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Sample records for crystal structure particle

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

    PubMed Central

    Vinothkumar, Kutti R

    2015-01-01

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

  2. Magnetic assembly of nonmagnetic particles into photonic crystal structures.

    PubMed

    He, Le; Hu, Yongxing; Kim, Hyoki; Ge, Jianping; Kwon, Sunghoon; Yin, Yadong

    2010-11-10

    We report the rapid formation of photonic crystal structures by assembly of uniform nonmagnetic colloidal particles in ferrofluids using external magnetic fields. Magnetic manipulation of nonmagnetic particles with size down to a few hundred nanometers, suitable building blocks for producing photonic crystals with band gaps located in the visible regime, has been difficult due to their weak magnetic dipole moment. Increasing the dipole moment of magnetic holes has been limited by the instability of ferrofluids toward aggregation at high concentration or under strong magnetic field. By taking advantage of the superior stability of highly surface-charged magnetite nanocrystal-based ferrofluids, in this paper we have been able to successfully assemble 185 nm nonmagnetic polymer beads into photonic crystal structures, from 1D chains to 3D assemblies as determined by the interplay of magnetic dipole force and packing force. In a strong magnetic field with large field gradient, 3D photonic crystals with high reflectance (83%) in the visible range can be rapidly produced within several minutes, making this general strategy promising for fast creation of large-area photonic crystals using nonmagnetic particles as building blocks.

  3. 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.

  4. Finite particle size drives defect-mediated domain structures in strongly confined colloidal liquid crystals

    NASA Astrophysics Data System (ADS)

    Gârlea, Ioana C.; Mulder, Pieter; Alvarado, José; Dammone, Oliver; Aarts, Dirk G. A. L.; Lettinga, M. Pavlik; Koenderink, Gijsje H.; Mulder, Bela M.

    2016-06-01

    When liquid crystals are confined to finite volumes, the competition between the surface anchoring imposed by the boundaries and the intrinsic orientational symmetry-breaking of these materials gives rise to a host of intriguing phenomena involving topological defect structures. For synthetic molecular mesogens, like the ones used in liquid-crystal displays, these defect structures are independent of the size of the molecules and well described by continuum theories. In contrast, colloidal systems such as carbon nanotubes and biopolymers have micron-sized lengths, so continuum descriptions are expected to break down under strong confinement conditions. Here, we show, by a combination of computer simulations and experiments with virus particles in tailor-made disk- and annulus-shaped microchambers, that strong confinement of colloidal liquid crystals leads to novel defect-stabilized symmetrical domain structures. These finite-size effects point to a potential for designing optically active microstructures, exploiting the as yet unexplored regime of highly confined liquid crystals.

  5. Finite particle size drives defect-mediated domain structures in strongly confined colloidal liquid crystals.

    PubMed

    Gârlea, Ioana C; Mulder, Pieter; Alvarado, José; Dammone, Oliver; Aarts, Dirk G A L; Lettinga, M Pavlik; Koenderink, Gijsje H; Mulder, Bela M

    2016-06-29

    When liquid crystals are confined to finite volumes, the competition between the surface anchoring imposed by the boundaries and the intrinsic orientational symmetry-breaking of these materials gives rise to a host of intriguing phenomena involving topological defect structures. For synthetic molecular mesogens, like the ones used in liquid-crystal displays, these defect structures are independent of the size of the molecules and well described by continuum theories. In contrast, colloidal systems such as carbon nanotubes and biopolymers have micron-sized lengths, so continuum descriptions are expected to break down under strong confinement conditions. Here, we show, by a combination of computer simulations and experiments with virus particles in tailor-made disk- and annulus-shaped microchambers, that strong confinement of colloidal liquid crystals leads to novel defect-stabilized symmetrical domain structures. These finite-size effects point to a potential for designing optically active microstructures, exploiting the as yet unexplored regime of highly confined liquid crystals.

  6. Defect structure of a nematic liquid crystal around a spherical particle: adaptive mesh refinement approach.

    PubMed

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

    2002-04-01

    We investigate numerically the structure of topological defects close to a spherical particle immersed in a uniformly aligned nematic liquid crystal. To this end we have implemented an adaptive mesh refinement scheme in an axi-symmetric three-dimensional system, which makes it feasible to take into account properly the large length scale difference between the particle and the topological defects. The adaptive mesh refinement scheme proves to be quite efficient and useful in the investigation of not only the macroscopic properties such as the defect position but also the fine structure of defects. It can be shown that a hyperbolic hedgehog that accompanies a particle with strong homeotropic anchoring takes the structure of a ring.

  7. Finite particle size drives defect-mediated domain structures in strongly confined colloidal liquid crystals

    PubMed Central

    Gârlea, Ioana C.; Mulder, Pieter; Alvarado, José; Dammone, Oliver; Aarts, Dirk G. A. L.; Lettinga, M. Pavlik; Koenderink, Gijsje H.; Mulder, Bela M.

    2016-01-01

    When liquid crystals are confined to finite volumes, the competition between the surface anchoring imposed by the boundaries and the intrinsic orientational symmetry-breaking of these materials gives rise to a host of intriguing phenomena involving topological defect structures. For synthetic molecular mesogens, like the ones used in liquid-crystal displays, these defect structures are independent of the size of the molecules and well described by continuum theories. In contrast, colloidal systems such as carbon nanotubes and biopolymers have micron-sized lengths, so continuum descriptions are expected to break down under strong confinement conditions. Here, we show, by a combination of computer simulations and experiments with virus particles in tailor-made disk- and annulus-shaped microchambers, that strong confinement of colloidal liquid crystals leads to novel defect-stabilized symmetrical domain structures. These finite-size effects point to a potential for designing optically active microstructures, exploiting the as yet unexplored regime of highly confined liquid crystals. PMID:27353002

  8. Crystal Structure and Proteomics Analysis of Empty Virus-like Particles of Cowpea Mosaic Virus.

    PubMed

    Huynh, Nhung T; Hesketh, Emma L; Saxena, Pooja; Meshcheriakova, Yulia; Ku, You-Chan; Hoang, Linh T; Johnson, John E; Ranson, Neil A; Lomonossoff, George P; Reddy, Vijay S

    2016-04-01

    Empty virus-like particles (eVLPs) of Cowpea mosaic virus (CPMV) are currently being utilized as reagents in various biomedical and nanotechnology applications. Here, we report the crystal structure of CPMV eVLPs determined using X-ray crystallography at 2.3 Å resolution and compare it with previously reported cryo-electron microscopy (cryo-EM) of eVLPs and virion crystal structures. Although the X-ray and cryo-EM structures of eVLPs are mostly similar, there exist significant differences at the C terminus of the small (S) subunit. The intact C terminus of the S subunit plays a critical role in enabling the efficient assembly of CPMV virions and eVLPs, but undergoes proteolysis after particle formation. In addition, we report the results of mass spectrometry-based proteomics analysis of coat protein subunits from CPMV eVLPs and virions that identify the C termini of S subunits undergo proteolytic cleavages at multiple sites instead of a single cleavage site as previously observed. PMID:27021160

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

    PubMed

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

    2015-02-01

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

  10. Crystal Structure and Proteomics Analysis of Empty Virus-like Particles of Cowpea Mosaic Virus.

    PubMed

    Huynh, Nhung T; Hesketh, Emma L; Saxena, Pooja; Meshcheriakova, Yulia; Ku, You-Chan; Hoang, Linh T; Johnson, John E; Ranson, Neil A; Lomonossoff, George P; Reddy, Vijay S

    2016-04-01

    Empty virus-like particles (eVLPs) of Cowpea mosaic virus (CPMV) are currently being utilized as reagents in various biomedical and nanotechnology applications. Here, we report the crystal structure of CPMV eVLPs determined using X-ray crystallography at 2.3 Å resolution and compare it with previously reported cryo-electron microscopy (cryo-EM) of eVLPs and virion crystal structures. Although the X-ray and cryo-EM structures of eVLPs are mostly similar, there exist significant differences at the C terminus of the small (S) subunit. The intact C terminus of the S subunit plays a critical role in enabling the efficient assembly of CPMV virions and eVLPs, but undergoes proteolysis after particle formation. In addition, we report the results of mass spectrometry-based proteomics analysis of coat protein subunits from CPMV eVLPs and virions that identify the C termini of S subunits undergo proteolytic cleavages at multiple sites instead of a single cleavage site as previously observed.

  11. Crystal structure of a signal recognition particle Alu domain in the elongation arrest conformation.

    PubMed

    Bousset, Luc; Mary, Camille; Brooks, Mark A; Scherrer, Anne; Strub, Katharina; Cusack, Stephen

    2014-12-01

    The signal recognition particle (SRP) is a conserved ribonucleoprotein particle that targets membrane and secreted proteins to translocation channels in membranes. In eukaryotes, the Alu domain, which comprises the 5' and 3' extremities of the SRP RNA bound to the SRP9/14 heterodimer, is thought to interact with the ribosome to pause translation elongation during membrane docking. We present the 3.2 Å resolution crystal structure of a chimeric Alu domain, comprising Alu RNA from the archaeon Pyrococcus horikoshii bound to the human Alu binding proteins SRP9/14. The structure reveals how intricate tertiary interactions stabilize the RNA 5' domain structure and how an extra, archaeal-specific, terminal stem helps constrain the Alu RNA into the active closed conformation. In this conformation, highly conserved noncanonical base pairs allow unusually tight side-by-side packing of 5' and 3' RNA stems within the SRP9/14 RNA binding surface. The biological relevance of this structure is confirmed by showing that a reconstituted full-length chimeric archaeal-human SRP is competent to elicit elongation arrest in vitro. The structure will be useful in refining our understanding of how the SRP Alu domain interacts with the ribosome.

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  13. The crystal structure of the signal recognition particle Alu RNA binding heterodimer, SRP9/14.

    PubMed Central

    Birse, D E; Kapp, U; Strub, K; Cusack, S; Aberg, A

    1997-01-01

    The mammalian signal recognition particle (SRP) is an 11S cytoplasmic ribonucleoprotein that plays an essential role in protein sorting. SRP recognizes the signal sequence of the nascent polypeptide chain emerging from the ribosome, and targets the ribosome-nascent chain-SRP complex to the rough endoplasmic reticulum. The SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide RNA molecule. SRP9 and SRP14 proteins form a heterodimer that binds to the Alu domain of SRP RNA which is responsible for translation arrest. We report the first crystal structure of a mammalian SRP protein, that of the mouse SRP9/14 heterodimer, determined at 2.5 A resolution. SRP9 and SRP14 are found to be structurally homologous, containing the same alpha-beta-beta-beta-alpha fold. This we designate the Alu binding module (Alu bm), an additional member of the family of small alpha/beta RNA binding domains. The heterodimer has pseudo 2-fold symmetry and is saddle like, comprising a strongly curved six-stranded amphipathic beta-sheet with the four helices packed on the convex side and the exposed concave surface being lined with positively charged residues. PMID:9233785

  14. 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.

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

    SciTech Connect

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

    2014-05-07

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

  16. Ionic colloidal crystals of oppositely charged particles.

    PubMed

    Leunissen, Mirjam E; Christova, Christina G; Hynninen, Antti-Pekka; Royall, C Patrick; Campbell, Andrew I; Imhof, Arnout; Dijkstra, Marjolein; van Roij, René; van Blaaderen, Alfons

    2005-09-01

    Colloidal suspensions are widely used to study processes such as melting, freezing and glass transitions. This is because they display the same phase behaviour as atoms or molecules, with the nano- to micrometre size of the colloidal particles making it possible to observe them directly in real space. Another attractive feature is that different types of colloidal interactions, such as long-range repulsive, short-range attractive, hard-sphere-like and dipolar, can be realized and give rise to equilibrium phases. However, spherically symmetric, long-range attractions (that is, ionic interactions) have so far always resulted in irreversible colloidal aggregation. Here we show that the electrostatic interaction between oppositely charged particles can be tuned such that large ionic colloidal crystals form readily, with our theory and simulations confirming the stability of these structures. We find that in contrast to atomic systems, the stoichiometry of our colloidal crystals is not dictated by charge neutrality; this allows us to obtain a remarkable diversity of new binary structures. An external electric field melts the crystals, confirming that the constituent particles are indeed oppositely charged. Colloidal model systems can thus be used to study the phase behaviour of ionic species. We also expect that our approach to controlling opposite-charge interactions will facilitate the production of binary crystals of micrometre-sized particles, which could find use as advanced materials for photonic applications.

  17. Crystal-structure prediction via the Floppy-Box Monte Carlo algorithm: Method and application to hard (non)convex particles

    NASA Astrophysics Data System (ADS)

    de Graaf, Joost; Filion, Laura; Marechal, Matthieu; van Roij, René; Dijkstra, Marjolein

    2012-12-01

    In this paper, we describe the way to set up the floppy-box Monte Carlo (FBMC) method [L. Filion, M. Marechal, B. van Oorschot, D. Pelt, F. Smallenburg, and M. Dijkstra, Phys. Rev. Lett. 103, 188302 (2009), 10.1103/PhysRevLett.103.188302] to predict crystal-structure candidates for colloidal particles. The algorithm is explained in detail to ensure that it can be straightforwardly implemented on the basis of this text. The handling of hard-particle interactions in the FBMC algorithm is given special attention, as (soft) short-range and semi-long-range interactions can be treated in an analogous way. We also discuss two types of algorithms for checking for overlaps between polyhedra, the method of separating axes and a triangular-tessellation based technique. These can be combined with the FBMC method to enable crystal-structure prediction for systems composed of highly shape-anisotropic particles. Moreover, we present the results for the dense crystal structures predicted using the FBMC method for 159 (non)convex faceted particles, on which the findings in [J. de Graaf, R. van Roij, and M. Dijkstra, Phys. Rev. Lett. 107, 155501 (2011), 10.1103/PhysRevLett.107.155501] were based. Finally, we comment on the process of crystal-structure prediction itself and the choices that can be made in these simulations.

  18. Crystal-structure prediction via the floppy-box Monte Carlo algorithm: method and application to hard (non)convex particles.

    PubMed

    de Graaf, Joost; Filion, Laura; Marechal, Matthieu; van Roij, René; Dijkstra, Marjolein

    2012-12-01

    In this paper, we describe the way to set up the floppy-box Monte Carlo (FBMC) method [L. Filion, M. Marechal, B. van Oorschot, D. Pelt, F. Smallenburg, and M. Dijkstra, Phys. Rev. Lett. 103, 188302 (2009)] to predict crystal-structure candidates for colloidal particles. The algorithm is explained in detail to ensure that it can be straightforwardly implemented on the basis of this text. The handling of hard-particle interactions in the FBMC algorithm is given special attention, as (soft) short-range and semi-long-range interactions can be treated in an analogous way. We also discuss two types of algorithms for checking for overlaps between polyhedra, the method of separating axes and a triangular-tessellation based technique. These can be combined with the FBMC method to enable crystal-structure prediction for systems composed of highly shape-anisotropic particles. Moreover, we present the results for the dense crystal structures predicted using the FBMC method for 159 (non)convex faceted particles, on which the findings in [J. de Graaf, R. van Roij, and M. Dijkstra, Phys. Rev. Lett. 107, 155501 (2011)] were based. Finally, we comment on the process of crystal-structure prediction itself and the choices that can be made in these simulations. PMID:23231211

  19. 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…

  20. X-ray Crystal Structure of the Vault, Largest Ribonucleoprotein Particle, with a Molecular Weight of 10 MDa

    NASA Astrophysics Data System (ADS)

    Tanaka, Hideaki; Kato, Koji; Yamashita, Eiki

    Vaults are among the largest cytoplasmic ribonucleoprotein particles and are found in numerous eukaryotic species. Although roles in multidrug resistance and innate immunity have been suggested, the cellular function remains unclear. We have determined the X-ray structure of rat liver vault at 3.5 Å resolution. A vault particle shell was composed of 78 MVP (Major vault protein) chains with 39-fold dihedral symmetry. The shoulder domain of MVP is structurally similar to SPFH (stomatin/prohibitin/flotillin/HflK/C) domain involved in lipid raft association.

  1. Colloidal particles embedded in liquid crystal droplets

    NASA Astrophysics Data System (ADS)

    Melchert, Drew; Sadati, Monirosadat; Zhou, Ye; de Pablo, Juan J.

    In this work, we encapsulate polystyrene and silica particles in nematic liquid crystal (LC) droplets dispersed in water using microfluidic glass capillary devices. While polystyrene particles induce planar anchoring on the surface, silica particles, treated with DMOAP, create homeotropic anchoring of the LC molecules at their surface. Sodium dodecyl sulfate (SDS) is added to the aqueous phase to stabilize LC droplets and promote a radial configuration with point defect in the center of LC droplet. Our experimental and computational studies show that, when trapped inside the LC droplets, particles with both anchoring types become mostly localized at the defect point (at the center) and interact with the radial configuration. Interestingly, a twisting structure is observed for polystyrene particle with strong planar anchoring. Although localization of the particles at the droplet center is the most stable state and with the lowest free energy, off-center positions also emerge, displacing the defect point from the center to near the surface of a radial droplet. - Corresponding author - Second affiliation: Argonne National Laboratory, Argonne, IL 60439, USA.

  2. 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.

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

    SciTech Connect

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

    2015-07-31

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

  4. Crystallization in a dense suspension of self-propelled particles.

    PubMed

    Bialké, Julian; Speck, Thomas; Löwen, Hartmut

    2012-04-20

    Using Brownian dynamics computer simulations, we show that a two-dimensional suspension of self-propelled ("active") colloidal particles crystallizes at sufficiently high densities. Compared to the equilibrium freezing of passive particles, the freezing density is both significantly shifted and depends on the structural or dynamical criterion employed. In nonequilibrium the transition is accompanied by pronounced structural heterogeneities. This leads to a transition region between liquid and solid in which the suspension is globally ordered but unordered liquidlike "bubbles" still persist.

  5. Self-assembling behavior of cellulose nanoparticles during freeze-drying: effect of suspension concentration, particle size, crystal structure, and surface charge.

    PubMed

    Han, Jingquan; Zhou, Chengjun; Wu, Yiqiang; Liu, Fangyang; Wu, Qinglin

    2013-05-13

    Cellulose nanocrystals and cellulose nanofibers with I and II crystalline allomorphs (designated as CNC I, CNC II, CNF I, and CNF II) were isolated from bleached wood fibers by alkaline pretreatment and acid hydrolysis. The effects of concentration, particle size, surface charge, and crystal structure on the lyophilization-induced self-assembly of cellulose particles in aqueous suspensions were studied. Within the concentration range of 0.5 to 1.0 wt %, cellulose particles self-organized into lamellar structured foam composed of aligned membrane layers with widths between 0.5 and 3 μm. At 0.05 wt %, CNC I, CNF I, CNC II, and CNF II self-assembled into oriented ultrafine fibers with mean diameters of 0.57, 1.02, 1.50, and 1.00 μm, respectively. The size of self-assembled fibers became larger when more hydroxyl groups and fewer sulfates (weaker electrostatic repulsion) were on cellulose surfaces. Possible formation mechanism was inferred from ice growth and interaction between cellulose nanoparticles in liquid-crystalline suspensions.

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

    PubMed

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

  7. Ionizing particle detection based on phononic crystals

    SciTech Connect

    Aly, Arafa H. E-mail: arafa.hussien@science.bsu.edu.eg; Mehaney, Ahmed; Eissa, Mostafa F.

    2015-08-14

    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.

  8. 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.

  9. Structural Color Painting by Rubbing Particle Powder

    NASA Astrophysics Data System (ADS)

    Park, Choojin; Koh, Kunsuk; Jeong, Unyong

    2015-02-01

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

  10. 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

  11. Dressed active particles in spherical crystals.

    PubMed

    Yao, Zhenwei

    2016-08-17

    We investigate the dynamics of an active particle in two-dimensional spherical crystals, which provide an ideal environment to illustrate the interplay between active particles and crystallographic defects. A moving active particle is observed to be surrounded by localized topological defects, becoming a dressed active particle. Such a physical picture characterizes both the lattice distortion around the moving particle and the healing of the distorted lattice in its trajectory. We find that the dynamical behaviors of an active particle in both random and ballistic motions uniformly conform to this featured scenario, whether the particle is initially a defect or not. We further observe that the defect pattern around a dressed ballistic active particle randomly oscillates between two well-defined wing-like defect motifs regardless of its speed. The established physical picture of dressed active particles in this work partially deciphers the complexity of the intriguing nonequilibrium behaviors in active crystals, and opens the promising possibility of introducing the activity to engineer defects, which has strong connections with the design of materials.

  12. Vaterite Crystals Contain Two Interspersed Crystal Structures

    NASA Astrophysics Data System (ADS)

    Kabalah-Amitai, Lee; Mayzel, Boaz; Kauffmann, Yaron; Fitch, Andrew N.; Bloch, Leonid; Gilbert, Pupa U. P. A.; Pokroy, Boaz

    2013-04-01

    Calcite, aragonite, and vaterite are the three anhydrous polymorphs of calcium carbonate, in order of decreasing thermodynamic stability. Although vaterite is not commonly found in geological settings, it is an important precursor in several carbonate-forming systems and can be found in biological settings. Because of difficulties in obtaining large, pure, single crystals, the crystal structure of vaterite has been elusive for almost a century. Using aberration-corrected high-resolution transmission electron microscopy, we found that vaterite is actually composed of at least two different crystallographic structures that coexist within a pseudo-single crystal. The major structure exhibits hexagonal symmetry; the minor structure, existing as nanodomains within the major matrix, is still unknown.

  13. Particles and curvatures in nematic liquid crystals

    NASA Astrophysics Data System (ADS)

    Serra, Francesca; Luo, Yimin; Yang, Shu; Kamien, Randall D.; Stebe, Kathleen J.

    Elastic interactions in anisotropic fluids can be harnessed to direct particle interactions. A strategy to smoothly manipulate the director field in nematic liquid crystals is to vary the topography of the bounding surfaces. A rugged landscape with peaks and valleys create local deformations of the director field which can interact with particles in solution. We study this complex interaction in two different settings. The first consists of an array of shallow pores in a poly-dimethyl-siloxane (PDMS) membrane, whose curvature can be tuned either by swelling the PDMS membrane or by mechanical stretching. The second is a set of grooves with wavy walls, fabricated by photolithography, with various parameters of curvature and shapes. In this contexts we study how the motion of colloidal particles in nematic liquid crystals can be influenced by their interaction with the peaks and valleys of the bottom substrate or of the side walls. Particles with different associated topological defects (hedgehogs or Saturn rings) behave differently as they interact with the topographical features, favoring the docking on peaks or valleys. These experimental systems are also ideal to study the ``lock and key'' mechanism of particles in holes and to investigate a possible route for particle sorting.

  14. 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.

  15. Crystal structure of propaquizafop

    PubMed Central

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

    2014-01-01

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

  16. 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)

  17. 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.

  18. Nucleation and structural growth of cluster crystals

    NASA Astrophysics Data System (ADS)

    Leitold, Christian; Dellago, Christoph

    2016-08-01

    We study the nucleation of crystalline cluster phases in the generalized exponential model with exponent n = 4. Due to the finite value of this pair potential for zero separation, at high densities the system forms cluster crystals with multiply occupied lattice sites. Here, we investigate the microscopic mechanisms that lead to the formation of cluster crystals from a supercooled liquid in the low-temperature region of the phase diagram. Using molecular dynamics and umbrella sampling, we calculate the free energy as a function of the size of the largest crystalline nucleus in the system, and compare our results with predictions from classical nucleation theory. Employing bond-order parameters based on a Voronoi tessellation to distinguish different crystal structures, we analyze the average composition of crystalline nuclei. We find that even for conditions where a multiply occupied fcc crystal is the thermodynamically stable phase, the nucleation into bcc cluster crystals is strongly preferred. Furthermore, we study the particle mobility in the supercooled liquid and in the cluster crystal. In the cluster crystal, the motion of individual particles is captured by a simple reaction-diffusion model introduced previously to model the kinetics of hydrogen bonds.

  19. Nucleation and structural growth of cluster crystals.

    PubMed

    Leitold, Christian; Dellago, Christoph

    2016-08-21

    We study the nucleation of crystalline cluster phases in the generalized exponential model with exponent n = 4. Due to the finite value of this pair potential for zero separation, at high densities the system forms cluster crystals with multiply occupied lattice sites. Here, we investigate the microscopic mechanisms that lead to the formation of cluster crystals from a supercooled liquid in the low-temperature region of the phase diagram. Using molecular dynamics and umbrella sampling, we calculate the free energy as a function of the size of the largest crystalline nucleus in the system, and compare our results with predictions from classical nucleation theory. Employing bond-order parameters based on a Voronoi tessellation to distinguish different crystal structures, we analyze the average composition of crystalline nuclei. We find that even for conditions where a multiply occupied fcc crystal is the thermodynamically stable phase, the nucleation into bcc cluster crystals is strongly preferred. Furthermore, we study the particle mobility in the supercooled liquid and in the cluster crystal. In the cluster crystal, the motion of individual particles is captured by a simple reaction-diffusion model introduced previously to model the kinetics of hydrogen bonds. PMID:27544116

  20. Crystal structure determination of Efavirenz

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  1. Symmetry considerations for the targeted assembly of entropically stabilized colloidal crystals via Voronoi particles.

    PubMed

    Schultz, Benjamin A; Damasceno, Pablo F; Engel, Michael; Glotzer, Sharon C

    2015-03-24

    The relationship between colloidal building blocks and their assemblies is an active field of research. As a strategy for targeting novel crystal structures, we examine the use of Voronoi particles, which are hard, space-filling particles in the shape of Voronoi cells of a target structure. Although Voronoi particles stabilize their target structure in the limit of high pressure by construction, the thermodynamic assembly of the same structure at moderate pressure, close to the onset of crystallization, is not guaranteed. Indeed, we find that a more symmetric crystal is often preferred due to additional entropic contributions arising from configurational or occupational degeneracy. We characterize the assembly behavior of the Voronoi particles in terms of the symmetries of the building blocks as well as the symmetries of crystal structures and demonstrate how controlling the degeneracies through a modification of particle shape and field-directed assembly can significantly improve the assembly propensity.

  2. Symmetry considerations for the targeted assembly of entropically stabilized colloidal crystals via Voronoi particles.

    PubMed

    Schultz, Benjamin A; Damasceno, Pablo F; Engel, Michael; Glotzer, Sharon C

    2015-03-24

    The relationship between colloidal building blocks and their assemblies is an active field of research. As a strategy for targeting novel crystal structures, we examine the use of Voronoi particles, which are hard, space-filling particles in the shape of Voronoi cells of a target structure. Although Voronoi particles stabilize their target structure in the limit of high pressure by construction, the thermodynamic assembly of the same structure at moderate pressure, close to the onset of crystallization, is not guaranteed. Indeed, we find that a more symmetric crystal is often preferred due to additional entropic contributions arising from configurational or occupational degeneracy. We characterize the assembly behavior of the Voronoi particles in terms of the symmetries of the building blocks as well as the symmetries of crystal structures and demonstrate how controlling the degeneracies through a modification of particle shape and field-directed assembly can significantly improve the assembly propensity. PMID:25692863

  3. Generation of crystal structures using known crystal structures as analogues

    PubMed Central

    Cole, Jason C.; Groom, Colin R.; Read, Murray G.; Giangreco, Ilenia; McCabe, Patrick; Reilly, Anthony M.; Shields, Gregory P.

    2016-01-01

    This analysis attempts to answer the question of whether similar molecules crystallize in a similar manner. An analysis of structures in the Cambridge Structural Database shows that the answer is yes – sometimes they do, particularly for single-component structures. However, one does need to define what we mean by similar in both cases. Building on this observation we then demonstrate how this correlation between shape similarity and packing similarity can be used to generate potential lattices for molecules with no known crystal structure. Simple intermolecular interaction potentials can be used to minimize these potential lattices. Finally we discuss the many limitations of this approach. PMID:27484374

  4. Micropolar crystal plasticity simulation of particle strengthening

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  5. 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 NO(x)). We show that SSZ-13 grows by two concerted mechanisms: nonclassical growth involving the attachment of amorphous aluminosilicate particles to crystal surfaces and classical layer-by-layer growth via the incorporation of molecules to advancing steps on the crystal surface. A facile, commercially viable method of tailoring SSZ-13 crystal size and morphology is introduced wherein growth modifiers are used to mediate precursor aggregation and attachment to crystal surfaces. We demonstrate that small quantities of polymers can be used to tune crystal size over 3 orders of magnitude (0.1-20 μm), 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

  6. Crystal structure of cyproconazole

    PubMed Central

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

    2015-01-01

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

  7. Crystal structure of flumioxazin

    PubMed Central

    Park, Hyunjin; Kim, Jineun; Kwon, Eunjin; Kim, Tae Ho

    2015-01-01

    The title compound {systematic name: 2-[7-fluoro-3,4-di­hydro-3-oxo-4-(prop-2-yn-1-yl)-2H-1,4-benzoxazin-6-yl]-4,5,6,7-tetra­hydro-1H-iso­indole-1,3(2H)-dione}, C19H15FN2O4, is a dicarboximide herbicide. The dihedral angle between the male­imide and benzene ring planes is 66.13 (5)°. In the crystal, C—H⋯O and C—H⋯F hydrogen bonds and weak C—H⋯π inter­actions [3.5601 (19) Å] link adjacent mol­ecules, forming two-dimensional networks extending parallel to the (110) plane. PMID:26594468

  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. Crystal structure determination of Efavirenz

    SciTech Connect

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

    2015-12-23

    Needle-shaped single crystals of the title compound, C{sub 14}H{sub 9}ClF{sub 3}NO{sub 2}, were obtained from a co-crystallization experiment of Efavirenz with maleic acid in a (1:1) ratio, using methanol as solvent. Crystal structure determination at room temperature revealed a significant anisotropy of the lattice expansion compared to the previously reported low-temperature structure. In both low- and room temperature structures the cyclopropylethynyl fragment in one of the asymmetric unit molecules is disordered. While at low-temperature only one C atom exhibits positional disorder, at room temperature the disorder is present for two C atoms of the cyclopropane ring.

  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. Predicting patchy particle crystals: variable box shape simulations and evolutionary algorithms.

    PubMed

    Bianchi, Emanuela; Doppelbauer, Günther; Filion, Laura; Dijkstra, Marjolein; Kahl, Gerhard

    2012-06-01

    We consider several patchy particle models that have been proposed in literature and we investigate their candidate crystal structures in a systematic way. We compare two different algorithms for predicting crystal structures: (i) an approach based on Monte Carlo simulations in the isobaric-isothermal ensemble and (ii) an optimization technique based on ideas of evolutionary algorithms. We show that the two methods are equally successful and provide consistent results on crystalline phases of patchy particle systems. PMID:22697525

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

    PubMed

    Tari, Tímea; Fekete, Zoltán; Szabó-Révész, Piroska; Aigner, Zoltán

    2015-01-15

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

  13. Crystal chemistry and real structure of crystals

    NASA Astrophysics Data System (ADS)

    Bartl, H.; Bats, J. W.; Dyck, W.; Fuess, H.; Gregory, A.; Joswig, W.; Lottermoser, W.; Koerfer, M.; Mueller, R.; Schweiss, B. P.

