being observed in several cases close to their deliquescence RH values (80%, 75%, and 62%, respectively). To our knowledge, these observations represent the highest reported efflorescence RH values for microdroplets of these salts. These results are particularly important for considering the phase state of NH4NO3, where the contact efflorescence RH (?20-60%) is in stark contrast to the observation that NH4NO3 microdroplets do not homogeneously effloresce, even when exposed to extremely arid conditions (<1% RH). Considering the occurrence of particle collisions in the atmosphere (i.e., coagulation), these observations of contact efflorescence challenge many assumptions made about the phase state of inorganic aerosol. PMID:26668396

  18. Can antimonide-based nanowires form wurtzite crystal structure?

    NASA Astrophysics Data System (ADS)

    Gorji Ghalamestani, Sepideh; Lehmann, Sebastian; Dick, Kimberly A.

    2016-01-01

    The epitaxial growth of antimonide-based nanowires has become an attractive subject due to their interesting properties required for various applications such as long-wavelength IR detectors. The studies conducted on antimonide-based nanowires indicate that they preferentially crystallize in the zinc blende (ZB) crystal structure rather than wurtzite (WZ), which is common in other III-V nanowire materials. Also, with the addition of small amounts of antimony to arsenide- and phosphide-based nanowires grown under conditions otherwise leading to WZ structure, the crystal structure of the resulting ternary nanowires favors the ZB phase. Therefore, the formation of antimonide-based nanowires with the WZ phase presents fundamental challenges and is yet to be explored, but is particularly interesting for understanding the nanowire crystal phase in general. In this study, we examine the formation of Au-seeded InSb and GaSb nanowires under various growth conditions using metalorganic vapor phase epitaxy. We address the possibility of forming other phases than ZB such as WZ and 4H in binary nanowires and demonstrate the controlled formation of WZ InSb nanowires. We further discuss the fundamental aspects of WZ growth in Au-seeded antimonide-based nanowires.The epitaxial growth of antimonide-based nanowires has become an attractive subject due to their interesting properties required for various applications such as long-wavelength IR detectors. The studies conducted on antimonide-based nanowires indicate that they preferentially crystallize in the zinc blende (ZB) crystal structure rather than wurtzite (WZ), which is common in other III-V nanowire materials. Also, with the addition of small amounts of antimony to arsenide- and phosphide-based nanowires grown under conditions otherwise leading to WZ structure, the crystal structure of the resulting ternary nanowires favors the ZB phase. Therefore, the formation of antimonide-based nanowires with the WZ phase presents fundamental challenges and is yet to be explored, but is particularly interesting for understanding the nanowire crystal phase in general. In this study, we examine the formation of Au-seeded InSb and GaSb nanowires under various growth conditions using metalorganic vapor phase epitaxy. We address the possibility of forming other phases than ZB such as WZ and 4H in binary nanowires and demonstrate the controlled formation of WZ InSb nanowires. We further discuss the fundamental aspects of WZ growth in Au-seeded antimonide-based nanowires. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr07362f

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

    SciTech Connect

    Uchiyama, Hiroaki Nakanishi, Shunsuke; Kozuka, Hiromitsu

    2014-09-15

    Crystalline SnO particles were obtained from Sn{sub 6}O{sub 4}(OH){sub 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. - Graphical abstract: Nanostructured SnO particles were obtained from Sn{sub 6}O{sub 4}(OH){sub 4} by the hydrothermal treatment in gelatin solutions. - Highlights: • SnO particles were prepared from Sn{sub 6}O{sub 4}(OH){sub 4} by the hydrothermal treatment. • The adsorption of gelatin suppressed the growth of SnO crystals. • The shape of SnO particles depends on the amount of gelatin. • Blocks, disks, stacked plates and unshaped aggregates were obtained.

  20. 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.

  1. Volume reflection and volume capture of ultrarelativistic particles in bent single crystals

    NASA Astrophysics Data System (ADS)

    Bellucci, S.; Chesnokov, Yu. A.; Maisheev, V. A.; Yazynin, I. A.

    2015-11-01

    The paper is devoted to the study of volume reflection and volume capture of high energy particles moving in planar fields of bent single crystals. The influence of volume capture on the process of volume reflection was considered analytically. Relations describing various distributions of particles involved in the process, the probability of volume capture and the behavior of channeling and dechanneling fractions of a beam were obtained. Results of the study will be useful in the realization of multicrystal devices for collimation and extraction of beams on modern and future accelerators.

  2. Crystal structure of fully oxidized human thioredoxin.

    PubMed

    Hwang, Jungwon; Nguyen, Loi T; Jeon, Young Ho; Lee, Chan Yong; Kim, Myung Hee

    2015-11-13

    In addition to the active cysteines located at positions 32 and 35 in humans, mammalian cytosolic thioredoxin (TRX) possesses additional conserved cysteine residues at positions 62, 69, and 73. These non-canonical cysteine residues, that are distinct from prokaryotic TRX and also not found in mammalian mitochondrial TRX, have been implicated in biological functions regulating signal transduction pathways via their post-translational modifications. Here, we describe for the first time the structure of a fully oxidized TRX. The structure shows a non-active Cys62-Cys69 disulfide bond in addition to the active Cys32-Cys35 disulfide. The non-active disulfide switches the ?3-helix of TRX, composed of residues Cys62 to Glu70, to a bulging loop and dramatically changes the environment of the TRX residues involved in the interaction with its reductase and other cellular substrates. This structural modification may have implications for a number of potential functions of TRX including the regulation of redox-dependent signaling pathways. PMID:26453009

  3. Hierarchical self-assembly of telechelic star polymers: from soft patchy particles to gels and diamond crystals

    NASA Astrophysics Data System (ADS)

    Capone, Barbara; Coluzza, Ivan; Blaak, Ronald; Lo Verso, Federica; Likos, Christos N.

    2013-09-01

    The design of self-assembling materials in the nanometer scale focuses on the fabrication of a class of organic and inorganic subcomponents that can be reliably produced on a large scale and tailored according to their vast applications for, e.g. electronics, therapeutic vectors and diagnostic imaging agent carriers, or photonics. In a recent publication (Capone et al 2012 Phys. Rev. Lett. 109 238301), diblock copolymer stars have been shown to be a novel system, which is able to hierarchically self-assemble first into soft patchy particles and thereafter into more complex structures, such as the diamond and cubic crystal. The self-aggregating single star patchy behavior is preserved from extremely low up to high densities. Its main control parameters are related to the architecture of the building blocks, which are the number of arms (functionality) and the fraction of attractive end-monomers. By employing a variety of computational and theoretical tools, ranging from the microscopic to the mesoscopic, coarse-grained level in a systematic fashion, we investigate the crossover between the formation of microstructure versus macroscopic phase separation, as well as the formation of gels and networks in these systems. We finally show that telechelic star polymers can be used as building blocks for the fabrication of open crystal structures, such as the diamond or the simple-cubic lattice, taking advantage of the strong correlation between single-particle patchiness and lattice coordination at finite densities.

  4. Multiplexed DNA detection using spectrally encoded porous SiO2 photonic crystal particles

    PubMed Central

    Meade, Shawn O.; Chen, Michelle Y.

    2009-01-01

    A particle-based multiplexed DNA assay based on encoded porous SiO2 photonic crystal disks is demonstrated. A spectral barcode is generated by electrochemical etch of a single-crystal silicon wafer using a programmed current-time waveform. A lithographic procedure is used to isolate cylindrical microparticles 25 microns in diameter and 10 microns thick, which are then oxidized, modified with a silane linker, and conjugated to various amino functionalized oligonucleotide probes via cyanuric chloride. It is shown that the particles can be decoded based on their reflectivity spectra, and that a multiple analyte assay can be performed in a single sample with a modified fluorescence microscope. The homogeneity of the reflectivity and fluorescence spectra, both within and across the microparticles is also reported. PMID:19271746

  5. 3D Structural Fluctuation of IgG1 Antibody Revealed by Individual Particle Electron Tomography

    PubMed Central

    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 (~13?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

  6. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    SciTech Connect

    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, 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.

  7. 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

  8. Structure of RCC1 chromatin factor bound to the nucleosome core particle

    SciTech Connect

    Makde, Ravindra D.; England, Joseph R.; Yennawar, Hemant P.; Tan, Song

    2010-11-11

    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. Although RCC1 has been shown to bind directly with the nucleosome, the molecular details of this interaction were not known. Here we determine the crystal structure of a complex of Drosophila RCC1 and the nucleosome core particle at 2.9 {angstrom} resolution, providing an 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 the nucleosomes forms a 145-base-pair nucleosome core particle, not the expected canonical 147-base-pair particle.

  9. Unusual Features of Crystal Structures of Some Simple Copper Compounds

    ERIC Educational Resources Information Center

    Douglas, Bodie

    2009-01-01

    Some simple copper compounds have unusual crystal structures. Cu[subscript 3]N is cubic with N atoms at centers of octahedra formed by 6 Cu atoms. Cu[subscript 2]O (cuprite) is also cubic; O atoms are in tetrahedra formed by 4 Cu atoms. These tetrahedra are linked by sharing vertices forming two independent networks without linkages between them.

  10. Discrete structures in continuum descriptions of defective crystals.

    PubMed

    Parry, G P

    2016-04-28

    I discuss various mathematical constructions that combine together to provide a natural setting for discrete and continuum geometric models of defective crystals. In particular, I provide a quite general list of 'plastic strain variables', which quantifies inelastic behaviour, and exhibit rigorous connections between discrete and continuous mathematical structures associated with crystalline materials that have a correspondingly general constitutive specification. PMID:27002070

  11. Unusual Features of Crystal Structures of Some Simple Copper Compounds

    ERIC Educational Resources Information Center

    Douglas, Bodie

    2009-01-01

    Some simple copper compounds have unusual crystal structures. Cu[subscript 3]N is cubic with N atoms at centers of octahedra formed by 6 Cu atoms. Cu[subscript 2]O (cuprite) is also cubic; O atoms are in tetrahedra formed by 4 Cu atoms. These tetrahedra are linked by sharing vertices forming two independent networks without linkages between them.…

  12. 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.

  13. 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

  14. Domain structures in nematic liquid crystals on a polycarbonate surface.

    PubMed

    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

  15. 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.

    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.

  16. Crystal structures at high pressures and temperatures

    NASA Astrophysics Data System (ADS)

    Caldwell, Wendel Alexander

    2000-10-01

    The diamond anvil cell (DAC) is a unique instrument that can generate pressures equivalent to those inside planetary interiors (pressures on the order of 1 million atmospheres) under sustained conditions. When combined with a bright source of collimated x-rays, the DAC can be used to probe the structure of materials in-situ at ultra-high pressures. An understanding of the high-pressure structure of materials is important in determining what types of processes may take place in the Earth at great depths. Motivated by previous studies showing that xenon becomes metallic at pressures above ˜1 megabar (100 GPa), we examined the stable structures and reactivity of xenon at pressures approaching that of the core-mantle boundary in the Earth. Our findings indicate the transformation of xenon from face-centered cubic (fcc) to hexagonal close-packed (hcp) structures is kinetically hindered at room temperature, with the equilibrium fcc--hcp phase boundary at 21 (+/-3) gigapascals, a pressure lower than was previously thought. Additionally, we find no tendency on the part of xenon to form a metal alloy with iron or platinum to at least 100 to 150 gigapascals, making it unlikely that the Earth's core serves as a reservoir for primordial xenon. Measurements of the compressibility of natural (Mg.75,Fe .25)2SiO4 gamma-spinel at pressures of the Earth's transition zone yield a pressure derivative of the bulk modulus K0 ' = 6.3 (+/-0.3). As gamma-spinel is considered to be a dominant mineral phase of the transition-zone of the Earth's mantle (400--670 km depth), the relatively high value of K0' for gamma-spinel may help explain the rapid increase with depth of seismic velocities through the transition zone. The thermodynamics, mechanisms and kinetics of pressure-induced amorphization are not well understood. We report here new studies indicating little or no entropy difference between the crystalline and glassy states of Ca(OH) 2 (portlandite). Additional work on the pressure-induced amorphization of AlPO4 (berlinite) shows that this material, which is a close analog to quartz, shows a rich behavior that is dependent upon the pressure, temperature, stress-state and time-scales of the experimental conditions.

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

    NASA Astrophysics Data System (ADS)

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

    2001-11-01

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

  18. Effect of Gravity Level on the Particle Shape and Size During Zeolite Crystal Growth

    NASA Technical Reports Server (NTRS)

    Song, Hong-Wei; Ilebusi, Olusegun J.; Sacco, Albert, Jr.

    2003-01-01

    A microscopic diffusion model is developed to represent solute transport in the boundary layer of a growing zeolite crystal. This model is used to describe the effect of gravity on particle shape and solute distribution. Particle dynamics and crystal growth kinetics serve as the boundary conditions of flow and convection-diffusion equations. A statistical rate theory is used to obtain the rate of solute transport across the growing interface, which is expressed in terms of concentration and velocity of solute species. Microgravity can significantly decrease the solute velocity across the growing interface compared to its earth-based counterpart. The extent of this reduction highly depends on solute diffusion constant in solution. Under gravity, the flow towards the crystal enhances solute transport rate across the growing interface while the flow away from crystals reduces this rate, suggesting a non-uniform growth rate and thus an elliptic final shape. However, microgravity can significantly reduce the influence of flow and obtain a final product with perfect spherical shape. The model predictions compare favorably with the data of space experiment of zeolites grown in space.

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

    SciTech Connect

    Rao Popuri, Srinivasa; Artemenko, Alla; Labrugere, Christine; Miclau, Marinela; Villesuzanne, Antoine; Pollet, Michal

    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.

  20. Crystal structure of new AsS2 compound

    NASA Astrophysics Data System (ADS)

    Bolotina, N. B.; Brazhkin, V. V.; Dyuzheva, T. I.; Lityagina, L. M.; Kulikova, L. F.; Nikolaev, N. A.; Verin, I. A.

    2013-01-01

    AsS2 single crystals have been obtained for the first time from an As2S3 melt at pressures above 6 GPa and temperatures above 800 K in the As2S3 ? AsS + AsS2 reaction. The monoclinic structure of the new high-pressure phase is solved by X-ray diffraction analysis and compared to the structure of high-pressure AsS phase, which was studied previously.

  1. Crystal growth, structure analysis and characterisation of 2 - (1, 3 - dioxoisoindolin - 2 - yl) acetic acid single crystal

    SciTech Connect

    Sankari, R. Siva; Perumal, Rajesh Narayana

    2014-04-24

    Single crystal of dielectric material 2 - (1, 3 - dioxoisoindolin - 2 - yl) acetic acid has been grown by slow evaporation solution growth method. The grown crystal was harvested in 25 days. The crystal structure was analyzed by Single crystal X - ray diffraction. UV-vis-NIR analysis was performed to examine the optical property of the grown crystal. The thermal property of the grown crystal was studied by thermogravimetric analysis (TGA) and differential thermal analysis (DTA). The dielectric measurements were carried out and the dielectric constant was calculated and plotted at all frequencies.

  2. Solvent-controlled assembly of crystal structures: From centrosymmetric structure to noncentrosymmetric structure

    NASA Astrophysics Data System (ADS)

    Zhang, Le; Dang, Lilong; Luo, Feng; Feng, Xuefeng

    2016-02-01

    Reported here are two isomeric organic crystals and two HgI2-based coordination compounds by solvo(hydro)thermal method: [(TPTA)·H2O]n (1, Cc), [(TPTA)·H2O]n (2, Pbca), [Hg1.5I3(TPTA)0.5(CH3CN)·(H2O)0.5]n (3, P21) and [HgI2(TPTA)·H2O]n (4, P21/c) (TPTA = N,N‧,N″-tris(3-pyridyl)trimesic amide). Single crystal X-ray diffraction show that they afford noncentrosymmetric and centrosymmetric structures, respectively. Note that this kind of formations can be precisely controlled by changing the reaction solvent, thus indicating a facile method towards generating noncentrosymmetric structure.

  3. 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.

  4. Structural evolution in the crystallization of rapid cooling silver melt

    SciTech Connect

    Tian, Z.A.; Dong, K.J.; Yu, A.B.

    2015-03-15

    The structural evolution in a rapid cooling process of silver melt has been investigated at different scales by adopting several analysis methods. The results testify Ostwald’s rule of stages and Frank conjecture upon icosahedron with many specific details. In particular, the cluster-scale analysis by a recent developed method called LSCA (the Largest Standard Cluster Analysis) clarified the complex structural evolution occurred in crystallization: different kinds of local clusters (such as ico-like (ico is the abbreviation of icosahedron), ico-bcc like (bcc, body-centred cubic), bcc, bcc-like structures) in turn have their maximal numbers as temperature decreases. And in a rather wide temperature range the icosahedral short-range order (ISRO) demonstrates a saturated stage (where the amount of ico-like structures keeps stable) that breeds metastable bcc clusters. As the precursor of crystallization, after reaching the maximal number bcc clusters finally decrease, resulting in the final solid being a mixture mainly composed of fcc/hcp (face-centred cubic and hexagonal-closed packed) clusters and to a less degree, bcc clusters. This detailed geometric picture for crystallization of liquid metal is believed to be useful to improve the fundamental understanding of liquid–solid phase transition. - Highlights: • A comprehensive structural analysis is conducted focusing on crystallization. • The involved atoms in our analysis are more than 90% for all samples concerned. • A series of distinct intermediate states are found in crystallization of silver melt. • A novelty icosahedron-saturated state breeds the metastable bcc state.

  5. Self-powdering and nonlinear optical domain structures in ferroelastic beta'-Gd{sub 2}(MoO{sub 4}){sub 3} crystals formed in glass

    SciTech Connect

    Tsukada, Y.; Honma, T.; Komatsu, T.

    2009-08-15

    Ferroelastic beta'-Gd{sub 2}(MoO{sub 4}){sub 3}, (GMO), crystals are formed through the crystallization of 21.25Gd{sub 2}O{sub 3}-63.75MoO{sub 3}-15B{sub 2}O{sub 3} glass (mol%), and two scientific curious phenomena are observed. (1) GMO crystals formed in the crystallization break into small pieces with a triangular prism or pyramid shape having a length of 50-500 {mu}m spontaneously during the crystallizations in the inside of an electric furnace, not during the cooling in air after the crystallization. This phenomenon is called 'self-powdering phenomenon during crystallization' in this paper. (2) Each self-powdered GMO crystal grain shows a periodic domain structure with different refractive indices, and a spatially periodic second harmonic generation (SHG) depending on the domain structure is observed. It is proposed from polarized micro-Raman scattering spectra and the azimuthal dependence of second harmonic intensities that GMO crystals are oriented in each crystal grain and the orientation of (MoO{sub 4}){sup 2-} tetrahedra in GMO crystals changes periodically due to spontaneous strains in ferroelastic GMO crystals. - Graphical abstract: This figure shows the polarized optical photograph at room temperature for a particle (piece) obtained by a heat treatment of the glass at 590 deg. C for 2 h in an electric furnace in air. This particle was obtained through the self-powdering behavior in the crystallization of glass. The periodic domain structure is observed. Ferroelastic beta'-Gd{sub 2}(MoO{sub 4}){sub 3} crystals are formed in the particle, and second harmonic generations are detected, depending on the domain structure.

