Three-dimensional Structures of Carotenoids by X-ray Crystallography

NASA Astrophysics Data System (ADS)

Helliwell, Madeleine

The number of crystal structures of carotenoid molecules and carotenoid derivatives deposited in the Cambridge Crystallographic Data Centre [1] is still relatively small, but has increased compared with the previous survey [2]. The list is summarized in Table 1.

Intermolecular C-H···O, Cl···Cl and π-π interactions in the 2-dichloromethyl derivative of vitamin K3.

PubMed

Soave, Raffaella; Colombo, Pietro

2013-12-15

The title 1,4-naphthoquinone, 2-dichloromethyl-3-methyl-1,4-dihydronaphthalene-1,4-dione, C12H8Cl2O2, is a chlorinated derivative of vitamin K3, which is a synthetic compound also known as menadione. Molecules of (I) are planar and lie on a crystallographic mirror plane (Z' = 0.5) in the space group Pnma. They are connected to each other by C-H···O hydrogen bonds, forming two-dimensional layers parallel to the ac plane. In addition, Cl···Cl and π-π interactions link adjacent molecules in different layers, thus forming zigzag ribbons along the b axis, such that a three-dimensional architecture is generated.

Magnetic field induced strong valley polarization in the three-dimensional topological semimetal LaBi

NASA Astrophysics Data System (ADS)

Kumar, Nitesh; Shekhar, Chandra; Klotz, J.; Wosnitza, J.; Felser, Claudia

2017-10-01

LaBi is a three-dimensional rocksalt-type material with a surprisingly quasi-two-dimensional electronic structure. It exhibits excellent electronic properties such as the existence of nontrivial Dirac cones, extremely large magnetoresistance, and high charge-carrier mobility. The cigar-shaped electron valleys make the charge transport highly anisotropic when the magnetic field is varied from one crystallographic axis to another. We show that the electrons can be polarized effectively in these electron valleys under a rotating magnetic field. We achieved a polarization of 60% at 2 K despite the coexistence of three-dimensional hole pockets. The valley polarization in LaBi is compared to the sister compound LaSb where it is found to be smaller. The performance of LaBi is comparable to the highly efficient bismuth.

A two-dimensional Zn coordination polymer with a three-dimensional supra-molecular architecture.

PubMed

Liu, Fuhong; Ding, Yan; Li, Qiuyu; Zhang, Liping

2017-10-01

The title compound, poly[bis-{μ 2 -4,4'-bis-[(1,2,4-triazol-1-yl)meth-yl]biphenyl-κ 2 N 4 : N 4' }bis-(nitrato-κ O )zinc(II)], [Zn(NO 3 ) 2 (C 18 H 16 N 6 ) 2 ] n , is a two-dimensional zinc coordination polymer constructed from 4,4'-bis-[(1 H -1,2,4-triazol-1-yl)meth-yl]-1,1'-biphenyl units. It was synthesized and characterized by elemental analysis and single-crystal X-ray diffraction. The Zn II cation is located on an inversion centre and is coordinated by two O atoms from two symmetry-related nitrate groups and four N atoms from four symmetry-related 4,4'-bis-[(1 H -1,2,4-triazol-1-yl)meth-yl]-1,1'-biphenyl ligands, forming a distorted octa-hedral {ZnN 4 O 2 } coordination geometry. The linear 4,4'-bis-[(1 H -1,2,4-triazol-1-yl)meth-yl]-1,1'-biphenyl ligand links two Zn II cations, generating two-dimensional layers parallel to the crystallographic (132) plane. The parallel layers are connected by C-H⋯O, C-H⋯N, C-H⋯π and π-π stacking inter-actions, resulting in a three-dimensional supra-molecular architecture.

Construction of the Seven Basic Crystallographic Units.

ERIC Educational Resources Information Center

Li, Thomas; Worrell, Jay H.

1989-01-01

Presents an exercise to get students more intimately involved in the three dimensional nature of basic units by constructing models. Uses balsa wood, glue, sandpaper, and a square. Studies seven crystals: cubic, hexagonal, monoclinic, orthorhombic, rhombohedral, tetragonal, and triclinic. Plans are available for a Macintosh computer. (MVL)

Three-dimensional imaging of dislocation dynamics during the hydriding phase transformation

NASA Astrophysics Data System (ADS)

Ulvestad, A.; Welland, M. J.; Cha, W.; Liu, Y.; Kim, J. W.; Harder, R.; Maxey, E.; Clark, J. N.; Highland, M. J.; You, H.; Zapol, P.; Hruszkewycz, S. O.; Stephenson, G. B.

2017-05-01

Crystallographic imperfections significantly alter material properties and their response to external stimuli, including solute-induced phase transformations. Despite recent progress in imaging defects using electron and X-ray techniques, in situ three-dimensional imaging of defect dynamics remains challenging. Here, we use Bragg coherent diffractive imaging to image defects during the hydriding phase transformation of palladium nanocrystals. During constant-pressure experiments we observe that the phase transformation begins after dislocation nucleation close to the phase boundary in particles larger than 300 nm. The three-dimensional phase morphology suggests that the hydrogen-rich phase is more similar to a spherical cap on the hydrogen-poor phase than to the core-shell model commonly assumed. We substantiate this using three-dimensional phase field modelling, demonstrating how phase morphology affects the critical size for dislocation nucleation. Our results reveal how particle size and phase morphology affects transformations in the PdH system.

Syntheses, structures, and magnetic properties of three new MnII-[MoIII(CN)7]4- molecular magnets.

PubMed

Wei, Xiao-Qin; Pi, Qian; Shen, Fu-Xing; Shao, Dong; Wei, Hai-Yan; Wang, Xin-Yi

2018-05-22

By reaction of K4[MoIII(CN)7]·2H2O, Mn(ClO4)2·6H2O and bidentate chelating ligands, three new cyano-bridged compounds, namely Mn2(3-pypz)(H2O)(CH3CN)[Mo(CN)7] (1), Mn2(1-pypz)(H2O)(CH3CN)[Mo(CN)7] (2) and Mn2(pyim)(H2O)(CH3CN)[Mo(CN)7] (3) (3-pypz = 2-(1H-pyrazol-3-yl)pyridine, 1-pypz = 2-(1H-pyrazol-1-yl)pyridine, pyim = 2-(1H-imidazol-2-yl)pyridine), have been synthesized and characterized structurally and magnetically. Single crystal X-ray analyses revealed that although the chelating ligands are different, compounds 1 to 3 are isomorphous and crystallize in the same monoclinic space group C2/m. Connected by the bridging cyano groups, one crystallographically unique [Mo(CN)7]4- unit and three crystallographically unique MnII ions of different coordination environments form similar three-dimensional frameworks, which have a four-nodal 3,4,4,7-connecting topological net with a vertex symbol of {43}{44·62}2{410·611}. Magnetic measurements revealed that compounds 1-3 display long-range magnetic ordering with critical temperatures of 64, 66 and 62 K, respectively. These compounds are rare examples of a small number of chelating co-ligand coordinated [Mo(CN)7]4--based magnetic materials. Specifically, the bidentate chelating ligands were successfully introduced into the heptacyanomolybdate system for the first time.

Long-range modulation of a composite crystal in a five-dimensional superspace

DOE PAGES

Guerin, Laurent; Mariette, Celine; Rabiller, Philippe; ...

2015-05-05

The intergrowth crystal of n-tetracosane/urea presents a misfit parameter, defined by the ratio γ = c h/c g (c host/c guest), that is very close to a commensurate value (γ ≅ 1/3). High-resolution diffraction studies presented here reveal an aperiodic misfit parameter of γ = 0.3369, which is found to be constant at all temperatures studied. A complex sequence of structural phases is reported. The high temperature phase (phase I) exists in the four-dimensional superspace group P6 122(00γ). At T c1 = 179(1) K, a ferroelastic phase transition increases the dimension of the crystallographic superspace. This orthorhombic phase (phase II)more » is characterized by the five-dimensional (5D) superspace group C222 1(00γ)(10δ) with a modulation vector a o* + c m* = a o* + δ · c h*, in which the supplementary misfit parameter is δ = 0.025(1) in host reciprocal units. Finally, this corresponds to the appearance of a modulation of very long period (about 440 ± 16 Å). At T c2 = 163.0(5) K, a 5D to 5D phase transition leads to the crystallographic superspace group P2 12 12 1(00γ)(00δ) with a very similar value of δ. This phase transition reveals a significant hysteresis effect.« less

Structure solution of network materials by solid-state NMR without knowledge of the crystallographic space group.

PubMed

Brouwer, Darren H

2013-01-01

An algorithm is presented for solving the structures of silicate network materials such as zeolites or layered silicates from solid-state (29)Si double-quantum NMR data for situations in which the crystallographic space group is not known. The algorithm is explained and illustrated in detail using a hypothetical two-dimensional network structure as a working example. The algorithm involves an atom-by-atom structure building process in which candidate partial structures are evaluated according to their agreement with Si-O-Si connectivity information, symmetry restraints, and fits to (29)Si double quantum NMR curves followed by minimization of a cost function that incorporates connectivity, symmetry, and quality of fit to the double quantum curves. The two-dimensional network material is successfully reconstructed from hypothetical NMR data that can be reasonably expected to be obtained for real samples. This advance in "NMR crystallography" is expected to be important for structure determination of partially ordered silicate materials for which diffraction provides very limited structural information. Copyright © 2013 Elsevier Inc. All rights reserved.

3D-printing zirconia implants; a dream or a reality? An in-vitro study evaluating the dimensional accuracy, surface topography and mechanical properties of printed zirconia implant and discs.

PubMed

Osman, Reham B; van der Veen, Albert J; Huiberts, Dennis; Wismeijer, Daniel; Alharbi, Nawal

2017-11-01

The aim of this study was to evaluate the dimensional accuracy, surface topography of a custom designed, 3D-printed zirconia dental implant and the mechanical properties of printed zirconia discs. A custom designed implant was 3D-printed in zirconia using digital light processing technique (DLP). The dimensional accuracy was assessed using the digital-subtraction technique. The mechanical properties were evaluated using biaxial flexure strength test. Three different build angles were adopted to print the specimens for the mechanical test; 0°(Vertical), 45° (Oblique) and 90°(Horizontal) angles. The surface topography, crystallographic phase structure and surface roughness were evaluated using scanning electron microscopy analysis (SEM), X-ray diffractometer and confocal microscopy respectively. The printed implant was dimensionally accurate with a root mean square (RMSE) value of 0.1mm. The Weibull analysis revealed a statistically significant higher characteristic strength (1006.6MPa) of 0° printed specimens compared to the other two groups and no significant difference between 45° (892.2MPa) and 90° (866.7MPa) build angles. SEM analysis revealed cracks, micro-porosities and interconnected pores ranging in size from 196nm to 3.3µm. The mean Ra (arithmetic mean roughness) value of 1.59µm (±0.41) and Rq (root mean squared roughness) value of 1.94µm (±0.47) was found. A crystallographic phase of primarily tetragonal zirconia typical of sintered Yttria tetragonal stabilized zirconia (Y-TZP) was detected. DLP prove to be efficient for printing customized zirconia dental implants with sufficient dimensional accuracy. The mechanical properties showed flexure strength close to those of conventionally produced ceramics. Optimization of the 3D-printing process parameters is still needed to improve the microstructure of the printed objects. Copyright © 2017 Elsevier Ltd. All rights reserved.

Crystallographic orientation mapping with an electron backscattered diffraction technique in (Bi, Pb)2Sr2Ca2Cu3O10 superconductor tapes

NASA Astrophysics Data System (ADS)

Tan, T. T.; Li, S.; Oh, J. T.; Gao, W.; Liu, H. K.; Dou, S. X.

2001-02-01

It is believed that grain boundaries act as weak links in limiting the critical current density (Jc) of bulk high-Tc superconductors. The weak-link problem can be greatly reduced by elimination or minimization of large-angle grain boundaries. It has been reported that the distribution of the Jc in (Bi, Pb)2Sr2Ca2Cu3O10+x (Bi2223) superconductor tapes presents a parabolic relationship in the transverse cross section of the tapes, with the lowest currents occurring at the centre of the tapes. It was proposed that the Jc distribution is strongly dependent on the local crystallographic orientation distribution of the Bi2223 oxides. However, the local three-dimensional crystallographic orientation distribution of Bi2223 crystals in (Bi, Pb)2Sr2Ca2Cu3O10+x superconductor tapes has not yet been experimentally determined. In this work, the electron backscattered diffraction technique was employed to map the crystallographic orientation distribution, determine the misorientation of grain boundaries and also map the misorientation distribution in Bi2223 superconductor tapes. Through crystallographic orientation mapping, the relationship between the crystallographic orientation distribution, the boundary misorientation distribution and the fabrication parameters may be understood. This can be used to optimize the fabrication processes thus increasing the critical current density in Bi2223 superconductor tapes.

Three-dimensional crystals of ribosomes and their subunits from eu- and archaebacteria.

PubMed

Glotz, C; Müssig, J; Gewitz, H S; Makowski, I; Arad, T; Yonath, A; Wittmann, H G

1987-11-01

Ordered three-dimensional crystals of 70S ribosomes as well as of 30S and 50S ribosomal subunits from various bacteria (E. coli, Bacillus stearothermophilus, Thermus thermophilus and Halobacterium marismortui) have been grown by vapour diffusion in hanging drops using mono- and polyalcohols. A new compact crystal form of 50S subunits has been obtained, and it is suitable for crystallographic studies at medium resolution. In addition, from one crystal form large crystals could be grown in X-ray capillaries. In all cases the crystals were obtained from functionally active ribosomal particles, and the particles from dissolved crystals retained their integrity and biological activity.

Synthesis and structure of cesium complexes of nitrilotris(methylenephosphonic) acid [Cs-μ6-NH(CH2PO3)3H4] and [Cs2-μ10-NH(CH2PO3H)3] · H2O

NASA Astrophysics Data System (ADS)

Somov, N. V.; Chausov, F. F.; Zakirov, R. M.

2017-07-01

3D coordination polymers cesium nitrilotris(methylenephosphonate) and dicesium nitrilotris( methylenephosphonate) are synthesized and their crystal structure is determined. In the crystal of [Cs-μ6-NH(CH2PO3)3H4] (space group P, Z = 2), cesium atoms occupy two crystallographically inequivalent positions with c.n. = 10 and c.n. = 14. The phosphonate ligand plays the bridging function; its denticity is nine. The crystal packing consists of alternating layers of Cs atoms in different environments with layers of ligand molecules between them. A ligand is bound to three Cs atoms of one layer and three Cs atoms of another layer. In the crystal of [Cs2-μ10-NH(CH2PO3H)3] · H2O (space group P, Z = 2), the complex has a dimeric structure: the bridging phosphonate ligand coordinates Cs to form a three-dimensional Cs4O6 cluster. The denticity of the ligand is equal to nine; the coordination numbers of cesium atoms are seven and nine. Two-dimensional corrugated layers of Cs4O6 clusters lie in the (002) plane, and layers of ligand molecules are located between them. Each ligand molecule coordinates eight Cs atoms of one layer and two Cs atoms of the neighboring layer.

Poly[[(μ2-acetato-κ3 O,O′:O′)aqua­bis­(μ3-isonicotinato-κ3 O:O′:N)samarium(III)silver(I)] perchlorate

PubMed Central

Zhu, Li-Cai; Zhu, Si-Ming

2011-01-01

The title compound, {[AgSm(C6H4NO2)2(CH3CO2)(H2O)]ClO4}n, is a three-dimensional heterobimetallic complex constructed from a repeating dimeric unit. Only half of the dimeric moiety is found in the asymmetric unit; the unit cell is completed by crystallographic inversion symmetry. The SmIII ion is eight-coordinated by four O atoms of four different isonicotinate ligands, three O atoms of two different acetate ligands, and one O atom of a water mol­ecule. The two-coordinate AgI ion is bonded to two N atoms of two different isonicotinate anions, thereby connecting the disamarium units. In addition, the isonicotinate ligands also act as bridging ligands, generating a three-dimensional network. The coordinated water mol­ecules link the carboxyl­ate group and acetate ligands by O—H⋯O hydrogen bonding. Another O—H⋯O hydrogen bond is observed in the crystal structure. The perchlorate ion is disordered over two sites with site-occupancy factors of 0.560 (11) and 0.440 (11), whereas the methyl group of the acetate ligand is disordered over two sites with site-occupancy factors of 0.53 (5) and 0.47 (5). PMID:22090841

A new antibacterial silver(I) complex incorporating 2,5-dimethylpyrazine and the anti-inflammatory diclofenac.

PubMed

Hamamci Alisir, Sevim; Dege, Necmi

2016-12-01

Ag I -containing coordination complexes have attracted attention because of their photoluminescence properties and antimicrobial activities and, in principle, these properties depend on the nature of the structural topologies. A novel two-dimensional silver(I) complex with the anti-inflammatory diclofenac molecule, namely bis{μ-2-[2-(2,6-dichloroanilino)phenyl]acetato-κ 3 O,O':O}bis(μ-2,5-dimethylpyrazine-κ 2 N:N')silver(I), [Ag 2 (C 14 H 10 Cl 2 NO 2 ) 2 (C 6 H 8 N 2 )] n , (I), has been synthesized and characterized by single-crystal X-ray diffraction, revealing that the Ag I ions are chelated by the carboxylate groups of the anionic 2-[2-(2,6-dichloroanilino)phenyl]acetate (dicl) ligand in a μ 3 -η 1 :η 2 coordination mode. Each dicl ligand links three Ag I atoms to generate a one-dimensional infinite chain. Adjacent chains are connected through 2,5-dimethylpyrazine (dmpyz) ligands to form a two-dimensional layer structure parallel to the crystallographic bc plane. The layers are further connected by C-H...π interactions to generate a three-dimensional supramolecular structure. Additionally, the most striking feature is that the structure contains an intramolecular C-H ...Ag anagostic interaction. Furthermore, the title complex has been tested for its in vitro antibacterial activity and is determined to be highly effective on the studied microorganisms.

Novel bimetallic thiocyanate-bridged Cu(II)-Hg(II) compounds—synthesis, X-Ray studies and magnetic properties

NASA Astrophysics Data System (ADS)

Machura, B.; Świtlicka, A.; Zwoliński, P.; Mroziński, J.; Kalińska, B.; Kruszynski, R.

2013-01-01

Seven novel heterobimetallic Cu/Hg polymers based on thiocyanate bridges have been synthesised and characterised by means of IR, EPR, magnetic measurements and single crystal X-Ray. Three of them, [Cu(pzH)4Hg(SCN)4]n (1) [Cu(indH)4Hg(SCN)4]n (2) and [Cu(ampy)2Hg(SCN)4]n (3), have one-dimensional coordination structure. Two compounds [Cu(pzH)2Hg(SCN)4]n (4) and [Cu(abzimH)Hg(SCN)4]n (5) form two-dimensional nets, whereas the complexes [Cu(pyCN)2Hg(SCN)4]n (6) and [Cu(pyCH(OH)(OMe))2Hg(SCN)4]n (7) are three-dimensional coordination polymers. The chains of 1 are connected by the intermolecular N-H•••N hydrogen bonds to the three dimensional net. In 2 the N-H•••S hydrogen bonds link the polymeric chains to the two dimensional layer extending along crystallographic (0 0 1) plane. The polymeric chains of compound 3 are joined by the intermolecular N-H•••N and N-H•••S hydrogen bonds to the three dimensional net. The polymeric layers of 4 are connected by the intermolecular N-H•••N hydrogen bonds to the three dimensional net.

Bromidotetra-kis-(1H-2-ethyl-5-methyl-imidazole-κN)copper(II) bromide.

PubMed

Godlewska, Sylwia; Baranowska, Katarzyna; Socha, Joanna; Dołęga, Anna

2011-12-01

The Cu(II) ion in the title compound, [CuBr(C(6)H(10)N(2))(4)]Br, is coordinated in a square-based-pyramidal geometry by the N atoms of four imidazole ligands and a bromide anion in the apical site. Both the Cu(II) and Br(-) atoms lie on a crystallographic fourfold axis. In the crystal, the [CuBr(C(6)H(10)N(2))(4)](+) complex cations are linked to the uncoordinated Br(-) anions (site symmetry [Formula: see text]) by N-H⋯Br hydrogen bonds, generating a three-dimensional network. The ethyl group of the imidazole ligand was modelled as disordered over two orientations with occupancies of 0.620 (8) and 0.380 (8).

Li15Al3Si6 (Li14.6Al3.4Si6), a compound displaying a heterographite-like anionic framework.

PubMed

Spina, Laurent; Tillard, Monique; Belin, Claude

2003-02-01

The title compound, lithium aluminium silicide (15/3/6), crystallizes in the hexagonal centrosymmetric space group P6(3)/m. The three-dimensional structure of this ternary compound may be depicted as two interpenetrating lattices, namely a graphite-like Li(3)Al(3)Si(6) layer and a distorted diamond-like lithium lattice. As is commonly found for LiAl alloys, the Li and Al atoms are found to share some crystallographic sites. The diamond-like lattice is built up of Li cations, and the graphite-like anionic layer is composed of Si, Al and Li atoms in which Si and Al are covalently bonded [Si-Al = 2.4672 (4) A].

Cloning, purification, crystallization and preliminary X-ray crystallographic analysis of MCAT from Synechocystis sp. PCC 6803.

PubMed

Liu, Yinghui; Zhang, Yanming; Cao, Xupeng; Xue, Song

2013-11-01

Malonyl-coenzymeA:acyl-carrier protein transacylase (MCAT), which catalyzes the transfer of the malonyl group from malonyl-CoA to acyl-carrier protein (ACP), is an essential enzyme in type II fatty-acid synthesis. The enzyme MCAT from Synechocystis sp. PCC 6803 (spMCAT), the first MCAT counterpart from a cyanobacterium, was cloned, purified and crystallized in order to determine its three-dimensional crystal structure. A higher-quality crystal with better diffraction was obtained by crystallization optimization. The crystal diffracted to 1.8 Å resolution and belonged to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 43.22, b = 149.21, c = 40.59 Å. Matthews coefficient calculations indicated that the crystal contained one spMCAT molecule in the asymmetric unit with a Matthews coefficient of 2.18 Å(3) Da(-1) and a solvent content of 43.65%.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aagesen, Larry K.; Coltrin, Michael Elliott; Han, Jung

Three-dimensional phase-field simulations of GaN growth by selective area epitaxy were performed. Furthermore, this model includes a crystallographic-orientation-dependent deposition rate and arbitrarily complex mask geometries. The orientation-dependent deposition rate can be determined from experimental measurements of the relative growth rates of low-index crystallographic facets. Growth on various complex mask geometries was simulated on both c-plane and a-plane template layers. Agreement was observed between simulations and experiment, including complex phenomena occurring at the intersections between facets. The sources of the discrepancies between simulated and experimental morphologies were also investigated. We found that the model provides a route to optimize masks andmore » processing conditions during materials synthesis for solar cells, light-emitting diodes, and other electronic and opto-electronic applications.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aagesen, Larry K.; Thornton, Katsuyo, E-mail: kthorn@umich.edu; Coltrin, Michael E.

Three-dimensional phase-field simulations of GaN growth by selective area epitaxy were performed. The model includes a crystallographic-orientation-dependent deposition rate and arbitrarily complex mask geometries. The orientation-dependent deposition rate can be determined from experimental measurements of the relative growth rates of low-index crystallographic facets. Growth on various complex mask geometries was simulated on both c-plane and a-plane template layers. Agreement was observed between simulations and experiment, including complex phenomena occurring at the intersections between facets. The sources of the discrepancies between simulated and experimental morphologies were also investigated. The model provides a route to optimize masks and processing conditions during materialsmore » synthesis for solar cells, light-emitting diodes, and other electronic and opto-electronic applications.« less

A three-dimensional polyhedral unit model for grain boundary structure in fcc metals

NASA Astrophysics Data System (ADS)

Banadaki, Arash Dehghan; Patala, Srikanth

2017-03-01

One of the biggest challenges in developing truly bottom-up models for the performance of polycrystalline materials is the lack of robust quantitative structure-property relationships for interfaces. As a first step in analyzing such relationships, we present a polyhedral unit model to classify the geometrical nature of atomic packing along grain boundaries. While the atomic structure in disordered systems has been a topic of interest for many decades, geometrical analyses of grain boundaries has proven to be particularly challenging because of the wide range of structures that are possible depending on the underlying macroscopic crystallographic character. In this article, we propose an algorithm that can partition the atomic structure into a connected array of three-dimensional polyhedra, and thus, present a three-dimensional polyhedral unit model for grain boundaries. A point-pattern matching algorithm is also provided for quantifying the distortions of the observed grain boundary polyhedral units. The polyhedral unit model is robust enough to capture the structure of high-Σ, mixed character interfaces and, hence, provides a geometric tool for comparing grain boundary structures across the five-parameter crystallographic phase-space. Since the obtained polyhedral units circumscribe the voids present in the structure, such a description provides valuable information concerning segregation sites within the grain boundary. We anticipate that this technique will serve as a powerful tool in the analysis of grain boundary structure. The polyhedral unit model is also applicable to a wide array of material systems as the proposed algorithm is not limited by the underlying lattice structure.

4-Benzyl-4-ethyl-morpholin-1-ium hexa-fluoro-phosphate.

PubMed

Yang, Fang; Zang, Hongjun; Cheng, Bowen; Xu, Xianlin; Ren, Yuanlin

2012-03-01

The asymmetric unit of the title compound, C(13)H(20)NO(+)·PF(6) (-), contains two cations, one complete anion and two half hexa-fluoro-phosphate anions having crystallographically imposed twofold rotation symmetry. In the cations, the morpholine rings are in a chair conformation. In the crystal, ions are linked by weak C-H⋯F hydrogen bonds into a three-dimensional network.

Large-angle illumination STEM: Toward three-dimensional atom-by-atom imaging

DOE PAGES

Ishikawa, Ryo; Lupini, Andrew R.; Hinuma, Yoyo; ...

2014-11-26

To completely understand and control materials and their properties, it is of critical importance to determine their atomic structures in all three dimensions. Recent revolutionary advances in electron optics – the inventions of geometric and chromatic aberration correctors as well as electron source monochromators – have provided fertile ground for performing optical depth sectioning at atomic-scale dimensions. In this study we theoretically demonstrate the imaging of top/sub-surface atomic structures and identify the depth of single dopants, single vacancies and the other point defects within materials by large-angle illumination scanning transmission electron microscopy (LAI-STEM). The proposed method also allows us tomore » measure specimen properties such as thickness or three-dimensional surface morphology using observations from a single crystallographic orientation.« less

Bromidotetra­kis­(1H-2-ethyl-5-methyl­imidazole-κN 3)copper(II) bromide

PubMed Central

Godlewska, Sylwia; Baranowska, Katarzyna; Socha, Joanna; Dołęga, Anna

2011-01-01

The CuII ion in the title compound, [CuBr(C6H10N2)4]Br, is coordinated in a square-based-pyramidal geometry by the N atoms of four imidazole ligands and a bromide anion in the apical site. Both the CuII and Br− atoms lie on a crystallographic fourfold axis. In the crystal, the [CuBr(C6H10N2)4]+ complex cations are linked to the uncoordinated Br− anions (site symmetry ) by N—H⋯Br hydrogen bonds, generating a three-dimensional network. The ethyl group of the imidazole ligand was modelled as disordered over two orientations with occupancies of 0.620 (8) and 0.380 (8). PMID:22199662

Crystalline liquids: the blue phases

NASA Astrophysics Data System (ADS)

Wright, David C.; Mermin, N. David

1989-04-01

The blue phases of cholesteric liquid crystals are liquids that exhibit orientational order characterized by crystallographic space-group symmetries. We present here a pedagogical introduction to the current understanding of the equilibrium structure of these phases accompanied by a general overview of major experimental results. Using the Ginzburg-Landau free energy appropriate to the system, we first discuss in detail the character and stability of the usual helical phase of cholesterics, showing that for certain parameter ranges the helical phase is unstable to the appearance of one or more blue phases. The two principal models for the blue phases are two limiting cases of the Ginzburg-Landau theory. We explore each limit and conclude with some general considerations of defects in both models and an exact minimization of the free energy in a curved three-dimensional space.

Subsurface Stress Fields in FCC Single Crystal Anisotropic Contacts

NASA Technical Reports Server (NTRS)

Arakere, Nagaraj K.; Knudsen, Erik; Swanson, Gregory R.; Duke, Gregory; Ham-Battista, Gilda

2004-01-01

Single crystal superalloy turbine blades used in high pressure turbomachinery are subject to conditions of high temperature, triaxial steady and alternating stresses, fretting stresses in the blade attachment and damper contact locations, and exposure to high-pressure hydrogen. The blades are also subjected to extreme variations in temperature during start-up and shutdown transients. The most prevalent high cycle fatigue (HCF) failure modes observed in these blades during operation include crystallographic crack initiation/propagation on octahedral planes, and non-crystallographic initiation with crystallographic growth. Numerous cases of crack initiation and crack propagation at the blade leading edge tip, blade attachment regions, and damper contact locations have been documented. Understanding crack initiation/propagation under mixed-mode loading conditions is critical for establishing a systematic procedure for evaluating HCF life of single crystal turbine blades. This paper presents analytical and numerical techniques for evaluating two and three dimensional subsurface stress fields in anisotropic contacts. The subsurface stress results are required for evaluating contact fatigue life at damper contacts and dovetail attachment regions in single crystal nickel-base superalloy turbine blades. An analytical procedure is presented for evaluating the subsurface stresses in the elastic half-space, based on the adaptation of a stress function method outlined by Lekhnitskii. Numerical results are presented for cylindrical and spherical anisotropic contacts, using finite element analysis (FEA). Effects of crystal orientation on stress response and fatigue life are examined. Obtaining accurate subsurface stress results for anisotropic single crystal contact problems require extremely refined three-dimensional (3-D) finite element grids, especially in the edge of contact region. Obtaining resolved shear stresses (RSS) on the principal slip planes also involves considerable post-processing work. For these reasons it is very advantageous to develop analytical solution schemes for subsurface stresses, whenever possible.

Protein crystallization studies

NASA Technical Reports Server (NTRS)

Lyne, James Evans

1996-01-01

The Structural Biology laboratory at NASA Marshall Spaceflight Center uses x-ray crystallographic techniques to conduct research into the three-dimensional structure of a wide variety of proteins. A major effort in the laboratory involves an ongoing study of human serum albumin (the principal protein in human plasma) and its interaction with various endogenous substances and pharmaceutical agents. Another focus is on antigenic and functional proteins from several pathogenic organisms including the human immunodeficiency virus (HIV) and the widespread parasitic genus, Schistosoma. My efforts this summer have been twofold: first, to identify clinically significant drug interactions involving albumin binding displacement and to initiate studies of the three-dimensional structure of albumin complexed with these agents, and secondly, to establish collaborative efforts to extend the lab's work on human pathogens.

Symmetry based assembly of a 2 dimensional protein lattice

DOE Office of Scientific and Technical Information (OSTI.GOV)

Poulos, Sandra; Agah, Sayeh; Jallah, Nikardi

2017-04-18

The design of proteins that self-assemble into higher order architectures is of great interest due to their potential application in nanotechnology. Specifically, the self-assembly of proteins into ordered lattices is of special interest to the field of structural biology. Here we designed a 2 dimensional (2D) protein lattice using a fusion of a tandem repeat of three TelSAM domains (TTT) to the Ferric uptake regulator (FUR) domain. We determined the structure of the designed (TTT-FUR) fusion protein to 2.3 Å by X-ray crystallographic methods. In agreement with the design, a 2D lattice composed of TelSAM fibers interdigitated by the FURmore » domain was observed. As expected, the fusion of a tandem repeat of three TelSAM domains formed 21 screw axis, and the self-assembly of the ordered oligomer was under pH control. We demonstrated that the fusion of TTT to a domain having a 2-fold symmetry, such as the FUR domain, can produce an ordered 2D lattice. The TTT-FUR system combines features from the rotational symmetry matching approach with the oligomer driven crystallization method. This TTT-FUR fusion was amenable to X-ray crystallographic methods, and is a promising crystallization chaperone.« less

Linking a completely three-dimensional nanostrain to a structural transformation eigenstrain.

PubMed

Tirry, Wim; Schryvers, Dominique

2009-09-01

Ni-Ti is one of the most popular shape-memory alloys, a phenomenon resulting from a martensitic transformation. Commercial Ni-Ti-based alloys are often thermally treated to contain Ni(4)Ti(3) precipitates. The presence of these precipitates can introduce an extra transformation step related to the so-called R-phase. It is believed that the strain field surrounding the precipitates, caused by the matrix-precipitate lattice mismatch, lies at the origin of this intermediate transformation step. Atomic-resolution transmission electron microscopy in combination with geometrical phase analysis is used to measure the elastic strain field surrounding these precipitates. By combining measurements from two different crystallographic directions, the three-dimensional strain matrix is determined from two-dimensional measurements. Comparison of the measured strain matrix to the eigenstrain of the R-phase shows that both are very similar and that the introduction of the R-phase might indeed compensate the elastic strain introduced by the precipitate.

Linking a completely three-dimensional nanostrain to a structural transformation eigenstrain

NASA Astrophysics Data System (ADS)

Tirry, Wim; Schryvers, Dominique

2009-09-01

Ni-Ti is one of the most popular shape-memory alloys, a phenomenon resulting from a martensitic transformation. Commercial Ni-Ti-based alloys are often thermally treated to contain Ni4Ti3 precipitates. The presence of these precipitates can introduce an extra transformation step related to the so-called R-phase. It is believed that the strain field surrounding the precipitates, caused by the matrix-precipitate lattice mismatch, lies at the origin of this intermediate transformation step. Atomic-resolution transmission electron microscopy in combination with geometrical phase analysis is used to measure the elastic strain field surrounding these precipitates. By combining measurements from two different crystallographic directions, the three-dimensional strain matrix is determined from two-dimensional measurements. Comparison of the measured strain matrix to the eigenstrain of the R-phase shows that both are very similar and that the introduction of the R-phase might indeed compensate the elastic strain introduced by the precipitate.

X-Ray Crystallography as a Tool to Determine Three-Dimensional Structures of Commercial Enzymes Subjected to Treatment in Pressurized Fluids.

PubMed

Feiten, Mirian Cristina; Di Luccio, Marco; Santos, Karine F; de Oliveira, Débora; Oliveira, J Vladimir

2017-06-01

The study of enzyme function often involves a multi-disciplinary approach. Several techniques are documented in the literature towards determining secondary and tertiary structures of enzymes, and X-ray crystallography is the most explored technique for obtaining three-dimensional structures of proteins. Knowledge of three-dimensional structures is essential to understand reaction mechanisms at the atomic level. Additionally, structures can be used to modulate or improve functional activity of enzymes by the production of small molecules that act as substrates/cofactors or by engineering selected mutants with enhanced biological activity. This paper presentes a short overview on how to streamline sample preparation for crystallographic studies of treated enzymes. We additionally revise recent developments on the effects of pressurized fluid treatment on activity and stability of commercial enzymes. Future directions and perspectives on the the role of crystallography as a tool to access the molecular mechanisms underlying enzymatic activity modulation upon treatment in pressurized fluids are also addressed.

Atomic structure and chemistry of human serum albumin

NASA Technical Reports Server (NTRS)

He, Xiao M.; Carter, Daniel C.

1992-01-01

The three-dimensional structure of human serum albumin has been determined crystallographically to a resolution of 2.8 A. It comprises three homologous domains that assemble to form a heart-shaped molecule. Each domain is a product of two subdomains that possess common structural motifs. The principal regions of ligand binding to human serum albumin are located in hydrophobic cavities in subdomains IIA and ILIA, which exhibit similar chemistry. The structure explains numerous physical phenomena and should provide insight into future pharmacokinetic and genetically engineered therapeutic applications of serum albumin.

Atomic structure and chemistry of human serum albumin

NASA Astrophysics Data System (ADS)

He, Xiao Min; Carter, Daniel C.

1992-07-01

The three-dimensional structure of human serum albumin has been determined crystallographically to a resolution of 2.8 Å. It comprises three homologous domains that assemble to form a heart-shaped molecule. Each domain is a product of two subdomains that possess common structural motifs. The principal regions of ligand binding to human serum albumin are located in hydrophobic cavities in subdomains IIA and IIIA, which exhibit similar chemistry. The structure explains numerous physical phenomena and should provide insight into future pharmacokinetic and genetically engineered therapeutic applications of serum albumin.

Crystallographic Orientation Effect on Electromigration in Ni-Sn Microbump

NASA Astrophysics Data System (ADS)

Huang, Yi-Ting; Chen, Chih-Hao; Chakroborty, Subhendu; Wu, Albert T.

2017-09-01

This article addresses the reliability challenges regarding electromigration in developing three-dimensional integrated circuits (3D-ICs). The line-type sandwich structure of Ni/Sn3.5Ag(15 μm)/Ni was used to simulate microbumps to examine the reliability of electromigration in 3D-IC technology. The solder strip of Ni/Sn3.5Ag(15 μm)/Ni was stressed with a current density of 1.0 × 104 A/cm2 at 150°C. The current stressing enhanced the reaction between the solder and Ni to form Ni3Sn4, which occupied the entire joint and transformed into a Ni/Ni3Sn4/Ni structure when the solder was completely consumed. Electron backscatter diffraction was used to analyze the crystallographic characteristics of Sn and Ni3Sn4 as related to the electromigration effect. The results indicated that the crystallographic orientation of Sn plays a significant role in the Ni/Sn3.5Ag/Ni, whereas the orientation of Ni3Sn4 is the dominant factor of diffusion behavior in the Ni/Ni3Sn4/Ni.

Advantages of Crystallographic Fragment Screening: Functional and Mechanistic Insights from a Powerful Platform for Efficient Drug Discovery

PubMed Central

Patel, Disha; Bauman, Joseph D.; Arnold, Eddy

2015-01-01

X-ray crystallography has been an under-appreciated screening tool for fragment-based drug discovery due to the perception of low throughput and technical difficulty. Investigators in industry and academia have overcome these challenges by taking advantage of key factors that contribute to a successful crystallographic screening campaign. Efficient cocktail design and soaking methodologies have evolved to maximize throughput while minimizing false positives/negatives. In addition, technical improvements at synchrotron beamlines have dramatically increased data collection rates thus enabling screening on a timescale comparable to other techniques. The combination of available resources and efficient experimental design has resulted in many successful crystallographic screening campaigns. The three-dimensional crystal structure of the bound fragment complexed to its target, a direct result of the screening effort, enables structure-based drug design while revealing insights regarding protein dynamics and function not readily obtained through other experimental approaches. Furthermore, this “chemical interrogation” of the target protein crystals can lead to the identification of useful reagents for improving diffraction resolution or compound solubility. PMID:25117499

Advantages of crystallographic fragment screening: functional and mechanistic insights from a powerful platform for efficient drug discovery.

PubMed

Patel, Disha; Bauman, Joseph D; Arnold, Eddy

2014-01-01

X-ray crystallography has been an under-appreciated screening tool for fragment-based drug discovery due to the perception of low throughput and technical difficulty. Investigators in industry and academia have overcome these challenges by taking advantage of key factors that contribute to a successful crystallographic screening campaign. Efficient cocktail design and soaking methodologies have evolved to maximize throughput while minimizing false positives/negatives. In addition, technical improvements at synchrotron beamlines have dramatically increased data collection rates thus enabling screening on a timescale comparable to other techniques. The combination of available resources and efficient experimental design has resulted in many successful crystallographic screening campaigns. The three-dimensional crystal structure of the bound fragment complexed to its target, a direct result of the screening effort, enables structure-based drug design while revealing insights regarding protein dynamics and function not readily obtained through other experimental approaches. Furthermore, this "chemical interrogation" of the target protein crystals can lead to the identification of useful reagents for improving diffraction resolution or compound solubility. Copyright © 2014. Published by Elsevier Ltd.

Chiral Silver-Lanthanide Metal-Organic Frameworks Comprised of One-Dimensional Triple Right-Handed Helical Chains Based on [Ln7(μ3-OH)8]13+ Clusters.

PubMed

Guo, Yan; Zhang, Lijuan; Muhammad, Nadeem; Xu, Yan; Zhou, Yunshan; Tang, Fang; Yang, Shaowei

2018-02-05

Three new isostructural chiral silver-lanthanide heterometal-organic frameworks [Ag 3 Ln 7 (μ 3 -OH) 8 (bpdc) 6 (NO 3 ) 3 (H 2 O) 6 ](NO 3 )·2H 2 O [Ln = Eu (1), Tb (2, Sm (3); H 2 bpdc = 2,2'-bipyridine-3,3'-dicarboxylic acid] based on heptanuclear lanthanide clusters [Ln 7 (μ 3 -OH) 8 ] 13+ comprised of one-dimensional triple right-handed helical chains were hydrothermally synthesized. Various means such as UV-vis spectroscopy, IR spectroscopy, elemental analysis, powder X-ray diffraction, and thermogravimetric/differential thermal analysis were used to characterize the compounds, wherein compound 3 was crystallographically characterized. In the structure of compound 3, eight μ 3 -OH - groups link seven Sm 3+ ions, forming a heptanuclear cluster, [Sm 7 (μ 3 -OH) 8 ] 13+ , and the adjacent [Sm 7 (μ 3 -OH) 8 ] 13+ clusters are linked by the carboxylic groups of bpdc 2- ligands, leading to the formation of a one-dimensional triple right-handed helical chain. The adjacent triple right-handed helical chains are further joined together by coordinating the pyridyl N atoms of the bpdc 2- ligands with Ag + , resulting in a chiral three-dimensional silver(I)-lanthanide(III) heterometal-organic framework with one-dimensional channels wherein NO 3 - anions and crystal lattice H 2 O molecules are trapped. The compounds were studied systematically with respect to their photoluminescence properties and energy-transfer mechanism, and it was found that H 2 bpdc (the energy level for the triplet states of the ligand H 2 bpdc is 21505 cm -1 ) can sensitize Eu 3+ luminescence more effectively than Tb 3+ and Sm 3+ luminescence because of effective energy transfer from bpdc 2- to Eu 3+ under excitation in compound 1.

Mesohysteresis model for ferromagnetic materials by minimization of the micromagnetic free energy

NASA Astrophysics Data System (ADS)

van den Berg, A.; Dupré, L.; Van de Wiele, B.; Crevecoeur, G.

2009-04-01

To study the connection between macroscopic hysteretic behavior and the microstructural properties, this paper presents and validates a new material dependent three-dimensional mesoscopic magnetic hysteresis model. In the presented mesoscopic description, the different micromagnetic energy terms are reformulated on the space scale of the magnetic domains. The sample is discretized in cubic cells, each with a local stress state, local bcc crystallographic axes, etc. The magnetization is assumed to align with one of the three crystallographic axes, in positive or negative sense, defining six volume fractions within each cell. The micromagnetic Gibbs free energy is described in terms of these volume fractions. Hysteresis loops are computed by minimizing the mesoscopic Gibbs free energy using a modified gradient search for a sequence of external applied fields. To validate the mesohysteresis model, we studied the magnetic memory properties. Numerical experiments reveal that (1) minor hysteresis loops are indeed closed and (2) the closed minor loops are erased from the memory.

2-Amino-2,3-dimethyl­butanamide

PubMed Central

Yin, Yongbiao

2010-01-01

The title compound, C6H14N2O, was synthesized by the reaction between 2-amino-2,3-dimethyl­butanonitrile and oil of vitriol (sulfuric acid). A racemic mixture of L- and R-2-amino-2,3-di­methyl­butanamide was characterized crystallographically. In the crystal structure, inter­molecular N—H⋯O hydrogen bonds link the two enanti­omers into a three-dimensional network. PMID:21579361

4-Benzyl-4-ethyl­morpholin-1-ium hexa­fluoro­phosphate

PubMed Central

Yang, Fang; Zang, Hongjun; Cheng, Bowen; Xu, Xianlin; Ren, Yuanlin

2012-01-01

The asymmetric unit of the title compound, C13H20NO+·PF6 −, contains two cations, one complete anion and two half hexa­fluoro­phosphate anions having crystallographically imposed twofold rotation symmetry. In the cations, the morpholine rings are in a chair conformation. In the crystal, ions are linked by weak C—H⋯F hydrogen bonds into a three-dimensional network. PMID:22412701

Crystal structure and Hirshfeld surface analysis of (2E,2'E)-3,3'-(1,4-phenyl-ene)bis-[1-(2,4-di-fluoro-phen-yl)prop-2-en-1-one].

PubMed

Kwong, Huey Chong; Sim, Aijia; Chidan Kumar, C S; Then, Li Yee; Win, Yip-Foo; Quah, Ching Kheng; Naveen, S; Warad, Ismail

2017-12-01

The asymmetric unit of the title compound, C 24 H 14 F 4 O 2 , comprises of one and a half mol-ecules; the half-mol-ecule is completed by crystallographic inversion symmetry. In the crystal, mol-ecules are linked into a three-dimensional network by C-H⋯F and C-H⋯O hydrogen bonds. Some of the C-H⋯F links are unusually short (< 2.20 Å). Hirshfeld surface analyses ( d norm surfaces and two-dimensional fingerprint plots) for the title compound are presented and discussed.

Crystal structure of the human adenovirus proteinase with its 11 amino acid cofactor.

PubMed Central

Ding, J; McGrath, W J; Sweet, R M; Mangel, W F

1996-01-01

The three-dimensional structure of the human adenovirus-2 proteinase complexed with its 11 amino acid cofactor, pVIc, was determined at 2.6 A resolution by X-ray crystallographic analysis. The fold of this protein has not been seen before. However, it represents an example of either subtly divergent or powerfully convergent evolution, because the active site contains a Cys-His-Glu triplet and oxyanion hole in an arrangement similar to that in papain. Thus, the adenovirus proteinase represents a new, fifth group of enzymes that contain catalytic triads. pVIc, which extends a beta-sheet in the main chain, is distant from the active site, yet its binding increases the catalytic rate constant 300-fold for substrate hydrolysis. The structure reveals several potential targets for antiviral therapy. Images PMID:8617222

Cytotoxic Flavones from the Stem Bark of Bougainvillea spectabilis Willd.

PubMed

Do, Lien T M; Aree, Thammarat; Siripong, Pongpun; Vo, Nga T; Nguyen, Tuyet T A; Nguyen, Phung K P; Tip-Pyang, Santi

2018-01-01

Five new flavones possessing a fully substituted A-ring with C-6 and C-8 methyl groups, bougainvinones I - M (1: -5: ), along with three known congeners, 2'-hydroxydemethoxymatteucinol (6: ), 5,7,3',4'-tetrahydroxy-3-methoxy-6,8-dimethylflavone (7: ) and 5,7,4'-trihydroxy-3-methoxy-6,8-dimethylflavone (8: ), were isolated from the EtOAc extract of the stem bark of Bougainvillea spectabilis . Their structures were established by means of spectroscopic data (ultraviolet, infrared, high-resolution electrospray ionization mass spectrometry, and one-dimensional and two-dimensional nuclear magnetic resonance) and single-crystal X-ray crystallographic analysis. The in vitro cytotoxicity of all isolated compounds against five cancer cell lines (KB, HeLa S-3, MCF-7, HT-29, and HepG2) was evaluated. Compound 5: showed promising cytotoxic activity against the KB and HeLa S-3 cell lines, with IC 50 values of 7.44 and 6.68 µM. The other compounds exhibited moderate cytotoxicity against the KB cell line. Georg Thieme Verlag KG Stuttgart · New York.

Phase-field simulations of GaN growth by selective area epitaxy on complex mask geometries

DOE PAGES

Aagesen, Larry K.; Coltrin, Michael Elliott; Han, Jung; ...

2015-05-15

Three-dimensional phase-field simulations of GaN growth by selective area epitaxy were performed. Furthermore, this model includes a crystallographic-orientation-dependent deposition rate and arbitrarily complex mask geometries. The orientation-dependent deposition rate can be determined from experimental measurements of the relative growth rates of low-index crystallographic facets. Growth on various complex mask geometries was simulated on both c-plane and a-plane template layers. Agreement was observed between simulations and experiment, including complex phenomena occurring at the intersections between facets. The sources of the discrepancies between simulated and experimental morphologies were also investigated. We found that the model provides a route to optimize masks andmore » processing conditions during materials synthesis for solar cells, light-emitting diodes, and other electronic and opto-electronic applications.« less

Constitutive and life modeling of single crystal blade alloys for root attachment analysis

NASA Technical Reports Server (NTRS)

Meyer, T. G.; Mccarthy, G. J.; Favrow, L. H.; Anton, D. L.; Bak, Joe

1988-01-01

Work to develop fatigue life prediction and constitutive models for uncoated attachment regions of single crystal gas turbine blades is described. At temperatures relevant to attachment regions, deformation is dominated by slip on crystallographic planes. However, fatigue crack initiation and early crack growth are not always observed to be crystallographic. The influence of natural occurring microporosity will be investigated by testing both hot isostatically pressed and conventionally cast PWA 1480 single crystal specimens. Several differnt specimen configurations and orientations relative to the natural crystal axes are being tested to investigate the influence of notch acuity and the material's anisotropy. Global and slip system stresses in the notched regions were determined from three dimensional stress analyses and will be used to develop fatigue life prediction models consistent with the observed lives and crack characteristics.

Revealing the sub-nanometere three-dimensional microscture of a metallic meteorite

NASA Astrophysics Data System (ADS)

Einsle, J. F.; Harrison, R.; Blukis, R.; Eggeman, A.; Saghi, Z.; Martineau, B.; Bagot, P.; Collins, S. M.; Midgley, P. A.

2017-12-01

Coming from from the core of differentiated planetesimals, iron-nickel meteorites provide some of the only direct material artefacts from planetary cores. Iron - nickel meteorites contain a record of their thermal and magnetic history, written in the intergrowth of iron-rich and nickel-rich phases that formed during slow cooling over millions of years. Of intense interest for understanding the thermal and magnetic history is the `'cloudy zone''. This nanoscale intergrowth that has recently been used to provide a record of magnetic activity on the parent body of stony-iron meteorites. The cloudy zone consists of islands of tetrataenite surrounded by a matrix phase, Here we use a multi-scale and multidimensional comparative study using high-resolution electron diffraction, scanning transmission electron tomography with chemical mapping, atom probe tomography and micromagnetic simulations to reveal the three-dimensional architecture of the cloudy zone with sub-nanometre spatial resolution. Machine learning data deconvolution strategies enable the three microanalytical techniques to converge on a consistent microstructural description for the cloudy zone. Isolated islands of tetrataenite are found, embedded in a continuous matrix of an FCC-supercell of Fe27Ni5 structure, never before identified in nature. The tetrataenite islands are arranged in clusters of three crystallographic variants, which control how magnetic information is encoded into the nanostructure during slow cooling. The new compositional, crystallographic and micromagnetic data have profound implications for how the cloudy zone acquires magnetic remanence, and requires a revision of the low-temperature metastable phase diagram of the Fe-Ni system. This can lead to a refinement of core dynamics in small planetoids.

Automated building of organometallic complexes from 3D fragments.

PubMed

Foscato, Marco; Venkatraman, Vishwesh; Occhipinti, Giovanni; Alsberg, Bjørn K; Jensen, Vidar R

2014-07-28

A method for the automated construction of three-dimensional (3D) molecular models of organometallic species in design studies is described. Molecular structure fragments derived from crystallographic structures and accurate molecular-level calculations are used as 3D building blocks in the construction of multiple molecular models of analogous compounds. The method allows for precise control of stereochemistry and geometrical features that may otherwise be very challenging, or even impossible, to achieve with commonly available generators of 3D chemical structures. The new method was tested in the construction of three sets of active or metastable organometallic species of catalytic reactions in the homogeneous phase. The performance of the method was compared with those of commonly available methods for automated generation of 3D models, demonstrating higher accuracy of the prepared 3D models in general, and, in particular, a much wider range with respect to the kind of chemical structures that can be built automatically, with capabilities far beyond standard organic and main-group chemistry.

Liquid metal micro heat pipes for space radiator applications

NASA Technical Reports Server (NTRS)

Gerner, F. M.; Henderson, H. T.

1995-01-01

Micromachining is a chemical means of etching three-dimensional structures, typically in single-crystalline silicon. These techniques are leading toward what is coming to be referred to as MEMS (micro electro mechanical systems), where in addition to the ordinary two dimensional (planar) microelectronics, it is possible to build three-dimensional micromotors, electrically-actuated microvalves, hydraulic systems, and much more on the same microchip. These techniques become possible because of differential etching rates of various crystallographic planes and materials used for semiconductor microfabrication. The University of Cincinnati group in collaboration with NASA Lewis formed micro heat pipes in silicon by the above techniques. Work is ongoing at a modest level, but several essential bonding and packaging techniques have been recently developed. Currently, we have constructed and filled water/silicon micro heat pipes. Preliminary thermal tests of arrays of 125 micro heat pipes etched in a 1 inch x 1 inch x 250 micron silicon wafer have been completed. These pipes are instrumented with extremely small P-N junctions to measure their effective conductivity and their maximum operating power. A relatively simple one-dimensional model has been developed in order to predict micro heat pipes' operating characteristics. This information can be used to optimize micro heat pipe design with respect to length, hydraulic diameter, and number of pipes. Work is progressing on the fabrication of liquid-metal micro heat pipes. In order to be compatible with liquid metal (sodium or potassium), the inside of the micro heat pipes will be coated with a refractory metal (such as tungsten, molybdenum, or titanium).

