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1

Magnetic assembly of nonmagnetic particles into photonic crystal structures.  

PubMed

We report the rapid formation of photonic crystal structures by assembly of uniform nonmagnetic colloidal particles in ferrofluids using external magnetic fields. Magnetic manipulation of nonmagnetic particles with size down to a few hundred nanometers, suitable building blocks for producing photonic crystals with band gaps located in the visible regime, has been difficult due to their weak magnetic dipole moment. Increasing the dipole moment of magnetic holes has been limited by the instability of ferrofluids toward aggregation at high concentration or under strong magnetic field. By taking advantage of the superior stability of highly surface-charged magnetite nanocrystal-based ferrofluids, in this paper we have been able to successfully assemble 185 nm nonmagnetic polymer beads into photonic crystal structures, from 1D chains to 3D assemblies as determined by the interplay of magnetic dipole force and packing force. In a strong magnetic field with large field gradient, 3D photonic crystals with high reflectance (83%) in the visible range can be rapidly produced within several minutes, making this general strategy promising for fast creation of large-area photonic crystals using nonmagnetic particles as building blocks. PMID:20945882

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

2010-11-10

2

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

Microsoft Academic Search

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

Ling Li; Keqiong Ye

2006-01-01

3

Fabrication of three-dimensional terahertz photonic crystals with diamond structure by particle manipulation assembly  

NASA Astrophysics Data System (ADS)

We reported the fabrication of terahertz photonic crystals by three-dimensional (3D) particle manipulation assembly. Our method, which is based on pick-and-place manipulation and interparticle laser welding, enabled accurate assembling of an arbitrary 3D structure, regardless of particle polydispersity. By using this method, we fabricated a diamond crystal from ZrO2/polyethylene composite particles (diameter of 400 ?m). The obtained crystal exhibited a photonic stop gap in the ?111? direction; this result was in good agreement with the theoretical result, suggesting that the crystal has a full photonic bandgap at around 0.2 THz.

Takagi, Kenta; Kawasaki, Akira

2009-01-01

4

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

PubMed

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

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

2001-10-21

5

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 BaTiO 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

6

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

7

Crystal structures of nucleosome core particles containing the '601' strong positioning sequence.  

PubMed

Nucleosome positioning plays a key role in genomic regulation by defining histone-DNA context and by modulating access to specific sites. Moreover, the histone-DNA register influences the double-helix structure, which in turn can affect the association of small molecules and protein factors. Analysis of genomic and synthetic DNA has revealed sequence motifs that direct nucleosome positioning in vitro; thus, establishing the basis for the DNA sequence dependence of positioning would shed light on the mechanics of the double helix and its contribution to chromatin structure in vivo. However, acquisition of well-diffracting nucleosome core particle (NCP) crystals is extremely dependent on the DNA fragment used for assembly, and all previous NCP crystal structures have been based on human ?-satellite sequences. Here, we describe the crystal structures of Xenopus NCPs containing one of the strongest known histone octamer binding and positioning sequences, the so-called '601' DNA. Two distinct 145-bp 601 crystal forms display the same histone-DNA register, which coincides with the occurrence of DNA stretching-overtwisting in both halves of the particle around five double-helical turns from the nucleosome center, giving the DNA an 'effective length' of 147 bp. As we have found previously with stretching around two turns from the nucleosome center for a centromere-based sequence, the terminal stretching observed in the 601 constructs is associated with extreme kinking into the minor groove at purine-purine (pyrimidine-pyrimidine) dinucleotide steps. In other contexts, these step types display an overall nonflexible behavior, which raises the possibility that DNA stretching in the nucleosome or extreme distortions in general have unique sequence dependency characteristics. Our findings indicate that DNA stretching is an intrinsically predisposed site-specific property of the nucleosome and suggest how NCP crystal structures with diverse DNA sequences can be obtained. PMID:20800598

Vasudevan, Dileep; Chua, Eugene Y D; Davey, Curt A

2010-10-15

8

Effects of particle morphology and crystal structure on the microwave properties of flake-like nanocrystalline Fe 3Co 2 particles  

Microsoft Academic Search

Flake-like nanocrystalline Fe3Co2 powders synthesized by mechanical alloying have been studied by morphological, structural and magnetic measurements, and compared with sphere-like samples. Complex permeability (?r=??r?i??r) and permittivity (?r=??r?i??r) was measured in microwave range of frequency (218GHz). Combined with the nature of nanostructure and the dynamics of magnetism, the particle morphology and crystal structure dependence of microwave properties for nanocrystalline particles

P. H. Zhou; L. J. Deng; J. L. Xie; D. F. Liang

2008-01-01

9

Colloidal Particles at Chiral Liquid Crystal Interfaces  

E-print Network

Colloidal particles trapped at an interface between two fluids can form a wide range of different structures. Replacing one of the fluid with a liquid crystal increases the complexity of interactions and results in a greater range of possible structures. New behaviour emerges when colloidal particles interact with defects in the liquid crystal phases. Here we discuss the templating of colloids at a cholesteric isotropic interface.

Anne Claire Pawsey; Juho Lintuvuori

2014-03-19

10

Inflammasome Activation by Pathogenic Crystals and Particles  

Microsoft Academic Search

\\u000a The NLRP3 inflammasome is a multiprotein complex that controls processing and secretion of bioactive IL-1? and IL-18, powerful\\u000a proinflammatory cytokines involved in several human diseases. The NLRP3 inflammasome is activated by pathogens, danger signals\\u000a released by necrotic cells, and crystals and particles of varied size and structure. These inflammasome-activating particles\\u000a have a causative role in human diseases such as gout,

Fabio Re

11

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

PubMed Central

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

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

2010-01-01

12

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

13

Random Dielectric Photonic Structures for Accelerating Particles  

Microsoft Academic Search

We investigate the applicability of random dielectric photonic structures to particle acceleration. Electromagnetic waves trapped within photonic crystal cavities can be used to accelerate charged particles. Whereas metallic cavities support higher harmonics, cavities in dielectric photonic crystals limit trapped oscillations to a frequency range within the bandgap of the surrounding crystal. This allows the cavity to contain only one frequency

C. A. Bauer; J. R. Cary; G. R. Werner

2006-01-01

14

Crystal Structures as Geobarometers  

NSDL National Science Digital Library

This exercise is based on the recent formulation of a geobarometer based on the crystal structure of clinopyroxene (Nimis, 1995; 1998; 1999). This method relates structural parameters (e.g., the volumes of the unit cell and the M1 polyhedron) to the pressure at which the mineral crystallizes within basic and ultrabasic magmas. students are guided into the American Mineralogist Crystal Structure Database to retrieve and download published crystal structure data for viewing in either the CrystalMaker or Xtaldraw visualization software packages. students are instructed on how to examine the structures to determine pressure-sensitive crystallographic parameters students are then asked a series of questions related to what they learn.

Ratajeski, Kent

15

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

16

Teaching With Crystal Structures  

NSDL National Science Digital Library

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 periodi

Smithenry, Dennis W.

2009-09-01

17

Olivine Crystal Structure  

NSDL National Science Digital Library

This exercise is based on recent crystallographic research on the olivine crystal structure published by Redfern et al. (2000). The authors of this study synthesized Fa50 olivine olivine (MgFeSiO4) in an experimental apparatus at temperatures ranging from 100 to 1250 °C, quenched the experiments, and used in situ neutron powder diffraction techniques to investigate changes in the synthesized olivines as a function of temperature. While this study reports cutting-edge materials research carried out with the latest crystallographic techniques, the results are educationally instructive and illustrate important concepts normally covered in an undergraduate mineralogy course. In this exercise, students are guided into the American Mineralogist Crystal Structure Database to retrieve and download published crystal structure data for viewing in either the CrystalMaker or XtalDraw visualization software packages. The students are instructed on how to manipulate the structures and are asked to plot some of the crystallographic data from this study on graphs using a spreadsheet program such as Excel.

Ratajeski, Kent

18

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

19

MODELLING AND ANALYSIS OF PARTICLE FORMATION DURING AGGLOMERATIVE CRYSTAL PRECIPITATION PROCESSES  

Microsoft Academic Search

While nucleation and crystal growth are normally considered to be the primary particle formation processes during industrial crystallization, secondary processes including crystal agglomeration and breakage can have a determining effect on product form, especially of precipitates. In addition to the usual overall size distribution, primary and secondary particle size, particle structure and morphology then become important characteristics affecting both product

ALAN G. JONES; JIRI HOSTOMSK; SHUN WACH

1996-01-01

20

The crystallization of small particles and droplets  

NASA Technical Reports Server (NTRS)

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

Weinberg, M. C.

1985-01-01

21

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.

22

New particle ID detector for Crystal  

E-print Network

MWPC Chambers PMTs MWPC=133mm 500mm PMT support ring beam · PID-II ­ removable! (redesigned MWPCNew particle ID detector for Crystal Ball at MAMI-C Daniel Watts, University of Edinburgh John ¡ · Good separation of p, with little overhead in material before MWPC and CB detectors PID-I #12;MWPC

Edinburgh, University of

23

Transport of Particles in Liquid Crystals  

E-print Network

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.

Oleg D. Lavrentovich

2013-11-26

24

Crystal Structure Lab  

NSDL National Science Digital Library

This activity is concerned with crystals, the basic building units that make up rocks and minerals. Students construct a model of the silicon-oxygen tetrahedron and discover that the smallest whole unit that could form a unique crystal is called a unit cell. They learn that a unit cell would have all the properties of a large crystal such as a diamond, but would be only molecular size (submicroscopic). If a crystal starts to form from a slowly cooling magma or from a drying up pool of salty sea water, unit cells add themselves one on top of another in order to develop the large crystals we can see and handle.

Fetcho, Ray

25

Directed Discovery of Crystal Structures  

NSDL National Science Digital Library

This contribution is modified from a published exercise "Directed Discovery of Crystal Structures Using Ball-and-Stick Models" [Mogk, 1997] . While the published exercise is based on student exploration of traditional ball-and-stick models of crystal structures, this modified version uses a similar "discovery-based" approach and the latest online crystallographic information and visualization software to teach the spatial relationships and crystal-chemical rules that govern the crystal structures of common minerals and crystalline solids. A few changes in the content have been made from the published exercise, mainly to accommodate the new digital media.

Mogk, Dave; Ratajeski, Kent

26

Crystal Structure in Nematic Emulsion  

SciTech Connect

We describe the experimental observation of a crystal structure formed by glycerol droplets suspended in a nematic liquid crystal. The structure exhibits a high density hexagonal ordering. We have experimentally observed a noticeable interaction between droplets with tangential boundary conditions. Within the scope of known models we discuss the nature of appropriate mechanisms of the interaction.

Nazarenko, V. G.; Nych, A. B.; Lev, B. I.

2001-08-13

27

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 Bialk; Thomas Speck; Hartmut Lwen

2011-12-22

28

Three-Dimensional Photonic Crystal Laser-Driven Accelerator Structures  

SciTech Connect

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

Cowan, B.; /SLAC

2006-09-07

29

Reliable and Highly Accurate Molecular Crystal Structures  

E-print Network

Dispersion-corrected DFT (DFT-D) #12;Reproduction of Crystal Structures 225 "organic only" crystal structures. B66, 544-558 #12;Reproduction of Crystal Structures 225 "organic only" crystal structures from Minimised Experimental #12;What about Wrong Structures? Unit cell free Acta Cryst. E test set No H

Magee, Joseph W.

30

Structural studies of orbivirus particles.  

PubMed

We are using crystallographic methods to investigate the structure of AHSV and BTV. Our initial approach was to investigate the structure of the major protein component of the viral core, VP7(T13). This trimeric protein has been studied in several crystal forms from both orbiviruses and reveals a structure made up of conserved domains, capable of conformational changes and possessing a cleavage site. Further crystallographic analyses of native particles have provided a picture of the VP7(T13) and VP3(T2) layers of the BTV core. The VP7(T13) layer consists of 260 trimers arranged rather symmetrically and possessing very similar structures, thereby following the rules of quasi equivalence. The VP3(T2) layer is thin and contains 120 copies of 100 kDa protein arranged as 60 approximate dimers. This type of icosahedral construction has not been observed before and appears to contain a genome which is highly ordered. We anticipate that all of these features will be common to AHSV. PMID:9785510

Stuart, D I; Gouet, P; Grimes, J; Malby, R; Diprose, J; Zientara, S; Burroughs, J N; Mertens, P P

1998-01-01

31

Crystal structure of triclopyr  

PubMed Central

In the title compound {systematic name: 2-[(3,5,6-trichloropyridin-2-yl)oxy]acetic acid}, the herbicide triclopyr, C7H4Cl3NO3, the asymmetric unit comprises two independent molecules in which the dihedral angles between the mean plane of the carboxylic acid group and the pyridyl ring plane are 79.3?(6) and 83.8?(5). In the crystal, pairs of intermolecular OH?O hydrogen bonds form dimers through an R 2 2(8) ring motif and are extended into chains along [100] by weak ?? interactions [ring centroid separations = 3.799?(4) and 3.810?(4)?]. In addition, short intermolecular Cl?Cl contacts [3.458?(2)?] connect the chains, yielding a two-dimensional architecture extending parallel to (020). The crystal studied was found to be non-merohedrally twinned with the minor component being 0.175?(4).

Cho, Seonghwa; Kim, Jineun; Jeon, Youngeun; Kim, Tae Ho

2014-01-01

32

Crystal structure of anilazine  

PubMed Central

The title compound [systematic name: 4,6-dichloro-N-(2-chlorophenyl)-1,3,5-triazin-2-amine], C9H5Cl3N4, is a triazine fungicide. The dihedral angle between the planes of the triazine and benzene rings is 4.04?(8). In the crystal, two weak CH?N hydrogen bonds and short Cl?Cl contacts [3.4222?(4)?] link adjacent molecules, forming two-dimensional networks parellel to the (112) plane. The planes are linked by weak intermolecular ?? interactions [3.6428?(5) and 3.6490?(5)?], resulting in a three-dimensional architecture.

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

2014-01-01

33

Crystal structure of anilazine.  

PubMed

THE TITLE COMPOUND [SYSTEMATIC NAME: 4,6-di-chloro-N-(2-chloro-phen-yl)-1,3,5-triazin-2-amine], C9H5Cl3N4, is a triazine fungicide. The dihedral angle between the planes of the triazine and benzene rings is 4.04?(8). In the crystal, two weak C-H?N hydrogen bonds and short Cl?Cl contacts [3.4222?(4)?] link adjacent mol-ecules, forming two-dimensional networks parellel to the (112) plane. The planes are linked by weak inter-molecular ?-? inter-actions [3.6428?(5) and 3.6490?(5)?], resulting in a three-dimensional architecture. PMID:25309255

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

2014-09-01

34

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 a system of identical particles interacting via a spherically symmetric potential. A weak first order transition was observed upon cooling a low-density isotropic liquid. It produced a liquid crystal composed of hexagonally packed parallel particle columns with liquid structure and significant intracolumn diffusion. Further cooling resulted in another transition transforming the liquid crystal into a crystal, as the columns became periodically ordered in three dimensions. This is the first observation of a liquid crystal formation in a simple one-component particle system. It indicates 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 force field.

Alfredo Metere; Tomas Oppelstrup; Sten Sarman; Mikhail Dzugutov

2014-06-30

35

Directional emission from photonic crystal waveguide terminations using particle swarm  

E-print Network

Directional emission from photonic crystal waveguide terminations using particle swarm optimization (Doc. ID 114908); published January 29, 2010 We report particle swarm optimization (PSO) of photonic M. Sathish Kumar,* Sergey Menabde, Sunkyu Yu, and Namkyoo Park Photonic Systems Laboratory, School

Park, Namkyoo

36

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

37

Crystal Structure of Neotame Anhydrate Polymorph G  

Microsoft Academic Search

Purpose. To determine the crystal structure of the neotame anhydrate polymorph G and to evaluate X-ray powder diffractometry (XRPD) with molecular modeling as an alternative method for determining the crystal structure of this conformationally flexible dipeptide.

Zedong Dong; Victor G. Young; Agam Sheth; Eric J. Munson; Steve A. Schroeder; Indra Prakash; David J. W. Grant

2002-01-01

38

Crystal Structure of Rochelle Salt  

Microsoft Academic Search

WE have succeeded in finding approximate positions for all the atoms of Rochelle salt (sodium potassium tartrate tetrahydrate) in the crystal structure. The unit cell has dimensions 11.93 A. 14.30 A. 6.17 A. (Z = 4), and the space group is P21212. The set of general positions expressing this symmetry is and the co-ordinates of the various atoms

C. A. Beevers; W. Hughes

1940-01-01

39

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.

40

The crystal structure of hopeite  

Microsoft Academic Search

The crystal structure of hopeite, Zns(POa)2.4Hro, has been solved by the Heavy Atom method from l42l graphite-monochromatized MoKa data and refined by full matrix least- squares to R = 0.026 (R. = 0.036). The structure is orthorhombic, pnma, a = 10.597(3), b : l8.3lE(8), c: 5.031(l) A, and Z: 4.Thezn atoms occur in two crystallographically distinct sites, one six-coordinated and

RooEnrcr J. Hrr; J. B. JoNes

41

Shear induced structures in crystallizing cocoa butter  

Microsoft Academic Search

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

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

2004-01-01

42

Crystal structure of lignin peroxidase  

SciTech Connect

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

Edwards, S.L. (Center for Advanced Research in Biotechnology, Rockville, MD (United States) National Institutes of Health, Bethesda, MD (United States)); Raag, R. (Center for Advanced Research in Biotechnology, Rockville, MD (United States)); Wariishi, Hiroyuki; Gold, M.H. (Oregon Graduate Institute of Science and Technology, Beaverton (United States)); Poulos, T.L. (Center for Advanced Reseaarch in Biotechnology, Rockville, MD (United States) Univ. of California, Irvine (United States))

1993-01-15

43

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.

44

The structural consequences of calcium crystal deposition.  

PubMed

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

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

2014-05-01

45

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

E-print Network

the phrase, "structure-property relations", without saying the word, "structure". #12;Simple crystal1. Understanding crystal structures: How are more complex crystal structures built up from simpler ones. 2. Structure-composition-property relations in inorganic materials: Some examples of subscript

Akhmedov, Azer

46

Isomorph invariance of the structure and dynamics of classical crystals  

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

47

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

48

Methane hydrate crystallization mechanism from in-situ particle sizing  

SciTech Connect

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

Herri, J.M. [Ecole des Mines de Saint-Etienne (France)] [Ecole des Mines de Saint-Etienne (France); [Institut Francais du Petrole, Rueil-Malmaison (France); Pic, J.S.; Gruy, F.; Cournil, M. [Ecole des Mines de Saint-Etienne (France)] [Ecole des Mines de Saint-Etienne (France)

1999-03-01

49

Crystal formation of dipolar particles in a helical geometry  

E-print Network

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

Pedersen, J K; Jensen, A S; Zinner, N T

2014-01-01

50

Analysis of the structure and morphology of fenoxycarb crystals.  

PubMed

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

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

2014-09-01

51

Crystal structure of prethrombin-1  

SciTech Connect

Prothrombin is the zymogen precursor of the clotting enzyme thrombin, which is generated by two sequential cleavages at R271 and R320 by the prothrombinase complex. The structure of prothrombin is currently unknown. Prethrombin-1 differs from prothrombin for the absence of 155 residues in the N-terminal domain and is composed of a single polypeptide chain containing fragment 2 (residues 156-271), A chain (residues 272-320), and B chain (residues 321-579). The X-ray crystal structure of prethrombin-1 solved at 2.2-{angstrom} resolution shows an overall conformation significantly different (rmsd = 3.6 {angstrom}) from that of its active form meizothrombin desF1 carrying a cleavage at R320. Fragment 2 is rotated around the y axis by 29{sup o} and makes only few contacts with the B chain. In the B chain, the oxyanion hole is disrupted due to absence of the I16-D194 ion pair and the Na{sup +} binding site and adjacent primary specificity pocket are highly perturbed. A remarkable feature of the structure is that the autolysis loop assumes a helical conformation enabling W148 and W215, located 17 {angstrom} apart in meizothrombin desF1, to come within 3.3 {angstrom} of each other and completely occlude access to the active site. These findings suggest that the zymogen form of thrombin possesses conformational plasticity comparable to that of the mature enzyme and have significant implications for the mechanism of prothrombin activation and the zymogen {yields} protease conversion in trypsin-like proteases.

Chen, Zhiwei; Pelc, Leslie A.; Di Cera, Enrico (St. Louis-MED)

2010-11-15

52

Structure of self - assembled two-dimensional spherical crystals  

NASA Astrophysics Data System (ADS)

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

Bausch, Andreas R.

2004-03-01

53

Ionic colloidal crystals of oppositely charged particles  

Microsoft Academic Search

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

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

2005-01-01

54

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

PubMed

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

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

2014-05-01

55

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

56

Introduction to Crystal Structure: Bond Strength  

NSDL National Science Digital Library

This exercise is designed to familiarize students with some basic crystal structures The exercise helps students fully understand the nature and significance of ionic bonds and Pauling's second rule It also builds a bit on Pauling's first rule (radius ratio principle) It is one of several related activities, all of which are intended to help students understand the nature of ionic crystals

Perkins, Dexter

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

ICSD Web: the Inorganic Crystal Structure Database  

NSDL National Science Digital Library

This site contains a free demonstration version of the Inorganic Crystal Structure Database. This database contains a 3325 structure subset of the 76,480 inorganic structures as of 2004. The demo version can be queried and accessed by a web-interface which allows multiple methods of searching, and the resulting crystal structures can then be viewed online (with the CHIME plug-in) or downloaded for viewing with other visualization software. Also included on the site are updates of bug fixes, conditions of use and prices, tips for displaying the structures, a gallery of images, a flash movie, and instructions for installing a ICSD server.

Alan, Hewat

60

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

61

Photonic-crystal mediated charged particle beam velocity modulation and electromagnetic wave generation  

Microsoft Academic Search

We present the first experimental results of a photonic crystal (PC) structure-mediated charged particle beam velocity modulation and energy exchange. Our structure was based on two photonic lattices working at 9.532 GHz: a modulation lattice (ML) driven by a 2.56 W signal to velocity-modulate an electron beam of dc voltage from 15 to 30 kV and current from 50 to

Yiming Xu; Rebecca Seviour

2012-01-01

62

Time dependence of the intensity of parametric X-ray radiation produced by relativistic particles passing through crystals  

NASA Astrophysics Data System (ADS)

The time evolution of parametric X-ray radiation (PXR) produced by a relativistic charged particle passing through a crystal is studied. It is shown that the duration of PXR pulses can be much longer than the particle flight time through the crystal. This enables a thorough experimental investigation of the time structure of parametric X-ray pulses generated by electron bunches available with modern accelerators. The complicated time structure of parametric radiation can also be observed in artificial (electromagnetic, photonic) crystals in optical, terahertz, and microwave ranges of wavelengths.

Anishchenko, S. V.; Baryshevsky, V. G.; Gurinovich, A. A.

2012-12-01

63

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

64

Crystallizing hard-sphere glasses by doping with active particles.  

PubMed

Crystallization and vitrification are two different routes to form a solid. Normally these two processes suppress each other, with the glass transition preventing crystallization at high density (or low temperature). This is even true for systems of colloidal hard spheres, which are commonly used as building blocks for novel functional materials with potential applications, e.g. photonic crystals. By performing Brownian dynamics simulations of glassy systems consisting of mixtures of active and passive hard spheres, we show that the crystallization of such hard-sphere glasses can be dramatically promoted by doping the system with small amounts of active particles. Surprisingly, even hard-sphere glasses of packing fraction up to ? = 0.635 crystallize, which is around 0.5% below the random close packing at ? ? 0.64. Our results suggest a novel way of fabricating crystalline materials from (colloidal) glasses. This is particularly important for materials that get easily kinetically trapped in glassy states, and the crystal nucleation hardly occurs. PMID:25079244

Ni, Ran; Cohen Stuart, Martien A; Dijkstra, Marjolein; Bolhuis, Peter G

2014-09-21

65

Natural photonic crystals: formation, structure, function  

NASA Astrophysics Data System (ADS)

The structure and properties of natural photonic crystals are discussed using the colored scales of the beetle Lamprocyphus augustus as an example. While the exact mechanism behind the formation of these biopolymeric photonic structures has yet to be fully explored, similarities of these structures to intracellular cubic membrane architectures are introduced. Some crucial parameters behind the formation of cubic membranes are discussed. Using these insights, intracellular cubic membrane structures are transformed into an extracellular environment.

Bartl, Michael H.; Dahlby, Michael R.; Barrows, Frank P.; Richens, Zachary J.; Terooatea, Tommy; Jorgensen, Matthew R.

2012-03-01

66

Paul trapping for micro-particles and its application for crystal growth  

Microsoft Academic Search

Recently, crystal growth in the microgravity is attracting attention because it has possibility to produce uniform crystal. The purpose of our study is to manipulate a particle with micrometer of diameter and to produce crystal coincidentally by Paul trapping. Cylindrical electrodes were prepared for Paul trapping and electrospray ionization was brought in to charge particles. A micro particle of solid,

Yukitoshi OTANI; Y. Mizutani; N. Yoshizawa

2009-01-01

67

Random hcp and fcc structures in thermoresponsive microgel crystals  

NASA Astrophysics Data System (ADS)

Monodisperse thermoresponsive poly(N-isopropylacrylamide) (PNIPAM) microgel particles having a diameter of 520 nm were synthesized by free-radical precipitation polymerization and centrifuged to obtain a concentrated suspension. The centrifuged mother suspension was made to self-order into a crystalline state by repeated annealing beyond the volume phase transition (VPT) of the particles. We report here the three-dimensional (3D) real space structure, determined using a confocal laser scanning microscope, of PNIPAM microgel crystal samples prepared by two different recrystallized routes: (1) solidifying a shear melted colloidal liquid (referred as as-prepared sample) and (2) slow cooling of a colloidal liquid (referred as recrystallized sample). We have recorded images of several regions of the crystal with each region containing 15 horizontal crystal planes for determining the in-plane [two-dimensional (2D)] and 3D pair-correlation functions. The 2D pair-correlation function g(r) revealed hexagonal long-range order of particles in the layers with a lattice constant of 620 nm. The analysis of stacking sequence of layers recorded on as-prepared sample has revealed the existence of stacking disorder with an average stacking probability ?~0.42. This value of ? together with the analysis of 3D pair-correlation function determined from particle positions revealed the structure of microgel crystals in the as-prepared sample to be random hexagonal close packing. We report the first observation of a split second peak in the 3D g(r) of the microgel crystals obtained from a shear melted liquid. Upon melting the sample above VPT and recrystallizing it the split second peak disappeared and the crystals are found to have a face centered cubic (fcc) structure with ?~0.95. From simulations, the split second peak is shown to arise from the displacement of some of the B-planes from the ideal hcp positions. The present results are discussed in light of those reported for charged and hard sphere colloidal crystals and plausible reasons for observing two different structures are also explained.

Brijitta, J.; Tata, B. V. R.; Joshi, R. G.; Kaliyappan, T.

2009-08-01

68

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, Universit 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, Universit di Trento, Via Sommarive 14, 38123 Trento (Italy); Montagna, M. [Dipartimento di Fisica, Universit di Trento, Via Sommarive 14, 38123 Trento (Italy)] [Dipartimento di Fisica, Universit di Trento, Via Sommarive 14, 38123 Trento (Italy)

2013-11-07

69

Critical single domain grain sizes in chains of interacting greigite particles: Implications for magnetosome crystals  

NASA Astrophysics Data System (ADS)

Magnetotactic bacteria contain chains of magnetically interacting crystals (magnetosomes), which aid navigation (magnetotaxis). To improve the efficiency of magnetotaxis, magnetosome crystals (which can consist of magnetite or greigite) should be magnetically stable single domain (SD) particles. Larger particles subdivide into nonuniform multidomain (MD) magnetic structures that produce weaker magnetic signals, while small SD particles become magnetically unstable due to thermal fluctuations and exhibit superparamagnetic (SP) behavior. In this study, we determined the stable SD range as a function of grain elongation and interparticle separation for chains of identical greigite grains using fundamental parameters recently determined for greigite. Interactions significantly increase the stable SD range. For example, for cube-shaped greigite grains the upper stable SD threshold size is increased from 107 nm for isolated grains to 204 nm for touching grains arranged in chains. The larger critical SD grain size for greigite means that, compared to magnetite magnetosomes, greigite magnetosomes can produce larger magnetic signals without the need for intergrain interactions.