  6. 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. ); Appella, E.; Clore, G.M.; Gronenborn, A.M. ); Yamada, Masaki ); Edwards, B.F.P. )

    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.

  7. 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 NH?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

  8. 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 α-MgCl(2) crystal lattice. PMID:22052708

  9. Azimuthal structures of produced particles in heavy-ion interactions

    SciTech Connect

    Vokal, S. Orlova, G. I.; Lehocka, S.

    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.

  10. Structural analysis of three-dimenstionl photonic crystals in nature

    NASA Astrophysics Data System (ADS)

    Yoon, Beom-Jin; Park, Jung Ok; Srinivasarao, Mohan

    2012-02-01

    We studied the structural origin of the color and photonic band structure in exoskeletons of Eupholus weevils and dorsal wings of lycaenids butterflies. The internal structures of the insects were systematically investigated using focused ion beam (FIB) milling, and the optical response of the insects was observed by optical microscopy and a microspectrophotometer. A series of sequential SEM images were obtained during the FIB milling process and 3D structures were reconstructed by image processing. The correlation of the structures and the optical responses were studied by theoretical modeling. Diamond-based 3D photonic crystal lattice existed in Eupholus weevils, while gyroid structure was in lycaenids butterflies. The calculated photonic band structures matched the measured optical response. Aluminum oxide and titanium oxide were deposited on the weevils and the butterflies in order to study the effect of refractive index contrast to the photonic band structure and the optical response.

  11. Structural and thermal properties of MnSi single crystal

    NASA Astrophysics Data System (ADS)

    Tite, T.; Shu, G. J.; Chou, F. C.; Chang, Y.-M.

    2010-07-01

    Polarized Raman spectroscopy of MnSi single crystal was carried out to characterize its phonons, crystal structure, and thermal stability. The Raman spectra show correct Raman selection rules and consistence with those of the other transition metal silicide compounds. The MnSi thermal stability and phase transformation is investigated by monitoring the evolution of Raman spectrum as a function of the laser intensity, in which three compositions, MnSi, MnSiO3, and Mn5Si3, can be identified. The involved oxidation reaction is then proposed and verified by performing the thermogravimetric and x-ray diffraction analysis.

  12. Crystal structure of alpha poly-p-xylylene.

    NASA Technical Reports Server (NTRS)

    Kubo, S.; Wunderlich, B.

    1971-01-01

    A crystal structure of alpha poly-p-xylylene is proposed with the help of data of oriented crystals grown during polymerization. The unit cell is monoclinic with the parameters a = 8.57 A, b = 10.62 A, c = 6.54 A (chain axis), and beta = 101.3 deg. Four repeating units per cell lead to a calculated density of 1.185 g/cu cm and a packing density of 0.71. The probable space group is P2 sub 1/m.

  13. Structural, magnetic and optical properties of two concomitant molecular crystals

    NASA Astrophysics Data System (ADS)

    Silva, Manuela Ramos; Milne, Bruce; Coutinho, Joana T.; Pereira, Laura C. J.; Martín-Ramos, Pablo; Pereira da Silva, Pedro S.; Martín-Gil, Jesús

    2016-03-01

    A new 1D complex has been prepared and characterized. X-ray single crystal structure confirms that the Cu(II) ions assemble in alternating chains with Cu … Cu distances of 2.5685(4) and 3.1760(4) Å. The temperature dependence of the magnetic susceptibility reveals an antiferromagnetic interaction between the paddle-wheel copper centers with an exchange of -300 cm-1. The exchange integral was also determined by quantum chemical ab-initio calculations, using polarised and unpolarised basis sets reproducing well the experimental value. The second harmonic generation efficiency of a concomitantly crystallized material was evaluated and was found to be comparable to urea.

  14. Structural transitions in vertically and horizontally coupled parabolic channels of Wigner crystals

    NASA Astrophysics Data System (ADS)

    Galvn-Moya, J. E.; Nelissen, K.; Peeters, F. M.

    2012-11-01

    Structural phase transitions in two vertically or horizontally coupled channels of strongly interacting particles are investigated. The particles are free to move in the x direction but are confined by a parabolic potential in the y direction. They interact with each other through a screened power-law potential (r-ne-r/?). In vertically coupled systems, the channels are stacked above each other in the direction perpendicular to the (x,y) plane, while in horizontally coupled systems both channels are aligned in the confinement direction. Using Monte Carlo (MC) simulations we obtain the ground-state configurations and the structural transitions as a function of the linear particle density and the separation between the channels. At zero temperature, the vertically coupled system exhibits a rich phase diagram with continuous and discontinuous transitions. On the other hand, the horizontally coupled system exhibits only a very limited number of phase transitions due to its symmetry. Further, we calculated the normal modes for the Wigner crystals in both cases. From MC simulations, we found that in the case of vertically coupled systems, the zigzag transition is only possible for low densities. A Ginzburg-Landau theory for the zigzag transition is presented, which predicts correctly the behavior of this transition from which we interpret the structural phase transition of the Wigner crystal through the reduction of the Brillouin zone.

  15. Influence of particle aspect ratio on the midinfrared extinction spectra of wavelength-sized ice crystals.

    PubMed

    Wagner, Robert; Benz, Stefan; Mhler, Ottmar; Saathoff, Harald; Schnaiter, Martin; Leisner, Thomas

    2007-12-20

    We have used the T-matrix method and the discrete dipole approximation to compute the midinfrared extinction cross-sections (4500-800 cm(-1)) of randomly oriented circular ice cylinders for aspect ratios extending up to 10 for oblate and down to 1/6 for prolate particle shapes. Equal-volume sphere diameters ranged from 0.1 to 10 microm for both particle classes. A high degree of particle asphericity provokes a strong distortion of the spectral habitus compared to the extinction spectrum of compactly shaped ice crystals with an aspect ratio around 1. The magnitude and the sign (increase or diminution) of the shape-related changes in both the absorption and the scattering cross-sections crucially depend on the particle size and the values for the real and imaginary part of the complex refractive index. When increasing the particle asphericity for a given equal-volume sphere diameter, the values for the overall extinction cross-sections may change in opposite directions for different parts of the spectrum. We have applied our calculations to the analysis of recent expansion cooling experiments on the formation of cirrus clouds, performed in the large coolable aerosol and cloud chamber AIDA of Forschungszentrum Karlsruhe at a temperature of 210 K. Depending on the nature of the seed particles and the temperature and relative humidity characteristics during the expansion, ice crystals of various shapes and aspect ratios could be produced. For a particular expansion experiment, using Illite mineral dust particles coated with a layer of secondary organic matter as seed aerosol, we have clearly detected the spectral signatures characteristic of strongly aspherical ice crystal habits in the recorded infrared extinction spectra. We demonstrate that the number size distributions and total number concentrations of the ice particles that were generated in this expansion run can only be accurately derived from the recorded infrared spectra when employing aspect ratios as high as 10 in the retrieval approach. Remarkably, the measured spectra could also be accurately fitted when employing an aspect ratio of 1 in the retrieval. The so-deduced ice particle number concentrations, however, exceeded the true values, determined with an optical particle counter, by more than 1 order of magnitude. Thus, the shape-induced spectral changes between the extinction spectra of platelike ice crystals of aspect ratio 10 and compactly shaped particles of aspect ratio 1 can be efficiently balanced by deforming the true number size distribution of the ice cloud. As a result of this severe size/shape ambiguity in the spectral analysis, we consider it indispensable to cross-check the infrared retrieval results of wavelength-sized ice particles with independent reference measurements of either the number size distribution or the particle morphology. PMID:18004822

  16. Can antimonide-based nanowires form wurtzite crystal structure?

    PubMed

    Gorji Ghalamestani, Sepideh; Lehmann, Sebastian; Dick, Kimberly A

    2016-01-28

    The epitaxial growth of antimonide-based nanowires has become an attractive subject due to their interesting properties required for various applications such as long-wavelength IR detectors. The studies conducted on antimonide-based nanowires indicate that they preferentially crystallize in the zinc blende (ZB) crystal structure rather than wurtzite (WZ), which is common in other III-V nanowire materials. Also, with the addition of small amounts of antimony to arsenide- and phosphide-based nanowires grown under conditions otherwise leading to WZ structure, the crystal structure of the resulting ternary nanowires favors the ZB phase. Therefore, the formation of antimonide-based nanowires with the WZ phase presents fundamental challenges and is yet to be explored, but is particularly interesting for understanding the nanowire crystal phase in general. In this study, we examine the formation of Au-seeded InSb and GaSb nanowires under various growth conditions using metalorganic vapor phase epitaxy. We address the possibility of forming other phases than ZB such as WZ and 4H in binary nanowires and demonstrate the controlled formation of WZ InSb nanowires. We further discuss the fundamental aspects of WZ growth in Au-seeded antimonide-based nanowires. PMID:26763161

  17. Crystal structure, physical properties and superconductivity in AxFe2Se2 single crystals

    NASA Astrophysics Data System (ADS)

    Luo, X. G.; Wang, X. F.; Ying, J. J.; Yan, Y. J.; Li, Z. Y.; Zhang, M.; Wang, A. F.; Cheng, P.; Xiang, Z. J.; Ye, G. J.; Liu, R. H.; Chen, X. H.

    2011-05-01

    We studied the correlation among structure, transport properties and superconductivity in different AxFe2Se2 single crystals (A=K, Rb and Cs). Two sets of (00l) reflections are observed in the x-ray single-crystal diffraction patterns, and they arise from the intrinsic inhomogeneous distribution of the intercalated alkali atoms. The occurrence of superconductivity is closely related to the c-axis lattice constant, and the A content is crucial to superconductivity. The hump observed in resistivity seems to be irrelevant to the superconductivity. There exist many deficiencies within the FeSe layers in AxFe2Se2, although their Tc does not change so much. In this sense, superconductivity is robust to the vacancies within the FeSe layers. Very high resistivity in the normal state should be ascribed to such defects in the conducting FeSe layers. AxFe2Se2 (A=K, Rb and Cs) single crystals show the same susceptibility behavior in the normal state, and no anomaly is observed in susceptibility at the hump temperature in resistivity. The clear jump in specific heat for RbxFe2Se2 and KxFe2Se2 single crystals indicates the good bulk superconductivity of these crystals.

  18. Magnetopause structure and the question of particle accessibility

    NASA Technical Reports Server (NTRS)

    Whipple, E. C.; Hill, J. R.; Nichols, J. D.

    1984-01-01

    A simple plane model of the magnetopause is used to address the question of particle accessibility. Particle motion in the current sheet region is analyzed, showing that the concept of gyromotion is useful even when the electric and magnetic fields vary significantly over the gyroradius, as long as the variation is perpendicular to the drift direction. The first adiabatic invariant for particle motion is defined in such a way that it is preserved in regions of large field gradients, provided that the gradients are in a direction primarily perpendicular to the particle drifts. This generalized invariant provides an adiabatically conserved quantity that can be used to characterize particles as they move from a source region through the drift region and into the magnetopause itself, helping to resolve the accessibility question. Some preliminary results are given for the magnetopause structure based on the location of particle guiding points.

  19. Anisole at 100 K: the first crystal structure determination.

    PubMed

    Seidel, Rüdiger W; Goddard, Richard

    2015-08-01

    The simplest alkyl aryl ether, anisole (methoxybenzene), C7H8O, is a feedstock chemical and is widely used in the pharmaceutical industry. The structure of anisole at 100 K, as determined by single-crystal X-ray analysis, is reported. A crystal (m.p. 236 K) suitable for X-ray diffraction was obtained from the melt. The title compound crystallizes in the centrosymmetric space group P2(1)/c with two molecules in the asymmetric unit (Z' = 2). Both crystallographically distinct molecules adopt a virtually flat (Cs-symmetric) conformation. The arrangement of the molecules in the solid state appears to be governed by close packing. No face-to-face π-π stacking of the molecules is observed, but rather edge-to-face interactions result in a herringbone packing motif. PMID:26243411

  20. Structure and melting behavior of classical bilayer crystals of dipoles

    SciTech Connect

    Lu Xin; Wu Changqin; Micheli, Andrea; Pupillo, Guido

    2008-07-01

    We study the structure and melting of a classical bilayer system of dipoles in a setup where the dipoles are oriented perpendicular to the planes of the layers and the density of dipoles is the same in each layer. Due to the anisotropic character of the dipole-dipole interactions, we find that the ground-state configuration is given by two hexagonal crystals positioned on top of each other, independent of the interlayer spacing and dipolar density. For large interlayer distances these crystals are independent, while in the opposite limit of small interlayer distances the system behaves as a two-dimensional crystal of paired dipoles. Within the harmonic approximation for the phonon excitations, the melting temperature of these crystalline configurations displays a nonmonotonic dependence on the interlayer distance, which is associated with a re-entrant melting behavior in the form of solid-liquid-solid-liquid transitions at fixed temperature.

  1. Crystal structure and density of helium to 232 kbar

    NASA Technical Reports Server (NTRS)

    Mao, H. K.; Wu, Y.; Jephcoat, A. P.; Hemley, R. J.; Bell, P. M.; Bassett, W. A.

    1988-01-01

    The properties of helium and hydrogen at high pressure are topics of great interest to the understanding of planetary interiors. These materials constitute 95 percent of the entire solar system. A technique was presented for the measurement of X-ray diffraction from single-crystals of low-Z condenses gases in a diamond-anvil cell at high pressure. The first such single-crystal X-ray diffraction measurements on solid hydrogen to 26.5 GPa were presented. The application of this technique to the problem of the crystal structure, equation of state, and phase diagram of solid helium is reported. Crucial for X-ray diffraction studies of these materials is the use of a synchrotron radiation source which provides high brillance, narrow collimation of the incident and diffracted X-ray beams to reduce the background noise, and energy-dispersive diffraction techniques with polychromatic (white) radiation, which provides high detection efficiency.

  2. Crystal structure and mechanistic investigation of the twister ribozyme.

    PubMed

    Liu, Yijin; Wilson, Timothy J; McPhee, Scott A; Lilley, David M J

    2014-09-01

    We present a crystal structure at 2.3- resolution of the recently described nucleolytic ribozyme twister. The RNA adopts a previously uncharacterized compact fold based on a double-pseudoknot structure, with the active site at its center. Eight highly conserved nucleobases stabilize the core of the ribozyme through the formation of one Watson-Crick and three noncanonical base pairs, and the highly conserved adenine 3' of the scissile phosphate is bound in the major groove of an adjacent pseudoknot. A strongly conserved guanine nucleobase directs its Watson-Crick edge toward the scissile phosphate in the crystal structure, and mechanistic evidence supports a role for this guanine as either a general base or acid in a concerted, general acid-base-catalyzed cleavage reaction. PMID:25038788

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

    PubMed

    Shonberg, Jeremy; Kling, Ralf C; Gmeiner, Peter; Lber, 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

  4. Myelin structures formed by thermotropic smectic liquid crystals

    NASA Astrophysics Data System (ADS)

    Peddireddy, Karthik Reddy; Kumar, Pramoda; Thutupalli, Shashi; Herminghaus, Stephan; Bahr, Christian

    2014-03-01

    We report on transient structures, formed by thermotropic smectic-A liquid crystals, resembling the myelin figures of lyotropic lamellar liquid crystals. The thermotropic myelin structures form during the solubilization of a smectic-A droplet in an aqueous phase containing a cationic surfactant at concentrations above the critical micelle concentration. Similar to the lyotropic myelin figures, the thermotropic myelins appear in an optical microscope as flexible tube-like structures growing at the smectic/aqueous interface. Polarizing microscopy and confocal fluorescence microscopy show that the smectic layers are parallel to the tube surface and form a cylindrically bent arrangement around a central line defect in the tube. We study the growth behavior of this new type of myelins and discuss similarities and differences to the classical lyotropic myelin figures.

  5. Crystal structure of a symbiosis-related lectin from octocoral.

    PubMed

    Kita, Akiko; Jimbo, Mitsuru; Sakai, Ryuichi; Morimoto, Yukio; Miki, Kunio

    2015-09-01

    D-Galactose-binding lectin from the octocoral, Sinularia lochmodes (SLL-2), distributes densely on the cell surface of microalgae, Symbiodinium sp., an endosymbiotic dinoflagellate of the coral, and is also shown to be a chemical cue that transforms dinoflagellate into a non-motile (coccoid) symbiotic state. SLL-2 binds with high affinity to the Forssman antigen (N-acetylgalactosamine(GalNAc)?1-3GalNAc?1-3Gal?1-4Gal?1-4Glc-ceramide), and the presence of Forssman antigen-like sugar on the surface of Symbiodinium CS-156 cells was previously confirmed. Here we report the crystal structures of SLL-2 and its GalNAc complex as the first crystal structures of a lectin involved in the symbiosis between coral and dinoflagellate. N-Linked sugar chains and a galactose derivative binding site common to H-type lectins were observed in each monomer of the hexameric SLL-2 crystal structure. In addition, unique sugar-binding site-like regions were identified at the top and bottom of the hexameric SLL-2 structure. These structural features suggest a possible binding mode between SLL-2 and Forssman antigen-like pentasaccharide. PMID:26022515

  6. Structural features of ?2 adrenergic receptor: crystal structures and beyond.

    PubMed

    Bang, Injin; Choi, Hee-Jung

    2015-01-01

    The beta2-adrenergic receptor (?2AR) family, which is the largest family of cell surface receptors in humans. Extra attention has been focused on the human GPCRs because they have been studied as important protein targets for pharmaceutical drug development. In fact, approximately 40% of marketed drugs directly work on GPCRs. GPCRs respond to various extracellular stimuli, such as sensory signals, neurotransmitters, chemokines, and hormones, to induce structural changes at the cytoplasmic surface, activating downstream signaling pathways, primarily through interactions with heterotrimeric G proteins or through G-protein independent pathways, such as arrestin. Most GPCRs, except for rhodhopsin, which contains covalently linked 11 cis-retinal, bind to diffusible ligands, having various conformational states between inactive and active structures. The first human GPCR structure was determined using an inverse agonist bound ?2AR in 2007 and since then, more than 20 distinct GPCR structures have been solved. However, most GPCR structures were solved as inactive forms, and an agonist bound fully active structure is still hard to obtain. In a structural point of view, ?2AR is relatively well studied since its fully active structure as a complex with G protein as well as several inactive structures are available. The structural comparison of inactive and active states gives an important clue in understanding the activation mechanism of ?2AR. In this review, structural features of inactive and active states of ?2AR, the interaction of ?2AR with heterotrimeric G protein, and the comparison with ?1AR will be discussed. PMID:25537861

  7. New 2-methylimidazole-dicarboxylic acid molecular crystals: crystal structure and proton conductivity

    NASA Astrophysics Data System (ADS)

    ?awniczak, P.; Pogorzelec-Glaser, K.; Pawlaczyk, Cz; Pietraszko, A.; Szcze?niak, L.