Energy-selective Neutron Imaging for Three-dimensional Non-destructive Probing of Crystalline Structures

NASA Astrophysics Data System (ADS)

Peetermans, S.; Bopp, M.; Vontobel, P.; Lehmann, E. H.

Common neutron imaging uses the full polychromatic neutron beam spectrum to reveal the material distribution in a non-destructive way. Performing it with a reduced energy band, i.e. energy-selective neutron imaging, allows access to local variation in sample crystallographic properties. Two sample categories can be discerned with different energy responses. Polycrystalline materials have an energy-dependent cross-section featuring Bragg edges. Energy-selective neutron imaging can be used to distinguish be- tween crystallographic phases, increase material sensitivity or penetration, improve quantification etc. An example of the latter is shown by the examination of copper discs prior to machining them into linear accelerator cavity structures. The cross-section of single crystals features distinct Bragg peaks. Based on their pattern, one can determine the orientation of the crystal, as in a Laue pattern, but with the tremendous advantage that the operation can be performed for each pixel, yielding crystal orientation maps at high spatial resolution. A wholly different method to investigate such samples is also introduced: neutron diffraction imaging. It is based on projections formed by neutrons diffracted from the crystal lattice out of the direct beam. The position of these projections on the detector gives information on the crystal orientation. The projection itself can be used to reconstruct the crystal shape. A three-dimensional mapping of local Bragg reflectivity or a grain orientation mapping can thus be obtained.

Supramolecular architectures in Co(II) and Cu(II) complexes with thiophene-2-carboxylate and 2-amino-4,6-dimethoxypyrimidine ligands.

PubMed

Karthikeyan, Ammasai; Thomas Muthiah, Packianathan; Perdih, Franc

2016-05-01

The coordination chemistry of mixed-ligand complexes continues to be an active area of research since these compounds have a wide range of applications. Many coordination polymers and metal-organic framworks are emerging as novel functional materials. Aminopyrimidine and its derivatives are flexible ligands with versatile binding and coordination modes which have been proven to be useful in the construction of organic-inorganic hybrid materials and coordination polymers. Thiophenecarboxylic acid, its derivatives and their complexes exhibit pharmacological properties. Cobalt(II) and copper(II) complexes of thiophenecarboxylate have many biological applications, for example, as antifungal and antitumor agents. Two new cobalt(II) and copper(II) complexes incorporating thiophene-2-carboxylate (2-TPC) and 2-amino-4,6-dimethoxypyrimidine (OMP) ligands have been synthesized and characterized by X-ray diffraction studies, namely (2-amino-4,6-dimethoxypyrimidine-κN)aquachlorido(thiophene-2-carboxylato-κO)cobalt(II) monohydrate, [Co(C5H3O2S)Cl(C6H9N3O2)(H2O)]·H2O, (I), and catena-poly[copper(II)-tetrakis(μ-thiophene-2-carboxylato-κ(2)O:O')-copper(II)-(μ-2-amino-4,6-dimethoxypyrimidine-κ(2)N(1):N(3))], [Cu2(C5H3O2S)4(C6H9N3O2)]n, (II). In (I), the Co(II) ion has a distorted tetrahedral coordination environment involving one O atom from a monodentate 2-TPC ligand, one N atom from an OMP ligand, one chloride ligand and one O atom of a water molecule. An additional water molecule is present in the asymmetric unit. The amino group of the coordinated OMP molecule and the coordinated carboxylate O atom of the 2-TPC ligand form an interligand N-H...O hydrogen bond, generating an S(6) ring motif. The pyrimidine molecules also form a base pair [R2(2)(8) motif] via a pair of N-H...N hydrogen bonds. These interactions, together with O-H...O and O-H...Cl hydrogen bonds and π-π stacking interactions, generate a three-dimensional supramolecular architecture. The one-dimensional coordination polymer (II) contains the classical paddle-wheel [Cu2(CH3COO)4(H2O)2] unit, where each carboxylate group of four 2-TPC ligands bridges two square-pyramidally coordinated Cu(II) ions and the apically coordinated OMP ligands bridge the dinuclear copper units. Each dinuclear copper unit has a crystallographic inversion centre, whereas the bridging OMP ligand has crystallographic twofold symmetry. The one-dimensional polymeric chains self-assemble via N-H...O, π-π and C-H...π interactions, generating a three-dimensional supramolecular architecture.

Two sodium and lanthanide(III) MOFs based on oxalate and V-shaped 4,4‧-oxybis(benzoate) ligands: Hydrothermal synthesis, crystal structure, and luminescence properties

NASA Astrophysics Data System (ADS)

Wang, Chongchen; Guo, Guangliang; Wang, Peng

2013-01-01

Two lanthanide based metal-organic frameworks, [NaLn(oba)(ox)(H2O)] (Lndbnd6 Eu(1) and Sm(2)) were obtained from 4,4'-oxybisbenzoic acid, sodium oxalate and corresponding lanthanide salts by hydrothermal synthesis. They were characterized by single-crystal X-ray diffraction, IR spectra, and photoluminescent spectra. The crystallographic data reveals that complexes 1 and 2 are isomorphous and isostructural, composed of three-dimensional framework built up of distorted tricapped trigonal EuO9 units, distorted octahedron NaO6 units, 4,4'-oxybis(benzoate) and oxalate. The carboxylate oxygen atoms of the 4,4'-oxybis(benzoate) and oxalate ligand are coordinated to lanthanide ions and sodium ions, resulting into two-dimensional inorganic sheets, which are further linked into three-dimensional network by organic ligands. Thermogravimetric analyses of 1-2 display a considerable thermal stability. Photoluminescent measurements indicated that europium complex 1 displayed strong red emission.

A crystallographic model for nickel base single crystal alloys

NASA Technical Reports Server (NTRS)

Dame, L. T.; Stouffer, D. C.

1988-01-01

The purpose of this research is to develop a tool for the mechanical analysis of nickel-base single-crystal superalloys, specifically Rene N4, used in gas turbine engine components. This objective is achieved by developing a rate-dependent anisotropic constitutive model and implementing it in a nonlinear three-dimensional finite-element code. The constitutive model is developed from metallurgical concepts utilizing a crystallographic approach. An extension of Schmid's law is combined with the Bodner-Partom equations to model the inelastic tension/compression asymmetry and orientation-dependence in octahedral slip. Schmid's law is used to approximate the inelastic response of the material in cube slip. The constitutive equations model the tensile behavior, creep response and strain-rate sensitivity of the single-crystal superalloys. Methods for deriving the material constants from standard tests are also discussed. The model is implemented in a finite-element code, and the computed and experimental results are compared for several orientations and loading conditions.

A crystallographic investigation of GaN nanostructures by reciprocal space mapping in a grazing incidence geometry.

PubMed

Lee, Sanghwa; Sohn, Yuri; Kim, Chinkyo; Lee, Dong Ryeol; Lee, Hyun-Hwi

2009-05-27

Reciprocal space mapping with a two-dimensional (2D) area detector in a grazing incidence geometry was applied to determine crystallographic orientations of GaN nanostructures epitaxially grown on a sapphire substrate. By using both unprojected and projected reciprocal space mapping with a proper coordinate transformation, the crystallographic orientations of GaN nanostructures with respect to that of a substrate were unambiguously determined. In particular, the legs of multipods in the wurtzite phase were found to preferentially nucleate on the sides of tetrahedral cores in the zinc blende phase.

Preparation, crystallization and preliminary X-ray crystallographic studies of diadenosine tetraphosphate hydrolase from Shigella flexneri 2a.

PubMed

Hu, Wenxin; Wang, Qihai; Bi, Ruchang

2005-12-01

Diadenosine tetraphosphate (Ap4A) hydrolase (EC 3.6.1.41) hydrolyzes Ap4A symmetrically in prokaryotes. It plays a potential role in organisms by regulating the concentration of Ap4A in vivo. To date, no three-dimensional structures of proteins with significant sequence homology to this protein have been determined. The 31.3 kDa Ap4A hydrolase from Shigella flexneri 2a has been cloned, expressed and purified using an Escherichia coli expression system. Crystals of Ap4A hydrolase have been obtained by the hanging-drop technique at 291 K using PEG 550 MME as precipitant. Ap4A hydrolase crystals diffract X-rays to 3.26 A and belong to space group P2(1), with unit-cell parameters a = 118.9, b = 54.6, c = 128.5 A, beta = 95.7 degrees.

Crystal structure of the cis and trans polymorphs of bis-[μ-2-(1,3-benzo-thia-zol-2-yl)phenolato]-κ3N,O:O;κ3O:N,O-bis-[fac-tri-carbonyl-rhenium(I)].

PubMed

Priyatharsini, Maruthupandiyan; Shankar, Bhaskaran; Sathiyendiran, Malaichamy; Srinivasan, Navaneethakrishnan; Krishnakumar, Rajaputi Venkatraman

2017-02-01

The title dinuclear complex, [Re 2 (C 13 H 8 NOS) 2 (CO) 6 ], crystallizes in two polymorphs where the 2-(1,3-benzo-thia-zol-2-yl)phenolate ligands and two carbonyl groups are trans - ( I ) or cis -arranged ( II ) with respect to the [Re 2 O 2 (CO) 4 ] core. Polymorphs I and II exhibit a crystallographically imposed centre of symmetry and a twofold rotation axis, respectively. The structures may be described as being formed by two octa-hedrally distorted metal-coordinating units fused through μ-oxido bridges, leading to edge-sharing dimers. The crystal packing is governed by C-H⋯O hydrogen-bonding inter-actions, forming chains parallel to the c axis in I and a three-dimensional network in II .

Comparison of quartz crystallographic preferred orientations identified with optical fabric analysis, electron backscatter and neutron diffraction techniques.

PubMed

Hunter, N J R; Wilson, C J L; Luzin, V

2017-02-01

Three techniques are used to measure crystallographic preferred orientations (CPO) in a naturally deformed quartz mylonite: transmitted light cross-polarized microscopy using an automated fabric analyser, electron backscatter diffraction (EBSD) and neutron diffraction. Pole figure densities attributable to crystal-plastic deformation are variably recognizable across the techniques, particularly between fabric analyser and diffraction instruments. Although fabric analyser techniques offer rapid acquisition with minimal sample preparation, difficulties may exist when gathering orientation data parallel with the incident beam. Overall, we have found that EBSD and fabric analyser techniques are best suited for studying CPO distributions at the grain scale, where individual orientations can be linked to their source grain or nearest neighbours. Neutron diffraction serves as the best qualitative and quantitative means of estimating the bulk CPO, due to its three-dimensional data acquisition, greater sample area coverage, and larger sample size. However, a number of sampling methods can be applied to FA and EBSD data to make similar approximations. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

Magnetic anisotropy and spin-flop transition of NiWO4 single crystals

NASA Astrophysics Data System (ADS)

Liu, C. B.; He, Z. Z.; Liu, Y. J.; Chen, R.; Shi, M. M.; Zhu, H. P.; Dong, C.; Wang, J. F.

2017-12-01

NiWO4 exhibits a spin chain structure built by magnetic Ni2+ ions, which may be considered as a one dimensional S = 1 system. In this work, large-sized single crystals of NiWO4 were successfully synthesized by a flux method and the crystal quality was confirmed by X-ray diffraction. Magnetic properties of obtained single crystals were studied by means of magnetic susceptibility and high field magnetization along crystallographic axes. The results demonstrate that NiWO4 is highly magnetic anisotropic and possesses a three-dimensional long range ordering below 60 K, where a spin flop transition can be observed at 17.5 T in applied magnetic fields along the magnetic easy axis (c-axis).

Magnetochemistry of the tetrahaloferrate (III) ions. 7. Crystal structure and magnetic ordering in (pyridinium){sub 3}Fe{sub 2}Br{sub 9}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lowe, C.B.; Shaviv, R.; Carlin, R.L.

1994-07-06

A monoclinic crystal structure was found by X-ray diffraction for bis [pyridinium tetrabromferrate(III)]-pyridinium bromide. The double salt contains two slightly distorted [FeBr{sub 4}]{sup -} tetrahedra, three pyridinium rings, and an uncoordinated halide in each asymmetric unit, as is characteristic of the A{sub 3}Fe{sub 2}X{sub 9} series of compounds. Unit cell parameters, monoclinic space group P2{sub 1}, are a = 7.656(3) {angstrom}, b = 14.237(5) {angstrom}, c = 13.725(5) {angstrom}, {beta} = 93.42(3){degrees}, and V = 1493(1) {angstrom}{sup 3}, using Mo K{alpha} radiation {lambda} = 0.710 69 {angstrom}, {rho}{sub calc} = 2.38 g cm{sup -3}, and Z = 2. The tetrahedramore » are aligned with their 3-fold axes parallel to the crystallographic c axis. Bond lengths (Fe-Br) range from 2.271(9) {angstrom} to 2.379(9) {angstrom} for the two different slightly distorted tetrahedral units. Magnetic susceptibility studies show that the material orders three-dimensionally at 7.4 {+-} 0.2 K. The data are compared to a HTS expansion of 1/{sub {chi}} for the S = 5/2 three-dimensional Heisenberg model antiferromagnet for a sc lattice with g = 1.98 and J/k{sub B} = -0.43 K. The specific heat measurements indicate two odd-shaped {lambda} features, at 7.3 and 8 K.« less

Overview of electron crystallography of membrane proteins: crystallization and screening strategies using negative stain electron microscopy.

PubMed

Nannenga, Brent L; Iadanza, Matthew G; Vollmar, Breanna S; Gonen, Tamir

2013-01-01

Electron cryomicroscopy, or cryoEM, is an emerging technique for studying the three-dimensional structures of proteins and large macromolecular machines. Electron crystallography is a branch of cryoEM in which structures of proteins can be studied at resolutions that rival those achieved by X-ray crystallography. Electron crystallography employs two-dimensional crystals of a membrane protein embedded within a lipid bilayer. The key to a successful electron crystallographic experiment is the crystallization, or reconstitution, of the protein of interest. This unit describes ways in which protein can be expressed, purified, and reconstituted into well-ordered two-dimensional crystals. A protocol is also provided for negative stain electron microscopy as a tool for screening crystallization trials. When large and well-ordered crystals are obtained, the structures of both protein and its surrounding membrane can be determined to atomic resolution.

Fusion proteins as alternate crystallization paths to difficult structure problems

NASA Technical Reports Server (NTRS)

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

1994-01-01

The three-dimensional structure of a peptide fusion product with glutathione transferase from Schistosoma japonicum (SjGST) has been solved by crystallographic methods to 2.5 A resolution. Peptides or proteins can be fused to SjGST and expressed in a plasmid for rapid synthesis in Escherichia coli. Fusion proteins created by this commercial method can be purified rapidly by chromatography on immobilized glutathione. The potential utility of using SjGST fusion proteins as alternate paths to the crystallization and structure determination of proteins is demonstrated.

Correcting pervasive errors in RNA crystallography through enumerative structure prediction.

PubMed

Chou, Fang-Chieh; Sripakdeevong, Parin; Dibrov, Sergey M; Hermann, Thomas; Das, Rhiju

2013-01-01

Three-dimensional RNA models fitted into crystallographic density maps exhibit pervasive conformational ambiguities, geometric errors and steric clashes. To address these problems, we present enumerative real-space refinement assisted by electron density under Rosetta (ERRASER), coupled to Python-based hierarchical environment for integrated 'xtallography' (PHENIX) diffraction-based refinement. On 24 data sets, ERRASER automatically corrects the majority of MolProbity-assessed errors, improves the average R(free) factor, resolves functionally important discrepancies in noncanonical structure and refines low-resolution models to better match higher-resolution models.

Simultaneously enhanced strength and ductility for 3D-printed stainless steel 316L by selective laser melting

NASA Astrophysics Data System (ADS)

Sun, Zhongji; Tan, Xipeng; Tor, Shu Beng; Chua, Chee Kai

2018-04-01

Laser-based powder-bed fusion additive manufacturing or three-dimensional printing technology has gained tremendous attention due to its controllable, digital, and automated manufacturing process, which can afford a refined microstructure and superior strength. However, it is a major challenge to additively manufacture metal parts with satisfactory ductility and toughness. Here we report a novel selective laser melting process to simultaneously enhance the strength and ductility of stainless steel 316L by in-process engineering its microstructure into a <011> crystallographic texture. We find that the tensile strength and ductility of SLM-built stainless steel 316L samples could be enhanced by 16% and 40% respectively, with the engineered <011> textured microstructure compared to the common <001> textured microstructure. This is because the favorable nano-twinning mechanism was significantly more activated in the <011> textured stainless steel 316L samples during plastic deformation. In addition, kinetic simulations were performed to unveil the relationship between the melt pool geometry and crystallographic texture. The new additive manufacturing strategy of engineering the crystallographic texture can be applied to other metals and alloys with twinning-induced plasticity. This work paves the way to additively manufacture metal parts with high strength and high ductility.

Are X-rays the key to integrated computational materials engineering?

DOE PAGES

Ice, Gene E.

2015-11-01

The ultimate dream of materials science is to predict materials behavior from composition and processing history. Owing to the growing power of computers, this long-time dream has recently found expression through worldwide excitement in a number of computation-based thrusts: integrated computational materials engineering, materials by design, computational materials design, three-dimensional materials physics and mesoscale physics. However, real materials have important crystallographic structures at multiple length scales, which evolve during processing and in service. Moreover, real materials properties can depend on the extreme tails in their structural and chemical distributions. This makes it critical to map structural distributions with sufficient resolutionmore » to resolve small structures and with sufficient statistics to capture the tails of distributions. For two-dimensional materials, there are high-resolution nondestructive probes of surface and near-surface structures with atomic or near-atomic resolution that can provide detailed structural, chemical and functional distributions over important length scales. Furthermore, there are no nondestructive three-dimensional probes with atomic resolution over the multiple length scales needed to understand most materials.« less

Cryo-quenched Fe-Ni-Cr alloy single crystals: A new decorative steel

DOE PAGES

Boatner, Lynn A.; Kolopus, James A.; Lavrik, Nicolay V.; ...

2016-08-31

In this paper, a decorative steel is described that is formed by a process that is unlike that of the fabrication methods utilized in making the original Damascus steels over 2000 years ago. The decorative aspect of the steel arises from a three-dimensional surface pattern that results from cryogenically quenching polished austenitic alloy single crystals into the martensitic phase that is present below 190 K. No forging operations are involved – the mechanism is entirely based on the metallurgical phase properties of the ternary alloy. The symmetry of the decorative pattern is determined and controlled by the crystallographic orientation andmore » symmetry of the 70%Fe,15%Ni,15%Cr alloy single crystals. Finally, in addition to using “cuts” made along principal crystallographic surface directions, an effectively infinite number of other random-orientation “cuts” can be utilized to produce decorative patterns where each pattern is unique after the austenitic-to-martensitic phase transformation.« less

PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps.

PubMed

Kuzu, Guray; Keskin, Ozlem; Nussinov, Ruth; Gursoy, Attila

2016-10-01

The structures of protein assemblies are important for elucidating cellular processes at the molecular level. Three-dimensional electron microscopy (3DEM) is a powerful method to identify the structures of assemblies, especially those that are challenging to study by crystallography. Here, a new approach, PRISM-EM, is reported to computationally generate plausible structural models using a procedure that combines crystallographic structures and density maps obtained from 3DEM. The predictions are validated against seven available structurally different crystallographic complexes. The models display mean deviations in the backbone of <5 Å. PRISM-EM was further tested on different benchmark sets; the accuracy was evaluated with respect to the structure of the complex, and the correlation with EM density maps and interface predictions were evaluated and compared with those obtained using other methods. PRISM-EM was then used to predict the structure of the ternary complex of the HIV-1 envelope glycoprotein trimer, the ligand CD4 and the neutralizing protein m36.

Al-doped ZnO seed layer-dependent crystallographic control of ZnO nanorods by using electrochemical deposition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Son, Hyo-Soo; Choi, Nak-Jung; Kim, Kyoung-Bo

Highlights: • Polar and semipolar ZnO NRs were successfully achieved by hydrothermal synthesis. • Semipolar and polar ZnO NRs were grown on ZnO and AZO/m-sapphire, respectively. • Al % of AZO/m-sapphire enhanced the lateral growth rate of polar ZnO NRs. - Abstract: We investigated the effect of an Al-doped ZnO film on the crystallographic direction of ZnO nanorods (NRs) using electrochemical deposition. From high-solution X-ray diffraction measurements, the crystallographic plane of ZnO NRs grown on (1 0 0) ZnO/m-plane sapphire was (1 0 1). The surface grain size of the (100) Al-doped ZnO (AZO) film decreased with increasing Al contentmore » in the ZnO seed layer, implying that the Al dopant accelerated the three-dimensional (3D) growth of the AZO film. In addition, it was found that with increasing Al doping concentration of the AZO seed layer, the crystal orientation of the ZnO NRs grown on the AZO seed layer changed from [1 0 1] to [0 0 1]. With increasing Al content of the nonpolar (1 0 0) AZO seed layer, the small surface grains with a few crystallographic planes of the AZO film changed from semipolar (1 0 1) ZnO NRs to polar (0 0 1) ZnO NRs due to the increase of the vertical [0 0 1] growth rate of the ZnO NRs owing to excellent electrical properties.« less

Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 7

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quesada, Odayme; Gurda, Brittney; Govindasamy, Lakshmanan

2007-12-01

Crystals of baculovirus-expressed adeno-associated virus serotype 7 capsids have been produced which diffract X-rays to ∼3.0 Å resolution. Crystals of baculovirus-expressed adeno-associated virus serotype 7 capsids diffract X-rays to ∼3.0 Å resolution. The crystals belong to the rhombohedral space group R3, with unit-cell parameters a = 252.4, c = 591.2 Å in the hexagonal setting. The diffraction data were processed and reduced to an overall completeness of 79.0% and an R{sub merge} of 12.0%. There are three viral capsids in the unit cell. The icosahedral threefold axis is coincident with the crystallographic threefold axis, resulting in one third of amore » capsid (20 monomers) per crystallographic asymmetric unit. The orientation of the viral capsid has been determined by rotation-function searches and is positioned at (0, 0, 0) by packing considerations.« less

Modeling of protein binary complexes using structural mass spectrometry data

PubMed Central

Kamal, J.K. Amisha; Chance, Mark R.

2008-01-01

In this article, we describe a general approach to modeling the structure of binary protein complexes using structural mass spectrometry data combined with molecular docking. In the first step, hydroxyl radical mediated oxidative protein footprinting is used to identify residues that experience conformational reorganization due to binding or participate in the binding interface. In the second step, a three-dimensional atomic structure of the complex is derived by computational modeling. Homology modeling approaches are used to define the structures of the individual proteins if footprinting detects significant conformational reorganization as a function of complex formation. A three-dimensional model of the complex is constructed from these binary partners using the ClusPro program, which is composed of docking, energy filtering, and clustering steps. Footprinting data are used to incorporate constraints—positive and/or negative—in the docking step and are also used to decide the type of energy filter—electrostatics or desolvation—in the successive energy-filtering step. By using this approach, we examine the structure of a number of binary complexes of monomeric actin and compare the results to crystallographic data. Based on docking alone, a number of competing models with widely varying structures are observed, one of which is likely to agree with crystallographic data. When the docking steps are guided by footprinting data, accurate models emerge as top scoring. We demonstrate this method with the actin/gelsolin segment-1 complex. We also provide a structural model for the actin/cofilin complex using this approach which does not have a crystal or NMR structure. PMID:18042684

Expression, purification, crystallization and X-ray crystallographic studies of different redox states of the active site of thioredoxin 1 from the whiteleg shrimp Litopenaeus vannamei

PubMed Central

Campos-Acevedo, Adam A.; Garcia-Orozco, Karina D.; Sotelo-Mundo, Rogerio R.; Rudiño-Piñera, Enrique

2013-01-01

Thioredoxin (Trx) is a 12 kDa cellular redox protein that belongs to a family of small redox proteins which undergo reversible oxidation to produce a cystine disulfide bond through the transfer of reducing equivalents from the catalytic site cysteine residues (Cys32 and Cys35) to a disulfide substrate. In this study, crystals of thioredoxin 1 from the Pacific whiteleg shrimp Litopenaeus vannamei (LvTrx) were successfully obtained. One data set was collected from each of four crystals at 100 K and the three-dimensional structures of the catalytic cysteines in different redox states were determined: reduced and oxidized forms at 2.00 Å resolution using data collected at a synchrotron-radiation source and two partially reduced structures at 1.54 and 1.88 Å resolution using data collected using an in-house source. All of the crystals belonged to space group P3212, with unit-cell parameters a = 57.5 (4), b = 57.5 (4), c = 118.1 (8) Å. The asymmetric unit contains two subunits of LvTrx, with a Matthews coefficient (V M) of 2.31 Å3 Da−1 and a solvent content of 46%. Initial phases were determined by molecular replacement using the crystallographic model of Trx from Drosophila melanogaster as a template. In the present work, LvTrx was overexpressed in Escherichia coli, purified and crystallized. Structural analysis of the different redox states at the Trx active site highlights its reactivity and corroborates the existence of a dimer in the crystal. In the crystallographic structures the dimer is stabilized by several interactions, including a disulfide bridge between Cys73 of each LvTrx monomer, a hydrogen bond between the side chain of Asp60 of each monomer and several hydrophobic interactions, with a noncrystallographic twofold axis. PMID:23695560

Crystallization of the photosystem II core complex and its chlorophyll binding subunit CP43 from transplastomic plants of Nicotiana tabacum.

PubMed

Piano, Dario; El Alaoui, Sabah; Korza, Henryk J; Filipek, Renata; Sabala, Izabela; Haniewicz, Patrycja; Buechel, Claudia; De Sanctis, Daniele; Bochtler, Matthias

2010-12-01

Photosystem II from transplastomic plants of Nicotiana tabacum with a hexahistidine tag at the N-terminal end of the PsbE subunit (α-chain of the cytochrome b(559)) was purified according to the protocol of Fey et al. (BBA 12:1501-1509, 2008). The protein sample was then subjected to two additional gel filtration runs in order to increase its homogeneity and to standardize the amount of detergent. Large three dimensional crystals of the core complex were obtained. Crystals of one of its chlorophyll binding subunits (CP43) in isolation grew in very similar conditions that differed only in the concentration of the detergent. Diffraction of Photosystem II and CP43 crystals at various synchrotron beamlines was limited to a resolution of 7 and 14 Å, respectively. In both cases the diffraction quality was insufficient for an unambiguous assignment of the crystallographic lattice or space group.

Preliminary crystallographic studies of four crystal forms of serum albumin

NASA Technical Reports Server (NTRS)

Carter, D. C.; Chang, B.; Ho, J. X.; Keeling, K.; Krishnasami, Z.

1994-01-01

Several crystal forms of serum albumin suitable for three-dimensional structure determination have been grown. These forms include crystals of recombinant and wild-type human serum albumin, baboon serum albumin, and canine serum albumin. The intrinsic limits of X-ray diffraction for these crystals are in the range 0.28-0.22 nm. Two of the crystal forms produced from human and canine albumin include incorporated long-chain fatty acids. Molecular replacement experiments have been successfully conducted on each crystal form using the previously determined atomic coordinates of human serum albumin illustrating the conserved tertiary structure.

1,3-Bis[(5-amino-furan-2-yl)meth-yl]-3,4,5,6-tetra-hydro-pyrimidin-1-ium hexa-fluoro-phosphate.

PubMed

Akkurt, Mehmet; Akkoç, Senem; Gök, Yetkin; Tahir, Muhammad Nawaz

2013-01-01

The asymmetric unit of the title salt, C16H21N2O2 (+)·PF6 (-), contains half of the whole ion pair, which has crystallographic mirror symmetry. Two F atoms related by the mirror plane are disordered over two sites of equal occupancy. The dihedral angle between the central ring and the furan ring is 59.3 ()°. In the crystal, the anions and cations are linked through C-H⋯F inter-actions, forming a three-dimensional network.

Uncovering three-dimensional gradients in fibrillar orientation in an impact-resistant biological armour.

PubMed

Zhang, Y; Paris, O; Terrill, N J; Gupta, H S

2016-05-23

The complex hierarchical structure in biological and synthetic fibrous nanocomposites entails considerable difficulties in the interpretation of the crystallographic texture from diffraction data. Here, we present a novel reconstruction method to obtain the 3D distribution of fibres in such systems. An analytical expression is derived for the diffraction intensity from fibres, explaining the azimuthal intensity distribution in terms of the angles of the three dimensional fibre orientation distributions. The telson of stomatopod (mantis shrimp) serves as an example of natural biological armour whose high impact resistance property is believed to arise from the hierarchical organization of alpha chitin nanofibrils into fibres and twisted plywood (Bouligand) structures at the sub-micron and micron scale. Synchrotron microfocus scanning X-ray diffraction data on stomatopod telson were used as a test case to map the 3D fibre orientation across the entire tissue section. The method is applicable to a range of biological and biomimetic structures with graded 3D fibre texture at the sub-micron and micron length scales.

Three-dimensional controlled growth of monodisperse sub-50 nm heterogeneous nanocrystals

PubMed Central

Liu, Deming; Xu, Xiaoxue; Du, Yi; Qin, Xian; Zhang, Yuhai; Ma, Chenshuo; Wen, Shihui; Ren, Wei; Goldys, Ewa M.; Piper, James A.; Dou, Shixue; Liu, Xiaogang; Jin, Dayong

2016-01-01

The ultimate frontier in nanomaterials engineering is to realize their composition control with atomic scale precision to enable fabrication of nanoparticles with desirable size, shape and surface properties. Such control becomes even more useful when growing hybrid nanocrystals designed to integrate multiple functionalities. Here we report achieving such degree of control in a family of rare-earth-doped nanomaterials. We experimentally verify the co-existence and different roles of oleate anions (OA−) and molecules (OAH) in the crystal formation. We identify that the control over the ratio of OA− to OAH can be used to directionally inhibit, promote or etch the crystallographic facets of the nanoparticles. This control enables selective grafting of shells with complex morphologies grown over nanocrystal cores, thus allowing the fabrication of a diverse library of monodisperse sub-50 nm nanoparticles. With such programmable additive and subtractive engineering a variety of three-dimensional shapes can be implemented using a bottom–up scalable approach. PMID:26743184

Applications of the Cambridge Structural Database in chemical education1

PubMed Central

Battle, Gary M.; Ferrence, Gregory M.; Allen, Frank H.

2010-01-01

The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal–organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout. PMID:20877495

Uncovering three-dimensional gradients in fibrillar orientation in an impact-resistant biological armour

NASA Astrophysics Data System (ADS)

Zhang, Y.; Paris, O.; Terrill, N. J.; Gupta, H. S.

2016-05-01

The complex hierarchical structure in biological and synthetic fibrous nanocomposites entails considerable difficulties in the interpretation of the crystallographic texture from diffraction data. Here, we present a novel reconstruction method to obtain the 3D distribution of fibres in such systems. An analytical expression is derived for the diffraction intensity from fibres, explaining the azimuthal intensity distribution in terms of the angles of the three dimensional fibre orientation distributions. The telson of stomatopod (mantis shrimp) serves as an example of natural biological armour whose high impact resistance property is believed to arise from the hierarchical organization of alpha chitin nanofibrils into fibres and twisted plywood (Bouligand) structures at the sub-micron and micron scale. Synchrotron microfocus scanning X-ray diffraction data on stomatopod telson were used as a test case to map the 3D fibre orientation across the entire tissue section. The method is applicable to a range of biological and biomimetic structures with graded 3D fibre texture at the sub-micron and micron length scales.

Uncovering three-dimensional gradients in fibrillar orientation in an impact-resistant biological armour

PubMed Central

Zhang, Y.; Paris, O.; Terrill, N. J.; Gupta, H. S.

2016-01-01

The complex hierarchical structure in biological and synthetic fibrous nanocomposites entails considerable difficulties in the interpretation of the crystallographic texture from diffraction data. Here, we present a novel reconstruction method to obtain the 3D distribution of fibres in such systems. An analytical expression is derived for the diffraction intensity from fibres, explaining the azimuthal intensity distribution in terms of the angles of the three dimensional fibre orientation distributions. The telson of stomatopod (mantis shrimp) serves as an example of natural biological armour whose high impact resistance property is believed to arise from the hierarchical organization of alpha chitin nanofibrils into fibres and twisted plywood (Bouligand) structures at the sub-micron and micron scale. Synchrotron microfocus scanning X-ray diffraction data on stomatopod telson were used as a test case to map the 3D fibre orientation across the entire tissue section. The method is applicable to a range of biological and biomimetic structures with graded 3D fibre texture at the sub-micron and micron length scales. PMID:27211574

Applications of the Cambridge Structural Database in chemical education.

PubMed

Battle, Gary M; Ferrence, Gregory M; Allen, Frank H

2010-10-01

The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal-organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout.

High antiferromagnetic transition temperature of a honeycomb compound SrRu 2O 6

DOE PAGES

Tian, Wei; Svoboda, Chris; Ochi, M.; ...

2015-09-14

We study the high-temperature magnetic order in a quasi-two-dimensional honeycomb compound SrRu 2O 6 by measuring magnetization and neutron powder diffraction with both polarized and unpolarized neutrons. SrRu 2O 6 crystallizes into the hexagonal lead antimonate (PbSb 2O 6, space group P31m) structure with layers of edge-sharing RuO6 octahedra separated by Sr 2+ ions. SrRu 2O 6 is found to order at T N = 565 K with Ru moments coupled antiferromagnetically both in plane and out of plane. The magnetic moment is 1.30(2) μ B/Ru at room temperature and is along the crystallographic c axis in the G-type magneticmore » structure. We perform density functional calculations with constrained random-phase approximation (RPA) to obtain the electronic structure and effective intra- and interorbital interaction parameters. The projected density of states shows strong hybridization between Ru 4d and O 2p. By downfolding to the target t 2g bands we extract the effective magnetic Hamiltonian and perform Monte Carlo simulations to determine the transition temperature as a function of interand intraplane couplings. We find a weak interplane coupling, 3% of the strong intraplane coupling, permits three-dimensional magnetic order at the observed T N .« less

Non-destructive and three-dimensional measurement of local strain development during tensile deformation in an aluminium alloy

NASA Astrophysics Data System (ADS)

Kobayashi, M.; Miura, H.; Toda, H.

2015-08-01

Anisotropy of mechanical responses depending on crystallographic orientation causes inhomogeneous deformation on the mesoscopic scale (grain size scale). Investigation of the local plastic strain development is important for discussing recrystallization mechanisms, because the sites with higher local plastic strain may act as potential nucleation sites for recrystallization. Recently, high-resolution X-ray tomography, which is non-destructive inspection method, has been utilized for observation of the materials structure. In synchrotron radiation X-ray tomography, more than 10,000 microstructural features, like precipitates, dispersions, compounds and hydrogen pores, can be observed in aluminium alloys. We have proposed employing these microstructural features as marker gauges to measure local strains, and then have developed a method to calculate the three-dimensional strain distribution by tracking the microstructural features. In this study, we report the development of local plastic strain as a function of the grain microstructure in an aluminium alloy by means of this three-dimensional strain measurement technique. Strongly heterogeneous strain development was observed during tensile loading to 30%. In other words, some parts of the sample deform little whereas another deforms a lot. However, strain in the whole specimen was keeping harmony. Comparing the microstructure with the strain concentration that is obtained by this method has a potential to reveal potential nucleation sites of recrystallization.

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

PubMed Central

Miao, Zhichao; Adamiak, Ryszard W.; Blanchet, Marc-Frédérick; Boniecki, Michal; Bujnicki, Janusz M.; Chen, Shi-Jie; Cheng, Clarence; Chojnowski, Grzegorz; Chou, Fang-Chieh; Cordero, Pablo; Cruz, José Almeida; Ferré-D'Amaré, Adrian R.; Das, Rhiju; Ding, Feng; Dokholyan, Nikolay V.; Dunin-Horkawicz, Stanislaw; Kladwang, Wipapat; Krokhotin, Andrey; Lach, Grzegorz; Magnus, Marcin; Major, François; Mann, Thomas H.; Masquida, Benoît; Matelska, Dorota; Meyer, Mélanie; Peselis, Alla; Popenda, Mariusz; Purzycka, Katarzyna J.; Serganov, Alexander; Stasiewicz, Juliusz; Szachniuk, Marta; Tandon, Arpit; Tian, Siqi; Wang, Jian; Xiao, Yi; Xu, Xiaojun; Zhang, Jinwei; Zhao, Peinan; Zok, Tomasz; Westhof, Eric

2015-01-01

This paper is a report of a second round of RNA-Puzzles, a collective and blind experiment in three-dimensional (3D) RNA structure prediction. Three puzzles, Puzzles 5, 6, and 10, represented sequences of three large RNA structures with limited or no homology with previously solved RNA molecules. A lariat-capping ribozyme, as well as riboswitches complexed to adenosylcobalamin and tRNA, were predicted by seven groups using RNAComposer, ModeRNA/SimRNA, Vfold, Rosetta, DMD, MC-Fold, 3dRNA, and AMBER refinement. Some groups derived models using data from state-of-the-art chemical-mapping methods (SHAPE, DMS, CMCT, and mutate-and-map). The comparisons between the predictions and the three subsequently released crystallographic structures, solved at diffraction resolutions of 2.5–3.2 Å, were carried out automatically using various sets of quality indicators. The comparisons clearly demonstrate the state of present-day de novo prediction abilities as well as the limitations of these state-of-the-art methods. All of the best prediction models have similar topologies to the native structures, which suggests that computational methods for RNA structure prediction can already provide useful structural information for biological problems. However, the prediction accuracy for non-Watson–Crick interactions, key to proper folding of RNAs, is low and some predicted models had high Clash Scores. These two difficulties point to some of the continuing bottlenecks in RNA structure prediction. All submitted models are available for download at http://ahsoka.u-strasbg.fr/rnapuzzles/. PMID:25883046

Metal-Organic Nanosheets Formed via Defect-Mediated Transformation of a Hafnium Metal-Organic Framework.

PubMed

Cliffe, Matthew J; Castillo-Martínez, Elizabeth; Wu, Yue; Lee, Jeongjae; Forse, Alexander C; Firth, Francesca C N; Moghadam, Peyman Z; Fairen-Jimenez, David; Gaultois, Michael W; Hill, Joshua A; Magdysyuk, Oxana V; Slater, Ben; Goodwin, Andrew L; Grey, Clare P

2017-04-19

We report a hafnium-containing MOF, hcp UiO-67(Hf), which is a ligand-deficient layered analogue of the face-centered cubic fcu UiO-67(Hf). hcp UiO-67 accommodates its lower ligand:metal ratio compared to fcu UiO-67 through a new structural mechanism: the formation of a condensed "double cluster" (Hf 12 O 8 (OH) 14 ), analogous to the condensation of coordination polyhedra in oxide frameworks. In oxide frameworks, variable stoichiometry can lead to more complex defect structures, e.g., crystallographic shear planes or modules with differing compositions, which can be the source of further chemical reactivity; likewise, the layered hcp UiO-67 can react further to reversibly form a two-dimensional metal-organic framework, hxl UiO-67. Both three-dimensional hcp UiO-67 and two-dimensional hxl UiO-67 can be delaminated to form metal-organic nanosheets. Delamination of hcp UiO-67 occurs through the cleavage of strong hafnium-carboxylate bonds and is effected under mild conditions, suggesting that defect-ordered MOFs could be a productive route to porous two-dimensional materials.

Electron crystallographic analysis of two-dimensional streptavidin crystals coordinated to metal-chelated lipid monolayers.

PubMed Central

Frey, W; Brink, J; Schief, W R; Chiu, W; Vogel, V

1998-01-01

Coordination of individual histidine residues located on a protein surface to metal-chelated lipid monolayers is a potentially general method for crystallizing proteins in two dimensions. It was shown recently by Brewster angle microscopy (BAM) that the model protein streptavidin binds via its surface histidines to Cu-DOIDA lipid monolayers, and aggregates into regularly shaped domains that have the appearance of crystals. We have used electron microscopy to confirm that the domains are indeed crystalline with lattice parameters similar to those of the same protein crystallized beneath biotinylated lipid monolayers. Although BAM demonstrates that the two-dimensional protein crystals grown via metal chelation are distinct from the biotin-bound crystals in both microscopic shape and thermodynamic behavior, the two crystal types show similar density projections and the same plane group symmetry. PMID:9591691

Spectroscopic investigation of phenolic groups ionization in the vipoxin neurotoxic phospholipase A 2: comparison with the X-ray structure in the region of the tyrosyl residues

NASA Astrophysics Data System (ADS)

Georgieva, Dessislava Nikolova; Genov, Nicolay; Rajashankar, Kanagalaghatta R.; Aleksiev, Boris; Betzel, Christian

1998-12-01

The neurotoxin vipoxin is the major lethal component of the venom of Vipera ammodites meridionalis, the most toxic snake in Europe. It is a complex between a toxic phospholipase A 2 (PLA 2) and a non-toxic protein inhibitor (Inh). Tyrosyl residues are involved in the catalytic site (Tyr 52 and 73) and in the substrate binding (Tyr 22). Spectroscopic studies demonstrated differences in the ionization behavior of the various phenolic hydroxyl groups in the toxic PLA 2. The tyrosyl side chains of the enzyme can be classified into three groups: (a) three phenolic hydroxyls are accessible to the solvent and titrate normally, with a p Keff=10.45; (b) three residues are partially 'buried' and participate in hydrogen bonds with neighboring functional groups. They titrate anomalously with a p Keff=12.17; (c) two tyrosines with a p Keff=13.23 are deeply 'buried' in the hydrophobic interior of PLA 2. They became accessible to the titrating agent only after alkaline denaturation of the protein molecule. The spectroscopic data are related to the X-ray structure of the vipoxin PLA 2. The refined model was investigated in the region of the tyrosyl side chains. The accessible surface area of each tyrosyl residue and each phenolic hydroxyl group was calculated. A good correlation between the spectrophotometric and the crystallographic data was observed. The ionization behavior of the phenolic groups is explained by peculiarities of the protein three-dimensional structure and the participation of tyrosines in the catalytic site hydrogen bond network. Attempts are made to assign the calculated p Keff values to individual residues. The high degree of 'exposure' on the protein surface of Tyr 22 and 75 is probably important for their function as parts of the substrate binding and pharmacological sites.

Poly[tetra­aqua­(μ6-9,10-dioxo-9,10-dihydro­anthracene-1,4,5,8-tetra­carboxyl­ato)dimanganese(II)

PubMed Central

Xu, Rui; Liu, Jian-Lan

2012-01-01

The title complex, [Mn2(C18H4O10)(H2O)4]n, was synthesized from manganese(II) chloride tetra­hydrate and 9,10-dioxo-9,10-dihydro­anthracene-1,4,5,8-tetra­carb­oxy­lic acid (H4AQTC) in water. The anthraquinone unit is located about a crystallographic center of inversion. Each asymmetric unit therefore contains one MnII atom, two water ligands and one half AQTC4− anion. The MnII atom is coordinated in a distorted octa­hedral geometry by four O atoms from three AQTC4− ligands and two water O atoms. Two of the carboxyl­ate groups coordinate one MnII atom in a chelating mode, whereas the others each coordinate two MnII atoms. Each AQTC4− tetra-anion therefore coordinates six different MnII ions and, as a result, a three-dimensional coordination polymer is formed. O—H⋯O hydrogen bonds, some of them bifurcated, between water ligands and neighboring water or anthraquinone ligands are observed in the crystal structure. PMID:22807779

Three sets of crystallographic sub-planar structures in quartz formed by tectonic deformation

NASA Astrophysics Data System (ADS)

Derez, Tine; Pennock, Gill; Drury, Martyn; Sintubin, Manuel

2016-05-01

In quartz, multiple sets of fine planar deformation microstructures that have specific crystallographic orientations parallel to planes with low Miller-Bravais indices are commonly considered as shock-induced planar deformation features (PDFs) diagnostic of shock metamorphism. Using polarized light microscopy, we demonstrate that up to three sets of tectonically induced sub-planar fine extinction bands (FEBs), sub-parallel to the basal, γ, ω, and π crystallographic planes, are common in vein quartz in low-grade tectonometamorphic settings. We conclude that the observation of multiple (2-3) sets of fine scale, closely spaced, crystallographically controlled, sub-planar microstructures is not sufficient to unambiguously distinguish PDFs from tectonic FEBs.

All-metal aromatic cationic palladium triangles can mimic aromatic donor ligands with Lewis acidic cations† †Electronic supplementary information (ESI) available: Reaction procedures, characterization of complexes, copies of all spectra and cif files, modelling details and XYZ coordinates. CCDC 1410440–1410442. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc03475j Click here for additional data file. Click here for additional data file.

PubMed Central

Wang, Yanlan; Monfredini, Anna; Deyris, Pierre-Alexandre; Blanchard, Florent; Derat, Etienne; Malacria, Max

2017-01-01

We present that cationic rings can act as donor ligands thanks to suitably delocalized metal–metal bonds. This could grant parent complexes with the peculiar properties of aromatic rings that are crafted with main group elements. We assembled Pd nuclei into equilateral mono-cationic triangles with unhindered faces. Like their main group element counterparts and despite their positive charge, these noble-metal rings form stable bonding interactions with other cations, such as positively charged silver atoms, to deliver the corresponding tetranuclear dicationic complexes. Through a mix of modeling and experimental techniques we propose that this bonding mode is an original coordination-like one rather than a 4-centre–2-electron bond, which have already been observed in three dimensional aromatics. The present results thus pave the way for the use of suitable metal rings as ligands. PMID:29163890

Three-dimensional Model of Human Platelet Integrin αIIbβ3 in Solution Obtained by Small Angle Neutron Scattering*

PubMed Central

Nogales, Aurora; García, Carolina; Pérez, Javier; Callow, Phil; Ezquerra, Tiberio A.; González-Rodríguez, José

2010-01-01

Integrin αIIbβ3 is the major membrane protein and adhesion receptor at the surface of blood platelets, which after activation plays a key role in platelet plug formation in hemostasis and thrombosis. Small angle neutron scattering (SANS) and shape reconstruction algorithms allowed formation of a low resolution three-dimensional model of whole αIIbβ3 in Ca2+/detergent solutions. Model projections after 90° rotation along its long axis show an elongated and “arched” form (135°) not observed before and a “handgun” form. This 20-nm-long structure is well defined, despite αIIbβ3 multidomain nature and expected segmental flexibility, with the largest region at the top, followed by two narrower and smaller regions at the bottom. Docking of this SANS envelope into the high resolution structure of αIIbβ3, reconstructed from crystallographic and NMR data, shows that the solution structure is less constrained, allows tentative assignment of the disposition of the αIIb and β3 subunits and their domains within the model, and points out the structural analogies and differences of the SANS model with the crystallographic models of the recombinant ectodomains of αIIbβ3 and αVβ3 and with the cryo-electron microscopy model of whole αIIbβ3. The ectodomain is in the bent configuration at the top of the model, where αIIb and β3 occupy the concave and convex sides, respectively, at the arched projection, with their bent knees at its apex. It follows the narrower transmembrane region and the cytoplasmic domains at the bottom end. αIIbβ3 aggregated in Mn2+/detergent solutions, which impeded to get its SANS model. PMID:19897481

Two novel mixed-ligand complexes containing organosulfonate ligands.

PubMed

Li, Mingtian; Huang, Jun; Zhou, Xuan; Fang, Hua; Ding, Liyun

2008-07-01

The structures reported herein, viz. bis(4-aminonaphthalene-1-sulfonato-kappaO)bis(4,5-diazafluoren-9-one-kappa(2)N,N')copper(II), [Cu(C(10)H(8)NO(3)S)(2)(C(11)H(6)N(2)O)(2)], (I), and poly[[[diaquacadmium(II)]-bis(mu-4-aminonaphthalene-1-sulfonato)-kappa(2)O:N;kappa(2)N:O] dihydrate], {[Cd(C(10)H(8)NO(3)S)(2)(H(2)O)(2)].2H(2)O}(n), (II), are rare examples of sulfonate-containing complexes where the anion does not fulfill a passive charge-balancing role, but takes an active part in coordination as a monodentate and/or bridging ligand. Monomeric complex (I) possesses a crystallographic inversion center at the Cu(II) atom, and the asymmetric unit contains one-half of a Cu atom, one complete 4-aminonaphthalene-1-sulfonate (ans) ligand and one 4,5-diazafluoren-9-one (DAFO) ligand. The Cu(II) atom has an elongated distorted octahedral coordination geometry formed by two O atoms from two monodentate ans ligands and by four N atoms from two DAFO molecules. Complex (II) is polymeric and its crystal structure is built up by one-dimensional chains and solvent water molecules. Here also the cation (a Cd(II) atom) lies on a crystallographic inversion center and adopts a slightly distorted octahedral geometry. Each ans anion serves as a bridging ligand linking two Cd(II) atoms into one-dimensional infinite chains along the [010] direction, with each Cd(II) center coordinated by four ans ligands via O and N atoms and by two aqua ligands. In both structures, there are significant pi-pi stacking interactions between adjacent ligands and hydrogen bonds contribute to the formation of two- and three-dimensional networks.

Crystallographic Topology 2: Overview and Work in Progress

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, C.K.

1999-08-01

This overview describes an application of contemporary geometric topology and stochastic process concepts to structural crystallography. In this application, crystallographic groups become orbifolds, crystal structures become Morse functions on orbifolds, and vibrating atoms in a crystal become vector valued Gaussian measures with the Radon-Nikodym property. Intended crystallographic benefits include new methods for visualization of space groups and crystal structures, analysis of the thermal motion patterns seen in ORTEP drawings, and a classification scheme for crystal structures based on their Heegaard splitting properties.

Sr-Al-Si co-segregated regions in eutectic Si phase of Sr-modified Al-10Si alloy.

PubMed

Timpel, M; Wanderka, N; Schlesiger, R; Yamamoto, T; Isheim, D; Schmitz, G; Matsumura, S; Banhart, J

2013-09-01

The addition of 200 ppm strontium to an Al-10 wt% Si casting alloy changes the morphology of the eutectic silicon phase from coarse plate-like to fine fibrous networks. In order to clarify this modification mechanism the location of Sr within the eutectic Si phase has been investigated by a combination of high-resolution methods. Whereas three-dimensional atom probe tomography allows us to visualise the distribution of Sr on the atomic scale and to analyse its local enrichment, transmission electron microscopy yields information about the crystallographic nature of segregated regions. Segregations with two kinds of morphologies were found at the intersections of Si twin lamellae: Sr-Al-Si co-segregations of rod-like morphology and Al-rich regions of spherical morphology. Both are responsible for the formation of a high density of multiple twins and promote the anisotropic growth of the eutectic Si phase in specific crystallographic directions during solidification. The experimental findings are related to the previously postulated mechanism of "impurity induced twinning". Copyright © 2012 Elsevier B.V. All rights reserved.

Novel bimetallic thiocyanate-bridged Cu(II)-Hg(II) compounds-synthesis, X-Ray studies and magnetic properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Machura, B., E-mail: basia@ich.us.edu.pl; Switlicka, A.; Zwolinski, P.

2013-01-15

Seven novel heterobimetallic Cu/Hg polymers based on thiocyanate bridges have been synthesised and characterised by means of IR, EPR, magnetic measurements and single crystal X-Ray. Three of them, [Cu(pzH){sub 4}Hg(SCN){sub 4}]{sub n} (1) [Cu(indH){sub 4}Hg(SCN){sub 4}]{sub n} (2) and [Cu(ampy){sub 2}Hg(SCN){sub 4}]{sub n} (3), have one-dimensional coordination structure. Two compounds [Cu(pzH){sub 2}Hg(SCN){sub 4}]{sub n} (4) and [Cu(abzimH)Hg(SCN){sub 4}]{sub n} (5) form two-dimensional nets, whereas the complexes [Cu(pyCN){sub 2}Hg(SCN){sub 4}]{sub n} (6) and [Cu(pyCH(OH)(OMe)){sub 2}Hg(SCN){sub 4}]{sub n} (7) are three-dimensional coordination polymers. The chains of 1 are connected by the intermolecular N-H Bullet Bullet Bullet N hydrogen bonds to the threemore » dimensional net. In 2 the N-H Bullet Bullet Bullet S hydrogen bonds link the polymeric chains to the two dimensional layer extending along crystallographic (0 0 1) plane. The polymeric chains of compound 3 are joined by the intermolecular N-H Bullet Bullet Bullet N and N-H Bullet Bullet Bullet S hydrogen bonds to the three dimensional net. The polymeric layers of 4 are connected by the intermolecular N-H Bullet Bullet Bullet N hydrogen bonds to the three dimensional net. - Graphical abstract: Novel bimetallic thiocyanate-bridged Cu(II)-Hg(II) compound-synthesis,X-Ray studies and magnetic properties. Highlights: Black-Right-Pointing-Pointer Novel heterobimetallic Cu/Hg coordination polymers were synthesised. Black-Right-Pointing-Pointer The multidimensional structures have been proved by single X-ray analysIs. Black-Right-Pointing-Pointer A variation in the crystalline architectures was observed depending on auxiliary ligands. Black-Right-Pointing-Pointer Magnetic measurements indicate weak exchange interaction between Cu(II) in the crystal lattices below 10 K.« less

Three-dimensional mesoscale heterostructures of ZnO nanowire arrays epitaxially grown on CuGaO2 nanoplates as individual diodes.