Muxworthy, Adrian R.; Williams, Wyn; Roberts, Andrew P.; Winklhofer, Michael; Chang, Liao; Psfai, Mihly

2013-12-01

70

Influence of Patch-Size Variability on the Crystallization of Tetrahedral Patchy Particles  

NASA Astrophysics Data System (ADS)

The understanding of disorder effects on crystallization is of fundamental and technological importance. It is well established by both theory and experiment that particle-size polydispersity hinders crystallization for isotropically interacting particles. Here, we address the effects of patch variability in a model for tetrahedral colloids, where polydispersity is introduced independently on the size, position, and strength of the attractive patches. Our simulations indicate that, unlike particle-size polydispersity, angular polydispersity has a minor impact on the crystallization properties of tetrahedral colloidal particles. Particles with angular polydispersity well within current experimental possibilities fully retain their crystallization properties, a result which should encourage the realization of colloidal crystals in experiment.

Romano, Flavio; Russo, John; Tanaka, Hajime

2014-09-01

71

Building Crystal Structure Ball Models Using Pre-Drilled Templates: Sheet Structures, Tridymite, and Cristobalite  

NSDL National Science Digital Library

This activity involves building crystal structure ball models in order to strengthen students' understanding of crystalline order, relative atomic size, atomic coordination, crystal chemistry, and crystal symmetry.

Hollocher, Kurt

72

Synthesis and crystal structure of maleopimaric acid.  

PubMed

The title compound maleopimaric acid was synthesized by a Diels-Alder reaction between maleic anhydride and Pinus elliottii engelm oleoresin at room temperature and it was characterized by single crystal X-ray diffraction. The white crystals crystallized in the orthorhombic system, space group P2(12121) with cell dimensions: a = 7.6960 (15) A, b = 11.851 (2) A, c = 24.577 (5) A, alpha = 90 degrees, beta = 90 degrees, gamma = 90 degrees, V = 2241.6(8) A(3), and R(1) = 0.0716, wR(2) = 0.1975. The two fused and unbridged cyclohexane rings form a trans ring junction with chair conformation with two methyl groups in axis positions, the anhydride ring is planar. Crystal water existed in the molecular and stabilized the structure through intermolecular hydrogen bonds. PMID:18626819

Rao, Xiaoping; Song, Zhanqian; Yao, Xujie; Han, Chunrui; Shang, Shibin

2008-01-01

73

Liquids more stable than crystals in particles with limited valence and flexible bonds  

NASA Astrophysics Data System (ADS)

All liquids (except helium owing to quantum effects) crystallize at low temperatures, forming ordered structures. The competition between disorder, which stabilizes the liquid phase, and energy, which leads to a preference for the crystalline structure, inevitably favours the crystal when the temperature is lowered and entropy becomes progressively less relevant. The liquid state survives at low temperatures only as a glass, an out-of-equilibrium arrested state of matter. This textbook description holds inevitably for atomic and molecular systems, where particle interactions are set by quantum-mechanical laws. The question remains whether it holds for colloidal particles, where interparticle interactions are usually short-ranged and tunable. Here we show that for patchy colloids with limited valence, conditions can be found for which the liquid phase is stable even in the zero-temperature limit. Our results offer fresh cues for understanding the stability of gels and the glass-forming ability of molecular network glasses.

Smallenburg, Frank; Sciortino, Francesco

2013-09-01

74

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 4C. Droplet size (0.17 versus 1.20?m), lipid composition (stearin versus olein) and cooling rate (1 versus 10Cmin(-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 (3.8-4.2nm). 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

75

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

76

Particle beam and crabbing and deflecting structure  

DOEpatents

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

Delayen, Jean (Yorktown, VA)

2011-02-08

77

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

78

Slip Flow through Colloidal Crystals of Varying Particle Diameter  

PubMed Central

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

Rogers, Benjamin J.; Wirth, Mary J.

2012-01-01

79

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

80

THE CRYSTAL STRUCTURE OF VANADYL BISACETYLACETONATE (thesis)  

Microsoft Academic Search

The crystal structure of the chelate vanadyl bisacetylacetonate has been ; determined by x-ray diffraction. The compound is not a polymer in the solid but ; forms separate molecules, and there is no intermolecular bonding other than the ; usual Van der Waals type. The main feature of interest in the result is the ; geometrical arrangement of oxygen atoms

Dodge

1958-01-01

81

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

82

Genesis of crystal structures of superconducting oxides  

SciTech Connect

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

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

1995-05-01

83

Generation of relativistic positronium atoms by high-energy photons and charged particles in aligned crystals  

Microsoft Academic Search

We consider different generation mechanisms of relativistic positronium (Ps) atoms (positronium atoms moving with relativistic velocity) by high-energy photons and charged particles in aligned crystals. Coherent effect in a crystal leads to sufficient enhancement in Ps yield at certain photon energies. The energy spectrum of singlet and triplet Ps atoms generated by high-energy charged particles penetrating through a crystal contains

Yury P. Kunashenko; Yury L. Pivovarov

2000-01-01

84

Anomalous diffusion of colloidal particles in a nematic liquid crystal  

NASA Astrophysics Data System (ADS)

We explore the Brownian motion of colloidal microspheres in a nematic liquid crystal within time scales below 100ms that was not accessible in previous experiments. Our experimental results point towards an apparent sub-diffusion of the colloids with a mean square displacement MSD t^1/2. For longer time scales, the particles exhibit normal diffusion with two anisotropic diffusion constants parallel and perpendicular to the nematic director n [1]. The nonlinear effect vanishes when the host is heated up to the isotropic phase; therefore the subdiffusive behavior can be attributed to the coupling of slow director fluctuations of the nematic with the colloidal particle dynamics. We also discuss the role of finite accuracy of measurements. [4pt] [1] J. C. Loudet, P. Hanusse and P. Poulin, Science 306, (2004).

Lazo, Israel; Lavrentovich, Oleg D.; Turiv, Taras; Brodin, Alexander; Nazarenko, Vassili

2012-02-01

85

Aggregate Structure and Free Energy Changes in Chromonic Liquid Crystals  

E-print Network

concerning the reasons why different aggre- gate structures are formed and why the liquid crystal phase crystal phase forms at higher concentrations. Keywords: aggregation; chromonic; liquid crystalsAggregate Structure and Free Energy Changes in Chromonic Liquid Crystals Alexandra J. Dickinson

Collings, Peter

86

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

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

2011-04-01

87

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

88

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

89

Predicting Polymeric Crystal Structures by Evolutionary Algorithms  

E-print Network

The recently developed evolutionary algorithm USPEX proved to be a tool that enables accurate and reliable prediction of structures for a given chemical composition. Here we extend this method to predict the crystal structure of polymers by performing constrained evolutionary search, where each monomeric unit is treated as one or several building blocks with fixed connectivity. This greatly reduces the search space and allows the initial structure generation with different sequences and packings using these blocks. The new constrained evolutionary algorithm is successfully tested and validated on a diverse range of experimentally known polymers, namely polyethylene (PE), polyacetylene (PA), poly(glycolic acid) (PGA), poly(vinyl chloride) (PVC), poly(oxymethylene) (POM), poly(phenylene oxide) (PPO), and poly (p-phenylene sulfide) (PPS). By fixing the orientation of polymeric chains, this method can be further extended to predict all polymorphs of poly(vinylidene fluoride) (PVDF), and the complex linear polymer crystals, such as 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.

Qiang Zhu; Vinit Sharma; Artem R Oganov; Rampi Ramprasad

2014-06-05

90

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

91

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

92

3D photonic crystals with a hierarchical pore structure  

NASA Astrophysics Data System (ADS)

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

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

2014-03-01

93

Exploring Crystal Structures with XtalDraw  

NSDL National Science Digital Library

At the end of this exercise students will be able to use computer-based software to draw crystal structures and visualize symmetries present in minerals. By varying the way in which atoms or groups of atoms are displayed, they will begin to see how atoms link through bonds. Students will also begin to investigate the effects of variable composition on bonding on unit cell parameters.

Panero, Wendy

94

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

PubMed Central

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

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

2011-01-01

95

About mechanics of the structured particles  

E-print Network

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

V. M. Somsikov

2011-03-15

96

~ 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. For instance, to make a movie of a crystal structure as a function of temperature we make a set of frames] INTRODUCTION The mineralogical literature is full of images of crystal structures. These images provide

Downs, Robert T.

97

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

98

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

PubMed

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

Mahlin, Denny; Berggren, Jonas; Alderborn, Gran; Engstrm, Sven

2004-01-01

99

Modeling Liquid crystal configurations 1 Modeling liquid crystal structures using MPI on a workstation cluster  

E-print Network

Modeling Liquid crystal configurations 1 Modeling liquid crystal structures using MPI Introduction Liquid crystals are so called because they exhibit some of the properties of both the liquid orientational and positional order, and the isotropic liquid phase, which exhibits neither. Liquid crystals re

Farrell, Paul A.

100

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

PubMed

Orientational and positional ordering properties of liquid crystal monolayers are examined by means of Fundamental-Measure Density Functional Theory. Particles forming the monolayer are modeled as hard parallelepipeds of square section of size ? and length L. Their shapes are controlled by the aspect ratio ? = L/? (>1 for prolate and <1 for oblate shapes). The particle centers of mass are restricted to a flat surface and three possible and mutually perpendicular orientations (in-plane and along the layer normal) of their uniaxial axes are allowed. We find that the structure of the monolayer depends strongly on particle shape and density. In the case of rod-like shapes, particles align along the layer normal in order to achieve the lowest possible occupied area per particle. This phase is a uniaxial nematic even at very low densities. In contrast, for plate-like particles, the lowest occupied area can be achieved by random in-plane ordering in the monolayer, i.e., planar nematic ordering takes place even at vanishing densities. It is found that the random in-plane ordering is not favorable at higher densities and the system undergoes an in-plane ordering transition forming a biaxial nematic phase or crystallizes. For certain values of the aspect ratio, the uniaxial-biaxial nematic phase transition is observed for both rod-like and plate-like shapes. The stability region of the biaxial nematic phase enhances with decreasing aspect ratios for plate-like particles, while the rod-like particles exhibit a reentrant phenomenon, i.e., a sequence of uniaxial-biaxial-uniaxial nematic ordering with increasing density if the aspect ratio is larger than 21.34. In addition to this, packing fraction inversion is observed with increasing surface pressure due to the alignment along the layers normal. At very high densities the nematic phase destabilizes to a nonuniform phases (columnar, smectic, or crystalline phases) for both shapes. PMID:24880324

Martnez-Ratn, Yuri; Varga, Szabolcs; Velasco, Enrique

2014-05-28

101

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

Microsoft Academic Search

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 hi gh salt and the P2 1 crystal form being obtained from lower concentration of salt and PEG. We report here the crystallization, preliminary stages of structure determination and t he detection of

Michael Baranowski; Boguslaw Stec

2007-01-01

102

Crystal structures of the benzene and ethanol solvates of neotame  

Microsoft Academic Search

The benzene and ethanol solvates of neotame crystallized from solutions of neotame anhydrate in benzene and ethanol, respectively. The crystal structures of the two solvates were determined by single-crystal X-ray diffraction using synchrotron radiation. The benzene solvate crystallizes in the monoclinic space group, P21, Z = 2, with one neotame molecule and one benzene molecule per asymmetric unit. The cell

Zedong Dong; Victor G. Young; Eric J. Munson; Steve A. Schroeder; Indra Prakash; David J. W. Grant

2003-01-01

103

The structural instabilities in ferronematic based on liquid crystal with negative diamagnetic susceptibility anisotropy  

NASA Astrophysics Data System (ADS)

The studied ferronematic is a nematic liquid crystal (ZLI1695) of low negative anisotropy of the diamagnetic susceptibility (?a<0) doped with the magnetic particles Fe 3O 4. Structural instabilities are interpreted within Burylov and Raikher's theory. The high magnetic fields were oriented perpendicular (Freedericksz transition) or parallel to the initial director. Using capacitance measurements the Freedericksz threshold magnetic field of the ferronematic BFN, and the critical magnetic field Bmax, at which the initial parallel orientation between the director and the magnetic moment of magnetic particles breaks down, have been determined. The values of these quantities have been used to estimate the surface density of the anchoring energy W of liquid crystal molecules on the surface of the magnetic particles. The obtained values indicate a soft anchoring of the liquid crystal on the magnetic particles with a preferred parallel orientation of the magnetic moment of magnetic particles and the director.

Kop?ansk, Peter; Tomaovi?ov, Natlia; Konerack, Martina; Timko, Milan; Zviov, Vlasta; ber, Nndor; Fodor-Csorba, Katalin; Tth-Katona, Tibor; Vajda, Anik; Jadzyn, Jan; Beaugnon, Eric; Chaud, Xavier

2010-11-01

104

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

SciTech Connect

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., E-mail: suvorova@ns.crys.ras.ru; Klechkovskaya, V. V. [Shubnikov Institute of Crystallography of Russian Academy of Sciences (Russian Federation)

2010-12-15

105

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

106

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

E-print Network

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

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

2014-01-01

107

In situ X-ray crystallographic study of the structural evolution of colloidal crystals upon heating  

PubMed Central

The structural evolution of colloidal crystals made of polystyrene hard spheres has been studied in situ upon incremental heating of a crystal in a temperature range below and above the glass transition temperature of polystyrene. Thin films of colloidal crystals having different particle sizes were studied in transmission geometry using a high-resolution small-angle X-ray scattering setup at the P10 Coherence Beamline of the PETRA III synchrotron facility. The transformation of colloidal crystals to a melted state has been observed in a narrow temperature interval of less than 10?K. PMID:24046496

Zozulya, A. V.; Meijer, J.-M.; Shabalin, A.; Ricci, A.; Westermeier, F.; Kurta, R. P.; Lorenz, U.; Singer, A.; Yefanov, O.; Petukhov, A. V.; Sprung, M.; Vartanyants, I. A.

2013-01-01

108

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

E-print Network

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

Toshiyuki Hamanaka; Akira Onuki

2006-05-10

109

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

SciTech Connect

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

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

2009-10-07

110

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

E-print Network

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

Davidchack, R. L.; Laird, Brian Bostian

2005-03-01

111

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 made available by large scale lifting was taken up by depositional growth of the ice crystals

Vali, Gabor

112

Structural Evolution of Colloidal Crystals with Increasing Ionic Strength  

E-print Network

. In Final Form: June 5, 2004 We have directly observed the structural evolution of colloidal crystalsStructural Evolution of Colloidal Crystals with Increasing Ionic Strength Michael A. Bevan sedimented onto a glass substrate in deionized water to create large, single domain crystals. The solution

Braun, Paul

113

The coexistence of molecules having different structures in organic crystals  

Microsoft Academic Search

A comparison of the structures of symmetrically independent molecules coexisting in organic crystals has been carried out on the basis of the statistical treatment of x-ray diffraction data. The analysis of 330 crystal structures containing such molecules showed that 20% of the crystals contain molecules with different Iconformations (the phenomenon of contact conformerism); in 80% of cases the symmetrically independent

P. M. Zorkii; A. E. Razumaeva

1979-01-01

114

Crystal structure of the Golgi casein kinase  

PubMed Central

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

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

2013-01-01

115

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? 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

116

Crystal Structure of Marburg Virus VP24  

PubMed Central

The VP24 protein plays an essential, albeit poorly understood role in the filovirus life cycle. VP24 is only 30% identical between Marburg virus and the ebolaviruses. Furthermore, VP24 from the ebolaviruses is immunosuppressive, while that of Marburg virus is not. The crystal structure of Marburg virus VP24, presented here, reveals that although the core is similar between the viral genera, Marburg VP24 is distinguished by a projecting ?-shelf and an alternate conformation of the N-terminal polypeptide. PMID:24574400

Zhang, Adrianna P. P.; Bornholdt, Zachary A.; Abelson, Dafna M.

2014-01-01

117

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

118

A particle's eye view of crystallizer fluid mechanics  

Microsoft Academic Search

It has been recognized for some time that flow and mixing in industrial crystallizers has an effect on the kinetics of growth, nucleation and agglomeration and consequently on the crystal size distribution. Yet, a common assumption in population balance modelling is that the fluid mechanical environment experienced by growing crystals is uniform. In practice, however, industrial crystallizers provide extremely varied

Chris D Rielly; Andrew J Marquis

2001-01-01

119

Structural studies of large nucleoprotein particles, vaults  

PubMed Central

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

TANAKA, Hideaki; TSUKIHARA, Tomitake

2012-01-01

120

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

E-print Network

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

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

2010-07-04

121

Tunability of LSPR using gold nano-particles embedded in a liquid crystal cell  

NASA Astrophysics Data System (ADS)

Tunability of localized surface plasmon resonance (LSPR) of an ordered array of gold nano-particles is investigated in this paper. Herein, the array is embedded in a liquid crystal cell and then sandwiched with two glass substrates. The extinction spectra are computed using the Finite-Difference Time Domain (FDTD) method. The LSPR tunability of gold nanostructures is compromised by the anchoring effects of surrounding LC molecules, this effect can be compensated by optimizing geometric parameters of gold nanostructures. Interestingly, double resonant peaks are achieved with optimized structure. Meanwhile, the tunability of LSPR is improved up to 72 nm with anchoring effects taken into account.

Wang, Huan; Vial, Alexandre

2014-10-01

122

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

123

Crystal Structure of Human Nicotinamide Riboside Kinase  

SciTech Connect

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

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

2007-01-01

124

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

2013-05-21

125

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

126

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

PubMed

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

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

2014-08-01

127

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

128

Bragg scattering and Brownian motion dynamics in optically induced crystals of submicron particles  

NASA Astrophysics Data System (ADS)

A set of four confocal laser beams of 1064-nm wavelength is used to prepare optically induced crystals of submicron particles in aqueous solution. Thousands of polystyrene spheres of about 200 nm in diameter are trapped in three dimensions. Bragg scattering patterns obtained with a probe beam of 532-nm wavelength are in agreement with the calculated lattice structure and its polarization dependence. The decay and rise of the Bragg scattering intensity upon switching the lattice off and on reveal the Brownian motion dynamics of the particles in the periodic optical trapping potential. Experimental results agree well with results from trajectory simulations based on the Langevin equation. The results exhibit the interplay between Brownian motion and deterministic forces in an inhomogeneous (near-)periodic optical trapping potential.

Sapiro, R. E.; Slama, B. N.; Raithel, G.

2013-05-01

129

Bragg scattering and Brownian motion dynamics in optically induced crystals of submicron particles.  

PubMed

A set of four confocal laser beams of 1064-nm wavelength is used to prepare optically induced crystals of submicron particles in aqueous solution. Thousands of polystyrene spheres of about 200 nm in diameter are trapped in three dimensions. Bragg scattering patterns obtained with a probe beam of 532-nm wavelength are in agreement with the calculated lattice structure and its polarization dependence. The decay and rise of the Bragg scattering intensity upon switching the lattice off and on reveal the Brownian motion dynamics of the particles in the periodic optical trapping potential. Experimental results agree well with results from trajectory simulations based on the Langevin equation. The results exhibit the interplay between Brownian motion and deterministic forces in an inhomogeneous (near-)periodic optical trapping potential. PMID:23767544

Sapiro, R E; Slama, B N; Raithel, G

2013-05-01

130

Crystal structure of Junin virus nucleoprotein.  

PubMed

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

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

2013-10-01

131

In situ proteolysis for protein crystallization and structure determination.  

PubMed

We tested the general applicability of in situ proteolysis to form protein crystals suitable for structure determination by adding a protease (chymotrypsin or trypsin) digestion step to crystallization trials of 55 bacterial and 14 human proteins that had proven recalcitrant to our best efforts at crystallization or structure determination. This is a work in progress; so far we determined structures of 9 bacterial proteins and the human aminoimidazole ribonucleotide synthetase (AIRS) domain. PMID:17982461

Dong, Aiping; Xu, Xiaohui; Edwards, Aled M; Chang, Changsoo; Chruszcz, Maksymilian; Cuff, Marianne; Cymborowski, Marcin; Di Leo, Rosa; Egorova, Olga; Evdokimova, Elena; Filippova, Ekaterina; Gu, Jun; Guthrie, Jennifer; Ignatchenko, Alexandr; Joachimiak, Andrzej; Klostermann, Natalie; Kim, Youngchang; Korniyenko, Yuri; Minor, Wladek; Que, Qiuni; Savchenko, Alexei; Skarina, Tatiana; Tan, Kemin; Yakunin, Alexander; Yee, Adelinda; Yim, Veronica; Zhang, Rongguang; Zheng, Hong; Akutsu, Masato; Arrowsmith, Cheryl; Avvakumov, George V; Bochkarev, Alexey; Dahlgren, Lars-Gran; Dhe-Paganon, Sirano; Dimov, Slav; Dombrovski, Ludmila; Finerty, Patrick; Flodin, Susanne; Flores, Alex; Grslund, Susanne; Hammerstrm, Martin; Herman, Maria Dolores; Hong, Bum-Soo; Hui, Raymond; Johansson, Ida; Liu, Yongson; Nilsson, Martina; Nedyalkova, Lyudmila; Nordlund, Pr; Nyman, Tomas; Min, Jinrong; Ouyang, Hui; Park, Hee-won; Qi, Chao; Rabeh, Wael; Shen, Limin; Shen, Yang; Sukumard, Deepthi; Tempel, Wolfram; Tong, Yufeng; Tresagues, Lionel; Vedadi, Masoud; Walker, John R; Weigelt, Johan; Welin, Martin; Wu, Hong; Xiao, Ting; Zeng, Hong; Zhu, Haizhong

2007-12-01

132

Crystal Structure of Bacillus subtilis Signal Peptide Peptidase A  

E-print Network

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

Paetzel, Mark

133

Nanoscale structure intercrystalline interactions in fat crystal networks  

Microsoft Academic Search

The functional attributes of fat-structured food products such as butter, margarine, chocolate, and ice cream are strongly influenced by the structure and physical properties of an underlying fat crystal network present in the material. Fat crystal networks are arranged in a hierarchical manner with characteristic and quantifiable nano and mesoscale structures. Recent studies carried out by our group have demonstrated

Nuria C. Acevedo; Fernanda Peyronel; Alejandro G. Marangoni

2011-01-01

134

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

135

Crystal structure of human uroporphyrinogen decarboxylase.  

PubMed Central

Uroporphyrinogen decarboxylase (URO-D) catalyzes the fifth step in the heme biosynthetic pathway, converting uroporphyrinogen to coproporphyrinogen by decarboxylating the four acetate side chains of the substrate. This activity is essential in all organisms, and subnormal activity of URO-D leads to the most common form of porphyria in humans, porphyria cutanea tarda (PCT). We have determined the crystal structure of recombinant human URO-D at 1.60 A resolution. The 40.8 kDa protein is comprised of a single domain containing a (beta/alpha)8-barrel with a deep active site cleft formed by loops at the C-terminal ends of the barrel strands. Many conserved residues cluster at this cleft, including the invariant side chains of Arg37, Arg41 and His339, which probably function in substrate binding, and Asp86, Tyr164 and Ser219, which may function in either binding or catalysis. URO-D is a dimer in solution (Kd = 0.1 microM), and this dimer also appears to be formed in the crystal. Assembly of the dimer juxtaposes the active site clefts of the monomers, suggesting a functionally important interaction between the catalytic centers. PMID:9564029

Whitby, F G; Phillips, J D; Kushner, J P; Hill, C P

1998-01-01

136

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

137

Crystal structure of a snake venom cardiotoxin  

SciTech Connect

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

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

1987-05-01

138

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

139

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, Danil; Smallenburg, Frank; Dijkstra, Marjolein

2009-10-30

140

The magnetic domain structures of small crystals  

Microsoft Academic Search

The first part of the article describes the calculation of magnetostatic energies (which are necessary to predict the critical sizes of crystals below which domains cease to form) and of the domain spacing or number of domains per crystal. Methods suitable for periodic magnetic charge distributions in semi-infinite crystals and for finite distributions are described, and both planar and cylindrical

D. J. Craik

1970-01-01

141

Hierarchical structuring of liquid crystal polymer-Laponite hybrid materials.  

PubMed

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

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

2013-09-01

142

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

143

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

NASA Astrophysics Data System (ADS)

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

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

2012-06-01

144

Crystal structure of a Trypanosoma brucei metacaspase.  

PubMed

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 . 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

2012-05-01

145

Crystal Structure of Human Kynurenine Aminotransferase ll*  

SciTech Connect

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

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

2008-01-01

146

Inelastic Collision of Particles with Structure Model  

NSDL National Science Digital Library

The Ejs Inelastic Collision of Particles with Structure model displays the inelastic collision between two equal particles with structure on a smooth horizontal surface. Each particle has two microscopic elements which interact through a massless spring of stiffness k and natural length L. The mass of one of the microscopic elements and the spring length of the connector spring can be changed via textboxes. You can modify this simulation if you have Ejs installed by right-clicking within the plot and selecting Open Ejs Model from the pop-up menu item. Ejs Inelastic Collision of Particles with Structure model was created using the Easy Java Simulations (Ejs) modeling tool. It is distributed as a ready-to-run (compiled) Java archive. Double clicking the ejs_ehu_oscillations_inelastic.jar file will run the program if Java is installed. Ejs is a part of the Open Source Physics Project and is designed to make it easier to access, modify, and generate computer models. Additional Ejs models for classical mechanics are available. They can be found by searching ComPADRE for Open Source Physics, OSP, or Ejs.

Aguirregabiria, Juan

2008-10-09

147

Langmuir-Blodgett assembly of colloidal photonic crystals using silica particles prepared without the use of surfactant molecules.  

PubMed

This short communication reports the observation that in contrast to most previously reported procedures, it is possible to prepare 3D photonic crystal structures from silica particles that have not been deliberately treated with surfactant molecules, using the Langmuir-Blodgett method. We find that colloidal particles prepared simply via the Stber method with diameters in the range 180-360 nm and dispersed in ethanol, may be effectively floated at the air/water interface and compressed into close packed layers prior to depositing the layers on a substrate. We also find, by comparing structures made with both particles treated with the surfactants 3-(trimethoxysilyl) propyl methacrylate or (3-aminopropyl)triethoxysilane and particles which have not been treated with any surfactant species, that the position of the Bragg peak and the reflectivity of the sample does not appear to be influenced by the presence of the surfactant molecules. PMID:19251265

Bardosova, Maria; Dillon, Frank C; Pemble, Martyn E; Povey, Ian M; Tredgold, Richard H

2009-05-15

148

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 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

149

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

SciTech Connect

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

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

1991-12-01

150

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

151

Spectroscopy and crystal structure of anabasine salts  

NASA Astrophysics Data System (ADS)

The anabasinium hydrochloride, hydriodide and perchlorate were characterized by IR and NMR spectroscopy as well as by X-ray diffraction. Anabasinium hydrochloride crystallizes with three independent ionic pairs in the asymmetric part of the orthorhombic unit cell, while anabasinium hydriodide and perchlorate crystals, being isostructural, are hexagonal and contain only one symmetry independent ionic pair. Despite these differences in the crystal data, both types of crystals display very similar helical solid-state patterns. The reported results combined with the CSD searches indicate an inherent tendency of anabasinium salts to crystallize with multiple asymmetric units, and to form folded arrangements in crystals. In the solid state the anabasinium cations predominantly adopt either synperiplanar or antiperiplanar conformations with respect to the mutual orientation of C *-H and pyridine C-C(N) bonds, with deformations towards, respectively, (+) synclinal or (+) anticlinal rotamers.

Wojciechowska-Nowak, Marzena; Boczo?, W?adys?aw; Rychlewska, Urszula; War?ajtis, Beata

2007-09-01

152

Growth, Crystal Structure, and Thermopower of Single Crystals of UNi 1.9Sn  

Microsoft Academic Search

We have grown single crystals of UNi1.9(1)Sn from a semi-levitated melt using the Kyropoulos technique. The crystal structure of UNi1.9(1)Sn was determined by single-crystal X-ray diffraction and refined to a residual value of R=0.0336. This compound crystallizes in the cubic MnCu2Al-type structure with the lattice parameter a=6.4633(4) . The temperature dependence of the thermoelectric power, different from that observed for

L. Shlyk; J. C. Waerenborgh; M. Almeida

2000-01-01

153

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

154

The Structure of Agglomerates consisting of Polydisperse Particles.  