    2009-08-01

    Three new proton conducting molecular crystals, 2-methylimidazole glutarate, 2-methylimidazole suberate and 2-methylimidazole azelate, were obtained and their structure was determined by the x-ray diffraction method. The structure of the crystals was found to be of layer-type. A hydrogen bond network between the heterocycle, glutaric acid and water molecules was apparent in a single layer of 2-methylimidazole glutarate, whereas chains consisting of two heterocyclic molecules linked with hydrogen bonds with dicarboxylic acid were distinguished in a single layer of 2-methylimidazole suberate and azelate crystals. Thermal stability of the crystals was characterized by differential scanning calorimetry and the electrical conductivity was studied by the impedance spectroscopy method. The maximum conductivity of 2-methylimidazole glutarate pellets amounts to 3.3 10-2 S m-1 at 325 K, in the case of 2-methylimidazole suberate pellets the maximum conductivity is 2.4 10-4 S m-1 at 348 K and for 2-methylimidazole azelate pellets the maximum conductivity reaches 6.9 10-4 S m-1 at 353 K.

  8. In-situ observations of aerosol particles remaining from evaporated cirrus crystals: Comparing clean and polluted air masses

    NASA Astrophysics Data System (ADS)

    Seifert, M.; Strm, J.; Krejci, R.; Minikin, A.; Petzold, A.; Gayet, J.-F.; Schumann, U.; Ovarlez, J.

    2003-07-01

    In-situ observations of aerosol particles contained in cirrus crystals are presented and compared to interstitial aerosol size distributions (non-activated particles in between the cirrus crystals). The observations were conducted in cirrus clouds in the Southern and Northern Hemisphere mid-latitudes during the INCA project. The first campaign in March and April 2000 was performed from Punta Arenas, Chile (54S) in pristine air. The second campaign in September and October 2000 was performed from Prestwick, Scotland (53N) in the vicinity of the North Atlantic flight corridor. Size distribution measurements of crystal residuals (particles remaining after evaporation of the crystals) show that small aerosol particles (Dp< 0.1 mm) dominate the number density of residuals. The crystal residual size distributions were significantly different in the two campaigns. On average the residual size distributions were shifted towards larger sizes in the Southern Hemisphere. For a given integral residual number density, the calculated particle volume was on average three times larger in the Southern Hemisphere. This may be of significance to the vertical redistribution of aerosol mass by clouds in the tropopause region. In both campaigns the mean residual size increased slightly with increasing crystal number density. The form of the residual size distribution did not depend on temperature as one might have expected considering different modes of nucleation. The observations of ambient aerosol particles were consistent with the expected higher pollution level in the Northern Hemisphere. The fraction of residual particles only contributes to approximately a percent or less of the total number of particles, which is the sum of the residual and interstitial particles. Excellent agreement between the CVI and FSSP-300 probes was found supporting the assumption that each crystal is associated with only one residual particle.

  9. Propagation through complex structured liquid crystal optical fibers

    NASA Astrophysics Data System (ADS)

    Ghasemi, Masih; Choudhury, Pankaj K.

    2014-01-01

    Wave propagation in optical mediums greatly depends on the materials of which the guides are composed. Among the other forms of optical mediums, liquid crystals are both inhomogeneous and optically anisotropic in nature, and exhibit strong electro-optic behavior, which allows alternation in their optical properties under the influence of external electrical fields. These features make optical fibers containing liquid crystals greatly useful for fabricating many optical devices for practical applications. As such, the analytical investigation of wave propagation through liquid crystal optical fibers, particularly a three-layer fiber with radially anisotropic liquid crystal material in the outermost clad section, remains interesting. The power confinement in the liquid crystal section of such fibers can be enhanced for these to be efficiently used in optical coupling and/or sensing applications. Furthermore, a control over the dispersion characteristics, and, hence, the confinement of power, in such fibers may be imposed by making the guide even more complex in the form of introducing a conducting sheath helix structure at the core-inner clad interface.

  10. 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, β=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.

  11. Exceptional groups and elementary-particle structures

    SciTech Connect

    Biedenharn, L.C.; Truini, P.

    1981-09-01

    A new finite-dimensional quantum mechanical space is constructed over the complex octonionic plane using the recently developed algebraic techniques of Jordan pairs and inner ideals. The automorphism group of this structure is E/sub 6/ x U(1), realized on precisely two E/sub 6/ irreps which is abstracted as a (topless) model for grand unification.

  12. Exceptional groups and elementary particle structures

    NASA Astrophysics Data System (ADS)

    Biedenharn, L. C.; Truini, P.

    1982-08-01

    We construct a new finite-dimensional quantum-mechanical space over the complex octonionic plane using the recently-developed algebraic techniques of Jordan pairs and inner ideals. The automorphism group of this structure is E6 × U(1), realized on precisely two irreducible representations (27) and (27 ∗) of E6 which we abstract as a (topless) model for grand unification.

  13. Fine structure of auroral particle acceleration

    SciTech Connect

    Lynch, K.A.

    1992-01-01

    A mass-analyzing capped hemispherical electrostatic analyzer was developed for the purpose of resolving the mass, energy, and pitch angle distributions of auroral ions. The instrument, the B-field Hemispherical Electrostatic Energy and Pitch Angle Spectrometer (BEEPS), is an extension of the HEEPS instrument, which uses a hemispherical analyzer and microchannel plates to measure the angular and energy distribution of ions. BEEPS uses a toroidal magnetic field constructed from rare-earth permanent magnets to separate ion measurements into two groups, protons and heavier ions. BEEPS was flown in February, 1991, from Poker Flat, Alaska, on the TOPAZ3 sounding rocket. This sounding rocket mission carried a full array of particle and field instrumentation to an altitude of over 1000 km. Electron data from the flight are presented and discussed in detail, and are shown in light of both ion and wave data taken during the same flight. Correspondences between the various data sets are presented. Particular note is made of the observation that ion heating seems to correspond with a field-aligned plateau in the electron distribution function below the peak electron energy. The growth rate of the n = -1 anomalous Doppler resonance of medium energy electrons with lower hybrid waves is discussed, and proposed as a mechanism for converting energy from the auroral electrons, the driver of the auroral activity, to the ion heating events.

  14. Crystal structure of inactive form of Rab3B

    SciTech Connect

    Zhang, Wei; Shen, Yang; Jiao, Ronghong; Liu, Yanli; Deng, Lingfu; Qi, Chao

    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.

  15. The crystal structure of GROEL at 2.8 {angstrom}.

    SciTech Connect

    Braig, K.; Otwinowski, Z.; Hegde, R.; Boisvert, D.; Joachimiak, A.; Horwich, A. L.; Sigler, P. B.; Center for Mechanistic Biology and Biotechnology; Yale Univ. School of Medicine; Yale Univ. School of Medicine

    1995-01-01

    The crystal structure of Escherichia coli GroEL shows a porous cylinder of 14 subunits made of two nearly 7-fold rotationally symmetrical rings stacked back-to-back with dyad symmetry. The subunits consist of three domains: a large equatorial domain that forms the foundation of the assembly at its waist and holds the rings together; a large loosely structured apical domain that forms the ends of the cylinder; and a small slender intermediate domain that connects the two, creating side windows. The three-dimensional structure places most of the mutationally defined functional sites on the channel walls and its outward invaginations, and at the ends of the cylinder.

  16. 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.

  17. The Rapid Crystallization Strategy for Structure-Based Inhibitor Design

    NASA Astrophysics Data System (ADS)

    Bergfors, Terese

    RAPID (Rapid Approaches to Pathogen Inhibitor Discovery) is an integrated center for structural biology, computational chemistry, and medicinal chemistry at Uppsala University, Sweden. The main target of the structural biology section is Mycobacterium tuberculosis. Key concepts in the crystallization strategy include minimal screening and buffer optimization. Examples are presented showing how these concepts have been successful in RAPID projects. Three screening methods are used: vapor-diffusion, micro-batch, and microfluidics. Our experiences may be relevant for other small, academic laboratories involved in structure-based inhibitor design.

  18. Structural engineering of three-dimensional phononic crystals

    NASA Astrophysics Data System (ADS)

    Delpero, Tommaso; Schoenwald, Stefan; Zemp, Armin; Bergamini, Andrea

    2016-02-01

    Artificially-structured materials are attracting the research interest of a growing community of scientists for the possibility to develop novel materials with advantageous properties that arise from the ability to tailor the propagation of elastic waves, and thus energy, through them. In this work, we propose a three-dimensional phononic crystal whose unit cell has been engineered to obtain a strong wave-attenuation band in the middle of the acoustic frequency range. The combination of its acoustic properties with the dimensions of the unit cell and its static mechanical properties makes it an interesting material for possibly several applications in civil and mechanical engineering, for instance as the core of an acoustically insulating sandwich panel. A sample of this crystal has been manufactured and experimentally tested with respect to its acoustic transmissibility. The performance of the phononic crystal core is remarkable both in terms of amplitude reduction in the transmissibility and width of the attenuation band. A parametric study has been finally conducted on selected geometrical parameters of the unit cell and on their effect on the macroscopic properties of the crystal. This work represents an application-oriented example of how the macroscopic properties of an artificially-structured material can be designed, according to specific needs, by a conventional engineering of its unit cell.

  19. Single-particle electron microscopy in the study of membrane protein structure.

    PubMed

    De Zorzi, Rita; Mi, Wei; Liao, Maofu; Walz, Thomas

    2016-02-01

    Single-particle electron microscopy (EM) provides the great advantage that protein structure can be studied without the need to grow crystals. However, due to technical limitations, this approach played only a minor role in the study of membrane protein structure. This situation has recently changed dramatically with the introduction of direct electron detection device cameras, which allow images of unprecedented quality to be recorded, also making software algorithms, such as three-dimensional classification and structure refinement, much more powerful. The enhanced potential of single-particle EM was impressively demonstrated by delivering the first long-sought atomic model of a member of the biomedically important transient receptor potential channel family. Structures of several more membrane proteins followed in short order. This review recounts the history of single-particle EM in the study of membrane proteins, describes the technical advances that now allow this approach to generate atomic models of membrane proteins and provides a brief overview of some of the membrane protein structures that have been studied by single-particle EM to date. PMID:26470917

  20. Crystal structure optimisation using an auxiliary equation of state.

    PubMed

    Jackson, Adam J; Skelton, Jonathan M; Hendon, Christopher H; Butler, Keith T; Walsh, Aron

    2015-11-14

    Standard procedures for local crystal-structure optimisation involve numerous energy and force calculations. It is common to calculate an energy-volume curve, fitting an equation of state around the equilibrium cell volume. This is a computationally intensive process, in particular, for low-symmetry crystal structures where each isochoric optimisation involves energy minimisation over many degrees of freedom. Such procedures can be prohibitive for non-local exchange-correlation functionals or other "beyond" density functional theory electronic structure techniques, particularly where analytical gradients are not available. We present a simple approach for efficient optimisation of crystal structures based on a known equation of state. The equilibrium volume can be predicted from one single-point calculation and refined with successive calculations if required. The approach is validated for PbS, PbTe, ZnS, and ZnTe using nine density functionals and applied to the quaternary semiconductor Cu2ZnSnS4 and the magnetic metal-organic framework HKUST-1. PMID:26567640

  1. Structural evolution in the crystallization of rapid cooling silver melt

    NASA Astrophysics Data System (ADS)

    Tian, Z. A.; Dong, K. J.; Yu, A. B.

    2015-03-01

    The structural evolution in a rapid cooling process of silver melt has been investigated at different scales by adopting several analysis methods. The results testify Ostwald's rule of stages and Frank conjecture upon icosahedron with many specific details. In particular, the cluster-scale analysis by a recent developed method called LSCA (the Largest Standard Cluster Analysis) clarified the complex structural evolution occurred in crystallization: different kinds of local clusters (such as ico-like (ico is the abbreviation of icosahedron), ico-bcc like (bcc, body-centred cubic), bcc, bcc-like structures) in turn have their maximal numbers as temperature decreases. And in a rather wide temperature range the icosahedral short-range order (ISRO) demonstrates a saturated stage (where the amount of ico-like structures keeps stable) that breeds metastable bcc clusters. As the precursor of crystallization, after reaching the maximal number bcc clusters finally decrease, resulting in the final solid being a mixture mainly composed of fcc/hcp (face-centred cubic and hexagonal-closed packed) clusters and to a less degree, bcc clusters. This detailed geometric picture for crystallization of liquid metal is believed to be useful to improve the fundamental understanding of liquid-solid phase transition.

  2. Crystal structure optimisation using an auxiliary equation of state

    NASA Astrophysics Data System (ADS)

    Jackson, Adam J.; Skelton, Jonathan M.; Hendon, Christopher H.; Butler, Keith T.; Walsh, Aron

    2015-11-01

    Standard procedures for local crystal-structure optimisation involve numerous energy and force calculations. It is common to calculate an energy-volume curve, fitting an equation of state around the equilibrium cell volume. This is a computationally intensive process, in particular, for low-symmetry crystal structures where each isochoric optimisation involves energy minimisation over many degrees of freedom. Such procedures can be prohibitive for non-local exchange-correlation functionals or other "beyond" density functional theory electronic structure techniques, particularly where analytical gradients are not available. We present a simple approach for efficient optimisation of crystal structures based on a known equation of state. The equilibrium volume can be predicted from one single-point calculation and refined with successive calculations if required. The approach is validated for PbS, PbTe, ZnS, and ZnTe using nine density functionals and applied to the quaternary semiconductor Cu2ZnSnS4 and the magnetic metal-organic framework HKUST-1.

  3. Material-binding peptide application--ZnO crystal structure control by means of a ZnO-binding peptide.

    PubMed

    Togashi, Takanari; Yokoo, Nozomi; Umetsu, Mitsuo; Ohara, Satoshi; Naka, Takashi; Takami, Seiichi; Abe, Hiroya; Kumagai, Izumi; Adschiri, Tadafumi

    2011-02-01

    Recently, a zinc oxide (ZnO)-binding peptide (ZnOBP) has been identified and has been used to assist the synthesis of unique crystalline ZnO particles. We analyzed the influence of ZnOBP on the crystal growth of ZnO structures formed from zinc hydroxide. The addition of ZnOBP in the hydrothermal synthesis of ZnO suppressed [0001] crystal growth in the ZnO particles, indicating that the specificity of the material-binding peptide for specific inorganic crystal faces controlled the crystal growth. Furthermore, the dipeptides with a partial sequence of ZnO-binding "hot spot" in ZnOBP were used to synthesize ZnO particles, and we found that the presence of these dipeptides more strictly suppressed (0001) growth in ZnO crystals than did the complete ZnOBP sequence. These results demonstrate the applicability of dipeptides selected from material-binding peptides to control inorganic crystal growth. PMID:20947422

  4. EVOEvolutionary algorithm for crystal structure prediction

    NASA Astrophysics Data System (ADS)

    Bahmann, Silvia; Kortus, Jens

    2013-06-01

    We present EVOan 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.

  5. Photonic crystals and plasmonic structures recorded by multi-exposure of holographic patterns

    NASA Astrophysics Data System (ADS)

    Menezes, Jacson W.; Braga, Edmundo S.; Cescato, Lucila

    2009-05-01

    Different technologies can be used for fabrication of photonic crystals such as: self-assembly of colloidal particles, ebeam lithography (EB), interference lithography (IL) and focused ion beam (FIB). Among them, the holographic lithography (HL) is the only technique that is able to fabricate both two-dimensional and three-dimensional photonic crystals, as well as plasmonic structures, in large areas. In this paper we demonstrate the use of the multi-exposure of two-beam interference patterns, with rotation of the sample around different axis, for fabrication of large areas 2D and 3 D photonic crystals and plasmonic structures. Using this technique, we achieved aspect ratios of about 4 in 2D photoresist templates recorded in 1 cm2 glass substrates. In order to generate the 2D photonic band gap layers and plasmonic structures, we combine the use the high aspect ratio photoresist templates with shadow evaporation of appropriated materials, with a further lift-off of the photoresist. The optical properties of the recorded structures, both photonic and plasmonic, were measured to demonstrate the applicability of the technique.

  6. Nanoscale potassium niobate crystal structure and phase transition

    PubMed Central

    2011-01-01

    Nanoscale potassium niobate (KNbO3) powders of orthorhombic structure were synthesized using the sol-gel method. The heat-treatment temperature of the gels had a pronounced effect on KNbO3 particle size and morphology. Field emission scanning electron microscopy and transmission electron microscopy were used to determine particle size and morphology. The average KNbO3 grain size was estimated to be less than 100 nm, and transmission electron microscopy images indicated that KNbO3 particles had a brick-like morphology. Synchrotron X-ray diffraction was used to identify the room-temperature structures using Rietveld refinement. The ferroelectric orthorhombic phase was retained even for particles smaller than 50 nm. The orthorhombic to tetragonal and tetragonal to cubic phase transitions of nanocrystalline KNbO3 were investigated using temperature-dependent powder X-ray diffraction. Differential scanning calorimetry was used to examine the temperature dependence of KNbO3 phase transition. The Curie temperature and phase transition were independent of particle size, and Rietveld analyses showed increasing distortions with decreasing particle size. PMID:21943345

  7. 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 2COOHClH 2O, crystallizes in space group Pnna (No. 52), with a=15.623(3), b=19.707(3), c=5.069(1) , 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) . 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.

  8. Crystal structure of tris­(hydroxyl­ammonium) orthophosphate

    PubMed Central

    Leinemann, Malte; Jess, Inke; Boeckmann, Jan; Näther, Christian

    2015-01-01

    The crystal structure of the title salt, ([H3NOH]+)3·[PO4]3−, consists of discrete hydroxyl­ammonium cations and ortho­phos­phate anions. The atoms of the cation occupy general positions, whereas the anion is located on a threefold rotation axis that runs through the phospho­rus atom and one of the phosphate O atoms. In the crystal structure, cations and anions are linked by inter­molecular O—H⋯O and N—H⋯O hydrogen bonds into a three-dimensional network. Altogether, one very strong O—H⋯O, two N—H⋯O hydrogen bonds of medium strength and two weaker bifurcated N—H⋯O inter­actions are observed. PMID:26594525

  9. Synthesis, structural and spectroscopic investigations of nanostructured samarium oxalate crystals

    NASA Astrophysics Data System (ADS)

    Vimal, G.; Mani, Kamal P.; Biju, P. R.; Joseph, Cyriac; Unnikrishnan, N. V.; Ittyachen, M. A.

