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1

Dependence of the crystal structure on particle size in barium titanate  

Microsoft Academic Search

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

Kenji Uchino; T. Hirose; E. Sadanaga

1989-01-01

2

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

NASA Astrophysics Data System (ADS)

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

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

2002-03-01

3

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

PubMed

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

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

2015-02-01

4

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

E-print Network

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

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

2010-05-27

5

Interaction of Fine Fe Particles with Structural Defects on {111} Faces of Synthetic Diamond Crystals in a Hydrogen Atmosphere  

Microsoft Academic Search

Data are presented on the interaction of fine Fe particles with structural defects on the octahedral faces of synthetic diamond crystals during catalyzed diamond gasification in a hydrogen atmosphere at 900°C. The defects were revealed by etching in molten NaNO3?. The results indicate that the penetration of metal particles into the crystal bulk is only possible at the outcrops of

V. M. Sonin

2004-01-01

6

Crystal structures of EV71 recombinant virus particles provide insights into vaccine design.  

PubMed

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 (CVA16). A desirable vaccine against HFMD is supposed to be multivalent and able to elicit protective responses against multiple HFMD causative agents. Previously, we have demonstrated that a thermo-stable 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 N-terminus of VP1 are transiently externalized. Together, our study provided insights into vaccine development against HFMD. PMID:25492868

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

2014-12-01

7

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

NASA Astrophysics Data System (ADS)

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

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

2006-05-01

8

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

SciTech Connect

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

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

2014-05-07

9

Nanodiamond particles forming photonic structures  

NASA Astrophysics Data System (ADS)

Colloid suspensions of irregularly shaped, highly charged detonation nanodiamond particles are found to have unexpected optical properties, similar to those of photonic crystals. This finding is all the more surprising since the particles used in this work are far more polydisperse than those typically forming photonic crystals. Intensely iridescent structures have been fabricated using the centrifugation of aqueous suspensions of nanodiamonds.

Grichko, Varvara; Tyler, Talmage; Grishko, Victor I.; Shenderova, Olga

2008-06-01

10

Ionic colloidal crystals of oppositely charged particles  

NASA Astrophysics Data System (ADS)

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.

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

11

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

NASA Astrophysics Data System (ADS)

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

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

2014-12-01

12

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

ERIC Educational Resources Information Center

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…

Smithenry, Dennis W.

2009-01-01

13

Passive particle dosimetry. [silver halide crystal growth  

NASA Technical Reports Server (NTRS)

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.

Childs, C. B.

1977-01-01

14

Structural Color Painting by Rubbing Particle Powder  

PubMed Central

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

Park, ChooJin; Koh, Kunsuk; Jeong, Unyong

2015-01-01

15

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.

16

Crystal structure of propaquizafop  

PubMed Central

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

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

2014-01-01

17

Data Mining Analysis of HIV1 Protease Crystal Structures  

Microsoft Academic Search

A data mining study has been done using HIV-1 protease crystal structures complexed with FDA approved HIV-1 protease inhibitor drugs. Chemical descriptors have been computed for the binding pockets of each crystal structure, yielding approximately 600 constitutional, topological, geometric, elecrotostatic, and quantum mechanical descriptors for each structure. Several supervised (hybrid binary particle swarm optimization- artificial neural network and random forest)

Gene M. Ko; A. Srinivas Reddy; Sunil Kumar; Rajni Garg

18

Demonstration of Crystal Structure.  

ERIC Educational Resources Information Center

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)

Neville, Joseph P.

1985-01-01

19

Soap Froths and Crystal Structures  

Microsoft Academic Search

We propose a physical mechanism to explain the crystal symmetries found in macromolecular and supramolecular micellar materials. We argue that the packing entropy of the hard micellar cores is frustrated by the entropic interaction of their brushlike coronas. The latter interaction is treated as a surface effect between neighboring Voronoi cells. The observed crystal structures correspond to the Kelvin and

Primoz Ziherl; Randall D. Kamien

2000-01-01

20

Crystallization in a dense suspension of self-propelled particles  

E-print Network

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 non-equilibrium 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 liquid-like "bubbles" still persist.

Julian Bialké; Thomas Speck; Hartmut Löwen

2011-12-22

21

Soap froths and crystal structures  

PubMed

We propose a physical mechanism to explain the crystal symmetries found in macromolecular and supramolecular micellar materials. We argue that the packing entropy of the hard micellar cores is frustrated by the entropic interaction of their brushlike coronas. The latter interaction is treated as a surface effect between neighboring Voronoi cells. The observed crystal structures correspond to the Kelvin and Weaire-Phelan minimal foams. We show that these structures are stable for reasonable areal entropy densities. PMID:11030938

Ziherl; Kamien

2000-10-16

22

Transport of particles in liquid crystals.  

PubMed

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

Lavrentovich, Oleg D

2014-03-01

23

CALYPSO: A method for crystal structure prediction  

NASA Astrophysics Data System (ADS)

We have developed a software package CALYPSO (Crystal structure AnaLYsis by Particle Swarm Optimization) to predict the energetically stable/metastable crystal structures of materials at given chemical compositions and external conditions (e.g., pressure). The CALYPSO method is based on several major techniques (e.g. particle-swarm optimization algorithm, symmetry constraints on structural generation, bond characterization matrix on elimination of similar structures, partial random structures per generation on enhancing structural diversity, and penalty function, etc.) for global structural minimization from scratch. All of these techniques have been demonstrated to be critical to the prediction of global stable structure. We have implemented these techniques into the CALYPSO code. Testing of the code on many known and unknown systems shows high efficiency and the highly successful rate of this CALYPSO method [Y. Wang, J. Lv, L. Zhu, Y. Ma, Phys. Rev. B 82 (2010) 094116] [29]. In this paper, we focus on descriptions of the implementation of CALYPSO code and why it works.

Wang, Yanchao; Lv, Jian; Zhu, Li; Ma, Yanming

2012-10-01

24

Crystal structure refinement with SHELXL  

PubMed Central

The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as ‘a CIF’) containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors. PMID:25567568

Sheldrick, George M.

2015-01-01

25

Crystal structure refinement with SHELXL.  

PubMed

The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors. PMID:25567568

Sheldrick, George M

2015-01-01

26

Brownian dynamics simulation of the crystallization dynamics of charged colloidal particles.  

PubMed

Crystal formation process of charged colloidal particles is investigated using Brownian dynamics (BD) simulations. The particles are assumed to interact with the pair-additive repulsive Yukawa potential. The time evolution of crystallization process and the crystal structure during the simulation are characterized by means of the radial distribution functions (RDF) and mean square displacement (MSD). The simulations show that when the interaction is featured with long-range, particles can spontaneously assemble into body-centered-cubic (BCC) arrays at relatively low particle number density. When the interaction is short-ranged, with increasing the number density particles become trapped into a stagnant disordered configuration before the crystallization could be actualized. The simulations further show that as long as the trapped configurations are bypassed, the face-centered-cubic (FCC) structures can be achieved and are actually more stable than BCC structures. PMID:20673671

Gu, Lingyun; Xu, Shenghua; Sun, Zhiwei; Wang, Jin Tong

2010-10-15

27

Crystal structure of fenpropathrin  

PubMed Central

In the title compound [systematic name: cyano­(3-phen­oxy­phen­yl)methyl 2,2,3,3-tetra­methyl­cyclo­propane­carboxyl­ate], C22H23NO3, which is the pyrethroid insecticide fenpropathrin, the dihedral angle between the cyclo­propane ring plane and the carboxyl­ate group plane is 88.25?(11)°. The dihedral angle between the benzene and phenyl rings in the phen­oxy­benzyl group is 82.99?(4)°. In the crystal, C—H?N hydrogen bonds and weak C—H?? inter­actions link adjacent mol­ecules, forming loop chains along the b-axis direction. PMID:25553036

Kang, Gihaeng; Jeon, Youngeun; Lee, Sangjin; Kim, Tae Ho

2014-01-01

28

Photonic Crystal Laser-Driven Accelerator Structures  

SciTech Connect

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.

Cowan, Benjamin M.

2007-08-22

29

Crystal structure of difenoconazole.  

PubMed

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

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

2014-11-01

30

The Crystal Structure of Talc  

Microsoft Academic Search

The crystal structure of a sample of talc from Harford County, Maryland, has been deter- mined by least squares refinement from X-ray diffraction photographs. A triclinic cell with a = 5.293, b = 9.179, c = 9.496A, a = 90'57 ~ = 98-91 ~ y = 90.03, space group cT is adopted. The layers of the structure have almost monoclinic

J. H. Rayner; G. BROWN

1973-01-01

31

Crystal structure of guggulsterone Z  

SciTech Connect

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.

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

2006-03-15

32

The crystallization processes in the aluminum particles production technology  

NASA Astrophysics Data System (ADS)

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.

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

2015-01-01

33

STUDY OF PHOTONIC CRYSTAL STRUCTURES YUGUANG ZHAO  

E-print Network

STUDY OF PHOTONIC CRYSTAL STRUCTURES BY THz-TDS By YUGUANG ZHAO Bachelor of Science Northwest CRYSTAL STRUCTURES BY THz-TDS Thesis Approved: Dr. Daniel Grischkowsky . Thesis Adviser Dr. Yumin Zhang photonic crystal structures ....................................................... 25 3.2 MEMS technology

Oklahoma State University

34

Isothermal Crystallization Kinetics of Highly Filled Wood Plastic Composites: Effect of Wood Particles Content and Compatibilizer  

Microsoft Academic Search

The isothermal crystallization behavior and crystal structure of the polypropylene (PP) component in Wood Plastic Composites (WPC) with respect to wood particle content and maleic anhydride grafted polypropylene (MAHPP) compatilizer were studied by means of polarized optical microscopy (POM), scanning electron microscopy (SEM), X-ray diffraction (XRD) and differential scanning calorimetry (DSC). It was found that under the experimental conditions of

PENG WANG; JIANYE LIU; WEI YU; CHIXING ZHOU

2011-01-01

35

American Mineralogist Crystal Structure Database  

NSDL National Science Digital Library

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

R. T. Downs

36

Crystal structures and freezing of dipolar fluids  

E-print Network

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

B. Groh; S. Dietrich

2000-10-21

37

Crystal structures and freezing of dipolar fluids.  

PubMed

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

Groh, B; Dietrich, S

2001-02-01

38

American Mineralogist Crystal Structure Database  

NSDL National Science Digital Library

The American Mineralogist Crystal Structure Database website, maintained by the Mineralogical Society of America and the Mineralogical Association of Canada and sponsored by the National Science Foundation, "includes every structure published in the American Mineralogist, The Canadian Mineralogist, and the European Journal of Mineralogy." The authors are also currently adding data from Physics and Chemistry of Minerals. Users can search the data by minerals, authors, chemistry, cell parameter and symmetry, or by a simple general search. This no frills website allows users to easily find and download data.

39

Crystal Structures Classifier for an Evolutionary Algorithm Structure Predictor  

E-print Network

Crystal Structures Classifier for an Evolutionary Algorithm Structure Predictor Mario Valle Data of Crystallography, Department of Materials ETH Z¨urich ABSTRACT USPEX is a crystal structure predictor based on an evolutionary algorithm. Every USPEX run produces hundreds or thousands of crystal structures, some of which may

Oganov, Artem R.

40

Crystal structure of lignin peroxidase.  

PubMed Central

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

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

1993-01-01

41

American Mineralogist Crystal Structure Database  

NSDL National Science Digital Library

This database includes the crystal structure for every mineral published in the American Mineralogist, The Canadian Mineralogist, European Journal of Mineralogy and Physics, and Chemistry of Minerals. Data is now being imported from Acta Crystallographica as well. The database is maintained under the care of the Mineralogical Society of America and the Mineralogical Association of Canada. The data can be displayed or downloaded and are searchable by mineral, author, mineral chemistry, unit cell parameters and symmetry, diffraction pattern, or a general search. Links are provided to additional information and to crystallographic software.

42

Study of structures in filled nematics with spherical particles  

NASA Astrophysics Data System (ADS)

The conditions for transitions between the possible structures in nematic liquid crystals with spherical particles (SPs) are studied. It has been shown that the divergent terms (K13 and K24) in Frank energy play an important role in such structures. The influence of charge of the SP and of an external electric field on the transitions between the structures is investigated.

Kuksenok, O. V.; Shiyanovskii, Serguey V.

1996-04-01

43

Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition.  

PubMed

U1 snRNP binds to the 5' exon-intron junction of pre-mRNA and thus plays a crucial role at an early stage of pre-mRNA splicing. We present two crystal structures of engineered U1 sub-structures, which together reveal at atomic resolution an almost complete network of protein-protein and RNA-protein interactions within U1 snRNP, and show how the 5' splice site of pre-mRNA is recognised by U1 snRNP. The zinc-finger of U1-C interacts with the duplex between pre-mRNA and the 5'-end of U1 snRNA. The binding of the RNA duplex is stabilized by hydrogen bonds and electrostatic interactions between U1-C and the RNA backbone around the splice junction but U1-C makes no base-specific contacts with pre-mRNA. The structure, together with RNA binding assays, shows that the selection of 5'-splice site nucleotides by U1 snRNP is achieved predominantly through basepairing with U1 snRNA whilst U1-C fine-tunes relative affinities of mismatched 5'-splice sites. PMID:25555158

Kondo, Yasushi; Oubridge, Chris; van Roon, Anne-Marie M; Nagai, Kiyoshi

2015-01-01

44

Photonic Band Structure of fcc Colloidal Crystals  

Microsoft Academic Search

Polystyrene colloidal crystals form three dimensional periodic dielectric structures which can be used for photonic band structure measurements in the visible regime. From transmission measurements the photonic band structure of an fcc crystal has been obtained along the directions between the L point and the W point. Kossel line patterns were used for locating the symmetry points of the lattice

I. Inanç Tarhan; George H. Watson

1996-01-01

45

Simulations of Photonic Crystal and Dielectric Structures  

SciTech Connect

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

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

2010-11-04

46

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

E-print Network

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

Alfredo Metere; Tomas Oppelstrup; Sten Sarman; Mikhail Dzugutov

2015-01-12

47

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

PubMed Central

High-resolution structural information is available for several soluble plasma apolipoproteins (apos) in a lipid-free state. However, this information provides limited insight into structure–function relationships, as this class of proteins primarily performs its functions of lipid transport and modulation of lipid metabolism in a lipid-bound state on lipoprotein particles. Here, the possibility of generating homogeneous lipoprotein particles that could be crystallized was explored, opening the possibility of obtaining high-resolution structural information by X-ray crystallography. To test this possibility, apoE4 complexed with the phospholipid dipalmitoylphosphatidylcholine was chosen. Uniform particles containing 50% lipid and 50% apoE4 were obtained and crystallized using the hanging-drop method. Two crystal forms diffract to beyond 8?Å resolution. PMID:16511213

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

2005-01-01

48

Crystal structure analysis of intermetallic compounds  

NASA Technical Reports Server (NTRS)

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.

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

1968-01-01

49

Old and New Particle Structure  

NASA Astrophysics Data System (ADS)

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

Wolff, Milo

2002-05-01

50

Crystal structure from one-electron theory  

Microsoft Academic Search

We have studied the crystal structures of all the 3d, 4d, and 5d transition metals at zero pressure and temperature by means of the linear muffin-tin orbital method and Andersen's force theorem. We find that, although the structural energy differences seem to be overestimated by the theory, the predicted crystal structures are in accord with experiment in all cases except

Hans L. Skriver

1985-01-01

51

Librarians, crystal structures and drug design.  

PubMed

There are now 355,000 published crystal structures of organic and metal-organic compounds, all of which have been acquired, validated, chemically annotated and organised for searching in the Cambridge Structural Database (CSD). The CSD is used in rational drug design and is beginning to answer important questions relevant to the formulation of pharmaceutical active ingredients. The value and credibility of this research are ultimately dependent on the accuracy and completeness of the underlying crystal-structure data. PMID:16228017

Allen, Frank H; Taylor, Robin

2005-11-01

52

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

PubMed

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

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

2013-01-01

53

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

NASA Technical Reports Server (NTRS)

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

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

1979-01-01

54

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

PubMed

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. PMID:24382495

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

2014-03-01

55

Process to make structured particles  

DOEpatents

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.

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

2014-02-04

56

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

DOEpatents

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.

Capone, D.W.; Dusek, J.

1994-10-18

57

Compact Couplers for Photonic Crystal Laser-Driven Accelerator Structures  

SciTech Connect

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

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

2012-07-02

58

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

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

59

Photonic-crystal fibre: Mapping the structure  

NASA Astrophysics Data System (ADS)

The demonstration of real-time and non-destructive Doppler-assisted tomography of the internal structure of photonic-crystal fibres could aid the fabrication of high-quality fibres with enhanced performance.

Markos, Christos

2015-01-01

60

Restricted dislocation mobility in crystals of peanut-shaped colloidal particles  

NASA Astrophysics Data System (ADS)

Recent advances in colloidal particle synthesis techniques have enabled the production of a variety of anisotropic yet monodisperse particles, including colloidal ``peanuts,'' which consist of two connected spherical lobes. Since their shape crudely approximates a dimer, colloidal peanut particles constitute a simple but fundamental extension of the classic system of colloidal spheres. Experimental investigations as well as simulations of colloidal peanut monolayers have shown that at high area fractions the particles form a degenerate crystal (DC). In this structure, the peanut particle lobes order into a triangular lattice, much like close-packed spheres, while the connections between lobe pairs are randomly oriented, uniformly populating the three crystalline directions of the underlying lattice. Comparative studies of crystal formation in rapidly compressed monolayers of peanut-shaped versus spherical particles show that DCs harbor many more defects than equivalent crystals of spheres. This suggests that defect annealing may be frustrated by the constraining rigid connections between particle lobes. To elucidate the interactions between these geometric constraints and defect mobility, we directly examine the mechanisms for dislocation nucleation and propagation in DCs. In particular, we show that obstacles formed by certain particle orientations severely limit the range over which dislocations can glide. Furthermore, we observe that transport over longer distances can proceed through dislocation reactions, which switch the direction of propagation and allow dislocations to bypass such obstacles. In this talk I will discuss the impact that these restricted mechanisms have on the macroscopic properties of DCs.

Cohen, Itai

2009-03-01

61

Predicting crystal structure by merging data mining with quantum mechanics  

E-print Network

ARTICLES Predicting crystal structure by merging data mining with quantum mechanics CHRISTOPHER C crystal structures will form in an alloy system. Crystal structure can only be predicted effectively the stable crystal structure of materials. C rystal structure occupies a central and often critical role

Ceder, Gerbrand

62

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

E-print Network

and symmetry, and a list of elements in the structure. This element list contains the atomic coordinates, siteABSTRACT The American Mineralogist Crystal Structure Database is a compilation of every crystal structure potentially of mineralogic or geologic interest. The database, seen as an outreach service

Downs, Robert T.

63

Formation of the structure of gold nanoclusters during crystallization  

SciTech Connect

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

Gafner, Yu. Ya., E-mail: ygafner@khsu.ru; Goloven'ko, Zh. V.; Gafner, S. L. [Khakassian State University (Russian Federation)] [Khakassian State University (Russian Federation)

2013-02-15

64

Crystal structure of trismorpholino phosphiniminocyclotrithiazene  

Microsoft Academic Search

The title compound (OC4H8N)3P=N–S3N3 crystallizes in a monoclinic crystal system with unit cell parameters a = 8.9996(3), b = 17.2895(7), and c = 12.3648(9) Å, ß = 90.63(5)°, Z = 4, and space group P21\\/n. Strikingly the exocylic S1–N4 bond length is 1.545(3) ÅR and is accompanied by the largest angle at P–N4–S1 as 131.2(2)°. The tricoordinated sulfur atom of

J. Srinivas; G. Sreenivasa Murthy; U. Swarnalatha; M. N. Sudheendra Rao

2001-01-01

65

Structures of cyano-biphenyl liquid crystals  

NASA Technical Reports Server (NTRS)

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.

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

1989-01-01

66

Interaction between two spherical particles in a nematic liquid crystal  

NASA Astrophysics Data System (ADS)

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

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

2004-04-01

67

DYNAMIC BEHAVIOR OF PARTICLE AGGLOMERATION OF EUROPIUM OXALATE DURING REACTION CRYSTALLIZATION IN SEMI-BATCH REACTOR  

Microsoft Academic Search

During reaction crystallization of europium oxalate in a semi-batch reactor, a monotonical increase in the mean particle size and corresponding reduction in the total particle population were observed due to particle agglomeration occurring simultaneously with particle nucleation and growth. However, since particle agglomeration was achieved via particle aggregation and molecular growth, the mean particle size and total particle population in

Woo-Sik Kim; Woon-Soo Kim; Kwang-Seok Kim; Joon-Soo Kim; Taesung Jung; Michael D. Ward

2006-01-01

68

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

NASA Astrophysics Data System (ADS)

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 self-assembled procedures of making composite crystals at micron scale are very promising, because the fabrication will only relies on solvent, additives, or combination of them without using sophisticated crystallizers.

Luo, Tzy-Jiun Mark

69

Fabrication and characterization of non-brownian particle-based crystals.  

PubMed

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 ?m) 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. PMID:24983125

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

2015-01-27

70

Liquid crystal light valve structures  

NASA Technical Reports Server (NTRS)

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

Koda, N. J. (inventor)

1985-01-01

71

High-temperature crystal structure of pyroxmangite  

Microsoft Academic Search

AssrRAcr High-temperature crystal-structure analysis of MnSiO, pyroxmangite indicates that ex- pansion of the structure takes place by expansion of the M cation

72

Crystal Structure of A-amylose: a Revisit from Synchrotron Microdiffraction Analysis of Single Crystals  

E-print Network

1 Crystal Structure of A-amylose: a Revisit from Synchrotron Microdiffraction Analysis of Single;2 Abstract The three-dimensional structure of A-amylose crystals, as a model of the crystal domains of A-sized single crystals. The resulting datasets allowed a determination of the structure with conventional X

Paris-Sud XI, Université de

73

Crystal structures of sialyltransferase from Photobacterium damselae.  

PubMed

Sialyltransferase structures fall into either GT-A or GT-B glycosyltransferase fold. Some sialyltransferases from the Photobacterium genus have been shown to contain an additional N-terminal immunoglobulin (Ig)-like domain. Photobacterium damselae ?2-6-sialyltransferase has been used efficiently in enzymatic and chemoenzymatic synthesis of ?2-6-linked sialosides. Here we report three crystal structures of this enzyme. Two structures with and without a donor substrate analog CMP-3F(a)Neu5Ac contain an immunoglobulin (Ig)-like domain and adopt the GT-B sialyltransferase fold. The binary structure reveals a non-productive pre-Michaelis complex, which are caused by crystal lattice contacts that prevent the large conformational changes. The third structure lacks the Ig-domain. Comparison of the three structures reveals small inherent flexibility between the two Rossmann-like domains of the GT-B fold. PMID:25451227

Huynh, Nhung; Li, Yanhong; Yu, Hai; Huang, Shengshu; Lau, Kam; Chen, Xi; Fisher, Andrew J

2014-12-20

74

Data mining chemistry and crystal structure  

NASA Astrophysics Data System (ADS)

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

Yang, Lusann W.

75

Phononic crystals of spherical particles: A tight binding approach  

SciTech Connect

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.

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

2013-11-07

76

Crystal structure and chirality of natural floridoside.  

PubMed

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

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

2003-10-31

77

The crystal structure and crystal chemistry of fernandinite and corvusite  

USGS Publications Warehouse

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

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

1994-01-01

78

Crystal structures and morphologies of fractionated milk fat in nanoemulsions.  

PubMed

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

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

2015-03-15

79

Automated protein crystal structure determination using elves  

PubMed Central

Efficient determination of protein crystal structures requires automated x-ray data analysis. Here, we describe the expert system elves and its use to determine automatically the structure of a 12-kDa protein. Multiwavelength anomalous diffraction analysis of a selenomethionyl derivative was used to image the Asn-16-Ala variant of the GCN4 leucine zipper. In contrast to the parallel, dimeric coiled coil formed by the WT sequence, the mutant unexpectedly formed an antiparallel trimer. This structural switch reveals how avoidance of core cavities at a single site can select the native fold of a protein. All structure calculations, including indexing, data processing, locating heavy atoms, phasing by multiwavelength anomalous diffraction, model building, and refinement, were completed without human intervention. The results demonstrate the feasibility of automated methods for determining high-resolution, x-ray crystal structures of proteins. PMID:14752198

Holton, James; Alber, Tom

2004-01-01

80

Many particle approach to excitons in crystals: Electron-electron and electron-phonon interactions  

NASA Astrophysics Data System (ADS)

A many particle system of electrons interacting one with another and also with the crystal lattice vibrations was studied theoretically. The particular diagonalization of the Hamiltonian was fulfilled and it was shown that the structure of bands (exciton structure) in the absorption spectra of the crystal is really the set of electron-phonon maxima. Numerical calculations showed also that full electron bands, valence and conductivity, are responsible for the formation of exciton maxima and even states located far from the edge of zones have significant effect on the occurrence of exciton peaks - which is in disagreement with the effective mass approximation (EMA). The results are compared with known experimental data for wide band ZnO and CdS crystals.

Yaremko, A. M.; Dzhagan, V. M.; Yukhymchuk, V. O.; Linnik, T. L.; Ratajczak, H.; Baran, J.; Barnes, A. J.

2010-07-01

81

Requirements for structure determination of aperiodic crystals  

SciTech Connect

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

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

1991-01-15

82

Surface-induced structures in nematic liquid crystal colloids.  

PubMed

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

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

2014-08-01

83

Surface-induced structures in nematic liquid crystal colloids  

NASA Astrophysics Data System (ADS)

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

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

2014-08-01

84

Surface induced structures in nematic liquid crystal colloids  

E-print Network

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

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

2014-05-30

85

Particle tracking from image sequences of complex plasma crystals  

SciTech Connect

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.

Hadziavdic, Vedad; Melandsoe, Frank; Hanssen, Alfred [Department of Physics and Technology, University of Tromsoe, NO-9037 Tromsoe (Norway)

2006-05-15

86

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

NASA Astrophysics Data System (ADS)

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.

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

2003-01-01

87

Shear induced structures in crystallizing cocoa butter  

NASA Astrophysics Data System (ADS)

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.

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

2004-03-01

88

Crystal Structure of Tetraphenyltin(1~) (a Redetermination)  

Microsoft Academic Search

The crystal structure of tetraphenyltin(1v) has been redetermined at 295(1) K, full-matrix least-squares refinement yielding a residual of 0.031 for 557 independent 'observed' reflections. The tin-phenyl carbon distance is 2.143(5) A, with the angles subtended at the tin atom being 108.9(2) and 110.5(2)\\

Lutz M. Engelhardt; Wing-Por Leung; Colin L. Raston; Allan H. White; W. A. Nedlands

89

Hammerhead Ribozyme Crystal Structures and Catalysis  

E-print Network

are comparatively large and complex catalytic RNAs, the identification of the hammerhead ribozyme offered hopeCHAPTER 4 Hammerhead Ribozyme Crystal Structures and Catalysis WILLIAM SCOTT Center in fact those of hammerhead ribozymes, but they seemed to create more questions than compelling

Scott, William

90

Crystal structure of a plectonemic RNA supercoil  

SciTech Connect

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.