PubMed

Agglomeration is encountered in many natural or industrial processes, like growth of aerosol particles in the atmosphere and during material synthesis or even flocculation of suspensions, granulation, crystallization and with colloidal particle processing. These particles collide by different mechanisms and stick together forming irregular or fractal-like agglomerates. Typically, the structure of these agglomerates is characterized with the fractal dimension, Df , and pre-exponential factor, kn , of simulated agglomerates of monodisperse primary particles (PP) for ballistic or diffusion-limited particle-cluster and cluster-cluster collision mechanisms. Here, the effect of PP polydispersity on Df and kn is investigated with agglomerates consisting of 16 - 1024 PP with closely controlled size distribution (geometric standard deviation, ? g = 1-3). These simulations are in excellent agreement with the classic structure (Df and kn ) of agglomerates consisting of monodisperse PPs made by four different collision mechanisms as well as with agglomerates of bi-, tri-disperse and normally distributed PPs. Broadening the PP size distribution of agglomerates decreases monotonically their Df and for sufficiently broad PP distributions (? g > 2.5) the Df reaches about 1.5 and kn about 1 regardless of collision mechanism. Furthermore with increasing PP polydispersity, the corresponding projected area exponent, D ? , and pre-exponential factor, ka , decrease monotonically from their standard values for agglomerates with monodisperse PPs. So Df as well as D ? and ka can be an indication for PP polydispersity in mass-mobility and light scattering measurements, if the dominant agglomeration mechanism is known, like diffusion-limited and/or ballistic cluster-cluster coagulation in aerosols. PMID:23729953

Eggersdorfer, M L; Pratsinis, S E

2012-03-01

155

Spectroscopic, thermal and structural studies on manganous malate crystals  

SciTech Connect

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

Thomas, J., E-mail: smartlabindia@gmail.com; Lincy, A., E-mail: lincymaria@gmail.com; Mahalakshmi, V.; Saban, K. V. [Smart Materials Analytic Research and Technology (SMART), Department of Physics, St. Berchmans College (India)] [Smart Materials Analytic Research and Technology (SMART), Department of Physics, St. Berchmans College (India)

2013-01-15

156

Anisotropic domain structure of KTiOPO{sub 4} crystals  

SciTech Connect

Highly anisotropic ferroelectric domain structure is observed in KTiOPO{sub 4} (KTP) crystals reversed by low electric field. The applied Miller--Weinreich model for sidewise motion of domain walls indicates that this anisotropy results from the peculiarities of KTP crystal lattice. The domain nuclei of dozen nanometer size, imaged by atomic force microscopy method, demonstrate regular hexagonal forms. The orientation of domain walls of the elementary nuclei coincides with the orientation of the facets of macroscopic KTP crystals. The observed strong domain elongation along one principal crystal axis allows us to improve tailoring of ferroelectric domain engineered structures for nonlinear optical converters. {copyright} 2001 American Institute of Physics.

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

2001-08-15

157

The Mechanics of the Systems of Structured Particles  

E-print Network

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

V. M. Somsikov

2009-01-19

158

Crystal structure and morphology control of calcium oxalate using biopolymeric additives in crystallization  

NASA Astrophysics Data System (ADS)

Using the acid-rich polymeric additives, poly- L-aspartate (polyD), poly- L-glutamate (polyE), and polyacrylate (polyAA), the structure and morphology of calcium oxalate crystals were controlled during crystallization. In crystallization without the polymeric additives, twinned calcium oxalate monohydrate (COM) crystals were preferentially produced. However, the structural shift of calcium oxalate from a monohydrate (COM) to a dihydrate (COD) form occurred gradually when increasing the polymeric additive concentration, then COD crystals were exclusively crystallized beyond certain critical concentrations of the additives. These critical concentrations actually depended on the molecular configurations of the additives that determined the capability to control the crystallization. When increasing the additive concentration far beyond the critical level, shape modifications without structural changes occurred from a normal octahedral shape (bi-pyramid) to a rod shape (elongated octahedral shape), followed by a dumbbell shape, and finally a sphere shape. Due to its high binding affinity to the crystal surface, polyAA exhibited the most effective elongation in the [0 0 1] direction and clearest development of {1 0 0} faces, while polyE had the least effect on the crystals.

Jung, Taesung; Kim, Woo-Sik; Kyun Choi, Chang

2005-05-01

159

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

160

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

NASA Astrophysics Data System (ADS)

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

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

2014-08-01

161

Single particle light scattering method for studying aging properties of Pickering emulsions stabilized by catanionic crystals  

Microsoft Academic Search

Single particle light scattering (SPLS) has been extended towards sizes near 100nm to measure particle size distributions with high precision and model free and thus to establish a diagnostic about the stage of aging emulsion properties. SPLS measurements on emulsions stabilized with catanionic crystals allowed to follow the evolution of droplet size distribution as a function of surface charge upon

Natascha Schelero; Heinz Lichtenfeld; Heidi Zastrow; Helmuth Mhwald; Monique Dubois; Thomas Zemb

2009-01-01

162

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

E-print Network

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

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

2001-08-31

163

On the Crystal Structure of Ln  

SciTech Connect

The crystal structures of La{sub 2}O{sub 2}CO{sub 3} II and Nd{sub 2}O{sub 2}CO{sub 3} II have been shown by means of high-resolution powder neutron (PND) and synchrotron X-ray diffraction (SXRD) combined with selected area electron diffraction (SAED) studies to be far more complex than earlier anticipated, owing to ordering of carbonate groups between (Ln{sub 2}O{sub 2}{sup +2}){sub n} layers. In contrast to earlier descriptions, the carbonate groups appear to be rather regular. Relative to an average model, the SAED patterns show additional scattering in the form of closely distributed, but essentially discrete, spots along < 1/3, 1/3, 1 >. Most of the observed scattering, H, can be described as H=G{+-}m q{sub 1}+n q{sub 2}, where G is the Bragg reflections of the underlying average P6{sub 3}/mmc lattice, q1=[1/3, 1/3, {+-}1/2]*, q2=[1/3, 1/3, {+-}2/3]*, and m and n are integers. The additional scattering reflects ordering of the carbonate groups into trigonal layers between the (Ln{sub 2}O{sub 2}{sup +2}){sub n} layers, but it remains open whether q{sub 1} and q{sub 2} represent two separate structures with different stacking sequences of such layers or whether they correspond to an even more complex stacking sequence. In any case, some disorder and rotational domain twinning are present. Two structure models, one for each modulation wave vector, were constructed. Rietveld-type refinements of PND data of La{sub 2}O{sub 2}CO{sub 3} II were performed, approximating the complex, and at least partly disordered, stacking sequence as a two-phase mixture of the two modulated phases. Satisfactory convergence was achieved with R{sub p}=6.4%, R{sub wp}=8.3%, and {chi}{sup 2}=3.32. The isothermal expansivities, {alpha}{sub p}, for La{sub 2}O{sub 2}CO{sub 3} II and Nd{sub 2}O{sub 2}CO{sub 3} II between 298 and 893 K were determined as 2.92x10{sup {minus}5} and 2.70x10{sup {minus}5} K{sup {minus}1}, respectively.

Olafsen, Anja; Larsson, Ann-Kristin; Fjellvaag, Helmer; Hauback, Bjoern C.

2001-04-01

164

The crystal structure of pyridinium hexafluoroantimonate(V  

E-print Network

TNE CRYSTAL STRUCTURE OF PYRIDINIUM HEXAFLUOROANTIMONATE(V) A Thesis By Richard Franklin Copelsnd, Jr, Submitted to the Graduate Scbool of the Agricultural and Mechanical College of Texas in partial fulfillment of the requirements... of Department) August 1963 Abstract CRYSTAL STRUCTURE OF PYRIDINIUM HEXAFLUOROANTIMONATE(V) (August 1963) Richard Franklin Copeland, Jr. , B S. , A. and M. College of Texas Directed by: Dr. Edward A, Meyers The structure of pyridinium hexafluoroantimonate...

Copeland, Richard Franklin

2012-06-07

165

Synthesis, Crystal Structure and Thermal Analysis of (TAGH) 2(TNR)  

Microsoft Academic Search

A new energetic compound (TAGH)2(TNR) (TAG: triaminoguanidine, TNR: 2,4,6-trinitroresorcinol) was prepared by reacting triaminoguanidine with 2,4,6-trinitroresorcinol (styphnic acid) in aqueous solution under nitrogen atmosphere, and characterized by elemental analysis and Fourier transform infrared (FTIR) spectra. Its crystal structure was determined by single crystal X-ray diffraction analysis. The crystal belonged to a monoclinic, C 2\\/c space group. The unit cell parameters

Zhenhua Liu; Guojun Ao; Tonglai Zhang; Li Yang; Jianguo Zhang; Yan Zang

2008-01-01

166

Crystal structure of CsTiSiO  

Microsoft Academic Search

Crystals of a new titanosilicate phase, CsTiSiO, were grown from a cesium vanadate flux. The compound has monoclinic symmetry, space group C2\\/c, with a = 13.386(5), b = 7.423(3), c = 15.134(5) , β = 107.71(3)°, Z = 4. The crystal structure was solved using single crystal X-ray data (MoKα radiation) and refined to R(F) = 0.039 for 1874 unique

I. E. Grey; R. S. Roth; M. L. Balmer

1997-01-01

167

Reconfigurable 3D photonic crystal structures  

NASA Astrophysics Data System (ADS)

The insertion of high dielectric rods in the low dielectric region of photonics crystal enables the optical properties to be reconfigurable. We show that for a square array of holes, the inserted rods define the waveguide region, wavelength of operation and functionality of the photonic crystal device (directional coupler presented). Also are examined the modification of the resonator state's wavelength and field profile when rods are introduced in the central region of two types of quasi-crystals. Based on these results more elaborate reconfigurable devices can be derived.

Gauthier, R. C.

2013-02-01

168

Structural study of Langmuir liquid crystal monolayer  

NASA Astrophysics Data System (ADS)

A systematic study is reported on monolayer characteristics of Ferroelectric Liquid Crystal (FLC) at the air-water interface, using surface pressure and surface potential isotherms at different temperatures. Dipole moment is calculated by using Helmholtz equation. No significant influence from the sub phase temperature was detected because liquid crystal remains in Sm-C* phase in temperature range 5C-40C. FLC was deposited on smooth quartz substrate with good transfer ratio. AFM topography reveals uniform deposition of liquid crystals having well defined domains.

Kaur, Ramneek; Raina, K. K.

2014-04-01

169

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

170

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

171

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; Mhler, Ottmar; Saathoff, Harald; Schnaiter, Martin

2014-07-01

172

Crystal and molecular structure of 4'-hexyloxyphenyl 4-pentylbenzoate  

NASA Astrophysics Data System (ADS)

The molecular and crystal structure of 4'-hexyloxyphenyl 4-pentylbenzoate, C6H13O-C6H4-COO-C6H4-C5H11, which is a liquid-crystal compound, was determined by X-ray diffraction. This compound forms a nematic phase upon melting. The crystal contains three crystallographically independent molecules. In one of them, the alkyl chain is disordered. This is indicative of the looseness of the crystal packing in the aliphatic region. The crystal structure is stabilized by the following two types of weak directional interactions: hydrogen bonds with the participation of the terminal O atom of the ester group and the C-H group of one of the benzene rings and C-H?-system interactions. Only one of the three independent molecules is involved in the latter type of interactions. Hence, the structurization of the mesophase is most likely determined by hydrogen bonding.

Gunina, M. A.; Lermontova, E. Kh.; Pestov, S. M.; Kuz'mina, L. G.

2012-09-01

173

Crystal structures of drugs: advances in determination, prediction and engineering  

Microsoft Academic Search

Most marketed pharmaceuticals consist of molecular crystals. The arrangement of the molecules in a crystal determines its physical properties and, in certain cases, its chemical properties, and so greatly influences the processing and formulation of solid pharmaceuticals, as well as key drug properties such as dissolution rate and stability. A thorough understanding of the relationships between physical structures and the

Sharmistha Datta; David J. W. Grant

2004-01-01

174

Formation of classical crystals of dipolar particles in a helical geometry  

NASA Astrophysics Data System (ADS)

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

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

2014-08-01

175

Formation of classical crystals of dipolar particles in a helical geometry  

E-print Network

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

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

2014-02-18

176

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

177

Purification and properties of virus particles, infectious subviral particles, cores and VP7 crystals of African horsesickness virus serotype 9.  

PubMed

Methods were developed for the purification, at high yield, of four different particle types of African horsesickness virus serotype 9 (AHSV-9). These products included virus particles purified on CsCl gradients which contain proteins apparently directly comparable to those of bluetongue virus (VP1 to VP7); virus particles purified on sucrose gradients which also contain, as a variable component, protein NS2; infectious subviral particles (ISVPs), containing chymotrypsin cleavage products of VP2; and cores, obtained by treating purified ISVPs with 1 M-MgCl2 to remove the components of the outer capsid layer (VP5 and VP2 cleavage products). Additional protein bands migrating with apparent M(r)s lower than that of VP5 were detected during SDS-PAGE analysis of virus particles. These appear to be conformational variants of VP5 and are identified as VP5' and VP5". BHK-21 cells infected with this strain of AHSV-9 produce large quantities of flat, usually hexagonal crystals of VP7, a major group antigen and core protein; these were also purified. Either 20 mg of virus particles, 20 mg of ISVPs or 10 mg of cores as well as 20 mg of VP7 crystals could be purified from approximately 8 x 10(9) infected cells. None of the preparations of particles or crystals showed any detectable contamination with BHK-21 cell proteins or antigens, as determined by SDS-PAGE or indirect ELISA. Virus particle and ISVP preparations had similar specific infectivities for BHK-21 cells (approximately 1 x 10(9) TCID50/A260 unit) but the infectivity of cores was approximately 10(5)-fold lower. PMID:8046387

Burroughs, J N; O'Hara, R S; Smale, C J; Hamblin, C; Walton, A; Armstrong, R; Mertens, P P

1994-08-01

178

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

179

Structural and mechanical studies of cadmium manganese thiocyanate crystal  

NASA Astrophysics Data System (ADS)

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

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

2012-06-01

180

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

181

Ice nucleation: elemental identification of particles in snow crystals.  

PubMed

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

Parungo, F P; Pueschel, R F

1973-06-01

182

Structurally Coloured Secondary Particles Composed of Black and White Colloidal Particles  

NASA Astrophysics Data System (ADS)

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.

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

2013-08-01

183

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

184

Crystal Structure of a Cyclotetraicosaphenylene by Peter Mllera  

E-print Network

Crystal Structure of a Cyclotetraicosaphenylene by Peter Müllera ), Isabel Uso?na ), Volker Henselb was performed using SAINT [9], and the data were corrected semiempirically for absorption and other effects

Müller, Peter

185

Characterization of liquid crystal structure using freely suspended films  

NASA Astrophysics Data System (ADS)

The exact structure that the molecules within many liquid phases adapt is a significant question that still requires clarification. Several procedures are available to elucidate this problem. Among them, the forming of freely suspended liquid crystal films is a powerful method to reveal the structure of the liquid crystal phases. Ultra-thin freely suspended films of smectic liquid crystals are layers of 2-dimensional fluids. Because the interaction between the layers is relatively weak, each layer can be approximated by a 2D model. The 2D c-directors, (projections of the average molecular long axis onto the film plane), studied under depolarized reflected light microscopy, (DRLM), give valuable information about the azimuthal orientation of the molecules. This azimuthal orientation is ordered from layer to layer defining the symmetry of each liquid crystal phase. By including the consideration that the symmetry of the freely suspended liquid crystal films are broken at the liquid crystal-air interfaces, the bulk phase can be characterized. In attempting to explain some novel liquid crystal phase structures, firstly I studied the textures appearing in their freely suspended films in terms of their optical bire-fringence. In one bent core molecular material, the ground state was determined to be a defect rich phase with a modulated polarization splay structure. In another, a T-shaped bolaamphiphile molecule, there exists a phase with 2-dimensional smectic order. These two materials exhibited complicated structures that rarely appear in liquid crystals. Secondly, I present the study of laser reflectivity measurements in connection with the symmetry properties of the films. The phase of one symmetrical bent-core molecular material was found to possess C1, (symmetric only under identity), and Ci, (symmetric under inversion), symmetries. This triclinic order, (C1 and Ci symmetries), was demonstrated for the first time to exist in fluid smectic layers. Lastly I address the influence of spontaneous polarization on topological defect structures in freely suspended films of chiral and achiral liquid crystal materials.

Chattham, Nattaporn

186

Detergent structure in tetragonal crystals of OmpF porin  

Microsoft Academic Search

Background: The high-resolution structures of five porins have been solved by X-ray crystallography including the trigonal crystal form of the trimeric OmpF porin from Escherichia coli. In an accompanying article, the structure of the tetragonal form of OmpF porin is presented. In contrast to the trigonal crystal form, the protein surfaces normally in contact with lipids in the membrane are

E Pebay-Peyroula; RM Garavito; JP Rosenbusch; M Zulauf; PA Timmins

1995-01-01

187

Allophycocyanin and phycocyanin crystal structures reveal facets of phycobilisome assembly.  

PubMed

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

Marx, Ailie; Adir, Noam

2013-03-01

188

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

189

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

190

Crystal structure of actinide metals at high compression  

SciTech Connect

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

Fast, L. [Uppsala Univ. (Sweden). Physics Dept.; Soederlind, P. [Lawrence Livermore National Lab., CA (United States). Physics Dept.

1995-08-01

191

Elemental composition and morphology of ice-crystal residual particles in cirrus clouds and contrails  

Microsoft Academic Search

Aircraft sampling of residual particles from evaporated ice crystals was performed using a Counterflow Virtual Impactor. Samples of crystals taken in both contrails and cirrus clouds were compared with interstitial aerosols found in natural cirrus. The samples were analyzed with a scanning electron microscope which was equipped with a windowless energy-dispersive X-ray detector (SEM\\/EDX). In the contrail and cirrus cases

A Petzold; J Strm; S Ohlsson; F. P Schrder

1998-01-01

192

The ground state and the character of the interaction between a colloidal particles in a liquid crystals  

E-print Network

In this article is proposed the general approach to determination the character of the interaction between colloidal particles in a different liquid crystals. The main idea of this approach are in the presentation of the colloidal particle as sours of the possible deformation of the ground state of the director field. The ground state of liquid crystal imposes restrictions on the possible deformations and as result determine the character of the interaction between the colloidal particles. Based on this approach the Coulomb like interaction between dipole particles in a cholesteric liquid crystal and changing of the character of the interaction in a smactic liquid crystal has been predicted.

B. I. Lev

2013-11-08

193

Reaction intermediates discovered in crystal structures of enzymes.  

PubMed

Crystal structures of enzymes have provided valuable information for the reaction mechanisms. Structures of the enzyme complex with different reaction intermediates are particularly valuable. In several cases, these structures of intermediates were discovered accidently, presumably by trapping in the crystal during freezing prior to X-ray data collection. High to atomic resolution structures reveal the detailed geometry of the reaction intermediate and its interactions within the enzyme active site. In other cases, the protein can be crystallized with its substrate, including examples of protease precursors that represent their own substrates. Examples are described of an FAD-dependent dehydrogenase, HIV protease and caspases, where the structures provide snapshots of steps in the reaction and the conformational changes occurring during the reaction. Complementary techniques such as computational chemistry, neutron crystallography, Laue crystallography, and time-resolved spectroscopy can give a more complete picture of the reaction. PMID:22607752

Weber, Irene T; Agniswamy, Johnson; Fu, Guoxing; Shen, Chen-Hsiang; Harrison, Robert W

2012-01-01

194

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

195

Mechanical Properties of Amorphous Metal with Dispersed Nanocrystalline Particles: Molecular Dynamics Study on Crystal Volume Fraction and Size Effects  

NASA Astrophysics Data System (ADS)

Large-scale molecular dynamics simulations of tensile deformation of amorphous metals with nanocrystalline particles were performed in order to clarify the effects of particle size and crystal volume fraction on the deformation property and the strength. It was clarified that the size effects of the particle are very small, whereas the influences of the crystal volume fraction are large. Youngs modulus and the flow stress become large as the crystal volume fraction increases. Even after the yielding of the amorphous phase, the stress of the crystal phase still continues to increase. Thus, the flow stress of the composite increases after yielding, which prevents plastic localization and improves the ductility. When the crystal volume fraction is small, the stress distribution is homogeneous in the particle including near the amorphous-crystal interface. Therefore, possibility of deformation is small, and inside-particle plastic deformation is negligible. When the crystal volume fraction is high, the particle undergoes plastic deformation even with small global deformation. After the yielding of the crystal particle, the flow stress decreases because defects are introduced into the crystal. It is expected that there is an ideal crystal volume fraction that gives the maximum ductility. A Lennard-Jones potential modified to enforce the continuity at the cut-off distance was used as an interatomic potential. The potential parameters were defined based on Inoues three basic principles.

Matsumoto, Ryosuke; Nakagaki, Michihiko

196

Variation Principle for Calculation of Many-Particle Effects in Crystals  

E-print Network

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

Halina V. Grushevskaya; Leonid I. Gurskii

2006-01-28

197

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

E-print Network

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

Gennady V. Kovalev

2014-10-12

198

Many-particle effects in accumulation kinetics of Frenkel defects in crystals  

Microsoft Academic Search

The analytical theory describing accumulation of immobile Frenkel defects created under irradiation in crystals and based on a hierarchy of equations for many-particle distribution functions of defect densities is presented and developed. Many-particle effects resulting in a radiation-induced aggregation of similar neutral defects (atoms or vacancies) are treated in detail. Their role in accumulation kinetics and the saturation concentration for

V. N. Kuzovkov; E. A. Kotomin

1984-01-01

199

The Mechanics of the Systems of Structured Particles and Irreversibility  

E-print Network

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

V. M. Somsikov

2009-08-21

200

Crystal structure of a theta-class glutathione transferase.  

PubMed Central

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

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

1995-01-01

201

Crystal structure, magnetic and electric properties of ternary neodymium stannides  

Microsoft Academic Search

New ternary Nd12Co6Sn and Nd6Co2Sn compounds were found in the Nd-rich part of the investigated NdCoSn system. The Nd12Co6Sn intermetallic compound crystallizes with the Sm12Ni6In structure type (space group Im3, a=0.9861(2) nm). The crystal structure of the Nd6Co2Sn stannide belongs to the Ho6Co2Ga structure type (space group Immm, a=0.9268(7) nm, b=0.9285(7) nm, c=0.9839(9) nm). A thermally induced transition was observed

V. Babyuk; P. Staszczuk; O. Bodak; Yu. Gorelenko; L. Romaka; Yu. Stadnyk

2004-01-01

202

Crystal structure of ScB/sub 12/  

SciTech Connect

The crystal structure of scandium dodecaboride was determined. The research material was a single crystal derived from an ingot obtained by fusion of metallic Sc and finely crystalline boron in an electric-arc furnace (Ar atmosphere). We used Laue, rotation, and inverse-lattice photography methods. The data confirmed that ScB/sub 12/ has a face-centered cubic structure. The investigation showed that with regard to the composition and structure of the resulting borides Sc exhibits complete analogy with Zr and is less similar to yttrium-group rare earth metals, for which the formation of tetraborides and hexaborides is characteristic.

Bruskov, V.A.; Zavalii, L.V.; Kuz'ma, Yu.B.

1988-08-01

203

Symmetry building Monte Carlo-based crystal structure prediction  

NASA Astrophysics Data System (ADS)

Methods are presented that allow for the automatic increase and preservation of symmetry during global optimization of crystal structures. This systematic building of symmetry allows for its incorporation into structure prediction simulations even when the space group information is not known a priori. It is shown that simulations that build and maintain symmetry converge much more rapidly to ground state crystal structures than when symmetry is ignored, allowing for the treatment of unit cells much larger than would otherwise be possible, especially when beginning from the P1 space group.

Michel, Kyle Jay; Wolverton, C.

2014-05-01

204

Band gap creation using quasiordered structures based on sonic crystals  

Microsoft Academic Search

It is well known that sonic crystals are periodic structures that present acoustic band gaps attenuation centered at frequencies related with the lattice constant of the structure. We present an approach based on genetic algorithms to create band gaps in a predetermined range of frequencies. The mechanism used by genetic algorithms to achieve this objective is the creation of vacancies

V. Romero-Garca; E. Fuster; L. M. Garca-Raffi; E. A. Snchez-Prez; M. Sopena; J. Llinares; J. V. Snchez-Prez

2006-01-01

205

On automation of the procedure for crystal structure model refinement  

SciTech Connect

The methods of automation of the procedure for crystal structure model refinement from experimental diffraction data, implemented in the ASTRA program package, are described. Such tools as statistical tests, parameter scanning, and data scanning reduce the time necessary for structural investigation. At strong correlations between parameters, especially when the data set is limited, parameter scanning has an advantage over the full-matrix refinement.

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

2008-03-15

206

Boron-oxygen polyanion in the crystal structure of tunellite  

USGS Publications Warehouse

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

Clark, J. R.

1963-01-01

207

Photonics of liquid-crystal structures: A review  

Microsoft Academic Search

The original results of studies of the electro-optical and laser effects which have been performed at the Laboratory of Liquid\\u000a Crystals of the Institute of Crystallography, Russian Academy of Sciences, over the last few years are reviewed. Cholesteric\\u000a liquid crystals as vivid representatives of photonic structures and their behavior in an electric field are considered in\\u000a detail. The formation of

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

2011-01-01

208

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 (5.010.0) and ionic strength (50200 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

209

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

E-print Network

Epitaxial growth, structure, and magnetism of epitaxial Ni80Fe20 single-crystal, bicrystal epitaxy MBE growth and structural and magnetic characterizations of high-quality single-crystal, bi the conclusion is made. II. SAMPLE PREPARATION AND MEASUREMENTS The crystal growth was carried out in a MBE

Huang, Jung-Chun

210

Photocurable pickering emulsion for colloidal particles with structural complexity.  