    2014-03-01

    Nanostructured samarium oxalate crystals were prepared via microwave assisted co-precipitation method. The crystal structure and morphology of the sample were analyzed using X-ray powder diffraction, Scanning electron microscopy and Transmission electron microscopy. The presence of functional groups is ascertained by Fourier transform infrared spectroscopy. Samarium oxalate nanocrystals of average size 20 nm were aggregated together to form nano-plate structure in sub-microrange. Detailed spectroscopic investigation of the prepared phosphor material was carried out by Judd-Ofelt analysis based on the UV-Visible-NIR absorption spectra and photoluminescence emission spectra. The analysis reveals that the transition from energy level 4G5/2 to 6H7/2 of Sm3+ ion has maximum branching ratio and the corresponding orange emission can be used for display applications.

  10. Crystal structure of naturally occurring mercury(II) amidonitrate

    NASA Astrophysics Data System (ADS)

    Randall, Charles J.; Peacor, Donald R.; Rouse, Roland C.; Dunn, Pete J.

    1982-05-01

    A naturally-occurring mercuroammonium compound from Pitkin County, Colorado, is shown to be the natural analog of synthetic HgNH 2NO 3. The crystals are isometric, P4 132 or P4 332, with a = 10.254(1) and twelve formula weights per cell. Using 437 symmetry-independent reflections, the crystal structure was partially determined and refined to a residual of 0.090. The positions of the Hg atoms and the N and O atoms of the nitrate group were determined, but the amide ion could not be located, probably due to positional disorder. The structure contains mercury atoms arranged in equilateral triangles 3.421(1) on a side. These triangles are linked through shared vertices into helical chains wound around the fourfold screw axes. Similar triangular units occur in other inorganic Hg(II) compounds. The distortion of the nitrate ion from trigonal planar symmetry is also discussed.

  11. Crystal structures and properties of nylon polymers from theory

    SciTech Connect

    Dasgupta, S.; Goddard, W.A. III; Hammond, W.B.

    1996-12-11

    A complete force field (MSXX) for simulation of all nylon polymers is derived from ab initio quantum calculations. Special emphasis is given to the accuracy of the hydrogen bond potential for the amide unit and the torsional potential between the peptide and alkane fragments. The MSXX force field was used to predict the structures, moduli, and detailed geometries of all nine nylons for which there are experimental crystal data plus one other. For nylon-(2n) with 2n = 6, the {alpha} crystal structure (with all-trans CH{sub 2} chains nearly coplanar with the hydrogen bonding plane) is more stable, while for 2n > 6, {gamma} (with the alkane plane twisted by 70{degree}) is more stable. This change results from the increased importance of methylene packing interactions over H bonds for larger 2n. We find the highest Young`s modulus for nylon-7. 51 refs., 6 figs., 7 tabs.

  12. Crystal structure of tris-(hydroxyl-ammonium) orthophosphate.

    PubMed

    Leinemann, Malte; Jess, Inke; Boeckmann, Jan; Nther, Christian

    2015-11-01

    The crystal structure of the title salt, ([H3NOH](+))3[PO4](3-), consists of discrete hydroxyl-ammonium cations and ortho-phos-phate anions. The atoms of the cation occupy general positions, whereas the anion is located on a threefold rotation axis that runs through the phospho-rus atom and one of the phosphate O atoms. In the crystal structure, cations and anions are linked by inter-molecular O-H?O and N-H?O hydrogen bonds into a three-dimensional network. Altogether, one very strong O-H?O, two N-H?O hydrogen bonds of medium strength and two weaker bifurcated N-H?O inter-actions are observed. PMID:26594525

  13. 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.

  14. Crystal Structures of Cisplatin Bound to a Human Copper Chaperone

    SciTech Connect

    Boal, Amie K.; Rosenzweig, Amy C.

    2010-08-16

    Copper trafficking proteins, including the chaperone Atox1 and the P{sub 1B}-type ATPase ATP7B, have been implicated in cellular resistance to the anticancer drug cisplatin. We have determined two crystal structures of cisplatin-Atox1 adducts that reveal platinum coordination by the conserved CXXC copper-binding motif. Direct interaction of cisplatin with this functionally relevant site has significant implications for understanding the molecular basis for resistance mediated by copper transport pathways.

  15. Crystal Structure of the Product of Mg 2+Insertion into V 2O 5Single Crystals

    NASA Astrophysics Data System (ADS)

    Shklover, V.; Haibach, T.; Ried, F.; Nesper, R.; Novák, P.

    1996-05-01

    Chemical (by interaction with a dibutylmagnesium solution) and electrochemical (in acetonitrile solution of magnesium perchlorate) insertion of Mg 2+into the single crystals of V 2O 5was performed. The morphology change of V 2O 5crystals as a result of the Mg 2+insertion was studied by scanning electron microscopy. The wavelength dispersive electron probe microanalysis clearly showed the presence of Mg (at least) at the surface of intercalated V 2O 5. Based on the single crystal X-ray diffraction study of intercalated V 2O 5(orthorhombic, Pmn2 1, a= 11.544(6), b= 4.383(3), c= 3.574(2) Å, Z= 4) the location of a small amount of Mg (˜1%) in the bulk V 2O 5may be suggested, with [6 + 4] oxygen atoms surrounding Mg. The resulting Mg-O separations essentially exceed the accepted values for the Mg-O distances in crystals with hexacoordinated Mg atoms, which may be correlated with the structural and electrochemical properties of Mg 2+-inserted V 2O 5.

  16. Combined crystal structure prediction and high-pressure crystallization in rational pharmaceutical polymorph screening

    PubMed Central

    Neumann, M. A.; van de Streek, J.; Fabbiani, F. P. A.; Hidber, P.; Grassmann, O.

    2015-01-01

    Organic molecules, such as pharmaceuticals, agro-chemicals and pigments, frequently form several crystal polymorphs with different physicochemical properties. Finding polymorphs has long been a purely experimental game of trial-and-error. Here we utilize in silico polymorph screening in combination with rationally planned crystallization experiments to study the polymorphism of the pharmaceutical compound Dalcetrapib, with 10 torsional degrees of freedom one of the most flexible molecules ever studied computationally. The experimental crystal polymorphs are found at the bottom of the calculated lattice energy landscape, and two predicted structures are identified as candidates for a missing, thermodynamically more stable polymorph. Pressure-dependent stability calculations suggested high pressure as a means to bring these polymorphs into existence. Subsequently, one of them could indeed be crystallized in the 0.02 to 0.50 GPa pressure range and was found to be metastable at ambient pressure, effectively derisking the appearance of a more stable polymorph during late-stage development of Dalcetrapib. PMID:26198974

  17. Phonon Dispersion and Elastic Properties of Two-Dimensional Soft Particle Colloidal Crystals and Glasses

    NASA Astrophysics Data System (ADS)

    Still, Tim; Chen, Ke; Yunker, Peter J.; Goodrich, Carl P.; Schoenholz, Samuel; Liu, Andrea J.; Yodh, A. G.

    2013-03-01

    We investigate phonon dispersion relations and associated mechanical properties of two-dimensional colloidal glasses and crystals composed of soft, thermoresponsive microgel particles whose temperature-sensitive size facilitates in-situ variation of particle packing fraction. The phonon modes were measured using particle tracking and displacement covariance matrix techniques. Measurements of the hexagonal crystal served to check our methodology and, as expected, the observed phonon dispersion was largely in agreement with theoretical expectations. Measurements of phonon dispersion in the glassy colloids, as a function of packing fraction above the jamming transition, permitted study of the scaling of bulk and shear moduli as a function of packing fraction. We performed numerical simulations and were able to recover the experimental findings. Moreover, the obtained shear moduli are in good agreement with rheological measurements. We gratefully acknowledge financial support from the NSF through DMR12-05463, the PENN MRSEC DMR11-20901, and NASA NNX08AO0G. T. S. acknowledges financial support from DAAD.

  18. Structural considerations on acridine/acridinium derivatives: Synthesis, crystal structure, Hirshfeld surface analysis and computational studies

    NASA Astrophysics Data System (ADS)

    Wera, Michał; Storoniak, Piotr; Serdiuk, Illia E.; Zadykowicz, Beata

    2016-02-01

    This article describes a detailed study of the molecular packing and intermolecular interactions in crystals of four derivatives of acridine, i.e. 9-methyl-, 9-ethyl, 9-bromomethyl- and 9-piperidineacridine (1, 2, 3 and 4, respectively) and three 10-methylacridinium salts containing the trifluoromethanesulphonate anion and 9-vinyl-, 9-bromomethyl, and 9-phenyl-10-methylacridinium cations (5, 6 and 7, respectively). The crystal structures of all of the compounds are stabilized by long-range electrostatic interactions, as well as by a network of short-range C-HṡṡṡO (in hydrates and salts 3 and 5-7, respectively), C-Hṡṡṡπ, π-π, C-Fṡṡṡπ and S-Oṡṡṡπ (in salts 5-7) interactions. Hirshfeld surface analysis shows that various intermolecular contacts play an important role in the crystal packing, graphically exhibiting the differences in spatial arrangements of the acridine/acridinium derivatives under scrutiny here. Additionally, computational methods have been used to compare the intermolecular interactions in the crystal structures of the investigated compounds. Computations have confirmed the great contribution of dispersive interactions for crystal lattice stability in the case of 9-substituted acridine and electrostatic interactions for the crystal lattice stability in the case of 9-substituted 10-methylacridinium trifluoromethanesulphonates. The value of crystal lattice energy and the electrostatic contribution in the crystal lattice energy of monohydrated acridine derivatives have confirmed that these compounds have behave as acridinium derivatives.

  19. Coherent transmission and reflection spectra of ordered structures from spherical alumina particles

    NASA Astrophysics Data System (ADS)

    Loiko, V. A.; Miskevich, A. A.

    2013-08-01

    We have studied the transmission of light through a multilayer system of plane-parallel monolayers of monodisperse nonabsorbing spherical alumina particles under conditions of normal illumination in the wavelength range of 0.3-1.0 μm. In the quasi-crystalline approximation of the theory of multiple scattering of waves, we have calculated the coefficients of coherent transmission and reflection of partially ordered monolayers of particles and monolayers of particles with a nearly regular packing (planar photonic crystals with a nonideal lattice). Based on these calculations, using the transfer matrix method, we have calculated the coefficients of coherent transmission and reflection of the multilayer system. The influence of the spatial distribution of particles in individual monolayers on the coherent transmission and reflection spectra of the system has been analyzed. Characteristic minima in transmission spectra of layers caused by the interference of waves have been described. One of these minima is determined by the concentration and optical properties of particles. It appears in the spectrum of a monolayer at ratios of wavelengths and particle sizes roughly corresponding to one of the main maxima of the extinction. The second minimum is determined by the regularity of distribution of particles in the plane of the monolayer. It occurs in the spectrum of the monolayer at particle sizes comparable with the wavelength. The third minimum is the photonic band gap. It appears in the spectrum of a multilayer structure at spacings between monolayers comparable with the wavelength and is caused by the periodicity of the structure. The results make it possible to solve problems of monitoring of the degree of ideality of packing of particles by analysis of the spectral dependences of the coefficients of coherent transmission and reflection, problems of creating multilayer selective reflectors and bandpass filters, diffusers, and other elements based on alumina, which is used, e.g., in novel display technologies. The results of calculations agree well with the available experimental data for the position of the photonic band gap.

  20. Computational method for the long time propagation of quantum channeled particles in crystals and carbon nanotubes

    NASA Astrophysics Data System (ADS)

    ?osi?, M.; Petrovi?, S.; Nekovi?, N.

    2014-07-01

    This work reports on the computational method for the long time propagation of the quantum channeled particles in infinite and finite harmonic interaction wells and in a realistic carbon nanotube interaction potential well. This method is based on the Chebyshev global propagation method for solving of the corresponding time dependent Schrdinger equation. For comparison, the computational method based on the Crank-Nicolson propagation method is also presented. In the case of quantum particle motion in infinite harmonic potential well, when the analytical solution of the corresponding time-dependent Schrdinger equation exists, we show that the obtained propagation method is efficient, very accurate and numerically stable. It is superior with respect to the method based on the Crank-Nicolson propagation method. A detailed study of the long time quantum particle motion in the finite harmonic interaction potential well shows that the obtained computational method based on the Chebyshev global propagation method can be successfully applied for following of the channeled quantum particle in crystals and carbon nanotubes. This is demonstrated in the case of quantum particle motion in a realistic carbon nanotube interaction potential well.

  1. Dynamics of colloidal particles in electrohydrodynamic convection of nematic liquid crystal.

    PubMed

    Takahashi, Kentaro; Kimura, Yasuyuki

    2014-07-01

    We have studied the dynamics of micrometer-sized colloidal particles in electrohydrodynamic convection of nematic liquid crystal. Above the onset voltage of electroconvection, the parallel array of convection rolls appears to be perpendicular to the nematic field at first. The particles are forced to rotate by convection flow and are trapped within a single roll in this voltage regime. A slow glide motion along the roll axis is also observed. The frequency of rotational motion and the glide velocity increase with the applied voltage. Under a much larger voltage where the roll axis temporally fluctuates, the particles occasionally hop to the neighbor rolls. In this voltage regime, the motion of the particles becomes two-dimensional. The motion perpendicular to the roll axis exhibits diffusion behavior at a long time period. The effective diffusion constant is 10(3)-10(4) times larger than the molecular one. The observed behavior is compared with the result obtained by a simple stochastic model for the transport of the particles in convection. The enhancement of diffusion can be quantitatively described well by the rotation frequency in a roll, the width of the roll, and the hopping probability to the neighbor rolls. PMID:25122319

  2. Surface and zeta-potentials of silver halide single crystals: pH-dependence in comparison to particle systems.

    PubMed

    Selmani, Atia; Ltzenkirchen, 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

  3. Structural contribution to the roughness of supersmooth crystal surface

    SciTech Connect

    Butashin, A. V.; Muslimov, A. E. Kanevsky, V. M.; Deryabin, A. N.; Pavlov, V. A.; Asadchikov, V. E.

    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.

  4. Growth and structural, optical, and electrical properties of zincite crystals

    SciTech Connect

    Kaurova, I. A.; Kuz'micheva, G. M.; Rybakov, V. B.

    2013-03-15

    An X-ray diffraction study of ZnO crystals grown by the hydrothermal method has revealed reflections that give grounds to assign them to the sp. gr. P3 rather than to P6{sub 3}mc. The distribution of Zn1, Zn2, O1, and O2 over structural positions, along with vacancies and incorporated zinc atoms, explains the dissymmetrization observed in terms of the kinetic (growth) phase transition of the order-disorder type, which is caused by ordering Zn and O atoms over structural positions. The color of crystals of refined compositions (Zn{sub 0.975}{open_square}{sub 0.025})Zn{sub i(0.015)}(O{sub 0.990}{open_square}{sub 0.010}) (green) and (Zn{sub 0.965}{open_square}{sub 0.035})Zn{sub i(0.035)}O (bright green) is related to different oxygen contents, which is confirmed by the results of electron probe X-ray microanalysis and absorption spectroscopy. The degree of the structural quality of crystals, their resistivity, and activation energy are also related to oxygen vacancies.

  5. Crystal Structures of the β2-Adrenergic Receptor

    NASA Astrophysics Data System (ADS)

    Weis, William I.; Rosenbaum, Daniel M.; Rasmussen, Søren G. F.; Choi, Hee-Jung; Thian, Foon Sun; Kobilka, Tong Sun; Yao, Xiao-Jie; Day, Peter W.; Parnot, Charles; Fung, Juan J.; Ratnala, Venkata R. P.; Kobilka, Brian K.; Cherezov, Vadim; Hanson, Michael A.; Kuhn, Peter; Stevens, Raymond C.; Edwards, Patricia C.; Schertler, Gebhard F. X.; Burghammer, Manfred; Sanishvili, Ruslan; Fischetti, Robert F.; Masood, Asna; Rohrer, Daniel K.

    G protein coupled receptors (GPCRs) constitute the largest family of membrane proteins in the human genome, and are responsible for the majority of signal transduction events involving hormones and neuro-transmitters across the cell membrane. GPCRs that bind to diffusible ligands have low natural abundance, are relatively unstable in detergents, and display basal G protein activation even in the absence of ligands. To overcome these problems two approaches were taken to obtain crystal structures of the β2-adrenergic receptor (β2AR), a well-characterized GPCR that binds cate-cholamine hormones. The receptor was bound to the partial inverse agonist carazolol and co-crystallized with a Fab made to a three-dimensional epitope formed by the third intracellular loop (ICL3), or by replacement of ICL3 with T4 lysozyme. Small crystals were obtained in lipid bicelles (β2AR-Fab) or lipidic cubic phase (β2AR-T4 lysozyme), and diffraction data were obtained using microfocus technology. The structures provide insights into the basal activity of the receptor, the structural features that enable binding of diffusible ligands, and the coupling between ligand binding and G-protein activation.

  6. Nanoconfinement-Induced Structures in Chiral Liquid Crystals

    PubMed Central

    Melle, Michael; Theile, Madlona; Hall, Carol K.; Schoen, Martin

    2013-01-01

    We employ Monte Carlo simulations in a specialized isothermal-isobaric and in the grand canonical ensemble to study structure formation in chiral liquid crystals as a function of molecular chirality. Our model potential consists of a simple Lennard-Jones potential, where the attractive contribution has been modified to represent the orientation dependence of the interaction between a pair of chiral liquid-crystal molecules. The liquid crystal is confined between a pair of planar and atomically smooth substrates onto which molecules are anchored in a hybrid fashion. Hybrid anchoring allows for the formation of helical structures in the direction perpendicular to the substrate plane without exposing the helix to spurious strains. At low chirality, we observe a cholesteric phase, which is transformed into a blue phase at higher chirality. More specifically, by studying the unit cell and the spatial arrangement of disclination lines, this blue phase can be established as blue phase II. If the distance between the confining substrates and molecular chirality are chosen properly, we see a third structure, which may be thought of as a hybrid, exhibiting mixed features of a cholesteric and a blue phase. PMID:23989605

  7. Optically driven translational and rotational motions of microrod particles in a nematic liquid crystal

    PubMed Central

    Eremin, Alexey; Hirankittiwong, Pemika; Chattham, Nattaporn; Nádasi, Hajnalka; Stannarius, Ralf; Limtrakul, Jumras; Haba, Osamu; Yonetake, Koichiro; Takezoe, Hideo

    2015-01-01

    A small amount of azo-dendrimer molecules dissolved in a liquid crystal enables translational and rotational motions of microrods in a liquid crystal matrix under unpolarized UV light irradiation. This motion is initiated by a light-induced trans-to-cis conformational change of the dendrimer adsorbed at the rod surface and the associated director reorientation. The bending direction of the cis conformers is not random but is selectively chosen due to the curved local director field in the vicinity of the dendrimer-coated surface. Different types of director distortions occur around the rods, depending on their orientations with respect to the nematic director field. This leads to different types of motions driven by the torques exerted on the particles by the director reorientations. PMID:25624507

  8. 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 β-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

  9. The first crystal structure of an archaeal helical repeat protein

    SciTech Connect

    Yoneda, Kazunari; Sakuraba, Haruhiko; Tsuge, Hideaki; Katunuma, Nobuhiko; Kuramitsu, Seiki; Kawabata, Takeshi; Ohshima, Toshihisa

    2005-07-01

    The crystal structure of ST1625p, a protein encoded by a hypothetical open reading frame ST1625 in the genome of the hyperthermophilic archaeon Sulfolobus tokodaii, was determined at 2.2 Å resolution. The structure of ST1625p consists of a unique superhelix with a low-level structure resemblance to doamins from other proteins with known three-dimensional structures. The crystal structure of ST1625p, a protein encoded by a hypothetical open reading frame ST1625 in the genome of the hyperthermophilic archaeon Sulfolobus tokodaii, was determined at 2.2 Å resolution. The only sequence similarity exhibited by the amino-acid sequence of ST1625p was a 33% identity with the sequence of SSO0983p from S. solfataricus. The 19 kDa monomeric protein was observed to consist of a right-handed superhelix assembled from a tandem repeat of ten α-helices. A structural homology search using the DALI and MATRAS algorithms indicates that this protein can be classified as a helical repeat protein.