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

2012-12-14

91

Crystal-structure calculations with distorted ions  

NASA Astrophysics Data System (ADS)

We present the polarization-included electron-gas (PEG) model for crystal structures, which is similar to the modified-electron-gas (MEG) model for crystal structures, but in which the anions can distort from spherical symmetry. This nonspherical distortion is important when the anions occupy low-symmetry positions. For SiO2 quartz, SiO2 cristobalite, BeF2 quartz, and the zeolite sodalite, which have open crystal structures, the structures and energies calculated with the PEG model are in much better agreement with experiment than those calculated with the MEG model. The improved structural results are due mainly to smaller and more accurate cation-anion-cation bond angles. For SiO2 stishovite, TiO2 rutile, and Mg2SiO4 spinel, which have more closely packed crystal structures, the structures are modeled well with both the PEG and MEG models, but the energies are more accurately calculated with the PEG model. The improved results for the energies are due to the stronger bonds formed when charge density moves into the bonding regions. Electron-distribution plots are in good agreement with those from accurate band-structure calculations for the cristobalite and stishovite phases of silica. The electron-distribution plots show that the nonspherical distortions increase from BeF2 to TiO2 to SiO2, demonstrating that the extent of covalent bonding increases from BeF2 to TiO2 to SiO2, in agreement with electronegativity differences. We find that covalent effects are not as important in MgSiO3 perovskite as they are in the silica polymorphs quartz, cristobalite and stishovite, and Mg2SiO4 spinel.

Lacks, Daniel J.; Gordon, Roy G.

1993-08-01

92

Crystal Structure of Human Enterovirus 71  

SciTech Connect

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.

Plevka, Pavel; Perera, Rushika; Cardosa, Jane; Kuhn, Richard J.; Rossmann, Michael G. (Purdue); (Sentinext)

2013-04-08

93

Crystal structure of human enterovirus 71.  

PubMed

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. PMID:22383808

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

2012-06-01

94

Crystal structures of dibromochloromethane and bromodichloromethane  

Microsoft Academic Search

The crystal structures of CHB2Cl and CHBrCl2 have been investigated using neutron powder profile techniques. These structures were found to be similar to that of CHBr3 in its lowest temperature triclinic phase. Whereas CHBr3 has three phases, both CHBr2Cl and CHBrCl2 have only one. The two CHBr3 phases which are absent in these compounds require the molecules to have threefold

B. H. Torrie; O. S. Binbrek; I. P. Swainson; B. M. Powell

1999-01-01

95

Crystal structures of dibromochloromethane and bromodichloromethane  

Microsoft Academic Search

The crystal structures of CHB2C1 and CHBrC12 have been investigated using neutron powder profile techniques. These structures were found to be similar to that of CHBr3 in its lowest temperature triclinic phase. Whereas CHBr3 has three phases, both CHBr2C1 and CHBrC12 have only one. The two CHBr3 phases which are absent in these compounds require the molecules to have threefold

B. H. TORRIE; O. S. BINBREK; I. P. SWAINSON; B. M. POWELL

1999-01-01

96

Crystal Structure of Cesium-V  

NASA Astrophysics Data System (ADS)

The crystal structure of the high-pressure phase cesium-V was investigated using monochromatic synchrotron x-ray diffraction. Full profile refinements of powder diffraction data resulted in a solution with space group Cmca and 16 atoms in the orthorhombic unit cell. The Cs-V structure can be viewed as a distorted fcc structure. Atoms occupy two different Wyckoff positions with 10-fold and 11-fold coordination, respectively. This new structure type is considered a possible candidate for high-pressure phases of other elemental metals.

Schwarz, U.; Takemura, K.; Hanfland, M.; Syassen, K.

1998-09-01

97

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

PubMed

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

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

2011-04-01

98

Integrable structure of modified melting crystal model  

E-print Network

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

Kanehisa Takasaki

2012-08-22

99

The crystal structure of nickel arsenide  

Microsoft Academic Search

The crystal structure has been redetermined using X-ray diffraction data collected from a triply twinned crystal, a=10.8568(8), b=6.2682(5), c=5.0340(7)AA, Cmc21 grown using I2 as the vapour transport agent. The weak orthorhombic superlattice originally observed by convergent-beam electron diffraction, corresponding to the freezing in of a q=1\\/3(1120) Sigma 6 sub-cell phonon mode, is confirmed, and magnitudes of the atomic displacements from

J. G. Thompson; A. D. Rae; R. L. Withers; T. R. Welberry; A. C. Willis

1988-01-01

100

Structure of nucleosome core particles of chromatin  

Microsoft Academic Search

Crystals have been obtained of nucleosome cores and analysed by X-ray diffraction and electron microscopy. The core is a flat particle of dimensions about 110 × 110 × 57 Å, somewhat wedge shaped, and strongly divided into two `layers', consistent with the DNA being wound into about 1¾ turns of a fiat superhelix of a pitch about 28 Å. The

J. T. Finch; L. C. Lutter; D. Rhodes; R. S. Brown; B. Rushton; M. Levitt; A. Klug

1977-01-01

101

Structure of the nucleosome core particle at 7 Å resolution  

Microsoft Academic Search

The crystal structure of the nucleosome core particle has been solved to 7 Å resolution. The right-handed B-DNA superhelix on the outside contains several sharp bends and makes numerous interactions with the histone octamer within. The central turn of superhelix and H3 . H4 tetramer have dyad symmetry, but the H2A . H2B dimers show departures due to interparticle associations.

T. J. Richmond; J. T. Finch; B. Rushton; D. Rhodes; A. Klug

1984-01-01

102

Crystal structure of low-symmetry rondorfite  

SciTech Connect

The crystal structure of an aluminum-rich variety of the mineral rondorfite with the composition Ca{sub 16}[Mg{sub 2}(Si{sub 7}Al)(O{sub 31}OH)]Cl{sub 4} from the skarns of the Verkhne-Chegemskoe plateau (the Kabardino-Balkarian Republic, the Northern Caucasus Region, Russia) was solved in the triclinic space group with the unit-cell parameters a = 15.100(2) Angstrom-Sign , b = 15.110(2) Angstrom-Sign , c = 15.092(2) Angstrom-Sign , {alpha} = 90.06(1) Degree-Sign , {beta} = 90.01(1) Degree-Sign , {gamma} = 89.93(1) Degree-Sign , Z = 4, sp. gr. P1. The structural model consisting of 248 independent atoms was determined by the phase-correction method and refined to R = 3.8% with anisotropic displacement parameters based on all 7156 independent reflections with 7156 F > 3{sigma}(F). The crystal structure is based on pentamers consisting of four Si tetrahedra linked by the central Mg tetrahedron. The structure can formally be refined in the cubic space group (a = 15.105 Angstrom-Sign , sp. gr. Fd 3 bar , seven independent positions) with anisotropic displacement parameters to R = 2.74% based on 579 reflections with F > 3{sigma}(F) without accounting for more than 1000 observed reflections, which are inconsistent with the cubic symmetry of the crystal structure.

Rastsvetaeva, R. K., E-mail: rast@ns.crys.ras.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Zadov, A. E. [NPO Neokhim (Russian Federation); Chukanov, N. V. [Russian Academy of Sciences, Institute of Problems of Chemical Physics (Russian Federation)

2008-03-15

103

Crystal structure of low-symmetry rondorfite  

SciTech Connect

The crystal structure of an aluminum-rich variety of the mineral rondorfite with the composition Ca{sub 16}[Mg{sub 2}(Si{sub 7}Al)(O{sub 31}OH)]Cl{sub 4} from the skarns of the Verkhne-Chegemskoe plateau (the Kabardino-Balkarian Republic, the Northern Caucasus Region, Russia) was solved in the triclinic space group with the unit-cell parameters a = 15.100(2) A, b = 15.110(2) A, c = 15.092(2) A, {alpha} = 90.06(1) deg., {beta} = 90.01(1) deg., {gamma} = 89.93(1) deg., Z = 4, sp. gr. P1. The structural model consisting of 248 independent atoms was determined by the phase-correction method and refined to R = 3.8% with anisotropic displacement parameters based on all 7156 independent reflections with 7156 F > 3{sigma}(F). The crystal structure is based on pentamers consisting of four Si tetrahedra linked by the central Mg tetrahedron. The structure can formally be refined in the cubic space group (a = 15.105 A, sp. gr. Fd-bar 3, seven independent positions) with anisotropic displacement parameters to R = 2.74% based on 579 reflections with F > 3{sigma}(F) without accounting for more than 1000 observed reflections, which are inconsistent with the cubic symmetry of the crystal structure.

Rastsvetaeva, R. K. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)], E-mail: rast@ns.crys.ras.ru; Zadov, A. E. [NPO Neokhim (Russian Federation); Chukanov, N. V. [Russian Academy of Sciences, Institute of Problems of Chemical Physics (Russian Federation)

2008-03-15

104

Persistent hydrogen bonding in polymorphic crystal structures.  

PubMed

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

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

2009-02-01

105

Single particle detection in CMOS compatible photonic crystal nanobeam cavities.  

PubMed

We report the label-free detection of single particles using photonic crystal nanobeam cavities fabricated in silicon-on-insulator platform, and embedded inside microfluidic channels fabricated in poly-dimethylsiloxane (PDMS). Our system operates in the telecommunication wavelength band, thus leveraging the widely available, robust and tunable telecom laser sources. Using this approach, we demonstrated the detection of polystyrene nanoparticles with dimensions down to 12.5nm in radius. Furthermore, binding events of a single streptavidin molecule have been observed. PMID:24514817

Quan, Qimin; Floyd, Daniel L; Burgess, Ian B; Deotare, Parag B; Frank, Ian W; Tang, Sindy K Y; Ilic, Rob; Loncar, Marko

2013-12-30

106

5.841 Crystal Structure Refinement, Fall 2006  

E-print Network

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

Mueller, Peter

107

5.067 Crystal Structure Refinement, Fall 2007  

E-print Network

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

Mueller, Peter

108

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

E-print Network

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 show that the large particle moves almost freely through the bulk of plasma crystal, while dust particles move along characteristic $\\alpha$-shaped pathways near the large particle. In the hydrodynamic approximation, we develop a theory of nonviscous dust particles motion about a large particle and calculate particle trajectories. A good agreement with experiment validates our approach.

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

2012-01-01

109

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

PubMed

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

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

110

A tri-objective Particle Swarm Optimizer for designing line defect Photonic Crystal Waveguides  

NASA Astrophysics Data System (ADS)

This paper proposes a novel tri-objective approach for optimizing the structure of line defect Photonic Crystal Waveguides (PCW). A nature-inspired algorithm called Multi-Objective Particle Swarm Optimization (MOPSO) is employed as the optimizer. The three objectives considered are maximization of group index, maximization of bandwidth, and minimization of Group Velocity Dispersion (GVD). In addition, the optimization process is subject to five constraints in order to guarantee the feasibility of the structures obtained and prevent bad mixing in the final optimized structures. The results show that the tri-objective MOPSO is able to find 20 optimized structures for line defect PCW. The comparative study verifies the significant improvement of the optimized structures compared to current structures. Moreover, post analysis of the results reveals the importance of holes and their possible physical behaviours in line defect PCW. Finally, the implementation considerations and investigations show that the optimized structures are feasible for manufacturing with a resolution of 1 nm.

Mirjalili, Seyed Mohammad; Mirjalili, Seyedali; Lewis, Andrew; Abedi, Kambiz

2014-04-01

111

Crystal structure of riboflavin synthase  

SciTech Connect

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.

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

2010-03-05

112

Crystal Structure of a Cyclotetraicosaphenylene by Peter Mllera  

E-print Network

Crystal Structure of a Cyclotetraicosaphenylene by Peter Müllera ), Isabel Uso�na ), Volker Henselb-rigid macrocycle is the cyclotetraicosaphenylene 1. Determining the X-ray crystal structure was a challenge which]. Although of great interest, a three-dimensional structure determination ± preferably a single-crystal X

Müller, Peter

113

Structural Evolution of Colloidal Crystals with Increasing Ionic Strength  

E-print Network

Structural Evolution of Colloidal Crystals with Increasing Ionic Strength Michael A. Bevan. In Final Form: June 5, 2004 We have directly observed the structural evolution of colloidal crystals-driven transport that also melted initial single domain crystals to yield polycrystalline and gel structures

Braun, Paul

114

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

ERIC Educational Resources Information Center

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)

Chesick, John P.

1989-01-01

115

Crystal structure of the bacterial conjugation  

E-print Network

. Here we present the 2.0 Ã? resolution X-ray crystal structure of FinO, lacking its flexible N to interact with traJ mRNA to occlude its ribo- some binding site, blocking traJ translation and thereby of the inhibition sys- tem, protects FinP against degradation. It binds to FinP and steri- cally blocks access

Glover, Mark

116

Observations on the crystal structures of lueshite  

NASA Astrophysics Data System (ADS)

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

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

2014-06-01

117

Crystal Structure of a Phosphorylated Smad2  

Microsoft Academic Search

Ligand-induced phosphorylation of the receptor-regulated Smads (R-Smads) is essential in the receptor Ser\\/Thr kinase-mediated TGF-? signaling. The crystal structure of a phosphorylated Smad2, at 1.8 Å resolution, reveals the formation of a homotrimer mediated by the C-terminal phosphoserine (pSer) residues. The pSer binding surface on the MH2 domain, frequently targeted for inactivation in cancers, is highly conserved among the Co-

Jia-Wei Wu; Min Hu; Jijie Chai; Joan Seoane; Morgan Huse; Carey Li; Daniel J. Rigotti; Saw Kyin; Tom W. Muir; Robert Fairman; Joan Massagué; Yigong Shi

2001-01-01

118

Photosensitive liquid crystals with nanoparticulate internal structure  

NASA Astrophysics Data System (ADS)

Stabilization of thermodynamic relaxation of photoinduced cis isomers of azobenzene liquid-crystal molecules is observed in nanoparticulate networks. The phenomenon permits bistability of the phase state (anisotropic and isotropic) of the material and reversible all-optical switching between those states, resulting in strong changes in the light-scattering properties of the material. Recording of complex optical structures with high spatial resolution with the aid of laser beams of different wavelengths is demonstrated.

Tabiryan, N.; Grozhik, V.; Serak, S.

2002-11-01

119

Predicting polymeric crystal structures by evolutionary algorithms.  

PubMed

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. PMID:25338876

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

2014-10-21

120

Predicting polymeric crystal structures by evolutionary algorithms  

NASA Astrophysics Data System (ADS)

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.

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

2014-10-01

121

Bio-Inspired Approaches to Crystals with Composite Structures  

NASA Astrophysics Data System (ADS)

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

Meldrum, Fiona

2013-03-01

122

Crystal structure and DFT calculations of andrographiside  

NASA Astrophysics Data System (ADS)

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

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

2010-02-01

123

Interaction of two-dimensional plasma crystals with upstream charged particles  

NASA Astrophysics Data System (ADS)

Two-dimensional plasma crystals are characterized by a strong up-and-down asymmetry not only due to gravity but also due to the presence of plasma flow at the location of particles. We study for the first time the interaction of a single-layer plasma crystal with charged extra particles located above it (upstream of the flow of ions). Upstream extra particles tend to move between the rows of particles in the crystal, accelerate to supersonic speeds, and excite attraction-dominated Mach cones and wakes in the crystal.

Du, C.-R.; Nosenko, V.; Zhdanov, S.; Thomas, H. M.; Morfill, G. E.

2012-09-01

124

Crystal Structure of Cryptosporidium parvum Pyruvate Kinase  

PubMed Central

Pyruvate kinase plays a critical role in cellular metabolism of glucose by serving as a major regulator of glycolysis. This tetrameric enzyme is allosterically regulated by different effector molecules, mainly phosphosugars. In response to binding of effector molecules and substrates, significant structural changes have been identified in various pyruvate kinase structures. Pyruvate kinase of Cryptosporidium parvum is exceptional among known enzymes of protozoan origin in that it exhibits no allosteric property in the presence of commonly known effector molecules. The crystal structure of pyruvate kinase from C. parvum has been solved by molecular replacement techniques and refined to 2.5 Å resolution. In the active site a glycerol molecule is located near the ?-phosphate site of ATP, and the protein structure displays a partially closed active site. However, unlike other structures where the active site is closed, the ?6' helix in C. parvum pyruvate kinase unwinds and assumes an extended conformation. In the crystal structure a sulfate ion is found at a site that is occupied by a phosphate of the effector molecule in many pyruvate kinase structures. A new feature of the C. parvum pyruvate kinase structure is the presence of a disulfide bond cross-linking the two monomers in the asymmetric unit. The disulfide bond is formed between cysteine residue 26 in the short N-helix of one monomer with cysteine residue 312 in a long helix (residues 303–320) of the second monomer at the interface of these monomers. Both cysteine residues are unique to C. parvum, and the disulfide bond remained intact in a reduced environment. However, the significance of this bond, if any, remains unknown at this time. PMID:23056503

Cook, William J.; Senkovich, Olga; Aleem, Khadijah; Chattopadhyay, Debasish

2012-01-01

125

PROTEIN STRUCTURE REPORT Crystal structure of the Yersinia type III  

E-print Network

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

126

Crystal structure of MboIIA methyltransferase.  

SciTech Connect

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.

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

2003-09-15

127

Vibrational Phonon Modes of Two-Dimensional Soft-Particle Colloidal Crystals with Hard-Particle Dopants  

NASA Astrophysics Data System (ADS)

We study the phonon modes of two-dimensional colloidal crystals consisting of random distributions of ``soft'' NIPA microgel particles and ``hard'' polystyrene particle dopants. Thus, the effective springs connecting nearest-neighbors are very stiff, very soft, or of intermediate stiffness, corresponding to three possible inter-particle potentials present in the crystals. We employ video microscopy to derive the phonon modes of corresponding ``shadow'' crystals with the same geometric configuration and interactions as the experimental colloidal system, but absent damping [1,2,3]. Long wavelength, Debye-like behavior is found at low frequencies, regardless of the number of hard polystyrene particles present in the crystal. Hard particles are primary participants at high frequencies, while soft spheres are primary participants at intermediate frequencies. [1] Chen et al., PRL 105, 025501 (2010). [2] Kaya et al., Science 329, 656 (2010). [3] Ghosh et al. PRL 104, 248305 (2010).

Gratale, Matthew; Yunker, Peter; Chen, Ke; Aptowicz, Kevin; Yodh, Arjun

2012-02-01

128

Crystal structure of a human GABAA receptor.  

PubMed

Type-A ?-aminobutyric acid receptors (GABAARs) are the principal mediators of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signalling triggers hyperactive neurological disorders such as insomnia, anxiety and epilepsy. Here we present the first three-dimensional structure of a GABAAR, the human ?3 homopentamer, at 3?Å resolution. This structure reveals architectural elements unique to eukaryotic Cys-loop receptors, explains the mechanistic consequences of multiple human disease mutations and shows an unexpected structural role for a conserved N-linked glycan. The receptor was crystallized bound to a previously unknown agonist, benzamidine, opening a new avenue for the rational design of GABAAR modulators. The channel region forms a closed gate at the base of the pore, representative of a desensitized state. These results offer new insights into the signalling mechanisms of pentameric ligand-gated ion channels and enhance current understanding of GABAergic neurotransmission. PMID:24909990

Miller, Paul S; Aricescu, A Radu

2014-08-21

129

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

Microsoft Academic Search

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

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

1975-01-01

130

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

NASA Astrophysics Data System (ADS)

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.

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

2010-12-01

131

The crystal structure of calcite III Joseph R. Smyth  

E-print Network

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

Smyth, Joseph R.

132

Prediction of binary hard-sphere crystal structures  

NASA Astrophysics Data System (ADS)

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, ?CuTi , ?IrV , 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.

Filion, Laura; Dijkstra, Marjolein

2009-04-01

133

Prediction of binary hard-sphere crystal structures.  

PubMed

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

Filion, Laura; Dijkstra, Marjolein

2009-04-01

134

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

E-print Network

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

Qi, Limin

135

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

E-print Network

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

Titov, Anatoly

136

Crystal structure of yeast Sco1  

SciTech Connect

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.

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

2010-03-05

137

The Crystal Structure of Human Argonaute2  

SciTech Connect

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.

Schirle, Nicole T.; MacRae, Ian J. (Scripps)

2012-07-18

138

Crystal structure of glucokinase regulatory protein.  

PubMed

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

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

2013-05-21

139

Crystal structures of dibromochloromethane and bromodichloromethane  

NASA Astrophysics Data System (ADS)

The crystal structures of CHB2Cl and CHBrCl2 have been investigated using neutron powder profile techniques. These structures were found to be similar to that of CHBr3 in its lowest temperature triclinic phase. Whereas CHBr3 has three phases, both CHBr2Cl and CHBrCl2 have only one. The two CHBr3 phases which are absent in these compounds require the molecules to have threefold axes. The degree of disorder of the halogen atoms has been examined and the results indicate that the Br and Cl atoms have definite preferences for some sites over others, so that the molecules on average do not have a threefold axis.

Torrie, B. H.; Binbrek, O. S.; Swainson, I. P.; Powell, B. M.

140

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

PubMed

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

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

2015-01-13

141

Crystal and Electronic Structure of Copper Sulfides  

NASA Astrophysics Data System (ADS)

Because of the complexity of the crystal structure of Cu2-xS, no electronic band structure studies have been performed in the past. These materials have S atoms on a (hcp) or at high-temperature (fcc) close packed lattice but the Cu atoms occupy various low-symmetry Wyckoff sites of which only the statistical distribution is known from X-ray diffraction experiments. Here, we constructed supercell models for the cubic and hexagonal phases with the Cu positions determined by a weighted random number generator. The electronic structure of both these models and the monoclinic structure are studied using the full-potential linearized muffin-tin orbital method in the local density approximation (LDA). Both LDA and GW quasiparticle calculations give a zero band gap for the latter. The supercell models gave small band gaps of order 0.1--0.2 eV. Adding a Cu-s shift as suggested by the antifluorite structure GW calculation and an analysis in terms of atomic orbitals, increases the gap to about 0.5 eV.

Lukashev, Pavel; Lambrecht, Walter R. L.

2007-03-01

142

Crystal Structure of Human Spermine Synthase  

PubMed Central

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

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

2008-01-01

143

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

ERIC Educational Resources Information Center

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)

Hong, Y. S.; And Others

1980-01-01

144

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

SciTech Connect

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.

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

2014-04-07

145

Inner structure of adsorbed ionic microgel particles.  

PubMed

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

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

2014-06-24

146

Broadband super-collimation in a hybrid photonic crystal structure  

E-print Network

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

Soljaèiæ, Marin

147

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

E-print Network

1 Cloud structure and crystal growth in nimbostratus clouds. Mengistu Wolde* , Gabor Vali-mail: mengistu.wolde@nrc.ca. #12;2 Abstract Cloud structure and crystal growth in two nimbostratus were examined using in situ and airborne radar observations. In both cases, structure throughout the cloud depth

Vali, Gabor

148

Cyanuryl-PNA monomer: synthesis and crystal structure.  

PubMed

[structure: see text] The chemical synthesis and crystal structure of the peptide nucleic acid (PNA) monomer 11 having cyanuric acid as the nucleobase is reported. The crystal structure of 11 shows molecular tapes arising from continuous intermolecular dimeric hydrogen bonding, with successive tapes held by single hydrogen bonds in the backbone. PMID:10964375

Sanjayan, G J; Pedireddi, V R; Ganesh, K N

2000-09-01

149

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

NASA Technical Reports Server (NTRS)

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

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

1979-01-01

150

Crystal structure of the ?-secretase component nicastrin  

PubMed Central

?-Secretase is an intramembrane protease responsible for the generation of amyloid-? (A?) peptides. Aberrant accumulation of A? leads to the formation of amyloid plaques in the brain of patients with Alzheimer's disease. Nicastrin is the putative substrate-recruiting component of the ?-secretase complex. No atomic-resolution structure had been identified on ?-secretase or any of its four components, hindering mechanistic understanding of ?-secretase function. Here we report the crystal structure of nicastrin from Dictyostelium purpureum at 1.95-Å resolution. The extracellular domain of nicastrin contains a large lobe and a small lobe. The large lobe of nicastrin, thought to be responsible for substrate recognition, associates with the small lobe through a hydrophobic pivot at the center. The putative substrate-binding pocket is shielded from the small lobe by a lid, which blocks substrate entry. These structural features suggest a working model of nicastrin function. Analysis of nicastrin structure provides insights into the assembly and architecture of the ?-secretase complex. PMID:25197054

Xie, Tian; Yan, Chuangye; Zhou, Rui; Zhao, Yanyu; Sun, Linfeng; Yang, Guanghui; Lu, Peilong; Ma, Dan; Shi, Yigong

2014-01-01

151

STRUCTURE NOTE Crystal Structure of a Truncated Version of the Phage  

E-print Network

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

152

Crystal Structures of Respiratory Pathogen Neuraminidases  

SciTech Connect

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.

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

2009-01-01

153

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

PubMed

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

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

2009-12-24

154

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

PubMed

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

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

2009-10-30

155

Crystal structure of betulinic acid methanol monosolvate  

PubMed Central

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

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

2014-01-01

156

Crystal structure of betulinic acid methanol monosolvate.  

PubMed

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

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

2014-12-01

157

Activation of the alternative pathway of complement by monosodium urate monohydrate crystals and other inflammatory particles.  

PubMed Central

Activation of serum C3 by monosodium urate monohydrate (MSU) crystals and other particles was determined by immunofixation following electrophoretic separation of C3 and its activation products. Densitometry allowed quantitation of results. MSU, hydroxyapatite, brushite, and calcium pyrophosphate dihydrate crystals split C3 under conditions which demonstrate activation via the alternative pathway (AP). Quantitatively similar results were obtained in immunoglobulin deficient serum. Activation was crystal specific and was reduced by heating, grinding, sonication, and aging of crystals. Other inflammatory particles (e.g., blackthorn) activated C3 via the AP: noninflammatory particles (e.g., diamond) caused insignificant activation. It is suggested that particle-induced activation of the alternative pathway of complement may be important in the initiation of crystal-induced synovitis. Images PMID:6407405

Doherty, M; Whicher, J T; Dieppe, P A

1983-01-01

158

The Crystal Structure of Triuranyl Diphosphate Tetrahydrate  

NASA Astrophysics Data System (ADS)

The hydrated neutral uranyl phosphate, (UO2)3(PO4)2(H2O)4, was synthesized by hydrothermal methods. Intensity data were collected using MoK? radiation and a CCD-based area detector. The crystal structure was solved by direct methods and refined by full-matrix least-squares techniques to agreement indices wR2=0.116 for all data, and R1=0.040, calculated for the 2764 unique observed reflections (?Fo??4?F). The compound is orthorhombic, space group Pnma, Z=4, a=7.063(1) Å, b=17.022(3) Å, c=13.172(3) Å, V=1583.5(5) Å3. The structure consists of sheets of phosphate tetrahedra and uranyl pentagonal bipyramids, with composition [(UO2)(PO4)]- and the uranophane sheet anion topology. The sheets are connected by a uranyl pentagonal bipyramid in the interlayer that shares corners with a phosphate tetrahedron on each of two adjacent sheets, resulting in an open framework with isolated H2O groups in the larger cavities of the structure.