    1984-03-01

    Elastic and inelastic scattering, X-ray diffraction and spectroscopy were combined to obtain a comprehensive picture of the properties of crystals. The electron density distribution allows one to verify the models of the theoretical chemistry. Systematic investigations of chemically similar anions (ClO3 and ClO4; S2O3, SO3 and SO4) show differences in bonding and reaction capability. The X-ray-neutron method applied to these anions shows maxima between 0.2 and 0.4 eXA to the power-3 in the bondings of the unbound electrons on S and D. For the SO3-group good agreement is found with theoretical calculations. The effect of the Mg (two times ionized) cation on the density is demonstrated on the water molecules of MgS2O3.6H2O and MgSO3.6H2O. Magnetic structure and magnetization density were investigated on CO3V2O8, Fe2SiO4 and Mn2SiO4 with polarized neutrons. The differences in magnetic moments of both cation states is also demonstrated for Fe2SiO4 with complementary Mossbauer measurements. Inelastic time of flight experiments allow predictions concerning the motion of the NH3-group in aniliniumbromide and of the water molecule in natural zeolites. The theoretical model to calculate the photon dispersion on CaSO4 shows good agreement with the measured dispersion curves.

  14. Crystal Structure of Bi

    SciTech Connect

    Borg, Stefan; Svensson, Goeran

    2001-02-15

    The room temperature structures of the two-layer Aurivillius phases Bi{sub 2.5}Me{sub 0.5}Nb{sub 2}O{sub 9} (Me=Na, K) have been refined with the Rietveld method from powder neutron diffraction data ({lambda}=1.470 {angstrom}). They consist of (Bi{sub 2}O{sub 2}){sup 2+} layers interleaved with perovskite (Bi{sub 0.5}Me{sub 0.5}Nb{sub 2}O{sub 7}){sup 2-} (Me=Na, K) slabs. The structures were refined in the orthorhombic space group A2{sub 1}am, Z=4, and the unit cell parameters of the two oxides are a= 5.4937(3), b=5.4571(4), c=24.9169(14) {angstrom} and a=5.5005(8), b=5.4958(8), c=25.2524(16) {angstrom}, respectively. The orthorhombic distortion increases with decreasing Me+ cation size in the perovskite layer (Bi/Me){sup 2+} site and the lone pair electrons from the Bi{sup 3+} cation are influencing the site distortion. This is in agreement with other two-layer Aurivillius phases and originates from bonding requirements depending on size and electronic environment.

  15. Photonic Crystal Laser-Driven Accelerator Structures

    SciTech Connect

    Cowan, Benjamin M.

    2007-08-22

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

  16. Crystal structure of guggulsterone Z

    SciTech Connect

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

    2006-03-15

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

  17. 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).

  18. 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.

  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. Full inactivation of alphaviruses in single particle and crystallized forms.

    PubMed

    Lawrence, Robert M; Zook, James D; Hogue, Brenda G

    2016-10-01

    Inherent in the study of viruses is the risk of pathogenic exposure, which necessitates appropriate levels of biosafety containment. Unfortunately, this also limits the availability of useful research instruments that are located at facilities not equipped to handle infectious pathogens. Abrogation of viral infectivity can be accomplished without severely disrupting the physical structure of the virus particle. Virus samples that are verifiably intact but not infectious may be enabled for study at research facilities where they would otherwise not be allowed. Inactivated viruses are also used in the development of vaccines, where immunogenicity is sought in the absence of active infection. We demonstrate the inactivation of Sindbis alphavirus particles in solution, as well as in crystallized form. Inactivation was accomplished by two different approaches: crosslinking of proteins by glutaraldehyde treatment, and crosslinking of nucleic acids by UV irradiation. Biophysical characterization methods, including dynamic light scattering and transmission electron microscopy, were used to demonstrate that the glutaraldehyde and UV inactivated Sindbis virus particles remain intact structurally. SDS-PAGE was also used to show evidence of the protein crosslinking that was expected with glutaraldehyde treatment, but also observed with UV irradiation. PMID:27465218

  1. The crystal structure of waxes.

    PubMed

    Dorset, D L

    1995-12-01

    Quantitative electron crystallographic studies have been carried out on epitaxially oriented multi-component waxes. Intensities from two paraffin-based samples, an artificial six-component medium wax (equimolar distribution of chain lengths) and a petroleum-based wax (Gaussian distribution of chain lengths) have been used to determine their crystal structures. As found earlier for binary paraffin solid solutions, differences in molecular volume are compensated by longitudinal molecular shifts within individual lamellae. Nevertheless, each lamellar surface must remain flat enough, and with enough crystallographic order intact, to nucleate the next lamella, thus accounting for the observed long-range correlation in these crystals. Recrystallized beeswax also has a layer packing somewhat similar to the paraffin waxes. However, in this case, the lamellar order is 'frustrated' so that a certain amount of 'nematically' ordered material must be present, spanning the nascent lamellar interfaces. PMID:8554724

  2. Methane hydrate crystallization mechanism from in-situ particle sizing

    SciTech Connect

    Herri, J.M. |; Pic, J.S.; Gruy, F.; Cournil, M.

    1999-03-01

    A new experimental setup that makes possible in-situ determinations of the population density function of the methane hydrate particles during its crystallization in a pressurized reactor is used. Thanks to this equipment, new results can be obtained, in particular concerning the granular aspects of the crystallization processes and the influence of the stirring rate. These results are discussed in the framework of a model including gas absorption, primary and secondary nucleation, crystal growth, agglomeration, and breakage. From this discussion, the relevant processes and parameters of methane hydrate crystallization can be determined and quantified.

  3. Quantum effects for particles channeling in a bent crystal

    NASA Astrophysics Data System (ADS)

    Feranchuk, Ilya; San, Nguyen Quang

    2016-09-01

    Quantum mechanical theory for channeling of the relativistic charged particles in the bent crystals is considered in the paper. Quantum effects of under-barrier tunneling are essential when the radius of the curvature is closed to its critical value. In this case the wave functions of the quasi-stationary states corresponding to the particles captured in a channel are presented in the analytical form. The efficiency of channeling of the particles and their angular distribution at the exit crystal surface are calculated. Characteristic experimental parameters for observation the quantum effects are estimated.

  4. 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.

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

    DOEpatents

    Lin, Shawn-Yu; Koops, Hans W. P.

    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.

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

    NASA Astrophysics Data System (ADS)

    Gürhan, Deniz; Çakal, Gaye Ö.; Eroğlu, İnci; Özkar, Saim

    2009-03-01

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

  7. Checking nucleic acid crystal structures.

    PubMed

    Das, U; Chen, S; Fuxreiter, M; Vaguine, A A; Richelle, J; Berman, H M; Wodak, S J

    2001-06-01

    The program SFCHECK [Vaguine et al. (1999), Acta Cryst. D55, 191-205] is used to survey the quality of the structure-factor data and the agreement of those data with the atomic coordinates in 105 nucleic acid crystal structures for which structure-factor amplitudes have been deposited in the Nucleic Acid Database [NDB; Berman et al. (1992), Biophys. J. 63, 751-759]. Nucleic acid structures present a particular challenge for structure-quality evaluations. The majority of these structures, and DNA molecules in particular, have been solved by molecular replacement of the double-helical motif, whose high degree of symmetry can lead to problems in positioning the molecule in the unit cell. In this paper, the overall quality of each structure was evaluated using parameters such as the R factor, the correlation coefficient and various atomic error estimates. In addition, each structure is characterized by the average values of several local quality indicators, which include the atomic displacement, the density correlation, the B factor and the density index. The latter parameter measures the relative electron-density level at the atomic position. In order to assess the quality of the model in specific regions, the same local quality indicators are also surveyed for individual groups of atoms in each structure. Several of the global quality indicators are found to vary linearly with resolution and less than a dozen structures are found to exhibit values significantly different from the mean for these indicators, showing that the quality of the nucleic acid structures tends to be rather uniform. Analysis of the mutual dependence of the values of different local quality indicators, computed for individual residues and atom groups, reveals that these indicators essentially complement each other and are not redundant with the B factor. Using several of these indicators, it was found that the atomic coordinates of the nucleic acid bases tend to be better defined than those of

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  9. 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.

  10. Septin crystallization for structural analysis.

    PubMed

    Valadares, N F; Garratt, R C

    2016-01-01

    Septins are filament-forming proteins found in many eukaryotes. Despite being important components of the cytoskeleton, only recently details of their macromolecular assemblies and crystal structures have started to appear in the literature. These are of fundamental importance to the understanding of cytoskeleton dynamics, membrane barrier formation, and bacterial caging, as well as essential cellular processes such as cell division, exocytosis, and vesicle trafficking. However, obtaining this data is frequently hindered by several experimental difficulties common to the majority of septin samples. Here we provide an overview of the current approaches to circumvent or minimize the experimental complications observed in septin crystallography focusing mainly, but not exclusively, on the choice of the septin construct and how to best prepare the sample itself. PMID:27473918

  11. [Theory and practice of electrospray crystallization in particle size reduction].

    PubMed

    Szunyogh, Tímea; Ambrus, Rita; Szabóné Révész, Piroska

    2015-01-01

    Nowdays, one of the most challenges for the researchers is the formulation of poorly water soluble drugs. Reduction of particle size of active agents to submicron range could result in a faster dissolution rate and higher bioavailability. Integration as crystallization process is an often used particle size decreasing technique. The aim of this study was to show the theoretical background and practical application of the electros pray crystallization as an innovative particle size decreasing technique. Our model drug was the niflumic acid (NIF), which belongs to the BCS Class II. After the optimization of the process parameters, the physico-chemical properties of the samples were characterized. Particle size and shape were visualized by scanning electron microscopy (SEM). Crystalline state of NIF and the samples were investigated using differential scanning calorimetry (DSC) and X-ray powder diffraction. Physico-chemical properties were determined using dissolution test from simulated media. The electrospray crytallization resulted in particle size reduction but the aggregation of nanonized NIF crystals (NIF-nano) could not avoid without excipient. Aggregates with poor secondary forces are suitable for production of the interactive physical mixture. It was found that NIF-nano could be well distributed on the surface of the mannitol as carrier and the Poloxamer R protected the NIF-nano crystals (320 nm)from aggregation. Consequently, the physical mixture resulted in product with higher polarity, better wettability and faster dissolution rate of NIF as raw NIF or NIF-nano.

  12. [Theory and practice of electrospray crystallization in particle size reduction].

    PubMed

    Szunyogh, Tímea; Ambrus, Rita; Szabóné Révész, Piroska

    2015-01-01

    Nowdays, one of the most challenges for the researchers is the formulation of poorly water soluble drugs. Reduction of particle size of active agents to submicron range could result in a faster dissolution rate and higher bioavailability. Integration as crystallization process is an often used particle size decreasing technique. The aim of this study was to show the theoretical background and practical application of the electros pray crystallization as an innovative particle size decreasing technique. Our model drug was the niflumic acid (NIF), which belongs to the BCS Class II. After the optimization of the process parameters, the physico-chemical properties of the samples were characterized. Particle size and shape were visualized by scanning electron microscopy (SEM). Crystalline state of NIF and the samples were investigated using differential scanning calorimetry (DSC) and X-ray powder diffraction. Physico-chemical properties were determined using dissolution test from simulated media. The electrospray crytallization resulted in particle size reduction but the aggregation of nanonized NIF crystals (NIF-nano) could not avoid without excipient. Aggregates with poor secondary forces are suitable for production of the interactive physical mixture. It was found that NIF-nano could be well distributed on the surface of the mannitol as carrier and the Poloxamer R protected the NIF-nano crystals (320 nm)from aggregation. Consequently, the physical mixture resulted in product with higher polarity, better wettability and faster dissolution rate of NIF as raw NIF or NIF-nano. PMID:26390735

  13. 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.

  14. 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.

  15. 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.

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

    PubMed

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

    2013-01-01

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

  17. Particle size measurement for the control of industrial crystallizers

    NASA Astrophysics Data System (ADS)

    Boxman, A.

    1992-01-01

    The need for on-line sensors to monitor particulate processes is rapidly increasing. Such systems are a necessity to understand the complex phenomena of particle formation, growth, and breakage. Some aspects of the design of an on-line sensor for particle size analysis are discussed. The technique used is based on forward light scattering, which covers a size range from about 1 to 2,000 micrometers. The observations are used to develop a physical model and subsequently an effective control strategy for a 970 liter continuous crystallizer. The purpose of the controller is to manipulate the dynamics of the size distribution. Therefore, a firm relation between process inputs and outputs (i.e., the crystal size distribution) must first be established. Secondly, an intelligent interpretation of the recorded data, in this case a light scattering pattern, is required. Chapter headings include the following: Validation of Light Scattering Models for Polydisperse Particle Systems; Deconvolution Algorithm for the Recovery of Particle Size Distributions; Automated Measurement and Interpretation of Scattering Patterns; On-line Measurement of Crystal Size Distribution in Industrial Crystallizers.

  18. Single particle 3D reconstruction for 2D crystal images of membrane proteins.

    PubMed

    Scherer, Sebastian; Arheit, Marcel; Kowal, Julia; Zeng, Xiangyan; Stahlberg, Henning

    2014-03-01

    In cases where ultra-flat cryo-preparations of well-ordered two-dimensional (2D) crystals are available, electron crystallography is a powerful method for the determination of the high-resolution structures of membrane and soluble proteins. However, crystal unbending and Fourier-filtering methods in electron crystallography three-dimensional (3D) image processing are generally limited in their performance for 2D crystals that are badly ordered or non-flat. Here we present a single particle image processing approach, which is implemented as an extension of the 2D crystallographic pipeline realized in the 2dx software package, for the determination of high-resolution 3D structures of membrane proteins. The algorithm presented, addresses the low single-to-noise ratio (SNR) of 2D crystal images by exploiting neighborhood correlation between adjacent proteins in the 2D crystal. Compared with conventional single particle processing for randomly oriented particles, the computational costs are greatly reduced due to the crystal-induced limited search space, which allows a much finer search space compared to classical single particle processing. To reduce the considerable computational costs, our software features a hybrid parallelization scheme for multi-CPU clusters and computer with high-end graphic processing units (GPUs). We successfully apply the new refinement method to the structure of the potassium channel MloK1. The calculated 3D reconstruction shows more structural details and contains less noise than the map obtained by conventional Fourier-filtering based processing of the same 2D crystal images.

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

    DOEpatents

    Capone, Donald W.; Dusek, Joseph

    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.

  20. 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.

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

    PubMed

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

    2014-05-01

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

  2. Exploiting MIC architectures for the simulation of channeling of charged particles in crystals

    NASA Astrophysics Data System (ADS)

    Bagli, Enrico; Karpusenko, Vadim

    2016-08-01

    Coherent effects of ultra-relativistic particles in crystals is an area of science under development. DYNECHARM + + is a toolkit for the simulation of coherent interactions between high-energy charged particles and complex crystal structures. The particle trajectory in a crystal is computed through numerical integration of the equation of motion. The code was revised and improved in order to exploit parallelization on multi-cores and vectorization of single instructions on multiple data. An Intel Xeon Phi card was adopted for the performance measurements. The computation time was proved to scale linearly as a function of the number of physical and virtual cores. By enabling the auto-vectorization flag of the compiler a three time speedup was obtained. The performances of the card were compared to the Dual Xeon ones.

  3. 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.

  4. Particle trapping and transport achieved via an adjustable acoustic field above a phononic crystal plate

    NASA Astrophysics Data System (ADS)

    Wang, T.; Ke, M.; Qiu, C.; Liu, Z.

    2016-06-01

    We present the design for an acoustic system that can achieve particle trapping and transport using the acoustic force field above a phononic crystal plate. The phononic crystal plate comprised a thin brass plate with periodic slits alternately embedded with two kinds of elastic inclusions. Enhanced acoustic transmission and localized acoustic fields were achieved when the structure was excited by external acoustic waves. Because of the different resonant frequencies of the two elastic inclusions, the acoustic field could be controlled via the working frequency. Particles were transported between adjacent traps under the influence of the adjustable acoustic field. This device provides a new and versatile avenue for particle manipulation that would complement other means of particle manipulation.

  5. Fabrication of colloidal crystals with defined and complex structures via layer-by-layer transfer.

    PubMed

    Li, Wei; Yang, Bai; Wang, Dayang

    2008-12-01

    A new and versatile way--using poly(dimethylsiloxane) (PDMS) sheets to layer-by-layer (LbL) transfer hexagonal-close-packed particle monolayers from preformed colloidal crystals and stack them on substrates-has been demonstrated to create colloidal crystals. This approach allows LbL control of the thickness of the resulting crystals and especially of the size and the packing structure of the particles in each layer. Furthermore, it also allows fabrication of binary colloidal crystals over large areas by deformation of the PDMS sheets during LbL transfer. Two new binary crystals-one composed of identically sized particles but in different densities and the other of a nonclose-packed monolayer of large particles and a close-packed monolayer of small particles-were created, which are hard grown by other colloidal crystallization techniques developed thus far. PMID:18986179

  6. Pair distribution function and structure factor of spherical particles

    SciTech Connect

    Howell, Rafael C.; Proffen, Thomas; Conradson, Steven D.

    2006-03-01

    The availability of neutron spallation-source instruments that provide total scattering powder diffraction has led to an increased application of real-space structure analysis using the pair distribution function. Currently, the analytical treatment of finite size effects within pair distribution refinement procedures is limited. To that end, an envelope function is derived which transforms the pair distribution function of an infinite solid into that of a spherical particle with the same crystal structure. Distributions of particle sizes are then considered, and the associated envelope function is used to predict the particle size distribution of an experimental sample of gold nanoparticles from its pair distribution function alone. Finally, complementing the wealth of existing diffraction analysis, the peak broadening for the structure factor of spherical particles, expressed as a convolution derived from the envelope functions, is calculated exactly for all particle size distributions considered, and peak maxima, offsets, and asymmetries are discussed.

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

    NASA Astrophysics Data System (ADS)

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

    1992-09-01

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

  8. Dynamics of particles and defects on spherical crystals

    NASA Astrophysics Data System (ADS)

    Guerra, Rodrigo; Kelleher, Colm; Chaikin, Paul

    Repulsive particles confined to two dimensions can form nearly perfect crystals that melt via the well-know Kosterlitz-Thouless two-step process. By contrast, when identical particles are confined to the surface of a sphere, the curvature and topology of the surface distorts the crystal lattice and forces it to accommodate point-like disclinations and chains of dislocations. Extensive numerical and theoretical investigation has shown that these extended scars are intrinsic to the ground-state-energy configuration of these packings, as they relieve some of the stress induced by the curvature of the surface. Nevertheless, the effect of these defects on the kinetics and phase behavior of spherical crystals is not at all well understood. Here we present results of computer simulations and experiments that suggest that these scars facilitate the motion of particles close to them and fundamentally alter the nature of the mobility and liquid-to-solid transition of packings of particles confined to spherical surfaces.

  9. Structural characterization of thin film photonic crystals

    SciTech Connect

    Subramania, G.; Biswas, R.; Constant, K.; Sigalas, M. M.; Ho, K. M.

    2001-06-15

    We quantitatively analyze the structure of thin film inverse-opal photonic crystals composed of ordered arrays of air pores in a background of titania. Ordering of the sphere template and introduction of the titania background were performed simultaneously in the thin film photonic crystals. Nondestructive optical measurements of backfilling with high refractive index liquids, angle-resolved reflectivity, and optical spectroscopy were combined with band-structure calculations. The analysis reveals a thin film photonic crystal structure with a very high filling fraction (92{endash}94%) of air and a substantial compression along the c axis ({similar_to}22{endash}25%).

  10. Budded baculovirus particle structure revisited.

    PubMed

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

    2016-02-01

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

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

    PubMed Central

    2011-01-01

    Characterizing nanoparticle dispersions and understanding the effect of parameters that alter dispersion properties are important for both environmental applications and toxicity investigations. The role of particle surface area, primary particle size, and crystal phase on TiO2 nanoparticle dispersion properties is reported. Hydrodynamic size, zeta potential, and isoelectric point (IEP) of ten laboratory synthesized TiO2 samples, and one commercial Degussa TiO2 sample (P25) dispersed in different solutions were characterized. Solution ionic strength and pH affect titania dispersion properties. The effect of monovalent (NaCl) and divalent (MgCl2) inert electrolytes on dispersion properties was quantified through their contribution to ionic strength. Increasing titania particle surface area resulted in a decrease in solution pH. At fixed pH, increasing the particle surface area enhanced the collision frequency between particles and led to a higher degree of agglomeration. In addition to the synthesis method, TiO2 isoelectric point was found to be dependent on particle size. As anatase TiO2 primary particle size increased from 6 nm to 104 nm, its IEP decreased from 6.0 to 3.8 that also results in changes in dispersion zeta potential and hydrodynamic size. In contrast to particle size, TiO2 nanoparticle IEP was found to be insensitive to particle crystal structure. PMID:27502650

  12. Fabrication and characterization of non-Brownian particle-based crystals.

    PubMed

    Lash, Melissa H; Fedorchak, Morgan V; Little, Steven R; McCarthy, Joseph J

    2015-01-27

    Particle-based crystals have been explored in the literature for applications in molecular electronics, photonics, sensors, and drug delivery. However, much of the research on these crystals has been focused on particles of nano- and submicrometer dimensions (so-called colloidal crystals) with limited attention directed toward building blocks with dimensions ranging from tens to hundreds of micrometers. This can be attributed, in part, to the fact that the underlying thermal effects in these larger systems typically cannot naturally overcome kinetic barriers at the meso- and macroscales so that many of the methods used for nanoscale particle assembly cannot be directly applied to larger components, as they become kinetically arrested in nonequilibrium states. In this work, ultrasonic agitation is being explored as a means of allowing large, non-Brownian microparticles (18-750 μm) to overcome the kinetic barriers to packing in the creation of close-packed, highly ordered, crystalline structures. In addition, we study how the energy input affects bulk particle behavior and describe several new ways to characterize particle-based crystals made from microparticles.

  13. Resonant optical propulsion of a particle inside a hollow-core photonic crystal fiber.

    PubMed

    Maslov, A V

    2016-07-01

    Resonant propulsion of small nonresonant particles inside metal waveguides due to the formation of resonant states by the guided modes below their cutoffs has been predicted in the past. Here it is shown that stable resonant propulsion exists in hollow-core photonic crystal fibers, which are all-dielectric structures and are a major platform for various photonic applications. Specific features of the resonant propulsion are discussed together with the fiber design issues. The results may enable power-efficient transport of particles over long distances, particle sorting, and sensitive detection.

  14. Pattern information extraction from crystal structures

    NASA Astrophysics Data System (ADS)

    Okuyan, Erhan; Güdükbay, Uğur; Gülseren, Oğuz

    2007-04-01

    Determining the crystal structure parameters of a material is an important issue in crystallography and material science. Knowing the crystal structure parameters helps in understanding the physical behavior of material. It can be difficult to obtain crystal parameters for complex structures, particularly those materials that show local symmetry as well as global symmetry. This work provides a tool that extracts crystal parameters such as primitive vectors, basis vectors and space groups from the atomic coordinates of crystal structures. A visualization tool for examining crystals is also provided. Accordingly, this work could help crystallographers, chemists and material scientists to analyze crystal structures efficiently. Program summaryTitle of program: BilKristal Catalogue identifier: ADYU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYU_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: None Programming language used: C, C++, Microsoft .NET Framework 1.1 and OpenGL Libraries Computer: Personal Computers with Windows operating system Operating system: Windows XP Professional RAM: 20-60 MB No. of lines in distributed program, including test data, etc.:899 779 No. of bytes in distributed program, including test date, etc.:9 271 521 Distribution format:tar.gz External routines/libraries: Microsoft .NET Framework 1.1. For visualization tool, graphics card driver should also support OpenGL Nature of problem: Determining crystal structure parameters of a material is a quite important issue in crystallography. Knowing the crystal structure parameters helps to understand physical behavior of material. For complex structures, particularly, for materials which also contain local symmetry as well as global symmetry, obtaining crystal parameters can be quite hard. Solution method: The tool extracts crystal parameters such as primitive vectors, basis vectors and identify the space group from

  15. Observations of specular reflective particles and layers in crystal clouds.

    PubMed

    Balin, Yurii S; Kaul, Bruno V; Kokhanenko, Grigorii P; Penner, Ioganes E

    2011-03-28

    In the present article, results of observations of high crystal clouds with high spatial and temporal resolution using the ground-based polarization LOSA-S lidar are described. Cases of occurrence of specularly reflective layers formed by particles oriented predominantly in the horizontal plane are demonstrated. Results of measuring echo-signal depolarization are compared for linear and circular polarization states of the initial laser beam.

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

    SciTech Connect

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

    2013-11-07

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

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

    PubMed

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

    2004-04-01

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

  18. Structures of cyano-biphenyl liquid crystals

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

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

  19. Two-Dimensional Crystal Structure Formed by Two Components of DNA Nanoparticles on a Substrate

    NASA Astrophysics Data System (ADS)

    Katsuno, Hiroyasu; Maegawa, Yuya; Sato, Masahide

    2016-07-01

    We study the two-dimensional crystal structure of two components of DNA nanoparticles on a substrate by Brownian dynamics simulation. We use the Lennard-Jones potential as the interaction potential between particles and assume that the interaction length between different types of particles, σAB, is smaller than that between the same types of particles, σ. Two types of particles form an alloy structure. With decreasing σAB/σ, the crystal structure changes from a triangular lattice, to a square lattice, a honeycomb lattice, a rectangular lattice, and a triangular lattice.

  20. 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.

  1. 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

  2. Crystal engineering: From design of crystal structures to fabrication of composite crystals

    NASA Astrophysics Data System (ADS)

    Luo, Tzy-Jiun Mark

    This thesis reports how to design and control co-crystal structures from a kinetic point of view, and demonstrates the control of crystal morphology through understanding the kinetics and crystal structures. In chapter one, the in-situ atomic force microscope (AFM) was utilized to investigate how side chain on a glycine 2,5-diketopiperazine (GLYDKP) backbone can affect the assembly of GLYDKP, and showed that methyl groups cause larger energy barrier for crystallization. Because the introduction of functional group on the side chain could inevitably slow down the assembly process, a different approach should be considered. Chapter two shows that formic acid at low concentration can accelerate the assembly process without incorporating into the crystal structure. Because formic acid only crystallizes with GLYDKP in concentrated solution, these results prove that co-crystallization is a better method for incorporating functionalized molecules into a solid than direct modification of molecule itself. Chapter three focuses on the rational design of GLYDKP cocrystals by utilizing the observation found in chapter two. Structure of GLYDKP and formic acid crystal was analyzed to search possible guest molecules for cocrystal studies. This method successfully identified eleven molecules that crystallize with GLYDKP, and proved that crystal structure can be controlled through weak interactions such as C-H•••O=C and C-H•••Cl interactions. Chapter four and chapter five explore the possibility of using self-assembled process to control morphology of crystals and surface epitaxy. Metal(II) bis(imidazolium 2,b-pyridinedicarboxylate) complexes were chosen and two morphologies associated with different metal ions were found: rhombohedral (Type I) and rectangular (Type II) crystals. In this study, an additive was found to change the morphology of crystal from type I to type II, and then methods of producing various shapes of composite crystals were also established. These

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

    PubMed

    Makde, Ravindra D; Tan, Song

    2013-11-15

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

  4. 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.

  5. Crystallization and Structure Analysis of Membrane Proteins

    NASA Astrophysics Data System (ADS)

    Newman, Richard

    In recent years, there has been great progress in the determination of high-resolution three-dimensional (3D) structures of membrane proteins. The first major breakthrough came with the crystallization (1) and X-ray crystallography (2,3) of the bacterial photosynthetic reaction center (see refs. 4 and 5 for reviews). The structure of another, entirely different membrane protein, the bacterial outer membrane porin from Rhodobacter capsulatus, has now been determined by X-ray crystallography (6). Recent results by electron crystallography of two-dimensional (2D) crystals have been most encouraging. The high-resolution 3D structure of bacteriorhodopsin (7) plant light-harvesting complex (8) and projection maps of several other membrane proteins at similar resolutions (9-11) have been obtained by this technique. Electron crystallography seems particularly appropriate for membrane proteins that are prone to form 2D crystals, and it is hoped that many more structures will be determined in this way.

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

    NASA Astrophysics Data System (ADS)

    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.

  7. Polypeptide-Coated Silica Particles Dispersed in Lyotropic Liquid Crystals of the Same Polypeptide.

    PubMed

    Rosu, Cornelia; Balamurugan, Sreelatha; Cueto, Rafael; Roy, Amitava; Russo, Paul S

    2016-07-28

    When a particle is introduced into a liquid crystal (LC), it distorts the LC director field, leading to new arrangements of the particles. This phenomenon is ordinarily studied using >100 nm particles and ∼2 nm mesogens. Usually the particle surface and mesogens are chemically distinct, which adds an enthalpic effect, even though the more interesting interactions are entropic. To raise the structures to the visible regime, while minimizing chemical differences between the particle surface and mesogen, silica particles coated with an α-helical polypeptide have been prepared and dispersed in lyotropic polypeptide LCs. The polypeptide is poly(γ-stearyl-α,l-glutamate) or PSLG. To make the particles easy to manipulate and easy to find, the silica core included superparamagnetic magnetite (Fe3O4) and covalently attached dye. Two methods were used to place polypeptides on these magnetic, fluorescent particles: a multistep grafting-to approach in which whole polypeptides were attached and a one-pot grafting-from approach in which the polymerization of the monomers was initiated from the particle surface. These approaches resulted in sparse and dense surface coverages, respectively. The influence of surface curvature and polypeptide molecular weight on the design of sparsely covered particles was investigated using the grafting-to approach. The aggregated grafting-from particles when freshly dispersed in a PSLG/solvent matrix disrupted the orientation of the characteristic cholesteric LC (ChLC) phase directors. In time, the hybrid particles were expelled from some domains, enabling the return of the familiar helical twist of the cholesteric mesophase. The sparsely coated grafting-to hybrid particles when inserted in the PSLG/solvent matrix assembled into stable islet-like formations that could not be disrupted even by an external magnetic field. The bulk particles aligned in chains that were easily manipulated by a magnetic field. These results indicate that

  8. Slip flow through colloidal crystals of varying particle diameter.

    PubMed

    Rogers, Benjamin J; Wirth, Mary J

    2013-01-22

    Slip flow of water through silica colloidal crystals was investigated experimentally for eight different particle diameters, which have hydraulic channel radii ranging from 15 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 10(10) 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.

  9. 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

  10. Crystal structure of levomepromazine maleate.

    PubMed

    Gál, Gyula Tamás; May, Nóra Veronika; Bombicz, Petra

    2016-05-01

    The asymmetric unit of the title salt, C19H25N2OS(+)·C4H3O4 (-) [systematic name: (S)-3-(2-meth-oxy-pheno-thia-zin-10-yl)-N,N,2-tri-methyl-propanaminium hydrogen maleate], comprises two (S)-levomepromazine cations and two hydrogen maleate anions. The conformations of the two cations are similar. The major difference relates to the orientation of the meth-oxy substituent at the pheno-thia-zine ring system. The crystal components form a three-dimensional supra-molecular network via N-H⋯O, C-H⋯O and C-H⋯π inter-actions. A comparison of the conformations of the levomepromazine cations with those of the neutral mol-ecule and similar protonated mol-ecules reveals significant conformational flexibility of the pheno-thia-zine ring system and the substituent at the pheno-thia-zine N atom. PMID:27308001

  11. Engineering the structures and shapes of colloidal particles

    NASA Astrophysics Data System (ADS)

    Lu, Yu

    Well-defined colloidal particles have wide applications in optics, electronics, catalysis and diagnostics. Considerable effort has recently been devoted to the design and controlled fabrication of colloidal particles with various functionalities. Effective strategies to build tailored colloidal particles reliably and predictably are required in order to meet the ever-increasing demands placed on colloidal materials science. The properties of colloidal particles strongly depend on their size, composition, shape, and spatial organization. This research will develop a few strategies to modify these parameters in producing new types of colloidal particles for a number of applications. The first goal is to coat colloidal particles of metals, metal oxides, and polymers with thin shells of different materials, such as oxides and polymers. The obtained core-shell materials generally have enhanced or specific performance due to the combined properties and/or structuring effects of the components. They will be used as new building blocks in constructing plasmonic waveguides and three-dimensional (3D) photonic crystals. The second goal of this research is to fabricate nonspherical colloidal particles with uniform sizes and shapes. Both direct and indirect methods will be used in producing monodispersed nonspherical colloidal samples. Self-assembly approaches will be explored to organize the nonspherical building blocks into 3D highly ordered lattices. The optical properties of the crystals with nonspherical lattice points will be also studied.