  10. Structure of the toxic core of ?-synuclein from invisible crystals.

    PubMed

    Rodriguez, Jose A; Ivanova, Magdalena I; Sawaya, Michael R; Cascio, Duilio; Reyes, Francis E; Shi, Dan; Sangwan, Smriti; Guenther, Elizabeth L; Johnson, Lisa M; Zhang, Meng; Jiang, Lin; Arbing, Mark A; Nannenga, Brent L; Hattne, Johan; Whitelegge, Julian; Brewster, Aaron S; Messerschmidt, Marc; Boutet, Sbastien; Sauter, Nicholas K; Gonen, Tamir; Eisenberg, David S

    2015-09-24

    The protein ?-synuclein is the main component of Lewy bodies, the neuron-associated aggregates seen in Parkinson disease and other neurodegenerative pathologies. An 11-residue segment, which we term NACore, appears to be responsible for amyloid formation and cytotoxicity of human ?-synuclein. Here we describe crystals of NACore that have dimensions smaller than the wavelength of visible light and thus are invisible by optical microscopy. As the crystals are thousands of times too small for structure determination by synchrotron X-ray diffraction, we use micro-electron diffraction to determine the structure at atomic resolution. The 1.4 resolution structure demonstrates that this method can determine previously unknown protein structures and here yields, to our knowledge, the highest resolution achieved by any cryo-electron microscopy method to date. The structure exhibits protofibrils built of pairs of face-to-face ?-sheets. X-ray fibre diffraction patterns show the similarity of NACore to toxic fibrils of full-length ?-synuclein. The NACore structure, together with that of a second segment, inspires a model for most of the ordered portion of the toxic, full-length ?-synuclein fibril, presenting opportunities for the design of inhibitors of ?-synuclein fibrils. PMID:26352473

  11. The crystal structure of aluminum doped {beta}-rhombohedral boron

    SciTech Connect

    Bykova, Elena; Materialphysik und Technologie, Lehrstuhl fuer Kristallographie, Physikalisches Institut, Universitaet Bayreuth, Universitaetsstrasse 30, D-95440 Bayreuth ; Parakhonskiy, Gleb; Materialphysik und Technologie, Lehrstuhl fuer Kristallographie, Physikalisches Institut, Universitaet Bayreuth, Universitaetsstrasse 30, D-95440 Bayreuth ; Dubrovinskaia, Natalia; Chernyshov, Dmitry; Dubrovinsky, Leonid

    2012-10-15

    A crystal structure of aluminum doped {beta}-rhombohedral boron was studied by single-crystal X-ray diffraction at 80 K. The crystals were synthesized using high-pressure high temperature technique at 3 GPa and 2100 K. The structure is based on three-dimensional framework made of B{sub 12} icosahedra with voids occupied by the B{sub 28}-B-B{sub 28} units, it has the R-3m space group with a=10.9014(3), c=23.7225(7) A lattice dimensions in hexagonal setting. Aluminum atoms are located in A1 and D special positions of the {beta}-B structure with occupancies of 82.7(6)% and 11.3(4)%, respectively. Additional boron atoms are located near the D-site. Their possible distribution is discussed. Finally we have found two appropriate structural models whose refinement suggests two possible chemical compositions, AlB{sub 44.8(5)} and AlB{sub 37.8(5)}, which are in a good agreement with the chemical analysis data obtained from EDX. The crystal structure of AlB{sub 44.8(5)} is described in detail. - Graphical abstract: The atomic distribution near the B(15) atom (non-labeled atom in the center of the picture) shown along the c axis. Anisotropic displacement ellipses for Al(2) (D-site) and B(15) are shown with 50 % probability level. The mirror plane with Miller indices (1 1 0) and related to it (-1 2 0) and (-2 1 0) generated by the 3-fold rotation-inversion axis parallel to the c axis splits the position of B(16) over two sites. Highlights: Black-Right-Pointing-Pointer The crystal structure of the AlB{sub 44.8(5)} has been refined. Black-Right-Pointing-Pointer Aluminum atoms partially fill certain types of voids (the A1- and D-sites). Black-Right-Pointing-Pointer We have got two possible models of atomic distribution near the D-site.

  12. 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 Mller-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 Mller-Plesset perturbation theory or higher. PMID:24754304

  13. Preparation of poly(BMA-co-MMA) particles by soap-free emulsion polymerization and its optical properties as photonic crystals.

    PubMed

    Lee, Ki-Chang; Choo, Hun-Seung

    2014-11-01

    Narrowly dispersed poly(BMA-co-MMA) and PBMA latices with particle diameters ranging within 216-435 nm were synthesized successfully by surfactant-free emulsion polymerization with KPS and AIBA. The average particle diameter and particle size distribution, average molecular weight and its distribution, glass transition temperature, reflectance spectra in visible wavelength, and refractive indices for the respective poly(BMA-co-MMA) latices and their photonic crystals were systematically investigated in terms of BMA/MMA ratio, BMA content, polymerization temperature, and DVB effect. The rate of polymerization increased with increasing MMA concentration in BMA/MMA ratio. The particle diameter increased with BMA concentration in BMA/MMA ratio. The molecular weight increased with BMA concentration in BMA/MMA ratio and monomer concentration. The drying of the latices offered self-assembled shiny colloidal crystal films showing the characteristic structural colors in visible wavelength. All the poly(BMA-co-MMA) latices prepared in the study were fallen within the range of photonic grade microspheres. The reflectance measurement on the colloidal photonic crystals having different particle diameters clearly exhibited narrow stopbands. The reflection maxima (?(max)) measured in this study were well close to the ?(max) calculated, derived from the Bragg's equation. The refractive indices of poly(BMA-co-MMA) photonic crystals were found to be almost same as the theoretical values and increased proportionally from 1.50 to 1.57 with BMA content in BMA/MMA ratios. It was, thus, found that the optical reflectance properties of the poly(BMA-co-MMA) colloidal photonic crystals can be controlled easily by adjusting the reaction conditions and BMA/MMA ratio in soap-free emulsion copolymerization of BMA and MMA. PMID:25958515

  14. Effect of crystal thickness and geometry on the alpha-particle resolution of CsI (Tl)

    USGS Publications Warehouse

    Martinez, P.; Senftle, F.E.

    1960-01-01

    The resolution of CsI(Tl) for Po210 alpha particles has been measured as a function of crystal thickness. The best resolution of a 12;-in. diam cylindrical crystal was obtained for a thickness of 0.38 mm, and the effect of thickness on the resolution is discussed. Based on the proposed model, a conical crystal was designed, which yielded a line width of 1.8% for Po 210 alpha particles with a selected photomultiplier tube. ?? 1960 The American Institute of Physics.

  15. Effect of Hf-Rich Particles on the Creep Life of a High-strength Nial Single Crystal Alloy

    NASA Technical Reports Server (NTRS)

    Garg, A.; Raj, S. V.; Darolia, R.

    1995-01-01

    Additions of small amounts of Hf and Si to NiAl single crystals significantly improve their high-temperature strength and creep properties. However, if large Hf-rich dendritic particles formed during casting of the alloyed single crystals are not dissolved completely during homogenization heat treatment, a large variation in creep rupture life can occur. This behavior, observed in five samples of a Hf containing NiAl single crystal alloy tested at 1144 K under an initial stress of 241.4 MPa, is described in detail highlighting the role of interdendritic Hf-rich particles in limiting creep rupture life.

  16. 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.

  17. Crystal structure of inactive form of Rab3B

    SciTech Connect

    Zhang, Wei; Shen, Yang; Jiao, Ronghong; Liu, Yanli; Deng, Lingfu; Qi, Chao

    2012-02-24

    Highlights: Black-Right-Pointing-Pointer This is the first structural information of human Rab3B. Black-Right-Pointing-Pointer To provides a structural basis for the GDP/GTP switch in controlling the activity of Rab3. Black-Right-Pointing-Pointer The charge distribution of Rab3B indicates its unique roles in vesicular trafficking. -- Abstract: 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 A 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.

  18. 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

  19. Crystal structure dependent thermal conductivity in two-dimensional phononic crystal nanostructures

    NASA Astrophysics Data System (ADS)

    Nakagawa, Junki; Kage, Yuta; Hori, Takuma; Shiomi, Junichiro; Nomura, Masahiro

    2015-07-01

    Thermal phonon transport in square- and triangular-lattice Si phononic crystal (PnC) nanostructures with a period of 300 nm was investigated by measuring the thermal conductivity using micrometer-scale time-domain thermoreflectance. The placement of circular nanoholes has a strong influence on thermal conductivity when the periodicity is within the range of the thermal phonon mean free path. A staggered hole structure, i.e., a triangular lattice, has lower thermal conductivity, where the difference in thermal conductivity depends on the porosity of the structure. The largest difference in conductivity of approximately 20% was observed at a porosity of around 30%. This crystal structure dependent thermal conductivity can be understood by considering the local heat flux disorder created by a staggered hole structure. Numerical simulation using the Monte Carlo technique was also employed and also showed the lower thermal conductivity for a triangular lattice structure. Besides gaining a deeper understanding of nanoscale thermal phonon transport, this information would be useful in the design of highly efficient thermoelectric materials created by nanopatterning.

  20. 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

  1. ASSOCIATION OF SUPRATHERMAL PARTICLES WITH COHERENT STRUCTURES AND SHOCKS

    SciTech Connect

    Tessein, J. A.; Matthaeus, W. H.; Wan, M.; Osman, K. T.; Ruffolo, D.; Giacalone, J.

    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. Crystal structures of two ()-exo-N-isobornylacetamides

    PubMed Central

    Stepanovs, Dmitrijs; Posevins, Daniels; Turks, Maris

    2015-01-01

    The title compounds consist of a bornane skeleton with attached acetamide, C12H21NO ()-(1) {systematic name: ()-N-[(1RS,2RS,4RS)-1,7,7-trimethylbicyclo[2.2.1]heptan-2-yl]acetamide}, and chloroacetamide, C12H20ClNO ()-(2) {systematic name: ()-2-chloro-N-[(1RS,2RS,4RS)-1,7,7-trimethylbicyclo[2.2.1]heptan-2-yl]acetamide}, functionalities to the 2-exo-position. The crystal structure of the first monoclinic polymorph of ()-(1) has been reported previously [Ung et al. (2014 ?). Monatsh. Chem. 145, 983992]. Compound ()-(1) crystallizes in the space group P21/n with two independent molecules in the asymmetric unit, in contrast to the above-mentioned polymorph which crystallized in the space group C2/c with one molecule in the asymmetric unit. In the title compounds, the bicyclic bornane moieties have normal geometries. In the crystals of both compounds, molecules are linked by NH?O hydrogen bonds, reinforced by CH?O contacts, forming trans-amide chains propagating along the a-axis direction. In the case of compound ()-(1), neighbouring chains are linked by further CH?O contacts, forming double-chain ribbons along [100]. PMID:26594386

  3. Crystal structures of two ()-exo-N-isobornyl-acetamides.

    PubMed

    Stepanovs, Dmitrijs; Posevins, Daniels; Turks, Maris

    2015-10-01

    The title compounds consist of a bornane skeleton with attached acetamide, C12H21NO ()-(1) {systematic name: ()-N-[(1RS,2RS,4RS)-1,7,7-tri-methylbi-cyclo-[2.2.1]heptan-2-yl]acetamide}, and chloro-acetamide, C12H20ClNO ()-(2) {systematic name: ()-2-chloro-N-[(1RS,2RS,4RS)-1,7,7-tri-methylbi-cyclo-[2.2.1]heptan-2-yl]-acetamide}, functionalities to the 2-exo-position. The crystal structure of the first monoclinic polymorph of ()-(1) has been reported previously [Ung et al. (2014 ?). Monatsh. Chem. 145, 983-992]. Compound ()-(1) crystallizes in the space group P21/n with two independent mol-ecules in the asymmetric unit, in contrast to the above-mentioned polymorph which crystallized in the space group C2/c with one mol-ecule in the asymmetric unit. In the title compounds, the bicyclic bornane moieties have normal geometries. In the crystals of both compounds, mol-ecules are linked by N-H?O hydrogen bonds, reinforced by C-H?O contacts, forming trans-amide chains propagating along the a-axis direction. In the case of compound ()-(1), neighbouring chains are linked by further C-H?O contacts, forming double-chain ribbons along [100]. PMID:26594386

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

    NASA Astrophysics Data System (ADS)

    Szafran, M.; Dega-Szafran, Z.; Thaimattam, R.; Jaskólski, M.

    2004-11-01

    A 1:1 complex between N-methylpiperidine betaine and hydrofluoric acid, MPB·HF, has been characterized by single crystal X-ray analysis, FTIR spectroscopy, and DFT calculations. The crystals are orthorhombic, space group Pbca, with a=11.656(2), b=9.395(2), c=16.331(3) Å. The piperidine ring adopts a chair conformation with the CH 3 group in an axial and the CH 2COO·H group in an equatorial position. In the crystal, the HF molecule is engaged in a very short O⋯H⋯F hydrogen bond (O⋯F=2.379(1) Å) with the proton most likely to reside in a single-minimum potential well shifted towards the F atom. The F - anion is engaged in three short N +⋯F - intermolecular electrostatic interactions and in several C-H⋯F contacts. Four conformers of MPB·HF (two axial and two equatorial) have been examined by the B3LYP/6-31G(d,p) method. Unlike in the crystal structure, the isolated molecule is most stable with axial CH 2COO·H group. Powder FTIR spectrum shows a broad and intense absorption in the 2500-600 cm -1 region typical for very strong hydrogen bonds.

  5. A novel characterization of organic molecular crystal structures for the purpose of crystal engineering.

    PubMed

    Thomas, Noel W

    2015-08-01

    A novel analytical approach is proposed for the characterization of organic molecular crystal structures where close packing is an important factor. It requires the identification of a unique reference axis within the crystal, along which three-dimensional space is divided into close-packed blocks (CPB) and junction zones (JZ). The degree of close packing along the reference axis is quantified by a two-dimensional packing function, ?2D, of symmetry determined by the space group. Values of ?2D reflect the degree of area-filling in planes perpendicular to this axis. The requirement of close packing within CPB allows the planar structures perpendicular to the reference axis to be analysed as tessellations of area-filling molecular-based cells (MBC), which are generally hexagonal. The form of these cells reflects the molecular shape in the cross-section, since their vertices are given by the centres of the voids between molecules. There are two basic types of MBC, Type 1, of glide or pseudo-glide symmetry, and Type 2, which is formed by lattice translations alone and generally requires a short unit-cell axis. MBC at layers of special symmetry are used to characterize the structures in terms of equivalent ellipses with parameters aell, bell and ?ell. The ratio aell/bell allows the established ?, ?, ? classification to be integrated into the current framework. The values of parameters aell and bell arising from all the structures considered, polynuclear aromatic hydrocarbons (PAH), substituted anthracenes and anthraquinones (SAA) and 2-benzyl-5-benzylidene (BBCP) are mapped onto a universal curve. The division of three-dimensional space into CPB and JZ is fundamentally useful for crystal engineering, since the structural perturbations brought about by substitution at hydrogen positions located within JZ are minimal. A contribution is also made to ongoing debate concerning the adoption of polar space groups, isomorphism and polymorphism. PMID:26208627

  6. Modification of near-wall coherent structures by inertial particles

    NASA Astrophysics Data System (ADS)

    Richter, David H.; Sullivan, Peter P.

    2014-10-01

    Direct numerical simulations are combined with two-way coupled Lagrangian point particles to study the effect of Reynolds number on particle-turbulence interaction. Turbulent planar Couette flow is simulated at a constant dispersed phase mass loading of ?m = 0.25 for particle Stokes numbers of StK = [O(1), O(10), O(100)] (based on the Stokes time scale of the particle and the Kolmogorov time scale of the flow) and bulk Reynolds numbers of Reb = [8100, 24000, 72000] (based on the plate velocity difference and separation distance). Statistics of swirling strength |?ci| are used to evaluate the impact of particles on near-wall motions which are responsible for turbulent, wall-normal momentum transport. Instantaneously, the number of high-strength swirling motions near the wall decreases significantly in the presence of particles, and this trend is enhanced with increasing Reb. Conditional averages are computed using linear stochastic estimation, providing the average structures responsible for ejection events near the wall. These conditional eddies are weakened substantially by the presence of the dispersed phase, and this effect is again enhanced with increasing Reb. We propose a mechanism where particles, by interfering with the hairpin regeneration process near the wall, can influence turbulent fluxes in a way that increases with Reb despite only having direct interaction with scales on the same order as their small physical size. At the same time, turbulent momentum flux concentrated at higher wavenumbers with increasing Reb allows small particles to be effective agents for altering turbulent transport.

  7. Crystal structure of new AsS{sub 2} compound

    SciTech Connect

    Bolotina, N. B.; Brazhkin, V. V.; Dyuzheva, T. I.; Lityagina, L. M.; Kulikova, L. F.; Nikolaev, N. A.; Verin, I. A.

    2013-01-15

    AsS{sub 2} single crystals have been obtained for the first time from an As{sub 2}S{sub 3} melt at pressures above 6 GPa and temperatures above 800 K in the As{sub 2}S{sub 3} {yields} AsS + AsS{sub 2} reaction. The monoclinic structure of the new high-pressure phase is solved by X-ray diffraction analysis and compared to the structure of high-pressure AsS phase, which was studied previously.