Locock, Andrew J.; Burns, Peter C.

2002-01-01

159

The structure of membrane crystals of the light-harvesting chlorophyll a/b protein complex  

PubMed Central

Membrane crystals of the light-harvesting chlorophyll a/b protein complex from pea chloroplasts were investigated using electron microscopy and image analysis. The membrane crystals formed upon precipitation of the detergent-solubilized complex with mono- and divalent cations in the presence of small amounts of Triton X-100. The crystalline fraction contained two polypeptides of 25,000 and 27,000 mol wt. Freeze-dried and freeze-etched specimens showed a periodic honeycomb structure on the surface of membrane crystals. Double replicas of freeze-fractured sheets showed a hexagonal lattice of particles on both fracture faces. Image analysis of negatively stained membrane crystals suggested that they had threefold rather than sixfold symmetry in projection. A projection map at 20-A resolution revealed two triangular structural units of opposite handedness per crystallographic unit cell. The structural units appeared to be inserted bidirectionally into the membrane, alternating in orientation perpendicular to the membrane plane. PMID:6341379

1983-01-01

160

The structure of particle cloud premixed flames  

NASA Technical Reports Server (NTRS)

The structure of premixed flames propagating in combustible systems containing uniformly distributed volatile fuel particles in an oxidizing gas mixture is analyzed. This analysis is motivated by experiments conducted at NASA Lewis Research Center on the structure of flames propagating in combustible mixtures of lycopodium particles and air. Several interesting modes of flame propagation were observed in these experiments depending on the number density and the initial size of the fuel particle. The experimental results show that steady flame propagation occurs even if the initial equivalence ratio of the combustible mixture based on the gaseous fuel available in the particles, phi sub u, is substantially larger than unity. A model is developed to explain these experimental observations. In the model, it is presumed that the fuel particles vaporize first to yield a gaseous fuel of known chemical composition which then reacts with oxygen in a one-step overall process. The activation energy of the chemical reaction is presumed to be large. The activation energy characterizing the kinetics of vaporization is also presumed to be large. The equations governing the structure of the flame were integrated numerically. It is shown that the interplay of vaporization kinetics and oxidation process can result in steady flame propagation in combustible mixtures where the value of phi sub u is substantially larger than unity. This prediction is in agreement with experimental observations.

Seshadri, K.; Berlad, A. L.

1992-01-01

161

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

E-print Network

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

Gennady V. Kovalev

2007-07-26

162

Track-Structure Simulations for Charged Particles  

PubMed Central

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

Dingfelder, Michael

2013-01-01

163

Research on TGS single crystal growth with modulated structure  

NASA Astrophysics Data System (ADS)

The experimental results of TGS crystal growth with modulated structure (periodic laminar of ferroelectric domains) is briefly discussed in this paper. The method used here is to add some DL-alanine additive in the solution of TGS and to apply the electric field during crystal growth, the direction of which is periodically varied. By using this method, TGS single crystals containing a nearly regular and flat periodic laminar structure of ferroelectric domains have been fabricated.

Wang, Wenshan; Qi, Ming

1986-12-01

164

Population structure and particle swarm performance  

Microsoft Academic Search

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

James Kennedy; Rui Mendes

2002-01-01

165

Crystallization and Characterization of Galdieria sulphuraria RUBISCO in Two Crystal Forms: Structural Phase Transition Observed in P21 Crystal Form  

PubMed Central

We have isolated ribulose-1,5-bisphosphate-carboxylase/oxygenase (RUBISCO) from the red algae Galdieria Sulphuraria. The protein crystallized in two different crystal forms, the I422 crystal form being obtained from high salt and the P21 crystal form being obtained from lower concentration of salt and PEG. We report here the crystallization, preliminary stages of structure determination and the detection of the structural phase transition in the P21 crystal form of G. sulphuraria RUBISCO. This red algae enzyme belongs to the hexadecameric class (L8S8) with an approximate molecular weight 0.6MDa. The phase transition in G. sulphuraria RUBISCO leads from two hexadecamers to a single hexadecamer per asymmetric unit. The preservation of diffraction power in a phase transition for such a large macromolecule is rare.

Baranowski, Michael; Stec, Boguslaw

2007-01-01

166

Undergraduates Improve upon Published Crystal Structure in Class Assignment  

ERIC Educational Resources Information Center

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…

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

2014-01-01

167

Use of Pom Pons to Illustrate Cubic Crystal Structures.  

ERIC Educational Resources Information Center

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)

Cady, Susan G.

1997-01-01

168

The crystal structural evolution of nano-Si anode caused by lithium insertion and extraction at room temperature  

Microsoft Academic Search

The crystal structure and morphology of nanosized Si particles and wires after Li-insertion\\/extraction electrochemically have been studied by ex-situ XRD, Raman spectroscopy and electronic microscopy. It is confirmed that the insertion of lithium ions at room temperature destroys the crystal structure of Si gradually and leads to the formation of metastable amorphous Li–Si alloy. Furthermore, local ordered structure of Si

Hong Li; Xuejie Huang; Liquan Chen; Guangwen Zhou; Ze Zhang; Dapeng Yu; Yu Jun Mo; Ning Pei

2000-01-01

169

Crystal structure of a Trypanosoma brucei metacaspase  

PubMed Central

Metacaspases are distantly related caspase-family cysteine peptidases implicated in programmed cell death in plants and lower eukaryotes. They differ significantly from caspases because they are calcium-activated, arginine-specific peptidases that do not require processing or dimerization for activity. To elucidate the basis of these differences and to determine the impact they might have on the control of cell death pathways in lower eukaryotes, the previously undescribed crystal structure of a metacaspase, an inactive mutant of metacaspase 2 (MCA2) from Trypanosoma brucei, has been determined to a resolution of 1.4 Å. The structure comprises a core caspase fold, but with an unusual eight-stranded ?-sheet that stabilizes the protein as a monomer. Essential aspartic acid residues, in the predicted S1 binding pocket, delineate the arginine-specific substrate specificity. In addition, MCA2 possesses an unusual N terminus, which encircles the protein and traverses the catalytic dyad, with Y31 acting as a gatekeeper residue. The calcium-binding site is defined by samarium coordinated by four aspartic acid residues, whereas calcium binding itself induces an allosteric conformational change that could stabilize the active site in a fashion analogous to subunit processing in caspases. Collectively, these data give insights into the mechanistic basis of substrate specificity and mode of activation of MCA2 and provide a detailed framework for understanding the role of metacaspases in cell death pathways of lower eukaryotes. PMID:22529389

McLuskey, Karen; Rudolf, Jana; Proto, William R.; Isaacs, Neil W.; Coombs, Graham H.; Moss, Catherine X.; Mottram, Jeremy C.

2012-01-01

170

Large scale structures in liquid crystal/clay colloids  

NASA Astrophysics Data System (ADS)

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

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

2005-04-01

171

Verification of the constant crystal growth model for attrition particles and its relevance to the modeling of crystallizers  

NASA Astrophysics Data System (ADS)

Potash alum-water system growth experiments have been carried out in a stagnant cell as reported by Garside and Larson for attrition particles with sizes L0 between 5 and 50 µm. Crystals with sizes Lo larger than 400 µm were investigated in a flow-through cell. In the stagnant growth cell large fluctuations of growth rate in the beginning have been observed. After about 5 to 10 min the growth rate of each crystal becomes constant. A constant linear growth rate of every fixed crystal has been measured in the flow-through cell. The growth rate dispersion according to the CCG model has been verified.

Wang, S.; Mersmann, A.; Kind, M.

1990-01-01

172

Coherent Effects of High-Energy Particles in a Graded Si1-xGex Crystal  

NASA Astrophysics Data System (ADS)

A graded Si1-xGex crystal has been manufactured for operation with high-energy protons to excite coherent interactions of the particles with the crystal such as channeling and volume reflection. The crystal had the shape of a parallelepiped though its (111) atomic planes were curved at a radius of 25.6 m because of the graded Ge content. The crystal was exposed to a 400GeV/c proton beam at the external lines of CERN Super Proton Synchrotron to probe its capability to steer high-energy particles. Measured deflection efficiency was 62.0% under planar channeling and 96.0% under volume reflection. Such values are critically compared to their counterparts for a standard bent Si crystal under peer conditions. A Monte Carlo simulation of the dynamics of channeled and volume reflected particles in a graded crystal including the effect of Ge impurities and of lattice dislocations has been carried out. We found that the effect of crystal imperfections spoiled the efficiency of channeling while it negligibly affected the performance of volume reflection. We finally propose the usage of the graded crystal as a primary scatterer to aid halo collimation for the new generation of hadronic machines. As a unique feature, a properly cut graded crystal circumvents the problem of the miscut angle, which is currently a severe limitation for implementation of crystal-assisted collimation.

Bagli, E.; Bandiera, L.; Guidi, V.; Mazzolari, A.; De Salvador, D.; Maggioni, G.; Berra, A.; Lietti, D.; Prest, M.; Vallazza, E.; Abrosimov, N. V.

2013-04-01

173

Fabrication of large binary colloidal crystals with a NaCl structure  

PubMed Central

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

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

2009-01-01

174

Cluster-Structured Adaptive Particle Swarm Optimization  

NASA Astrophysics Data System (ADS)

A new cluster-structured Particle Swarm Optimization (PSO) with interaction and diversity of parameters is proposed in this letter. After a swarm of PSO is divided into some sub-swarms (clusters), interactions between sub-swarms and diversity of PSO parameters are added so as to improve the search ability of PSO in the proposed cluster-structured PSO. The feasibility and the advantage of the proposed cluster-structured PSO are demonstrated through numerical simulations using two typical optimization test problems.

Yazawa, Kazuyuki; Motoki, Makoto; Ishigame, Atsushi; Yasuda, Keiichiro

175

Flash Nanoprecipitation: Particle Structure and Stability  

PubMed Central

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

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

176

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

PubMed Central

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

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

2013-01-01

177

Synthesis, crystal structure and superconductivity of LaNiPO  

Microsoft Academic Search

Single crystals of LaNiPO were synthesized by reacting La, P and NiO at 1173K in a tin flux under argon atmosphere. A phase analysis and crystal structure determination was carried out using X-ray powder and single crystal methods. The quaternary phosphide oxide crystallizes in the tetragonal ZrCuSiAs structure (P4\\/nmm, a=404.53(1)pm, c=810.54(3)pm, Z=2), which is characterized by layers of edge-sharing [La4\\/4O]?2

Marcus Tegel; Daniel Bichler; Dirk Johrendt

2008-01-01

178

Crystal structure of 2-pentyl­oxybenzamide  

PubMed Central

In the title mol­ecule, C12H17NO2, the amide NH2 group is oriented toward the pent­yloxy substituent and an intra­molecular N—H?O hydrogen bond is formed with the pent­yloxy O atom. The benzene ring forms dihedral angles of 2.93?(2) and 5.60?(2)° with the amide group and the pent­yloxy group mean planes, respectively. In the crystal, mol­ecules are linked by pairs of N—H?O hydrogen bonds, forming inversion dimers with their mol­ecular planes parallel, but at an offset of 0.45?(1)?Å to each other. These dimers are ordered into two types of symmetry-related columns extended along the a axis, with the mean plane of one set of dimers in a column approximately parallel to (121) and the other in a column approximately parallel to (1-21). The two planes form a dihedral angle of 85.31?(2)°, and are linked via C—H?O hydrogen bonds and C—H?? inter­actions, forming a three-dimensional framework structure. PMID:25484660

Bugenhagen, Bernhard; Al Jasem, Yosef; Thiemann, Thies

2014-01-01

179

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

NASA Astrophysics Data System (ADS)

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

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

2012-11-01

180

Unconventional structure-assisted optical manipulation of high-index nanowires in liquid crystals.  

PubMed

Stable optical trapping and manipulation of high-index particles in low-index host media is often impossible due to the dominance of scattering forces over gradient forces. Here we explore optical manipulation in liquid crystalline structured hosts and show that robust optical manipulation of high-index particles, such as GaN nanowires, is enabled by laser-induced distortions in long-range molecular alignment, via coupling of translational and rotational motions due to helicoidal molecular arrangement, or due to elastic repulsive interactions with confining substrates. Anisotropy of the viscoelastic liquid crystal medium and particle shape give rise to a number of robust unconventional trapping capabilities, which we use to characterize defect structures and study rheological properties of various thermotropic liquid crystals. PMID:22453452

Engström, David; Varney, Michael C M; Persson, Martin; Trivedi, Rahul P; Bertness, Kris A; Goksör, Mattias; Smalyukh, Ivan I

2012-03-26

181

Quasi-Cherenkov Radiation from Relativistic Particles Passing Through a Photonic Crystal  

E-print Network

The expressions for spectral-angular distribution of quasi-Cherenkov radiation emitted by a relativistic particle traversing a photonic crystal are derived. It is shown that for a relativistic particle, passing through a photonic crystal formed by periodically strained threads, the intensity of quasi-Cherenkov radiation emitted at small angles to the direction of particle motion, as contrasted to ordinary Cherenkov radiation, exhibits anisotropic properties as the the photon momentum is rotated about the direction of particle motion (as the crystal is rotated about the direction of particle motion at fixed-angle observation of the outcoming photon). The intensity of quasi-Cherenkov radiation in terahertz and optical ranges is shown to be high enough to allow the experimental study of quasi-Cherenkov radiation in these frequency ranges.

Baryshevsky, V G

2014-01-01

182

Photonic crystals for monitoring fatigue phenomena in steel structures  

NASA Astrophysics Data System (ADS)

This paper introduces the concept and development of a strain sensing system for structural application based on the properties of photonic crystals. Photonic crystals are artificially created periodic structures, usually produced in the thinfilm form, where optical properties are tailored by a periodicity in the refractive index. The idea of using the crystal as a sensor is based on the observation that a distortion in the crystal structure produces a change in the reflected bandwidth. When a photonic crystal is designed to operate in the visible part of the spectrum, a permanent distortion of the film results in a change in its apparent color. This property makes photonic crystals suitable for permanent monitoring of structural elements, as any critical changes in the strain field can be promptly and easily detected by visual inspection. A simple and low-cost example of photonic crystals consists of opals synthesized by vertical deposition. In this contribution we introduce a target application for the fatigue monitoring of wind turbines, and then provide the reader with some basic information concerning modeling of the crystal architecture and fabrication of these structures. Next we discuss their application to strain measurement, specifying how reflection and transmission properties of the opals have to be designed to satisfy the expected strain response of the sensor. Finally, we present the preliminary results of a laboratory validation carried out on thin films applied to a rubber support.

Zonta, Daniele; Chiappini, Andrea; Chiasera, Alessandro; Ferrari, Maurizio; Pozzi, Matteo; Battisti, Lorenzo; Benedetti, Matteo

2009-03-01

183

Structural and Thermoelectric Properties of Tungsten Diselenide Crystals  

NASA Astrophysics Data System (ADS)

Crystals of Tungsten diselenide (WSe2) have been grown by direct vapour transport (DVT) technique using micro processor controlled dual zone horizontal furnace. The chemical composition and structure of grown crystals were confirmed using energy dispersive analysis of X-ray (EDAX) and X-ray diffraction (XRD). In the present investigation thermoelectric power measurements (TEP) have been carried out on the grown crystals. Different electrical transport parameters of semiconductors have been determined and discussed in the paper.

Patel, K. K.; Patel, K. D.; Patel, Mayur; Patel, C. A.; Pathak, V. M.; Srivastava, R.

2011-12-01

184

Crystal and molecular structure of organophosphorus insecticides. 12. Dowco 214  

Microsoft Academic Search

The crystal and molecular structure of Dowco 214 (O,O-dimethyl O-(3,5,6-trichloro-2-pyridyl) phosphorothioate) has been determined by single crystal X-ray techniques. It crystallizes in space group P1 with ..cap alpha.. = 11.598 (2), b = 13.619 (3), c = 8.281 (1) A, ..cap alpha.. = 94.65 (1), ..beta.. = 94.87 (2), and ..gamma.. = 79.97 (2)° with four molecules per unit cell

Debra E. Beckman; Robert A. Jacobson

1979-01-01

185

Particle-swarm structure prediction on clusters  

NASA Astrophysics Data System (ADS)

We have developed an efficient method for cluster structure prediction based on the generalization of particle swarm optimization (PSO). A local version of PSO algorithm was implemented to utilize a fine exploration of potential energy surface for a given non-periodic system. We have specifically devised a technique of so-called bond characterization matrix (BCM) to allow the proper measure on the structural similarity. The BCM technique was then employed to eliminate similar structures and define the desirable local search spaces. We find that the introduction of point group symmetries into generation of cluster structures enables structural diversity and apparently avoids the generation of liquid-like (or disordered) clusters for large systems, thus considerably improving the structural search efficiency. We have incorporated Metropolis criterion into our method to further enhance the structural evolution towards low-energy regimes of potential energy surfaces. Our method has been extensively benchmarked on Lennard-Jones clusters with different sizes up to 150 atoms and applied into prediction of new structures of medium-sized Lin (n = 20, 40, 58) clusters. High search efficiency was achieved, demonstrating the reliability of the current methodology and its promise as a major method on cluster structure prediction.

Lv, Jian; Wang, Yanchao; Zhu, Li; Ma, Yanming

2012-08-01

186

Particle-swarm structure prediction on clusters.  

PubMed

We have developed an efficient method for cluster structure prediction based on the generalization of particle swarm optimization (PSO). A local version of PSO algorithm was implemented to utilize a fine exploration of potential energy surface for a given non-periodic system. We have specifically devised a technique of so-called bond characterization matrix (BCM) to allow the proper measure on the structural similarity. The BCM technique was then employed to eliminate similar structures and define the desirable local search spaces. We find that the introduction of point group symmetries into generation of cluster structures enables structural diversity and apparently avoids the generation of liquid-like (or disordered) clusters for large systems, thus considerably improving the structural search efficiency. We have incorporated Metropolis criterion into our method to further enhance the structural evolution towards low-energy regimes of potential energy surfaces. Our method has been extensively benchmarked on Lennard-Jones clusters with different sizes up to 150 atoms and applied into prediction of new structures of medium-sized Li(n) (n = 20, 40, 58) clusters. High search efficiency was achieved, demonstrating the reliability of the current methodology and its promise as a major method on cluster structure prediction. PMID:22938215

Lv, Jian; Wang, Yanchao; Zhu, Li; Ma, Yanming

2012-08-28

187

Photonic crystal structures with tunable structure color as colorimetric sensors.  

PubMed

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

Wang, Hui; Zhang, Ke-Qin

2013-01-01

188

Photonic Crystal Structures with Tunable Structure Color as Colorimetric Sensors  

PubMed Central

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

Wang, Hui; Zhang, Ke-Qin

2013-01-01

189

Novel photonic crystal cavities and related structures.  

SciTech Connect

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.

Luk, Ting Shan

2007-11-01

190

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

SciTech Connect

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.

Hung, T.-S.; Ho, Y.-C.; Wong, S.-J.; Chen, S.-Y. [Department of Physics, National Central University, Jhong-Li 320, Taiwan (China); Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan (China); Chang, Y.-L. [Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan (China); Department of Physics, National Chung Cheng University, Chia-Yi 621, Taiwan (China); Chu, H.-H. [Department of Physics, National Central University, Jhong-Li 320, Taiwan (China); Lin, J.-Y. [Department of Physics, National Chung Cheng University, Chia-Yi 621, Taiwan (China); Wang, J. [Department of Physics, National Central University, Jhong-Li 320, Taiwan (China); Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan (China); Department of Physics, National Taiwan University, Taipei 106, Taiwan (China)

2012-06-15

191

Hertzian Fracture in Single Crystals with the Diamond Structure  

Microsoft Academic Search

Extension of an earlier theory of Hertzian fracture in brittle isotropic materials is here made to include the case of brittle single crystals, with particular reference to crystals having the diamond structure. A detailed description is first given of the inhomogeneous stress field in a flat, elastic specimen loaded normally with a hard sphere. The geometry of cracks growing in

B. R. Lawn

1968-01-01

192

Crystal Structure, Physical Properties, and Electrochemistry of Copper Substituted LiFePO4 Single Crystals  

E-print Network

indicate that the dark brown color originates from interionic d-d transitions. A part of the lithium ions phosphate, with the olivine structure, has been synthesized hydrothermally as dark-brown single crystals

Ceder, Gerbrand

193

The crystal structure of SnP3 and a note on the crystal structure of GeP3  

Microsoft Academic Search

SnP3 crystallizes in the trigonal space group R3m with six formula units in a unit cell of dimensions a = 7.378Å and c = 10.512Å. The detailed atomic arrangement has been determined from three-dimensional single crystal X ray data. The structure is characterized as a layer structure related to the As-type structure (A7). The identical layers consist of puckered P6

Jan Gullman; Olle Olofsson

1972-01-01

194

Band structures of bilayer radial phononic crystal plate with crystal gliding  

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

195

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

Microsoft Academic Search

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

Tadafumi Adschiri; Katsuhito Kanazawa; Kunio Arai

1992-01-01

196

Online measurement of particle size distribution during crystallization using ultrasonic spectroscopy  

Microsoft Academic Search

Particle growth during crystallization of paracetamol was monitored on-line using a new modified method based on ultrasonic spectroscopy. The model was earlier developed and tested with inert particles systems and accounts for low angle scattering and probe geometry. A graphic user interface was developed and integrated with the model based deconvolution algorithm for real-time data acquisition, analysis and display of

Abhishek Shukla; Anand Prakash; Sohrab Rohani

2010-01-01

197

FAST TRACK COMMUNICATION: Silicon crystal for channelling of negatively charged particles  

NASA Astrophysics Data System (ADS)

Efficient channelling of negatively charged-particle beams in a bent crystal demands operation in axial mode, preferably along the lang1 1 1rang axis due to the strong confining potential generated along this direction. We propose a bent crystal suitable for steering negatively charged particle beams via axial channelling (AC) for operation at some gigaelectronvolt energy. The crystal is a quasi-mosaic crystal, relying on mechanical anisotropy of crystalline silicon. By use of high-resolution x-ray diffraction, we investigated the lattice bending of a crystal under the high-deformation regime. Anticlastic bending was found to weaken under a high deformation regime while anisotropic bending holds also under strong deformation. This circumstance envisages a versatile way to manage beams by AC.

Guidi, V.; Mazzolari, A.; De Salvador, D.; Carnera, A.

2009-09-01

198

Crystal Structure of Human Plasma Platelet-Activating Factor Acetylhydrolase  

SciTech Connect

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.

Samanta, U.; Bahnson, B

2008-01-01

199

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

SciTech Connect

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.

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

200

English Verb-particle Constructions: Two Types, Two Structures  

E-print Network

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

Zoerner, Ed

1996-01-01

201

Prediction and Observation of Crystal Structures of Oppositely Charged Colloids  

NASA Astrophysics Data System (ADS)

We studied crystal structures in mixtures of large and small oppositely charged spherical colloids with size ratio 0.31 using Monte Carlo simulations and confocal microscopy. We developed an interactive method based on simulated annealing to predict new binary crystal structures with stoichiometries from 1 to 8. Employing these structures in Madelung energy calculations using a screened Coulomb potential, we constructed a ground-state phase diagram, which shows a remarkably rich variety of crystals. Our phase diagram displays colloidal analogs of simple-salt structures and of the doped fullerene C60 structures, but also novel structures that do not have an atomic or molecular analog. We found three of the predicted structures experimentally, which provides confidence that our method yields reliable results.

Hynninen, A.-P.; Christova, C. G.; van Roij, R.; van Blaaderen, A.; Dijkstra, M.

2006-04-01

202

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

NASA Astrophysics Data System (ADS)

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.

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

2014-07-01

203

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

NASA Astrophysics Data System (ADS)

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

Abedi, Kambiz; Mirjalili, Seyed Mohammad

2015-03-01

204

Wear particles of single-crystal silicon carbide in vacuum  

NASA Technical Reports Server (NTRS)

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.

Miyoshi, K.; Buckley, D. H.

1980-01-01

205

A machine learning approach to crystal structure prediction  

E-print Network

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

Fischer, Christopher Carl

2007-01-01

206

Crystal structure engineering for improved performance of emerging nanoscale devices  

NASA Astrophysics Data System (ADS)

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

Chimalgi, Vinay Uday

207

Structural, optical and electrical characteristics of a new NLO crystal  

NASA Astrophysics Data System (ADS)

A new nonlinear optical (NLO) organic crystal 1-[4-({(E)-[4-(methylsulfanyl)phenyl]methylidene}amino)phenyl]ethanone (MMP) has been grown by slow evaporation technique at ambient temperature. The crystal structure of MMP was determined by single crystal X-ray diffraction. MMP crystallizes in non-centrosymmetric monoclinic system with space group P21. The FT-IR spectrum recorded for new crystal confirmed the presence of various functional groups in the material. MMP was found to be thermally stable up to 300 °C. The grown crystal was optically transparent in the wavelength range of 400-1100 nm. The second harmonic generation (SHG) efficiency of the crystal was measured by the classical powder technique using Nd:YAG laser and was found to be 4.13 times more efficient than reference material, urea. Third order nonlinear parameters were measured by employing the Z-scan technique. The laser damage threshold for MMP crystal was determined to be 4.26 GW/cm2. The Brewster angle technique was employed to measure the refractive index of the crystal and the values for green and red wavelengths were found to be 1.35 and 1.33, respectively. The dielectric and electrical measurements were carried out to study the different polarization mechanisms and conductivity of the crystal.

D'silva, E. D.; Krishna Podagatlapalli, G.; Venugopal Rao, S.; Dharmaprakash, S. M.

2012-09-01

208

Determination of channeling perspectives for complex crystal structures  

SciTech Connect

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

Allen, W.R.