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

    USGS Publications Warehouse

    Evans, H.T.; 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

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

    PubMed

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

    2006-07-14

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

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

    PubMed

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

    2006-07-14

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

  15. 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.

  16. Particle beam and crabbing and deflecting structure

    DOEpatents

    Delayen, Jean

    2011-02-08

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

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

    PubMed

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

    2012-07-01

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

  18. Crystal structure of canagliflozin hemihydrate

    PubMed Central

    Liu, Kai-Hang; Gu, Jian-Ming; Hu, Xiu-Rong; Tang, Gu-Ping

    2016-01-01

    There are two canagliflozin mol­ecules (A and B) and one water mol­ecule in the asymmetric unit of the title compound, C24H25FO5S·0.5H2O [systematic name: (2S,3R,4R,5S,6R)-2-(3-{[5-(4-fluoro­phen­yl)thio­phen-2-yl]meth­yl}-4-methylphen­yl)-6-(hy­droxy­meth­yl)-3,4,5,6-tetra­hydro-2H-pyran-3,4,5-triol hemihydrate]. The dihedral angles between the methyl­benzene and thio­phene rings are 115.7 (4) and 111.7 (4)°, while the dihedral angles between the fluoro­benzene and thio­phene rings are 24.2 (6) and 20.5 (9)° in mol­ecules A and B, respectively. The hydro­pyran ring exhibits a chair conformation in both canagliflozin mol­ecules. In the crystal, the canagliflozin mol­ecules and lattice water mol­ecules are connected via O—H⋯O hydrogen bonds into a three-dimensional supra­molecular architecture. PMID:27308030

  19. Crystal structure of canagliflozin hemihydrate.

    PubMed

    Liu, Kai-Hang; Gu, Jian-Ming; Hu, Xiu-Rong; Tang, Gu-Ping

    2016-05-01

    There are two canagliflozin mol-ecules (A and B) and one water mol-ecule in the asymmetric unit of the title compound, C24H25FO5S·0.5H2O [systematic name: (2S,3R,4R,5S,6R)-2-(3-{[5-(4-fluoro-phen-yl)thio-phen-2-yl]meth-yl}-4-methylphen-yl)-6-(hy-droxy-meth-yl)-3,4,5,6-tetra-hydro-2H-pyran-3,4,5-triol hemihydrate]. The dihedral angles between the methyl-benzene and thio-phene rings are 115.7 (4) and 111.7 (4)°, while the dihedral angles between the fluoro-benzene and thio-phene rings are 24.2 (6) and 20.5 (9)° in mol-ecules A and B, respectively. The hydro-pyran ring exhibits a chair conformation in both canagliflozin mol-ecules. In the crystal, the canagliflozin mol-ecules and lattice water mol-ecules are connected via O-H⋯O hydrogen bonds into a three-dimensional supra-molecular architecture. PMID:27308030

  20. Computing stoichiometric molecular composition from crystal structures

    PubMed Central

    Gražulis, Saulius; Merkys, Andrius; Vaitkus, Antanas; Okulič-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

  1. Charged-particle spectroscopy in organic semiconducting single crystals

    NASA Astrophysics Data System (ADS)

    Ciavatti, A.; Sellin, P. J.; Basiricò, L.; Fraleoni-Morgera, A.; Fraboni, B.

    2016-04-01

    The use of organic materials as radiation detectors has grown, due to the easy processability in liquid phase at room temperature and the possibility to cover large areas by means of low cost deposition techniques. Direct charged-particle detectors based on solution-grown Organic Semiconducting Single Crystals (OSSCs) are shown to be capable to detect charged particles in pulse mode, with very good peak discrimination. The direct charged-particle detection in OSSCs has been assessed both in the planar and in the vertical axes, and a digital pulse processing algorithm has been used to perform pulse height spectroscopy and to study the charge collection efficiency as a function of the applied bias voltage. Taking advantage of the charge spectroscopy and the good peak discrimination of pulse height spectra, an Hecht-like behavior of OSSCs radiation detectors is demonstrated. It has been possible to estimate the mobility-lifetime value in organic materials, a fundamental parameter for the characterization of radiation detectors, whose results are equal to μτcoplanar = (5 .5 ± 0.6 ) × 10-6 cm2/V and μτsandwich = (1 .9 ± 0.2 ) × 10-6 cm2/V, values comparable to those of polycrystalline inorganic detectors. Moreover, alpha particles Time-of-Flight experiments have been carried out to estimate the drift mobility value. The results reported here indicate how charged-particle detectors based on OSSCs possess a great potential as low-cost, large area, solid-state direct detectors operating at room temperature. More interestingly, the good detection efficiency and peak discrimination observed for charged-particle detection in organic materials (hydrogen-rich molecules) are encouraging for their further exploitation in the detection of thermal and high-energy neutrons.

  2. 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

  3. 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 μm), lipid composition (stearin versus olein) and cooling rate (1 versus 10°C min(-1)) had an influence on the structural properties. Five crystal polymorphs (α, β'1, β'2, β1, and β2) 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.

  4. 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).

  5. Crystal structure of the eukaryotic ribosome.

    PubMed

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

    2010-11-26

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

  6. 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.

  7. 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.

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

    SciTech Connect

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

    2008-04-01

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

  9. Crystal structure of monobasic sodium tartrate monohydrate

    SciTech Connect

    Titaeva, E. K. Somov, N. V.; Portnov, V. N.; Titaev, D. N.

    2015-01-15

    Crystals of a new polymorphic modification of monobasic sodium tartrate monohydrate NaHC{sub 4}H{sub 4}O{sub 6} · H{sub 2}O have been grown in a metasilicate gel. Their atomic structure is solved by X-ray diffraction.

  10. Crystal structure of methane oxidation enzyme determined

    SciTech Connect

    Baum, R.

    1994-01-10

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

  11. Structure analysis on synthetic emerald crystals

    NASA Astrophysics Data System (ADS)

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

    2013-05-01

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

  12. 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.

  13. 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.

  14. 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.

  15. Phase separation of two-dimensional Coulombic crystals of mesoscale dipolar particles from mesoscale polarizable ``solvent''

    NASA Astrophysics Data System (ADS)

    Kaufman, George K.; Reches, Meital; Thomas, Samuel W.; Feng, Ji; Shaw, Bryan F.; Whitesides, George M.

    2009-01-01

    This letter describes the formation of two-dimensional (2D) crystals of dipolar particles (TN) made of electrostatically charged, joined, millimeter-scale Teflon (T) and nylon-6,6 (N) spheres, and the separation of these crystals, as a distinct phase, from a mixture of TN and similar, capacitively charged particles that were coated with gold (Au2). The extent of separation increased with increasing amplitude of agitation, and with decreasing density of particles. Above a threshold in the amplitude of agitation, the crystals broke apart and the particles remixed. This system is a 2D model of the nucleation of crystals of polar molecules in a polarizable liquid.

  16. Crystal structure refinement from electron diffraction data

    SciTech Connect

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

    2008-05-15

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

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

    PubMed Central

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

    2011-01-01

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

  18. 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.

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

    PubMed Central

    Shen, Tongye; Wolynes, Peter G.

    2004-01-01

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

  20. Persistent hydrogen bonding in polymorphic crystal structures.

    PubMed

    Galek, Peter T A; Fábián, László; Allen, Frank H

    2009-02-01

    The significance of hydrogen bonding and its variability in polymorphic crystal structures is explored using new automated structural analysis methods. The concept of a chemically equivalent hydrogen bond is defined, which may be identified in pairs of structures, revealing those types of bonds that may persist, or not, in moving from one polymorphic form to another. Their frequency and nature are investigated in 882 polymorphic structures from the Cambridge Structural Database. A new method to compare conformations of equivalent molecules is introduced and applied to derive distinct subsets of conformational and packing polymorphs. The roles of chemical functionality and hydrogen-bond geometry in persistent interactions are systematically explored. Detailed structural comparisons reveal a large majority of persistent hydrogen bonds that are energetically crucial to structural stability. PMID:19155561

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

    PubMed Central

    Schmidt-Krey, Ingeborg; Rubinstein, John L.

    2010-01-01

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

  2. The crystal structure of methane phase III

    NASA Astrophysics Data System (ADS)

    Neumann, Marcus A.; Press, Werner; Nöldeke, Christian; Asmussen, Bernd; Prager, Michael; Ibberson, Richard M.

    2003-07-01

    Methane is the simplest organic molecule, and like many supposedly simple molecular materials it has a rich phase diagram. While crystal structures could be determined for two of the solid phases, that of the low temperature phase III remained unsolved. Using high-resolution neutron powder diffraction and a direct-space Monte Carlo simulated annealing approach, this fundamental structure has now finally been solved. It is orthorhombic with space group Cmca, and 16 molecules in the unit cell. The structure is closely related to that of phase II, yet is no subgroup of it.

  3. Coagulation factor XII protease domain crystal structure

    PubMed Central

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

    2015-01-01

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

  4. Novel Approach for Clustering Zeolite Crystal Structures.

    PubMed

    Lach-Hab, M; Yang, S; Vaisman, I I; Blaisten-Barojas, E

    2010-04-12

    Informatics approaches play an increasingly important role in the design of new materials. In this work we apply unsupervised statistical learning for identifying four framework-type attractors of zeolite crystals in which several of the zeolite framework types are grouped together. Zeolites belonging to these super-classes manifest important topological, chemical and physical similarities. The zeolites form clusters located around four core framework types: LTA, FAU, MFI and the combination of EDI, HEU, LTL and LAU. Clustering is performed in a 9-dimensional space of attributes that reflect topological, chemical and physical properties for each individual zeolite crystalline structure. The implemented machine learning approach relies on hierarchical top-down clustering approach and the expectation maximization method. The model is trained and tested on ten partially independent data sets from the FIZ/NIST Inorganic Crystal Structure Database.

  5. Crystal structure of an archaeal actin homolog.

    PubMed

    Roeben, Annette; Kofler, Christine; Nagy, István; Nickell, Stephan; Hartl, F Ulrich; Bracher, Andreas

    2006-04-21

    Prokaryotic homologs of the eukaryotic structural protein actin, such as MreB and ParM, have been implicated in determination of bacterial cell shape, and in the segregation of genomic and plasmid DNA. In contrast to these bacterial actin homologs, little is known about the archaeal counterparts. As a first step, we expressed a predicted actin homolog of the thermophilic archaeon Thermoplasma acidophilum, Ta0583, and determined its crystal structure at 2.1A resolution. Ta0583 is expressed as a soluble protein in T.acidophilum and is an active ATPase at physiological temperature. In vitro, Ta0583 forms sheets with spacings resembling the crystal lattice, indicating an inherent propensity to form filamentous structures. The fold of Ta0583 contains the core structure of actin and clearly belongs to the actin/Hsp70 superfamily of ATPases. Ta0583 is approximately equidistant from actin and MreB on the structural level, and combines features from both eubacterial actin homologs, MreB and ParM. The structure of Ta0583 co-crystallized with ADP indicates that the nucleotide binds at the interface between the subdomains of Ta0583 in a manner similar to that of actin. However, the conformation of the nucleotide observed in complex with Ta0583 clearly differs from that in complex with actin, but closely resembles the conformation of ParM-bound nucleotide. On the basis of sequence and structural homology, we suggest that Ta0583 derives from a ParM-like actin homolog that was once encoded by a plasmid and was transferred into a common ancestor of Thermoplasma and Ferroplasma. Intriguingly, both genera are characterized by the lack of a cell wall, and therefore Ta0583 could have a function in cellular organization.

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

    PubMed

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

    2015-07-01

    Systems of soft-core particles interacting via a two-scale potential are studied. The potential is responsible for peaks in the structure factor of the liquid state at two different but comparable length scales and a similar bimodal structure is evident in the dispersion relation. Dynamical density functional theory in two dimensions is used to identify two unusual states of this system: a crystal-liquid state, in which the majority of the particles are located on lattice sites but a minority remains free and so behaves like a liquid, and a 12-fold quasicrystalline state. Both are present even for deeply quenched liquids and are found in a regime in which the liquid is unstable with respect to modulations on the smaller scale only. As a result, the system initially evolves towards a small-scale crystal state; this state is not a minimum of the free energy, however, and so the system subsequently attempts to reorganize to generate the lower-energy larger-scale crystals. This dynamical process generates a disordered state with quasicrystalline domains and takes place even when this large scale is linearly stable, i.e., it is a nonlinear process. With controlled initial conditions, a perfect quasicrystal can form. The results are corroborated using Brownian dynamics simulations. PMID:26274178

  7. 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.

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

    SciTech Connect

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

    2010-12-15

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

  9. Characterization of the interior structure of synthetic diamond particles

    NASA Astrophysics Data System (ADS)

    Gu, Jiteng; Huang, Kai; Fang, Keming; Wang, Xiao; Li, Zhihai; Si, Zhihua

    2016-10-01

    TEM observation was originally presented about the interior microstructure of a diamond particle, and three different kinds of carbon allotropes were found existing in diamond. The synthetic diamond particle was constituted of many tiny columnar monocrystals with the approximate diameter of 10 nm and length of more than several hundred nanometer. These nanocrystals were assembled into clusters along the <111> lattice plane, while between these nanocrystals there were the amorphous carbons filled with, and this study originally revealed the microstructure of the synthetic diamond particle. Internal structure with crystal defects was also demonstrated clearly. These findings show the interior microstructure more explicitly, which may give useful inspiration to the technical progress of diamond synthesis.

  10. 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)

  11. 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

  12. Lagrangian coherent structures and inertial particle dynamics

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  13. Lagrangian coherent structures and inertial particle dynamics.

    PubMed

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

    2016-03-01

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

  14. Determining crystal structures through crowdsourcing and coursework

    NASA Astrophysics Data System (ADS)

    2016-09-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

  15. Determining crystal structures through crowdsourcing and coursework.

    PubMed

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A; Cooper, Seth; Flatten, Jeff; Rogawski, David S; Koropatkin, Nicole M; Hailu, Tsinatkeab T; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S; Chapman, Matthew R; Sikkema, Andrew P; Skiba, Meredith A; Maloney, Finn P; Beinlich, Felix R M; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C A

    2016-09-16

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

  16. Determining crystal structures through crowdsourcing and coursework.

    PubMed

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A; Cooper, Seth; Flatten, Jeff; Rogawski, David S; Koropatkin, Nicole M; Hailu, Tsinatkeab T; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S; Chapman, Matthew R; Sikkema, Andrew P; Skiba, Meredith A; Maloney, Finn P; Beinlich, Felix R M; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C A

    2016-01-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality. PMID:27633552

  17. Determining crystal structures through crowdsourcing and coursework

    PubMed Central

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Roque, Paulo Sergio Silveira Belo Nascimento; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

    2016-01-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality. PMID:27633552

  18. 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.

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

    PubMed

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

    2015-09-01

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

  20. The crystallization of biological macromolecules under microgravity: a way to more accurate three-dimensional structures?

    PubMed

    Lorber, Bernard

    2002-09-23

    The crystallization of proteins and other biological particles (including nucleic acids, nucleo-protein complexes and large assemblies such as nucleosomes, ribosomal subunits or viruses) in a microgravity environment can produce crystals having lesser defects than crystals prepared under normal gravity on earth. Such microgravity-grown crystals can diffract X-rays to a higher resolution and have a lower mosaic spread. The inferred electron density maps can be richer in details owing to which more accurate three-dimensional structure models can be built. Major results reported in this field of research are reviewed. Novel ones obtained with the Advanced Protein Crystallization Facility are presented. For structural biology, practical applications and implications associated with crystallization and crystallography onboard the International Space Station are discussed.

  1. 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.

  2. 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.

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

    PubMed

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

    2015-01-01

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

  4. 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.

  5. Crystal Structure Prediction from First Principles: The Crystal Structures of Glycine

    PubMed Central

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

    2015-01-01

    Here we present the results of our unbiased searches of glycine polymorphs obtained using the Genetic Algorithms search implemented in 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. PMID:25843964

  6. Flowing crystals: nonequilibrium structure of foam.

    PubMed

    Garstecki, Piotr; Whitesides, George M

    2006-07-14

    Bubbles pushed through a quasi-two-dimensional channel self-organize into a variety of periodic lattices. The structures of these lattices correspond to local minima of the interfacial energy. The "flowing crystals" are long-lived metastable states, a small subset of possible local minima of confined quasi-two-dimensional foams [P. Garstecki and G. M. Whitesides, Phys. Rev. E 73, 031603 (2006)10.1103/PhysRevE.73.031603]. Experimental results suggest that the choice of the structures that we observe is dictated by the dynamic stability of the cyclic processes of their formation. Thus, the dynamic system that we report provides a unique example of nonequilibrium self-organization that results in structures that correspond to local minima of the relevant energy functional. PMID:16907453

  7. Crystal structure of plant photosystem I

    NASA Astrophysics Data System (ADS)

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

    2003-12-01

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

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

    PubMed

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

    2014-08-01

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

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

    PubMed

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

    2014-08-01

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

  10. Crystal structure of a DNA catalyst.

    PubMed

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

    2016-01-14

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

  11. Crystal structure of a DNA catalyst.

    PubMed

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

    2016-01-14

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

  12. 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.

  13. Crystal structure of 2,2-dimethyl succinic acid.

    PubMed

    Ozcan, Yusuf; Osmanoğlu, Semsettin; Ide, Semra

    2003-08-01

    The title compound crystallizes triclinically in space group of P1. The C2-COOH and C3-COOH molecular groups are planar. The crystal structure is stabilized by the formation of intermolecular (O-HO) hydrogen bonds. PMID:12945684

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

    DOE PAGES

    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

  15. Self-assembly patterning of colloidal crystals constructed from opal structure or NaCl structure.

    PubMed

    Masuda, Yoshitake; Itoh, Tetsuya; Itoh, Minoru; Koumoto, Kunihito

    2004-06-22

    We developed a novel self-assembly process to fabricate an orderly array of particle wires constructed from a close-packed colloidal crystal without preparation of patterned templates. A substrate was immersed vertically into a SiO2 colloidal solution, and the liquid surface moved downward upon evaporation of solution. Particles formed a mono-/multiparticle layer, which was cut by the periodic drop-off of solution. The orderly array of particle wires was successfully fabricated, showing the suitability of the self-assembly process for the fabrication of nano-/microstructures constructed from nano-/microparticles or blocks. The mechanism of the assembly process and control of thickness, width, and interval of particle wires were further discussed. Moreover, an array of particle wires constructed not from close-packed face-centered cubic (or hexagonal close packed) structure but from two kinds of particles was realized to fabricate an array of particle wires with NaCl structure by this self-assembly process.

  16. 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.

  17. Track-Structure Simulations for Charged Particles

    PubMed Central

    Dingfelder, Michael

    2013-01-01

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

  18. The measurement results of carbon ion beam structure extracted by bent crystal from U-70 accelerator

    NASA Astrophysics Data System (ADS)

    Afonin, A. G.; Barnov, E. V.; Britvich, G. I.; Chesnokov, Yu A.; Chirkov, P. N.; Durum, A. A.; Kostin, M. Yu; Maisheev, V. A.; Pitalev, V. I.; Reshetnikov, S. F.; Yanovich, A. A.; Nazhmudinov, R. M.; Kubankin, A. S.; Shchagin, A. V.

    2016-07-01

    The carbon ion +6C beam with energy 25 GeV/nucleon was extracted by bent crystal from the U-70 ring. The bent angle of silicon crystal was 85 mrad. About 2×105 particles for 109 circulated ions in the ring were observed in beam line 4a after bent crystal. Geometrical parameters, time structure and ion beam structure were measured. The ability of the bent monocrystal to extract and generate ion beam with necessary parameters for regular usage in physical experiments is shown in the first time.

  19. Crystal Structure of Human DNA Methyltransferase 1.

    PubMed

    Zhang, Zhi-Min; Liu, Shuo; Lin, Krystal; Luo, Youfu; Perry, John Jefferson; Wang, Yinsheng; Song, Jikui

    2015-07-31

    DNMT1 (DNA methyltransferase 1) is responsible for propagating the DNA methylation patterns during DNA replication. DNMT1 contains, in addition to a C-terminal methyltransferase domain, a large N-terminal regulatory region that is composed of an RFTS (replication foci targeting sequence) domain, a CXXC zinc finger domain and a pair of BAH (bromo adjacent homology) domains. The regulatory domains of DNMT1 mediate a network of protein-protein and protein-DNA interactions to control the recruitment and enzymatic activity of DNMT1. Here we report the crystal structure of human DNMT1 with all the structural domains (hDNMT1, residues 351-1600) in complex with S-adenosyl-l-homocysteine at 2.62Å resolution. The RFTS domain directly associates with the methyltransferase domain, thereby inhibiting the substrate binding of hDNMT1. Through structural analysis, mutational, biochemical and enzymatic studies, we further identify that a linker sequence between the CXXC and BAH1 domains, aside from its role in the CXXC domain-mediated DNMT1 autoinhibition, serves as an important regulatory element in the RFTS domain-mediated autoinhibition. In comparison with the previously determined structure of mouse DNMT1, this study also reveals a number of distinct structural features that may underlie subtle functional diversity observed for the two orthologues. In addition, this structure provides a framework for understanding the functional consequence of disease-related hDNMT1 mutations.

  20. The crystal structure of vyuntspakhite: A redetermination

    NASA Astrophysics Data System (ADS)

    Yakubovich, O. V.; Steele, I. M.

    2009-09-01

    The crystal structure of the mineral vyuntspakhite (Y, TR)6{Al2(OH)3[H1.48Si1.88O7][SiO4][SiO3(OH)]}2( a = 5.7551(11) Å, b = 14.752(3) Å, c = 15.906(4) Å, β = 96.046(4)°, sp. gr. P21/ n, Z = 2), which had been established earlier in the pseudo-unit cell, is redetermined by X-ray diffraction ( R = 0.040, T = 100 K). The redetermination of the structure shows that pronounced pseudotranslation along the axis c' = c/3 is associated with the fact that Y( TR) atoms are related by a 1/3 translation along the [001] direction. Most of the hydrogen atoms are located. The crystal-chemical function of hydrogen bonds is analyzed. In the unit cell of vyuntspakhite, the cationic layers consisting of edge-sharing (Y, TR) eight-vertex polyhedra alternate along the b axis with mixed anionic layers composed of isolated Si tetrahedra (orthotetrahedra), Si2O7 double-tetrahedra (diortho) groups, Al five-vertex polyhedra, and Al2O8 double-tetrahedra groups linked by shared vertices and through hydrogen bonding.

  1. Fine crystal structure of porous corundum ceramics

    NASA Astrophysics Data System (ADS)

    Grigoriev, M. V.; Kulkov, S. N.

    2011-05-01

    The microstructure of corundum ceramics based on powders with a varying grain size has been investigated. Both commercial alumina powders and those fabricated by denitration of aluminum salts in a high-frequency discharge plasma were used. An increase in the plasma-chemical Al2O3 powder content in the sample was found to change the pore structure of the corundum ceramics from a high-porosity ceramic skeleton with a well-developed system of channel-forming pores to ceramics with isolated pores. The change in the pore structure was observed for 50% porosity and caused an increase in the level of crystal lattice microdistortions. An increase in the sintering temperature from 1200 to 1650°C is shown to be responsible for a two-fold increase in the average crystallite size and for annealing of lattice defects along grain boundaries.

  2. Crystal structure of mammalian acid sphingomyelinase

    PubMed Central

    Gorelik, Alexei; Illes, Katalin; Heinz, Leonhard X.; Superti-Furga, Giulio; Nagar, Bhushan

    2016-01-01

    Acid sphingomyelinase (ASMase, ASM, SMPD1) converts sphingomyelin into ceramide, modulating membrane properties and signal transduction. Inactivating mutations in ASMase cause Niemann–Pick disease, and its inhibition is also beneficial in models of depression and cancer. To gain a better understanding of this critical therapeutic target, we determined crystal structures of mammalian ASMase in various conformations. The catalytic domain adopts a calcineurin-like fold with two zinc ions and a hydrophobic track leading to the active site. Strikingly, the membrane interacting saposin domain assumes either a closed globular conformation independent from the catalytic domain, or an open conformation, which establishes an interface with the catalytic domain essential for activity. Structural mapping of Niemann–Pick mutations reveals that most of them likely destabilize the protein's fold. This study sheds light on the molecular mechanism of ASMase function, and provides a platform for the rational development of ASMase inhibitors and therapeutic use of recombinant ASMase. PMID:27435900

  3. Crystal structure of mammalian acid sphingomyelinase.

    PubMed

    Gorelik, Alexei; Illes, Katalin; Heinz, Leonhard X; Superti-Furga, Giulio; Nagar, Bhushan

    2016-01-01

    Acid sphingomyelinase (ASMase, ASM, SMPD1) converts sphingomyelin into ceramide, modulating membrane properties and signal transduction. Inactivating mutations in ASMase cause Niemann-Pick disease, and its inhibition is also beneficial in models of depression and cancer. To gain a better understanding of this critical therapeutic target, we determined crystal structures of mammalian ASMase in various conformations. The catalytic domain adopts a calcineurin-like fold with two zinc ions and a hydrophobic track leading to the active site. Strikingly, the membrane interacting saposin domain assumes either a closed globular conformation independent from the catalytic domain, or an open conformation, which establishes an interface with the catalytic domain essential for activity. Structural mapping of Niemann-Pick mutations reveals that most of them likely destabilize the protein's fold. This study sheds light on the molecular mechanism of ASMase function, and provides a platform for the rational development of ASMase inhibitors and therapeutic use of recombinant ASMase. PMID:27435900

  4. 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.

  5. Structure, thermodynamics, and crystallization of amorphous hafnia

    SciTech Connect

    Luo, Xuhui; Demkov, Alexander A.

    2015-09-28

    We investigate theoretically amorphous hafnia using the first principles melt and quench method. We identify two types of amorphous structures of hafnia. Type I and type II are related to tetragonal and monoclinic hafnia, respectively. We find type II structure to show stronger disorder than type I. Using the phonon density of states, we calculate the specific heat capacity for type II amorphous hafnia. Using the nudged elastic band method, we show that the averaged transition barrier between the type II amorphous hafnia and monoclinic phase is approximately 0.09 eV/HfO{sub 2}. The crystallization temperature is estimated to be 421 K. The calculations suggest an explanation for the low thermal stability of amorphous hafnia.

  6. 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

  7. Crystal Structure of Human Nicotinamide Riboside Kinase

    SciTech Connect

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

    2007-01-01

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

  8. 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.

  9. Prediction of binary hard-sphere crystal structures.

    PubMed

    Filion, Laura; Dijkstra, Marjolein

    2009-04-01

    We present a method based on a combination of a genetic algorithm and Monte Carlo simulations to predict close-packed crystal structures in hard-core systems. We employ this method to predict the binary crystal structures in a mixture of large and small hard spheres with various stoichiometries and diameter ratios between 0.4 and 0.84. In addition to known binary hard-sphere crystal structures similar to NaCl and AlB2, we predict additional crystal structures with the symmetry of CrB, gammaCuTi, alphaIrV, HgBr2, AuTe2, Ag2Se, and various structures for which an atomic analog was not found. In order to determine the crystal structures at infinite pressures, we calculate the maximum packing density as a function of size ratio for the crystal structures predicted by our GA using a simulated annealing approach. PMID:19518387

  10. Structural Transitions in Cholesteric Liquid Crystal Droplets.

    PubMed

    Zhou, Ye; Bukusoglu, Emre; Martínez-González, José A; Rahimi, Mohammad; Roberts, Tyler F; Zhang, Rui; Wang, Xiaoguang; Abbott, Nicholas L; de Pablo, Juan J

    2016-07-26

    Confinement of cholesteric liquid crystals (ChLC) into droplets leads to a delicate interplay between elasticity, chirality, and surface energy. In this work, we rely on a combination of theory and experiments to understand the rich morphological behavior that arises from that balance. More specifically, a systematic study of micrometer-sized ChLC droplets is presented as a function of chirality and surface energy (or anchoring). With increasing chirality, a continuous transition is observed from a twisted bipolar structure to a radial spherical structure, all within a narrow range of chirality. During such a transition, a bent structure is predicted by simulations and confirmed by experimental observations. Simulations are also able to capture the dynamics of the quenching process observed in experiments. Consistent with published work, it is found that nanoparticles are attracted to defect regions on the surface of the droplets. For weak anchoring conditions at the nanoparticle surface, ChLC droplets adopt a morphology similar to that of the equilibrium helical phase observed for ChLCs in the bulk. As the anchoring strength increases, a planar bipolar structure arises, followed by a morphological transition to a bent structure. The influence of chirality and surface interactions are discussed in the context of the potential use of ChLC droplets as stimuli-responsive materials for reporting molecular adsorbates.

  11. 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

  12. Crystal structures of five 6-mercaptopurine derivatives.

    PubMed

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

    2016-03-01

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

  13. Crystal structure of strontium dinickel iron orthophosphate

    PubMed Central

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

    2015-01-01

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

  14. 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.

  15. 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

  16. The crystal structure Escherichia coli Spy.

    PubMed

    Kwon, Eunju; Kim, Dong Young; Gross, Carol A; Gross, John D; Kim, Kyeong Kyu

    2010-11-01

    Escherichia coli spheroplast protein y (EcSpy) is a small periplasmic protein that is homologous with CpxP, an inhibitor of the extracytoplasmic stress response. Stress conditions such as spheroplast formation induce the expression of Spy via the Cpx or the Bae two-component systems in E. coli, though the function of Spy is unknown. Here, we report the crystal structure of EcSpy, which reveals a long kinked hairpin-like structure of four α-helices that form an antiparallel dimer. The dimer contains a curved oval shape with a highly positively charged concave surface that may function as a ligand binding site. Sequence analysis reveals that Spy is highly conserved over the Enterobacteriaceae family. Notably, three conserved regions that contain identical residues and two LTxxQ motifs are placed at the horizontal end of the dimer structure, stabilizing the overall fold. CpxP also contains the conserved sequence motifs and has a predicted secondary structure similar to Spy, suggesting that Spy and CpxP likely share the same fold.

  17. Accurate crystal molecular dynamics simulations using particle-mesh-Ewald: RNA dinucleotides — ApU and GpC

    NASA Astrophysics Data System (ADS)

    Lee, Hsing; Darden, Thomas; Pedersen, Lee

    1995-09-01

    Long molecular dynamics (MD) simulations for two crystal RNA dinucleotides ApU (2.0 ns) and GpC (1.5 ns) were performed, starting from the crystallographic positions of all heavy atoms in the crystals. By employing the particle-mesh-Ewald algorithm [Darden et al., J. Chem. Phys. 98 (1993) 10089] to accommodate the long-range Coulomb interactions, highly accurate MD structures were obtained for both crystals. The instantaneous root-mean-square positional deviations of the heavy atoms equilibrate at approximately 0.4 Å for both systems, while the experimental and calculated temperature factors are comparable in size. These results describe the first successful crystal MD simulation of RNA molecules.

