Science.gov

Sample records for crystal structure particle

  1. Defect structures in nematic liquid crystals around charged particles.

    PubMed

    Tojo, K; Furukawa, A; Araki, T; Onuki, A

    2009-09-01

    We numerically study the orientation deformations in nematic liquid crystals around charged particles. We set up a Ginzburg-Landau theory with inhomogeneous electric field. If the dielectric anisotropy epsilon 1 is positive, Saturn-ring defects are formed around the particles. For epsilon 1< 0 , novel "ansa" defects appear, which are disclination lines with their ends on the particle surface. We find unique defect structures around two charged particles. To lower the free energy, oppositely charged particle pairs tend to be aligned in the parallel direction for epsilon 1> 0 and in the perpendicular plane for epsilon 1< 0 with respect to the background director. For identically charged pairs the preferred directions for epsilon 1> 0 and epsilon 1< 0 are exchanged. We also examine competition between the charge-induced anchoring and the short-range anchoring. If the short-range anchoring is sufficiently strong, it can be effective in the vicinity of the surface, while the director orientation is governed by the long-range electrostatic interaction far from the surface. PMID:19756793

  2. Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA-binding Ligands

    E-print Network

    Gates, Kent. S.

    Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA-binding Ligands Research Institute, La Jolla, CA 92037 USA We determined the crystal structures of three nucleosome core.65 superhelical turns. Crystal structures of NCPs reconstituted with histones from different species,1 ­4

  3. X-ray Crystal Structure of the Rotavirus Inner Capsid Particle at 3.8 Resolution

    E-print Network

    Harrison, Stephen C.

    X-ray Crystal Structure of the Rotavirus Inner Capsid Particle at 3.8 Å Resolution Brian McClain1 January 2010; accepted 22 January 2010 Available online 1 February 2010 The rotavirus inner capsid the crystal structure of the bovine rotavirus DLP. There is one full particle (outer diameter 700 Å

  4. 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

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

    E-print Network

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

    2010-05-28

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

  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 DNA–DNA 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. Nematic liquid crystal around a spherical particle: Investigation of the defect structure and its stability using adaptive mesh refinement.

    PubMed

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

    2004-01-01

    We investigate the orientation profile and the structure of topological defects of a nematic liquid crystal around a spherical particle using an adaptive mesh refinement scheme developed by us previously. The previous work [J. Fukuda et al., Phys. Rev. E 65, 041709 (2002)] was devoted to the investigation of the fine structure of a hyperbolic hedgehog defect that the particle accompanies and in this paper we present the equilibrium profile of the Saturn ring configuration. The radius of the Saturn ring r(d) in units of the particle radius R(0) increases weakly with the increase of Epsilon, the ratio of the nematic coherence length to R(0). Next we discuss the energetic stability of a hedgehog and a Saturn ring. The use of adaptive mesh refinement scheme together with a tensor orientational order parameter Q (alpha, beta) allows us to calculate the elastic energy of a nematic liquid crystal without any assumption of the structure and the energy of the defect core as in the previous similar studies. The reduced free energy of a nematic liquid crystal, F= F/L1RO, with L(1) being the elastic constant, is almost independent of Epsilon in the hedgehog configuration, while it shows a logarithmic dependence in the Saturn ring configuration. This result clearly indicates that the energetic stability of a hedgehog to a Saturn ring for a large particle is definitely attributed to the large defect energy of the Saturn ring with a large radius. PMID:15024619

  8. Crystal Structure of an Aquabirnavirus Particle: Insights into Antigenic Diversity and Virulence Determinism?

    PubMed Central

    Coulibaly, Fasséli; Chevalier, Christophe; Delmas, Bernard; Rey, Félix A.

    2010-01-01

    Infectious pancreatic necrosis virus (IPNV), a pathogen of salmon and trout, imposes a severe toll on the aquaculture and sea farming industries. IPNV belongs to the Aquabirnavirus genus in the Birnaviridae family of bisegmented double-stranded RNA viruses. The virions are nonenveloped with a T=13l icosahedral capsid made by the coat protein VP2, the three-dimensional (3D) organization of which is known in detail for the family prototype, the infectious bursal disease virus (IBDV) of poultry. A salient feature of the birnavirus architecture is the presence of 260 trimeric spikes formed by VP2, projecting radially from the capsid. The spikes carry the principal antigenic sites as well as virulence and cell adaptation determinants. We report here the 3.4-Å resolution crystal structure of a subviral particle (SVP) of IPNV, containing 20 VP2 trimers organized with icosahedral symmetry. We show that, as expected, the SVPs have a very similar organization to the IBDV counterparts, with VP2 exhibiting the same overall 3D fold. However, the spikes are significantly different, displaying a more compact organization with tighter packing about the molecular 3-fold axis. Amino acids controlling virulence and cell culture adaptation cluster differently at the top of the spike, i.e., in a central bowl in IBDV and at the periphery in IPNV. In contrast, the spike base features an exposed groove, conserved across birnavirus genera, which contains an integrin-binding motif. Thus, in addition to revealing the viral antigenic determinants, the structure suggests that birnaviruses interact with different receptors for attachment and for cell internalization during entry. PMID:20007275

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

  10. 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.

  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. Exclusion of impurity particles in charged colloidal crystals.

    PubMed

    Yoshizawa, Koki; Toyotama, Akiko; Okuzono, Tohru; Yamanaka, Junpei

    2014-05-21

    Uniformly shaped, charged colloidal particles dispersed in water form ordered "crystal" structures when the interaction between the particles is sufficiently strong. Herein, we report the behavior of "impurity" particles, whose sizes and/or charge numbers are different from those of the bulk, on addition to the charged colloidal crystals. These impurities were excluded from the crystals during the homogeneous crystallization, crystal grain growth, and unidirectional crystallization processes. Such systems will be useful as models for studying the refinement of materials and crystal defects. PMID:24807633

  13. 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…

  14. Module: Material Structure Focus: Crystal Structures

    E-print Network

    Rowley, Clarence W.

    Module: Material Structure Focus: Crystal Structures Duration: 43 minute period Contact: Daniel with the class crystalline structure. 2. Students will perform a lab on crystal structure. Assignment: 1. dsteinbe@princeton.edu #12;Module: Material Structure Focus: Crystal Structures Duration: 43 minute period

  15. 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.

  16. 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

  17. Crystal Structures Academic Resource Center

    E-print Network

    Heller, Barbara

    structure: the manner in which atoms, ions, or molecules are spatially arranged. #12;Unit cell: small repeating entity of the atomic structure. The basic building block of the crystal structure. It defines the entire crystal structure with the atom positions within. #12;Lattice: 3D array of points coinciding

  18. 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.

  19. 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; Cölfen, 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

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. Crystal structure of dimethomorph

    PubMed Central

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

    2015-01-01

    In the title compound, C21H22ClNO4 [systematic name: (E)-3-(4-chloro­phen­yl)-3-(3,4-di­meth­oxy­phen­yl)-1-(morpholin-4-yl)prop-2-en-1-one], which is the morpholine fungicide dimethomorph, the dihedral angles between the mean planes of the central chloro­phenyl and the terminal benzene and morpholine (r.m.s. deviation = 0.2233?Å) rings are 71.74?(6) and 63.65?(7)°, respectively. In the crystal, molecules are linked via C—H?O hydrogen bonds and weak Cl?? interactions [3.8539?(11)?Å], forming a three-dimensional structure. PMID:26396887

  5. 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)

  6. Restricted Dislocation Motion in Crystals of Colloidal Dimer Particles

    E-print Network

    Sharon J. Gerbode; Stephanie H. Lee; Chekesha M. Liddell; Itai Cohen

    2008-11-07

    At high area fractions, monolayers of colloidal dimer particles form a degenerate crystal (DC) structure in which the particle lobes occupy triangular lattice sites while the particles are oriented randomly along any of the three lattice directions. We report that dislocation glide in DCs is blocked by certain particle orientations. The mean number of lattice constants between such obstacles is 4.6 +/- 0.2 in experimentally observed DC grains and 6.18 +/- 0.01 in simulated monocrystalline DCs. Dislocation propagation beyond these obstacles is observed to proceed through dislocation reactions. We estimate that the energetic cost of dislocation pair separation via such reactions in an otherwise defect free DC grows linearly with final separation, hinting that the material properties of DCs may be dramatically different from those of 2-D crystals of spheres.

  7. 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.

  8. Transport of particles in liquid crystals.

    PubMed

    Lavrentovich, Oleg D

    2014-03-01

    Colloidal particles in a liquid crystal (LC) behave very differently from their counterparts in isotropic fluids. Elastic nature of the orientational order and surface anchoring of the director cause long-range anisotropic interactions and lead to the phenomenon of levitation. The LC environment enables new mechanisms of particle transport that are reviewed in this work. Among them the motion of particles caused by gradients of the director, and effects in the electric field: backflow powered by director reorientations, dielectrophoresis in LC with varying dielectric permittivity and LC-enabled nonlinear electrophoresis with velocity that depends on the square of the applied electric field and can be directed differently from the field direction. PMID:24651158

  9. Crystal structure of pseudoguainolide.

    PubMed

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

    2015-03-01

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

  10. 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.

  11. 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 Mac OS X operating systems, and is particularly suitable for multiple-core processors. PMID:25567568

  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. 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

  14. 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

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

    PubMed

    Kumar, Manjesh; Luo, Helen; Román-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 NOx). 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

  16. 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.

  17. Crystal structure of fenbuconazole

    PubMed Central

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

    2015-01-01

    In the title compound, C19H17ClN4 [systematic name: (RS)-4-(4-chloro­phen­yl)-2-phenyl-2-(1H-1,2,4-triazol-1-ylmeth­yl)butyro­nitrile], which is the conazole fungicide fenbuconazole, the dihedral angles between the planes of the central benzene and the terminal chloro­phenyl and triazole rings are 32.77?(5) and 32.97?(5)°, respectively. The C—C—C—C linkage between the tertiary C atom and the benzene ring has an anti orientation [torsion angle = 174.47?(12)°]. In the crystal, C—H?N hydrogen bonds and very weak C—Cl?? inter­actions [Cl?? = 3.7892?(9)?Å] link adjacent mol­ecules, forming two-dimensional networks lying parellel to the (101) plane. The planes are linked by weak ?–? inter­actions [centroid–centroid separation = 3.8597?(9)?Å], resulting in a three-dimensional architecture. PMID:26396902

  18. Crystal structure of difenoconazole

    PubMed Central

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

    2014-01-01

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

  19. 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 N—H?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)?Å] and Cl?Cl [3.2837?(7)?Å] contacts, as well as weak inter­molecular ?–? inter­actions [ring centroid separation = 3.6100?(11) and 3.7764?(13)?Å], resulting in a two-dimensional architecture parallel to (111). PMID:25705506

  20. Crystal structure of difenoconazole.

    PubMed

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

    2014-11-01

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

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

    NASA Astrophysics Data System (ADS)

    Gopalan, Shridhar

    1999-10-01

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

  2. 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.

  3. 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

  4. 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).

  5. Quadrupolar particles in a nematic liquid crystal: effects of particle size and shape.

    PubMed

    Hung, Francisco R

    2009-02-01

    We investigate the effects of particle size and shape on the quadrupolar (Saturn-ring-like) defect structures formed by a nematic liquid crystal around nm-sized and mum -sized particles with spherical and spherocylindrical shapes. We also report results for the potentials of mean force in our systems, calculated using a mesoscale theory for the tensor order parameter Q of the nematic. Our results indicate that for pairs of nm-sized particles in close proximity, the nematic forms "entangled hyperbolic" defect structures regardless of the shape of the nanoparticles. In our calculations with nanoparticles we did not observe any other entangled or unentangled defect structures, in contrast to what was reported for pairs of mum -sized spherical particles. Such a finding suggests that the "entangled hyperbolic" defect structures are the most stable for pairs of nanoparticles in close proximity. For pairs of mum -sized particles, our results indicate that the nematic forms entangled "figure-of-eight" defect structures around pairs of spheres and spherocylinders. Our results suggest that the transition between "entangled hyperbolic" and figure-of-eight defect structures takes place when the diameter of the particle is between D=100 nm and 1 microm . We have also calculated the torques that develop when pairs of spherocylindrical nanoparticles in a nematic approach each other. Our calculations suggest that the nematic-mediated interactions between the nm-sized particles are fairly strong, up to 5700 k{B}T for the case of pairs of spherocylindrical nanoparticles arranged with their long axis parallel to each other. Furthermore, these interactions can make the particles to bind together at specific locations, and thus could be used to assemble the particles into ordered structures with different morphologies. PMID:19391763

  6. 1. Understanding crystal structures: How are more complex crystal structures built up from simpler ones.

    E-print Network

    Bigelow, Stephen

    1. Understanding crystal structures: How are more complex crystal structures built up from simpler http://www.mrl.ucsb.edu/~seshadri +++ seshadri@mrl.ucsb.edu #12;1. Understanding crystal structures: How are more complex crystal structures built up from simpler ones. http

  7. Structural colours through photonic crystals

    NASA Astrophysics Data System (ADS)

    McPhedran, R. C.; Nicorovici, N. A.; McKenzie, D. R.; Rouse, G. W.; Botten, L. C.; Welch, V.; Parker, A. R.; Wohlgennant, M.; Vardeny, V.

    2003-10-01

    We discuss two examples of living creatures using photonic crystals to achieve iridescent colouration. The first is the sea mouse (Aphroditidae, Polychaeta), which has a hexagonal close packed structure of holes in its spines and lower-body felt, while the second is the jelly fish Bolinopsis infundibulum, which has an oblique array of high index inclusions in its antennae. We show by measurements and optical calculations that both creatures can achieve strong colours despite having access only to weak refractive index contrast.

  8. The crystallization processes in the aluminum particles production technology

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  9. Module: Material Structure Focus: Hydrogen Bonding & Crystallization.

    E-print Network

    Rowley, Clarence W.

    and demonstrate the process of growing crystals. Materials: Water Copper Sulfate Cup Petri Dish Petri Dish Water sulfate in each Petri dish to act as a "seed" crystal. I came across another crystal growing exerciseModule: Material Structure Focus: Hydrogen Bonding & Crystallization. Duration: 43 minute period

  10. 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

  11. Crystal structures and freezing of dipolar fluids

    E-print Network

    B. Groh; S. Dietrich

    2000-10-21

    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 $\\sim r^{-n}$. 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.

  12. Studies on Crystals of Intact Bacterial Ribosomal Particles

    E-print Network

    Yonath, Ada E.

    severe limitations. Our efforts are directed at growing three-dimensional crystals of ribo- somes from7 Studies on Crystals of Intact Bacterial Ribosomal Particles A. YONATH, M. A. SAPER, and H. G crystal growth is at all possible. Nevertheless, natural periodic organizations of ordered arrays

  13. Compound structure one-dimensional photonic crystal

    E-print Network

    Wu, Xiang-Yao; Liu, Xiao-Jing; Liang, Yu; Wang, Zhi-Guo; Fang, Yun-Tuan

    2015-01-01

    In this paper, we have proposed a new compound structure one-dimensional photonic crystal, which include series connection, parallel connection and positive and negative feedback compound structure photonic crystal. We have studied their transmission characteristics and obtained some new results, which should be help to design new type optical devices, such as optical amplifier, photonic crystal laser and so on.

  14. The American Mineralogist Crystal Structure Database is a compilation of every crystal structure potentially of

    E-print Network

    Downs, Robert T.

    ABSTRACT The American Mineralogist Crystal Structure Database is a compilation of every crystal for instructors, allowing direct access to crystal structures of almost any mineral, and many at various, instructors, and researchers to easily access various crystal structures. Suggestions for using the database

  15. STRUCTURE NOTE Crystal Structure of Stilbene Synthase From Arachis

    E-print Network

    Suh, Dae-Yeon

    STRUCTURE NOTE Crystal Structure of Stilbene Synthase From Arachis hypogaea Yasuhito Shomura,1, respectively. The crystal structure and molecu- lar mechanism of CHS from Medicago sativa (alfalfa) have was not clear. More recently, the crystal structure of STS from Pinus silvestris (pine) was reported

  16. 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

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

    NASA Astrophysics Data System (ADS)

    Albrechtsen, Dan E.; Olsen, Andreas E.; Pedersen, Ulf R.; Schrøder, 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 Wahnström 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.

  18. `clumpy' fluid crystallizes, the resulting solid retains the clumpy structure to form a regular

    E-print Network

    Sciortino, Francesco

    `clumpy' fluid crystallizes, the resulting solid retains the clumpy structure to form a regular about whether soft matter can adopt an unconventional crystal structure at high densities -- it can is typical of standard crystals), but also locally disordered because of the random number of particles

  19. Structural Dynamics of the Vault Ribonucleoprotein Particle

    NASA Astrophysics Data System (ADS)

    Casañas, Arnau; Querol, Jordi; Fita, Ignasi; Verdaguer, Núria

    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 Å 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.

  20. Large Silver Halide Single Crystals as Charged Particle Track Detectors

    NASA Technical Reports Server (NTRS)

    Kusmiss, J. H.

    1972-01-01

    The trajectory of the particle is made visible under a microscope by the accumulation of metallic silver at regions of the lattice damaged by the particle. This decoration of the particle track is accomplished by exposure of the crystal to light. The decoration of normally present lattice imperfections such as dislocations can be suppressed by the addition to the crystal of less than ten parts per million of a suitable polyvalent metal impurity. An account of some preliminary attempts to grow thin single crystals of AgCl is given also, and suggestions for a more refined technique are offered.

  1. Structure and Growth of Rod-Shaped Mn Ultrafine Particle

    NASA Astrophysics Data System (ADS)

    Kido, Osamu; Suzuki, Hitoshi; Saito, Yoshio; Kaito, Chihiro

    2003-09-01

    The structure of rod-shaped Mn ultrafine particles was elucidated by electron microscopy. Mn ultrafine particles have characteristic tristetrahedron (?-Mn), rhombic dodecahedron (?-Mn) and rod-shape crystal habits. It was found that the rod-shaped particle resulted from the parallel coalescence of ?-Mn particles with the size of 50 nm. Detailed analysis of the defects seen in large rod-shaped particles with the width of 100 nm indicated a mixture of ?- and ?-phases. A size effect on the phase transition from ? to ? was observed throughout the rod-shaped crystal structure. The structure and growth of Mn particles were discussed based on the outline of the smoke and the temperature distribution in the smoke.

  2. 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.

  3. Confinement Induced Plastic Crystal-to-Crystal Transitions in Rodlike Particles with Long-Ranged Repulsion

    NASA Astrophysics Data System (ADS)

    Liu, Bing; Besseling, Thijs H.; van Blaaderen, Alfons; Imhof, Arnout

    2015-08-01

    Colloidal particles in geometrical confinement display a complex variety of packing structures different from their three-dimensional (3D) bulk counterpart. Here, we confined charged rodlike colloids with long-ranged repulsions to a thin wedge-shaped cell and show, by quantitative 3D confocal microscopy, that not only their positional but also their orientational order depends sensitively upon the slit width. Synchronized with transitions in lattice symmetry and number of layers confinement induces plastic crystal-to-crystal transitions. A model analysis suggests that this complex sequence of more or less rotationally ordered states originates from the subtle competition between the electrostatic repulsion of a rod with the wall and with its neighbors.

  4. 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.

  5. Module: Material Structure Focus: Crystal Structures

    E-print Network

    Rowley, Clarence W.

    to observe and diagram various crystal defects. Materials: Copper Sulfate Crystals Microscope Procedures: 1 in the copper sulfate crystals they made in a previous lab. Assignment: 1. Complete lab write up. Assessment: 1 of yesterday's lab, students are to place a few of their copper sulfate crystals on a microscope slide

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

    PubMed

    Zeglinski, Jacek; Svärd, Michael; Karpinska, Jolanta; Kuhs, Manuel; Rasmuson, Åke 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

  7. Elastic octopoles and colloidal structures in nematic liquid crystals

    E-print Network

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

    2013-05-14

    We propose a simple theoretical model which explains a formation of dipolar 2D and 3D colloidal structures in nematic liquid crystal. Colloidal particles are treated as effective hard spheres interacting via their elastic dipole, quadrupole and octopole moments. It is shown that octopole moment plays an important role in the formation of 2D and 3D nematic colloidal crystals. We generalize this assumption on the case of the external electric field and theoretically explain a giant electrostriction effect in 3D crystals observed recently [A. Nych et al., Nature Communications \\textbf{4}, 1489 (2013)].

  8. Structural Properties and Melting of 2D-Plasma Crystals

    SciTech Connect

    Knapek, C.; Samsonov, D.; Zhdanov, S.; Konopka, U.; Morfill, G.E.

    2005-10-31

    Melting of a monolayer plasma crystal was induced by an electric pulse. We investigated, how structural parameters like defect fraction and correlation lengths as well as dynamical properties like the particle kinetic energy changed during the recrystallisation. As an indication of the phase transition, the change of the Lindemann parameter and the Coulomb coupling parameter were considered.

  9. Formation of a Columnar Liquid Crystal in a Simple One-Component System of Particles

    E-print Network

    Alfredo Metere; Tomas Oppelstrup; Sten Sarman; Mikhail Dzugutov

    2015-03-18

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

  10. 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.

  11. 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.

  12. Structure of self - assembled two-dimensional spherical crystals

    NASA Astrophysics Data System (ADS)

    Bausch, Andreas R.

    2004-03-01

    Dense spherical particles on a flat surface usually pack into a simple triangular lattice, similar to billiard balls at the start of a game. The minimum energy configuration for interacting particles on the curved surface of a sphere, however, presents special difficulties, as recognized already by J.J. Thomson. We describe experimental investigations of the structure of two-dimensional spherical crystals. The crystals, formed by beads self-assembled on water droplets in oil, serve as model systems for exploring very general theories about the minimum energy configurations of particles with arbitrary repulsive interactions on curved surfaces. Above a critical system size we find that crystals develop distinctive high-angle grain boundaries or "scars" not found in planar crystals. The number of excess defects in a scar is shown to grow linearly with the dimensionless system size. First experiments where the melting of the crystal structure was observable will be discussed. Dynamic triangulation methods allow the analysis of the dynamics of the defects. Possible modifications towards mechanically stabilized self assembly structures result in so called Colloidosomes, which are promising for many different encapsulation purposes.

  13. Theoretical prediction of crystal structures of rubrene

    NASA Astrophysics Data System (ADS)

    Obata, Shigeaki; Miura, Toshiaki; Shimoi, Yukihiro

    2014-01-01

    We theoretically predict crystal structures and molecular arrangements for rubrene molecule using CONFLEX program and compare them with the experimental ones. The most, second-most, and fourth-most stable predicted crystal structures show good agreement with the triclinic, orthorhombic, and monoclinic polymorphs of rubrene, respectively. The change in molecular conformation is also predicted between crystalline and gas phases: the tetracene backbone takes flat conformation in crystalline phase as in the observed structure. Meanwhile, it is twisted in gas phase. The theoretical prediction method used in this work provides the successful results on the determination of the three kinds of crystal structures and molecular arrangements for rubrene molecule.

  14. 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.

  15. 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.

  16. Crystal structure of benzimidazolium salicylate

    PubMed Central

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

    2015-01-01

    In the anion of the title mol­ecular salt, C7H7N2 +·C7H5O3 ? (systematic name: 1H-benzimidazol-3-ium 2-hy­droxy­ben­zo­ate), there is an intra­molecular 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 ?–? inter­actions [inter-centroid distances = 3.4156?(7) and 3.8196?(8)?Å], forming a three-dimensional structure. PMID:26594483

  17. Self-organized assemblies of colloidal particles obtained from an aligned chromonic liquid crystal dispersion.

    PubMed

    Zimmermann, Natalie; Jünnemann-Held, Gisela; Collings, Peter J; Kitzerow, Heinz-S

    2015-02-28

    The behavior of mono-disperse colloidal particles in a chromonic liquid crystal was investigated. Poly(methyl methacrylate) spherical particles with three different functionalizations, with and without surface charges, were utilized in the nematic and columnar phases of disodium cromoglycate solutions. The nematic phase was completely aligned parallel to the glass substrates by a simple rubbing technique, and the columnar phase showed regions of similar alignment. The behavior of the colloidal particles in the chromonic liquid crystal depended critically on the functionality, with bromine functionalized particles not dispersing at all, and cationic trimethylammonium and epoxy functionalized particles dispersing well in the isotropic phase of the liquid crystal. At the transition to the nematic and especially the columnar phase, the colloidal particles were expelled into the remaining isotropic phase. Since the columnar phase grew in parallel ribbons, the colloidal particles ended up in chain-like assemblies. Such behavior opens the possibility of producing patterned assemblies of colloidal particles by taking advantage of the self-organized structure of chromonic liquid crystals. PMID:25589441

  18. 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

  19. 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.

  20. 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).

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

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

    PubMed

    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. PMID:12786160

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Structural phase transitions in low-dimensional ion crystals

    SciTech Connect

    Fishman, Shmuel; Chiara, Gabriele de; Calarco, Tommaso; Morigi, Giovanna

    2008-02-01

    A chain of singly charged particles, confined by a harmonic potential, exhibits a sudden transition to a zigzag configuration when the radial potential reaches a critical value, depending on the particle number. This structural change is a phase transition of second order, whose order parameter is the crystal displacement from the chain axis. We study analytically the transition using Landau theory and find full agreement with numerical predictions by Schiffer [Phys. Rev. Lett. 70, 818 (1993)] and Piacente et al. [Phys. Rev. B 69, 045324 (2004)]. Our theory allows us to determine analytically the system's behavior at the transition point.

  10. The Systems Dynamics of the Structured Particles

    E-print Network

    V. M. Somsikov

    2010-06-16

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

  11. 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.

  12. 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 4°C. Droplet size (0.17 versus 1.20 ?m), lipid composition (stearin versus olein) and cooling rate (1 versus 10°C 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

  13. 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.