1993-03-01

209

Teaching Mineralogy with Crystal Structure Databases and Visualization Software  

NSDL National Science Digital Library

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

Kent Ratajeski

2002-01-01

210

Fractal structure of the equilibrium crystal shape S. E. Burkov  

E-print Network

317 Fractal structure of the equilibrium crystal shape S. E. Burkov Landau Institute décroît avec la distance plus rapidement que r-4. Nous montrons que la surface du cristal a une structure continue aux arêtes. Le bord d'une face a également une structure fractale. Elle consiste en un nombre

Paris-Sud XI, Université de

211

The crystal structure of faustite and its copper analogue turquoise  

Microsoft Academic Search

The crystal structure of faustite, ZnAI6(P04MOHhAH20, was determined using single-crystal data (Mo-KIX X-radiation, CCD area detector, 1624 unique reflections, RI = 4.91 %, wR2 = 9.23%), and compared with results of a reinvestigation of the structure of its copper analogue turquoise, CuAI6(P04MOH)gAH20 (2737 unique reflections, RI = 2.81%, wR2 = 6.90%). Both are isostructural and crystallize in space group PI,

U. Kolitsch; G. Giester

2000-01-01

212

Quantitative crystal structure descriptors from multiplicative congruential generators.  

PubMed

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

Hornfeck, Wolfgang

2012-03-01

213

Submicrometer Single Crystal Diffractometry for Highly Accurate Structure Determination  

NASA Astrophysics Data System (ADS)

Submicrometer single crystal diffractometry for highly accurate structure determination was developed using the extremely stable and highly brilliant synchrotron radiation from SPring-8. This was achieved using a microbeam focusing system and the submicrometer precision low-eccentric goniometer system. We demonstrated the structure analyses with 2×2×2 ?m3 cytidine, 600×600×300 nm3 BaTiO3, and 1×1×1 ?m3 silicon. The observed structure factors of the silicon crystal were in agreement with the structure factors determined by the Pendellösung method and do not require absorption and extinction corrections.

Yasuda, Nobuhiro; Fukuyama, Yoshimitsu; Toriumi, Koshiro; Kimura, Shigeru; Takata, Masaki

2010-06-01

214

Submicrometer Single Crystal Diffractometry for Highly Accurate Structure Determination  

SciTech Connect

Submicrometer single crystal diffractometry for highly accurate structure determination was developed using the extremely stable and highly brilliant synchrotron radiation from SPring-8. This was achieved using a microbeam focusing system and the submicrometer precision low-eccentric goniometer system. We demonstrated the structure analyses with 2x2x2 {mu}m{sup 3} cytidine, 600x600x300 nm{sup 3} BaTiO{sub 3}, and 1x1x1 {mu}m{sup 3} silicon. The observed structure factors of the silicon crystal were in agreement with the structure factors determined by the Pendelloesung method and do not require absorption and extinction corrections.

Yasuda, Nobuhiro; Fukuyama, Yoshimitsu; Kimura, Shigeru [Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5198 (Japan); Japan Science and Technology Agency, CREST, 5, Sanbancho, Chiyoda, Tokyo 102-0075 (Japan); Toriumi, Koshiro [Japan Science and Technology Agency, CREST, 5, Sanbancho, Chiyoda, Tokyo 102-0075 (Japan); University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297 (Japan); Takata, Masaki [Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5198 (Japan); Japan Science and Technology Agency, CREST, 5, Sanbancho, Chiyoda, Tokyo 102-0075 (Japan); RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148 (Japan)

2010-06-23

215

Crystal structure prediction for cyclotrimethylene trinitramine (RDX) from first principles.  

PubMed

Crystal structure prediction and molecular dynamics methods were applied to the cyclotrimethylene trinitramine (RDX) crystal to explore the stability rankings of various polymorphs using a recently developed nonempirical potential energy function that describes the RDX dimer interactions. The energies of 500 high-density structures resulting from molecular packing were minimized and the 14 lowest-energy structures were subjected to isothermal-isostress molecular dynamics (NsT-MD) simulations. For both crystal structure prediction methods and molecular dynamics simulations, the lowest-energy polymorph corresponded to the experimental structure; furthermore, the lattice energy of this polymorph was lower than that of the other polymorphs by at least 1.1 kcal mol(-1). Crystal parameters and densities of the low-energy crystal produced by the NsT-MD simulations matched those of the experimental crystal to within 1% of density and cell edge lengths and 0.01 degrees of the cell angle. The arrangement of the molecules within the time-averaged unit cell were in equally outstanding agreement with experiment, with the largest deviation of the location of the molecular mass centers being less than 0.07 A and the largest deviation in molecular orientation being less than 2.8 degrees . NsT-MD simulations were also used to calculate crystallographic parameters as functions of temperature and pressure and the results were in a reasonable agreement with experiment. PMID:19551222

Podeszwa, Rafal; Rice, Betsy M; Szalewicz, Krzysztof

2009-07-14

216

STRUCTURE NOTE Crystal Structure of Gene Locus At3g16990 from  

E-print Network

STRUCTURE NOTE Crystal Structure of Gene Locus At3g16990 from Arabidopsis thaliana Paul G. Blommel thaliana was given a suitable score for study, with the only major demerits being a large cysteine residue, we report the crystal structure of the protein from Arabidopsis thaliana gene locus At3g16990

Rayment, Ivan

217

Predicting inclusion behaviour and framework structures in organic crystals.  

PubMed

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

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

2009-12-01

218

Structurally Coloured Secondary Particles Composed of Black and White Colloidal Particles  

PubMed Central

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

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

2013-01-01

219

Structural characteristics and second order nonlinear optical properties of borate crystals  

E-print Network

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

Osnabrück, Universität

220

Glass crystallization synthesis of ultrafine hexagonal M-type ferrites: Particle morphology and magnetic characteristics  

Microsoft Academic Search

This review concerns the synthesis and functional properties of ultrafine particles of M-type hexagonal ferrites prepared\\u000a by the most advanced process of oxide glass crystallization. Hexaferrite phase formation during the heat treatment of multicomponent\\u000a oxide glasses of various chemical compositions containing boron and\\/or silicon oxides as glass formers is considered. This\\u000a route is useful to prepare assemblies of single-crystal strontium

P. E. Kazin; L. A. Trusov; D. D. Zaitsev; Yu. D. Tret’yakov

2009-01-01

221

Effects of crystal structures on gas sensing properties of nanocrystalline ITO thick films  

Microsoft Academic Search

Two kinds of nanocrystalline indium tin oxide (ITO) powders with different crystal structures—rhombohedral and cubic—were prepared using a coprecipitation process through the control of pH of a mixing solution and aging time after coprecipitation. The two powders have the same particle size of 15nm in diameter but different morphologies (spherical for rhombohedral and rectangular for cubic). The gaseous ethanol sensing

Bong-Chull Kim; Jae-Yeol Kim; Duk-Dong Lee; Jeong-Ok Lim; Jeung-Soo Huh

2003-01-01

222

Liquid Crystal Phase Behaviour of Attractive Disc-Like Particles  

PubMed Central

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

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

2013-01-01

223

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

PubMed

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

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

2014-05-01

224

Observation of particle pairing in a two-dimensional plasma crystal.  

PubMed

The observation is presented of naturally occurring pairing of particles and their cooperative drift in a two-dimensional plasma crystal. A single layer of plastic microspheres was suspended in the plasma sheath of a capacitively coupled radio-frequency discharge in argon at a low pressure of 1 Pa. The particle dynamics were studied by combining the top-view and side-view imaging of the suspension. Cross-analysis of the particle trajectories allowed us to identify naturally occurring metastable pairs of particles. The lifetime of pairs was long enough for their reliable identification. PMID:25353582

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

2014-02-01

225

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

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

226

Crystal structure of a nematode-infecting virus.  

PubMed

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

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

2014-09-01

227

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

228

Voids and yolk-shells from crystals that coat particles.  

PubMed

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

Sindoro, Melinda; Granick, Steve

2014-10-01

229

The crystal structure of some rhenium and technetium dichalcogenides  

Microsoft Academic Search

The crystal structures of ReSe., ReS., ReSSe and TeS2 are determined using single crystal X-ray diffraction. The compounds are triclinic with space groupPl. ReSe., ReS, and ReSSe have a distorted CdCl2-type structure: TeS2 has a distorted Cd(OH)-type structure. In the case of ReS, there are two sandwiches in the unit cell, related by symmetry centers. The other compounds have one

H.-J. Lamfers; A. Meetsma; G. A. Wiegers; J. L. de Boer

1996-01-01

230

Crystal structure solution from experimentally determined atomic pair distribution functions  

Microsoft Academic Search

The paper describes an extension of the Liga algorithm for structure solution from atomic pair distribution function (PDF), to handle periodic crystal structures with multiple elements in the unit cell. The procedure is performed in 2 separate steps - at first the Liga algorithm is used to find unit cell sites consistent with pair distances extracted from the experimental PDF.

Pavol Juhas; Luke Granlund; Saurabh R. Gujarathi; Phillip M. Duxbury; Simon J. L. Billinge

2010-01-01

231

Nitric Oxide Myoglobin: Crystal Structure and Analysis of Ligand Geometry  

E-print Network

Nitric Oxide Myoglobin: Crystal Structure and Analysis of Ligand Geometry Eric Allen Brucker,1 John School of Medicine, Cleveland, Ohio ABSTRACT The structure of the ferrous nitric oxide form of native oxide ligand is bent with respect to the heme plane: the Fe-N-O angle is 112°. This angle is smaller

Phillips, George N. Jr.

232

Formation, structure, and crystallization of Al-rich metallic glasses  

Microsoft Academic Search

The formation, structure, and the crystallization of Al85YxNi15?x are studied using x-ray diffraction and differential scanning calorimetry. The results show two distinct glasses depending on composition. Y-rich glasses (x?8) are homogeneous with a well-defined glass transition. The x-ray diffraction patterns have a single main peak. These glasses crystallize through a nucleation and growth process. Y-poor glasses (x<8) do not show

R. Sabet-Sharghi; Z. Altounian; W. B. Muir

1994-01-01

233

The effect of crystal imperfections on particle fracture behaviour.  

PubMed

Micronisation of active pharmaceutical ingredients is a process which is sometimes difficult to control. The main purpose of this study was to assess the effect of the pre-existing flaws in the material to be milled. The rate of breakage of four samples of a model compound (sodium chloride), originating from different sources, was determined in a jet mill. It appeared that each type of sodium chloride has a distinct particle rate of breakage and breakage pattern. The numbers of flaws in the different types of sodium chloride have been determined by immersing the sodium chloride particles in a liquid with the same refractive index. This makes the cracks better visible. Microphotographs were made and flaws were counted manually. The study shows that the flaw density has an impact on the fracture behaviour of particles. The degree of fracture tends to increase with increasing flaw density. The paper shows however that the mechanical properties of the material as well as the starting particle size dominate the significance of the impact of flaws on fracture behaviour. PMID:16597489

de Vegt, Onno; Vromans, Herman; Pries, Wim; van der Voort Maarschalk, Kees

2006-07-01

234

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

PubMed

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

Hudait, Arpa; Molinero, Valeria

2014-06-01

235

Polymorphism of Scyllo-Inositol: Joining Crystal Structure Prediction with Experiment to Elucidate the Structures of Two  

E-print Network

Polymorphism of Scyllo-Inositol: Joining Crystal Structure Prediction with Experiment to Elucidate, 2006; ReVised Manuscript ReceiVed July 19, 2006 ABSTRACT: We report on the crystal structures of two in parallel with the crystallization experiments. When a single crystal was finally grown, its structure

de Gispert, Adrià

236

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

SciTech Connect

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.

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

2010-10-15

237

Theory of coherent x-ray radiation by relativistic particles in a single crystal  

NASA Astrophysics Data System (ADS)

A quantum theory is developed for a type of coherent x-ray radiation observed recently. It is shown that the lowest-order coherent-radiation processes due to the interaction between the particle and the crystal electrons are classified into two kinds: electronic bremsstrahlung and x-ray radiation. An analytical expression for the radiation probability is derived using quantum electrodynamics. For ultrarelativistic particles, our quantum expression yields the classical formula by Ter-Mikaelian, in agreement with the experimental results.

Nitta, H.

1992-04-01

238

Creation and Evolution of Excited States in ? Particle Tracks in Anthracene Crystals  

Microsoft Academic Search

The kinematics of excited states in anthracene crystals bombarded by 5 MeV x particles is studied. The elementary processes which account for the transitions from the primary excited states to the lowest singlet S1, and triplet T1, excited states is described. The equations governing the evolution of the S1 and T1 excitons in the x particle track are then solved,

G. Klein

1978-01-01

239

The Crystal Structures of the Tryparedoxin-Tryparedoxin Peroxidase Couple Unveil the Structural Determinants of  

E-print Network

The Crystal Structures of the Tryparedoxin-Tryparedoxin Peroxidase Couple Unveil the Structural-swapped dimer. In LmTXNPx, crystallized in reducing condition, both the locally unfolded (LU) and fully folded cysteine which facilitates Cys52 to form an inter-chain disulfide bond with the resolving cysteine (Cys173

Paris-Sud XI, Université de

240

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

DOEpatents

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.

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

1994-01-01

241

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

DOEpatents

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

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

1994-08-23

242

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

PubMed Central

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

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

2014-01-01

243

Structural colored gels for tunable soft photonic crystals.  

PubMed

A periodically ordered interconnecting porous structure can be embodied in chemical gels by using closest-packed colloidal crystals as templates. The interconnecting porosity not only provides a quick response but also endows the porous gels with structural color arising from coherent Bragg optical diffraction. The structural colors revealed by porous gels can be regulated by several techniques, and thus, it is feasible to obtain desirable, smart, soft materials. A well-known thermosensitive monomer, N-isopropylacrylamide (NIPA), and other minor monomers were used to fabricate various structural colored gels. The selection of minor monomers depended on the targeted properties. This review focuses on the synthesis of templates, structural colored porous gels, and the applications of structural colored gel as smart soft materials for tunable photonic crystals. PMID:19306332

Harun-Ur-Rashid, Mohammad; Seki, Takahiro; Takeoka, Yukikazu

2009-01-01

244

Quench crystallization of linear polyethylene: Crystallization kinetics, morphology and structure investigation  

NASA Astrophysics Data System (ADS)

The behavior of semi-crystalline polymers at large supercoolings has always been of great interest in the industry and academia alike. It is well known that the resulting crystal morphology and microstructure are strongly dependent on supercooling or quench depth, and ultimately control a variety of physical, mechanical, chemical and optical properties. One of the main goals of the current research was to extend the crystallization range of linear polyethylene beyond currently accessible supercoolings. The current study reports the development of a simple yet effective "depolarized reflection light microscopy" technique that allows quench-crystallization at unprecedented onset crystallization temperatures well below 90°C, but more importantly allows concurrent spherulitic and bulk growth rates to be measured for kinetic analyses. Application of this technique to linear polyethylene, which is perhaps the fastest crystallizing polymer, generated new insights into the morphology, microstructure, crystallization kinetics, and reorganization-thickening processes prior to the melting of the crystals formed under deep quench conditions. The predominant morphology was found to vary substantially with the crystallization temperature from fully developed and impinged spherulites in isothermal conditions to a very high density of small isolated, un-impinged spherulites in deep quench. At the lowest temperatures the micrographs revealed sizeable areas of amorphous material, consistent with the low degree of crystallinity (˜35%) measured by X-ray diffraction. Predominant surface nucleation gave rise to hemispheres or "half-spherulites" on both surfaces in contact with dissimilar substrates. The quenched samples exhibited crystallite orientation effects; in particular the growth of the b axis direction of the unit cell was approximately perpendicular to the film surface. A quantitative analysis of the Herman's orientation factor revealed that the degree of orientation was fairly moderate and therefore had no major influence on the growth rate of the crystals. Crystallization kinetics measurements of bulk and spherulitic growth rates demonstrated for the first time, the (elusive) characteristic maximum and the crossover to the diffusion-controlled side of the growth rate-temperature dependence. The growth rates at temperatures below the maximum conform to a single linear fit characteristic of regime III which suggests conformity with the mechanism of the regime theory of secondary nucleation. However the stability and nature of the fold surface of the quenched crystals that are capable of further crystallization was substantially altered. Combined DSC, transmitted light intensity method, and temperature-resolved X-ray scattering methods were used to investigate the structural reorganization processes that take place prior to melting. Finally the mechanism of the recrystallization-lamellar thickening of quenched crystals was proposed.

Patki, Rahul P.

245

Crystal structure tuning in GaAs nanowires using HCl  

NASA Astrophysics Data System (ADS)

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

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

2014-06-01

246

Dynamic structure of superionic protons in hydrogen fluoride crystal  

NASA Astrophysics Data System (ADS)

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

Ohde, Yoshiyuki; Tsumuraya, Kazuo

2013-03-01

247

Modeling liquid crystal bilayer structures with minimal surfaces J. D. Enlowa)  

E-print Network

Modeling liquid crystal bilayer structures with minimal surfaces J. D. Enlowa) and R. L. Enlow crystal phase used in familiar liquid crystal displays, but the term also refers to structures with far that surfactant liquid crystals can have structures whose shapes are based on minimal surfaces. II. MINIMAL

Gruner, Sol M.

248

J. Mol. Biol. (1978) 123, 607-630 Crystal Structure of Yeast Phenylalanine Transfer RNA  

E-print Network

J. Mol. Biol. (1978) 123, 607-630 Crystal Structure of Yeast Phenylalanine Transfer RNA I phenylalanine transfer RNA in an orthorhombic crystal form. The crystal structure of the transfer KNA has been to the crystal structure of yeast phenylalanine tRNA are described in this paper. A complete list of atomic co

Church, George M.

249

Crystal Structure of Streptococcus mutans Pyrophosphatase  

Microsoft Academic Search

Background:Streptococcus mutans pyrophosphatase (Sm-PPase) is a member of a relatively uncommon but widely dispersed sequence family (family II) of inorganic pyrophosphatases. A structure will answer two main questions: is it structurally similar to the family I PPases, and is the mechanism similar?Results: The first family II PPase structure, that of homodimeric Sm-PPase complexed with metal and sulfate ions, has been

Michael C Merckel; Igor P Fabrichniy; Anu Salminen; Nisse Kalkkinen; Alexander A Baykov; Reijo Lahti; Adrian Goldman

2001-01-01

250

The crystal structure of GXGD membrane protease FlaK  

SciTech Connect

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.

Hu, Jian; Xue, Yi; Lee, Sangwon; Ha, Ya (Yale-MED)

2011-09-20

251

The Crystal Structure of GXGD Membrane Protease FlaK  

SciTech Connect

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.

J Hu; Y Xue; S Lee; Y Ha

2011-12-31

252

Why biomolecules prefer only a few crystal structures  

NASA Astrophysics Data System (ADS)

We have shown that, in determining the biomolecule-crystal symmetry, the occupation of low-site-symmetry Wyckoff positions is crucial, which contrasts with the overwhelming majority of nonmolecular, inorganic crystals where atoms mainly reside in high-symmetry Wyckoff positions. We consider the general relation between the symmetry of an isolated molecule and the possible symmetries of biomolecular crystals it can generate. We reveal that the improper symmetry operations (inversion and mirror symmetries) are prohibited in the chirally pure biomolecular crystals. Next, we show that the low (C1) symmetry of large biological molecules substantially decreases the space in a crystal where the molecules can reside. The space “forbidden” for molecule centers is found to be in the R vicinity of the higher-symmetry Wyckoff positions on symmetry lines, where R is the molecule characteristic size. The remaining free space and hence the probability for the structure to exist are shown to be drastically increased when replacing any rotation axis by a screw one. Based on the proposed model, we have explained the peculiar distribution of biomolecular crystals over the space groups, which can be obtained from biomolecule-crystal databases.

Kitaev, Yu. E.; Panfilov, A. G.; Smirnov, V. P.; Tronc, P.

2003-01-01

253

Crystal structure of an amphiphilic foldamer reveals a 48-mer assembly comprising a hollow truncated octahedron  

PubMed Central

Foldamers provide an attractive medium to test the mechanisms by which biological macromolecules fold into complex three-dimensional structures, and ultimately to design novel protein-like architectures with properties unprecedented in nature. Here, we describe a large cage-like structure formed from an amphiphilic arylamide foldamer crystallized from aqueous solution. Forty eight copies of the foldamer assemble into a 5 nm cage-like structure, an omnitruncated octahedron filled with well-ordered ice-like water molecules. The assembly is stabilised by a mix of arylamide stacking interaction, hydrogen bonding and hydrophobic forces. The omnitruncated octahedra tessellate to form a cubic crystal. These findings may provide an important step towards the design of nanostructured particles resembling spherical viruses. PMID:24705140

Pavone, Vincenzo; Zhang, Shao-Qing; Merlino, Antonello; Lombardi, Angela; Wu, Yibing; DeGrado, William F.

2014-01-01

254

Crystal structure of an amphiphilic foldamer reveals a 48-mer assembly comprising a hollow truncated octahedron.  

PubMed

Foldamers provide an attractive medium to test the mechanisms by which biological macromolecules fold into complex three-dimensional structures, and ultimately to design novel protein-like architectures with properties unprecedented in nature. Here, we describe a large cage-like structure formed from an amphiphilic arylamide foldamer crystallized from aqueous solution. Forty-eight copies of the foldamer assemble into a 5-nm cage-like structure, an omnitruncated octahedron filled with well-ordered ice-like water molecules. The assembly is stabilized by a mix of arylamide stacking interaction, hydrogen bonding and hydrophobic forces. The omnitruncated octahedra tessellate to form a cubic crystal. These findings may provide an important step towards the design of nanostructured particles resembling spherical viruses. PMID:24705140

Pavone, Vincenzo; Zhang, Shao-Qing; Merlino, Antonello; Lombardi, Angela; Wu, Yibing; DeGrado, William F

2014-01-01

255

Microscopic characterization of defect structure in RDX crystals.  

PubMed

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

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

2013-12-01

256

INVESTIGATION OF THE CRYSTAL STRUCTURES OF NUCLEOSIDES CONTAINING SULFUR  

Microsoft Academic Search

The crystal structures of three nucleosides containing sulfur have been determined by X-ray analysis: 4'-thiouridine, 5-fluoro-4'-thio-(alpha)-2'-deoxyuridine and 2,2'-anhydro-3'-O-acetyl-2'-thio-1-(beta)-D-arabinofuranosylcytosine hydrochloride.\\u000aThe study of the crystal structures of 4'-thiouridine and 5-fluoro-4'-thio-(alpha)-2'-deoxyuridine showed that the substitution of the ring oxygen by sulfur alters substantially the stereochemical features of furanoside nucleosides. The g('-) orientation of O(5') is favored more and the g('+) less. The

Jacqueline Vitali

1986-01-01

257

BY AN UNBEATEN WAY Interactions of particles and -radiation with crystals and application of  

E-print Network

, excited by the initial radiation with continuous spectrum of an X-ray tube (or of a radioactive source73 BY AN UNBEATEN WAY Interactions of particles and -radiation with crystals and application of the diffraction methods in very different fields of physics (P.I.Lukirski could not see the ready device

Titov, Anatoly

258

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

NASA Astrophysics Data System (ADS)

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

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

2015-01-01

259

Hybrid crystals comprising metal-organic frameworks and functional particles: synthesis and applications.  

PubMed

Hybrid crystals containing encapsulated functional species exhibit promising novel physical and chemical properties. The realization of many properties critically depends on the selection of suitable functional species for incorporation, the rational control of the crystallinity of the host materials, and the manipulation of the distribution of the encapsulated species; only a few hybrid crystals achieve this. Here, a novel synthetic method enables the encapsulation of functional species within crystalline metal-organic frameworks (MOFs). Various kinds of single-crystalline MOFs with incorporated particles are presented. The encapsulated particles can be distributed in a controllable manner, and the hybrid crystals are applied to the heterogeneous catalysis of the reduction of nitroarenes. These findings suggest a general approach for the construction of MOF materials with potential applications; by combining species and MOFs with suitable functionalities, new properties--not possible by other means--may arise. PMID:25048076

Li, Shaozhou; Huo, Fengwei

2014-11-12

260

Theoretical and Experimental Study of Photonic Crystal Based Structures for Optical Communication Applications  

E-print Network

Theoretical and Experimental Study of Photonic Crystal Based Structures for Optical Communication 01854 ABSTRACT Photonic crystal based structures have been considered for optical communication applications. A class of novel symmetric structures consisting of cavities and waveguides have been proposed

Chen, Ray

261

Crystal structure of the human spastin AAA domain  

PubMed Central

Hereditary spastic paraplegia (HSP) is a motor neuron disease caused by a progressive degeneration of the motor axons of the corticospinal tract. Point mutations or exon deletions in the microtubule-severing ATPase, spastin, are responsible for approximately 40% of cases of autosomal dominant HSP. Here, we report the 3.3 Å X-ray crystal structure of a hydrolysis- deficient mutant (E442Q) of the human spastin protein AAA domain. This structure is analyzed in the context of the existing Drosophila melanogaster spastin AAA domain structure and crystal structures of other closely related proteins in order to build a more unifying framework for understanding the structural features of this group of microtubule-severing ATPases. PMID:22446388

Taylor, Jennifer L.; White, Susan Roehl; Lauring, Brett; Kull, F. Jon

2012-01-01

262

Crystal structure of the human spastin AAA domain.  

PubMed

Hereditary spastic paraplegia (HSP) is a motor neuron disease caused by a progressive degeneration of the motor axons of the corticospinal tract. Point mutations or exon deletions in the microtubule-severing ATPase, spastin, are responsible for approximately 40% of cases of autosomal dominant HSP. Here, we report the 3.3 Å X-ray crystal structure of a hydrolysis-deficient mutant (E442Q) of the human spastin protein AAA domain. This structure is analyzed in the context of the existing Drosophila melanogaster spastin AAA domain structure and crystal structures of other closely related proteins in order to build a more unifying framework for understanding the structural features of this group of microtubule-severing ATPases. PMID:22446388

Taylor, Jennifer L; White, Susan Roehl; Lauring, Brett; Kull, F Jon

2012-08-01

263

The crystal structure of URu3B2  

NASA Astrophysics Data System (ADS)

The crystal structure of URu 3B 2 has been determined by single crystal X-ray analysis. URu 3B 2 crystallizes in the trigonal space group P3¯ (C 131) with hexagonal lattice a = 1.09531(14), c = 0.59353 (8) nm, Z = 8. Intensity measurements were obtained from a fourcircle diffractometer. The structure was solved by Patterson methods and refined by full matrix least squares calculation. The final R-value, R = ? | ?F|/? F0, is 0.052 for an asymètric set of 962 independent reflections ( l- F0l > 2 ? ( F0)). The crystal structure is a twofold superstructure (distortion-derivative) of the CeCo3B2-type cell ( a = 2 a', c = 2 c' and thus closely related to the CaCu5 type structure. The coordination numbers of U are 2 U + 12 Ru + (6 B) and those of Ru atoms 4 U + 6 Ru + 4 B. The isolated boron atoms have tetrakaidekahedral metal coordination 6 Ru + 3 U; no boron-boron contacts occur. The structural chemistry of ( Th, U, RE) Ru3B2 phases is discussed.

Rogl, Peter

1980-09-01

264

CRYSTAL STRUCTURE ANALYSIS OF A PUTATIVE OXIDOREDUCTASE FROM KLEBSIELLA PNEUMONIAE  

SciTech Connect

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.