  18. 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.

  19. Crystal Structure of the VS ribozyme

    PubMed Central

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

    2015-01-01

    Varkud Satellite (VS) ribozyme mediates rolling circle replication of a plasmid found in the Neurospora mitochondria. We report crystal structures of this ribozyme at 3.1Å resolution, revealing an intertwined dimer formed by an exchange of substrate helices. Within 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 significance 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

  20. Exploring structural phase transitions of ion crystals

    PubMed Central

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

    2016-01-01

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

  1. Crystal structure of a snake venom cardiotoxin

    SciTech Connect

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

    1987-05-01

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

  2. Soot Aerosol Particles as Cloud Condensation Nuclei: from Ice Nucleation Activity to Ice Crystal Morphology

    NASA Astrophysics Data System (ADS)

    Pirim, Claire; Ikhenazene, Raouf; Ortega, Isamel Kenneth; Carpentier, Yvain; Focsa, Cristian; Chazallon, Bertrand; Ouf, François-Xavier

    2016-04-01

    Emissions of solid-state particles (soot) from engine exhausts due to incomplete fuel combustion is considered to influence ice and liquid water cloud droplet activation [1]. The activity of these aerosols would originate from their ability to be important centers of ice-particle nucleation, as they would promote ice formation above water homogeneous freezing point. Soot particles are reported to be generally worse ice nuclei than mineral dust because they activate nucleation at higher ice-supersaturations for deposition nucleation and at lower temperatures for immersion freezing than ratios usually expected for homogeneous nucleation [2]. In fact, there are still numerous opened questions as to whether and how soot's physico-chemical properties (structure, morphology and chemical composition) can influence their nucleation ability. Therefore, systematic investigations of soot aerosol nucleation activity via one specific nucleation mode, here deposition nucleation, combined with thorough structural and compositional analyzes are needed in order to establish any association between the particles' activity and their physico-chemical properties. In addition, since the morphology of the ice crystals can influence their radiative properties [3], we investigated their morphology as they grow over both soot and pristine substrates at different temperatures and humidity ratios. In the present work, Combustion Aerosol STandart soot samples were produced from propane using various experimental conditions. Their nucleation activity was studied in deposition mode (from water vapor), and monitored using a temperature-controlled reactor in which the sample's relative humidity is precisely measured with a cryo-hygrometer. Formation of water/ice onto the particles is followed both optically and spectroscopically, using a microscope coupled to a Raman spectrometer. Vibrational signatures of hydroxyls (O-H) emerge when the particle becomes hydrated and are used to characterize ice

  3. Crystal Structure of Amylomaltase from Corynebacterium glutamicum.

    PubMed

    Joo, Seongjoon; Kim, Sangwoo; Seo, Hogyun; Kim, Kyung-Jin

    2016-07-20

    Amylomaltase is an essential enzyme in maltose utilization and maltodextrin metabolism, and it has been industrially used for the production of cyclodextrin and modification of starch. We determined the crystal structure of amylomaltase from Corynebacterium glutamicum (CgAM) at a resolution of 1.7 Å. Although CgAM forms a dimer without NaCl, it exists as a monomer in physiological concentration of NaCl. CgAM is composed of N- and C-terminal domains, which can be further divided into two and four subdomains, respectively. It exhibits a unique structural feature at the functionally unknown N-domain and also shows two striking differences at the C-domain compared to other amylomaltases. These differences at extended edge of the substrate-binding site might affect substrate specificity for large cyclodextrin formation. The bis-tris methane and sulfate molecules bound at the substrate-binding site of our current structure mimic the binding of the hydroxyl groups of glucose bound at subsites -1 and -2, respectively. PMID:27366969

  4. Efficient method for predicting crystal structures at finite temperature: variable box shape simulations.

    PubMed

    Filion, Laura; Marechal, Matthieu; van Oorschot, Bas; Pelt, Daniël; Smallenburg, Frank; Dijkstra, Marjolein

    2009-10-30

    We present an efficient and robust method based on Monte Carlo simulations for predicting crystal structures at finite temperature. We apply this method, which is surprisingly easy to implement, to a variety of systems, demonstrating its effectiveness for hard, attractive, and anisotropic interactions, binary mixtures, semi-long-range soft interactions, and truly long-range interactions where the truly long-range interactions are treated using Ewald sums. In the case of binary hard-sphere mixtures, star polymers, and binary Lennard-Jones mixtures, the crystal structures predicted by this algorithm are consistent with literature, providing confidence in the method. Finally, we predict new crystal structures for hard asymmetric dumbbell particles, bowl-like particles and hard oblate cylinders and present the phase diagram for the oblate cylinders based on full free energy calculations. PMID:19905838

  5. 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)

  6. Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

    PubMed

    Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

    2009-12-24

    In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure.

  7. Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

    PubMed

    Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

    2009-12-24

    In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure. PMID:19950907

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

    PubMed

    Kim, Sung-Jo; Kim, Jong-Hyun

    2014-04-21

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

  9. Dynamics of ordered colloidal particle monolayers at nematic liquid crystal interfaces.

    PubMed

    Wei, Wei-Shao; Gharbi, Mohamed Amine; Lohr, Matthew A; Still, Tim; Gratale, Matthew D; Lubensky, T C; Stebe, Kathleen J; Yodh, A G

    2016-05-25

    We prepare two-dimensional crystalline packings of colloidal particles on surfaces of the nematic liquid crystal (NLC) 5CB, and we investigate the diffusion and vibrational phonon modes of these particles using video microscopy. Short-time particle diffusion at the air-NLC interface is well described by a Stokes-Einstein model with viscosity similar to that of 5CB. Crystal phonon modes, measured by particle displacement covariance techniques, are demonstrated to depend on the elastic constants of 5CB through interparticle forces produced by LC defects that extend from the interface into the underlying bulk material. The displacement correlations permit characterization of transverse and longitudinal sound velocities of the crystal packings, as well as the particle interactions produced by the LC defects. All behaviors are studied in the nematic phase as a function of increasing temperature up to the nematic-isotropic transition. PMID:27109759

  10. Crystal structures of Bacillus subtilis Lon protease.

    PubMed

    Duman, Ramona E; Löwe, Jan

    2010-08-27

    Lon ATP-dependent proteases are key components of the protein quality control systems of bacterial cells and eukaryotic organelles. Eubacterial Lon proteases contain an N-terminal domain, an ATPase domain, and a protease domain, all in one polypeptide chain. The N-terminal domain is thought to be involved in substrate recognition, the ATPase domain in substrate unfolding and translocation into the protease chamber, and the protease domain in the hydrolysis of polypeptides into small peptide fragments. Like other AAA+ ATPases and self-compartmentalising proteases, Lon functions as an oligomeric complex, although the subunit stoichiometry is currently unclear. Here, we present crystal structures of truncated versions of Lon protease from Bacillus subtilis (BsLon), which reveal previously unknown architectural features of Lon complexes. Our analytical ultracentrifugation and electron microscopy show different oligomerisation of Lon proteases from two different bacterial species, Aquifex aeolicus and B. subtilis. The structure of BsLon-AP shows a hexameric complex consisting of a small part of the N-terminal domain, the ATPase, and protease domains. The structure shows the approximate arrangement of the three functional domains of Lon. It also reveals a resemblance between the architecture of Lon proteases and the bacterial proteasome-like protease HslUV. Our second structure, BsLon-N, represents the first 209 amino acids of the N-terminal domain of BsLon and consists of a globular domain, similar in structure to the E. coli Lon N-terminal domain, and an additional four-helix bundle, which is part of a predicted coiled-coil region. An unexpected dimeric interaction between BsLon-N monomers reveals the possibility that Lon complexes may be stabilised by coiled-coil interactions between neighbouring N-terminal domains. Together, BsLon-N and BsLon-AP are 36 amino acids short of offering a complete picture of a full-length Lon protease.

  11. 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

  12. 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.}

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

    NASA Astrophysics Data System (ADS)

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

    2010-06-01

    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 γ-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 - 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 γ-Al 2O 3 particles with mesostructures after further calcination at 1173 K, whereas coexisting SO 42- can promote above morphology evolution and then transformed into γ-Al 2O 3 nanofibers after calcination at 1173 K. Moreover nearly all materials retain relatively high specific surface areas larger than 100 m 2 g -1 even after calcinations at 1173 K.

  14. 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.

  15. 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; Muševič, 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

  16. 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.

  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.

  18. 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.

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

    NASA Technical Reports Server (NTRS)

    Miyoshi, K.; Buckley, D. H.

    1980-01-01

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

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

    PubMed

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

    2013-07-16

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

  1. 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…

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

    PubMed

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

    2006-08-01

    Modern methods of quantum mechanics have proved to be effective tools to understand and even predict materials properties. An essential element of the materials design process, relevant to both new materials and the optimization of existing ones, is knowing which crystal structures will form in an alloy system. Crystal structure can only be predicted effectively with quantum mechanics if an algorithm to direct the search through the large space of possible structures is found. We present a new approach to the prediction of structure that rigorously mines correlations embodied within experimental data and uses them to direct quantum mechanical techniques efficiently towards the stable crystal structure of materials.

  3. Enhanced high-temperature ice nucleation ability of crystallized aerosol particles after preactivation at low temperature

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

    In cloud chamber experiments with crystallized aqueous ammonium sulfate, oxalic acid, and succinic acid solution droplets, we have studied a preactivation mechanism that markedly enhances the particles' heterogeneous ice nucleation ability. First cloud expansion experiments were performed at a high temperature (267-244 K) where the crystallized particles did not promote any heterogeneous ice nucleation. Ice nucleation at this temperature, however, could be triggered by temporarily cooling the crystallized particles to a lower temperature. This is because upon crystallization, residuals of the aqueous solution are trapped within the crystals. These captured liquids can freeze when cooled below their respective homogeneous or heterogeneous freezing temperature, leading to the formation of ice pockets in the crystalline particles. When warmed again to the higher temperature, ice formation by the preactivated particles occurred via depositional and deliquescence-induced ice growth, with ice active fractions ranging from 1 to 4% and from 4 to 20%, respectively. Preactivation disappeared above the eutectic temperature, which for the organic acids are close to the melting point of ice. This mechanism could therefore contribute to the very small fraction of atmospheric aerosol particles that are still ice active well above 263 K.

  4. Effect of direction of an external force on crystallization of colloidal particles in a V-shaped groove by sedimentation

    NASA Astrophysics Data System (ADS)

    Sato, Masahide

    2016-09-01

    We carried out Langevin dynamics simulations to study the effect of the direction of a uniform external force on the crystallization of colloidal particles in a V-shaped groove. When the inclination of the side walls of a groove was set to a suitable value and the external force bisected the angle, the face-centered-cubic (fcc) structure grew with a {100} growth interface. When the external force was inclined, the number of solidified particles decreased with increasing inclination, which is different from the growth in an inverted pyramidal container.

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

    NASA Technical Reports Server (NTRS)

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

    1990-01-01

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

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

    ERIC Educational Resources Information Center

    Cady, Susan G.

    1997-01-01

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

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

    PubMed

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

    2009-09-22

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

  8. Topological defects and self-assembly of cuboidal colloidal particles with sharp edges in a nematic liquid crystal

    NASA Astrophysics Data System (ADS)

    de Pablo, Juan J.; Sadati, Monirosadat; Armas-Perez, Julio C.; Soni, Vishal; Irvine, William T. M.

    The geometry of colloidal particles defines the topology and self-assembly of colloidal superstructures in nematic liquid crystals. Past research has largely focused on the defects that arise around spherical colloids, and the defect-induced aggregation between them. In this work, we examine experimentally and theoretically, the effect of edge curvature of colloidal particles on their defect configurations and self-assembly in a nematic liquid crystal (5CB). The polarized images of the particles with homeotropic surface anchoring in 5CB show that the presence of sharp edges can reshape completely the defect ring. The defect makes sharp turns and follows the edge of the cube particles, which significantly affects the interaction between particles and their eventual self-assembly. In agreement with our experimental results, our computational studies indicate that the gradual increase of the edges sharpness that occurs as we transition from spheres to cubes, changes the defect structure from a Saturn ring to a twisted ring, which is pinned to the edges of the cube particle. The wide variety of topological defects achievable by changing the curvature could provide new tools to tune colloidal self-assembly.

  9. Crystal structure of Clostridium difficile toxin A.

    PubMed

    Chumbler, Nicole M; Rutherford, Stacey A; Zhang, Zhifen; Farrow, Melissa A; Lisher, John P; Farquhar, Erik; Giedroc, David P; Spiller, Benjamin W; Melnyk, Roman A; Lacy, D Borden

    2016-01-01

    Clostridium difficile infection is the leading cause of hospital-acquired diarrhoea and pseudomembranous colitis. Disease is mediated by the actions of two toxins, TcdA and TcdB, which cause the diarrhoea, as well as inflammation and necrosis within the colon(1,2). The toxins are large (308 and 270 kDa, respectively), homologous (47% amino acid identity) glucosyltransferases that target small GTPases within the host(3,4). The multidomain toxins enter cells by receptor-mediated endocytosis and, upon exposure to the low pH of the endosome, insert into and deliver two enzymatic domains across the membrane. Eukaryotic inositol-hexakisphosphate (InsP6) binds an autoprocessing domain to activate a proteolysis event that releases the N-terminal glucosyltransferase domain into the cytosol. Here, we report the crystal structure of a 1,832-amino-acid fragment of TcdA (TcdA1832), which reveals a requirement for zinc in the mechanism of toxin autoprocessing and an extended delivery domain that serves as a scaffold for the hydrophobic α-helices involved in pH-dependent pore formation. A surface loop of the delivery domain whose sequence is strictly conserved among all large clostridial toxins is shown to be functionally important, and is highlighted for future efforts in the development of vaccines and novel therapeutics. PMID:27571750

  10. Crystal structure of Clostridium difficile toxin A

    PubMed Central

    Chumbler, Nicole M.; Rutherford, Stacey A.; Zhang, Zhifen; Farrow, Melissa A.; Lisher, John P.; Farquhar, Erik; Giedroc, David P.; Spiller, Benjamin W.; Melnyk, Roman A.; Lacy, D. Borden

    2016-01-01

    Clostridium difficile infection is the leading cause of hospital-acquired diarrhoea and pseudomembranous colitis. Disease is mediated by the actions of two toxins, TcdA and TcdB, which cause the diarrhoea, as well as inflammation and necrosis within the colon1,2. The toxins are large (308 and 270 kDa, respectively), homologous (47% amino acid identity) glucosyltransferases that target small GTPases within the host3,4. The multidomain toxins enter cells by receptor-mediated endocytosis and, upon exposure to the low pH of the endosome, insert into and deliver two enzymatic domains across the membrane. Eukaryotic inositol-hexakisphosphate (InsP6) binds an autoprocessing domain to activate a proteolysis event that releases the N-terminal glucosyltransferase domain into the cytosol. Here, we report the crystal structure of a 1,832-amino-acid fragment of TcdA (TcdA1832), which reveals a requirement for zinc in the mechanism of toxin autoprocessing and an extended delivery domain that serves as a scaffold for the hydrophobic α-helices involved in pH-dependent pore formation. A surface loop of the delivery domain whose sequence is strictly conserved among all large clostridial toxins is shown to be functionally important, and is highlighted for future efforts in the development of vaccines and novel therapeutics. PMID:27571750

  11. Anisotropic domain structure of KTiOPO4 crystals

    NASA Astrophysics Data System (ADS)

    Urenski, P.; Lesnykh, M.; Rosenwaks, Y.; Rosenman, G.; Molotskii, M.

    2001-08-01

    Highly anisotropic ferroelectric domain structure is observed in KTiOPO4 (KTP) crystals reversed by low electric field. The applied Miller-Weinreich model for sidewise motion of domain walls indicates that this anisotropy results from the peculiarities of KTP crystal lattice. The domain nuclei of dozen nanometer size, imaged by atomic force microscopy method, demonstrate regular hexagonal forms. The orientation of domain walls of the elementary nuclei coincides with the orientation of the facets of macroscopic KTP crystals. The observed strong domain elongation along one principal crystal axis allows us to improve tailoring of ferroelectric domain engineered structures for nonlinear optical converters.

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

    PubMed

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

    2013-07-29

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

  13. 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.

  14. Photonic crystal channel drop filters based on fractal structures

    NASA Astrophysics Data System (ADS)

    Dideban, Ali; Habibiyan, Hamidreza; Ghafoorifard, Hassan

    2014-09-01

    In this paper we introduce new configurations of channel drop filters based on two-dimensional photonic crystals. Structures consist of two photonic crystal waveguides and a fractal-shaped resonator between them. The effect of structural parameters on resonance frequency and drop efficiency is investigated. Calculations of band structure and propagation of electromagnetic field through devices are done by plane wave expansion (PWE) and finite difference time domain (FDTD) methods, respectively. In our designs more than 95% drop efficiency with quality factor of ~1150 is achievable at wavelength near 1540 nm, which in comparison with other photonic crystal resonator structures is a very satisfactory and acceptable result.

  15. 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.

  16. 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.

  17. Novel photonic crystal cavities and related structures.

    SciTech Connect

    Luk, Ting Shan

    2007-11-01

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

  18. 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

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

    PubMed

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

    2012-03-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2012-03-01

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

  2. Crystal structure of an HIV assembly and maturation switch

    PubMed Central

    Wagner, Jonathan M; Zadrozny, Kaneil K; Chrustowicz, Jakub; Purdy, Michael D; Yeager, Mark; Ganser-Pornillos, Barbie K; Pornillos, Owen

    2016-01-01

    Virus assembly and maturation proceed through the programmed operation of molecular switches, which trigger both local and global structural rearrangements to produce infectious particles. HIV-1 contains an assembly and maturation switch that spans the C-terminal domain (CTD) of the capsid (CA) region and the first spacer peptide (SP1) of the precursor structural protein, Gag. The crystal structure of the CTD-SP1 Gag fragment is a goblet-shaped hexamer in which the cup comprises the CTD and an ensuing type II β-turn, and the stem comprises a 6-helix bundle. The β-turn is critical for immature virus assembly and the 6-helix bundle regulates proteolysis during maturation. This bipartite character explains why the SP1 spacer is a critical element of HIV-1 Gag but is not a universal property of retroviruses. Our results also indicate that HIV-1 maturation inhibitors suppress unfolding of the CA-SP1 junction and thereby delay access of the viral protease to its substrate. DOI: http://dx.doi.org/10.7554/eLife.17063.001 PMID:27416583

  3. Crystal structure of an HIV assembly and maturation switch.

    PubMed

    Wagner, Jonathan M; Zadrozny, Kaneil K; Chrustowicz, Jakub; Purdy, Michael D; Yeager, Mark; Ganser-Pornillos, Barbie K; Pornillos, Owen

    2016-01-01

    Virus assembly and maturation proceed through the programmed operation of molecular switches, which trigger both local and global structural rearrangements to produce infectious particles. HIV-1 contains an assembly and maturation switch that spans the C-terminal domain (CTD) of the capsid (CA) region and the first spacer peptide (SP1) of the precursor structural protein, Gag. The crystal structure of the CTD-SP1 Gag fragment is a goblet-shaped hexamer in which the cup comprises the CTD and an ensuing type II β-turn, and the stem comprises a 6-helix bundle. The β-turn is critical for immature virus assembly and the 6-helix bundle regulates proteolysis during maturation. This bipartite character explains why the SP1 spacer is a critical element of HIV-1 Gag but is not a universal property of retroviruses. Our results also indicate that HIV-1 maturation inhibitors suppress unfolding of the CA-SP1 junction and thereby delay access of the viral protease to its substrate. PMID:27416583

  4. 'Crystal Collimator' Measurement of CESR particle-beam Source Size

    SciTech Connect

    Finkelstein, K.D.; Bazarov, Ivan; White, Jeffrey; Revesz, Peter

    2004-05-12

    We have measured electron and positron beam source size at CHESS when the Cornell Electron Storage Ring (CESR) is run dedicated for the production of synchrotron radiation. Horizontal source size at several beamlines is expected to shrink by a factor of two but synchrotron (visible) light measurements only provide the vertical size. Therefore a 'crystal collimator' using two Bragg reflection in dispersive (+,+) orientation has been built to image the horizontal (vertical) source by passing x-rays parallel to within 5 microradians to an imaging screen and camera. With the 'crystal collimator' we observe rms sizes of 1.2 mm horizontal by 0.28 mm vertical, in good agreement with the 1.27 mm size calculated from lattice functions, and 0.26 mm observed using a synchrotron light interferometer.

  5. 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

  6. 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

  7. A Investigation of Crystal Surface Structure and Electron Beam-Induced Interaction by Srem.

    NASA Astrophysics Data System (ADS)

    Ou, Herng-Jia Henry

    Scanning Reflection Electron Microscopy (SREM) has recently become an effective technique for surface science study. Nanodiffraction patterns are used to characterize the local surface structure of a region as small as the resolution limit of SREM image. Two instrumentation developments were attempted: (1) Reflection Electron Microscopy and Electron Reflection Diffraction at Intermediate Energy (REMEDIE) microscope system, and (2) In-situ specimen treatment chamber of VG-HB5 STEM microscope. Two different individual experiments were carried out, one in each microscope: (1) investigations of Si(111)2 x 1 domain structure of an in -situ cleaved crystal surface in the REMEDIE system, and (2) investigations of electron beam-induced interaction between the in-situ deposited small metallic particles and MgO crystal surface in VG-HG5 microscope. Alternative arrangements of Si(111)2 x 1 B domain structure, C domain structure and the regular 1x1 structure region were observed, suggesting a bonding relationship between them. On the (100) MgO surface, the as-deposited Cu particles prefer to align on 001 , the incident beam direction, and/or decorate the big surface steps. But after exposure to air, these Cu particles appear randomly, decorating the fine surface steps. At room temperature and T(,s) = 90(DEGREES)C, as-deposited Pd particles decorate the MgO surface in the same way as Cu particles do. At T(,s) = 150(DEGREES)C, the electron beam-induced growth process of the epitaxed Pd particles on the crystal surface steps is observed, a core of particles is formed, and the extension of the growth process is guided by the condensed electron beam. Pd particles of 10(ANGSTROM) in diameter were observed during the growth process. At T(,s) = 250(DEGREES)C, the periodic surface fringe decorated by the as-deposited Pd particles show (TURN)25(ANGSTROM) periodicity, presumably associated with the surface structure of the substrate. SREM images of the periodic arrays of surface steps on

  8. Two-particle problem in comblike structures

    NASA Astrophysics Data System (ADS)

    Agliari, Elena; Cassi, Davide; Cattivelli, Luca; Sartori, Fabio

    2016-05-01

    Encounters between walkers performing a random motion on an appropriate structure can describe a wide variety of natural phenomena ranging from pharmacokinetics to foraging. On homogeneous structures the asymptotic encounter probability between two walkers is (qualitatively) independent of whether both walkers are moving or one is kept fixed. On infinite comblike structures this is no longer the case and here we deepen the mechanisms underlying the emergence of a finite probability that two random walkers will never meet, while one single random walker is certain to visit any site. In particular, we introduce an analytical approach to address this problem and even more general problems such as the case of two walkers with different diffusivity, particles walking on a finite comb and on arbitrary bundled structures, possibly in the presence of loops. Our investigations are both analytical and numerical and highlight that, in general, the outcome of a reaction involving two reactants on a comblike architecture can strongly differ according to whether both reactants are moving (no matter their relative diffusivities) or only one is moving and according to the density of shortcuts among the branches.

  9. Two-particle problem in comblike structures.

    PubMed

    Agliari, Elena; Cassi, Davide; Cattivelli, Luca; Sartori, Fabio

    2016-05-01

    Encounters between walkers performing a random motion on an appropriate structure can describe a wide variety of natural phenomena ranging from pharmacokinetics to foraging. On homogeneous structures the asymptotic encounter probability between two walkers is (qualitatively) independent of whether both walkers are moving or one is kept fixed. On infinite comblike structures this is no longer the case and here we deepen the mechanisms underlying the emergence of a finite probability that two random walkers will never meet, while one single random walker is certain to visit any site. In particular, we introduce an analytical approach to address this problem and even more general problems such as the case of two walkers with different diffusivity, particles walking on a finite comb and on arbitrary bundled structures, possibly in the presence of loops. Our investigations are both analytical and numerical and highlight that, in general, the outcome of a reaction involving two reactants on a comblike architecture can strongly differ according to whether both reactants are moving (no matter their relative diffusivities) or only one is moving and according to the density of shortcuts among the branches. PMID:27300834

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

    SciTech Connect

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

    2015-09-25

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

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

    SciTech Connect

    Samanta, U.; Bahnson, B

    2008-01-01

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

  12. 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.

  13. Structural and mechanical studies of cadmium manganese thiocyanate crystal

    NASA Astrophysics Data System (ADS)

    Manikandan, M. R.; Vijayaprasath, G.; babu, G. Anandha; Bhagavannarayan, G.; Vijayan, N.; Ravi, G.

    2012-06-01

    Single crystals of cadmium manganese thiocyanate (CMTC) have been synthesized successfully and grown by slow evaporation method. The structural perfection of the grown crystals has been analyzed by High resolution X-ray diffraction (HRXRD), which shows the crystalline perfection of the grown crystal is quite good. Optical behavior was assessed by UV-Vis analysis and found that no absorption in the UV visible region and it may be useful for second harmonic applications. The mechanical hardness of the grown crystals was studied and Vicker's microhardness, Stiffness constant was calculated.

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

    PubMed

    Matsuyama, Akihiko

    2009-11-28

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

  15. Molecular structures and crystal packings of 2-styrylquinoxaline derivatives

    NASA Astrophysics Data System (ADS)

    Kuz'mina, L. G.; Sitin, A. G.; Gulakova, E. N.; Fedorova, O. A.; Lermontova, E. Kh.; Churakov, A. V.

    2012-01-01

    The crystal and molecular structures of 2-styrylquinoxaline derivatives with different substituents in the styryl fragment are determined. The degree of planarity of the molecules studied varies in a very wide range, from 1.7° to 33.5°. In the ethylene fragment, the double bond is essentially localized. The bicycle-pedal disordering of the ethylene fragment is found in the crystals of the methoxy and oxyacetyl derivatives of 2-styrylquinoxaline. None of the packings contains packing motifs favorable for the photocycloaddition (PCA) reaction with single crystal retention. The crystal packings of these compounds and that of 2-(4-methylstyryl)quinoxaline are characterized by a stacking motif of the head-to-head type, which eliminates the possibility of PCA taking place with single crystal retention but is suitable for this reaction in polycrystalline films. The crystal packing of 2-(3,4-dimethoxystyryl)quinoxaline does not contain elements with stacking interactions.

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

    NASA Technical Reports Server (NTRS)

    Bahadur, H.; Parshad, R.

    1981-01-01

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

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

    SciTech Connect

    Bondarenco, M. V.

    2010-10-15

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

  18. Symmetry breaking and interaction of colloidal particles in nematic liquid crystals.

    PubMed

    Lev, B I; Chernyshuk, S B; Tomchuk, P M; Yokoyama, H

    2002-02-01

    We propose a general approach to the description of the long-ranged elastic interaction in the nematic colloids, based on the symmetry breaking of the director field. The type of the far-field interaction between particles immersed in a nematic host is determined by the way the symmetry is broken in the near-field region around the colloidal particle. This is caused both by the particle's shape and the anchoring at the surface. If the director field near the particle has a set of three symmetry planes, the far-field interaction falls off as d(-5) with d being the distance between particles. If one symmetry plane is absent, a dipolar moment perpendicular to it is allowed and yields dipole-dipole interactions, which decays as d(-3). If both the horizontal and vertical mirror symmetries are broken (it is equivalent to the case when the nonzero torque moment is applied to the particle by the nematic liquid crystal), the particles are shown to attract each other following the Coulomb law. We propose a simple method for the experimental observation of this Coulomb attraction. The behavior of colloid particles in curved director fields is analyzed. Quadrupolar particles with planar anchoring are shown to be attracted toward the regions with high splay deformations, while quadrupoles with homeotropic anchoring are depleted from such regions. When there are many colloidal particles in the nematic solvent, the distortions of the director from all of them are overlapped and lead to the exponential screening in the elastic pair interaction potential. This is a many-body interaction effect. This screening is essential in the real dense colloid systems, such as ferronematics--suspensions of magnetic cylindrical grains in the nematic liquid crystal. External magnetic field induces an elastic Yukawa attraction between them. We apply this attraction to the explanation of the cellular texture in magnetically doped liquid crystals.

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

    PubMed

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

    2015-12-01

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

  20. 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...

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

    PubMed

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

    2016-03-24

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  3. 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.

  4. Crystal structure of actinide metals at high compression

    SciTech Connect

    Fast, L.; Soederlind, P.

    1995-08-01

    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.

  5. 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

  6. Selective modulation of infrared radiation by an Al2O3 particles — liquid crystal system

    NASA Astrophysics Data System (ADS)

    Ibragimov, T. D.; Allakhverdiev, E. A.; Bairamov, G. M.; Imamaliev, A. R.

    2011-07-01

    We have developed a dual-frequency liquid crystal consisting of 4-n-pentyl-4'-cyanobiphenyl (5CB), 4-hexyloxyphenyl-4'-hexyloxy-3-nitrobenzoate (C2), and 4-butyl-4'-(hexyloxyphenyloxycarbonyl)phenyl carbonate (H22). We have measured the frequency dependences of the longitudinal and transverse components of the dielectric constant of the mixture and we have determined the frequency regions of positive and negative dielectric anisotropy. We show that for certain changes in the frequency of the applied electric field while the magnitude of the field remains the same, the transmission region of the Al2O3 particles — dual-frequency liquid crystal system switches from one wavelength to the other. The experimental results are explained by the optical homogeneity of the system in a narrow wavelength interval when the refractive indices of the particle material and the matrix are close, and also by reorientation of the liquid crystal molecules as the frequency of the applied voltage changes.

  7. 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 β-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 β-lactose in α-lactose based on powder X-ray diffraction (PXRD), which is described here.

  8. 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.

  9. Growth, characterization, and crystal structure of a new chalcone derivative single crystal

    NASA Astrophysics Data System (ADS)

    Shettigar, Venkataraya; Dharmaprakash, S. M.

    2006-09-01

    A new organic nonlinear optical (NLO) chalcone derivative viz.1- ( 4- methoxyphenyl )-3- (3,4 - dimethoxy phenyl ) - 2 - propene-1-one, has been synthesized by Claisen-Schmidt condensation method. The synthesized compound was purified by repeated recrystallization process. To confirm the identity of the synthesized compound, FTIR spectra was recorded and various functional groups present were identified. NMR spectra were recorded for structural identity and purity confirmation of the synthesized compound. Good quality single crystals were grown by solvent evaporation and slow cooling technique using acetone as solvent. The grown crystals were characterized by UV-Visible , differential thermal analysis and linear refractive index measurement. The hardness of the crystal was determined using Vicker's indentation method. The single crystal structure analysis of the crystal was performed and it is found that the crystal belongs to monoclinic system with space group P2 I. The powder second harmonic generation(SHG)frequency conversion efficiency of the crystal was determined using Nd: YAG laser(λ = 1064nm)and it is 15 times that of Urea.