  14. 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

  15. Crystal structure of 9-methacryloylanthracene

    PubMed Central

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

    2015-01-01

    In the title compound, C18H14O, with systematic name 1-(anthracen-9-yl)-2-methyl­prop-2-en-1-one, the ketonic C atom lies 0.2030?(16)?Å out of the anthryl-ring-system plane. The dihedral angle between the planes of the anthryl and methacryloyl moieties is 88.30?(3)° and the stereochemistry about the Csp 2—Csp 2 bond in the side chain is transoid. In the crystal, the end rings of the anthryl units in adjacent mol­ecules associate in parallel–planar orientations [shortest centroid–centroid distance = 3.6320?(7)?Å]. A weak hydrogen bond is observed between an aromatic H atom and the O atom of a mol­ecule displaced by translation in the a-axis direction, forming sheets of parallel-planar anthryl groups packing in this direction. PMID:26029389

  16. Computing stoichiometric molecular composition from crystal structures

    PubMed Central

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

    2015-01-01

    Crystallographic investigations deliver high-accuracy information about positions of atoms in crystal unit cells. For chemists, however, the structure of a molecule is most often of interest. The structure must thus be reconstructed from crystallographic files using symmetry information and chemical properties of atoms. Most existing algorithms faithfully reconstruct separate molecules but not the overall stoichiometry of the complex present in a crystal. Here, an algorithm that can reconstruct stoichiometrically correct multimolecular ensembles is described. This algorithm uses only the crystal symmetry information for determining molecule numbers and their stoichiometric ratios. The algorithm can be used by chemists and crystallographers as a standalone implementation for investigating above-molecular ensembles or as a function implemented in graphical crystal analysis software. The greatest envisaged benefit of the algorithm, however, is for the users of large crystallographic and chemical databases, since it will permit database maintainers to generate stoichiometrically correct chemical representations of crystal structures automatically and to match them against chemical databases, enabling multidisciplinary searches across multiple databases. PMID:26089747

  17. 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).

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. Nematic liquid crystals in inverted microstrip structures

    NASA Astrophysics Data System (ADS)

    Piotrowski, Jerzy; Parka, Janusz; Nowinowski-Kruszelnicki, Edward

    2013-07-01

    Nematic liquid crystals are promising dielectrics for tunable microwave devices due to their significant birefringence and moderately low loss. Dielectric anisotropy or refractive index anisotropy of liquid crystal is one of the important parameter for the design of variety of reconfigurable devices. In this work, transmission line method is used for the broadband investigation of nematic liquid crystals in the frequency range of 1-10 GHz. For this purpose, a measurement device is proposed with a tunable liquid crystal transduces based on an inverted microstrip structure section placed between two segments of layered microstrip lines terminated by microstrip-coaxial line transitions. Measurements of the scattering parameters of the device with standard liquid crystal 6CHBT as well as with a novel highly anisotropic mixture W1825 have been conducted. Based on these measurements, a high effective refractive index anisotropy of 0.31 for the W1825 mixture compared to 0.12 for 6CHBT have been determined. These values are lower of 26% and 18% than anisotropy of the refractive indices appointed by a resonator method for W1825 and 6CHBT, respectively. Progress in highly anisotropic mixtures opens new low-cost liquid crystal applications in microwave devices.

  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. Colloidal aggregation in a nematic liquid crystal: topological arrest of particles by a single-stroke disclination line.

    PubMed

    Araki, Takeaki; Tanaka, Hajime

    2006-09-22

    We numerically study many-body interactions among colloidal particles suspended in a nematic liquid crystal, using a fluid particle dynamics method, which properly incorporates dynamical coupling among particles, nematic orientation, and flow field. Based on simulation results, we propose a new type of interparticle interaction in addition to well-known quadrupolar interaction for particles accompanying Saturn-ring defects. This interaction is mediated by the defect of the nematic phase: upon nematic ordering, a closed disclination loop binds more than two particles to form a sheetlike dynamically arrested structure. The interaction depends upon the topology of a disclination loop binding particles, which is determined by aggregation history. PMID:17025998

  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. 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.

  8. Integrable structure of modified melting crystal model

    E-print Network

    Kanehisa Takasaki

    2012-08-22

    Our previous work on a hidden integrable structure of the melting crystal model (the U(1) Nekrasov function) is extended to a modified crystal model. As in the previous case, "shift symmetries" of a quantum torus algebra plays a central role. With the aid of these algebraic relations, the partition function of the modified model is shown to be a tau function of the 2D Toda hierarchy. We conjecture that this tau function belongs to a class of solutions (the so called Toeplitz reduction) related to the Ablowitz-Ladik hierarchy.

  9. Pauli Crystals: hidden geometric structures of the quantum statistics

    E-print Network

    Mariusz Gajda; Jan Mostowski; Tomasz Sowi?ski; Magdalena Za?uska-Kotur

    2015-11-05

    The micro-world is governed by the laws of Quantum Theory. Although we cannot directly experience Quantum Mechanics in action, it imperceptibly enters our everyday life. It explains the structure of matter on the one hand and stands behind all modern technologies on the other. It also gives a completely different meaning to the classical concept of identical objects. Quantum identical particles are identical not only because they share the same mass, spin, charge, etc., but also because they cannot be identified by tracing their history. Indistinguishability results in a division of the world of elementary particles into fundamentally different families: fermions (e.g. electrons, protons, neutrons) and bosons (e.g. photons, gluons, Higgs boson). Identical fermions subjected to the Fermi-Dirac statistics cannot occupy the same quantum state. Here we show yet another, so far undiscovered, consequence of quantum indistinguishability. We show that identical fermions confined by an external trapping potential arrange themselves in spectacular geometric structures although no mutual interaction is present. This is because the indistinguishability of fermions, formulated in the language of the Pauli exclusion principle, prevents any two fermions from being at the same location. These unexplored geometric structures, Pauli crystals, emerge repeatedly in single-shot pictures of the many-body system. Pauli crystals form a previously unknown form of particles' organization. Our results shed some light on the role of quantum statistics -- one of the fundamentals of quantum mechanics of many-body systems.

  10. Spherical particle immersed in a nematic liquid crystal: effects of confinement on the director field configurations.

    PubMed

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

    2003-01-01

    The effects of confinement on the director field configurations are studied for a spherical particle immersed in a nematic liquid crystal. The liquid crystal is confined in a cylindrical geometry and the particle is located on the axis of symmetry. A finite element method is used to minimize the Frank free energy for various sizes of the system. The liquid crystal is assumed to possess strong anchoring at all the surfaces in the system. Two structures are examined for strong homeotropic anchoring at the surface of the particle: configuration with a Saturn ring disclination line and configuration with a satellite point defect (hedgehog defect). It is shown that the equilibrium locations of the Saturn ring and of the hedgehog point defect change with confinement. It is also found that confinement induces an increase in the elastic free energy that differs substantially with the type of topological defect under consideration. In particular, the evaluation of the total free energy that includes an approximate contribution for the core defect shows that, for micrometer-sized particles in confined systems, the Saturn ring configuration appears to be more stable than the hedgehog defect. This result is in contrast to the bulk situation, where the hedgehog is more stable than the Saturn ring, and it helps explain recent experimental observations of Saturn ring defects around confined micrometer-sized solid particles. PMID:12636512

  11. 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.

  12. 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 laboratory’s 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

  13. Soviet research on crystal channeling of charged particle beams

    NASA Astrophysics Data System (ADS)

    Kassel, S.

    1985-03-01

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

  14. 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)

  15. 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.

  16. 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.

  17. 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 63±3 nm. A flow enhancement of 20±2 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

  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. COMMUNICATION The Crystal Structure of 3

    E-print Network

    van Aalten, Daan

    of Biochemistry University of Dundee, Dundee DD1 5EH, UK The active-site geometry of the ®rst crystal structure carbon atom of the sub- strate, Á3 -enoyl-CoA, to the C4 atom of the product, Á2 -enoyl-CoA. Site- directed mutagenesis has been performed to con®rm that this glutamate residue is essential for catalysis

  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 C–H?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.

  2. 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 arrangement—transport macropores between particles and mesopores inside the shell—are promising for application in optical gas sensors.

  3. 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.

  4. Particle beam and crabbing and deflecting structure

    DOEpatents

    Delayen, Jean (Yorktown, VA)

    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.

  5. 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, ? = ? = ? = 90°, and contain one particle per asymmetric unit.

  6. 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.

  7. 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.

  8. Crystallization Pathways of Sulfate-Nitrate-Ammonium Aerosol Particles Julie C. Schlenker and Scot T. Martin*

    E-print Network

    Crystallization Pathways of Sulfate-Nitrate-Ammonium Aerosol Particles Julie C. Schlenker and Scot into the nonlinear crystallization pathways of sulfate-nitrate-ammonium aerosol particles. 1. Introduction The physicochemical behavior of the sulfate particles is strongly influenced by the presence of nitrate and ammonium.3

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

    E-print Network

    , 2005; FINAL REVISION July 15, 2005; ACCEPTED July 27, 2005) Abstract The plague-causing bacterium of oligomerization is discussed. Keywords: Yersinia pestis; plague; type III secretion; YscE; crystal structure Yersinia pestis, the causative agent of plague, utilizes a type III secretion system (T3SS) to inject

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

    E-print Network

    Davidchack, Ruslan L.; Laird, Brian Bostian

    2005-03-01

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

  11. Crystal Structure of a Cyclotetraicosaphenylene by Peter Mllera

    E-print Network

    Müller, Peter

    Crystal Structure of a Cyclotetraicosaphenylene by Peter Müllera ), Isabel UsoÂna ), Volker Henselb-rigid macrocycle is the cyclotetraicosaphenylene 1. Determining the X-ray crystal structure was a challenge which . In the crystal these channels are filled with liquid solvent which is amorphously frozen during data collection

  12. Crystal structure of natural phaeosphaeride A.

    PubMed

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

    2015-08-01

    The asymmetric unit of the title compound, C15H23NO5, contains two independent mol-ecules. 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 mol-ecules form layered structures. Nearly planar sheets, parallel to the (001) plane, form bilayers of two-dimensional hydrogen-bonded networks with the hy-droxy groups located on the inter-ior 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 inter-digitate 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

  13. 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

  14. The First Mammalian Aldehyde Oxidase Crystal Structure

    PubMed Central

    Coelho, Catarina; Mahro, Martin; Trincão, José; Carvalho, Alexandra T. P.; Ramos, Maria João; Terao, Mineko; Garattini, Enrico; Leimkühler, Silke; Romão, Maria João

    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

  15. 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.

  16. 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.

  17. 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.

  18. The crystal structure of calcite III Joseph R. Smyth

    E-print Network

    Smyth, Joseph R.

    The crystal structure of calcite III Joseph R. Smyth Department of Geological Sciences, University of Technology, Pasadena, CA. Abstract. The crystal structure of calcite III has been deduced from existing high of the calcite I structure. The structure is monoclinic with space group C2 and a Z of 6. There are two Ca

  19. 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

  20. Crystal structure of the Golgi casein kinase.

    PubMed

    Xiao, Junyu; Tagliabracci, Vincent S; Wen, Jianzhong; Kim, Soo-A; Dixon, Jack E

    2013-06-25

    The family with sequence similarity 20 (Fam20) kinases phosphorylate extracellular substrates and play important roles in biomineralization. Fam20C is the Golgi casein kinase that phosphorylates secretory pathway proteins within Ser-x-Glu/pSer motifs. Mutations in Fam20C cause Raine syndrome, an osteosclerotic bone dysplasia. Here we report the crystal structure of the Fam20C ortholog from Caenorhabditis elegans. The nucleotide-free and Mn/ADP-bound structures unveil an atypical protein kinase-like fold and highlight residues critical for activity. The position of the regulatory ?C helix and the lack of an activation loop indicate an architecture primed for efficient catalysis. Furthermore, several distinct elements, including the presence of disulfide bonds, suggest that the Fam20 family diverged early in the evolution of the protein kinase superfamily. Our results reinforce the structural diversity of protein kinases and have important implications for patients with disorders of biomineralization. PMID:23754375

  1. 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.

  2. Phase behaviour of liquid-crystal monolayers of rod-like and plate-like particles

    NASA Astrophysics Data System (ADS)

    Martínez-Ratón, Yuri; Varga, Szabolcs; Velasco, Enrique

    2014-05-01

    Orientational and positional ordering properties of liquid crystal monolayers are examined by means of Fundamental-Measure Density Functional Theory. Particles forming the monolayer are modeled as hard parallelepipeds of square section of size ? and length L. Their shapes are controlled by the aspect ratio ? = L/? (>1 for prolate and <1 for oblate shapes). The particle centers of mass are restricted to a flat surface and three possible and mutually perpendicular orientations (in-plane and along the layer normal) of their uniaxial axes are allowed. We find that the structure of the monolayer depends strongly on particle shape and density. In the case of rod-like shapes, particles align along the layer normal in order to achieve the lowest possible occupied area per particle. This phase is a uniaxial nematic even at very low densities. In contrast, for plate-like particles, the lowest occupied area can be achieved by random in-plane ordering in the monolayer, i.e., planar nematic ordering takes place even at vanishing densities. It is found that the random in-plane ordering is not favorable at higher densities and the system undergoes an in-plane ordering transition forming a biaxial nematic phase or crystallizes. For certain values of the aspect ratio, the uniaxial-biaxial nematic phase transition is observed for both rod-like and plate-like shapes. The stability region of the biaxial nematic phase enhances with decreasing aspect ratios for plate-like particles, while the rod-like particles exhibit a reentrant phenomenon, i.e., a sequence of uniaxial-biaxial-uniaxial nematic ordering with increasing density if the aspect ratio is larger than 21.34. In addition to this, packing fraction inversion is observed with increasing surface pressure due to the alignment along the layers normal. At very high densities the nematic phase destabilizes to a nonuniform phases (columnar, smectic, or crystalline phases) for both shapes.

  3. 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.

  4. 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.

  5. Near Surface Structure of Organic Semiconductor Tetracene Single Crystal

    NASA Astrophysics Data System (ADS)

    Wakabayashi, Yusuke; Morisaki, Hazuki; Kimura, Tsuyoshi; Miwa, Kazumoto; Koretsune, Takashi; Takeya, Jun

    2014-03-01

    Electric conduction in organic crystals is highly anisotropic because of the anisotropic molecular orbitals. Crystal structure governs the transfer through the overlap integral among the highest occupied (or lowest unoccupied) molecular orbitals. In case of organic devices, the place where electrons conduct is the interface. Therefore, the surface structure of organic single crystals is relevant. Surface relaxation of the structure of rubrene single crystal was firstly observed by means of surface x-ray diffraction a few years ago. This time we performed similar measurement on tetracene single crystal, whose molecular shape has large similarity with rubrene while the crystal structure is very different. Tetracene single crystal was grown by the physical vapor transport method, and the surface x-ray diffraction experiments were performed at BL-3A and 4C of the Photon Factory, KEK, Japan. Obtained electron density profile shows a large structural deformation at the surface layer of tetracene.

  6. Transitions among crystal, glass, and liquid in a binary mixture with changing particle size ratio and temperature

    E-print Network

    Toshiyuki Hamanaka; Akira Onuki

    2006-05-10

    Using molecular dynamics simulation we examine changeovers among crystal, glass, and liquid at high density in a two dimensional binary mixture. We change the ratio between the diameters of the two components and the temperature. The transitions from crystal to glass or liquid occur with proliferation of defects. We visualize the defects in terms of a disorder variable "D_j(t)" representing a deviation from the hexagonal order for particle j. The defect structures are heterogeneous and are particularly extended in polycrystal states. They look similar at the crystal-glass crossover and at the melting. Taking the average of "D_j(t)" over the particles, we define a disorder parameter "D(t)", which conveniently measures the degree of overall disorder. Its relaxation after quenching becomes slow at low temperature in the presence of size dispersity. Its steady state average is small in crystal and large in glass and liquid.

  7. About mechanics of the structured particles

    E-print Network

    Somsikov, V M

    2011-01-01

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

  8. About mechanics of the structured particles

    E-print Network

    V. M. Somsikov

    2011-03-15

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

  9. 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.

  10. 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

  11. 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.

  12. Structural Modifications in Liquid Crystals and Liquid Crystal Polymers.

    NASA Astrophysics Data System (ADS)

    Legge, Coulton Heath

    Available from UMI in association with The British Library. The effect of doping liquid crystals and liquid crystal polymers with either photoactive molecules or cross links was investigated. Selective irradiation of low molar mass and polymer liquid crystals doped with a photoactive unit results in either a Eto Z or Zto E isomerisation of the photoactive unit. (4-butyl -4^'methoxyazobenzene and methyl beta-(1-naphthyl)propenoate were the photoactive molecules investigated.) The effect of the isomerisation is such as to cause a depression of the LC to I phase transition temperature of the system, which may be monitored optically. Both the overall depression and response is found to be dependent upon the concentration of chromophore present (a maximum depression of 50^circC in T_{rm Nl} was observed in one system). Orientational changes of the molecular units in some liquid crystal polymer samples were also observed as a result of the isomerisation. The changes were found to differ if the isomerisation took place in the glass phase of the polymer, where only the chromophore units rotated, or in the liquid crystal phase, where both chromophore and liquid crystal units rotated. In some low molar mass mixtures the incorporation of the photoactive molecule resulted in a biphasic liquid crystal + isotropic region whose breadth was dependant upon the chromophore concentration. Incorporation of cross-links into liquid crystal polymers to yield free-standing monodomain samples are shown to have a complete memory of the orientational configuration at the time of crosslinking. This memory is demonstrated through samples in which the parent polymer system is first aligned in a magnetic field prior to crosslinking. The resulting films exhibit a remarkable memory effect, in that the sample may be held in the isotropic phase for >2 weeks, but on cooling into the liquid crystal phase region, both the original director and the degree of preferred orientation are recovered.

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

    ERIC Educational Resources Information Center

    Hong, Y. S.; And Others

    1980-01-01

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

  14. Crystal Structure of Staphylococcus aureus Cas9.

    PubMed

    Nishimasu, Hiroshi; Cong, Le; Yan, Winston X; Ran, F Ann; Zetsche, Bernd; Li, Yinqing; Kurabayashi, Arisa; Ishitani, Ryuichiro; Zhang, Feng; Nureki, Osamu

    2015-08-27

    The RNA-guided DNA endonuclease Cas9 cleaves double-stranded DNA targets with a protospacer adjacent motif (PAM) and complementarity to the guide RNA. Recently, we harnessed Staphylococcus aureus Cas9 (SaCas9), which is significantly smaller than Streptococcus pyogenes Cas9 (SpCas9), to facilitate efficient in vivo genome editing. Here, we report the crystal structures of SaCas9 in complex with a single guide RNA (sgRNA) and its double-stranded DNA targets, containing the 5'-TTGAAT-3' PAM and the 5'-TTGGGT-3' PAM, at 2.6 and 2.7 Å resolutions, respectively. The structures revealed the mechanism of the relaxed recognition of the 5'-NNGRRT-3' PAM by SaCas9. A structural comparison of SaCas9 with SpCas9 highlighted both structural conservation and divergence, explaining their distinct PAM specificities and orthologous sgRNA recognition. Finally, we applied the structural information about this minimal Cas9 to rationally design compact transcriptional activators and inducible nucleases, to further expand the CRISPR-Cas9 genome editing toolbox. PMID:26317473

  15. Crystal Structure of Bacillus subtilis Signal Peptide Peptidase A

    E-print Network

    Paetzel, Mark

    Crystal Structure of Bacillus subtilis Signal Peptide Peptidase A Sung-Eun Nam, Apollos C. Kim Bacillus subtilis SppA (SppABS). *Corresponding author. E-mail address: mpaetzel@sfu.ca. Abbreviations used the first crystal structure of a Gram-positive bacterial SppA. The 2.4-Å- resolution structure of Bacillus

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

    E-print Network

    Soljaèiæ, Marin

    Broadband super-collimation in a hybrid photonic crystal structure Rafif E. Hamam, Mihai Ibanescu, USA rafif@mit.edu Abstract: We propose a two dimensional (2D) photonic crystal (PhC) structure of holes). We theoretically and numerically investigate the collimation mechanism in our 2D structure

  17. Synthesis of Calcite Single Crystals with Porous Surface by Templating of Polymer Latex Particles

    E-print Network

    Qi, Limin

    Synthesis of Calcite Single Crystals with Porous Surface by Templating of Polymer Latex Particles in solution. After template removal, well-defined, calcite single crystals exhibiting a rhombohedral morphology and uniform surface pores are obtained. The surface pore size of the calcite single crystals can

  18. Crystal Structure of the West Nile Virus Envelope Glycoprotein?

    PubMed Central

    Nybakken, Grant E.; Nelson, Christopher A.; Chen, Beverly R.; Diamond, Michael S.; Fremont, Daved H.

    2006-01-01

    The envelope glycoprotein (E) of West Nile virus (WNV) undergoes a conformational rearrangement triggered by low pH that results in a class II fusion event required for viral entry. Herein we present the 3.0-Å crystal structure of the ectodomain of WNV E, which reveals insights into the flavivirus life cycle. We found that WNV E adopts a three-domain architecture that is shared by the E proteins from dengue and tick-borne encephalitis viruses and forms a rod-shaped configuration similar to that observed in immature flavivirus particles. Interestingly, the single N-linked glycosylation site on WNV E is displaced by a novel ?-helix, which could potentially alter lectin-mediated attachment. The localization of histidines within the hinge regions of E implicates these residues in pH-induced conformational transitions. Most strikingly, the WNV E ectodomain crystallized as a monomer, in contrast to other flavivirus E proteins, which have crystallized as antiparallel dimers. WNV E assembles in a crystalline lattice of perpendicular molecules, with the fusion loop of one E protein buried in a hydrophobic pocket at the DI-DIII interface of another. Dimeric E proteins pack their fusion loops into analogous pockets at the dimer interface. We speculate that E proteins could pivot around the fusion loop-pocket junction, allowing virion conformational transitions while minimizing fusion loop exposure. PMID:16987985

  19. Crystal Structure, Rotational Symmetry and Quasicrystals Frank Rioux

    E-print Network

    Rioux, Frank

    Crystal Structure, Rotational Symmetry and Quasicrystals Frank Rioux Department of Chemistry College of St. Benedict St. John's University Prior to 1991 crystals were defined to be solids having only with the crystal lattice, followed as required by the uncertainty principle, a delocalization of the momentum

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

    PubMed Central

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

    2010-01-01

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

  1. STRUCTURE NOTE Crystal Structure of a Truncated Version of the Phage

    E-print Network

    STRUCTURE NOTE Crystal Structure of a Truncated Version of the Phage Protein gpD Changsoo Chang,1 utilized in this technique are of considerable interest. The high-resolution crystal structure of gp crystallized in a larger cell with two trimers in the asymmetric unit, the structure of this truncated version

  2. 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 ?-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

  3. 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.

  4. 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-Å 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

  5. Crystal structures of the human adiponectin receptors.

    PubMed

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

    2015-04-16

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

  6. 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.

  7. 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.

  8. 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 [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 inter­action with the two carboxyl­ate O-atom acceptors of the anion. The second aminium-H atom forms an inter-species N—H?Ocarboxyl­ate 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 inter­actions, forming a supra­molecular layer parallel to (01-1). PMID:26594560

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

    PubMed

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

    2015-09-01

    In this study, the formation and structure of a single-particle layer of organo-zinc oxide are investigated using surface-pressure-area (?-A) isotherms, out-of-plane X-ray diffraction (XRD) analysis, and atomic force microscopy (AFM). Further, techniques for achieving the solubilization of inorganic fine particles in general solvents have been proposed, and a single-particle layer has been formed using such an inorganic solution as a "spreading solution" for an interfacial film. Surface modification of ZnO is performed using a long-chain carboxylic acid. Accordingly, a regular arrangement of ZnO can be easily achieved in order to overcome the relatively weak van der Walls interactions between inorganic materials. A condensed Langmuir monolayer of these particles is also formed. A multiparticle layered structure is constructed by the Langmuir-Blodgett (LB) technique. Out-of-plane XRD measurement results for a single-particle layer of organo-ZnO clearly show a sharp peak at 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

  10. 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.

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

    PubMed

    Cattaneo, Laura; Kos, Žiga; Savoini, Matteo; Kouwer, Paul; Rowan, Alan; Ravnik, Miha; Muševi?, 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

  12. Inner structure of adsorbed ionic microgel particles.

    PubMed

    Wellert, Stefan; Hertle, Yvonne; Richter, Marcel; Medebach, Martin; Magerl, David; Wang, Weinan; Demé, Bruno; Radulescu, Aurel; Müller-Buschbaum, Peter; Hellweg, Thomas; von Klitzing, Regine

    2014-06-24

    Microgel particles of cross-linked poly(NIPAM-co-acrylic acid) with different acrylic acid contents are investigated in solution and in the adsorbed state. As a substrate, silicon with a poly(allylamine hydrochloride) (PAH) coating is used. The temperature dependence of the deswelling of the microgel particles was probed with atomic force microscopy (AFM). The inner structure of the adsorbed microgel particles was detected with grazing incidence small angle neutron scattering (GISANS). Small angle neutron scattering (SANS) on corresponding microgel suspensions was performed for comparison. Whereas the correlation length of the polymer network shows a divergence in the bulk samples, in the adsorbed microgel particles it remains unchanged over the entire temperature range. In addition, GISANS indicates changes in the particles along the surface normal. This suggests that the presence of a solid surface suppresses the divergence of internal fluctuations in the adsorbed microgels close to the volume phase transition. PMID:24920223

  13. 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.