  8. The first crystal structure of an archaeal helical repeat protein

    PubMed Central

    Yoneda, Kazunari; Sakuraba, Haruhiko; Tsuge, Hideaki; Katunuma, Nobuhiko; Kuramitsu, Seiki; Kawabata, Takeshi; Ohshima, Toshihisa

    2005-01-01

    The crystal structure of ST1625p, a protein encoded by a hypothetical open reading frame ST1625 in the genome of the hyperthermophilic archaeon Sulfolobus tokodaii, was determined at 2.2? resolution. The only sequence similarity exhibited by the amino-acid sequence of ST1625p was a 33% identity with the sequence of SSO0983p from S. solfataricus. The 19?kDa monomeric protein was observed to consist of a right-handed superhelix assembled from a tandem repeat of ten ?-helices. A structural homology search using the DALI and MATRAS algorithms indicates that this protein can be classified as a helical repeat protein. PMID:16511116

  9. Fusion proteins as alternate crystallization paths to difficult structure problems

    NASA Technical Reports Server (NTRS)

    Carter, Daniel C.; Rueker, Florian; Ho, Joseph X.; Lim, Kap; Keeling, Kim; Gilliland, Gary; Ji, Xinhua

    1994-01-01

    The three-dimensional structure of a peptide fusion product with glutathione transferase from Schistosoma japonicum (SjGST) has been solved by crystallographic methods to 2.5 A resolution. Peptides or proteins can be fused to SjGST and expressed in a plasmid for rapid synthesis in Escherichia coli. Fusion proteins created by this commercial method can be purified rapidly by chromatography on immobilized glutathione. The potential utility of using SjGST fusion proteins as alternate paths to the crystallization and structure determination of proteins is demonstrated.

  10. Holographic liquid crystal polarization grating with Fabry-Perot structure.

    PubMed

    Sakamoto, Moritsugu; Yamaguchi, Haruki; Noda, Kohei; Sasaki, Tomoyuki; Kawatsuki, Nobuhiro; Ono, Hiroshi

    2016-03-15

    A holographic liquid crystal polarization grating with a Fabry-Perot structure was developed. Because of its resonant structure, the device offers high levels of control of the diffraction properties of incident-polarized light beams, depending on the resonance conditions. The diffracted light beams are emitted in both the reflection and transmission directions, and the device thus works as a multibranch polarization grating with double optical paths, unlike a conventional polarization grating. These device features were experimentally demonstrated and were also explained theoretically. PMID:26977643

  11. Tuning the self-assembled monolayer formation on nanoparticle surfaces with different curvatures: Investigations on spherical silica particles and plane-crystal-shaped zirconia particles

    PubMed Central

    Feichtenschlager, Bernhard; Lomoschitz, Christoph J.; Kickelbick, Guido

    2011-01-01

    The ordering of dodecyl-chain self-assembled monolayers (SAM) on different nanoscopic surfaces was investigated by FT-IR studies. As model systems plane-crystal-shaped ZrO2 nanoparticles and spherical SiO2 nanoparticles were examined. The type of capping agent was chosen dependent on the substrate, therefore dodecylphosphonic acid and octadecylphosphonic acid were used for ZrO2 and dodecyltrimethoxysilane for SiO2 samples. The plane ZrO2 nanocrystals yielded more ordered alkyl-chain structures whereas spherical SiO2 nanoparticles showed significantly lower alkyl-chain ordering. Submicron-sized silica spheres revealed a significantly higher alkyl chain ordering, comparable to an analogously prepared SAM on a non-curved plane oxidized Si-wafer. In the case of ZrO2 nanocrystals an intense alkyl-chain alignment could be disturbed by decreasing the grafting density from the maximum of 2.1molecules/nm2 through the variation of coupling agent concentration to lower values. Furthermore, the co-adsorption of a different coupling agent, such as phenylphosphonic acid for ZrO2 and phenyltrimethoxysilane for SiO2, resulted in a significantly lower alkyl-chain ordering for ZrO2 plane crystals and for large SiO2 spherical particles at high grafting density. An increasing amount of order-disturbing molecules leads to a gradual decrease in alkyl-chain alignment on the surface of the inorganic nanoparticles. In the case of the ZrO2 nanoparticle system it is shown via dynamic light scattering (DLS) that the mixed monolayer formation on the particle surface impacts the dispersion quality in organic solvents such as n-hexane. PMID:21549385

  12. Crystals and liquids of ionic microgel particles: Osmotic pressure and phase coexistence

    NASA Astrophysics Data System (ADS)

    Pelaez-Fernandez, Miguel; Souslov, Anton; Lyon, L. Andrew; Goldbart, Paul M.; Fernandez-Nieves, Alberto; School of Chemistry and Biochemistry Collaboration; School of Physics Team

    2014-03-01

    We quantify the phase behavior of suspensions comprised of swollen, ionic microgels while measuring the system osmotic pressure. Surprisingly, the osmotic pressure of dilute suspensions is much larger than that expected for an ideal gas. Furthermore, we find that the width of the liquid-crystal phase coexistence region increases as the microgels are made softer; this is true in terms of a generalized volume fraction, ? = nV0, with n the particle density and V0 the dilute microgel volume. We will discuss the role played by the ions in our observations and compare with expectations based on computer simulations.

  13. Synthesis of bulk nanostructured aluminum containing in situ crystallized amorphous particles

    NASA Astrophysics Data System (ADS)

    Zhang, Zhihui

    5083 Al containing in situ crystallized Al85Ni10La 5 amorphous particles (10% and 20% in volume fraction) was synthesized through a powder metallurgy route consisting of cold isostatic pressing, degassing and hot extrusion. The nanostructured 5083 Al powders (grain size 28 nm) were produced through mechanical milling in liquid nitrogen. The Al 85Ni10La5 powders were produced via gas atomization using helium gas and the fraction in the size range of <500 mesh (<25 mum), which appeared to be fully amorphous on the basis of X-ray diffraction studies, was isolated for further investigation. The amorphous Al85Ni10La5 alloy exhibited a glass transition at 259C (at a heating rate of 40C/min) and nanoscale crystallites (< 100 nm) with an equiaxed morphology formed during the subsequent crystallization reactions. At temperatures higher than 283C, only the equilibrium phases Al, Al3Ni and Al11La 3 were formed. An unusually high nucleation density (1021-22 /m3) was recorded in the crystallization process. The copious nucleation sites were rationalized from the presence of quenched-in Al nuclei, which were evidenced by isothermal calorimetric tracing (235C) and a direct HRTEM observation of the amorphous Al85Ni10La 5 powders. The feasibility of preparation of nanocrystalline/amorphous particles via melt spinning followed by ball milling was also studied. In the as-extruded composites, the amorphous Al85Ni10 La5 particles underwent complete crystallization resulting in a grain size of 100 200 nm; the 5083 Al matrix had a grain size around 200 nm in the fine-grained region interspersed by coarse-grained region with a grain size of 600 1500 nm. A metallurgical bond formed between the 5083 Al matrix and Al85Ni10La5 particles showing a grain-boundary-like interface. The compressive fracture strength of the as-extruded 10% and 20% Al85Ni10La5 composites were determined to be 1025 MPa and 837 MPa, respectively. The influence of secondary processing, i.e., swaging, following extrusion on the mechanical behavior was also studied. The coarse grain formation in cryomilled 5083 Al during the thermomechanical process was discussed and it was evident that grain rotation and coalescence played an important role in the overall mechanism.

  14. Ordered Structures of Functionalized Silica Nanoparticles on Gold Surfaces: Correlation of Quartz Crystal Microbalance with Structural Characterization.

    PubMed

    Grunewald, Christian; Schmudde, Madlen; Noufele, Christelle Njiki; Graf, Christina; Risse, Thomas

    2015-10-20

    Quartz crystal microbalance (QCM) is frequently used to investigate adsorption of nanometer-sized objects such as proteins, viruses, or organic as well as inorganic nanoparticles from solution. The interpretation of the data obtained for heterogeneous adsorbate layers is not straightforward in particular if the systems exhibit sizable amounts of dissipation. In this study we investigate the deposition of monodisperse, amine functionalized silica nanoparticles on gold surfaces using QCM with dissipation (QCM-D) to obtain frequency and dissipation changes during adsorption from the liquid phase. These investigations are combined with ex situ scanning electron microscopy (SEM) measurements to study both coverage as well as lateral arrangement of the particles. An ordered layer of particles is found at saturation coverage due to the charged particle surface resulting in a repulsive interaction between the particles. The repulsion ensures a minimal distance between the particles, which leads to a saturation coverage of 15% for particles of 137 nm diameter. The frequency shift is shown to be a linear function of coverage which is a behavior expected for an elastic medium according to the Sauerbrey equation. However, the system shows a strong dependence of the normalized frequency shift on the overtones as well as a large dissipation, which is a clear indication for a system with viscoelastic properties. The analysis of the data show that a reliable determination of the adsorbed mass solely on the basis of QCM-D results is not possible, but additional information as determined by SEM in the present case is required to determine the coverage. From a correlation of the QCM-D results with the structural characterization it is possible to infer that the dissipation is a long ranged phenomenon. A lower boundary of the interaction length could be derived being twice the particle diameter for the particles studied here. In contrast to that the frequency response behaves like local phenomenon. PMID:26394850

  15. Structural Insights into the Regulatory Particle of the Proteasome from Methanocaldococcus jannaschii

    SciTech Connect

    Zhang, F.; Hu, M; Tian, G; Zhang, P; Finley, D; Jeffrey, P; Shi, Y

    2009-01-01

    Eukaryotic proteasome consists of a core particle (CP), which degrades unfolded protein, and a regulatory particle (RP), which is responsible for recognition, ATP-dependent unfolding, and translocation of polyubiquitinated substrate protein. In the archaea Methanocaldococcus jannaschii, the RP is a homohexameric complex of proteasome-activating nucleotidase (PAN). Here, we report the crystal structures of essential elements of the archaeal proteasome: the CP, the ATPase domain of PAN, and a distal subcomplex that is likely the first to encounter substrate. The distal subcomplex contains a coiled-coil segment and an OB-fold domain, both of which appear to be conserved in the eukaryotic proteasome. The OB domains of PAN form a hexameric ring with a 13 A pore, which likely constitutes the outermost constriction of the substrate translocation channel. These studies reveal structural codes and architecture of the complete proteasome, identify potential substrate-binding sites, and uncover unexpected asymmetry in the RP of archaea and eukaryotes.

  16. 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).

  17. Interplay between size and crystal structure of molybdenum dioxide nanoparticles--synthesis, growth mechanism, and electrochemical performance.

    PubMed

    Koziej, Dorota; Rossell, Marta D; Ludi, Bettina; Hintennach, Andreas; Novk, Petr; Grunwaldt, Jan-Dierk; Niederberger, Markus

    2011-02-01

    A detailed study is presented on the formation of MoO(2) nanoparticles from the dissolution of the precursor to the final rodlike product, with a focus on the exploration of the inorganic reaction occurring ahead of the nucleation step, and interplay between size and crystal structure of MoO(2). In situ X-ray absorption spectroscopy experiments show that the crystallization and the growth process of MoO(2) nanorods is initiated by rapid reduction of the MoO(2) Cl(2) precursor in benzyl alcohol and acetophenone. This reaction triggers the nucleation of 2 nm MoO(2) particles with spherical shape and hexagonal crystal structure. The transformation from spheres into rods emerges as a complex process driven by oriented attachment. High-resolution transmission electron microscopy and X-ray diffraction results provide evidence that the 2 nm particles first aggregate into 5-20 nm-large oriented assemblies. The increase in particle size induces the phase transition from hexagonal to the less symmetrical monoclinic crystal structure, and finally the transformation into rods. Is it shown that electrodes for lithium-ion batteries based on MoO(2) nanorods have a long-term cycling life. The specific discharge capacity even after 200 cycles at a discharge rate of 1 C is about 300 Ah kg(-1) . PMID:21294267

  18. Equilibrium structures of anisometric, quadrupolar particles confined to a monolayer.

    PubMed

    Heinemann, Thomas; Antlanger, Moritz; Mazars, Martial; Klapp, Sabine H L; Kahl, Gerhard

    2016-02-21

    We investigate the structural properties of a two-dimensional system of ellipsoidal particles carrying a linear quadrupole moment in their center. These particles represent a simple model for a variety of uncharged, non-polar conjugated organic molecules. Using optimization tools based on ideas of evolutionary algorithms, we first examine the ground state structures as we vary the aspect ratio of the particles and the pressure. Interestingly, we find, besides the intuitively expected T-like configurations, a variety of complex structures, characterized with up to three different particle orientations. In an effort to explore the impact of thermal fluctuations, we perform constant-pressure molecular dynamics simulations within a range of rather low temperatures. We observe that ground state structures formed by particles with a large aspect ratio are in particular suited to withstand fluctuations up to rather high temperatures. Our comprehensive investigations allow for a deeper understanding of molecular or colloidal monolayer arrangements under the influence of a typical electrostatic interaction on a coarse-grained level. PMID:26896992

  19. Crystal structure of the 80S yeast ribosome.

    PubMed

    Jenner, Lasse; Melnikov, Sergey; Garreau de Loubresse, Nicolas; Ben-Shem, Adam; Iskakova, Madina; Urzhumtsev, Alexandre; Meskauskas, Arturas; Dinman, Jonathan; Yusupova, Gulnara; Yusupov, Marat

    2012-12-01

    The first X-ray structure of the eukaryotic ribosome at 3.0? resolution was determined using ribosomes isolated and crystallized from the yeast Saccharomyces cerevisiae (Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, Yusupov M: The structure of the eukaryotic ribosome at 3.0 A resolution. Science 2011, 334:1524-1529). This accomplishment was possible due to progress in yeast ribosome biochemistry as well as recent advances in crystallographic methods developed for structure determination of prokaryotic ribosomes isolated from Thermus thermophilus and Escherichia coli. In this review we will focus on the development of isolation procedures that allowed structure determination (both cryo-EM and X-ray crystallography) to be successful for the yeast S. cerevisiae. Additionally we will introduce a new nomenclature that facilitates comparison of ribosomes from different species and kingdoms of life. Finally we will discuss the impact of the yeast 80S ribosome crystal structure on perspectives for future investigations. PMID:22884264

  20. From protein structure to function via single crystal optical spectroscopy

    PubMed Central

    Ronda, Luca; Bruno, Stefano; Bettati, Stefano; Storici, Paola; Mozzarelli, Andrea

    2015-01-01

    The more than 100,000 protein structures determined by X-ray crystallography provide a wealth of information for the characterization of biological processes at the molecular level. However, several crystallographic artifacts, including conformational selection, crystallization conditions and radiation damages, may affect the quality and the interpretation of the electron density maps, thus limiting the relevance of structure determinations. Moreover, for most of these structures, no functional data have been obtained in the crystalline state, thus posing serious questions on their validity in infereing protein mechanisms. In order to solve these issues, spectroscopic methods have been applied for the determination of equilibrium and kinetic properties of proteins in the crystalline state. These methods are UV-vis spectrophotometry, spectrofluorimetry, IR, EPR, Raman, and resonance Raman spectroscopy. Some of these approaches have been implemented with on-line instruments at X-ray synchrotron beamlines. Here, we provide an overview of investigations predominantly carried out in our laboratory by single crystal polarized absorption UV-vis microspectrophotometry, the most applied technique for the functional characterization of proteins in the crystalline state. Studies on hemoglobins, pyridoxal 5?-phosphate dependent enzymes and green fluorescent protein in the crystalline state have addressed key biological issues, leading to either straightforward structure-function correlations or limitations to structure-based mechanisms. PMID:25988179

  1. Manganese oxide minerals: Crystal structures and economic and environmental significance

    PubMed Central

    Post, Jeffrey E.

    1999-01-01

    Manganese oxide minerals have been used for thousands of yearsby the ancients for pigments and to clarify glass, and today as ores of Mn metal, catalysts, and battery material. More than 30 Mn oxide minerals occur in a wide variety of geological settings. They are major components of Mn nodules that pave huge areas of the ocean floor and bottoms of many fresh-water lakes. Mn oxide minerals are ubiquitous in soils and sediments and participate in a variety of chemical reactions that affect groundwater and bulk soil composition. Their typical occurrence as fine-grained mixtures makes it difficult to study their atomic structures and crystal chemistries. In recent years, however, investigations using transmission electron microscopy and powder x-ray and neutron diffraction methods have provided important new insights into the structures and properties of these materials. The crystal structures for todorokite and birnessite, two of the more common Mn oxide minerals in terrestrial deposits and ocean nodules, were determined by using powder x-ray diffraction data and the Rietveld refinement method. Because of the large tunnels in todorokite and related structures there is considerable interest in the use of these materials and synthetic analogues as catalysts and cation exchange agents. Birnessite-group minerals have layer structures and readily undergo oxidation reduction and cation-exchange reactions and play a major role in controlling groundwater chemistry. PMID:10097056

  2. Automated detection and characterization of microstructural features: application to eutectic particles in single crystal Ni-based superalloys

    NASA Astrophysics Data System (ADS)

    Tschopp, M. A.; Groeber, M. A.; Fahringer, R.; Simmons, J. P.; Rosenberger, A. H.; Woodward, C.

    2010-03-01

    Serial sectioning methods continue to produce an abundant amount of image data for quantifying the three-dimensional nature of material microstructures. Here, we discuss a methodology to automate detecting and characterizing eutectic particles taken from serial images of a production turbine blade made of a heat-treated single crystal Ni-based superalloy (PWA 1484). This method includes two important steps for unassisted eutectic particle characterization: automatically identifying a seed point within each particle and segmenting the particle using a region growing algorithm with an automated stop point. Once detected, the segmented eutectic particles are used to calculate microstructural statistics for characterizing and reconstructing statistically representative synthetic microstructures for single crystal Ni-based superalloys. The significance of this work is its ability to automate characterization for analysing the 3D nature of eutectic particles.