  10. Crystal structure of the co-crystal butyl-paraben-isonicotinamide (1/1).

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  12. Crystal structure of the co-crystal butyl-paraben-isonicotinamide (1/1).

    PubMed

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

    2016-01-01

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

  13. Predicting inclusion behaviour and framework structures in organic crystals.

    PubMed

    Cruz-Cabeza, Aurora J; Day, Graeme M; Jones, William

    2009-12-01

    We have used well-established computational methods to generate and explore the crystal structure landscapes of four organic molecules of well-known inclusion behaviour. Using these methods, we are able to generate both close-packed crystal structures and high-energy open frameworks containing voids of molecular dimensions. Some of these high-energy open frameworks correspond to real structures observed experimentally when the appropriate guest molecules are present during crystallisation. We propose a combination of crystal structure prediction methodologies with structure rankings based on relative lattice energy and solvent-accessible volume as a way of selecting likely inclusion frameworks completely ab initio. This methodology can be used as part of a rational strategy in the design of inclusion compounds, and also for the anticipation of inclusion behaviour in organic molecules. PMID:19876969

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  15. Evolution of molecular crystal optical phonons near structural phase transitions

    NASA Astrophysics Data System (ADS)

    Michki, Nigel; Niessen, Katherine; Xu, Mengyang; Markelz, Andrea

    Molecular crystals are increasingly important photonic and electronic materials. For example organic semiconductors are lightweight compared to inorganic semiconductors and have inexpensive scale up processing with roll to roll printing. However their implementation is limited by their environmental sensitivity, in part arising from the weak intermolecular interactions of the crystal. These weak interactions result in optical phonons in the terahertz frequency range. We examine the evolution of intermolecular interactions near structural phase transitions by measuring the optical phonons as a function of temperature and crystal orientation using terahertz time-domain spectroscopy. The measured orientation dependence of the resonances provides an additional constraint for comparison of the observed spectra with the density functional calculations, enabling us to follow specific phonon modes. We observe crystal reorganization near 350 K for oxalic acid as it transforms from dihydrate to anhydrous form. We also report the first THz spectra for the molecular crystal fructose through its melting point.

  16. Effect of particle size on hydroxyapatite crystal-induced tumor necrosis factor alpha secretion by macrophages.

    PubMed

    Nadra, Imad; Boccaccini, Aldo R; Philippidis, Pandelis; Whelan, Linda C; McCarthy, Geraldine M; Haskard, Dorian O; Landis, R Clive

    2008-01-01

    Macrophages may promote a vicious cycle of inflammation and calcification in the vessel wall by ingesting neointimal calcific deposits (predominantly hydroxyapatite) and secreting tumor necrosis factor (TNF)alpha, itself a vascular calcifying agent. Here we have investigated whether particle size affects the proinflammatory potential of hydroxyapatite crystals in vitro and whether the nuclear factor (NF)-kappaB pathway plays a role in the macrophage TNFalpha response. The particle size and nano-topography of nine different crystal preparations was analyzed by X-ray diffraction, Raman spectroscopy, scanning electron microscopy and gas sorbtion analysis. Macrophage TNFalpha secretion was inversely related to hydroxyapatite particle size (P=0.011, Spearman rank correlation test) and surface pore size (P=0.014). A necessary role for the NF-kappaB pathway was demonstrated by time-dependent I kappaB alpha degradation and sensitivity to inhibitors of I kappaB alpha degradation. To test whether smaller particles were intrinsically more bioactive, their mitogenic activity on fibroblast proliferation was examined. This showed close correlation between TNFalpha secretion and crystal-induced fibroblast proliferation (P=0.007). In conclusion, the ability of hydroxyapatite crystals to stimulate macrophage TNFalpha secretion depends on NF-kappaB activation and is inversely related to particle and pore size, with crystals of 1-2 microm diameter and pore size of 10-50 A the most bioactive. Microscopic calcific deposits in early stages of atherosclerosis may therefore pose a greater inflammatory risk to the plaque than macroscopically or radiologically visible deposits in more advanced lesions.

  17. 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

  18. 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.

  19. Crystal structure of a nematode-infecting virus

    PubMed Central

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

    2014-01-01

    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–δ 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, β-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

  20. Optical and structural properties of chalcone NLO single crystals

    NASA Astrophysics Data System (ADS)

    Rajesh Kumar, P. C.; Ravindrachary, V.; Janardhana, K.; Manjunath, H. R.; Karegouda, Prakash; Crasta, Vincent; Sridhar, M. A.

    2011-11-01

    Organic compound (E)-1-(4-methoxyphenyl)-3-(2,3,5-trichlorophenyl)prop-2-en-1-one [MPTCPP] with molecular formula C 16H 11Cl 3O 2 was synthesized using Claisen-Schmidt condensation reaction method. 1H NMR spectra was recorded to identify the various functional groups present in the compound and confirm the chemical structure. The single crystals were grown using slow evaporation solution growth technique. The UV-Visible spectrum study reveals that the crystal is transparent in the entire visible region and the absorption is observed at 364 nm. The Kurtz powder second harmonic generation (SHG) test shows that the MPTCPP is NLO active and its SHG efficiency is three times that of urea. Single crystal XRD study shows that the compound crystallizes in the monoclinic system with a space group Cc. The corresponding lattice parameters of the crystal are a = 28.215(5) Å, b = 3.9740(4) Å, c = 16.178(3) Å and V = 1503.0(4) Å 3. The micro hardness test was carried out and the work hardening coefficient value ( n) of the crystal was found to be 1.48. This indicates that the crystal is hard and is suitable for device application. The thermal study reveals that the thermal stability of the crystal is good.

  1. 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.

  2. Origin of particle accumulation structures in liquid bridges: Particle-boundary-interactions versus inertia

    NASA Astrophysics Data System (ADS)

    Muldoon, Frank H.; Kuhlmann, Hendrik C.

    2016-07-01

    The formation of particle-accumulation structures in the flow in a cylindrical liquid bridge driven by the thermocapillary effect is studied with the aim of determining the physical mechanism which forms the structures. The flow is modeled using the incompressible Navier-Stokes and energy equations with the assumption of constant fluid properties except for surface tension, which is assumed to depend linearly on temperature. Different models for the motion of small non-interacting spherical particles at low concentration are employed, taking into account particle inertia due to density differences between fluid and particles and the restricted particle motion near the boundaries of the flow domain. Attention is focused on differences in formation time between particle-accumulation structures arising as a result of inertial effects only, particle-boundary-interaction effects only, and a combination of the two.

  3. The different conformations and crystal structures of dihydroergocristine

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  4. Observation and Analysis of Polymer Crystal Structures at the Stem Level. Implications Regarding Polymer Crystallization Processes.

    NASA Astrophysics Data System (ADS)

    Lotz, Bernard

    2003-03-01

    The building element of chain folded polymer crystals is the individual stem that spans the lamellar thickness. For chiral but racemic helical polymers such as polyolefins (e.g. isotactic and syndiotactic polypropylene and poly(1-butene)), stems can be right- or left-handed helices. These polymers can exist in various crystal polymorphs that are either "racemic" or "chiral" (made of both, or of only one helical hand). Upon crystallization, each stem has a conformational "choice", but must adapt to the crystal structure and, once crystallized, is characterized by a "conformational tag" (right or left hand). Various means exist to determine or observe helical hands in polyolefin lamellae: Atomic Force Microscopy on epitaxially crystallized samples, or, for the alpha phase of isotactic polypropylene, analysis of its specific lamellar branching. These observations and analyses indicate that the helical hand of stems is tightly determined by the substrate or growth face topography, i.e. indicate that the depositing stem probes and adapts to the surface structure prior to successful attachment. This "post-mortem" analysis of the crystal structure and stem chirality emphasizes the "sequential" nature of the growth process (successive attachment of individual stems). It is in line with early views on polymer crystallization. It is at variance with recently introduced models or scenarios that assume either some pre-ordering of the polymer melt as a result of spinodal decomposition and/or accretion of polymer chains in pseudo-crystalline bundles followed by (solid state) reorganization of the bundles to generate fully grown lamellae.

  5. 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.

  6. 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

  7. Heterogeneous Crystallization on Pairs of Pre-Structured Seeds.

    PubMed

    Jungblut, Swetlana; Dellago, Christoph

    2016-09-01

    Studying the effects of small pre-structured seeds on the crystallization transition in an undercooled monodisperse Lennard-Jones fluid with transition interface path sampling combined with molecular dynamics simulations, we analyze the impact of the simultaneous presence of two seeds with various structures. In the presence of seeds with face- and body-centered cubic structures, we find that decreasing the seed-to-seed distance enhances the probability of the crystalline clusters formed on one of the seeds to grow beyond the critical size, thus, increasing the crystal nucleation rates. In contrast, when seeds have an icosahedral structure, the crystalline clusters form mostly in the bulk. The crystal nucleation rate, however, is also determined by the distance between the seeds with regular structure in which the lattice spacing is equal to the bulk lattice constant, pointing to a heterogeneous crystal nucleation that occurs away from the icosahedrally structured seeds. For slightly squeezed seeds, the effects of the presence of seeds with face- and body-centered cubic structures are reduced in comparison to the regular seeds, and we do not see any effect of the presence of the second seed for seeds with squeezed icosahedral structure. PMID:27479875

  8. Heterogeneous Crystallization on Pairs of Pre-Structured Seeds

    PubMed Central

    2016-01-01

    Studying the effects of small pre-structured seeds on the crystallization transition in an undercooled monodisperse Lennard-Jones fluid with transition interface path sampling combined with molecular dynamics simulations, we analyze the impact of the simultaneous presence of two seeds with various structures. In the presence of seeds with face- and body-centered cubic structures, we find that decreasing the seed-to-seed distance enhances the probability of the crystalline clusters formed on one of the seeds to grow beyond the critical size, thus, increasing the crystal nucleation rates. In contrast, when seeds have an icosahedral structure, the crystalline clusters form mostly in the bulk. The crystal nucleation rate, however, is also determined by the distance between the seeds with regular structure in which the lattice spacing is equal to the bulk lattice constant, pointing to a heterogeneous crystal nucleation that occurs away from the icosahedrally structured seeds. For slightly squeezed seeds, the effects of the presence of seeds with face- and body-centered cubic structures are reduced in comparison to the regular seeds, and we do not see any effect of the presence of the second seed for seeds with squeezed icosahedral structure. PMID:27479875

  9. 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.

  10. Isolation, crystallization and crystal structure determination of bovine kidney Na(+),K(+)-ATPase.

    PubMed

    Gregersen, Jonas Lindholt; Mattle, Daniel; Fedosova, Natalya U; Nissen, Poul; Reinhard, Linda

    2016-04-01

    Na(+),K(+)-ATPase is responsible for the transport of Na(+) and K(+) across the plasma membrane in animal cells, thereby sustaining vital electrochemical gradients that energize channels and secondary transporters. The crystal structure of Na(+),K(+)-ATPase has previously been elucidated using the enzyme from native sources such as porcine kidney and shark rectal gland. Here, the isolation, crystallization and first structure determination of bovine kidney Na(+),K(+)-ATPase in a high-affinity E2-BeF3(-)-ouabain complex with bound magnesium are described. Crystals belonging to the orthorhombic space group C2221 with one molecule in the asymmetric unit exhibited anisotropic diffraction to a resolution of 3.7 Å with full completeness to a resolution of 4.2 Å. The structure was determined by molecular replacement, revealing unbiased electron-density features for bound BeF3(-), ouabain and Mg(2+) ions. PMID:27050261

  11. Structural effects of monovalent anions on polymorphic lysozyme crystals.

    PubMed

    Vaney, M C; Broutin, I; Retailleau, P; Douangamath, A; Lafont, S; Hamiaux, C; Prangé, T; Ducruix, A; Riès-Kautt, M

    2001-07-01

    Understanding direct salt effects on protein crystal polymorphism is addressed by comparing different crystal forms (triclinic, monoclinic, tetragonal and orthorhombic) for hen, turkey, bob white quail and human lysozymes. Four new structures of hen egg-white lysozyme are reported: crystals grown in the presence of NapTS diffracted to 1.85 A, of NaI to 1.6 A, of NaNO(3) to 1.45 A and of KSCN to 1.63 A. These new structures are compared with previously published structures in order to draw a mapping of the surface of different lysozymes interacting with monovalent anions, such as nitrate, chloride, iodide, bromide and thiocyanate. An analysis of the structural sites of these anions in the various lysozyme structures is presented. This study shows common anion sites whatever the crystal form and the chemical nature of anions, while others seem specific to a given geometry and a particular charge environment induced by the crystal packing.

  12. 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

  13. 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

  14. 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.

  15. 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

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

    DOEpatents

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

    1994-01-01

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

  17. 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.

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

    PubMed

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

    2013-11-21

    In this work, we propose "single-image analysis", as opposed to multi-image averaging, for extracting valuable information from AFM images of single bio-particles. This approach allows us to study molecular systems imaged by AFM under general circumstances without restrictions on their structural forms. As feature exhibition is a resolution correlation, we have performed AFM imaging on surfaces of tobacco mosaic virus (TMV) to demonstrate variations of structural patterns with probing resolution. Two AFM images were acquired with the same tip at different probing resolutions in terms of pixel width, i.e., 1.95 and 0.49 nm per pixel. For assessment, we have constructed an in silico topograph based on the three-dimensional crystal structure of TMV as a reference. The prominent artifacts observed in the AFM-determined shape of TMV were attributed to tip convolutions. The width of TMV rod was systematically overestimated by ~10 nm at both probing resolutions of AFM. Nevertheless, the effects of tip convolution were less severe in vertical orientation so that the estimated height of TMV by AFM imaging was in close agreement with the in silico X-ray topograph. Using dedicated image processing algorithms, we found that at low resolution (i.e., 1.95 nm per pixel), the extracted surface features of TMV can be interpreted as a partial or full helical repeat (three complete turns with ~7.0 nm in length), while individual protein subunits (~2.5 nm) were perceivable only at high resolution. The present study shows that the scales of revealed structural features in AFM images are subject to both probing resolution and processing algorithms for image analysis. PMID:24056758

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

    PubMed Central

    Toyotama, Akiko; Okuzono, Tohru; Yamanaka, Junpei

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Toyotama, Akiko; Okuzono, Tohru; Yamanaka, Junpei

    2016-03-01

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

  1. Modulated crystal structure of InMo4O6.

    PubMed

    Schultz, Peter; Simon, Arndt; Oeckler, Oliver

    2016-08-01

    The (3 + 1)-dimensional modulated crystal structure of the metal-rich cluster compound InMo4O6 was solved and refined from single-crystal data in the superspace group P4/mbm(00γ)00ss [q = 0, 0, 0.1536 (4); a = 9.6664 (9), c = 2.8645 (3) Å; R1(all) = 0.046, wR(all) = 0.076]. The crystal structure is closely related to the NaMo4O6 structure type. It is built from rods of Mo6 clusters condensed via trans edges. These form channels parallel to [001], in which In6 and In7 oligomers alternate. Weak diffuse planes parallel to (001)* interconnect the satellite reflections; they occur due to two-dimensional rod disorder of the In oligomer chains. PMID:27484384

  2. The high-resolution crystal structure of human LCAT.

    PubMed

    Piper, Derek E; Romanow, William G; Gunawardane, Ruwanthi N; Fordstrom, Preston; Masterman, Stephanie; Pan, Oscar; Thibault, Stephen T; Zhang, Richard; Meininger, David; Schwarz, Margrit; Wang, Zhulun; King, Chadwick; Zhou, Mingyue; Walker, Nigel P C

    2015-09-01

    LCAT is intimately involved in HDL maturation and is a key component of the reverse cholesterol transport (RCT) pathway which removes excess cholesterol molecules from the peripheral tissues to the liver for excretion. Patients with loss-of-function LCAT mutations exhibit low levels of HDL cholesterol and corneal opacity. Here we report the 2.65 Å crystal structure of the human LCAT protein. Crystallization required enzymatic removal of N-linked glycans and complex formation with a Fab fragment from a tool antibody. The crystal structure reveals that LCAT has an α/β hydrolase core with two additional subdomains that play important roles in LCAT function. Subdomain 1 contains the region of LCAT shown to be required for interfacial activation, while subdomain 2 contains the lid and amino acids that shape the substrate binding pocket. Mapping the naturally occurring mutations onto the structure provides insight into how they may affect LCAT enzymatic activity. PMID:26195816

  3. Synthesis, growth, structural, optical, thermal and mechanical properties of an organic Urea maleic acid single crystals for nonlinear optical applications

    NASA Astrophysics Data System (ADS)

    Vinothkumar, P.; Kumar, R. Mohan; Jayavel, R.; Bhaskaran, A.

    2016-07-01

    A potential organic urea maleic acid (UMA) was synthesized and single crystals were grown at room temperature by slow evaporation and seed rotation methods. The grown crystal has been subjected to single crystal XRD analysis and found to have been crystallized in a noncentrosymmetric monoclinic crystal system with Cc as space group. The High resolution X-ray diffraction analysis revealed that the specimen is free from structural grain boundaries. The transparency of the grown crystal was confirmed by optical absorption and transmittance spectra with lower cut-off wavelength of 285 nm. The microhardness test was carried out on different planes to study the load dependent hardness values. The dislocation density of the UMA crystal was estimated from the etching studies. The dielectric permittivity and dielectric loss of the grown crystal was carried out as a function of frequency for different temperatures along three crystallographic axes. Thermal properties of UMA crystals were studied by TG-DTA analysis and it is stable upto 112 °C. The laser induced surface damage threshold of the grown crystal was measured using Nd: YAG laser. The birefringence of the crystal measured in the visible region was found to vary with the wavelength. The particle size dependent SHG of the sample was measured with different input energies by Kurtz's powder method using Nd:YAG laser.

  4. Directed self-assembly of colloidal particles onto the chemically anchoring patterned surface in a nematic liquid crystal

    NASA Astrophysics Data System (ADS)

    Li, Xiao; Armas-Pérez, Julio; Hernandez-Ortiz, Juan; de Pablo, Juan; Nealey, Paul

    The defects assisted assembly of colloidal particles works are more focused on the defects created in the bulk or the interface of nematic liquid crystal, which usually observe a group of particles spontaneously forming a chain or aggregating over the defects. The confining surface with specific 3D sculptured structures, such as pyramid or zig-zag grooves, offers the opportunity to isolate the trapped particles into certain position. Here, we explore a new method to direct self-assemble the colloidal particles through manipulating defects on the 2D geometry confined anchoring surface. Since the director of the preferred planar orientation of LCs could be manipulated by the pattern geometry and dimension, the topological defects could be engineered based on multi-stable orientation by designed 2D geometry pattern of different controllable direction at sub-micrometer dimension. We demonstrate that the designed one single middle straight stripe with disjoint two groups of straight stripe array on both side of the middle stripe as 45 angle of different orientation director could control the distortion of the disjoint gap space thus acting as defects template to trap the colloidal particles directed self-assembly at the designed positions. Through anchoring distribution on the pattern areas, geometry design of pattern, and also the external electric field applied on the system, those defects areas could be generate, erase, resume or even correct.

  5. Structural and magnetic characterization of electro-crystallized magnetite nanoparticles under constant current

    SciTech Connect

    Mosivand, Saba; Kazeminezhad, Iraj

    2015-10-15

    Graphical abstract: Structural and magnetic properties of electro-crystallized magnetite nanoparticles under constant current were studied. All samples were characterized using XRD, SEM, VSM, and Mössbauer spectrometry. - Highlights: • The effect of applied current on morphology and properties of Fe{sub 3}O{sub 4} is studied. • The particle size and morphology are controllable by adjusting the current. • The magnetization depends on particle size, type of surfactant and applied current. • The clear correlation between magnetization and the mean particle size is observed. - Abstract: The effect of applied current on the morphology, particle size, structure, and magnetic properties of magnetite nanoparticles prepared by electro-crystallization method was studied. The synthesis was performed in an electrochemical cell containing two iron electrodes and an aqueous solution of sodium sulfate, and either thiourea, sodium butanoate, or β-cyclodextrine as organic stabilizer. All the samples were characterized by XRD, SEM, VSM, and Mössbauer spectroscopy. X-ray diffraction patterns, clearly confirmed that all products have the cubic spinel Fe{sub 3}O{sub 4} crystal structure. Electron microscope images of the samples showed that their mean particle size is in the range 20–80 nm, and depends critically on the applied current and type of the organic additives. Specific magnetization of the samples at room temperature ranges from 60 to 90 A m{sup 2} kg{sup −1}, depending on the growth conditions. Room temperature Mössbauer spectra are typical of nonstoichiometric Fe{sub 3−δ}O{sub 4}, with a small excess of Fe{sup 3+}, 0.06 ≤ δ ≤ 0.17.

  6. Microscopic characterization of defect structure in RDX crystals.

    PubMed

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

    2013-12-01

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

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

    PubMed Central

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

    2013-01-01

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

  8. Pattern phase transitions of self-propelled particles: gases, crystals, liquids, and mills

    NASA Astrophysics Data System (ADS)

    Cheng, Zhao; Chen, Zhiyong; Vicsek, Tamás; Chen, Duxin; Zhang, Hai-Tao

    2016-10-01

    To understand the collective behaviors of biological swarms, flocks, and colonies, we investigated the non-equilibrium dynamic patterns of self-propelled particle systems using statistical mechanics methods and H-stability analysis of Hamiltonian systems. By varying the individual vision range, we observed phase transitions between four phases, i.e., gas, crystal, liquid, and mill-liquid coexistence patterns. In addition, by varying the inter-particle force, we detected three distinct milling sub-phases, i.e., ring, annulus, and disk. Based on the coherent analysis for collective motions, one may predict the stability and adjust the morphology of the phases of self-propelled particles, which has promising potential applications in natural self-propelled particles and artificial multi-agent systems.

  9. Electronic structure of the CuBS2 crystal

    NASA Astrophysics Data System (ADS)

    Basalaev, Yu. M.; Gordienko, A. B.; Filippov, S. I.

    2012-09-01

    The band structure and spectra of the total and projected densities of states of a new crystal of the chalcopyrite family, namely, CuBS2, have been calculated in terms of the density functional theory. It has been found that the crystal is a pseudo-direct-band-gap semiconductor, and the best theoretical estimate of the optical band gap is 3.44 eV. The upper valence band of the CuBS2 crystal basically consists of the contributions from the p states of S atoms and the d states of Cu atoms. The crystal splitting is 0.2 eV. The bottom of the conduction band is basically formed by the sp states of boron and sulfur atoms with an admixture of the s states of copper atoms.

  10. Crystal Structure of the Human Astrovirus Capsid Protein

    PubMed Central

    Toh, Yukimatsu; Harper, Justin; Dryden, Kelly A.; Yeager, Mark; Méndez, Ernesto

    2016-01-01

    ABSTRACT Human astrovirus (HAstV) is a leading cause of viral diarrhea in infants and young children worldwide. HAstV is a nonenveloped virus with a T=3 capsid and a positive-sense RNA genome. The capsid protein (CP) of HAstV is synthesized as a 90-kDa precursor (VP90) that can be divided into three linear domains: a conserved N-terminal domain, a hypervariable domain, and an acidic C-terminal domain. Maturation of HAstV requires proteolytic processing of the astrovirus CP both inside and outside the host cell, resulting in the removal of the C-terminal domain and the breakdown of the rest of the CP into three predominant protein species with molecular masses of ∼34, 27/29, and 25/26 kDa, respectively. We have now solved the crystal structure of VP9071–415 (amino acids [aa] 71 to 415 of VP90) of human astrovirus serotype 8 at a 2.15-Å resolution. VP9071–415 encompasses the conserved N-terminal domain of VP90 but lacks the hypervariable domain, which forms the capsid surface spikes. The structure of VP9071–415 is comprised of two domains: an S domain, which adopts the typical jelly-roll β-barrel fold, and a P1 domain, which forms a squashed β-barrel consisting of six antiparallel β-strands similar to what was observed in the hepatitis E virus (HEV) capsid structure. Fitting of the VP9071–415 structure into the cryo-electron microscopy (EM) maps of HAstV produced an atomic model for a continuous, T=3 icosahedral capsid shell. Our pseudoatomic model of the human HAstV capsid shell provides valuable insights into intermolecular interactions required for capsid assembly and trypsin-mediated proteolytic maturation needed for virus infectivity. Such information has potential applications in the development of a virus-like particle (VLP) vaccine as well as small-molecule drugs targeting astrovirus assembly/maturation. IMPORTANCE Human astrovirus (HAstV) is a leading cause of viral diarrhea in infants and young children worldwide. As a nonenveloped virus

  11. The crystal structure of GXGD membrane protease FlaK

    SciTech Connect

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

    2011-09-20

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

  12. The Crystal Structure of GXGD Membrane Protease FlaK

    SciTech Connect

    J Hu; Y Xue; S Lee; Y Ha

    2011-12-31

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

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

    PubMed Central

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

    2015-01-01

    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

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

    PubMed

    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.

  15. 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.

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

    PubMed

    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. PMID:25679634

  17. Photonic crystals, light manipulation, and imaging in complex nematic structures

    NASA Astrophysics Data System (ADS)

    Ravnik, Miha; Å timulak, Mitja; Mur, Urban; Čančula, Miha; Čopar, Simon; Žumer, Slobodan

    2016-03-01

    Three selected approaches for manipulation of light by complex nematic colloidal and non-colloidal structures are presented using different own custom developed theoretical and modelling approaches. Photonic crystals bands of distorted cholesteric liquid crystal helix and of nematic colloidal opals are presented, also revealing distinct photonic modes and density of states. Light propagation along half-integer nematic disclinations is shown with changes in the light polarization of various winding numbers. As third, simulated light transmission polarization micrographs of nematic torons are shown, offering a new insight into the complex structure characterization. Finally, this work is a contribution towards using complex soft matter in optics and photonics for advanced light manipulation.

  18. 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.

  19. 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.

  20. Structure and NLO property relationship in a novel chalcone co-crystal

    NASA Astrophysics Data System (ADS)

    Ravindra, H. J.; Chandrashekaran, K.; Harrison, W. T. A.; Dharmaprakash, S. M.

    2009-03-01

    Single crystals of a chalcone co-crystal (C18H19NO4/C17H16NO3Br; 0.972/0.028) have been grown by slow evaporation from solution. The powder second harmonic generation (SHG) efficiency of this chalcone co-crystal is 7 times that of urea. The dependence of second harmonic (SH) intensity on particle size revealed the existence of phase matching direction in this crystal. The large SHG efficiency observed is mainly due to the unidirectional alignment of molecular dipoles, in which the dipole moment of each molecule adds to establish a net polarization. The weak N-H ṡṡṡO hydrogen-bond interactions help to stabilize the noncentrosymmetric crystal packing and also contribute partly to the SHG. The better thermal stability, transparency and high laser damage resistance (>1.5 GW cm-2 at 532 nm, 8 ns) of this chalcone co-crystal indicate that it is a promising material for frequency doubling of diode lasers down to 470 nm. This molecule also shows a third-order NLO response and good optical limiting property of 8 ns laser pulses at 532 nm. The mechanism for optical limiting in this chalcone was attributed to two-photon induced excited state absorption that leads to reverse saturable absorption. The structure-property relationship in this chalcone and related compounds is discussed based on the experimental results and semiempherical hyperpolarizability calculations.

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

    SciTech Connect

    Uchiyama, Hiroaki Nakanishi, Shunsuke; Kozuka, Hiromitsu

    2014-09-15

    Crystalline SnO particles were obtained from Sn{sub 6}O{sub 4}(OH){sub 4} by the hydrothermal treatment in aqueous solutions containing gelatin at 150 °C for 24 h, where the morphologies of the SnO products changed from blocks to layered disks, stacked plates and unshaped aggregates with increasing amount of gelatin in the solutions. Such morphological changes of SnO particles were thought to be attributed to the suppression of the growth of SnO crystals by the adsorbed gelatin. - Graphical abstract: Nanostructured SnO particles were obtained from Sn{sub 6}O{sub 4}(OH){sub 4} by the hydrothermal treatment in gelatin solutions. - Highlights: • SnO particles were prepared from Sn{sub 6}O{sub 4}(OH){sub 4} by the hydrothermal treatment. • The adsorption of gelatin suppressed the growth of SnO crystals. • The shape of SnO particles depends on the amount of gelatin. • Blocks, disks, stacked plates and unshaped aggregates were obtained.

  2. Laser trapping of small colloidal particles in a nematic liquid crystal: clouds and ghosts.

    PubMed

    Musevic, I; Skarabot, M; Babic, D; Osterman, N; Poberaj, I; Nazarenko, V; Nych, A

    2004-10-29

    We show that, contrary to intuition, small (< or =1 microm) transparent particles can be trapped and manipulated in a nematic liquid crystal using an intense laser beam, although their index of refraction is lower than both refractive indices of the surrounding birefringent fluid. Two mechanisms are identified that are responsible for this anomalous trapping: (i) surface-induced distortion of the birefringent media around the particle, creating a high-index "cloud" around the colloid, and (ii) laser-induced distortion or (partial) melting of a nematic, creating a ghost colloid.

  3. 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

  4. Synthesis, crystal structure, crystal growth and physical properties of N,N-diethyl anilinium picrate

    NASA Astrophysics Data System (ADS)

    Subramaniyan @ Raja, R.; Anandha Babu, G.; Ramasamy, P.

    2011-11-01

    Crystalline substance of N,N-diethyl anilinium picrate (NNDEAP) has been synthesized and single crystals of NNDEAP were successfully grown for the first time by the slow evaporation solution growth technique at room temperature with dimensions 14×10×10 mm3. The formation of the new crystal has been confirmed by single crystal X-ray diffraction studies. The structural perfection of the grown crystal was analyzed by high resolution X-ray diffraction (HRXRD) measurements. The functional groups of NNDEAP have been identified by Fourier transform infrared spectral studies. Thermogravimetric analysis (TGA) and differential thermal analysis (DTA) have also been carried out and the thermal behavior of NNDEAP has been studied. The UV-vis-NIR studies have been carried out to identify the optical transmittance and the cut off wavelength of NNDEAP is identified. The dielectric loss and the dielectric constant as a function of frequency and temperature were measured for the grown crystal and the nature of variation of dielectric constant εr and dielectric losses (tan δ) were studied. Vicker's hardness test has been carried out on NNDEAP to measure the load dependent hardness. The laser induced surface damage threshold for the grown crystal was measured using Nd:YAG laser.

  5. Crystallization Behavior of Amorphous Si3N4 and Particle Size Control of the Crystallized α-Si3N4.

    PubMed

    Chung, Yong-Kwon; Kim, Shin-A; Koo, Jae-Hong; Oh, Hyeon-Cheol; Chi, Eun-Ok; Hahn, Jee-Hyun; Park, Chan

    2016-05-01

    Amorphous silicon nitride powder prepared by low-temperature vapor-phase reaction was heat treated at various temperatures for different periods of time to examine the crystallization behavior. The effects of the heat-treatment temperature and duration on the degree of crystallization were investigated along with the effect of the heat-up rate on the particle size, and its distribution, of the crystallized α-phase silicon nitride powder. A phase transition from amorphous to α-phase occurred at a temperature above 1400 degrees C. The crystallization. process was completed after heat treatment at 1500 degrees C for 3 h or at 1550 degrees C for 1 h. The crystallization process starts at the surface of the amorphous particle: while the outer regions of the particle become crystalline, the inner part remains amorphous. The re-arrangement of the Si and N atoms on the surface of the amorphous particle leads to the formation of hexagonal crystals that are separated from the host amorphous particle. The particle size and size distribution can be controlled by varying the heat-treatment profile (namely, the heat-treatment temperature, heating rate, and heating duration at the specified temperature), which can be used to control the relative extent of the nucleation and growth. The completion of most of the nucleation process by lowering the heat-up rate can be used to achieve a singlet particle size distribution. Bimodal particle size distribution can be achieved by fast heat-up during the crystallization process. PMID:27483939

  6. Photonics of liquid-crystal structures: A review

    SciTech Connect

    Palto, S. P. Blinov, L. M.; Barnik, M. I.; Lazarev, V. V.; Umanskii, B. A.; Shtykov, N. M.