  14. 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 Å, 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

  15. 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 Å in its ligand-free form. Our structural data allow the assignment of human NaPRTase to the type II phosphoribosyltransferase subfamily and reveal that the enzyme consists of two domains and functions as a dimer with the active site located at the interface of the monomers. The substrate-binding mode was analyzed by molecular docking simulation and provides hints into the catalytic mechanism. Moreover, structural comparison of human NaPRTase with the other two human type II phosphoribosyltransferases involved in NAD biosynthesis, quinolinate phosphoribosyltransferase and nicotinamide phosphoribosyltransferase, reveals that while the three enzymes share a conserved overall structure, a few distinctive structural traits can be identified. In particular, we show that NaPRTase lacks a tunnel that, in nicotinamide phosphoribosiltransferase, represents the binding site of its potent and selective inhibitor FK866, currently used in clinical trials as an antitumoral agent. PMID:26042198

  16. Crystal structure of human nicotinic acid phosphoribosyltransferase

    PubMed Central

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

    2015-01-01

    Nicotinic acid phosphoribosyltransferase (EC 2.4.2.11) (NaPRTase) is the rate-limiting enzyme in the three-step Preiss–Handler pathway for the biosynthesis of NAD. The enzyme catalyzes the conversion of nicotinic acid (Na) and 5-phosphoribosyl-1-pyrophosphate (PRPP) to nicotinic acid mononucleotide (NaMN) and pyrophosphate (PPi). Several studies have underlined the importance of NaPRTase for NAD homeostasis in mammals, but no crystallographic data are available for this enzyme from higher eukaryotes. Here, we report the crystal structure of human NaPRTase that was solved by molecular replacement at a resolution of 2.9 Å in its ligand-free form. Our structural data allow the assignment of human NaPRTase to the type II phosphoribosyltransferase subfamily and reveal that the enzyme consists of two domains and functions as a dimer with the active site located at the interface of the monomers. The substrate-binding mode was analyzed by molecular docking simulation and provides hints into the catalytic mechanism. Moreover, structural comparison of human NaPRTase with the other two human type II phosphoribosyltransferases involved in NAD biosynthesis, quinolinate phosphoribosyltransferase and nicotinamide phosphoribosyltransferase, reveals that while the three enzymes share a conserved overall structure, a few distinctive structural traits can be identified. In particular, we show that NaPRTase lacks a tunnel that, in nicotinamide phosphoribosiltransferase, represents the binding site of its potent and selective inhibitor FK866, currently used in clinical trials as an antitumoral agent. PMID:26042198

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

    PubMed

    Rödström, 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

  18. Structural studies of large nucleoprotein particles, vaults

    PubMed Central

    TANAKA, Hideaki; TSUKIHARA, Tomitake

    2012-01-01

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

  19. Crystal Structure of the Ribosome at 5.5 Resolution

    E-print Network

    Economou, Tassos

    Crystal Structure of the Ribosome at 5.5 Å Resolution Marat M. Yusupov,1 * Gulnara Zh. Yusupova,1 the crystal structure of the complete Thermus thermophilus 70S ribosome containing bound messenger RNA and transfer RNAs (tRNAs) at 5.5 angstrom resolution. All of the 16S, 23S, and 5S ribosomal RNA (rRNA) chains

  20. Symmetrybroken crystal structure of elemental boron at low temperature

    E-print Network

    Widom, Michael

    Symmetry­broken crystal structure of elemental boron at low temperature M. Widom Department Academy of Sciences, Bratislava, Slovakia (Dated: November 6, 2007) The crystal structure of boron­ lations found its energy to be greater than the energy of the #­rhombohedral (red) form, implying # cannot

  1. Hybrid Single-Nanowire Photonic Crystal and Microresonator Structures

    E-print Network

    Loncar, Marko

    Hybrid Single-Nanowire Photonic Crystal and Microresonator Structures Carl J. Barrelet, Jiming Bao that combines chemically synthesized single nanowire emitters with lithographically defined photonic crystal and racetrack microresonator structures. Finite-difference time-domain calculations were used to design nanowire

  2. 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…

  3. 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)

  4. 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

  5. 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; Noé, 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

  6. 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.

  7. A Possibility of Volume Refraction of Negative Relativistic Particles in Bent Crystals

    E-print Network

    Gennady V. Kovalev

    2007-07-26

    The volume coherent deflection of high-energy positive and negative particles in uniformly bent crystals is studied. The general analysis of potential scattering shows that the standard screening potential for a large class of collisions can cause the volume refraction for negative particles (antiprotons, electrons) instead of the volume reflection for positive particles (proton, positrons).

  8. 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.

  9. INELASTIC LIGHT SCATTERING BY LARGE STRUCTURED PARTICLES

    E-print Network

    Berne, Bruce J.

    INELASTIC LIGHT SCATTERING BY LARGE STRUCTURED PARTICLES BRUCE J. BERNE and RALPH NOSSAL From than the wavelength of scattered light. Particular attention is given to models of motile, and dumbbell-shaped scatterers are derived and compared. 1. INTRODUCTION Several recent studies have

  10. A Dominant Factor for Structural Classification of Protein Crystals.

    PubMed

    Qi, Fei; Fudo, Satoshi; Neya, Saburo; Hoshino, Tyuji

    2015-08-24

    With the increasing number of solved protein crystal structures, much information on protein shape and atom geometry has become available. It is of great interest to know the structural diversity for a single kind of protein. Our preliminary study suggested that multiple crystal structures of a single kind of protein can be classified into several groups from the viewpoint of structural similarity. In order to broadly examine this finding, cluster analysis was applied to the crystal structures of hemoglobin (Hb), myoglobin (Mb), human serum albumin (HSA), hen egg-white lysozyme (HEWL), and human immunodeficiency virus type 1 protease (HIV-1 PR), downloaded from the Protein Data Bank (PDB). As a result of classification by cluster analysis, 146 crystal structures of Hb were separated into five groups. The crystal structures of Mb (n = 284), HEWL (n = 336), HSA (n = 63), and HIV-1 PR (n = 488) were separated into six, five, three, and six groups, respectively. It was found that a major factor causing these structural separations is the space group of crystals and that crystallizing agents have an influence on the crystal structures. Amino acid mutation is a minor factor for the separation because no obvious point mutation making a specific cluster group was observed for the five kinds of proteins. In the classification of Hb and Mb, the species of protein source such as humans, rabbits, and mice is another significant factor. When the difference in amino sequence is large among species, the species of protein source is the primary factor causing cluster separation in the classification of crystal structures. PMID:26230289

  11. 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

  12. 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 Å 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

  13. 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

  14. 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

  15. 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.

  16. 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

  17. 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

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

    SciTech Connect

    Avanesov, A.G.; Zhorin, V.V.; Pisarenko, V.F.

    1994-11-01

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

  19. Crystal Structures of Human NUDT5 Reveal Insights into the Structural Basis of the Substrate Specificity

    E-print Network

    Tian, Weidong

    Crystal Structures of Human NUDT5 Reveal Insights into the Structural Basis of the Substrate-ribosylation by hydrolyzing ADPR to AMP and ribose 5-phosphate. We report here the crystal structures of hNUDT5 in apo form- sugars over other sugar nucleotides. Structural comparisons with E. coli ADPRase ORF209 and ADPXase ORF

  20. 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.

  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. 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.

  3. 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.

  4. Optically generated reconfigurable photonic structures of elastic quasiparticles in frustrated cholesteric liquid crystals.

    PubMed

    Smalyukh, Ivan I; Kaputa, Daniel; Kachynski, Aliaksandr V; Kuzmin, Andrey N; Ackerman, Paul J; Twombly, Christopher W; Lee, Taewoo; Trivedi, Rahul P; Prasad, Paras 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 ~10 V applied to the transparent electrodes. PMID:22453364

  5. 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.

  6. 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.

  7. Crystal Structure of Mycobacterium tuberculosis D-3-Phosphoglycerate Dehydrogenase

    E-print Network

    Grant, Gregory

    Crystal Structure of Mycobacterium tuberculosis D-3-Phosphoglycerate Dehydrogenase EXTREME of D-3-phosphoglyc- erate dehydrogenase from Mycobacterium tuberculosis has been determined at 2.3 Å bacteria such as Mycobacterium, Bacillus subtilis, Corynebacterium, plants such as Arabidopsis, and higher

  8. A machine learning approach to crystal structure prediction

    E-print Network

    Fischer, Christopher Carl

    2007-01-01

    This thesis develops a machine learning framework for predicting crystal structure and applies it to binary metallic alloys. As computational materials science turns a promising eye towards design, routine encounters with ...

  9. The Effect of High Pressure on Crystal Structure Topology 

    E-print Network

    Wood, Peter Andrew

    2008-01-01

    This thesis describes the effects of the application of high pressure to single crystals of small organic compounds. A range of different structural analysis techniques have been used with the emphasis on whole molecule ...

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

    E-print Network

    Hamam, Rafif E.

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

  11. Structure and properties of detonation soot particles

    SciTech Connect

    MalKOV, I.Y.; Titiov, V.M.

    1996-05-01

    The influence of TNT/RDX (50/50) detonation parameters and conservation conditions of detonation products during their expansion in hermetic detonation chamber on structure and phase composition of the detonation carbon has been considered. Systematic studies made it possible to establish the real structure of detonation carbon depending on experimental conditions. It has been shown that both during explosion in a chamber and thermal annealing in vacuum the nanoparticles of diamond have the tendency to transform not into graphite particles, as was assumed earlier, but into onionlike structures of fullerene series, composed of closed concentric carbon shells, the so-called carbon onions. The nanometer carbon particles have been obtained which comprise a diamond nucleus surrounded by a graphite-like mantle composed of quasi-spherical carbon shells which are the intermediate products of annealing of nanodiamond. The influence of initial sizes of the diamond particles and temperature on the annealing of diamond has been studied. {copyright} {ital 1996 American Institute of Physics.}

  12. 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

  13. 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.

  14. Fabricating large two-dimensional single colloidal crystals by doping with active particles

    E-print Network

    B. van der Meer; L. Filion; M. Dijkstra

    2015-11-06

    Using simulations we explore the behaviour of two-dimensional colloidal (poly)crystals doped with active particles. We show that these active dopants can provide an elegant new route to removing grain boundaries in polycrystals. Specifically, we show that active dopants both generate and are attracted to defects, such as vacancies and interstitials, which leads to clustering of dopants at grain boundaries. The active particles both broaden and enhance the mobility of the grain boundaries, causing rapid coarsening of the crystal domains. The remaining defects recrystallize upon turning off the activity of the dopants, resulting in a large-scale single-domain crystal.

  15. A model for the interaction of high-energy particles in straight and bent crystals implemented in Geant4

    NASA Astrophysics Data System (ADS)

    Bagli, E.; Asai, M.; Brandt, D.; Dotti, A.; Guidi, V.; Wright, D. H.

    2014-08-01

    A model for the simulation of orientational effects in straight and bent periodic atomic structures is presented. The continuum potential approximation has been adopted.The model allows the manipulation of particle trajectories by means of straight and bent crystals and the scaling of the cross sections of hadronic and electromagnetic processes for channeled particles. Based on such a model, an extension of the Geant4 toolkit has been developed. The code has been validated against data from channeling experiments carried out at CERN.

  16. Simulation of structural phase transition in two dimensional ionic crystal

    NASA Astrophysics Data System (ADS)

    Zhang, Dongsheng; Vernizzi, Graziano; Olvera de La Cruz, Monica

    2010-03-01

    We investigate the structure of a two-dimensional monovalent ionic crystal observed in cationic-anionic molecules adsorbed into surfaces by molecular dynamics simulations. The pair interaction between ions include a short-range Lennard-Jones term and a long-range electrostatic term. When the dielectric constant is small, electrostatic interactions dominate and the crystal form a regular square lattice. At large values of the dielectric constant the Lennard-Jones attraction dominates, and the crystal form a triangular lattice. We study the phase diagram of this model and the properties of the structural transition.

  17. Band structure mapping of photonic crystal intersubband detectors

    NASA Astrophysics Data System (ADS)

    Schartner, S.; Golka, S.; Pflügl, 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.

  18. 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.}

  19. The distorted close-packed crystal structure of methane A

    NASA Astrophysics Data System (ADS)

    Maynard-Casely, H. E.; Bull, C. L.; Guthrie, M.; Loa, I.; McMahon, M. I.; Gregoryanz, E.; Nelmes, R. J.; Loveday, J. S.

    2010-08-01

    We have determined the full crystal structure of the high-pressure phase methane A. X-ray single-crystal diffraction data were used to determine the carbon-atom arrangement, and neutron powder diffraction data from a deuterated sample allowed the deuterium atoms to be located. It was then possible to refine all the hydrogen positions from the single-crystal x-ray data. The structure has 21 molecules in a rhombohedral unit cell, and is quite strongly distorted from the cubic close-packed structure of methane I, although some structural similarities remain. Full knowledge of this structure is important for modeling of methane at higher pressures, including in relation to the mineralogy of the outer solar system. We discuss interesting structural parallels with the carbon tetrahalides.

  20. Phase transitions of aqueous atmospheric particles: Crystallization of ammonium salts promoted by oxide mineral constituents

    NASA Astrophysics Data System (ADS)

    Han, Jeong-Ho

    2001-09-01

    Knowledge of the hygroscopic response of aerosols is a fundamental factor necessary for the accurate quantitative modeling of visibility degradation, global warming, PM-10 health issues, cloud microphysics, and the oxidizing capacity of the troposphere. At the present time, however, our current understanding of phase transitions is insufficient to develop accurate quantitative models. The discrepancy between current atmospheric models and field measurements originates mainly from a lack of understanding of the efflorescence of real atmospheric particles. While there have been many studies on the homogeneous nucleation of the soluble organic, inorganic, or multi-component materials, many recent in situ field measurements with single-particle mass spectrometry reveal that the individual particles in the troposphere are primarily composed of more than one component. One of the common mixed component particle types contains both water- soluble and insoluble components. Through atmospheric processes, the soluble component can be expected to form a coating around the insoluble constituents. This type of atmospheric particles is very important because the insoluble constituent can play a role as a template for the crystallization of the soluble components by heterogeneous nucleation. In the atmosphere, the most prevalent insoluble constituents are mineral dusts, which have their origin from Saharan and Gobbi deserts. The existence of these coated particles has been supported by several field measurements as well as model studies. Therefore, it becomes imperative to simulate more realistic atmospheric particles for more exact (or realistic) understanding the phase transition of the ambient aerosol particles in the real world. In this context, a series of studies has been completed to solve the aforementioned problems in the phase transition study and to better understand the heterogeneous nucleation of these internally mixed particles. An in-line tube furnace has been developed and characterized to generate the internally mixed particles consisting of the soluble and insoluble components. Spray pyrolysis was employed in order to have the control of the size and crystalline phase of the insoluble constituents and combined with the in-line tube furnace to manipulate the coated particles (i.e., internally mixed particles). Employing the stable and well- characterized generation source for the coated particles, the roles of the insoluble constituents (i.e., metal oxides) in heterogeneous nucleation were investigated extensively in terms of their size (i.e., surface area) and crystalline structure as nucleation templates. Ammonium sulfate and ammonium nitrate were selected as the soluble components because they are the most common atmospheric aerosol particles from anthropogenic activities. As for insoluble components, corundum (?-Al2O3), hematite (?- Al2O3), mullite (Al6Si 2O13), silica (am-SiO2), rutile (TiO2), ZrO2, and ?-Al2O3 were selected with the reasoning that some of them represent the abundant crustal components in the atmosphere and that others have interesting chemical compositions and/or crystalline structures.

  1. Collective Diffusion of Colloidal Hard Rods in Smectic Liquid Crystals: Effect of Particle Anisotropy

    E-print Network

    Alessandro Patti; Djamel El Masri; René van Roij; Marjolein Dijkstra

    2010-04-16

    We study the layer-to-layer diffusion in smectic-A liquid crystals of colloidal hard rods with different length-to-diameter ratios using computer simulations. The layered arrangement of the smectic phase yields a hopping-type diffusion due to the presence of permanent barriers and transient cages. Remarkably, we detect stringlike clusters composed of inter-layer rods moving cooperatively along the nematic director. Furthermore, we find that the structural relaxation in equilibrium smectic phases shows interesting similarities with that of out-of-equilibrium supercooled liquids, although there the particles are kinetically trapped in transient rather than permanent cages. Additionally, at fixed packing fraction we find that the barrier height increases with increasing particle anisotropy, and hence the dynamics is more heterogeneous and non-Gaussian for longer rods, yielding a lower diffusion coefficient along the nematic director and smaller clusters of inter-layer particles that move less cooperatively. At fixed barrier height, the dynamics becomes more non-Gaussian and heterogeneous for longer rods that move more collectively giving rise to a higher diffusion coefficient along the nematic director.

  2. Chapter 9 Crystal Structure Although the symmetry and beauty of crystals have always excited curiosity and wonder, the

    E-print Network

    Lee, Ho Sung

    1-1 Chapter 9 Crystal Structure Although the symmetry and beauty of crystals have always excited by the fact that when he accidently dropped a crystal of calcite (a form of calcium carbonate), it fractured into smaller crystals that had the same interfacial angles between their plane surface as did the original

  3. 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.

  4. The Mechanics of the Systems of Structured Particles

    E-print Network

    V. M. Somsikov

    2012-10-02

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

  5. 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.

  6. 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.

  7. Crystal structure transfer in core/shell nanowires.

    PubMed

    Algra, Rienk E; Hocevar, Moïra; 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

  8. 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...

  9. 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

  10. Structural characteristics and second order nonlinear optical properties of borate crystals

    E-print Network

    Osnabrück, Universität

    Structural characteristics and second order nonlinear optical properties of borate crystals D. Xue optical (NLO) responses of some typical borate crystals with various crystal structures have been the reported inorganic crystal structures there are in total only 15% of noncentrosymmetric structure

  11. THE ELECTRONIC STRUCTURE OF SMOOTHLY DEFORMED CRYSTALS: WANNIER FUNCTIONS AND THE CAUCHY-BORN

    E-print Network

    Lu, Jianfeng

    THE ELECTRONIC STRUCTURE OF SMOOTHLY DEFORMED CRYSTALS: WANNIER FUNCTIONS AND THE CAUCHY-BORN RULE WEINAN E AND JIANFENG LU Abstract. The electronic structure of a smoothly deformed crystal is ana- lyzed structure of perfect crystals, particularly the equilibrium structure. Here by "perfect crystals" we mean

  12. Manipulation of particles by laser tweezers-induced gradient of order in the nematic liquid crystal

    NASA Astrophysics Data System (ADS)

    Škarabot, Miha; Osterman, Natan; Lokar, Žiga; Muševi?, Igor

    2014-09-01

    Manipulation and transport of microparticles and even fluorescent molecules by thermally induced gradient of the order parameter is demonstrated in the nematic liquid crystal. IR light absorption of a focused beam of the laser tweezers is used to heat locally a thin layer of the nematic liquid crystal by several degrees, thus creating a spatial gradient of temperature of the nematic liquid crystal over tens of micrometers. It is observed that a colloidal particle with dipolar symmetry of the director configuration is attracted into the hot spot of the tweezers. The strength of trapping potential increases linearly with particle radius, which indicates that the trapping is due to elastic energy of the distorted nematic liquid crystal around the particle. By using fluorescent molecules instead of colloidal particles, we observed that this thermal trapping of colloidal particles is efficient down to the nanoscale, as fluorescent molecules are also attracted to the hotter regions of the liquid crystal. This effect is absent in the isotropic phase.

  13. 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.

  14. 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

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. Colloidal particles in liquid crystal films and at interfaces

    E-print Network

    Mykola Tasinkevych; Denis Andrienko

    2010-11-04

    This mini-review discusses the recent contribution of theoretical and computational physics as well as experimental efforts to the understanding of the behavior of colloidal particles in confined geometries and at liquid crystalline interfaces. Theoretical approaches used to study trapping, long- and short-range interactions, and assembly of solid particles and liquid inclusions are outlined. As an example, an interaction of a spherical colloidal particle with a nematic-isotropic interface and a pair interaction potential between two colloids at this interface are obtained by minimizing the Landau-de Gennes free energy functional using the finite-element method with adaptive meshes.

  20. Formation of lanthanum beryllate real structure under different crystallization conditions

    SciTech Connect

    Tsvetkov, E.G. . E-mail: tsvetkov@uiggm.nsc.ru; Rylov, G.M.; Matrosov, V.N.

    2006-02-02

    The aim of this paper is to characterize the major structural defects of lanthanum beryllate single crystals grown by the Czochralski method, including those doped with rare-earth elements, and to reveal their relationship to specific properties of the crystal structure of La{sub 2}Be{sub 2}O{sub 5} and with their crystallization conditions. As a basic method for research, we used transmission X-ray topography. It was established that the defect state of La{sub 2}Be{sub 2}O{sub 5} crystals prepared by this method can be caused by different types of dislocations and their ordered assemblies, solid-phase inclusions of crucible metal and eutectically co-crystallizing phases, as well as by face growth sectors with elevated content of dopant. We show a possibility for growing single crystals of doped lanthanum beryllate having a minimum quantity of structural defects that could be suitable for manufacture of high quality laser rods.

  1. 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

  2. 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

  3. 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.

  4. Understanding molecular crystal structures at extreme conditions 

    E-print Network

    Funnell, Nicholas Paul

    2012-06-22

    Understanding the structure of matter in the solid state could be considered as being one of ‘the big questions’ in chemistry. Whereas the structural behaviour of molecules in the gas phase is relatively well-understood, ...

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

    E-print Network

    Glaser, Rainer

    Dipole Parallel Alignment in the Crystal Structure of a Polar Biphenyl: 4-Acetyl-4-Methoxybiphenyl) was synthesized via a catalytic Suzuki cross-coupling reaction, and the crystal structure was determined, and the crystals are noncentrosymmetric, space group Pna21. The crystal structure of AMB features parallel

  6. Crystal structure of human muscle creatine kinase

    E-print Network

    Shen, Yue-quan; Tang, Liang; Zhou, Hai-Meng; Lin, Zheng-jiong

    2001-08-01

    (Muhlebach et al., 1994) and they have high amino-acid sequence identity. Since 1996, several creatine kinase crystal struc- tures have been solved, including mitochondrial CK from sarcomas (sMtCK; Fritz- Wolf et al., 1996), MM-type CK from rabbit (RCK; Rao... of rabbit muscle creatine kinase determined at 2.4 A Ê (Rao et al., 1998) with high sequence identity (?96%) was selected as a search model. Residues with discrepant sequences were replaced with alanine. In the early stage of the molecular replacement...

  7. 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

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

    DOEpatents

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

    1994-01-01

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

  10. 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.

  11. Dynamic structure of superionic protons in hydrogen fluoride crystal

    NASA Astrophysics Data System (ADS)

    Ohde, Yoshiyuki; Tsumuraya, Kazuo

    2013-03-01

    Hydrogen fluoride crystal forms zig-zag chains of hydrogen fluoride molecules forming covalent bond between them. Goldman et al.(J. Chem. Phys.125,044501(2006).) have found the superionic state of the protons in the hydrogen fluoride crystal at 900 K and beyond the pressures at 33 GPa. The present study elucidates the dynamic structure of the protons in the superionic state of the crystal at the extreme conditions with the first principles molecular dynamics method. The strong covalent bond between the proton and the fluorine in the conductor has shown a different dynamic structure from that in the ?-CuI The protons in the conductor are bonded with the nearest fluorine and the other protons are located at incommensurate sites of the bcc fluorine lattice. This is a different dynamic structure from the formation of the incommensurate dynamic copper dimers in the ?-CuI.(Tsumuraya et al . J. Phys. Soc. Jpn. 81,055603(2012).)

  12. 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

  13. Anisotropy of bond projections in simple crystal structures

    NASA Astrophysics Data System (ADS)

    Šim?nek, Antonín

    2011-10-01

    The nearest-neighbor bond distances represented by the stick-and-ball model of a crystal are projected into planes in order to find the directions from where the projections have maximum or minimum values. The projection directions and their corresponding values of the maxima and minima are presented for simple cubic, body-centered-cubic, face-centered-cubic, sodium chloride, zinc sulfide, diamond, fluorite, cesium chloride, hexagonal close-packed, tungsten carbide, wurtzite, graphite, graphene, and aluminum boride structures. The purely geometrical considerations quantitatively reflect an anisotropy of the bond projections and provide data for a large amount of materials crystallizing in these structures. The presented results can be applied to the description, analysis, and understanding of anisotropic effects related to bond projection in 14 crystal structures. The application of hardness anisotropy for BN, SiC, and TiC is shown.

  14. 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

  15. Crystal Structure of Bacillus subtilis ?-Amylase in Complex with Acarbose

    PubMed Central

    Kagawa, Masayuki; Fujimoto, Zui; Momma, Mitsuru; Takase, Kenji; Mizuno, Hiroshi

    2003-01-01

    The crystal structure of Bacillus subtilis ?-amylase, in complex with the pseudotetrasaccharide inhibitor acarbose, revealed an hexasaccharide in the active site as a result of transglycosylation. After comparison with the known structure of the catalytic-site mutant complexed with the native substrate maltopentaose, it is suggested that the present structure represents a mimic intermediate in the initial stage of the catalytic process. PMID:14617662

  16. 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

  17. 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 ?m 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

  18. 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.

  19. The crystal structure of methenyltetrahydromethanopterin cyclohydrolase from Methanobrevibacter ruminantium.

    PubMed

    Carbone, Vincenzo; Schofield, Linley R; Beattie, Amy K; Sutherland-Smith, Andrew J; Ronimus, Ron S

    2013-11-01

    Methenyltetrahydromethanopterin cyclohydrolase (Mch) is involved in the methanogenesis pathway of archaea as a C1 unit carrier where N(5) -formyl-tetrahydromethanopterin is converted to methenyl-tetrahydromethanopterin. Mch from Methanobrevibacter ruminantium was cloned, purified, crystallized and its crystal structure solved at 1.37 Å resolution. A biologically active trimer, the enzyme is composed of two domains including an N-terminal domain of six ?-helices encompassing a series of four ?-sheets and a predominantly anti-parallel ?-sheet at the C-terminus flanked on one side by ?-helices. Sequence and structural alignments have helped identify residues involved in substrate binding and trimer formation. PMID:23873651

  20. 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.

  1. 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

  2. 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.

  3. The Resonance Scattering Phenomenon of Fast Negatively Charged Particles in a Single Crystal

    E-print Network

    Gennady V. Kovalev

    2014-12-12

    The energy spectrum of the extended attractive potential of a crystallographic row for negatively charged particles has quasi-bound states. It follows that a negatively charged particle with small transversal momentum component ($p_{\\bot} R crystal, when fast electrons move with a small glancing angle ($\\theta_0 << 1/pR$) to a crystallographic axis. The calculated results for the electrons and angular widths of resonance peaks are consistent with experimental data.

  4. Variation Principle for Calculation of Many-Particle Effects in Crystals

    E-print Network

    Halina V. Grushevskaya; Leonid I. Gurskii

    2006-01-28

    Variation principle has been developed to calculate many-particle effects in crystals. Within the framework of quasi-particle concept the variation principle has been used to find one-electron states with taking into account of effects due to non-locality of electronic density functional in electromagnetic fields. A secondary quantized density matrix was used to find the Green function of a quasiparticle and changes of its effective mass due to correlated motion of interacting electrons.

  5. Potential of mean force between a spherical particle suspended in a nematic liquid crystal and a substrate: sphere size effects.