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

2009-01-01

265

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

PubMed

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

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

2014-08-28

266

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

NASA Astrophysics Data System (ADS)

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

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

2013-03-01

267

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

NASA Astrophysics Data System (ADS)

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

Merlini, M.

2013-12-01

268

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

SciTech Connect

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.

Tsukada, Y.; Honma, T. [Department of Materials Science and Technology, Nagaoka University of Technology, 1603-1 Kamitomioka-cho, Nagaoka 940-2188 (Japan); Komatsu, T., E-mail: komatsu@mst.nagaokaut.ac.j [Department of Materials Science and Technology, Nagaoka University of Technology, 1603-1 Kamitomioka-cho, Nagaoka 940-2188 (Japan)

2009-08-15

269

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)

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.

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

2001-11-01

270

Phase behavior and structure of a new colloidal model system of bowl-shaped particles.  

PubMed

We study the phase behavior of bowl-shaped (nano)particles using confocal microscopy and computer simulations. Experimentally, we find the formation of a wormlike fluid phase in which the bowl-shaped particles have a strong tendency to stack on top of each other. However, using free energy calculations in computer simulations, we show that the wormlike phase is out-of-equilibrium and that the columnar phase is thermodynamically stable for sufficiently deep bowls and high densities. In addition, we employ a novel technique based on simulated annealing to predict the crystal structures for shallow bowls. We find four exotic new crystal structures and we determine their region of stability using free energy calculations. We discuss the implications of our results for the development of materials consisting of molecular mesogens or nanoparticles. PMID:20387799

Marechal, Matthieu; Kortschot, Rob J; Demirörs, Ahmet Faik; Imhof, Arnout; Dijkstra, Marjolein

2010-05-12

271

Analytical calculation of the Stokes drag of the spherical particle in a nematic liquid crystal  

E-print Network

As an approach to the motion of particles in an anisotropic liquid, we analytically study the Stokes drag of spherical particles in a nematic liquid crystal. The Stokes drag of spherical particles for a general anisotropic case is derived in terms of multipoles. In the case of weak anchoring, we use the well-known distribution of the elastic director field around the spherical particle. In the case of strong anchoring, the multipole expansion may be also used by modifying the size of a particle to the size of the deformation coating. For the case of zero anchoring (uniform director field) we found that the viscosities along the director $\\eta_{\\parallel}$ and perpendicular direction $\\eta_{\\perp}$ are almost the same, which is quite reasonable because in this case the liquid behaves as isotropic. In the case of non-zero anchoring, the general ratio $\\eta_{\\parallel}/\\eta_{\\perp}$ is about 2 which is satisfied by experimental observations.

M. V. Kozachok; B. I. Lev

2014-03-06

272

Intrinsic focusing of the particle size distribution in colloids containing nanocrystals of two different crystal phases.  

PubMed

We have studied the Ostwald ripening of colloids containing nanocrystals of two different crystal phases of the same material. Ostwald ripening in such polymorphic systems is shown to result in an intrinsic focusing of the particle size distribution of the thermodynamically preferred phase while the particles of the less stable phase completely dissolve. Experimentally, a colloidal system of this kind was realized by mixing small NaEuF4 nanocrystals of the cubic ?-phase with particles of the hexagonal ?-phase having the same mean size and size distribution. The temporal evolution of the particle sizes of both phases can be understood and numerically simulated within the framework of LSW theory. The simulations show that small differences in the bulk solubility or the surface energy of the two phases are sufficient to explain the experimentally observed narrowing of the particle size distribution. PMID:24206197

Voss, Benjamin; Haase, Markus

2013-12-23

273

Measurement of particle size distribution of tripalmitin crystals in a model solution using a laser diffraction method  

Microsoft Academic Search

The form and size distribution of tripalmitin (PPP) crystals formed by quenching a solution in a batch crystallizer have been\\u000a studied using scanning electron microscopy and a laser diffraction technique. Although the accuracy of the laser technique\\u000a for particle sizing was affected by the nonsphericity of the crystals, the technique proved to be effective and very reproducible.\\u000a Crystals recovered by

Andrea M. Fitzgerald; O. John Barnes; Ian Smart; D. Ian Wilson

2001-01-01

274

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

SciTech Connect

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.

Sankari, R. Siva, E-mail: sivasankari.sh@act.edu.in [Department of Physics, Agni College of Technology, Thalambur, Chennai-603103 (India); Perumal, Rajesh Narayana [Department of Physics, SSN College of Engineering, Kalavakkam, Chennai-603110 (India)

2014-04-24

275

Magnetic properties and crystal structure of ?-Ta  

NASA Astrophysics Data System (ADS)

Polycrystalline samples of ?-Ta with Frank-Kasper ?-phase structure prepared by electrolysis are studied. The atomic parameters are determined by the Rietveld method. The magnetic susceptibility is measured in the temperature range 4.2 < T < 273 K and the dependence of the magnetization on the magnetic field strength is measured at 4.2 and 77 K. The analysis of interatomic distances and the results of magnetic measurements indicate that clusters with a localized excess charge exist in ?-Ta. The data obtained in this study suggest structural changes in ?-Ta at T < 77 K.

Shamra?, V. F.; Warhulska, J. K.; Arakcheeva, A. V.; Grinevich, V. V.

2004-11-01

276

[Band electronic structures and crystal packing forces  

SciTech Connect

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

Not Available

1993-01-01

277

RECENT CRYSTAL STRUCTURE DETERMINATIONS BY NEUTRON DIFFRACTION AT OAK RIDGE  

E-print Network

469. RECENT CRYSTAL STRUCTURE DETERMINATIONS BY NEUTRON DIFFRACTION AT OAK RIDGE By GEORGE M. BROWN and HENRI A. LEVY, Chemistry Division Oak Ridge National Laboratory (1), Oak Ridge, Tennessee, U. S. A ont été relevées grace au diffractomètre à neutrons d'Oak Ridge position- nant automatiquement les

Paris-Sud XI, Université de

278

The diammoniate of diborane: crystal structure and hydrogen release.  

PubMed

[(NH(3))(2)BH(2)](+)[BH(4)](-) is formed from the room temperature decomposition of NH(4)(+)BH(4)(-), via a NH(3)BH(3) intermediate. Its crystal structure has been determined and contains disordered BH(4)(-) ions in 2 distinct sites. Hydrogen release is similar to that from NH(3)BH(3) but with faster kinetics. PMID:20941402

Bowden, Mark; Heldebrant, David J; Karkamkar, Abhi; Proffen, Thomas; Schenter, Gregory K; Autrey, Tom

2010-12-01

279

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

E-print Network

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

Downs, Robert T.

280

Diffusion-Driven Crystal Structure Transformation: Synthesis of Heusler Alloy  

E-print Network

Diffusion-Driven Crystal Structure Transformation: Synthesis of Heusler Alloy Fe3Si Nanowires Materials Research Team, KBSI, Daejeon 305-333, Korea ABSTRACT We report fabrication of Heusler alloy Fe3Si transformation, magnetic materials, Heusler alloy M etal silicide nanowires (NWs) can have diverse metal

Kim, Bongsoo

281

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

NASA Technical Reports Server (NTRS)

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.

1975-01-01

282

Crystal Structures of Thermostable Xylose Isomerases from Thermus caldophilus and  

E-print Network

of XI makes it a useful enzyme for converting glucose to fructose for the industrial production of high-fructose corn syrup. However, XIs in general have higher KM and lower kcat for D-glucose than for D of Science and Technology, Daejon 305-333, Korea The crystal structures of highly thermostable xylose

Suh, Se Won

283

Domain Structures in Nematic Liquid Crystals on a Polycarbonate Surface  

PubMed Central

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

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

2013-01-01

284

Nanoscale structural features determined by AFM for single virus particles  

NASA Astrophysics Data System (ADS)

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.

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

2013-10-01

285

Improved synthesis of fine zinc borate particles using seed crystals  

Microsoft Academic Search

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

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

2009-01-01

286

Transformation of the snow crystal to a particle of ice  

Microsoft Academic Search

To study the physical properties of snow under different meteorological conditions a mathematical model and numerical computer\\u000a program were created and applied for some numerical modelling estimates. The non-linear mathematical model consists of partial\\u000a differential equations and can be subdivided into a thermal part with phase changes in porous media, diffusion, structural\\u000a transformation and mechanical parts. The model was applied

Elena Guseva-Lozinski

1999-01-01

287

Crystal structure of cyclin-dependent kinase 2  

Microsoft Academic Search

Cyclin-dependent kinase 2 (CDK2) is a member of a highly conserved family of protein klnases that regulate the eukaryotic cell cycle. The crystal structures of the human CDK2 apoenzyme and its Mg2+ATP complex have been determined to 2.4Å resolution. The structure is bi-lobate, like that of the cyclic AMP-dependent protein kinase, but contains a unique helix-loop segment that interferes with

Hendrik L. de Bondt; Jody Rosenblatt; Jarmila Jancarik; Heather D. Jones; David O. Morgant; Sung-Hou Kim

1993-01-01

288

Crystal structure and chemical bonding in tin(II) acetate  

Microsoft Academic Search

Tin(II) acetate was prepared and its crystal structure was solved from X-ray powder diffraction data. Tin(II) acetate adopts a polymeric structure consisting of infinite Sn(CH3COO)2 chains running along the c-axis which are packed into groups of four. The acetate groups bridge the Sn atoms along the chains. The Sn atoms are asymmetrically surrounded by four oxygen atoms with two short

Varvara S. Stafeeva; Alexander S. Mitiaev; Artem M. Abakumov; Alexander A. Tsirlin; Artem M. Makarevich; Evgeny V. Antipov

2007-01-01

289

Crystal Structure of the Phosphorus Oxynitride P 4ON 6  

Microsoft Academic Search

The ab initio crystal structure determination of the phosphorus oxynitride P4ON6 has been performed by the X-ray powder diffraction technique (space group Pnnm; a = 6.8424(1)Å, b = 6.0714(2)Å, c = 6.8176(1)Å, Z = 2; RBragg = 4.8%, Gof = 1.35) A structure refinement of neutron data incorporating anisotropic temperature coefficients for oxygen and nitrogen reduces the RBragg-factor down to

J. Ronis; B. Bondars; A. Vitola; T. Millers; J. Schneider; F. Frey

1995-01-01

290

Crystal Structure of Chaperonin-60 from Paracoccus denitrificans  

Microsoft Academic Search

The crystal structure of chaperonin-60 from Paracoccus denitrificans (P.cpn60) has been determined at 3.2Å resolution by the molecular replacement method. Two heptameric rings of identical subunits of P.cpn60 in adjacent asymmetric units are stacked in a back-to-back manner and form a cylinder, as found in GroEL, cpn60 from Escherichia coli. With respect to the unliganded GroEL structure, each subunit of

Takaaki A. Fukami; Masafumi Yohda; Hideki Taguchi; Masasuke Yoshida; Kunio Miki

2001-01-01

291

TUNABLE PHOTONIC STRUCTURES BASED ON SILICON AND LIQUID CRYSTALS  

Microsoft Academic Search

This paper is focused on the design, fabrication and characterization of the conventional and tunable photonic devices based on grooved silicon, serving as one-dimensional (1D) photonic crystal. The advantages of these photonic structures are as follows: the large refractive index contrast, in-plane moulding of the light flow, the possibility to fabricate a composite photonic structures by filling the grooves with

Tatiana S. Perova; Vladimir A. Tolmacheva; Ekaterina V. Astrova

292

Intermetallic crystal structures as foams. Beyond frank-kasper.  

PubMed

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

Bonneau, Charlotte; O'Keeffe, Michael

2015-02-01

293

Tailor-made force fields for crystal-structure prediction.  

PubMed

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

Neumann, Marcus A

2008-08-14

294

Crystal Structure and Calculated Electronic Band Structure of ZrTe 3  

Microsoft Academic Search

Because of inconsistencies in literature data, the crystal structure of ZrTe3was redetermined from single-crystal data and the electronic band structure was calculated using density functional theory in the local density approximation (LDA) and the linear muffin tin orbital method (LMTO). ZrTe3crystallizes in the monoclinic space groupP21\\/mwitha=589.8(1) pm,b=392.69(3) pm,c=1010.3(1) pm, and?=97.81(1)° (Z=2) in the ZrSe3structure type (?data collection,Rw=1.88%). In the layer

Klaus Stöwe; Frank R Wagner

1998-01-01

295

Structural analysis of three-dimenstionl photonic crystals in nature  

NASA Astrophysics Data System (ADS)

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

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

2012-02-01

296

Crystal structures of dibromodichloromethane and bromotrichloromethane  

NASA Astrophysics Data System (ADS)

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

Lee-Dadswell, S. E.

297

Crystal structure of human chorionic gonadotropin  

Microsoft Academic Search

The three-dimensional structure of human chorionic gonadotropin shows that each of its two different subunits has a similar topology, with three disulphide bonds forming a cystine knot. This same folding motif is found in some protein growth factors. The heterodimer is stabilized by a segment of the beta-subunit which wraps around the alpha-subunit and is covalently linked like a seat

A. J. Lapthorn; D. C. Harris; A. Littlejohn; J. W. Lustbader; R. E. Canfield; K. J. Machin; F. J. Morgan; N. W. Isaacs

1994-01-01

298

The EMBO Journal Vol.16 No.13 pp.37873796, 1997 Crystal structure of a deubiquitinating enzyme  

E-print Network

processing (OlveraKeywords: crystal structure/cysteine protease/substrate and Wool, 1993; Haas et al., 1996The EMBO Journal Vol.16 No.13 pp.3787­3796, 1997 Crystal structure of a deubiquitinating enzyme-terminus of ubiquitin. We have modification of chromatin structure (Bradbury, 1992),determined the crystal structure

Hill, Chris

299

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

NASA Astrophysics Data System (ADS)

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

Terentjev, E. M.

1995-02-01

300

English Verb-Particle Constructions: Two Types, Two Structures.  

ERIC Educational Resources Information Center

This paper proposes that resultative verb-particle constructions (VPCs) have an underlyingly different structure from idiomatic VPCs; both structures differ from the Small Clause analysis of R. Kayne (1985) et al and the verb-particle complex analysis of K. Johnson (1991). Empirical support for the new proposal comes from anaphor deletion facts…

Zoerner, Ed

1996-01-01

301

Smectic Layer Structures in Complex Geometries—Modelling Complex Layer Structures in Smectic Liquid Crystals  

Microsoft Academic Search

In order to understand the operation of liquid crystal devices based on tilted smectic materials it is highly important to also understand the formation of the smectic liquid crystal layer structures. However, in many situations this is not easy to do. It is well established that in devices filled with materials that have an upper lying SmA phase a “chevron”

Steve J. Elston; Lesley A. Parry-Jones

2005-01-01

302

Crystal structure of tin(IV) chloride octa­hydrate  

PubMed Central

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

Hennings, Erik; Schmidt, Horst; Voigt, Wolfgang

2014-01-01

303

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

PubMed

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

Hennings, Erik; Schmidt, Horst; Voigt, Wolfgang

2014-12-01

304

Fractal Particles: Titan's Thermal Structure and IR Opacity  

NASA Technical Reports Server (NTRS)

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.

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

1998-01-01

305

Projection structure of frog rhodopsin in two crystal forms.  

PubMed Central

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

Schertler, G F; Hargrave, P A

1995-01-01

306

Use of Pom Pons To Illustrate Cubic Crystal Structures  

NASA Astrophysics Data System (ADS)

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.

Cady, Susan G.

1997-07-01

307

Crystal structure and mechanistic investigation of the twister ribozyme.  

PubMed

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

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

2014-09-01

308

Uptake of different crystal structures of TiO? nanoparticles by Caco-2 intestinal cells.  

PubMed

The gastrointestinal uptake of different crystal structures of TiO2 was investigated using Caco-2 intestinal cells. Caco-2 monolayers exhibited time-dependent, saturable uptake of Ti from TiO2 exposures of 1 mgl(-1) over 24h, which was influenced by crystal type. Initial uptake rates were 5.3, 3.73, 3.58 and 4.48 nmol mg(-1)protein h(-1) for bulk, P25, anatase and rutile forms respectively. All exposures caused elevations of Ti in the cells relative to the control (ANOVA P<0.05). Electron micrographs of the Caco-2 monolayer showed the presence of particles inside the cells, and energy dispersive spectroscopy (EDS) confirmed the composition as TiO2. Incubating the cells with 120 IU nystatin (putative endocytosis inhibitor) or 100 ?mol l(-1) vanadate (ATPase inhibitor) caused large increases in Ti accumulation for all crystal types relative to controls (ANOVA P<0.05), except for the rutile form with vanadate. Incubating the cells with 90 ?mol l(-1) genistein (tyrosine kinase inhibitor) or 27 ?mol l(-1) chloropromazine (clathrin-mediated endocytosis inhibitor) caused a large decrease in Ti accumulation relative to the controls (ANOVA P<0.05). Cell viability measures were generally good (low LDH leak, normal cell morphology), but there were some changes in the electrolyte composition (K(+), Na(+), Ca(2+), Mg(2+)) of exposed cells relative to controls. A rise in total Ca(2+) concentration in the cells was observed for all TiO2 crystal type exposures. Overall, the data shows that Ti accumulation for TiO2 NP exposure in Caco-2 cells is crystal structure-dependent, and that the mechanism(s) involves endocytosis of intact particles. PMID:24576787

Gitrowski, Constantinos; Al-Jubory, Aliaa R; Handy, Richard D

2014-05-01

309

Trapping of topological-structural defects in Coulomb crystals.  

PubMed

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

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

2013-03-29

310

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

PubMed

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

Hashemi, S Masoomeh; Ejtehadi, Mohammad Reza

2015-01-01

311

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

NASA Astrophysics Data System (ADS)

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.

Hashemi, S. Masoomeh; Ejtehadi, Mohammad Reza

2015-01-01

312

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

E-print Network

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

S. Masoomeh Hashemi; Mohammad Reza Ejtehadi

2015-01-25

313

Synthesis and crystal structure of CuZrTiO{sub 5}-A new crystal structure type  

SciTech Connect

A new compound, CuZrTiO{sub 5}, was synthesized as strongly pleochroic green crystals from the oxides between 995 and 1010 deg. C, 1 atm. Its crystal structure was determined by single crystal XRD, resulting in R (F{sup 2}>2sigma(F{sup 2}))=0.032 and wR (all data)=0.079). CuZrTiO{sub 5} is orthorhombic, space group P2{sub 1}2{sub 1}2{sub 1}, a=3.5871(3) A, b=6.6968(4) A, c=14.6679(9) A, V=352.35(4) A{sup 3}, Z=4. The structure is topologically similar to In{sub 2}TiO{sub 5} but differs in space group and cation coordination. CuZrTiO{sub 5} has relatively regular TiO{sub 6} polyhedra, but coordination is 7+1 for Zr, and 4+2 for Cu due to the Jahn-Teller effect. Ordering of the long Cu-O bonds causes reduction in symmetry relative to In{sub 2}TiO{sub 5}. Layers of Cu alternate with Ti+Zr on (001), giving rise to a distinct cleavage. Bond valence sums on Ti and Zr are far from ideal, which appears due to the limited ability of this structural topology to avoid close next-nearest neighbour distances. - Graphical abstract: The new compound CuZrTiO{sub 5} is orthorhombic (P2{sub 1}2{sub 1}2{sub 1}), with a=3.5871(3) A, b=6.6968(4) A, c=14.6679(9) A. The structure, determined with single crystal XRD, represents a new crystal structure type that is a slight distortion of that of In{sub 2}TiO{sub 5} but differs in space group and cation coordination.

Troitzsch, Ulrike [Research School of Earth Sciences, Australian National University, Canberra ACT 0200 (Australia); Christy, Andrew G., E-mail: Andrew.Christy@anu.edu.a [Research School of Earth Sciences, Australian National University, Canberra ACT 0200 (Australia); Willis, Anthony C. [Research School of Chemistry, Australian National University, Canberra ACT 0200 (Australia); Ellis, David J. [Research School of Earth Sciences, Australian National University, Canberra ACT 0200 (Australia)

2010-03-15

314

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

E-print Network

Crystallization of atmospheric sulfate-nitrate-ammonium particles Scot T. Martin, Julie C the crystallization RH (CRH) at 293 K of particles throughout the entire sulfate-nitrate-ammonium composition space. Malinowski, H.-M. Hung, and Y. Rudich, Crystallization of atmospheric sulfate- nitrate-ammonium particles

315

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

NASA Astrophysics Data System (ADS)

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

Miskevich, Alexander A.; Loiko, Valery A.

2014-03-01

316

Edinburgh Research Explorer Europium-IV: An Incommensurately Modulated Crystal Structure  

E-print Network

Edinburgh Research Explorer Europium-IV: An Incommensurately Modulated Crystal Structure 2012, 'Europium-IV: An Incommensurately Modulated Crystal Structure in the Lanthanides' Physical Review to the work immediately and investigate your claim. Download date: 27. Jun. 2014 #12;Europium

Millar, Andrew J.

317

Is the methanation reaction over Ru single crystals structure dependent?  

PubMed

The influence of monoatomic steps and defects on the methanation reaction over ruthenium has been investigated. The experiments are performed on a Ru(0 1 54) ruthenium single crystal, which contains one monoatomic step atom for each 27 terrace atoms. The methanation activity is measured at one bar of hydrogen and CO in a high pressure cell, which enables simultaneous measurements of the local reactivity of the well defined single crystal surface and the global reactivity of the entire crystal and its auxiliary support. By adding sulfur we observe that the measured activity from the well defined stepped front-side of the crystal is poisoned faster than the entire crystal containing more defects. We also observe that additional sputtering of the well-defined front-side increases the reactivity measured on the surface. Based on this, we conclude that the methanation reaction takes place on undercoordinated sites, such as steps and kinks, and that the methanation reaction is extremely structure dependent. Simulations of the flow, temperature, and product distributions in the high pressure cell are furthermore presented as supplementary information. PMID:21258708

Vendelbo, Søren B; Johansson, Martin; Nielsen, Jane H; Chorkendorff, Ib

2011-03-14

318

Crystals in magma: flow dynamics and rheology of particle-bearing melts  

NASA Astrophysics Data System (ADS)

Volcanic activity is naturally linked to the flow of magma. For the assessment of hazards associated with a volcanic eruption, i.e. the prediction and modeling of magmatic flow processes, it is of pivotal importance to understand the basic principles of magma rheology as accurately as possible. Magma rheology depends primarily on melt chemistry and on the relative proportions of the three phases melt-gas-crystals. Whilst the viscosity of many melt compositions has been accurately measured, the effect of adding particles to them is still poorly constrained. Unlike bubbles, the presence of crystals in a Newtonian melt - due to their rigid character - always increases the viscosity of the mixture and may additionally introduce various non-Newtonian rheological effects. The viscosity of the mixture is a function of both the concentration and geometry of the added particles and can be several orders of magnitude larger than the viscosity of the pure melt. We have performed analogue experiments on suspensions of particles with different geometries in Newtonian silicone oil. The particles used were glass beads (spherical), glitter (oblate), wollastonite (prolate), and SiC grit (angular), in a size range of 100-350µm. Rheological properties, including viscoelasticity, have been measured using a Haake MARS rotational rheometer. The effects of the respective particles on suspension rheology during two experimental phases (transient flow initiation and steady flow) have been determined: (I) When flow commences, the initially randomly distributed particles realign and reorganize in less flow-resisting configurations. Depending on the particle geometry, this motion results in distinctive strain-dependent viscosity patterns. (II) During steady shear flow, the suspended particles cause different degrees of relative viscosity increase, shear thinning and yield strength behaviour, mainly depending on their aspect ratio. These effects have been quantified and fitted to existing rheology models.

Mueller, S.; Mader, H. M.; Llewellin, E. W.

2009-04-01

319

Crystal structure of four-stranded Oxytricha telomeric DNA  

NASA Technical Reports Server (NTRS)

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.

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

1992-01-01

320

Crystal structure of homoisocitrate dehydrogenase from Schizosaccharomyces pombe  

PubMed Central

Homoisocitrate dehydrogenase (HICDH) catalyzes the conversion of homoisocitrate to 2-oxoadipate, the third enzymatic step in the ?-aminoadipate pathway by which lysine is synthesized in fungi and certain archaebacteria. This enzyme represents a potential target for anti-fungal drug design. Here, we describe the first crystal structures of a fungal HICDH, including structures of an apoenzyme and a binary complex with a glycine tri-peptide. The structures illustrate the homology of HICDH with other ?-hydroxyacid oxidative decarboxylases and reveal key differences with the active site of Thermus thermophilus HICDH that provide insights into the differences in substrate specificity of these enzymes. PMID:22105743

Bulfer, Stacie L.; Hendershot, Jenna M.; Trievel, Raymond C.

2013-01-01

321

Multiplexed DNA detection using spectrally encoded porous SiO2 photonic crystal particles  

PubMed Central

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

Meade, Shawn O.; Chen, Michelle Y.

2009-01-01

322

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

PubMed

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

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

2011-02-01

323

Phonon-mediated detection of elementary particles using silicon crystal acoustic detectors  

NASA Astrophysics Data System (ADS)

A research group at Stanford is developing Silicon Crystal Acoustic Detectors (SiCADs) which operate at cryogenic temperatures and sense phonons generated when an incident particle scatters off a nucleus or electron in the crystalline Si wafer substrate. In the present design photon sensors consist of a thin film labyrinth pattern of superconducting titanium, which is dc current biased at a temperature just below its superconducting to normal transition (approx. 430 mK). The motivation for developing SiCADs includes their many direct applications to neutrino physics, particle astrophysics, and solid state physics.

Young, Betty Aileen

1991-06-01

324

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

NASA Astrophysics Data System (ADS)

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

Uchiyama, Hiroaki; Nakanishi, Shunsuke; Kozuka, Hiromitsu

2014-09-01

325

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

E-print Network

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

Kovalev, Gennady V

2015-01-01

326

Rigidity analysis of protein biological assemblies and periodic crystal structures  

PubMed Central

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, and would not have been observed only from the asymmetric unit. For the Ribonuclease A protein (PDB file 5RSA), which is functionally active in the crystallized form, we found that the individual protein and its crystal form retain the flexibility parameters between the two states. In contrast, a derivative of Ribonuclease A (PDB file 9RSA), has no functional activity, and the protein in both the asymmetric and crystalline forms, is very rigid. For the vaccinia virus D13 scaffolding protein (PDB file 3SAQ), which has two biological assemblies, we observed a striking asymmetry in the rigidity cluster decomposition of one of them, which seems implausible, given its symmetry. Upon careful investigation, we tracked the cause to a placement decision by the Reduce software concerning the hydrogen atoms, thus affecting the distribution of certain hydrogen bonds. The surprising result is that the presence or lack of a very few, but critical, hydrogen bonds, can drastically affect the rigid cluster decomposition of the biological assembly. Conclusion The rigidity analysis of a single asymmetric unit may not accurately reflect the protein's behavior in the tightly packed crystal environment. Using our KINARI software, we demonstrated that additional functional and rigidity information can be gained by analyzing a protein's biological assembly and/or crystal structure. However, performing a larger scale study would be computationally expensive (due to the size of the molecules involved). Overcoming this limitation will require novel mathematical and computational extensions to our software. PMID:24564201

2013-01-01

327

Structural and magnetic properties of barium hexaferrite nanostructured particles prepared by the combustion method  

NASA Astrophysics Data System (ADS)

The combustion method, a fast and simple way of preparing sub-micrometer sized particles from a solution of the corresponding metal nitrates and a reducing agent (ODH, TFTA) which is used as a fuel, was adapted to the synthesis of barium hexaferrite particles. Structural and magnetic properties were investigated by X-ray diffraction, transmission electronic microscopy, magnetic measurements and Mössbauer spectrometry on nanostructured as well as on microstructured particles resulting from annealing treatments under different conditions. High values of the coercive field (5.3 kOe) and of the magnetization (57.8 emu/g), at 13.5 kOe, were obtained on well crystallized BaFe12O19 particles annealed at 850°C.