    2011-07-15

    The original results of studies of the electro-optical and laser effects which have been performed at the Laboratory of Liquid Crystals of the Institute of Crystallography, Russian Academy of Sciences, over the last few years are reviewed. Cholesteric liquid crystals as vivid representatives of photonic structures and their behavior in an electric field are considered in detail. The formation of higher harmonics in the periodic distribution of the director field in a helical liquid crystal structure and, correspondingly, the new (anharmonic) mode of electro-optical effects are discussed. Another group of studies is devoted to bistable light switching by an electric field in chiral nematics. Polarization diffraction gratings controlled by an electric field are also considered. The results of studies devoted to microlasers on various photonic structures with cholesteric and nematic liquid crystals are considered in detail. Particular attention is given to the new regime: leaky-mode lasing. Designs of liquid crystal light amplifiers and their polarization, field, and spectral characteristics are considered in the last section.

  7. Orientational order and translational dynamics of magnetic particle assemblies in liquid crystals.

    PubMed

    Peroukidis, Stavros D; Klapp, Sabine H L

    2016-08-10

    Implementing extensive molecular dynamics simulations we explore the organization of magnetic particle assemblies (clusters) in a uniaxial liquid crystalline matrix comprised of rodlike particles. The magnetic particles are modelled as soft dipolar spheres with diameter significantly smaller than the width of the rods. Depending on the dipolar strength coupling the magnetic particles arrange into head-to-tail configurations forming various types of clusters including rings (closed loops) and chains. In turn, the liquid crystalline matrix induces long range orientational ordering to these structures and promotes their diffusion along the director of the phase. Different translational dynamics are exhibited as the liquid crystalline matrix transforms either from isotropic to nematic or from nematic to smectic state. This is caused due to different collective motion of the magnetic particles into various clusters in the anisotropic environments. Our results offer a physical insight for understanding both the structure and dynamics of magnetic particle assemblies in liquid crystalline matrices.

  8. Orientational order and translational dynamics of magnetic particle assemblies in liquid crystals.

    PubMed

    Peroukidis, Stavros D; Klapp, Sabine H L

    2016-08-10

    Implementing extensive molecular dynamics simulations we explore the organization of magnetic particle assemblies (clusters) in a uniaxial liquid crystalline matrix comprised of rodlike particles. The magnetic particles are modelled as soft dipolar spheres with diameter significantly smaller than the width of the rods. Depending on the dipolar strength coupling the magnetic particles arrange into head-to-tail configurations forming various types of clusters including rings (closed loops) and chains. In turn, the liquid crystalline matrix induces long range orientational ordering to these structures and promotes their diffusion along the director of the phase. Different translational dynamics are exhibited as the liquid crystalline matrix transforms either from isotropic to nematic or from nematic to smectic state. This is caused due to different collective motion of the magnetic particles into various clusters in the anisotropic environments. Our results offer a physical insight for understanding both the structure and dynamics of magnetic particle assemblies in liquid crystalline matrices. PMID:27460190

  9. Orientation control of liquid crystals using carbon-nanotube-magnetic particle hybrid materials.

    PubMed

    Jeong, Hyeon Su; Youn, Sang Cheon; Kim, Yun Ho; Jung, Hee-Tae

    2013-06-28

    We have developed a simple yet versatile method for aligning liquid crystals (LCs) by using magnetic-field oriented single-walled carbon nanotubes (SWNTs) that were modified with magnetic particles. A high degree of homeotropic/planar LC alignment was achieved by SWNTs being exposed to a very low strength magnetic field, combined with strong π-π interactions between the biphenyl group in the LCs and the wall of the SWNTs. PMID:23676827

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

    SciTech Connect

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

    2009-01-01

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

  11. 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.

  12. The crystal structure of samarosporin I at atomic resolution.

    PubMed

    Gessmann, Renate; Axford, Danny; Evans, Gwyndaf; Brückner, Hans; Petratos, Kyriacos

    2012-11-01

    The atomic resolution structures of samarosporin I have been determined at 100 and 293 K. This is the first crystal structure of a natural 15-residue peptaibol. The amino acid sequence in samarosporin I is identical to emerimicin IV and stilbellin I. Samarosporin is a peptide antibiotic produced by the ascomycetous fungus Samarospora rostrup and belongs to peptaibol subfamily 2. The structures at both temperatures are very similar to each other adopting mainly a 3₁₀-helical and a minor fraction of α-helical conformation. The helices are significantly bent and packed in an antiparallel fashion in the centered monoclinic lattice leaving among them an approximately 10-Å channel extending along the crystallographic twofold axis. Only two ordered water molecules per peptide molecule were located in the channel. Comparisons have been carried out with crystal structures of subfamily 2 16-residue peptaibols antiamoebin and cephaibols. The repercussion of the structural analysis of samarosporin on membrane function is discussed.

  13. Precise characterization of grain structures, stacking disorders, and lattice disorders of a close-packed colloidal crystal

    NASA Astrophysics Data System (ADS)

    Suzuki, Yoshihisa; Mori, Atsushi; Fujiwara, Takahisa; Tamura, Katsuhiro

    2011-05-01

    The perpendicular fracture surface of a dried colloidal crystal with pillar-like grains, obtained by centrifugation of a dispersion of polystyrene particles, was observed using a scanning electron microscope. Many grain boundaries on the fracture surface were observed at the particle level. Most of the particles on the surface showed a face-centered cubic (FCC) array. Although some grains were single FCC ones, other FCC grains contained some stacking disorders. Most of the surface was covered with such grains, and the grain boundaries formed a mosaic-like pattern. From these results, we confirmed that the colloidal crystals obtained by centrifugation formed a bundle structure of pillar-like FCC grains. A fracture surface adjacent to the side wall of the growth cell was also observed. The surface was composed of several layers. In the uppermost layer closest to the wall, numerous point defects and mismatches of triangular lattices between the neighboring two-dimensional islands were observed. These mismatches and point defects probably generated several lattice defects in the crystal. Similar generation of lattice defects probably occurred at the bottom of the container or the growth front of the crystals. Screw dislocations were also found in the layers, although they were not observed frequently. From these results, it was concluded that two-dimensional nucleation growth and spiral growth probably occurred on the crystal-dispersion interfaces of colloidal crystals as well as on the surface of atomic crystals.

  14. Crystal structure of HINT from Helicobacter pylori.

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  16. Particles as Fundaments of Discourse Structuring.

    ERIC Educational Resources Information Center

    Fernandez-Vest, M. M. Jocelyne

    A serious study of discourse particles (DIPs) must be founded on the analysis of orality in its two main dimensions: oral communication in its ordinary functioning (i.e., discourse, conversation, enunciation), but also in expression ritualized by the oral tradition of cultures that do not have a writing system. The association of the two…

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

    NASA Astrophysics Data System (ADS)

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

    2001-11-01

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

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

    PubMed Central

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

    2015-01-01

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

  19. Interleukin-22 and its crystal structure.

    PubMed

    Nagem, Ronaldo Alves Pinto; Ferreira Júnior, José Ribamar; Dumoutier, Laure; Renauld, Jean-Christophe; Polikarpov, Igor

    2006-01-01

    Interleukin-22 (IL-22) is a cytokine that regulates the production of acute phase proteins of the immunological response. On binding to its cognate receptor (IL-22R1), which is associated to the interleukin-10 receptor 2 (IL-10R2), IL-22 promotes activation of signal transducer and activator of transcription (STAT) pathway and several other cellular responses. A soluble receptor termed interleukin-22 binding protein (IL-22BP) is also able to bind to IL-22 as a natural protein antagonist, and probably provides systemic regulation of IL-22 activity. This inflammatory response system is analyzed here in terms of its molecular physiology and structural assembly. Three-dimensional (3D) model of IL-22 and structural basis of its interactions with the cognate receptors are discussed.

  20. Three-dimensional Dielectric Photonic Crystal Structures for Laser-driven Acceleration

    SciTech Connect

    Cowan, Benjamin M.; /Tech-X, Boulder /SLAC

    2007-12-14

    We present the design and simulation of a three-dimensional photonic crystal waveguide for linear laser-driven acceleration in vacuum. The structure confines a synchronous speed-of-light accelerating mode in both transverse dimensions. We report the properties of this mode, including sustainable gradient and optical-to-beam efficiency. We present a novel method for confining a particle beam using optical fields as focusing elements. This technique, combined with careful structure design, is shown to have a large dynamic aperture and minimal emittance growth, even over millions of optical wavelengths.

  1. Structural and optical properties of a new chalcone single crystal

    NASA Astrophysics Data System (ADS)

    Rajesh Kumar, P. C.; Ravindrachary, V.; Janardhana, K.; Poojary, Boja

    2012-09-01

    A new nonlinear optical material 1-(4-methylthiophenyl)-3-(4-methoxyphenyl)prop-2-en-1-one with molecular formula C17H16O2S was synthesized by using the Claisen-Schmidt condensation reaction method. The Various functional groups present in the compound were identified using recorded FT-IR spectrum. The crystal growth parameters have been studied using solubility test and acetone is found to be a very good solvent for the crystal growth at an ambient temperature. The transparent high quality single crystals up to a size of 26×2×2 mm3 were grown using the slow evaporation solution growth technique. UV-visible study was carried out and the spectrum reveals that the crystal is transparent in the entire visible region and absorptive in the UV region. The refractive index is determined using Brewster's angle method. The optical energy band gap of the material is measured using Tauc's plot and the direct method. The single crystal XRD of MMPP crystal shows the following cell parameters: a=5.9626(2) Å, b=15.3022(6) Å, c=16.0385(7) Å, α=β=γ=90°, volume=1463.37(10) Å3 with a space group of Pna21. The compound MMPP exhibits optical nonlinearity (NLO) and its second order NLO efficiency is 3.15 times to that of urea. The effect of functional groups OCH3 and SCH3 on the non-linearity as well as the structural property of the compound has been discussed. The crystal is thermally stable. High NLO efficiency, good thermal stability, good transparency and ability to grow as a high quality single crystal make this material very attractive for opto-electronic applications.

  2. 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.

  3. 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

  4. 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

  5. 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.…

  6. Redetermination of the crystal structure of NbF4.

    PubMed

    Bandemehr, Jascha; Conrad, Matthias; Kraus, Florian

    2016-08-01

    Single crystals of NbF4, niobium(IV) tetra-fluoride, were synthesized by disproportionation of Nb2F5 at 1273 K in a sealed niobium tube, extracted and studied by single-crystal X-ray diffraction. Previous reports on the crystal structure of NbF4 were based on X-ray powder diffraction data and the observed isotypicity to SnF4 [Gortsema & Didchenko (1965 ▸). Inorg. Chem. 4, 182-186; Schäfer et al. (1965 ▸). J. Less Common Met. 9, 95-104]. The data obtained from a single-crystal X-ray diffraction study meant the atomic coordinates could now be refined as well as their anisotropic displacement parameters, leading to a significant improvement of the structural model of NbF4. In the structure, the Nb atom is octahedron-like surrounded by six F atoms of which four are bridging to other NbF6 octa-hedra, leading to a layer structure extending parallel to the ab plane. PMID:27536416

  7. Redetermination of the crystal structure of NbF4

    PubMed Central

    Bandemehr, Jascha; Conrad, Matthias; Kraus, Florian

    2016-01-01

    Single crystals of NbF4, niobium(IV) tetra­fluoride, were synthesized by disproportionation of Nb2F5 at 1273 K in a sealed niobium tube, extracted and studied by single-crystal X-ray diffraction. Previous reports on the crystal structure of NbF4 were based on X-ray powder diffraction data and the observed isotypicity to SnF4 [Gortsema & Didchenko (1965 ▸). Inorg. Chem. 4, 182–186; Schäfer et al. (1965 ▸). J. Less Common Met. 9, 95–104]. The data obtained from a single-crystal X-ray diffraction study meant the atomic coordinates could now be refined as well as their anisotropic displacement parameters, leading to a significant improvement of the structural model of NbF4. In the structure, the Nb atom is octahedron-like surrounded by six F atoms of which four are bridging to other NbF6 octa­hedra, leading to a layer structure extending parallel to the ab plane. PMID:27536416

  8. 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.

  9. The diammoniate of diborane: Crystal structure and hydrogen release

    SciTech Connect

    Bowden, Mark E.; Heldebrant, David J.; Karkamkar, Abhijeet J.; Proffen, Thomas E.; Schenter, Gregory K.; Autrey, Thomas

    2010-10-12

    [(NH3)2BH2]+[BH4]- is formed from the room temperature decomposition of NH4+BH4-, via a NH3BH3 intermediate. Its crystal structure has been determined and contains disordered BH4- ions in 2 distinct sites. Hydrogen release is similar to that from NH3BH3 but with faster kinetics.

  10. Analysis of voids in crystal structures: the methods of 'dual' crystal chemistry.

    PubMed

    Blatov, V A; Shevchenko, A P

    2003-01-01

    The theoretical basics of the analysis of voids in crystal structures by means of Voronoi-Dirichlet polyhedra (VDP) and of the graph theory are stated. Topological relations are considered between VDPs and atomic domains in a crystal field. These relations allow the separation of two non-intersecting topological subspaces in a crystal structure, whose connectednesses are defined by two finite 'reduced' graphs. The first, 'direct', subspace includes the atoms (VDP centres) and the network of interatomic bonds (VDP faces), the second, 'dual', one comprises the void centres (VDP vertices) and the system of channels (VDP edges) between them. Computer methods of geometrical-topological analysis of the 'dual' subspace are developed and implemented within the program package TOPOS. They are designed for automatically restoring the system of channels, visualizing and sizing voids and void conglomerates, dimensional analysis of continuous void systems, and comparative topological analysis of 'dual' subspaces for various substances. The methods of analysis of 'dual' and 'direct' subspaces are noted to differ from each other only in some details that allows the term 'dual' crystal chemistry to be introduced. The efficiency of the methods is shown with the analysis of compounds of different chemical nature: simple substances, ionic structures, superionic conductors, zeolites, clathrates, organic supramolecular complexes. PMID:12496460

  11. 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.

  12. 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.

  13. Structural characterization of particle systems using spherical harmonics

    SciTech Connect

    Feinauer, Julian; Spettl, Aaron; Manke, Ingo; Strege, Stefan; Kwade, Arno; Pott, Andres; Schmidt, Volker

    2015-08-15

    Many important properties of particulate materials are heavily influenced by the size and shape of the constituent particles. Thus, in order to control and improve product quality, it is important to develop a good understanding of the shape and size of the particles that make up a given particulate material. In this paper, we show how the spherical harmonics expansion can be used to approximate particles obtained from tomographic 3D images. This yields an analytic representation of the particles which can be used to calculate structural characteristics. We present an estimation method for the optimal length of expansion depending on individual particle shapes, based on statistical hypothesis testing. A suitable choice of this parameter leads to a smooth approximation that preserves the main shape features of the original particle. To show the wide applicability of this procedure, we use it to approximate particles obtained from two different tomographic 3D datasets of particulate materials. The first one describes an anode material from lithium-ion cells that consists of sphere-like particles with different sizes. The second dataset describes a powder of highly non-spherical titanium dioxide particles. - Highlights: • Complex particle shapes are described analytically by spherical harmonics expansion. • The optimal length of the expansion is estimated for each particle individually. • Characteristics like, e.g., particle surface areas can be calculated efficiently. • The method is applied to two tomographic datasets of particulate materials.

  14. Band structures in Sierpinski triangle fractal porous phononic crystals

    NASA Astrophysics Data System (ADS)

    Wang, Kai; Liu, Ying; Liang, Tianshu

    2016-10-01

    In this paper, the band structures in Sierpinski triangle fractal porous phononic crystals (FPPCs) are studied with the aim to clarify the effect of fractal hierarchy on the band structures. Firstly, one kind of FPPCs based on Sierpinski triangle routine is proposed. Then the influence of the porosity on the elastic wave dispersion in Sierpinski triangle FPPCs is investigated. The sensitivity of the band structures to the fractal hierarchy is discussed in detail. The results show that the increase of the hierarchy increases the sensitivity of ABG (Absolute band gap) central frequency to the porosity. But further increase of the fractal hierarchy weakens this sensitivity. On the same hierarchy, wider ABGs could be opened in Sierpinski equilateral triangle FPPC; whilst, a lower ABG could be opened at lower porosity in Sierpinski right-angled isosceles FPPCs. These results will provide a meaningful guidance in tuning band structures in porous phononic crystals by fractal design.

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

    PubMed

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

    2013-01-01

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

  16. 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.

  17. Crystal structure and stereochemistry study of 2-substituted benzoxazole derivatives.

    PubMed

    Mabied, Ahmed F; Shalaby, Elsayed M; Zayed, Hamdia A; El-Kholy, Esmat; Farag, Ibrahim S A; Ahmed, Naima A

    2014-01-01

    The structure of 2-[(4-chlorophenylazo) cyanomethyl] benzoxazole, C15H9ClN4O (I), has triclinic ([Formula: see text]) symmetry. The structure displays N-H ⋯ N hydrogen bonding. The structure of 2-[(arylidene) cyanomethyl] benzoxazoles, C17H10N2O3 (II), has triclinic ([Formula: see text]) symmetry. The structure displays C-H ⋯ N, C-H ⋯ C hydrogen bonding. In (I), the chlorophenyl and benzoxazole groups adopt a trans configuration with respect to the central cyanomethyle hydrazone moiety. Compound (II) crystallized with two molecules in the asymmetric unit shows cisoid conformation between cyano group and benzoxazole nitrogen, contrary to (I). In (II) the benzodioxole has an envelope conformation (the C17 atom is the flap atom). The molecular geometry obtained using molecular mechanics (MM) calculations has been discussed along with the results of single crystal analysis.

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2013-01-01

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

  20. Crystallization studies of lunar igneous rocks: crystal structure of synthetic armalcolite.

    PubMed

    Lind, M D; Housley, R M

    1972-02-01

    Crystals of armalcolite, Mg(0.5)Fe(0.5)Ti(2)O(5), up to several millimeters in length have been grown from a glass initially having the composition of lunar rock 10017. A single-crystal x-ray study has confirmed that the crystals are isomorphous with pseudobrookite and has shown that the cations are strongly ordered, with the Ti(4+) ions occupying the 8f sites and the Fe(2+) and Mg(2+) ions randomly distributed over the 4c sites. An examination of karrooite, MgTi(2)O(5), has revealed a similar distribution of Mg(2+) and Ti(4+) ions. A reexamination of earlier x-ray and Mössbauer data for pseudobrookite, Fe(2)TiO(5), has shown that it is more consistent with this type of ordering than with the inverse structure that has been generally assumed.

  1. Concentrating colloids with electric field gradients. I. Particle transport and growth mechanism of hard-sphere-like crystals in an electric bottle.

    PubMed

    Leunissen, Mirjam E; Sullivan, Matthew T; Chaikin, Paul M; van Blaaderen, Alfons

    2008-04-28

    This work concerns the use of electric field gradients to manipulate the local particle concentration in a hard-sphere-like suspension. Inside a specially designed "electric bottle," we observed our colloids to collect in the regions of lowest field strength ("negative dielectrophoresis"). This allows for the use of larger field gradients and stronger dielectrophoretic forces than in the original electric bottle design, which was based on positive dielectrophoresis [M. T. Sullivan et al., Phys. Rev. Lett. 96, 015703 (2006)]. We used confocal scanning laser microscopy to quantitatively follow the time-dependent change in the particle density and the suspension structure. Within a few days, the dielectrophoretic compression was seen to initiate a heterogeneouslike growth of large single crystals, which took place far out-of-equilibrium. The crystals had a random hexagonal close-packed structure and displayed an intriguing growth mechanism, during which the entire crystal was continuously transported, while growing both on the "high-field" and the "low-field" sides, although at different rates. After switching off the electric field, the compressed crystals were found to relax to a lower packing fraction and melt, at a much slower rate than the crystal growth. Besides revealing the particular (far out-of-equilibrium) crystal growth mechanism in these electric bottles, our observations also shed light on the role of the different particle transport processes in the cell and some of the relevant tuning parameters. This is useful for different types of experiments, for instance, focusing more on melting, homogeneous crystallization, or the glass transition.

  2. Serendibite, a Complicated, New, Inorganic Crystal Structure

    PubMed Central

    Buerger, Martin J.; Venkatakrishnan, V.

    1974-01-01

    Serendibite with very similar analyses is known from Ceylon and New York. The triclinic cell of symmetry P[unk] and volume 670.9 Å3 contains 2Ca1.64Mg2.64Fe0.27IIAl4.64B1.66Si3O20, with 14 metal atoms and 20 oxygen atoms in the asymmetric unit. It was solved by the “direct” method of transforming the ordinary three-dimensional Patterson function into an approximation of the electron density by using conjugate peaks and minimum functions, followed by successive Fourier syntheses and least-squares refinement to R = 7.1%. This new structure is composed of interrupted brucite-type layers which form an octahedral framework, and winged single chains of tetrahedra. The structure has units of similar, but not identical, geometry to those of the minerals sapphirine and aenigmatite, and these similar units are assembled in a different way. PMID:16592193

  3. 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.

  4. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    DOE PAGES

    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

  5. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    SciTech Connect

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

    2015-05-05

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

  6. 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.

  7. Crystal structure of new AsS2 compound

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

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

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

    SciTech Connect

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

    2015-03-15

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

  9. Tailor-made force fields for crystal-structure prediction.

    PubMed

    Neumann, Marcus A

    2008-08-14

    A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom.

  10. Tailor-made force fields for crystal-structure prediction.

    PubMed

    Neumann, Marcus A

    2008-08-14

    A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom. PMID:18642947

  11. Separation-independent attractive force between like particles mediated by nematic-liquid-crystal distortions.

    PubMed

    Fukuda, Jun-Ichi; Yokoyama, Hiroshi

    2005-04-15

    We investigate numerically with the aid of the Landau-de Gennes continuum theory the interaction between two spherical particles carrying the same topological charges +1 mediated by the elastic distortion of a nematic liquid crystal. We consider the case where an escaped nontopological ring disclination is situated between the particles; the director is continuous everywhere and no counterdefects are present. We find that the interaction is attractive and its potential energy depends linearly on the interparticle distance D. This behavior yields the D-independent interaction force, which was observed experimentally by Poulin, Cabuil, and Weitz [Phys. Rev. Lett. 79, 4862 (1997)] in the presence of narrow strings of birefringent regions ("bubble-gum" configuration) between the particles. PMID:15904120

  12. Thermodynamics of sublimation, crystal lattice energies, and crystal structures of racemates and enantiomers: (+)- and (+/-)-ibuprofen.

    PubMed

    Perlovich, German L; Kurkov, Sergey V; Hansen, Lars Kr; Bauer-Brandl, Annette

    2004-03-01

    Thermodynamic differences between ibuprofen (IBP) racemate and the (+)-enantiomer were studied by X-ray diffraction, thermoanalysis, and crystal energy calculations. The thermodynamic functions of sublimation (as a measure of crystal lattice energy) were obtained by the transpiration method. The sublimation enthalpies (DeltaH(sub)) of (+/-)-IBP and (+)-IBP are 115.8 +/- 0.6 and 107.4 +/- 0.5 kJ. mol(-1), respectively. Using the temperature dependency of the saturated vapor pressure, the relative fractions of enthalpy and entropy of the sublimation process were calculated, and the sublimation process for both the racemate and the enantiomer was found to be enthalpy driven (62%). Two different force fields, Mayo et al. (M) and Gavezzotti (G), were used for comparative analysis of crystal lattice energies. Both force fields revealed that the van der Waals term contributes more to the packing energy in (+)-IBP than in (+/-)-IBP. The hydrogen bonding energy, however, contributes at 29.7 and 32.3% to the total crystal lattice energy in (+)-IBP and (+/-)-IBP (M), respectively. Furthermore, different structure fragments of the IBP molecule were analyzed with respect to their contribution to nonbonded van der Waals interactions. The effect of the C-H distance on the van der Waals term of the crystal lattice energy was also studied.

  13. Crystal structure of 4-carbamoylpyridinium chloride.

    PubMed

    Fellows, Simon M; Prior, Timothy J

    2016-04-01

    The hydro-chloride salt of isonicotinamide, C6H7N2O(+)·Cl(-), has been synthesized from a dilute solution of hydro-chloric acid in aceto-nitrile. The compound displays monoclinic symmetry (space group C2/c) at 150 K, similar to the related hydro-chloride salt of nicotinamide. The asymmetric unit contains one protonated isonicotinamide mol-ecule and a chloride anion. An array of hydrogen-bonding inter-actions, including a peculiar bifurcated pyridinium-chloride inter-action, results in linear chains running almost perpendicularly in the [150] and [1-50] directions within the structure. A description of the hydrogen-bonding network and comparison with similar compounds are presented. PMID:27375858

  14. Crystal structure of 4-carbamoylpyridinium chloride

    PubMed Central

    Fellows, Simon M.; Prior, Timothy J.

    2016-01-01

    The hydro­chloride salt of isonicotinamide, C6H7N2O+·Cl−, has been synthesized from a dilute solution of hydro­chloric acid in aceto­nitrile. The compound displays monoclinic symmetry (space group C2/c) at 150 K, similar to the related hydro­chloride salt of nicotinamide. The asymmetric unit contains one protonated isonicotinamide mol­ecule and a chloride anion. An array of hydrogen-bonding inter­actions, including a peculiar bifurcated pyridinium–chloride inter­action, results in linear chains running almost perpendicularly in the [150] and [1-50] directions within the structure. A description of the hydrogen-bonding network and comparison with similar compounds are presented. PMID:27375858

  15. Crystal structures of Ziegler-Natta catalyst supports.

    PubMed

    Malizia, Federica; Fait, Anna; Cruciani, Giuseppe

    2011-12-01

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

  16. On calculating the equilibrium structure of molecular crystals.

    SciTech Connect

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

    2010-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  18. Modeling liquid crystal bilayer structures with minimal surfaces.

    PubMed

    Enlow, J D; Enlow, R L; McGrath, K M; Tate, M W

    2004-01-22

    This paper describes a new convenient and accurate method of calculating x-ray diffraction integrated intensities from detailed cubic bilayer structures. The method is employed to investigate the structure of a particular surfactant system (didodecyldimethylammonium bromide in a solution of oil and heavy water), for which single-crystal experimental data have recently been collected. The diffracted peak intensities correlate well with theoretical structures based on mathematical minimal surfaces. Optimized electron density profiles of the bilayer are presented, providing new insight into key features of the bilayer structure.

  19. Mechanism and kinetics of organic matter degradation based on particle structure variation during pig manure aerobic composting.

    PubMed

    Ge, Jinyi; Huang, Guangqun; Huang, Jing; Zeng, Jianfei; Han, Lujia

    2015-07-15

    Characterization of the dynamic structure of composting particles may facilitate our understanding of the mechanisms of organic matter degradation during pig manure-wheat straw aerobic composting. In this study, changes in the size, shape, pores, chemical compositions, and crystal structures of pig manure particles during composting were investigated. The results showed that the median diameter (D50) decreased exponentially, while the particle aspect ratio and sphericity were unchanged, suggesting that particles were degraded uniformly along different radial directions. Pores had a mean diameter of 15-30 μm and were elliptical. The particle porosity increased linearly mainly because of hemicellulose degradation. Furthermore, the influence of particle structure variation on the first order rate constant (k) of organic matter degradation was corrected, which may facilitate the optimization of operation conditions. The k value was proportional to the reciprocal of D50 according to the specific surface area of particles, and it decreased with increased porosity due to the stabilized chemical compositions and crystal structures of particles. However, the applicability of these data to other composting materials should be verified. PMID:25781372

  20. Thin film solar cell design based on photonic crystal and diffractive grating structures.

    PubMed

    Mutitu, James G; Shi, Shouyuan; Chen, Caihua; Creazzo, Timothy; Barnett, Allen; Honsberg, Christiana; Prather, Dennis W

    2008-09-15

    In this paper we present novel light trapping designs applied to multiple junction thin film solar cells. The new designs incorporate one dimensional photonic crystals as band pass filters that reflect short light wavelengths (400 - 867 nm) and transmit longer wavelengths(867 -1800 nm) at the interface between two adjacent cells. In addition, nano structured diffractive gratings that cut into the photonic crystal layers are incorporated to redirect incoming waves and hence increase the optical path length of light within the solar cells. Two designs based on the nano structured gratings that have been realized using the scattering matrix and particle swarm optimization methods are presented. We also show preliminary fabrication results of the proposed devices.

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

    PubMed

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

    2016-02-01

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

  2. Projection structure of frog rhodopsin in two crystal forms.

    PubMed Central

    Schertler, G F; Hargrave, P A

    1995-01-01

    Rhodopsin is the G protein-coupled receptor that upon light activation triggers the visual transduction cascade. Rod cell outer segment disc membranes were isolated from dark-adapted frog retinas and were extracted with Tween detergents to obtain two-dimensional rhodopsin crystals for electron crystallography. When Tween 80 was used, tubular structures with a p2 lattice (a = 32 A, b = 83 A, gamma = 91 degrees) were formed. The use of a Tween 80/Tween 20 mixture favored the formation of larger p22(1)2(1) lattices (a = 40 A, b = 146 A, gamma = 90 degrees). Micrographs from frozen hydrated frog rhodopsin crystals were processed, and projection structures to 7-A resolution for the p22(1)2(1) form and to 6-A resolution for the p2 form were calculated. The maps of frog rhodopsin in both crystal forms are very similar to the 9-A map obtained previously for bovine rhodopsin and show that the arrangement of the helices is the same. In a tentative topographic model, helices 4, 6, and 7 are nearly perpendicular to the plane of the membrane. In the higher-resolution projection maps of frog rhodopsin, helix 5 looks more tilted than it appeared previously. The quality of the two frog rhodopsin crystals suggests that they would be suitable to obtain a three-dimensional structure in which all helices would be resolved. Images Fig. 1 Fig. 2 Fig. 6 PMID:8524807

  3. Band structure and optical properties of diglycine nitrate crystal

    NASA Astrophysics Data System (ADS)

    Andriyevsky, Bohdan; Ciepluch-Trojanek, Wioleta; Romanyuk, Mykola; Patryn, Aleksy; Jaskólski, Marcin

    2005-07-01

    Experimental and theoretical investigations of the electron energy characteristics and optical spectra for diglycine nitrate crystal (DGN), (NH 2CH 2COOH) 2·HNO 3, in the paraelectric phase ( T=295 K) are presented. Spectral dispersion of light reflection R( E) have been measured in the range of 3-22 eV and the optical functions n( E) and k( E) have been calculated using Kramers-Kronig relations. First principal calculations of the electron energy characteristic and optical spectra of DGN crystal have been performed in the frame of density functional theory using CASTEP code (CAmbridge Serial Total Energy Package). Optical transitions forming the low-energy edge of fundamental absorption are associated with the nitrate groups NO 3. Peculiarities of the band structure and DOS projected onto glycine and NO 3 groups confirm the molecular character of DGN crystal.