PubMed

We prepared polymeric microparticles with coordinated patches using oil-in-water emulsion droplets which were stabilized by adsorbed colloidal polystyrene (PS) latex particles. The oil phase was photocurable ethoxylated trimethylolpropane triacrylate (ETPTA), and the particle-armored oil droplets were solidified by UV irradiation within a few seconds to produce ETPTA-PS composite microparticles without disturbing the structures. Large armored emulsion drops became raspberry-like particles, while small emulsion drops with a few anchored particles were transformed into colloidal clusters with well-coordinated patches. For high-molecular-weight PS particles with low chemical affinity to the ETPTA monomer, the morphology of the patchy particle was determined by the volume of the emulsion drop and the contact angle of the emulsion interface on the PS particle surface. Meanwhile, for low-molecular-weight PS particles with high affinity, the ETPTA monomers were likely to swell the adsorbed PS particles, and distinctive morphologies were induced during the shrinkage of emulsion drops and the phase separation of ETPTA from the swollen PS particles. In addition, colloidal particles with large open windows were produced by dissolving the PS particles from the patchy particles. We observed photoluminescent emission from the patchy particles in which dye molecules were dispersed in the ETPTA phase. Finally, we used Surface Evolver simulation to predict equilibrium structures of patchy particles and estimate surface energies which are essential to understand the underlying physics. PMID:18237213

Kim, Shin-Hyun; Yi, Gi-Ra; Kim, Kyu Han; Yang, Seung-Man

2008-03-18

211

Structure of ice crystallized from supercooled water  

PubMed Central

The freezing of water to ice is fundamentally important to fields as diverse as cloud formation to cryopreservation. At ambient conditions, ice is considered to exist in two crystalline forms: stable hexagonal ice and metastable cubic ice. Using X-ray diffraction data and Monte Carlo simulations, we show that ice that crystallizes homogeneously from supercooled water is neither of these phases. The resulting ice is disordered in one dimension and therefore possesses neither cubic nor hexagonal symmetry and is instead composed of randomly stacked layers of cubic and hexagonal sequences. We refer to this ice as stacking-disordered ice I. Stacking disorder and stacking faults have been reported earlier for metastable ice I, but only for ice crystallizing in mesopores and in samples recrystallized from high-pressure ice phases rather than in water droplets. Review of the literature reveals that almost all ice that has been identified as cubic ice in previous diffraction studies and generated in a variety of ways was most likely stacking-disordered ice I with varying degrees of stacking disorder. These findings highlight the need to reevaluate the physical and thermodynamic properties of this metastable ice as a function of the nature and extent of stacking disorder using well-characterized samples. PMID:22232652

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

2012-01-01

212

Large Eddy Simulations and stereoscopic particle image velocimetry measurements in a scraped heat exchanger crystallizer  

E-print Network

Large Eddy Simulations and stereoscopic particle image velocimetry measurements in a scraped heat *Corresponding author: M.Rodriguez@tudelft.nl Abstract The transport phenomena in scraped heat exchanger crystallizers are critical for the process performance. Fluid flow and turbulence close to the heat exchanger

Paris-Sud XI, Université de

213

Drying dissipative structures of lycopodium spore particles in aqueous dispersion  

Microsoft Academic Search

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

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

2010-01-01

214

Using polarimetric remote sensing measurements to estimate ice particle size, optical depth and ice water path during CRYSTAL-FACE  

Microsoft Academic Search

In situ observations made during the CRYSTAL-FACE field experiment have indicated that ice crystals have smaller sizes and are more reflective than is commonly assumed in most current climate models. The size of the particles appears to be principally determined by temperature with the smallest particles being found at the coldest temperatures. Previous analyses of polarimetric measurements in non-absorbing bands

I. Geogdzhayev; B. Cairns; M. I. Mishchenko; L. D. Travis

2006-01-01

215

Crystal growth and twinned crystal structure of Sr2CaWO6.  

PubMed

Single crystals of Sr(2)CaWO(6) have been prepared by sintering at high temperature. Powder samples were compressed into rods and heated up to 1953 K. This seems a promising new route for further studies of the structure and physical properties of double perovskites. The structural model of Sr(2)CaWO(6) includes a quantitative description of the twinning shown by the diffraction pattern that should be present in almost any single-crystal specimen for this type of compound. PMID:20305344

Madariaga, G; Faik, A; Breczewski, T; Igartua, J M

2010-04-01

216

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

217

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

218

Three-dimensional structure and defects in colloidal photonic crystals revealed by tomographic scanning transmission X-ray microscopy.  

PubMed

Self-assembled colloidal crystals have attracted major attention because of their potential as low-cost three-dimensional (3D) photonic crystals. Although a high degree of perfection is crucial for the properties of these materials, little is known about their exact structure and internal defects. In this study, we use tomographic scanning transmission X-ray microscopy (STXM) to access the internal structure of self-assembled colloidal photonic crystals with high spatial resolution in three dimensions for the first time. The positions of individual particles of 236 nm in diameter are identified in three dimensions, and the local crystal structure is revealed. Through image analysis, structural defects, such as vacancies and stacking faults, are identified. Tomographic STXM is shown to be an attractive and complementary imaging tool for photonic materials and other strongly absorbing or scattering materials that cannot be characterized by either transmission or scanning electron microscopy or optical nanoscopy. PMID:22260512

Hilhorst, Jan; van Schooneveld, Matti M; Wang, Jian; de Smit, Emiel; Tyliszczak, Tolek; Raabe, Jrg; Hitchcock, Adam P; Obst, Martin; de Groot, Frank M F; Petukhov, Andrei V

2012-02-21

219

Crystal structure tuning in GaAs nanowires using HCl.  

PubMed

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

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

2014-07-21

220

Crystal structure of simple metals at high pressures  

SciTech Connect

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

Degtyareva, Olga (Edinburgh)

2010-10-22

221

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

NASA Astrophysics Data System (ADS)

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

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

2010-11-01

222

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

SciTech Connect

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

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

2007-12-12

223

New crystal structures of PII-type ATPases: excitement continues.  

PubMed

P-type ATPases are ATP-powered ion pumps, classified into five subfamilies (PI-PV). Of these, PII-type ATPases, including Ca2+-ATPase, Na+,K+-ATPase and gastric H+,K+-ATPase, among others, have been the most intensively studied. Best understood structurally and biochemically is Ca2+-ATPase from sarcoplasmic reticulum of fast twitch skeletal muscle (sarco(endo)plasmic reticulum Ca2+-ATPase 1a, SERCA1a). Since publication of the first crystal structure in 2000, it has continuously been a source of excitement, as crystal structures for new reaction intermediates always show large structural changes. Crystal structures now exist for most of the reaction intermediates, almost covering the entire reaction cycle. This year the crystal structure of a missing link, the E1Mg2+ state, finally appeared, bringing another surprise: bound sarcolipin (SLN). The current status of two other important PII-type ATPases, Na+,K+-ATPase and H+,K+-ATPase, is also briefly described. PMID:23871101

Toyoshima, Chikashi; Cornelius, Flemming

2013-08-01

224

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

225

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

226

Electronic structure of the CuBS2 crystal  

NASA Astrophysics Data System (ADS)

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

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

2012-09-01

227

Internal motion in protein crystal structures  

PubMed Central

The binding states of the substrates and the environment have significant influence on protein motion. We present the analysis of such motion derived from anisotropic atomic displacement parameters (ADPs) in a set of atomic resolution protein structures. Local structural motion caused by ligand binding as well as functional loops showing cooperative patterns of motion could be inferred. The results are in line with proposed protonation states, hydrogen bonding patterns and the location of distinctly flexible regions: we could locate the mobile active site loop in a virus integrase, distinguish the subdomains in RNAse A and hydroxynitrile lyase, and reconstruct the molecular architecture in a xylanase. We demonstrate that the ADP-based motion analysis provides information at high level of detail and that the structural changes needed for substrate attachment or release may be derived from single X-ray structures. PMID:20198682

Schmidt, Andrea; Lamzin, Victor S

2010-01-01

228

Internal motion in protein crystal structures.  

PubMed

The binding states of the substrates and the environment have significant influence on protein motion. We present the analysis of such motion derived from anisotropic atomic displacement parameters (ADPs) in a set of atomic resolution protein structures. Local structural motion caused by ligand binding as well as functional loops showing cooperative patterns of motion could be inferred. The results are in line with proposed protonation states, hydrogen bonding patterns and the location of distinctly flexible regions: we could locate the mobile active site loop in a virus integrase, distinguish the subdomains in RNAse A and hydroxynitrile lyase, and reconstruct the molecular architecture in a xylanase. We demonstrate that the ADP-based motion analysis provides information at high level of detail and that the structural changes needed for substrate attachment or release may be derived from single X-ray structures. PMID:20198682

Schmidt, Andrea; Lamzin, Victor S

2010-05-01

229

Crystal growth of lead carbonates: Influence of the medium and relationship between structure and habit  

NASA Astrophysics Data System (ADS)

The crystal-growth features of cerussite and hydrocerussite formed by two different chemical reactions are studied. With respect to the former, acid-vapour oxidation and latter carbonation of metallic lead produced a nanocrystalline precipitate for the lead carbonates. In the latter, cerussite and hydrocerusite are precipitated after mixing two mother solutions in liquid and solid porous media, forming diverse polyhedral morphologies. Crystal growth in gel medium gives rise to pseudo-cubic morphologies by the aggregation of one-micron-sized particles of cerussite. Skeletal morphologies composed of cyclically twinned crystals of cerussite also occur in gel-growth experiments. These morphologies were determined by kinetic factors, in particular by high supersaturation conditions that led to high growth rates. Kinetics also favoured the predominance of weak over strong interactions during crystal growth. The habit observed for cerussite crystals has been explained based on crystal-structure considerations and quantum-mechanical calculations. In particular, the crystal growth along the a direction in cyclically twinned crystals is explained by the binding forces between the CO32- molecular group and Pb2+, defining an uninterrupted chain of strong bonds along that direction. However, the preferred growth along the c direction observed for the cerussite crystal formed in gel media is here attributed to an intermolecular interaction through C-C bonds. The occurrence of a chemical bonding between the C atoms of the CO32- molecular groups aligned along the c direction is clearly shown by the theoretical analysis of the electron density with the quantum theory of atoms in molecules (QTAIM).

Snchez-Navas, Antonio; Lpez-Cruz, Olimpia; Velilla, Nicols; Vidal, Isaac

2013-08-01

230

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; Demirrs, Ahmet Faik; Imhof, Arnout; Dijkstra, Marjolein

2010-05-12

231

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

NASA Astrophysics Data System (ADS)

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

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

2014-04-01

232

Photonics of liquid-crystal structures: A review  

SciTech Connect

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

Palto, S. P., E-mail: palto@online.ru; Blinov, L. M.; Barnik, M. I.; Lazarev, V. V.; Umanskii, B. A.; Shtykov, N. M. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

2011-07-15

233

Single-crystal YBa/sub 2/Cu/sub 3/O/sub 7/ particle formation by aerosol decomposition  

SciTech Connect

Single-crystal YBa/sub 2/Cu/sub 3/O/sub 7/ particles have been formed in a carbon-free gaseous flow system by thermally decomposing droplets containing the nitrate salts of Y, Ba, and Cu in water followed by calcining and annealing in the gas phase. The electron diffraction pattern for particles ranging in size from 0.1 to 1.5 ..mu..m corresponded to single crystals of orthorhombic YBa/sub 2/Cu/sub 3/O/sub 7/ while the powder x-ray diffraction pattern confirmed the presence of single-phase material. Energy dispersive spectroscopy showed a similar composition for all particles examined. Iodometric titration showed that the particles were fully oxygenated. Two types of single-crystal particles were observed, equiaxed and elongated. Formation of solid single-crystal particles is favored by operation near the melting point of the material and by long reactor-residence times.

Kodas, T.; Datye, A.; Lee, V.; Engler, E.

1989-03-01

234

Crystal structure and microstructure of cholesteryl oleyl carbonate.  

PubMed

The crystal structure as well as the microstructure, i.e., size and strain, of crystallites of cholesteryl oleyl carbonate was determined from X-ray powder diffraction data. The X-ray line broadening was analyzed through the refinement of TCH-pseudo-Voigt function parameters (isotropic effects) and the refinement of multipolar functions, i.e., symmetrized cubic harmonics (anisotropic effects). The crystal structure turns out to be primitive monoclinic, space group Pc, type I monolayer having two molecules per unit cell with parameters: a=18.9210.006?, b=12.9520.003?, c=9.2760.002? and ?=91.320.03. The average size of a well ground specimen of crystallites was 60nm. The average micro-strain, e.g., 4510(-4) has been tentatively attributed to fatty chain conformational disorder. The unit cell parameters, including the lamellar thickness, of COC crystal is very closely similar to those of another, structurally similar cholesterol ester, e.g., cholesteryl oleate (CO) crystal, space group P2(1), type II monolayer. Type I monolayer structure has been established for COC on the basis of the intensity calculations of the XRD profiles of both CO and COC. The dipolar and structural disorder in a 4:1 molar, binary mixture of CO and COC can be accommodated in an induced smectic phase with a lamellar thickness, which is nearly equal to that of pure CO or pure COC. PMID:20951687

Das, Pradip; De, Joyes

2011-01-01

235

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 proteins relationship to disease treatment such as that for pneumonia and other related pathologies.

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

2009-01-01

236

[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

237

Crystal structure and vibrational spectral studies of a new organic-inorganic crystal: 4-Benzylpiperidinium trioxonitrate  

NASA Astrophysics Data System (ADS)

Single crystals of a new organic-inorganic crystal, 4-benzylpiperidinium trioxonitrate (4-BPPN) were grown by slow evaporation at room temperature and were characterized by X-ray diffraction, DTA-TG measurement, FT-IR and FT-Raman spectroscopies. The title compound crystallizes in the monoclinic system P21/c at room temperature with the following parameters: a = 12.787(8) , b = 9.007(5) , c = 11.120(5) , ? = 95.974(2) and Z = 4. Its crystal structure is packing of alternated inorganic and organic layers parallel to (a, c) planes. The different components are connected by a bi-dimensional network of N-H⋯O hydrogen bonds. The ability of ions to form spontaneous three-dimensional structure through N-H⋯O hydrogen bond is fully utilized. These hydrogen bonds give notable vibrational effects. The optimized molecular structure and the vibrational spectra were calculated by the Density Functional Theory (DFT) method using the B3LYP function with the 6-31G(d) basis set. All observed vibrational bands have been discussed and assigned to normal mode or to combinations on the basis of our DFT calculations as a primary source of attribution and also by comparison with the previous results for similar compounds. Good consistency is found between the calculated results and the experimental structure, IR, and Raman spectra.

Kessentini, Yassmin; Ben Ahmed, Ali; Al-Juaid, Salih S.; Mhiri, Tahar; Elaoud, Zakaria

2014-08-01

238

Crystal structure and vibrational spectral studies of a new organic-inorganic crystal: 4-Benzylpiperidinium trioxonitrate.  

PubMed

Single crystals of a new organic-inorganic crystal, 4-benzylpiperidinium trioxonitrate (4-BPPN) were grown by slow evaporation at room temperature and were characterized by X-ray diffraction, DTA-TG measurement, FT-IR and FT-Raman spectroscopies. The title compound crystallizes in the monoclinic system P21/c at room temperature with the following parameters: a=12.787(8), b=9.007(5), c=11.120(5), ?=95.974(2) and Z=4. Its crystal structure is packing of alternated inorganic and organic layers parallel to (a, c) planes. The different components are connected by a bi-dimensional network of N-H?O hydrogen bonds. The ability of ions to form spontaneous three-dimensional structure through N-H?O hydrogen bond is fully utilized. These hydrogen bonds give notable vibrational effects. The optimized molecular structure and the vibrational spectra were calculated by the Density Functional Theory (DFT) method using the B3LYP function with the 6-31G(d) basis set. All observed vibrational bands have been discussed and assigned to normal mode or to combinations on the basis of our DFT calculations as a primary source of attribution and also by comparison with the previous results for similar compounds. Good consistency is found between the calculated results and the experimental structure, IR, and Raman spectra. PMID:24755637

Kessentini, Yassmin; Ben Ahmed, Ali; Al-Juaid, Salih S; Mhiri, Tahar; Elaoud, Zakaria

2014-08-14

239

Evidence from Crystal Structures in Regard to Atomic Structures  

Microsoft Academic Search

The distribution of valence electrons in the diamond and similar crystals.-Because of the cubical symmetry, the equivalent scattering power of all the atoms, and the absence of pyro- and piezo-electric effect, the atoms in the diamond cannot be held together as a result of the transfer of electrons from atom to atom. Symmetry requirements also eliminate any cubical arrangement of

Maurice L. Huggins

1926-01-01

240

Molecular dynamics simulation of fast particle irradiation on the single crystal CeO2  

NASA Astrophysics Data System (ADS)

We used a molecular dynamics method to simulate structural relaxation caused by the high-energy-ion irradiation of single crystal CeO2. As the initial condition, we assumed high thermal energy was supplied to the individual atoms within a cylindrical region of nanometer-order diameter located in the center of the single crystal. The potential proposed by Inaba et al. was utilized to calculate interactions between atoms [H. Inaba, R. Sagawa, H. Hayashi, K. Kawamura, Solid State Ionics 122 (1999) 95-103]. The supplied thermal energy was first spent to change the crystal structure into an amorphous one within a short period of about 0.3 ps, then it was dissipated in the crystal. We compared the obtained results with those of computer simulations for UO2 and found that CeO2 was more stable than UO2 when supplied with high thermal energy.

Sasajima, Y.; Ajima, N.; Osada, T.; Ishikawa, N.; Iwase, A.

2013-11-01

241

Crystal structure of catechol O-methyltransferase.  

PubMed

Catechol O-methyltransferase (COMT, EC 2.1.1.6) is important in the central nervous system because it metabolizes catecholamine neurotransmitters such as dopamine. The enzyme catalyses the transfer of the methyl group from S-adenosyl-L-methionine (AdoMet) to one hydroxyl group of catechols. COMT also inactivates catechol-type compounds such as L-DOPA. With selective inhibitors of COMT in combination with L-DOPA, a new principle has been realized in the therapy of Parkinson's disease. Here we solve the atomic structure of COMT to 2.0 A resolution, which provides new insights into the mechanism of the methyl transfer reaction. The co-enzyme-binding domain is strikingly similar to that of an AdoMet-dependent DNA methylase, indicating that all AdoMet methylases may have a common structure. PMID:8127373

Vidgren, J; Svensson, L A; Liljas, A

1994-03-24

242

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

243

Unusual Features of Crystal Structures of Some Simple Copper Compounds  

ERIC Educational Resources Information Center

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

Douglas, Bodie

2009-01-01

244

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

245

Structure of desheptapeptide (B24B30) insulin in a new crystal form  

Microsoft Academic Search

The structure of desheptapeptide (B24B30) insulin (DHPI) in a new crystal form (form B) has been determined and refined to\\u000a 0.2 nm resolution. The crystals were obtained under the same crystallization condition as previously reported crystal form\\u000a (form A). The overall structures of the two crystal forms are similar but obvious differences can be observed in crystal packing\\u000a and local

Sujin Bao; Jiping Zhang; Wenrui Chang; Dongcai Liang

1999-01-01

246

Crystal structure of photolysed carbonmonoxy-myoglobin.  

PubMed

Myoglobin is a globular haem protein that reversibly binds ligands such as O2 and CO. Single photons of visible light can break the covalent bond between CO and the haem iron in carbon-monoxy-myoglobin (MbCO) and thus form an unstable intermediate, Mb*CO, with the CO inside the protein. The ensuing rebinding process has been extensively studied as a model for the interplay of dynamics, structure and function in protein reactions. We have used X-ray crystallography at liquid-helium temperatures to determine the structure of Mb*CO to a resolution of 1.5 A. The photodissociated CO lies on top of the haem pyrrole ring C. Comparison with the CO-bound and unligated myoglobin structures reveals that on photodissociation of the CO, the haem 'domes', the iron moves partially out of the haem plane, the iron-proximal histidine bonds is compressed, the F helix is strained and the distal histidine swings towards the outside of the ligand-binding pocket. PMID:7935843

Schlichting, I; Berendzen, J; Phillips, G N; Sweet, R M

1994-10-27

247

Crystal Structure and Stereochemistry Study of 2-Substituted Benzoxazole Derivatives  

PubMed Central

The structure of 2-[(4-chlorophenylazo) cyanomethyl] benzoxazole, C15H9ClN4O (I), has triclinic (P1?) symmetry. The structure displays NH ? N hydrogen bonding. The structure of 2-[(arylidene) cyanomethyl] benzoxazoles, C17H10N2O3 (II), has triclinic (P1?) symmetry. The structure displays CH ? N, CH ? C hydrogen bonding. In (I), the chlorophenyl and benzoxazole groups adopt a trans configuration with respect to the central cyanomethyle hydrazone moiety. Compound (II) crystallized with two molecules in the asymmetric unit shows cisoid conformation between cyano group and benzoxazole nitrogen, contrary to (I). In (II) the benzodioxole has an envelope conformation (the C17 atom is the flap atom). The molecular geometry obtained using molecular mechanics (MM) calculations has been discussed along with the results of single crystal analysis. PMID:24944828

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

2014-01-01

248

Photonic Crystal Electrode to be Used in Organic LED Structures  

NASA Astrophysics Data System (ADS)

In this work we report the possibility to obtain a high refractive index grid anode directly on the substrate surface by fabricating a relatively large-area photonic crystal (PC) structure using the combinations of electron beam lithography (EBL) and focused ion beam (FIB) techniques. The performance of the realized photonic crystal (PC) structure were enhanced by milling the ITO layer until the glass substrate and by removing the further refractive index jump between the PC and the substrate. The good properties of highly conductive poly(3,4 ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS), ensured a continuous path for the current and a high refractive index jump for the PC structure by filling the holes in the PC structure.

Petti, L.; Rippa, M.; Capasso, R.; Nenna, G.; De Girolamo Del Mauro, A.; La Ferrara, V.; Pacheri Madathil, A.; Minarini, C.

2013-01-01

249

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

250

Crystal Structure of the Bacillus subtilis Superoxide Dismutase  

SciTech Connect

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

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

2008-06-01

251

Structure and switching dynamics in ferroelectric crystal and liquid crystal thin films  

NASA Astrophysics Data System (ADS)

The structure and switching dynamics of ferroelectric solid state and liquid crystal thin films were investigated experimentally using x-ray scattering, dielectric measurements, and optical microspectroscopy. Crystalline piezoelectric ferroelectric films, formed by sol-gel and sputter deposition, were developed and analyzed for application as high speed nonvolatile memories. Ferroelectric liquid crystal devices were studied for application as fast electro-optic light valves in spatial light modulator applications. A novel thermo-optical effect in ferroelectric lead magnesium niobate suitable for use in pressure sensing applications was discovered.

Clark, Noel A.; Scott, James F.

1993-03-01

252

Molecular and crystal structures of 4-acylphenyl 4'-alkyloxybenzoates  

NASA Astrophysics Data System (ADS)

The crystal structures of four liquid-crystal (LC) compounds belonging to 4-acylphenyl 4'-alkyloxybenzoates with the general formula C n H2 n + 1-C(O)-C6H4-O-C(O)-C6H4-O-C m H2 m + 1 numbered as 1/6, 1/7, 2/7, and 3/7 (the numbers in the code indicate the ratios of the numbers of alkyl-chain units, n/ m) are determined. Compounds 1/6 and 1/7 form smectic and nematic phases, but they are monotropic mesogens, whereas compounds 2/7 and 3/7 form only an enantiotropic smectic phase. Compound 3/7 crystallizes in two crystal modificationstriclinic with Z' = 2 ( 3/7 tr ) and monoclinic with Z' = 4 (sp. gr. P2, 3/7 mon ). All crystals consist of alternating aromatic and aliphatic regions and are characterized by the presence of weak directional interactions, such as C-H...O hydrogen bonds and ?-stacking interactions. This provides the necessary conditions for the formation of a mesophase, and the existence of two types of structure-forming units is in line with the formation of a smectic phase. An explanation is proposed for the monotropic properties of 1/6 and 1/7.

Konstantinov, I. I.; Churakov, A. V.; Kuz'mina, L. G.

2013-01-01

253

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

254

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

NASA Astrophysics Data System (ADS)

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; Perumal, Rajesh Narayana

2014-04-01

255

Dynamics and Structure of Nanocrystalline Carbon Particles  

Microsoft Academic Search

Ultrathin amorphous carbon films deposited on SiO2 substrates have been crystallized to form isolated nanocrystallites for Raman scattering and transmission electron microscope studies. Interference enhanced Raman scattering as a function of film thickness (0.7-2nm) has indicated substantial changes in the low frequency scattering below 1000cm-1. A decrease in the separation between the two main features in the disorder induced Raman

V. I. Merkulov; J. S. Lannin; J. M. Cowley

1996-01-01

256

Synthesis, crystal structure, and photoluminescence of a zinc metalloporphyrin  

NASA Astrophysics Data System (ADS)

A zinc metalloporphyrin, ZnTCPP(acetone) ( 1) (TCPP = meso-tetra(4-carboxyphenyl)porphyrin), has been prepared via a solvothermal reaction and structurally characterized by single-crystal X-ray diffraction. Compound 1 features an isolated structure with a planar macrocycle and an embedded zinc ion binded to four pyrrole nitrogen atoms and one acetone oxygen atom. Photoluminescent investigation reveals that compound 1 displays an intensive emission in the red region.

Chen, Wen-Tong; Yi, Xiu-Guang; Luo, Zhi-Gang; Fu, Hong-Ru; Liu, Juan

2014-07-01

257

Crystal structure of new AsS2 compound  

NASA Astrophysics Data System (ADS)

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

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

2013-01-01

258

The crystal structure of gold telluride iodide AuTel  

Microsoft Academic Search

The crystal structure of AuTel has been determined. It is monoclinic with space group P21\\/c, a = 7.3130, b = 7.6242, c = 7.2550 , beta = 106.263, and Z = 4. Intensities were measured on an automatic diffractometer, and the structure was refined, with anisotropic temperature factors, to R = 0.055. With a distorted square-planar coordination by three bridging

J. Fenner; D. Mootz

1978-01-01

259

Crystal structure of interleukin 8: Symbiosis of NMR and crystallography  

SciTech Connect

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

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

1991-01-15

260

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

PubMed

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

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

2011-09-26

261

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

NASA Astrophysics Data System (ADS)

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

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

2013-09-01

262

Crystal structure and physical characterization of neotame methanol solvate  

Microsoft Academic Search

The crystal structure of the methanol solvate (empirical formula: 2C20H30N2O53CH3OH) of a new dipeptide sweetener, neotame (N-(3,3-dimethylbutyl)-L-a-aspartyl-L-phenylalanine 1-methyl ester), has been determined. Crystal data: a = 9.8989(1), b = 18.1331(1), c = 27.5725(1) , orthorhombic, space group P212121, with Z = 4. Each unit cell includes 8 neotame and 12 methanol molecules. Disorder exists in one neotame molecule and one

Zedong Dong; Victor G. Young; Brian E. Padden; Steve A. Schroeder; Indra Prakash; Eric J. Munson; David J. W. Grant

1999-01-01

263

Laser Trapping of Small Colloidal Particles in a Nematic Liquid Crystal: Clouds and Ghosts  

NASA Astrophysics Data System (ADS)

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

Muevi?, I.; karabot, M.; Babi?, D.; Osterman, N.; Poberaj, I.; Nazarenko, V.; Nych, A.

2004-10-01

264

Laser crystal analysis using the OLCAO electronic structure method  

NASA Astrophysics Data System (ADS)

This work investigates the theoretical analysis of laser crystals through the band structure method of Orthogonalized Linear Combination of Atomic Orbitals. A review of the more traditional theoretical method, the Crystal Field Theory, is provided for comparison with the Orthogonalized Linear Combination of Atomic Orbitals theory. The benefits of the more computationally intensive band structure method in analyzing the complicated crystal structures typical of laser materials are presented. The method is then utilized to study Cr4+-doped yttrium aluminum garnet and its application as a passive Q-switch device. The detailed analysis provided by the Orthogonalized Linear Combination of Atomic Orbitals method leads to an alternate model for optical transitions within the passive Q-switch application, and experimental evidence validating this model is presented. The method is then used to study undoped, bulk yttrium aluminum garnet and gadolinium scandium gallium garnet crystals with emphasis on the radiation hardness of laser rods using these hosts. Plans for future work are presented, including a suggestion of how this powerful theoretical method can be used in a predictive mode to facilitate the design of novel laser materials.

Brickeen, Brian Keith

1999-12-01

265

Electronic structures of lead iodide based low-dimensional crystals  

NASA Astrophysics Data System (ADS)

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

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

2003-04-01

266

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

267

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

PubMed

A particle-based multiplexed DNA assay based on encoded porous SiO(2) 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 microm in diameter and 10 microm 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; Sailor, Michael J; Miskelly, Gordon M

2009-04-01

268

Particles as Fundaments of Discourse Structuring.  

ERIC Educational Resources Information Center

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

Fernandez-Vest, M. M. Jocelyne

269

Structural characteristics and second order nonlinear optical properties of borate crystals  

E-print Network

and related effects of an assigned crystal. It might not only form the basis but also provide an opportunityStructural 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

Osnabrück, Universität

270

Structure of RCC1 chromatin factor bound to the nucleosome core particle  

SciTech Connect

The small GTPase Ran enzyme regulates critical eukaryotic cellular functions including nuclear transport and mitosis through the creation of a RanGTP gradient around the chromosomes. This concentration gradient is created by the chromatin-bound RCC1 (regulator of chromosome condensation) protein, which recruits Ran to nucleosomes and activates Ran's nucleotide exchange activity. Although RCC1 has been shown to bind directly with the nucleosome, the molecular details of this interaction were not known. Here we determine the crystal structure of a complex of Drosophila RCC1 and the nucleosome core particle at 2.9 {angstrom} resolution, providing an atomic view of how a chromatin protein interacts with the histone and DNA components of the nucleosome. Our structure also suggests that the Widom 601 DNA positioning sequence present in the nucleosomes forms a 145-base-pair nucleosome core particle, not the expected canonical 147-base-pair particle.