Castro, S.; Gayoso, M.; Rivas, J.; Greneche, J. M.; Mira, J.; Rodríguez, C.

1996-01-01

328

EVO—Evolutionary algorithm for crystal structure prediction  

NASA Astrophysics Data System (ADS)

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

Bahmann, Silvia; Kortus, Jens

2013-06-01

329

A Model of Voltage Gating Developed Using the KvAP Channel Crystal Structure  

E-print Network

A Model of Voltage Gating Developed Using the KvAP Channel Crystal Structure Indira H. Shrivastava Having inspected the crystal structure of the complete KvAP channel protein, we suspect that the voltage interactions with the central pore-forming domain. On the other hand, a second crystal structure

Benos, Takis

330

Fabrication of polymer photonic crystal superprism structures using polydimethylsiloxane soft molds  

E-print Network

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

Jiang, Wei

331

Space group selection for crystal structure prediction of solvates{ Aurora J. Cruz Cabeza,a  

E-print Network

Space group selection for crystal structure prediction of solvates{ Aurora J. Cruz Cabeza,a Elna with common solvents are presented to assist crystal structure prediction calculations on these complex systems. Introduction Many programs for the computer generation of crystal structures (e.g. UPACK,1

de Gispert, Adrià

332

INFLUENCE OF OPTICAL BAND STRUCTURES ON THE DIFFRACTION OF PHOTONIC COLLOIDAL CRYSTALS  

E-print Network

INFLUENCE OF OPTICAL BAND STRUCTURES ON THE DIFFRACTION OF PHOTONIC COLLOIDAL CRYSTALS WILLEM L crystal structures - e.g. the diamond structure [9]. In this case, no wave with an energy within the gap diffraction studies on colloidal crystals with large re- fractive index mismatches up to 1

Vos, Willem L.

333

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

E-print Network

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

Dennis, Edward A.

334

An Assessment of Lattice Energy Minimization for the Prediction of Molecular Organic Crystal Structures  

E-print Network

in the predicted lists are used to determine the efficacy of lattice energy minimization in crystal structure Computational methods of predicting the most likely crystal structures of a molecule from its atomic con in the pro- cessing cycle of a pharmaceutical molecule. The field of crystal structure prediction (CSP) has

de Gispert, Adrià

335

Tunable all-optical switching in periodic structures with liquid-crystal defects  

E-print Network

Tunable all-optical switching in periodic structures with liquid-crystal defects Andrey E in periodic pho- tonic structures with liquid-crystal defects. We consider a one-dimensional periodic structure of Si layers with a local defect created by infiltrating a liquid crystal into a pore

336

Realizing Predicted Crystal Structures at Extreme Conditions: The Low-Temperature and High-Pressure  

E-print Network

Realizing Predicted Crystal Structures at Extreme Conditions: The Low-Temperature and High-Pressure Crystal Structures of 2-Chlorophenol and 4-Fluorophenol Iain D. H. Oswald, David R. Allan, Graeme M. Day but a small group at high pressure. We show that Crystal Structure Prediction methodologies reproduce all four

de Gispert, Adrià

337

The crystal structure of a Cys25!Ala mutant of human procathepsin S elucidates enzymeprosequence  

E-print Network

: crystal structure; cysteine proteinase; procathepsin S; propeptide Cathepsin S (EC 3The crystal structure of a Cys25!Ala mutant of human procathepsin S elucidates enzyme; ACCEPTED August 8, 2006) Abstract The crystal structure of the active-site mutant Cys25!Ala of glycosylated

Lübeck, Universität zu

338

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

PubMed

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. PMID:24334063

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

2014-03-25

339

Synthesis, structural and spectroscopic investigations of nanostructured samarium oxalate crystals  

NASA Astrophysics Data System (ADS)

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

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

2014-03-01

340

Crystallizing membrane proteins for structure determination: use of lipidic mesophases.  

PubMed

The principal route to determine the structure and the function and interactions of membrane proteins is via macromolecular crystallography. For macromolecular crystallography to be successful, structure-quality crystals of the target protein must be forthcoming, and crystallogenesis represents a major challenge. Several techniques are employed to crystallize membrane proteins, and the bulk of these techniques make direct use of solubilized protein-surfactant complexes by the more traditional, so-called in surfo methods. An alternative in meso approach, which employs a bicontinuous lipidic mesophase, has emerged as a method with considerable promise in part because it involves reconstitution of the solubilized protein back into a stabilizing and organizing lipid bilayer reservoir as a prelude to crystallogenesis. A hypothesis for how the method works at the molecular level and experimental evidence in support of the proposal are reviewed here. The latest advances, successes, and challenges associated with the method are described. PMID:19086821

Caffrey, Martin

2009-01-01

341

Crystal structure of N'-hy-droxy-pyrimidine-2-carboximidamide.  

PubMed

The title compound, C5H6N4O, is approximately planar, with an angle of 11.04?(15)° between the planes of the pyrimidine ring and the non-H atoms of the carboximidamide unit. The mol-ecule adopts an E configuration about the C=N double bond. In the crystal, adjacent mol-ecules are linked by pairs of N-H?O hydrogen bonds, forming inversion dimers with an R 2 (2)(10) ring motif. The dimers are further linked via N-H?N and O-H?N hydrogen bonds into a sheet structure parallel to the ac plane. The crystal structure also features N-H?O and weak C-H?O hydrogen bonds and offset ?-? stacking inter-actions between adjacent pyrimidine rings [centroid-centroid distance = 3.622?(1)?Å]. PMID:25484698

Jasmine, Nithianantham Jeeva; Muthiah, Packianathan Thomas; Stanley, Nithianantham

2014-10-01

342

Crystal Structures of Aedes Aegypt Alanine Glyoxylate Aminotransferase  

SciTech Connect

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.

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

2006-01-01

343

Structural studies of metabolic products of dopamine. IV. Crystal and molecular structure of (-)-noradrenaline.  

PubMed

The crystal structure of (-)-noradrenaline has been determined by X-ray methods, using 1000 observed reflections collected by counter diffractometer techniques. The crystals are orthorhombic, space group P212121, with a=8.611(2), B=6.138(2), And c=14.912(4) A. Least-squares refinements yielded a conventional R-factor of 0.036. Standard deviations in bond lengths are 0.003 A and in bond angles 0.2 degrees. The crystal structure of (-)-noradrenaline corresponds closely to that of (-)-adrenaline in molecular geometry, conformation, and arrangement in the crystals. The results of the structure investigations are discussed in relation to the biological activity of these biogenic amines. PMID:1202890

Andersen, A M

1975-01-01

344

Defect structures mediate the isotropic-nematic transition in strongly confined liquid crystals.  

PubMed

Using Monte Carlo simulations, we study rod-like lyotropic liquid crystals confined to a square slab-like geometry with lateral dimensions comparable to the length of the particles. We observe that this system develops linear defect structures upon entering the planar nematic phase. These defect structures flank a lens-shaped nematic region oriented along a diagonal of the square box. We interpret these structures as a compromise between the 2-fold order of the bulk nematic phase and the 4-fold order imposed by the lateral boundaries. A simple Onsager-type theory that effectively implements these competing tendencies is used to model the phase behavior in the center of the box and shows that the free-energy cost of forming the defect structures strongly offsets the transition-inducing effects of both the transverse and lateral confinement. PMID:25435377

Gârlea, Ioana C; Mulder, Bela M

2014-12-17

345

Crystal structure of the Src family tyrosine kinase Hck  

Microsoft Academic Search

The crystal structure of the haematopoietic cell kinase Hck has been determined at 2.6\\/2.9 Å resolution. Inhibition of enzymatic activity is a consequence of intramolecular interactions of the enzyme's Src-homology domains SH2 and SH3, with concomitant displacement of elements of the catalytic domain. The conformation of the active site has similarities with that of inactive cyclin-dependent protein kinases.

Frank Sicheri; Ismail Moarefi; John Kuriyan

1997-01-01

346

Lithium niobate: Summary of physical properties and crystal structure  

Microsoft Academic Search

Ferroelectric lithium niobate (LiNbO3) is widely used in integrated and guided-wave optics because of its favorable optical, piezoelectric, electro-optic, elastic, photoelastic, and photorefractive properties. However, detailed summaries of its pertinent physical properties and crystal structure are not readily available. In this tutorial paper, the important tensor physical properties and their mathematical descriptions are compiled and presented. The essential features of

R. S. Weis; T. K. Gaylord

1985-01-01

347

Crystal Structures of Cisplatin Bound to a Human Copper Chaperone  

SciTech Connect

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.

Boal, Amie K.; Rosenzweig, Amy C.; (NWU)

2010-08-16

348

Electronic structure of hole centers in aluminum doped fluorite crystals  

Microsoft Academic Search

UDC 535.37 A wealth of experimental data are currently available on point defects and processes with their participation in scintillation crystals based on CaF 2 containing rare earth elements (REE). The electronic and spatial structure of a number of hole and electron centers was studied theoretically. The ab initio Hartree-Fock method and the scattered wave method were used to calculate

S. N. Mysovskii

1999-01-01

349

Crystal Structure and Formation Energy of -carbide Using First  

E-print Network

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

Cambridge, University of

350

Crystal Structures of Cisplatin Bound to a Human Copper Chaperone  

Microsoft Academic Search

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

Amie K. Boal; Amy C. Rosenzweig

2010-01-01

351

Crystal structures of cisplatin bound to a human copper chaperone.  

PubMed

Copper trafficking proteins, including the chaperone Atox1 and the P(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. PMID:19807176

Boal, Amie K; Rosenzweig, Amy C

2009-10-14

352

Polymer crystallization enabled nanotube functionalization: Morphology, structure and applications  

NASA Astrophysics Data System (ADS)

Carbon Nanotubes (CNT) have attracted tremendous attention and numerous potential applications have been proposed. In this thesis study, a unique means to modify CNT surface with polymer crystals via controlled polymer crystallization method has been developed. CNTs were wrapped in polymer single crystal lamellae in a periodic manner, resulting in nano hybrid shish-kebab (NHSK) structures. The periodicity of the polymer lamellae can be varied from 20-150 nm. The kebabs are ˜5 nm thick (along CNT direction) with a lateral size of ˜20 nm to micrometers, which can be readily controlled by varying crystallization conditions. PE, Nylon 66 and PE-b-SBR were successfully decorated on single-walled carbon nanotubes (SWNT), multi-walled carbon nanotubes (MWNT), as well as vapor grown carbon nanofibers (CNF). The formation mechanism was attributed to "size dependent soft epitaxy". Efforts were focused on PE/SWNT system to understand the growth mechanism and the effect of experimental parameters on the periodicity. It was found that weight ratio of SWNT and PE (defined as R) played an important role and periodicity increases with increasing R. This was attributed to a reduced polymer concentration at the crystal growth front. Since NHSK formation conditions depend upon CNT structures, it further provides a unique opportunity for CNT separation. Applications of using NHSK in CNT dispersions, separation and nanocomposites have also been successfully developed. This unique means is different from all the reported methods and it opens a gateway to achieving periodically functionalized CNT for a variety of applications ranging from nanocomposites, sensors, fuel cells etc.

Li, Lingyu

353

Flow-Induced Crystallization Precursor Structure in Entangled Polymer Melt.  

NASA Astrophysics Data System (ADS)

Flow-induced crystallization has long been an important subject in polymer processing. Varying processing conditions can produce different morphologies, which lead to different properties. Recent studies indicated that the final morphology is in fact dictated by the initial formation of crystallization precursor structures (i.e., shish kebabs) under flow. In this talk, factors that affect the shish-kebab formation in entangled polymer melts are systematically reviewed, including the concept of coil-stretch transition, chain dynamics, critical orientation molecular weight, phase transition during shish and kebab formations. In particular, recent experimental results from in-situ rheo-X-ray studies and ex-situ microscopic examinations have been presented to illustrate several new findings of flow-induced shish-kebab structures in polymer melts. (1) The shish entity consists of stretched chains (or chain segments) that can be in the amorphous, mesomorphic or crystalline state. (2) The kebab entity mainly arises from the crystallization of coiled chains (or chain segments), which seems to follow a diffusion-control growth process. (3) A shish-kebab structure with multiple shish was seen in the ultra-high molecular weight polyethylene (UHMWPE) precursor. Based on the above results and recent simulation work from other laboratories, a modified molecular mechanism for the shish-kebab formation in entangled melt is presented.

Hsiao, Benjamin

2006-03-01

354

Nanoconfinement-induced structures in chiral liquid crystals.  

PubMed

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

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

2013-01-01

355

Nanoconfinement-Induced Structures in Chiral Liquid Crystals  

PubMed Central

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

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

2013-01-01

356

Structural contribution to the roughness of supersmooth crystal surface  

SciTech Connect

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

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

2013-05-15

357

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

PubMed

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

Michielsen, K; Stavenga, D G

2008-01-01

358

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

PubMed

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

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

2014-09-16

359

Crystal Structure of Uronate Dehydrogenase from Agrobacterium tumefaciens*  

PubMed Central

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

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

2011-01-01

360

Structure of crystal defects in damaged RDX as revealed by an AFM  

SciTech Connect

An atomic force microscope (AFM) was employed to reveal the structure of defects produced in single crystals of cyclotrimethylenetrinitramine (RDX), damaged either by indentation, heat or underwater shock. In general, all of these stimuli produced dislocation pits, cracks, fissures and mosaics, however, the details were different. Indentation generated a large number of triangular dislocation pits, which in their turn produced fissures, cracks and holes by coalescing. Heat produced fine parallel cracks. Slivers as thin as sixty molecules across were observed. Shock caused the crystal to become a three-dimensional mosaic structure, 100-500 nm in size, produced by intensive cleavage and delamination. In all cases very fine particles, 20-500 nm in size, were ejected onto the surface as debris from the formation of defects. The AFM has revealed for the first time un-etched dislocation pits in their pristine condition, so that their internal structure could be investigated. A dislocation density of 10{sup 6} cm{sup -2} has been observed. RDX is found to behave like a very fragile crystal in which numerous imperfections show up at a level of the stimuli, far below that necessary for the start of chemical reaction.

Sharma, J.; Hoover, S. M.; Coffey, C. S.; Tompa, A. S.; Sandusky, H. W.; Armstrong, R. W.; Elban, W. L. [Carderock Division Naval Surface Warfare Center, Bethesda, Maryland 20817 (United States); Indian Head Division Naval Surface Warfare Center, Indian Head, Maryland 20640 (United States); University of Maryland, College Park, Maryland 20742 (United States); Loyola College, Baltimore, Maryland 21210 (United States)

1998-07-10

361

Crystal structure, microstructure and magnetic properties of Ni nanoparticles elaborated by hydrothermal route  

NASA Astrophysics Data System (ADS)

We report on the crystal structure, microstructure and magnetic properties of Ni nanoparticles (NPs), with an average diameter of around 40 nm, produced by hydrothermal method. A series of Ni powders was synthesized at relatively low temperature (140 °C) by varying the NaOH concentration. The crystal structure, microstructure and magnetic properties were investigated by means of XRD, MEB coupled to EDX and VSM magnetometry. The XRD patterns show Bragg reflections corresponding to Ni with face centred cubic (fcc) crystal structure. EDX spectra confirm the purity of Ni powders. Moreover, the SEM micrographs show that the Ni-NPs are agglomerated forming entities of 1-5 ?m in average size with different morphologies that change as the NaOH concentration increases. While those entities exhibit a flower-like form at the lowest concentration, a dendritic shape appears for the highest one. The room temperature values for the coercive field (<200 Oe) and saturation magnetization (?52 Am2/kg) were obtained from the magnetic hysteresis loops. We discuss about the influence of the particle morphology on the magnetic behaviour.

Bouremana, A.; Guittoum, A.; Hemmous, M.; Rahal, B.; Sunol, J. J.; Martínez-Blanco, D.; Blanco, J. A.; Gorria, Pedro; Benrekaa, N.

2014-05-01

362

Crystal Structures of Calcium IV and V under High Pressure  

NASA Astrophysics Data System (ADS)

High-pressure phases IV and V of calcium discovered in 2005 have the highest superconducting transition temperature of 25 K among all the elements; however, their crystal structures have not been determined. From the x-ray powder diffraction data, both Ca IV and V have been found to form unique and complex structures with a coordination number of 7. They were confirmed to be identical to the theoretical models that were recently predicted [Ishikawa , Phys. Rev. BPRBMDO0163-1829 77 020101(R) (2008)10.1103/PhysRevB.77.020101].

Fujihisa, Hiroshi; Nakamoto, Yuki; Shimizu, Katsuya; Yabuuchi, Takahiro; Gotoh, Yoshito

2008-08-01

363

Crystal structure refinement of an arsenic-bearing argentian tetrahedrite  

Microsoft Academic Search

The crystal structure of a synthetic tetrahedrite, composition cu6.aaAEz.tzFer.u Sb2 7sAs1.3sS13, has been refined using full-matrix least-squares methods to a weighted disagreement index of 4.6Vo for 169 independent observed difractions. The effects of the substitutions of Ag for Cu and As for Sb on the distances and bond-angles in the tetrahedrite structure are separable, as has been noted previously for

Meny L. JouusoN

364

Crystal and molecular structure of triethanolammonium nitrate (TEAN)  

Microsoft Academic Search

The crystal and molecular structure of crystalline triethanolammonium nitrate (TEAN) was determined. TEAN is monoclinic with space groupP21\\/c and has lattice parametersa=6.592(1),b=16.358(1),c=9.3850(8)Å andß=90.87(1)°. Based on four formula weights of TEAN per unit cell, the computed density is 1.393 g\\/cm-3. The structure is a three-dimensional hydrogen bonded network of cations and anions. An interesting feature of the cation conformation is the

A. J. Bracuti

1993-01-01

365

Fusion proteins as alternate crystallization paths to difficult structure problems  

NASA Technical Reports Server (NTRS)

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.

Carter, Daniel C.; Rueker, Florian; Ho, Joseph X.; Lim, Kap; Keeling, Kim; Gilliland, Gary; Ji, Xinhua

1994-01-01

366

The first crystal structure of an archaeal helical repeat protein  

PubMed Central

The crystal structure of ST1625p, a protein encoded by a hypothetical open reading frame ST1625 in the genome of the hyperthermophilic archaeon Sulfolobus tokodaii, was determined at 2.2?Å resolution. The only sequence similarity exhibited by the amino-acid sequence of ST1625p was a 33% identity with the sequence of SSO0983p from S. solfataricus. The 19?kDa monomeric protein was observed to consist of a right-handed superhelix assembled from a tandem repeat of ten ?-­helices. A structural homology search using the DALI and MATRAS algorithms indicates that this protein can be classified as a helical repeat protein. PMID:16511116

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

2005-01-01

367

Separation-Independent Attractive Force between Like Particles Mediated by Nematic-Liquid-Crystal Distortions  

NASA Astrophysics Data System (ADS)

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), PRLTAO, 0031-9007, 10.1103/PhysRevLett.79.4862] in the presence of narrow strings of birefringent regions (“bubble-gum” configuration) between the particles.

Fukuda, Jun-Ichi; Yokoyama, Hiroshi

2005-04-01

368

Structure of the Maize Streak Virus Geminate Particle  

Microsoft Academic Search

The Geminiviridae is an extensive family of plant viruses responsible for economically devastating diseases in crops worldwide. Geminiviruses package circular, single-stranded DNA (ssDNA) genomes. The characteristic twinned or “geminate” particles, which consist of two joined, incomplete T = 1 icosahedra, are unique among viruses. We have determined the first structure of a geminivirus particle, the Nigerian strain of Maize streak

Wei Zhang; Norman H. Olson; Timothy S. Baker; Lee Faulkner; Mavis Agbandje-McKenna; Margaret I. Boulton; Jeffrey W. Davies; Robert McKenna

2001-01-01

369

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

NASA Astrophysics Data System (ADS)

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

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

2014-01-01

370

Manganese oxide minerals: Crystal structures and economic and environmental significance  

PubMed Central

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

Post, Jeffrey E.

1999-01-01

371

Water structure in vitamin B12 coenzyme crystals. II. Structural characteristics of the solvent networks.  

PubMed Central

The geometrical details of the solvent structure in vitamin B12 coenzyme crystals with respect to hydrogen bonding and nonbonded contacts, are described. The individual H-bond geometries varied over wide ranges, similar to those observed in small molecule structures. Large deviations from tetrahedral coordination were found around a majority of the waters. The mutual positions and orientations of the water molecules could not be adequately explained in terms of the H-bonding relationships present in the structure. However, additional investigations, which focused on the short range nonbonded contacts around water positions in a variety of crystal hydrates, revealed several structural regularities (Savage, 1986b). These features relate to the nonbonded O...O, H...O, and H...H interactions, and give rise to a set of repulsive restrictions that are seen to be very much stronger stereochemical restraints than those associated with H-bonding. The short-range restrictions appear largely to govern the local orientational correlations and packing arrangements of the water structure within the coenzyme (and other hydrate) crystals. In more general terms, the inclusion of the nonbonding relationships as well as the attractive H-bonding interactions, leads to a significant increase in our understanding of water structure(s). The repulsive restrictions can be used as stereochemical restraints in the interpretation and refinement of solvent structures within larger hydrate systems, such as protein crystals. They may also be included in potential functions used to simulate solvent structures in aqueous solutions and hydrate systems. PMID:3790697

Savage, H

1986-01-01

372

Self-Assembly of Colloidal Particles on Template Structures  

NASA Technical Reports Server (NTRS)

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.

Yodh, Arjun G.

2002-01-01

373

Identifying duplicate crystal structures: XTALCOMP, an open-source solution  

NASA Astrophysics Data System (ADS)

We describe the implementation of XTALCOMP, an efficient, reliable, and open-source library that tests if two crystal descriptions describe the same underlying structure. The algorithm has been tested and found to correctly identify duplicate structures in spite of the "real-world" difficulties that arise from working with numeric crystal representations: degenerate unit cell lattices, numerical noise, periodic boundaries, and the lack of a canonical coordinate origin. The library is portable, open, and not dependent on any external packages. A web interface to the algorithm is publicly accessible at http://xtalopt.openmolecules.net/xtalcomp/xtalcomp.html. Program summaryProgram title: XtalComp Catalogue identifier: AEKV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: "New" (3-clause) BSD [1] No. of lines in distributed program, including test data, etc.: 3148 No. of bytes in distributed program, including test data, etc.: 21 860 Distribution format: tar.gz Programming language: C++ Computer: No restrictions Operating system: All operating systems with a compliant C++ compiler. Classification: 7.8 Nature of problem: Computationally identifying duplicate crystal structures taken from the output of modern solid state calculations is a non-trivial exercise for many reasons. The translation vectors in the description are not unique — they may be transformed into linear combinations of themselves and continue to describe the same extended structure. The coordinates and cell parameters contain numerical noise. The periodic boundary conditions at the unit cell faces, edges, and corners can cause very small displacements of atomic coordinates to result in very different representations. The positions of all atoms may be uniformly translated by an arbitrary vector without modifying the underlying structure. Additionally, certain applications may consider enantiomorphic structures to be identical. Solution method: The XtalComp algorithm overcomes these issues to detect duplicate structures regardless of differences in representation. It begins by performing a Niggli reduction on the inputs, standardizing the translation vectors and orientations. A transform search is performed to identify candidate sets of rotations, reflections, and translations that potentially map the description of one crystal onto the other, solving the problems of enantiomorphs and rotationally degenerate lattices. The atomic positions resulting from each candidate transform are then compared, using a cell-expansion technique to remove periodic boundary issues. Computational noise is treated by comparing non-integer quantities using a specified tolerance. Running time: The test run provided takes less than a second to complete.

Lonie, David C.; Zurek, Eva

2012-03-01

374

Protein dynamics derived from clusters of crystal structures.  

PubMed Central

A method is presented to mathematically extract concerted structural transitions in proteins from collections of crystal structures. The "essential dynamics" procedure is used to filter out small-amplitude fluctuations from such a set of structures; the remaining large conformational changes describe motions such as those important for the uptake/release of substrate/ligand and in catalytic reactions. The method is applied to sets of x-ray structures for a number of proteins, and the results are compared with the results from essential dynamics as applied to molecular dynamics simulations of those proteins. A significant degree of similarity is found, thereby providing a direct experimental basis for the application of such simulations to the description of large concerted motions in proteins. Images FIGURE 1 PMID:9414203

van Aalten, D M; Conn, D A; de Groot, B L; Berendsen, H J; Findlay, J B; Amadei, A

1997-01-01

375

The crystal and molecular structure of triethanol-ammonium nitrate  

NASA Astrophysics Data System (ADS)

The liquid propellant used in the 155-mm regenerative liquid propellant gun is XM46. XM46 is a solution of 60 percent hydroxyl ammonium nitrate (HAN), 20 percent triethanolammonium nitrate (TEAN), and 20 percent water. This material exhibits rather unusual liquid properties that have been attributed to its being a 'molten eutectic' of fused salts rather than a normal aqueous solution of two different nitrate salts. A hydrogen-bonded liquid structure for eutectic LP1946 was proposed previously based on the known structures of neat HAN and water and a best-guess estimate of the TEAN structure. To verify this estimate, the molecular structure of neat TEAN was recently determined. This investigation revealed TEAN has very unusual and interesting bifurcated intermolecular and trifurcated intramolecular hydrogen bonding configurations within the crystal. If these hydrogen bonding configurations are retained in aqueous solution, they could be responsible in some part to the observed unusual liquid properties of liquid propellant XM46.

Bracuti, A. J.

1992-12-01

376

Crystal Structure of a Fructokinase Homolog from Halothermothrix orenii  

SciTech Connect

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.