    PubMed

    Kim, Evelina B; de Pablo, Juan J

    2004-06-01

    The expanded ensemble density of states method (ExEDOS) is used to investigate the effective interaction of a spherical colloidal particle suspended in a confined liquid crystal (LC) with a substrate. The potential of mean force (PMF) is determined as a function of the normal distance between the particle and the substrate's surface. The presence of the substrate induces a layered structure of the LC, which in turn greatly influences the PMF. We analyze the structure of the Saturn ring defect that accompanies the colloidal sphere, and find that the ring is displaced slightly towards the surface when the sphere is within the first LC surface layer. A transition occurs from an overall attraction of the colloid to the substrate to a global repulsion when the sphere's radius is roughly twice the length of the LC molecules. PMID:15244594

  6. 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

  7. 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.

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

    E-print Network

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

    2015-01-01

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

  9. 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.

  10. 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.

  11. Crystal structure of a eukaryotic phosphate transporter.

    PubMed

    Pedersen, Bjørn P; Kumar, Hemant; Waight, Andrew B; Risenmay, Aaron J; Roe-Zurz, Zygy; Chau, Bryant H; Schlessinger, Avner; Bonomi, Massimiliano; Harries, William; Sali, Andrej; Johri, Atul K; Stroud, Robert M

    2013-04-25

    Phosphate is crucial for structural and metabolic needs, including nucleotide and lipid synthesis, signalling and chemical energy storage. Proton-coupled transporters of the major facilitator superfamily (MFS) are essential for phosphate uptake in plants and fungi, and also have a function in sensing external phosphate levels as transceptors. Here we report the 2.9?Å structure of a fungal (Piriformospora indica) high-affinity phosphate transporter, PiPT, in an inward-facing occluded state, with bound phosphate visible in the membrane-buried binding site. The structure indicates both proton and phosphate exit pathways and suggests a modified asymmetrical 'rocker-switch' mechanism of phosphate transport. PiPT is related to several human transporter families, most notably the organic cation and anion transporters of the solute carrier family (SLC22), which are implicated in cancer-drug resistance. We modelled representative cation and anion SLC22 transporters based on the PiPT structure to surmise the structural basis for substrate binding and charge selectivity in this important family. The PiPT structure demonstrates and expands on principles of substrate transport by the MFS transporters and illuminates principles of phosphate uptake in particular. PMID:23542591

  12. 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.

  13. Measurement of elastic forces between iron colloidal particles in a nematic liquid crystal.

    PubMed

    Noël, C M; Bossis, G; Chaze, A-M; Giulieri, F; Lacis, S

    2006-06-01

    The forces that arise between two iron particles in a nematic liquid crystal with a strong homeotropic anchoring were studied. For the first time, the short range repulsive force resulting from the presence of a hedgehog defect between two particles was precisely determined thanks to application of a small magnetic field and observation of the equilibrium position resulting from the balance between the elastic and magnetic forces. Above a given threshold force, the particles stuck together whereas the hedgehog defect was expelled and transformed into a Saturn ring located between the particles. The attractive part of the interparticle force was determined with the same method on the entire range of separation distances; we found that the equilibrium distance between two particles was r = 1.19 +/- 0.05 ( was the average diameter of the pair of particles). PMID:16803274

  14. 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.

  15. Tunable metamaterial binary nano-particle dispersed liquid crystal cells

    NASA Astrophysics Data System (ADS)

    Aylo, Rola; Banerjee, Partha P.; Nehmetallah, Georges

    2010-08-01

    Metamaterials with tunable properties are of great importance due to potential applications in super-resolution lensing and sensors. In this paper we study the feasibility of the fabrication of a metamaterial using binary nanoparticle-dispersed liquid crystal cell (NDLCC). Depending on the angle between the director axis of the LCC and the incident beam, types, radii, and volume filling fractions of the nanoparticles, a negative index of refraction cell is obtained in a certain range of frequencies. The effective index of refraction is calculated using the effective medium theory. The scattering, extinction, and absorption of such a NDLCC cell is also found. Finally, the influence of the various parameters to obtain such a negative index metamaterial has been investigated.

  16. Volume 184, number 1 FEBS 2468 May 1985 Characterization and crystallization of ribosomal particles

    E-print Network

    Yonath, Ada E.

    Volume 184, number 1 FEBS 2468 May 1985 Characterization and crystallization of ribosomal particles Chemistry, Rehovot, Israel Received 22 February 1985 Ribosomes and their subunits have been isolated from of the large ribosomal subunits have been obta- ined. Electron microscopy of positively stained thin sections

  17. CRYSTAL STRUCTURES OF THE AND PHASES PRESSURE(GPa)

    E-print Network

    Rodríguez, Fernando

    CRYSTAL STRUCTURES OF THE AND PHASES . PRESSURE(GPa) TEMPERATURE (K) PHASE DIAGRAM FOR CuMoO4 ab.302 7.977 94.76 103.35 103.26 -phase -phase COLOUR: GREEN BROWNISH RED Coordination geometry around Cu2 (brownish red phase). · The -phase is more compact than the normal -phase. The phase transition is of first

  18. 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.

  19. Crystal Structure and Formation Energy of -carbide Using First

    E-print Network

    Cambridge, University of

    Crystal Structure and Formation Energy of -carbide Using First Principles CalculationsIntroduction · Martensite (') -carbide -carbide -carbide Cementite () · Silicon promotes the formation of -carbide below-456(2008) 900, 100s 200, 20s 250, 30 s Ms = 302(1.0 wt%Si), 293 (1.7 wt%Si) 1.0wt% Si : No -carbide 1.7wt% Si

  20. 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.…

  1. ~ Animation of Crystal Structure Variations with Pressure, Temperature and Composition

    E-print Network

    Downs, Robert T.

    ~ Animation of Crystal Structure Variations with Pressure, Temperature and Composition Robert T as a function of temperature, pressure and composition. Examples of these animations are found on the cover another is an effective way to make the computer animations. This paper presents an outline

  2. Crystal Perfection of Particle Monolayer at the Air-Water Interface.

    PubMed

    Shinotsuka, Kei; Kajita, Yasuhito; Hongo, Koki; Hatta, Yoshihisa

    2015-10-27

    Crystal growth in colloidal particle monolayers fabricated by Langmuir-Blodgett method on 4 in. sapphire wafers was investigated under the condition of two techniques, that is, ultrasonic annealing at 1.2 to 1.5 MHz and barrier-sway process at 0.2 to 0.5 Hz. Significant increases of the ordered area were obtained by the both techniques and more than 60 times growth was confirmed. The remaining crystal defects after the growth were categorized as grain boundary, vacancy, and line defect. Both techniques exhibited different features regarding the component ratio of the defects, and different mechanisms for the reorientation of particles are discussed. The driving force of these reorientations is thought to be associated with the 2D Ostwald ripening of colloidal crystals. PMID:26434777

  3. 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.

  4. Selective Crystal Growth and Structural, Optical, and Electronic Studies of Mn3Ta2O8

    E-print Network

    Medvedeva, Julia E.

    Selective Crystal Growth and Structural, Optical, and Electronic Studies of Mn3Ta2O8 Karl Rickert-long single crystal via the optical floating-zone technique. Single-crystal absorbance studies determine these materials, however, the structure solution of a CCTN is difficult without a single crystal. Furthermore

  5. 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.

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

    E-print Network

    V. M. Somsikov

    2009-08-21

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

  7. [Band electronic structures and crystal packing forces

    SciTech Connect

    Not Available

    1993-01-01

    We investigated the electronic and structural properties of low-dimensional materials and explored the structure-property correlations governing their physical properties. Progress was made on how to interpret the scanning tunneling microscopy and atomic force microscopy images of layered materials and on how to account for charge density wave instabilities in 2-D metals. Materials studied included transition metal chalcogenides, transition metal halides, organic conducting salts, Mo bronzes, A[sub 2]PdH[sub 2], fullerenes, squarate tetrahydrate polymers Fe, Cu(C[sub 4]O[sub 4])4[center dot]H[sub 2]O, BEDT salts, etc.

  8. 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, Michaël

    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.

  9. 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.

  10. Crystallization and immersion freezing ability of oxalic and succinic acid in multicomponent aqueous organic aerosol particles

    NASA Astrophysics Data System (ADS)

    Wagner, Robert; Höhler, Kristina; Möhler, Ottmar; Saathoff, Harald; Schnaiter, Martin

    2015-04-01

    This study reports on heterogeneous ice nucleation efficiency of immersed oxalic and succinic acid crystals in the temperature range from 245 to 215 K, as investigated with expansion cooling experiments using suspended particles. In contrast to previous laboratory work with emulsified solution droplets where the precipitation of solid inclusions required a preceding freezing/evaporation cycle, we show that immersed solids readily form by homogeneous crystallization within aqueous solution droplets of multicomponent organic mixtures, which have noneutonic compositions with an excess of oxalic or succinic acid. Whereas succinic acid crystals did not act as heterogeneous ice nuclei, immersion freezing by oxalic acid dihydrate crystals led to a reduction of the ice saturation ratio at freezing onset by 0.066-0.072 compared to homogeneous freezing, which is by a factor of 2 higher than previously reported laboratory data. These observations emphasize the importance of oxalic acid in heterogeneous ice nucleation.

  11. TE-polarized graphene modes sustained by photonic crystal structures.

    PubMed

    Degli-Eredi, I; Sipe, J E; Vermeulen, N

    2015-05-01

    We present the design of a supporting photonic crystal structure that would allow for the excitation of the predicted transverse electric (TE) polarized excitation in a single layer of graphene. We show that it is possible to measure this excitation at room temperature, and that adding an extra layer of dielectric material on top of the structure would further facilitate the experimental observation of the graphene mode. PMID:25927788

  12. Single Crystal Structure Determination of Alumina to 1 Mbar

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    PubMed

    Bonneau, Charlotte; O'Keeffe, Michael

    2015-02-01

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

  14. 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.

  15. Crystal structure of GnsA from Escherichia coli.

    PubMed

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

    2015-06-19

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

  16. Quantum-Mechanical Description of Spin-1/2 Particles and Nuclei Channeled in Bent Crystals

    E-print Network

    A. J. Silenko

    2015-08-02

    General quantum-mechanical description of relativistic particles and nuclei with spin 1/2 channeled in bent crystals is performed with the use of the cylindrical coordinate system. The previously derived Dirac equation in this system is added by terms characterizing anomalous magnetic and electric dipole moments. A transformation to the Foldy-Wouthuysen representation, a derivation of the quantum-mechanical equations of motion for particles and their spins, and a determination of classical limit of these equations are fulfilled in the general case. A physical nature of main peculiarities of description of particles and nuclei in the cylindrical coordinate system is ascertained.

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

    NASA Astrophysics Data System (ADS)

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

    1999-08-01

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

  18. About the probability of close collisions during stochastic deflection of positively charged particles by a bent crystal

    NASA Astrophysics Data System (ADS)

    Chesnokov, Yu. A.; Kirillin, I. V.; Scandale, W.; Shul'ga, N. F.; Truten', V. I.

    2014-04-01

    The probability of close interactions of high-energy positively charged particle with atoms in a bent crystal was considered as a function of the angle between the initial particle momentum and the bending plane. The results of simulation of particle motion presented in the article show the great efficiency of high-energy positively charged particle deflection by a bent crystal due to the stochastic deflection mechanism and strong reduction of the probability of close collisions during the stochastic deflection in comparison to the planar channeling in a bent crystal.

  19. 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.

  20. 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.

  1. Crystal structures of dibromodichloromethane and bromotrichloromethane

    NASA Astrophysics Data System (ADS)

    Lee-Dadswell, S. E.

    The neutron powder profiles for CBr2Cl2 and CBrCl3 have been recorded at temperatures ranging from about 260 K to 5 K. The profiles at the highest temperatures are consistent with fcc structures with a = 8.597(2)A and a = 8.526(2)A respectively. CBrCl3 has a second plastic phase observed at 245 K. The remaining profiles, below 250 K for CBr2Cl2, or below 225 K for CBrCl3, can be analysed in terms of the C2/c space group with Z = 32. This is the same as for the ordered phases of CBr4 and CCl4. Orientational disorder of the molecules leads to the structural similarity of all members of the family. Tests for partial ordering were not successful.

  2. 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

  3. 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.

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

    PubMed

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

    2015-07-15

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

  5. Thin polymer-layer decorated, structure adjustable crystals of nanoparticles.

    PubMed

    Cao, Xue-Zheng; Duan, Zhi-Guang; Wang, Jun-Shu; Cui, Wei; Liu, Yong-Song; Wu, Chen-Xu

    2015-09-21

    Flattened polymer chain decorated crystals of nanoparticles (NPs) are observed for polymer-NP mixtures confined between two parallel substrates. In order to minimize the entropy loss, polymer chains instead of NPs aggregate at the substrate surfaces when the number of NPs is high enough to have the conformation of chains significantly disturbed. Increasing NP concentration to be much higher than that of polymer chains leads to an ordered arrangement of NPs in the central region, which are sandwiched between two thin layers of polymer chains. A scaling model regarding polymer chains consisting of packed correlation blobs is provided to clarify the physics mechanism behind the formation of thin polymer layer and the crystallization of NPs. The order structure of the crystallized NPs is shown to be switchable through an adjustment of the bulk concentrations of polymer chains and NPs. PMID:26268892

  6. 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.

  7. 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.

  8. 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.

  9. Controlling the crystal structure of Ni nanoparticles by the use of alkylamines

    NASA Astrophysics Data System (ADS)

    Mourdikoudis, S.; Simeonidis, K.; Vilalta-Clemente, A.; Tuna, F.; Tsiaoussis, I.; Angelakeris, M.; Dendrinou-Samara, C.; Kalogirou, O.

    2009-09-01

    Ni nanoparticles were prepared via thermal decomposition of nickel acetate tetrahydrate in the presence of long-chain amines, which acted as both solvents and reducing agents. By tuning the reaction temperature, Ni nanostructures with either hcp or fcc crystal structure were obtained. In principle, higher temperatures favored the formation of hcp nanoparticles. The employment of additional surfactants such as 1-adamantanecarboxylic acid and trioctylphosphine-oxide facilitated the tuning of the particles' growth limit. The size of the particles varied between 5 and 120 nm. The magnetic features of fcc-Ni nanoparticles were quite similar to the corresponding 'bulk' ones. On the other hand, the hcp-Ni particles showed weak magnetic features, reflected by low magnetization values, the absence of saturation magnetization and by blocking temperatures far below room temperature.

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

    PubMed

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

    2015-11-01

    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 ?-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

  11. 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 ?-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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

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

    NASA Astrophysics Data System (ADS)

    Seifert, M.; Ström, 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 < 0.1µm) 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.

  17. 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

  18. Synthetic antibodies for specific recognition and crystallization of structured RNA

    PubMed Central

    Ye, Jing-Dong; Tereshko, Valentina; Frederiksen, John K.; Koide, Akiko; Fellouse, Frederic A.; Sidhu, Sachdev S.; Koide, Shohei; Kossiakoff, Anthony A.; Piccirilli, Joseph A.

    2008-01-01

    Antibodies that bind protein antigens are indispensable in biochemical research and modern medicine. However, knowledge of RNA-binding antibodies and their application in the ever-growing RNA field is lacking. Here we have developed a robust approach using a synthetic phage-display library to select specific antigen-binding fragments (Fabs) targeting a large functional RNA. We have solved the crystal structure of the first Fab–RNA complex at 1.95 ?. Capability in phasing and crystal contact formation suggests that the Fab provides a potentially valuable crystal chaperone for RNA. The crystal structure reveals that the Fab achieves specific RNA binding on a shallow surface with complementarity-determining region (CDR) sequence diversity, length variability, and main-chain conformational plasticity. The Fab–RNA interface also differs significantly from Fab–protein interfaces in amino acid composition and light-chain participation. These findings yield valuable insights for engineering of Fabs as RNA-binding modules and facilitate further development of Fabs as possible therapeutic drugs and biochemical tools to explore RNA biology. PMID:18162543

  19. 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.

  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. 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.

  2. 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

  3. 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.

  4. Effects of crystal structure on the uptake of metals by lake trout (Salvelinus namaycush)

    E-print Network

    Effects of crystal structure on the uptake of metals by lake trout (Salvelinus namaycush) otoliths radii), the crystalline structure, and the development state of the fish. Chemistry and crystal hexagonal crystal structure, whereas larger cations such as Sr (1.32 Å) and Ba (1.49 Å) were preferentially

  5. Crystal structure of rabbit muscle creatine kinase J.K. Mohana RaoY

    E-print Network

    Crystal structure of rabbit muscle creatine kinase J.K. Mohana RaoY *, Grzegorz BujaczY , Alexander Abstract The crystal structure of rabbit muscle creatine kinase, solved at 2.35 Aî resolution by X; Rabbit muscle; Enzyme; Crystal structure 1. Introduction Creatine kinase [1^3] (CK; adenosine 5P

  6. Binary hard-sphere crystals with the cesium chloride structure A. B. Schofield

    E-print Network

    Schofield, Andrew B.

    Binary hard-sphere crystals with the cesium chloride structure A. B. Schofield Department The possibility of binary hard-sphere colloids crystallizing with the cesium chloride CsCl structure was examined to have the CsCl structure. Over a period of time some of the CsCl crystals disappeared indicating

  7. Crystallization and Structure Determination of a Hepatitis Delta Virus Ribozyme: Use of the

    E-print Network

    Doudna, Jennifer A.

    Crystallization and Structure Determination of a Hepatitis Delta Virus Ribozyme: Use of the RNA complex crystallized readily, and its structure was solved using standard techniques for heavy crystallization method should be useful for the structure determination of other bio- chemically important RNAs

  8. Computation of the band structure of two-dimensional Photonic Crystals with hp Finite Elements

    E-print Network

    Grohs, Philipp

    Computation of the band structure of two-dimensional Photonic Crystals with hp Finite Elements K structure of 2D photonic crystals and their eigenmodes can be efficiently computed with the finite element and phrases: hp-FEM, exponential convergence, corner singularities, photonic crystals, photonic band structure

  9. THE ELECTRONIC STRUCTURE OF SMOOTHLY DEFORMED CRYSTALS: CAUCHY-BORN RULE FOR THE NONLINEAR

    E-print Network

    Lu, Jianfeng

    THE ELECTRONIC STRUCTURE OF SMOOTHLY DEFORMED CRYSTALS: CAUCHY-BORN RULE FOR THE NONLINEAR TIGHT-BINDING MODEL WEINAN E AND JIANFENG LU Abstract. The electronic structure of a smoothly deformed crystal is ana to the study of the elec- tronic structure of smoothly or elastically deformed crystals, by analyzing various

  10. Structures of Two Novel Crystal Forms of Naja naja naja Phospholipase A2 Lacking Ca2

    E-print Network

    Dennis, Edward A.

    Structures of Two Novel Crystal Forms of Naja naja naja Phospholipase A2 Lacking Ca2 Reveal characterized crystal belong to the tetragonal space group P43212 (a b 88.6 AÊ , c 107.4 AÊ ). The structure naja naja enzyme. # 1998 Academic Press Limited Keywords: lipase; crystal; structure; trimer

  11. Fabrication of polymer photonic crystal superprism structures using polydimethylsiloxane soft molds

    E-print Network

    Jiang, Wei

    Fabrication of polymer photonic crystal superprism structures using polydimethylsiloxane soft molds photonic crystal superprism structures using elastomeric polydimethylsiloxane templates. Dense two-dimensional photonic crystal superprism structures with feature sizes of 150­500 nm and aspect ratios of up to 1

  12. Crystal structures and compressibilities of synthetic 2M1 and 3T phengite micas

    E-print Network

    Smyth, Joseph R.

    Crystal structures and compressibilities of synthetic 2M1 and 3T phengite micas JOSEPH R. SMYTH,1 University, Tempe, AZ 84532, USA *e-mail: joseph.smyth@colorado.edu Abstract: The crystal structures of co, crystal structure, compression Introduction Relatively few hydrous silicate phases are stable

  13. 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.

  14. EVO—Evolutionary algorithm for crystal structure prediction

    NASA Astrophysics Data System (ADS)

    Bahmann, Silvia; Kortus, Jens

    2013-06-01

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

  15. 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

  16. Micro-spectroscopic mapping: revealing internal structures of zircon crystals

    NASA Astrophysics Data System (ADS)

    Nasdala, L.; Reiners, P. W.; Hanchar, J. M.

    2003-04-01

    Natural zircon crystals typically deviate from perfect crystallinity and ideal chemical composition. If non-ideality features are not homogeneously distributed within a crystal but show a heterogeneity pattern, this is referred to as its "internal structure". Internal structures of zircon are mostly first caused by the heterogeneous incorporation of trace elements during crystal growth. Over time, these primary patterns may become more complex after being overprinted by radioactive self-irradiation and heterogeneous alteration or recrystallization. Internal structures may provide valuable information about the origin and post-growth history of zircon crystals. Further, they need to be recognized for sound microprobe dating, for instance to avoid biased results when straddling zones of different age. Revealing internal structures has thus become an important tool in zircon research. It is mostly done by means of backscattered electrons or cathodoluminescence imaging. These two techniques are advantageous over optical microscopy in the cross-polarized mode as the volume resolution is better and simple polished mounts instead of doubly-sided sections are needed. A disadvantage, however, is that the impact of electron beam during analysis causes local structural changes. Quantitative studies of the real structure of zircon samples, such as determination of the degree of the radiation damage, is therefore tainted with potential uncertainty when being done after electron probe analysis. As an alternative, we present images of internal zircon structures generated through visible laser excitation and mapping of the Raman and photoluminescence light. Due to the time-consuming mapping procedure, such images will perhaps not be routinely used. For detailed studies, however, they may provide most valuable information. Photoluminescence maps provide, for instance, information on both the distribution of rare earth elements (band integrals) and the short-range order (band broadening) whereas Raman-based images are most sensitive for revealing patterns of heterogeneous radiation damage. Application of micro-spectroscopic mappings to the study of zircon crystals from the Gold Butte block, Nevada, and the Adirondack Mountains, New York State, are presented.

  17. Avoiding problems with hydrogen misplacement in reporting crystal structures.

    PubMed

    Bernal, Ivan; Watkins, Steven F

    2013-08-01

    Intermolecular hydrogen bonding is an integral part of many crystal structures. Hydrogen bonding sometimes results in one-, two- or three-dimensional supramolecular assemblies, a common feature of which is positional disorder of H atoms related to space-group symmetry. Yet some reported structures fail to include all possible donor–acceptor close contacts, or to seek H-atom electron densities associated with apparent D-H???A trios, while some H-atom positions violate principles of chemistry or crystal physics. Modern diffraction equipment and sophisticated computing systems provide high-quality data; thus, failure to characterize and report fully an accurate, complete and physically correct hydrogen-bonding model should not be acceptable. We illustrate the relevant issues with three published examples in the hope of slowing the proliferation of these problems, with the scientifically desirable goal of improving the accuracy of crystallographic models while also providing improved search keys for information retrieval. PMID:23907863

  18. 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.

  19. Structure development in silicon sheet by shaped crystallization

    NASA Technical Reports Server (NTRS)

    Leipold, M. H.; De Angelis, R. J.

    1978-01-01

    Models are presented for the development of a parallel twinned structure of the 110 plane type and the 112 line type in silicon ribbons. The models are believed to be mutually compatible and operable. The first model relates the requirements for super-cooling during crystallization. The existence of reentrant angles associated with the twin structure is proposed to provide a rough interface to reduce super-cooling. The spacing of the twins is proposed to be limited by the geometrical relationship between the thermal gradient in the liquid and the dimensions of the twinned crystallization front. The second model relates the thermal stress configuration to detail dislocation reactions which would be expected to develop twins. While a specific dislocation mechanism cannot yet be defined, a number of alternatives are presented. All of these various dislocation mechanisms would result in the observed crystalline configuration and the choice among them is not critical.

  20. 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

  1. The crystal structure of ice under mesospheric conditions

    NASA Astrophysics Data System (ADS)

    Murray, Benjamin J.; Malkin, Tamsin L.; Salzmann, Christoph G.

    2015-05-01

    Ice clouds form in the summer high latitude mesopause region, which is the coldest part of the Earth's atmosphere. At these very low temperatures (<150 K) ice can exist in metastable forms, but the nature of these ices remains poorly understood. In this paper we show that ice which is grown at mesospherically relevant temperatures does not have a structure corresponding to the well-known hexagonal form or the metastable cubic form. Instead, the ice which forms under mesospheric conditions is a material in which cubic and hexagonal sequences of ice are randomly arranged to produce stacking disordered ice (ice Isd). The structure of this ice is in the trigonal crystal system, rather than the cubic or hexagonal systems, and is expected to produce crystals with aspect ratios consistent with lidar observations.

  2. Crystal Structures of Aedes Aegypt Alanine Glyoxylate Aminotransferase

    SciTech Connect

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

    2006-01-01

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

  3. Incommensurate composite crystal structure of scandium-II

    SciTech Connect

    Fujihisa, Hiroshi; Gotoh, Yoshito; Yamawaki, Hiroshi; Sakashita, Mami; Takeya, Satoshi; Honda, Kazumasa; Akahama, Yuichi; Kawamura, Haruki

    2005-10-01

    The long-unknown crystal structure of the high pressure phase scandium-II was solved by powder x-ray diffraction and was found to have tetragonal host channels along the c axis and guest chains that are incommensurate with the host, as well as the high pressure phases of Ba, Sr, Bi, and Sb. The pressure dependences of the lattice constants, the incommensurability, the atomic distances, and the atomic volume were investigated.

  4. 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

  5. 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

  6. 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.

  7. 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

  8. 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.

  9. Crystal structure of a COG4313 outer membrane channel

    PubMed Central

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

    2015-01-01

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

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

    SciTech Connect

    Sheldrick, George M.

    2015-01-01

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

  11. 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, Sébastien; 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 Å 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

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

    E-print Network

    S. Masoomeh Hashemi; Mohammad Reza Ejtehadi

    2015-01-25

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

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

    NASA Astrophysics Data System (ADS)

    Hashemi, S. Masoomeh; Ejtehadi, Mohammad Reza

    2015-01-01

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

  14. 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.

  15. 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 (~1–3?nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions. PMID:25940394

  16. 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

  17. 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

  18. 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.

  19. 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

  20. 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.

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

    NASA Astrophysics Data System (ADS)

    Uchiyama, Hiroaki; Nakanishi, Shunsuke; Kozuka, Hiromitsu

    2014-09-01

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

  3. 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.