  4. 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.

  5. 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.

  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. Use of Pom Pons To Illustrate Cubic Crystal Structures

    NASA Astrophysics Data System (ADS)

    Cady, Susan G.

    1997-07-01

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

  8. Crystal structure of Brinzolamide: a carbonic anhydrase inhibitor.

    PubMed

    Zheng, Huirong; Lou, Benyong

    2016-05-01

    In crystal structure of the title compound, C12H21N3O5S3 [systematic name: (R)-4-ethyl-amino-2-(3-meth-oxy-prop-yl)-3,4-di-hydro-2H-thieno[3,2-e][1,2]thia-zine-6-sulfonamide 1,1-dioxide], there exist three kinds of hydrogen-bonding inter-actions. The sulfonamide group is involved in hydrogen bonding with the secondary amine and the meth-oxy O atom, resulting in the formation of layers parallel to the bc plane. The layers are linked by an N-H⋯O hydrogen bond involving a sulfonamide O atom as acceptor and the secondary amine H atom as donor, which gives rise to the formation of a unique bilayer structure. The absolute structure of the mol-ecule in the crystal was determined by resonant scattering [Flack parameter = 0.01 (4)]. PMID:27308020

  9. First principles investigation of the structure of a bacteriochlorophyll crystal

    SciTech Connect

    Marchi, M. |; Hutter, J.; Parrinello, M.

    1996-08-21

    In this communication we present an ab initio study of the crystal of methyl bacteriophorbide (MeBPheo) a, a bacteriochlorophyll derivative, and high-precision structure of which is available. Our main purpose has been to investigate the viability of the technique toward complex molecular systems relevant to biologically important phenomena, in this particular case photosynthesis. Here we present the following results: First, we show that DFT is capable of calculating nuclear positions in excellent agreement with the experimental X-ray structure. Second, the calculated electronic density of the HOMO orbital reveals a {pi} type bond between rings I and III, consistent with the one-dimensional chain structure of the MeBPheo a molecules in the crystal. Finally, after performing the optimization of the molecular geometry with one electron in the LUMO state, we find localized bond length changes near the ring II of the MeBPheo a. 19 refs., 3 figs.

  10. Myelin structures formed by thermotropic smectic liquid crystals.

    PubMed

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

    2013-12-17

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

  11. Thermally triggered solid-state single-crystal-to-single-crystal structural transformation accompanies property changes.

    PubMed

    Li, Quan-Quan; Ren, Chun-Yan; Huang, Yang-Yang; Li, Jian-Li; Liu, Ping; Liu, Bin; Liu, Yang; Wang, Yao-Yu

    2015-03-16

    The 1D complex [(CuL0.5H2O)⋅H2O]n (1) (H4L = 2,2'-bipyridine-3,3',6,6'-tetracarboxylic acid) undergoes an irreversible thermally triggered single-crystal-to-single-crystal (SCSC) transformation to produce the 3D anhydrous complex [CuL0.5]n (2). This SCSC structural transformation was confirmed by single-crystal X-ray diffraction analysis, thermogravimetric (TG) analysis, powder X-ray diffraction (PXRD) patterns, variable-temperature powder X-ray diffraction (VT-PXRD) patterns, and IR spectroscopy. Structural analyses reveal that in complex 2, though the initial 1D chain is still retained as in complex 1, accompanied with the Cu-bound H2O removed and new O(carboxyl)-Cu bond forming, the coordination geometries around the Cu(II) ions vary from a distorted trigonal bipyramid to a distorted square pyramid. With the drastic structural transition, significant property changes are observed. Magnetic analyses show prominent changes from antiferromagnetism to weak ferromagnetism due to the new formed Cu1-O-C-O-Cu4 bridge. The catalytic results demonstrate that, even though both solid-state materials present high catalytic activity for the synthesis of 2-imidazolines derivatives and can be reused, the activation temperature of complex 1 is higher than that of complex 2. In addition, a possible pathway for the SCSC structural transformations is proposed.

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

    PubMed

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

    2015-09-01

    D-Galactose-binding lectin from the octocoral, Sinularia lochmodes (SLL-2), distributes densely on the cell surface of microalgae, Symbiodinium sp., an endosymbiotic dinoflagellate of the coral, and is also shown to be a chemical cue that transforms dinoflagellate into a non-motile (coccoid) symbiotic state. SLL-2 binds with high affinity to the Forssman antigen (N-acetylgalactosamine(GalNAc)α1-3GalNAcβ1-3Galα1-4Galβ1-4Glc-ceramide), and the presence of Forssman antigen-like sugar on the surface of Symbiodinium CS-156 cells was previously confirmed. Here we report the crystal structures of SLL-2 and its GalNAc complex as the first crystal structures of a lectin involved in the symbiosis between coral and dinoflagellate. N-Linked sugar chains and a galactose derivative binding site common to H-type lectins were observed in each monomer of the hexameric SLL-2 crystal structure. In addition, unique sugar-binding site-like regions were identified at the top and bottom of the hexameric SLL-2 structure. These structural features suggest a possible binding mode between SLL-2 and Forssman antigen-like pentasaccharide. PMID:26022515

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

    PubMed

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

    2015-09-01

    D-Galactose-binding lectin from the octocoral, Sinularia lochmodes (SLL-2), distributes densely on the cell surface of microalgae, Symbiodinium sp., an endosymbiotic dinoflagellate of the coral, and is also shown to be a chemical cue that transforms dinoflagellate into a non-motile (coccoid) symbiotic state. SLL-2 binds with high affinity to the Forssman antigen (N-acetylgalactosamine(GalNAc)α1-3GalNAcβ1-3Galα1-4Galβ1-4Glc-ceramide), and the presence of Forssman antigen-like sugar on the surface of Symbiodinium CS-156 cells was previously confirmed. Here we report the crystal structures of SLL-2 and its GalNAc complex as the first crystal structures of a lectin involved in the symbiosis between coral and dinoflagellate. N-Linked sugar chains and a galactose derivative binding site common to H-type lectins were observed in each monomer of the hexameric SLL-2 crystal structure. In addition, unique sugar-binding site-like regions were identified at the top and bottom of the hexameric SLL-2 structure. These structural features suggest a possible binding mode between SLL-2 and Forssman antigen-like pentasaccharide.

  14. Photoinduced Directional Motions of Microparticles at Air-Liquid-Crystal Interfaces of Azobenzene-Doped Liquid-Crystal Films with Homeotropic or Homogeneous Alignment Structures

    NASA Astrophysics Data System (ADS)

    Yamamoto, Takahiro; Yoshida, Masaru

    2012-10-01

    We investigated the effects of liquid-crystal (LC) alignments on photoinduced motions of microparticles at air-LC interfaces of azobenzene-doped LC films. In homeotropically aligned LC films, the lattice spacings of pseudo-hexagonal structures of microparticles site-selectively exhibited reversible expansion or contraction on alternating irradiation with ultraviolet and visible light. The particle motions were probably driven by photochemical deformation of LC surfaces. In homogeneously aligned films, alternating irradiation induced macroscopic convective flows followed by rapid gathering or dispersion of linear chains of microparticles. Particle motions were significantly influenced by LC alignments as well as the light wavelength.

  15. Rigidity analysis of protein biological assemblies and periodic crystal structures

    PubMed Central

    2013-01-01

    Background We initiate in silico rigidity-theoretical studies of biological assemblies and small crystals for protein structures. The goal is to determine if, and how, the interactions among neighboring cells and subchains affect the flexibility of a molecule in its crystallized state. We use experimental X-ray crystallography data from the Protein Data Bank (PDB). The analysis relies on an effcient graph-based algorithm. Computational experiments were performed using new protein rigidity analysis tools available in the new release of our KINARI-Web server http://kinari.cs.umass.edu. Results We provide two types of results: on biological assemblies and on crystals. We found that when only isolated subchains are considered, structural and functional information may be missed. Indeed, the rigidity of biological assemblies is sometimes dependent on the count and placement of hydrogen bonds and other interactions among the individual subchains of the biological unit. Similarly, the rigidity of small crystals may be affected by the interactions between atoms belonging to different unit cells. We have analyzed a dataset of approximately 300 proteins, from which we generated 982 crystals (some of which are biological assemblies). We identified two types of behaviors. (a) Some crystals and/or biological assemblies will aggregate into rigid bodies that span multiple unit cells/asymmetric units. Some of them create substantially larger rigid cluster in the crystal/biological assembly form, while in other cases, the aggregation has a smaller effect just at the interface between the units. (b) In other cases, the rigidity properties of the asymmetric units are retained, because the rigid bodies did not combine. We also identified two interesting cases where rigidity analysis may be correlated with the functional behavior of the protein. This type of information, identified here for the first time, depends critically on the ability to create crystals and biological assemblies

  16. Structural engineering of three-dimensional phononic crystals

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  17. One dimensional coordination polymers: Synthesis, crystal structures and spectroscopic properties

    NASA Astrophysics Data System (ADS)

    Karaağaç, Dursun; Kürkçüoğlu, Güneş Süheyla; Şenyel, Mustafa; Şahin, Onur

    2016-11-01

    Two new one dimensional (1D) cyanide complexes, namely [M(4-aepy)2(H2O)2][Pt(CN)4], (4-aepy = 4-(2-aminoethyl)pyridine M = Cu(II) (1) or Zn(II) (2)), have been synthesized and characterized by vibrational (FT-IR and Raman) spectroscopy, single crystal X-ray diffraction, thermal and elemental analyses techniques. The crystallographic analyses reveal that 1 and 2 are isomorphous and isostructural, and crystallize in the monoclinic system and C2 space group. The Pt(II) ions are coordinated by four cyanide-carbon atoms in the square-planar geometry and the [Pt(CN)4]2- ions act as a counter ion. The M(II) ions display an N4O2 coordination sphere with a distorted octahedral geometry, the nitrogen donors belonging to four molecules of the organic 4-aepy that act as unidentate ligands and two oxygen atoms from aqua ligands. The crystal structures of 1 and 2 are similar each other and linked via intermolecular hydrogen bonding, Pt⋯π interactions to form 3D supramolecular network. Vibration assignments of all the observed bands are given and the spectral features also supported to the crystal structures of the complexes.

  18. Lattice dynamics of crystals having R2MX6 structure

    NASA Astrophysics Data System (ADS)

    Torres, D. I.; Freire, J. D.; Katiyar, R. S.

    1997-10-01

    The theory of lattice dynamics in the harmonic approximation using a rigid-ion model due to Born and Huang [Dynamical Theory of Crystal Lattices (Oxford University Press, New York, 1954)], is applied to ionic crystals of the R2MX6 type with antifluorite structure namely, K2SnCl6, K2PtBr6, Cs2SnBr6, and Rb2SnBr6 in the cubic phase. The model expresses the potential energy as the sum of long-range Coulomb interactions and repulsive short-range interactions between ions in the primitive cell. A function of axially symmetric type is used to approximate the short-range part, and the number of force constant parameters were reduced utilizing stability conditions in the manner described by Katiyar [J. Phys. C 3, 1087 (1970)]. The remaining constants were determined by a nonlinear least-squares analysis of some experimental frequencies at the critical point Γ. The long-range contributions were calculated using the Ewald transformation as described by Cowley [Acta Crystallogr. 15, 687 (1962)]. Phonon frequencies and the normal modes of vibrations at the zone center were obtained; of particular interest is the resulting lowest librational frequency for each crystal. We obtained excellent agreement between the calculated and the observed frequencies. The resulting effective charge parameters indicated that these crystals are partially ionic. In general, the results offered a better vision of the structural phase transition mechanism involving the rotational mode T1g.

  19. 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.

  20. 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.

  1. 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.

  2. Thermodynamic stability and structural properties of cluster crystals formed by amphiphilic dendrimers

    NASA Astrophysics Data System (ADS)

    Lenz, Dominic A.; Mladek, Bianca M.; Likos, Christos N.; Blaak, Ronald

    2016-05-01

    We pursue the goal of finding real-world examples of macromolecular aggregates that form cluster crystals, which have been predicted on the basis of coarse-grained, ultrasoft pair potentials belonging to a particular mathematical class [B. M. Mladek et al., Phys. Rev. Lett. 46, 045701 (2006)]. For this purpose, we examine in detail the phase behavior and structural properties of model amphiphilic dendrimers of the second generation by means of monomer-resolved computer simulations. On augmenting the density of these systems, a fluid comprised of clusters that contain several overlapping and penetrating macromolecules is spontaneously formed. Upon further compression of the system, a transition to multi-occupancy crystals takes place, the thermodynamic stability of which is demonstrated by means of free-energy calculations, and where the FCC is preferred over the BCC-phase. Contrary to predictions for coarse-grained theoretical models in which the particles interact exclusively by effective pair potentials, the internal degrees of freedom of these molecules cause the lattice constant to be density-dependent. Furthermore, the mechanical stability of monodisperse BCC and FCC cluster crystals is restricted to a bounded region in the plane of cluster occupation number versus density. The structural properties of the dendrimers in the dense crystals, including their overall sizes and the distribution of monomers are also thoroughly analyzed.

  3. 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.

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

    NASA Astrophysics Data System (ADS)

    Ćosić, M.; Petrović, S.; Nešković, N.

    2014-07-01

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

  5. 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

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

    PubMed

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

    2015-02-10

    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

  7. Surface-enhanced Raman Scattering from Virus-like Particle Crystals

    NASA Astrophysics Data System (ADS)

    Dufort, Christopher; Dragnea, Bogdan

    2008-03-01

    Recently, a method for the encapsidation of gold nanoparticules by an icosahedral virus protein coat, termed a virus-like particle (VLP), has been developed. Of particular interest is in observing their spectroscopic properties upon arrangement into a three-dimensional crystal lattice. Here we present the surface-enhanced Raman scattering spectrum of such an assembly. This is made possible by the plasmonic coupling of adjacent gold nanoparticules when excited near their plasmon resonant frequency. To determine whether the SERS effect is arising from isolated hot spots or a large number of junctions acting in unison we employed scanning confocal Raman spectroscopy. This seems to indicate the latter, as a uniform Raman intensity is observed across entire crystals.

  8. Crystal structure optimisation using an auxiliary equation of state

    SciTech Connect

    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 Cu{sub 2}ZnSnS{sub 4} and the magnetic metal-organic framework HKUST-1.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. Coupled particle dispersion by three-dimensional vortex structures

    SciTech Connect

    Troutt, T.R.; Chung, J.N.; Crowe, C.T.

    1996-12-31

    The primary objective of this research program is to obtain understanding concerning the role of three-dimensional vortex structures in the dispersion of particles and droplets in free shear flows. This research program builds on previous studies which focused on the nature of particle dispersion in large scale quasi two-dimensional vortex structures. This investigation employs time dependent experimental and numerical techniques to provide information concerning the particulate dispersion produced by three dimensional vortex structures in free shear layers. The free shear flows investigated include modified plane mixing layers, and modified plane wakes. The modifications to these flows involve slight perturbations to the initiation boundary conditions such that three-dimensional vortex structures are rapidly generated by the experimental and numerical flow fields. Recent results support the importance of these vortex structures in the particle dispersion process.

  14. 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

  15. How evolutionary crystal structure prediction works--and why.

    PubMed

    Oganov, Artem R; Lyakhov, Andriy O; Valle, Mario

    2011-03-15

    Once the crystal structure of a chemical substance is known, many properties can be predicted reliably and routinely. Therefore if researchers could predict the crystal structure of a material before it is synthesized, they could significantly accelerate the discovery of new materials. In addition, the ability to predict crystal structures at arbitrary conditions of pressure and temperature is invaluable for the study of matter at extreme conditions, where experiments are difficult. Crystal structure prediction (CSP), the problem of finding the most stable arrangement of atoms given only the chemical composition, has long remained a major unsolved scientific problem. Two problems are entangled here: search, the efficient exploration of the multidimensional energy landscape, and ranking, the correct calculation of relative energies. For organic crystals, which contain a few molecules in the unit cell, search can be quite simple as long as a researcher does not need to include many possible isomers or conformations of the molecules; therefore ranking becomes the main challenge. For inorganic crystals, quantum mechanical methods often provide correct relative energies, making search the most critical problem. Recent developments provide useful practical methods for solving the search problem to a considerable extent. One can use simulated annealing, metadynamics, random sampling, basin hopping, minima hopping, and data mining. Genetic algorithms have been applied to crystals since 1995, but with limited success, which necessitated the development of a very different evolutionary algorithm. This Account reviews CSP using one of the major techniques, the hybrid evolutionary algorithm USPEX (Universal Structure Predictor: Evolutionary Xtallography). Using recent developments in the theory of energy landscapes, we unravel the reasons evolutionary techniques work for CSP and point out their limitations. We demonstrate that the energy landscapes of chemical systems have an

  16. Exceptional groups and elementary-particle structures

    SciTech Connect

    Biedenharn, L.C.; Truini, P.

    1981-09-01

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

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

    PubMed

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

    2014-03-25

    Nanostructured samarium oxalate crystals were prepared via microwave assisted co-precipitation method. The crystal structure and morphology of the sample were analyzed using X-ray powder diffraction, Scanning electron microscopy and Transmission electron microscopy. The presence of functional groups is ascertained by Fourier transform infrared spectroscopy. Samarium oxalate nanocrystals of average size 20 nm were aggregated together to form nano-plate structure in sub-microrange. Detailed spectroscopic investigation of the prepared phosphor material was carried out by Judd-Ofelt analysis based on the UV-Visible-NIR absorption spectra and photoluminescence emission spectra. The analysis reveals that the transition from energy level (4)G5/2 to (6)H7/2 of Sm(3+) ion has maximum branching ratio and the corresponding orange emission can be used for display applications.

  18. 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.

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

    SciTech Connect

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

    2015-06-04

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

  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. Synthesis and crystal structure of EuBi{sub 2}

    SciTech Connect

    Sun Zhongming; Mao Jianggao . E-mail: mjg@ms.fjirsm.ac.cn

    2004-10-01

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

  2. 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.

  3. Structure and magnetic properties of Nd2Fe14B fine particles produced by spark erosion

    NASA Astrophysics Data System (ADS)

    Wan, H.; Berkowitz, A. E.

    1994-11-01

    At present Nd2Fe14B is the best permanent magnet because of its extremely high coercivity and energy product. Optimum properties of Nd2Fe14B magnets can be attained by producing single domain particles, and then aligning and compacting them. Due to the reactivity of the Nd constitutent, it is challenging to produce and handle a large amount of fine particles of this material. We have prepared fine particles of Nd2Fe14B by spark erosion with various dielectric media. Yield, size, size distribution, structure, and magnetic properties are discussed. The Nd2Fe14B particles were made by the sharker pot spark erosion method. Relaxation oscillators or a pulse generator were used to power the park erosion. Commercial Neomax 35 was employed as the primary material. The dielectric media were liquid Ar, Ar gas, and hydrocarbons, which provided an oxygen free environment. Structure and size were studied by transmission electron microscopy (TEM), scanning electron microscopy (SEM), and x-ray diffraction. Magnetic properties were measured by vibrating sample magnetometer (VSM) with temperatures in range of 4.2-1200 K. The particles produced in these three different dielectric media had different microstructures and crystal structures. The particles made in Ar gas were pure Nd2Fe14B phase. The particles made in liquid Ar were a mixture of amorphous and crystalline Nd2Fe14B, because the liquid Ar provided a much higher quench rate than Ar gas, which produced some amorphous Nd2Fe14B. Upon annealing, the amorphous particles became crystalline. The fine particles produced in hydrocarbons, such as pentane and dodecane, had more complex mixed phases, since the rare earth reacted with the hydrocarbons during the sparking process. The phases were NdC2, alpha-Fe, and amorphous and crystalline Nd2Fe14B. The effects of power parameters, such as voltage and capacitance, on particle size were investigated. Particle sizes from 20 nm to 50 microns were obtained.

  4. 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

  5. High frequency single mode traveling wave structure for particle acceleration

    NASA Astrophysics Data System (ADS)

    Ivanyan, M. I.; Danielyan, V. A.; Grigoryan, B. A.; Grigoryan, A. H.; Tsakanian, A. V.; Tsakanov, V. M.; Vardanyan, A. S.; Zakaryan, S. V.

    2016-09-01

    The development of the new high frequency slow traveling wave structures is one of the promising directions in accomplishment of charged particles high acceleration gradient. The disc and dielectric loaded structures are the most known structures with slowly propagating modes. In this paper a large aperture high frequency metallic two-layer accelerating structure is studied. The electrodynamical properties of the slowly propagating TM01 mode in a metallic tube with internally coated low conductive thin layer are examined.

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

    SciTech Connect

    Boal, Amie K.; Rosenzweig, Amy C.

    2010-08-16

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

  7. Crystal Structure of the Human Laminin Receptor Precursor

    SciTech Connect

    Jamieson,K.; Wu, J.; Hubbard, S.; Meruelo, D.

    2008-01-01

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

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  10. 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.

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

    PubMed

    Weil, Matthias

    2015-01-01

    Single crystals of poly[μ4-tartrato-κ(6) O (1),O (3):O (1'):O (2),O (4):O (4')-lead], [Pb(C4H4O6)] n , were grown in a gel medium. In comparison with the previous structure determination of this compound from laboratory powder X-ray diffraction data [De Ridder et al. (2002 ▶). Acta Cryst. C58, m596-m598], the redetermination on the basis of single-crystal data reveals the absolute structure, all atoms with anisotropic displacement parameters and a much higher accuracy in terms of bond lengths and angles. It could be shown that a different space group or incorporation of water as reported for similarly gel-grown lead tartrate crystals is incorrect. In the structure, each Pb(2+) cation is bonded to eight O atoms of five tartrate anions, while each tartrate anion links four Pb(2+) cations. The resulting three-dimensional framework is stabilized by O-H⋯O hydrogen bonds between the OH groups of one tartrate anion and the carboxyl-ate O atoms of adjacent anions.

  12. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

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

    SciTech Connect

    Bykova, Elena; Parakhonskiy, Gleb; 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. 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.

  16. 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

  17. 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].

  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. 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.

  20. 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.

  1. 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.

  2. Crystal structures explain functional properties of two E. coli porins

    NASA Astrophysics Data System (ADS)

    Cowan, S. W.; Schirmer, T.; Rummel, G.; Steiert, M.; Ghosh, R.; Pauptit, R. A.; Jansonius, J. N.; Rosenbusch, J. P.

    1992-08-01

    Porins form aqueous channels that aid the diffusion of small hydrophilic molecules across the outer membrane of Gram-negative bacteria. The crystal structures of matrix porin and phosphoporin both reveal trimers of identical subunits, each subunit consisting of a 16-stranded anti-parallel β-barrel containing a pore. A long loop inside the barrel contributes to a constriction of the channel where the charge distribution affects ion selectivity. The structures explain at the molecular level functional characteristics and their alterations by known mutations.

  3. Crystal structure of new AsS{sub 2} compound

    SciTech Connect

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

    2013-01-15

    AsS{sub 2} single crystals have been obtained for the first time from an As{sub 2}S{sub 3} melt at pressures above 6 GPa and temperatures above 800 K in the As{sub 2}S{sub 3} {yields} AsS + AsS{sub 2} reaction. The monoclinic structure of the new high-pressure phase is solved by X-ray diffraction analysis and compared to the structure of high-pressure AsS phase, which was studied previously.

  4. Holographic liquid crystal polarization grating with Fabry-Perot structure.

    PubMed

    Sakamoto, Moritsugu; Yamaguchi, Haruki; Noda, Kohei; Sasaki, Tomoyuki; Kawatsuki, Nobuhiro; Ono, Hiroshi

    2016-03-15

    A holographic liquid crystal polarization grating with a Fabry-Perot structure was developed. Because of its resonant structure, the device offers high levels of control of the diffraction properties of incident-polarized light beams, depending on the resonance conditions. The diffracted light beams are emitted in both the reflection and transmission directions, and the device thus works as a multibranch polarization grating with double optical paths, unlike a conventional polarization grating. These device features were experimentally demonstrated and were also explained theoretically.

  5. Holographic liquid crystal polarization grating with Fabry-Perot structure.

    PubMed

    Sakamoto, Moritsugu; Yamaguchi, Haruki; Noda, Kohei; Sasaki, Tomoyuki; Kawatsuki, Nobuhiro; Ono, Hiroshi

    2016-03-15

    A holographic liquid crystal polarization grating with a Fabry-Perot structure was developed. Because of its resonant structure, the device offers high levels of control of the diffraction properties of incident-polarized light beams, depending on the resonance conditions. The diffracted light beams are emitted in both the reflection and transmission directions, and the device thus works as a multibranch polarization grating with double optical paths, unlike a conventional polarization grating. These device features were experimentally demonstrated and were also explained theoretically. PMID:26977643

  6. The Cambridge Structural Database: a quarter of a million crystal structures and rising.

    PubMed

    Allen, Frank H

    2002-06-01

    The Cambridge Structural Database (CSD) now contains data for more than a quarter of a million small-molecule crystal structures. The information content of the CSD, together with methods for data acquisition, processing and validation, are summarized, with particular emphasis on the chemical information added by CSD editors. Nearly 80% of new structural data arrives electronically, mostly in CIF format, and the CCDC acts as the official crystal structure data depository for 51 major journals. The CCDC now maintains both a CIF archive (more than 73,000 CIFs dating from 1996), as well as the distributed binary CSD archive; the availability of data in both archives is discussed. A statistical survey of the CSD is also presented and projections concerning future accession rates indicate that the CSD will contain at least 500,000 crystal structures by the year 2010.

  7. Crystal structure and crystal chemistry of melanovanadite, a natural vanadium bronze.

    USGS Publications Warehouse

    Konnert, J.A.; Evans, H.T.

    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.

  8. Internal stresses and dislocation structure of large single crystals of germanium for IR optics

    NASA Astrophysics Data System (ADS)

    Kaplunov, I. A.

    2006-02-01

    The thermoelastic stresses that appear during crystallization have been theoretically estimated for single crystals of germanium grown in the shape of a disk. It is shown that there is a correlation between the stress distribution and the dislocation structure of large single crystals of germanium obtained by the Stepanov method and by directed crystallization.

  9. 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

  10. Crystal structure of the 80S yeast ribosome.

    PubMed

    Jenner, Lasse; Melnikov, Sergey; Garreau de Loubresse, Nicolas; Ben-Shem, Adam; Iskakova, Madina; Urzhumtsev, Alexandre; Meskauskas, Arturas; Dinman, Jonathan; Yusupova, Gulnara; Yusupov, Marat

    2012-12-01

    The first X-ray structure of the eukaryotic ribosome at 3.0Å resolution was determined using ribosomes isolated and crystallized from the yeast Saccharomyces cerevisiae (Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, Yusupov M: The structure of the eukaryotic ribosome at 3.0 A resolution. Science 2011, 334:1524-1529). This accomplishment was possible due to progress in yeast ribosome biochemistry as well as recent advances in crystallographic methods developed for structure determination of prokaryotic ribosomes isolated from Thermus thermophilus and Escherichia coli. In this review we will focus on the development of isolation procedures that allowed structure determination (both cryo-EM and X-ray crystallography) to be successful for the yeast S. cerevisiae. Additionally we will introduce a new nomenclature that facilitates comparison of ribosomes from different species and kingdoms of life. Finally we will discuss the impact of the yeast 80S ribosome crystal structure on perspectives for future investigations.

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

    PubMed

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

    2013-09-01

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

  12. 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

  13. Gravitationally induced particle production and its impact on structure formation

    NASA Astrophysics Data System (ADS)

    Nunes, Rafael C.

    2016-08-01

    In this paper we investigate the influence of a continuous particles creation processes on the linear and nonlinear matter clustering, and its consequences on the weak lensing effect induced by structure formation. We study the line of sight behavior of the contribution to the bispectrum signal at a given angular multipole l, showing that the scale where the nonlinear growth overcomes the linear effect depends strongly of particles creation rate.

  14. 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.

  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. Self-Assembly and Electrostriction of Arrays and Chains of Hopfion Particles in Chiral Liquid Crystals

    SciTech Connect

    Ackerman, P. J.; van de Lagemaat, J.; Smalyukh, I. I.

    2015-01-21

    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.

  17. Self-Assembly and Electrostriction of Arrays and Chains of Hopfion Particles in Chiral Liquid Crystals

    DOE PAGES

    Ackerman, P. J.; van de Lagemaat, J.; Smalyukh, I. I.

    2015-01-21

    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 thatmore » 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.« less

  18. 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

  19. 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.

  20. Crystal Structures of Intermediates in the Nitroalkane Oxidase Reaction

    SciTech Connect

    Heroux, A.; Bozinovski, D; Valley, M; Fitzpatrick, P; Orville, A

    2009-01-01

    The flavoenzyme nitroalkane oxidase is a member of the acyl-CoA dehydrogenase superfamily. Nitroalkane oxidase catalyzes the oxidation of neutral nitroalkanes to nitrite and the corresponding aldehydes or ketones. Crystal structures to 2.2 {angstrom} resolution or better of enzyme complexes with bound substrates and of a trapped substrate-flavin adduct are described. The D402N enzyme has no detectable activity with neutral nitroalkanes. The structure of the D402N enzyme crystallized in the presence of 1-nitrohexane or 1-nitrooctane shows the presence of the substrate in the binding site. The aliphatic chain of the substrate extends into a tunnel leading to the enzyme surface. The oxygens of the substrate nitro group interact both with amino acid residues and with the 2'-hydroxyl of the FAD. When nitroalkane oxidase oxidizes nitroalkanes in the presence of cyanide, an electrophilic flavin imine intermediate can be trapped (Valley, M. P., Tichy, S. E., and Fitzpatrick, P. F. (2005) J. Am. Chem. Soc. 127, 2062-2066). The structure of the enzyme trapped with cyanide during oxidation of 1-nitrohexane shows the presence of the modified flavin. A continuous hydrogen bond network connects the nitrogen of the CN-hexyl-FAD through the FAD 2'-hydroxyl to a chain of water molecules extending to the protein surface. Together, our complementary approaches provide strong evidence that the flavin cofactor is in the appropriate oxidation state and correlates well with the putative intermediate state observed within each of the crystal structures. Consequently, these results provide important structural descriptions of several steps along the nitroalkane oxidase reaction cycle.

  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 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

  3. 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.

  4. 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.

  5. Impact of surfactants on the crystallization of aqueous suspensions of celecoxib amorphous solid dispersion spray dried particles.

    PubMed

    Chen, Jie; Ormes, James D; Higgins, John D; Taylor, Lynne S

    2015-02-01

    Amorphous solid dispersions are frequently prepared by spray drying. It is important that the resultant spray dried particles do not crystallize during formulation, storage, and upon administration. The goal of the current study was to evaluate the impact of surfactants on the crystallization of celecoxib amorphous solid dispersions (ASD), suspended in aqueous media. Solid dispersions of celecoxib with hydroxypropylmethylcellulose acetate succinate were manufactured by spray drying, and aqueous suspensions were prepared by adding the particles to acidified media containing various surfactants. Nucleation induction times were evaluated for celecoxib in the presence and absence of surfactants. The impact of the surfactants on drug and polymer leaching from the solid dispersion particles was also evaluated. Sodium dodecyl sulfate and Polysorbate 80 were found to promote crystallization from the ASD suspensions, while other surfactants including sodium taurocholate and Triton X100 were found to inhibit crystallization. The promotion or inhibition of crystallization was found to be related to the impact of the surfactant on the nucleation behavior of celecoxib, as well as the tendency to promote leaching of the drug from the ASD particle into the suspending medium. It was concluded that surfactant choice is critical to avoid failure of amorphous solid dispersions through crystallization of the drug.