PubMed

Forticaux, Audrey; Hacialioglu, Salih; DeGrave, John P; Dziedzic, Rafal; Jin, Song

2013-09-24

We report a three-dimensional (3D) mesoscale heterostructure composed of one-dimensional (1D) nanowire (NW) arrays epitaxially grown on two-dimensional (2D) nanoplates. Specifically, three facile syntheses are developed to assemble vertical ZnO NWs on CuGaO2 (CGO) nanoplates in mild aqueous solution conditions. The key to the successful 3D mesoscale integration is the preferential nucleation and heteroepitaxial growth of ZnO NWs on the CGO nanoplates. Using transmission electron microscopy, heteroepitaxy was found between the basal planes of CGO nanoplates and ZnO NWs, which are their respective (001) crystallographic planes, by the observation of a hexagonal Moiré fringes pattern resulting from the slight mismatch between the c planes of ZnO and CGO. Careful analysis shows that this pattern can be described by a hexagonal supercell with a lattice parameter of almost exactly 11 and 12 times the a lattice constants for ZnO and CGO, respectively. The electrical properties of the individual CGO-ZnO mesoscale heterostructures were measured using a current-sensing atomic force microscopy setup to confirm the rectifying p-n diode behavior expected from the band alignment of p-type CGO and n-type ZnO wide band gap semiconductors. These 3D mesoscale heterostructures represent a new motif in nanoassembly for the integration of nanomaterials into functional devices with potential applications in electronics, photonics, and energy.

Final Report: DOE Award Number: DE-SC0006398, University of CA, San Diego

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cha, Jennifer

The focus of the proposed research is to direct the assembly of single or binary nanoparticles into meso- or macroscale three-dimensional crystals of any desired configuration and crystallographic orientation without using prohibitively expensive lithographic processes. The epitaxial nucleation of defect-free, surface-bound bulk single crystals will revolutionize technologies for energy to generate new types of solar cells that yield maximum conversion efficiencies. It has been proposed that having a nanostructured bulk hetero-interface will enable efficient charge-carrier separations, similar to organic based heterojunction cells but with potential improvements, including thermal and long-term stability, tunability of energy levels, large adsorption coefficients and carriermore » multiplication. However, engineering such devices requires nanoscale control and ordering in both 2- and 3-dimensions over macroscopic areas and this has yet to be achieved. In Nature, bulk organic and inorganic materials are arranged into precise and ordered programmed assemblies through the sequestration of raw materials into confined spaces and association through highly specific non-covalent interactions between biomolecules. Using similar strategies, the proposed research will focus on confining metal and semiconductor nanocrystals to pre-determined surface patterns and controlling their arrangement through tunable, orthogonal biomolecular binding. Once a perfect two-dimensional seed layer has been constructed, successive layers of single nanocrystals will be nucleated epitaxially with long-range order and tunable crystallographic orientations. The proposed research exploits the ability of biomolecules to bind specific targets in a tunable, orthogonal, multivalent, and reversible manner to the arrangements of DNA-nanoparticle conjugates on chemically defined surfaces. Through careful balance of the attractive and repulsive forces between the particles, the array, and the outside surface, it is envisioned that single or mixed nanoparticles can be packed to adopt uniform crystal orientation in two and three dimensions from simple mixing and annealing of biomolecule-nanoparticle conjugates with biomolecule-stamped surfaces. To control the crystallographic alignment of each particle with its neighbors, the nanoparticles will be assembled using a mixture of non-covalent biomolecular interactions. To create solar cells in which layers of donor and acceptor nanocrystals that are not only oriented normal to the top and bottom electrodes but are also arranged in a checkerboard pattern, multicomponent nanocrystals (e.g. CdSe, CdTe) will be conjugated with biochemical linkers such that only interactions between the CdTe and CdSe promote particle packing within the array. The proposed research will: (1) elucidate the role of single and binary cooperative particle-DNA interactions in influencing nanoparticle crystallographic orientation in two and three dimensions; (2) understand how confinement of nanoparticles on patterned arrays of biomolecules and modification of the surrounding substrate can nucleate long-range order over macroscopic areas via predefined grain boundaries; and (3) synthesize and characterize DNA conjugated semiconductor nanocrystals and assemble them into 2- and 3-D binary superlattice arrays for photovoltaics.« less

Cs2Bi(PO4)(WO4)

PubMed Central

Terebilenko, Kateryna V.; Zatovsky, Igor V.; Baumer, Vyacheslav N.; Slobodyanik, Nikolay S.

2009-01-01

Dicaesium bis­muth(III) phosphate(V) tungstate(VI), Cs2Bi(PO4)(WO4), has been synthesized during complex investigation in a molten pseudo-quaternary Cs2O–Bi2O3–P2O5–WO3 system. It is isotypic with K2Bi(PO4)(WO4). The three-dimensional framework is built up from [Bi(PO4)(WO4)] nets, which are organized by adhesion of [BiPO4] layers and [WO4] tetra­hedra above and below of those layers. The inter­stitial space is occupied by Cs atoms. Bi, W and P atoms lie on crystallographic twofold axes. PMID:21577386

Surface crystallographic structures of cellulose nanofiber films and overlayers of pentacene

NASA Astrophysics Data System (ADS)

Nakayama, Yasuo; Mori, Toshiaki; Tsuruta, Ryohei; Yamanaka, Soichiro; Yoshida, Koki; Imai, Kento; Koganezawa, Tomoyuki; Hosokai, Takuya

2018-03-01

Cellulose nanofibers or nanocellulose is a promising recently developed biomass and biodegradable material used for various applications. In order to utilize this material as a substrate in organic electronic devices, thorough understanding of the crystallographic structures of the surfaces of the nanocellulose composites and of their interfaces with organic semiconductor molecules is essential. In this work, surface crystallographic structures of nanocellulose films (NCFs) and overlayers of pentacene were investigated by two-dimensional grazing-incidence X-ray diffraction. The NCFs are found to crystallize on solid surfaces with the crystal lattice preserving the same structure of the known bulk phase, whereas distortion of interchain packing toward the surface normal direction is suggested. The pentacene overlayers on the NCFs are found to form the thin-film phase with an in-plane mean crystallite size of over 10 nm.

Friction force microscopy: a simple technique for identifying graphene on rough substrates and mapping the orientation of graphene grains on copper

NASA Astrophysics Data System (ADS)

Marsden, A. J.; Phillips, M.; Wilson, N. R.

2013-06-01

At a single atom thick, it is challenging to distinguish graphene from its substrate using conventional techniques. In this paper we show that friction force microscopy (FFM) is a simple and quick technique for identifying graphene on a range of samples, from growth substrates to rough insulators. We show that FFM is particularly effective for characterizing graphene grown on copper where it can correlate the graphene growth to the three-dimensional surface topography. Atomic lattice stick-slip friction is readily resolved and enables the crystallographic orientation of the graphene to be mapped nondestructively, reproducibly and at high resolution. We expect FFM to be similarly effective for studying graphene growth on other metal/locally crystalline substrates, including SiC, and for studying growth of other two-dimensional materials such as molybdenum disulfide and hexagonal boron nitride.

Solid-state NMR study of various mono- and divalent cation forms of the natural zeolite natrolite.

PubMed

Park, Min Bum; Vicente, Aurélie; Fernandez, Christian; Hong, Suk Bong

2013-05-28

Here we present the one-dimensional (29)Si and (27)Al MAS NMR and two-dimensional (27)Al MQMAS and DQF-STMAS NMR spectra of the monovalent (Na(+), K(+), Rb(+), Cs(+) and NH4(+)) and divalent (Ca(2+), Sr(2+) and Ba(2+)) cation forms of the natural zeolite natrolite (framework type NAT) with complete Si-Al ordering over the crystallographically distinct tetrahedral sites and with the same hydration state (hydrated, partially dehydrated or fully dehydrated). In the case of monovalent cation-exchanged natrolites, the differences in their crystal symmetry evidenced by (29)Si MAS NMR were found to be in good agreement with those determined by crystallographic analyses. However, (27)Al DQF-STMAS NMR spectroscopy shows the presence of two distinct Al sites in dehydrated K-NAT, Rb-NAT and NH4-NAT, suggesting that their actual crystal symmetry is lower than the reported one (i.e., orthorhombic Fdd2). The MAS NMR results also show that the space group of hydrated Ca-NAT is lower than that (monoclinic F1d1) of hydrated scolecite, the natural calcium counterpart of natrolite, which is also the case with hydrated Sr-NAT and Ba-NAT. We believe that the unexpected diversity in the crystal symmetry of natrolite caused by exchange of various mono- and divalent ions, as well as by dehydration, may be inherently due to the high framework flexibility of this natural zeolite.

Development of synchrotron X-ray micro-tomography under extreme conditions of pressure and temperature.

PubMed

Álvarez-Murga, M; Perrillat, J P; Le Godec, Y; Bergame, F; Philippe, J; King, A; Guignot, N; Mezouar, M; Hodeau, J L

2017-01-01

X-ray tomography is a non-destructive three-dimensional imaging/microanalysis technique selective to a wide range of properties such as density, chemical composition, chemical states and crystallographic structure with extremely high sensitivity and spatial resolution. Here the development of in situ high-pressure high-temperature micro-tomography using a rotating module for the Paris-Edinburgh cell combined with synchrotron radiation is described. By rotating the sample chamber by 360°, the limited angular aperture of ordinary high-pressure cells is surmounted. Such a non-destructive high-resolution probe provides three-dimensional insight on the morphological and structural evolution of crystalline as well as amorphous phases during high pressure and temperature treatment. To demonstrate the potentials of this new experimental technique the compression behavior of a basalt glass is investigated by X-ray absorption tomography, and diffraction/scattering tomography imaging of the structural changes during the polymerization of C 60 molecules under pressure is performed. Small size and weight of the loading frame and rotating module means that this apparatus is portable, and can be readily installed on most synchrotron facilities to take advantage of the diversity of three-dimensional imaging techniques available at beamlines. This experimental breakthrough should open new ways for in situ imaging of materials under extreme pressure-temperature-stress conditions, impacting diverse areas in physics, chemistry, geology or materials sciences.

Three-dimensional imaging of dislocation dynamics during the hydriding phase transformation

DOE PAGES

Ulvestad, A.; Welland, M. J.; Cha, W.; ...

2017-01-16

Crystallographic imperfections can significantly alter material properties and responses to external stimuli, including solute induced phase transformations and crystal growth and dissolution . Despite recent progress in imaging defects using both electron and x-ray techniques, in situ three-dimensional imaging studies of defect dynamics, necessary to understand and engineer nanoscale processes, remains challenging. Here, we report in situ three-dimensional imaging of defect dynamics during the hydriding phase transformation of individual palladium nanocrystals by Bragg Coherent Diffractive Imaging (BCDI) . During constant pressure experiments, we observed that the phase transformation begins after the nucleation of dislocations in large (300 nm) particles. Themore » 3D dislocation network shows that dislocations are close to the phase boundary. The 3D phase morphology resolved by BCDI suggests that the hydrogen-rich phase is more similar to a spherical cap on the hydrogen-poor phase than the core-shell model commonly assumed. We substantiate this conclusion using 3D phase field modeling and demonstrate how phase morphology affects the critical size for dislocation nucleation. We determine the size dependence of the transformation pressure for large (150-300 nm) palladium nanocrystals using variable pressure experiments. Our results reveal a pathway for solute induced structural phase transformations in nanocrystals and demonstrate BCDI as a novel method for understanding dislocation dynamics in phase transforming systems at the nanoscale.« less

Tunable and laser-reconfigurable 2D heterocrystals obtained by epitaxial stacking of crystallographically incommensurate Bi2Se3 and MoS2 atomic layers

PubMed Central

Vargas, Anthony; Liu, Fangze; Lane, Christopher; Rubin, Daniel; Bilgin, Ismail; Hennighausen, Zachariah; DeCapua, Matthew; Bansil, Arun; Kar, Swastik

2017-01-01

Vertical stacking is widely viewed as a promising approach for designing advanced functionalities using two-dimensional (2D) materials. Combining crystallographically commensurate materials in these 2D stacks has been shown to result in rich new electronic structure, magnetotransport, and optical properties. In this context, vertical stacks of crystallographically incommensurate 2D materials with well-defined crystallographic order are a counterintuitive concept and, hence, fundamentally intriguing. We show that crystallographically dissimilar and incommensurate atomically thin MoS2 and Bi2Se3 layers can form rotationally aligned stacks with long-range crystallographic order. Our first-principles theoretical modeling predicts heterocrystal electronic band structures, which are quite distinct from those of the parent crystals, characterized with an indirect bandgap. Experiments reveal striking optical changes when Bi2Se3 is stacked layer by layer on monolayer MoS2, including 100% photoluminescence (PL) suppression, tunable transmittance edge (1.1→0.75 eV), suppressed Raman, and wide-band evolution of spectral transmittance. Disrupting the interface using a focused laser results in a marked the reversal of PL, Raman, and transmittance, demonstrating for the first time that in situ manipulation of interfaces can enable “reconfigurable” 2D materials. We demonstrate submicrometer resolution, “laser-drawing” and “bit-writing,” and novel laser-induced broadband light emission in these heterocrystal sheets. PMID:28740860

Synthesis and Crystallographic Insight into the Structural Aspects of Some Novel Adamantane-Based Ester Derivatives.

PubMed

Kumar, C S Chidan; Kwong, Huey Chong; Mah, Siau Hui; Chia, Tze Shyang; Loh, Wan-Sin; Quah, Ching Kheng; Lim, Gin Keat; Chandraju, Siddegowda; Fun, Hoong-Kun

2015-10-16

Adamantyl-based compounds are commercially important in the treatments for neurological conditions and type-2 diabetes, aside from their anti-viral abilities. Their values in drug design are chronicled as multi-dimensional. In the present study, a series of 2-(adamantan-1-yl)-2-oxoethyl benzoates, 2(a-q), and 2-(adamantan-1-yl)-2-oxoethyl 2-pyridinecarboxylate, 2r, were synthesized by reacting 1-adamantyl bromomethyl ketone with various carboxylic acids using potassium carbonate in dimethylformamide medium at room temperature. Three-dimensional structures studied using X-ray diffraction suggest that the adamantyl moiety can serve as an efficient building block to synthesize 2-oxopropyl benzoate derivatives with synclinal conformation with a looser-packed crystal packing system. Compounds 2a, 2b, 2f, 2g, 2i, 2j, 2m, 2n, 2o, 2q and 2r exhibit strong antioxidant activities in the hydrogen peroxide radical scavenging test. Furthermore, three compounds, 2p, 2q and 2r, show good anti-inflammatory activities in the evaluation of albumin denaturation.

Rational redesign of inhibitors of furin/kexin processing proteases by electrostatic mutations.

PubMed

Cai, Xiao-hui; Zhang, Qing; Ding, Da-fu

2004-12-01

To model the three-dimensional structure and investigate the interaction mechanism of the proprotein convertase furin/kexin and their inhibitors (eglin c mutants). The three-dimensional complex structures of furin/kexin with its inhibitors, eglin c mutants, were generated by modeller program using the newly published X-ray crystallographical structures of mouse furin and yeast kexin as templates. The electrostatic interaction energy of each complex was calculated and the results were compared with the experimentally determined inhibition constants to find the correlation between them. High quality models of furin/kexin-eglin c mutants were obtained and used for calculation of the electrostatic interaction energies between the proteases and their inhibitors. The calculated electrostatic energies of interaction showed a linear correlation to the experimental inhibition constants. The modeled structures give good explanations of the specificity of eglin c mutants to furin/kexin. The electrostatic interactions play important roles in inhibitory activity of eglin c mutants to furin/kexin. The results presented here provided quantitative structural and functional information concerning the role of the charge-charge interactions in the binding of furin/kexin and their inhibitors.

Bilinear magnetoelectric resistance as a probe of three-dimensional spin texture in topological surface states

NASA Astrophysics Data System (ADS)

He, Pan; Zhang, Steven S.-L.; Zhu, Dapeng; Liu, Yang; Wang, Yi; Yu, Jiawei; Vignale, Giovanni; Yang, Hyunsoo

2018-05-01

Surface states of three-dimensional topological insulators exhibit the phenomenon of spin-momentum locking, whereby the orientation of an electron spin is determined by its momentum. Probing the spin texture of these states is of critical importance for the realization of topological insulator devices, but the main technique currently available is spin- and angle-resolved photoemission spectroscopy. Here we reveal a close link between the spin texture and a new kind of magnetoresistance, which depends on the relative orientation of the current with respect to the magnetic field as well as the crystallographic axes, and scales linearly with both the applied electric and magnetic fields. This bilinear magnetoelectric resistance can be used to map the spin texture of topological surface states by simple transport measurements. For a prototypical Bi2Se3 single layer, we can map both the in-plane and out-of-plane components of the spin texture (the latter arising from hexagonal warping). Theoretical calculations suggest that the bilinear magnetoelectric resistance originates from conversion of a non-equilibrium spin current into a charge current under application of the external magnetic field.

Three Dimensional Characterization of Tin Crystallography and Cu6Sn5 Intermetallics in Solder Joints by Multiscale Tomography

NASA Astrophysics Data System (ADS)

Kirubanandham, A.; Lujan-Regalado, I.; Vallabhaneni, R.; Chawla, N.

2016-11-01

Decreasing pitch size in electronic packaging has resulted in a drastic decrease in solder volumes. The Sn grain crystallography and fraction of intermetallic compounds (IMCs) in small-scale solder joints evolve much differently at the smaller length scales. A cross-sectional study limits the morphological analysis of microstructural features to two dimensions. This study utilizes serial sectioning technique in conjunction with electron backscatter diffraction to investigate the crystallographic orientation of both Sn grains and Cu6Sn5 IMCs in Cu/Pure Sn/Cu solder joints in three dimensional (3D). Quantification of grain aspect ratio is affected by local cooling rate differences within the solder volume. Backscatter electron imaging and focused ion beam serial sectioning enabled the visualization of morphology of both nanosized Cu6Sn5 IMCs and the hollow hexagonal morphology type Cu6Sn5 IMCs in 3D. Quantification and visualization of microstructural features in 3D thus enable us to better understand the microstructure and deformation mechanics within these small scale solder joints.

Three-dimensional structure of Schistosoma japonicum glutathione S-transferase fused with a six-amino acid conserved neutralizing epitope of gp41 from HIV

NASA Technical Reports Server (NTRS)

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

1994-01-01

The 3-dimensional crystal structure of glutathione S-transferase (GST) of Schistosoma japonicum (Sj) fused with a conserved neutralizing epitope on gp41 (glycoprotein, 41 kDa) of human immunodeficiency virus type 1 (HIV-1) was determined at 2.5 A resolution. The structure of the 3-3 isozyme rat GST of the mu gene class was used as a molecular replacement model. The structure consists of a 4-stranded beta-sheet and 3 alpha-helices in domain 1 and 5 alpha-helices in domain 2. The space group of the Sj GST crystal is P4(sub 3)2(sub 1)2 with unit cell dimensions of a = b = 94.7 A, and c = 58.1 A. The crystal has 1 GST monomer per asymmetric unit, and 2 monomers that form an active dimer are related by crystallographic 2-fold symmetry. In the binding site, the ordered structure of reduced glutathione is observed. The gp41 peptide (Glu-Leu-Asp-Lys-Trp-Ala) fused to the C-terminus of Sj GST forms a loop stabilized by symmetry-related GSTs. The Sj GST structure is compared with previously determined GST structures of mammalian gene classes mu, alpha, and pi. Conserved amino acid residues among the 4 GSTs that are important for hydrophobic and hydrophilic interactions for dimer association and glutathione binding are discussed.

Photoconductivity in the chalcohalide semiconductor, SbSeI: a new candidate for hard radiation detection.

PubMed

Wibowo, Arief C; Malliakas, Christos D; Liu, Zhifu; Peters, John A; Sebastian, Maria; Chung, Duck Young; Wessels, Bruce W; Kanatzidis, Mercouri G

2013-06-17

We investigated an antimony chalcohalide compound, SbSeI, as a potential semiconductor material for X-ray and γ-ray detection. SbSeI has a wide band gap of 1.70 eV with a density of 5.80 g/cm(3), and it crystallizes in the orthorhombic Pnma space group with a one-dimensional chain structure comprised of infinite zigzag chains of dimers [Sb2Se4I8]n running along the crystallographic b axis. In this study, we investigate conditions for vertical Bridgman crystal growth using combinations of the peak temperature and temperature gradients as well as translation rate set in a three-zone furnace. SbSeI samples grown at 495 °C peak temperature and 19 °C/cm temperature gradient with 2.5 mm/h translation rate produced a single phase of columnar needlelike crystals aligned along the translational direction of the growth. The ingot sample exhibited an n-type semiconductor with resistivity of ∼10(8) Ω·cm. Photoconductivity measurements on these specimens allowed us to determine mobility-lifetime (μτ) products for electron and hole carriers that were found to be of similar order of magnitude (∼10(-4) cm(2)/V). Further, the SbSeI ingot with well-aligned, one-dimensional columnar needlelike crystals shows an appreciable response of Ag Kα X-ray.

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of human histidine triad nucleotide-binding protein 2 (hHINT2)

PubMed Central

Dolot, Rafał; Włodarczyk, Artur; Bujacz, Grzegorz D.; Nawrot, Barbara

2013-01-01

Histidine triad nucleotide-binding protein 2 (HINT2) is a mitochondrial adenosine phosphoramidase mainly expressed in the pancreas, liver and adrenal gland. HINT2 possibly plays a role in apoptosis, as well as being involved in steroid biosynthesis, hepatic lipid metabolism and regulation of hepatic mitochondria function. The expression level of HINT2 is significantly down-regulated in hepatocellular carcinoma patients. To date, endogenous substrates for this enzyme, as well as the three-dimensional structure of human HINT2, are unknown. In this study, human HINT2 was cloned, overexpressed in Escherichia coli and purified. Crystallization was performed at 278 K using PEG 4000 as the main precipitant; the crystals, which belonged to the tetragonal space group P41212 with unit-cell parameters a = b = 76.38, c = 133.25 Å, diffracted to 2.83 Å resolution. Assuming two molecules in the asymmetric unit, the Matthews coefficient and the solvent content were calculated to be 2.63 Å3 Da−1 and 53.27%, respectively. PMID:23832208

Crystallization of beef heart cytochrome c oxidase

NASA Astrophysics Data System (ADS)

Yoshikawa, Shinya; Shinzawa, Kyoko; Tsukihara, Tomitake; Abe, Toshio; Caughey, Winslow S.

1991-03-01

The three-dimensional structure of cytochrome c oxidase, a complex (multimetal, multisubunit) membrane protein is critical to elucidation of the mechanism of the enzymic reactions and their control. Our recent developments in the crystallization of the enzyme isolated from beef hearts are presented. The crystals appeared more readily at higher protein concentration, lower ionic strength, higher detergent concentration (Brij-35) and lower temperature. Large crystals were obtained by changing one of these parameters to the crystallization point as slowly as possible, keeping the other parameters constant. Increasing the detergent concentration was the most successful method, producing green crystals of the resting oxidized form as hexagonal bipyramids with typical dimensions of 0.6 mm. The usual procedures for crystallization of water soluble proteins, such as increasing ionic strength by vapor diffusion, were not applicable for this enzyme. Crystals of the resting oxidized enzyme belong to a space group of P6 2 or P6 4 with cell dimensions, a = b = 208.7 Å and c = 282.3 Å. The Patterson function shows that the crystal exhibited a non-crystallographic two-fold axis parallel to the c-axis in the asymmetric unit.

Crystal growth, structure and characterization of p-Toluidinium picrate

NASA Astrophysics Data System (ADS)

Muthu, K.; Meenakshisundaram, Subbiah

2012-08-01

p-Toluidinium picrate (PTP), is a proton transfer complex of 2,4,6-trinitrophenol as an electron acceptor with p-toluidine as electron donor, crystallizing in the monoclinic system with four molecules in the unit cell (space group P21/c). The vibrational patterns of the organic crystal PTP in comparison with that of the parent compound clearly evidences the complex formation. Loss of hydroxyl proton at O1 leading to specific electron delocalization around C1 is observed. Crystallographic data are reported as a=12.9304(6) Å, b=15.7176(7) Å, c=7.5403(4) Å, β=101.837(5)°. The crystalline cohesion is achieved by N-H…O and C-H…O hydrogen bonds and the ions are linked into three dimensional network. Intermolecular hydrogen bonding between nitrogen of p-toluidine and phenolate ion of picric acid results in charge transfer. A sharp endotherm in the DSC curve, no decomposition up to the melting point and poor absorbance in the visible region indicate the suitability of the material for potential applications.

Hydrothermal Synthesis, Crystal Structure and Electrochemical Behavior of 2d Hybrid Coordination Polymer

NASA Astrophysics Data System (ADS)

Fan, Weiqiang; Zhu, Lin; Shi, Weidong; Chen, Fuxiao; Bai, Hongye; Song, Shuyan; Yan, Yongsheng

2013-04-01

A novel metal-organic coordination polymer [Cu(phen)(L)0.5(H2O)]n (H4L = (N,N‧-5,5‧-bis(isophthalic acid)-p-xylylenediamine, and phen = 1,10-phenanthroline) has been hydrothermally synthesized and characterized by elemental analysis, IR, TGA, and single-crystal X-ray diffraction. The crystallographic data show that the title compound crystallizes in monoclinic space group P21/n with a = 10.682(2), b = 15.682(3), c = 11.909(2) Å, β = 91.39(3)°, V = 1994.3(7) Å3, C24H17CuN3O5, Mr = 490.95, Dc = 1.635 g/cm3, F(000) = 1004, Z = 4, μ(MoKα) = 1.141 mm-1, the final R = 0.0418 and wR = 0.0983 for 3578 observed reflections (I > 2σ(I)). The structural analyses reveal that the title compound exhibits shows a 2D layer structure, which are further linked by hydrogen bonding interactions to form a three-dimensional supramolecular network. In addition, the thermal stability and electrochemical behavior of title compound has been studied. CCDC: 900413.

Origin of polymorphism of the two-dimensional group-IV monochalcogenides

NASA Astrophysics Data System (ADS)

Wu, Minghui; Wei, Su-Huai; Huang, Li

2017-11-01

Unlike other two-dimensional (2D) isovalent materials, the 2D group IV monochalcogenides, M X (M =Si , Ge, Sn, and Pb; X =S , Se, and Te), are found to be either in a black phosphorene-derived distorted NaCl-type (d -NaCl) structure or a recently predicted P m a 2 structure. Both M and X atoms in the d -NaCl structure are threefold coordinated, whereas M and X in the P m a 2 structure are fourfold and twofold coordinated, respectively. Using first-principles total energy and electronic structure calculations and a global structural search technique, we systematically investigated the mechanism underlying the polymorphism of the 2D group-IV monochalcogenides. Our analysis show that the relative stability of the two distinct crystallographic phases depends on the strength of the M -M covalent bond and the electronegativity difference between the constituent elements M and X . For small cations, the covalency plays more important role, whereas for large cations the Coulomb interaction becomes more dominant. Therefore, the Si X and Ge X compounds assume the P m a 2 structure, whereas the M X compounds with heavy cation elements (M =Sn and Pb) tend to adopt the d -NaCl structure.

Metal–Organic Nanosheets Formed via Defect-Mediated Transformation of a Hafnium Metal–Organic Framework

PubMed Central

2017-01-01

We report a hafnium-containing MOF, hcp UiO-67(Hf), which is a ligand-deficient layered analogue of the face-centered cubic fcu UiO-67(Hf). hcp UiO-67 accommodates its lower ligand:metal ratio compared to fcu UiO-67 through a new structural mechanism: the formation of a condensed “double cluster” (Hf12O8(OH)14), analogous to the condensation of coordination polyhedra in oxide frameworks. In oxide frameworks, variable stoichiometry can lead to more complex defect structures, e.g., crystallographic shear planes or modules with differing compositions, which can be the source of further chemical reactivity; likewise, the layered hcp UiO-67 can react further to reversibly form a two-dimensional metal–organic framework, hxl UiO-67. Both three-dimensional hcp UiO-67 and two-dimensional hxl UiO-67 can be delaminated to form metal–organic nanosheets. Delamination of hcp UiO-67 occurs through the cleavage of strong hafnium-carboxylate bonds and is effected under mild conditions, suggesting that defect-ordered MOFs could be a productive route to porous two-dimensional materials. PMID:28343394

Air and moisture stable covalently-bonded tin(ii) coordination polymers.

PubMed

de Lima, G M; Walton, R I; Clarkson, G J; Bitzer, R S; Ardisson, J D

2018-06-05

Four covalently-bonded tin(ii) coordination polymers, (1)-(4), were hydrothermally prepared in aqueous alkaline media by the reactions of SnSO4 with 1,2,4,5-benzenetetracarboxylic acid (1), 1,3,5-benzenetricarboxylic acid (2), 4-hydroxypyridine-2,6-dicarboxylic acid (3), and 1,3,5-cyclohexanetricarboxylic acid (4). All products were structurally authenticated by single-crystal X-ray diffraction, and the number of different tin centres and their oxidation states were confirmed by 119Sn Mössbauer spectroscopy. In addition, the comparison between experimental and simulated X-ray powder diffraction patterns confirmed the authenticity of the samples. Our crystallographic results for (1)-(4) show that the Sn(ii) centres are tetracoordinated and exhibit distorted disphenoidal geometries, corroborating the presence of one stereochemically active lone electron pair at each metal site. Products (1) and (2) display bi-dimensional polymeric structures, (3) exhibits a one-dimensional architecture, whereas (4) shows a remarkable three-dimensional coordination network. Hirshfeld surface and supramolecular analyses for the repeating units of (1)-(4) were also performed in order to identify structurally important non-covalent interactions.

Production, Purification and Preliminary X-ray Crystallographic Studies of Adeno-Associated Virus Serotype 9

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mitchell, M.; Nam, H; Carter, A

2009-01-01

Adeno-associated virus (AAV) serotype 9, which is under development for gene-delivery applications, shows significantly enhanced capsid-associated transduction efficiency in muscle compared with other AAV serotypes. With the aim of characterizing the structural determinants of this property, the purification, crystallization and preliminary X-ray crystallographic analyses of the AAV9 viral capsid are reported. The crystals diffracted X-rays to 2.8 A resolution using synchrotron radiation and belonged to the trigonal space group P32, with unit-cell parameters a = b = 251.0, c = 640.0 A. There are three complete viral capsids in the crystal unit cell. The orientation and position of the asymmetricmore » unit capsid have been determined by molecular-replacement methods and structure determination is in progress.« less

Validating two-dimensional leadership models on three-dimensionally structured fish schools

PubMed Central

Nagy, Máté; Holbrook, Robert I.; Biro, Dora; Burt de Perera, Theresa

2017-01-01

Identifying leader–follower interactions is crucial for understanding how a group decides where or when to move, and how this information is transferred between members. Although many animal groups have a three-dimensional structure, previous studies investigating leader–follower interactions have often ignored vertical information. This raises the question of whether commonly used two-dimensional leader–follower analyses can be used justifiably on groups that interact in three dimensions. To address this, we quantified the individual movements of banded tetra fish (Astyanax mexicanus) within shoals by computing the three-dimensional trajectories of all individuals using a stereo-camera technique. We used these data firstly to identify and compare leader–follower interactions in two and three dimensions, and secondly to analyse leadership with respect to an individual's spatial position in three dimensions. We show that for 95% of all pairwise interactions leadership identified through two-dimensional analysis matches that identified through three-dimensional analysis, and we reveal that fish attend to the same shoalmates for vertical information as they do for horizontal information. Our results therefore highlight that three-dimensional analyses are not always required to identify leader–follower relationships in species that move freely in three dimensions. We discuss our results in terms of the importance of taking species' sensory capacities into account when studying interaction networks within groups. PMID:28280582

Three-dimensional structure of human serum albumin

NASA Technical Reports Server (NTRS)

Carter, Daniel C.; He, Xiao-Min; Twigg, Pamela D.; Casale, Elena

1991-01-01

The binding locations to human serum albumin (HSA) of several drug molecules were determined at low resolution using crystallographic methods. The principal binding sites are located within subdomains IIA and IIIA. Preliminary studies suggest that an approach to increasing the in vivo efficacy of drugs which are rendered less effective or ineffective by virtue of their interaction with HSA, would be the use of competitive displacement in drug therapies and/or the development of a general inhibitor to the site within subdomain IIIA. These findings also suggest that the facilitated transfer of various ligands across organ/circulatory interfaces such as liver, kidney, and brain may be associated with binding to the IIIA subdomain.

Poly[[diaqua­hemi-μ4-oxalato-μ2-oxalato-praseodymium(III)] monohydrate

PubMed Central

Yang, Ting-Hai; Chen, Qiang; Zhuang, Wei; Wang, Zhe; Yue, Bang-Yi

2009-01-01

In the title complex, {[Pr(C2O4)1.5(H2O)2]·H2O}n, the PrIII ion, which lies on a crystallographic inversion centre, is coordinated by seven O atoms from four oxalate ligands and two O atoms from two water ligands; further Pr—O coordination from tetra­dentate oxalate ligands forms a three-dimensional structure. The compound crystallized as a monohydrate, the water mol­ecule occupying space in small voids and being secured by O—H⋯O hydrogen bonding as an acceptor from ligand water H atoms and as a donor to oxalate O-acceptor sites. PMID:21577485

Uncovering a reconstructive solid-solid phase transition in a metal-organic framework.

PubMed

Longley, L; Li, N; Wei, F; Bennett, T D

2017-11-01

A nanoporous three-dimensional metal-organic framework (MOF), ZnPurBr undergoes a transition to a previously unreported high-temperature phase, ZnPurBr-ht. The transition, which proceeds without mass loss, is uncovered through the use of differential scanning calorimetry (DSC). The new crystal structure was solved using single-crystal X-ray diffraction, and the mechanical properties of both phases investigated by nanoindentation and density functional theory. The anisotropy of the calculated Young's moduli showed good agreement with the crystallographic alignment of the stiff purinate organic linker. The results provide a prototypical example of the importance of the use of DSC in the MOF field, where its use is not currently standard in characterization.

A collaborative molecular modeling environment using a virtual tunneling service.

PubMed

Lee, Jun; Kim, Jee-In; Kang, Lin-Woo

2012-01-01

Collaborative researches of three-dimensional molecular modeling can be limited by different time zones and locations. A networked virtual environment can be utilized to overcome the problem caused by the temporal and spatial differences. However, traditional approaches did not sufficiently consider integration of different computing environments, which were characterized by types of applications, roles of users, and so on. We propose a collaborative molecular modeling environment to integrate different molecule modeling systems using a virtual tunneling service. We integrated Co-Coot, which is a collaborative crystallographic object-oriented toolkit, with VRMMS, which is a virtual reality molecular modeling system, through a collaborative tunneling system. The proposed system showed reliable quantitative and qualitative results through pilot experiments.

The three-dimensional structure of a T-cell antigen receptor V alpha V beta heterodimer reveals a novel arrangement of the V beta domain.

PubMed Central

Housset, D; Mazza, G; Grégoire, C; Piras, C; Malissen, B; Fontecilla-Camps, J C

1997-01-01

The crystal structure of a mouse T-cell antigen receptor (TCR) Fv fragment complexed to the Fab fragment of a specific anti-clonotypic antibody has been determined to 2.6 A resolution. The polypeptide backbone of the TCR V alpha domain is very similar to those of other crystallographically determined V alphas, whereas the V beta structure is so far unique among TCR V beta domains in that it displays a switch of the c" strand from the inner to the outer beta-sheet. The beta chain variable region of this TCR antigen-binding site is characterized by a rather elongated third complementarity-determining region (CDR3beta) that packs tightly against the CDR3 loop of the alpha chain, without leaving any intervening hydrophobic pocket. Thus, the conformation of the CDR loops with the highest potential diversity distinguishes the structure of this TCR antigen-binding site from those for which crystallographic data are available. On the basis of all these results, we infer that a significant conformational change of the CDR3beta loop found in our TCR is required for binding to its cognate peptide-MHC ligand. PMID:9250664

Three Bianthraquinone Derivatives from the Mangrove Endophytic Fungus Alternaria sp. ZJ9-6B from the South China Sea

PubMed Central

Huang, Cai-Huan; Pan, Jia-Hui; Chen, Bin; Yu, Miao; Huang, Hong-Bo; Zhu, Xun; Lu, Yong-Jun; She, Zhi-Gang; Lin, Yong-Cheng

2011-01-01

Three new bianthraquinone derivatives, alterporriol K (1), L (2) and M (3), along with six known compounds were obtained from extracts of the endophytic fungus Alternaria sp. ZJ9-6B, isolated from the mangrove Aegiceras corniculatum collected in the South China Sea. Their structures were elucidated by one- and two-dimensional NMR spectroscopy, MS data analysis and circular dichroism measurements. Compounds 1, 2 and 3 were first isolated alterporriols with a C-2–C-2′ linkage. The crystallographic data of tetrahydroaltersolanol B (7) was reported for the first time. In the primary bioassays, alterporriol K and L exhibited moderate cytotoxic activity towards MDA-MB-435 and MCF-7 cells with IC50 values ranging from 13.1 to 29.1 μM. PMID:21673892

Crystallographic education in the 21st century

PubMed Central

Gražulis, Saulius; Sarjeant, Amy Alexis; Moeck, Peter; Stone-Sundberg, Jennifer; Snyder, Trevor J.; Kaminsky, Werner; Oliver, Allen G.; Stern, Charlotte L.; Dawe, Louise N.; Rychkov, Denis A.; Losev, Evgeniy A.; Boldyreva, Elena V.; Tanski, Joseph M.; Bernstein, Joel; Rabeh, Wael M.; Kantardjieff, Katherine A.

2015-01-01

There are many methods that can be used to incorporate concepts of crystallography into the learning experiences of students, whether they are in elementary school, at university or part of the public at large. It is not always critical that those who teach crystallography have immediate access to diffraction equipment to be able to introduce the concepts of symmetry, packing or molecular structure in an age- and audience-appropriate manner. Crystallography can be used as a tool for teaching general chemistry concepts as well as general research techniques without ever having a student determine a crystal structure. Thus, methods for younger students to perform crystal growth experiments of simple inorganic salts, organic compounds and even metals are presented. For settings where crystallographic instrumentation is accessible (proximally or remotely), students can be involved in all steps of the process, from crystal growth, to data collection, through structure solution and refinement, to final publication. Several approaches based on the presentations in the MS92 Microsymposium at the IUCr 23rd Congress and General Assembly are reported. The topics cover methods for introducing crystallography to undergraduate students as part of a core chemistry curriculum; a successful short-course workshop intended to bootstrap researchers who rely on crystallography for their work; and efforts to bring crystallography to secondary school children and non-science majors. In addition to these workshops, demonstrations and long-format courses, open-format crystallographic databases and three-dimensional printed models as tools that can be used to excite target audiences and inspire them to pursue a deeper understanding of crystallography are described. PMID:26664347

Towards the synthesis of prenylated phloroglucinol derivatives: An X-ray crystallographic and DFT study of unexpected reaction products

NASA Astrophysics Data System (ADS)

Akerman, Matthew P.; Mkhize, Zimbili; van Heerden, Fanie R.

2018-07-01

Owing to their bioactivity and prevalence in medicinal plant extracts, prenylated phloroglucinols have garnered significant interest. Towards the synthesis of prenylated phloroglucinol derivatives, 2,4,6-trihydroxy-3-(3-methylbut-2-enyl)acetophenone is required as an intermediate. Herein, this was synthesised by a tandem Claisen-Cope rearrangement reaction on 2,4-bis(methoxymethoxy)-6-(3-methylbut-2-enyloxy)acetophenone and a subsequent hydrolysis to remove protecting groups. This reaction yielded the desired product as well as three by-products. Two of these by-products were isomeric chromane derivatives (2 and 3) and the third was a methoxy derivative (4). These compounds have been studied by single crystal X-ray crystallography and DFT methods. Compound (2) crystallised in the P21/c space group with two hydrogen-bonded molecules in the asymmetric unit (Z = 8). Compound (4) crystallised in the Pbca space group with a single molecule in the asymmetric unit (Z = 8). Both compounds formed extensive supramolecular structures supported by hydrogen bonds in the solid state. Compound (2) forms a simple one-dimensional hydrogen-bonded chain co-linear with the a-axis. Compound (4) forms a two-dimensional supramolecular structure comprising "pentameric" hydrogen-bonded motifs linked by additional H-bonds to form the supramolecular structure. Both structures showed intramolecular hydrogen bonds between the acetyl oxygen and adjacent OH group. DFT simulations were used to probe the relative energies of the molecules and hydrogen bonds. These simulations showed that the intramolecular hydrogen bond has a substantial stabilising effect with an interaction strength of 70.64 kJ mol-1. The formation of the hydrogen-bonded dimer of (2) from which the supramolecular structure is formed has a ΔHassoc constant of -42.32 kJ mol-1, illustrating that the formation of the hydrogen-bonded structure is energetically favourable.

Crystallographic Information Resources

ERIC Educational Resources Information Center

Glasser, Leslie

2016-01-01

Crystallographic information provides the fundamental basis for understanding the properties and behavior of materials. This data, such as chemical composition, unit cell dimensions, space group, and atomic positions, derives from the primary literature--that is, from published experimental measurement or theoretical calculation. Although the…

The role of the cubic structure in freezing of a supercooled water droplet on an ice substrate

NASA Astrophysics Data System (ADS)

Takahashi, T.; Kobayashi, T.

1983-12-01

The possibility of the formation of a metastable cubic (diamond) structure and its role in freezing of a supercooled water droplet on an ice substrate are discussed in terms of two-dimensional nucleation. The mode of stacking sequence of new layers formed by two-dimensional nucleation is divided into single and multi-nucleation according to the degree of supercooling and to the size of the supercooled droplet. In the case of single nucleation a frozen droplet develops into a complete hexagonal single crystal or an optically single crystal (containing discontinuous stacking faults). In the case of multi-nucleation attention is paid to the size effect and the stacking direction of the nucleus to calculate the waiting time in the nucleation. Then the frozen droplets are crystallographically divided into three categories: completely single crystals, optically single crystals (containing a small cubic structure, i.e. stacking faults) and polycrystals with a misorientation of 70.53° between the c-axes.

Three-Dimensional Stress Fields and Slip Systems for Single Crystal Superalloy Notched Specimens

NASA Technical Reports Server (NTRS)

Magnan, Shannon M.; Throckmorton, David (Technical Monitor)

2002-01-01

Single crystal superalloys have become increasingly popular for turbine blade and vane applications due to their high strength, and creep and fatigue resistance at elevated temperatures. The crystallographic orientation of a single crystal material greatly affects its material properties, including elastic modulus, shear modulus, and ductility. These directional properties, along with the type of loading and temperature, dictate an anisotropic response in the yield strength, creep resistance, creep rupture ductility, fatigue resistance, etc. A significant amount of research has been conducted to determine the material properties in the <001> orientation, yet the material properties deviating from the <001> orientation have not been assessed for all cases. Based on the desired application and design criteria, a crystal orientation is selected to yield the maximum properties. Currently, single crystal manufacturing is able to control the primary crystallographic orientation within 15 of the target orientation, which is an acceptable deviation to meet both performance and cost guidelines; the secondary orientation is rarely specified. A common experiment is the standard load-controlled tensile test, in which specimens with different orientations can be loaded to observe the material response. The deformation behavior of single-crystal materials under tension and compression is known to be a function of not only material orientation, but also of varying microdeformation (i.e. dislocation) mechanisms. The underlying dislocation motion causes deformation via slip, and affects the activation of specific slip systems based on load and orientation. The slip can be analyzed by observing the visible traces left on the surface of the specimen from the slip activity within the single crystal material. The goal of this thesis was to predict the slip systems activated in three-dimensional stress fields of a notched tensile specimen, as a function of crystal orientation, using finite element analysis without addressing microstructural deformation mechanisms that govern their activation. Out of three orientations tested, the specimen with a [110] load orientation and a [001] growth direction had the lowest maximum resolved shear stress; this specimen orientation appears to be the best design candidate for a tensile application.

Bilinear magnetoelectric resistance as a probe of three-dimensional spin texture in topological surface states

DOE PAGES

He, Pan; Zhang, Steven S. -L.; Zhu, Dapeng; ...

2018-02-05

Surface states of three-dimensional topological insulators exhibit the phenomenon of spin-momentum locking, whereby the orientation of an electron spin is determined by its momentum. Probing the spin texture of these states is of critical importance for the realization of topological insulator devices, but the main technique currently available is spin-and angle-resolved photoemission spectroscopy. Here in this paper we reveal a close link between the spin texture and a new kind of magnetoresistance, which depends on the relative orientation of the current with respect to the magnetic field as well as the crystallographic axes, and scales linearly with both the appliedmore » electric and magnetic fields. This bilinear magnetoelectric resistance can be used to map the spin texture of topological surface states by simple transport measurements. For a prototypical Bi 2Se 3 single layer, we can map both the in-plane and out-of-plane components of the spin texture (the latter arising from hexagonal warping). Theoretical calculations suggest that the bilinear magnetoelectric resistance originates from conversion of a non-equilibrium spin current into a charge current under application of the external magnetic field.« less

Bilinear magnetoelectric resistance as a probe of three-dimensional spin texture in topological surface states

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Pan; Zhang, Steven S. -L.; Zhu, Dapeng

Surface states of three-dimensional topological insulators exhibit the phenomenon of spin-momentum locking, whereby the orientation of an electron spin is determined by its momentum. Probing the spin texture of these states is of critical importance for the realization of topological insulator devices, but the main technique currently available is spin-and angle-resolved photoemission spectroscopy. Here in this paper we reveal a close link between the spin texture and a new kind of magnetoresistance, which depends on the relative orientation of the current with respect to the magnetic field as well as the crystallographic axes, and scales linearly with both the appliedmore » electric and magnetic fields. This bilinear magnetoelectric resistance can be used to map the spin texture of topological surface states by simple transport measurements. For a prototypical Bi 2Se 3 single layer, we can map both the in-plane and out-of-plane components of the spin texture (the latter arising from hexagonal warping). Theoretical calculations suggest that the bilinear magnetoelectric resistance originates from conversion of a non-equilibrium spin current into a charge current under application of the external magnetic field.« less

Isomorphous rare-earth bis[bis(2,6-diisopropylphenyl)phosphate] complexes and their self-assembly into two-dimensional frameworks by intramolecular hydrogen bonds.

PubMed

Minyaev, Mikhail E; Nifant'ev, Ilya E; Tavtorkin, Alexander N; Korchagina, Sof'ya A; Zeynalova, Shadana Sh; Ananyev, Ivan V; Churakov, Andrei V

2017-10-01

The crystal structures of rare-earth diaryl- or dialkylphosphate derivatives are poorly explored. Crystals of bis[bis(2,6-diisopropylphenyl)phosphato-κO]chloridotetrakis(methanol-κO)neodymium methanol disolvate, [Nd(C 24 H 34 O 4 P)Cl(CH 4 O) 4 ]·2CH 3 OH, (1), and of the lutetium, [Lu(C 24 H 34 O 4 P)Cl(CH 4 O) 4 ]·2CH 3 OH, (2), and yttrium, [Y(C 24 H 34 O 4 P)Cl(CH 4 O) 4 ]·2CH 3 OH, (3), analogues have been obtained by reactions between lithium bis(2,6-diisopropylphenyl)phosphate and LnCl 3 (H 2 O) 6 (in a 2:1 ratio) in methanol. Compounds (1)-(3) crystallize in the C2/c space group. Their crystal structures are isomorphous. The molecule possesses C 2 symmetry with a twofold crystallographic axis passing through the Ln and Cl atoms. The bis(2,6-diisopropylphenyl)phosphate ligands all display a κ 1 O-monodentate coordination mode. The coordination polyhedron for the metal atom [coordination number (CN) = 7] is a distorted pentagonal bipyramid. Each [Ln{O 2 P(O-2,6- i Pr 2 C 6 H 3 ) 2 } 2 Cl(CH 3 OH) 4 ] molecular unit exhibits two intramolecular O-H...O hydrogen bonds, forming six-membered rings, and two intramolecular O-H...Cl interactions, forming four-membered rings. Intermolecular O-H...O hydrogen bonds connect each unit via four noncoordinating methanol molecules with four other units, forming a two-dimensional hydrogen-bond network. Crystals of bis[bis(2,6-diisopropylphenyl)phosphato-κO]tetrakis(methanol-κO)(nitrato-κ 2 O,O')neodymium methanol disolvate, [Nd(C 24 H 34 O 4 P)(NO 3 )(CH 4 O) 4 ]·2CH 3 OH, (4), have been obtained in an analogous manner from NdCl 3 (H 2 O) 6 . Compound (4) also crystalizes in the C2/c space group. Its crystal structure is similar to those of (1)-(3). The κ 2 O,O'-bidentate nitrate anion is disordered over a twofold axis, being located nearly on it. Half of the molecule is crystallographically unique (CN Nd = 8). Unlike (1)-(3), complex (4) exhibits disorder of all three methanol molecules, one isopropyl group of the phosphate ligand and the NO 3 - ligand. The structure of (4) displays intra- and intermolecular O-H...O hydrogen bonds similar to those in (1)-(3). Compounds (1)-(4) represent the first reported mononuclear bis[bis(diaryl/dialkyl)phosphate] rare-earth complexes.

High pressure synthesis and magnetic studies of quasi one dimensional systems Sr(n-1)Cu(n+1)O(2n) (n=3,5)

NASA Technical Reports Server (NTRS)

Azuma, M.; Hiroi, Z.; Takano, M.; Ishida, K.; Kitaoka, Y.

1995-01-01

SrCu2O3 and Sr2Cu3O5 containing two-leg and three-leg S = 1/2 ladders made of antiferromagnetic Cu-O-Cu linear bonds, respectively, were synthesized at high pressure, and their crystallographic and magnetic properties were investigated. Both susceptibility and T(1) data of NMR (nuclear magnetic resonance) revealed the existence of a large spin gap only for SrCu2O3. Superconductivity, which had been predicted theoretically for carrier-doped SrCu2O3 could not be realized although partial substitution of La(3+) for Sr(2+) seemed to be carried out successfully. Electron carriers injected seems to remain localized.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Estrozi, L.F.; Neumann, E.; Squires, G.

The blood-sucking reduviid bug Triatoma infestans, one of the most important vector of American human trypanosomiasis (Chagas disease) is infected by the Triatoma virus (TrV). TrV has been classified as a member of the Cripavirus genus (type cricket paralysis virus) in the Dicistroviridae family. This work presents the three-dimensional cryo-electron microscopy (cryo-EM) reconstruction of the TrV capsid at about 25 A resolution and its use as a template for phasing the available crystallographic data by the molecular replacement method. The main structural differences between the cryo-EM reconstruction of TrV and other two viruses, one from the same family, the cricketmore » paralysis virus (CrPV) and the human rhinovirus 16 from the Picornaviridae family are presented and discussed.« less

New software for statistical analysis of Cambridge Structural Database data

PubMed Central

Sykes, Richard A.; McCabe, Patrick; Allen, Frank H.; Battle, Gary M.; Bruno, Ian J.; Wood, Peter A.

2011-01-01

A collection of new software tools is presented for the analysis of geometrical, chemical and crystallographic data from the Cambridge Structural Database (CSD). This software supersedes the program Vista. The new functionality is integrated into the program Mercury in order to provide statistical, charting and plotting options alongside three-dimensional structural visualization and analysis. The integration also permits immediate access to other information about specific CSD entries through the Mercury framework, a common requirement in CSD data analyses. In addition, the new software includes a range of more advanced features focused towards structural analysis such as principal components analysis, cone-angle correction in hydrogen-bond analyses and the ability to deal with topological symmetry that may be exhibited in molecular search fragments. PMID:22477784

Crystal structure of ethyl (E)-2-cyano-3-(thio-phen-2-yl)acrylate: two conformers forming a discrete disorder.