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

2010-11-11

271

Crystal structure and mechanistic investigation of the twister ribozyme.  

PubMed

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

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

2014-09-01

272

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

273

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

NASA Technical Reports Server (NTRS)

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

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

2003-01-01

274

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

275

Structure of the nucleosome core particle at 8 A resolution.  

PubMed

The x-ray crystallographic structure of the nucleosome core particle has been determined using 8 A resolution diffraction data. The particle has a mean diameter of 106 A and a maximum thickness of 65 A in the superhelical axis direction. The longest chord through the histone core measures 85 A and is in a non-axial direction. The 1.87 turn superhelix consists of B-DNA with about 78 base pairs or 7.6 helical repeats per superhelical turn. The mean DNA helical repeat contains 10.2 +/- 0.05 base pairs and spans 35 A, slightly more than standard B-DNA. The superhelix varies several Angstroms in radius and pitch, and has three distinct domains of curvature (with radii of curvature of 60, 45 and 51 A). These regions are separated by localized sharper bends +/- 10 and +/- 40 base pairs from the center of the particle, resulting in an overall radius of curvature about 43 A. Compression of superhelical DNA grooves on the inner surface and expansion on the outer surface can be seen throughout the DNA electron density. This density has been fit with a double helical ribbon model providing groove width estimates of 12 +/- 1 A inside vs. 19 +/- 1 A outside for the major groove, and 8 +/- 1 A inside vs. 13 +/- 1 A outside for the minor groove. The histone core is primarily contained within the bounds defined by the superhelical DNA, contacting the DNA where the phosphate backbone faces in toward the core. Possible extensions of density between the gyres have been located, but these are below the significance level of the electron density map. In cross-section, a tripartite organization of the histone octamer is apparent, with the tetramer occupying the central region and the dimers at the extremes. Several extensions of histone density are present which form contacts between nucleosomes in the crystal, perhaps representing flexible or "tail" histone regions. The radius of gyration of the histone portion of the electron density is calculated to be 30.4 A (in reasonable agreement with solution scattering values), and the histone core volume in the map is 93% of its theoretical volume. PMID:2684220

Uberbacher, E C; Bunick, G J

1989-08-01

276

Crystal and molecular structure of N-methylpiperidine betaine hydrochloride  

NASA Astrophysics Data System (ADS)

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

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

2003-06-01

277

Band structures of phononic-crystal plates in the form of a sandwich-layered structure.  

PubMed

This study investigates the propagation of Lamb waves in phononic-crystal plates in the form of a sandwich-layered structure. The composite plates are composed of periodic layers bilaterally deposited on both sides of the homogeneous core layer. Using the analyses of the band structures and the transmission spectra, it is revealed that the core layer may induce significant modulations to the lower-order Lamb modes. The modulations are ascribed to the reshaped particle displacement fields of the eigenmodes. Prominently, the core layer made of soft material (rubber) combines the identical eigenmodes of the periodic layers into a pair of asymmetric and symmetric modes in which case the periodic layers vibrate independently. However, the core layer made of hard material (tungsten) or medium hardness material (silicon) couples the periodic layers tightly, in which case the composites vibrate as a whole. In addition, it is found that the phononic band gaps are very sensitive to the thickness of the core layer; this could be indispensable to practical applications such as bandgap tuning. PMID:22087902

Cheng, Y; Liu, X J; Wu, D J

2011-11-01

278

Crystal structure of a putative isochorismatase hydrolase from Oleispira antarctica  

PubMed Central

Isochorismatase-like hydrolases (IHL) constitute a large family of enzymes divided into five structural families (by SCOP). IHLs are crucial for siderophore-mediated ferric iron acquisition by cells. Knowledge of the structural characteristics of these molecules will enhance the understanding of the molecular basis of iron transport, and perhaps resolve which of the mechanisms previously proposed in the literature is the correct one. We determined the crystal structure of the apo-form of a putative isochorismatase hydrolase OaIHL (PDB code: 3LQY) from the antarctic ?-proteobacterium Oleispira antarctica, and did comparative sequential and structural analysis of its closest homologs. The characteristic features of all analyzed structures were identified and discussed. We also docked isochorismate to the solved crystal structure by in silico methods, to highlight the interactions of the active center with the substrate. The putative isochorismate hydrolase OaIHL from Oleispira antarctica possesses the typical catalytic triad for IHL proteins. Its active center resembles those IHLs with a D-K-C catalytic triad, rather than those variants with a D-K-X triad. OaIHL shares some structural and sequential features with other members of the IHL superfamily. In silico docking results showed that despite small differences in active site composition, isochorismate binds to in the structure of OaIHL in a similar mode to its binding in phenazine biosynthesis protein PhzD (PDB code 1NF8). PMID:22350524

Goral, Anna M.; Tkaczuk, Karolina L.; Chruszcz, Maksymilian; Kagan, Olga; Savchenko, Alexei; Minor, Wladek

2012-01-01

279

Dissipative Particle Dynamics Simulation of Structure Properties of Lipid Micelles  

NASA Astrophysics Data System (ADS)

We chose dissipative particle dynamics (DPD) simulation to study the micelle structure properties. The self-assembly lipid is modeled by a flexible chain with head and tail particles. By changing interaction parameters between the solution particles and the lipid particles, three types of solution are considered: water, oil and water-oil mixture. It is found that the tail/head chains forming the micelle core have a very disorder distribution. The relation between the core radius with the aggregation number as well as the number of oil particles inside is obtained based on the simulation results and the molecular packing parameter. The mean density of particles in the core is higher than that in the simulation box. For micelles without oils inside, the density depends on the number of head particles in a lipid molecule, and the dependence becomes weaker as more oil particles are captured. At the core surface, head particles form clusters with water particles incorporated between the clusters. Comparisons with results from other simulation method such as MD show that DPD achieves high performance in simulating micelle formation and structure properties.

Zhang, Jinsuo; Jiang, Yi

2006-03-01

280

A Binary Particle Swarm Optimization for Structural Topology Optimization  

Microsoft Academic Search

Binary particle swarm optimization (BPSO) algorithm is applied to continuum structural topology design. An overview of the PSO and binary PSO algorithms are first described. A discretized topology design representation and the method for mapping each binary particle into toplogy representation are then detailed. Subsequently, a modified BPSO algorithm adopting binary bit-string type code and logic AND, OR and XOR

Guan-Chun Luh; Chun-Yi Lin

2010-01-01

281

Designing 'Smart' Particles for the Assembly of Complex Macroscopic Structures**  

PubMed Central

Surface functionalization with a branched copolymer surfactant is used to create responsive inorganic particles that can self-assemble in complex structures. The assembly process is triggered by a pH switch that reversibly activates multiple hydrogen bonds between ceramic particles and soft templates. PMID:23780923

Barg, S.; Bell, R.; Weaver, J.; Walter, C.; Goyos, L.; Saiz, E.

2013-01-01

282

Chirality in Liquid Crystals: from Microscopic Origins to Macroscopic Structure  

E-print Network

Molecular chirality leads to a wonderful variety of equilibrium structures, from the simple cholesteric phase to the twist-grain-boundary phases, and it is responsible for interesting and technologically important materials like ferroelectric liquid crystals. This paper will review some recent advances in our understanding of the connection between the chiral geometry of individual molecules and the important phenomenological parameters that determine macroscopic chiral structure. It will then consider chiral structure in columnar systems and propose a new equilibrium phase consisting of a regular lattice of twisted ropes.

T. C. Lubensky; A. B. Harris; Randall D. Kamien; Gu Yan

1997-10-31

283

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

284

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

285

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

286

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

287

Single-particle resonances in continuum nuclear structure calculations  

SciTech Connect

Accuracy and stability of single-particle resonance parameters under changes of a resonance wave function'' are examined in the context of a projection technique. Implications for their use in nuclear structure calculations are discussed.

Teruya, N.; de Toledo Piza, A.F.R.; Dias, H. (Instituto de Fisica, Universidade de Sao Paulo, Caixa Postal 20516, 01498 Sao Paulo, SP, Brazil (BR))

1991-07-01

288

Photon structure functions with heavy particle mass effects  

E-print Network

In the framework of the perturbative QCD we investigate heavy particle mass effects on the unpolarized and polarized photon structure functions, $F_2^\\gamma$ and $g_1^\\gamma$, respectively. We present our basic formalism to treat heavy particle mass effects to NLO in perturbative QCD. We also study heavy quark effects on the QCD sum rule for the first moment of $g_1^\\gamma$, which is related to axial anomaly. The photon structure function in supersymmetric QCD is also briefly discussed.

Tsuneo Uematsu

2012-08-16

289

Crystal Structure of a Hyperactive Escherichia coli Glycerol Kinase Mutant Gly230 f Asp Obtained Using Microfluidic Crystallization Devices,  

E-print Network

Crystal Structure of a Hyperactive Escherichia coli Glycerol Kinase Mutant Gly230 f Asp Obtained ABSTRACT: The crystal structure of an Escherichia coli glycerol kinase mutant Gly230 f Asp (GKG230D GK monomer conformations in the presence of glycerol and in the absence of a nucleotide substrate

Quake, Stephen R.

290

Three-dimensional structure of polystyrene colloidal crystal by synchrotron radiation X-ray phase-contrast computed tomography  

NASA Astrophysics Data System (ADS)

Colloidal crystal with long-range ordered structure has attracted great attention for their applications in various fields. Although perfect colloidal crystals have been achieved by some fabrications for utilization, little is known about their exact structures and internal defects. In this study, we use synchrotron radiation (SR) phase-contrast computed tomography (CT) to noninvasively access the internal structure of polystyrene (PS) colloidal crystals in three dimensions (3D). The phase-attenuation duality Paganin algorithm phase retrieval was employed to achieve a satisfactory contrast and outline of the spheres. After CT reconstruction, the positions of individual PS particles and structural defects are identified in three dimensions, and the local crystal structure is revealed. Further quantitative analysis of the void system in colloidal crystal illustrates that single voids can be mostly attributed to tetrahedron void of sphere close packing, but the interconnected voids with large volume induce a sphere volume fraction of 59.39 % that reflects a metastable glass behavior of colloidal crystal arrangement. The void orientation result reveals that the 3D close-packing difficulty mainly lies in the stacking of interlayer.

Fu, Yanan; Xie, Honglan; Deng, Biao; Du, Guohao; Chen, Rongchang; Xiao, Tiqiao

2014-06-01

291

Crystal structure and electronic structure of CePt2In7.  

PubMed

We report a corrected crystal structure for the CePt2In7 superconductor, refined from single crystal x-ray diffraction data. The corrected crystal structure shows a different Pt-In stacking along the c-direction in this layered material than was previously reported. In addition, all of the atomic sites are fully occupied with no evidence of atom site mixing, resolving a discrepancy between the observed high resistivity ratio of the material and the atomic disorder present in the previous structural model. The Ce-Pt distance and coordination is typical of that seen in all other reported CenMmIn3n+2?m compounds. Our band structure calculations based on the correct structure reveal three bands at the Fermi level that are more 3D than those previously proposed, and density functional theory (DFT) calculations show that the new structure has a significantly lower energy. PMID:25211386

Klimczuk, T; Walter, O; Mchler, L; Krizan, J W; Kinnart, F; Cava, R J

2014-10-01

292

Crystal structure and electronic structure of CePt2In7  

NASA Astrophysics Data System (ADS)

We report a corrected crystal structure for the CePt2In7 superconductor, refined from single crystal x-ray diffraction data. The corrected crystal structure shows a different Pt-In stacking along the c-direction in this layered material than was previously reported. In addition, all of the atomic sites are fully occupied with no evidence of atom site mixing, resolving a discrepancy between the observed high resistivity ratio of the material and the atomic disorder present in the previous structural model. The Ce-Pt distance and coordination is typical of that seen in all other reported CenMmIn3n+2?m compounds. Our band structure calculations based on the correct structure reveal three bands at the Fermi level that are more 3D than those previously proposed, and density functional theory (DFT) calculations show that the new structure has a significantly lower energy.

Klimczuk, T.; Walter, O.; Mchler, L.; Krizan, J. W.; Kinnart, F.; Cava, R. J.

2014-10-01

293

Micro-spectroscopic mapping: revealing internal structures of zircon crystals  

NASA Astrophysics Data System (ADS)

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

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

2003-04-01

294

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

295

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

296

Crystal structure of BIS(Betaine) hydrochloride monohydrate  

NASA Astrophysics Data System (ADS)

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

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

1990-11-01

297

Crystal structure of bis(pyridine betaine) hydrochloride monohydrate  

NASA Astrophysics Data System (ADS)

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

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

1990-04-01

298

A particle method for elastic and visco-plastic structures and fluid-structure interactions  

Microsoft Academic Search

A new particle method is proposed for elastic and visco-plastic structures based on the concept of MPS (Moving Particle Semi-implicit)\\u000a method which was developed for fluid dynamics. Particle interaction models for differential operators are prepared in MPS\\u000a method. The government equations of elastic structures are interpreted into interactions among particles. These interactions\\u000a are equivalent to those of normal and tangential

Y. Chikazawa; S. Koshizuka; Y. Oka

2001-01-01

299

Drying dissipative structures of lycopodium spore particles in aqueous dispersion.  

PubMed

Drying dissipative structures of aqueous dispersions of lycopodium particles (31 microm in average diameter) from the spores of Lycopodium clavatum were studied as a function of the particle concentrations in the presence and the absence of sodium chloride. The drying patterns formed on a cover glass, a watch glass and a Petri glass dish were observed macroscopically and microscopically. Lycopodium particles were the combination of hemisphere and tetrahedron in their shape and possessed the weakly acidic groups on their surfaces. The vague broad ring structure was observed even for the very large colloidal particles, and their size on a cover glass decreased as particle concentration decreased. Microscopic drying patterns almost disappeared except the short chain-like patterns. These observations support that the convectional contribution on the dissipative drying pattern formation is still effective in the lycopodium suspensions, though the convectional forces in the suspension are very weak compared with the sedimentation forces. PMID:20598865

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

2010-10-15

300

Acetylcholinesterase inhibition by fasciculin: Crystal structure of the complex  

Microsoft Academic Search

The crystal structure of the snake toxin fasciculin, bound to mouse acetylcholinesterase (mAChE), at 3.2 resolution reveal s a synergistic three-point anchorage consistent with the picomolar dissociation constant of the complex. Loop II of fasciculin contains a cluster of hydrophobic residues that interact with the peripheral anionic site of the enzyme and sterically occlude substrate access to the catalytic

Yves Bourne; Palmer Taylor; Pascale Marchot

1995-01-01

301

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

302

Crystal structures explain functional properties of two E. coli porins  

Microsoft Academic Search

Porins form aqueous channels that aid the diffusion of small hydrophilic molecules across the outer membrane of Gram-negative bacteria. The crystal structures of matrix porin and phosphoporin both reveal trimers of identical subunits, each subunit consisting of a 16-stranded anti-parallel beta-barrel containing a pore. A long loop inside the barrel contributes to a constriction of the channel where the charge

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

1992-01-01

303

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

304

Incommensurate composite crystal structure of scandium-II  

SciTech Connect

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

Fujihisa, Hiroshi; Gotoh, Yoshito; Yamawaki, Hiroshi; Sakashita, Mami; Takeya, Satoshi; Honda, Kazumasa [National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565 (Japan); Akahama, Yuichi; Kawamura, Haruki [Graduate School of Material Science, University of Hyogo, 3-2-1 Koto, Kamigohri, Hyogo 678-1297 (Japan)

2005-10-01

305

Micro-machined infrared emitter with metallic photonic crystals structure  

NASA Astrophysics Data System (ADS)

Infrared emitter (IR) with photonic crystal structure formed by a hexagonal array of holes has been designed. The processes for fabricating the emitter are developed basing on using silicon-on-insulator (SOI) wafer. The emission spectrum of the IR emitter is measured with spectroradiometer. The experimental results show that the infrared emitter exhibits a strong narrow-band emission in middle infrared range. The wavelengths of the measured emission peaks agree well with the theoretical prediction.

Li, Fangqiang; San, Haisheng; Cheng, Meijing; Chen, Xuyuan

2009-05-01

306

Interferometric studies of domain structures in potassium niobate single crystals  

Microsoft Academic Search

Interferometric studies of domain structures in KNbO3 single crystals, grown by using excess of K2CO3 as a flux are reported. The surface deformations produced on the pseudocubic (001) planes by the stable patterns of 90, 60 and 180 domains have been studied and discussed. If the observed plane is not the plane of the shear, the 90 domains are inclined

K G Deshmukh; S G Ingle

1971-01-01

307

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

NASA Astrophysics Data System (ADS)

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

Urrutia-Bauelos, Efran; Aranda-Espinosa, Helim; Chasvez-Paez, Martin

2008-03-01

308

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

SciTech Connect

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

Kaurova, I. A., E-mail: kaurova_irina@mail.ru [Moscow Open State University (Russian Federation); Kuz'micheva, G. M. [Lomonosov State Academy of Fine Chemical Technology (Russian Federation)] [Lomonosov State Academy of Fine Chemical Technology (Russian Federation); Rybakov, V. B. [Moscow State University (Russian Federation)] [Moscow State University (Russian Federation)

2013-03-15

309

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

310

Structured Nanocomposites: Organization of Particles Templated in Self-Assembled PEO-PPO-PEO Mesophases  

NASA Astrophysics Data System (ADS)

The design of materials with tailored properties and function requires control over their structure in the nanometer scale. It is advantageous to many engineering applications that this is carried out using self-assembly processes that occur at reasonable concentrations (10^20 particles/L) and short timescales (ns -- ?s). In this work, we have developed a novel approach using an ordered template to control the nanoscale structure of materials that would not otherwise order in solution. We use close-packed cubic and cylindrical mesophases of a thermoreversible block copolymer (PEO-PPO-PEO) to impart spatial order on dispersed nanoparticles. The thermoreversible nature of the template allows for the dispersion of particles synthesized outside the template. This feature extends the applicability of this templating method to many particle-polymer systems and also permits a systematic evaluation of the impact of design parameters on the structure and mechanical properties of the nanocomposites. The approach is extremely robust and we have successfully templated solutions of silica and gold inorganic nanoparticles as well as a series of proteins, which act as organic nanoparticles in our system. The influence of relative size (particle to template sites), relative concentration, temperature and shear are experimentally determined using small angle neutron scattering (SANS) and rheology. SANS with contrast variation is used to characterize the structure of the polymer mesophase and the templated particles in a nanocomposite independently. SANS experiments also demonstrate that shear can be used to align the nanocomposites into single-crystal macro-domains; the first demonstration of the formation of single-crystal nanoparticle superlattices. The outcome of this work serves as a basis for designing new soft nanocomposite materials.

Walker, Lynn

2006-03-01

311

Unified approach for determining tetragonal tungsten bronze crystal structures.  

PubMed

Tetragonal tungsten bronze (TTB) oxides are one of the most important classes of ferroelectrics. Many of these framework structures undergo ferroelastic transformations related to octahedron tilting deformations. Such tilting deformations are closely related to the rigid unit modes (RUMs). This paper discusses the whole set of RUMs in an ideal TTB lattice and possible crystal structures which can emerge owing to the condensation of some of them. Analysis of available experimental data for the TTB-like niobates lends credence to the obtained theoretical predictions. PMID:24815976

Smirnov, M; Saint-Grgoire, P

2014-05-01

312

Exceptional groups and elementary-particle structures  

SciTech Connect

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

Biedenharn, L.C.; Truini, P.

1981-09-01

313

Substrate selectivity of bacterial monoacylglycerol lipase based on crystal structure.  

PubMed

Lipases, which are conserved from bacteria to mammals, catalyze the hydrolysis of acylglycerol to free fatty acids and glycerol. Monoacylglycerol lipase (MGL) specifically catalyzes the hydrolysis of monoacylglycerol. Although there have been numerous studies of the structure of lipases, there have been few studies of MGL. Here, we report the crystal structure of authentic MGL isolated from Bacillus sp. H257 (bMGL). The crystal diffracts to 1.96 resolution. It belongs to space group P21212, and the unit cell parameters are a=99.7 , b=106.1 and c=43.0 . As in other lipases, three structural features for lipase activity are conserved in bMGL: the glycine-X-serine-X-glycine motif, catalytic triad and cap region. The structure of bMGL appears to be closed, as the cap region covers the active site entrance. The isolated bMGL hydrolyzed 2-AG, a known human MGL-specific substrate. Based on a 2-AG bound model, we discuss the substrate selectivity. The functional and structural features of bMGL provide insight how its substrate selectivity is determined and how specific inhibitors of bacterial MGL could be designed, which may be useful for development of novel antibiotics. PMID:24894647

Tsurumura, Toshiharu; Tsuge, Hideaki

2014-09-01

314

Crystal Structures of Intermediates in the Nitroalkane Oxidase Reaction  

SciTech Connect

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

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

2009-01-01

315

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

USGS Publications Warehouse

The crystal structure of melanovanadite from Minas Ragra, Peru, has been determined in space group P1. The triclinic unit cell (non-standard) has a 6.360(2), b 18.090(9), c 6.276(2) A, alpha 110.18(4)o, beta 101.62(3)o, gamma 82.86(4)o. A subcell with b' = b/2 was found by crystal-structure analysis to contain CaV4O10.5H2O. The subcell has a layer structure in which the vanadate sheet consists of corner-shared tetrahedral VO4 and double square-pyramidal V2O8 groups, similar to that previously found in synthetic CsV2O5. Refinement of the full structure (R = 0.056) showed that the Ca atom, which half-occupies a general position in the subcell, is 90% ordered at one of these sites in the whole unit cell. Bond length-bond strength estimates indicate that the tetrahedra contain V5+, and the square pyramids, V4+.-J.A.Z.

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

1987-01-01

316

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

317

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

USGS Publications Warehouse

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

Martinez, P.; Senftle, F. E.

1960-01-01

318

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

PubMed

Isoflavonoids play important roles in plant defense and exhibit a range of mammalian health-promoting activities. Isoflavone reductase (IFR) specifically recognizes isoflavones and catalyzes a stereospecific NADPH-dependent reduction to (3R)-isoflavanone. The crystal structure of Medicago sativa IFR with deletion of residues 39-47 has been determined at 1.6A resolution. Structural analysis, molecular modeling and docking, and comparison with the structures of other NADPH-dependent enzymes, defined the putative binding sites for co-factor and substrate and potential key residues for enzyme activity and substrate specificity. Further mutagenesis has confirmed the role of Lys144 as a catalytic residue. This study provides a structural basis for understanding the enzymatic mechanism and substrate specificity of IFRs as well as the functions of IFR-like proteins. PMID:16600295

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

2006-05-19

319

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

320

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

PubMed

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

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

2014-07-01

321

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

PubMed Central

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

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

2014-01-01

322

Modulated crystal structure of Pr2SbO2.  

PubMed

The crystal structure of commensurately modulated Pr2SbO2 was solved in the orthorhombic superspace group Immm(0?0)000, q = 3/4b*, a = 13.5790?(15), b = 3.9818?(18), c = 4.0041?(18)? (T = 40?K) from a crystal twinned by reticular pseudomerohedry applying the twin law (1?0?0, 0?0?1, 0?-1?0), corresponding to a rotation by 90 along the reciprocal a axis. The formation of Zintl-type Sb(2-)-Sb(2-) dumbbells in Pr2(3+)Sb(2-)O2(2-) is considered to be accountable for its semiconducting properties, as observed previously. The space group for the three-dimensional commensurate supercell a = 13.5790?(15), b = 15.9272?(18), c = 4.0041?(18)? (T = 40?K) is Pmnm. PMID:24253079

Magdysyuk, Oxana V; Nuss, Jrgen; Jansen, Martin

2013-12-01

323

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

324

STRUCTURE NOTE Crystal Structure of YdcE Protein From Bacillus subtilis  

E-print Network

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

Shapiro, Lawrence

325

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 2.1molecules/nm2 through the variation of coupling agent concentration to lower values. Furthermore, the co-adsorption of a different coupling agent, such as phenylphosphonic acid for ZrO2 and phenyltrimethoxysilane for SiO2, resulted in a significantly lower alkyl-chain ordering for ZrO2 plane crystals and for large SiO2 spherical particles at high grafting density. An increasing amount of order-disturbing molecules leads to a gradual decrease in alkyl-chain alignment on the surface of the inorganic nanoparticles. In the case of the ZrO2 nanoparticle system it is shown via dynamic light scattering (DLS) that the mixed monolayer formation on the particle surface impacts the dispersion quality in organic solvents such as n-hexane. PMID:21549385

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

2011-01-01

326

Diterbium hepta-nickel: 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, 12801282; Lemaire & Paccard (1969). Bull. Soc. Fr. Mineral. Cristallogr. 92, 916; Buschow & van der Goot (1970). J. Less-Common Met. 22, 419428], the present redetermination affords refined coordinates and anisotropic displacement parameters for all atoms. A partial occupation for one Tb atom results in the non-stoichiometric composition Tb1.962?(4)Ni7. The title compound adopts the Ce2Ni7 structure type and can also be derived from the CaCu5 structure type as an intergrowth structure. The asymmetric unit contains two Tb sites (both site symmetries 3m.) and five Ni sites (.m., mm2, 3m., 3m., -3m.). The two different coordination polyhedra of Tb are a FrankKasper polyhedron formed by four Tb and 12 Ni atoms and a pseudo FrankKasper polyhedron formed by two Tb and 18 Ni atoms. The four different coordination polyhedra of Ni are FrankKasper icosahedra formed by five Tb and seven Ni atoms, four Tb and eight Ni atoms, three Tb and nine Ni atoms, and six Tb and six Ni atoms, respectively. PMID:25249871

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

2014-01-01

327

Symmetry and structure of freely suspended liquid crystal films  

NASA Astrophysics Data System (ADS)

Smectic liquid crystals can be regarded as stacks of layers, each of which is essentially a two-dimensional liquid of rod-like molecules. In the tilted smectics, the azimuthal orientation of n, the unit vector giving the local average long axis of the molecules, is ordered from layer to layer. This global structure defines the bulk symmetry for a given smectic phase. These bulk structures can be elucidated by studying freely suspended films of an integer number of smectic layers. This thesis addresses the connection between the broken symmetry at the liquid crystal-air interface and the two macroscopic properties: optical birefringence and spontaneous polarization. These properties are probed by depolarized reflected light microscopy while applying an electric field to reveal the underlying structure of bulk smectic phases. In this way, the ground state structures of polar ordered phases of bent core molecules and of several other novel phases were determined. This same technique was also applied to the well-known smectic A and smectic C phases. These studies reveal (i) the existence of ground state anticlinic smectic C surface layers on smectic A films and (ii) that the smectic C materials of DOBAMBC and TFMHPOBC have antiferroelectric minima in their interlayer orientation potential. In addition, the long-standing problem of ring formation in rotating electric films has been studied and an analytic solution found for relaxation in the limit of a single elastic constant.

Link, Darren Roy

328

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 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

329

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 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

330

Particle detection and non-equilibrium phonons: Experience with large germanium crystals and NTD Ge thermistors  

NASA Astrophysics Data System (ADS)

We have studied particle detectors consisting of neutron transmutation doped (NTD) Ge phonon sensors attached with a eutectic bonding process to large mass germanium crystals. These thermistors remain one of the most performant temperature sensors at temperatures as low as 20 mK. We summarize the experimental evidence for the significant role of non-equilibrium phonons in their observed behavior. However, the difficulties of forming a high transparency interface and the lack of inelastic channels appear to limit their effectiveness as non-equilibrium phonon sensors.

Sadoulet, B.; Akerib, D.; Barnes, P. D.; Cummings, A.; Da Silva, A.; Diaz, R.; Emes, J.; Golwala, S.; Haller, E. E.; Itoh, K.; Knowlton, W.; Queinnec, F.; Ross, R. R.; Seitz, D.; Shutt, T.; Smith, G.; Stockwell, W.; White, S.