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

2010-01-01

377

PROTEIN STRUCTURE REPORT Crystal structure of the protease-resistant core  

E-print Network

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

378

Integrable structure of melting crystal model with external potentials  

E-print Network

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

Toshio Nakatsu; Kanehisa Takasaki

2010-02-23

379

Morphology, crystal structure and hydration of calcined and modified anhydrite  

NASA Astrophysics Data System (ADS)

The effects of calcination and modification on the morphology (shapes and textures) and crystal structure of anhydrite powders were studied. The results show that, calcination at 100°C causes anhydrite to disintegrate into smaller crystals, accompanied by a slight increase in d-spacing. Without calcination and modification, the solidification time and curing time of anhydrite are 15 and 77 h, respectively. After the treatment, however, the solidification time and curing time are shortened significantly to 9.5 and 14 min, respectively. The compressive and flexural strengths of hydration products made from the treated anhydrite reach 10.2 and 2.0 MPa, respectively. The much shorter solidification and curing time make it possible to use anhydrite as a building and construction material.

Niu, Xiao-qing; Chen, Ji-chun

2014-10-01

380

Crystal structure of cesium aquanickelo(II)undecatungstophosphate dihydrate  

SciTech Connect

The title compound, Cs/sub 5/(PNi(H/sub 2/O)W/sub 11/O/sub 39/) x 2H/sub 2/O, is tetragonal with space group P4/sub 2//ncm and cell dimensions a = 20.908(5), c = 10.391(6) A. The single-crystal structure determination (diffractometer data, Mo radiation, R = 0.054 for 1484 unique reflexions) shows that two types of disorder are present; the Ni atom substituting for W in the parent ..cap alpha..-PW/sub 12/O/sub 40//sup 3 -/ anion is distributed equally over all twelve W sites and, in addition, the anion lies at a crystal site of symmetry 2/m in two equally weighted orientations related by the two-fold axis. The dimensions of the anion are normal.

Weakley, T.J. R.

1987-06-01

381

Crystal structure of jinshajiangite from the Norra Kaerr complex (Sweden)  

SciTech Connect

The structure of the mineral jinshajiangite from the Norra Kaerr alkaline complex (Sweden) was determined by single-crystal X-ray diffraction and refined to R = 6.7%. The monoclinic unit-cell parameters are a = 5.350(2) A, b = 6.909(6) A, c = 20.96(1) A, {beta} = 99.83(4){sup o}, sp. gr. P2/m. This mineral is an Fe-rich analogue of surkhobite and perraultite, but it crystallizes in a different space group, and the unit-cell parameters a and b are two times smaller than those of these two minerals. The framework of jinshajiangite from Norra Kaerr contains narrow and wide channels, which are occupied by Ca, Na, Ba, and K atoms in an ordered fashion.

Rastsvetaeva, R. K., E-mail: rast@ns.crys.ras.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Chukanov, N. V. [Russian Academy of Sciences, Institute of Problems of Chemical Physics in Chernogolovka (Russian Federation); Rozenberg, K. A. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

2008-07-15

382

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

E-print Network

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

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

2012-05-02

383

The crystal structure of superoxide dismutase from Plasmodium falciparum  

PubMed Central

Background Superoxide dismutases (SODs) are important enzymes in defence against oxidative stress. In Plasmodium falciparum, they may be expected to have special significance since part of the parasite life cycle is spent in red blood cells where the formation of reactive oxygen species is likely to be promoted by the products of haemoglobin breakdown. Thus, inhibitors of P. falciparum SODs have potential as anti-malarial compounds. As a step towards their development we have determined the crystal structure of the parasite's cytosolic iron superoxide dismutase. Results The cytosolic iron superoxide dismutase from P. falciparum (PfFeSOD) has been overexpressed in E. coli in a catalytically active form. Its crystal structure has been solved by molecular replacement and refined against data extending to 2.5 Å resolution. The structure reveals a two-domain organisation and an iron centre in which the metal is coordinated by three histidines, an aspartate and a solvent molecule. Consistent with ultracentrifugation analysis the enzyme is a dimer in which a hydrogen bonding lattice links the two active centres. Conclusion The tertiary structure of PfFeSOD is very similar to those of a number of other iron-and manganese-dependent superoxide dismutases, moreover the active site residues are conserved suggesting a common mechanism of action. Comparison of the dimer interfaces of PfFeSOD with the human manganese-dependent superoxide dismutase reveals a number of differences, which may underpin the design of parasite-selective superoxide dismutase inhibitors. PMID:17020617

Boucher, Ian W; Brzozowski, Andrzej M; Brannigan, James A; Schnick, Claudia; Smith, Derek J; Kyes, Sue A; Wilkinson, Anthony J

2006-01-01

384

Crystal Structure of the Japanese Encephalitis Virus Envelope Protein  

SciTech Connect

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.

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

2012-03-13

385

Syntheses and crystal structures of two new organically templated borates  

NASA Astrophysics Data System (ADS)

Two new organically templated borates, [H 3N(C 6H 10)NH 3][B 4O 5(OH) 4] (1) and [H 3N(C 6H 10)NH 3][B 5O 8(OH)] (2) have been synthesized in the presence of trans-1,4-diaminocyclohexane acting as a structure-directing agent under mild solvothermal conditions. The structures were determined by single crystal X-ray diffraction and further characterized by FTIR, elemental analysis and thermogravimetric analysis. Compound 1 crystallizes in the monoclinic system, space group C2/ c (No. 15), a=9.1325(3) Å, b=11.4869(3) Å, c=12.2756(5) Å, ?=105.258(6)°, V=1242.37(7) Å, Z=4. The structure contains supramolecular hydrogen-bonded network formed by isolated [B 4O 5(OH) 4] 2- polyanions. 2 is monoclinic, space group P2( 1)/ n (No. 14), a=6.5176(2) Å, b=16.8861(5) Å, c=11.1522(7) Å, ?=91.897(6)°, V=1226.70(9) Å, Z=4. The structure consists of layers of 3,9-membered boron rings constructed from pentaborate anion groups [B 5O 8(OH)] 2-. The adjacent borate layers are further linked with each other by hydrogen bond to form a 3D supramolecular network. It is the first example of layered borates templated by an organic amine.

Wang, Guo-Ming; Sun, Yan-Qiong; Yang, Guo-Yu

2004-12-01

386

Crystal Structure of Cruxrhodopsin-3 from Haloarcula vallismortis  

PubMed Central

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

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

2014-01-01

387

Crystal structure of thioltransferase at 2.2 A resolution.  

PubMed Central

We report here the first three-dimensional structure of a mammalian thioltransferase as determined by single crystal X-ray crystallography at 2.2 A resolution. The protein is known for its thiol-redox properties and dehydroascorbate reductase activity. Recombinant pig liver thioltransferase expressed in Escherichia coli was crystallized in its oxidized form by vapor diffusion technique. The structure was determined by multiple isomorphous replacement method using four heavy-atom derivatives. The protein folds into an alpha/beta structure with a four-stranded mixed beta-sheet in the core, flanked on either side by helices. The fold is similar to that found in other thiol-redox proteins, viz. E. coli thioredoxin and bacteriophage T4 glutaredoxin, and thus seems to be conserved in these functionally related proteins. The active site disulfide (Cys 22-Cys 25) is located on a protrusion on the molecular surface. Cys 22, which is known to have an abnormally low pKa of 3.8, is accessible from the exterior of the molecule. Pro 70, which is in close proximity to the disulfide bridge, assumes a conserved cis-peptide configuration. Mutational data available on the protein are in agreement with the three-dimensional structure. PMID:8535236

Katti, S. K.; Robbins, A. H.; Yang, Y.; Wells, W. W.

1995-01-01

388

Crystal structure of the human CSN6 MPN domain.  

PubMed

The mammalian COP9 signalosome is an eight-subunit (CSN1-CSN8) complex that plays essential roles in multiple cellular and physiological processes. CSN5 and CSN6 are the only two MPN (Mpr1-Pad1-N-terminal) domain-containing subunits in the complex. Unlike the CSN5 MPN domain, CSN6 lacks a metal-binding site and isopeptidase activity. Here, we report the crystal structure of the human CSN6 MPN domain. Each CSN6 monomer contains nine ? sheets surrounded by three helices. Two forms of dimers are observed in the crystal structure. Interestingly, a domain swapping of ?8 and ?9 strands occurs between two neighboring monomers to complete a typical MPN fold. Analyses of the pseudo metal-binding motif in CSN6 suggest that the loss of two key histidine residues may contribute to the lack of catalytic activity in CSN6. Comparing the MPN domain of our CSN6 with that in the CSN complex shows that apart from the different ?8-?9 conformation, they have minor conformational differences at two insertion regions (Ins-1 and Ins-2). Besides, the interacting mode of CSN6-CSN6 in our structure is distinct from that of CSN5-CSN6 in the CSN complex structure. Moreover, the functional implications for Ins-1 and Ins-2 are discussed. PMID:25242525

Ma, Xiao-li; Xu, Min; Jiang, Tao

2014-10-10

389

Diterbium hepta­nickel: a crystal structure redetermination  

PubMed Central

The crystal structure of the title compound, Tb2Ni7, was redetermined from single-crystal X-ray diffraction data. In comparison with previous studies based on powder X-ray diffraction data [Lemaire et al. (1967). C. R. Acad. Sci. Ser. B, 265, 1280–1282; Lemaire & Paccard (1969). Bull. Soc. Fr. Mineral. Cristallogr. 92, 9–16; Buschow & van der Goot (1970). J. Less-Common Met. 22, 419–428], the present redetermination affords refined coordinates and anisotropic displacement parameters for all atoms. A partial occupation for one Tb atom results in the non-stoichiometric composition Tb1.962?(4)Ni7. The title compound adopts the Ce2Ni7 structure type and can also be derived from the CaCu5 structure type as an inter­growth structure. The asymmetric unit contains two Tb sites (both site symmetries 3m.) and five Ni sites (.m., mm2, 3m., 3m., -3m.). The two different coordination polyhedra of Tb are a Frank–Kasper polyhedron formed by four Tb and 12 Ni atoms and a pseudo Frank–Kasper polyhedron formed by two Tb and 18 Ni atoms. The four different coordination polyhedra of Ni are Frank–Kasper icosa­hedra formed by five Tb and seven Ni atoms, four Tb and eight Ni atoms, three Tb and nine Ni atoms, and six Tb and six Ni atoms, respectively. PMID:25249871

Levytskyy, Volodymyr; Babizhetskyy, Volodymyr; Kotur, Bohdan; Smetana, Volodymyr

2014-01-01

390

Lithium-cation conductivity and crystal structure of lithium diphosphate  

SciTech Connect

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

Voronin, V.I., E-mail: voronin@imp.uran.ru [Institute of Metal Physics Urals Branch RAS, S.Kovalevskoy Street 18, 620041 Ekaterinburg (Russian Federation); Sherstobitova, E.A. [Institute of Metal Physics Urals Branch RAS, S.Kovalevskoy Street 18, 620041 Ekaterinburg (Russian Federation); Blatov, V.A., E-mail: blatov@samsu.ru [Samara Center for Theoretical Materials Science (SCTMS), Samara State University, Ac.Pavlov Street 1, 443011 Samara (Russian Federation); Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589 (Saudi Arabia); Shekhtman, G.Sh., E-mail: shekhtman@ihte.uran.ru [Institute of High Temperature Electrochemistry Urals Branch RAS, Akademicheskaya 20, 620990 Ekaterinburg (Russian Federation)

2014-03-15

391

Crystal and molecular structure of perindopril erbumine salt  

NASA Astrophysics Data System (ADS)

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 ? = 97.153(4), ? = 94.417(4), ? = 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.

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

2011-06-01

392

Crystal structures of hexakis-(2,6-di- O-methyl)-cyclomaltohexaose (dimethyl-?-cyclodextrin) crystallized from acetone, and crystallized from hot water  

Microsoft Academic Search

X-ray diffraction studies were carried out on hexakis-(2,6-di-O-methyl)-cyclomaltohexaose (dimethyl-?-cyclodextrin, DIMEA) crystallized at room temperature from solutions in pure acetone as the 1:1 inclusion complex, and crystallized from aqueous solution at 80 °C without water of hydration. In both crystal structures, the DIMEA molecules adopt a round shape stabilized by systematic intramolecular O-3?H … O-2 hydrogen bonds between neighbouring glucose units,

Thomas Steiner; Fumitoshi Hirayama; Wolfram Saenger

1996-01-01

393

Anomalous modal structure in a waveguide with a photonic crystal core  

E-print Network

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

Fan, Shanhui

394

PROBLEMS AND PROCEDURES IN COLLECTION OF THREE-DIMENSIONAL NEUTRON DIFFRACTION DATA FOR CRYSTAL STRUCTURE DETERMINATION  

E-print Network

FOR CRYSTAL STRUCTURE DETERMINATION By GEORGE M. BROWN and HENRI A. LEVY, Chemistry Division Oak Ridge data from the smaller crystals are chosen for structure refinement. For the other reflections, data for crystals of thirteen different compounds on the Oak Ridge automatic three-circle neutron diffractometer

Paris-Sud XI, Université de

395

Surface Structure of Zeolite (MFI) Crystals Isabel Diaz,, Efrosini Kokkoli, Osamu Terasaki, and Michael Tsapatsis*,  

E-print Network

Articles Surface Structure of Zeolite (MFI) Crystals Isabel Di´az,,§ Efrosini Kokkoli, Osamu type MFI) is an important zeolite that, in addition to conventional applications such as adsorption in studies of zeolite crystal growth. The surface structure of silicalite-1 crystals with two different

Kokkoli, Efie

396

STRUCTURE OF A HYBRID ALIGNBD CHOLESTERIC LIQUID CRYSTAL CELL I. DOZOV and I. PENCHEV  

E-print Network

373 STRUCTURE OF A HYBRID ALIGNBD CHOLESTERIC LIQUID CRYSTAL CELL I. DOZOV and I. PENCHEV Institute'un crystal liquide cholestérique est étu- diée expérimentalement et théoriquement. Pour des petites. Abstract.- The structure of a hybrid ali- gned cholesteric liquid crystal sample is investigated both

Boyer, Edmond

397

Optically bound particle structures in evanescent wave traps  

NASA Astrophysics Data System (ADS)

We present a study of the manipulation of microparticles and the formation of optically bound structures of particles in evanescent wave traps. Two trapping geometries are considered: the first is a surface trap where the evanescent field above a glass prism is formed by the interference of a number of laser beams incident on the prism-water interface; the second uses the evanescent field surrounding a biconical tapered optical fiber that has been stretched to produce a waist of submicron diameter. In the surface trap we observe optical binding of microparticles in to one-dimensional chain structures. In the tapered optical fiber trap we demonstrate both particle transport for long distances along the fiber, and the formation of stable arrays of particles. In both experiments we use video microscopy to track the particle locations and make quantitative measures of the particle dynamics. The experimental studies of particle structures are complemented by light scattering calculations based on Mie theory to infer how the geometries of the observed particle structures are controlled by the underlying incident and scattered optical fields.

Sergides, Marios; Skelton, Susan E.; Karczewska, Ewa; Thorneycroft, Kelly; Maragó, Onofrio M.; Jones, Philip H.

2012-10-01

398

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

NASA Technical Reports Server (NTRS)

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.

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

1995-01-01

399

Structure, Hydrodynamics, and Phase Transition of Freely Suspended Liquid Crystals  

NASA Technical Reports Server (NTRS)

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

Clark, Noel A.

2000-01-01

400

Crystal Structure of the Human Ephrin-A5 Ectodomain  

SciTech Connect

The Eph receptors, the largest subfamily of receptor tyrosine kinases, and their ephrin ligands are important mediators of cell-cell communication regulating cell attachment, pathfinding, and mobility in the nervous and cardiovascular systems. Recent structural studies have revealed unique molecular features that explain many of the biochemical and signaling properties of Ephs and ephrins. Nevertheless, open questions remain, including understanding the precise molecular mechanism underlining their binding-partner preferences and subclass specificity. In this study, we have determined and present the crystal structure of the extracellular domain of ephrin-A5--the first structure of an unbound A-class ephrin. The structure, determined at 2.1 Angstroms resolution, is a variation of the Greek key {beta}-barrel folding topology, containing eight {beta}-strands, and stabilized by two disulphide bonds. Overall, ephrin-A5 is structurally very similar to ephrin-B1 and ephrin-B2 but, unlike ephrin-B2, it does not show dimerization either in solution or in the crystals. Comparing free ephrin-A5 to the previously published structure of EphB2-bound ephrin-A5 reveals that significant conformational changes occur only around the G-H ephrin loop that upon binding bends toward the receptor. Interestingly, the G-H loop undergoes a very similar conformational rearrangement in ephrin-B2 upon receptor binding. The results of this study further emphasize the importance of the G-H loop for receptor recognition and selectivity, and could serve as a starting point for the development of structure-based Eph antagonists.

Nikolov,D.; Li, C.; Lackmann, M.; Jeffrey, P.; Himanen, J.

2007-01-01

401

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

PubMed

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

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

2015-02-10

402

Crystal structure and phase transitions in Sr3WO6.  

PubMed

The crystal structures of the beta and gamma polymorphs of Sr(3)WO(6) and the gamma<-->beta phase transition have been investigated using electron diffraction, synchrotron X-ray powder diffraction, and neutron powder diffraction. The gamma-Sr(3)WO(6) polymorph is stable above T(c) approximately 470 K and adopts a monoclinically distorted double perovskite A(2)BB'O(6) = Sr(2)SrWO(6) structure (space group Cc, a = 10.2363(1)A, b = 17.9007(1)A, c = 11.9717(1)A, beta = 125.585(1)(o) at T = 1373 K, Z = 12, corresponding to a = a(p) + 1/2b(p) - 1/2c(p), b = 3/2b(p) + 3/2c(p), c = -b(p) + c(p), a(p),b(p), c(p), lattice vectors of the parent Fm3m double perovskite structure). Upon cooling it undergoes a continuous phase transition into the triclinically distorted beta-Sr(3)WO(6) phase (space group C1, a = 10.09497(3)A, b = 17.64748(5)A, c = 11.81400(3)A, alpha = 89.5470(2)(o), beta = 125.4529(2)(o), gamma = 90.2889(2)(o) at T = 300 K). Both crystal structures of Sr(3)WO(6) belong to a family of double perovskites with broken corner sharing connectivity of the octahedral framework. A remarkable feature of the gamma-Sr(3)WO(6) structure is a non-cooperative rotation of the WO(6) octahedra. One third of the WO(6) octahedra are rotated by approximately 45 degrees about either the b(p) or the c(p) axis of the parent double perovskite structure. As a result, the WO(6) octahedra do not share corners but instead share edges with the coordination polyhedra of the Sr cations at the B positions increasing their coordination number from 6 to 7 or 8. The crystal structure of the beta-phase is very close to the structure of the gamma-phase; decreasing symmetry upon the gamma-->beta transformation occurs because of unequal octahedral rotation angles about the b(p) and c(p) axes and increasing distortions of the WO(6) octahedra. PMID:20527961

King, Graham; Abakumov, Artem M; Hadermann, J; Alekseeva, Anastasiya M; Rozova, Marina G; Perkisas, Tyche; Woodward, Patrick M; Van Tendeloo, Gustaaf; Antipov, Evgeny V

2010-07-01

403

Dynamics of colloidal particles in electrohydrodynamic convection of nematic liquid crystal  

NASA Astrophysics Data System (ADS)

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 103-104 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.

Takahashi, Kentaro; Kimura, Yasuyuki

2014-07-01

404

Germanium FCC structure from a colloidal crystal template  

SciTech Connect

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

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

2000-05-16

405

Tuning the self-assembled monolayer formation on nanoparticle surfaces with different curvatures: Investigations on spherical silica particles and plane-crystal-shaped zirconia particles  

PubMed Central

The ordering of dodecyl-chain self-assembled monolayers (SAM) on different nanoscopic surfaces was investigated by FT-IR studies. As model systems plane-crystal-shaped ZrO2 nanoparticles and spherical SiO2 nanoparticles were examined. The type of capping agent was chosen dependent on the substrate, therefore dodecylphosphonic acid and octadecylphosphonic acid were used for ZrO2 and dodecyltrimethoxysilane for SiO2 samples. The plane ZrO2 nanocrystals yielded more ordered alkyl-chain structures whereas spherical SiO2 nanoparticles showed significantly lower alkyl-chain ordering. Submicron-sized silica spheres revealed a significantly higher alkyl chain ordering, comparable to an analogously prepared SAM on a non-curved plane oxidized Si-wafer. In the case of ZrO2 nanocrystals an intense alkyl-chain alignment could be disturbed by decreasing the grafting density from the maximum of 2.1 molecules/nm2 through the variation of coupling agent concentration to lower values. Furthermore, the co-adsorption of a different coupling agent, such as phenylphosphonic acid for ZrO2 and phenyltrimethoxysilane for SiO2, resulted in a significantly lower alkyl-chain ordering for ZrO2 plane crystals and for large SiO2 spherical particles at high grafting density. An increasing amount of order-disturbing molecules leads to a gradual decrease in alkyl-chain alignment on the surface of the inorganic nanoparticles. In the case of the ZrO2 nanoparticle system it is shown via dynamic light scattering (DLS) that the mixed monolayer formation on the particle surface impacts the dispersion quality in organic solvents such as n-hexane. PMID:21549385

Feichtenschlager, Bernhard; Lomoschitz, Christoph J.; Kickelbick, Guido

2011-01-01

406

Characteristics and crystal structure of bacterial inosine-5'-monophosphate dehydrogenase.  

SciTech Connect

IMP dehydrogenase (IMPDH) is an essential enzyme that catalyzes the first step unique to GTP synthesis. To provide a basis for the evaluation of IMPDH inhibitors as antimicrobial agents, we have expressed and characterized IMPDH from the pathogenic bacterium Streptococcus pyogenes. Our results show that the biochemical and kinetic characteristics of S. pyogenes IMPDH are similar to other bacterial IMPDH enzymes. However, the lack of sensitivity to mycophenolic acid and the K{sub m} for NAD (1180 {mu}M) exemplify some of the differences between the bacterial and mammalian IMPDH enzymes, making it an attractive target for antimicrobial agents. To evaluate the basis for these differences, we determined the crystal structure of the bacterial enzyme at 1.9 {angstrom} with substrate bound in the catalytic site. The structure was determined using selenomethionine-substituted protein and multiwavelength anomalous (MAD) analysis of data obtained with synchrotron radiation from the undulator beamline (19ID) of the Structural Biology Center at Argonne's Advanced Photon Source. S. pyogenes IMPDH is a tetramer with its four subunits related by a crystallographic 4-fold axis. The protein is composed of two domains: a TIM barrel domain that embodies the catalytic framework and a cystathione {beta}-synthase (CBS) dimer domain of so far unknown function. Using information provided by sequence alignments and the crystal structure, we prepared several site-specific mutants to examine the role of various active site regions in catalysis. These variants implicate the active site flap as an essential catalytic element and indicate there are significant differences in the catalytic environment of bacterial and mammalian IMPDH enzymes. Comparison of the structure of bacterial IMPDH with the known partial structures from eukaryotic organisms will provide an explanation of their distinct properties and contribute to the design of specific bacterial IMPDH inhibitors.

Zhang, R.; Evans, G.; Rotella, F. J.; Westbrook, E. M.; Beno, D.; Huberman, E.; Joachimiak, A.; Collart, F. R.

1999-01-01

407

Applications of the particle-in-cell technique to liquid crystal optical devices  

NASA Astrophysics Data System (ADS)

For the first time we demonstrate the application of the particle-in-cell (PIC) technique in modeling liquid crystal (LC) optical devices. We apply the technique to a two-dimensional cell including splay and bend deformations. The simulation method is validated by comparing the numerical results with analytical theory of Fredericksz transition in a parallel-plate LC cell. The phenomenon of the Fredericksz transition and the formation and dynamics of defect walls in highly inhomogeneous electric fields are investigated, demonstrating the applicability of the technique for modeling the dynamic behavior of LC devices.

Singh, Nagendra; Leung, W. C.

1998-10-01

408

Synthesis of bulk nanostructured aluminum containing in situ crystallized amorphous particles  

NASA Astrophysics Data System (ADS)

5083 Al containing in situ crystallized Al85Ni10La 5 amorphous particles (10% and 20% in volume fraction) was synthesized through a powder metallurgy route consisting of cold isostatic pressing, degassing and hot extrusion. The nanostructured 5083 Al powders (grain size ˜28 nm) were produced through mechanical milling in liquid nitrogen. The Al 85Ni10La5 powders were produced via gas atomization using helium gas and the fraction in the size range of <500 mesh (<25 mum), which appeared to be fully amorphous on the basis of X-ray diffraction studies, was isolated for further investigation. The amorphous Al85Ni10La5 alloy exhibited a glass transition at ˜259°C (at a heating rate of 40°C/min) and nanoscale crystallites (< 100 nm) with an equiaxed morphology formed during the subsequent crystallization reactions. At temperatures higher than 283°C, only the equilibrium phases Al, Al3Ni and Al11La 3 were formed. An unusually high nucleation density (1021-22 /m3) was recorded in the crystallization process. The copious nucleation sites were rationalized from the presence of quenched-in Al nuclei, which were evidenced by isothermal calorimetric tracing (235°C) and a direct HRTEM observation of the amorphous Al85Ni10La 5 powders. The feasibility of preparation of nanocrystalline/amorphous particles via melt spinning followed by ball milling was also studied. In the as-extruded composites, the amorphous Al85Ni10 La5 particles underwent complete crystallization resulting in a grain size of 100 ˜ 200 nm; the 5083 Al matrix had a grain size around 200 nm in the fine-grained region interspersed by coarse-grained region with a grain size of 600 ˜ 1500 nm. A metallurgical bond formed between the 5083 Al matrix and Al85Ni10La5 particles showing a grain-boundary-like interface. The compressive fracture strength of the as-extruded 10% and 20% Al85Ni10La5 composites were determined to be 1025 MPa and 837 MPa, respectively. The influence of secondary processing, i.e., swaging, following extrusion on the mechanical behavior was also studied. The coarse grain formation in cryomilled 5083 Al during the thermomechanical process was discussed and it was evident that grain rotation and coalescence played an important role in the overall mechanism.

Zhang, Zhihui

409

Crystal structure of the yeast metacaspase Yca1.  

PubMed

Yca1, the only metacaspase in Saccharomyces cerevisiae, is thought to be a clan CD cysteine protease that includes the caspase subfamily. Although yeast is a single cell eukaryote, it can undergo a cell death process reminiscent of apoptosis. Yca1 has been reported to play an important role in the regulation of such apoptotic process. However, the structure and functional mechanism of Yca1 remain largely enigmatic. In this study, we report the crystal structure of the Yca1 metacaspase at 1.7 Å resolution, confirming a caspase-like fold. In sharp contrast to canonical caspases, however, Yca1 exists as a monomer both in solution and in the crystals. Canonical caspase contains six ?-strands, with strand ?6 pairing up with ?6 of another caspase molecule to form a homodimerization interface. In Yca1, an extra pair of antiparallel ?-strands forms a continuous ?-sheet with the six caspase-common ?-strands, blocking potential dimerization. Yca1 was reported to undergo autocatalytic processing in yeast; overexpression in bacteria also led to autoprocessing of Yca1 into two fragments. Unexpectedly, we found that both the autocatalytic processing and the proteolytic activity of Yca1 are greatly facilitated by the presence of calcium (Ca(2+)), but not other divalent cations. Our structural and biochemical characterization identifies Yca1 as a Ca(2+)-activated cysteine protease that may cleave specific substrates during stress response in yeast. PMID:22761449

Wong, Ada Hang-Heng; Yan, Chuangye; Shi, Yigong

2012-08-24

410

Phase-field-crystal methodology for modeling of structural transformations.  