PubMed

Castro Agudelo, Brian; Cárdenas, Juan C; Macías, Mario A; Ochoa-Puentes, Cristian; Sierra, Cesar A

2017-09-01

In the title compound, C 10 H 9 NO 2 S, all the non-H atoms, except for the ethyl fragment, lie nearly in the same plane. Despite the mol-ecular planarity, the ethyl fragment presents more than one conformation, giving rise to a discrete disorder, which was modelled with two different crystallographic sites for the eth-oxy O and eth-oxy α-C atoms, with occupancy values of 0.5. In the crystal, the three-dimensional array is mainly directed by C-H⋯(O,N) inter-actions, giving rise to inversion dimers with R 2 2 (10) and R 2 2 (14) motifs and infinite chains running along the [100] direction.

Novel half-magnetization plateau and nematiclike transition in the S =1 skew chain Ni2V2O7

NASA Astrophysics Data System (ADS)

Ouyang, Z. W.; Sun, Y. C.; Wang, J. F.; Yue, X. Y.; Chen, R.; Wang, Z. X.; He, Z. Z.; Xia, Z. C.; Liu, Y.; Rao, G. H.

2018-04-01

A quantized magnetization plateau is usually not expected when a classic spin-flop transition occurs in a low-dimensional antiferromagnet. Here, we report an experimental observation of a spin-flop transition followed by a wide half-magnetization plateau in the S =1 skew-chain system Ni2V2O7 . This plateau, which is stabilized in fields of 8-30 T, is realized through an exotic nematiclike phase transition for magnetic fields applied along all three crystallographic axes, resulting in rich anisotropic phase diagrams. We discuss a possible mechanism whereby the magnetic frustration and interchain interactions may cause this half-magnetization plateau, which is in agreement with our exact diagonalization result.

A Collaborative Molecular Modeling Environment Using a Virtual Tunneling Service

PubMed Central

Lee, Jun; Kim, Jee-In; Kang, Lin-Woo

2012-01-01

Collaborative researches of three-dimensional molecular modeling can be limited by different time zones and locations. A networked virtual environment can be utilized to overcome the problem caused by the temporal and spatial differences. However, traditional approaches did not sufficiently consider integration of different computing environments, which were characterized by types of applications, roles of users, and so on. We propose a collaborative molecular modeling environment to integrate different molecule modeling systems using a virtual tunneling service. We integrated Co-Coot, which is a collaborative crystallographic object-oriented toolkit, with VRMMS, which is a virtual reality molecular modeling system, through a collaborative tunneling system. The proposed system showed reliable quantitative and qualitative results through pilot experiments. PMID:22927721

Preparation and Characterization of Monomodal Grapevine Virus A Capsid Protein.

PubMed

Santana, Vinícius S; Mariutti, Ricardo B; Eberle, Raphael J; Ullah, Anwar; Caruso, Icaro P; Arni, Raghuvir K

2015-01-01

Grapevine virus A (GVA), a flexible filament of approximately 800 nm in length is composed of capsid subunits that spontaneously assembles around a positive sense genomic RNA. In addition to encapsidation, plant viruses capsid proteins (CPs) participate in other processes throughout infection and GVA CP is involved in cell-to-cell translocation of the virus. A protocol was developed to obtain low-molecular weight GVA-CP that is not prone to aggregation and spontaneous assembly and this was characterized by circular dichroism and dynamic light scattering. These results indicate the suitably of GVA-CP for X-ray crystallographic and NMR studies that should lead to the elucidation of the first three-dimensional structure of a flexible filamentous virus from the Betaflexiviridae family.

SdsA polymorph isolation and improvement of their crystal quality using nonconventional crystallization techniques

DOE Office of Scientific and Technical Information (OSTI.GOV)

De la Mora, Eugenio; Flores-Hernández, Edith; Jakoncic, Jean

SdsA, a sodium dodecyl sulfate hydrolase, from Pseudomonas aeruginosa was crystallized in three different crystal polymorphs and their three-dimensional structure was determined. The different polymorphs present different crystal packing habits. One of the polymorphs suggests the existence of a tetramer, an oligomeric state not observed previously, while the crystal packing of the remaining two polymorphs obstructs the active site entrance but stabilizes flexible regions of the protein. Nonconventional crystallization methods that minimize convection, such as counterdiffusion in polyvinyl alcohol gel coupled with the influence of a 500 MHz (10.2 T) magnetic field, were necessary to isolate the poorest diffracting polymorphmore » and increase its internal order to determine its structure by X-ray diffraction. In conclusion, the results obtained show the effectiveness of nonconventional crystallographic methods to isolate different crystal polymorphs.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kalsi, Deepti; Rayaprol, S.; Siruguri, V.

We report the crystallographic properties of RE{sub 2}NiGe{sub 3} (RE=La, Ce) synthesized by arc melting. Rietveld refinement on the powder neutron diffraction (ND) data suggest both compounds are isostructural and crystallize in the non-centrosymmetric Er{sub 2}RhSi{sub 3} type structure having hexagonal space group P6{sup ¯}2c. In the crystal structure of RE{sub 2}NiGe{sub 3}, two dimensional arrangements of nickel and germanium atoms lead to the formation of hexagonal layers with rare earth atoms sandwiched between them. Magnetic susceptibility measurements performed in low fields exhibit antiferromagnetic ordering in cerium compound around (T{sub o}=) 3.2 K. Neutron diffraction measurements at 2.8 K (i.e.,more » at T« less

Hydrogen-bonded structures from adamantane-based catechols

NASA Astrophysics Data System (ADS)

Kawahata, Masatoshi; Matsuura, Miku; Tominaga, Masahide; Katagiri, Kosuke; Yamaguchi, Kentaro

2018-07-01

Adamantane-based bis- and tris-catechols were synthesized to examine the effect of hydrogen bonds on the arrangement and packing of the components in the crystalline state. Single-crystal X-ray crystallographic analysis revealed that hydrogen bonds formed by the hydroxyl groups of catechol groups play essential roles in the production of various types of unique structures. 1,3-Bis(3,4-dihydroxyphenyl)adamantane (1) provided hydrogen-bonded network structures composed of helical chains in crystal from chloroform/methanol, and layer structures in crystal from ethyl acetate/hexane. The complexation of 1 with 1,3,5-trinitrobenzene or 1,2,4,5-tetracyanobenzene resulted in the formation of co-crystals, respectively. One-dimensional hydrogen-bonded structures were constructed from the adamantane-based molecules, which participated in charge-transfer interactions with guests. 1,3,5-Tris(3,4-dihydroxyphenyl)adamantane also afforded crystal, and the components were assembled into infinite polymers.

Post-synthetic halide conversion and selective halogen capture in hybrid perovskites† †Electronic supplementary information (ESI) available. CCDC 1048945–1048947. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c5sc01135c

PubMed Central

Solis-Ibarra, D.; Smith, I. C.

2015-01-01

Reaction with halogen vapor allows us to post-synthetically exchange halides in both three- (3D) and two-dimensional (2D) organic–inorganic metal-halide perovskites. Films of 3D Pb–I perovskites cleanly convert to films of Pb–Br or Pb–Cl perovskites upon exposure to Br2 or Cl2 gas, respectively. This gas–solid reaction provides a simple method to produce the high-quality Pb–Br or Pb–Cl perovskite films required for optoelectronic applications. Reactivity with halogens can be extended to the organic layers in 2D metal-halide perovskites. Here, terminal alkene groups placed between the inorganic layers can capture Br2 gas through chemisorption to form dibromoalkanes. This reaction's selectivity for Br2 over I2 allows us to scrub Br2 to obtain high-purity I2 gas streams. We also observe unusual halogen transfer between the inorganic and organic layers within a single perovskite structure. Remarkably, the perovskite's crystallinity is retained during these massive structural rearrangements. PMID:29218171

Expression, purification and preliminary crystallographic analysis of oligopeptidase B from Trypanosoma brucei

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rea, Dean; Hazell, Carole; Andrews, Norma W.

2006-08-01

Recombinant oligopeptidase B from T. brucei has been prepared and crystallized. Data were collected to 2.7 Å. Heavy-atom soaks and preparation of selenomethionine-substituted protein are in progress for structure determination by MAD or MIR. African sleeping sickness, also called trypanosomiasis, is a significant cause of morbidity and mortality in sub-Saharan Africa. Peptidases from Trypanosoma brucei, the causative agent, include the serine peptidase oligopeptidase B, a documented virulence factor and therapeutic target. Determination of the three-dimensional structure of oligopeptidase B is desirable to facilitate the development of novel inhibitors. Oligopeptidase B was overexpressed in Escherichia coli as an N-terminally hexahistidine-tagged fusionmore » protein, purified using metal-affinity chromatography and crystallized using the hanging-drop vapour-diffusion technique in 7%(w/v) polyethylene glycol 6000, 1 M LiCl, 0.1 M bis-tris propane pH 7.5. Diffraction data to 2.7 Å resolution were collected using synchrotron radiation. The crystals belong to space group P3{sub 1}21 or P3{sub 2}21, with unit-cell parameters a = b = 124.5, c = 249.9 Å. A complete data set to 2.7 Å was collected using synchrotron radiation.« less

Bacterial expression of the phosphodiester-binding site of the cation-independent mannose 6-phosphate receptor for crystallographic and NMR studies

PubMed Central

Olson, Linda J.; Jensen, Davin R.; Volkman, Brian F.; Kim, Jung-Ja P.; Peterson, Francis C.; Gundry, Rebekah L.; Dahms, Nancy M.

2015-01-01

The cation-independent mannose 6-phosphate receptor (CI-MPR) is a multifunctional protein that interacts with diverse ligands and plays central roles in autophagy, development, and tumor suppression. By delivering newly synthesized phosphomannosyl-containing acid hydrolases from the Golgi to endosomal compartments, CI-MPR is an essential component in the generation of lysosomes that are critical for the maintenance of cellular homeostasis. The ability of CI-MPR to interact with ~60 different acid hydrolases is facilitated by its large extracellular region, with four out of its 15 domains binding phosphomannosyl residues. Although the glycan specificity of CI-MPR has been elucidated, the molecular basis of carbohydrate binding has not been determined for two out of these four carbohydrate recognition domains (CRD). Here we report expression of CI-MPR’s CRD located in domain 5 that preferentially binds phosphodiester-containing glycans. Domain 5 of CI-MPR was expressed in Escherichia coli BL21 (DE3) cells as a fusion protein containing an N-terminal histidine tag and the small ubiquitin-like modifier (SUMO) protein. The His6-SUMO-CRD construct was recovered from inclusion bodies, refolded in buffer to facilitate disulfide bond formation, and subjected to Ni-NTA affinity chromatography and size exclusion chromatography. Surface plasmon resonance analyses demonstrated that the purified protein was active and bound phosphorylated glycans. Characterization by NMR spectroscopy revealed high quality 1H–15N HSQC spectra. Additionally, crystallization conditions were identified and a crystallographic data set of the CRD was collected to 1.8 Å resolution. Together, these studies demonstrate the feasibility of producing CI-MPR’s CRD suitable for three-dimensional structure determination by NMR spectroscopic and X-ray crystallographic approaches. PMID:25863146

Virtual Reality Training With Three-Dimensional Video Games Improves Postural Balance and Lower Extremity Strength in Community-Dwelling Older Adults.

PubMed

Lee, Yongwoo; Choi, Wonjae; Lee, Kyeongjin; Song, Changho; Lee, Seungwon

2017-10-01

Avatar-based three-dimensional technology is a new approach to improve physical function in older adults. The aim of this study was to use three-dimensional video gaming technology in virtual reality training to improve postural balance and lower extremity strength in a population of community-dwelling older adults. The experimental group participated in the virtual reality training program for 60 min, twice a week, for 6 weeks. Both experimental and control groups were given three times for falls prevention education at the first, third, and fifth weeks. The experimental group showed significant improvements not only in static and dynamic postural balance but also lower extremity strength (p < .05). Furthermore, the experimental group was improved to overall parameters compared with the control group (p < .05). Therefore, three-dimensional video gaming technology might be beneficial for improving postural balance and lower extremity strength in community-dwelling older adults.

Non-crystallographic nets: characterization and first steps towards a classification.

PubMed

Moreira de Oliveira, Montauban; Eon, Jean Guillaume

2014-05-01

Non-crystallographic (NC) nets are periodic nets characterized by the existence of non-trivial bounded automorphisms. Such automorphisms cannot be associated with any crystallographic symmetry in realizations of the net by crystal structures. It is shown that bounded automorphisms of finite order form a normal subgroup F(N) of the automorphism group of NC nets (N, T). As a consequence, NC nets are unstable nets (they display vertex collisions in any barycentric representation) and, conversely, stable nets are crystallographic nets. The labelled quotient graphs of NC nets are characterized by the existence of an equivoltage partition (a partition of the vertex set that preserves label vectors over edges between cells). A classification of NC nets is proposed on the basis of (i) their relationship to the crystallographic net with a homeomorphic barycentric representation and (ii) the structure of the subgroup F(N).

Three phase crystallography and solute distribution analysis during residual austenite decomposition in tempered nanocrystalline bainitic steels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caballero, F.G.; Yen, Hung-Wei; Australian Centre for Microscopy and Microanalysis, The University of Sydney, NSW 2006

2014-02-15

Interphase carbide precipitation due to austenite decomposition was investigated by high resolution transmission electron microscopy and atom probe tomography in tempered nanostructured bainitic steels. Results showed that cementite (θ) forms by a paraequilibrium transformation mechanism at the bainitic ferrite–austenite interface with a simultaneous three phase crystallographic orientation relationship. - Highlights: • Interphase carbide precipitation due to austenite decomposition • Tempered nanostructured bainitic steels • High resolution transmission electron microscopy and atom probe tomography • Paraequilibrium θ with three phase crystallographic orientation relationship.

Fine refinement of solid state structure of racemic form of phospho-tyrosine employing NMR Crystallography approach.

PubMed

Paluch, Piotr; Pawlak, Tomasz; Oszajca, Marcin; Lasocha, Wieslaw; Potrzebowski, Marek J

2015-02-01

We present step by step facets important in NMR Crystallography strategy employing O-phospho-dl-tyrosine as model sample. The significance of three major techniques being components of this approach: solid state NMR (SS NMR), X-ray diffraction of powdered sample (PXRD) and theoretical calculations (Gauge Invariant Projector Augmented Wave; GIPAW) is discussed. Each experimental technique provides different set of structural constraints. From the PXRD measurement the size of the unit cell, space group and roughly refined molecular structure are established. SS NMR provides information about content of crystallographic asymmetric unit, local geometry, molecular motion in the crystal lattice and hydrogen bonding pattern. GIPAW calculations are employed for validation of quality of elucidation and fine refinement of structure. Crystal and molecular structure of O-phospho-dl-tyrosine solved by NMR Crystallography is deposited at Cambridge Crystallographic Data Center under number CCDC 1005924. Copyright © 2014 Elsevier Inc. All rights reserved.

Crystallographic analysis of ground and space thermostable T1 lipase crystal obtained via counter diffusion method approach.

PubMed

Mohamad Aris, Sayangku Nor Ariati; Thean Chor, Adam Leow; Mohamad Ali, Mohd Shukuri; Basri, Mahiran; Salleh, Abu Bakar; Raja Abd Rahman, Raja Noor Zaliha

2014-01-01

Three-dimensional structure of thermostable lipase is much sought after nowadays as it is important for industrial application mainly found in the food, detergent, and pharmaceutical sectors. Crystallization utilizing the counter diffusion method in space was performed with the aim to obtain high resolution diffracting crystals with better internal order to improve the accuracy of the structure. Thermostable T1 lipase enzyme has been crystallized in laboratory on earth and also under microgravity condition aboard Progress spacecraft to the ISS in collaboration with JAXA (Japanese Aerospace Exploration Agency). This study is conducted with the aims of improving crystal packing and structure resolution. The diffraction data set for ground grown crystal was collected to 1.3 Å resolution and belonged to monoclinic C2 space group with unit cell parameters a = 117.40 Å, b = 80.95 Å, and c = 99.81 Å, whereas the diffraction data set for space grown crystal was collected to 1.1 Å resolution and belonged to monoclinic C2 space group with unit cell parameters a = 117.31 Å, b = 80.85 Å, and c = 99.81 Å. The major difference between the two crystal growth systems is the lack of convection and sedimentation in microgravity environment resulted in the growth of much higher quality crystals of T1 lipase.

Diaqua­bis­(4-meth­oxy­benzoato-κO 1)bis­(nicotinamide-κN 1)cobalt(II) dihydrate

PubMed Central

Hökelek, Tuncer; Dal, Hakan; Tercan, Barış; Tenlik, Erdinç; Necefoğlu, Hacali

2010-01-01

In the mononuclear title compound, [Co(C8H7O3)2(C6H6N2O)2(H2O)2]·2H2O, the CoII ion is located on a crystallographic inversion center. The asymmetric unit is completed by one 4-meth­oxy­benzoate anion, one nicotinamide (NA) ligand and one coordinated and one uncoordinated water mol­ecule. All ligands act in a monodentate mode. The four O atoms in the equatorial plane around the CoII ion form a slightly distorted square-planar arrangement, while the slightly distorted octa­hedral coordination is completed by the two pyridine N atoms of the NA ligands in the axial positions. The dihedral angle between the carboxyl­ate group and the attached benzene ring is 6.47 (7)°, while the pyridine and benzene rings are oriented at a dihedral angle of 72.80 (4)°. An O—H⋯O hydrogen bond links the uncoordinated water mol­ecule to one of the carboxyl­ate groups. In the crystal structure, inter­molecular O—H⋯O, N—H⋯O and C—H⋯O hydrogen bonds link the mol­ecules into a three-dimensional network. PMID:21588149

Non Fermi Liquid Crossovers in a Quasi-One-Dimensional Conductor in an Inclined Magnetic Field

NASA Astrophysics Data System (ADS)

Lebed, Andrei

We consider a theoretical problem of electron-electron scattering time in a quasi-one-dimensional (Q1D) conductor in a magnetic field, perpendicular to its conducting axis. We show that inverse electron-electron scattering time becomes of the order of characteristic electron energy, 1 / τ ~ ɛ ~ T , in a high magnetic field, directed far from the main crystallographic axes, which indicates breakdown of the Fermi liquid theory. In a magnetic field, directed close to one of the main crystallographic axis, inverse electron-electron scattering time becomes much smaller than characteristic electron energy and, thus, applicability of Fermi liquid theory restores. We suggest that there exist crossovers between Fermi liquid and some non Fermi liquid states in a strong enough inclined magnetic field. Application of our results to the Q1D conductor (Per)2Au(mnt)2 shows that it has to be possible to observe the above mentioned phenomenon in feasibly high magnetic fields of the order of H >=H* ~= 25 T . It was partially supported by NFS grant DMR-1104512.

Non-destructive identification of unknown minor phases in polycrystalline bulk alloys using three-dimensional X-ray diffraction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Yiming, E-mail: yangyiming1988@outlook.com

Minor phases make considerable contributions to the mechanical and physical properties of metals and alloys. Unfortunately, it is difficult to identify unknown minor phases in a bulk polycrystalline material using conventional metallographic methods. Here, a non-destructive method based on three-dimensional X-ray diffraction (3DXRD) is developed to solve this problem. Simulation results demonstrate that this method is simultaneously able to identify minor phase grains and reveal their positions, orientations and sizes within bulk alloys. According to systematic simulations, the 3DXRD method is practicable for an extensive sample set, including polycrystalline alloys with hexagonal, orthorhombic and cubic minor phases. Experiments were alsomore » conducted to confirm the simulation results. The results for a bulk sample of aluminum alloy AA6061 show that the crystal grains of an unexpected γ-Fe (austenite) phase can be identified, three-dimensionally and nondestructively. Therefore, we conclude that the 3DXRD method is a powerful tool for the identification of unknown minor phases in bulk alloys belonging to a variety of crystal systems. This method also has the potential to be used for in situ observations of the effects of minor phases on the crystallographic behaviors of alloys. - Highlights: •A method based on 3DXRD is developed for identification of unknown minor phase. •Grain position, orientation and size, is simultaneously acquired. •A systematic simulation demonstrated the applicability of the proposed method. •Experimental results on a AA6061 sample confirmed the practicability of the method.« less

Influence of different kinds of rolling on the crystallographic texture and magnetic induction of a NOG 3 wt% Si steel

NASA Astrophysics Data System (ADS)

Silva, J. M.; Baêta Júnior, E. S.; Moraes, N. R. D. C.; Botelho, R. A.; Felix, R. A. C.; Brandao, L.

2017-01-01

The purpose of this work was to study the influence of different kinds of rolling on the magnetic properties of NOG steel, an electric steel widely used in electrical motors. These properties are highly correlated with the crystallographic texture of the material, which can be changed by rolling. Three kinds of rolling were examined: conventional rolling, cross-rolling and asymmetrical rolling. The crystallographic texture was determined by X-ray diffraction and the magnetic properties were calculated from a theoretical model that related the magnetic induction to crystallographic texture through the anisotropy energy. The results show that cross-rolling yields higher values of magnetic induction than the other processes.

The role of three-dimensional imaging in optimizing diagnosis, classification and surgical treatment of hepatocellular carcinoma with portal vein tumor thrombus.

PubMed

Wei, Xu-Biao; Xu, Jie; Li, Nan; Yu, Ying; Shi, Jie; Guo, Wei-Xing; Cheng, Hong-Yan; Wu, Meng-Chao; Lau, Wan-Yee; Cheng, Shu-Qun

2016-03-01

Accurate assessment of characteristics of tumor and portal vein tumor thrombus is crucial in the management of hepatocellular carcinoma. Comparison of the three-dimensional imaging with multiple-slice computed tomography in the diagnosis and treatment of hepatocellular carcinoma with portal vein tumor thrombus. Patients eligible for surgical resection were divided into the three-dimensional imaging group or the multiple-slice computed tomography group according to the type of preoperative assessment. The clinical data were collected and compared. 74 patients were enrolled into this study. The weighted κ values for comparison between the thrombus type based on preoperative evaluation and intraoperative findings were 0.87 for the three-dimensional reconstruction group (n = 31) and 0.78 for the control group (n = 43). Three-dimensional reconstruction was significantly associated with a higher rate of en-bloc resection of tumor and thrombus (P = 0.025). Using three-dimensional reconstruction, significant correlation existed between the predicted and actual volumes of the resected specimens (r = 0.82, P < 0.01), as well as the predicted and actual resection margins (r = 0.97, P < 0.01). Preoperative three-dimensional reconstruction significantly decreased tumor recurrence and tumor-related death, with hazard ratios of 0.49 (95% confidential interval, 0.27-0.90) and 0.41 (95% confidential interval, 0.21-0.78), respectively. For hepatocellular carcinoma with portal vein tumor thrombus, three-dimensional imaging was efficient in facilitating surgical treatment and benefiting postoperative survivals. Copyright © 2015 International Hepato-Pancreato-Biliary Association Inc. Published by Elsevier Ltd. All rights reserved.

VO.sub.2 precipitates for self-protected optical surfaces

DOEpatents

Gea, Laurence A.; Boatner, Lynn A.

1999-01-01

A method for forming crystallographically coherent precipitates of vanadium dioxide in the near-surface region of sapphire and the resulting product is disclosed. Ions of vanadium and oxygen are stoichiometrically implanted into a sapphire substrate (Al.sub.2 O.sub.3), and subsequently annealed to form vanadium dioxide precipitates in the substrate. The embedded VO.sub.2 precipitates, which are three-dimensionally oriented with respect to the crystal axes of the Al.sub.2 O.sub.3 host lattice, undergo a first-order monoclinic-to-tetragonal (and also semiconducting-to-metallic) phase transition at .about.77.degree. C. This transformation is accompanied by a significant variation in the optical transmission of the implanted region and results in the formation of an optically active, thermally "switchable" surface region on Al.sub.2 O.sub.3.

Poly[[tetra-μ3-acetato-hexa-μ2-acetato­diaqua-μ2-oxalato-tetra­lanthanum(III)] dihydrate

PubMed Central

Di, Wen-Jing; Lan, Shao-Min; Zhang, Qun; Liang, Yun-Xiao

2011-01-01

The title compound, {[La4(CH3CO2)10(C2O4)(H2O)2]·2H2O}n, exhibits a two-dimensional layered structure with the oxalate and acetate ligands acting as bridges. The asymmetric unit contains two crystallographically independent lanthanum(III) ions, half of an oxalate ligand, five acetate ligands, one coordinated water mol­ecule and one uncoordinated water mol­ecule. The coordination numbers of the two La ions are 9 and 10. Adjacent layers of the structure, which extend parallel to (100), are linked by O–H⋯O hydrogen bonds and are also held together by van der Waals inter­actions between the CH3 groups of the acetate anions. PMID:22064832

Sterically Hindered Chiral Organometallic Complexes: AN X-Ray Crystallographic, NMR Spectroscopic and Ehmo Study.

NASA Astrophysics Data System (ADS)

Malisza, Krisztina Laura

Sterically crowded organometallic complexes present fascinating problems of structure and molecular dynamics. Tetrahedral clusters such as (RCequivCR ^')rm(C_5H_5)_2M _2(CO)_4, where M = Mo or W, crystallize in conformations possessing three terminal carbonyls while the fourth is semi-bridging. However, these ligands undergo a rapid exchange process which can be followed by variable -temperature NMR spectroscopy. When the R substituent is derived from a chiral natural product, the low temperature NMR spectra reveal the presence of diastereomers which are interconvertible via rotations of the organometallic vertices. The fluxional behaviour of tetrahedral clusters containing such vertices as Co(CO)_3, Fe(CO)_3 or rm(C_5H _5)Mo(CO)_2 can be rationalized by means of molecular orbital calculations at the extended Huckel level of approximation. These studies show that the barriers to vertex rotation can usually be traced to one principal orbital interaction in each case. However, in rm(C_5H_5)_2Mo_2(CO) _4(R-CequivC-R) clusters, the barriers are primarily steric in character. The ability of transition metal clusters to delocalize electronic charge is well known and, in principle, could be used to stabilize intermediates of biochemical significance. Treatment of 2-methylcyclopentanone with an alkyne anion was carried out in order to generate 1-alkynyl-2-methylcyclopentanols in which the methyl and alkynyl groups are trans diaxial; the aim was to mimic the "D"-ring of the steroidal contraceptive mestranol. In fact, the major epimer was the one in which the methyl and alkynyl substituents were disposed in a cis manner. The conformation of 2-methyl-1-phenylethynylcyclopentanol 47 was elucidated by two-dimensional NMR techniques. Moreover, the structure of 47 and also of its rm Co _2(CO)_6 derivative have been determined crystallographically. Protonation of the dicobalt or dimolybdenum complexes of 47 lead to stable cations; treatment of these cations with nucleophiles results in elimination of water to yield 2-methylcyclopentene derivatives of which the dimolybdenum cluster has been characterized by x-ray crystallography. The sterically crowded complexes rm(C _6H_5)_3SiOH[ Cr(CO)_3 ]_{n}, where n = 1,2,3, have also been characterized X-ray crystallographically and all three have propellor-type geometries. The question of whether the phenyl ring rotations are correlated has been studied by variable-temperature NMR spectroscopy. These systems do not yield stable silicenium cations, but the analogous Cr(CO)_3 complex of triphenylcarbinol not only shows fluxional behaviour but also yields a metal -stabilized cation. The pathway for phenyl rotations in such systems can be followed via a Dunitz-type trajectory approach in which a number of x-ray structures were analyzed.

Synthesis, crystal structure, and magnetic characterization of the three-dimensional compound [Co2(cbut)(H2O)3]n (H4cbut = 1,2,3,4-cyclobutanetetracarboxylic acid).

PubMed

Díaz-Gallifa, Pau; Fabelo, Oscar; Pasán, Jorge; Cañadillas-Delgado, Laura; Rodríguez-Carvajal, Juan; Lloret, Francesc; Julve, Miguel; Ruiz-Pérez, Catalina

2014-06-02

A novel cobalt(II) complex of formula [Co2(cbut)(H2O)3]n (1) (H4cbut = 1,2,3,4-cyclobutanetetracarboxylic acid) has been synthesized under hydrothermal conditions and its crystal structure has been determined by means of synchrotron radiation and neutron powder diffraction. The crystal structure of 1 consists of layers of cobalt(II) ions extending in the bc-plane which are pillared along the crystallographic a-axis through the skeleton of the cbut(4-) ligand. Three crystallographically independent cobalt(II) ions [Co(1), Co(2), and Co(3)] occur in 1. They are all six-coordinate with four carboxylate-oxygens [Co(1)-Co(3)] and two cis-[Co(1)] or trans-water molecules [Co(2) and Co(3)] building distorted octahedral surroundings. Regular alternating double oxo(carboxylate) [between Co(1) and Co(1a)] and oxo(carboxylate) plus one aqua and a syn-syn carboxylate bridges [between Co(1) and Co(2)] occur along the crystallographic b-axis, the values of the cobalt-cobalt separation being 3.1259(8) and 3.1555(6) Å, respectively. These chains are connected to the Co(3) atoms through the OCO carboxylate along the [011] direction leading to the organic-inorganic bc-layers with Co(1)-OCO(anti-syn)-Co(3) and Co(2)-OCO(anti-anti)-Co(3) distances of 5.750(2) and 4.872(1) Å. The shortest interlayer cobalt-cobalt separation through the cbut(4-) skeleton along the crystallographic a-axis is 7.028(2) Å. Variable-temperature magnetic susceptibility measurements show the occurrence of antiferromagnetic ordering with a Néel temperature of 5.0 K, followed by a field-induced ferromagnetic transition under applied dc fields larger than 1500 Oe. The magnetic structure of 1 has been elucidated at low temperatures in zero field by neutron powder diffraction measurements and was found to be formed by ferromagnetic chains running along the b-axis which are antiferromagnetically coupled with the Co(3) ions through the c-axis giving rise to noncompensated magnetic moments within each bc-layer (ferrimagnetic plane). The occurrence of an antitranslation operation between these layers produces a weak interlayer antiferromagnetic coupling along the a-axis which is overcome by dc fields greater than 1500 Oe resulting in a phase transition toward a ferromagnetic state (metamagnetic behavior).

Tubular Crystals and Helical Arrays: Structural Determination of HIV-1 Capsid Assemblies Using Iterative Helical Real-Space Reconstruction

PubMed Central

Zhang, Peijun; Meng, Xin; Zhao, Gongpu

2013-01-01

Helical structures are important in many different life forms and are well-suited for structural studies by cryo-EM. A unique feature of helical objects is that a single projection image contains all the views needed to perform a three-dimensional (3D) crystallographic reconstruction. Here, we use HIV-1 capsid assemblies to illustrate the detailed approaches to obtain 3D density maps from helical objects. Mature HIV-1 particles contain a conical- or tubular-shaped capsid that encloses the viral RNA genome and performs essential functions in the virus life cycle. The capsid is composed of capsid protein (CA) oligomers which are helically arranged on the surface. The N-terminal domain (NTD) of CA is connected to its C-terminal domain (CTD) through a flexible hinge. Structural analysis of two- and three-dimensional crystals provided molecular models of the capsid protein (CA) and its oligomer forms. We determined the 3D density map of helically assembled HIV-1 CA hexamers at 16 Å resolution using an iterative helical real-space reconstruction method. Docking of atomic models of CA-NTD and CA-CTD dimer into the electron density map indicated that the CTD dimer interface is retained in the assembled CA. Furthermore, molecular docking revealed an additional, novel CTD trimer interface. PMID:23132072

Three-dimensional lattice rotation in GaAs nanowire growth on hydrogen-silsesquioxane covered GaAs (001) using molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Tran, Dat Q.; Pham, Huyen T.; Higashimine, Koichi; Oshima, Yoshifumi; Akabori, Masashi

2018-05-01

We report on crystallographic behaviors of inclined GaAs nanowires (NWs) self-crystallized on GaAs (001) substrate. The NWs were grown on hydrogen-silsesquioxane (HSQ) covered substrates using molecular beam epitaxy (MBE). Commonly, the epitaxial growth of GaAs < 111>B (B-polar) NWs is prominently observed on GaAs (001); however, we yielded a remarkable number of epitaxially grown GaAs < 111>A (A-polar) NWs in addition to the majorly obtained B-polar NWs. Such NW orientations are always accompanied by a typical inclined angle of 35° from (001) plane. NWs with another inclined angle of 74° were additionally observed and attributed to be < 111>-oriented, not in direct epitaxial relation with the substrate. Such 74° NWs' existence is related to first-order three-dimensional (3D) lattice rotation taking place at the very beginning of the growth. It turns out that spatially 60° lattice rotation around < 111> directions at GaAs seeds is essentially in charge of A- and B-polar 74° NWs. Transmission electron microscope observations reveal a high density of twinning in the B-polar NWs and twin-free characteristic in the A-polar NWs.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ulvestad, A.; Welland, M. J.; Cha, W.

Crystallographic imperfections can significantly alter material properties and responses to external stimuli, including solute induced phase transformations and crystal growth and dissolution . Despite recent progress in imaging defects using both electron and x-ray techniques, in situ three-dimensional imaging studies of defect dynamics, necessary to understand and engineer nanoscale processes, remains challenging. Here, we report in situ three-dimensional imaging of defect dynamics during the hydriding phase transformation of individual palladium nanocrystals by Bragg Coherent Diffractive Imaging (BCDI) . During constant pressure experiments, we observed that the phase transformation begins after the nucleation of dislocations in large (300 nm) particles. Themore » 3D dislocation network shows that dislocations are close to the phase boundary. The 3D phase morphology resolved by BCDI suggests that the hydrogen-rich phase is more similar to a spherical cap on the hydrogen-poor phase than the core-shell model commonly assumed. We substantiate this conclusion using 3D phase field modeling and demonstrate how phase morphology affects the critical size for dislocation nucleation. We determine the size dependence of the transformation pressure for large (150-300 nm) palladium nanocrystals using variable pressure experiments. Our results reveal a pathway for solute induced structural phase transformations in nanocrystals and demonstrate BCDI as a novel method for understanding dislocation dynamics in phase transforming systems at the nanoscale.« less

Three-dimensional structure of Schistosoma japonicum glutathione S-transferase fused with a six-amino acid conserved neutralizing epitope of gp41 from HIV

NASA Technical Reports Server (NTRS)

Lim, K.; Ho, J. X.; Keeling, K.; Gilliland, G. L.; Ji, X.; Ruker, F.; Carter, D. C.

1994-01-01

The 3-dimensional crystal structure of glutathione S-transferase (GST) of Schistosoma japonicum (Sj) fused with a conserved neutralizing epitope on gp41 (glycoprotein, 41 kDa) of human immunodeficiency virus type 1 (HIV-1) (Muster T et al., 1993, J Virol 67:6642-6647) was determined at 2.5 A resolution. The structure of the 3-3 isozyme rat GST of the mu gene class (Ji X, Zhang P, Armstrong RN, Gilliland GL, 1992, Biochemistry 31:10169-10184) was used as a molecular replacement model. The structure consists of a 4-stranded beta-sheet and 3 alpha-helices in domain 1 and 5 alpha-helices in domain 2. The space group of the Sj GST crystal is P4(3)2(1)2, with unit cell dimensions of a = b = 94.7 A, and c = 58.1 A. The crystal has 1 GST monomer per asymmetric unit, and 2 monomers that form an active dimer are related by crystallographic 2-fold symmetry. In the binding site, the ordered structure of reduced glutathione is observed. The gp41 peptide (Glu-Leu-Asp-Lys-Trp-Ala) fused to the C-terminus of Sj GST forms a loop stabilized by symmetry-related GSTs. The Sj GST structure is compared with previously determined GST structures of mammalian gene classes mu, alpha, and pi. Conserved amino acid residues among the 4 GSTs that are important for hydrophobic and hydrophilic interactions for dimer association and glutathione binding are discussed.

ITQ-54: a multi-dimensional extra-large pore zeolite with 20 × 14 × 12-ring channels

DOE PAGES

Jiang, Jiuxing; Yun, Yifeng; Zou, Xiaodong; ...

2015-01-01

A multi-dimensional extra-large pore silicogermanate zeolite, named ITQ-54, has been synthesised by in situ decomposition of the N,N-dicyclohexylisoindolinium cation into the N-cyclohexylisoindolinium cation. Its structure was solved by 3D rotation electron diffraction (RED) from crystals of ca. 1 μm in size. The structure of ITQ-54 contains straight intersecting 20 × 14 × 12-ring channels along the three crystallographic axes and it is one of the few zeolites with extra-large channels in more than one direction. ITQ-54 has a framework density of 11.1 T atoms per 1000 Å 3, which is one of the lowest among the known zeolites. ITQ-54 wasmore » obtained together with GeO 2 as an impurity. A heavy liquid separation method was developed and successfully applied to remove this impurity from the zeolite. ITQ-54 is stable up to 600 °C and exhibits permanent porosity. The structure was further refined using powder X-ray diffraction (PXRD) data for both as-made and calcined samples.« less

Three-dimensional kinetic Monte Carlo simulations of cubic transition metal nitride thin film growth

NASA Astrophysics Data System (ADS)

Nita, F.; Mastail, C.; Abadias, G.

2016-02-01

A three-dimensional kinetic Monte Carlo (KMC) model has been developed and used to simulate the microstructure and growth morphology of cubic transition metal nitride (TMN) thin films deposited by reactive magnetron sputtering. Results are presented for the case of stoichiometric TiN, chosen as a representative TMN prototype. The model is based on a NaCl-type rigid lattice and includes deposition and diffusion events for both N and Ti species. It is capable of reproducing voids and overhangs, as well as surface faceting. Simulations were carried out assuming a uniform flux of incoming particles approaching the surface at normal incidence. The ballistic deposition model is parametrized with an interaction parameter r0 that mimics the capture distance at which incoming particles may stick on the surface, equivalently to a surface trapping mechanism. Two diffusion models are implemented, based on the different ways to compute the site-dependent activation energy for hopping atoms. The influence of temperature (300-500 K), deposition flux (0.1-100 monolayers/s), and interaction parameter r0 (1.5-6.0 Å) on the obtained growth morphology are presented. Microstructures ranging from highly porous, [001]-oriented straight columns with smooth top surface to rough columns emerging with different crystallographic facets are reproduced, depending on kinetic restrictions, deposited energy (seemingly captured by r0), and shadowing effect. The development of facets is a direct consequence of the diffusion model which includes an intrinsic (minimum energy-based) diffusion anisotropy, although no crystallographic diffusion anisotropy was explicitly taken into account at this stage. The time-dependent morphological evolution is analyzed quantitatively to extract the growth exponent β and roughness exponent α , as indicators of kinetic roughening behavior. For dense TiN films, values of α ≈0.7 and β =0.24 are obtained in good agreement with existing experimental data. At this stage a single lattice is considered but the KMC model will be extended further to address more complex mechanisms, such as anisotropic surface diffusion and grain boundary migration at the origin of the competitive columnar growth observed in polycrystalline TiN-based films.

Open Access Internet Resources for Nano-Materials Physics Education

NASA Astrophysics Data System (ADS)

Moeck, Peter; Seipel, Bjoern; Upreti, Girish; Harvey, Morgan; Garrick, Will

2006-05-01

Because a great deal of nano-material science and engineering relies on crystalline materials, materials physicists have to provide their own specific contributions to the National Nanotechnology Initiative. Here we briefly review two freely accessible internet-based crystallographic databases, the Nano-Crystallography Database (http://nanocrystallography.research.pdx.edu) and the Crystallography Open Database (http://crystallography.net). Information on over 34,000 full structure determinations are stored in these two databases in the Crystallographic Information File format. The availability of such crystallographic data on the internet in a standardized format allows for all kinds of web-based crystallographic calculations and visualizations. Two examples of which that are dealt with in this paper are: interactive crystal structure visualizations in three dimensions and calculations of lattice-fringe fingerprints for the identification of unknown nanocrystals from their atomic-resolution transmission electron microscopy images.

Role of a computer-generated three-dimensional laryngeal model in anatomy teaching for advanced learners.

PubMed

Tan, S; Hu, A; Wilson, T; Ladak, H; Haase, P; Fung, K

2012-04-01

(1) To investigate the efficacy of a computer-generated three-dimensional laryngeal model for laryngeal anatomy teaching; (2) to explore the relationship between students' spatial ability and acquisition of anatomical knowledge; and (3) to assess participants' opinion of the computerised model. Forty junior doctors were randomised to undertake laryngeal anatomy study supplemented by either a three-dimensional computer model or two-dimensional images. Outcome measurements comprised a laryngeal anatomy test, the modified Vandenberg and Kuse mental rotation test, and an opinion survey. Mean scores ± standard deviations for the anatomy test were 15.7 ± 2.0 for the 'three dimensions' group and 15.5 ± 2.3 for the 'standard' group (p = 0.7222). Pearson's correlation between the rotation test scores and the scores for the spatial ability questions in the anatomy test was 0.4791 (p = 0.086, n = 29). Opinion survey answers revealed significant differences in respondents' perceptions of the clarity and 'user friendliness' of, and their preferences for, the three-dimensional model as regards anatomical study. The three-dimensional computer model was equivalent to standard two-dimensional images, for the purpose of laryngeal anatomy teaching. There was no association between students' spatial ability and functional anatomy learning. However, students preferred to use the three-dimensional model.

I Situ Surface X-Ray Diffraction Studies of Electrochemically Deposited Monolayers

NASA Astrophysics Data System (ADS)

Yee, Dennis

1995-01-01

In situ x-ray diffraction has been used to determine the detailed atomic structure of electrochemically deposited lead, thallium, and bismuth monolayers on the silver (111) electrode surface. A review of our previously published lead and thallium monolayer results and the first in situ surface x-ray crystallographic study of the bismuth monolayer structure is presented. The crystallographic analysis of the bismuth Bragg rod intensities and the interference between the bismuth Bragg rod and silver crystal truncation rod scattering were used to determine the detailed atomic structure of the bismuth on silver (111) system at the liquid-solid interface. Our previous in situ x-ray diffraction studies showed that the bismuth monolayer lattice is rectangular and uniaxially incommensurate with the underlying hexagonal silver surface. A crystallographic analysis of the measured structure factor magnitudes reveals that the monolayer forms chains of atoms on the silver surface, similar to the bulk Bi(110)_{rh} plane, with a near neighbor distance of 3.12 +/- 0.01 A and a bond angle of 93 +/- 1^circ, consistent with the bulk Bi(110) _{rh} plane values. The crystallographic refinement also shows that the bismuth monolayer atoms are anisotropically disordered with a rms disorder of 0.25 +/- 0.03 A in the incommensurate direction and 0.09 +/- 0.03 A rms in the commnensurate direction. The interference between the Bi(20) Bragg rod and the Ag(10L)_ {h} crystal truncation rod scattering reveals that one set of bismuth atoms is registered near the bridge sites of the silver (111) surface while another set is registered near the 3-fold hollow sites. In addition, the Bi-Ag d-spacing (3.1 +/- 0.1 A) is found to be consistent with the bulk bismuth near neighbor distance. The bismuth z-direction rms disorder (1.01 +/- 0.08 A) is found to be dominated by the roughness of the underlying silver (sigma_{Ag} = 0.9 +/- 0.1 A rms). Using the estimated bismuth-bismuth spring constant of 1.41 +/- 0.07 eV/A^2 from our measured bismuth two-dimensional compressibility, two simple models are used to try and understand the origin of the anisotropic disorder. A simple two-dimensional isotropic thermal fluctuation model shows that thermal fluctuations are not large enough to account for all of the measured excess disorder in the incommensurate direction. A simple one-dimensional Frenkel-Kontorova model shows that the substrate-induced disorder can account for the anisotropic disorder, assuming a substrate sinusoidal potential strength of 0.35 +/- 0.02 eV.

Crystallographic site swapping of La3+ ion in BaA'LaTeO6 (A' = Na, K, Rb) double perovskite type compounds: diffraction and photoluminescence evidence for the site swapping.

PubMed

Phatak, R; Gupta, S K; Krishnan, K; Sali, S K; Godbole, S V; Das, A

2014-02-28

Double perovskite type compounds of the formula BaA'LaTeO6 (A' = Na, K, Rb) were synthesized by solid state route and their crystal structures were determined by Rietveld analysis using powder X-ray diffraction and neutron diffraction data. Na compound crystallizes in the monoclinic system with P2₁/n space group whereas, K and Rb compounds crystallize in Fm3m space group. All the three compounds show rock salt type ordering at B site. Crystal structure analysis shows that La ion occupies A site in Na compound whereas, it occupies B site in K and Rb compounds according to the general formula of AA'BB'O6 for a double perovskite type compound. Effect of this crystallographic site swapping of the La ion was also observed in the photoluminescence study by doping Eu(3+) in La(3+) site. The large decrease in the intensity of the electric dipole ((5)D0-(7)F2) transition in the Rb compound compared to the Na compound indicates that Eu(3+) ion resides in the centrosymmetric octahedral environment in the Rb compound.

Identical phase oscillators with global sinusoidal coupling evolve by Mobius group action.

PubMed

Marvel, Seth A; Mirollo, Renato E; Strogatz, Steven H

2009-12-01

Systems of N identical phase oscillators with global sinusoidal coupling are known to display low-dimensional dynamics. Although this phenomenon was first observed about 20 years ago, its underlying cause has remained a puzzle. Here we expose the structure working behind the scenes of these systems by proving that the governing equations are generated by the action of the Mobius group, a three-parameter subgroup of fractional linear transformations that map the unit disk to itself. When there are no auxiliary state variables, the group action partitions the N-dimensional state space into three-dimensional invariant manifolds (the group orbits). The N-3 constants of motion associated with this foliation are the N-3 functionally independent cross ratios of the oscillator phases. No further reduction is possible, in general; numerical experiments on models of Josephson junction arrays suggest that the invariant manifolds often contain three-dimensional regions of neutrally stable chaos.

Geometric actions for three-dimensional gravity

NASA Astrophysics Data System (ADS)

Barnich, G.; González, H. A.; Salgado-Rebolledo, P.

2018-01-01

The solution space of three-dimensional asymptotically anti-de Sitter or flat Einstein gravity is given by the coadjoint representation of two copies of the Virasoro group in the former and the centrally extended BMS3 group in the latter case. Dynamical actions that control these solution spaces are usually constructed by starting from the Chern–Simons formulation and imposing all boundary conditions. In this note, an alternative route is followed. We study in detail how to derive these actions from a group-theoretical viewpoint by constructing geometric actions for each of the coadjoint orbits, including the appropriate Hamiltonians. We briefly sketch relevant generalizations and potential applications beyond three-dimensional gravity.

Carbohydrate recognition by the rhamnose-binding lectin SUL-I with a novel three-domain structure isolated from the venom of globiferous pedicellariae of the flower sea urchin Toxopneustes pileolus.

PubMed

Hatakeyama, Tomomitsu; Ichise, Ayaka; Unno, Hideaki; Goda, Shuichiro; Oda, Tatsuya; Tateno, Hiroaki; Hirabayashi, Jun; Sakai, Hitomi; Nakagawa, Hideyuki

2017-08-01

The globiferous pedicellariae of the venomous sea urchin Toxopneustes pileolus contains several biologically active proteins. We have cloned the cDNA of one of the toxin components, SUL-I, which is a rhamnose-binding lectin (RBL) that acts as a mitogen through binding to carbohydrate chains on target cells. Recombinant SUL-I (rSUL-I) was produced in Escherichia coli cells, and its carbohydrate-binding specificity was examined with the glycoconjugate microarray analysis, which suggested that potential target carbohydrate structures are galactose-terminated N-glycans. rSUL-I exhibited mitogenic activity for murine splenocyte cells and toxicity against Vero cells. The three-dimensional structure of the rSUL-I/l-rhamnose complex was determined by X-ray crystallographic analysis at a 1.8 Å resolution. The overall structure of rSUL-I is composed of three distinctive domains with a folding structure similar to those of CSL3, a RBL from chum salmon (Oncorhynchus keta) eggs. The bound l-rhamnose molecules are mainly recognized by rSUL-I through hydrogen bonds between its 2-, 3-, and 4-hydroxy groups and Asp, Asn, and Glu residues in the binding sites, while Tyr and Ser residues participate in the recognition mechanism. It was also inferred that SUL-I may form a dimer in solution based on the molecular size estimated via dynamic light scattering as well as possible contact regions in its crystal structure. © 2017 The Protein Society.

A 2:1 co-crystal of p-nitro-benzoic acid and N,N'-bis-(pyridin-3-ylmeth-yl)ethanedi-amide: crystal structure and Hirshfeld surface analysis.

PubMed

Syed, Sabrina; Halim, Siti Nadiah Abdul; Jotani, Mukesh M; Tiekink, Edward R T

2016-01-01

The title 2:1 co-crystal, 2C7H5NO4·C14H14N4O2, in which the complete di-amide mol-ecule is generated by crystallographic inversion symmetry, features a three-mol-ecule aggregate sustained by hydroxyl-O-H⋯N(pyrid-yl) hydrogen bonds. The p-nitro-benzoic acid mol-ecule is non-planar, exhibiting twists of both the carb-oxy-lic acid and nitro groups, which form dihedral angles of 10.16 (9) and 4.24 (4)°, respectively, with the benzene ring. The di-amide mol-ecule has a conformation approximating to a Z shape, with the pyridyl rings lying to either side of the central, almost planar di-amide residue (r.m.s. deviation of the eight atoms being 0.025 Å), and forming dihedral angles of 77.22 (6)° with it. In the crystal, three-mol-ecule aggregates are linked into a linear supra-molecular ladder sustained by amide-N-H⋯O(nitro) hydrogen bonds and orientated along [10-4]. The ladders are connected into a double layer via pyridyl- and benzene-C-H⋯O(amide) inter-actions, which, in turn, are connected into a three-dimensional architecture via π-π stacking inter-actions between pyridyl and benzene rings [inter-centroid distance = 3.6947 (8) Å]. An evaluation of the Hirshfeld surfaces confirm the importance of inter-molecular inter-actions involving oxygen atoms as well as the π-π inter-actions.

Structure and energy of non-canonical basepairs: comparison of various computational chemistry methods with crystallographic ensembles.

PubMed

Panigrahi, Swati; Pal, Rahul; Bhattacharyya, Dhananjay

2011-12-01

Different types of non-canonical basepairs, in addition to the Watson-Crick ones, are observed quite frequently in RNA. Their importance in the three dimensional structure is not fully understood, but their various roles have been proposed by different groups. We have analyzed the energetics and geometry of 32 most frequently observed basepairs in the functional RNA crystal structures using different popular empirical, semi-empirical and ab initio quantum chemical methods and compared their optimized geometry with the crystal data. These basepairs are classified into three categories: polar, non-polar and sugar-mediated, depending on the types of atoms involved in hydrogen bonding. In case of polar basepairs, most of the methods give rise to optimized structures close to their initial geometry. The interaction energies also follow similar trends, with the polar ones having more attractive interaction energies. Some of the C-H...O/N hydrogen bond mediated non-polar basepairs are also found to be significantly stable in terms of their interaction energy values. Few polar basepairs, having amino or carboxyl groups not hydrogen bonded to anything, such as G:G H:W C, show large flexibility. Most of the non-polar basepairs, except A:G s:s T and A:G w:s C, are found to be stable; indicating C-H...O/N interaction also plays a prominent role in stabilizing the basepairs. The sugar mediated basepairs show variability in their structures, due to the involvement of flexible ribose sugar. These presumably indicate that the most of the polar basepairs along with few non-polar ones act as seed for RNA folding while few may act as some conformational switch in the RNA.

Uncovering the true nature of deformation microstructures using 3D analysis methods

NASA Astrophysics Data System (ADS)

Ferry, M.; Quadir, M. Z.; Afrin, N.; Xu, W.; Loeb, A.; Soe, B.; McMahon, C.; George, C.; Bassman, L.

2015-08-01

Three-dimensional electron backscatter diffraction (3D EBSD) has emerged as a powerful technique for generating 3D crystallographic information in reasonably large volumes of a microstructure. The technique uses a focused ion beam (FIB) as a high precision serial sectioning device for generating consecutive ion milled surfaces of a material, with each milled surface subsequently mapped by EBSD. The successive EBSD maps are combined using a suitable post-processing method to generate a crystallographic volume of the microstructure. The first part of this paper shows the usefulness of 3D EBSD for understanding the origin of various structural features associated with the plastic deformation of metals. The second part describes a new method for automatically identifying the various types of low and high angle boundaries found in deformed and annealed metals, particularly those associated with grains exhibiting subtle and gradual variations in orientation. We have adapted a 2D image segmentation technique, fast multiscale clustering, to 3D EBSD data using a novel variance function to accommodate quaternion data. This adaptation is capable of segmenting based on subtle and gradual variation as well as on sharp boundaries within the data. We demonstrate the excellent capabilities of this technique with application to 3D EBSD data sets generated from a range of cold rolled and annealed metals described in the paper.

The 2008 Lindau Nobel Laureate Meeting: Robert Huber, Chemistry 1988. Interview by Klaus J. Korak.