  3. Crystal structures of intermediates in the nitroalkane oxidase reaction.

    PubMed

    Hroux, Annie; Bozinovski, Dragana M; Valley, Michael P; Fitzpatrick, Paul F; Orville, Allen M

    2009-04-21

    The flavoenzyme nitroalkane oxidase is a member of the acyl-CoA dehydrogenase superfamily. Nitroalkane oxidase catalyzes the oxidation of neutral nitroalkanes to nitrite and the corresponding aldehydes or ketones. Crystal structures to 2.2 A resolution or better of enzyme complexes with bound substrates and of a trapped substrate-flavin adduct are described. The D402N enzyme has no detectable activity with neutral nitroalkanes [Valley, M. P., and Fitzpatrick, P. F. (2003) J. Am. Chem. Soc. 125, 8738-8739]. The structure of the D402N enzyme crystallized in the presence of 1-nitrohexane or 1-nitrooctane shows the presence of the substrate in the binding site. The aliphatic chain of the substrate extends into a tunnel leading to the enzyme surface. The oxygens of the substrate nitro group interact both with amino acid residues and with the 2'-hydroxyl of the FAD. When nitroalkane oxidase oxidizes nitroalkanes in the presence of cyanide, an electrophilic flavin imine intermediate can be trapped [Valley, M. P., Tichy, S. E., and Fitzpatrick, P. F. (2005) J. Am. Chem. Soc. 127, 2062-2066]. The structure of the enzyme trapped with cyanide during oxidation of 1-nitrohexane shows the presence of the modified flavin. A continuous hydrogen bond network connects the nitrogen of the CN-hexyl-FAD through the FAD 2'-hydroxyl to a chain of water molecules extending to the protein surface. Together, our complementary approaches provide strong evidence that the flavin cofactor is in the appropriate oxidation state and correlates well with the putative intermediate state observed within each of the crystal structures. Consequently, these results provide important structural descriptions of several steps along the nitroalkane oxidase reaction cycle. PMID:19265437

  4. Crystal Structures of Intermediates in the Nitroalkane Oxidase Reaction

    SciTech Connect

    Heroux, A.; Bozinovski, D; Valley, M; Fitzpatrick, P; Orville, A

    2009-01-01

    The flavoenzyme nitroalkane oxidase is a member of the acyl-CoA dehydrogenase superfamily. Nitroalkane oxidase catalyzes the oxidation of neutral nitroalkanes to nitrite and the corresponding aldehydes or ketones. Crystal structures to 2.2 {angstrom} resolution or better of enzyme complexes with bound substrates and of a trapped substrate-flavin adduct are described. The D402N enzyme has no detectable activity with neutral nitroalkanes. The structure of the D402N enzyme crystallized in the presence of 1-nitrohexane or 1-nitrooctane shows the presence of the substrate in the binding site. The aliphatic chain of the substrate extends into a tunnel leading to the enzyme surface. The oxygens of the substrate nitro group interact both with amino acid residues and with the 2'-hydroxyl of the FAD. When nitroalkane oxidase oxidizes nitroalkanes in the presence of cyanide, an electrophilic flavin imine intermediate can be trapped (Valley, M. P., Tichy, S. E., and Fitzpatrick, P. F. (2005) J. Am. Chem. Soc. 127, 2062-2066). The structure of the enzyme trapped with cyanide during oxidation of 1-nitrohexane shows the presence of the modified flavin. A continuous hydrogen bond network connects the nitrogen of the CN-hexyl-FAD through the FAD 2'-hydroxyl to a chain of water molecules extending to the protein surface. Together, our complementary approaches provide strong evidence that the flavin cofactor is in the appropriate oxidation state and correlates well with the putative intermediate state observed within each of the crystal structures. Consequently, these results provide important structural descriptions of several steps along the nitroalkane oxidase reaction cycle.

  5. Identifying duplicate crystal structures: XTALCOMP, an open-source solution

    NASA Astrophysics Data System (ADS)

    Lonie, David C.; Zurek, Eva

    2012-03-01

    We describe the implementation of XTALCOMP, an efficient, reliable, and open-source library that tests if two crystal descriptions describe the same underlying structure. The algorithm has been tested and found to correctly identify duplicate structures in spite of the "real-world" difficulties that arise from working with numeric crystal representations: degenerate unit cell lattices, numerical noise, periodic boundaries, and the lack of a canonical coordinate origin. The library is portable, open, and not dependent on any external packages. A web interface to the algorithm is publicly accessible at http://xtalopt.openmolecules.net/xtalcomp/xtalcomp.html. Program summaryProgram title: XtalComp Catalogue identifier: AEKV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: "New" (3-clause) BSD [1] No. of lines in distributed program, including test data, etc.: 3148 No. of bytes in distributed program, including test data, etc.: 21 860 Distribution format: tar.gz Programming language: C++ Computer: No restrictions Operating system: All operating systems with a compliant C++ compiler. Classification: 7.8 Nature of problem: Computationally identifying duplicate crystal structures taken from the output of modern solid state calculations is a non-trivial exercise for many reasons. The translation vectors in the description are not unique they may be transformed into linear combinations of themselves and continue to describe the same extended structure. The coordinates and cell parameters contain numerical noise. The periodic boundary conditions at the unit cell faces, edges, and corners can cause very small displacements of atomic coordinates to result in very different representations. The positions of all atoms may be uniformly translated by an arbitrary vector without modifying the underlying structure. Additionally, certain applications may consider enantiomorphic structures to be identical. Solution method: The XtalComp algorithm overcomes these issues to detect duplicate structures regardless of differences in representation. It begins by performing a Niggli reduction on the inputs, standardizing the translation vectors and orientations. A transform search is performed to identify candidate sets of rotations, reflections, and translations that potentially map the description of one crystal onto the other, solving the problems of enantiomorphs and rotationally degenerate lattices. The atomic positions resulting from each candidate transform are then compared, using a cell-expansion technique to remove periodic boundary issues. Computational noise is treated by comparing non-integer quantities using a specified tolerance. Running time: The test run provided takes less than a second to complete.

  6. Crystal structure and crystal chemistry of melanovanadite, a natural vanadium bronze.

    USGS Publications Warehouse

    Konnert, J.A.; Evans, H.T., Jr.

    1987-01-01

    The crystal structure of melanovanadite from Minas Ragra, Peru, has been determined in space group P1. The triclinic unit cell (non-standard) has a 6.360(2), b 18.090(9), c 6.276(2) A, alpha 110.18(4)o, beta 101.62(3)o, gamma 82.86(4)o. A subcell with b' = b/2 was found by crystal-structure analysis to contain CaV4O10.5H2O. The subcell has a layer structure in which the vanadate sheet consists of corner-shared tetrahedral VO4 and double square-pyramidal V2O8 groups, similar to that previously found in synthetic CsV2O5. Refinement of the full structure (R = 0.056) showed that the Ca atom, which half-occupies a general position in the subcell, is 90% ordered at one of these sites in the whole unit cell. Bond length-bond strength estimates indicate that the tetrahedra contain V5+, and the square pyramids, V4+.-J.A.Z.

  7. 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

  8. Crystal and molecular structure of N-methylpiperidine betaine hydrobromide

    NASA Astrophysics Data System (ADS)

    Dega-Szafran, Zofia; Tykarska, Ewa; Dulewicz, Ewa; Szafran, Mirosław

    2002-03-01

    The molecular and crystal structure of N-methylpiperidine betaine hydrobromide, MPBHBr, has been solved by X-ray diffraction methods at 100 K and refined to the R=0.017 ( I>2 σ( I)). The crystals are monoclinic, space group P2 1/ c, a=6.193(1), b=13.275(3), c=13.056(3) Å, β=103.38(3)°, V=1044.2(4) Å 3, Z=4. Piperidine ring adopts a chair conformation with the CH 2COOH group in an axial and the CH 3 group in an equatorial position. The carboxylic group is engaged in a weak hydrogen bond with the bromide ion, O-H⋯Br - (Br -⋯O 3.130(1) Å). Powder FTIR spectrum was measured and assignments of the observed bands to vibrations of the hydrogen bond are proposed. In the crystal, the hydroxy proton in the COOH group is in syn conformation relative to the CO bond, while in the PM3-optimized structure it is in anti.

  9. N-methylcodeinium iodide—Crystal structure and spectroscopic elucidation

    NASA Astrophysics Data System (ADS)

    Seidel, R. W.; Bakalska, B. R.; Kolev, T.; Vassilev, D.; Mayer-Figge, H.; Spiteller, M.; Sheldrick, W. S.; Koleva, B. B.

    2009-07-01

    The correlation between the structure and the spectroscopic properties of N-methylcodeinium iodide ( 1) has been studied, using the methods of single crystal X-ray diffraction, IR-LD spectroscopy of oriented samples as a suspension in nematic liquid crystals, UV-vis spectroscopy and 1H and 13C NMR spectroscopy. HPLC tandem mass spectrometry (HPLC ESI MS/MS) and thermal methods were also employed. Quantum chemical calculations have been performed with a view to obtaining the electronic structure and vibrational properties of the title compound. Compound ( 1) crystallizes in the space group P2 12 12 1 and its cations and anions are joined by moderate intermolecular OH…I - interaction of length 3.442 Å. The codeine molecule exhibits the classical T-shape for opiates. A dihedral angle value of 86.4(5)° between the A/B/C and D/E planes is obtained. Rings A and B are effectively coplanar with an interplanar angle of 3.6(3)°.

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

    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.

  11. 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

  12. Crystal structures of three (trichloromethyl)(carbamoyl)disulfanes

    PubMed Central

    Goldenberg, Barbara L.; Young Jr, Victor G.; Barany, George

    2015-01-01

    The present paper reports crystallographic studies on three related compounds that were of inter­est as precursors for synthetic and mechanistic work in organosulfur chemistry, as well as to model nitro­gen-protecting groups: (N-methyl­carbamo­yl)(tri­chloro­meth­yl)disulfane, C3H4Cl3NOS2, (1), (N-benzyl­carbamo­yl)(tri­chloro­meth­yl)disulfane, C9H8Cl3NOS2, (2), and (N-methyl-N-phenyl­carbamo­yl)(tri­chloro­meth­yl)disulfane, C9H8Cl3NOS2, (3). Their mol­ecular structures, with similar bond lengths and angles for the CCl3SS(C=O)N moieties, are confirmed. Compounds (1) and (3) both crystallized with two independent mol­ecules in the asymmetric unit. Classical hydrogen bonding, as well as chlorine-dense regions, are evident in the crystal packing for (1) and (2). In the crystal of (1), mol­ecules are linked via N—H⋯O hydrogen bonds forming chains along [110], which are linked by short Cl⋯Cl and S⋯O contacts forming sheets parallel to (001). In the crystal of (2), mol­ecules are linked via N—H⋯O hydrogen bonds forming chains along [001], which in turn are linked by pairs of short O⋯Cl contacts forming ribbons along the c-axis direction. In the crystal of (3), there are no classical hydrogen bonds present and the chlorine-dense regions observed in (1) and (2) are lacking. PMID:26594398

  13. Crystal structures of three (trichloromethyl)(carbamoyl)disulfanes.

    PubMed

    Goldenberg, Barbara L; Young, Victor G; Barany, George

    2015-10-01

    The present paper reports crystallographic studies on three related compounds that were of inter-est as precursors for synthetic and mechanistic work in organosulfur chemistry, as well as to model nitro-gen-protecting groups: (N-methyl-carbamo-yl)(tri-chloro-meth-yl)disulfane, C3H4Cl3NOS2, (1), (N-benzyl-carbamo-yl)(tri-chloro-meth-yl)disulfane, C9H8Cl3NOS2, (2), and (N-methyl-N-phenyl-carbamo-yl)(tri-chloro-meth-yl)disulfane, C9H8Cl3NOS2, (3). Their mol-ecular structures, with similar bond lengths and angles for the CCl3SS(C=O)N moieties, are confirmed. Compounds (1) and (3) both crystallized with two independent mol-ecules in the asymmetric unit. Classical hydrogen bonding, as well as chlorine-dense regions, are evident in the crystal packing for (1) and (2). In the crystal of (1), mol-ecules are linked via N-H?O hydrogen bonds forming chains along [110], which are linked by short Cl?Cl and S?O contacts forming sheets parallel to (001). In the crystal of (2), mol-ecules are linked via N-H?O hydrogen bonds forming chains along [001], which in turn are linked by pairs of short O?Cl contacts forming ribbons along the c-axis direction. In the crystal of (3), there are no classical hydrogen bonds present and the chlorine-dense regions observed in (1) and (2) are lacking. PMID:26594398

  14. Optically induced periodic structures in smectic-C liquid crystals.

    PubMed

    Jákli, A; Kósa, T; Vajda, A; Benkler, E; Jánossy, I; Palffy-Muhoray, P

    2001-01-01

    We explore periodic structures of smectic-C (SmC) liquid crystals, induced optically by a polarization grating. The studied cells contain a passive surface of rubbed polyimide and an active photosensitive substrate of azo-dye doped polyimide. In a nematic phase the director field can be periodic independent of the angle between the grating vector and the rubbing direction. In the SmA phase periodic structure can be induced only by layer undulations. The SmC behaves similarly to the nematic phase, but the director can rotate only on a cone, which results in a more complex geometry. The periodic pattern is superimposed with four different director and layer structures. In spite of the coexistence of the nonuniform structures the diffraction efficiency is better in the SmC, than in the nematic phase. PMID:11304276

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

    SciTech Connect

    Wang Mingzhu; Liu Lin; Wang Yanli; Wei Zhiyi; Zhang Ping; Li Yikun; Jiang Xiaohua; Xu Hang Gong Weimin

    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.

  16. 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.

  17. Crystal structure of isoflavone reductase from alfalfa (Medicago sativa L.).

    PubMed

    Wang, Xiaoqiang; He, Xianzhi; Lin, Jianqiao; Shao, Hui; Chang, Zhenzhan; Dixon, Richard A

    2006-05-19

    Isoflavonoids play important roles in plant defense and exhibit a range of mammalian health-promoting activities. Isoflavone reductase (IFR) specifically recognizes isoflavones and catalyzes a stereospecific NADPH-dependent reduction to (3R)-isoflavanone. The crystal structure of Medicago sativa IFR with deletion of residues 39-47 has been determined at 1.6A resolution. Structural analysis, molecular modeling and docking, and comparison with the structures of other NADPH-dependent enzymes, defined the putative binding sites for co-factor and substrate and potential key residues for enzyme activity and substrate specificity. Further mutagenesis has confirmed the role of Lys144 as a catalytic residue. This study provides a structural basis for understanding the enzymatic mechanism and substrate specificity of IFRs as well as the functions of IFR-like proteins. PMID:16600295

  18. Equation of State and Structure of Electrostatic Colloidal Crystals: Osmotic Pressure and Scattering Study

    NASA Astrophysics Data System (ADS)

    Reus, V.; Belloni, L.; Zemb, T.; Lutterbach, N.; Versmold, H.

    1997-04-01

    Electrostatically stabilized aqueous suspensions of bromopolystyrene particles have been studied by scattering and osmotic pressure measurements. We investigated their structure and the interparticle interactions as a function of the volume fraction at very low salinity of the order of micromole/l. At slow crystallization speed we observe perfect crystals, body centrered cubic crystals by light scattering for volume fractions between 0.04 and 0.7% and face centrered cubic crystals by Ultra Small Angle X ray Scattering (USAXS) for higher volume fractions (2 12%). After shear the crystal displays other structures. At low volume fractions (0.1 0.3%), some reflexions disappear by light scattering whereas a strong diffuse prepeak" appears before the first Bragg peak for higher concentrations (2 12%) evidenced by USAXS. This prepeak" can be attributed to defects in the crystal. Osmotic pressures have been measured by difference between the hydrostatic pressure in the solution and in the reservoir separated by an hemipermeable membrane. The experimental data are very well reproduced by the Poisson Boltzmann Cell (PBC) theory which shows that the interaction between particles is purely repulsive. No attractive contribution has been experimentally detected. By calculating the mean square displacement of a particle inside its cage from the eccentric PBC model, we have verified that the Lindemann criterion for the existence of crystals (against melting) is satisfied. This study has allowed to determine the equation of state of an electrostatical colloidal crystal and is equivalent to an ultraprecise force/distance measurement between latex particles since the measured forces are of the order of 10^{-12} N for distances of the order of 4000 . Des suspensions aqueuses de particules de bromopolystyrne ont t caractrises par diffusion de lumire, diffusion de rayons X aux petits angles et par des mesures de pression osmotique. Nous avons ainsi tudi leur structure et les interactions interparticulaires en fonction de la fraction volumique salinit constante de l'ordre de la micromole/l. Lorsque la cristallisation est lente, nous observons des cristaux parfaits cubiques centrs par diffusion de lumire pour des fractions volumiques comprises entre 0,04 et 0,7 % et cubiques faces centres pax diffusion de rayons X aux petits angles pour des fractions volumiques plus leves (2 12 %). Aprs cisaillement, des dfauts apparaissent dans les cristaux ; ils sont caractriss par la disparition de certaines raies de Bragg en diffusion de lumire pour des chantillons de fraction volumique comprise entre 0,1 et 0,3 % et par la prsence d'un pr pic observ par diffusion de rayons X aux petits angles avant le premier pic de Bragg, pour des chantillons plus concentrs (2 12 %). Les pressions osmotiques ont t mesures par diffrence de pression hydrostatique entre la solution et le rservoir spars par une membrane hmipermable. Les donnes exprimentales sont bien reproduites par la thorie Poisson Boltzmann Rseau (PBR) qui montre que les interactions sont purement rpulsives. Aucune force attractive faible de longue porte n'a t dtecte exprimentalement. En calculant le dplacement moyen d'une particule l'intrieur de sa cage l'aide du modle PBR "excentr", nous avons vrifi que le critre de Lindemann tait satisfait pour tous les cristaux observs. Cette tude a permis de dterminer l'quation d'tat d'un cristal colloidal lectrostatique. Les rsultats sont quivalents une mesure de force ultraprcise puisque les forces d'interaction mesures entre particules sont de l'ordre de 10^{-12} N pour des distances centre centre de l'ordre de 4000 .

  19. Crystal structure of (1Z,2E)-cinnamaldehyde oxime

    PubMed Central

    Bugenhagen, Bernhard; Al Soom, Nuha; Al Jasem, Yosef; Thiemann, Thies

    2015-01-01

    The title compound, C9H9NO, crystallized with two independent molecules (A and B) in the asymmetric unit. The conformation of the two molecules differs slightly with the phenyl ring in molecule A, forming a dihedral angle of 15.38?(12) with the oxime group (ON=C), compared to the corresponding angle of 26.29?(11) in molecule B. In the crystal, the A and B molecules are linked head-to-head by OH?N hydrogen bonds, forming ABAB zigzag chains along [010]. Within the chains and between neighbouring chains there are CH?? interactions present, forming a three-dimensional structure.

  20. Syntheses and crystal structures of three barium uranium sulfides

    NASA Astrophysics Data System (ADS)

    Mesbah, Adel; Ibers, James A.

    2013-03-01

    The barium uranium sulfides Ba3.69US6, BaUS3, and BaU2S5 have been synthesized at 1273, 1323, and 1323 K, respectively. The structures of these compounds have been determined by single-crystal X-ray diffraction methods. They crystallize in space groups D3d6-R3c, D2h16-Pnma, and C2h5-P21/c, respectively. Among these three ternaries and Ba2US6 the coordination geometries about the U atoms vary considerably. Ba3.69US6 is a mixed U4+/U5+compound whereas the others are U4+ compounds. The decreasing dimensionality of the four compounds with increasing Ba-to-U content shows the expected trend.

  1. Structural chemistry and number theory amalgamized: crystal structure of Na11Hg52.

    PubMed

    Hornfeck, Wolfgang; Hoch, Constantin

    2015-12-01

    The recently elucidated crystal structure of the technologically important amalgam Na11Hg52 is described by means of a method employing some fundamental concept of number theory, namely modular arithmetical (congruence) relations observed between a slightly idealized set of atomic coordinates. In combination with well known ideas from group theory, regarding lattice-sublattice transformations, these allow for a deeper mutual understanding of both and provide the structural chemist with a slightly different kind of spectacles, thus enabling a distinct viw on complex crystal structures in general. PMID:26634733

  2. Characterization of scintillator crystals for usage as prompt gamma monitors in particle therapy

    NASA Astrophysics Data System (ADS)

    Roemer, K.; Pausch, G.; Bemmerer, D.; Berthel, M.; Dreyer, A.; Golnik, C.; Hueso-González, F.; Kormoll, T.; Petzoldt, J.; Rohling, H.; Thirolf, P.; Wagner, A.; Wagner, L.; Weinberger, D.; Fiedler, F.