1996-02-01

331

Degeneracy and Inversion of Band Structure for Wigner Crystals on a Toroidal Helix  

E-print Network

We explore the formation of Wigner crystals for charged particles on a toroidal helix. Focusing on certain commensurate cases we show that the ground state undergoes a pitchfork bifurcation from the totally symmetric polygonic to a zig-zag-like configuration with increasing radius of the helix. Remarkably, we find that for a specific value of the helix radius, below the bifurcation point, the vibrational frequency spectrum collapses to a single frequency. This allows for an essentially independent small-amplitude motion of the individual particles and consequently localized excitations can propagate in time without significant spreading. Increasing the radius beyond the degeneracy point, the band structure is inverted, with the out-of-phase oscillation mode becoming lower in frequency than the mode corresponding to the center of mass motion.

Zampetaki, A V; Schmelcher, P

2014-01-01

332

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

333

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

334

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

335

ASSOCIATION OF SUPRATHERMAL PARTICLES WITH COHERENT STRUCTURES AND SHOCKS  

SciTech Connect

Various mechanisms have been proposed to explain observed suprathermal particle populations in the solar wind, including direct acceleration at flares, stochastic acceleration, shock acceleration, and acceleration by random compression or reconnection sites. Using magnetic field and suprathermal particle data from the Advanced Composition Explorer (ACE), we identify coherent structures and interplanetary shocks, and analyze the temporal association of energetic particle fluxes with these coherent structures. Coherent structures having a range of intensities are identified using the magnetic Partial Variance of Increments statistic, essentially a normalized vector increment. A stronger association of energetic particle flux in the 0.047-4.75 MeV range is found with intense magnetic discontinuities than is found with shocks. Nevertheless, the average profile of suprathermals near shocks is quite consistent with standard models of diffusive shock acceleration, while a significant amount of the energetic particles measured and strong discontinuities are found by ACE within six hours of a shock. This evidence supports the view that multiple mechanisms contribute to the acceleration and transport of interplanetary suprathermal particles.

Tessein, J. A.; Matthaeus, W. H.; Wan, M. [Department of Physics and Astronomy, University of Delaware, Newark, DE 19716 (United States)] [Department of Physics and Astronomy, University of Delaware, Newark, DE 19716 (United States); Osman, K. T. [Centre for Fusion, Space and Astrophysics, University of Warwick, Coventry CV4 7AL (United Kingdom)] [Centre for Fusion, Space and Astrophysics, University of Warwick, Coventry CV4 7AL (United Kingdom); Ruffolo, D. [Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400 (Thailand)] [Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400 (Thailand); Giacalone, J. [Department of Planetary Sciences and Lunar and Planetary Laboratory, University of Arizona, 1629 East University Boulevard, Tucson, AZ 85721 (United States)] [Department of Planetary Sciences and Lunar and Planetary Laboratory, University of Arizona, 1629 East University Boulevard, Tucson, AZ 85721 (United States)

2013-10-10

336

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

337

Structure of a tractable stochastic mimic of soft particles.  

PubMed

The structure and assembly of soft particles is difficult to characterize because their interpenetrability allows them to be packed at ever higher density albeit with an increasing penalty in energy and/or pressure. Alternatively, the use of impenetrable particles (such as hard spheres) as a reference model for soft particles can fail because the packing densities are limited by the impossibility of complete space filling. We recently introduced the stochastic penetration algorithm (SPA) so as to allow for the computationally efficient integration of hard sphere models while including overlaps seen in soft interactions [Craven et al., J. Chem. Phys., 2013, 138, 244901]. Moving beyond the initial one-dimensional case studied earlier, we now consider the spatial properties of systems of stochastically penetrable spheres in dimensions d? 3 through the use of molecular dynamics simulations and analytic methods. The stochastic potential allows spheres to either interpenetrate with a probability ? or collide elastically otherwise. For ? > 0 the particles interpenetrate (overlap), reducing the effective volume occupied by the particles in the system. We find that the occupied volume can be accurately predicted using analytic expressions derived from mean field arguments for the particle overlap probabilities with the exception of an observed clustering regime. This anomalous clustering behavior occurs at high densities and small ?. We find that this regime is coincident with that observed in deterministic penetrable models. The behavior of the stochastic penetrable particles also indicates that soft particles would be characterizable through a single reduced parameter that captures their overlap probability. PMID:24935651

Craven, Galen T; Popov, Alexander V; Hernandez, Rigoberto

2014-08-01

338

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 Road, Cambridge CB2 1EZ, England Received October 14, 2004 ABSTRACT: A crystal of 2-chlorophenol

de Gispert, Adrià

339

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

ERIC Educational Resources Information Center

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

Bindel, Thomas H.

2008-01-01

340

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

E-print Network

demonstrated that when two differently sized sets of these hard spheres are mixed together then they can co-crystallize to form binary crystal structures analogous to those seen in atomic systems 4­6 . The exact binary crystal structure formed and its stoichiometry is found to be depen- dant on the radius ratio of the two different

Schofield, Andrew B.

341

Crystal Structure of a Lipid G Protein?Coupled Receptor  

SciTech Connect

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

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

2012-03-01

342

Emergent Structure of Multidislocation Ground States in Curved Crystals  

NASA Astrophysics Data System (ADS)

We study the structural features and underlying principles of multidislocation ground states of a crystalline spherical cap. In the continuum limit where the ratio of crystal size to lattice spacing W/a diverges, dislocations proliferate and ground states approach a characteristic sequence of structures composed of radial grain boundaries ("neutral scars"), extending radially from the boundary and terminating in the bulk. Employing a combination of numerical simulations and asymptotic analysis of continuum elasticity theory, we prove that an energetic hierarchy gives rise to a structural hierarchy, whereby dislocation number and scar number diverge as a/W?0 while scar length and dislocation number per scar become independent of lattice spacing. We characterize a secondary transition occurring as scar length grows, where the n-fold scar symmetry is broken and ground states are characterized by polydisperse, forked-scar morphologies.

Azadi, Amir; Grason, Gregory M.

2014-06-01

343

Crystal structure and physical properties in Fe-Te-Br  

NASA Astrophysics Data System (ADS)

Within a spin fluctuation driven scenario of superconductivity the results indicate that FeTe with doping is a likely higher-temperature superconductor. However, Fe1+xTe forms the same tetragonal structure with 0.06 y 0.17. The excess Fe (2) not only stabilizes the PbO-type crystal structure with space group P4/nmm but also is strongly magnetic as an electron donor while the deficit of Fe in Fe1-xTe will result in the hexagonal structure with space group P63/mmc. In this work, five single tetragonal phase samples with space group P4/nmm and three single hexagonal phase samples with space group P63/mmc have been made in Fe-Te-Br. Magnetic and electrical properties as well as the possibility of high-Tc superconductivity in the Fe-Te-Br system investigated will be discussed.

Ho, C. H.; Chen, S. C.; Syu, K. J.; Lee, W. H.

2013-03-01

344

Crystal structure of deglycosylated human IgG4-Fc  

PubMed Central

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

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

2014-01-01

345

Crystal structures of ethylene glycol and ethylene glycol monohydrate  

NASA Astrophysics Data System (ADS)

We have carried out a neutron powder diffraction study of deuterated ethylene glycol (1,2-ethanediol), and deuterated ethylene glycol monohydrate with the D2B high-resolution diffractometer at the Institut Laue-Langevin. Using these data, we have refined the complete structure, including all hydrogen atoms, of the anhydrous phase at 220 K. In addition, we have determined the structure of ethylene glycol monohydrate at 210 K using direct space methods. Anhydrous ethylene glycol crystallizes in space-group P212121 with four formula units in a unit-cell of dimensions a = 5.0553(1) A?, b = 6.9627(1) A?, c = 9.2709(2) A?, and V = 326.319(8) A?3 [?calcdeuterated = 1386.26(3) kg m-3] at 220 K. Ethylene glycol monohydrate crystallizes in space-group P21/c with four formula units in a unit-cell of dimensions a = 7.6858(3) A?, b = 7.2201(3) A?, c = 7.7356(4) A?, ? = 92.868(3), and V = 428.73(2) A?3 [?calcdeuterated = 1365.40(7) kg m-3] at 210 K. Both the structures are characterized by the gauche conformation of the ethylene glycol molecule; however, the anhydrous phase contains the tGg' rotamer (or its mirror, g'Gt), whereas the monohydrate contains the gGg' rotamer. In the monohydrate, each water molecule is tetrahedrally coordinated, donating two hydrogen bonds to, and accepting two hydrogen bonds from the hydroxyl groups of neighboring ethylene glycol molecules. There are substantial differences in the degree of weak C-D...O hydrogen bonding between the two crystals, which calls into question the role of these interactions in determining the conformation of the ethylene glycol molecule.

Fortes, A. Dominic; Suard, Emmanuelle

2011-12-01

346

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

347

Crystal Structure of the Monomeric Porin OmpG  

SciTech Connect

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

Subbarao,G.; van den Berg, B.

2006-01-01

348

High resolution crystal structure of Rubrivivax gelatinosus cytochrome c'.  

PubMed

The structure of the cytochrome c' from the purple non-sulfur phototrophic bacterium Rubrivivax gelatinosus was determined using two crystals grown independently at pH 6.3 and pH 8. The resolution attained for the two structures (1.29 A and 1.50 A for the crystals at high and low pH, respectively) is the highest to date for this class of proteins. The two structures were compared in detail in an attempt to investigate the influence of pH on the geometry of the haem and of the coordination environment of the Fe(III) ion. However, while the results suggest some small propensity for the movement of the metal atom out of the plane of the haem ring upon pH increase, the accuracy of the measurements at these two pH below the pK of the axial histidine is not sufficient to provide hard evidence of a shift in the iron position and associated changes. PMID:18295896

Benini, Stefano; Rypniewski, Wojciech R; Wilson, Keith S; Ciurli, Stefano

2008-01-01

349

Analysis of the crystal structure of an active MCM hexamer.  

PubMed

In a previous Research article (Froelich et al., 2014), we suggested an MCM helicase activation mechanism, but were limited in discussing the ATPase domain because it was absent from the crystal structure. Here we present the crystal structure of a nearly full-length MCM hexamer that is helicase-active and thus has all features essential for unwinding DNA. The structure is a chimera of Sulfolobus solfataricus N-terminal domain and Pyrococcus furiosus ATPase domain. We discuss three major findings: 1) a novel conformation for the A-subdomain that could play a role in MCM regulation; 2) interaction of a universally conserved glutamine in the N-terminal Allosteric Communication Loop with the AAA+ domain helix-2-insert (h2i); and 3) a recessed binding pocket for the MCM ssDNA-binding motif influenced by the h2i. We suggest that during helicase activation, the h2i clamps down on the leading strand to facilitate strand retention and regulate ATP hydrolysis. PMID:25262915

Miller, Justin M; Arachea, Buenafe T; Epling, Leslie B; Enemark, Eric J

2014-01-01

350

Crystal Structure of the Pseudomonas aeruginosa Virulence Factor Regulator  

SciTech Connect

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

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

2012-09-07

351

Alkyltributylphosphonium chloride ionic liquids: synthesis, physicochemical properties and crystal structure.  

PubMed

A series of alkyltributylphosphonium chloride ionic liquids, prepared from tributylphosphine and the respective 1-chloroalkane, C(n)H(2n+1)Cl (where n = 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12 or 14), is reported. This work is a continuation of an extended series of tetraalkylphosphonium ionic liquids, where the focus is on the variability of n and its impact on the physical properties, such as melting points/glass transitions, thermal stability, density and viscosity. Experimental density and viscosity data were interpreted using QPSR and group contribution methods and the crystal structure of propyl(tributyl)phosphonium chloride is detailed. PMID:22679620

Adamov, Gabriela; Gardas, Ramesh L; Nieuwenhuyzen, Mark; Puga, Alberto V; Rebelo, Lus Paulo N; Robertson, Allan J; Seddon, Kenneth R

2012-07-21

352

Crystal structure of 4-chloro-2-iodo-aniline  

PubMed Central

In the crystal structure of the title compound, C6H5ClIN, the amino group engages in NH?N hydrogen bonding, creating [100] chains. A Cl?I contact is observed [3.7850?(16)?]. The parallel planes of neigbouring molecules reveal highly offset ?-stacking characterized by a centroidcentroid distance of 4.154?(1), a centroid-to-plane distance of 3.553?(3) and ring-offset slippage of 2.151?(6)?.

Quinn, Taylor R.; Tanski, Joseph M.

2014-01-01

353

Crystal and molecular structure of muurolene and cadinene dihydrochlorides  

Microsoft Academic Search

An x-ray structural investigation (? Mo Ka2?\\/? scanning for 2?12121, mp 117C. The crystals of (II) belong to the monoclinic system, with a=9.842(4), b=11.627(6), c=13.677(9) , =95.10(4), Z=4, sp. gr. P21, mp 86C. The six-membered rings of the molecules (I) and (II) have the chair conformation with equatorial alkyl groups. The chlorine atoms have the axial arrangement. The molecule of

Yu. Gatilov; S. A. Oadchii; Zh. V. Dubovenko

1981-01-01

354

Theory of elastic interaction between arbitrary colloidal particles in confined nematic liquid crystals  

NASA Astrophysics Data System (ADS)

We develop the method proposed by Chernyshuk and Lev [Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.81.041701 81, 041701 (2010)] for theoretical investigation of elastic interactions between colloidal particles of arbitrary shape and chirality (polar as well as azimuthal anchoring) in the confined nematic liquid crystal (NLC). General expressions for six different types of multipole elastic interactions are obtained in the confined NLC: monopole-monopole (Coulomb type), monopole-dipole, monopole-quadrupole, dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole interactions. The obtained formulas remain valid in the presence of the external electric or magnetic fields. The exact equations are found for all multipole coefficients for the weak anchoring case. For the strong anchoring coupling, the connection between the symmetry of the shape or director and multipole coefficients is obtained, which enables us to predict which multipole coefficients vanish and which remain nonzero. The particles with azimuthal helicoid anchoring are considered as an example. Dipole-dipole interactions between helicoid cylinders and cones are found in the confined NLC. In addition, the banana-shaped particles in homeotropic and planar nematic cells are considered. It is found that the dipole-dipole interaction between banana-shaped particles differs greatly from the dipole-dipole interaction between the axially symmetrical particles in the nematic cell. There is a crossover from attraction to repulsion between banana particles along some directions in nematic cells. It is shown that monopoles do not feel the type of nematic cell: monopole-monopole interaction turns out to be the same in homeotropic and planar nematic cells and converges to the Coulomb law as thickness increases, L??.

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

2012-12-01

355

Enhancing transmission efficiency of bending waveguide based on graded sonic crystals using antireflection structures  

NASA Astrophysics Data System (ADS)

The conventional antireflection coating (ARC) structure for sonic crystal devices is to place the cylinders at the interface between a sonic crystal device and a background medium. The radius of ARC cylinders and the distance between the ARC and the sonic crystal device are adjusted to obtain an optimal antireflection effect. We propose that ARC structures are directly designed by using the conventional ARC theory instead of scanning the geometric and spatial parameters of the conventional ARC structures. According to the concept of the effective refractive index of sonic crystals, the exact ARC structures can be implemented by sonic crystals. The transmission efficiency of a bending waveguide designed by graded sonic crystals can be enhanced by introducing the ARC structures based on sonic crystals. The performances of different ARC structure designs are compared and discussed.

Wu, Liang-Yu; Chen, Lien-Wen

2012-06-01

356

Simultaneous occurrence of structure-directed and particle-resonance-induced phononic gaps in colloidal films.  

PubMed

We report on the observation of two hypersonic phononic gaps of different nature in three-dimensional colloidal films of nanospheres using Brillouin light scattering. One is a Bragg gap occurring at the edge of the first Brillouin zone along a high-symmetry crystal direction. The other is a hybridization gap in crystalline and amorphous films, originating from the interaction of the band of quadrupole particle eigenmodes with the acoustic effective-medium band, and its frequency position compares well with the computed lowest eigenfrequency. Structural disorder eliminates the Bragg gap, while the hybridization gap is robust. PMID:18518452

Still, T; Cheng, W; Retsch, M; Sainidou, R; Wang, J; Jonas, U; Stefanou, N; Fytas, G

2008-05-16

357

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

358

Probing the molecular structure of interfacial films and crystals  

NASA Astrophysics Data System (ADS)

The properties of outside surfaces were found to play an important role in the nucleation and crystallization processes. Thus controlling the surface properties would provide an effective means for crystal engineering. Hydrophobic surface is prepared by self-assembled monolayer (SAM) formation of octadecyltrichlorosilane (OTS) on silicon surface, with the hydrophobicity adjusted by the monolayer coverage. Silicon wafer treated by RCA method is hydrophilic, so are SAMs formed by two amine-terminated organosilanes on silicon. However these three hydrophilic surfaces are unstable, due to contamination of the amine-terminated SAMs and hydrolysis of RCA treated silicon. Polymethine dyes, BDH+Cl- and BDH +ClO4-, are synthesized and characterized by UV spectra and crystal morphology. They have identical UV spectrum in dilute solutions due to the same chromophore, and J-aggregation happens at much higher concentrations. IR spectra are analyzed to monitor the crystallization process of BDH+Cl- OTS SAM surface and the crystallization process of BDH+Cl- on substrates with varying hydrophobicity was monitored by optical microscopy and compared. Due to the extreme flexibility of polysiloxane, silicone surfactants can arrange themselves at the interfaces quickly to adopt configurations with minimum free energy. Polysiloxane is hydrophobic but not oleophilic, which makes them effective emulsifiers and stabilizers in aqueous and nonaqueous media. The interaction between an AFM Si3N4 tip and a hydrophobic surface in silicone polyether (SPE) solution in the presence of ethanol was investigated by Atomic Force Microscopy (AFM) force measurement. ABA triblock type and comb-type SPE surfactants, adsorbed at the liquid-solid interface, provide steric barriers, even with significant addition of ethanol. On the contrary, conventional low-molecular weight and polymeric alkyl surfactants display no steric barrier even in the presence of moderate amount of ethanol. This unique property makes SPEs to be used as emulsion-stabilizers in products or processes involving alcohols or other organic solvents. Formation of polymer brush structure at the interface is essential to the existence of steric barrier. ABA-type SPEs adopt buoy-anchor-buoy configuration to fulfill this requirement, and comb-type SPEs attach to hydrophobic surface with siloxane backbone with many polyether buoys. Both configurations contribute to the formation of polymer brush structure. As a general trend, increase of ethanol content leads to smaller force maximum and critical barrier thickness. ABA-type SPEs display better alcohol tolerance than comb-type ones. The incorporation of propylene oxide (PO) segments in the polyether chain was found to improve the alcohol tolerance. Two competing factors are involved upon ethanol content increase: extension of the polyether chain and reduction of adsorption density of the surfactants at the interface.

Wang, Anfeng

359

Control of Polymer Structures in Phase-Separated Liquid Crystal-Polymer Composite Systems Qingbing WANG, Jung O. PARK1  

E-print Network

: liquid crystal, polymerization, phase separation, polymer morphology, polymer dispersed liquid crystal 1 optical and scanning electron microscopies. Two processes, spatially nonuniform polymerization structure to a heterogeneous polymer dispersed liquid crystal (PDLC) structure. A variation in cell

Srinivasarao, Mohan

360

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

E-print Network

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

361

The Crystal Structure of the Escherichia coli RNase E Apoprotein and a Mechanism for  

E-print Network

Structure Article The Crystal Structure of the Escherichia coli RNase E Apoprotein and a Mechanism of structured RNA precursors in Escheri- chia coli. Here, we present the crystal structure of the E. coli RNase- radation of most mRNA in E. coli (Mudd et al., 1990; Babitzke and Kushner, 1991). In addition to its purely

Scott, William

362

Crystal Structure of the Avian Astrovirus Capsid Spike  

PubMed Central

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

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

2013-01-01

363

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

NASA Astrophysics Data System (ADS)

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

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

2013-06-01

364

Crystal structures of superconducting sodium intercalates of hafnium nitride chloride  

SciTech Connect

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

Oro-Sole, J. [Institut de Ciencia de Materials de Barcelona (CSIC), Campus UAB, 08193 Bellaterra (Spain); Frontera, C. [Institut de Ciencia de Materials de Barcelona (CSIC), Campus UAB, 08193 Bellaterra (Spain); Beltran-Porter, D. [Institut de Ciencia de Materials de la Universitat de Valencia, PO Box 2085, Poligono 'La Coma' s/n, 46980 Paterna (Spain); Lebedev, O.I. [EMAT, RUCA, Groenenborgerlaan 171, Antwerp 2020 (Belgium); Van Tendeloo, G. [EMAT, RUCA, Groenenborgerlaan 171, Antwerp 2020 (Belgium); Fuertes, A. [Institut de Ciencia de Materials de Barcelona (CSIC), Campus UAB, 08193 Bellaterra (Spain)]. E-mail: amparo.fuertes@icmab.es

2006-05-25

365

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, 469478], 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 HgS bond lengths of 2.3954?(11), 2.4481?(8) and 2.7653?(6)? in comparison with values of 2.24, 2.43 and 2.77?. All atoms in the crystal structure are located on mirror planes. The Hg2+ cation is surrounded by four S atoms in a seesaw shape [SHgS 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 KN bond lengths of the distorted KN7 polyhedra lie between 2.926?(2) and 3.051?(3)?. PMID:25309170

Weil, Matthias; Hausler, Thomas

2014-01-01

366

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

PubMed

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

Weil, Matthias; Husler, Thomas

2014-09-01

367

Crystal Structure of 3S-hydroxy-7 Melleine  

NASA Astrophysics Data System (ADS)

A new compound, 3S-hydroxy-7 melleine was isolated from the endophytic fungus Xylariasp No.2508 from the mangrove tree on the South China Sea coast. It was the first time that this kind of compound was isolated from marine fungus. The structure was elucidated by NMR data, infrared spectrum (IR) and mass spectrometry (MS). In addition, its structure was determined by the single-crystal X-ray diffraction analysis. It crystallized in monoclinic, space group P21 with a=10.8884(19) , b=7.2284(13) , c=13.398(2) , ?=104.217(3), C10H10O4H2O, Mr=212.20, V=1022.2(3) 3, Z=4, Dc=1.379 mg/m3, F(000)=448, ?=0.112 mm-1, the final R=0.0498, ?R=0.101 for 2407 observed reflections (I>2?(I)). The molecular backbone of the compound includes a benzopyran ring. By comparing with the melting point and the optical rotation of the known 3R-hydroxy-7 melleine in literature, the absolute configuration of the compound was determined as 3S. It didn't exhibit antibacterial activity against Gram-positive bacterium Staphylococcus aureus at 200 ?g/disk in the preliminary test.

Liu, Xiao-hong; Xu, Fang; Zhang, Yi; Liu, Li-hong; Huang, Hua-rong; She, Zhi-gang; Lin, Yong-cheng; Chan, Winglai

2006-10-01

368

Crystal structure of bovine 3-hydroxyanthranilate 3,4-dioxygenase.  

PubMed

3-Hydroxyanthranilate 3,4-dioxygenase, the enzyme that catalyzes the conversion of 3-hydroxyanthranilate to quinolinic acid, has been extracted and purified from bovine kidney, crystallized and its structure determined at 2.5 A resolution. The enzyme, which crystallizes in the triclinic P1 space group, is a monomer, characterized by the so-called cupin fold. The monomer of the bovine enzyme mimics the dimer present in lower species, such as bacteria and yeast, since it is composed of two domains: one of them is equivalent to one monomer, whilst the second domain corresponds to only a portion of it. The active site consists of an iron ion coordinated by two histidine residues, one glutamate and an external ligand, which has been interpreted as a solvent molecule. It is contained in the N-terminal domain, whilst the function of the C-terminal domain is possibly structural. The catalytic mechanism very likely has been conserved through all species, since the positions of all residues considered relevant for the reaction are present from bacteria to humans. PMID:19226621

Dilovi?, Ivica; Gliubich, Francesca; Malpeli, Giorgio; Zanotti, Giuseppe; Matkovi?-Calogovi?, Dubravka

2009-12-01

369

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, 16071615], all atoms were refined with anisotropic displacement parameters, leading to higher precision in terms of bond lengths and angles [e.g. HgHg = 2.5031?(7) compared to 2.500?(3)]. 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 OHgHgO bonds to the sulfate tetrahedra into chains extending parallel to [20-1]. More remote OHgHgO bonds connect these chains into a three-dimensional framework.

Weil, Matthias

2014-01-01

370

Crystal structure of the bacterial nucleoside transporter Tsx.  

PubMed

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 beta-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

2004-08-18

371

Crystal structures of group IVa metals at ultrahigh pressures  

SciTech Connect

High-pressure energy-dispersive x-ray-diffraction studies were carried out on the group IVa metals hafnium (Hf) to 252 GPa (to a volume compression {ital V}/{ital V}{sub 0} of 0.48) and titanium (Ti) to 87 GPa using a synchrotron source. Two new structural phase transformations between an hcp phase and an {omega} phase and between the {omega} phase and a bcc phase (isostructural with group V transition metals) were observed during both compression and decompression in Hf. Equilibrium transformation pressures for Hf are 38{plus minus}8 and 71{plus minus}1 GPa for the hcp-to-{omega} and {omega}-to-bcc phase transformations, respectively, at room temperature. In Ti, only the hcp-to-{omega} phase transition was observed above 8 GPa, and the {omega} phase was stable to 87 GPa. The crystal structure sequences of Ti, Zr, and Hf at ultrahigh pressures are discussed.

Xia, H.; Parthasarathy, G.; Luo, H.; Vohra, Y.K.; Ruoff, A.L. (Department of Materials Science and Engineering, Cornell University, Ithaca, NY (USA))

1990-10-01

372

Atomic resolution crystal structure of hydroxynitrile lyase from Hevea brasiliensis.  

PubMed

The X-ray crystal structure of native hydroxynitrile lyase from Hevea brasiliensis (Hb-HNL) has been determined at 1.1 A resolution. It refined to a final R of 11.5% for all data and an Rfree of 14.4%. The favorable data-to-parameter ratio at atomic resolution made the refinement of individual anisotropic displacement parameters possible. The data also allowed a clear distinction of the alternate orientations of all histidine and the majority of asparagine and glutamine side chains. A number of hydrogen atoms, including one on the imidazole of the mechanistically important His-235, became visible as peaks in a difference electron density map. The structure revealed a discretely disordered sidechain of Ser-80, which is part of the putative catalytic triad. Analysis of the anisotropy indicated an increased mobility of residues near the entrance to the active site and within the active site. PMID:10494852

Gruber, K; Gugganig, M; Wagner, U G; Kratky, C

1999-01-01

373

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

PubMed Central

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

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

2009-01-01

374

Crystal Structure and Dielectric Property of Bismuth Layer-Structured Dielectric Films with c-Axis Preferential Crystal Orientation  

NASA Astrophysics Data System (ADS)

Thin films of bismuth layer-structured dielectrics (BLSDs), CaBi4Ti4O15, and SrBi4Ti4O15, were prepared by a chemical solution deposition (CSD) technique on various substrates, such as (111)Pt/TiO2/(100)Si, (100)LaNiO3/(111)Pt/TiO2/(100)Si, and (100)SrRuO3?(100)SrTiO3 substrates. Conductive perovskite oxide LaNiO3 with (100) preferential crystal orientation was introduced into the interface between the BLSD film and the (111)Pt/TiO2/(100)Si substrate to control the crystal orientation of BLSD by lattice matching between pseudo-perovskite blocks in the BLSD crystal and the (100)LaNiO3 plane with the perovskite structure. The (00l) planes of BLSD crystals were preferentially oriented on the substrate surface of the (100)LaNiO3/(111)Pt/TiO2/(100)Si, whereas randomly-oriented BLSD crystals with lower crystallinity were only obtained on the surface of (111)Pt/TiO2/(100)Si substrate. The (001)-oriented BLSD films exhibited the leakage current densities below 10-7 A/cm2 at 50 kV/cm, which is significantly lower than those for randomly-oriented films, above 10-6 A/cm2, The room-temperature dielectric constants (?r) of CaBi4Ti4O15 and SrBi4Ti4O15 thin films on the (100)LaNiO3/(111)Pt/TiO2/(100)Si substrate were both approximately 250, while those on the (100)SrRuO3?(100)SrTiO3 substrate were approximately 220. The temperature dependence of the capacitances for the CaBi4Ti4O15 and SrBi4Ti4O15 films on the (100)LaNiO3/(111)Pt/TiO2/(100)Si substrate were approximately +17 and +10%, respectively, in the temperature range from 25 to 400 C. These values were slightly larger than those of epitaxial BLSD films, but smaller than those of (Ba,Sr)TiO3 films.