PubMed

Huber, Robert

2008-11-25

Robert Huber and his colleagues, Johann Deisenhofer and Hartmut Michel, elucidated the three-dimensional structure of the Rhodopseudomonas viridis photosynthetic reaction center. This membrane protein complex is a basic component of photosynthesis - a process fundamental to life on Earth - and for their work, Huber and his colleagues received the 1988 Nobel Prize in Chemistry. Because structural information is central to understanding virtually any biological process, Huber likens their discovery to "switching on the light" for scientists trying to understand photosynthesis. Huber marvels at the growth of structural biology since the time he entered the field, when crystallographers worked with hand-made instruments and primitive computers, and only "a handful" of crystallographers would meet annually in the Bavarian Alps. In the "explosion" of structural biology since his early days of research, Huber looks to the rising generation of scientists to solve the remaining mysteries in the field - such as the mechanisms that underlie protein folding. A strong proponent of science mentorship, Huber delights in meeting young researchers at the annual Nobel Laureate Meetings in Lindau, Germany. He hopes that among these young scientists is an "Einstein of biology" who, he says with a twinkle in his eye, "doesn't know it yet." The interview was conducted by JoVE co-founder Klaus J. Korak at the Lindau Nobel Laureate Meeting 2008 in Lindau, Germany.

The 2008 Lindau Nobel Laureate Meeting: Robert Huber, Chemistry 1988

PubMed Central

Huber, Robert

2008-01-01

Robert Huber and his colleagues, Johann Deisenhofer and Hartmut Michel, elucidated the three-dimensional structure of the Rhodopseudomonas viridis photosynthetic reaction center. This membrane protein complex is a basic component of photosynthesis – a process fundamental to life on Earth – and for their work, Huber and his colleagues received the 1988 Nobel Prize in Chemistry. Because structural information is central to understanding virtually any biological process, Huber likens their discovery to “switching on the light” for scientists trying to understand photosynthesis. Huber marvels at the growth of structural biology since the time he entered the field, when crystallographers worked with hand-made instruments and primitive computers, and only “a handful” of crystallographers would meet annually in the Bavarian Alps. In the “explosion” of structural biology since his early days of research, Huber looks to the rising generation of scientists to solve the remaining mysteries in the field – such as the mechanisms that underlie protein folding. A strong proponent of science mentorship, Huber delights in meeting young researchers at the annual Nobel Laureate Meetings in Lindau, Germany. He hopes that among these young scientists is an “Einstein of biology” who, he says with a twinkle in his eye, “doesn’t know it yet.” The interview was conducted by JoVE co-founder Klaus J. Korak at the Lindau Nobel Laureate Meeting 2008 in Lindau, Germany. PMID:19066525

Molecular structure of leucine aminopeptidase at 2. 7- angstrom resolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burley, S.K.; David, P.R.; Lipscomb, W.N.

1990-09-01

The three-dimensional structure of bovine lens leucine aminopeptidase complexed with bestatin, a slow-binding inhibitor, has been solved to 3.0-{angstrom} resolution by the multiple isomorphous replacement method with phase combination and density modification. In addition, the structure of the isomorphous native enzyme has been refined at 2.7-{angstrom} resolution, and the current crystallographic R factor is 0.169 for a model that includes the two zinc ions and all 487 amino acid residues comprising the asymmetric unit. The enzyme is physiologically active as a hexamer, which has 32 symmetry and is triangular in shape with a triangle edge length of 115 {angstrom} andmore » maximal thickness of 90 {angstrom}. The monomers are crystallographically equivalent and each is folded into two unequal {alpha}/{beta} domains connected by an {alpha}-helix to give a comma-like shape with approximate maximal dimensions of 90 x 55 x 55 {angstrom}{sup 3}. The secondary structural composition is 40% {alpha}-helix and 19% {beta}-strand. The active site also contains two positively charged residues, Lys-250 and Arg-336. The six active sites are themselves located in the interior of the hexamer, where they line a disk-shaped cavity of radius 15 {angstrom} and thickness 10 {angstrom}. Access to this cavity is provided by solvent channels that run along the twofold symmetry axes.« less

BioProgrammable One, Two, and Three Dimensional Materials

DTIC Science & Technology

2017-01-18

or three- dimensional architectures. The Mirkin group has used DNA-functionalized nanoparticles as “programmable atom equivalents (PAEs)” as material...with electron beam lithography to simultaneously control material structure at the nano- and macroscopic length scales. The Nguyen group has...synthesized and assembled small molecule-DNA hybrids (SMDHs) as part of programmable atom equivalents . The Rosi group identified design rules for using

Hydrothermal synthesis, crystal structure, and magnetic properties of a new inorganic vanadium(III) phosphate with a chain structure.

PubMed

Ferdov, Stanislav; Reis, Mario S; Lin, Zhi; Ferreira, Rute A Sá

2008-11-03

A new vanadium(III) phosphate, Na3V(OH)(HPO4)(PO4), has been synthesized by using mild hydrothermal conditions under autogeneous pressure. This material represents a very rare example of sodium vanadium(III) phosphate with a chain structure. The crystal structure has been determined by refinement of powder X-ray diffraction data, starting from the atomic coordinates of an isotypic compound, Na3Al(OH)(HPO4)(PO4), which was obtained under high temperature and high pressure. The phase crystallizes in monoclinic space group C2/m (No. 12) with lattice parameters a = 15.423(9) A, b = 7.280(0) A, c = 7.070(9) A, beta = 96.79(7) degrees, V = 788.3(9) A(3), and Z = 4. The structure consists of one-dimensional chains composed of corner-sharing VO5(OH) octahedra running along the b direction. They are decorated by isolated PO4 and HPO4 tetrahedra sharing two of their corners with the ones of the vanadium octahedra. The interconnection between the chains is assured by three crystallographically distinct Na(+) cations. Magnetic investigation confirms the 3+ oxidation state of the vanadium ions and reveals an antiferromagnetic arrangement between those ions through the chain.

High-level Expression Purification Crystallization and Preliminary X-ray Crystallographic Studies of the Receptor Binding Domain of botulinum neurotoxin Serotype D

DOE Office of Scientific and Technical Information (OSTI.GOV)

Y Zhang; X Gao; G Buchko

2011-12-31

Botulinum neurotoxins (BoNTs) are highly toxic proteins for humans and animals that are responsible for the deadly neuroparalytic disease botulism. Here, details of the expression and purification of the receptor-binding domain (HCR) of BoNT/D in Escherichia coli are presented. Using a codon-optimized cDNA, BoNT/D{_}HCR was expressed at a high level (150-200 mg per litre of culture) in the soluble fraction. Following a three-step purification protocol, very pure (>98%) BoNT/D{_}HCR was obtained. The recombinant BoNT/D{_}HCR was crystallized and the crystals diffracted to 1.65 {angstrom} resolution. The crystals belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 60.8,more » b = 89.7, c = 93.9 {angstrom}. Preliminary crystallographic data analysis revealed the presence of one molecule in the asymmetric unit.« less

High-level expression, purification, crystallization and preliminary X-ray crystallographic studies of the receptor-binding domain of botulinum neurotoxin serotype D

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Y.; Robinson, H.; Gao, X.

2010-12-01

Botulinum neurotoxins (BoNTs) are highly toxic proteins for humans and animals that are responsible for the deadly neuroparalytic disease botulism. Here, details of the expression and purification of the receptor-binding domain (HCR) of BoNT/D in Escherichia coli are presented. Using a codon-optimized cDNA, BoNT/D{_}HCR was expressed at a high level (150-200 mg per litre of culture) in the soluble fraction. Following a three-step purification protocol, very pure (>98%) BoNT/D{_}HCR was obtained. The recombinant BoNT/D{_}HCR was crystallized and the crystals diffracted to 1.65 {angstrom} resolution. The crystals belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 60.8,more » b = 89.7, c = 93.9 {angstrom}. Preliminary crystallographic data analysis revealed the presence of one molecule in the asymmetric unit.« less

Insulin Mimetic Peptide Disrupts the Primary Binding Site of the Insulin Receptor*

PubMed Central

Lawrence, Callum F.; Margetts, Mai B.; Menting, John G.; Smith, Nicholas A.; Smith, Brian J.; Ward, Colin W.; Lawrence, Michael C.

2016-01-01

Sets of synthetic peptides that interact with the insulin receptor ectodomain have been discovered by phage display and reported in the literature. These peptides were grouped into three classes termed Site 1, Site 2, and Site 3 based on their mutual competition of binding to the receptor. Further refinement has yielded, in particular, a 36-residue Site 2-Site 1 fusion peptide, S519, that binds the insulin receptor with subnanomolar affinity and exhibits agonist activity in both lipogenesis and glucose uptake assays. Here, we report three-dimensional crystallographic detail of the interaction of the C-terminal, 16-residue Site 1 component (S519C16) of S519 with the first leucine-rich repeat domain (L1) of the insulin receptor. Our structure shows that S519C16 binds to the same site on the L1 surface as that occupied by a critical component of the primary binding site, namely the helical C-terminal segment of the insulin receptor α-chain (termed αCT). In particular, the two phenylalanine residues within the FYXWF motif of S519C16 are seen to engage the insulin receptor L1 domain surface in a fashion almost identical to the respective αCT residues Phe701 and Phe705. The structure provides a platform for the further development of peptidic and/or small molecule agents directed toward the insulin receptor and/or the type 1 insulin-like growth factor receptor. PMID:27281820

A molecular dynamics study of the three-dimensional model of human synovial fluid phospholipase A2--transition state mimic complexes.

PubMed

Hariprasad, V; Kulkarni, V M

1996-01-01

Different modes of binding of transition state mimics: amide, phosphonate and difluoro ketone, to human synovial fluid phospholipase A2 (HSF PLA2) are studies by molecular dynamics simulations computed in solvent. The results are analysed in the light of primary binding sites. Hydrogen bonding interaction plays an important role for amino acids such as Gly32, Val30, and Glu55, apart from the well known active site residues viz Asp48, Gly25, Gly29, Gly31, His27, His47, Lys62, Phe23, Asn114 and Tyr112. In addition, the hydrogen bonding interaction between Sn-1 tetrahedral phosphonate group of amide and difluoro ketone inhibitors and crystallographic water molecules (H2O 523, H2O 524 and H2O 401) seems to have a significant role. Many of the active site charged residues display considerable movement upon ligand binding. The structural effects of ligand binding were analyzed from RMS deviations of C alpha in the resulting energy-minimized average structures of the receptor-ligand complexes. The values of the RMS deviations differ among the HSF PLA2s, in a pattern that is not the same for the three complexes. This suggests that ligands with different pharmacological efficacies induce different types of conformational changes of the receptor. Our active-orientation model is, at least qualitatively, consistent with experimental data and should be useful for the rational design of more potent inhibitors.

High pressure synthesis and magnetic studies of quasi one dimensional systems Sr{sub n-1} Cu{sub n+1} O{sub 2n} (n=3,5)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Azuma, M.; Hiroi, Z.; Takano, M.

1994-12-31

SrCu{sub 2}O{sub 3} and Sr{sub 2}Cu{sub 3}O{sub 5} containing two-leg and three-leg S=1/2 ladders made of antiferromagnetic Cu-O-Cu linear bonds, respectively, were synthesized at high pressure, and their crystallographic and magnetic properties were investigated. Both susceptibility and T{sub 1} data of NMR revealed the existence of a large spin gap only for SrCu{sub 2}O{sub 3}. Superconductivity, which had been predicted theoretically for carrier-doped SrCu{sub 2}O{sub 3} could not be realized although partial substitution of La{sup 3+} for Sr{sup 2+} seemed to be carried out successfully. Electron carriers injected seems to remain localized.

VO{sub 2} precipitates for self-protected optical surfaces

DOEpatents

Gea, L.A.; Boatner, L.A.

1999-03-23

A method for forming crystallographically coherent precipitates of vanadium dioxide in the near-surface region of sapphire and the resulting product is disclosed. Ions of vanadium and oxygen are stoichiometrically implanted into a sapphire substrate (Al{sub 2}O{sub 3}), and subsequently annealed to form vanadium dioxide precipitates in the substrate. The embedded VO{sub 2} precipitates, which are three-dimensionally oriented with respect to the crystal axes of the Al{sub 2}O{sub 3} host lattice, undergo a first-order monoclinic-to-tetragonal (and also semiconducting-to-metallic) phase transition at ca. 77 C. This transformation is accompanied by a significant variation in the optical transmission of the implanted region and results in the formation of an optically active, thermally ``switchable`` surface region on Al{sub 2}O{sub 3}. 5 figs.

Lattice engineering through nanoparticle–DNA frameworks

DOE PAGES

Tian, Ye; Zhang, Yugang; Wang, Tong; ...

2016-02-22

Advances in self-assembly over the past decade have demonstrated that nano- and microscale particles can be organized into a large diversity of ordered three-dimensional (3D) lattices. However, the ability to generate different desired lattice types from the same set of particles remains challenging. Here, we show that nanoparticles can be assembled into crystalline and open 3D frameworks by connecting them through designed DNA-based polyhedral frames. The geometrical shapes of the frames, combined with the DNA-assisted binding properties of their vertices, facilitate the well-defined topological connections between particles in accordance with frame geometry. With this strategy, different crystallographic lattices using themore » same particles can be assembled by introduction of the corresponding DNA polyhedral frames. As a result, this approach should facilitate the rational assembly of nanoscale lattices through the design of the unit cell.« less

Synthesis, characterization and crystal structure of a 1D thiocyanato bridged [Cu(en)2Zn(NCS)4]ṡH2O. Comparison of the three structures with the same [Cu(en)2Zn(NCS)4] unit - different in structural terms

NASA Astrophysics Data System (ADS)

Wrzeszcz, Grzegorz; Muzioł, Tadeusz M.; Tereba, Natalia

2015-03-01

In this paper we report the synthesis method and the structure of a one-dimensional thiocyanato bridged heterometallic compound, [Cu(en)2Zn(NCS)4]ṡH2O (1). Moreover, we compare the structure of (1) with the previously described structures of [Cu(en)2Zn(NCS)4]ṡ0.5H2O (2) and [Cu(en)2Zn(NCS)4]ṡCH3CN (3) Pryma et al. (2003) [7]. The compound (1) has been characterized by thermal decomposition, IR, Vis and EPR spectra, and magnetic studies. Structure has been determined by X-ray analysis. Described coordination polymer crystallizes in the orthorhombic Cmcm space group with a = 12.414(2), b = 10.3276(14), c = 14.967(2) Å, α = β = γ = 90°, V = 1918.8(5) Å3 and Z = 4. Each distorted tetrahedral zinc(II) centre (with N-bonded NCS-) links two tetragonally distorted octahedral copper(II) centres by two end-to-end thiocyanato bridges and vice versa forming a zigzag type of CuZn chain. The structures of (1), (2) and (3) differ in crystallographic system, space group and/or CuZn chain type as well as in details. Variable temperature magnetic susceptibility measurements show very weak antiferromagnetic interactions between the paramagnetic copper(II) ions for compound (1).

Crystallographic alignment of high-density gallium nitride nanowire arrays.

PubMed

Kuykendall, Tevye; Pauzauskie, Peter J; Zhang, Yanfeng; Goldberger, Joshua; Sirbuly, Donald; Denlinger, Jonathan; Yang, Peidong

2004-08-01

Single-crystalline, one-dimensional semiconductor nanostructures are considered to be one of the critical building blocks for nanoscale optoelectronics. Elucidation of the vapour-liquid-solid growth mechanism has already enabled precise control over nanowire position and size, yet to date, no reports have demonstrated the ability to choose from different crystallographic growth directions of a nanowire array. Control over the nanowire growth direction is extremely desirable, in that anisotropic parameters such as thermal and electrical conductivity, index of refraction, piezoelectric polarization, and bandgap may be used to tune the physical properties of nanowires made from a given material. Here we demonstrate the use of metal-organic chemical vapour deposition (MOCVD) and appropriate substrate selection to control the crystallographic growth directions of high-density arrays of gallium nitride nanowires with distinct geometric and physical properties. Epitaxial growth of wurtzite gallium nitride on (100) gamma-LiAlO(2) and (111) MgO single-crystal substrates resulted in the selective growth of nanowires in the orthogonal [1\\[Evec]0] and [001] directions, exhibiting triangular and hexagonal cross-sections and drastically different optical emission. The MOCVD process is entirely compatible with the current GaN thin-film technology, which would lead to easy scale-up and device integration.

Stereoselective green synthesis and molecular structures of highly functionalized spirooxindole-pyrrolidine hybrids - A combined experimental and theoretical investigation

NASA Astrophysics Data System (ADS)

Kumar, Raju Suresh; Almansour, Abdulrahman I.; Arumugam, Natarajan; Soliman, Saied M.; Kumar, Raju Ranjith; Altaf, Mohammad; Ghabbour, Hazem A.; Krishnamoorthy, Bellie Sundaram

2018-01-01

Highly functionalized spirooxindole-pyrrolidine hybrids have been synthesized stereoselectively through a [3 + 2] cycloaddition strategy in an ionic liquid, 1-butyl-3-methylimidazolium bromide ([bmim]Br). The structure of these spiro heterocyclic hybrids was elucidated using one and two dimensional NMR spectroscopy, single crystal X-ray crystallographic studies and Density Functional Theory (DFT) calculations. The calculated geometric parameters are in good agreement with the experimental data obtained from the X-ray structures. The Natural Bond Orbital (NBO) calculations on these molecules confirm the electron rich carbonyl oxygen and electron deficient NH groups. The 1H and 13C NMR chemical shifts calculated using GIAO method are in good agreement with the experimental data. The DFT computed polarizability values also suggest the possible NLO activity of these molecules.

Effects of 3 dimensional crystal geometry and orientation on 1D and 2D time-scale determinations of magmatic processes using olivine and orthopyroxene

NASA Astrophysics Data System (ADS)

Shea, Thomas; Krimer, Daniel; Costa, Fidel; Hammer, Julia

2014-05-01

One of the achievements in recent years in volcanology is the determination of time-scales of magmatic processes via diffusion in minerals and its addition to the petrologists' and volcanologists' toolbox. The method typically requires one-dimensional modeling of randomly cut crystals from two-dimensional thin sections. Here we address the question whether using 1D (traverse) or 2D (surface) datasets exploited from randomly cut 3D crystals introduces a bias or dispersion in the time-scales estimated, and how this error can be improved or eliminated. Computational simulations were performed using a concentration-dependent, finite-difference solution to the diffusion equation in 3D. The starting numerical models involved simple geometries (spheres, parallelepipeds), Mg/Fe zoning patterns (either normal or reverse), and isotropic diffusion coefficients. Subsequent models progressively incorporated more complexity, 3D olivines possessing representative polyhedral morphologies, diffusion anisotropy along the different crystallographic axes, and more intricate core-rim zoning patterns. Sections and profiles used to compare 1, 2 and 3D diffusion models were selected to be (1) parallel to the crystal axes, (2) randomly oriented but passing through the olivine center, or (3) randomly oriented and sectioned. Results show that time-scales estimated on randomly cut traverses (1D) or surfaces (2D) can be widely distributed around the actual durations of 3D diffusion (~0.2 to 10 times the true diffusion time). The magnitude over- or underestimations of duration are a complex combination of the geometry of the crystal, the zoning pattern, the orientation of the cuts with respect to the crystallographic axes, and the degree of diffusion anisotropy. Errors on estimated time-scales retrieved from such models may thus be significant. Drastic reductions in the uncertainty of calculated diffusion times can be obtained by following some simple guidelines during the course of data collection (i.e. selection of crystals and concentration profiles, acquisition of crystallographic orientation data), thus allowing derivation of robust time-scales.

Learning the Cell Structures with Three-Dimensional Models: Students' Achievement by Methods, Type of School and Questions' Cognitive Level

NASA Astrophysics Data System (ADS)

Lazarowitz, Reuven; Naim, Raphael

2013-08-01

The cell topic was taught to 9th-grade students in three modes of instruction: (a) students "hands-on," who constructed three-dimensional cell organelles and macromolecules during the learning process; (b) teacher demonstration of the three-dimensional model of the cell structures; and (c) teaching the cell topic with the regular learning material in an expository mode (which use one- or two-dimensional cell structures as are presented in charts, textbooks and microscopic slides). The sample included 669, 9th-grade students from 25 classes who were taught by 22 Biology teachers. Students were randomly assigned to the three modes of instruction, and two tests in content knowledge in Biology were used. Data were treated with multiple analyses of variance. The results indicate that entry behavior in Biology was equal for all the study groups and types of schools. The "hands-on" learning group who build three-dimensional models through the learning process achieved significantly higher on academic achievements and on the high and low cognitive questions' levels than the other two groups. The study indicates the advantages students may have being actively engaged in the learning process through the "hands-on" mode of instruction/learning.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schafer, Marion; Bobev, Svilen

This paper presents results from our exploratory work in the systems K-Cd-Ge, Rb-Cd-Ge, and Cs-Cd-Ge, which yielded the novel type-I clathrates with refined compositions K 8Cd 3.77(7)Ge 42.23, Rb 8Cd 3.65(7)Ge 42.35, and Cs 7.80(1)Cd 3.65(6)Ge 42.35. The three compounds represent rare examples of clathrates of germanium with the alkali metals, where a d 10 element substitutes a group 14 element. The three structures, established by single-crystal X-ray diffraction, indicate that the framework-building Ge atoms are randomly substituted by Cd atoms on only one of the three possible crystallographic sites. Furthermore, this and several other details of the crystal chemistrymore » are elaborated.« less

The relationship between facial 3-D morphometry and the perception of attractiveness in children.

PubMed

Ferrario, V F; Sforza, C; Poggio, C E; Colombo, A; Tartaglia, G

1997-01-01

The aim of this investigation was to determine whether attractive children differ in their three-dimensional facial characteristics from nonattractive children of the same age, race, and sex. The facial characteristics of 36 boys and 44 girls aged 8 to 9 years were investigated. Frontal and profile photographs were analyzed independently by 21 judges, and, for each view, four groups were obtained: attractive boys, nonattractive boys, attractive girls, and nonattractive girls. For each child, the three-dimensional coordinates of 16 standardized soft tissue facial landmarks were automatically collected using an infrared system and used to calculate several three-dimensional angles, linear distances, and linear distance ratios. Mean values were computed in the eight groups, and attractive and nonattractive children were compared within sex and view. Most children received a different esthetic evaluation in the separate frontal and profile assessments; concordance in both attractive and nonattractive groups was only 50%. Moreover, three-dimensional facial morphometry was not able to separate attractive and nonattractive children.

Synthesis and crystallographic characterization of a mononuclear cobalt(III) complex possessing both thiol­ate and thio­ether donors: reactivity of an thiol­ate-bridged penta­nuclear Co2Ag3 complex with iodo­methane

PubMed Central

Fukuda, Yosuke; Yoshinari, Nobuto; Konno, Takumi

2017-01-01

Treatment of an S-bridged penta­nuclear AgI 3CoIII 2 complex, [Ag3{Co(L)}2]3+ [L 3– = N(CH2NHCH2CH2S−)3], in which two tris­(thiol­ate)-type mononuclear CoIII units ([Co(L)]) are bridged by three AgI ions through S atoms, with iodo­methane (CH3I) gave a new CoIII mononuclear complex, [Co(LMe2)]2+ [LMe2 − = N(CH2NHCH2CH2S−)(CH2NHCH2CH2SCH3)2], systematic name: {2-[(bis{[2-(methylsulfanyl)ethyl]aminomethyl}aminomethyl)amino]ethanethiolato}cobalt(III) bis(hexafluoridophosphate). This cationic complex was crystallized with PF6 − anions to form the title compound, [Co(LMe2)](PF6)2. In the [Co(LMe2)]2+ cation, two of three thiol­ate groups in [Co(L)] are methyl­ated while one thiol­ate group remains unreacted. Although a total of eight stereoisomers are possible for [Co(LMe2)]2+, only a pair of enanti­omers {ΛRR- and ΔSS-[Co(LMe2)]2+} are selectively formed. In the crystal, the complex cations and the PF­6 − anions are connected through weak N—H⋯F, C—H⋯F and C—H⋯S hydrogen bonds into a three-dimensional structure. Two F atoms in one PF6 anion are disordered over two sets of sites with refined occupancies of 0.61 (4) and 0.39 (4) and two F atoms in the other PF6 − anion are disordered over two sets of sites with occupancies of 0.5. PMID:28529774

Preoperative planning and real-time assisted navigation by three-dimensional individual digital model in partial nephrectomy with three-dimensional laparoscopic system.

PubMed

Wang, Dongwen; Zhang, Bin; Yuan, Xiaobin; Zhang, Xuhui; Liu, Chen

2015-09-01

To evaluate the feasibility and effectiveness of preoperative planning and real-time assisted surgical navigation for three-dimensional laparoscopic partial nephrectomy under the guidance of three-dimensional individual digital model (3D-IDM) created using three-dimensional medical image reconstructing and guiding system (3D-MIRGS). Between May 2012 and February 2014, 44 patients with cT1 renal tumors underwent retroperitoneal laparoscopic partial nephrectomy (LPN) using a three-dimensional laparoscopic system. The 3D-IDMs were created using the 3D-MIRGS in 21 patients (3D-MIRGS group) between February 2013 and February 2014. After preoperative planning, operations were real-time assisted using composite 3D-IDMs, which were fused with two-dimensional retrolaparoscopic images. The remaining 23 patients underwent surgery without 3D-MIRGS between May 2012 and February 2013; 14 of these patients were selected as a control group. Preoperative aspects and dimensions used for an anatomical score, "radius; exophytic/endophytic; nearness; anterior/posterior; location" nephrometry score, tumor size, operative time (OT), segmental renal artery clamping (SRAC) time, estimated blood loss (EBL), postoperative hospitalization, the preoperative serum creatinine level and ipsilateral glomerular filtration rate (GFR), as well as postoperative 6-month data were compared between groups. All the SRAC procedures were technically successful, and each targeted tumor was excised completely; final pathological margin results were negative. The OT was shorter (159.0 vs. 193.2 min; p < 0.001), and EBL (148.1 vs. 176.1 mL; p < 0.001) was reduced in the 3D-MIRGS group compared with controls. No statistically significant differences in SRAC time or postoperative hospitalization were found between the groups. Neither group showed any statistically significant increases in serum creatinine level or decreases in ipsilateral GFR postoperatively. Preoperative planning and real-time assisted surgical navigation using the 3D-IDM reconstructed from 3D-MIRGS and combined with the 3D laparoscopic system can facilitate LPN and result in precise SRAC and accurate excision of tumor that is both effective and safe.

Three new alkaloids from Xylopia vielana and their antiinflammatory activities.

PubMed

Guo, Yi-Gong; Ding, Yun-He; Wu, Guo-Jing; Zhu, Sheng-Lan; Sun, Yuan-Fang; Yan, Shi-Kai; Qian, Feng; Jin, Hui-Zi; Zhang, Wei-Dong

2018-02-05

Three new aporphine alkaloids, xylopialoids A-C (1-3), along with three known aporphine alkioids (4-6) and three other known compounds (7-9) were isolated from the roots of Xylopia vielana. Among these three new aporphine alkaloids, xylopialoid C (3) showed a special carbamido group directly connected to the nitrogen. The chemical structures of these nine compounds were determined by a combination of 1D and 2D NMR, MS, CD spectrum and Cu Kα X-ray crystallographic analyses. All these six alkaloids were firstly tested for the inhibitory activities against the production of NO in RAW264.7 cells stimulated by lipopolysaccharide (LPS). Among these compounds, 4 showed a potential inhibitory activity against the production of nitric oxide with IC 50 value of 1.39 μM. Copyright © 2018. Published by Elsevier B.V.

Anisotropic Fermi surface and quantum limit transport in high mobility three-dimensional Dirac semimetal Cd 3As 2

DOE PAGES

Zhao, Yanfei; Liu, Haiwen; Zhang, Chenglong; ...

2015-09-16

Three-dimensional (3D) topological Dirac semimetals have a linear dispersion in the 3D momentum space and are viewed as the 3D analogues of graphene. Here, we report angle dependent magnetotransport on the newly revealed Cd 3As 2 single crystals and clearly show how the Fermi surface evolves with crystallographic orientations. Remarkably, when the magnetic field lies in [112] or [44more » $$\\bar{1}$$] axis, magnetoresistance oscillations with only single period are present. However, the oscillation shows double periods when the field is applied along [1$$\\bar{1}$$0] direction. Moreover, aligning the magnetic field at certain directions also gives rise to double period oscillations. We attribute the observed anomalous oscillation behavior to the sophisticated geometry of Fermi surface and illustrate a complete 3D Fermi surfaces with two nested anisotropic ellipsoids around the Dirac points. Additionally, a sub-millimeter mean free path at 6 K is found in Cd 3As 2 crystals, indicating ballistic transport in this material. By measuring the magnetoresistance up to 60 T, we reach the quantum limit (n = 1 Landau level) at about 43 T. Lastly, these results improve the knowledge of the Dirac semimetal material Cd 3As 2, and also pave the way for proposing new electronic applications based on 3D Dirac materials.« less

Visualizing One-Dimensional Electronic States and their Scattering in Semi-conducting Nanowires

NASA Astrophysics Data System (ADS)

Beidenkopf, Haim; Reiner, Jonathan; Norris, Andrew; Nayak, Abhay Kumar; Avraham, Nurit; Shtrikman, Hadas

One-dimensional electronic systems constitute a fascinating playground for the emergence of exotic electronic effects and phases, within and beyond the Tomonaga-Luttinger liquid paradigm. More recently topological superconductivity and Majorana modes were added to that long list of phenomena. We report scanning tunneling microscopy and spectroscopy measurements conducted on pristine, epitaxialy grown InAs nanowires. We resolve the 1D electronic band structure manifested both via Van-Hove singularities in the local density-of-states, as well as by the quasi-particle interference patterns, induced by scattering from surface impurities. By studying the scattering of the one-dimensional electronic states off various scatterers, including crystallographic defects and the nanowire end, we identify new one-dimensional relaxation regimes and yet unexplored effects of interactions. Some of these may bear implications on the topological superconducting state and Majorana modes therein. The authors acknowledge support from the Israeli Science Foundation (ISF).

Chiral tunneling in gated inversion symmetric Weyl semimetal.

PubMed

Bai, Chunxu; Yang, Yanling; Chang, Kai

2016-02-18

Based on the chirality-resolved transfer-matrix method, we evaluate the chiral transport tunneling through Weyl semimetal multi-barrier structures created by periodic gates. It is shown that, in sharp contrast to the cases of three dimensional normal semimetals, the tunneling coefficient as a function of incident angle shows a strong anisotropic behavior. Importantly, the tunneling coefficients display an interesting periodic oscillation as a function of the crystallographic angle of the structures. With the increasement of the barriers, the tunneling current shows a Fabry-Perot type interferences. For superlattice structures, the fancy miniband effect has been revealed. Our results show that the angular dependence of the first bandgap can be reduced into a Lorentz formula. The disorder suppresses the oscillation of the tunneling conductance, but would not affect its average amplitude. This is in sharp contrast to that in multi-barrier conventional semiconductor structures. Moreover, numerical results for the dependence of the angularly averaged conductance on the incident energy and the structure parameters are presented and contrasted with those in two dimensional relativistic materials. Our work suggests that the gated Weyl semimetal opens a possible new route to access to new type nanoelectronic device.

Lysine N[superscript zeta]-Decarboxylation Switch and Activation of the [beta]-Lactam Sensor Domain of BlaR1 Protein of Methicillin-resistant Staphylococcus aureus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borbulevych, Oleg; Kumarasiri, Malika; Wilson, Brian

The integral membrane protein BlaR1 of methicillin-resistant Staphylococcus aureus senses the presence of {beta}-lactam antibiotics in the milieu and transduces the information to the cytoplasm, where the biochemical events that unleash induction of antibiotic resistance mechanisms take place. We report herein by two-dimensional and three-dimensional NMR experiments of the sensor domain of BlaR1 in solution and by determination of an x-ray structure for the apo protein that Lys-392 of the antibiotic-binding site is posttranslationally modified by N{sup {zeta}}-carboxylation. Additional crystallographic and NMR data reveal that on acylation of Ser-389 by antibiotics, Lys-392 experiences N{sup {zeta}}-decarboxylation. This unique process, termed themore » lysine N{sup {zeta}}-decarboxylation switch, arrests the sensor domain in the activated ('on') state, necessary for signal transduction and all the subsequent biochemical processes. We present structural information on how this receptor activation process takes place, imparting longevity to the antibiotic-receptor complex that is needed for the induction of the antibiotic-resistant phenotype in methicillin-resistant S. aureus.« less

Chiral tunneling in gated inversion symmetric Weyl semimetal

PubMed Central

Bai, Chunxu; Yang, Yanling; Chang, Kai

2016-01-01

Based on the chirality-resolved transfer-matrix method, we evaluate the chiral transport tunneling through Weyl semimetal multi-barrier structures created by periodic gates. It is shown that, in sharp contrast to the cases of three dimensional normal semimetals, the tunneling coefficient as a function of incident angle shows a strong anisotropic behavior. Importantly, the tunneling coefficients display an interesting periodic oscillation as a function of the crystallographic angle of the structures. With the increasement of the barriers, the tunneling current shows a Fabry-Perot type interferences. For superlattice structures, the fancy miniband effect has been revealed. Our results show that the angular dependence of the first bandgap can be reduced into a Lorentz formula. The disorder suppresses the oscillation of the tunneling conductance, but would not affect its average amplitude. This is in sharp contrast to that in multi-barrier conventional semiconductor structures. Moreover, numerical results for the dependence of the angularly averaged conductance on the incident energy and the structure parameters are presented and contrasted with those in two dimensional relativistic materials. Our work suggests that the gated Weyl semimetal opens a possible new route to access to new type nanoelectronic device. PMID:26888491

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

NASA Astrophysics Data System (ADS)

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

2016-11-01

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

Shaping highly regular glass architectures: A lesson from nature

PubMed Central

Schoeppler, Vanessa; Reich, Elke; Vacelet, Jean; Rosenthal, Martin; Pacureanu, Alexandra; Rack, Alexander; Zaslansky, Paul; Zolotoyabko, Emil; Zlotnikov, Igor

2017-01-01

Demospongiae is a class of marine sponges that mineralize skeletal elements, the glass spicules, made of amorphous silica. The spicules exhibit a diversity of highly regular three-dimensional branched morphologies that are a paradigm example of symmetry in biological systems. Current glass shaping technology requires treatment at high temperatures. In this context, the mechanism by which glass architectures are formed by living organisms remains a mystery. We uncover the principles of spicule morphogenesis. During spicule formation, the process of silica deposition is templated by an organic filament. It is composed of enzymatically active proteins arranged in a mesoscopic hexagonal crystal-like structure. In analogy to synthetic inorganic nanocrystals that show high spatial regularity, we demonstrate that the branching of the filament follows specific crystallographic directions of the protein lattice. In correlation with the symmetry of the lattice, filament branching determines the highly regular morphology of the spicules on the macroscale. PMID:29057327

Crystallization of PTP Domains.

PubMed

Levy, Colin; Adams, James; Tabernero, Lydia

2016-01-01

Protein crystallography is the most powerful method to obtain atomic resolution information on the three-dimensional structure of proteins. An essential step towards determining the crystallographic structure of a protein is to produce good quality crystals from a concentrated sample of purified protein. These crystals are then used to obtain X-ray diffraction data necessary to determine the 3D structure by direct phasing or molecular replacement if the model of a homologous protein is available. Here, we describe the main approaches and techniques to obtain suitable crystals for X-ray diffraction. We include tools and guidance on how to evaluate and design the protein construct, how to prepare Se-methionine derivatized protein, how to assess the stability and quality of the sample, and how to crystallize and prepare crystals for diffraction experiments. While general strategies for protein crystallization are summarized, specific examples of the application of these strategies to the crystallization of PTP domains are discussed.

The structure of Escherichia coli signal recognition particle revealed by scanning transmission electron microscopy.

PubMed

Mainprize, Iain L; Beniac, Daniel R; Falkovskaia, Elena; Cleverley, Robert M; Gierasch, Lila M; Ottensmeyer, F Peter; Andrews, David W

2006-12-01

Structural studies on various domains of the ribonucleoprotein signal recognition particle (SRP) have not converged on a single complete structure of bacterial SRP consistent with the biochemistry of the particle. We obtained a three-dimensional structure for Escherichia coli SRP by cryoscanning transmission electron microscopy and mapped the internal RNA by electron spectroscopic imaging. Crystallographic data were fit into the SRP reconstruction, and although the resulting model differed from previous models, they could be rationalized by movement through an interdomain linker of Ffh, the protein component of SRP. Fluorescence resonance energy transfer experiments determined interdomain distances that were consistent with our model of SRP. Docking our model onto the bacterial ribosome suggests a mechanism for signal recognition involving interdomain movement of Ffh into and out of the nascent chain exit site and suggests how SRP could interact and/or compete with the ribosome-bound chaperone, trigger factor, for a nascent chain during translation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, A. D.; Pham, Q.; Fortin, E. V.

Here, three-dimensional x-ray tomography (XRT) provides a nondestructive technique to characterize the size, shape, and location of damage in dynamically loaded metals. A shape-fitting method comprising the inertia tensors of individual damage sites was applied to study differences of spall damage development in face-centered-cubic (FCC) and hexagonal-closed-packed (HCP) multicrystals and for a suite of experiments on high-purity copper to examine the influence of loading kinetics on the spall damage process. Applying a volume-weighted average to the best-fit ellipsoidal aspect-ratios allows a quantitative assessment for determining the extent of damage coalescence present in a shocked metal. It was found that incipientmore » transgranular HCP spall damage nucleates in a lenticular shape and is heavily oriented along particular crystallographic slip directions. In polycrystalline materials, shape distributions indicate that a decrease in the tensile loading rate leads to a transition to coalesced damage dominance and that the plastic processes driving void growth are time dependent.« less

Characterizing the boundary lateral to the shear direction of deformation twins in magnesium

DOE PAGES

Liu, Y.; Li, N.; Shao, S.; ...

2016-06-01

The three-dimensional nature of twins, especially the atomic structures and motion mechanisms of the boundary lateral to the shear direction of the twin, has never been characterized at the atomic level, because such boundary is, in principle, crystallographically unobservable. We thus refer to it here as the dark side of the twin. Here, using high-resolution transmission electron microscopy and atomistic simulations, we characterize the dark side of {101 ⁻2} deformation twins in magnesium. It is found that the dark side is serrated and comprised of {101 ⁻2} coherent twin boundaries and semi-coherent twist prismatic–prismatic {211 ⁻0} boundaries that control twinmore » growth. The conclusions we find in this work apply to the same twin mode in other hexagonal close-packed materials, and the conceptual ideas discussed here should hold for all twin modes in crystalline materials.« less

Crystal structures of two bis-(iodo-meth-yl)benzene derivatives: similarities and differences in the crystal packing.

PubMed

McAdam, C John; Hanton, Lyall R; Moratti, Stephen C; Simpson, Jim

2015-12-01

The isomeric derivatives 1,2-bis-(iodo-meth-yl)benzene, (I), and 1,3-bis-(iodo-meth-yl)benzene (II), both C8H8I2, were prepared by metathesis from their di-bromo analogues. The ortho-derivative, (I), lies about a crystallographic twofold axis that bis-ects the C-C bond between the two iodo-methyl substituents. The packing in (I) relies solely on C-H⋯I hydrogen bonds supported by weak parallel slipped π-π stacking inter-actions [inter-centroid distance = 4.0569 (11) Å, inter-planar distance = 3.3789 (8) Å and slippage = 2.245 Å]. While C-H⋯I hydrogen bonds are also found in the packing of (II), type II, I⋯I halogen bonds [I⋯I = 3.8662 (2) Å] and C-H⋯π contacts feature prominently in stabilizing the three-dimensional structure.

Hidden impacts of ocean acidification to live and dead coral framework.

PubMed

Hennige, S J; Wicks, L C; Kamenos, N A; Perna, G; Findlay, H S; Roberts, J M

2015-08-22

Cold-water corals, such as Lophelia pertusa, are key habitat-forming organisms found throughout the world's oceans to 3000 m deep. The complex three-dimensional framework made by these vulnerable marine ecosystems support high biodiversity and commercially important species. Given their importance, a key question is how both the living and the dead framework will fare under projected climate change. Here, we demonstrate that over 12 months L. pertusa can physiologically acclimate to increased CO2, showing sustained net calcification. However, their new skeletal structure changes and exhibits decreased crystallographic and molecular-scale bonding organization. Although physiological acclimatization was evident, we also demonstrate that there is a negative correlation between increasing CO2 levels and breaking strength of exposed framework (approx. 20-30% weaker after 12 months), meaning the exposed bases of reefs will be less effective 'load-bearers', and will become more susceptible to bioerosion and mechanical damage by 2100. © 2015 The Authors.

Superlattices assembled through shape-induced directional binding

NASA Astrophysics Data System (ADS)

Lu, Fang; Yager, Kevin G.; Zhang, Yugang; Xin, Huolin; Gang, Oleg

2015-04-01

Organization of spherical particles into lattices is typically driven by packing considerations. Although the addition of directional binding can significantly broaden structural diversity, nanoscale implementation remains challenging. Here we investigate the assembly of clusters and lattices in which anisotropic polyhedral blocks coordinate isotropic spherical nanoparticles via shape-induced directional interactions facilitated by DNA recognition. We show that these polyhedral blocks--cubes and octahedrons--when mixed with spheres, promote the assembly of clusters with architecture determined by polyhedron symmetry. Moreover, three-dimensional binary superlattices are formed when DNA shells accommodate the shape disparity between nanoparticle interfaces. The crystallographic symmetry of assembled lattices is determined by the spatial symmetry of the block's facets, while structural order depends on DNA-tuned interactions and particle size ratio. The presented lattice assembly strategy, exploiting shape for defining the global structure and DNA-mediation locally, opens novel possibilities for by-design fabrication of binary lattices.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Fang; Yager, Kevin G.; Zhang, Yugang

Organization of spherical particles into lattices is typically driven by packing considerations. Although the addition of directional binding can significantly broaden structural diversity, nanoscale implementation remains challenging. Here we investigate the assembly of clusters and lattices in which anisotropic polyhedral blocks coordinate isotropic spherical nanoparticles via shape-induced directional interactions facilitated by DNA recognition. We show that these polyhedral blocks—cubes and octahedrons—when mixed with spheres, promote the assembly of clusters with architecture determined by polyhedron symmetry. Moreover, three-dimensional binary superlattices are formed when DNA shells accommodate the shape disparity between nanoparticle interfaces. The crystallographic symmetry of assembled lattices is determined bymore » the spatial symmetry of the block’s facets, while structural order depends on DNA-tuned interactions and particle size ratio. Lastly, the presented lattice assembly strategy, exploiting shape for defining the global structure and DNA-mediation locally, opens novel possibilities for by-design fabrication of binary lattices.« less

Applied and implied semantics in crystallographic publishing

PubMed Central

2012-01-01

Background Crystallography is a data-rich, software-intensive scientific discipline with a community that has undertaken direct responsibility for publishing its own scientific journals. That community has worked actively to develop information exchange standards allowing readers of structure reports to access directly, and interact with, the scientific content of the articles. Results Structure reports submitted to some journals of the International Union of Crystallography (IUCr) can be automatically validated and published through an efficient and cost-effective workflow. Readers can view and interact with the structures in three-dimensional visualization applications, and can access the experimental data should they wish to perform their own independent structure solution and refinement. The journals also layer on top of this facility a number of automated annotations and interpretations to add further scientific value. Conclusions The benefits of semantically rich information exchange standards have revolutionised the scholarly publishing process for crystallography, and establish a model relevant to many other physical science disciplines. PMID:22932420

Crystal structure of (S)-sec-butyl­ammonium l-tartrate monohydrate

PubMed Central

Publicover, Ernlie A.; Kolwich, Jennifer; Stack, Darcie L.; Doué, Alyssa J.; Ylijoki, Kai E. O.

2017-01-01

The title hydrated mol­ecular salt, C4H12N+·C4H5O6 −·H2O, was prepared by deprotonation of enanti­opure l-tartaric acid with racemic sec-butyl­amine in water. Only one enanti­omer was observed crystallographically, resulting from the combination of (S)-sec-butyl­amine with l-tartaric acid. The sec-butyl­ammonium moiety is disordered over two conformations related by rotation around the CH–CH2 bond; the refined occupancy ratio is 0.68 (1):0.32 (1). In the crystal, mol­ecules are linked through a network of O—H⋯O and N—H⋯O hydrogen-bonding inter­actions, between the ammonium H atoms, the tartrate hy­droxy H atoms, and the inter­stitial water, forming a three-dimensional supra­molecular structure. PMID:28529783

Dark-field hyperspectral X-ray imaging

PubMed Central

Egan, Christopher K.; Jacques, Simon D. M.; Connolley, Thomas; Wilson, Matthew D.; Veale, Matthew C.; Seller, Paul; Cernik, Robert J.

2014-01-01

In recent times, there has been a drive to develop non-destructive X-ray imaging techniques that provide chemical or physical insight. To date, these methods have generally been limited; either requiring raster scanning of pencil beams, using narrow bandwidth radiation and/or limited to small samples. We have developed a novel full-field radiographic imaging technique that enables the entire physio-chemical state of an object to be imaged in a single snapshot. The method is sensitive to emitted and scattered radiation, using a spectral imaging detector and polychromatic hard X-radiation, making it particularly useful for studying large dense samples for materials science and engineering applications. The method and its extension to three-dimensional imaging is validated with a series of test objects and demonstrated to directly image the crystallographic preferred orientation and formed precipitates across an aluminium alloy friction stir weld section. PMID:24808753

Superlattices assembled through shape-induced directional binding

DOE PAGES

Lu, Fang; Yager, Kevin G.; Zhang, Yugang; ...

2015-04-23

Organization of spherical particles into lattices is typically driven by packing considerations. Although the addition of directional binding can significantly broaden structural diversity, nanoscale implementation remains challenging. Here we investigate the assembly of clusters and lattices in which anisotropic polyhedral blocks coordinate isotropic spherical nanoparticles via shape-induced directional interactions facilitated by DNA recognition. We show that these polyhedral blocks—cubes and octahedrons—when mixed with spheres, promote the assembly of clusters with architecture determined by polyhedron symmetry. Moreover, three-dimensional binary superlattices are formed when DNA shells accommodate the shape disparity between nanoparticle interfaces. The crystallographic symmetry of assembled lattices is determined bymore » the spatial symmetry of the block’s facets, while structural order depends on DNA-tuned interactions and particle size ratio. Lastly, the presented lattice assembly strategy, exploiting shape for defining the global structure and DNA-mediation locally, opens novel possibilities for by-design fabrication of binary lattices.« less

Tailoring Selective Laser Melting Process Parameters for NiTi Implants

NASA Astrophysics Data System (ADS)

Bormann, Therese; Schumacher, Ralf; Müller, Bert; Mertmann, Matthias; de Wild, Michael

2012-12-01

Complex-shaped NiTi constructions become more and more essential for biomedical applications especially for dental or cranio-maxillofacial implants. The additive manufacturing method of selective laser melting allows realizing complex-shaped elements with predefined porosity and three-dimensional micro-architecture directly out of the design data. We demonstrate that the intentional modification of the applied energy during the SLM-process allows tailoring the transformation temperatures of NiTi entities within the entire construction. Differential scanning calorimetry, x-ray diffraction, and metallographic analysis were employed for the thermal and structural characterizations. In particular, the phase transformation temperatures, the related crystallographic phases, and the formed microstructures of SLM constructions were determined for a series of SLM-processing parameters. The SLM-NiTi exhibits pseudoelastic behavior. In this manner, the properties of NiTi implants can be tailored to build smart implants with pre-defined micro-architecture and advanced performance.

Systematic Comparison of Crystal and NMR Protein Structures Deposited in the Protein Data Bank

PubMed Central

Sikic, Kresimir; Tomic, Sanja; Carugo, Oliviero

2010-01-01

Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of the crystallographic and NMR results deposited in the files of the Protein Data Bank, in order to find out to which extent these information can be aggregated in bioinformatics. A non-redundant data set containing 109 NMR – X-ray structure pairs of nearly identical proteins was derived from the Protein Data Bank. A series of comparisons were performed by focusing the attention towards both global features and local details. It was observed that: (1) the RMDS values between NMR and crystal structures range from about 1.5 Å to about 2.5 Å; (2) the correlation between conformational deviations and residue type reveals that hydrophobic amino acids are more similar in crystal and NMR structures than hydrophilic amino acids; (3) the correlation between solvent accessibility of the residues and their conformational variability in solid state and in solution is relatively modest (correlation coefficient = 0.462); (4) beta strands on average match better between NMR and crystal structures than helices and loops; (5) conformational differences between loops are independent of crystal packing interactions in the solid state; (6) very seldom, side chains buried in the protein interior are observed to adopt different orientations in the solid state and in solution. PMID:21293729

Trichomonas vaginalis metalloproteinase TvMP50 is a monomeric Aminopeptidase P-like enzyme.

PubMed

Arreola, Rodrigo; Villalpando, José Luis; Puente-Rivera, Jonathan; Morales-Montor, Jorge; Rudiño-Piñera, Enrique; Alvarez-Sánchez, María Elizbeth

2018-06-23

Previously, metalloproteinase was isolated and identified from Trichomonas vaginalis, belonging to the aminopeptidase P-like metalloproteinase subfamily A/B, family M24 of clan MG, named TvMP50. The native and recombinant TvMP50 showed proteolytic activity, determined by gelatin zymogram, and a 50 kDa band, suggesting that TvMP50 is a monomeric active enzyme. This was an unexpected finding since other Xaa-Pro aminopeptidases/prolidases are active as a biological unit formed by dimers/tetramers. In this study, the evolutionary history of TvMP50 and the preliminary crystal structure of the recombinant enzyme determined at 3.4 Å resolution is reported. TvMP50 was shown to be a type of putative, eukaryotic, monomeric aminopeptidase P, and the crystallographic coordinates showed a monomer on a "pseudo-homodimer" array on the asymmetric unit that resembles the quaternary structure of the M24B dimeric family and suggests a homodimeric aminopeptidase P-like enzyme as a likely ancestor. Interestingly, TvMP50 had a modified N-terminal region compared with other Xaa-Pro aminopeptidases/prolidases with three-dimensional structures; however, the formation of the standard dimer is structurally unstable in aqueous solution, and a comparably reduced number of hydrogen bridges and lack of saline bridges were found between subunits A/B, which could explain why TvMP50 portrays monomeric functionality. Additionally, we found that the Parabasalia group contains two protein lineages with a "pita bread" fold; the ancestral monomeric group 1 was probably derived from an ancestral dimeric aminopeptidase P-type enzyme, and group 2 has a probable dimeric kind of ancestral eukaryotic prolidase lineage. The implications of such hypotheses are also presented.

Maxwell Strata and Cut Locus in the Sub-Riemannian Problem on the Engel Group

NASA Astrophysics Data System (ADS)

Ardentov, Andrei A.; Sachkov, Yuri L.

2017-12-01

We consider the nilpotent left-invariant sub-Riemannian structure on the Engel group. This structure gives a fundamental local approximation of a generic rank 2 sub-Riemannian structure on a 4-manifold near a generic point (in particular, of the kinematic models of a car with a trailer). On the other hand, this is the simplest sub-Riemannian structure of step three. We describe the global structure of the cut locus (the set of points where geodesics lose their global optimality), the Maxwell set (the set of points that admit more than one minimizer), and the intersection of the cut locus with the caustic (the set of conjugate points along all geodesics). The group of symmetries of the cut locus is described: it is generated by a one-parameter group of dilations R+ and a discrete group of reflections Z2 × Z2 × Z2. The cut locus admits a stratification with 6 three-dimensional strata, 12 two-dimensional strata, and 2 one-dimensional strata. Three-dimensional strata of the cut locus are Maxwell strata of multiplicity 2 (for each point there are 2 minimizers). Two-dimensional strata of the cut locus consist of conjugate points. Finally, one-dimensional strata are Maxwell strata of infinite multiplicity, they consist of conjugate points as well. Projections of sub-Riemannian geodesics to the 2-dimensional plane of the distribution are Euler elasticae. For each point of the cut locus, we describe the Euler elasticae corresponding to minimizers coming to this point. Finally, we describe the structure of the optimal synthesis, i. e., the set of minimizers for each terminal point in the Engel group.

Reliability of tunnel angle in ACL reconstruction: two-dimensional versus three-dimensional guide technique.