  4. 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; Novák, 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

  5. 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.

  6. 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

  7. 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

  8. 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, 983–992]. 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 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

  9. Crystal structure of the PB1 domain of NBR1.

    PubMed

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

    2006-01-01

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

  10. 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.

  11. 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

  12. 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 years—by 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

  13. Epitaxial growth, structure, and magnetism of epitaxial Ni80Fe20 single-crystal, bicrystal, and quad-crystal films

    E-print Network

    Huang, Jung-Chun

    Epitaxial growth, structure, and magnetism of epitaxial Ni80Fe20 single-crystal, bicrystal, and quad-crystal films J. C. A. Huang,1,2, * C. C. Yu,2 C. M. Fu,3 and C. H. Lee4 1 Physics Department planes and MgO 110 substrate have been studied. Single-crystal Ni80Fe20 110 films were prepared on Mg

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. Crystal structure of the Fe-member of usovite

    PubMed Central

    Weil, Matthias

    2015-01-01

    Crystals of the title compound, with the idealized composition Ba2CaFeAl2F14, dibarium calcium iron(II) dialuminium tetra­deca­fluoride, were obtained serendipitously by reacting a mixture of the binary fluorides BaF2, CaF2 and AlF3 in a leaky steel reactor. The compound crystallizes in the usovite structure type (Ba2CaMgAl2F14), with Fe2+ cations replacing the Mg2+ cations. The principal building units are distorted [CaF8] square-anti­prisms (point group symmetry 2), [FeF6] octa­hedra (point group symmetry -1) and [AlF6] octa­hedra that are condensed into undulating 2 ?[CaFeAl2F14]4? layers parallel (100). The Ba2+ cations separate the layers and exhibit a coordination number of 12. Two crystal structure models with a different treatment of the disordered Fe site [mixed Fe/Ca occupation, model (I), versus underoccupation of Fe, model (II)], are discussed, leading to different refined formulae Ba2Ca1.310?(15)Fe0.690?(15)Al2F14 [model (I)] and Ba2CaFe0.90?(1)Al2F14 [model (II)]. PMID:26090139

  19. 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.

  20. STRUCTURE NOTE Crystal Structure of YdcE Protein From Bacillus subtilis

    E-print Network

    Shapiro, Lawrence

    STRUCTURE NOTE Crystal Structure of YdcE Protein From Bacillus subtilis Arhonda Gogos,1 Haiyan Mu,2 from Bacillus subtilis, Mycobacte- rium tuberculosis, Chlamydia pneumoniae, Xylella fastidiosa. subtilis, the first from COG2337. Methods. We amplified the ydcE gene by polymerase chain reaction (PCR

  1. 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

  2. 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

  3. 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 Å. Des suspensions aqueuses de particules de bromopolystyrène ont été caractérisées par diffusion de lumière, diffusion de rayons X aux petits angles et par des mesures de pression osmotique. Nous avons ainsi étudié leur structure et les interactions interparticulaires en fonction de la fraction volumique à salinité constante de l'ordre de la micromole/l. Lorsque la cristallisation est lente, nous observons des cristaux parfaits cubiques centrés par diffusion de lumière pour des fractions volumiques comprises entre 0,04 et 0,7 % et cubiques faces centrées pax diffusion de rayons X aux petits angles pour des fractions volumiques plus élevées (2 12 %). Après cisaillement, des défauts apparaissent dans les cristaux ; ils sont caractérisés par la disparition de certaines raies de Bragg en diffusion de lumière pour des échantillons de fraction volumique comprise entre 0,1 et 0,3 % et par la présence d'un pré pic observé par diffusion de rayons X aux petits angles avant le premier pic de Bragg, pour des échantillons plus concentrés (2 12 %). Les pressions osmotiques ont été mesurées par différence de pression hydrostatique entre la solution et le réservoir séparés par une membrane hémiperméable. Les données expérimentales sont bien reproduites par la théorie Poisson Boltzmann Réseau (PBR) qui montre que les interactions sont purement répulsives. Aucune force attractive faible de longue portée n'a été détectée expérimentalement. En calculant le déplacement moyen d'une particule à l'intérieur de sa cage à l'aide du modèle PBR "excentré", nous avons vérifié que le critère de Lindemann était satisfait pour tous les cristaux observés. Cette étude a permis de déterminer l'équation d'état d'un cristal colloidal électrostatique. Les résultats sont équivalents à une mesure de force ultraprécise puisque les forces d'interaction mesurées entre particules sont de l'ordre de 10^{-12} N pour des distances centre à centre de l'ordre de 4000 Å.

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

    NASA Astrophysics Data System (ADS)

    Seifert, M.; Ström, 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 (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< 0.1 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.

  5. The Crystal Structure of a Parallel-stranded Guanine Tetraplex at 0.95 A Resolution

    E-print Network

    to stabilize the crystal lattice. We present evidence that the sugar conformation is strained and proposeThe Crystal Structure of a Parallel-stranded Guanine Tetraplex at 0.95 AÊ Resolution Kathryn, and recombination sites. We report the crystal structure at 0.95 AÊ resolution of a parallel- stranded tetraplex

  6. Crystal structure of human muscle aldolase complexed with fructose 1,6-bisphosphate

    E-print Network

    Crystal structure of human muscle aldolase complexed with fructose 1,6-bisphosphate: Mechanistic. Crystals were also soaked with the natural substrate ~fructose 1,6-bisphosphate!, and the crystal structure's base intermediate between the sugar and the enzyme. The type II enzymes are metal-containing enzymes

  7. Weak Protein-Protein Interactions in Lectins: The Crystal Structure of a Vegetative Lectin from the

    E-print Network

    Hamelryck, Thomas

    - sent, the crystal structures of 21 native or sugar- E-mail address of the corresponding author: lievenWeak Protein-Protein Interactions in Lectins: The Crystal Structure of a Vegetative Lectin from a role in the regulation of receptor crosslinking and subsequent signal transduction. The crystal

  8. he shapes of crystals found in bio-mineral structures such as the

    E-print Network

    Dove, Patricia M.

    T he shapes of crystals found in bio- mineral structures such as the skeletons of marine organisms dif- fer dramatically from those of crystals grown in pure solution. The formation of these complex, often hierarchical structures is difficult to reconcile with the simple mechanistic model of crystal

  9. Crystal Structure of ChrR--A Quinone Reductase with the Capacity to Reduce Chromate

    E-print Network

    Matin, A.C.

    Crystal Structure of ChrR--A Quinone Reductase with the Capacity to Reduce Chromate Subramaniam, such as in chromate bioremediation. Its crystal structure, solved at 2.2 A° resolution, shows that it belongsR crystallized as a tetramer, and size exclusion chromatography showed that this is the oligomeric form

  10. Exploring Solid-State Structure and Physical Properties: A Molecular and Crystal Model Exercise

    ERIC Educational Resources Information Center

    Bindel, Thomas H.

    2008-01-01

    A crystal model laboratory exercise is presented that allows students to examine relations among the microscopic-macroscopic-symbolic levels, using crystalline mineral samples and corresponding crystal models. Students explore the relationship between solid-state structure and crystal form. Other structure-property relationships are explored. The…

  11. Anomalous modal structure in a waveguide with a photonic crystal core

    E-print Network

    Fan, Shanhui

    Anomalous modal structure in a waveguide with a photonic crystal core Xiaofang Yu Department properties of photonic crystals, the modal structures of such waveguides are unusual. In particular a dielectric waveguide with a photonic crystal core. Using constant frequency contour analysis, we show

  12. Crystal Structure of the Oxygen-dependant Coproporphyrinogen Oxidase (Hem13p) of Saccharomyces cerevisiae*

    E-print Network

    Hill, Chris

    Crystal Structure of the Oxygen-dependant Coproporphyrinogen Oxidase (Hem13p) of Saccharomyces employing members of the highly con- served oxygen-dependent CPO family. Here, we report the crystal, as shown by the crystal structure of Escherichia coli oxygen-independent CPO (5), are radical S

  13. Integrable structure of melting crystal model with external potentials

    E-print Network

    Toshio Nakatsu; Kanehisa Takasaki

    2010-02-23

    This is a review of the authors' recent results on an integrable structure of the melting crystal model with external potentials. The partition function of this model is a sum over all plane partitions (3D Young diagrams). By the method of transfer matrices, this sum turns into a sum over ordinary partitions (Young diagrams), which may be thought of as a model of q -deformed random partitions. This model can be further translated to the language of a complex fermion system. A fermionic realization of the quantum torus Lie algebra is shown to underlie therein. With the aid of hidden symmetry of this Lie algebra, the partition function of the melting crystal model turns out to coincide, up to a simple factor, with a tau function of the 1D Toda hierarchy. Some related issues on 4D and 5D supersymmetric Yang-Mills theories, topological strings and the 2D Toda hierarchy are briefly discussed.

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

    PubMed

    Wagner, Robert; Benz, Stefan; Möhler, 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

  15. 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

  16. Structure of finite sphere packings via exact enumeration: Implications for colloidal crystal nucleation

    E-print Network

    Robert S. Hoy; Jared Harwayne-Gidansky; Corey S. O'Hern

    2012-05-02

    We analyze the geometric structure and mechanical stability of a complete set of isostatic and hyperstatic sphere packings obtained via exact enumeration. The number of nonisomorphic isostatic packings grows exponentially with the number of spheres $N$, and their diversity of structure and symmetry increases with increasing $N$ and decreases with increasing hyperstaticity $H \\equiv N_c - N_{ISO}$, where $N_c$ is the number of pair contacts and $N_{ISO} = 3N-6$. Maximally contacting packings are in general neither the densest nor the most symmetric. Analyses of local structure show that the fraction $f$ of nuclei with order compatible with the bulk (RHCP) crystal decreases sharply with increasing $N$ due to a high propensity for stacking faults, 5- and near-5-fold symmetric structures, and other motifs that preclude RHCP order. While $f$ increases with increasing $H$, a significant fraction of hyperstatic nuclei for $N$ as small as 11 retain non-RHCP structure. Classical theories of nucleation that consider only spherical nuclei, or only nuclei with the same ordering as the bulk crystal, cannot capture such effects. Our results provide an explanation for the failure of classical nucleation theory for hard-sphere systems of $N\\lesssim 10$ particles; we argue that in this size regime, it is essential to consider nuclei of unconstrained geometry. Our results are also applicable to understanding kinetic arrest and jamming in systems that interact via hard-core-like repulsive and short-ranged attractive interactions.

  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. 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, 1280–1282; Lemaire & Paccard (1969). Bull. Soc. Fr. Mineral. Cristallogr. 92, 9–16; Buschow & van der Goot (1970). J. Less-Common Met. 22, 419–428], 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 Frank–Kasper polyhedron formed by four Tb and 12 Ni atoms and a pseudo Frank–Kasper polyhedron formed by two Tb and 18 Ni atoms. The four different coordination polyhedra of Ni are Frank–Kasper 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

  19. 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.

  20. 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.

  1. 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 300–1050 K. At 913 K low temperature triclinic form of Li{sub 4}P{sub 2}O{sub 7} transforms into high temperature monoclinic one, space group P2{sub 1}/n, a=8.8261(4) Å, b=5.2028(4) Å, c=13.3119(2) Å, ?=104.372(6)°. The migration maps of Li{sup +} cations based on experimental data implemented into program package TOPOS have been explored. It was found that lithium cations in both low- and high temperature forms of Li{sub 4}P{sub 2}O{sub 7} migrate in three dimensions. Cross sections of the migrations channels extend as the temperature rises, but at the phase transition point have a sharp growth showing a strong “crystal structure – ion conductivity” correlation. -- Graphical abstract: Crystal structure of Li{sub 4}P{sub 2}O{sub 7} at 950 K. Red balls represent oxygen atoms; black lines show Li{sup +} ion migration channels in the layers perpendicular to [001] direction. Highlights: • Structure of Li{sub 4}P{sub 2}O{sub 7} has been refined using high temperature neutron diffraction. • At 913 K triclinic form of Li{sub 4}P{sub 2}O{sub 7} transforms into high temperature monoclinic one. • The migration maps of Li{sup +} implemented into program package TOPOS have been explored. • Cross sections of the migrations channels at the phase transition have a sharp growth.

  2. 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.

  3. Fluorescence enhancement by a photonic crystal with a nanorod-structured high index layer

    E-print Network

    Cunningham, Brian

    -dimensional photonic crystal slab incorporating a nanorod-structured TiO2 high index layer. The photonic crystal emission and the highly porous TiO2 film, not only increases the surface area of the device but more

  4. Inorganic chiral 3-D photonic crystals with bicontinuous gyroid structure replicated from butterfly wing scales.

    PubMed

    Mille, Christian; Tyrode, Eric C; Corkery, Robert W

    2011-09-21

    Three dimensional silica photonic crystals with the gyroid minimal surface structure have been synthesized. The butterfly Callophrys rubi was used as a biotemplate. This material represents a significant addition to the small family of synthetic bicontinuous photonic crystals. PMID:21818463

  5. Crystal structure and characterization of a novel organic crystal: 4-Dimethylaminobenzophenone

    SciTech Connect

    Anandha babu, G.; Ramasamy, P.; Ravikumar, K.; Sridhar, B.

    2009-06-03

    Single crystals of a novel organic material, dimethylaminobenzophenone were grown from aqueous solution employing the technique of controlled evaporation. Dimethylaminobenzophenone belongs to the monoclinic system, with a = 12.5755(7) A, b = 7.9749(4) A, c = 13.0946(7) A, {alpha} = 90{sup o}, {beta} = 111.6380(10){sup o} and {gamma} = 90{sup o}. Fourier transform infrared study has been performed to identify the functional groups. The transmittance of dimethylaminobenzophenone has been used to calculate the refractive index n; the extinction coefficient K and both the real {epsilon}{sub r} and imaginary {epsilon}{sub i} components of the dielectric constant as functions of photon energy. The optical band gap of dimethylaminobenzophenone is 2.9 eV. The structural prefection of the grown crystals has been analyzed by high-resolution X-ray diffraction rocking curve measurements. Thermo gravimetric analysis and differential thermal analysis have also been carried out, and the thermal behavior of dimethylaminobenzophenone crystal has been studied. The dielectric properties and mechanical properties have been investigated.

  6. Self-Assembly of Colloidal Particles on Template Structures

    NASA Technical Reports Server (NTRS)

    Yodh, Arjun G.

    2002-01-01

    I will discuss recent experiments from my lab, which use surface templates to induce ordered colloidal structures. Particle assembly driven by entropic depletion, fluid convection, and sedimentation will be described. Confocal microscopy was used to visualize most of these samples.

  7. Theoretical studies of the crystal structure of rare earths and actinides at zero temperature

    SciTech Connect

    Wills, J.M.; Eriksson, O.

    1993-07-01

    Accurate total energy electronic structure calculations have recently been carried out over a range of volumes for selected rare-earth and actinide elements in crystal structures, experimentally observed in these elements. Correct zero temperature crystal structures are obtained, and calculated equilibrium properties are in reasonable agreement with experiment. Results of these calculations indicate that the interactions underlying crystal structure stability are similar in itinerant f-electron metals and transition metals. The stable crystal structure at a particular volume is determined by a balance between one-electron bandwidths and band fillings and the electrostatic energy of the crystal lattice. Broad bands favor high-symmetry, close-packed structures while narrow bands favor low-symmetry, open structures; allowing for expansion as well as contraction, both transition and actinide elements can be stabilized in both low- and high-symmetry crystal structures.

  8. 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.

  9. All-Optical Reconstruction of Crystal Band Structure.

    PubMed

    Vampa, G; Hammond, T J; Thiré, N; Schmidt, B E; Légaré, F; McDonald, C R; Brabec, T; Klug, D D; Corkum, P B

    2015-11-01

    The band structure of matter determines its properties. In solids, it is typically mapped with angle-resolved photoemission spectroscopy, in which the momentum and the energy of incoherent electrons are independently measured. Sometimes, however, photoelectrons are difficult or impossible to detect. Here we demonstrate an all-optical technique to reconstruct momentum-dependent band gaps by exploiting the coherent motion of electron-hole pairs driven by intense midinfrared femtosecond laser pulses. Applying the method to experimental data for a semiconductor ZnO crystal, we identify the split-off valence band as making the greatest contribution to tunneling to the conduction band. Our new band structure measurement technique is intrinsically bulk sensitive, does not require a vacuum, and has high temporal resolution, making it suitable to study reactions at ambient conditions, matter under extreme pressures, and ultrafast transient modifications to band structures. PMID:26588381

  10. All-Optical Reconstruction of Crystal Band Structure

    NASA Astrophysics Data System (ADS)

    Vampa, G.; Hammond, T. J.; Thiré, N.; Schmidt, B. E.; Légaré, F.; McDonald, C. R.; Brabec, T.; Klug, D. D.; Corkum, P. B.

    2015-11-01

    The band structure of matter determines its properties. In solids, it is typically mapped with angle-resolved photoemission spectroscopy, in which the momentum and the energy of incoherent electrons are independently measured. Sometimes, however, photoelectrons are difficult or impossible to detect. Here we demonstrate an all-optical technique to reconstruct momentum-dependent band gaps by exploiting the coherent motion of electron-hole pairs driven by intense midinfrared femtosecond laser pulses. Applying the method to experimental data for a semiconductor ZnO crystal, we identify the split-off valence band as making the greatest contribution to tunneling to the conduction band. Our new band structure measurement technique is intrinsically bulk sensitive, does not require a vacuum, and has high temporal resolution, making it suitable to study reactions at ambient conditions, matter under extreme pressures, and ultrafast transient modifications to band structures.

  11. Crystal structure of the bacteriophage P2 integrase catalytic domain.

    PubMed

    Skaar, Karin; Claesson, Magnus; Odegrip, Richard; Högbom, Martin; Haggård-Ljungquist, Elisabeth; Stenmark, Pål

    2015-11-30

    Bacteriophage P2 is a temperate phage capable of integrating its DNA into the host genome by site-specific recombination upon lysogenization. Integration and excision of the phage genome requires P2 integrase, which performs recognition, cleavage and joining of DNA during these processes. This work presents the high-resolution crystal structure of the catalytic domain of P2 integrase, and analysis of the structure-function relationship of several previously identified non-functional P2 integrase mutants. The DNA binding area is characterized by a large positively charged patch, harboring key residues. The structure reveals potential for large dimer flexibility, likely essential for rearrangement of DNA strands upon integration and excision of the phage DNA. PMID:26453836

  12. Crystal Structure of a Self-Spliced Group II Intron

    SciTech Connect

    Toor, Navtej; Keating, Kevin S.; Taylor, Sean D.; Pyle, Anna Marie

    2008-04-10

    Group II introns are self-splicing ribozymes that catalyze their own excision from precursor transcripts and insertion into new genetic locations. Here we report the crystal structure of an intact, self-spliced group II intron from Oceanobacillus iheyensis at 3.1 angstrom resolution. An extensive network of tertiary interactions facilitates the ordered packing of intron subdomains around a ribozyme core that includes catalytic domain V. The bulge of domain V adopts an unusual helical structure that is located adjacent to a major groove triple helix (catalytic triplex). The bulge and catalytic triplex jointly coordinate two divalent metal ions in a configuration that is consistent with a two-metal ion mechanism for catalysis. Structural and functional analogies support the hypothesis that group II introns and the spliceosome share a common ancestor.

  13. Crystal Structure of Antagonist Bound Human Lysophosphatidic Acid Receptor 1.

    PubMed

    Chrencik, Jill E; Roth, Christopher B; Terakado, Masahiko; Kurata, Haruto; Omi, Rie; Kihara, Yasuyuki; Warshaviak, Dora; Nakade, Shinji; Asmar-Rovira, Guillermo; Mileni, Mauro; Mizuno, Hirotaka; Griffith, Mark T; Rodgers, Caroline; Han, Gye Won; Velasquez, Jeffrey; Chun, Jerold; Stevens, Raymond C; Hanson, Michael A

    2015-06-18

    Lipid biology continues to emerge as an area of significant therapeutic interest, particularly as the result of an enhanced understanding of the wealth of signaling molecules with diverse physiological properties. This growth in knowledge is epitomized by lysophosphatidic acid (LPA), which functions through interactions with at least six cognate G protein-coupled receptors. Herein, we present three crystal structures of LPA1 in complex with antagonist tool compounds selected and designed through structural and stability analyses. Structural analysis combined with molecular dynamics identified a basis for ligand access to the LPA1 binding pocket from the extracellular space contrasting with the proposed access for the sphingosine 1-phosphate receptor. Characteristics of the LPA1 binding pocket raise the possibility of promiscuous ligand recognition of phosphorylated endocannabinoids. Cell-based assays confirmed this hypothesis, linking the distinct receptor systems through metabolically related ligands with potential functional and therapeutic implications for treatment of disease. PMID:26091040

  14. Crystal structure of a lipid G protein-coupled receptor.

    PubMed

    Hanson, Michael A; Roth, Christopher B; Jo, Euijung; Griffith, Mark T; Scott, Fiona L; Reinhart, Greg; Desale, Hans; Clemons, Bryan; Cahalan, Stuart M; Schuerer, Stephan C; Sanna, M Germana; Han, Gye Won; Kuhn, Peter; Rosen, Hugh; Stevens, Raymond C

    2012-02-17

    The lyso-phospholipid sphingosine 1-phosphate modulates lymphocyte trafficking, endothelial development and integrity, heart rate, and vascular tone and maturation by activating G protein-coupled sphingosine 1-phosphate receptors. Here, we present the crystal structure of the sphingosine 1-phosphate receptor 1 fused to T4-lysozyme (S1P(1)-T4L) in complex with an antagonist sphingolipid mimic. Extracellular access to the binding pocket is occluded by the amino terminus and extracellular loops of the receptor. Access is gained by ligands entering laterally between helices I and VII within the transmembrane region of the receptor. This structure, along with mutagenesis, agonist structure-activity relationship data, and modeling, provides a detailed view of the molecular recognition and requirement for hydrophobic volume that activates S1P(1), resulting in the modulation of immune and stromal cell responses. PMID:22344443

  15. Low Temperature Crystal Structure and Magnetic Properties of RAl2

    SciTech Connect

    Pathak, Arjun K.; Paudyal, Durga; Gschneidner, Karl A.; Pecharsky, Vitalij K.

    2014-01-08

    Low temperature crystal structure and magnetic properties of RAl2 (R?=?Pr and Nd) have been studied using temperature dependent powder x-ray diffraction, magnetization, and heat capacity measurements. Unlike PrAl2, NdAl2 retains cubic MgCu2-type structure from room temperature down to 5?K, which is also confirmed from first principles electronic structure calculations. The magnetization measurements show both PrAl2 and NdAl2 order ferromagnetically at TC?=?32?K and 77?K, respectively. However, the magnetization measurements show the former is a hard ferromagnet compared to the latter which is a soft ferromagnetic material. The magnetic entropy change obtained from heat capacity measurements at ?H?=?30 kOe for PrAl2 and NdAl2 are 3.15?J?mol?1 K?1 and 1.18?J?mol?1 K?1, respectively.

  16. Crystal Structure of a Lipid G Protein?Coupled Receptor

    SciTech Connect

    Hanson, Michael A.; Roth, Christopher B.; Jo, Euijung; Griffith, Mark T.; Scott, Fiona L.; Reinhart, Greg; Desale, Hans; Clemons, Bryan; Cahalan, Stuart M.; Schuerer, Stephan C.; Sanna, M. Germana; Han, Gye Won; Kuhn, Peter; Rosen, Hugh; Stevens, Raymond C.

    2012-03-01

    The lyso-phospholipid sphingosine 1-phosphate modulates lymphocyte trafficking, endothelial development and integrity, heart rate, and vascular tone and maturation by activating G protein-coupled sphingosine 1-phosphate receptors. Here, we present the crystal structure of the sphingosine 1-phosphate receptor 1 fused to T4-lysozyme (S1P{sub 1}-T4L) in complex with an antagonist sphingolipid mimic. Extracellular access to the binding pocket is occluded by the amino terminus and extracellular loops of the receptor. Access is gained by ligands entering laterally between helices I and VII within the transmembrane region of the receptor. This structure, along with mutagenesis, agonist structure-activity relationship data, and modeling, provides a detailed view of the molecular recognition and requirement for hydrophobic volume that activates S1P{sub 1}, resulting in the modulation of immune and stromal cell responses.

  17. Germanium FCC structure from a colloidal crystal template

    SciTech Connect

    Miguez, H.; Meseguer, F.; Lopez, C.; Holgado, M.; Andreasen, G.; Mifsud, A.; Fornes, V.

    2000-05-16

    Here, the authors show a method to fabricate a macroporous structure in which the pores, essentially identical, arrange regularly in a face-centered cubic (FCC) lattice. The result is a network of air spheres in a germanium medium. This structure presents the highest dielectric contrast ({epsilon}{sub Ge}/{epsilon}{sub air} = 16) ever achieved in the optical regime in such periodic structures, which could result in important applications in photonics. The authors employ solid silica colloidal crystals (opals) as templates within which a cyclic germanium growth process is carried out. Thus, the three-dimensional periodicity of the host is inherited by the guest. Afterward, the silica is removed and a germanium opal replica is obtained.

  18. Crystal structure of Homo sapiens protein LOC79017

    SciTech Connect

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

    2010-02-08

    LOC79017 (MW 21.0 kDa, residues 1-188) was annotated as a hypothetical protein encoded by Homo sapiens chromosome 7 open reading frame 24. It was selected as a target by the Center for Eukaryotic Structural Genomics (CESG) because it did not share more than 30% sequence identity with any protein for which the three-dimensional structure is known. The biological function of the protein has not been established yet. Parts of LOC79017 were identified as members of uncharacterized Pfam families (residues 1-95 as PB006073 and residues 104-180 as PB031696). BLAST searches revealed homologues of LOC79017 in many eukaryotes, but none of them have been functionally characterized. Here, we report the crystal structure of H. sapiens protein LOC79017 (UniGene code Hs.530024, UniProt code O75223, CESG target number go.35223).