Mizutani, Yuki; Kiguchi, Takanori; Konno, Toyohiko J.; Funakubo, Hiroshi; Uchida, Hiroshi

2010-09-01

375

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

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

2004-02-10

376

Structural study of crystallization of a-Ge using extended x-ray-absorption fine structure  

NASA Astrophysics Data System (ADS)

Extended x-ray-absorption fine-structure measurements have been made on amorphous Ge and crystalline Ge at temperatures up to 450 C. The first-neighbor distance, variance of the bond-length distribution, and third-order cumulant increase with increasing temperature. Temperature dependence of the variance of the bond-length distribution is in agreement with Filipponi's calculation. The amorphous-to-crystalline transition takes place at 450 C. During the crystallization, these structural parameters decrease. The radial bond-energy change on crystallization is estimated to be one-tenth of the crystallization enthalpy. Anharmonicity effects are discussed by investigating the relationships between the first-neighbor distance, variance of the bond-length distribution, and third-order cumulant.

Wakagi, M.; Maeda, Y.

1994-11-01

377

The crystal structures of potassium and cesium trivanadates  

USGS Publications Warehouse

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

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

1966-01-01

378

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

379

Optical Crystals  

ERIC Educational Resources Information Center

Discusses the production and structure of a sequence of optical crystals which can serve as one-, two-, and three-dimensional diffraction plates to illustrate diffraction patterns by using light rather than x-rays or particles. Applications to qualitative presentations of Laue theory at the secondary and college levels are recommended. (CC)

Bergsten, Ronald

1974-01-01

380

Exploring protein flexibility: incorporating structural ensembles from crystal structures and simulation into virtual screening protocols.  

PubMed

The capacity of proteins to adapt their structure in response to various perturbations including covalent modifications, and interactions with ligands and other proteins plays a key role in biological processes. Here, we explore the ability of molecular dynamics (MD), replica exchange molecular dynamics (REMD), and a library of structures of crystal-ligand complexes, to sample the protein conformational landscape and especially the accessible ligand binding site geometry. The extent of conformational space sampled is measured by the diversity of the shapes of the ligand binding sites. Since our focus here is the effect of this plasticity on the ability to identify active compounds through virtual screening, we use the structures generated by these techniques to generate a small ensemble for further docking studies, using binding site shape hierarchical clustering to determine four structures for each ensemble. These are then assessed for their capacity to optimize enrichment and diversity in docking. We test these protocols on three different receptors: androgen receptor (AR), HIV protease, and CDK2. We show that REMD enhances structural sampling slightly as compared both to MD, and the distortions induced by ligand binding as reflected in the crystal structures. The improved sampling of the simulation methods does not translate directly into improved docking performance, however. The ensemble approach did improve enrichment and diversity, and the ensemble derived from the crystal structures performed somewhat better than those derived from the simulations. PMID:22424156

Osguthorpe, David J; Sherman, Woody; Hagler, Arnold T

2012-06-14

381

Crystal and molecular structure of the antimalarial agent enpiroline.  

PubMed Central

To identify common spatial and structural features of amino alcohol antimalarial agents with the eventual goal of designing more effective drugs and a better understanding of the mechanism of action of this class of antimalarial agents, the three-dimensional crystal and molecular structure of enpiroline, a new antimalarial agent active against chloroquine-resistant Plasmodium falciparum, was determined by X-ray crystallography and compared with the crystal structures of the cinchona alkaloids and of the new antimalarial agent WR 194,965. The aromatic rings of the phenyl-pyridine ring system of enpiroline are twisted from each other by approximately 18 degrees. The intramolecular aliphatic N-O distance in enpiroline was 2.80 A (1 A = 0.1 nm), which is close to the N-O distance found in the antimalarial cinchona alkaloids. Enpiroline contains both an intramolecular hydrogen bond between the aliphatic nitrogen and oxygen atoms and an intermolecular hydrogen bond between the aliphatic nitrogen and oxygen atoms of two neighboring molecules. One enantiomer of enpiroline superimposed best with quinine, and the other enantiomer of enpiroline superimposed best with quinidine, suggesting that both enantiomers of enpiroline possess antimalarial activity. Since a common feature of the crystal structures of the amino alcohol antimalarial agents is the formation of intermolecular hydrogen bonds, the common spatial direction of hydrogen bond formation indicates the potential ability of these antimalarial agents to bind to a common receptor site. The crystallographic parameters were as follows: C19H18F6N5O; Mr = 404.3; symmetry of unit cell, monoclinic; space group, P2(1)/a; parameters of unit cell---a = 9.454 +/- 0.004 A, b = 18.908 +/- 0.008 A, c = 10.300 +/- 0.004 A, and beta = 96.55 +/- 0.03 degrees: V (volume of unit cell) = 1829.2 A3; Z (number of molecules per unit cell) = 4; Dchi (calculated density) = 1.46 g cm-3; source of radiation, CuK alpha (lambda = 1.54178 A); mu (absorption coefficient) = 11.49 cm-1; F(000) (sum of atomic scattering factors at zero scattering angle) = 832; room temperature; final R = 8.7% for 1,798 reflections with [F0] > 3 sigma. PMID:2782859

Karle, J M; Karle, I L

1989-01-01

382

Crystal and molecular structure of the antimalarial agent enpiroline.  

PubMed

To identify common spatial and structural features of amino alcohol antimalarial agents with the eventual goal of designing more effective drugs and a better understanding of the mechanism of action of this class of antimalarial agents, the three-dimensional crystal and molecular structure of enpiroline, a new antimalarial agent active against chloroquine-resistant Plasmodium falciparum, was determined by X-ray crystallography and compared with the crystal structures of the cinchona alkaloids and of the new antimalarial agent WR 194,965. The aromatic rings of the phenyl-pyridine ring system of enpiroline are twisted from each other by approximately 18 degrees. The intramolecular aliphatic N-O distance in enpiroline was 2.80 A (1 A = 0.1 nm), which is close to the N-O distance found in the antimalarial cinchona alkaloids. Enpiroline contains both an intramolecular hydrogen bond between the aliphatic nitrogen and oxygen atoms and an intermolecular hydrogen bond between the aliphatic nitrogen and oxygen atoms of two neighboring molecules. One enantiomer of enpiroline superimposed best with quinine, and the other enantiomer of enpiroline superimposed best with quinidine, suggesting that both enantiomers of enpiroline possess antimalarial activity. Since a common feature of the crystal structures of the amino alcohol antimalarial agents is the formation of intermolecular hydrogen bonds, the common spatial direction of hydrogen bond formation indicates the potential ability of these antimalarial agents to bind to a common receptor site. The crystallographic parameters were as follows: C19H18F6N5O; Mr = 404.3; symmetry of unit cell, monoclinic; space group, P2(1)/a; parameters of unit cell---a = 9.454 +/- 0.004 A, b = 18.908 +/- 0.008 A, c = 10.300 +/- 0.004 A, and beta = 96.55 +/- 0.03 degrees: V (volume of unit cell) = 1829.2 A3; Z (number of molecules per unit cell) = 4; Dchi (calculated density) = 1.46 g cm-3; source of radiation, CuK alpha (lambda = 1.54178 A); mu (absorption coefficient) = 11.49 cm-1; F(000) (sum of atomic scattering factors at zero scattering angle) = 832; room temperature; final R = 8.7% for 1,798 reflections with [F0] > 3 sigma. PMID:2782859

Karle, J M; Karle, I L

1989-07-01

383

A particle method for elastic and visco-plastic structures and fluid-structure interactions  

NASA Astrophysics Data System (ADS)

A new particle method is proposed for elastic and visco-plastic structures based on the concept of MPS (Moving Particle Semi-implicit) method which was developed for fluid dynamics. Particle interaction models for differential operators are prepared in MPS method. The government equations of elastic structures are interpreted into interactions among particles. These interactions are equivalent to those of normal and tangential springs. Therefore the present particle method is simple and corresponding physical meaning is clear. Model for visco-plastic structure is represented to replace these elastic springs into visco-plastic ones. Elements or grids are not necessary. A tensile plate and a cantilever beam as elastic structures are analyzed by the present method. The results are in good agreement with theoretical solutions. Visco-plastic analysis for creep deformation and fracture of a cracked plate is also carried out and the result is in good agreement with an experiment. The present particle method for elastic structures is combined with MPS method for fluid-structural interaction problems. Since both methods are based on the same particle modeling in Lagrangian coordinates, large deformation of the interfaces can be easily analyzed. Water falling on a cantilever beam is analyzed by the combined method. Crash of water and resultant displacement of the beam are successfully analyzed. Structural analysis in a breakwater is carried out with wave propagation. The calculated pressure distribution on the breakwater is in good agreement with a theory.

Chikazawa, Y.; Koshizuka, S.; Oka, Y.

384

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

NASA Technical Reports Server (NTRS)

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

Authier, B.

1978-01-01

385

Structure and dissolution of L-leucine-coated salbutamol sulphate aerosol particles.  

PubMed

L-Leucine formed different crystalline coatings on salbutamol sulphate aerosol particles depending on the saturation conditions of L-leucine. The work emphasizes a careful characterization of powders where structural compartments such as crystal size and particle coating may affect the performance of drug when administered. The sublimation of L-leucine from the aerosol particles took place 90C lower temperature than the bulk L-leucine which was attributed to result from the sublimation of L-leucine from nano-sized crystalline domains. The dissolution slowed down and initial dissolution rate decreased with increasing L-leucine content. Decreasing crystalline domains to nano-scale improve heat and mass transfer which was observed as the lowered decomposition temperature of the drug salbutamol sulphate and the sublimation temperature of surface material L-leucine as well as the altered dissolution characteristics of the drug. The structure of the coated drug particles was studied by means of thermal analysis techniques (DSC and TG), and the dissolution of salbutamol sulphate was studied as an on-line measurement in a diffusion cell. PMID:22562614

Raula, Janne; Seppl, Jukka; Malm, Jari; Karppinen, Maarit; Kauppinen, Esko I

2012-06-01

386

Crystal Structures of Yellowtail Ascites Virus VP4 Protease  

PubMed Central

Yellowtail ascites virus (YAV) is an aquabirnavirus that causes ascites in yellowtail, a fish often used in sushi. Segment A of the YAV genome codes for a polyprotein (pVP2-VP4-VP3), where processing by its own VP4 protease yields the capsid protein precursor pVP2, the ribonucleoprotein-forming VP3, and free VP4. VP4 protease utilizes the rarely observed serine-lysine catalytic dyad mechanism. Here we have confirmed the existence of an internal cleavage site, preceding the VP4/VP3 cleavage site. The resulting C-terminally truncated enzyme (ending at Ala716) is active, as shown by a trans full-length VP4 cleavage assay and a fluorometric peptide cleavage assay. We present a crystal structure of a native active site YAV VP4 with the internal cleavage site trapped as trans product complexes and trans acyl-enzyme complexes. The acyl-enzyme complexes confirm directly the role of Ser633 as the nucleophile. A crystal structure of the lysine general base mutant (K674A) reveals the acyl-enzyme and empty binding site states of VP4, which allows for the observation of structural changes upon substrate or product binding. These snapshots of three different stages in the VP4 protease reaction mechanism will aid in the design of anti-birnavirus compounds, provide insight into previous site-directed mutagenesis results, and contribute to understanding of the serine-lysine dyad protease mechanism. In addition, we have discovered that this protease contains a channel that leads from the enzyme surface (adjacent to the substrate binding groove) to the active site and the deacylating water. PMID:23511637

Chung, Ivy Yeuk Wah; Paetzel, Mark

2013-01-01

387

Crystal Structure of Liganded Rat Peroxisomal Multifunctional Enzyme Type 1  

PubMed Central

The crystal structure of the full-length rat peroxisomal multifunctional enzyme, type 1 (rpMFE1), has been determined at 2.8 ? resolution. This enzyme has three catalytic activities and two active sites. The N-terminal part has the crotonase fold, which builds the active site for the ?3,?2-enoyl-CoA isomerase and the ?2-enoyl-CoA hydratase-1 catalytic activities, and the C-terminal part has the (3S)-hydroxyacyl-CoA dehydrogenase fold and makes the (3S)-hydroxyacyl-CoA dehydrogenase active site. rpMFE1 is a multidomain protein having five domains (AE). The crystal structure of full-length rpMFE1 shows a flexible arrangement of the A-domain with respect to the BE-domains. Because of a hinge region near the end of the A-domain, two different positions of the A-domain were observed for the two protein molecules (A and B) of the asymmetric unit. In the most closed conformation, the mode of binding of CoA is stabilized by domains A and B (helix-10), as seen in other crotonase fold members. Domain B, although functionally belonging to the N-terminal part, is found tightly associated with the C-terminal part, i.e. fixed to the E-domain. The two active sites of rpMFE1 are ?40 ? apart, separated by a tunnel, characterized by an excess of positively charged side chains. Comparison of the structures of rpMFE1 with the monofunctional crotonase and (3S)-hydroxyacyl-CoA dehydrogenase superfamily enzymes, as well as with the bacterial ?2?2-fatty acid oxidation multienzyme complex, reveals that this tunnel could be important for substrate channeling, as observed earlier on the basis of the kinetics of rpMFE1 purified from rat liver. PMID:20463028

Kasaragod, Prasad; Venkatesan, Rajaram; Kiema, Tiila R.; Hiltunen, J. Kalervo; Wierenga, Rik K.

2010-01-01

388

Simulations of Relativistic Collisionless Shocks: Shock Structure and Particle Acceleration  

SciTech Connect

We discuss 3D simulations of relativistic collisionless shocks in electron-positron pair plasmas using the particle-in-cell (PIC) method. The shock structure is mainly controlled by the shock's magnetization (''sigma'' parameter). We demonstrate how the structure of the shock varies as a function of sigma for perpendicular shocks. At low magnetizations the shock is mediated mainly by the Weibel instability which generates transient magnetic fields that can exceed the initial field. At larger magnetizations the shock is dominated by magnetic reflections. We demonstrate where the transition occurs and argue that it is impossible to have very low magnetization collisionless shocks in nature (in more than one spatial dimension). We further discuss the acceleration properties of these shocks, and show that higher magnetization perpendicular shocks do not efficiently accelerate nonthermal particles in 3D. Among other astrophysical applications, this may pose a restriction on the structure and composition of gamma-ray bursts and pulsar wind outflows.

Spitkovsky, Anatoly; /KIPAC, Menlo Park

2006-04-10

389

Chromatic patchy particles: effect of specific interactions on liquid structure  

E-print Network

We study the structural properties of patchy particle liquid, with special focus on the role of "color", i.e. specific. interactions between individual patches. One experimental realization of such "chromatic" patchy particles is by decorating them with single-strained DNA linkers. The complementarity of the linkers will promote formation of bonds only between predetermined pairs of patches. By using the MD simulation, we compare local coordination, the short range order, and other structural properties of the aggregates formed by "colored" and "colorless" systems. The analysis is done for spherical particles with two different patch arrangement (tetrahedral and cubic). The additional color constraint results in a less connected liquid structure which is also less stable thermodynamically. From our data, we estimate the configurational entropy loss due coloring to be about $2 k_B T$ per particle, which in turn should improve the relative stability of the corresponding ordered phases. Despite having slightly lower connectivity, the colored liquid exhibits significantly better local bond orientational order measured by PDFs of the Steinhardt's rotational invariants $q_l$ and $w_l$. We associate this with lower strain due to the removed bonds.

Oleg A. Vasilyev; Boris A. Klumov; Alexei V. Tkachenko

2014-07-01

390

Crystal structure of sulfotransferase STF9 from Mycobacterium avium.  

PubMed

Sulfotransferases catalyze the sulfate conjugation of a wide variety of endogenous and exogenous molecules. Human pathogenic mycobacteria produce numerous sulfated molecules including sulfolipids which are well related to the virulence of several strains. The genome of Mycobacterium avium encodes eight putative sulfotransferases (stf1, stf4-stf10). Among them, STF9 shows higher similarity to human heparan sulfate 3-O-sulfotransferase isoforms than to the bacterial STs. Here, we determined the crystal structure of sulfotransferase STF9 in complex with a sulfate ion and palmitic acid at a resolution of 2.6 . STF9 has a spherical structure utilizing the classical sulfotransferase fold. STF9 exclusively possesses three N-terminal ?-helices (?1, ?2, ?3) parallel to the 3'-phosphoadenosine-5'-phosphosulfate (PAPS) binding motif. The sulfate ion binds to the PAPS binding structural motif and the palmitic acid molecule binds in the deep cleft of the predicted substrate binding site suggesting the nature of endogenous acceptor substrate of STF9 resembles palmitic acid. The substrate binding site is covered by a flexible loop which may have involvement in endogenous substrate recognition. Based on the mutational study (Hossain et al., Mol Cell Biochem 350:155-162; 2011) and structural resemblance of STF9-sulfate ion-palmitic acid complex to the hHS3OST3 complex with PAP (3'-phosphoadenosine-5'-phosphate) and an acceptor sugar chain, Glu170 and Arg96 are appeared to be catalytic residues in STF9 sulfuryl transfer mechanism. PMID:21959978

Hossain, Md Murad; Moriizumi, Yuuji; Tanaka, Shotaro; Kimura, Makoto; Kakuta, Yoshimitsu

2012-02-01

391

Crystal Structure of a Thermally Stable Rhodopsin Mutant  

PubMed Central

We determined the structure of the rhodopsin mutant N2C/D282C expressed in mammalian cells; the first structure of a recombinantly produced G protein-coupled receptor (GPCR). The mutant was designed to form a disulfide bond between the N-terminus and loop E3 which allows handling of opsin in detergent solution and increases thermal stability of rhodopsin by 10C. It furthermore allowed us to crystallize a fully deglycosylated rhodopsin (N2C/N15D/D282C). N15 mutations are normally misfolding and cause retinitis pigmentosa in humans. Microcrystallographic techniques and a 5?m x-ray beam were used to collect data along a single needle measuring 5x5x90?m3. The disulfide introduces only minor changes but fixes the N-terminal cap over the ?-sheet lid covering the ligand binding site, a likely explanation for the increased stability. This work allows structural investigation of rhodopsin mutants and shows the problems encountered during structure determination of GPCRs and other mammalian membrane proteins. PMID:17825322

Standfuss, Jrg; Xie, Guifu; Edwards, Patricia C.; Burghammer, Manfred; Oprian, Daniel D.; Schertler, Gebhard F. X.

2007-01-01

392

Crystal structure of lipid phosphatase Escherichia coli phosphatidylglycerophosphate phosphatase B.  

PubMed

Membrane-integrated type II phosphatidic acid phosphatases (PAP2s) are important for numerous bacterial to human biological processes, including glucose transport, lipid metabolism, and signaling. Escherichia coli phosphatidylglycerol-phosphate phosphatase B (ecPgpB) catalyzes removing the terminal phosphate group from a lipid carrier, undecaprenyl pyrophosphate, and is essential for transport of many hydrophilic small molecules across the membrane. We determined the crystal structure of ecPgpB at a resolution of 3.2 . This structure shares a similar folding topology and a nearly identical active site with soluble PAP2 enzymes. However, the substrate binding mechanism appears to be fundamentally different from that in soluble PAP2 enzymes. In ecPgpB, the potential substrate entrance to the active site is located in a cleft formed by a V-shaped transmembrane helix pair, allowing lateral movement of the lipid substrate entering the active site from the membrane lipid bilayer. Activity assays of point mutations confirmed the importance of the catalytic residues and potential residues involved in phosphate binding. The structure also suggests an induced-fit mechanism for the substrate binding. The 3D structure of ecPgpB serves as a prototype to study eukaryotic PAP2 enzymes, including human glucose-6-phosphatase, a key enzyme in the homeostatic regulation of blood glucose concentrations. PMID:24821770

Fan, Junping; Jiang, Daohua; Zhao, Yan; Liu, Jianfeng; Zhang, Xuejun Cai

2014-05-27

393

Crystal structure of substrate free form of glycerol dehydratase  

SciTech Connect

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

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

2010-03-08

394

Supramolecule Structure for Amphiphilic Molecule by Dissipative Particle Dynamics Simulation  

E-print Network

Meso-scale simulation of structure formation for AB-dimers in solution W monomers was performed by dissipative particle dynamics (DPD) algorithm. As a simulation model, modified Jury Model was adopted Jury, S. et al. "Simulation of amphiphilic mesophases using dissipative particle dynamics," Phys. Chem. Chem. Phys. vol.1(1999) pp. 2051-2056, which represents mechanics of self-assembly for surfactant hexaethylene glycol dodecyl ether (C12E6) and water(H2 O). The same phase diagram as Jury's result was obtained. We also found that it takes a longer time to form the hexagonal phase (H1) than to form the lamellar phase (Lalpha).

Hiroaki Nakamura

2006-04-12

395

Gas-flow-induced reorientation to centimeter-sized two-dimensional colloidal single crystal of polystyrene particle.  

PubMed

Centimeter-sized two-dimensional (2D) colloidal single crystals of polystyrene (PS) particles were fabricated at the water/air interface by capillary-modulated self-assembly. Different from previous reports, in this work, emulsifier was used to facilitate the stress release during 2D colloidal crystal formation by adjusting the interparticle lateral interactions. With the assistance of compressed nitrogen flow, 2D hexagonal colloidal single crystals of centimeter size were obtained under appropriate emulsifier concentrations. A new method was also developed to transfer the 2D colloidal crystals from the air/water interface to the desired substrate without obvious disturbance. This new transferring method was proven not to be sensitive to surface wettability nor curvature, thus 2D colloidal single crystals with large areas could be obtained on different kinds of substrate. PMID:24588268

Meng, Xiaohui; Qiu, Dong

2014-03-25

396

Magnetic particles confined in a modulated channel: structural transitions tunable by tilting a magnetic field  

E-print Network

The ground state of colloidal magnetic particles in a modulated channel are investigated as function of the tilt angle of an applied magnetic field. The particles are confined by a parabolic potential in the transversal direction while in the axial direction a periodic substrate potential is present. By using Monte Carlo (MC) simulations, we construct a phase diagram for the different crystal structures as a function of the magnetic field orientation, strength of the modulated potential and the commensurability factor of the system. Interestingly, we found first and second order phase transitions between different crystal structures, which can be manipulated by the orientation of the external magnetic field. A re-entrant behavior is found between two- and four-chain configurations, with continuous second order transitions. Novel configurations are found consisting of frozen in solitons. By changing the orientation and/or strength of the magnetic field and/or the strength and the spatial frequency of the periodic substrate potential, the system transits through different phases.

J. E. Galvn-Moya; D. Lucena; W. P. Ferreira; F. M. Peeters

2014-01-03

397

Magnetic particles confined in a modulated channel: structural transitions tunable by tilting a magnetic field.  

PubMed

The ground state of colloidal magnetic particles in a modulated channel are investigated as a function of the tilt angle of an applied magnetic field. The particles are confined by a parabolic potential in the transversal direction while in the axial direction a periodic substrate potential is present. By using Monte Carlo simulations, we construct a phase diagram for the different crystal structures as a function of the magnetic field orientation, strength of the modulated potential, and the commensurability factor of the system. Interestingly, we found first- and second-order phase transitions between different crystal structures, which can be manipulated by the orientation of the external magnetic field. A reentrant behavior is found between two- and four-chain configurations, with continuous second-order transitions. Novel configurations are found consisting of frozen solitons of defects. By changing the orientation and/or strength of the magnetic field and/or the strength and periodicity of the substrate potential, the system transits through different phases. PMID:24730844

Galvn-Moya, J E; Lucena, D; Ferreira, W P; Peeters, F M

2014-03-01

398

Formation and structure of a soliton in an antiferroelectric liquid crystal in an electric field  

Microsoft Academic Search

The soliton structure in an antiferroelectric liquid crystal in an electric field is calculated in the discrete phenomenological Landau model for phase transitions. The anticlinic structure of the antiferroelectric crystal gives rise to nontrivial features of the soliton structure and the stability of the soliton. The soliton is topologically stable in a metastable state if the electric field is much

P. V. Dolganov; V. M. Zhilin; V. K. Dolganov; E. I. Kats

2009-01-01

399

Data Mining Approach to Ab-Initio Prediction of Crystal Structure Dane Morgan, Gerbrand Ceder  

E-print Network

Data Mining Approach to Ab-Initio Prediction of Crystal Structure Dane Morgan, Gerbrand Ceder are a powerful tool for predicting crystal structure, but are too slow to explore the extremely large space of possible structures for new alloys. Here we describe ongoing work on a novel method (Data Mining of Quantum

Curtarolo, Stefano

400

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

NASA Astrophysics Data System (ADS)

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

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

2013-06-01

401

Crystal and molecular structure of four adamantyl-substituted tetrazoles  

SciTech Connect

Four adamantyltetrazoles-1-(1-adamantyl)tetrazole (I), 2-(1-adamantyl)tetrazole (II), 2-(3-aminoadamantyl-1)tetrazole (III), and 2-(3-aminoadamantyl-1)-5-methyltetrazole (IV)-are synthesized, and their crystal structures are studied. It is found that the tetrazole rings in the 1-substituted molecule I and 2-substituted molecules II-IV have close linear parameters but differ significantly in endocyclic angles. The degree of delocalization of double bonds in I is somewhat smaller than that in II-IV. The identical relative orientation of the tetrazole ring and adamantyl fragment in I-IV is stabilized by intramolecular C-H...N interactions (H...N, 2.57(2)-2.76(2) A). The molecular packings of crystals I-IV are determined by weak intermolecular C-H...N interactions; in III and IV, the packings are in addition affected by N-H...N interactions that involve NH{sub 2} groups. In the series of compounds I-IV, a qualitative dependence of the lengths of intermolecular H...N contacts and antiviral activity on the basicity of nitrogen atoms in the molecules is revealed.

Polyakova, I. N., E-mail: polyakova@igic.ras.ru [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation); Saraev, V. V.; Gavrilov, A. S.; Golod, E. L. [St. Petersburg State Technological Institute (Technical University) (Russian Federation)

2009-05-15

402

Crystal and molecular structure of four adamantyl-substituted tetrazoles  

NASA Astrophysics Data System (ADS)

Four adamantyltetrazoles1-(1-adamantyl)tetrazole ( I), 2-(1-adamantyl)tetrazole ( II), 2-(3-aminoadamantyl-1)tetrazole ( III), and 2-(3-aminoadamantyl-1)-5-methyltetrazole ( IV)are synthesized, and their crystal structures are studied. It is found that the tetrazole rings in the 1-substituted molecule I and 2-substituted molecules II- IV have close linear parameters but differ significantly in endocyclic angles. The degree of delocalization of double bonds in I is somewhat smaller than that in II- IV. The identical relative orientation of the tetrazole ring and adamantyl fragment in I- IV is stabilized by intramolecular C-H...N interactions (H...N, 2.57(2)-2.76(2) ). The molecular packings of crystals I- IV are determined by weak intermolecular C-H...N interactions; in III and IV, the packings are in addition affected by N-H...N interactions that involve NH2 groups. In the series of compounds I- IV, a qualitative dependence of the lengths of intermolecular H...N contacts and antiviral activity on the basicity of nitrogen atoms in the molecules is revealed.

Polyakova, I. N.; Saraev, V. V.; Gavrilov, A. S.; Golod, E. L.

2009-05-01

403

Identification of a Novel "Fishbone" Structure in the Dendritic Growth of Columnar Ice Crystals  

E-print Network

Identification of a Novel "Fishbone" Structure in the Dendritic Growth of Columnar Ice Crystals will be an interesting challenge in understanding diffusion-limited crystal growth in the presence of highly anisotropic branching along growth directions that are not aligned with respect to the ice crystal lattice. Examples

Libbrecht, Kenneth G.

404

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

E-print Network

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

Wu, Chien H.