PubMed

We introduce and characterize free-energy functionals for modeling of solids with different crystallographic symmetries within the phase-field-crystal methodology. The excess free energy responsible for the emergence of periodic phases is inspired by classical density-functional theory, but uses only a minimal description for the modes of the direct correlation function to preserve computational efficiency. We provide a detailed prescription for controlling the crystal structure and introduce parameters for changing temperature and surface energies, so that phase transformations between body-centered-cubic (bcc), face-centered-cubic (fcc), hexagonal-close-packed (hcp), and simple-cubic (sc) lattices can be studied. To illustrate the versatility of our free-energy functional, we compute the phase diagram for fcc-bcc-liquid coexistence in the temperature-density plane. We also demonstrate that our model can be extended to include hcp symmetry by dynamically simulating hcp-liquid coexistence from a seeded crystal nucleus. We further quantify the dependence of the elastic constants on the model control parameters in two and three dimensions, showing how the degree of elastic anisotropy can be tuned from the shape of the direct correlation functions. PMID:21517507

Greenwood, Michael; Rottler, Jörg; Provatas, Nikolas

2011-03-01

411

Crystal Structure and Cation Distribution in Freibergite and Tetrahedrite  

Microsoft Academic Search

The crystal structure of a freibergite (Ag- tetrahedrite) from Keno Hill, Yukon, Canada, and a tetrahedrite from Turquetil Lake, NWT, Canada, have been refined. The freibergite, CUS.84Ag4.22Fe1.59ZnO.43 Sb4.1oAso.13S13, a = 10.610(2) A, and the tetrahedrite, CU,O.24Fe,.Q3ZnO.97Ago.osSb3.66Aso.28S,3' a = 10.364(2) A, were both refined in space group 143m. The refinements confirm that Ag does occupy the threefold coordinated metal site as

R. C. Peterson; I. MILLER

1986-01-01

412

Crystal chemistry and structural design of iron-based superconductors  

NASA Astrophysics Data System (ADS)

The second class of high-temperature superconductors (HTSCs), iron-based pnictides and chalcogenides, necessarily contain Fe2X2 (“X" refers to a pnictogen or a chalcogen element) layers, just like the first class of HTSCs which possess the essential CuO2 sheets. So far, dozens of iron-based HTSCs, classified into nine groups, have been discovered. In this article, the crystal-chemistry aspects of the known iron-based superconductors are reviewed and summarized by employing “hard and soft acids and bases (HSAB)" concept. Based on these understandings, we propose an alternative route to exploring new iron-based superconductors via rational structural design.

Jiang, Hao; Sun, Yun-Lei; Xu, Zhu-An; Cao, Guang-Han

2013-08-01

413

Crystal structure of human platelet-derived growth factor BB.  

PubMed Central

The crystal structure of the homodimeric BB isoform of human recombinant platelet-derived growth factor (PDGF-BB) has been determined by X-ray analysis to 3.0 A resolution. The polypeptide chain is folded into two highly twisted antiparallel pairs of beta-strands and contains an unusual knotted arrangement of three intramolecular disulfide bonds. Dimerization leads to the clustering of three surface loops at each end of the elongated dimer, which most probably form the receptor recognition sites. Images PMID:1396586

Oefner, C; D'Arcy, A; Winkler, F K; Eggimann, B; Hosang, M

1992-01-01

414

The crystal structure of pyridinium hexafluoroantimonate(V  

E-print Network

in the antimony-fluorine bond distances, and because it was felt that a less symmetrical cation might induce some changes in the packing of the hexa fluoroantimonate(V) group due to hydrogen bonding or other weak interactions between cation and anion..., it was decided to carry out an analysis of the structure of pyridinium hexa- fluoroantimonate(V), (C&NH6) Sbp&. CHAPTER I I PREPARATION Crystals of pyridinium hexafluoroantimonate(V) were supplied by Mr. Albert C. Kunkle of the Department of Chemistry...

Copeland, Richard Franklin

1963-01-01

415

Structure and Dynamics of Freely Suspended Liquid Crystals  

NASA Technical Reports Server (NTRS)

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

Clark, Noel A.

2004-01-01

416

Structure of RCC1 chromatin factor bound to the nucleosome core particle  

PubMed Central

The small GTPase Ran enzyme regulates critical eukaryotic cellular functions including nuclear transport and mitosis through the creation of a RanGTP gradient around the chromosomes. This concentration gradient is created by the chromatin bound RCC1 (regulator of chromosome condensation) protein which recruits Ran to nucleosomes and activates Ran’s nucleotide exchange activity. While RCC1 has been shown to bind directly with the nucleosome, the molecular details of this interaction were not known. We have determined the crystal structure of the RCC1-nucleosome core particle complex at 2.9 Å resolution, providing the first atomic view of how a chromatin protein interacts with the histone and DNA components of the nucleosome. Our structure also suggests that the Widom 601 DNA positioning sequence present in our nucleosomes forms a 145 bp and not the expected canonical 147 bp nucleosome core particle. PMID:20739938

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

2011-01-01

417

Quick, large-area assembly of a single-crystal monolayer of spherical particles by unidirectional rubbing.  

PubMed

Rubbing a dry powder of particles in one direction between two rubbery substrates is found to be a quick and highly reproducible, yet inexpensive fabrication technique for assembling particle monolayers with perfect spatial registry on flat or curved surfaces. The optimum rubbing conditions - pressure and speed - for a single-crystal monolayer are shown to depend on particle size. Potential applications are in biosensors, photovoltaics, and light manipulators. PMID:24711205

Park, ChooJin; Lee, Taeil; Xia, Younan; Shin, Tae Joo; Myoung, Jaemin; Jeong, Unyong

2014-07-16

418

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

NASA Technical Reports Server (NTRS)

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

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

1994-01-01

419

Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: Photoconversion and signal transduction  

SciTech Connect

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

Yang, Xiaojing; Kuk, Jane; Moffat, Keith (UC)

2008-11-12

420

Structural, optical, mechanical and dielectric studies of pure and doped L-Prolinium Trichloroacetate single crystals  

NASA Astrophysics Data System (ADS)

In the present work, pure and metal substituted L-Prolinium trichloroacetate (LPTCA) single crystals were grown by slow evaporation method. The grown crystals were subjected to single crystal X-ray diffraction (XRD), powder X-ray diffraction, FTIR, UV-Visible-NIR, hardness, photoluminescence and dielectric studies. The dopant concentration in the crystals was measured by inductively coupled plasma (ICP) analysis. Single crystal X-ray diffraction studies of the pure and metal substituted LPTCA revealed that the grown crystals belong to the trigonal system. Ni2+ and Co2+ doping slightly altered the lattice parameters of LPTCA without affecting the basic structure of the crystal. FTIR spectral analysis confirms the presence of various functional groups in the grown crystals. The mechanical behavior of pure and doped crystals was analyzed by Vickers's microhardness test. The optical transmittance, dielectric and photoluminescence properties of the pure and doped crystals were analyzed.

Renuka, N.; Ramesh Babu, R.; Vijayan, N.; Vasanthakumar, Geetha; Krishna, Anuj; Ramamurthi, K.

2015-02-01

421

The introduction of structure types into the Inorganic Crystal Structure Database ICSD  

PubMed Central

Both the approach used and the progress made in the assignment of structure types to the crystal structures contained in the ICSD database are reported. Extending earlier work, an hierarchical set of criteria for the separation of isopointal structures into isoconfigurational structure types is used. It is shown how these criteria, which include the space group (number), Wyckoff sequence and Pearson symbol, c/a ratio, ? ranges, ANX formulae and, in certain cases, the necessary elements and forbidden elements, may be used to uniquely identify the representative structure types of the compounds contained in the ICSD database. PMID:17703075

Allmann, Rudolf; Hinek, Roland

2007-01-01

422

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

SciTech Connect

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

Pitscheider, Almut [Institut fuer Allgemeine, Anorganische und Theoretische Chemie, Leopold-Franzens-Universitaet Innsbruck, Innrain 52a, A-6020 Innsbruck (Austria); Kaindl, Reinhard [Institut fuer Mineralogie und Petrographie, Leopold-Franzens-Universitaet Innsbruck, Innrain 52, A-6020 Innsbruck (Austria); Oeckler, Oliver [Department Chemie, Ludwig-Maximilians-Universitaet Muenchen, Butenandtstrasse 5-13, D-81377 Muenchen (Germany); Huppertz, Hubert, E-mail: Hubert.Huppertz@uibk.ac.a [Institut fuer Allgemeine, Anorganische und Theoretische Chemie, Leopold-Franzens-Universitaet Innsbruck, Innrain 52a, A-6020 Innsbruck (Austria)

2011-01-15

423

Crystal structure of K[Hg(SCN)3] – a redetermination  

PubMed Central

The crystal structure of the room-temperature modification of K[Hg(SCN)3], potassium tri­thio­cyanato­mercurate(II), was redetermined based on modern CCD data. In comparison with the previous report [Zhdanov & Sanadze (1952 ?). Zh. Fiz. Khim. 26, 469–478], reliability factors, standard deviations of lattice parameters and atomic coordinates, as well as anisotropic displacement parameters, were revealed for all atoms. The higher precision and accuracy of the model is, for example, reflected by the Hg—S bond lengths of 2.3954?(11), 2.4481?(8) and 2.7653?(6)?Å in comparison with values of 2.24, 2.43 and 2.77?Å. All atoms in the crystal structure are located on mirror planes. The Hg2+ cation is surrounded by four S atoms in a seesaw shape [S—Hg—S angles range from 94.65?(2) to 154.06?(3)°]. The HgS4 polyhedra share a common S atom, building up chains extending parallel to [010]. All S atoms of the resulting 1 ?[HgS2/1S2/2] chains are also part of SCN? anions that link these chains with the K+ cations into a three-dimensional network. The K—N bond lengths of the distorted KN7 polyhedra lie between 2.926?(2) and 3.051?(3)?Å. PMID:25309170

Weil, Matthias; Häusler, Thomas

2014-01-01

424

Fundamental Particle Structure in the Cosmological Dark Matter  

NASA Astrophysics Data System (ADS)

The nonbaryonic dark matter of the universe is assumed to consist of new stable forms of matter. Their stability reflects symmetry of micro-world and mechanisms of its symmetry breaking. Particle candidates for cosmological dark matter are lightest particles that bear new conserved quantum numbers. Dark matter particles may represent ideal gas of noninteracting particles. Self-interacting dark matter weakly or superweakly coupled to ordinary matter is also possible, reflecting nontrivial pattern of particle symmetry in the hidden sector of particle theory. In the early universe the structure of particle symmetry breaking gives rise to cosmological phase transitions, from which macroscopic cosmological defects or primordial nonlinear structures can be originated. Primordial black holes (PBHs) can be not only a candidate for dark matter, but also represent a universal probe for superhigh energy physics in the early universe. Evaporating PBHs turn to be a source of even superweakly interacting particles, while clouds of massive PBHs can serve as nonlinear seeds for galaxy formation. The observed broken symmetry of the three known families may provide a simultaneous solution for the problems of the mass of neutrino and strong CP-violation in the unique framework of models of horizontal unification. Dark matter candidates can also appear in the new families of quarks and leptons and the existence of new stable charged leptons and quarks is possible, hidden in elusive "dark atoms." Such possibility, strongly restricted by the constraints on anomalous isotopes of light elements, is not excluded in scenarios that predict stable double charged particles. The excessive -2 charged particles are bound in these scenarios with primordial helium in O-helium "atoms," maintaining specific nuclear-interacting form of the dark matter, which may provide an interesting solution for the puzzles of the direct dark matter searches. In the context of cosmoparticle physics, studying fundamental relationship of micro- and macro-worlds, the problem of cosmological dark matter implies cross disciplinary theoretical, experimental and observational studies for its solution.

Khlopov, Maxim

2013-11-01

425

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

PubMed

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

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

2015-01-01

426

Crystal structure of the multifunctional G?5–RGS9 complex  

PubMed Central

Regulators of G-protein signaling (RGS) proteins enhance the intrinsic GTPase activity of G protein ? (G?) subunits and are vital for proper signaling kinetics downstream of G protein–coupled receptors (GPCRs). R7 subfamily RGS proteins specifically and obligately dimerize with the atypical G protein ?5 (G?5) subunit through an internal G protein ? (G?)-subunit–like (GGL) domain. Here we present the 1.95-Å crystal structure of the G?5–RGS9 complex, which is essential for normal visual and neuronal signal transduction. This structure reveals a canonical RGS domain that is functionally integrated within a molecular complex that is poised for integration of multiple steps during G-protein activation and deactivation. PMID:18204463

Cheever, Matthew L; Snyder, Jason T; Gershburg, Svetlana; Siderovski, David P; Harden, T Kendall; Sondek, John

2009-01-01

427

Crystal structure of Hg2SO4 – a redetermination  

PubMed Central

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

Weil, Matthias

2014-01-01

428

Crystal structure of the bacterial nucleoside transporter Tsx  

PubMed Central

Tsx is a nucleoside-specific outer membrane (OM) transporter of Gram-negative bacteria. We present crystal structures of Escherichia coli Tsx in the absence and presence of nucleosides. These structures provide a mechanism for nucleoside transport across the bacterial OM. Tsx forms a monomeric, 12-stranded ?-barrel with a long and narrow channel spanning the outer membrane. The channel, which is shaped like a keyhole, contains several distinct nucleoside-binding sites, two of which are well defined. The base moiety of the nucleoside is located in the narrow part of the keyhole, while the sugar occupies the wider opening. Pairs of aromatic residues and flanking ionizable residues are involved in nucleoside binding. Nucleoside transport presumably occurs by diffusion from one binding site to the next. PMID:15272310

Ye, Jiqing; van den Berg, Bert

2004-01-01

429

Crystal Structure of a Phosphorylation-coupled Saccharide Transporter  

SciTech Connect

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

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

2011-12-31

430

Hierarchical structures of ZnO spherical particles synthesized solvothermally  

NASA Astrophysics Data System (ADS)

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.

Saito, Noriko; Haneda, Hajime

2011-12-01

431

Crystal structure of sucrose phosphorylase from Bifidobacterium adolescentis.  

PubMed

Around 80 enzymes are implicated in the generic starch and sucrose pathways. One of these enzymes is sucrose phosphorylase, which reversibly catalyzes the conversion of sucrose and orthophosphate to d-Fructose and alpha-d-glucose 1-phosphate. Here, we present the crystal structure of sucrose phosphorylase from Bifidobacterium adolescentis (BiSP) refined at 1.77 A resolution. It represents the first 3D structure of a sucrose phosphorylase and is the first structure of a phosphate-dependent enzyme from the glycoside hydrolase family 13. The structure of BiSP is composed of the four domains A, B, B', and C. Domain A comprises the (beta/alpha)(8)-barrel common to family 13. The catalytic active-site residues (Asp192 and Glu232) are located at the tips of beta-sheets 4 and 5 in the (beta/alpha)(8)-barrel, as required for family 13 members. The topology of the B' domain disfavors oligosaccharide binding and reduces the size of the substrate access channel compared to other family 13 members, underlining the role of this domain in modulating the function of these enzymes. It is remarkable that the fold of the C domain is not observed in any other known hydrolases of family 13. BiSP was found as a homodimer in the crystal, and a dimer contact surface area of 960 A(2) per monomer was calculated. The majority of the interactions are confined to the two B domains, but interactions between the loop 8 regions of the two barrels are also observed. This results in a large cavity in the dimer, including the entrance to the two active sites. PMID:14756551

Sprogøe, Desiree; van den Broek, Lambertus A M; Mirza, Osman; Kastrup, Jette S; Voragen, Alphons G J; Gajhede, Michael; Skov, Lars K

2004-02-10

432

Structure of HDL: Particle Subclasses and Molecular Components.  

PubMed

A molecular understanding of high-density lipoprotein (HDL) will allow a more complete grasp of its interactions with key plasma remodelling factors and with cell-surface proteins that mediate HDL assembly and clearance. However, these particles are notoriously heterogeneous in terms of almost every physical, chemical and biological property. Furthermore, HDL particles have not lent themselves to high-resolution structural study through mainstream techniques like nuclear magnetic resonance and X-ray crystallography; investigators have therefore had to use a series of lower resolution methods to derive a general structural understanding of these enigmatic particles. This chapter reviews current knowledge of the composition, structure and heterogeneity of human plasma HDL. The multifaceted composition of the HDL proteome, the multiple major protein isoforms involving translational and posttranslational modifications, the rapidly expanding knowledge of the HDL lipidome, the highly complex world of HDL subclasses and putative models of HDL particle structure are extensively discussed. A brief history of structural studies of both plasma-derived and recombinant forms of HDL is presented with a focus on detailed structural models that have been derived from a range of techniques spanning mass spectrometry to molecular dynamics. PMID:25522985

Kontush, Anatol; Lindahl, Mats; Lhomme, Marie; Calabresi, Laura; Chapman, M John; Davidson, W Sean

2015-01-01

433

Slow encounters of particle pairs in branched structures  

NASA Astrophysics Data System (ADS)

On infinite homogeneous structures, two random walkers meet with certainty if and only if the structure is recurrent; i.e., a single random walker returns to its starting point with probability 1. However, on general inhomogeneous structures this property does not hold, and, although a single random walker will certainly return to its starting point, two moving particles may never meet. This striking property has been shown to hold, for instance, on infinite combs. Due to the huge variety of natural phenomena which can be modeled in terms of encounters between two (or more) particles diffusing in comblike structures, it is fundamental to investigate if and, if so, to what extent similar effects may take place in finite structures. By means of numerical simulations we provide evidence that, indeed, even on finite structures, the topological inhomogeneity can qualitatively affect the two-particle problem. In particular, the mean encounter time can be polynomially larger than the time expected from the related one-particle problem.

Agliari, Elena; Blumen, Alexander; Cassi, Davide

2014-05-01

434

The crystal structure of NlpI A prokaryotic tetratricopeptide repeat protein with a globular fold  

E-print Network

The crystal structure of NlpI A prokaryotic tetratricopeptide repeat protein with a globular fold-dimensional structure of a globular protein. The NlpI struc- ture is also the first TPR structure from a prokaryote

Mochrie, Simon

435

Oxide Thermoelectrics: The Role of Crystal Structure on Thermopower in Strongly Correlated Spinels  

E-print Network

Oxide Thermoelectrics: The Role of Crystal Structure on Thermopower in Strongly Correlated Spinels Structure on Thermopower in Strongly Correlated Spinels Abstract This dissertation reports on the synthesis of strongly correlated spinels. General structure property relationships for electrical and thermal transport

Sparks, Taylor D.

436

Crystal structure of human cystatin C stabilized against amyloid formation.  

PubMed

Human cystatin C (HCC) is a family 2 cystatin inhibitor of papain-like (C1) and legumain-related (C13) cysteine proteases. In pathophysiological processes, the nature of which is not understood, HCC is codeposited in the amyloid plaques of Alzheimer's disease or Down's syndrome. The amyloidogenic properties of HCC are greatly increased in a naturally occurring L68Q variant, resulting in fatal cerebral amyloid angiopathy in early adult life. In all crystal structures of cystatin C studied to date, the protein has been found to form 3D domain-swapped dimers, created through a conformational change of a beta-hairpin loop, L1, from the papain-binding epitope. We have created monomer-stabilized human cystatin C, with an engineered disulfide bond (L47C)-(G69C) between the structural elements that become separated upon domain swapping. The mutant has drastically reduced dimerization and fibril formation properties, but its inhibition of papain is unaltered. The structure confirms the success of the protein engineering experiment to abolish 3D domain swapping and, in consequence, amyloid fibril formation. It illustrates for the first time the fold of monomeric cystatin C and allows verification of earlier predictions based on the domain-swapped forms and on the structure of chicken cystatin. Importantly, the structure defines the so-far unknown conformation of loop L1, which is essential for the inhibition of papain-like cysteine proteases. PMID:20175878

Kolodziejczyk, Robert; Michalska, Karolina; Hernandez-Santoyo, Alejandra; Wahlbom, Maria; Grubb, Anders; Jaskolski, Mariusz

2010-04-01

437

Crystal structure of lipoprotein GNA1946 from Neisseria meningitidis.  

PubMed

GNA1946, a conserved outer membrane lipoprotein from Neisseria meningitidis, has been identified as a candidate antigen for an urgently needed broad-spectrum meningococcal vaccine. It has been predicted to be a periplasmic receptor in the D-methionine uptake ABC transporter system. The crystal structure of GNA1946 was solved by the single-wavelength anomalous dispersion (SAD) method to a resolution of 2.25 A, and it reveals a Venus flytrap-like structure. GNA1946 consists of two globular lobes connected by a hinge region. Surprisingly, the structure showed an L-methionine bound within the cleft between the lobes. A comparison of GNA1946 with two other outer membrane lipoproteins, the L-methionine-binding Tp32 from Treponema pallidum and the dipeptide GlyMet-binding protein Pg110 from Staphylococcus aureus, revealed that although these three proteins share low sequence similarities, there is a high degree of structural conservation and similar substrate-binding frameworks. Our results reveal that GNA1946 is an L-methionine binding lipoprotein in the outer membrane, and should function as an initial receptor for ABC transporters with high affinity and specificity. The GNA1946 structure reported here should provide a valuable starting point for the development of a broad-spectrum meningococcal vaccine. PMID:19733245

Yang, Xue; Wu, Zhenhua; Wang, Xiangyu; Yang, Chunting; Xu, Honglin; Shen, Yuequan

2009-12-01

438

A computational tool to design and generate crystal structures  

NASA Astrophysics Data System (ADS)

The evolution of computers, more specifically regarding the increased storage and data processing capacity, allowed the construction of computational tools for the simulation of physical and chemical phenomena. Thus, practical experiments are being replaced, in some cases, by computational ones. In this context, we can highlight models used to simulate different phenomena on atomic scale. The construction of these simulators requires, by developers, the study and definition of accurate and reliable models. This complexity is often reflected in the construction of complex simulators, which simulate a limited group of structures. Such structures are sometimes expressed in a fixed manner using a limited set of geometric shapes. This work proposes a computational tool that aims to generate a set of crystal structures. The proposed tool consists of a) a programming language, which is used to describe the structures using for this purpose their characteristic functions and CSG (Constructive Solid Geometry) operators, and b) a compiler/interpreter that examines the source code written in the proposed language, and generates the objects accordingly. This tool enables the generation of an unrestricted number of structures, which can be incorporated in simulators such as the Monte Carlo Spin Engine, developed by our group at UFJF.

Ferreira, R. C.; Vieira, M. B.; Dantas, S. O.; Lobosco, M.

2014-03-01

439

SHELXT – Integrated space-group and crystal-structure determination  

PubMed Central

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

Sheldrick, George M.

2015-01-01

440

Crystal Structure of Arginine Methyltransferase 6 from Trypanosoma brucei  

PubMed Central

Arginine methylation plays vital roles in the cellular functions of the protozoan Trypanosoma brucei. The T. brucei arginine methyltransferase 6 (TbPRMT6) is a type I arginine methyltransferase homologous to human PRMT6. In this study, we report the crystal structures of apo-TbPRMT6 and its complex with the reaction product S-adenosyl-homocysteine (SAH). The structure of apo-TbPRMT6 displays several features that are different from those of type I PRMTs that were structurally characterized previously, including four stretches of insertion, the absence of strand ?15, and a distinct dimerization arm. The comparison of the apo-TbPRMT6 and SAH-TbPRMT6 structures revealed the fine rearrangements in the active site upon SAH binding. The isothermal titration calorimetry results demonstrated that SAH binding greatly increases the affinity of TbPRMT6 to a substrate peptide derived from bovine histone H4. The western blotting and mass spectrometry results revealed that TbPRMT6 methylates bovine histone H4 tail at arginine 3 but cannot methylate several T. brucei histone tails. In summary, our results highlight the structural differences between TbPRMT6 and other type I PRMTs and reveal that the active site rearrangement upon SAH binding is important for the substrate binding of TbPRMT6. PMID:24498306

Chen, Jiajia; Li, Xu; Peng, Junhui; Chen, Jiajing; Zou, Yang; Zhang, Zhiyong; Jin, Hong; Yang, Pengyuan; Wu, Jihui; Niu, Liwen; Gong, Qingguo; Teng, Maikun; Shi, Yunyu

2014-01-01

441

Orientational glass in mixtures of elliptic and circular particles: structural heterogeneities, rotational dynamics, and rheology.  

PubMed

Using molecular dynamics simulation with an angle-dependent Lennard-Jones potential, we study orientational glass with quadrupolar symmetry in mixtures of elliptic particles and circular impurities in two dimensions. With a mild aspect ratio (= 1.23) and a mild size ratio (= 1.2), we realize a plastic crystal at relatively high temperature T. With further lowering T, we find a structural phase transition for very small impurity concentration c and pinned disordered orientations for not small c. The ellipses are anchored by the impurities in the planar alignment. With increasing c, the orientation domains composed of isosceles triangles gradually become smaller, resulting in orientational glass with crystal order. In our simulation, the impurity distribution becomes heterogeneous during quenching from liquid, which then produces rotational dynamic heterogeneities. We also examine rheology in orientational glass to predict a shape memory effect and a superelasticity effect, where a large fraction of the strain is due to collective orientation changes. PMID:25353473

Takae, Kyohei; Onuki, Akira

2014-02-01

442

Ellman's reagent in promoting crystallization and structure determination of Anabaena CcbP.  

PubMed

Obtaining crystals presented a bottleneck in the structural study of Anabaena cyanobacterial Ca2+-binding protein (CcbP). In this report, the promoting effect of Ellman's reagent [5,5'-dithiobis(2-nitrobenzoic acid); DTNB] on the crystallization of CcbP is described. CcbP contains one free cysteine. A quick and simple oxidation reaction with DTNB blocked the free cysteine in purified CcbP and generated a homogenous monomeric protein for crystallization. The crystal structure of DTNB-modified CcbP was determined by the single-wavelength anomalous diffraction method. Structure analysis indicated that DTNB modification facilitated crystallization of CcbP by inducing polar interactions in the crystal lattice. DTNB-mediated cysteine modification was demonstrated to have little effect on the overall structure and the Ca2+ binding of CcbP. Thus, DTNB modification may provide a simple and general approach for protein modifi