PubMed

Leiter, Jeff R S; de Korompay, Nevin; Macdonald, Lindsey; McRae, Sheila; Froese, Warren; Macdonald, Peter B

2011-08-01

To compare the reliability of tibial tunnel position and angle produced with a standard ACL guide (two-dimensional guide) or Howell 65° Guide (three-dimensional guide) in the coronal and sagittal planes. In the sagittal plane, the dependent variables were the angle of the tibial tunnel relative to the tibial plateau and the position of the tibial tunnel with respect to the most posterior aspect of the tibia. In the coronal plane, the dependent variables were the angle of the tunnel with respect to the medial joint line of the tibia and the medial and lateral placement of the tibial tunnel relative to the most medial aspect of the tibia. The position and angle of the tibial tunnel in the coronal and sagittal planes were determined from anteroposterior and lateral radiographs, respectively, taken 2-6 months postoperatively. The two-dimensional and three-dimensional guide groups included 28 and 24 sets of radiographs, respectively. Tibial tunnel position was identified, and tunnel angle measurements were completed. Multiple investigators measured the position and angle of the tunnel 3 times, at least 7 days apart. The angle of the tibial tunnel in the coronal plane using a two-dimensional guide (61.3 ± 4.8°) was more horizontal (P < 0.05) than tunnels drilled with a three-dimensional guide (64.7 ± 6.2°). The position of the tibial tunnel in the sagittal plane was more anterior (P < 0.05) in the two-dimensional (41.6 ± 2.5%) guide group compared to the three-dimensional guide group (43.3 ± 2.9%). The Howell Tibial Guide allows for reliable placement of the tibial tunnel in the coronal plane at an angle of 65°. Tibial tunnels were within the anatomical footprint of the ACL with either technique. Future studies should investigate the effects of tibial tunnel angle on knee function and patient quality of life. Case-control retrospective comparative study, Level III.

Cluster Analysis of Time-Dependent Crystallographic Data: Direct Identification of Time-Independent Structural Intermediates

PubMed Central

Kostov, Konstantin S.; Moffat, Keith

2011-01-01

The initial output of a time-resolved macromolecular crystallography experiment is a time-dependent series of difference electron density maps that displays the time-dependent changes in underlying structure as a reaction progresses. The goal is to interpret such data in terms of a small number of crystallographically refinable, time-independent structures, each associated with a reaction intermediate; to establish the pathways and rate coefficients by which these intermediates interconvert; and thereby to elucidate a chemical kinetic mechanism. One strategy toward achieving this goal is to use cluster analysis, a statistical method that groups objects based on their similarity. If the difference electron density at a particular voxel in the time-dependent difference electron density (TDED) maps is sensitive to the presence of one and only one intermediate, then its temporal evolution will exactly parallel the concentration profile of that intermediate with time. The rationale is therefore to cluster voxels with respect to the shapes of their TDEDs, so that each group or cluster of voxels corresponds to one structural intermediate. Clusters of voxels whose TDEDs reflect the presence of two or more specific intermediates can also be identified. From such groupings one can then infer the number of intermediates, obtain their time-independent difference density characteristics, and refine the structure of each intermediate. We review the principles of cluster analysis and clustering algorithms in a crystallographic context, and describe the application of the method to simulated and experimental time-resolved crystallographic data for the photocycle of photoactive yellow protein. PMID:21244840

In silico ligand binding studies of cyanogenic β-glucosidase, dhurrinase-2 from Sorghum bicolor.

PubMed

Mahajan, Chavi; Patel, Krunal; Khan, Bashir M; Rawal, Shuban S

2015-07-01

Dhurrinase, a cyanogenic β-glucosidase from Sorghum bicolor is the key enzyme responsible for the hydrolysis of dhurrin to produce toxic hydrogen cyanide, as a part of plant defence mechanism. Dhurrinase 1 (SbDhr1) and dhurrinase 2 (SbDhr2), two isozymes have been isolated and characterized from S. bicolor. However, there is no information in the literature about the three dimensional (3D) structure of SbDhr2 and molecular interactions involved between the protein and ligand. In this study, the three dimensional structure of SbDhr2 was built based on homology modeling by using the X-ray crystallographic structure of its close homologue SbDhr1 as the template. The generated 3D model was energy minimized and the quality was validated by Ramachndran plot, various bioinformatic tools and their relevant parameters. Stability, folding-unfolding and flexibility of the modeled SbDhr2 was evaluated on the basis of RMSD, radius of gyration (Rg) and RMSF values respectively, obtained through molecular dynamic (MD) simulation. Further, molecular docking was performed with its natural substrate dhurrin, one substrate analogue, three un-natural substrates, and one inhibitor. Analysis of molecular interactions in the SbDhr2-ligand complexes revealed the key amino acid residues responsible to stabilize the ligands within the binding pocket through non-bonded interactions and some of them were found to be conserved (Glu239, Tyr381, Trp426, Glu454, Trp511). Reasonably broader substrate specificity of SbDhr2 was explained through the wider entrance passage observed in comparison to SbDhr1.

Maxillary reaction patterns identified by three-dimensional analysis of casts from infants with unilateral cleft lip and palate.

PubMed

Neuschulz, J; Schaefer, I; Scheer, M; Christ, H; Braumann, B

2013-07-01

In order to visualize and quantify the direction and extent of morphological upper-jaw changes in infants with unilateral cleft lip and palate (UCLP) during early orthodontic treatment, a three-dimensional method of cast analysis for routine application was developed. In the present investigation, this method was used to identify reaction patterns associated with specific cleft forms. The study included a cast series reflecting the upper-jaw situations of 46 infants with complete (n=27) or incomplete (n=19) UCLP during week 1 and months 3, 6, and 12 of life. Three-dimensional datasets were acquired and visualized with scanning software (DigiModel®; OrthoProof, The Netherlands). Following interactive identification of landmarks on the digitized surface relief, a defined set of representative linear parameters were three-dimensionally measured. At the same time, the three-dimensional surfaces of one patient series were superimposed based on a defined reference plane. Morphometric differences were statistically analyzed. Thanks to the user-friendly software, all landmarks could be identified quickly and reproducibly, thus, allowing for simultaneous three-dimensional measurement of all defined parameters. The measured values revealed that significant morphometric differences were present in all three planes of space between the two patient groups. Patients with complete UCLP underwent significantly larger reductions in cleft width (p<0.001), and sagittal growth in the complete UCLP group exceeded sagittal growth in the incomplete UCLP group by almost 50% within the first year of life. Based on patients with incomplete versus complete UCLP, different reaction patterns were identified that depended not on apparent severities of malformation but on cleft forms.

Crystallization of FcpA from Leptospira, a novel flagellar protein that is essential for pathogenesis.

PubMed

San Martin, Fabiana; Mechaly, Ariel E; Larrieux, Nicole; Wunder, Elsio A; Ko, Albert I; Picardeau, Mathieu; Trajtenberg, Felipe; Buschiazzo, Alejandro

2017-03-01

The protein FcpA is a unique component of the flagellar filament of spirochete bacteria belonging to the genus Leptospira. Although it plays an essential role in translational motility and pathogenicity, no structures of FcpA homologues are currently available in the PDB. Its three-dimensional structure will unveil the novel motility mechanisms that render pathogenic Leptospira particularly efficient at invading and disseminating within their hosts, causing leptospirosis in humans and animals. FcpA from L. interrogans was purified and crystallized, but despite laborious attempts no useful X ray diffraction data could be obtained. This challenge was solved by expressing a close orthologue from the related saprophytic species L. biflexa. Three different crystal forms were obtained: a primitive and a centred monoclinic form, as well as a hexagonal variant. All forms diffracted X-rays to suitable resolutions for crystallographic analyses, with the hexagonal type typically reaching the highest limits of 2.0 Å and better. A variation of the quick-soaking procedure resulted in an iodide derivative that was instrumental for single-wavelength anomalous diffraction methods.

Ca(5)Zr(3)F(22).

PubMed

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

2012-04-01

Single crystals of Ca(5)Zr(3)F(22), penta-calcium trizirconium docosafluoride, were obtained unexpectedly by solid-state reaction between CaF(2) and ZrF(4) in the presence of AgF. The structure of the title compound is isotypic with that of Sr(5)Zr(3)F(22) and can be described as being composed of layers with composition [Zr(3)F(20)](8-) made up from two different [ZrF(8)](4-) square anti-prisms (one with site symmetry 2) by corner-sharing. The layers extending parallel to the (001) plane are further linked by Ca(2+) cations, forming a three-dimensional network. Amongst the four crystallographically different Ca(2+) ions, three are located on twofold rotation axes. The Ca(2+) ions exhibit coordination numbers ranging from 8 to 12, depending on the cut off, with very distorted fluorine environments. Two of the Ca(2+) ions occupy inter-stices between the layers whereas the other two are located in void spaces of the [Zr(3)F(20)](8-) layer and alternate with the two Zr atoms along [010]. The crystal under investigation was an inversion twin.

Columnar to Nematic Mesophase Transition: Binary Mixtures of Unlike Copper Soaps

NASA Astrophysics Data System (ADS)

Seghrouchni, R.; Skoulios, A.

1995-10-01

Copper (II) soaps are known to produce columnar mesophases at high temperature. The polar groups of the soap molecules are stacked over one another within columns surrounded by the alkyl chains in a disordered conformation and laterally arranged according to a two-dimensional hexagonal lattice. The present work studies the mesomorphic behaviour of binary mixtures of copper soaps using differential scanning calorimetry, polarizing microscopy, and X-ray diffraction. When the soaps are of comparable molecular sizes the mixtures are homogeneous and columnar at all compositions. The columns of the two soaps, remaining intact in the mixture, are distributed randomly on the nodes of a hexagonal Bravais lattice. Crystallographic homogeneity is obtained by transfer of methylene groups from cell to cell. When, on the other hand, the soaps are different enough in molecular sizes, the columnar structure of the mixtures is interrupted in the middle range of compositions for the benefit of a nematic one. The transfer of methylene groups gets indeed harder to achieve and the distortion of the hexagonal units cells becomes important. The columnar to nematic phase transition is discussed on a molecular and a topological level.

One-dimensional pinning behavior in Co-doped BaFe2As2 thin films

NASA Astrophysics Data System (ADS)

Mishev, V.; Seeböck, W.; Eisterer, M.; Iida, K.; Kurth, F.; Hänisch, J.; Reich, E.; Holzapfel, B.

2013-12-01

Angle-resolved transport measurements revealed that planar defects dominate flux pinning in the investigated Co-doped BaFe2As2 thin film. For any given field and temperature, the critical current depends only on the angle between the crystallographic c-axis and the applied magnetic field but not on the angle between the current and the field. The critical current is therefore limited only by the in-plane component of the Lorentz force but independent of the out-of-plane component, which is entirely balanced by the pinning force exerted by the planar defects. This one-dimensional pinning behavior shows similarities and differences to intrinsic pinning in layered superconductors.

Dipolar Second-Order Nonlinear Optical Chromophores Containing Ferrocene, Octamethylferrocene, and Ruthenocene Donors and Strong π-Acceptors: Crystal Structures and Comparison of π-Donor Strengths

PubMed Central

Kinnibrugh, Tiffany L.; Salman, Seyhan; Getmanenko, Yulia A.; Coropceanu, Veaceslav; Porter, William W.; Timofeeva, Tatiana V.; Matzger, Adam J.; Brédas, Jean-Luc; Marder, Seth R.; Barlow, Stephen

2009-01-01

Crystal structures have been determined for six dipolar polyene chromophores with metallocenyl – ferrocenyl (Fc), octamethylferrocenyl (Fc″), or ruthenocenyl (Rc) – donors and strong heterocyclic acceptors based on 1,3-diethyl-2-thiobarbituric acid or 3-dicyanomethylidene-2,3-dihydrobenzothiophene-1,1-dioxide. In each case, crystals were found to belong to centrosymmetric space groups. For one example, polymer-induced heteronucleation revealed the existence of two additional polymorphs, which were inactive in second-harmonic generation, suggesting that they were also centrosymmetric. The bond-length alternations between the formally double and single bonds of the polyene bridges are reduced compared to simple polyenes, indicating significant contribution from charge-separated resonance structures, although the metallocenes are not significantly distorted towards the [(η6-fulvene)(η5-cyclopentadienyl)metal(II)]+ extreme. DFT geometries are in excellent agreement with those determined crystallographically; while the π-donor strengths of the three metallocenyl groups are insufficiently different to result in detectable differences in the crystallographic bond-length alternations, the DFT geometries, as well as DFT-calculations of partial charges for atoms, suggest that π-donor strength decreases in the order Fc″ ≫ Fc > Rc. NMR, IR and electrochemical evidence also suggests that octamethylferrocenyl is the stronger π-donor, exhibiting similar π-donor strength to a p-(dialkylamino)phenyl group, while ferrocenyl and ruthenocenyl show very similar π-donor strengths to one another in chromophores of this type. PMID:20047010

A Novel Silicon Micromachined Integrated MCM Thermal Management System

NASA Technical Reports Server (NTRS)

Kazmierczak, M. J.; Henderson, H. T.; Gerner, F. M.

1997-01-01

"Micromachining" is a chemical means of etching three-dimensional structures, typically in single- crystalline silicon. These techniques are leading toward what is coming to be referred to as MEMS (Micro Electro Mechanical Systems), where in addition to the ordinary two-dimensional (planar) microelectronics, it is possible to build three-dimensional n-ticromotors, electrically- actuated raicrovalves, hydraulic systems and much more on the same microchip. These techniques become possible because of differential etching rates of various crystallographic planes and materials used for semiconductor n-ticrofabfication. The University of Cincinnati group in collaboration with Karl Baker at NASA Lewis were the first to form micro heat pipes in silicon by the above techniques. Current work now in progress using MEMS technology is now directed towards the development of the next generation in MCM (Multi Chip Module) packaging. Here we propose to develop a complete electronic thermal management system which will allow densifica6on in chip stacking by perhaps two orders of magnitude. Furthermore the proposed technique will allow ordinary conu-nercial integrated chips to be utilized. Basically, the new technique involves etching square holes into a silicon substrate and then inserting and bonding commercially available integrated chips into these holes. For example, over a 100 1/4 in. by 1 /4 in. integrated chips can be placed on a 4 in. by 4 in. silicon substrate to form a Multi-Chip Module (MCM). Placing these MCM's in-line within an integrated rack then allows for three-diniensional stacking. Increased miniaturization of microelectronic circuits will lead to very high local heat fluxes. A high performance thermal management system will be specifically designed to remove the generated energy. More specifically, a compact heat exchanger with milli / microchannels will be developed and tested to remove the heat through the back side of this MCM assembly for moderate and high heat flux applications, respectively. The high heat load application of particular interest in mind is the motor controller developed by Martin Marietta for Nasa to control the thruster's directional actuators on space vechicles. Work is also proposed to develop highly advanced and improved porous wick structures for use in advanced heat loops. The porous wick will be micromachined from silicon using MEMS technology, thus permitting far superior control of pore size and pore distribution (over wicks made from sintered n-ietals), which in turn is expected to led to significantly improved heat loop performance.

Crystallization and preliminary X-ray crystallographic analysis of agkicetin-C from Deinagkistrodon acutus venom

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Gufeng; Departments of Molecular and Cell Biology, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026; Huang, Qingqiu

2005-01-01

The crystallization and preliminary crystallographic analysis of agkicetin-C, a well known platelet glycoprotein Ib (GPIb) antagonist from the venom of Deinagkistrodon acutus found in Anhui Province, China is reported. The crystallization and preliminary crystallographic analysis of agkicetin-C, a well known platelet glycoprotein Ib (GPIb) antagonist from the venom of Deinagkistrodon acutus found in Anhui Province, China is reported. Crystals of agkicetin-C suitable for structure determination were obtained from 1.8 M ammonium sulfate, 40 mM MES pH 6.5 with 2%(v/v) PEG 400. Interestingly, low buffer concentrations of MES seem to be necessary for crystal growth. The crystals of agkicetin-C belong tomore » space group C2, with unit-cell parameters a = 177.5, b = 97.7, c = 106.8 Å, β = 118.5°, and diffract to 2.4 Å resolution. Solution of the phase problem by the molecular-replacement method shows that there are four agkicetin-C molecules in the asymmetric unit, with a V{sub M} value of 3.4 Å{sup 3} Da{sup −1}, which corresponds to a high solvent content of approximately 64%. Self-rotation function calculations show a single well defined non-crystallographic twofold axis with features that may represent additional elements of non-crystallographic symmetry.« less

A synthesis, X-ray crystallographic and vibrational studies of guanidinium o-nitrobenzoate hydrate. New NLO crystal in guanidinium nitrobenzoate family

NASA Astrophysics Data System (ADS)

Drozd, Marek; Daszkiewicz, Marek

2018-06-01

According to literature data the two crystals are known: guanidinium m-nitrobenzoate and guanidinium p-nitrobenzoate. Both compounds belong to noncetrosymmetric crystallographic systems are consider as second order generators in nonlinear optic (NLO). For each of these crystals the detailed crystallographic, theoretical calculations and vibrational studies were performed. It is interesting that nitrobenzoic acid create tree variety of compounds ((2) ortho-, (3) meta- and (4) para-) what any data for third member of guanidinium nitrobenzoate crystal were not known. The guanidinium o-nitrobenzoate hydrate crystal was synthesized first time. The performed X-ray crystallographic study shown that crystal belongs to space group without macroscopic symmetry center. Additionally, the vibrational spectra (intensities, frequencies and PED analysis) of investigated compound are presented. These results are compared with theoretical calculations for equilibrium geometry and vibrational properties. Furthermore, the results of the theoretical approach include HOMO and LUMO energies and first order hyperpolarizability were obtained, also. On the basis of these data the crystal was classified as second order generator. All obtained results are compared with previous literature data of guanidinium m-nitrobenzoate and guanidinium p-nitrobenzoate compounds. Surprisingly, each of examined crystal belongs to different crystallographic system and shows different vibrational properties.

Structural similarities in tetraaryltins described by virtual non-crystallographic rotations or translations: Kitaigorodskii's morphotropism is revisited.

PubMed

Kálmán, Alajos; Fábián, László

2007-06-01

Recently Kálmán [(2005), Acta Cryst. B61, 536-547] revealed that semirigid molecules or their patterns held together e.g. by hydrogen bonds may perform non-crystallographic rotations (through 180, 90 degrees etc.) around themselves whenever a substitution, ring enlargement or isomerization destroys the existing close packing, i.e. the novel substituent or the enlarged ring can no longer fit in the hollows formed between the molecules. In other words, the old and new arrangements of such chemically similar molecules can be converted into each other by virtual rotations. However, when a semirigid molecule without substitution, but under the influence of solvents, temperature etc., is fully or partly rearranged in the solid state, the corresponding non-crystallographic rotation (hereinafter ncr) is real and gives rise to polymorphism. Such polymorphs are hallmarked by full or partial isostructurality and show that ncrs always occur together with isostructurality. First Kitaigorodskii [(1961), Organic Chemical Crystallography, New York: Consultants Bureau] reported on the structural similarity of three tetraaryltins, (p-RC(6)H(4))(4)Sn, R = H, CH(3), CH(3)O, which is terminated by the larger C(2)H(5)O group. A revisit to these structures revealed that the tetragonal --> monoclinic conversion termed by Kitaigorodskii as a ;morphotropic step' is also performed by an ncr. Similarly, other tetraaryltins in the literature are related by ncrs or the nc translation of the semirigid tetrahedra, or they remain isostructural. Since one of the definitions of morphotropism, a word of Greek origin, is 'turn of form', the ncrs of semirigid molecules can be denoted--following Kitaigorodskii--by this word, whereas its alternative definition in the morphological crystallography of ;unidirectional changes' [applied by Groth (1870). Ber. Chem. Ges. 3, 449-457] covers the non-crystallographic translations described first in this work.

Low Loss Substrates for Microwave Applications and Sol-Gel Processing of Superconductors

DTIC Science & Technology

1994-03-31

crystallographic axis normal to solid state technology, in the growth of ferrimagnetic garnets the substrate plane) or. better, in "epitaxial" films (i.e...hay- by liquid phase epitaxy ( LPE ). is from a melt using a para- ing their three crystallographic axes related to those of a magnetic garnet structure...yttrium barium cuprate (YBCO) films and their microwave applications have been carried out. Several promising new hosts such as Sr(All/2Tal/2)03, Sr(Al1

XAS Characterization of the Zn Site of Non-structural Protein 3 (NS3) from Hepatitis C Virus

NASA Astrophysics Data System (ADS)

Ascone, I.; Nobili, G.; Benfatto, M.; Congiu-Castellano, A.

2007-02-01

XANES spectra of non structural protein 3 (NS3) have been calculated using 4 Zn coordination models from three crystallographic structures in the Protein Data Base (PDB): 1DY9, subunit B, 1CU1 subunit A and B, and 1JXP subunit B. Results indicate that XANES is an appropriate tool to distinguish among them. Experimental XANES spectra have been simulated refining crystallographic data. The model obtained by XAS is compared with the PDB models.

Identification, display, and use of symmetry elements in atomic and electronic structure models.

PubMed

Khosrovani, N; Kung, P W; Freeman, C M; Gorman, A M; Kölmel, C M; Levine, S M; Newsam, J M

1999-01-01

Crystallographic symmetry plays an important role in structure determination from diffraction or scattering data, in spectroscopy and in simulations. It is convenient and insightful to integrate the display and use of such symmetry data with data analysis and modeling methods. We outline the integration of a suite of crystallographic algorithms, closely coupled with interactive graphical displays. These include techniques for identifying the unit cell of a solid, for automatically determining space and point group symmetries, for generalized displays of symmetry elements overlaid on structural models, and for construction, editing, and transformation of models subject to symmetry constraints. In addition, electron densities derived from periodic density functional calculations can be symmetrized and displayed with the corresponding symmetry elements. Applications of these various capabilities in crystallographic research are illustrated by topical examples.

Role of Different Kinds of Boundaries Against Cleavage Crack Propagation in Low-Temperature Embrittlement of Low-Carbon Martensitic Steel

NASA Astrophysics Data System (ADS)

Tsuboi, Mizuki; Shibata, Akinobu; Terada, Daisuke; Tsuji, Nobuhiro

2017-07-01

The present paper investigated the relationship between low-temperature embrittlement and microstructure of lath martensite in a low-carbon steel from both microstructural and crystallographic points of view. The fracture surface of the specimen after the miniaturized Charpy impact test at 98 K (-175 °C) mainly consisted of cleavage fracture facets parallel to crystallographic {001} planes of martensite. Through the crystallographic orientation analysis of micro-crack propagation, we found that the boundaries which separated different martensite variants having large misorientation angles of {001} cleavage planes could inhibit crack propagation. It was then concluded that the size of the aggregations of martensite variants belonging to the same Bain deformation group could control the low-temperature embrittlement of martensitic steels.

Crystallization and preliminary crystallographic study of 3 alpha, 20 beta-hydroxysteroid dehydrogenase from Streptomyces hydrogenans.

PubMed

Fitzgerald, P M; Duax, W L; Punzi, J S; Orr, J C

1984-05-15

3 alpha, 20 beta-Hydroxysteroid dehydrogenase, an NADH-dependent oxidoreductase isolated from Streptomyces hydrogenans , is a tetramer containing four subunits each of Mr 25,000. The enzyme has been crystallized by the vapor diffusion technique using either phosphate or borate buffered ammonium sulfate (pH between 6.0 and 8.7) as the precipitant. The crystals are hexagonal bipyramids ; they have the symmetry of space group P6(4)22 (or P6(2)22), with unit cell dimensions a = 127.3 A, c = 112.2 A. Volume and density considerations imply that the crystallographic asymmetric unit contains two monomers, and therefore that the tetramer possesses a 2-fold axis of symmetry that is coincident with a crystallographic 2-fold symmetry element.

Physical nature of ethidium and proflavine interactions with nucleic acid bases in the intercalation plane.

PubMed

Langner, Karol M; Kedzierski, Pawel; Sokalski, W Andrzej; Leszczynski, Jerzy

2006-05-18

On the basis of the crystallographic structures of three nucleic acid intercalation complexes involving ethidium and proflavine, we have analyzed the interaction energies between intercalator chromophores and their four nearest bases, using a hybrid variation-perturbation method at the second-order Møller-Plesset theory level (MP2) with a 6-31G(d,p) basis set. A total MP2 interaction energy minimum precisely reproduces the crystallographic position of the ethidium chromophore in the intercalation plane between UA/AU bases. The electrostatic component constitutes the same fraction of the total energy for all three studied structures. The multipole electrostatic interaction energy, calculated from cumulative atomic multipole moments (CAMMs), was found to converge only after including components above the fifth order. CAMM interaction surfaces, calculated on grids in the intercalation planes of these structures, reasonably reproduce the alignment of intercalators in crystal structures; they exhibit additional minima in the direction of the DNA grooves, however, which also need to be examined at higher theory levels if no crystallographic data are given.

Imaging and three-dimensional reconstruction of chemical groups inside a protein complex using atomic force microscopy

NASA Astrophysics Data System (ADS)

Kim, Duckhoe; Sahin, Ozgur

2015-03-01

Scanning probe microscopes can be used to image and chemically characterize surfaces down to the atomic scale. However, the localized tip-sample interactions in scanning probe microscopes limit high-resolution images to the topmost atomic layer of surfaces, and characterizing the inner structures of materials and biomolecules is a challenge for such instruments. Here, we show that an atomic force microscope can be used to image and three-dimensionally reconstruct chemical groups inside a protein complex. We use short single-stranded DNAs as imaging labels that are linked to target regions inside a protein complex, and T-shaped atomic force microscope cantilevers functionalized with complementary probe DNAs allow the labels to be located with sequence specificity and subnanometre resolution. After measuring pairwise distances between labels, we reconstruct the three-dimensional structure formed by the target chemical groups within the protein complex using simple geometric calculations. Experiments with the biotin-streptavidin complex show that the predicted three-dimensional loci of the carboxylic acid groups of biotins are within 2 Å of their respective loci in the corresponding crystal structure, suggesting that scanning probe microscopes could complement existing structural biological techniques in solving structures that are difficult to study due to their size and complexity.

The relationship between three-dimensional imaging and group decision making: an exploratory study.

PubMed

Litynski, D M; Grabowski, M; Wallace, W A

1997-07-01

This paper describes an empirical investigation of the effect of three dimensional (3-D) imaging on group performance in a tactical planning task. The objective of the study is to examine the role that stereoscopic imaging can play in supporting face-to-face group problem solving and decision making-in particular, the alternative generation and evaluation processes in teams. It was hypothesized that with the stereoscopic display, group members would better visualize the information concerning the task environment, producing open communication and information exchanges. The experimental setting was a tactical command and control task, and the quality of the decisions and nature of the group decision process were investigated with three treatments: 1) noncomputerized, i.e., topographic maps with depth cues; 2) two-dimensional (2-D) imaging; and 3) stereoscopic imaging. The results were mixed on group performance. However, those groups with the stereoscopic displays generated more alternatives and spent less time on evaluation. In addition, the stereoscopic decision aid did not interfere with the group problem solving and decision-making processes. The paper concludes with a discussion of potential benefits, and the need to resolve demonstrated weaknesses of the technology.

A Factor Increasing Venous Contamination on Bolus Chase Three-dimensional Magnetic Resonance Imaging: Charcot Neuroarthropathy.

PubMed

Çildağ, Mehmet B; Ertuğrul, Mustafa B; Köseoğlu, Ömer Fk; Armstrong, David G

2018-01-01

The study aimed to evaluate the ratio of venous contamination in diabetic cases without foot lesion, with foot lesion and with Charcot neuroarthropathy (CN). Bolus-chase three-dimensional magnetic resonance (MR) of 396 extremities of patients with diabetes mellitus was analyzed, retrospectively. Extremities were divided into three groups as follows: diabetic patients without foot ulcer or Charcot arthropathy (Group A), patients with diabetic foot ulcers (Group B) and patients with CN accompanying diabetic foot ulcers (Group C). Furthermore, amount of venous contamination classified as no venous contamination, mild venous contamination, and severe venous contamination. The relationship between venous contamination and extremity groups was investigated. Severe venous contamination was seen in Group A, Group B, and Group C, 5.6%, 15.2%, and 34.1%, respectively. Statistically significant difference was seen between groups with regard to venous contamination. Venous contamination following bolus chase MR was higher in patients with CN.

Three-dimensional mapping of the lateral ventricles in autism

PubMed Central

Vidal, Christine N.; Nicolsonln, Rob; Boire, Jean-Yves; Barra, Vincent; DeVito, Timothy J.; Hayashi, Kiralee M.; Geaga, Jennifer A.; Drost, Dick J.; Williamson, Peter C.; Rajakumar, Nagalingam; Toga, Arthur W.; Thompson, Paul M.

2009-01-01

In this study, a computational mapping technique was used to examine the three-dimensional profile of the lateral ventricles in autism. T1-weighted three-dimensional magnetic resonance images of the brain were acquired from 20 males with autism (age: 10.1 ± 3.5 years) and 22 male control subjects (age: 10.7 ± 2.5 years). The lateral ventricles were delineated manually and ventricular volumes were compared between the two groups. Ventricular traces were also converted into statistical three-dimensional maps, based on anatomical surface meshes. These maps were used to visualize regional morphological differences in the thickness of the lateral ventricles between patients and controls. Although ventricular volumes measured using traditional methods did not differ significantly between groups, statistical surface maps revealed subtle, highly localized reductions in ventricular size in patients with autism in the left frontal and occipital horns. These localized reductions in the lateral ventricles may result from exaggerated brain growth early in life. PMID:18502618

Three-dimensional printing and pediatric liver disease.

PubMed

Alkhouri, Naim; Zein, Nizar N

2016-10-01

Enthusiastic physicians and medical researchers are investigating the role of three-dimensional printing in medicine. The purpose of the current review is to provide a concise summary of the role of three-dimensional printing technology as it relates to the field of pediatric hepatology and liver transplantation. Our group and others have recently demonstrated the feasibility of printing three-dimensional livers with identical anatomical and geometrical landmarks to the native liver to facilitate presurgical planning of complex liver surgeries. Medical educators are exploring the use of three-dimensional printed organs in anatomy classes and surgical residencies. Moreover, mini-livers are being developed by regenerative medicine scientist as a way to test new drugs and, eventually, whole livers will be grown in the laboratory to replace organs with end-stage disease solving the organ shortage problem. From presurgical planning to medical education to ultimately the bioprinting of whole organs for transplantation, three-dimensional printing will change medicine as we know in the next few years.

Conformational analysis of an acyclic tetrapeptide: ab-initio structure determination from X-ray powder diffraction, Hirshfeld surface analysis and electronic structure.

PubMed

Das, Uday; Naskar, Jishu; Mukherjee, Alok Kumar

2015-12-01

A terminally protected acyclic tetrapeptide has been synthesized, and the crystal structure of its hydrated form, Boc-Tyr-Aib-Tyr-Ile-OMe·2H2O (1), has been determined directly from powder X-ray diffraction data. The backbone conformation of tetrapeptide (1) exhibiting two consecutive β-turns is stabilized by two 4 → 1 intramolecular N-H · · · O hydrogen bonds. In the crystalline state, the tetrapeptide molecules are assembled through water-mediated O-H · · · O hydrogen bonds to form two-dimensional molecular sheets, which are further linked by intermolecular C-H · · · O hydrogen bonds into a three-dimensional supramolecular framework. The molecular electrostatic potential (MEP) surface of (1) has been used to supplement the crystallographic observations. The nature of intermolecular interactions in (1) has been analyzed quantitatively through the Hirshfeld surface and two-dimensional fingerprint plot. The DFT optimized molecular geometry of (1) agrees closely with that obtained from the X-ray structure analysis. The present structure analysis of Boc-Tyr-Aib-Tyr-Ile-OMe·2H2 O (1) represents a case where ab-initio crystal structure of an acyclic tetrapeptide with considerable molecular flexibility has been accomplished from laboratory X-ray powder diffraction data. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.

Honeycombs of triangles and magnetic frustration in SrL{sub 2}O{sub 4} (L=Gd, Dy, Ho, Er, Tm, and Yb)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karunadasa, H.; Regan, K.A.; Cava, R.J.

2005-04-01

The crystal structures, magnetic order, and susceptibility have been investigated for magnetically frustrated SrDy{sub 2}O{sub 4}, SrHo{sub 2}O{sub 4}, SrEr{sub 2}O{sub 4}, SrTm{sub 2}O{sub 4}, and SrYb{sub 2}O{sub 4}. Powder neutron-diffraction structural refinements reveal columns of LO{sub 6} octahedra that run along one crystallographic direction, with Sr-O polyhedra in the interstices. The lanthanide sublattice displays multiple triangular interconnections: one-dimensional strings form the backbones of four types of chains of lanthanide triangles sharing edges arranged in a honeycomb pattern. This crystal structure produces strong geometric frustration for the magnetic system that is evidenced in both magnetic susceptibility and neutron-scattering data atmore » low temperatures. The susceptibility measurements for the series, including SrGd{sub 2}O{sub 4} for which data are also reported, lack the sharp features characteristic of three-dimensional long-range magnetic ordering. Metamagnetic behavior is observed in the magnetization vs applied field data at 1.8 K for the cases of L=Dy, Er, and Ho. Magnetic neutron-scattering studies for the Dy and Er materials show only very broad magnetic scattering at low temperatures, while the Ho system exhibits long-range two-dimensional order. Any magnetic scattering in the Tm and Yb compounds, if present, was too weak to be detected in these measurements.« less

Validation of a Three-Dimensional Ablation and Thermal Response Simulation Code

NASA Technical Reports Server (NTRS)

Chen, Yih-Kanq; Milos, Frank S.; Gokcen, Tahir

2010-01-01

The 3dFIAT code simulates pyrolysis, ablation, and shape change of thermal protection materials and systems in three dimensions. The governing equations, which include energy conservation, a three-component decomposition model, and a surface energy balance, are solved with a moving grid system to simulate the shape change due to surface recession. This work is the first part of a code validation study for new capabilities that were added to 3dFIAT. These expanded capabilities include a multi-block moving grid system and an orthotropic thermal conductivity model. This paper focuses on conditions with minimal shape change in which the fluid/solid coupling is not necessary. Two groups of test cases of 3dFIAT analyses of Phenolic Impregnated Carbon Ablator in an arc-jet are presented. In the first group, axisymmetric iso-q shaped models are studied to check the accuracy of three-dimensional multi-block grid system. In the second group, similar models with various through-the-thickness conductivity directions are examined. In this group, the material thermal response is three-dimensional, because of the carbon fiber orientation. Predictions from 3dFIAT are presented and compared with arcjet test data. The 3dFIAT predictions agree very well with thermocouple data for both groups of test cases.

An extended approach for computing the critical properties in the two-and three-dimensional lattices within the effective-field renormalization group method

NASA Astrophysics Data System (ADS)

de Albuquerque, Douglas F.; Santos-Silva, Edimilson; Moreno, N. O.

2009-10-01

In this letter we employing the effective-field renormalization group (EFRG) to study the Ising model with nearest neighbors to obtain the reduced critical temperature and exponents ν for bi- and three-dimensional lattices by increasing cluster scheme by extending recent works. The technique follows up the same strategy of the mean field renormalization group (MFRG) by introducing an alternative way for constructing classical effective-field equations of state takes on rigorous Ising spin identities.

Crystal and Magnetic Structures in Layered, Transition Metal Dihalides and Trihalides

DOE PAGES

McGuire, Michael A.

2017-04-27

Materials composed of two dimensional layers bonded to one another through weak van der Waals interactions often exhibit strongly anisotropic behaviors and can be cleaved into very thin specimens and sometimes into monolayer crystals. Interest in such materials is driven by the study of low dimensional physics and the design of functional heterostructures. Binary compounds with the compositions MX 2 and MX 3 where M is a metal cation and X is a halogen anion often form such structures. Magnetism can be incorporated by choosing a transition metal with a partially filled d-shell for M, enabling ferroic responses for enhancedmore » functionality. Here we give a brief overview of binary transition metal dihalides and trihalides, summarizing their crystallographic properties and long-range-ordered magnetic structures, focusing on those materials with layered crystal structures and partially filled d-shells required for combining low dimensionality and cleavability with magnetism.« less

Two-dimensional wetting: the role of atomic steps on the nucleation of thin water films on BaF2(111) at ambient conditions.

PubMed

Cardellach, M; Verdaguer, A; Santiso, J; Fraxedas, J

2010-06-21

The interaction of water with freshly cleaved BaF(2)(111) surfaces at ambient conditions (room temperature and under controlled humidity) has been studied using scanning force microscopy in different operation modes. The images strongly suggest a high surface diffusion of water molecules on the surface indicated by the accumulation of water at step edges forming two-dimensional bilayered structures. Steps running along the 110 crystallographic directions show a high degree of hydrophilicity, as evidenced by small step-film contact angles, while steps running along other directions exhibiting a higher degree of kinks surprisingly behave in a quite opposite way. Our results prove that morphological defects such as steps can be crucial in improving two-dimensional monolayer wetting and stabilization of multilayer grown on surfaces that show good lattice mismatch with hexagonal ice.

On the symmetries of integrability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bellon, M.; Maillard, J.M.; Viallet, C.

1992-06-01

In this paper the authors show that the Yang-Baxter equations for two-dimensional models admit as a group of symmetry the infinite discrete group A{sub 2}{sup (1)}. The existence of this symmetry explains the presence of a spectral parameter in the solutions of the equations. The authors show that similarly, for three-dimensional vertex models and the associated tetrahedron equations, there also exists an infinite discrete group of symmetry. Although generalizing naturally the previous one, it is a much bigger hyperbolic Coxeter group. The authors indicate how this symmetry can help to resolve the Yang-Baxter equations and their higher-dimensional generalizations and initiatemore » the study of three-dimensional vertex models. These symmetries are naturally represented as birational projective transformations. They may preserve non-trivial algebraic varieties, and lead to proper parametrizations of the models, be they integrable or not. The authors mention the relation existing between spin models and the Bose-Messner algebras of algebraic combinatorics. The authors' results also yield the generalization of the condition q{sup n} = 1 so often mentioned in the theory of quantum groups, when no q parameter is available.« less

A catalytic metal ion interacts with the cleavage site G•U wobble in the HDV ribozyme†

PubMed Central

Chen, Jui-Hui; Gong, Bo; Bevilacqua, Philip C.; Carey, Paul R.; Golden, Barbara L.

2009-01-01

The HDV ribozyme self-cleaves by a chemical mechanism involving general acid-base catalysis to generate a 2′,3′-cyclic phosphate and a 5′-hydroxyl termini. Biochemical studies from several laboratories have implicated C75 as the general acid and hydrated magnesium as the general base. We have previously shown that C75 has a pKa shifted > 2 pH units toward neutrality [Gong, B., Chen, J. H., Chase, E., Chadalavada, D. M., Yajima, R., Golden, B. L., Bevilacqua, P. C., and Carey, P. R. (2007) J. Am. Chem. Soc. 129, 13335–13342.], while in crystal structures, it is well-positioned for proton transfer. However no crystallographic evidence for a hydrated magnesium poised to serve as a general base in the reaction has been observed in high-resolution crystal structures of various reaction states and mutants. Herein, we use solution kinetic experiments and parallel Raman crystallographic studies to examine the effects of pH on rate and Mg2+-binding properties of wild-type and 7-deazaguanosine mutants of the HDV ribozyme. These data suggest that a previously-unobserved hydrated magnesium ion interacts with the N7 of the cleavage site G•U wobble base pair. Integrating this metal ion binding site with the available crystal structures provides a new three-dimensional model for the active site of the ribozyme that accommodates all available biochemical data and appears competent for catalysis. The position of this metal is consistent with a role of a magnesium-bound hydroxide as a general base as dictated by biochemical data. PMID:19178151

Toward in situ x-ray diffraction imaging at the nanometer scale

NASA Astrophysics Data System (ADS)

Zatsepin, Nadia A.; Dilanian, Ruben A.; Nikulin, Andrei Y.; Gable, Brian M.; Muddle, Barry C.; Sakata, Osami

2008-08-01

We present the results of preliminary investigations determining the sensitivity and applicability of a novel x-ray diffraction based nanoscale imaging technique, including simulations and experiments. The ultimate aim of this nascent technique is non-destructive, bulk-material characterization on the nanometer scale, involving three dimensional image reconstructions of embedded nanoparticles and in situ sample characterization. The approach is insensitive to x-ray coherence, making it applicable to synchrotron and laboratory hard x-ray sources, opening the possibility of unprecedented nanometer resolution with the latter. The technique is being developed with a focus on analyzing a technologically important light metal alloy, Al-xCu (where x is 2.0-5.0 %wt). The mono- and polycrystalline samples contain crystallographically oriented, weakly diffracting Al2Cu nanoprecipitates in a sparse, spatially random dispersion within the Al matrix. By employing a triple-axis diffractometer in the non-dispersive setup we collected two-dimensional reciprocal space maps of synchrotron x-rays diffracted from the Al2Cu nanoparticles. The intensity profiles of the diffraction peaks confirmed the sensitivity of the technique to the presence and orientation of the nanoparticles. This is a fundamental step towards in situ observation of such extremely sparse, weakly diffracting nanoprecipitates embedded in light metal alloys at early stages of their growth.

Controlled synthesis of nanostructured molybdenum oxide electrodes for high performance supercapacitor devices

NASA Astrophysics Data System (ADS)

Maheswari, Nallappan; Muralidharan, Gopalan

2017-09-01

Well defined crystallographic and one dimensional morphological structure of molybdenum oxide were successfully synthesized by adjusting the duration of hydrothermal treatment. The prepared molybdenum oxide was examined through XRD, SEM, FTIR, TEM, BET and electrochemical studies. The XRD patterns illustrate that MoOx prepared by variying the hydrothermal reaction time are in different crystallographic structure of MoyOx (Mo8O23 and MoO3). SEM studies reveal the different morphological structures ranging from flake like morphology to nanorods. TEM images confirm the excellent nanorod structure. The nanorod structure ensures good cyclic behaviour with maximum capacitance of 1080 F g-1 at a current density of 2 A g-1. This large capacity of the MoO3 nanostructures enabled fabrication of symmetric and asymmertic supercapacitor devices. The asymmertic device exhibits a maximum specific capacitance of 145 F g-1 at 2 mV s-1 with highest energy density of 38.6 W h kg-1 at 374.7 W kg-1 power density.

Analytical three-dimensional neutron transport benchmarks for verification of nuclear engineering codes. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ganapol, B.D.; Kornreich, D.E.

Because of the requirement of accountability and quality control in the scientific world, a demand for high-quality analytical benchmark calculations has arisen in the neutron transport community. The intent of these benchmarks is to provide a numerical standard to which production neutron transport codes may be compared in order to verify proper operation. The overall investigation as modified in the second year renewal application includes the following three primary tasks. Task 1 on two dimensional neutron transport is divided into (a) single medium searchlight problem (SLP) and (b) two-adjacent half-space SLP. Task 2 on three-dimensional neutron transport covers (a) pointmore » source in arbitrary geometry, (b) single medium SLP, and (c) two-adjacent half-space SLP. Task 3 on code verification, includes deterministic and probabilistic codes. The primary aim of the proposed investigation was to provide a suite of comprehensive two- and three-dimensional analytical benchmarks for neutron transport theory applications. This objective has been achieved. The suite of benchmarks in infinite media and the three-dimensional SLP are a relatively comprehensive set of one-group benchmarks for isotropically scattering media. Because of time and resource limitations, the extensions of the benchmarks to include multi-group and anisotropic scattering are not included here. Presently, however, enormous advances in the solution for the planar Green`s function in an anisotropically scattering medium have been made and will eventually be implemented in the two- and three-dimensional solutions considered under this grant. Of particular note in this work are the numerical results for the three-dimensional SLP, which have never before been presented. The results presented were made possible only because of the tremendous advances in computing power that have occurred during the past decade.« less

Physical Webbing: Collaborative Kinesthetic Three-Dimensional Mind Maps[R

ERIC Educational Resources Information Center

Williams, Marian H.

2012-01-01

Mind Mapping has predominantly been used by individuals or collaboratively in groups as a paper-based or computer-generated learning strategy. In an effort to make Mind Mapping kinesthetic, collaborative, and three-dimensional, an innovative pedagogical strategy, termed Physical Webbing, was devised. In the Physical Web activity, groups…

Media Compositions for Three Dimensional Mammalian Tissue Growth Under Microgravity Culture Conditions

NASA Technical Reports Server (NTRS)

Goodwin, Thomas J. (Inventor)

1998-01-01

Normal mammalian tissue and the culturing process has been developed for the three groups of organ, structural and blood tissue. The cells are grown in vitro under microgravity culture conditions and form three dimensional cells aggregates with normal cell function. The microgravity culture conditions may be microgravity or simulated microgravity created in a horizontal rotating wall culture vessel.

Media Compositions for Three-Dimensional Mammalian Tissue Growth under Microgravity Culture Conditions

NASA Technical Reports Server (NTRS)

Goodwin, Thomas J. (Inventor)

1998-01-01

Normal mammalian tissue and the culturing process has been developed for the three groups of organ, structural and blood tissue.The cells are grown in vitro under microgravity culture conditions and form three dimensional cells aggregates with normal cell function. The microgravity culture conditions may be microgravity or simulated microgravity created in a horizontal rotating wall culture vessel.

Towards a better understanding of honeycomb alternating magnetic networks.

PubMed

Marino, Nadia; Armentano, Donatella; De Munno, Giovanni; Lloret, Francesc; Cano, Joan; Julve, Miguel

2015-06-28

Two new two-dimensional homometallic compounds {[M2(bpm)(ox)2]n·5nH2O} with M = Co(II) (1) and Zn(II) (2) and the mononuclear nickel(II) complex [Ni(bpm)2(ox)]·2H2O (3) [bpm = 2,2'-bipyrimidine and ox = oxalate] have been prepared and structurally characterized. 1 and 2 are isostructural compounds whose structures are made up of oxalate-bridged M(II) cations cross-linked by bis-bidentate bpm molecules to afford a honeycomb layered network extending in the crystallographic ab plane. The layers are eclipsed along the crystallographic c axis and show graphitic-like interactions between the bpm rings. The three-dimensional supramolecular network deriving from such interactions is characterized by hexagonal-shaped channels extending in the same direction. Each M(II) ion in 1 and 2 is tris-chelated with four oxygen atoms from two oxalate groups and two bpm-nitrogen atoms building a distorted octahedral surrounding. The reduced values of the angles subtended by the bis-chelating bpm [77.69(8) (1) and 76.59(8)° (2)] and oxalate [79.69(6) (1) and 80.01(5)° (2)] are the main factors accounting for this distortion. The values of the metal-metal separation through bridging bpm are 5.6956(7) (1) and 5.7572(9) Å (2), whereas those across the bis-bidentate oxalate are 5.4306(4) (1) and 5.4058(5) Å (2). 3 is a neutral mononuclear nickel(II) complex where each metal ion is six-coordinate with four nitrogen atoms from two bpm ligands in a cis arrangement and two oxalate-oxygen atoms building a somewhat distorted octahedral surrounding. The values of the angles subtended at the nickel(II) ion by bpm and oxalate are 78.14(4) and 80.95(5)°, respectively. The magnetic properties of 1 have been investigated in the temperature range 1.9-295 K. They are typical of an overall antiferromagnetic coupling with a maximum of the magnetic susceptibility at 22.0 K. The analysis of the susceptibility data of 1 through an effective spin Hamiltonian allowed a satisfactory simulation in the temperature range 10-295 K with the best-fit parameters λ = -110 cm(-1), α = 1.1, |Δ| = 400 cm(-1), J(ox) = -11.1 cm(-1) and J(bpm) = -5.0 cm(-1). The values of the antiferromagnetic coupling through bpm and ox in 1 have also been supported by electronic structure calculations based on Density Functional Theory (DFT) and they compare well with those reported in the literature for bpm-bridged dicobalt(II) complexes and oxalate-bridged cobalt(II) chains.

The Holographic F Theorem

NASA Astrophysics Data System (ADS)

Taylor, Marika; Woodhead, William

2017-12-01

The F theorem states that, for a unitary three dimensional quantum field theory, the F quantity defined in terms of the partition function on a three sphere is positive, stationary at fixed point and decreases monotonically along a renormalization group flow. We construct holographic renormalization group flows corresponding to relevant deformations of three-dimensional conformal field theories on spheres, working to quadratic order in the source. For these renormalization group flows, the F quantity at the IR fixed point is always less than F at the UV fixed point, but F increases along the RG flow for deformations by operators of dimension between 3/2 and 5/2. Therefore the strongest version of the F theorem is in general violated.

GIXSGUI : a MATLAB toolbox for grazing-incidence X-ray scattering data visualization and reduction, and indexing of buried three-dimensional periodic nanostructured films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Zhang

GIXSGUIis a MATLAB toolbox that offers both a graphical user interface and script-based access to visualize and process grazing-incidence X-ray scattering data from nanostructures on surfaces and in thin films. It provides routine surface scattering data reduction methods such as geometric correction, one-dimensional intensity linecut, two-dimensional intensity reshapingetc. Three-dimensional indexing is also implemented to determine the space group and lattice parameters of buried organized nanoscopic structures in supported thin films.

Rapid reversible borane to boryl hydride exchange by metal shuttling on the carborane cluster surface† †Electronic supplementary information (ESI) available. CCDC 1545735 and 1545736. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc01846k

PubMed Central

Eleazer, Bennett J.; Smith, Mark D.

2017-01-01

In this work, we introduce a novel concept of a borane group vicinal to a metal boryl bond acting as a supporting hemilabile ligand in exohedrally metalated three-dimensional carborane clusters. The (POBOP)Ru(Cl)(PPh3) pincer complex (POBOP = 1,7-OP(i-Pr)2-m-2-carboranyl) features extreme distortion of the two-center-two-electron Ru–B bond due to the presence of a strong three-center-two-electron B–H···Ru vicinal interaction. Replacement of the chloride ligand with a hydride afforded the (POBOP)Ru(H)(PPh3) pincer complex, which possesses B–Ru, B–H···Ru, and Ru–H bonds. This complex was found to exhibit a rapid exchange between hydrogen atoms of the borane and the terminal hydride through metal center shuttling between two boron atoms of the carborane cage. This exchange process, which involves sequential cleavage and formation of strong covalent metal–boron and metal–hydrogen bonds, is unexpectedly facile at temperatures above –50 °C corresponding to an activation barrier of 12.2 kcal mol–1. Theoretical calculations suggested two equally probable pathways for the exchange process through formally Ru(0) or Ru(iv) intermediates, respectively. The presence of this hemilabile vicinal B–H···Ru interaction in (POBOP)Ru(H)(PPh3) was found to stabilize a latent coordination site at the metal center promoting efficient catalytic transfer dehydrogenation of cyclooctane under nitrogen and air at 170 °C. PMID:28970919

Solidification microstructures in single-crystal stainless steel melt pools

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sipf, J.B.; Boatner, L.A.; David, S.A.

1994-03-01

Development of microstructure of stationary melt pools of oriented stainless steel single crystals (70%Fe-15%Ni-15%Cr was analyzed. Stationary melt pools were formed by electron-beam and gas-tungsten-arc heating on (001), (011), and (111) oriented planes of the austenitic, fcc-alloy crystals. Characterization and analysis of resulting microstructure was carried out for each crystallographic plane and welding method. Results showed that crystallography which favors ``easy growth`` along the <100> family of directions is a controlling factor in the microstructural formation along with the melt-pool shape. The microstructure was found to depend on the melting method, since each method forms a unique melt-pool shape. Thesemore » results are used in making a three-dimensional reconstruction of the microstructure for each plane and melting method employed. This investigation also suggests avenues for future research into the microstructural properties of electron-beam welds as well as providing an experimental basis for mathematical models for the prediction of solidification microstructures.« less

Crystal structure of octane-1,8-diaminium 4,4′-(diazene-1,2-di­yl)dibenzoate monohydrate

PubMed Central

Elkin, Igor; Christopherson, Jan-Constantin; Borchers, Tristan H.; Barrett, Christopher J.

2018-01-01

The title salt, C8H22N2 2+·C14H8N2O4 2−·H2O, represents a pseudo-polymer ionic material, resulting from the self-organizing behavior of 4,4′-azinodibenzoate dianions and doubly protonated, 1,8-diaminium-octane cations in aqueous solution. The asymmetric unit consists of two halves of octane 1,8-diaminium cations (the complete cations are both generated by crystallographic inversion symmetry), a 4,4′-azinodibenzoate anion [dihedral angle between the aromatic rings = 10.22 (4)°] and a water mol­ecule of crystallization. One of the cations is in a fully extended linear conformation while the second one has a terminal C—C—C—N gauche conformation. In the crystal, the cations, anions and water mol­ecules are linked into a three-dimensional network via a complex pattern of charge-assisted N—H⋯O and O—H⋯O hydrogen bonds. PMID:29850100

Mechanism of aquaporin-4's fast and highly selective water conduction and proton exclusion.