  19. Critical exponents for the cloud-crystal phase transition of charged particles in a Paul Trap

    E-print Network

    Weiss, D K; Blümel, R

    2015-01-01

    It is well known that charged particles stored in a Paul trap, one of the most versatile tools in atomic and molecular physics, may undergo a phase transition from a disordered cloud state to a geometrically well-ordered crystalline state (the Wigner crystal). In this paper we show that the average lifetime $\\bar\\tau_m$ of the metastable cloud state preceding the cloud $\\rightarrow$ crystal phase transition follows a powerlaw, $\\bar\\tau_m \\sim (\\gamma-\\gamma_c)^{-\\beta}$, $\\gamma>\\gamma_c$, where $\\gamma_c$ is the critical value of the damping constant $\\gamma$ at which the cloud $\\rightarrow$ crystal phase transition occurs. The critical exponent $\\beta$ depends on the trap control parameter $q$, but is independent of the number of particles $N$ stored in the trap and the trap control parameter $a$, which determines the shape (oblate, prolate, or spherical) of the cloud. For $q=0.15,0.20$, and $0.25$, we find $\\beta=1.20\\pm 0.03$, $\\beta=1.61\\pm 0.09$, and $\\beta=2.38\\pm 0.12$, respectively. In addition we f...

  20. Crystal structure of deglycosylated human IgG4-Fc

    PubMed Central

    Davies, Anna M.; Jefferis, Roy; Sutton, Brian J.

    2014-01-01

    The Fc region of IgG antibodies, important for effector functions such as antibody-dependent cell-mediated cytotoxicity, antibody-dependent cellular phagocytosis and complement activation, contains an oligosaccharide moiety covalently attached to each CH2 domain. The oligosaccharide not only orients the CH2 domains but plays an important role in influencing IgG effector function, and engineering the IgG-Fc oligosaccharide moiety is an important aspect in the design of therapeutic monoclonal IgG antibodies. Recently we reported the crystal structure of glycosylated IgG4-Fc, revealing structural features that could explain the anti-inflammatory biological properties of IgG4 compared with IgG1. We now report the crystal structure of enzymatically deglycosylated IgG4-Fc, derived from human serum, at 2.7 ? resolution. Intermolecular CH2-CH2 domain interactions partially bury the CH2 domain surface that would otherwise be exposed by the absence of oligosaccharide, and two Fc molecules are interlocked in a symmetric, open conformation. The conformation of the CH2 domain DE loop, to which oligosaccharide is attached, is altered in the absence of carbohydrate. Furthermore, the CH2 domain FG loop, important for Fc? receptor and C1q binding, adopts two different conformations. One loop conformation is unique to IgG4 and would disrupt binding, consistent with IgG4's anti-inflammatory properties. The second is similar to the conserved conformation found in IgG1, suggesting that in contrast to IgG1, the IgG4 CH2 FG loop is dynamic. Finally, crystal packing reveals a hexameric arrangement of IgG4-Fc molecules, providing further clues about the interaction between C1q and IgG. PMID:24956411

  1. Crystal structures of titanate nanotubes: a Raman scattering study.

    PubMed

    Gao, Tao; Fjellvåg, Helmer; Norby, Poul

    2009-02-16

    Crystal structures of titanate nanotubes prepared from a NaOH treatment of TiO(2) with subsequent acid washing were discussed from a viewpoint of vibrational spectroscopy. The correlation between the vibrational feature and the polymerization nature of the TiO(6) octahedron was established by analyzing Raman scattering data of crystalline TiO(2) (anatase and rutile) and layered protonic titanates. Then, the polymerization nature of TiO(6) octahedra in the titanate nanotubes was identified by comparing their Raman scattering spectra with those of the crystalline TiO(2) and layered protonic titanates. It demonstrated that the titanate nanotubes consist of two-dimensional TiO(6) octahedral host layers with a lepidocrocite (gamma-FeOOH)-type layered structure. This conclusion was confirmed further by considering the Raman scattering properties of a restacked titanate prepared by assembling TiO(6) octahedral layers derived from the original scroll-like titanate nanotubes. Our findings offered a convenient approach to validate the crystal structures of the products from an alkaline treatment of TiO(2) under different experimental conditions. PMID:19143511

  2. Crystal structure of a Baeyer-Villiger monooxygenase.

    PubMed

    Malito, Enrico; Alfieri, Andrea; Fraaije, Marco W; Mattevi, Andrea

    2004-09-01

    Flavin-containing Baeyer-Villiger monooxygenases employ NADPH and molecular oxygen to catalyze the insertion of an oxygen atom into a carbon-carbon bond of a carbonylic substrate. These enzymes can potentially be exploited in a variety of biocatalytic applications given the wide use of Baeyer-Villiger reactions in synthetic organic chemistry. The catalytic activity of these enzymes involves the formation of two crucial intermediates: a flavin peroxide generated by the reaction of the reduced flavin with molecular oxygen and the "Criegee" intermediate resulting from the attack of the flavin peroxide onto the substrate that is being oxygenated. The crystal structure of phenylacetone monooxygenase, a Baeyer-Villiger monooxygenase from the thermophilic bacterium Thermobifida fusca, exhibits a two-domain architecture resembling that of the disulfide oxidoreductases. The active site is located in a cleft at the domain interface. An arginine residue lays above the flavin ring in a position suited to stabilize the negatively charged flavin-peroxide and Criegee intermediates. This amino acid residue is predicted to exist in two positions; the "IN" position found in the crystal structure and an "OUT" position that allows NADPH to approach the flavin to reduce the cofactor. Domain rotations are proposed to bring about the conformational changes involved in catalysis. The structural studies highlight the functional complexity of this class of flavoenzymes, which coordinate the binding of three substrates (molecular oxygen, NADPH, and phenylacetone) in proximity of the flavin cofactor with formation of two distinct catalytic intermediates. PMID:15328411

  3. Crystal structure of a Baeyer–Villiger monooxygenase

    PubMed Central

    Malito, Enrico; Alfieri, Andrea; Fraaije, Marco W.; Mattevi, Andrea

    2004-01-01

    Flavin-containing Baeyer–Villiger monooxygenases employ NADPH and molecular oxygen to catalyze the insertion of an oxygen atom into a carbon–carbon bond of a carbonylic substrate. These enzymes can potentially be exploited in a variety of biocatalytic applications given the wide use of Baeyer–Villiger reactions in synthetic organic chemistry. The catalytic activity of these enzymes involves the formation of two crucial intermediates: a flavin peroxide generated by the reaction of the reduced flavin with molecular oxygen and the “Criegee” intermediate resulting from the attack of the flavin peroxide onto the substrate that is being oxygenated. The crystal structure of phenylacetone monooxygenase, a Baeyer–Villiger monooxygenase from the thermophilic bacterium Thermobifida fusca, exhibits a two-domain architecture resembling that of the disulfide oxidoreductases. The active site is located in a cleft at the domain interface. An arginine residue lays above the flavin ring in a position suited to stabilize the negatively charged flavin-peroxide and Criegee intermediates. This amino acid residue is predicted to exist in two positions; the “IN” position found in the crystal structure and an “OUT” position that allows NADPH to approach the flavin to reduce the cofactor. Domain rotations are proposed to bring about the conformational changes involved in catalysis. The structural studies highlight the functional complexity of this class of flavoenzymes, which coordinate the binding of three substrates (molecular oxygen, NADPH, and phenylacetone) in proximity of the flavin cofactor with formation of two distinct catalytic intermediates. PMID:15328411

  4. Crystal Structure of the Monomeric Porin OmpG

    SciTech Connect

    Subbarao,G.; van den Berg, B.

    2006-01-01

    The outer membrane (OM) of Gram-negative bacteria contains a large number of channel proteins that mediate the uptake of ions and nutrients necessary for growth and functioning of the cell. An important group of OM channel proteins are the porins, which mediate the non-specific, diffusion-based passage of small (<600 Da) polar molecules. All porins of Gram-negative bacteria that have been crystallized to date form stable trimers, with each monomer composed of a 16-stranded {beta}-barrel with a relatively narrow central pore. In contrast, the OmpG porin is unique, as it appears to function as a monomer. We have determined the X-ray crystal structure of OmpG from Escherichia coli to a resolution of 2.3 Angstroms. The structure shows a 14-stranded {beta}{beta}-barrel with a relatively simple architecture. Due to the absence of loops that fold back into the channel, OmpG has a large ({approx}13 Angstroms) central pore that is considerably wider than those of other E. coli porins, and very similar in size to that of the toxin a-hemolysin. The architecture of the channel, together with previous biochemical and other data, suggests that OmpG may form a non-specific channel for the transport of larger oligosaccharides. The structure of OmpG provides the starting point for engineering studies aiming to generate selective channels and for the development of biosensors.

  5. Refinement of the crystal structure of lithium-bearing uvite

    SciTech Connect

    Rozhdestvenskaya, I. V. Frank-Kamenetskaya, O. V.; Kuznetsova, L. G.; Bannova, I. I.; Bronzova, Yu. M.

    2007-03-15

    The crystal structure of a natural calcium tourmaline, i.e., uvite with a high lithium content (0.51 au per formula (aupf) at the Y site, is refined to R = 0.019, R{sub w} = 0.020, and S = 1.11. It is shown that, in nature, there exist uvites in which the charge balance in the case where the Z site is occupied by trivalent cations is provided by the replacement of part of the divalent magnesium cations at the Y site by univalent cations, divalent calcium cations at the X site by sodium cations, and univalent anions at the W site by oxygen anions. The W site is found to be split into two sites, namely, the W1 and W11 sites (the W1-W11 distance is 0.14 A), which are partially occupied by the fluorine and oxygen anions, respectively. An analysis of the results obtained in this study and the data available in the literature on the crystal structure of uvites allows the conclusion that uvite can be considered a superspecies and that the nomenclature of this mineral group needs refinement with the use of structural data.

  6. Supressed Water Crystallization in Nano-Structured Physical Hydrogel

    NASA Astrophysics Data System (ADS)

    Wiener, Clinton; Vogt, Bryan; Weiss, Robert

    2015-03-01

    Suppressed water crystallization occurs in some organisms, such as the common wood frog, which allows it to hibernate in a frozen state without damage to its cells. Knowledge of the behavior of supercooled water and alternate ice forms may have many implications to many fields of science. Supercooling of water by several degrees below the normal freezing point is often observed in hydrogels that have attractive interactions with water, e.g., hydrogen bonding. Repulsive confinement, such as in hydrophobic porous carbon, can have even more significant effects on the supercooling of the entrapped water. This talk describes the freezing behavior in nano-structured, hydrophobically modified poly(dimethyl acrylamide) hydrogels that possess attractive and repulsive interactions with water and are physically crosslinked by hydrophobic nanodomains. Three distinct water freezing regimes were observed in the hydrogel swollen to about 50% water by weight. Differential scanning calorimetry detected three crystallization exotherms at 254K, 244K, and 227K. Quasi-elastic neutron scattering experiments have shown that although the water mobility was suppressed at room temperature, the water remained significantly mobile below the normal freezing point of water. The talk will discuss how tuning the concentration of the hydrophobic composition of the hydrogel affects the porous length scales in the hydrogel, which may alter the state of water and the crystal form produced by supercooling.

  7. Natural pseudowollastonite: Crystal structure, associated minerals, and geological context

    NASA Astrophysics Data System (ADS)

    Seryotkin, Yurii V.; Sokol, Ella V.; Kokh, Svetlana N.

    2012-03-01

    Pseudowollastonite, an extremely rare constituent of ultrahigh-temperature combustion metamorphic and igneous rocks, has been found as a rock-forming mineral in Ca-rich paralava veins of Nabi Musa fossil mud volcano (Dead Sea area). Pseudowollastonite-bearing paralavas are the products of combustion metamorphism associated with spontaneous burning of methane. The melt began to crystallize at 1480-1500 °C about the ambient pressure. Pseudowollastonite enters two mineral assemblages: (1) rankinite, larnite, nagelschmidtite, wollastonite (1T), gehlenite-rich melilite, Ti-rich andradite, cuspidine, and fluorapatite; (2) parawollastonite (2M), wollastonite (1T), gehlenite-rich melilite, Ti-rich andradite, fluorellestadite. In this study we present the first single-crystal structure determination of natural pseudowollastonite. Pseudowollastonite from Nabi Musa dome is stoichiometric CaSiO3 and belongs to the most widespread four-layer polytype: a = 6.83556(10) Å, b = 11.86962(18) Å, c = 19.6255(3) Å, ? = 90.6805(13)°, V = 1592.21(4) Å3, space group C2/c. We argue that pseudowollastonite is so scarce in nature because its formation requires joint action of several uncommon factors: availability of hot melts of T > 1200 °C that bear free calcium but are poor in Mg and Fe (mostly as Fe3 +) and their crystallization in the shallow crust followed by quenching.

  8. Planar defects and heterostructure in diamond structure photonic crystals

    NASA Astrophysics Data System (ADS)

    Dai, Wei; Wang, Hong

    2012-12-01

    Three dimensional diamond structure photonic crystals with planar defects and heterostructure fabricated by rapid prototyping and gel casting with alumina were studied. The influence of ordinary planar defect and twinned planar defect on the transmission properties of the electromagnetic wave in the photonic crystals was first investigated. The normalized resonant intensities are 0.5 and 0.58 for ordinary and twinned planar defect photonic crystals (PCs). The resonant intensity of electromagnetic wave in the twinned planar defect PC is stronger than that in the ordinary planar defect PC and the resonant peak width of the twinned planar defect PC is narrower and steeper than that of the ordinary planar defect PC. The resonant peak intensity and frequency of planar defect modes increase firstly and then decrease with the increase of the planar defect sizes. The strongest resonant peak intensity lies at the defect size with 0.5 mm. If the defect size is more than 2.5 mm, the resonant mode will disappear. In the heterostructure PC, which was realized by combining two perfect PCs with different lattice constants of 9 mm and 12 mm, the band gaps of the two different PCs can be united together.

  9. Crystal structure and 35Cl NQR of (±) ?- (trichloromethyl) -?-propiolactone

    NASA Astrophysics Data System (ADS)

    Basaran, Reha; Dou, Shi-qi; Weiss, Alarich

    1991-09-01

    The crystal structure of (±) ?- (trichloromethyl) -?-propiolactone, C 4H 3Cl 30 2, is reported ( T=294 K); space group C52hP2 l/ c, a=1002(1) pm, b=565.O(5) pm, c=1225(l) pm, ?=9397 (3)? Z=4, V=691.85(2)×10 6pm 3. A weak hydrogen bond is observed between H (C(3)) and the carbonyl oxygen 0(2). The 35Cl NQR spectrum shows three lines in the range 77? T(K)?310. At 77K the resonance frequencies are observed at 39.822(5) MHz, 38.905(5) MHz and 38.322(5) MHz.

  10. XANES study of 3d oxides: Dependence on crystal structure

    NASA Astrophysics Data System (ADS)

    Knapp, G. S.; Veal, B. W.; Pan, H. K.; Klippert, T.

    1982-12-01

    XANES measurements are reported for a number of transition metal oxides. Oxide phases, in which the transition element could be widely varied (within the 3d series) while preserving the crystal structure, were systematically examined. The materials examined include monoxides, perovskites, zircons and spinels. For those samples of a given oxide phase, the near edge spectra are nearly identical but spectra for different phases are dissimilar. These observations are consistent with the simplest view of the x-ray absorption process, namely that dipole selection rules are obeyed and spectral features predominately result from transitions between the K shell and empty states with p-character.

  11. Crystal structure of human tooth enamel studied by neutron diffraction

    NASA Astrophysics Data System (ADS)

    Ouladdiaf, Bachir; Rodriguez-Carvajal, Juan; Goutaudier, Christelle; Ouladdiaf, Selma; Grosgogeat, Brigitte; Pradelle, Nelly; Colon, Pierre

    2015-02-01

    Crystal structure of human tooth enamel was investigated using high-resolution neutron powder diffraction. Excellent agreement between observed and refined patterns is obtained, using the hexagonal hydroxyapatite model for the tooth enamel, where a large hydroxyl deficiency ˜70% is found in the 4e site. Rietveld refinements method combined with the difference Fourier maps have revealed, however, that the hydroxyl ions are not only disordered along the c-axis but also within the basal plane. Additional H ions located at the 6h site and forming HPO42- anions were found.

  12. Crystal Structure of the Pseudomonas aeruginosa Virulence Factor Regulator ?†

    PubMed Central

    Cordes, Timothy J.; Worzalla, Gregory A.; Ginster, Aaron M.; Forest, Katrina T.

    2011-01-01

    Virulence factor regulator (Vfr) enhances Pseudomonas aeruginosa pathogenicity through its role as a global transcriptional regulator. The crystal structure of Vfr shows that it is a winged-helix DNA-binding protein like its homologue cyclic AMP receptor protein (CRP). In addition to an expected primary cyclic AMP-binding site, a second ligand-binding site is nestled between the N-terminal domain and the C-terminal helix-turn-helix domain. Unlike CRP, Vfr is a symmetric dimer in the absence of DNA. Removal of seven disordered N-terminal residues of Vfr prevents the growth of P. aeruginosa. PMID:21665969

  13. A neutron diffraction study of the crystal structure of ferrocene

    E-print Network

    Takusagawa, Fusao; Koetzle, Thomas F.

    1979-05-01

    stream_size 36565 stream_content_type text/plain stream_name Takusagawa_1979_B35_1074.pdf.txt stream_source_info Takusagawa_1979_B35_1074.pdf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 1074... National Laboratory, Upton, New York 11973, USA (.Received 14 October 1978; accepted 21 November 1978) Abstract The structure of ferrocene has been refined with single-crystal neutron diffraction data measured at tempera-tures of 173 and 298 K [Fe(^ 5-C...

  14. Crystal Structure of the Pseudomonas aeruginosa Virulence Factor Regulator

    SciTech Connect

    Cordes, Timothy J.; Worzalla, Gregory A.; Ginster, Aaron M.; Forest, Katrina T.

    2012-09-07

    Virulence factor regulator (Vfr) enhances Pseudomonas aeruginosa pathogenicity through its role as a global transcriptional regulator. The crystal structure of Vfr shows that it is a winged-helix DNA-binding protein like its homologue cyclic AMP receptor protein (CRP). In addition to an expected primary cyclic AMP-binding site, a second ligand-binding site is nestled between the N-terminal domain and the C-terminal helix-turn-helix domain. Unlike CRP, Vfr is a symmetric dimer in the absence of DNA. Removal of seven disordered N-terminal residues of Vfr prvents the growth of P. aeruginosa.

  15. Structural evolution analysis and cold-crystallization kinetics of spherical crystals in poly(trimethylene terephthalate) film using Raman spectroscopy.

    PubMed

    Hu, Chenglong; Chen, Shaoyun; Zhang, Weihong; Xie, Fangyan; Chen, Jian; Chen, Xudong

    2015-09-14

    Dynamic processes and the structural evolution of cold-crystallized poly(trimethylene terephthalate) (PTT) film were investigated using Raman spectroscopy. Raman scattering of C[double bond, length as m-dash]O stretching vibration was related to the molecular chain movement and structure evolution in PTT during cold crystallization. In particular, information about each phase of crystallization, including induction, nucleation, nucleus growth, and secondary crystallization, was thoroughly revealed. The experimental results indicated that the kinetic parameters measured by the Raman method were in good agreement with those obtained by differential scanning calorimetry (DSC) and infrared spectroscopy. The blue-shifted C[double bond, length as m-dash]O stretching vibration resulting from the crystallization process is a popular phenomenon and may therefore have many potential applications in a wide range of areas. PMID:26235149

  16. 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.

  17. 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.

  18. Structure and Dynamics of Freely Suspended Liquid Crystals

    NASA Technical Reports Server (NTRS)

    Clark, Noel A.

    2004-01-01

    Smectic liquid crystals are phases of rod shaped molecules organized into one dimensionally (1 D) periodic arrays of layers, each layer being between one and two molecular lengths thick. In the least ordered smectic phases, the smectics A and C, each layer is a two dimensional (2D) liquid. Additionally there are a variety of more ordered smectic phases having hexatic short range translational order or 2D crystalline or quasi long range translational order within the layers. The inherent fluid-layer structure and low vapor pressure of smectic liquid crystals enables the long term stabilization of freely suspended, single component, layered fluid films as thin as 30A, a single molecular layer. The layering forces the films to be an integral number of smectic layers thick, quantizing their thickness in layer units and forcing a film of a particular number of layers to be physically homogeneous with respect to its layer structure over its entire area. Optical reflectivity enables the precise determination of the number of layers. These ultrathin freely suspended liquid crystal films are structures of fundamental interest in condensed matter and fluid physics. They are the thinnest known stable fluid structures and have the largest surface-to-volume ratio of any stable fluid preparation, making them ideal for the study of the effects of reduced dimensionality on phase behavior and on fluctuation and interface phenomena. Their low vapor pressure and quantized thickness enable the effective use of microgravity to extend the study of basic capillary phenomena to ultrathin fluid films. Freely suspended films have been a wellspring of new LC physics. They have been used to provide unique experimental conditions for the study of condensed phase transitions in two dimensions. They are the only system in which the hexatic has been unambiguously identified as a phase of matter, and the only physical system in which fluctuations of a 2D XY system and Kosterlitz Thouless phase transition has been observed and 2D XY quasi long range order verified. Smectic films have enabled the precise determination of smectic layer electron density and positional fluctuation profiles and have been used to show that the interlayer interactions in antiferroelectric tilted smectics do not extend significantly beyond nearest neighbors. Freely suspended films played a pivotal role in the recent discovery of macroscopic chiral-polar ordering in fluids of achiral molecules. The interactions which are operative in liquid crystals are generally weak in comparison to those in crystalline phases, leading to the facile manipulation of the order in liquid crystals by external agents such as applied fields and surfaces. Effects arising from weak ordering are significantly enhanced in ultrathin free films and filaments, in which the intermolecular coupling is effectively further reduced by loss of neighbors. Over the past four years this research, which we now detail, has produced a host of exciting new discoveries and unexpected results, maintaining the study of freely suspended liquid crystal structures as one of most exciting and fruitful areas of complex fluid physics. In addition, a class of experiments on the behavior of 1D interfaces in 2D films have been pursued with results that point to potentially quite interesting effects in microgravity.

  19. Crystal Structure Prediction (CSP) of Flexible Molecules using Parallel Genetic Algorithms with a Standard Force Field

    PubMed Central

    Kim, Seonah; Orendt, Anita M.; Ferraro, Marta B.; Facelli, Julio C.

    2009-01-01

    This paper describes the application of our distributed computing framework for crystal structure prediction (CSP), Modified Genetic Algorithms for Crystal and Cluster Prediction (MGAC) to predict the crystal structure of flexible molecules using the General Amber Force Field (GAFF) and the CHARMM program. The MGAC distributed computing framework which includes a series of tightly integrated computer programs for generating the molecule’s force field, sampling crystal structures using a distributed parallel genetic algorithm, local energy minimization of the structures followed by the classifying, sorting and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential. PMID:19130496

  20. The Influence of Gravity on Nucleation, Growth, Stability and Structure in Crystallizing Colloidal Suspensions

    NASA Technical Reports Server (NTRS)

    Gast, Alice P.

    1996-01-01

    Our goal is to understand the dynamics of particles within colloidal crystals. In particular, we focus on the influence of the cell walls and gravity on the particle dynamics. In this study, we will use a novel light scattering experiment, known as diffusing wave spectroscopy, to probe particle motions in turbid suspensions. This is a noninvasive experimental probe of interparticle dynamics.

  1. Anisotropic nanoparticles immersed in a nematic liquid crystal: defect structures and potentials of mean force.

    PubMed

    Hung, Francisco R; Guzmán, Orlando; Gettelfinger, Brian T; Abbott, Nicholas L; de Pablo, Juan J

    2006-07-01

    We report results for the potential of mean force (PMF) and the defect structures that arise when spherocylindrical nanoparticles are immersed in a nematic liquid crystal. Using a dynamic field theory for the tensor order parameter Q of the liquid crystal, we analyzed configurations, including one, two, and three elongated particles, with strong homeotropic anchoring at their surfaces. For systems with one nanoparticle, the most stable configuration is achieved when the spherocylinder is placed with its long axis perpendicular to the far-field director, for which the defect structure consists of an elongated Saturn ring. For systems with two or three nanoparticles with their long axes placed perpendicular to the far-field director, at small separations the defect structures consist of incomplete Saturn rings fused with new disclination rings orthogonal to the original ones, in analogy to results previously observed for spherical nanoparticles. The shape of these orthogonal rings depends on the nanoparticles' configuration, i.e., triangular, linear, or parallel with respect to their long axis. A comparison of the PMFs indicates that the latter configuration is the most stable. The stability of the different arrays depends on whether orthogonal disclination rings form or not, their size, and the curvature effects in the interparticle regions. Our results suggest that the one-elastic-constant approximation is valid for the considered systems; similar results were obtained when a three-constant expression is used to represent the elastic free energy. The attractive interactions between the elongated particles were compared to those observed for spheres of similar diameters. Similar interparticle energies were observed for linear arrays; in contrast, parallel and triangular arrays of spherocylinders yielded interactions that were up to 3.4 times stronger than those observed for spherical particles. PMID:16907115

  2. Structural, mechanical and light yield characterisation of heat treated LYSO:Ce single crystals for medical imaging applications

    NASA Astrophysics Data System (ADS)

    Mengucci, P.; André, G.; Auffray, E.; Barucca, G.; Cecchi, C.; Chipaux, R.; Cousson, A.; Davì, F.; Di Vara, N.; Rinaldi, D.; Santecchia, E.

    2015-06-01

    Five single crystals of cerium-doped lutetium yttrium oxyorthosilicate (LYSO:Ce) grown by the Czochralski method were submitted to structural characterisation by X-ray (XRD) and neutron (ND) diffraction, scanning (SEM) and transmission (TEM) electron microscopy and energy dispersive microanalysis (EDS). The Ultimate Tensile Strength (UTS), the Young Modulus (YM) and the Light Yield (LY) of the samples were also measured in order to correlate the mechanical and the optical behaviour of the crystals with the characteristics of their microstructure. Two of the samples analysed were also heat treated at 300 °C for 10 h to evidence possible variations induced by the temperature in the optical and mechanical response of the crystals. Results showed that the mean compositional variations evidenced by the structural analyses do not affect the mechanical and optical behaviour of the samples. On the contrary, the thermal treatment could induce the formation of coherent spherical particles (size 10 to 15 nm), not uniformly distributed inside the sample, that strongly reduce the UTS and YM values, but it does not affect the optical response of the crystal. This latter result was attributed to the low value of the heating temperature (300 °C) that is not sufficiently high to induce annealing of the oxygen vacancies traps that are responsible of the deterioration of the scintillation properties of the LYSO:Ce crystals. This study was carried out in the framework of the Crystal Clear Collaboration (CCC).