405

Band structures tunability of bulk 2D phononic crystals made of magneto-elastic materials  

E-print Network

(2011) Evanescent waves and deaf bands in sonic crystals AIP Advances 1, 041601 (2011) AdditionalBand structures tunability of bulk 2D phononic crystals made of magneto-elastic materials J. O phononic crystal slabs using a hybrid lattice dynamics-continuum mechanics technique AIP Advances 1, 041403

Deymier, Pierre

406

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 forms of Naja naja naja phospholipase A2 were discovered through random crystallization screening, including two heretofore uncharacterized forms. The crystallization conditions for both of these novel

Dennis, Edward A.

407

Optimization of 3D Plasmonic Crystal Structures for Refractive Index Sensing Joana Maria,  

E-print Network

Optimization of 3D Plasmonic Crystal Structures for Refractive Index Sensing Joana Maria, Tu T study the refractive index sensitive transmission of a 3D plasmonic crystal that consists of a square in sensitivity by an order of magnitude when the plasmonic crystal characteristics are optimized. 1. Introduction

Rogers, John A.

408

Application of a Crystal Septum to Replace a Magnet in a Charged Particle Beam and Study of Dechanneling and Feeding-In Effects in a Single Silicon Crystal  

NASA Astrophysics Data System (ADS)

First part of this thesis describes the first application of a crystal septum to replace a magnetic septum at the Fermilab Meson area M-Bottom secondary beam line. As a result the maximum momentum of the beam that could be transmitted to the experimental area was raised from the magnetic septum limit of 225 Gev/c to the full primary beam momentum of 400 Gev/c. Transmission properties of the crystal septum has been studied at energies of 60, 100 and 200 Gev/c. Beam properties at 200 Gev/c with the crystal septum operation has also been studied. The second part consists of a study of planar (110) and axial <112> feeding-in and dechanneling effects in a single silicon crystal. Three surface barrier semiconductor detectors along the crystal were used to measure the energy loss of the charged particles. For each particle incident and outgoing angles and the energy losses in the three crystal mounted detectors were recorded on magnetic tapes. Channeled particles were identified by their low energy losses. Data was acquired at energies of 30, 60, 100 and 200 Gev for planar channeling and 60 and 100 Gev for axial channeling. Feeding -in effects were observed for both planar and axial cases. The basic probabilistic equation was used to derive a simple theoretical model which contains the characteristic dechanneling and feeding-in length. The dechanneling lengths have been calculated for both planar and axial channeling and the incident angle dependence of feeding-in has been studied for planar channeling at above all energies.

Wijayawardana, Ranjith Laxman

1985-12-01

409

Crystallization, crystal-structure refinement, and IR spectroscopy of a synthetic hexahydroborite analog  

SciTech Connect

The crystal structure of the hexahydroborite analog Ca[B(OH){sub 4}]{sub 2} {center_dot} 2H{sub 2}O (a = 7.9941(3) Angstrom-Sign , b = 6.6321(2) Angstrom-Sign , c = 7.9871(3) Angstrom-Sign , {beta} = 104.166(4) Degree-Sign , V = 410.58(3) Angstrom-Sign {sup 3}, sp. gr. P2/c, Z = 2, {rho}{sub calc} = 1.891 g/cm{sup 3}; Xcalibur S CCD automated diffractometer, 1196 reflections with I > 2{sigma}(I), {lambda}MoK{sub {alpha}}), which was synthesized by the hydrothermal method via the recrystallization of calciborite CaB{sub 2}O{sub 4} (M) in the M - B{sub 2}O{sub 3} - H{sub 2}O system (t = 250 Degree-Sign C and P = 70-80 atm), was refined by the least-squares method with anisotropic displacement parameters (H atoms were located; R{sub 1} = 0.0260). The structure of synthetic hexahydroborite consists of infinite columns running along the c axis. The columns are formed by Ca polyhedra linked together and to [B(OH){sub 4}] orthotetrahedra by sharing edges. Along the two other axes, the translationally equivalent columns are linked only by hydrogen bonds. The presence of a stronger bond between the discrete (Ca-B-O) columns along the shortest (b = 6.6 Angstrom-Sign ) axis accounts for the possibility of the shift of the columns by 1/2T{sub b} and the formation of the second modification of Ca[B(OH){sub 4}]{sub 2} {center_dot} 2H{sub 2}O. The crystals of synthetic hexahydroborite were studied by IR spectroscopy. A crystal-chemical analysis was performed for a series of natural metaborates with the general formula CaB{sub 2}O{sub 4} {center_dot} nH{sub 2}O (CaO: B{sub 2}O{sub 3} = 1: 1, n = 0-6), including calciborite CaB{sub 2}O{sub 4} and hexahydroborite CaB{sub 2}O{sub 4} {center_dot} 6H{sub 2}O as the end members.

Yamnova, N. A., E-mail: natalia-yamnova@yandex.ru; Borovikova, E. Yu.; Dimitrova, O. V. [Moscow State University, Faculty of Geology (Russian Federation)

2011-11-15

410

VO2 (A): Reinvestigation of crystal structure, phase transition and crystal growth mechanisms  

NASA Astrophysics Data System (ADS)

Well crystallized VO2 (A) microrods were grown via a single step hydrothermal reaction in the presence of V2O5 and oxalic acid. With the advantage of high crystalline samples, we propose P4/ncc as an appropriate space group at room temperature. From morphological studies, we found that the oriented attachment and layer by layer growth mechanisms are responsible for the formation of VO2 (A) micro rods. The structural and electronic transitions in VO2 (A) are strongly first order in nature, and a marked difference between the structural transition temperatures and electronic transitions temperature was evidenced. The reversible intra- (LTP-A to HTP-A) and irreversible inter- (HTP-A to VO2 (M1)) structural phase transformations were studied by in-situ powder X-ray diffraction. Attempts to increase the size of the VO2 (A) microrods are presented and the possible formation steps for the flower-like morphologies of VO2 (M1) are described.

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

2014-05-01

411

A new structure type of phosphate: Crystal structure of Na 2Zn 5(PO 4) 4  

NASA Astrophysics Data System (ADS)

A new compound, Na 2Zn 5(PO 4) 4, was identified in the system ZnO sbnd Na 2O sbnd P 2O 5 and high-quality crystal was obtained by the melt method. The crystal structure of this compound was solved by direct method from single crystal X-ray diffraction data. The structure was then refined anisotropically using a full-matrix least square refinement on F2 and the refinement converged to R1=0.0233 and w R2=0.0544. This compound crystallizes in the orthorhombic system with space group Pbcn, lattice parameters a=10.381(2) , b=8.507(1) , c=16.568(3) and Z=4. The structure is made up of 3D [Zn 5P 4O 16] n2 n- covalent framework consisting of [Zn 4P 4O 16] n4 n- layers. The powder diffraction pattern of Na 9Zn 21(PO 4) 17 is explained by simulating a theoretical pattern with NaZnPO 4 and Na 2Zn 5(PO 4) 4 in the molar ratio of 1:4 and then by Rietveld refinement of experimental pattern. Na 2Zn 5(PO 4) 4 melts congruently at 855 C and its conductivity is 5.6310 -9 S/cm.

Ji, L. N.; Ma, H. W.; Li, J. B.; Liang, J. K.; Sun, B. J.; Liu, Y. H.; Zhang, J. Y.; Rao, G. H.

2007-08-01

412

Crystal structure of cindoxin, the P450cin redox partner.  

PubMed

The crystal structure of the flavin mononucleotide (FMN)-containing redox partner to P450cin, cindoxin (Cdx), has been determined to 1.3 resolution. The overall structure is similar to that of the FMN domain of human cytochrome P450 reductase. A Brownian dynamics-molecular dynamics docking method was used to produce a model of Cdx with its redox partner, P450cin. This Cdx-P450cin model highlights the potential importance of Cdx Tyr96 in bridging the FMN and heme cofactors as well P450cin Arg102 and Arg346. Each of the single-site Ala mutants exhibits ~10% of the wild-type activity, thus demonstrating the importance of these residues for binding and/or electron transfer. In the well-studied P450cam system, redox partner binding stabilizes the open low-spin conformation of P450cam and greatly decreases the stability of the oxy complex. In sharp contrast, Cdx does not shift P450cin to a low-spin state, although the stability of oxy-P450cin is decreased 10-fold in the presence of Cdx. This indicates that Cdx may have a modest effect on the open-closed equilibrium in P450cin compared to that in P450cam. It has been postulated that part of the effector role of Pdx on P450cam is to promote a significant structural change that makes available a proton relay network involving Asp251 required for O2 activation. The structure around the corresponding Asp in P450cin, Asp241, provides a possible structural reason for why P450cin is less dependent on its redox partner for functionally important structural changes. PMID:24533927

Madrona, Yarrow; Hollingsworth, Scott A; Tripathi, Sarvind; Fields, James B; Rwigema, Jean-Christophe N; Tobias, Douglas J; Poulos, Thomas L

2014-03-11

413

Crystal Structure of Hyperthermophilic Endo-?-1,4-glucanase  

PubMed Central

Endo-?-1,4-glucanase from thermophilic Fervidobacterium nodosum Rt17-B1 (FnCel5A), a new member of glycosyl hydrolase family 5, is highly thermostable and exhibits the highest activity on carboxymethylcellulose among the reported homologues. To understand the structural basis for the thermostability and catalytic mechanism, we report here the crystal structures of FnCel5A and the complex with glucose at atomic resolution. FnCel5A exhibited a (?/?)8-barrel structure typical of clan GH-A of the glycoside hydrolase families with a large and deep catalytic pocket located in the C-terminal end of the ?-strands that may permit substrate access. A comparison of the structure of FnCel5A with related structures from thermopile Clostridium thermocellum, mesophile Clostridium cellulolyticum, and psychrophile Pseudoalteromonas haloplanktis showed significant differences in intramolecular interactions (salt bridges and hydrogen bonds) that may account for the difference in their thermostabilities. The substrate complex structure in combination with a mutagenesis analysis of the catalytic residues implicates a distinctive catalytic module Glu167-His226-Glu283, which suggests that the histidine may function as an intermediate for the electron transfer network between the typical Glu-Glu catalytic module. Further investigation suggested that the aromatic residues Trp61, Trp204, Phe231, and Trp240 as well as polar residues Asn51, His127, Tyr228, and His235 in the active site not only participated in substrate binding but also provided a unique microenvironment suitable for catalysis. These results provide substantial insight into the unique characteristics of FnCel5A for catalysis and adaptation to extreme temperature. PMID:22128157

Zheng, Baisong; Yang, Wen; Zhao, Xinyu; Wang, Yuguo; Lou, Zhiyong; Rao, Zihe; Feng, Yan

2012-01-01

414

Synthetical bone-like and biological hydroxyapatites: a comparative study of crystal structure and morphology.  

PubMed

Phase composition, crystal structure and morphology of biological hydroxyapatite (BHAp) extracted from human mandible bone, and carbonated hydroxyapatite (CHAp), synthesized by the chemical precipitation method, were studied by x-ray powder diffraction (XRD), Fourier transform infrared (FTIR) and Raman (R) spectroscopy techniques, combined with transmission electron microscopy (TEM). Structural and microstructural parameters were determined through Rietveld refinement of recorded XRD data, performed using the FullProf computing program, and TEM. Microstructural analysis shows anisotropic extension along the [00l] crystallographic direction (i.e. elongated crystallites shape) of both investigated samples. The average crystallite sizes of 10 and 8 nm were estimated for BHAp and CHAp, respectively. The FTIR and R spectroscopy studies show that carbonate ions substitute both phosphate and hydroxyl ions in the crystal structure of BHAp as well as in CHAp, indicating that both of them are mixed AB-type of CHAp. The thermal behaviour and carbonate content were analysed using thermogravimetric and differential thermal analysis. The carbonate content of about 1 wt.% and phase transition, at near 790 C, from HAp to ?-tricalcium phosphate were determined in both samples. The quality of synthesized CHAp powder, particularly, the particle size distribution and uniformity of morphology, was analysed by a particle size analyser based on laser diffraction and field emission scanning electron microscopy, respectively. These data were used to discuss similarity between natural and synthetic CHAp. Good correlation between the unit cell parameters, average crystallite size, morphology, carbonate content and crystallographic positions of carbonate ions in natural and synthetic HAp samples was found. PMID:21659698

Markovi?, Smilja; Veselinovi?, Ljiljana; Luki?, Miodrag J; Karanovi?, Ljiljana; Bra?ko, Ines; Ignjatovi?, Nenad; Uskokovi?, Dragan

2011-08-01

415

Crystal structure of CD155 and electron microscopic studies of its complexes with polioviruses  

SciTech Connect

When poliovirus (PV) recognizes its receptor, CD155, the virus changes from a 160S to a 135S particle before releasing its genome into the cytoplasm. CD155 is a transmembrane protein with 3 Ig-like extracellular domains, D1-D3, where D1 is recognized by the virus. The crystal structure of D1D2 has been determined to 3.5-{angstrom} resolution and fitted into {approx}8.5-{angstrom} resolution cryoelectron microscopy reconstructions of the virus-receptor complexes for the 3 PV serotypes. These structures show that, compared with human rhinoviruses, the virus-receptor interactions for PVs have a greater dependence on hydrophobic interactions, as might be required for a virus that can inhabit environments of different pH. The pocket factor was shown to remain in the virus during the first recognition stage. The present structures, when combined with earlier mutational investigations, show that in the subsequent entry stage the receptor moves further into the canyon when at a physiological temperature, thereby expelling the pocket factor and separating the viral subunits to form 135S particles. These results provide a detailed analysis of how a nonenveloped virus can enter its host cell.

Zhang, Ping; Mueller, Steffen; Morais, Marc C.; Bator, Carol M.; Bowman, Valorie D.; Hafenstein, Susan; Wimmer, Eckard; Rossmann, Michael G. (SBU); (Purdue)

2010-11-02

416

Crystal Structure of Calcium-Deficient Carbonated Hydroxyapatite. Thermal Decomposition  

Microsoft Academic Search

Full Rietveld refinement of the crystal structure of the synthetic calcium-deficient carbonated apatite Ca13.40[Ca25.90 (NH4)0.10][(PO4)4.95(CO3)1.05(H2O)0.30][(OH)1.65(H2O)0.45] (space group P63\\/m; a=9.437(1), c=6.888(1) ; Z=1; Rwp=5.23%) was carried out using X-ray powder diffraction data. The use of the model with the split position of O3 atom made it possible to find two orientations of CO3 triangles sharing one of their edges. They occupy

T. I. Ivanova; O. V. Frank-Kamenetskaya; A. B. Kol'tsov; V. L. Ugolkov

2001-01-01

417

Structural Order in Liquids Induced by Interfaces with Crystals  

NASA Astrophysics Data System (ADS)

Interfaces between solids and liquids are important for a range of materials processes, including soldering and brazing, liquid-phase sintering, crystal growth, and lubrication. There is a wealth of fundamental studies on solid-liquid interfaces in materials, primarily focused on thermodynamics (relative interface energies and segregation effects) from high-temperature wetting experiments, which is often applied to processing design. Less is known about the atomistic structure at solid-liquid interfaces, mainly because of the difficulty involved in obtaining such information experimentally. This work reviews both theoretical and experimental studies of atomistic configurations at solid-liquid interfaces, focusing on the issue of ordering in the liquid adjacent to crystalline solids.

Kaplan, Wayne D.; Kauffmann, Yaron

2006-08-01

418

Crystal structure of a heterotetrameric NMDA receptor ion channel  

PubMed Central

N -methyl-D-aspartate (NMDA) receptors belong to the family of ionotropic glutamate receptors, which mediate most excitatory synaptic transmission in mammalian brains. Calcium permeation triggered by activation of NMDA receptors is the pivotal event for initiation of neuronal plasticity. Here we show the crystal structure of the intact heterotetrameric GluN1/GluN2B NMDA receptor ion channel at 4 . The NMDA receptors are arranged as a dimer of GluN1-GluN2B heterodimers with the two-fold symmetry axis running through the entire molecule composed of an amino terminal domain (ATD), a ligand-binding domain (LBD), and a transmembrane domain (TMD). The ATD and LBD are much more highly packed in the NMDA receptors than non-NMDA receptors, which may explain why ATD regulates ion channel activity in NMDA receptors but not in non-NMDA receptors. PMID:24876489

Karakas, Erkan; Furukawa, Hiro

2014-01-01

419

Structural conditionality of the piezoelectric properties of langasite family crystals  

SciTech Connect

The atomic displacements upon isomorphic substitutions in crystals of the langasite family have been analyzed. The thermal parameters are determined and the probability density function of atoms is analyzed. Local potential energy minima are found which can be occupied by atoms under external effects. The contributions of cations in all four independent crystallographic positions and anions in all three such positions to the piezoelectric properties are established. One specific structural feature is the constant (at isomorphic substitutions) or possible (under external effects) but always opposite displacements of two cations along symmetry axis 2. Large cations in eight-vertex polyhedra make the main contribution to the piezoelectric properties. The cations in the tetrahedra on symmetry axis 2 weaken these properties. The cations in the octahedra in the origin of coordinates and in the tetrahedra on symmetry axes 3 only slightly affect the piezoelectricity.

Dudka, A. P., E-mail: dudka@ns.crys.ras.ru; Simonov, V. I. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

2011-11-15

420

Design, synthesis, crystal structure analysis, and insecticidal evaluation of phenylazoneonicotinoids.  

PubMed

On the basis of research of the proposed modes of action between neonicotinoids and insect nicotinic acetylcholine receptor (nAChR), a series of phenylazoneonicotinoids were designed and synthesized to further promote the ?-? interaction between molecule and amino acid residues. The target compounds have been identified on the basis of satisfactory analytical and spectral ((1)H NMR, (13)C NMR, HRMS, and X-ray) data. The preliminary results revealed that tiny differences in substitutes resulted in different configurations and great bioactivity variations. Some compounds with electron-donating groups on positions 2 and 6 of the phenyl ring presented higher insecticidal activity than imidacloprid against cowpea aphids ( Aphis craccivora ). The impressive crystal structure of the excellent insecticidal activity compound 9q clearly proved that the functional electronegative pharmacophore was approximately vertical to the methyleneimidazolidine plane. The differences in the mode of interaction on nAChR of typical compounds 9h and 9q remain unclear. PMID:21894959

Ye, Zhenjun; Xia, Shuang; Shao, Xusheng; Cheng, Jiagao; Xu, Xiaoyong; Xu, Zhiping; Li, Zhong; Qian, Xuhong

2011-10-12

421

Vibrational and crystal structure analysis of a phenylenedioxydiacetic acid derivative  

NASA Astrophysics Data System (ADS)

Computationally derived data has successfully assisted the characterisation of the Raman and infrared vibrational spectra of the phenylenedioxydiacetic acid (PDA) derivative 2,2'-[(4-nitro-1,2-phenylene)bis(oxy)]diacetate (I) in the solid state. X-ray diffraction analysis of (I), which crystallised in the non-centrosymmetric achiral space group Pca2 1, revealed the computationally predicted minimum energy geometry differed to that observed in the solid state molecule due to significant inter-molecular bonding, this was also confirmed computationally. Importantly, large deviations between the wavenumber of predicted and experimental vibrational modes only occurred with functional groups that engaged in inter-molecular bonding. From a comparison of the energies of the calculated and X-ray structural data the crystal packing forces in the solid-state was estimated at ?240 kJ/mol.

Cunning, Benjamin V.; Hope, Gregory A.; Healy, Peter C.; Brown, Christopher L.

2011-02-01

422

Crystal structure of Saccharomyces cerevisiae 6-phosphogluconate dehydrogenase Gnd1  

PubMed Central

Background As the third enzyme of the pentose phosphate pathway, 6-phosphogluconate dehydrogenase (6PGDH) is the main generator of cellular NADPH. Both thioredoxin reductase and glutathione reductase require NADPH as the electron donor to reduce oxidized thioredoxin or glutathione (GSSG). Since thioredoxin and GSH are important antioxidants, it is not surprising that 6PGDH plays a critical role in protecting cells from oxidative stress. Furthermore the activity of 6PGDH is associated with several human disorders including cancer and Alzheimer's disease. The 3D structural investigation would be very valuable in designing small molecules that target this enzyme for potential therapeutic applications. Results The crystal structure of 6-phosphogluconate dehydrogenase (6PGDH/Gnd1) from Saccharomyces cerevisiae has been determined at 2.37 resolution by molecular replacement. The overall structure of Gnd1 is a homodimer with three domains for each monomer, a Rossmann fold NADP+ binding domain, an all-? helical domain contributing the majority to hydrophobic interaction between the two subunits and a small C-terminal domain penetrating the other subunit. In addition, two citrate molecules occupied the 6PG binding pocket of each monomer. The intact Gnd1 had a Km of 50 9 ?M for 6-phosphogluconate and of 35 6 ?M for NADP+ at pH 7.5. But the truncated mutants without the C-terminal 35, 39 or 53 residues of Gnd1 completely lost their 6PGDH activity, despite remaining the homodimer in solution. Conclusion The overall tertiary structure of Gnd1 is similar to those of 6PGDH from other species. The substrate and coenzyme binding sites are well conserved, either from the primary sequence alignment, or from the 3D structural superposition. Enzymatic activity assays suggest a sequential mechanism of catalysis, which is in agreement with previous studies. The C-terminal domain of Gnd1 functions as a hook to further tighten the dimer, but it is not necessary for the dimerization. This domain also works as a lid on the substrate binding pocket to control the binding of substrate and the release of product, so it is indispensable for the 6PGDH activity. Moreover, the co-crystallized citrate molecules, which mimic the binding mode of the substrate 6-phosphogluconate, provided us a novel strategy to design the 6PDGH inhibitors. PMID:17570834

He, Weiwei; Wang, Yi; Liu, Wei; Zhou, Cong-Zhao

2007-01-01

423

Light propagation in liquid crystals and liquid crystalline structures  

NASA Astrophysics Data System (ADS)

Liquid crystals are optically complex materials, characterized in general by anisotropy, loss and chirality. Understanding light propagation both in uniform samples, and in stratified structures consisting of layers of such materials is of considerable interest for fundamental reasons. It is also essential for the effective use of these materials in technology. Light propagation in matter can be understood classically in terms of solutions to Maxwell's equations. In this work, analytical solutions of Maxwell's equations have been obtained for the first time for general linear optical media[l], that is, biaxial, lossy and optically active material. This result is a key achivement of this dissertation. The explicit expressions are useful for understanding light propagation in optically complex media, including optically active media where both natural and magnetic optical activities are present and lossy biaxial media where the real and imaginary parts of dielectric tensor do not commute. Four, rather than two distinct optical eigenmodes are predicted in the general case. Special representations of the Poynting vector and boundary conditions have been obtained for optically active media. Based on the analytical solution of Maxwell's equations, a new 4 x 4 propagation matrix method has been developed for numerical calculation of light propagation in statified (1-d) liquid crystalline structures. This method has been implemented, and the demonstration software has been coded. It has been shown that this scheme is efficient, accurate and can be used in the general case of chiral materials. We have also studied light propagation in periodic structures with optically complex elements. These are 1-d photonic band gap materials; characteristic propagation matrices have been used to analyse the band structure The results are useful for developing optical devices such as switchable mirrors and the cholesteric laser. A Wave Guide Based Cholesteric Liquid Crystal Display (WGCLCD) has been invented with theoretical and numerical support. Prototype WGCLCDs have been built and demonstrated. These prototypes show good viewing angles, high optical efficiency and contrast ratio, and have faster switching speeds and lower switching voltages than typical conventional cholesteric displays. Because of their simple structure, low cost and easy fabrication, WGCLCDs may be useful for commercial displays.

Yuan, Haijun

424

[Galactic heavy charged particles damaging effect on biological structures].  

PubMed

A concept of the radiation risk of the manned interplanetary flights is proposed and substantiated. Heavy charged particles that are a component of the galactic cosmic rays (GCR) have a high damaging effect on the biological structures as great amount of energy is deposited in heavy particle tracks. The high biological effectiveness of heavy ions is observed in their action on cell genetic structures and the whole organism, including the brain structures. The hippocampus is the part of the central nervous system that is the most sensitive to radiation--first of all, to heavy charged particles. Irradiation of animals with accelerated iron ions at doses corresponding to the real fluxes of GCR heavy nuclei, to which Mars mission crews can be exposed, leads to marked behavioral function disorders in the post-irradiation period. To evaluate the radiation risk for the interplanetary flight crews, the concept of successful mission accomplishment is introduced. In these conditions, the central nervous system structures can be the critical target of GCR heavy nuclei. Their damage can modify the higher integrative functions of the brain and cause disorders in the crew members' operator performances. PMID:23789432

Grigor'ev, A I; Krasavin, E A; Ostrovski?, M A

2013-03-01

425

The Electronic Structure of Smoothly Deformed Crystals: Wannier Functions and the Cauchy-Born Rule  

NASA Astrophysics Data System (ADS)

The electronic structure of a smoothly deformed crystal is analyzed for the case when the effective Hamiltonian is a given function of the nuclei by considering the regime when the scale of the deformation is much larger than the lattice parameter. Wannier functions are defined by projecting the Wannier functions for the undeformed crystal to the space spanned by the wave functions of the deformed crystal. The exponential decay of such Wannier functions is proved for the case when the undeformed crystal is an insulator. The celebrated Cauchy-Born rule for crystal lattices is extended to the present situation for electronic structure analysis.

E, Weinan; Lu, Jianfeng

2011-02-01

426

Using polarimetric remote sensing measurements to estimate ice particle size, optical depth and ice water path during CRYSTAL-FACE  

NASA Astrophysics Data System (ADS)

In situ observations made during the CRYSTAL-FACE field experiment have indicated that ice crystals have smaller sizes and are more reflective than is commonly assumed in most current climate models. The size of the particles appears to be principally determined by temperature with the smallest particles being found at the coldest temperatures. Previous analyses of polarimetric measurements in non-absorbing bands have suggested that either bubble inclusions (inhomogeneous hexagonal mono-crystals) or distortions of the hexagonal crystal shape (distorted chain aggregates) are responsible for the observed general absence of haloes, smooth angular variation of reflectance and brightness of ice clouds. In this paper we use multi-angle measurements made by the Research Scanning Polarimeter (RSP) to examine the polarized and unpolarized reflectance of cirrus clouds in bands where ice is non-absorbing (670 and 865 nm) and absorbing (1590, 1880 and 2250 nm). During CRSYTAL-FACE the RSP scan was biased so that the view angle range was from 0 to 75 degrees to the rear of the Proteus aircraft and from 0 to 45 degrees to the front and was oriented to scan along the groundtrack of the aircraft. This allowed observations of a single target over a wide scattering angle range particularly when consecutive flight legs could be combined which allows for basic discrimination of crystal habit using the non-absorbing bands, similar to previous studies (at least in the gross sense of being able to separate columns from plates from distorted crystals from spheroidal shapes). However, compared with non-absorbing bands, the reflectance in absorbing bands is different depending on whether ice particles are geometrically distorted or contain air bubble inclusions because the path length of light inside an ice crystal is quite short which limits scattering off the bubble inclusions. Consequently the retrieved particle size is also sensitive to whether ice crystals are modeled as being distorted or containing air bubbles. We examine how the RSP size retrievals, with an appropriate vertical weighting determined by Green's function calculations, compare with in situ measurements and examine the angular and spectral polarized and unpolarized residuals from the retrievals. This allows us to identify the most appropriate crystal habit for use in the remote sensing of cirrus clouds formed by convection over land, such as those observed during CRYSTAL-FACE, and provide best estimates for the particle size, optical depth and ice water path determined using solar reflectance measurements.

Geogdzhayev, I.; Cairns, B.; Mishchenko, M. I.; Travis, L. D.

2006-12-01

427

Interferometric technique for the measurement of photonic band structure in colloidal crystals  

NASA Astrophysics Data System (ADS)

Under suitable conditions polystyrene microsphere colloids form photonic crystals capable of diffracting visible light, analogous to x-ray diffraction from atomic crystal planes. The lattice spacings of these crystals can be tailored to satisfy the Bragg condition along a certain direction for a particular desired wavelength. A modified Mach-Zehnder interferometer has been developed for accurately measuring relative phase shifts of light propagating in photonic crystals to determine the dispersion resulting from photonic band structure near the band edges.

Tarhan, I. Inanc; Zinkin, Martin P.; Watson, George H.

1995-07-01