PubMed

Tani, Kazutoshi; Mitsuma, Tadanori; Hiroaki, Yoko; Kamegawa, Akiko; Nishikawa, Kouki; Tanimura, Yukihiro; Fujiyoshi, Yoshinori

2009-06-19

Members of the aquaporin (AQP) family are expressed in almost every organism, including 13 homologues in humans. Based on the electron crystallographic structure of AQP1, the hydrogen-bond isolation mechanism was proposed to explain why AQPs are impermeable to protons despite their very fast water conduction. The mechanism by which AQPs exclude protons remained controversial, however. Here we present the structure of AQP4 at 2.8 A resolution obtained by electron crystallography of double-layered two-dimensional crystals. The resolution has been improved from the previous 3.2 A, with accompanying improvement in data quality resulting in the ability to identify individual water molecules. Our structure of AQP4, the predominant water channel in the brain, reveals eight water molecules in the channel. The arrangement of the waters provides support for the hydrogen-bond isolation mechanism. Our AQP4 structure also visualizes five lipids, showing that direct interactions of the extracellular surface of AQP4 with three lipids in the adjoining membrane help stabilize the membrane junction.

Structure of a human monoclonal antibody Fab fragment against gp41 of human immunodeficiency virus type

NASA Technical Reports Server (NTRS)

He, X. M.; Ruker, F.; Casale, E.; Carter, D. C.

1992-01-01

The three-dimensional structure of a human monoclonal antibody (Fab), which binds specifically to a major epitope of the transmembrane protein gp41 of the human immunodeficiency virus type 1, has been determined by crystallographic methods to a resolution of 2.7 A. It has been previously determined that this antibody recognizes the epitope SGKLICTTAVPWNAS, belongs to the subclass IgG1 (kappa), and exhibits antibody-dependent cellular cytotoxicity. The quaternary structure of the Fab is in an extended conformation with an elbow bend angle between the constant and variable domains of 175 degrees. Structurally, four of the hypervariable loops can be classified according to previously recognized canonical structures. The third hypervariable loops of the heavy (H3) and light chain (L3) are structurally distinct. Hypervariable loop H3, residues 102H-109H, is unusually extended from the surface. The complementarity-determining region forms a hydrophobic binding pocket that is created primarily from hypervariable loops L3, H3, and H2.

Structure of a human monoclonal antibody Fab fragment against gp41 of human immunodeficiency virus type 1

NASA Technical Reports Server (NTRS)

He, Xiao M.; Rueker, Florian; Casale, Elena; Carter, Daniel C.

1992-01-01

The three-dimensional structure of a human monoclonal antibody (Fab), which binds specifically to a major epitope of the transmembrane protein gp41 of the human immunodeficiency virus type 1, has been determined by crystallographic methods to a resolution of 2.7 A. It has been previously determined that this antibody recognizes the epitope SGKLICTTAVPWNAS, belongs to the subclass IgG1 (kappa), and exhibits antibody-dependent cellular cytotoxicity. The quaternary structure of the Fab is in an extended conformation with an elbow bend angle between the constant and variable domains of 175 deg. Structurally, four of the hypervariable loops can be classified according to previously recognized canonical structures. The third hypervariable loops of the heavy (H3) and light chain (L3) are structurally distinct. Hypervariable loop H3, residues 102H-109H, is unusually extended from the surface. The complementarity-determining region forms a hydrophobic binding pocket that is created primarily from hypervariable loops L3, H3, and H2.

Reversible mechanical protection: building a 3D “suit” around a T-shaped benzimidazole axle† †Electronic supplementary information (ESI) available: Synthetic details and full characterisation of all new compounds. CCDC 1533271 and 1533272. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc00790f Click here for additional data file. Click here for additional data file.

PubMed Central

Baggi, Giorgio; Vukotic, V. Nicholas

2017-01-01

The T-shaped benzimidazolium/crown ether recognition motif was used to prepare suit[1]anes. These novel mechanically interlocked molecules (MIMs) were fully characterized by 1H and 13C NMR spectroscopy, single-crystal X-ray diffraction, UV-vis absorption and fluorescence spectroscopy. By conversion to a suit[1]ane, a simple benzimidazole was shown to be protected from deprotonation by strong base. Moreover, it was demonstrated that this unique three-dimensional encapsulation can be made reversible, thus introducing the concept of “reversible mechanical protection”; a protecting methodology that may have potential applications in synthetic organic chemistry and the design of molecular machinery. PMID:28626559

Nitridation- and Buffer-Layer-Free Growth of [1100]-Oriented GaN Domains on m-Plane Sapphire Substrates by Using Hydride Vapor Phase Epitaxy

NASA Astrophysics Data System (ADS)

Seo, Yeonwoo; Lee, Sanghwa; Jue, Miyeon; Yoon, Hansub; Kim, Chinkyo

2012-12-01

Over a wide range of growth conditions, GaN domains were grown on bare m-plane sapphire substrates by using hydride vapor phase epitaxy (HVPE), and the relation between these growth conditions and three possible preferred crystallographic orientations ([1100], [1103], [1122]) of GaN domains was investigated. In contrast with the previous reports by other groups, our results revealed that preferentially [1100]-oriented GaN domains were grown without low-temperature nitridation or a buffer layer, and that the growth condition of preferentially [1100]-oriented GaN was insensitive to V/III ratio.

Absorption Efficiencies of Forsterite. I: DDA Explorations in Grain Shape and Size

NASA Technical Reports Server (NTRS)

Lindsay, Sean S.; Wooden, Diane; Harker, David E.; Kelley, Michael S.; Woodward, Charles E.; Murphy, Jim R.

2013-01-01

We compute the absorption efficiency (Q(sub abs)) of forsterite using the discrete dipole approximation (DDA) in order to identify and describe what characteristics of crystal grain shape and size are important to the shape, peak location, and relative strength of spectral features in the 8 - 40 micron wavelength range. Using the DDSCAT code, we compute Q(sub abs) for non-spherical polyhedral grain shapes with a(sub eff) = 0.1 micron. The shape characteristics identified are: 1) elongation/reduction along one of three crystallographic axes; 2) asymmetry, such that all three crystallographic axes are of different lengths; and 3) the presence of crystalline faces that are not parallel to a specific crystallographic axis, e.g., non-rectangular prisms and (di)pyramids. Elongation/reduction dominates the locations and shapes of spectral features near 10, 11, 16, 23.5, 27, and 33.5 micron, while asymmetry and tips are secondary shape effects. Increasing grain sizes (0.1 - 1.0 micron) shifts the 10, 11 micron features systematically towards longer wavelengths and relative to the 11 micron feature increases the strengths and slightly broadens the longer wavelength features. Seven spectral shape classes are established for crystallographic a-, b-, and c-axes and include columnar and platelet shapes plus non-elongated or equant grain shapes. The spectral shape classes and the effects of grain size have practical application in identifying or excluding columnar, platelet or equant forsterite grain shapes in astrophysical environs. Identification of the shape characteristics of forsterite from 8 - 40 micron spectra provides a potential means to probe the temperatures at which forsterite formed.

Left ventricular mechanics in isolated mild mitral stenosis: a three dimensional speckle tracking study.

PubMed

Poyraz, Esra; Öz, Tuğba Kemaloğlu; Zeren, Gönül; Güvenç, Tolga Sinan; Dönmez, Cevdet; Can, Fatma; Güvenç, Rengin Çetin; Dayı, Şennur Ünal

2017-09-01

In a fraction of patients with mild mitral stenosis, left ventricular systolic function deteriorates despite the lack of hemodynamic load imposed by the dysfunctioning valve. Neither the predisposing factors nor the earlier changes in left ventricular contractility were understood adequately. In the present study we aimed to evaluate left ventricular mechanics using three-dimensional (3D) speckle tracking echocardiography. A total of 31 patients with mild rheumatic mitral stenosis and 27 healthy controls were enrolled to the study. All subjects included to the study underwent echocardiographic examination to collect data for two- and three-dimensional speckle-tracking based stain, twist angle and torsion measurements. Data was analyzed offline with a echocardiographic data analysis software. Patients with rheumatic mild MS had lower global longitudinal (p < 0.001) circumferential (p = 0.02) and radial (p < 0.01) strain compared to controls, despite ejection fraction was similar for both groups [(p = 0.45) for three dimensional and (p = 0.37) for two dimensional measurement]. While the twist angle was not significantly different between groups (p = 0.11), left ventricular torsion was significantly higher in mitral stenosis group (p = 0.03). All strain values had a weak but significant positive correlation with mitral valve area measured with planimetry. Subclinical left ventricular systolic dysfunction develops at an early stage in rheumatic mitral stenosis. Further work is needed to elucidate patients at risk for developing overt systolic dysfunction.

Helix-packing motifs in membrane proteins.

PubMed

Walters, R F S; DeGrado, W F

2006-09-12

The fold of a helical membrane protein is largely determined by interactions between membrane-imbedded helices. To elucidate recurring helix-helix interaction motifs, we dissected the crystallographic structures of membrane proteins into a library of interacting helical pairs. The pairs were clustered according to their three-dimensional similarity (rmsd

Crystal structure of tri­hydrogen bis­{[1,1,1-tris­(2-oxido­ethyl­amino­meth­yl)ethane]­cobalt(III)} trinitrate

PubMed Central

Sethi, Waqas; Johannesen, Heini V.; Morsing, Thorbjørn J.; Piligkos, Stergios; Weihe, Høgni

2015-01-01

The title compound, [Co2(L)2]3+·3NO3 − [where L = CH3C(CH2NHCH2CH2OH1/2)3], has been synthesized from the ligand 1,1,1-tris­(2-hy­droxy­ethyl­amino­meth­yl)ethane. The cobalt(III) dimer has an inter­esting and uncommon O—H⋯O hydrogen-bonding motif with the three bridging hy­droxy H atoms each being equally disordered over two positions. In the dimeric trication, the octa­hedrally coordinated CoIII atoms and the capping C atoms lie on a threefold rotation axis. The N atoms of two crystallographically independent nitrate anions also lie on threefold rotation axes. N—H⋯O hydrogen bonding between the complex cations and nitrate anions leads to the formation of a three-dimensional network structure. The compound is a racemic conglomerate of crystals containing either d or l mol­ecules. The crystal used for this study is a d crystal. PMID:26870462

Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase from Shewanella oneidensis at 1.6 angstrom: Identification of Farnesyl pyrophosphate Trapped in a Hydrophobic Cavity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ni, Shuisong; Robinson, Howard; Marsing, Gregory C.

2004-11-01

1. Introduction Enzymes in the non-mevalonate pathway for isoprenoid synthesis have gained recent attention because of their potential value as targets for antibiotic drug development. 2C-methyl-D-erythritol-2,4 cyclophosphate (MECDP) synthase is the fifth enzyme in the seven enzyme non-mevalonate pathway for synthesis of isopentenyl diphosphate. Four groups have published structures of MECDP synthase at resolutions varying from 1.6Å to 2.8Å, either in the presence or absence of substrate from Escherichia coli (Richard et al., 2002; Kemp et al., 2002; Steinbacher et al., 2002) or from Thermus thermophilus (Kishida et al., 2003). Among these structures, the protein always exists as a homotrimermore » either with a crystallographic or a non-crystallographic three-fold symmetry axis and an active site formed in a cleft between adjacent monomers. While the overall shape of the proteins is highly similar among these structures, each of the four reported structures contain different combinations of metal ions in the active site including a Zn2+ ion only (Steinbacher et al., 2002), a Mn2+ ion only (Richard et al., 2002), Zn2+ and Mn2+ ions (Kemp et al., 2002) or two Mg2+ ions (Kishida et al., 2003). Furthermore, two of the structures are reported to contain a hydrophobic channel along the three-fold symmetry axis that is capped by a cluster of three arginine side chains (one from each monomer) at one end of the cavity and a cluster of three glutamic acid side chains (one from each monomer) at the other side of the cavity. In a 1.8Å resolution structure, Kemp et al. (2002) reported a sulfate ion coordinated to the arginine cap and solvent trapped in a hydrophobic cavity. In a lower 2.8Å resolution structure, Richard et al. (2002) concluded that geranyl diphosphate, GPP, was most likely trapped by the arginine cap and hydrophobic cavity (Richard et al., 2002), however, the low resolution of the data together with the presence of the crystallographic symmetry axis prohibited a definitive analysis of the identity and mode of binding of the bound molecule. Kishida et al. (2003) reported that no cavity existed in a 1.6Å structure of the SO3437 homolog from Thermus thermophilus, presumably due to tighter packing of the protein from the thermophilic organism. Steinbacher et al. (2002) make no description of a hydrophobic cavity in a lower resolution (2.5-3.2Å) of the Escherichia coli protein. Here, we report a high-resolution (1.6Å) structure of MECDP synthase from Shewanella oneidensis in the absence of substrate in the active site. We provide unambiguous data that confirms the presence of Zn2+ in one of the metal binding sites and observe what appears to be farnesyl diphosphate (FPP) bound in the hydrophobic cavity along the non-crystallographic three-fold symmetry axis of the homotrimer. The high-resolution structure clarifies the mode of binding of the pyrophosphate of FPP in the arginine cluster that caps the hydrophobic cavity.« less

Spinorial characterizations of surfaces into three-dimensional homogeneous manifolds

NASA Astrophysics Data System (ADS)

Roth, Julien

2010-06-01

We give spinorial characterizations of isometrically immersed surfaces into three-dimensional homogeneous manifolds with four-dimensional isometry group in terms of the existence of a particular spinor field. This generalizes works by Friedrich for R3 and Morel for S3 and H3. The main argument is the interpretation of the energy-momentum tensor of such a spinor field as the second fundamental form up to a tensor depending on the structure of the ambient space.

Computer-Based Learning: Graphical Integration of Whole and Sectional Neuroanatomy Improves Long-Term Retention

PubMed Central

Naaz, Farah; Chariker, Julia H.; Pani, John R.

2013-01-01

A study was conducted to test the hypothesis that instruction with graphically integrated representations of whole and sectional neuroanatomy is especially effective for learning to recognize neural structures in sectional imagery (such as MRI images). Neuroanatomy was taught to two groups of participants using computer graphical models of the human brain. Both groups learned whole anatomy first with a three-dimensional model of the brain. One group then learned sectional anatomy using two-dimensional sectional representations, with the expectation that there would be transfer of learning from whole to sectional anatomy. The second group learned sectional anatomy by moving a virtual cutting plane through the three-dimensional model. In tests of long-term retention of sectional neuroanatomy, the group with graphically integrated representation recognized more neural structures that were known to be challenging to learn. This study demonstrates the use of graphical representation to facilitate a more elaborated (deeper) understanding of complex spatial relations. PMID:24563579

Calculation of unsteady aerodynamics for four AGARD standard aeroelastic configurations

NASA Technical Reports Server (NTRS)

Bland, S. R.; Seidel, D. A.

1984-01-01

Calculated unsteady aerodynamic characteristics for four Advisory Group for Aeronautical Research Development (AGARD) standard aeroelastic two-dimensional airfoils and for one of the AGARD three-dimensional wings are reported. Calculations were made using the finite-difference codes XTRAN2L (two-dimensional flow) and XTRAN3S (three-dimensional flow) which solve the transonic small disturbance potential equations. Results are given for the 36 AGARD cases for the NACA 64A006, NACA 64A010, and NLR 7301 airfoils with experimental comparisons for most of these cases. Additionally, six of the MBB-A3 airfoil cases are included. Finally, results are given for three of the cases for the rectangular wing.

Structure and thermodynamic stability of UTa 3 O 10 , a U( v )-bearing compound

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Xiaofeng; Lipp, Christian; Tiferet, Eitan

Heating a mixture of uranyl(VI) nitrate and tantalum(V) oxide in the molar ratio of 2 : 3 to 1400 °C resulted in the formation of a new compound, UTa 3O 10. The honey colored to yellow brown crystals of UTa 3O 10 crystallize in an orthorhombic structure with the space group Fddd (no. 70), lattice parameters a = 7.3947(1), b = 12.7599(2), c = 15.8156(2) Å, and Z = 8. Vertex sharing [TaO 6] 7- octahedra of two crystallographically distinct Ta cations form a three dimensional tantalate framework. Within this framework, six membered rings of [TaO 6] 7- octahedra aremore » formed within the (001) plane. The center of these rings is occupied by the uranyl cations [UO 2] +, with an oxidation state of +5 for uranium. The pentavalence of U and Ta was confirmed by X-ray photoelectron spectroscopy and X-ray adsorption spectroscopy. The enthalpy of formation of UTa 3O 10 from Ta 2O 5, β-U 3O 7, and U 3O 8 has been determined to be 13.1 ± 18.1 kJ mol -1 using high temperature oxide melt solution calorimetry with sodium molybdate as the solvent at 700 °C. The close to zero enthalpy of formation of UTa 3O 10 can be explained by closely balanced structural stabilizing and destabilizing factors, which may also apply to other UM 3O 10 compounds.« less

Synthesis and crystal structure determination of yttrium ultraphosphate YP 5O 14

NASA Astrophysics Data System (ADS)

Mbarek, A.; Graia, M.; Chadeyron, G.; Zambon, D.; Bouaziz, J.; Fourati, M.

2009-03-01

The crystal structure of monoclinic YP 5O 14 (space group C2/ c, a=12.919(2) Å, b=12.796(4) Å, c=12.457(2) Å, β=91.30(1)°, Z=8) has been refined from single-crystal X-ray diffraction data. Full-matrix least-squares refinement on F2 using 2249 independent reflections for 183 refinable parameters results in a final R value of 0.027 ( ωR=0.069). The structure is isotypic with HoP 5O 14. This structure is built up from infinite layers of PO 4 tetrahedra linked through isolated YO 8 polyhedra. The three-dimensional cohesion of the framework results from Y-O-P bridges. This crystal structure refinement leads to the calculated X-ray diffraction powder pattern of this monoclinic polymorph, which has been the starting point of a thorough study of the solid-state synthesis of this ultraphosphate. This investigation further leads to a better outstanding of features observed during the synthesis of powdered samples. The thermal behavior of this ultraphosphate has been studied by DTA and TGA analyses. The infrared and Raman spectroscopic characterizations have been carried out on polycrystalline samples. The luminescence properties of the Eu 3+ ion incorporated in the monoclinic C2/ c polymorph of YP 5O 14 as local structural probe show that in YP 5O 14: 5% Eu 3+ sample, the Eu 3+ ions are distributed over the two Y 3+ crystallographic sites of C 2 symmetry of this structure.

Synthesis, X-ray crystal structures and thermal analyses of some new antimicrobial zinc complexes: New configurations and nano-size structures.

PubMed

Masoudiasl, A; Montazerozohori, M; Naghiha, R; Assoud, A; McArdle, P; Safi Shalamzari, M

2016-04-01

Some new five coordinated ZnLX2 complexes, where L is N3-Schiff base ligand obtained by condensation reaction between diethylenetriamine and (E)-3-(2-nitrophenyl)acrylaldehyde and X (Cl(-), Br(-), I(-), N3(-) and NCS(-)), were synthesized and characterized by FT-IR, (1)H and (13)CNMR, UV-visible, ESI-mass spectra and molar conductivity measurements. The structures of zinc iodide and thiocyanate complexes were determined by X-ray crystallographic analysis. The X-ray results showed that the Zn (II) center in these complexes is five-coordinated in a distorted trigonal-bipyramidal configuration. Zinc iodide and thiocyanate complexes crystallize in the monoclinic and triclinic systems with space groups of C2/c and P1- with eight and two molecules per unit cell respectively. The crystal packing of the complexes consists of intermolecular interactions such as C-H(…)O and C-H(…)I, C-H(···)S, N(…)O, together with π-π stacking and some other unexpected interactions. The mentioned interactions cause three-dimensional supramolecular structure in the solid state. Zinc complexes were also prepared in nano-structure by sonochemical method confirmed by XRD, SEM and TEM analyses. Moreover, ZnO nanoparticles were synthesized by direct thermolysis of zinc iodide complex. Furthermore, antimicrobial and thermal properties of the compounds were completely investigated. Copyright © 2016 Elsevier B.V. All rights reserved.

Crystallization and preliminary crystallographic analysis of Abp, a GH27 β-L-arabinopyranosidase from Geobacillus stearothermophilus.

PubMed

Lansky, Shifra; Salama, Rachel; Solomon, Vered H; Belrhali, Hassan; Shoham, Yuval; Shoham, Gil

2013-06-01

Geobacillus stearothermophilus T-6 is a thermophilic soil bacterium that possesses an extensive system for the utilization of hemicellulose. The bacterium produces a small number of endo-acting extracellular enzymes that cleave high-molecular-weight hemicellulolytic polymers into short decorated oligosaccharides, which are further hydrolysed into the respective sugar monomers by a battery of intracellular glycoside hydrolases. One of these intracellular processing enzymes is β-L-arabinopyranosidase (Abp), which is capable of removing β-L-arabinopyranose residues from naturally occurring arabino-polysaccharides. As arabino-polymers constitute a significant part of the hemicellulolytic content of plant biomass, their efficient enzymatic degradation presents an important challenge for many potential biotechnological applications. This aspect has led to an increasing interest in the biochemical characterization and structural analysis of this and related hemicellulases. Abp from G. stearothermophilus T-6 has recently been cloned, overexpressed, purified, biochemically characterized and crystallized in our laboratory, as part of its complete structure-function study. The best crystals obtained for this enzyme belonged to the primitive orthorhombic space group P2(1)2(1)2(1), with average unit-cell parameters a = 107.7, b = 202.2, c = 287.3 Å. Full diffraction data sets to 2.3 Å resolution have been collected for both the wild-type enzyme and its D197A catalytic mutant from flash-cooled crystals at 100 K, using synchrotron radiation. These data are currently being used for a high-resolution three-dimensional structure determination of Abp.

Clinical application of three-dimensional printing to the management of complex univentricular hearts with abnormal systemic or pulmonary venous drainage.

PubMed

McGovern, Eimear; Kelleher, Eoin; Snow, Aisling; Walsh, Kevin; Gadallah, Bassem; Kutty, Shelby; Redmond, John M; McMahon, Colin J

2017-09-01

In recent years, three-dimensional printing has demonstrated reliable reproducibility of several organs including hearts with complex congenital cardiac anomalies. This represents the next step in advanced image processing and can be used to plan surgical repair. In this study, we describe three children with complex univentricular hearts and abnormal systemic or pulmonary venous drainage, in whom three-dimensional printed models based on CT data assisted with preoperative planning. For two children, after group discussion and examination of the models, a decision was made not to proceed with surgery. We extend the current clinical experience with three-dimensional printed modelling and discuss the benefits of such models in the setting of managing complex surgical problems in children with univentricular circulation and abnormal systemic or pulmonary venous drainage.

Three-dimensional morphological imaging of human induced pluripotent stem cells by using low-coherence quantitative phase microscopy

NASA Astrophysics Data System (ADS)

Yamauchi, Toyohiko; Kakuno, Yumi; Goto, Kentaro; Fukami, Tadashi; Sugiyama, Norikazu; Iwai, Hidenao; Mizuguchi, Yoshinori; Yamashita, Yutaka

2014-03-01

There is an increasing need for non-invasive imaging techniques in the field of stem cell research. Label-free techniques are the best choice for assessment of stem cells because the cells remain intact after imaging and can be used for further studies such as differentiation induction. To develop a high-resolution label-free imaging system, we have been working on a low-coherence quantitative phase microscope (LC-QPM). LC-QPM is a Linnik-type interference microscope equipped with nanometer-resolution optical-path-length control and capable of obtaining three-dimensional volumetric images. The lateral and vertical resolutions of our system are respectively 0.5 and 0.93 μm and this performance allows capturing sub-cellular morphological features of live cells without labeling. Utilizing LC-QPM, we reported on three-dimensional imaging of membrane fluctuations, dynamics of filopodia, and motions of intracellular organelles. In this presentation, we report three-dimensional morphological imaging of human induced pluripotent stem cells (hiPS cells). Two groups of monolayer hiPS cell cultures were prepared so that one group was cultured in a suitable culture medium that kept the cells undifferentiated, and the other group was cultured in a medium supplemented with retinoic acid, which forces the stem cells to differentiate. The volumetric images of the 2 groups show distinctive differences, especially in surface roughness. We believe that our LC-QPM system will prove useful in assessing many other stem cell conditions.

Fermionic spin liquid analysis of the paramagnetic state in volborthite

NASA Astrophysics Data System (ADS)

Chern, Li Ern; Schaffer, Robert; Sorn, Sopheak; Kim, Yong Baek

2017-10-01

Recently, thermal Hall effect has been observed in the paramagnetic state of volborthite, which consists of distorted kagome layers with S =1 /2 local moments. Despite the appearance of magnetic order below 1 K , the response to external magnetic field and unusual properties of the paramagnetic state above 1 K suggest possible realization of exotic quantum phases. Motivated by these discoveries, we investigate possible spin liquid phases with fermionic spinon excitations in a nonsymmorphic version of the kagome lattice, which belongs to the two-dimensional crystallographic group p 2 g g . This nonsymmorphic structure is consistent with the spin model obtained in the density functional theory calculation. Using projective symmetry group analysis and fermionic parton mean field theory, we identify twelve distinct Z2 spin liquid states, four of which are found to have correspondence in the eight Schwinger boson spin liquid states we classified earlier. We focus on the four fermionic states with bosonic counterpart and find that the spectrum of their corresponding root U (1 ) states features spinon Fermi surface. The existence of spinon Fermi surface in candidate spin liquid states may offer a possible explanation of the finite thermal Hall conductivity observed in volborthite.

Influence of misfit stresses on dislocation glide in single crystal superalloys: A three-dimensional discrete dislocation dynamics study

NASA Astrophysics Data System (ADS)

Gao, Siwen; Fivel, Marc; Ma, Anxin; Hartmaier, Alexander

2015-03-01

In the characteristic γ / γ ‧ microstructure of single crystal superalloys, misfit stresses occur due to a significant lattice mismatch of those two phases. The magnitude of this lattice mismatch depends on the chemical composition of both phases as well as on temperature. Furthermore, the lattice mismatch of γ and γ ‧ phases can be either positive or negative in sign. The internal stresses caused by such lattice mismatch play a decisive role for the micromechanical processes that lead to the observed macroscopic athermal deformation behavior of these high-temperature alloys. Three-dimensional discrete dislocation dynamics (DDD) simulations are applied to investigate dislocation glide in γ matrix channels and shearing of γ ‧ precipitates by superdislocations under externally applied uniaxial stresses, by fully taking into account internal misfit stresses. Misfit stress fields are calculated by the fast Fourier transformation (FFT) method and hybridized with DDD simulations. For external loading along the crystallographic [001] direction of the single crystal, it was found that the different internal stress states for negative and positive lattice mismatch result in non-uniform dislocation movement and different dislocation patterns in horizontal and vertical γ matrix channels. Furthermore, positive lattice mismatch produces a lower deformation rate than negative lattice mismatch under the same tensile loading, but for an increasing magnitude of lattice mismatch, the deformation resistance always diminishes. Hence, the best deformation performance is expected to result from alloys with either small positive, or even better, vanishing lattice mismatch between γ and γ ‧ phase.

Unsteady Performance of Finite-Span Pitching Propulsors in Mixtures of Side-by-Side and In-Line Arrangements

NASA Astrophysics Data System (ADS)

Kurt, Melike; Moored, Keith

2016-11-01

Birds, insects, and fish propel themselves by flapping their wings or oscillating their fins in unsteady motions. Many of these animals fly or swim in groups or collectives, typically described as flocks, swarms and schools. The three-dimensional steady flow interactions and the two dimensional unsteady flow interactions that occur in collectives are well characterized. However, the interactions that occur among three-dimensional unsteady propulsors remain relatively unexplored. The aim of the current study is to measure the forces acting on and the energetics of two finite-span pitching wings. The wings are arranged in mixtures of canonical in-line and side-by-side configurations while the phase delay between the pitching wings is varied. The thrust force, fluid-mediated interaction force between the wings and the propulsive efficiency are quantified. The three-dimensional interaction mechanisms are compared and contrasted with previously examined two-dimensional mechanisms. Stereoscopic particle image velocimetry is employed to characterize the three-dimensional flow structures along the span of the pitching wings.

CIF2Cell: Generating geometries for electronic structure programs

NASA Astrophysics Data System (ADS)

Björkman, Torbjörn

2011-05-01

The CIF2Cell program generates the geometrical setup for a number of electronic structure programs based on the crystallographic information in a Crystallographic Information Framework (CIF) file. The program will retrieve the space group number, Wyckoff positions and crystallographic parameters, make a sensible choice for Bravais lattice vectors (primitive or principal cell) and generate all atomic positions. Supercells can be generated and alloys are handled gracefully. The code currently has output interfaces to the electronic structure programs ABINIT, CASTEP, CPMD, Crystal, Elk, Exciting, EMTO, Fleur, RSPt, Siesta and VASP. Program summaryProgram title: CIF2Cell Catalogue identifier: AEIM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPL version 3 No. of lines in distributed program, including test data, etc.: 12 691 No. of bytes in distributed program, including test data, etc.: 74 933 Distribution format: tar.gz Programming language: Python (versions 2.4-2.7) Computer: Any computer that can run Python (versions 2.4-2.7) Operating system: Any operating system that can run Python (versions 2.4-2.7) Classification: 7.3, 7.8, 8 External routines: PyCIFRW [1] Nature of problem: Generate the geometrical setup of a crystallographic cell for a variety of electronic structure programs from data contained in a CIF file. Solution method: The CIF file is parsed using routines contained in the library PyCIFRW [1], and crystallographic as well as bibliographic information is extracted. The program then generates the principal cell from symmetry information, crystal parameters, space group number and Wyckoff sites. Reduction to a primitive cell is then performed, and the resulting cell is output to suitably named files along with documentation of the information source generated from any bibliographic information contained in the CIF file. If the space group symmetries is not present in the CIF file the program will fall back on internal tables, so only the minimal input of space group, crystal parameters and Wyckoff positions are required. Additional key features are handling of alloys and supercell generation. Additional comments: Currently implements support for the following general purpose electronic structure programs: ABINIT [2,3], CASTEP [4], CPMD [5], Crystal [6], Elk [7], exciting [8], EMTO [9], Fleur [10], RSPt [11], Siesta [12] and VASP [13-16]. Running time: The examples provided in the distribution take only seconds to run.

Method for Producing Non-Neoplastic, Three Dimensional, Mammalian Tissue and Cell Aggregates Under Microgravity Culture Conditions and the Products Produced Therefrom

NASA Technical Reports Server (NTRS)

Goodwin, Thomas J. (Inventor); Wolf, David A. (Inventor); Spaulding, Glenn F. (Inventor); Prewett, Tracey L. (Inventor)

1996-01-01

Normal mammalian tissue and the culturing process has been developed for the three groups of organ, structural, and blood tissue. The cells are grown in vitro under microgravity culture conditions and form three dimensional cells aggregates with normal cell function. The microgravity culture conditions may be microgravity or simulated microgravity created in a horizontal rotating wall culture vessel.

Highly luminescent colloidal nanoplates of perovskite cesium lead halide and their oriented assemblies

DOE PAGES

Bekenstein, Yehonadav; Koscher, Brent A.; Eaton, Samuel W.; ...

2015-12-15

Anisotropic colloidal quasi-two-dimensional nanoplates (NPLs) hold great promise as functional materials due to their combination of low dimensional optoelectronic properties and versatility through colloidal synthesis. Recently, lead-halide perovskites have emerged as important optoelectronic materials with excellent efficiencies in photovoltaic and light-emitting applications. Here we report the synthesis of quantum confined all inorganic cesium lead halide nanoplates in the perovskite crystal structure that are also highly luminescent (PLQY 84%). The controllable self-assembly of nanoplates either into stacked columnar phases or crystallographic-oriented thin-sheet structures is demonstrated. Furthermore, the broad accessible emission range, high native quantum yields, and ease of self-assembly make perovskitemore » NPLs an ideal platform for fundamental optoelectronic studies and the investigation of future devices.« less

Hot Electrons Regain Coherence in Semiconducting Nanowires

NASA Astrophysics Data System (ADS)

Reiner, Jonathan; Nayak, Abhay Kumar; Avraham, Nurit; Norris, Andrew; Yan, Binghai; Fulga, Ion Cosma; Kang, Jung-Hyun; Karzig, Toesten; Shtrikman, Hadas; Beidenkopf, Haim

2017-04-01

The higher the energy of a particle is above equilibrium, the faster it relaxes because of the growing phase space of available electronic states it can interact with. In the relaxation process, phase coherence is lost, thus limiting high-energy quantum control and manipulation. In one-dimensional systems, high relaxation rates are expected to destabilize electronic quasiparticles. Here, we show that the decoherence induced by relaxation of hot electrons in one-dimensional semiconducting nanowires evolves nonmonotonically with energy such that above a certain threshold hot electrons regain stability with increasing energy. We directly observe this phenomenon by visualizing, for the first time, the interference patterns of the quasi-one-dimensional electrons using scanning tunneling microscopy. We visualize the phase coherence length of the one-dimensional electrons, as well as their phase coherence time, captured by crystallographic Fabry-Pèrot resonators. A remarkable agreement with a theoretical model reveals that the nonmonotonic behavior is driven by the unique manner in which one-dimensional hot electrons interact with the cold electrons occupying the Fermi sea. This newly discovered relaxation profile suggests a high-energy regime for operating quantum applications that necessitate extended coherence or long thermalization times, and may stabilize electronic quasiparticles in one dimension.

Analysis of different fractionations of three-dimensional conformable radiotherapy for esophageal cancer.

PubMed

Ma, Zhiqian; Zhang, Yan; Chen, Xiaofang; Liu, Chaoxing; Xu, Huijun; Zhao, Peng

2015-01-01

This study aims to observe and discuss the curative and side effects of three different fractionation regimen of three-dimensional conformable radiotherapy (3DCRT) for esophageal cancer. A total of 169 untreated patients of esophageal cancer were randomized into three groups: groups A (conventional group, 2.0 Gy per time), B (2.5 Gy group, 2 Gy per time), and C (3.0 Gy group, 3.0 Gy per time), respectively. Groups A, B, and C are similar in terms of partial response (P = 0.35). However, the three groups had no significant differences in terms of the complete response (P = 0.63). The three-year survival rate of group B was higher than those of the other two groups, and the difference was significant (P = 0.047). For the three-year local control rate, that of group B was also higher than those of groups A and C, but the difference was not significant (P = 0.067). The incidence rate of 3 level esophagitis and bronchitis was highest in group C (P = 0.023 and P = 0.064). The 3 level tardive radioactive esophagitis in group C was higher than those in other two groups (P = 0.037 and P = 0.04). The incidence rate of the 3 level advanced lung reaction was also the highest in the three groups (P = 0.041). The effect is better and the side effect is tolerable for the 2.5 Gy per fraction, 5 times per week; thus, it can be used clinically for 3DCRT for esophageal carcinoma.

Developing a Learning Progression for Three-Dimensional Learning of the Patterns of Evolution

ERIC Educational Resources Information Center

Wyner, Yael; Doherty, Jennifer H.

2017-01-01

This paper examines how students make progress toward three-dimensional (3D) understanding of the patterns of evolution. Specifically, it proposes a learning progression that explains how scientific practices, crosscutting concepts, and disciplinary core ideas come together in naming and grouping, length of change over time, and the role of common…

Scaling up Three-Dimensional Science Learning through Teacher-Led Study Groups across a State

ERIC Educational Resources Information Center

Reiser, Brian J.; Michaels, Sarah; Moon, Jean; Bell, Tara; Dyer, Elizabeth; Edwards, Kelsey D.; McGill, Tara A. W.; Novak, Michael; Park, Aimee

2017-01-01

The vision for science teaching in the Framework for K-12 Science Education and the Next Generation Science Standards requires a radical departure from traditional science teaching. Science literacy is defined as three-dimensional (3D), in which students engage in science and engineering practices to develop and apply science disciplinary ideas…

Teaching Point-Group Symmetry with Three-Dimensional Models

ERIC Educational Resources Information Center

Flint, Edward B.

2011-01-01

Three tools for teaching symmetry in the context of an upper-level undergraduate or introductory graduate course on the chemical applications of group theory are presented. The first is a collection of objects that have the symmetries of all the low-symmetry and high-symmetry point groups and the point groups with rotational symmetries from 2-fold…

Missing depth cues in virtual reality limit performance and quality of three dimensional reaching movements

PubMed Central

Mayo, Johnathan; Baur, Kilian; Wittmann, Frieder; Riener, Robert; Wolf, Peter

2018-01-01

Background Goal-directed reaching for real-world objects by humans is enabled through visual depth cues. In virtual environments, the number and quality of available visual depth cues is limited, which may affect reaching performance and quality of reaching movements. Methods We assessed three-dimensional reaching movements in five experimental groups each with ten healthy volunteers. Three groups used a two-dimensional computer screen and two groups used a head-mounted display. The first screen group received the typically recreated visual depth cues, such as aerial and linear perspective, occlusion, shadows, and texture gradients. The second screen group received an abstract minimal rendering lacking those. The third screen group received the cues of the first screen group and absolute depth cues enabled by retinal image size of a known object, which realized with visual renderings of the handheld device and a ghost handheld at the target location. The two head-mounted display groups received the same virtually recreated visual depth cues as the second or the third screen group respectively. Additionally, they could rely on stereopsis and motion parallax due to head-movements. Results and conclusion All groups using the screen performed significantly worse than both groups using the head-mounted display in terms of completion time normalized by the straight-line distance to the target. Both groups using the head-mounted display achieved the optimal minimum in number of speed peaks and in hand path ratio, indicating that our subjects performed natural movements when using a head-mounted display. Virtually recreated visual depth cues had a minor impact on reaching performance. Only the screen group with rendered handhelds could outperform the other screen groups. Thus, if reaching performance in virtual environments is in the main scope of a study, we suggest applying a head-mounted display. Otherwise, when two-dimensional screens are used, achievable performance is likely limited by the reduced depth perception and not just by subjects’ motor skills. PMID:29293512

Influence of Objective Three-Dimensional Measures and Movement Images on Surgeon Treatment Planning for Lip Revision Surgery

PubMed Central

Trotman, Carroll-Ann; Phillips, Ceib; Faraway, Julian J.; Hartman, Terry; van Aalst, John A.

2013-01-01

Objective To determine whether a systematic evaluation of facial soft tissues of patients with cleft lip and palate, using facial video images and objective three-dimensional measurements of movement, change surgeons’ treatment plans for lip revision surgery. Design Prospective longitudinal study. Setting The University of North Carolina School of Dentistry. Patients, Participants A group of patients with repaired cleft lip and palate (n = 21), a noncleft control group (n = 37), and surgeons experienced in cleft care. Interventions Lip revision. Main Outcome Measures (1) facial photographic images; (2) facial video images during animations; (3) objective three-dimensional measurements of upper lip movement based on z scores; and (4) objective dynamic and visual three-dimensional measurement of facial soft tissue movement. Results With the use of the video images plus objective three-dimensional measures, changes were made to the problem list of the surgical treatment plan for 86% of the patients (95% confidence interval, 0.64 to 0.97) and the surgical goals for 71% of the patients (95% confidence interval, 0.48 to 0.89). The surgeon group varied in the percentage of patients for whom the problem list was modified, ranging from 24% (95% confidence interval, 8% to 47%) to 48% (95% confidence interval, 26% to 70%) of patients, and the percentage for whom the surgical goals were modified, ranging from 14% (94% confidence interval, 3% to 36%) to 48% (95% confidence interval, 26% to 70%) of patients. Conclusions For all surgeons, the additional assessment components of the systematic valuation resulted in a change in clinical decision making for some patients. PMID:23855676

Macromolecular diffractive imaging using imperfect crystals

PubMed Central

Ayyer, Kartik; Yefanov, Oleksandr; Oberthür, Dominik; Roy-Chowdhury, Shatabdi; Galli, Lorenzo; Mariani, Valerio; Basu, Shibom; Coe, Jesse; Conrad, Chelsie E.; Fromme, Raimund; Schaffer, Alexander; Dörner, Katerina; James, Daniel; Kupitz, Christopher; Metz, Markus; Nelson, Garrett; Lourdu Xavier, Paulraj; Beyerlein, Kenneth R.; Schmidt, Marius; Sarrou, Iosifina; Spence, John C. H.; Weierstall, Uwe; White, Thomas A.; Yang, Jay-How; Zhao, Yun; Liang, Mengning; Aquila, Andrew; Hunter, Mark S.; Robinson, Joseph S.; Koglin, Jason E.; Boutet, Sébastien; Fromme, Petra; Barty, Anton; Chapman, Henry N.

2016-01-01

The three-dimensional structures of macromolecules and their complexes are predominantly elucidated by X-ray protein crystallography. A major limitation is access to high-quality crystals, to ensure X-ray diffraction extends to sufficiently large scattering angles and hence yields sufficiently high-resolution information that the crystal structure can be solved. The observation that crystals with shrunken unit-cell volumes and tighter macromolecular packing often produce higher-resolution Bragg peaks1,2 hints that crystallographic resolution for some macromolecules may be limited not by their heterogeneity but rather by a deviation of strict positional ordering of the crystalline lattice. Such displacements of molecules from the ideal lattice give rise to a continuous diffraction pattern, equal to the incoherent sum of diffraction from rigid single molecular complexes aligned along several discrete crystallographic orientations and hence with an increased information content3. Although such continuous diffraction patterns have long been observed—and are of interest as a source of information about the dynamics of proteins4 —they have not been used for structure determination. Here we show for crystals of the integral membrane protein complex photosystem II that lattice disorder increases the information content and the resolution of the diffraction pattern well beyond the 4.5 Å limit of measurable Bragg peaks, which allows us to directly phase5 the pattern. With the molecular envelope conventionally determined at 4.5 Å as a constraint, we then obtain a static image of the photosystem II dimer at 3.5 Å resolution. This result shows that continuous diffraction can be used to overcome long-supposed resolution limits of macromolecular crystallography, with a method that puts great value in commonly encountered imperfect crystals and opens up the possibility for model-free phasing6,7. PMID:26863980

Effect of a mutation at arginine 301 on the stability, crystal quality and the preliminary crystallographic analysis of recombinant canavalin from Canavalia ensiformis

NASA Astrophysics Data System (ADS)

Elizabeth Green, M.; Kirkland, Natalie; Ng, Joseph D.

2001-11-01

The technique of site-directed mutagenesis was used to implement rational amino acid changes in the plant storage protein canavalin, the major seed storage protein of the jack bean ( Canavali ensiformis). The mutations were targeted to amino acids previously demonstrated to be involved in either the intra- or intermolecular salt bridges, thought to be responsible for maintaining the three-dimensional structure of the trimer. The amino acid changes were designed to disrupt the salt bridge interactions by substituting a neutral alanine for a negatively charged aspartate or glutamate, or by substituting a negatively charged glutamate for a positively charged arginine. The resulting recombinant mutants were subsequently expressed, purified, and crystallized. The crystals of the mutant versions of canavalin were compared to those of the wild-type canavalin by visual inspection and X-ray analysis. Of the crystals obtained for the mutants, those for the Arg301Glu mutation appeared to be more stable with fewer surface defects than any of the other mutants or the wild-type protein. The I/ σ ratio of reflections versus the resolution for the Arg301Glu mutation was approximately 30% greater over the entire resolution range than that obtained for any of the other mutations or for the wild-type. Additionally, the crystals of Arg301Glu mutations displayed lower mosaicity. Finally, the Arg301Glu mutation displayed a striking increase in the transition temperature when subjected to thermal denaturation. This paper describes the rationale and techniques behind the mutation of canavalin and suggests possible explanations for the observed and measured differences between the Arg301Glu mutant and the wild-type protein. We show the initial crystallographic structure analysis of this mutant and its preliminary implications.

Crystal structure of delta9 stearoyl-acyl carrier protein desaturase from castor seed and its relationship to other di-iron proteins.

PubMed Central

Lindqvist, Y; Huang, W; Schneider, G; Shanklin, J

1996-01-01

The three-dimensional structure of recombinant homodimeric delta9 stearoyl-acyl carrier protein desaturase, the archetype of the soluble plant fatty acid desaturases that convert saturated to unsaturated fatty acids, has been determined by protein crystallographic methods to a resolution of 2.4 angstroms. The structure was solved by a combination of single isomorphous replacement, anomalous contribution from the iron atoms to the native diffraction data and 6-fold non-crystallographic symmetry averaging. The 363 amino acid monomer consists of a single domain of 11 alpha-helices. Nine of these form an antiparallel helix bundle. The enzyme subunit contains a di-iron centre, with ligands from four of the alpha-helices in the helix bundle. The iron ions are bound in a highly symmetric environment, with one of the irons forming interactions with the side chains of E196 and H232 and the second iron with the side chains of E105 and H146. Two additional glutamic acid side chains, from E143 and E229, are within coordination distance to both iron ions. A water molecule is found within the second coordination sphere from the iron atoms. The lack of electron density corresponding to a mu-oxo bridge, and the long (4.2 angstroms) distance between the iron ions suggests that this probably represents the diferrous form of the enzyme. A deep channel which probably binds the fatty acid extends from the surface into the interior of the enzyme. Modelling of the substrate, stearic acid, into this channel places the delta9 carbon atom in the vicinity of one of the iron ions. Images PMID:8861937

Crystal structure of delta9 stearoyl-acyl carrier protein desaturase from castor seed and its relationship to other di-iron proteins.

PubMed

Lindqvist, Y; Huang, W; Schneider, G; Shanklin, J

1996-08-15

The three-dimensional structure of recombinant homodimeric delta9 stearoyl-acyl carrier protein desaturase, the archetype of the soluble plant fatty acid desaturases that convert saturated to unsaturated fatty acids, has been determined by protein crystallographic methods to a resolution of 2.4 angstroms. The structure was solved by a combination of single isomorphous replacement, anomalous contribution from the iron atoms to the native diffraction data and 6-fold non-crystallographic symmetry averaging. The 363 amino acid monomer consists of a single domain of 11 alpha-helices. Nine of these form an antiparallel helix bundle. The enzyme subunit contains a di-iron centre, with ligands from four of the alpha-helices in the helix bundle. The iron ions are bound in a highly symmetric environment, with one of the irons forming interactions with the side chains of E196 and H232 and the second iron with the side chains of E105 and H146. Two additional glutamic acid side chains, from E143 and E229, are within coordination distance to both iron ions. A water molecule is found within the second coordination sphere from the iron atoms. The lack of electron density corresponding to a mu-oxo bridge, and the long (4.2 angstroms) distance between the iron ions suggests that this probably represents the diferrous form of the enzyme. A deep channel which probably binds the fatty acid extends from the surface into the interior of the enzyme. Modelling of the substrate, stearic acid, into this channel places the delta9 carbon atom in the vicinity of one of the iron ions.

Non-Abelian string and particle braiding in topological order: Modular SL (3 ,Z ) representation and (3 +1 ) -dimensional twisted gauge theory

NASA Astrophysics Data System (ADS)

Wang, Juven C.; Wen, Xiao-Gang

2015-01-01

String and particle braiding statistics are examined in a class of topological orders described by discrete gauge theories with a gauge group G and a 4-cocycle twist ω4 of G 's cohomology group H4(G ,R /Z ) in three-dimensional space and one-dimensional time (3 +1 D ) . We establish the topological spin and the spin-statistics relation for the closed strings and their multistring braiding statistics. The 3 +1 D twisted gauge theory can be characterized by a representation of a modular transformation group, SL (3 ,Z ) . We express the SL (3 ,Z ) generators Sx y z and Tx y in terms of the gauge group G and the 4-cocycle ω4. As we compactify one of the spatial directions z into a compact circle with a gauge flux b inserted, we can use the generators Sx y and Tx y of an SL (2 ,Z ) subgroup to study the dimensional reduction of the 3D topological order C3 D to a direct sum of degenerate states of 2D topological orders Cb2 D in different flux b sectors: C3 D=⊕bCb2 D . The 2D topological orders Cb2 D are described by 2D gauge theories of the group G twisted by the 3-cocycle ω3 (b ), dimensionally reduced from the 4-cocycle ω4. We show that the SL (2 ,Z ) generators, Sx y and Tx y, fully encode a particular type of three-string braiding statistics with a pattern that is the connected sum of two Hopf links. With certain 4-cocycle twists, we discover that, by threading a third string through two-string unlink into a three-string Hopf-link configuration, Abelian two-string braiding statistics is promoted to non-Abelian three-string braiding statistics.

Two-dimensional 3d-4f heterometallic coordination polymers: syntheses, crystal structures, and magnetic properties of six new Co(II)-Ln(III) compounds.

PubMed

Díaz-Gallifa, Pau; Fabelo, Oscar; Pasán, Jorge; Cañadillas-Delgado, Laura; Lloret, Francesc; Julve, Miguel; Ruiz-Pérez, Catalina

2014-06-16

Six new heterometallic cobalt(II)-lanthanide(III) complexes of formulas [Ln(bta)(H2O)2]2[Co(H2O)6]·10H2O [Ln = Nd(III) (1) and Eu(III) (2)] and [Ln2Co(bta)2(H2O)8]n·6nH2O [Ln = Eu(III) (3), Sm(III) (4), Gd(III) (5), and Tb(III) (6)] (H4bta = 1,2,4,5-benzenetretracaboxylic acid) have been synthesized and characterized via single-crystal X-ray diffraction. 1 and 2 are isostructural compounds with a structure composed of anionic layers of [Ln(bta)(H2O)2]n(n-) sandwiching mononuclear [Co(H2O)6](2+) cations plus crystallization water molecules, which are interlinked by electrostatic forces and hydrogen bonds, leading to a supramolecular three-dimensional network. 3-6 are also isostructural compounds, and their structure consists of neutral layers of formula [Ln2Co(bta)2(H2O)8]n and crystallization water molecules, which are connected through hydrogen bonds to afford a supramolecular three-dimensional network. Heterometallic chains formed by the regular alternation of two nine-coordinate lanthanide(III) polyhedra [Ln(III)O9] and one compressed cobalt(II) octahedron [Co(II)O6] along the crystallographic c-axis are cross-linked by bta ligands within each layer of 3-6. Magnetic susceptibility measurements on polycrystalline samples for 3-6 have been carried out in the temperature range of 2.0-300 K. The magnetic behavior of these types of Ln(III)-Co(II) complexes, which have been modeled by using matrix dagonalization techniques, reveals the lack of magnetic coupling for 3 and 4, and the occurrence of weak antiferromagnetic interactions within the Gd(III)-Gd(III) (5) and Tb(III)-Tb(III) (6) dinuclear units through the exchange pathway provided by the double oxo(carboxylate) and double syn-syn carboxylate bridges.

Classification of Arnold-Beltrami flows and their hidden symmetries

NASA Astrophysics Data System (ADS)

Fré, P.; Sorin, A. S.

2015-07-01

In the context of mathematical hydrodynamics, we consider the group theory structure which underlies the so named ABC flows introduced by Beltrami, Arnold and Childress. Main reference points are Arnold's theorem stating that, for flows taking place on compact three manifolds ℳ3, the only velocity fields able to produce chaotic streamlines are those satisfying Beltrami equation and the modern topological conception of contact structures, each of which admits a representative contact one-form also satisfying Beltrami equation. We advocate that Beltrami equation is nothing else but the eigenstate equation for the first order Laplace-Beltrami operator ★ g d, which can be solved by using time-honored harmonic analysis. Taking for ℳ3, a torus T 3 constructed as ℝ3/Λ, where Λ is a crystallographic lattice, we present a general algorithm to construct solutions of the Beltrami equation which utilizes as main ingredient the orbits under the action of the point group B A of three-vectors in the momentum lattice *Λ. Inspired by the crystallographic construction of space groups, we introduce the new notion of a Universal Classifying Group which contains all space groups as proper subgroups. We show that the ★ g d eigenfunctions are naturally arranged into irreducible representations of and by means of a systematic use of the branching rules with respect to various possible subgroups we search and find Beltrami fields with non trivial hidden symmetries. In the case of the cubic lattice the point group is the proper octahedral group O24 and the Universal Classifying Group is a finite group G1536 of order |G1536| = 1536 which we study in full detail deriving all of its 37 irreducible representations and the associated character table. We show that the O24 orbits in the cubic lattice are arranged into 48 equivalence classes, the parameters of the corresponding Beltrami vector fields filling all the 37 irreducible representations of G1536. In this way we obtain an exhaustive classification of all generalized ABC- flows and of their hidden symmetries. We make several conceptual comments about the need of a field-theory yielding Beltrami equation as a field equation and/or an instanton equation and on the possible relation of Arnold-Beltrami flows with (supersymmetric) Chern-Simons gauge theories. We also suggest linear generalizations of Beltrami equation to higher odd-dimensions that are different from the non-linear one proposed by Arnold and possibly make contact with M-theory and the geometry of flux-compactifications.

Proton-transfer compounds with 4-amino-N-(4,6-dimethylpyrimidin-2-yl)benzenesulfonamide (sulfamethazine): the structures and hydrogen bonding in the salts with 5-nitrosalicylic acid and picric acid.