  3. 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

  4. Effects of Ice-Crystal Structure on Halo Formation: Cirrus Cloud Experimental and Ray-Tracing Modeling Studies

    NASA Technical Reports Server (NTRS)

    Sassen, Kenneth; Knight, Nancy C.; Takano, Yoshihide; Heymsfield, Andrew J.

    1994-01-01

    During the 1986 Project FIRE (First International Satellite Cloud Climatology Project Regional Experiment) field campaign, four 22 deg halo-producing cirrus clouds were studied jointly from a ground-based polarization lidar and an instrumented aircraft. The lidar data show the vertical cloud structure and the relative position of the aircraft, which collected a total of 84 slides by impaction, preserving the ice crystals for later microscopic examination. Although many particles were too fragile to survive impaction intact, a large fraction of the identifiable crystals were columns and radial bullet rosettes, with both displaying internal cavitations and radial plate-column combinations. Particles that were solid or displayed only a slight amount of internal structure were relatively rare, which shows that the usual model postulated by halo theorists, i.e., the randomly oriented, solid hexagonal crystal, is inappropriate for typical cirrus clouds. With the aid of new ray-tracing simulations for hexagonal hollow-ended column and bullet-rosette models, we evaluate the effects of more realistic ice-crystal structures on halo formation and lidar depolarization and consider why the common halo is not more common in cirrus clouds.

  5. 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.

  6. Crystal Structure of the Avian Astrovirus Capsid Spike

    PubMed Central

    DuBois, Rebecca M.; Freiden, Pamela; Marvin, Shauna; Reddivari, Muralidhar; Heath, Richard J.; White, Stephen W.

    2013-01-01

    Astroviruses are small, nonenveloped, single-stranded RNA viruses that cause diarrhea in a wide variety of mammals and birds. On the surface of the viral capsid are globular spikes that are thought to be involved in attachment to host cells. To understand the basis of species specificity, we investigated the structure of an avian astrovirus capsid spike and compared it to a previously reported human astrovirus capsid spike structure. Here we report the crystal structure of the turkey astrovirus 2 (TAstV-2) capsid surface spike domain, determined to 1.5-Å resolution, and identify three conserved patches on the surface of the spike that are candidate avian receptor-binding sites. Surprisingly, the overall TAstV-2 capsid spike structure is unique, with only distant structural similarities to the human astrovirus capsid spike and other viral capsid spikes. There is an absence of conserved putative receptor-binding sites between the human and avian spikes. However, there is evidence for carbohydrate-binding sites in both human and avian spikes, and studies with human astrovirus 1 (HAstV-1) suggest a minor role in infection for chondroitin sulfate but not heparin. Overall, our structural and functional studies provide new insights into astrovirus host cell entry, species specificity, and evolution. PMID:23658448

  7. Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: Photoconversion and signal transduction

    SciTech Connect

    Yang, Xiaojing; Kuk, Jane; Moffat, Keith

    2008-11-12

    Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria via reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here we report the crystal structure at 2.9 {angstrom} resolution of a bacteriophytochrome from Pseudomonas aeruginosa with an intact, fully photoactive photosensory core domain in its dark-adapted Pfr state. This structure reveals how unusual interdomain interactions, including a knot and an 'arm' structure near the chromophore site, bring together the PAS (Per-ARNT-Sim), GAF (cGMP phosphodiesterase/adenyl cyclase/FhlA), and PHY (phytochrome) domains to achieve Pr/Pfr photoconversion. The PAS, GAF, and PHY domains have topologic elements in common and may have a single evolutionary origin. We identify key interactions that stabilize the chromophore in the Pfr state and provide structural and mutational evidence to support the essential role of the PHY domain in efficient Pr/Pfr photoconversion. We also identify a pair of conserved residues that may undergo concerted conformational changes during photoconversion. Modeling of the full-length bacteriophytochrome structure, including its output histidine kinase domain, suggests how local structural changes originating in the photosensory domain modulate interactions between long, cross-domain signaling helices at the dimer interface and are transmitted to the spatially distant effector domain, thereby regulating its histidine kinase activity.

  8. Single crystal structures of thallium (I) thorium fluorides and crystal chemistry of monovalent tetravalent cation pentafluorides

    NASA Astrophysics Data System (ADS)

    Oudahmane, Abdelghani; El-Ghozzi, Malika; Jouffret, Laurent; Avignant, Daniel

    2015-12-01

    Two thallium (I) thorium (IV) fluorides, TlTh3F13 and TlThF5 were obtained by solid state synthesis and their crystal structures determined from single crystal X-ray diffraction data recorded at room temperature with an APEX-II CCD diffractometer. TlTh3F13 is orthorhombic, space group Pmc21, with a=8.1801(2) Å, b=7.4479(2) Å, c=8.6375(2) Å, V=526.24(2) Å3, Z=2 and TlThF5 is monoclinic, space group P21/n, with a=8.1128(5) Å, b=7.2250(4) Å, c=8.8493(6) Å, ?=116.683(3)°, V=463.46(5) Å3, Z=4. The structure of TlTh3F13 comprises layers of corner and edge-sharing ThF9 polyhedra further linked by chains of trans connected tricapped trigonal prisms ThF9 through corners and edges. The three dimensional thorium frameworks delimits channels parallel to [0 0 1] where the 11-coordinated Tl+ ions are arranged into double columns located in mirror planes of the structure. TlTh3F13 is isotypic with RbTh3F13, RbU3F13 and with one of the two polymorphs of CsTh3F13. The structure of TlThF5 may be regarded as a layer structure built up from the regular succession of 2?[ M ?F5 ] - corrugated layers further held by the Tl+ ions along the [1 0 1 ?] direction. The layers are built up from edge and corner-sharing thorium polyhedra where each (ThF9)5- monocapped square antiprism is connected to five others by sharing three edges and two corners. TlThF5 is isostructural with ?-NH4UF5 and with one of the polymorphs of CsThF5. A comparison of the different structural types of MM?F5 pentafluorides is presented and a diagram of repartition of their structures is given. From the comparison of the Tl structures with their Rb or Cs homologs, where very similar monovalent cation environments are observed it should be concluded to a stereochemically inactivity of the 6s2 lone pair of Tl(I) in both TlTh3F13 and TlThF5, contrary to what is observed in richer Tl(I) content Tl3ThF7 fluorothorate.

  9. The crystal structure of {pi}-ErBO{sub 3}: New single-crystal data for an old problem

    SciTech Connect

    Pitscheider, Almut; Kaindl, Reinhard; Oeckler, Oliver; Huppertz, Hubert

    2011-01-15

    Single crystals of the orthoborate {pi}-ErBO{sub 3} were synthesized from Er{sub 2}O{sub 3} and B{sub 2}O{sub 3} under high-pressure/high-temperature conditions of 2 GPa and 800 {sup o}C in a Walker-type multianvil apparatus. The crystal structure was determined on the basis of single-crystal X-ray diffraction data, collected at room temperature. The title compound crystallizes in the monoclinic pseudowollastonite-type structure, space group C2/c, with the lattice parameters a=1128.4(2) pm, b=652.6(2) pm, c=954.0(2) pm, and {beta}=112.8(1){sup o} (R{sub 1}=0.0124 and wR{sub 2}=0.0404 for all data). -- graphical abstract: The first satisfying single-crystal structure determination of {pi}-ErBO{sub 3} sheds light on the extensively discussed structure of {pi}-orthoborates. The application of light pressure during the solid state synthesis yielded in high-quality crystals, due to pressure-induced crystallization. Research highlights: {yields} High-quality single crystals of {pi}-ErBO{sub 3} were prepared via high-pressure-induced crystallization. {yields} At least five different space groups for the rare-earth {pi}-orthoborates are reported. {yields} {pi}-ErBO{sub 3} is isotypic to the pseudowollastonite-type CaSiO{sub 3}. {yields} Remaining ambiguities regarding the structure of the rare-earth {pi}-orthoborates are resolved.

  10. 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

  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 2.1 molecules/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. 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.

  13. Structural Insights Into The Regulatory Particle Of The Proteasome From Methanocaldococcus jannaschii

    PubMed Central

    Zhang, Fan; Hu, Min; Tian, Geng; Zhang, Ping; Finley, Daniel; Jeffrey, Philip D.; Shi, Yigong

    2010-01-01

    Summary 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-Å 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. PMID:19481527

  14. Crystal structures of superconducting sodium intercalates of hafnium nitride chloride

    SciTech Connect

    Oro-Sole, J.; Frontera, C.; Beltran-Porter, D.; Van Tendeloo, G.; Fuertes, A. . E-mail: amparo.fuertes@icmab.es

    2006-05-25

    Sodium intercalation compounds of HfNCl have been prepared at room temperature in naphtyl sodium solutions in tetrahydrofuran and their crystal structure has been investigated by Rietveld refinement using X-ray powder diffraction data and high-resolution electron microscopy. The structure of two intercalates with space group R3-bar m and lattice parameters a=3.58131(6)A, c=57.752(6)A, and a=3.58791(8)A, c=29.6785(17)A is reported, corresponding to the stages 2 and 1, respectively, of Na{sub x}HfNCl. For the stage 2 phase an ordered model is presented, showing two crystallographically independent [HfNCl] units with an alternation of the Hf-Hf interlayer distance along the c-axis, according with the occupation by sodium atoms of one out of two van der Waals gaps. Both stages 1 and 2 phases are superconducting with critical temperatures between 20 and 24K, they coexist in different samples with proportions depending on the synthesis conditions, and show a variation in c spacing that can be correlated with the sodium stoichiometry. High-resolution electron microscopy images of the host and intercalated samples show bending of the HfNCl bilayers as well as stacking faults in some regions, which coexist in the same crystal with ordered domains.

  15. Crystal structure of K[Hg(SCN)3] - a redetermination.

    PubMed

    Weil, Matthias; Häusler, Thomas

    2014-09-01

    The crystal structure of the room-temperature modification of K[Hg(SCN)3], potassium tri-thio-cyanato-mercurate(II), was redetermined based on modern CCD data. In comparison with the previous report [Zhdanov & Sanadze (1952 ?). Zh. Fiz. Khim. 26, 469-478], reliability factors, standard deviations of lattice parameters and atomic coordinates, as well as anisotropic displacement parameters, were revealed for all atoms. The higher precision and accuracy of the model is, for example, reflected by the Hg-S bond lengths of 2.3954?(11), 2.4481?(8) and 2.7653?(6)?Å in comparison with values of 2.24, 2.43 and 2.77?Å. All atoms in the crystal structure are located on mirror planes. The Hg(2+) cation is surrounded by four S atoms in a seesaw shape [S-Hg-S angles range from 94.65?(2) to 154.06?(3)°]. The HgS4 polyhedra share a common S atom, building up chains extending parallel to [010]. All S atoms of the resulting (1) ?[HgS2/1S2/2] chains are also part of SCN(-) anions that link these chains with the K(+) cations into a three-dimensional network. The K-N bond lengths of the distorted KN7 polyhedra lie between 2.926?(2) and 3.051?(3)?Å. PMID:25309170

  16. Crystal structure and thermal behaviour of pyridinium styphnate

    PubMed Central

    Muthulakshmi, Selvarasu; Kalaivani, Doraisamyraja

    2015-01-01

    In the crystal structure of the title mol­ecular salt, C5H6N+·C6H2N3O8 ? (systematic name: pyridinium 3-hy­droxy-2,4,6-tri­nitro­phenolate), the pyridin­ium cation and the 3-hy­droxy-2,4,6-tri­nitro­phenolate anion are linked through bifurcated N—H?(O,O) hydrogen bonds, forming an R 1 2(6) ring motif. The nitro group para with respect to phenolate ion forms an intra­molecular hydrogen bond with the adjacent phenolic –OH group, which results in an S(6) ring motif. The nitro group flanked by the phenolate ion and the phenolic –OH group deviates noticeably from the benzene ring, subtending a dihedral angle of 89.2?(4)°. The other two nitro groups deviate only slightly from the plane of the benzene ring, making dihedral angles of 2.8?(4) and 3.4?(3)°. In the crystal, the 3-hy­droxy-2,4,6-tri­nitro­phenolate anions are linked through O—H?O hydrogen bonds, forming chains along [100]. These anionic chains, to which the cations are attached, are linked via C—H?O hydrogen bonds, forming a three-dimensional structure. Impact friction sensitivity tests and TGA/DTA studies on the title mol­ecular salt imply that it is an insensitive high-energy-density material. PMID:25878796

  17. Crystal structures of oxidized and reduced forms of NADH peroxidase.

    PubMed

    Yeh, Joanne I; Claiborne, Al

    2002-01-01

    X-ray structural characterization of cysteine-sulfenic acid-containing proteins is one of the most defining approaches to characterizing this rapidly growing class of protein functional groups. Although outside the scope of this chapter, these structural analyses can lead to kinetic measurements in the crystal that allow intermediate states to be trapped, visualized, and studied. An understanding of the biochemistry of these reactive groups can be more fully gained by studying the localized protein environment in which these groups function. Increased perception of how elements of a protein can stabilize and contribute to modulation of function in these systems will allow novel means of enhancing or inhibiting function in important classes of protein molecules, including transcription factors and redox-regulated enzymes. PMID:12078517

  18. Crystal structure of carbapenem synthase (CarC).

    PubMed

    Clifton, Ian J; Doan, Linh X; Sleeman, Mark C; Topf, Maya; Suzuki, Hikokazu; Wilmouth, Rupert C; Schofield, Christopher J

    2003-06-01

    The proposed biosynthetic pathway to the carbapenem antibiotics proceeds via epimerization/desaturation of a carbapenam in an unusual process catalyzed by an iron- and 2-oxoglutarate-dependent oxygenase, CarC. Crystal structures of CarC complexed with Fe(II) and 2-oxoglutarate reveal it to be hexameric (space group C2221), consistent with solution studies. CarC monomers contain a double-stranded beta-helix core that supports ligands binding a single Fe(II) to which 2-oxoglutarate complexes in a bi-dentate manner. A structure was obtained with l-N-acetylproline acting as a substrate analogue. Quantum mechanical/molecular mechanical modeling studies with stereoisomers of carbapenams and carbapenems were used to investigate substrate binding. The combined work will stimulate further mechanistic studies and aid in the engineering of carbapenem biosynthesis. PMID:12611886

  19. Crystal structure of a catalytic intermediate of the maltose transporter

    SciTech Connect

    Oldham, Michael L.; Khare, Dheeraj; Quiocho, Florante A.; Davidson, Amy L.; Chen, Jue

    2008-08-20

    The maltose uptake system of Escherichia coli is a well-characterized member of the ATP-binding cassette transporter superfamily. Here we present the 2.8-{angstrom} crystal structure of the intact maltose transporter in complex with the maltose-binding protein, maltose and ATP. This structure, stabilized by a mutation that prevents ATP hydrolysis, captures the ATP-binding cassette dimer in a closed, ATP-bound conformation. Maltose is occluded within a solvent-filled cavity at the interface of the two transmembrane subunits, about halfway into the lipid bilayer. The binding protein docks onto the entrance of the cavity in an open conformation and serves as a cap to ensure unidirectional translocation of the sugar molecule. These results provide direct evidence for a concerted mechanism of transport in which solute is transferred from the binding protein to the transmembrane subunits when the cassette dimer closes to hydrolyse ATP.

  20. Crystal structure of Hg2SO4 – a redetermination

    PubMed Central

    Weil, Matthias

    2014-01-01

    The crystal structure of mercury(I) sulfate (or mercurous sulfate), Hg2SO4, was re-determined based on modern CCD data. In comparison with the previous determination from Weissenberg film data [Dorm (1969 ?). Acta Chem. Scand. 23, 1607–1615], all atoms were refined with anisotropic displacement parameters, leading to higher precision in terms of bond lengths and angles [e.g. Hg—Hg = 2.5031?(7) compared to 2.500?(3)Å]. The structure consists of alternating rows along [001] of Hg2 2+ dumbbells (generated by inversion symmetry) and SO4 2? tetra­hedra (symmetry 2). The dumbbells are linked via short O—Hg—Hg—O bonds to the sulfate tetra­hedra into chains extending parallel to [20-1]. More remote O—Hg—Hg—O bonds connect these chains into a three-dimensional framework. PMID:25309168

  1. Crystal Structure of a Phosphorylation-coupled Saccharide Transporter

    SciTech Connect

    Y Cao; X Jin; E Levin; H Huang; Y Zong; W Hendrickson; J Javitch; K Rajashankar; M Zhou; et al.

    2011-12-31

    Saccharides have a central role in the nutrition of all living organisms. Whereas several saccharide uptake systems are shared between the different phylogenetic kingdoms, the phosphoenolpyruvate-dependent phosphotransferase system exists almost exclusively in bacteria. This multi-component system includes an integral membrane protein EIIC that transports saccharides and assists in their phosphorylation. Here we present the crystal structure of an EIIC from Bacillus cereus that transports diacetylchitobiose. The EIIC is a homodimer, with an expansive interface formed between the amino-terminal halves of the two protomers. The carboxy-terminal half of each protomer has a large binding pocket that contains a diacetylchitobiose, which is occluded from both sides of the membrane with its site of phosphorylation near the conserved His250 and Glu334 residues. The structure shows the architecture of this important class of transporters, identifies the determinants of substrate binding and phosphorylation, and provides a framework for understanding the mechanism of sugar translocation.

  2. 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 ˜259°C (at a heating rate of 40°C/min) and nanoscale crystallites (< 100 nm) with an equiaxed morphology formed during the subsequent crystallization reactions. At temperatures higher than 283°C, 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 (235°C) 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.

  3. Crystal Structure of the Outer Membrane Protein OpdK from Pseudomonas aeruginosa

    E-print Network

    Movileanu, Liviu

    Structure Article Crystal Structure of the Outer Membrane Protein OpdK from Pseudomonas aeruginosa in the outer membrane. Comparison of the OpdK structure with that of Pseudomonas aeruginosa OprD provides

  4. 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.

  5. Tuning light matter interaction in magnetic nanofluid based field induced photonic crystal-glass structure by controlling optical path length

    E-print Network

    Junaid M. Laskar; Baldev Raj; John Philip

    2015-09-04

    The ability to control the light matter interaction and simultaneous tuning of both structural order and disorder in materials, although are important in photonics, but still remain as major challenges. In this paper, we show that optical path length dictates light-matter interaction in the same crystal structure formed by the ordering of magnetic nanoparticle self-assembled columns inside magnetic nanofluid under applied field. When the optical path length (L=80 {\\mu}m) is shorter than the optical (for wavelength, {\\lambda}=632.8 nm) coherence length inside the magnetic nanofluid under applied field, a Debye diffraction ring pattern is observed; while for longer path length (L=1mm), a corona ring of scattered light is observed. Analysis of Debye diffraction ring pattern suggests the formation of 3D hexagonal crystal structure, where the longitudinal and lateral inter-column spacings are 5.281 and 7.344 microns, respectively. Observation of speckles within the Debye diffraction pattern confirms the presence of certain degree of structural disorder within the crystal structure, which can be tuned by controlling the applied field strength, nanoparticle size and particle volume fraction. Our results provide a new approach to develop next generation of tunable photonic devices, based on simultaneous harnessing of the properties of disordered photonic glass and 3D photonic crystal.

  6. Automated High Throughput Protein Crystallization Screening at Nanoliter Scale and Protein Structural Study on Lactate Dehydrogenase

    SciTech Connect

    Fenglei Li

    2006-08-09

    The purposes of our research were: (1) To develop an economical, easy to use, automated, high throughput system for large scale protein crystallization screening. (2) To develop a new protein crystallization method with high screening efficiency, low protein consumption and complete compatibility with high throughput screening system. (3) To determine the structure of lactate dehydrogenase complexed with NADH by x-ray protein crystallography to study its inherent structural properties. Firstly, we demonstrated large scale protein crystallization screening can be performed in a high throughput manner with low cost, easy operation. The overall system integrates liquid dispensing, crystallization and detection and serves as a whole solution to protein crystallization screening. The system can dispense protein and multiple different precipitants in nanoliter scale and in parallel. A new detection scheme, native fluorescence, has been developed in this system to form a two-detector system with a visible light detector for detecting protein crystallization screening results. This detection scheme has capability of eliminating common false positives by distinguishing protein crystals from inorganic crystals in a high throughput and non-destructive manner. The entire system from liquid dispensing, crystallization to crystal detection is essentially parallel, high throughput and compatible with automation. The system was successfully demonstrated by lysozyme crystallization screening. Secondly, we developed a new crystallization method with high screening efficiency, low protein consumption and compatibility with automation and high throughput. In this crystallization method, a gas permeable membrane is employed to achieve the gentle evaporation required by protein crystallization. Protein consumption is significantly reduced to nanoliter scale for each condition and thus permits exploring more conditions in a phase diagram for given amount of protein. In addition, evaporation rate can be controlled or adjusted in this method during the crystallization process to favor either nucleation or growing processes for optimizing crystallization process. The protein crystals gotten by this method were experimentally proven to possess high x-ray diffraction qualities. Finally, we crystallized human lactate dehydrogenase 1 (H4) complexed with NADH and determined its structure by x-ray crystallography. The structure of LDH/NADH displays a significantly different structural feature, compared with LDH/NADH/inhibitor ternary complex structure, that subunits in LDH/NADH complex show open conformation or two conformations on the active site while the subunits in LDH/NADH/inhibitor are all in close conformation. Multiple LDH/NADH crystals were obtained and used for x-ray diffraction experiments. Difference in subunit conformation was observed among the structures independently solved from multiple individual LDH/NADH crystals. Structural differences observed among crystals suggest the existence of multiple conformers in solution.

  7. Crystal structure of the human glucose transporter GLUT1

    NASA Astrophysics Data System (ADS)

    Deng, Dong; Xu, Chao; Sun, Pengcheng; Wu, Jianping; Yan, Chuangye; Hu, Mingxu; Yan, Nieng

    2014-06-01

    The glucose transporter GLUT1 catalyses facilitative diffusion of glucose into erythrocytes and is responsible for glucose supply to the brain and other organs. Dysfunctional mutations may lead to GLUT1 deficiency syndrome, whereas overexpression of GLUT1 is a prognostic indicator for cancer. Despite decades of investigation, the structure of GLUT1 remains unknown. Here we report the crystal structure of human GLUT1 at 3.2 Å resolution. The full-length protein, which has a canonical major facilitator superfamily fold, is captured in an inward-open conformation. This structure allows accurate mapping and potential mechanistic interpretation of disease-associated mutations in GLUT1. Structure-based analysis of these mutations provides an insight into the alternating access mechanism of GLUT1 and other members of the sugar porter subfamily. Structural comparison of the uniporter GLUT1 with its bacterial homologue XylE, a proton-coupled xylose symporter, allows examination of the transport mechanisms of both passive facilitators and active transporters.

  8. The crystal structures of potassium and cesium trivanadates

    USGS Publications Warehouse

    Evans, H.T., Jr.; Block, S.

    1966-01-01

    Potassium and cesium trivanadates are monoclinic and isomorphous, space group P21/m, with the following dimensions (Z = 2): KV3O8, a = 7.640 A, b = 8.380 A, c = 4.979 A, ??= 96?? 57???; CsV3O8, a = 8.176 A, b = 8.519 A, c = 4.988 A, ?? = 95?? 32???. The crystal structure of KV3O8 has been determined from hk0, 0kl, and h0l Weissenberg data with an R factor of 0.15. The structure of CsV3O8 has been refined with 1273 hkl Weissenberg data to an R factor of 0.089. The structures consist of corrugated sheets based on a linkage of distorted VO6, octahedra. Two of the vanadium atoms lie in double, square-pyramid groups V2O8, which are linked through opposite basal corners into chains along the b axis. The chains are joined laterally along the c axis into sheets by the third vanadium atom in VO groups, also forming part of a square-pyramid coordination. Various aspects of these structures are compared with other known oxovanadate structures.

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

    PubMed Central

    Sheldrick, George M.

    2015-01-01

    The new computer program SHELXT employs a novel dual-space algorithm to solve the phase problem for single-crystal reflection data expanded to the space group P1. Missing data are taken into account and the resolution extended if necessary. All space groups in the specified Laue group are tested to find which are consistent with the P1 phases. After applying the resulting origin shifts and space-group symmetry, the solutions are subject to further dual-space recycling followed by a peak search and summation of the electron density around each peak. Elements are assigned to give the best fit to the integrated peak densities and if necessary additional elements are considered. An isotropic refinement is followed for non-centrosymmetric space groups by the calculation of a Flack parameter and, if appropriate, inversion of the structure. The structure is assembled to maximize its connectivity and centred optimally in the unit cell. SHELXT has already solved many thousand structures with a high success rate, and is optimized for multiprocessor computers. It is, however, unsuitable for severely disordered and twinned structures because it is based on the assumption that the structure consists of atoms. PMID:25537383

  10. Water polygons in high-resolution protein crystal structures

    PubMed Central

    Lee, Jonas; Kim, Sung-Hou

    2009-01-01

    We have analyzed the interstitial water (ISW) structures in 1500 protein crystal structures deposited in the Protein Data Bank that have greater than 1.5 Å resolution with less than 90% sequence similarity with each other. We observed varieties of polygonal water structures composed of three to eight water molecules. These polygons may represent the time- and space-averaged structures of “stable” water oligomers present in liquid water, and their presence as well as relative population may be relevant in understanding physical properties of liquid water at a given temperature. On an average, 13% of ISWs are localized enough to be visible by X-ray diffraction. Of those, averages of 78% are water molecules in the first water layer on the protein surface. Of the localized ISWs beyond the first layer, almost half of them form water polygons such as trigons, tetragons, as well as expected pentagons, hexagons, higher polygons, partial dodecahedrons, and disordered networks. Most of the octagons and nanogons are formed by fusion of smaller polygons. The trigons are most commonly observed. We suggest that our observation provides an experimental basis for including these water polygon structures in correlating and predicting various water properties in liquid state. PMID:19551896

  11. Crystal Structure of the BARD1 BRCT Domains

    SciTech Connect

    Birrane,G.; Varma, A.; Soni, A.; Ladias, J.