  6. Nonlinear optical diglycine hydrochloride: Synthesis, crystal growth and structural characteristics

    NASA Astrophysics Data System (ADS)

    Narayana Moolya, B.; Darmaprakash, S. M.

    2006-07-01

    Diglycine hydrochloride (DGHCl), a new semiorganic nonlinear optical material with the molecular formula C 4H 11O 4Cl, was synthesized at ambient temperature. The solubility of DGHCl in water at varying temperatures was determined. Bulk single crystals were grown by the slow evaporation method at constant temperature. Powder X-ray diffraction patterns of the grown DGHCl were recorded and indexed. Functional groups present in the sample crystals were identified by FTIR spectral analysis. The chemical composition of the synthesized material was confirmed by CHN analysis. Thermal characteristics of DGHCl were determined from the TGA/DTA response curve. The Kurtz powder second harmonic generation (SHG) test showed potential for optical SHG. The UV cut-off of transmission was identified from the UV-VIS absorption spectra. The SHG of DGHCl is discussed on the basis of structural characteristics of the title compound.

  7. Crystal structure of isoflavone reductase from alfalfa (Medicago sativa L.).

    PubMed

    Wang, Xiaoqiang; He, Xianzhi; Lin, Jianqiao; Shao, Hui; Chang, Zhenzhan; Dixon, Richard A

    2006-05-19

    Isoflavonoids play important roles in plant defense and exhibit a range of mammalian health-promoting activities. Isoflavone reductase (IFR) specifically recognizes isoflavones and catalyzes a stereospecific NADPH-dependent reduction to (3R)-isoflavanone. The crystal structure of Medicago sativa IFR with deletion of residues 39-47 has been determined at 1.6A resolution. Structural analysis, molecular modeling and docking, and comparison with the structures of other NADPH-dependent enzymes, defined the putative binding sites for co-factor and substrate and potential key residues for enzyme activity and substrate specificity. Further mutagenesis has confirmed the role of Lys144 as a catalytic residue. This study provides a structural basis for understanding the enzymatic mechanism and substrate specificity of IFRs as well as the functions of IFR-like proteins.

  8. 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.

  9. Single crystal growth and X-ray structure analysis of non-peripheral octahexyl phthalocyanine

    NASA Astrophysics Data System (ADS)

    Ohmori, Masashi; Nakano, Chika; Higashi, Takuya; Miyano, Tetsuya; Tohnai, Norimitsu; Fujii, Akihiko; Ozaki, Masanori

    2016-07-01

    The single-crystal structure of metal-free non-peripheral octahexyl-substituted phthalocyanine (C6PcH2) has been investigated by single-crystal X-ray structure analysis. Two types of C6PcH2 single crystal, bulk and needle crystals, were separately grown by controlling the recrystallization conditions. The structures of the two types of crystal were determined, and were found to be completely different, that is, C6PcH2 exhibits structural polymorphism. It has been clarified that the C6PcH2 microcrystals in thin films used in previously reported electronic devices have the needle structure.

  10. 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.

  11. Enhanced High-Temperature Ice Nucleation Ability of Crystallized Aerosol Particles after Pre-Activation at Low Temperature

    NASA Astrophysics Data System (ADS)

    Wagner, R.; Moehler, O.; Saathoff, H.; Schnaiter, M.

    2014-12-01

    The term pre-activation in heterogeneous ice nucleation describes the observation that the ice nucleation ability of solid ice nuclei may improve after they have already been involved in ice crystal formation or have been exposed to a temperature lower than 235 K. This can be explained by the retention of small ice embryos in cavities or crevices at the particle surface or by the capillary condensation and freezing of supercooled water, respectively. In recent cloud chamber experiments with crystallized aqueous ammonium sulfate, oxalic acid, and succinic acid solution droplets, we have unraveled a further pre-activation mechanism under ice subsaturated conditions which does not require the preceding growth of ice on the seed aerosol particles (Wagner, R. et al., J. Geophys. Res. Atmos., 119, doi: 10.1002/2014JD021741). First cloud expansion experiments were performed at a high temperature (267 - 244 K) where the crystallized particles did not promote any heterogeneous ice nucleation. Ice nucleation at this temperature, however, could be triggered by temporarily cooling the crystallized particles to a lower temperature. This is because upon crystallization, residuals of the aqueous solution are trapped within the crystals. These captured liquids can freeze when cooled below their respective homogeneous or heterogeneous freezing temperature, leading to the formation of ice pockets in the crystalline particles. When warmed again to the higher temperature, ice formation by the pre-activated particles occurred via depositional and deliquescence-induced ice growth, with ice active fractions ranging from 1 to 4% and 4 to 20%, respectively. Pre-activation disappeared above the eutectic temperature, which for the organic acids are close to the melting point of ice. This mechanism could therefore contribute to the very small fraction of atmospheric aerosol particles that are still ice active well above 263 K.

  12. 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.

  13. The interplanetary magnetic structure that guides solar relativistic particles

    NASA Astrophysics Data System (ADS)

    Masson, S.; Démoulin, P.; Dasso, S.; Klein, K.-L.

    2012-02-01

    Context. Relating in-situ measurements of relativistic solar particles to their parent activity in the corona requires understanding the magnetic structures that guide them from their acceleration site to the Earth. Relativistic particle events are observed at times of high solar activity, when transient magnetic structures such as interplanetary coronal mass ejections (ICMEs) often shape the interplanetary magnetic field (IMF). They may introduce interplanetary paths that are longer than nominal, and magnetic connections rooted far from the nominal Parker spiral. Aims: We present a detailed study of the IMF configurations during ten relativistic solar particle events of the 23rd activity cycle to elucidate the actual IMF configuration that guides the particles to the Earth, where they are measured by neutron monitors. Methods: We used magnetic field (MAG) and plasma parameter measurements (SWEPAM) from the ACE spacecraft and determined the interplanetary path lengths of energetic particles through a modified version of the velocity dispersion analysis based on energetic particle measurements with SoHO/ERNE. Results: We find that the majority (7/10) of the events is detected in the vicinity of an ICME. Their interplanetary path lengths are found to be longer (1.5-2.6 AU) than those of the two events propagating in the slow solar wind (1.3 AU). The longest apparent path length is found in an event within the fast solar wind, probably caused by enhanced pitch angle scattering. The derived path lengths imply that the first energetic and relativistic protons are released at the Sun at the same time as electron beam emitting type III radio bursts. Conclusions: The timing of the first high-energy particle arrival on Earth is mainly determined by the type of IMF in which the particles propagate. Initial arrival times are as expected from Parker's model in the slow solar wind, and significantly longer in or near transient structures such as ICMEs.

  14. Nematic-field-driven positioning of particles in liquid crystal droplets.

    PubMed

    Whitmer, Jonathan K; Wang, Xiaoguang; Mondiot, Frederic; Miller, Daniel S; Abbott, Nicholas L; de Pablo, Juan J

    2013-11-27

    Common nematic oils, such as 5CB, experience planar anchoring at aqueous interfaces. When these oils are emulsified, this anchoring preference and the resulting topological constraints lead to the formation of droplets that exhibit one or two point defects within the nematic phase. Here, we explore the interactions of adsorbed particles at the aqueous interface through a combination of experiments and coarse-grained modeling, and demonstrate that surface-active particles, driven by elastic forces in the droplet, readily localize to these defect regions in a programmable manner. When droplets include two nanoparticles, these preferentially segregate to the two poles, thereby forming highly regular dipolar structures that could serve for hierarchical assembly of functional structures. Addition of sufficient concentrations of surfactant changes the interior morphology of the droplet, but pins defects to the interface, resulting in aggregation of the two particles.

  15. Nematic-Field Driven Positioning of Particles in Liquid Crystal Droplets

    PubMed Central

    Whitmer, Jonathan K.; Wang, Xiaoguang; Mondiot, Frederic; Miller, Daniel S.; Abbott, Nicholas L.; de Pablo, Juan J.

    2015-01-01

    Common nematic oils, such as 5CB, experience planar anchoring at aqueous interfaces. When these oils are emulsified, this anchoring preference and the resulting topological constraints lead to formation of droplets that exhibit one or two point defects within the nematic phase. Here, we explore the interactions of adsorbed particles at the aqueous interface through a combination of experiments and coarse-grained modeling, and demonstrate that surface-active particles, driven by elastic forces in the droplet, readily localize to these defect regions in a programmable manner. When droplets include two nanoparticles, these preferentially segregate to the two poles, thereby forming highly regular dipolar structures that could serve for hierarchical assembly of functional structures. Addition of sufficient concentrations of surfactant changes the interior morphology of the droplet, but pins defects to the interface, resulting in aggregation of the two particles. PMID:24329470

  16. 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.

  17. 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.

  18. Crystal structure of the major peanut allergen Ara h 1.

    PubMed

    Cabanos, Cerrone; Urabe, Hiroyuki; Tandang-Silvas, Mary Rose; Utsumi, Shigeru; Mikami, Bunzo; Maruyama, Nobuyuki

    2011-10-01

    Ara h 1, a 7S globulin, is one of the three major peanut allergens. We previously reported the crystallization of the core region of recombinant Ara h 1. Here, we present the crystal structure of the Ara h 1 core at a resolution of 2.43 Å. We also assayed the Ara h 1 core thermal stability and compared its final structure against other 7S globulins. The Ara h 1 core has a thermal denaturation temperature of 88.3°C and a structure that is very similar to other 7S globulins. Previously identified linear IgE epitopes were also mapped on the three-dimensional structure. Most linear epitopes were found in the extended loop domains and the coils between the N- and C-terminal modules, while others were found in the less accessible β-sheets of the C-terminal core β-barrel domain of each monomer. Most of these epitopes become either slightly or significantly buried upon trimer formation, implying that allergen digestion in the gut is required for these epitopes to be accessible to immunoglobulins. Our findings also suggest that both intact and partially degraded allergens should be employed in future diagnostic and immunotherapeutic strategies. PMID:21903274

  19. 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.

  20. Crystal Structure of Cruxrhodopsin-3 from Haloarcula vallismortis

    PubMed Central

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

    2014-01-01

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

  1. Crystal structure studies on sulfur oxygenase reductase from Acidianus tengchongensis

    SciTech Connect

    Li Mei; Chen Zhiwei; Zhang Pingfeng; Pan Xiaowei; Jiang Chengying; An Xiaomin; Liu Shuangjiang; Chang Wenrui

    2008-05-09

    Sulfur oxygenase reductase (SOR) simultaneously catalyzes oxidation and reduction of elemental sulfur to produce sulfite, thiosulfate, and sulfide in the presence of molecular oxygen. In this study, crystal structures of wild type and mutants of SOR from Acidianus tengchongensis (SOR-AT) in two different crystal forms were determined and it was observed that 24 identical SOR monomers form a hollow sphere. Within the icosatetramer sphere, the tetramer and trimer channels were proposed as the paths for the substrate and products, respectively. Moreover, a comparison of SOR-AT with SOR-AA (SOR from Acidianus ambivalens) structures showed that significant differences existed at the active site. Firstly, Cys31 is not persulfurated in SOR-AT structures. Secondly, the iron atom is five-coordinated rather than six-coordinated, since one of the water molecules ligated to the iron atom in the SOR-AA structure is lost. Consequently, the binding sites of substrates and a hypothetical catalytic process of SOR were proposed.

  2. Crystal Structure of a Ube2S-Ubiquitin Conjugate

    PubMed Central

    Lorenz, Sonja; Bhattacharyya, Moitrayee; Feiler, Christian; Rape, Michael; Kuriyan, John

    2016-01-01

    Protein ubiquitination occurs through the sequential formation and reorganization of specific protein-protein interfaces. Ubiquitin-conjugating (E2) enzymes, such as Ube2S, catalyze the formation of an isopeptide linkage between the C-terminus of a “donor” ubiquitin and a primary amino group of an “acceptor” ubiquitin molecule. This reaction involves an intermediate, in which the C-terminus of the donor ubiquitin is thioester-bound to the active site cysteine of the E2 and a functionally important interface is formed between the two proteins. A docked model of a Ube2S-donor ubiquitin complex was generated previously, based on chemical shift mapping by NMR, and predicted contacts were validated in functional studies. We now present the crystal structure of a covalent Ube2S-ubiquitin complex. The structure contains an interface between Ube2S and ubiquitin in trans that resembles the earlier model in general terms, but differs in detail. The crystallographic interface is more hydrophobic than the earlier model and is stable in molecular dynamics (MD) simulations. Remarkably, the docked Ube2S-donor complex converges readily to the configuration seen in the crystal structure in 3 out of 8 MD trajectories. Since the crystallographic interface is fully consistent with mutational effects, this indicates that the structure provides an energetically favorable representation of the functionally critical Ube2S-donor interface. PMID:26828794

  3. 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.

  4. Crystal and molecular structure of perindopril erbumine salt

    NASA Astrophysics Data System (ADS)

    Remko, M.; Bojarska, J.; Ježko, P.; Sieroń, L.; Olczak, A.; Maniukiewicz, W.

    2011-06-01

    The crystal structure of perindopril (2S,3aS,7aS)-1-[(2S)-2-[[(2S)-1-ethoxy-1-oxopentan-2-yl]amino]propanoyl]-2,3,3a,4,5,6,7,7a-octahydroindole-2-carboxylic acid) erbumine salt C 23H 43N 3O 5, angiotensin-converting enzyme inhibitor, was determined from single-crystal X-ray diffraction data. The compound crystallizes in the triclinic, non-centrosymetric space group P1, with unit cell dimensions a = 6.575(3), b = 12.165(5), c = 16.988(8) Å and α = 97.153(4), β = 94.417(4), γ = 90.349(4)°, Z = 2. The structure was refined by full matrix least squares methods to R = 0.037. In the solid state ionized molecules of perindopril and erbumine are linked together forming a complex via O⋯HN + hydrogen bonds between the positively charged amino groups of the erbuminium cations and oxygen atoms of the perindopril carboxylate groups. Intermolecular N sbnd H⋯O and C sbnd H⋯O contacts seem to be effective in the stabilization of the structure, resulting in the formation of a three-dimensional network. The gas-phase structure of perindopril-erbumine complex was optimized by the HF/6-31G(d) and Becke3LYP/6-31G(d) methods. The conformational behavior of this salt in water was examined using the CPCM and Onsager models. In both the gas phase and water solution the perindopril erbumine will exist in prevailing triclinic form.

  5. 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.

  6. Structural elucidation of crystallization centers in aluminium inoculated with titanium

    SciTech Connect

    Banerji, A.; Reif, W. . Inst. fuer Metallforschung-Metallkunde); Feng, Q. . Dept. of Materials Science and Engineering)

    1993-08-01

    The heterogeneous nucleation process in commercially pure aluminium (99.7%) castings inoculated with hypoperitectic titanium additions (<0.15%) was investigated. Electron diffraction of the crystallization center particles, which formed in situ by reaction of added titanium with carbon impurity in the melt and subsequently nucleated [alpha]-aluminium, showed that they were essentially composed of Ti[sub 2]C, having orthorhombic lattice with a = 1.2 nm, b = 1.06 nm and c = 0.50 nm, and stoichiometric TiC, having cubic lattice with a = 0.4380 nm. Traces of Ti[sub 3]AlC and Al[sub 4]C[sub 3] were recorded only in rare cases.

  7. 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

  8. Peculiarities of electro-optic properties of the ferroelectric particles-liquid crystal colloids

    NASA Astrophysics Data System (ADS)

    Ibragimov, T. D.; Imamaliyev, A. R.; Bayramov, G. M.

    2016-04-01

    Influence of ferroelectric barium titanate particles on electro-optic properties of the liquid crystal (LC) 4-cyano-4'-pentylbiphenyl (5CB) with positive dielectric anisotropy and the LC mixture (H37) consisting of 4-methoxybezylidene-4'-butylaniline and 4-ethoxybezylidene-4'-butylaniline with negative dielectric anisotropy was investigated. It was shown that a presence of particles (1 wt%) in 5CB and H37 decreased the clearing temperature from 35.2 °C to 32.4°C and from 61.2°C to 60.1°C, respectively. The threshold voltage of the Freedericksz effect became 0.3 V for the BaTiO3-5CB colloid while the beginning of this effect for the pure 5CB was observed at 2.1 V. The threshold voltage of the Freedericksz effect increased from 2.8 V to up 3.1 V at additive of particles in H37. A rise time of the BaTiO3-5CB colloid improved while a decay time worsened in comparison with the pure 5CB at all applied voltages. The inverse trends were observed for the H37 matrix, namely, a rise time worsened and a decay time improved. Among other things, the pecularities of Williams' domain formation (WDF) were also investigated in the colloid based on the H37 matrix. It was established that the WDF voltage decreased, a rise time increased and a decay time decreased in comparison with the pure H37. Experimental results are explained by appearance of local electric fields near the polarized ferroelectric particles at application of external electric field and an existence of the additional obstacles (particles) for movement of ions.

  9. 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.

  10. Chemical characterization of individual particles and residuals of cloud droplets and ice crystals collected on board research aircraft in the ISDAC 2008 study

    NASA Astrophysics Data System (ADS)

    Hiranuma, N.; Brooks, S. D.; Moffet, R. C.; Glen, A.; Laskin, A.; Gilles, M. K.; Liu, P.; MacDonald, A. M.; Strapp, J. W.; McFarquhar, G. M.

    2013-06-01

    Ambient particles and the dry residuals of mixed-phase cloud droplets and ice crystals were collected during the Indirect and Semi-Direct Aerosol Campaign (ISDAC) near Barrow, Alaska, in spring of 2008. The collected particles were analyzed using Computer Controlled Scanning Electron Microscopy with Energy Dispersive X-ray analysis and Scanning Transmission X-ray Microscopy coupled with Near Edge X-ray Absorption Fine Structure spectroscopy to identify physico-chemical properties that differentiate cloud-nucleating particles from the total aerosol population. A wide range of individually mixed components was identified in the ambient particles and residuals including organic carbon compounds, inorganics, carbonates, and black carbon. Our results show that cloud droplet residuals differ from the ambient particles in both size and composition, suggesting that both properties may impact the cloud-nucleating ability of aerosols in mixed-phase clouds. The percentage of residual particles which contained carbonates (47%) was almost four times higher than those in ambient samples. Residual populations were also enhanced in sea salt and black carbon and reduced in organic compounds relative to the ambient particles. Further, our measurements suggest that chemical processing of aerosols may improve their cloud-nucleating ability. Comparison of results for various time periods within ISDAC suggests that the number and composition of cloud-nucleating particles over Alaska can be influenced by episodic events bringing aerosols from both the local vicinity and as far away as Siberia.

  11. Structural properties of composites of polyvinylidene fluoride and mechanically activated BaTiO3 particles

    NASA Astrophysics Data System (ADS)

    Pavlović, V. P.; Pavlović, V. B.; Vlahović, B.; Božanić, D. K.; Pajović, J. D.; Dojčilović, R.; Djoković, V.

    2013-11-01

    Nanocomposites of electroactive ceramics and ferroelectric polymers exploit favorable features of the matrix polymer and the nanostructured filler to produce new functional materials for pressure and IR sensors. In this study, the influence of mechanical activation of barium titanate (BaTiO3) particles on the structural properties of BaTiO3/polyvinylidene fluoride (PVDF) nanocomposites was investigated. Nanocomposite films were prepared by the solution casting method and characterized by scanning electron microscopy, x-ray diffraction and Raman spectroscopy. It was found that mechanically activated fillers promote the formation of a ferroelectric β-phase during crystallization of PVDF.

  12. Crystal structure, defects and plasticity in pentacene thin films

    NASA Astrophysics Data System (ADS)

    Drummy, Lawrence Fisher, Jr.

    Pentacene is a crystalline organic molecular material currently under investigation for use as the active layer in all-organic flexible electronic devices. For pentacene and materials like it to be developed and integrated into useful devices, a greater understanding of their growth, crystal structure, defects and mechanical behavior in the thin film form must be obtained. Low-dose High Resolution Electron Microscopy (HREM) was used to image pentacene structure and defects with lattice resolution. A new technique, Low Voltage Electron Microscopy (LVEM), was used to characterize pentacene and other organic thin films with high contrast. Pentacene thin films were produced by vacuum sublimation onto various crystalline and amorphous substrates. The crystal structure and morphology of the films were characterized using microscopy and diffraction techniques, and a new orthorhombic crystal structure was found in very thin films. Although the bulk energy of this orthorhombic phase is higher than the pentacene triclinic phase, it is thermodynamically stable at low film thickness because of its low (001) surface energy. Single crystal growth of the triclinic phase was studied by complementing molecular mechanics simulations of surface energies with experimental images of pentacene films. Details of the structural relaxations near defects in pentacene thin films were investigated using HREM and Electron Diffraction (ED). Characteristic streaking in ED patterns gave evidence for anisotropic relaxations near molecular vacancies. Direct images of grain boundaries in the as-grown films gave insight into molecular reorganization under internal strain. Finally, the plasticity of pentacene was investigated by rubbing, scratching and nanoindentation. Alignment of the thermally evaporated films was achieved under a controlled load scratch. Evidence for single crystalline texturing inside the scratched region was seen using HREM, with the contact plane being {110} type

  13. Three new crystal structures in the Na-Pb system: solving structures without additional experimental input.

    PubMed

    Ward, Logan; Michel, Kyle; Wolverton, Chris

    2015-09-01

    The structures of three Na-Pb compounds, γ, δ and δ', have remained incompletely solved for nearly 60 years. The space group, lattice parameters and positions of the Pb atoms of these three structures have been determined, but the positions of the Na atoms are still unknown. In this work, the First-Principles Assisted Structure Solution (FPASS) method [Meredig & Wolverton (2013). Nat. Mater. 12, 123-127] has been used to complete the description of these three structures using only experimental information available from the literature as input. The paper also discusses the relative advantages of constrained crystal structure prediction tools, like FPASS, in comparison to conventional crystal structure prediction methods in reference to their abilities to complete the solution of other unsolved structures. PMID:26317197

  14. Effect of fluid motion on the impact erosion by a micro-particle on quartz crystals

    NASA Astrophysics Data System (ADS)

    Cai, D. H.; Qi, H.; Wen, D. H.; Zhang, L.; Yuan, Q. L.; Chen, Z. Z.

    2016-08-01

    Abrasive slurry jet (ASJ) is a promising technology to process a variety of materials with advantages of high flexibility, no heat affected zone and high cutting efficiency. In this paper, the impressions generated on a quartz crystal specimen by the impacts of micro-particles laden in a water flow and the associated impact erosion mechanisms are presented and discussed in order to effectively and efficiently control the machining quality. Both brittle and ductile mode erosions coexist in the machining process due to the influence of the fluid motion on the trajectories of particles near the target surface. Large-scale craters produced by brittle conchoidal fractures associated with crashed zone, radial and lateral cracks, dominate the erosion process at large jet impact angles while small-scale craters involving micro-ploughing and micro-cutting are produced by the ductile mode erosion at small jet impact angles. The relation between the process parameters and the overall average volume of craters has also been quantitatively analyzed. A combination of small jet impact angle and abrasive particles and low water pressure is preferred for improving the surface quality after the ASJ machining process caused by the more formation of ductile mode induced craters on the target material, but it is at the sacrifice of the material removal rate as well.

  15. Novel type of tunable infrared filters based on the Al 2O 3 particles - Liquid crystal system

    NASA Astrophysics Data System (ADS)

    Ibragimov, Tahir D.; Bayramov, Gazanfar M.

    2012-01-01

    The optical transmission of small aluminum oxide particles in liquid crystal 4-methoxybenzylidene-4'-butylaniline (MBBA) and dual-frequency liquid crystal mixture consisting of 4-n-pentyl-4'-cyanobiphenyl (5CB), 4-hexyloxyphenyl ester 4'-hexyloxy-3-nitrobenzoic acid (C2), 4-n-pentanoyloxy-benzoic acid-4'-hexyloxyphenyl ester (H 22) was studied. It was established that there was a transmission band which was shifted on application of a voltage and depended on temperature. At using the dual-frequency liquid crystal as a matrix, a transmission band maximum switched at changing of the frequency. The experimental results are explained by the optical homogeneity of the system in a narrow wavenumber interval when the refractive indices of the particle material and the matrix are close, and also by re-orientation of the liquid crystal molecules when a voltage is applied. The obtained results can be used in constructing of tunable filters and compact monochromators.

  16. Draft crystal structure of the vault shell at 9-A resolution.

    PubMed

    Anderson, Daniel H; Kickhoefer, Valerie A; Sievers, Stuart A; Rome, Leonard H; Eisenberg, David

    2007-11-01

    Vaults are the largest known cytoplasmic ribonucleoprotein structures and may function in innate immunity. The vault shell self-assembles from 96 copies of major vault protein and encapsulates two other proteins and a small RNA. We crystallized rat liver vaults and several recombinant vaults, all among the largest non-icosahedral particles to have been crystallized. The best crystals thus far were formed from empty vaults built from a cysteine-tag construct of major vault protein (termed cpMVP vaults), diffracting to about 9-A resolution. The asymmetric unit contains a half vault of molecular mass 4.65 MDa. X-ray phasing was initiated by molecular replacement, using density from cryo-electron microscopy (cryo-EM). Phases were improved by density modification, including concentric 24- and 48-fold rotational symmetry averaging. From this, the continuous cryo-EM electron density separated into domain-like blocks. A draft atomic model of cpMVP was fit to this improved density from 15 domain models. Three domains were adapted from a nuclear magnetic resonance substructure. Nine domain models originated in ab initio tertiary structure prediction. Three C-terminal domains were built by fitting poly-alanine to the electron density. Locations of loops in this model provide sites to test vault functions and to exploit vaults as nanocapsules.

  17. Complexity of coherent structures computed from braids of passive particles

    NASA Astrophysics Data System (ADS)

    Budisic, Marko; Thiffeault, Jean-Luc

    2015-11-01

    Transport in fluids can be characterized by tracking passive particles advected by the fluid flow. When particles are distributed densely, as can be achieved in laboratory, the fluid velocity field can be reconstructed through Particle Tracking Velocimetry, enabling computation of Lyapunov exponents or other numerical analyses. When particles are sparse, as in drifter measurements of oceans, the velocity field cannot be reliably reconstructed. Nevertheless, the amount of entanglement of particle paths over time can be used to estimate the dynamical complexity of the flow by computing the Finite-Time Braiding Exponent (FTBE). The technique is based on braid dynamics and measures the rate at which particle motion stretches topological loops, i.e., the ``rubber bands'' enclosing subsets of particles. Allshouse and Thiffeault showed that minimally-stretching loops correspond to the structures coherent under material transport in flows. We extend their work and couple it to the FTBE calculations in order to characterize the spatial distribution of flow complexity. Analysis is demonstrated on the Hackborn rotor-oscillator model, which exhibits regions of chaotic and regular dynamics, and can be realized both numerically and experimentally. Funded by NSF CMMI-1233935.

  18. Lagrangian coherent structures and the dynamics of inertial particles

    NASA Astrophysics Data System (ADS)

    Madhavan, Sudharsan

    Dynamics of inertial particles in two-dimensional planar flow have been investigated by evaluating finite-time Lyapunov exponents (FTLE). The first part of our work deals with inertial particle dynamics. The Maxey-Riley equations have been employed to track particles. Patterns formed by inertial particles are reported along with their dependance on Strokes number and density of particles relative to the carrier-fluid density. Our results distinguish patterns formed by particles denser than the fluid (aerosols) from those formed by particles lighter than the fluid (bubbles). Preferential concentration of these particles at specific regions of the flow have been observed. The attenuating, low-pass filter effect of Stokes drag on bubbles are reported for the first time. The results from this part of the work motivated further investigations into the underlying organizing structures of the flow, namely the Lagrangian coherent structures (LCS). LCS is traditionally evaluated using FTLE. In the next part of the work, our objective was to interpret the dynamics of inertial particles by evaluating finite-time Lyapunov exponents on their trajectories. A main result is that aerosols were found to be attracted and preferentially concentrated along ridges of negative finite-time Lyapunov exponents (nFTLE) of the underlying flow. On the other hand bubbles were found to be repelled from these structures and were therefore observed preferentially concentrating away from these zones. These results, being reported for the first time, supplement the existing literature on preferential concentration of inertial particles. Despite having an effect on particle trajectories, increasing the Stokes number had very little effect on inertial finite-time Lyapunov exponents (iFTLE). Furthermore, increasing Stokes number resulted in an increase in the ridges of iFTLE contours for aerosols, whereas for bubbles the opposite was observed. These findings indicate that optimum mixing occurs at

  19. Revealing Three-Dimensional Structure of an Individual Colloidal Crystal Grain by Coherent X-Ray Diffractive Imaging

    NASA Astrophysics Data System (ADS)

    Shabalin, A. G.; Meijer, J.-M.; Dronyak, R.; Yefanov, O. M.; Singer, A.; Kurta, R. P.; Lorenz, U.; Gorobtsov, O. Y.; Dzhigaev, D.; Kalbfleisch, S.; Gulden, J.; Zozulya, A. V.; Sprung, M.; Petukhov, A. V.; Vartanyants, I. A.

    2016-09-01

    We present results of a coherent x-ray diffractive imaging experiment performed on a single colloidal crystal grain. The full three-dimensional (3D) reciprocal space map measured by an azimuthal rotational scan contained several orders of Bragg reflections together with the coherent interference signal between them. Applying the iterative phase retrieval approach, the 3D structure of the crystal grain was reconstructed and positions of individual colloidal particles were resolved. As a result, an exact stacking sequence of hexagonal close-packed layers including planar and linear defects were identified.

  20. Characterization of the structure of heterogeneous materials and particle packings

    NASA Astrophysics Data System (ADS)

    Jiao, Yang

    In this dissertation, we present a combination of computational and theoretical results concerning the characterization of the microstructure of heterogeneous materials and hard-particle packings. An overview of the dissertation is provided in Chapter 1. In Part I of this dissertation, we focus on the characterization of multi-phase heterogeneous materials. In Chapter 2, we present a detailed discussion of the correlation functions that statistically characterize the microstructure of a heterogeneous material. Examples of such materials include composites, colloids, foams and biological media. In Chapter 3, we introduce a microstructure reconstruction/construction procedure developed by Yeong and Torquato and devise a powerful universal sampling scheme, called the lattice-point scheme, that enables one to incorporate the widest class of lower-order correlation functions known to date into the Yeong-Torquato procedure, which opens the door to many fruitful applications. In Chapter 4, we present two major applications of our lattice-point scheme including modelling heterogeneous materials via two-point correlation functions and identifying superior microstructure descriptors of random media. These developments suggest novel approach for material design and more accurate rigorous structure-property relations; they also have ramifications in atomic and molecular systems. In Part II of this dissertation, we focus on quantitatively describing the structure of hard-particle packings, which have been employed to model a wide spectrum of condensed matters such as simple liquid, disordered/crystalline solids and granular media as well as biological systems. In Chapter 5, we present two major numerical packing protocols, namely the Donev-Torquato-Stillinger (DTS) event-driven molecular dynamics (MD) algorithm for smooth convex particles and the adaptive-shrinking-cell (ASC) scheme for hard polyhedral particles. In Chapter 6, the DTS event-driven MD algorithm is employed to