    2015-10-01

    Particle therapy in oncology is advantageous compared to classical radiotherapy due to its well-defined penetration depth. In the so-called Bragg peak, the highest dose is deposited; the tissue behind the cancerous area is not exposed. Different factors influence the range of the particle and thus the target area, e.g. organ motion, mispositioning of the patient or anatomical changes. In order to avoid over-exposure of healthy tissue and under-dosage of cancerous regions, the penetration depth of the particle has to be monitored, preferably already during the ongoing therapy session. The verification of the ion range can be performed using prompt gamma emissions, which are produced by interactions between projectile and tissue, and originate from the same location and time of the nuclear reaction. The prompt gamma emission profile and the clinically relevant penetration depth are correlated. Various imaging concepts based on the detection of prompt gamma rays are currently discussed: collimated systems with counting detectors, Compton cameras with (at least) two detector planes, or the prompt gamma timing method, utilizing the particle time-of-flight within the body. For each concept, the detection system must meet special requirements regarding energy, time, and spatial resolution. Nonetheless, the prerequisites remain the same: the gamma energy region (2 to 10 MeV), high counting rates and the stability in strong background radiation fields. The aim of this work is the comparison of different scintillation crystals regarding energy and time resolution for optimized prompt gamma detection.

  3. Lagrangian chaos and particle diffusion in electroconvection of planar nematic liquid crystals.

    PubMed

    Hidaka, Yoshiki; Hashiguchi, Megumi; Oikawa, Noriko; Kai, Shoichi

    2015-09-01

    Two types of spatiotemporal chaos in the electroconvection of nematic liquid crystals, such as defect turbulence and spatiotemporal intermittency, have been statistically investigated according to the Lagrangian picture. Here fluctuations are traced using the motion of a single particle driven by chaotic convection. In the defect turbulence (fluctuating normal rolls), a particle is mainly trapped in a roll but sometimes jumps to a neighboring roll. Its activation energy is then obtained from the jumping (hopping) rate. This research clarifies that diffusion in the defect turbulence regime in electroconvection can be regarded as a kind of hopping process. The spatiotemporal intermittency appears as a coexistent state of ordered grid domains and turbulent domains. The motion of a single particle shows weak and strong diffusion, respectively, in the ordered and turbulent domains. The diffusion characteristics intermittently change from one to another with certain durations as the domains change. This research has found that the distribution function of the duration that a particle remains in an ordered area has a power-law decay for which the index is different from that obtained by the Eulerian measurement. PMID:26465542

  4. Theory of elastic interaction between arbitrary colloidal particles in confined nematic liquid crystals.

    PubMed

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

    2012-12-01

    We develop the method proposed by Chernyshuk and Lev [Phys. Rev. E 81, 041701 (2010)] for theoretical investigation of elastic interactions between colloidal particles of arbitrary shape and chirality (polar as well as azimuthal anchoring) in the confined nematic liquid crystal (NLC). General expressions for six different types of multipole elastic interactions are obtained in the confined NLC: monopole-monopole (Coulomb type), monopole-dipole, monopole-quadrupole, dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole interactions. The obtained formulas remain valid in the presence of the external electric or magnetic fields. The exact equations are found for all multipole coefficients for the weak anchoring case. For the strong anchoring coupling, the connection between the symmetry of the shape or director and multipole coefficients is obtained, which enables us to predict which multipole coefficients vanish and which remain nonzero. The particles with azimuthal helicoid anchoring are considered as an example. Dipole-dipole interactions between helicoid cylinders and cones are found in the confined NLC. In addition, the banana-shaped particles in homeotropic and planar nematic cells are considered. It is found that the dipole-dipole interaction between banana-shaped particles differs greatly from the dipole-dipole interaction between the axially symmetrical particles in the nematic cell. There is a crossover from attraction to repulsion between banana particles along some directions in nematic cells. It is shown that monopoles do not "feel" the type of nematic cell: monopole-monopole interaction turns out to be the same in homeotropic and planar nematic cells and converges to the Coulomb law as thickness increases, L??. PMID:23367965

  5. Theory of elastic interaction between arbitrary colloidal particles in confined nematic liquid crystals

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

    We develop the method proposed by Chernyshuk and Lev [Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.81.041701 81, 041701 (2010)] for theoretical investigation of elastic interactions between colloidal particles of arbitrary shape and chirality (polar as well as azimuthal anchoring) in the confined nematic liquid crystal (NLC). General expressions for six different types of multipole elastic interactions are obtained in the confined NLC: monopole-monopole (Coulomb type), monopole-dipole, monopole-quadrupole, dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole interactions. The obtained formulas remain valid in the presence of the external electric or magnetic fields. The exact equations are found for all multipole coefficients for the weak anchoring case. For the strong anchoring coupling, the connection between the symmetry of the shape or director and multipole coefficients is obtained, which enables us to predict which multipole coefficients vanish and which remain nonzero. The particles with azimuthal helicoid anchoring are considered as an example. Dipole-dipole interactions between helicoid cylinders and cones are found in the confined NLC. In addition, the banana-shaped particles in homeotropic and planar nematic cells are considered. It is found that the dipole-dipole interaction between banana-shaped particles differs greatly from the dipole-dipole interaction between the axially symmetrical particles in the nematic cell. There is a crossover from attraction to repulsion between banana particles along some directions in nematic cells. It is shown that monopoles do not “feel” the type of nematic cell: monopole-monopole interaction turns out to be the same in homeotropic and planar nematic cells and converges to the Coulomb law as thickness increases, L→∞.

  6. Controlling Chirality of Entropic Crystals

    NASA Astrophysics Data System (ADS)

    Damasceno, Pablo F.; Karas, Andrew S.; Schultz, Benjamin A.; Engel, Michael; Glotzer, Sharon C.

    2015-10-01

    Colloidal crystal structures with complexity and diversity rivaling atomic and molecular crystals have been predicted and obtained for hard particles by entropy maximization. However, thus far homochiral colloidal crystals, which are candidates for photonic metamaterials, are absent. Using Monte Carlo simulations we show that chiral polyhedra exhibiting weak directional entropic forces self-assemble either an achiral crystal or a chiral crystal with limited control over the crystal handedness. Building blocks with stronger faceting exhibit higher selectivity and assemble a chiral crystal with handedness uniquely determined by the particle chirality. Tuning the strength of directional entropic forces by means of particle rounding or the use of depletants allows for reconfiguration between achiral and homochiral crystals. We rationalize our findings by quantifying the chirality strength of each particle, both from particle geometry and potential of mean force and torque diagrams.

  7. Controlling Chirality of Entropic Crystals.

    PubMed

    Damasceno, Pablo F; Karas, Andrew S; Schultz, Benjamin A; Engel, Michael; Glotzer, Sharon C

    2015-10-01

    Colloidal crystal structures with complexity and diversity rivaling atomic and molecular crystals have been predicted and obtained for hard particles by entropy maximization. However, thus far homochiral colloidal crystals, which are candidates for photonic metamaterials, are absent. Using Monte Carlo simulations we show that chiral polyhedra exhibiting weak directional entropic forces self-assemble either an achiral crystal or a chiral crystal with limited control over the crystal handedness. Building blocks with stronger faceting exhibit higher selectivity and assemble a chiral crystal with handedness uniquely determined by the particle chirality. Tuning the strength of directional entropic forces by means of particle rounding or the use of depletants allows for reconfiguration between achiral and homochiral crystals. We rationalize our findings by quantifying the chirality strength of each particle, both from particle geometry and potential of mean force and torque diagrams. PMID:26550757

  8. 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.

  9. Crystal Structure of the Japanese Encephalitis Virus Envelope Protein

    SciTech Connect

    Luca, Vincent C.; AbiMansour, Jad; Nelson, Christopher A.; Fremont, Daved H.

    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.

  10. 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 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

  11. Crystal Structure of Rat Carnitine Palmitoyltransferase II (CPT-II)

    SciTech Connect

    Hsiao,Y.; Jogl, G.; Esser, V.; Tong, L.

    2006-01-01

    Carnitine palmitoyltransferase II (CPT-II) has a crucial role in the {beta}-oxidation of long-chain fatty acids in mitochondria. We report here the crystal structure of rat CPT-II at 1.9 Angstroms resolution. The overall structure shares strong similarity to those of short- and medium-chain carnitine acyltransferases, although detailed structural differences in the active site region have a significant impact on the substrate selectivity of CPT-II. Three aliphatic chains, possibly from a detergent that is used for the crystallization, were found in the structure. Two of them are located in the carnitine and CoA binding sites, respectively. The third aliphatic chain may mimic the long-chain acyl group in the substrate of CPT-II. The binding site for this aliphatic chain does not exist in the short- and medium-chain carnitine acyltransferases, due to conformational differences among the enzymes. A unique insert in CPT-II is positioned on the surface of the enzyme, with a highly hydrophobic surface. It is likely that this surface patch mediates the association of CPT-II with the inner membrane of the mitochondria.

  12. Crystal Structure of a Ube2S-Ubiquitin Conjugate

    PubMed Central

    Lorenz, Sonja; Bhattacharyya, Moitrayee; Feiler, Christian; Rape, Michael; Kuriyan, John

    2016-01-01

    Protein ubiquitination occurs through the sequential formation and reorganization of specific protein-protein interfaces. Ubiquitin-conjugating (E2) enzymes, such as Ube2S, catalyze the formation of an isopeptide linkage between the C-terminus of a “donor” ubiquitin and a primary amino group of an “acceptor” ubiquitin molecule. This reaction involves an intermediate, in which the C-terminus of the donor ubiquitin is thioester-bound to the active site cysteine of the E2 and a functionally important interface is formed between the two proteins. A docked model of a Ube2S-donor ubiquitin complex was generated previously, based on chemical shift mapping by NMR, and predicted contacts were validated in functional studies. We now present the crystal structure of a covalent Ube2S-ubiquitin complex. The structure contains an interface between Ube2S and ubiquitin in trans that resembles the earlier model in general terms, but differs in detail. The crystallographic interface is more hydrophobic than the earlier model and is stable in molecular dynamics (MD) simulations. Remarkably, the docked Ube2S-donor complex converges readily to the configuration seen in the crystal structure in 3 out of 8 MD trajectories. Since the crystallographic interface is fully consistent with mutational effects, this indicates that the structure provides an energetically favorable representation of the functionally critical Ube2S-donor interface. PMID:26828794

  13. Crystal Structure of a Ube2S-Ubiquitin Conjugate.

    PubMed

    Lorenz, Sonja; Bhattacharyya, Moitrayee; Feiler, Christian; Rape, Michael; Kuriyan, John

    2016-01-01

    Protein ubiquitination occurs through the sequential formation and reorganization of specific protein-protein interfaces. Ubiquitin-conjugating (E2) enzymes, such as Ube2S, catalyze the formation of an isopeptide linkage between the C-terminus of a "donor" ubiquitin and a primary amino group of an "acceptor" ubiquitin molecule. This reaction involves an intermediate, in which the C-terminus of the donor ubiquitin is thioester-bound to the active site cysteine of the E2 and a functionally important interface is formed between the two proteins. A docked model of a Ube2S-donor ubiquitin complex was generated previously, based on chemical shift mapping by NMR, and predicted contacts were validated in functional studies. We now present the crystal structure of a covalent Ube2S-ubiquitin complex. The structure contains an interface between Ube2S and ubiquitin in trans that resembles the earlier model in general terms, but differs in detail. The crystallographic interface is more hydrophobic than the earlier model and is stable in molecular dynamics (MD) simulations. Remarkably, the docked Ube2S-donor complex converges readily to the configuration seen in the crystal structure in 3 out of 8 MD trajectories. Since the crystallographic interface is fully consistent with mutational effects, this indicates that the structure provides an energetically favorable representation of the functionally critical Ube2S-donor interface. PMID:26828794

  14. Crystal structure studies on sulfur oxygenase reductase from Acidianus tengchongensis

    SciTech Connect

    Li Mei; Chen Zhiwei; Zhang Pingfeng; Pan Xiaowei; Jiang Chengying; An Xiaomin; Liu Shuangjiang; Chang Wenrui

    2008-05-09

    Sulfur oxygenase reductase (SOR) simultaneously catalyzes oxidation and reduction of elemental sulfur to produce sulfite, thiosulfate, and sulfide in the presence of molecular oxygen. In this study, crystal structures of wild type and mutants of SOR from Acidianus tengchongensis (SOR-AT) in two different crystal forms were determined and it was observed that 24 identical SOR monomers form a hollow sphere. Within the icosatetramer sphere, the tetramer and trimer channels were proposed as the paths for the substrate and products, respectively. Moreover, a comparison of SOR-AT with SOR-AA (SOR from Acidianus ambivalens) structures showed that significant differences existed at the active site. Firstly, Cys31 is not persulfurated in SOR-AT structures. Secondly, the iron atom is five-coordinated rather than six-coordinated, since one of the water molecules ligated to the iron atom in the SOR-AA structure is lost. Consequently, the binding sites of substrates and a hypothetical catalytic process of SOR were proposed.

  15. Crystal Structure of a Rhomboid Family Intramembrane Protease.

    SciTech Connect

    Wang,Y.; Zhang, Y.; Ha, Y.

    2006-01-01

    Escherichia coli GlpG is an integral membrane protein that belongs to the widespread rhomboid protease family. Rhomboid proteases, like site-2 protease (S2P) and {gamma}-secretase, are unique in that they cleave the transmembrane domain of other membrane proteins. Here we describe the 2.1 {angstrom} resolution crystal structure of the GlpG core domain. This structure contains six transmembrane segments. Residues previously shown to be involved in catalysis, including a Ser-His dyad, and several water molecules are found at the protein interior at a depth below the membrane surface. This putative active site is accessible by substrate through a large 'V-shaped' opening that faces laterally towards the lipid, but is blocked by a half-submerged loop structure. These observations indicate that, in intramembrane proteolysis, the scission of peptide bonds takes place within the hydrophobic environment of the membrane bilayer. The crystal structure also suggests a gating mechanism for GlpG that controls substrate access to its hydrophilic active site.

  16. Diterbium heptanickel: a crystal structure redetermination

    PubMed Central

    Levytskyy, Volodymyr; Babizhetskyy, Volodymyr; Kotur, Bohdan; Smetana, Volodymyr

    2014-01-01

    The crystal structure of the title compound, Tb2Ni7, was redetermined from single-crystal X-ray diffraction data. In comparison with previous studies based on powder X-ray diffraction data [Lemaire et al. (1967). C. R. Acad. Sci. Ser. B, 265, 12801282; Lemaire & Paccard (1969). Bull. Soc. Fr. Mineral. Cristallogr. 92, 916; Buschow & van der Goot (1970). J. Less-Common Met. 22, 419428], the present redetermination affords refined coordinates and anisotropic displacement parameters for all atoms. A partial occupation for one Tb atom results in the non-stoichiometric composition Tb1.962?(4)Ni7. The title compound adopts the Ce2Ni7 structure type and can also be derived from the CaCu5 structure type as an intergrowth structure. The asymmetric unit contains two Tb sites (both site symmetries 3m.) and five Ni sites (.m., mm2, 3m., 3m., -3m.). The two different coordination polyhedra of Tb are a FrankKasper polyhedron formed by four Tb and 12 Ni atoms and a pseudo FrankKasper polyhedron formed by two Tb and 18 Ni atoms. The four different coordination polyhedra of Ni are FrankKasper icosahedra formed by five Tb and seven Ni atoms, four Tb and eight Ni atoms, three Tb and nine Ni atoms, and six Tb and six Ni atoms, respectively. PMID:25249871

  17. Crystal Structure of Baculovirus RNA Triphosphatase Complexed with Phosphate

    SciTech Connect

    Changela, Anita; Martin, Alexandra; Shuman, Stewart; Mondragon, Alfonso

    2010-03-05

    Baculovirus RNA 5'-triphosphatase (BVP) exemplifies a family of RNA-specific cysteine phosphatases that includes the RNA triphosphatase domains of metazoan and plant mRNA capping enzymes. Here we report the crystal structure of BVP in a phosphate-bound state at 1.5 {angstrom} resolution. BVP adopts the characteristic cysteine-phosphatase {alpha}/{beta} fold and binds two phosphate ions in the active site region, one of which is proposed to mimic the phosphate of the product complex after hydrolysis of the covalent phosphoenzyme intermediate. The crystal structure highlights the role of backbone amides and side chains of the P-loop motif {sup 118}HCTHGXNRT{sup 126} in binding the cleavable phosphate and stabilizing the transition state. Comparison of the BVP structure to the apoenzyme of mammalian RNA triphosphatase reveals a concerted movement of the Arg-125 side chain (to engage the phosphate directly) and closure of an associated surface loop over the phosphate in the active site. The structure highlights a direct catalytic role of Asn-124, which is the signature P-loop residue of the RNA triphosphatase family and a likely determinant of the specificity of BVP for hydrolysis of phosphoanhydride linkages.

  18. Synthesis and crystal structure of three silver indium double phosphates

    NASA Astrophysics Data System (ADS)

    Strelkov, M. A.; Zhizhin, M. G.; Komissarova, L. N.

    2006-12-01

    Three new silver indium double phosphates Ag 3In(PO 4) 2 (I), β-(II) and α-Ag 3In 2(PO 4) 3 (III) were synthesized by solid state method (I and II—700 °C, III—900 °C). Compounds I and II crystallize into a monoclinic system (I—sp. gr. C2/ m, Z=2, a=8.7037(1)Å, b=5.4884(1)Å, c=7.3404(1)Å, β=93.897(1)°; II—sp. gr. C2/ c, Z=4, a=12.6305(1)Å, b=12.8549(1)Å, c=6.5989(1)Å, β=113.842(1)°), and compound III crystallize into a hexagonal system (sp. gr. R-3 c, Z=6, a=8.9943(1)Å, c=22.7134(1)Å). Their crystal structures were determined by the Rietveld analysis (I— R=6.47, R=8.54; II— R=5.67, R=6.40; III— R=7.30, R=9.91). Structure of Ag 3In(PO 4) 2 is related to the sodium chromate structure type and is isotypic to α-Na 3In(PO 4) 2. The polymorphous modifications of β- and α-Ag 3In 2(PO 4) 3 are isostructural to sodium analogs ( β- and α-Na 3In 2(PO 4) 3) and are related to alluaudite (II) and NASICON (III) structure types. Compounds I and II are not stable at temperature above 850 °C. Ag 3In(PO 4) 2 is decomposed providing silver orthophosphate Ag 3PO 4 and α-Ag 3In 2(PO 4) 2. β-Ag 3In 2(PO 4) 3 is transformed to α-Ag 3In 2(PO 4) 3.

  19. Lithium-cation conductivity and crystal structure of lithium diphosphate

    SciTech Connect

    Voronin, V.I.; Sherstobitova, E.A.; Blatov, V.A.; Shekhtman, G.Sh.

    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 3001050 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) , b=5.2028(4) , c=13.3119(2) , ?=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.

  20. 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.