    2007-01-01

    The interaction of the breast tumor suppressor BRCA1 with the protein BARD1 results in the formation of a heterodimeric complex that has ubiquitin ligase activity and plays central roles in cell cycle checkpoint control and DNA repair. Both BRCA1 and BARD1 possess a pair of tandem BRCT domains that interact in a phosphorylation-dependent manner with target proteins. We determined the crystal structure of the human BARD1 BRCT repeats (residues 568-777) at 1.9 {angstrom} resolution. The composition and structure of the BARD1 phosphoserine-binding pocket P{sub 1} are strikingly similar to those of the BRCA1 and MDC1 BRCT domains, suggesting a similar mode of interaction with the phosphate group of the ligand. By contrast, the BARD1 BRCT selectivity pocket P{sub 2} exhibits distinct structural features, including two prominent histidine residues, His685 and His686, which may be important for ligand binding. The protonation state of these histidines has a marked effect on the calculated electrostatic potential in the vicinity of P{sub 2}, raising the possibility that ligand recognition may be regulated by changes in pH. Importantly, the BARD1 BRCT structure provides insights into the mechanisms by which the cancer-associated missense mutations C645R, V695L, and S761N may adversely affect the structure and function of BARD1.

  12. Octa-O-propanoyl-B-maltose: crystal structure, acyl stacking, related structures and conformational anaylsis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The crystal structure of beta-maltose octapropanoate (1) was solved to increase knowledge of the influences on conformations of di-, oligo- and polysaccharides. The O6 and O6' atoms are in gg and gt conformations, respectively. Extrapolation of the coordinates of the non-reducing residue and observe...

  13. Solid State Sciences 2 (2000) 109118 Synthesis and crystal structures of yttrium sulfates

    E-print Network

    Wang, Xiqu

    2000-01-01

    Solid State Sciences 2 (2000) 109­118 Synthesis and crystal structures of yttrium sulfates Y.092(1)°. The coordination environments of the yttrium atoms in the four structures vary from highly irregular 6+2, 6+3, 7´dicales Elsevier SAS. All rights reserved. Keywords: Hydrothermal synthesis; Crystal structure; Yttrium sulfate

  14. Crystal structure retrieval by maximum entropy analysis of atomic resolution incoherent images

    E-print Network

    Pennycook, Steve

    Crystal structure retrieval by maximum entropy analysis of atomic resolution incoherent images A. J, TN 37831-6031, U.S.A. Key words. Atomic resolution, crystal structure retrieval, incoherent imaging be used to yield important information on unexpected atomic structures. Introduction The physical

  15. Band gap widening by photonic crystal heterostructures composed of two dimensional holes and diamond structure

    NASA Astrophysics Data System (ADS)

    Chen, Shibin; Li, Dichen; Zhi-Hui, Yuan

    2013-06-01

    A new kind of heterostructures containing 3D diamond and 2D holes structures, and diamond-structure photonic crystals and 2D holes-structure photonic crystals fabricated by stereolithography and gel-casting with alumina were studied at microwave range, respectively. The heterostructures were designed by 2D holes structure embedded in 3D diamond structure, in which the lattice of three kinds of structures was equivalent. It was found that the band gaps of photonic crystal heterostructure were broadened by 124.6% and 150% comparing to that of diamond-structure crystal and 2D aerial holes structure. Experimental results showed the band gap broadened was not connected with a linear superposition of the band gap of 2D and 3D photonic crystals, which was the superposition of partial overlap.

  16. Crystal Structure of the Human Cytomegalovirus Glycoprotein B

    PubMed Central

    Burke, Heidi G.; Heldwein, Ekaterina E.

    2015-01-01

    Human cytomegalovirus (HCMV), a dsDNA, enveloped virus, is a ubiquitous pathogen that establishes lifelong latent infections and caused disease in persons with compromised immune systems, e.g., organ transplant recipients or AIDS patients. HCMV is also a leading cause of congenital viral infections in newborns. Entry of HCMV into cells requires the conserved glycoprotein B (gB), thought to function as a fusogen and reported to bind signaling receptors. gB also elicits a strong immune response in humans and induces the production of neutralizing antibodies although most anti-gB Abs are non-neutralizing. Here, we report the crystal structure of the HCMV gB ectodomain determined to 3.6-Å resolution, which is the first atomic-level structure of any betaherpesvirus glycoprotein. The structure of HCMV gB resembles the postfusion structures of HSV-1 and EBV homologs, establishing it as a new member of the class III viral fusogens. Despite structural similarities, each gB has a unique domain arrangement, demonstrating structural plasticity of gB that may accommodate virus-specific functional requirements. The structure illustrates how extensive glycosylation of the gB ectodomain influences antibody recognition. Antigenic sites that elicit neutralizing antibodies are more heavily glycosylated than those that elicit non-neutralizing antibodies, which suggest that HCMV gB uses glycans to shield neutralizing epitopes while exposing non-neutralizing epitopes. This glycosylation pattern may have evolved to direct the immune response towards generation of non-neutralizing antibodies thus helping HCMV to avoid clearance. HCMV gB structure provides a starting point for elucidation of its antigenic and immunogenic properties and aid in the design of recombinant vaccines and monoclonal antibody therapies. PMID:26484870

  17. Optical tuning of silicon photonic structures with nematic liquid crystal claddings

    E-print Network

    Fainman, Yeshaiahu

    of silicon strip waveguides with methyl red doped nematic liquid crystal claddings is presented. Under lowOptical tuning of silicon photonic structures with nematic liquid crystal claddings Joanna materials; (160.3710) Liquid crystals; (160.5320) Photorefractive materials; (220.0220) Optical design

  18. A CRYSTAL STRUCTURE-BASED EIGENTRANSFORMATION AND ITS WORK-CONJUGATE MATERIAL STRESS

    E-print Network

    Wu, Chien H.

    A CRYSTAL STRUCTURE-BASED EIGENTRANSFORMATION AND ITS WORK-CONJUGATE MATERIAL STRESS CHIEN H. WU examine the configurational changes brought about by atomic diffusion in a nonuniform alloy crystal. The transformation from a reference, single-parameter simple cubic cell to a six-parameter alloy crystal cell, called

  19. Studies on synthesis, growth, structural, optical properties of organic 8-hydroxyquinolinium succinate single crystals

    SciTech Connect

    Thirumurugan, R. Anitha, K.

    2014-04-24

    8-hydroxyquinolinium succinate (8HQSU), an organic material has been synthesized and single crystals were grown by employing the technique of slow evaporation. The structure of the grown crystal was elucidated by using single crystal X-ray diffraction analysis. 8HQSU crystal belongs to the monoclinic crystallographic system with non-centro symmetric space group of P2{sub 1}. FT-IR spectral investigation has been carried out to identify the various functional groups present in the grown crystal. UV–vis spectral studies reveal that 8HQSU crystals are transparent in the entire visible region and the cut-off wavelength has been found to be 220nm.

  20. Crystallization of atmospheric sulfate-nitrate-ammonium particles Scot T. Martin, Julie C. Schlenker, Adam Malinowski, and Hui-Ming Hung

    E-print Network

    Crystallization of atmospheric sulfate-nitrate-ammonium particles Scot T. Martin, Julie C the crystallization RH (CRH) at 293 K of particles throughout the entire sulfate-nitrate-ammonium composition space the same particle for compositions enriched in nitrate or somewhat acidic, although the CRH is under 30

  1. One-dimensional correlation in the dipolar Ising crystal tricyclohexylmethanol: crystal structure revisited and heat capacity.

    PubMed

    Yamamura, Yasuhisa; Saitoh, Hideki; Sumita, Masato; Saito, Kazuya

    2007-04-30

    The crystal structure of an organic weak-ferroelectrics, tricyclohexylmethanol (TCHM), was re-examined by single-crystal x-ray diffraction at room temperature. TCHM forms a dimer through hydrogen bonding at the centre of the dimer, where two hydroxyl groups are arranged in tandem and their direction is disordered in two possible orientations, which brings about a dipolar Ising nature. The heat capacity measured by adiabatic calorimetry from 6 to 400 K shows three anomalies including fusion at 368 K. The entropy of the ferroelectric transition is 1.9 J K(-1) mol(-1), supporting the order-disorder mechanism of dimer dipoles. A broad anomaly at 348 K is related to the breakage of the intra-dimer hydrogen bond. Detailed analysis of the temperature dependence of heat capacity due to the phase transition showed the presence of a broad hump in the excess heat capacity around 160 K. The temperature dependences of the excess heat capacity and the existing dielectric constant can be analysed in terms of a highly anisotropic Ising model. PMID:21690964

  2. Silicon crystals: Process for manufacturing wafer-like silicon crystals with a columnar structure

    NASA Technical Reports Server (NTRS)

    Authier, B.

    1978-01-01

    Wafer-like crystals suitable for making solar cells are formed by pouring molten Si containing suitable dopants into a mold of the desired shape and allowing it to solidify in a temperature gradient, whereby the large surface of the melt in contact with the mold is kept at less than 200 D and the free surface is kept at a temperature of 200-1000 D higher, but below the melting point of Si. The mold can also be made in the form of a slit, whereby the 2 sides of the mold are kept at different temperatures. A mold was milled in the surface of a cylindrical graphite block 200 mm in diameter. The granite block was induction heated and the bottom of the mold was cooled by means of a water-cooled Cu plate, so that the surface of the mold in contact with one of the largest surfaces of the melt was held at approximately 800 D. The free surface of the melt was subjected to thermal radiation from a graphite plate located 2 mm from the surface and heated to 1500 D. The Si crystal formed after slow cooling to room temperature had a columnar structure and was cut with a diamond saw into wafers approximately 500 mm thick. Solar cells prepared from these wafers had efficiencies of 10 to 11%.

  3. Features of forming structure of titanium pseudosingle crystal during ? ? ? (bcc ? hcp) polymorphic transformation

    NASA Astrophysics Data System (ADS)

    Khlebnikova, Yu. V.; Rodionov, D. P.; Sazonova, V. A.; Egorova, L. Yu.; Kaletina, Yu. V.

    2013-09-01

    The structure of a titanium iodide single crystal obtained by zone melting has been studied by metallography, X-ray diffraction, and electron microscopy. It has been shown that the initial bcc titanium single crystal becomes a pseudosingle crystal upon cooling below the temperature of the ? ? ? polymorphic transition. The pseudosingle crystal consists of macroscopic packets, i.e., crystals of lath morphology with a size of 0.1-0.5 cm2 in different crystal sections. Each packet consists of ?-phase laths of the same orientation, which are separated by dislocation boundaries. A total of six different types of packets in the pseudosingle crystal volume is realized in accordance with the Burgers orientation relationships. The structural heredity in the titanium pseudosingle crystal after the cycle of the ? ? ? ? ? transformations is confirmed.

  4. Synthesis and crystal structure of tetramethylammonium fluoride octadecasil

    SciTech Connect

    Yang Xiaobo . E-mail: Xiaobo.Yang@pci.uni-hannover.de

    2006-01-05

    Octadecasil, a clathrate-type inclusion compound, has been synthesized hydrothermally at 453 K with a gel having the composition 1.0SiO{sub 2}:0.53tetramethylammonium (TMA{sup +}):0.54fluoride:86H{sub 2}O. The crystal structure has been determined based on powder X-ray diffraction data taken at 298 K, and has been refined using Rietveld method. The result confirms the AST-type, all-silica framework model developed by Caullet et al. [P. Caullet, J.L. Guth, J. Hazm, J.M. Lamblin, H. Gies, Eur. J. Solid State Inorg. Chem. 28 (1991) 345]. Furthermore, by using a rigid body model the position and orientation of the occluded TMA{sup +} cation in the rhombododecahedral [4{sup 6}6{sup 12}] cage can be determined; F{sup -} anion has been located in the hexahedral [4{sup 6}] cage. The unit cell parameters, in the tetragonal space group I4/m, have been refined as: a = b = 9.07 A, c = 13.44 A, cell volume = 1104.97 A{sup 3}. The refined unit cell composition is |[N(CH{sub 3}){sub 4} {sup +}]{sub 2.0}F{sup -} {sub 1.9}|[Si{sub 20}O{sub 40}], i.e., both TMA{sup +} and F{sup -} ions possess near full occupancies, and compensate each other's electronic charges. The crystallization of the AST framework structure is the result of a cooperative structure-directing effect of both ions.

  5. Self-assembly and electrostriction of arrays and chains of hopfion particles in chiral liquid crystals

    NASA Astrophysics Data System (ADS)

    Ackerman, Paul J.; van de Lagemaat, Jao; Smalyukh, Ivan I.

    2015-01-01

    Some of the most exotic condensed matter phases, such as twist grain boundary and blue phases in liquid crystals and Abrikosov phases in superconductors, contain arrays of topological defects in their ground state. Comprised of a triangular lattice of double-twist tubes of magnetization, the so-called ‘A-phase’ in chiral magnets is an example of a thermodynamically stable phase with topologically nontrivial solitonic field configurations referred to as two-dimensional skyrmions, or baby-skyrmions. Here we report that three-dimensional skyrmions in the form of double-twist tori called ‘hopfions’, or ‘torons’ when accompanied by additional self-compensating defects, self-assemble into periodic arrays and linear chains that exhibit electrostriction. In confined chiral nematic liquid crystals, this self-assembly is similar to that of liquid crystal colloids and originates from long-range elastic interactions between particle-like skyrmionic torus knots of molecular alignment field, which can be tuned from isotropic repulsive to weakly or highly anisotropic attractive by low-voltage electric fields.

  6. Self-assembly and electrostriction of arrays and chains of hopfion particles in chiral liquid crystals

    PubMed Central

    Ackerman, Paul J.; van de Lagemaat, Jao; Smalyukh, Ivan I.

    2015-01-01

    Some of the most exotic condensed matter phases, such as twist grain boundary and blue phases in liquid crystals and Abrikosov phases in superconductors, contain arrays of topological defects in their ground state. Comprised of a triangular lattice of double-twist tubes of magnetization, the so-called ‘A-phase’ in chiral magnets is an example of a thermodynamically stable phase with topologically nontrivial solitonic field configurations referred to as two-dimensional skyrmions, or baby-skyrmions. Here we report that three-dimensional skyrmions in the form of double-twist tori called ‘hopfions’, or ‘torons’ when accompanied by additional self-compensating defects, self-assemble into periodic arrays and linear chains that exhibit electrostriction. In confined chiral nematic liquid crystals, this self-assembly is similar to that of liquid crystal colloids and originates from long-range elastic interactions between particle-like skyrmionic torus knots of molecular alignment field, which can be tuned from isotropic repulsive to weakly or highly anisotropic attractive by low-voltage electric fields. PMID:25607778

  7. Ca2SnS4: Crystal structure, optical property, and electronic structure

    NASA Astrophysics Data System (ADS)

    Zhou, Molin; Jiang, Xingxing; Li, Chao; Lin, Zheshuai; Yao, Jiyong; Wu, Yicheng

    2016-01-01

    single crystals of Ca2SnS4were obtained by traditional high temperature solid-state reaction. The compound crystallizes in space group Pnma of the orthorhombic system. Its structure contains bi-layers built from corner-sharing Ca1S6 octahedra and Ca2S6 octahedra with isolated SnS4 tetrahedra residing in the cavities along the b axis. UV-vis-NIR spectroscopy measurement indicates that Ca2SnS4 has a band gap of 2.32(3) eV, comparable to the calculated value 2.72 eV.

  8. 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.

  9. 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

  10. Charge Structure and Counterion Distribution in Hexagonal DNA Liquid Crystal

    PubMed Central

    Dai, Liang; Mu, Yuguang; Nordenskiöld, Lars; Lapp, Alain; van der Maarel, Johan R. C.

    2007-01-01

    A hexagonal liquid crystal of DNA fragments (double-stranded, 150 basepairs) with tetramethylammonium (TMA) counterions was investigated with small angle neutron scattering (SANS). We obtained the structure factors pertaining to the DNA and counterion density correlations with contrast matching in the water. Molecular dynamics (MD) computer simulation of a hexagonal assembly of nine DNA molecules showed that the inter-DNA distance fluctuates with a correlation time around 2 ns and a standard deviation of 8.5% of the interaxial spacing. The MD simulation also showed a minimal effect of the fluctuations in inter-DNA distance on the radial counterion density profile and significant penetration of the grooves by TMA. The radial density profile of the counterions was also obtained from a Monte Carlo (MC) computer simulation of a hexagonal array of charged rods with fixed interaxial spacing. Strong ordering of the counterions between the DNA molecules and the absence of charge fluctuations at longer wavelengths was shown by the SANS number and charge structure factors. The DNA-counterion and counterion structure factors are interpreted with the correlation functions derived from the Poisson-Boltzmann equation, MD, and MC simulation. Best agreement is observed between the experimental structure factors and the prediction based on the Poisson-Boltzmann equation and/or MC simulation. The SANS results show that TMA is too large to penetrate the grooves to a significant extent, in contrast to what is shown by MD simulation. PMID:17098791

  11. Crystal structure of substrate free form of glycerol dehydratase

    SciTech Connect

    Liao, Der-Ing; Dotson, Garry; Turner, Jr., Ivan; Reiss, Lisa; Emptage, Mark

    2010-03-08

    Glycerol dehydratase (GDH) and diol dehydratase (DDH) are highly homologous isofunctional enzymes that catalyze the elimination of water from glycerol and 1,2-propanediol (1,2-PD) to the corresponding aldehyde via a coenzyme B{sub 12}-dependent radical mechanism. The crystal structure of substrate free form of GDH in complex with cobalamin and K{sup +} has been determined at 2.5 {angstrom} resolution. Its overall fold and the subunit assembly closely resemble those of DDH. Comparison of this structure and the DDH structure, available only in substrate bound form, shows the expected change of the coordination of the essential K{sup +} from hexacoordinate to heptacoordinate with the displacement of a single coordinated water by the substrate diol. In addition, there appears to be an increase in the rigidity of the K{sup +} coordination (as measured by lower B values) upon the binding of the substrate. Structural analysis of the locations of conserved residues among various GDH and DDH sequences has aided in identification of residues potentially important for substrate preference or specificity of protein-protein interactions.

  12. Effect of the Inhomogeneity of Ice Crystals on Retrieving Ice Cloud Optical Thickness and Effective Particle Size

    NASA Technical Reports Server (NTRS)

    Xie, Yu; Minnis, Patrick; Hu, Yong X.; Kattawar, George W.; Yang, Ping

    2008-01-01

    Spherical or spheroidal air bubbles are generally trapped in the formation of rapidly growing ice crystals. In this study the single-scattering properties of inhomogeneous ice crystals containing air bubbles are investigated. Specifically, a computational model based on an improved geometric-optics method (IGOM) has been developed to simulate the scattering of light by randomly oriented hexagonal ice crystals containing spherical or spheroidal air bubbles. A combination of the ray-tracing technique and the Monte Carlo method is used. The effect of the air bubbles within ice crystals is to smooth the phase functions, diminish the 22deg and 46deg halo peaks, and substantially reduce the backscatter relative to bubble-free particles. These features vary with the number, sizes, locations and shapes of the air bubbles within ice crystals. Moreover, the asymmetry factors of inhomogeneous ice crystals decrease as the volume of air bubbles increases. Cloud reflectance lookup tables were generated at wavelengths 0.65 m and 2.13 m with different air-bubble conditions to examine the impact of the bubbles on retrieving ice cloud optical thickness and effective particle size. The reflectances simulated for inhomogeneous ice crystals are slightly larger than those computed for homogenous ice crystals at a wavelength of 0.65 microns. Thus, the retrieved cloud optical thicknesses are reduced by employing inhomogeneous ice cloud models. At a wavelength of 2.13 microns, including air bubbles in ice cloud models may also increase the reflectance. This effect implies that the retrieved effective particle sizes for inhomogeneous ice crystals are larger than those retrieved for homogeneous ice crystals, particularly, in the case of large air bubbles.

  13. Orientational Coherent Effects of High-Energy Particles in a LiNbO3 Crystal

    NASA Astrophysics Data System (ADS)

    Bagli, E.; Guidi, V.; Mazzolari, A.; Bandiera, L.; Germogli, G.; Sytov, A. I.; De Salvador, D.; Argiolas, A.; Bazzan, M.; Carnera, A.; Berra, A.; Bolognini, D.; Lietti, D.; Prest, M.; Vallazza, E.

    2015-07-01

    A bent lithium niobate strip was exposed to a 400 -GeV /c proton beam at the external lines of CERN Super Proton Synchrotron to probe its capabilities versus coherent interactions of the particles with the crystal such as channeling and volume reflection. Lithium niobate (LiNbO3 ) exhibits an interplanar electric field comparable to that of Silicon (Si) and remarkable piezoelectric properties, which could be exploited for the realization of piezo-actuated devices for the control of high-energy particle beams. In contrast to Si and germanium (Ge), LiNbO3 shows an intriguing effect; in spite of a low channeling efficiency (3%), the volume reflection maintains a high deflection efficiency (83%). Such discrepancy was ascribed to the high concentration (1 04 per cm2 ) of dislocations in our sample, which was obtained from a commercial wafer. Indeed, it has been theoretically shown that a channeling efficiency comparable with that of Si or Ge would be attained with a crystal at low defect concentration (less than ten per cm2 ). To better understand the role of dislocations on volume reflection, we have worked out computer simulation via dynecharm++ Monte Carlo code to study the effect of dislocations on volume reflection. The results of the simulations agree with experimental records, demonstrating that volume reflection is more robust than channeling in the presence of dislocations.

  14. Orientational Coherent Effects of High-Energy Particles in a LiNbO3 Crystal.

    PubMed

    Bagli, E; Guidi, V; Mazzolari, A; Bandiera, L; Germogli, G; Sytov, A I; De Salvador, D; Argiolas, A; Bazzan, M; Carnera, A; Berra, A; Bolognini, D; Lietti, D; Prest, M; Vallazza, E

    2015-07-01

    A bent lithium niobate strip was exposed to a 400-GeV/c proton beam at the external lines of CERN Super Proton Synchrotron to probe its capabilities versus coherent interactions of the particles with the crystal such as channeling and volume reflection. Lithium niobate (LiNbO3) exhibits an interplanar electric field comparable to that of Silicon (Si) and remarkable piezoelectric properties, which could be exploited for the realization of piezo-actuated devices for the control of high-energy particle beams. In contrast to Si and germanium (Ge), LiNbO3 shows an intriguing effect; in spite of a low channeling efficiency (3%), the volume reflection maintains a high deflection efficiency (83%). Such discrepancy was ascribed to the high concentration (10(4)?per?cm2) of dislocations in our sample, which was obtained from a commercial wafer. Indeed, it has been theoretically shown that a channeling efficiency comparable with that of Si or Ge would be attained with a crystal at low defect concentration (less than ten per cm2). To better understand the role of dislocations on volume reflection, we have worked out computer simulation via dynecharm++ Monte Carlo code to study the effect of dislocations on volume reflection. The results of the simulations agree with experimental records, demonstrating that volume reflection is more robust than channeling in the presence of dislocations. PMID:26182106

  15. 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.

  16. Manufacturing and characterization of bent silicon crystals for studies of coherent interactions with negatively charged particles beams

    NASA Astrophysics Data System (ADS)

    Germogli, G.; Mazzolari, A.; Bandiera, L.; Bagli, E.; Guidi, V.

    2015-07-01

    Efficient steering of GeV-energy negatively charged particle beams was demonstrated to be possible with a new generation of thin bent silicon crystals. Suitable crystals were produced at the Sensor Semiconductor Laboratory of Ferrara starting from Silicon On Insulator wafers, adopting proper revisitation of silicon micromachining techniques such as Low Pressure Chemical Vapor Deposition, photolithography and anisotropic chemical etching. Mechanical holders, which allow to properly bend the crystal and to reduce unwanted torsions, were employed. Crystallographic directions and crystal holder design were optimized in order to excite quasi-mosaic effect along (1 1 1) planes. Prior to exposing the crystal to particle beams, a full set of characterizations were performed. Infrared interferometry was used to measure crystal thickness with high accuracy. White-light interferometry was employed to characterize surface deformational state and its torsion. High-resolution X-rays diffraction was used to precisely measure crystal bending angle along the beam. Manufactured crystals were installed and tested at the MAMI MAinz MIcrotron to steer sub-GeV electrons, and at SLAC to deflect an electron beam in the 1 to 10 GeV energy range.

  17. Additives Induced Structural Transformation of ABC Triblock Copolymer Particles.

    PubMed

    Xu, Jiangping; Yang, Yi; Wang, Ke; Li, Jingyi; Zhou, Huamin; Xie, Xiaolin; Zhu, Jintao

    2015-10-13

    Here we report the structural control of polystyrene-b-polyisoprene-b-poly(2-vinylpyridine) (PS-b-PI-b-P2VP) asymmetric ABC triblock copolymer particles under 3D confinement by tuning the interactions among blocks. The additives, including 3-n-pentadecylphenol, homopolystyrene, and solvents, which can modulate the interactions among polymer blocks, play significant roles in the particle morphology. Moreover, the structured particles can be disassembled into isolated micellar aggregates with novel morphologies or mesoporous particles with tunable pore shape. Interestingly, the formed pupa-like PS-b-PI-b-P2VP particles display interesting dynamic stretch-retraction behavior when the solvent property is changed after partial cross-linking of the P2VP block. We further prove that such dynamic behavior is closely related to the density of cross-linking. The strategies presented here are believed to be promising routes to rationally design and fabricate block copolymer particles with desirable shape and internal structure. PMID:26388457

  18. 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.

  19. 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

  20. Crystal structure and phase stability of tungsten borides

    NASA Astrophysics Data System (ADS)

    Li, Quan; Zhou, Dan; Ma, Yanming; Chen, Changfeng

    2013-03-01

    We address the longstanding and controversial issue of ground-state structures of technically important tungsten borides using a first-principles structural search method via a particle-swarm optimization (PSO) algorithm. We have explored a large set of stable chemical compositions (convex hull) and clarified the ground-state structures for a wide range of boron concentrations, including W2B, W3B2,WB,W2B3, WB2,W2B5, WB3, and WB4. We further assessed relative stability of various tungsten borides and compared the calculated results with previously reported experimental data. The phase diagram predicted by the presented calculations may serve as a useful guide for synthesis of a variety of tungsten borides. This work was supported by DOE Grant No. DE-FC52-06NA26274.