PubMed

Smith, Graham; Wermuth, Urs D

2013-05-01

The structures of the anhydrous proton-transfer compounds of the sulfa drug sulfamethazine with 5-nitrosalicylic acid and picric acid, namely 2-(4-aminobenzenesulfonamido)-4,6-dimethylpyrimidinium 2-hydroxy-5-nitrobenzoate, C12H15N4O2S(+)·C7H4NO4(-), (I), and 2-(4-aminobenzenesulfonamido)-4,6-dimethylpyrimidinium 2,4,6-trinitrophenolate, C12H15N4O2S(+)·C6H2N3O7(-), (II), respectively, have been determined. In the asymmetric unit of (I), there are two independent but conformationally similar cation-anion heterodimer pairs which are formed through duplex intermolecular N(+)-H···O(carboxylate) and N-H···O(carboxylate) hydrogen-bond pairs, giving a cyclic motif [graph set R2(2)(8)]. These heterodimers form separate and different non-associated substructures through aniline N-H···O hydrogen bonds, one one-dimensional, involving carboxylate O-atom acceptors, the other two-dimensional, involving both carboxylate and hydroxy O-atom acceptors. The overall two-dimensional structure is stabilized by π-π interactions between the pyrimidinium ring and the 5-nitrosalicylate ring in both heterodimers [minimum ring-centroid separation = 3.4580 (8) Å]. For picrate (II), the cation-anion interaction involves a slightly asymmetric chelating N-H···O R2(1)(6) hydrogen-bonding association with the phenolate O atom, together with peripheral conjoint R1(2)(6) interactions between the same N-H groups and O atoms of the ortho-related nitro groups. An inter-unit amine N-H···O(sulfone) hydrogen bond gives one-dimensional chains which extend along a and inter-associate through π-π interactions between the pyrimidinium rings [centroid-centroid separation = 3.4752 (9) Å]. The two structures reported here now bring to a total of four the crystallographically characterized examples of proton-transfer salts of sulfamethazine with strong organic acids.

Critical examination of quantum oscillations in SmB6

NASA Astrophysics Data System (ADS)

Riseborough, Peter S.; Fisk, Z.

2017-11-01

We critically review the results of magnetic torque measurements on SmB6 that show quantum oscillations. Similar studies have been given two different interpretations. One interpretation is based on the existence of metallic surface states, while the second interpretation is in terms of a three-dimensional Fermi surface involving neutral fermionic excitations. We suggest that the low-field oscillations that are seen by both groups for B fields as small as 6 T might be due to metallic surface states. The high-field three-dimensional oscillations are only seen by one group for fields B >18 T. The phenomenon of magnetic breakthrough occurs at high fields and involves the formation of Landau orbits that produces a directional-dependent suppression of Bragg scattering. We argue that the measurements performed under higher-field conditions are fully consistent with expectations based on a three-dimensional semiconducting state with magnetic breakthrough.

Petrology and deformation style of lithospheric mantle beneath the Heldburg Dike swarm (Central Germany) subset of Central European Volcanic Province

NASA Astrophysics Data System (ADS)

Kukuła, Anna; Puziewicz, Jacek; Hidas, Károly; Ntaflos, Theodoros; Matusiak-Małek, Magdalena; Milke, Ralf

2017-04-01

The Heldburg Dike swarm is a set of Cenozoic alkali basalt dikes occurring in the central part of Germany at the border between Thuringia and Bavaria. We studied xenoliths from Strauf, Feldstein, Bramberg and from the active quarry in Zeilberg. The peridotites from Strauf, Feldstein and Bramberg have the composition of spinel lherzolite (15), spinel harzburgite (9) and dunite (3). They vary in size from 1.5 cm (Strauf) up to 20 cm (Zeilberg). We distinguish groups (A, A- and B) of peridotites based on different forsterite content in olivine. Group A consists of olivine (89.6 - 91.8 Fo), orthopyroxene (Mg# 0.90-0.93, Al 0.05-0.18 a pfu), clinopyroxene (Mg# 0.87-0.95, Al 0.06-0.26 a pfu) and spinel (Cr# 0.13-0.65, Mg# 0.54-0.78). Clinopyroxene rare earth elements (REE) patterns are S-shaped (Feldstein, Bramberg) or U-shaped (Strauf); spoon-shaped patterns occur occasionally. Trace element (TE) patterns show negative Nb, Ta, Zr, Hf, Ti and positive Th, U anomalies. The most magnesian clinopyroxene (xenolith 3140, Feldstein) is strongly aluminous and LREE depletedwith weak anomalies in TE patterns. Group A- is contains olivine (88.9-89.5 Fo), orthopyroxene (Mg# 0.89-0.90, Al 0.10-0.13 a pfu) and clinopyroxene (Mg# 0.90-0.92, Al 0.10-0.17 a pfu). Clinopyroxene is increasingly enriched in REEs from Lu to La. TE patterns are similar to those of group A but with less pronounced anomalies. Group B (3 xenoliths only) consists of olivine Fo 86.7-88.9, orthopyroxene (Mg# 0.88-0.89, Al 0.07-0.19 a pfu), clinopyroxene (Mg# 0.88-0.90, Al 0.10-0.26 a pfu). Clinopyroxene is enriched in LREE, concave upward in Pr. TE patterns are similar to those in group A. One of group B harzburgites contains grains (up to 0.5 mm) of Ca-Mg carbonate located in interstices. The clinopyroxene chemical composition plots away from the melting trend in the MgO-Al2O3 diagram of Upton et al. (2011), suggesting a later addition of the clinopyroxene. The composition of orthopyroxene corresponds to ca. 15-30 % of melting of primitive mantle, which was overprinted by silicate and/or carbonatite metasomatism. The xenolith 3140 seems not to be affected by metasomatic overprint. Based on the EBSD analyses of 15 xenoliths, olivine grains are characterized by relatively strong CPO (crystal preferred orientation) with J indices 4.4 - 13.3, and they have orthorhombic (8 xenoliths) or [100]-fiber CPO (6 xenoliths) symmetries except for one [010]-fiber symmetry observed in group B (Tommasi et al., 1999). Pyroxenes have weaker CPO and the distribution of their crystallographic axes is inconsistent with their coeval deformation with olivine. We propose that their CPO postdates that of olivine, hence strongly support a later origin for pyroxenes. Funding. This study was possible thanks to the project NCN UMO-2014/15/B/ST10/00095 of Polish National Centre for Science to JP Tommasi, A., B. Tikoff, and A. Vauchez (1999). Upper mantle tectonics: three-dimensional deformation, olivine crystallographic fabrics and seismic properties, Earth Planet Sc Lett,168, 173-186. Upton, B.G.J., Downes, H., Kirstein, L.A., Bonadiman, C., Hill, P.G., Ntaflos, T. (2011). The lithospheric mantle and lower crust-mantle relationships under Scotland: a xenolithic perspective. J Geol Soc, 168, 873-886.

Electronic structure of CuTeO 4 and its relationship to cuprates

DOE PAGES

Botana, Antia S.; Norman, Michael R.

2017-03-13

Based on first-principles calculations, the electronic structure of CuTeO 4 is discussed in the context of superconducting cuprates. Despite some significant crystallographic differences, we find that CuTeO 4 is similar to these cuprates, exhibiting a quasi-two-dimensional electronic structure that involves hybridized Cu- d and O-p states in the vicinity of the Fermi level, along with an antiferromagnetic insulating ground state. Lastly, hole- doping this material by substituting Te 6+ with Sb 5+ would be of significant interest.

Analysis of Crystallographic Structure of a Japanese Sword by the Pulsed Neutron Transmission Method

NASA Astrophysics Data System (ADS)

Kino, K.; Ayukawa, N.; Kiyanagi, Y.; Uchida, T.; Uno, S.; Grazzi, F.; Scherillo, A.

We measured two-dimensional transmission spectra of pulsed neutron beams for a Japanese sword sample. Atom density, crystalline size, and preferred orientation of crystals were obtained using the RITS code. The position dependence of the atomic density is consistent with the shape of the sample. The crystalline size is very small and shows position dependence, which is understood by the unique structure of Japanese swords. The preferred orientation has strong position dependence. Our study shows the usefulness of the pulsed neutron transmission method for cultural metal artifacts.

Effectiveness of Three-Dimensional Digital Animation in Teaching Human Anatomy in an Authentic Classroom Context

ERIC Educational Resources Information Center

Hoyek, Nady; Collet, Christian; Di Rienzo, Franck; De Almeida, Mickael; Guillot, Aymeric

2014-01-01

Three-dimensional (3D) digital animations were used to teach the human musculoskeletal system to first year kinesiology students. The purpose of this study was to assess the effectiveness of this method by comparing two groups from two different academic years during two of their official required anatomy examinations (trunk and upper limb…

NASA Tech Briefs, April 2005

NASA Technical Reports Server (NTRS)

2005-01-01

Gas-Tolerant Device Senses Electrical Conductivity of Liquid Nanoactuators Based on Electrostatic Forces on Dielectrics Replaceable Microfluidic Cartridges for a PCR Biosensor CdZnTe Image Detectors for Hard-X-Ray Telescopes High-Aperture-Efficiency Horn Antenna Full-Circle Resolver-to-Linear-Analog Converter Continuous, Full-Circle Arctangent Circuit Advanced Three-Dimensional Display System Automatic Focus Adjustment of a Microscope Topics covered include: FastScript3D - A Companion to Java 3D; Generating Mosaics of Astronomical Images; Simulating Descent and Landing of a Spacecraft; Simulating Vibrations in a Complex Loaded Structure; Rover Sequencing and Visualization Program; Software Template for Instruction in Mathematics; Support for User Interfaces for Distributed Systems; Nanostructured MnO2-Based Cathodes for Li-Ion/Polymer Cells; Multi-Layer Laminated Thin Films for Inflatable Structures; Two-Step Laser Ranging for Precise Tracking of a Spacecraft; Growing Aligned Carbon Nanotubes for Interconnections in ICs; Multilayer Composite Pressure Vessels; Texturing Blood-Glucose-Monitoring Optics Using Oxygen Beams; Fault-Tolerant Heat Exchanger; Atomic Clock Based on Opto-Electronic Oscillator; Microfocus/Polycapillary-Optic Crystallographic X-Ray Sys; Depth-Penetrating Luminescence Thermography of Thermal- Barrier Coatings; One-Dimensional Photonic Crystal Superprisms; Measuring Low-Order Aberrations in a Segmented Telescope; Mapping From an Instrumented Glove to a Robot Hand; Application of the Hilbert-Huang Transform to Financial Data; Optimizing Parameters for Deep-Space Optical Communication; and Low-Shear Microencapsulation and Electrostatic Coating.

Critical Intermediate Structure That Directs the Crystalline Texture and Surface Morphology of Organo-Lead Trihalide Perovskite.

PubMed

Chia, Hao-Chung; Sheu, Hwo-Shuenn; Hsiao, Yu-Yun; Li, Shao-Sian; Lan, Yi-Kang; Lin, Chung-Yao; Chang, Je-Wei; Kuo, Yen-Chien; Chen, Chia-Hao; Weng, Shih-Chang; Su, Chun-Jen; Su, An-Chung; Chen, Chun-Wei; Jeng, U-Ser

2017-10-25

We have identified an often observed yet unresolved intermediate structure in a popular processing with dimethylformamide solutions of lead chloride and methylammonium iodide for perovskite solar cells. With subsecond time-resolved grazing-incidence X-ray scattering and X-ray photoemission spectroscopy, supplemental with ab initio calculation, the resolved intermediate structure (CH 3 NH 3 ) 2 PbI 2 Cl 2 ·CH 3 NH 3 I features two-dimensional (2D) perovskite bilayers of zigzagged lead-halide octahedra and sandwiched CH 3 NH 3 I layers. Such intermediate structure reveals a hidden correlation between the intermediate phase and the composition of the processing solution. Most importantly, the 2D perovskite lattice of the intermediate phase is largely crystallographically aligned with the [110] planes of the three-dimensional perovskite cubic phase; consequently, with sublimation of Cl ions from the organo-lead octahedral terminal corners in prolonged annealing, the zigzagged octahedral layers of the intermediate phase can merge with the intercalated methylammonium iodide layers for templated growth of perovskite crystals. Regulated by annealing temperature and the activation energies of the intermediate and perovskite, deduced from analysis of temperature-dependent structural kinetics, the intermediate phase is found to selectively mature first and then melt along the layering direction for epitaxial conversion into perovskite crystals. The unveiled epitaxial conversion under growth kinetics controls might be general for solution-processed and intermediate-templated perovskite formation.

Defect Passivation of Organic–Inorganic Hybrid Perovskites by Diammonium Iodide toward High-Performance Photovoltaic Devices

DOE PAGES

Zhao, Ting; Chueh, Chu-Chen; Chen, Qi; ...

2016-09-12

The polycrystalline feature of solutionprocessed perovskite film and its ionic nature inevitably incur substantial crystallographic defects, especially at the film surface and the grain boundaries (GBs). Here, a simple defect passivation method was exploited by post-treating CH 3NH 3PbI 3 (MAPbI 3) film with a rationally selected diammonium iodide. The molecular structure of the used diammonium iodide was discovered to play a critical role in affecting the phase purity of treated MAPbI 3. Both NH 3I(CH 2) 4NH 3I and NH 3I(CH 2) 2O(CH 2) 2NH 3I (EDBE) induce three-dimensional (3D) to two-dimensional (2D) perovskite phase transformation during the treatmentmore » while only NH 3I(CH 2) 8NH 3I (C 8) successfully passivates perovskite surface and GBs without forming 2D perovskite because of the elevated activation energy arising from its unique anti-gauche isomerization. In conclusion, defect passivation of MAPbI 3 was clearly confirmed by scanning Kelvin probe microscopy (SKPM) and time-resolved photoluminescence (TRPL) studies, which results in the reduced recombination loss in derived devices. Consequently, the perovskite solar cell with C 8 passivation showed a much improved power conversion efficiency (PCE) of 17.60% compared to the control device PCE of 14.64%.« less

A series of three-dimensional lanthanide coordination polymers with rutile and unprecedented rutile-related topologies.

PubMed

Qin, Chao; Wang, Xin-Long; Wang, En-Bo; Su, Zhong-Min

2005-10-03

The complexes of formulas Ln(pydc)(Hpydc) (Ln = Sm (1), Eu (2), Gd (3); H2pydc = pyridine-2,5-dicarboxylic acid) and Ln(pydc)(bc)(H2O) (Ln = Sm (4), Gd (5); Hbc = benzenecarboxylic acid) have been synthesized under hydrothermal conditions and characterized by elemental analysis, IR, TG analysis, and single-crystal X-ray diffraction. Compounds 1-3 are isomorphous and crystallize in the orthorhombic system, space group Pbcn. Their final three-dimensional racemic frameworks can be considered as being constructed by helix-linked scalelike sheets. Compounds 4 and 5 are isostructural and crystallize in the monoclinic system, space group P2(1)/c. pydc ligands bridge dinuclear lanthanide centers to form the three-dimensional frameworks featuring hexagonal channels along the a-axis that are occupied by one-end-coordinated bc ligands. From the topological point of view, the five three-dimensional nets are binodal with six- and three-connected nodes, the former of which exhibit a rutile-related (4.6(2))(2)(4(2).6(9).8(4)) topology that is unprecedented within coordination frames, and the latter two species display a distorted rutile (4.6(2))(2)(4(2).6(10).8(3)) topology. Furthermore, the luminescent properties of 2 were studied.

Three-dimensionally networked graphene hydroxide with giant pores and its application in supercapacitors

PubMed Central

Lee, Dongwook; Seo, Jiwon

2014-01-01

The three-dimensionally networked and layered structure of graphene hydroxide (GH) was investigated. After lengthy immersion in a NaOH solution, most of the epoxy groups in the graphene oxide were destroyed, and more hydroxyl groups were generated, transforming the graphene oxide into graphene hydroxide. Additionally, benzoic acid groups were formed, and the ether groups link the neighboring layers, creating a near-3D structure in the GH. To utilize these unique structural features, electrodes with large pores for use in supercapacitors were fabricated using thermal reduction in vacuum. The reduced GH maintained its layered structure and developed a lot of large of pores between/inside the layers. The GH electrodes exhibited high gravimetric as well as high volumetric capacitance. PMID:25492227

Three-dimensionally networked graphene hydroxide with giant pores and its application in supercapacitors

NASA Astrophysics Data System (ADS)

Lee, Dongwook; Seo, Jiwon

2014-12-01

The three-dimensionally networked and layered structure of graphene hydroxide (GH) was investigated. After lengthy immersion in a NaOH solution, most of the epoxy groups in the graphene oxide were destroyed, and more hydroxyl groups were generated, transforming the graphene oxide into graphene hydroxide. Additionally, benzoic acid groups were formed, and the ether groups link the neighboring layers, creating a near-3D structure in the GH. To utilize these unique structural features, electrodes with large pores for use in supercapacitors were fabricated using thermal reduction in vacuum. The reduced GH maintained its layered structure and developed a lot of large of pores between/inside the layers. The GH electrodes exhibited high gravimetric as well as high volumetric capacitance.

Three-dimensionally networked graphene hydroxide with giant pores and its application in supercapacitors.

PubMed

Lee, Dongwook; Seo, Jiwon

2014-12-10

The three-dimensionally networked and layered structure of graphene hydroxide (GH) was investigated. After lengthy immersion in a NaOH solution, most of the epoxy groups in the graphene oxide were destroyed, and more hydroxyl groups were generated, transforming the graphene oxide into graphene hydroxide. Additionally, benzoic acid groups were formed, and the ether groups link the neighboring layers, creating a near-3D structure in the GH. To utilize these unique structural features, electrodes with large pores for use in supercapacitors were fabricated using thermal reduction in vacuum. The reduced GH maintained its layered structure and developed a lot of large of pores between/inside the layers. The GH electrodes exhibited high gravimetric as well as high volumetric capacitance.

Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, Edward B.; Gurda-Whitaker, Brittney; Govindasamy, Lakshmanan

2006-12-01

Crystals of baculovirus-expressed adeno-associated virus serotype 1 (AAV1) capsids have been grown in the rhombohedral space group R32 (unit-cell parameters a = 254.7 Å, α = 62.3°) and shown to diffract X-rays to at least 2.5 Å resolution. Crystals of baculovirus-expressed adeno-associated virus serotype 1 (AAV1) capsids have been grown in the rhombohedral space group R32 (unit-cell parameters a = 254.7 Å, α = 62.3°) and shown to diffract X-rays to at least 2.5 Å resolution. The diffraction data were subsequently processed and reduced with an overall R{sub sym} of 12.3% and a completeness of 89.0%. Based on the unit-cellmore » volume, rotation-function and translation-function results and packing considerations, there is one virus capsid (60 viral proteins) per unit cell and there are ten viral proteins per crystallographic asymmetric unit. The AAV1 capsid shares both the twofold and threefold crystallographic symmetry operators. The AAV1 data have been initially phased using a polyalanine model (based on the crystal structure of AAV4) to 4.0 Å resolution and the structure determination and refinement is in progress using tenfold noncrystallographic symmetry electron-density averaging.« less

Refolding, crystallization and preliminary X-ray crystallographic studies of the β-barrel domain of BamA, a membrane protein essential for outer membrane protein biogenesis.

PubMed

Ni, Dongchun; Yang, Kun; Huang, Yihua

2014-03-01

In Gram-negative bacteria, the assembly of outer membrane proteins (OMPs) requires a five-protein β-barrel assembly machinery (BAM) complex, of which BamA is an essential and evolutionarily conserved integral outer membrane protein. Here, the refolding, crystallization and preliminary X-ray crystallographic characterization of the β-barrel domain of BamA from Escherichia coli (EcBamA) are reported. Native and selenomethionine-substituted EcBamA proteins were crystallized at 16°C and X-ray diffraction data were collected to 2.6 and 3.7 Å resolution, respectively. The native crystals belonged to space group P21212, with unit-cell parameters a = 118.492, b = 159.883, c = 56.000 Å and two molecules in one asymmetric unit; selenomethionine-substituted protein crystals belonged to space group P4322, with unit-cell parameters a = b = 163.162, c = 46.388 Å and one molecule in one asymmetric unit. Initial phases for EcBamA β-barrel domain were obtained from a SeMet SAD data set. These preliminary X-ray crystallographic studies paved the way for further structural determination of the β-barrel domain of EcBamA.

5,11,17,23-Tetra-tert-butyl-25,26,27,28-tetra­methoxy­calix[4]arene dichloro­methane hemisolvate

PubMed Central

Fischer, Conrad; Gruber, Tobias; Seichter, Wilhelm; Schindler, Diana; Weber, Edwin

2008-01-01

In the title compound, C48H64O4·0.5CH2Cl2, both crystallographically independent calixarene mol­ecules display a partial cone conformation. Their crystal packing is stabilized by C—H⋯π contacts involving the meth­oxy groups. The solvent mol­ecule is located inter­stitially between two calixarene units with C—H⋯Cl contacts to meth­oxy and tert-butyl groups. One tert-butyl residue of each calixarene mol­ecule is disordered over two positions (occupancies 0.60/0.40 and 0.63/0.37), resulting in bond distances that deviate from ideal values. The tetra­mer calixarene mol­ecules present models with approximate non-crystallographic Cs symmetry. PMID:21202066

Attitude Estimation or Quaternion Estimation?

NASA Technical Reports Server (NTRS)

Markley, F. Landis

2003-01-01

The attitude of spacecraft is represented by a 3x3 orthogonal matrix with unity determinant, which belongs to the three-dimensional special orthogonal group SO(3). The fact that all three-parameter representations of SO(3) are singular or discontinuous for certain attitudes has led to the use of higher-dimensional nonsingular parameterizations, especially the four-component quaternion. In attitude estimation, we are faced with the alternatives of using an attitude representation that is either singular or redundant. Estimation procedures fall into three broad classes. The first estimates a three-dimensional representation of attitude deviations from a reference attitude parameterized by a higher-dimensional nonsingular parameterization. The deviations from the reference are assumed to be small enough to avoid any singularity or discontinuity of the three-dimensional parameterization. The second class, which estimates a higher-dimensional representation subject to enough constraints to leave only three degrees of freedom, is difficult to formulate and apply consistently. The third class estimates a representation of SO(3) with more than three dimensions, treating the parameters as independent. We refer to the most common member of this class as quaternion estimation, to contrast it with attitude estimation. We analyze the first and third of these approaches in the context of an extended Kalman filter with simplified kinematics and measurement models.

First-principles study of crystallographic slip modes in ω-Zr.

PubMed

Kumar, Anil; Kumar, M Arul; Beyerlein, Irene J

2017-08-21

We use first-principles density functional theory to study the preferred modes of slip in the high-pressure ω phase of Zr. The generalized stacking fault energy surfaces associated with shearing on nine distinct crystallographic slip modes in the hexagonal ω-Zr crystal are calculated, from which characteristics such as ideal shear stress, the dislocation Burgers vector, and possible accompanying atomic shuffles, are extracted. Comparison of energy barriers and ideal shear stresses suggests that the favorable modes are prismatic 〈c〉, prismatic-II [Formula: see text] and pyramidal-II 〈c + a〉, which are distinct from the ground state hexagonal close packed α phase of Zr. Operation of these three modes can accommodate any deformation state. The relative preferences among the identified slip modes are examined using a mean-field crystal plasticity model and comparing the calculated deformation texture with the measurement. Knowledge of the basic crystallographic modes of slip is critical to understanding and analyzing the plastic deformation behavior of ω-Zr or mixed α-ω phase-Zr.

The effects of absence of stereopsis on performance of a simulated surgical task in two-dimensional and three-dimensional viewing conditions

PubMed Central

Bloch, Edward; Uddin, Nabil; Gannon, Laura; Rantell, Khadija; Jain, Saurabh

2015-01-01

Background Stereopsis is believed to be advantageous for surgical tasks that require precise hand-eye coordination. We investigated the effects of short-term and long-term absence of stereopsis on motor task performance in three-dimensional (3D) and two-dimensional (2D) viewing conditions. Methods 30 participants with normal stereopsis and 15 participants with absent stereopsis performed a simulated surgical task both in free space under direct vision (3D) and via a monitor (2D), with both eyes open and one eye covered in each condition. Results The stereo-normal group scored higher, on average, than the stereo-absent group with both eyes open under direct vision (p<0.001). Both groups performed comparably in monocular and binocular monitor viewing conditions (p=0.579). Conclusions High-grade stereopsis confers an advantage when performing a fine motor task under direct vision. However, stereopsis does not appear advantageous to task performance under 2D viewing conditions, such as in video-assisted surgery. PMID:25185439

Synthesis, crystal structure and characterization of chiral, three-dimensional anhydrous potassium tris(oxalato)ferrate(III)

NASA Astrophysics Data System (ADS)

Saritha, A.; Raju, B.; Ramachary, M.; Raghavaiah, P.; Hussain, K. A.

2012-11-01

The synthesis, crystal structure and physical properties of chiral, three-dimensional anhydrous potassium tris(oxalato)ferrate(III) [K3Fe(C2O4)3] are described. X-ray analysis reveals that the compound crystallized in the chiral space group P4132 of cubic system with a=b=c=13.5970(2), Z=4. The structure of the complex consists of infinite anionic [Fe(C2O4)3]3- units with distorted octahedral environment of iron surrounded by six oxygen atoms of three oxalato groups. The anionic units are interlinked through K+ ions of three different coordination environments of distorted octahedral, bicapped trigonal prismatic and trigonal prismatic yielding a three-dimensional motif. The two broad absorption bands at 644 and 924 nm from UV-vis-NIR transmittance spectra were ascribed to a ligand-to-metal charge transfer. The room temperature crystalline EPR spectra indicate the high-spin (S=5/2) of Fe(III) ion. The vibrating sample magnetometer measurement shows the paramagnetic nature at room temperature. Thermal studies of the compound confirm the absence of water molecule.

Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage $${\\Phi}$$6 Major Capsid Protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nemecek, Daniel; Plevka, Pavel; Boura, Evzen

2013-11-29

Bacteriophagemore » $${\\Phi}$$6 is a double-stranded RNA virus that has been extensively studied as a model organism. In this paper we describe structure determination of $${\\Phi}$$6 major capsid protein P1. The protein crystallized in base centered orthorhombic space group C2221. Matthews’s coefficient indicated that the crystals contain from four to seven P1 subunits in the crystallographic asymmetric unit. The self-rotation function had shown presence of fivefold axes of non-crystallographic symmetry in the crystals. Thus, electron density map corresponding to a P1 pentamer was excised from a previously determined cryoEM reconstruction of the $${\\Phi}$$6 procapsid at 7 Å resolution and used as a model for molecular replacement. The phases for reflections at higher than 7 Å resolution were obtained by phase extension employing the fivefold non-crystallographic symmetry present in the crystal. Lastly, the averaged 3.6 Å-resolution electron density map was of sufficient quality to allow model building.« less

Extracellular overproduction and preliminary crystallographic analysis of a family I.3 lipase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Angkawidjaja, Clement; You, Dong-Ju; Matsumura, Hiroyoshi

2007-03-01

A family I.3 lipase from Pseudomonas sp. MIS38 was secreted from Escherichia coli cells to the external medium, purified and crystallized and preliminary crystallographic studies were performed. A family I.3 lipase from Pseudomonas sp. MIS38 was secreted from Escherichia coli cells to the external medium, purified and crystallized and preliminary crystallographic studies were performed. The crystal was grown at 277 K by the hanging-drop vapour-diffusion method. Native X-ray diffraction data were collected to 1.7 Å resolution using synchrotron radiation at station BL38B1, SPring-8. The crystal belongs to space group P2{sub 1}, with unit-cell parameters a = 48.79, b = 84.06,more » c = 87.04 Å. Assuming the presence of one molecule per asymmetric unit, the Matthews coefficient V{sub M} was calculated to be 2.73 Å{sup 3} Da{sup −1} and the solvent content was 55%.« less

Production, purification, crystallization and preliminary X-ray analysis of adeno-associated virus serotype 8

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lane, Michael Douglas; Nam, Hyun-Joo; Padron, Eric

2005-06-01

The production, purification, crystallization and preliminary X-ray crystallographic analysis of adeno-associated virus serotype 8 is reported. Adeno-associated viruses (AAVs) are actively being developed for clinical gene-therapy applications and the efficiencies of the vectors could be significantly improved by a detailed understanding of their viral capsid structures and the structural determinants of their tissue-transduction interactions. AAV8 is ∼80% identical to the more widely studied AAV2, but its liver-transduction efficiency is significantly greater than that of AAV2 and other serotypes. The production, purification, crystallization and preliminary X-ray crystallographic analysis of AAV8 viral capsids are reported. The crystals diffract X-rays to 3.0 Åmore » resolution using synchrotron radiation and belong to the hexagonal space group P6{sub 3}22, with unit-cell parameters a = 257.5, c = 443.5 Å. The unit cell contains two viral particles, with ten capsid viral protein monomers per crystallographic asymmetric unit.« less

Detailed characterization of thermal expansion tensor in monoclinic K Re(WO 4) 2 (where Re = Gd, Y, Lu, Yb)

NASA Astrophysics Data System (ADS)

Loiko, P. A.; Yumashev, K. V.; Kuleshov, N. V.; Rachkovskaya, G. E.; Pavlyuk, A. A.

2011-11-01

Linear thermal expansion coefficients αT were measured in monoclinic potassium (rare-earth) double tungstates K Re(WO 4) 2 ( Re = Gd, Y, Lu, Yb) by a dilatometric technique in the directions of a1, b1, c1∗ crystallographic axes (I2/c space group) and optical indicatrix axes Nm and Ng. Thermal expansion tensor αij was evaluated in the { Nm, Np, Ng} frame and then diagonalized. The orientation of corresponding frame {Xi'} with respect to crystallographic and optical indicatrix frames was determined, considering two different crystallographic settings (C2/c and I2/c). Potassium lutetium tungstate KLu(WO 4) 2 was found to possess the lower thermal expansion anisotropy among K Re(WO 4) 2 family. Athermal orientations of laser elements were proposed for K Re(WO 4) 2-based lasers under diode pumping, taking into account temperature dependence of the refractive index and bulging of crystal end faces.

Crystallographic studies of gas sorption in metal–organic frameworks

PubMed Central

Carrington, Elliot J.; Vitórica-Yrezábal, Iñigo J.; Brammer, Lee

2014-01-01

Metal–organic frameworks (MOFs) are a class of porous crystalline materials of modular design. One of the primary applications of these materials is in the adsorption and separation of gases, with potential benefits to the energy, transport and medical sectors. In situ crystallography of MOFs under gas atmospheres has enabled the behaviour of the frameworks under gas loading to be investigated and has established the precise location of adsorbed gas molecules in a significant number of MOFs. This article reviews progress in such crystallographic studies, which has taken place over the past decade, but has its origins in earlier studies of zeolites, clathrates etc. The review considers studies by single-crystal or powder diffraction using either X-rays or neutrons. Features of MOFs that strongly affect gas sorption behaviour are discussed in the context of in situ crystallographic studies, specifically framework flexibility, and the presence of (organic) functional groups and unsaturated (open) metal sites within pores that can form specific interactions with gas molecules. PMID:24892587

Unsteady Flow Interactions Between Pitching Wings In Schooling Arrangements

NASA Astrophysics Data System (ADS)

Kurt, Melike; Moored, Keith

2017-11-01

In nature, many fish aggregate into large groups or schools for protection against predators, for social interactions and to save energy during migrations. Regardless of their prime motivation, fish experience three-dimensional flow interactions amongst themselves that can improve or hamper swimming performance and give rise to fluid-mediated forces between individuals. To date, the unsteady, three-dimensional flow interactions among schooling fish remains relatively unexplored. In order to study these interactions, the caudal fins of two interacting fish are idealized as two finite span pitching wings arranged in mixtures of canonical in-line and side-by-side arrangements. The forces and moments acting on the wings in the streamwise and cross-stream directions are quantified as the arrangement and the phase delay between the wings is altered. Particle image velocimetry is employed to characterize the flow physics during high efficiency locomotion. Finally, the forces and flowfields of two-dimensional pitching wings are compared with three-dimensional wings to distinguish how three-dimensionality alters the flow interactions in schools of fish.

N-(2-Chloro­eth­yl)morpholine-4-carbox­amide

PubMed Central

Ujam, Oguejiofo T.; Asegbeloyin, Jonnie N.; Nicholson, Brian K.; Ukoha, Pius O.; Ukwueze, Nkechi N.

2014-01-01

The title compound, C7H13ClN2O2, synthesized by the reaction of 2-chloro­ethyl iso­cyanate and morpholine, crystallizes with four molecules in the asymmetric unit, which have similar conformations and comprise two pairs each related by approximate non-crystallographic inversion centres. Two of them have a modest orientational disorder of the 2-chloro­ethyl fragments [occupancy ratio of 0.778 (4):0.222 (4)]. In the crystal, mol­ecules are linked by N—H⋯O=C hydrogen bonds, forming three crystallographically different kinds of infinite hydrogen-bonded chains extending along [001]. PMID:24826162

A Dimensional Analysis of College Student Satisfaction.

ERIC Educational Resources Information Center

Betz, Ellen L.; And Others

Further research on the College Student Satisfaction Questionnaire (CSSQ) is reported herein (see TM 000 049). Item responses of two groups of university students were separately analyzed by three different factor analytic methods. Three factors consistently appeared across groups and methods: Compensation, Social Life, and Working Conditions. Two…

Three-Dimensional Audio Client Library

NASA Technical Reports Server (NTRS)

Rizzi, Stephen A.

2005-01-01

The Three-Dimensional Audio Client Library (3DAudio library) is a group of software routines written to facilitate development of both stand-alone (audio only) and immersive virtual-reality application programs that utilize three-dimensional audio displays. The library is intended to enable the development of three-dimensional audio client application programs by use of a code base common to multiple audio server computers. The 3DAudio library calls vendor-specific audio client libraries and currently supports the AuSIM Gold-Server and Lake Huron audio servers. 3DAudio library routines contain common functions for (1) initiation and termination of a client/audio server session, (2) configuration-file input, (3) positioning functions, (4) coordinate transformations, (5) audio transport functions, (6) rendering functions, (7) debugging functions, and (8) event-list-sequencing functions. The 3DAudio software is written in the C++ programming language and currently operates under the Linux, IRIX, and Windows operating systems.

A randomized controlled trial of conventional fraction and late course accelerated hyperfraction three-dimensional conformal radiotherapy for esophageal cancer.

PubMed

Wang, Jian-Hua; Lu, Xu-Jing; Zhou, Jian; Wang, Feng

2012-01-01

We compared the curative and side-effects in esophageal carcinoma treated by conventional fraction (CF) and late course accelerated hyperfraction (LCAF) three-dimensional conformal radiotherapy. Ninety-eight patients were randomly assigned to two different radiotherapy model groups. Fifty patients were treated using CF three-dimensional conformal radiotherapy at a total dose of 60-68 Gy; 2 Gy/F; 5 fractions/week (median 64 Gy), 48 patients were treated with LCAF (First CF-treated at the dose 40 Gy. Later, LCAF-treated 1.5 Gy/F; 2 fractions/day; 21-27 Gy; a total dose of 61-67 Gy; median 64 Gy). The data showed that the 1-, 2- and 3-year-survival rates in LCAF group were 79.2, 56.3, and 43.8%, compared to 74, 54, and 36% in CF group (P = 0.476). The 1-, 2- and 3-year-local control rates in LCAF group were 81.3, 62.5, and 50%, compared to 78, 58, and 42% in CF group (P = 0.454). In CF group, the incidence of radiation-induced esophagitis was lower than that in LCAF group (72 vs. 93.8%; P = 0.008) and there was no significant difference between rates of radiation-induced pneumonitis in CF and LCAF groups (10 vs. 6.25%; P = 0.498). It was concluded that the 1-, 2- and 3-year-local control and survival rates of esophageal carcinoma patients treated with LCAF were slightly better than CF radiotherapy; however, the radiation side-effects in LCAF group were greater than those in CF group.

HealthLines

MedlinePlus

... a particular order, and identified shapes on a computer screen. They were divided into three groups. One ... some people. Virtual colonoscopy uses X-ray and computer technology to create three-dimensional images of the ...

Design, fabrication, and testing of nanostructured carbons and composites

NASA Astrophysics Data System (ADS)

Wang, Zhiyong

Many applications, such as catalysis, sensing, separation and energy storage and conversion, will benefit from the miniaturization of materials to nanometer length scales. This dissertation details my study of nanocomposites based on three-dimensionally ordered macroporous (3DOM) carbons and zirconia, and three-dimensionally ordered macroporous/mesoporous (3DOM/m) carbons. The macropores of these materials were produced using colloidal crystal templates while the mesopores were generated using surfactant templates. These solids are composed of close-packed and three-dimensionally interconnected spherical macropores surrounded by nanoscale solid or mesoporous wall skeletons. This unique architecture offers large surface areas, pore volumes, and good access into the bulk via a macroporous network. 3DOM carbons have been demonstrated as promising electrode materials for lithium ion batteries and sensors, but their electrochemical performance still needs to be improved. As a model system for the modification of the electrode, 3DOM C/TiO2 was synthesized by fabricating a conformal coating of TiO2 nanoparticles on the macropore walls of 3DOM C. My research further extended the micro-structural design of monolithic carbon from 3DOM to 3DOM/m. 3DOM/m C monoliths with high surface areas, controllable mesopore sizes, and mesopore ordering, were synthesized by three methods. One of the methods is simpler and more environment benign than previously reported methods. The mesopores in 3DOM/m C-based electrode provide room to accommodate secondary phases, such as graphitic carbon, SnO2 and Si which can improve the conductivity or lithium capacity of the electrode. Owing to this advantage, 3DOM/m C/C and 3DOM/m C/SnO2 exhibited significantly improved rate performance, lithium capacity and cycleability, compared with 3DOM C. To meet the demands of nano-sized functional materials in applications such as nano-device fabrication and drug delivery, mesoporous carbon nanoparticles with cubic, spherical and tetrapod shapes were also synthesized. In addition, new methods were developed to assemble nanocomposites of bifunctional catalyst components. These materials were designed for the potential direct conversion of synthesis gas to clean liquid fuels. Coatings of zeolite and cobalt nanoparticles were fabricated on 3DOM promoted zirconia. The 3DOM zirconia-based nanocomposites were characterized by a wide variety of techniques to illustrate their morphologies, internal structures, chemical compositions, porosity, and crystallographic phases.

Three-dimensional high-definition neuroendoscopic surgery: a controlled comparative laboratory study with two-dimensional endoscopy and clinical application.

PubMed

Inoue, Daisuke; Yoshimoto, Koji; Uemura, Munenori; Yoshida, Masaki; Ohuchida, Kenoki; Kenmotsu, Hajime; Tomikawa, Morimasa; Sasaki, Tomio; Hashizume, Makoto

2013-11-01

The purpose of this research was to investigate the usefulness of three-dimensional (3D) endoscopy compared with two-dimensional (2D) endoscopy in neuroendoscopic surgeries in a comparative study and to test the clinical applications. Forty-three examinees were divided into three groups according to their endoscopic experience: novice, beginner, or expert. Examinees performed three separate tasks using 3D and 2D endoscopy. A recently developed 3D high-definition (HD) neuroendoscope, 4.7 mm in diameter (Shinko Optical Co., Ltd., Tokyo, Japan) was used. In one of the three tasks, we developed a full-sized skull model of acrylic-based plastic using a 3D printer and a patient's thin slice computed tomography data, and evaluated the execution time and total path length of the tip of the pointer using an optical tracking system. Sixteen patients underwent endoscopic transnasal transsphenoidal pituitary surgery using both 3D and 2D endoscopy. Horizontal motion was evaluated using task 1, and anteroposterior motion was evaluated with task 3. Execution time and total path length in task 3 using the 3D system in both novice and beginner groups were significantly shorter than with the 2D system (p < 0.05), although no significant difference between 2D and 3D systems in task 1 was seen. In both the novice and beginner groups, the 3D system was better for depth perception than horizontal motion. No difference was seen in the expert group in this regard. The 3D HD endoscope was used for the pituitary surgery and was found very useful to identify the spatial relationship of carotid arteries and bony structures. The use of a 3D neuroendoscope improved depth perception and task performance. Our results suggest that 3D endoscopes could shorten the learning curve of young neurosurgeons and play an important role in both general surgery and neurosurgery. Georg Thieme Verlag KG Stuttgart · New York.

’MBTI3D’ (A Three-Dimensional Interpretation)

DTIC Science & Technology

1993-04-01

preferential relationship --individuals are pigeonholed into personality types based solely on preference inclination and with disregard for actual preference...values. Consequently, individual and group relationships , as represented by the MBTI, are not integrated the way most organizations perceive. The MBTI’s...somewhat cerebral definition and its two-dimensional visual display present a limited portrayal of real life multi-dimensional relationships . This

[Comparison of treatment outcomes in patients with maxillary dentoalveolar protrusion by applying different anchorage methods: a three-dimensional model study].

PubMed

Ning, Ma; Weiran, Li

2015-02-01

This study aims to compare the treatment outcomes in patients with maxillary dentoalveolar protrusion by applying different anchorage methods via three-dimensional model measurement. A total of 46 patients with maxillary dentoalveolar protrusion treated with bilateral maxillary first premolar extractions and high anchorage were selected. The subjects were randomly divided into three groups according to the type of anchorage applied, which included implant, extraoral, and Nance arch anchorages. The maxillary dental models were made before treatment and after space closure of maxilla. The movements of the maxillary central incisors and first molars were measured via a three-dimensional model measurement, and the amounts of movement were compared among the three groups. The sagittal lingual movements of the maxillary central incisors were (-6.661 ± 1.328), (-5.939 ± 1.806), and (-5.788 ± 2.009) mm for the implant, extraoral, and Nance arch anchorage groups, respectively, with no significant difference among the three groups (P = 0.121). The corresponding vertical movements of the maxillary central incisors were (0.129 ± 1.815) mm intrusion, and (-2.162 ± 2.026), (-2.623 ± 1.776) mm extrusion. Significant difference was found between the implant anchorage group and the other groups (P < 0.05). The corresponding sagittal mesial movements of the maxillary first molars were (0.608 ± 1.045), (1.445 ± 1.462), and (1.503 ± 0.945) mm. The corresponding vertical movements of the maxillary first molars were (0.720 ± 0.805) mm intrusion, (0.076 ± 0.986) mm intrusion, and (-0.072 ± 0.690) mm extrusion. Significant difference was found between the implant anchorage group and the other two groups (P < 0.05). In the transverse direction, the first molars all moved lingually with no significant difference among the three groups (P > 0.05). Implant anchorage may be superior in the vertical control of the maxillary incisors and in the sagittal, as well as in the vertical control of the maxillary molars, compared with the traditional anchorages during the treatment of patients with maxillary dentoalveolar protrusion.

[COMPARISON OF FEMORAL CONDYLAR TWIST ANGLE IN THREE DIMENSIONAL RECONSTRUCTION DIGITAL MODELS OF KNEE JOINT BASED ON TWO DIMENSIONAL IMAGES OF MRI AND CT].

PubMed

Huang, Zan; Li, Yanlin; Hu, Meng; Li, Jian; You, Zhimin; Wang, Guoliang; He, Chuan

2015-02-01

To study the difference of femoral condylar twist angle (CTA) measurement in three dimensional (3-D) reconstruction digital models of human knee joint based on the two dimensional (2-D) images of MRI and CT so as to provide a reference for selecting the best method of CTA measurement in preoperative design for the femoral prosthesis rotational position. The CTA of 10 human cadaveric knee joint was measured in 3-D digital models based on MRI (group A), in 3-D digital models based on CT (group B), in the cadaveric knee joint with cartilage (group C), and in the cadaveric knee joint without cartilage (group D), respectively. The statistical analysis of the differences was made among the measurements of the CTA. The CTA values measured in 3-D digital models were (6.43 ± 0.53) degrees in group A and (3.31 ± 1.07) degrees in group B, showing significant difference (t = 10.235, P = 0.000). The CTA values measured in the cadaveric knee joint were (5.21 ± 1.28) degrees in group C and (3.33 ± 1.12) degrees in group D, showing significant difference (t = 5.770, P = 0.000). There was significant difference in the CTA values between group B and group C (t = 5.779, P = 0.000), but no significant difference was found between group A and group C (t = 3.219, P = 0.110). The CTA values measured in the 3-D digital models based on MRI are closer to the actual values measured in the knee joint with cartilage, and benefit for preoperative plan.

Three-dimensional nanometer scale analyses of precipitate structures and local compositions in titanium aluminide engineering alloys

NASA Astrophysics Data System (ADS)

Gerstl, Stephan S. A.

Titanium aluminide (TiAl) alloys are among the fastest developing class of materials for use in high temperature structural applications. Their low density and high strength make them excellent candidates for both engine and airframe applications. Creep properties of TiAl alloys, however, have been a limiting factor in applying the material to a larger commercial market. In this research, nanometer scale compositional and structural analyses of several TiAl alloys, ranging from model Ti-Al-C ternary alloys to putative commercial alloys with 10 components are investigated utilizing three dimensional atom probe (3DAP) and transmission electron microscopies. Nanometer sized borides, silicides, and carbide precipitates are involved in strengthening TiAl alloys, however, chemical partitioning measurements reveal oxygen concentrations up to 14 at. % within the precipitate phases, resulting in the realization of oxycarbide formation contributing to the precipitation strengthening of TiAl alloys. The local compositions of lamellar microstructures and a variety of precipitates in the TiAl system, including boride, silicide, binary carbides, and intermetallic carbides are investigated. Chemical partitioning of the microalloying elements between the alpha2/gamma lamellar phases, and the precipitate/gamma-matrix phases are determined. Both W and Hf have been shown to exhibit a near interfacial excess of 0.26 and 0.35 atoms nm-2 respectively within ca. 7 nm of lamellar interfaces in a complex TiAl alloy. In the case of needle-shaped perovskite Ti3AlC carbide precipitates, periodic domain boundaries are observed 5.3+/-0.8 nm apart along their growth axis parallel to the TiAl[001] crystallographic direction with concomitant composition variations after 24 hrs. at 800°C.

Solution structure of the DNA-binding domain of the heat shock transcription factor determined by multidimensional heteronuclear magnetic resonance spectroscopy.

PubMed Central

Damberger, F. F.; Pelton, J. G.; Harrison, C. J.; Nelson, H. C.; Wemmer, D. E.

1994-01-01

The solution structure of the 92-residue DNA-binding domain of the heat shock transcription factor from Kluyveromyces lactis has been determined using multidimensional NMR methods. Three-dimensional (3D) triple resonance, 1H-13C-13C-1H total correlation spectroscopy, and 15N-separated total correlation spectroscopy-heteronuclear multiple quantum correlation experiments were used along with various 2D spectra to make nearly complete assignments for the backbone and side-chain 1H, 15N, and 13C resonances. Five-hundred eighty-three NOE constraints identified in 3D 13C- and 15N-separated NOE spectroscopy (NOESY)-heteronuclear multiple quantum correlation spectra and a 4-dimensional 13C/13C-edited NOESY spectrum, along with 35 phi, 9 chi 1, and 30 hydrogen bond constraints, were used to calculate 30 structures by hybrid distance geometry/stimulated annealing protocol, of which 24 were used for structural comparison. The calculations revealed that a 3-helix bundle packs against a small 4-stranded antiparallel beta-sheet. The backbone RMS deviation (RMSD) for the family of structures was 1.03 +/- 0.19 A with respect to the average structure. The topology is analogous to that of the C-terminal domain of the catabolite gene activator protein and appears to be in the helix-turn-helix family of DNA-binding proteins. The overall fold determined by the NMR data is consistent with recent crystallographic work on this domain (Harrison CJ, Bohm AA, Nelson HCM, 1994, Science 263:224) as evidenced by RMSD between backbone atoms in the NMR and X-ray structures of 1.77 +/- 0.20 A. Several differences were identified some of which may be due to protein-protein interactions in the crystal. PMID:7849597

In situ 3D-X-ray diffraction tracking of individual grains of olivine during high-pressure/ high-temperature phase transitions

NASA Astrophysics Data System (ADS)

Rosa, A. D.; Merkel, S.; Ghosh, S.; Hilairet, N.; Perrillat, J.; Mezouar, N.; Vaughan, G.

2013-12-01

The series of phase transitions between olivine, wadsleyite and ringwoodite play an essential role for large scale dynamical processes in the Earth mantle. Detailed knowledge of the microscopic mechanism at the origin of these high-pressure and high-temperature phase transformations is useful to connect global seismic observations and geodynamics. Indeed, the textures of these phases can be induced either during mantle flow or during the phase transformations and they greatly affect the characteristics of seismic wave propagation. Here, we present a new design of diamond anvil cell experiments to collect three-dimensional diffraction images and track individual grains inside a polycristalline sample at high pressure and high temperature. The instrumentation includes a new resistively heated diamond anvil cell developed at beamline ID27 of the ESRF which provided stable and homogenous temperature condition over more than 24 hours. In our experiments, the pressure is first increased up to 12 GPa at a constant temperature of T = 800 K. The temperature is then further increased to 1300 K to reach the stability field of the high-pressure polymorph. Upon further compression the transformation of olivine to its high-pressure polymorph is successfully monitored. At each pressure-temperature step and while the sample is transforming the crystallographic parameters, the orientations and positions of grains within the sample are tracked in situ using three-dimensional X-ray diffraction. This will provide important information on the micromechanical properties of olivine including orientation statistics, orientation relations between parent and daughter phases, and transformation textures at different stages of the phase transition. This in turn will help in interpreting the geophysical observations. Details of the experimental and analytical approach used in this study will be given.

The Effect of Hydrostatic Pressure on Three-Dimensional Chondroinduction of Human Adipose–Derived Stem Cells

PubMed Central

Mizuno, Shuichi; Murphy, George F.; Orgill, Dennis P.

2009-01-01

Background The optimal production of three-dimensional cartilage in vitro requires both inductive factors and specified culture conditions (e.g., hydrostatic pressure [HP], gas concentration, and nutrient supply) to promote cell viability and maintain phenotype. In this study, we optimized the conditions for human cartilage induction using human adipose–derived stem cells (ASCs), collagen scaffolds, and cyclic HP treatment. Methods Human ASCs underwent primary culture and three passages before being seeded into collagen scaffolds. These constructs were incubated for 1 week in an automated bioreactor using cyclic HP at 0–0.5 MPa, 0.5 Hz, and compared to constructs exposed to atmospheric pressure. In both groups, chondrogenic differentiation medium including transforming growth factor-β1 was employed. One, 2, 3, and 4 weeks after incubation, the cell constructs were harvested for histological, immunohistochemical, and gene expression evaluation. Results In histological and immunohistochemical analyzes, pericellular and extracellular metachromatic matrix was observed in both groups and increased over 4 weeks, but accumulated at a higher rate in the HP group. Cell number was maintained in the HP group over 4 weeks but decreased after 2 weeks in the atmospheric pressure group. Chondrogenic-specific gene expression of type II and X collagen, aggrecan, and SRY-box9 was increased in the HP group especially after 2 weeks. Conclusion Our results demonstrate chondrogenic differentiation of ASCs in a three-dimensional collagen scaffolds with treatment of a cyclic HP. Cyclic HP was effective in enhancing accumulation of extracellular matrix and expression of genes indicative of chondrogenic differentiation. PMID:19290804

Preliminary crystallographic analysis of the oxidized form of a two mono-nuclear iron centres protein from Desulfovibrio desulfuricans ATCC 27774.

PubMed Central

Coelho, A. V.; Matias, P. M.; Carrondo, M. A.; Tavares, P.; Moura, J. J.; Moura, I.; Fülop, V.; Hajdu, J.; Le Gall, J.

1996-01-01

Crystals of the fully oxidized form of desulfoferrodoxin were obtained by vapor diffusion from a solution containing 20% PEG 4000, 0.1 M HEPES buffer, pH 7.5, and 0.2 M CaCl2. Trigonal and/or rectangular prisms could be obtained, depending on the temperature used for the crystal growth. Trigonal prisms belong to the rhombohedral space group R32, with a = 112.5 A and c = 63.2 A; rectangular prisms belong to the monoclinic space group C2, with a = 77.7 A, b = 80.9 A, c = 53.9 A, and beta = 98.1 degrees. The crystallographic asymmetric unit of the rhombohedral crystal form contains one molecule. There are two molecules in the asymmetric unit of the monoclinic form, in agreement with the self-rotation function. PMID:8762151

Preparation, crystallization and preliminary crystallographic analysis of old yellow enzyme from Trypanosoma cruzi

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sugiyama, Shigeru; Tokuoka, Keiji; Uchiyama, Nahoko

2007-10-01

Old yellow enzyme from Trypanosoma cruzi, has been crystallized using the hanging-drop vapour-diffusion method. Old yellow enzyme (OYE) is an NADPH oxidoreductase that contains a flavin mononucleotide as a prosthetic group. The OYE from Trypanosoma cruzi, which produces prostaglandin F{sub 2α}, a potent mediator of various physiological and pathological processes, from prostaglandin H2. The protein was recombinantly expressed and purified from Escherichia coli and was crystallized using the hanging-drop vapour-diffusion method. The crystal belongs to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 56.3, b = 78.8, c = 78.8 Å, β = 93.4° and two moleculesmore » per asymmetric unit. The crystals were suitable for X-ray crystallographic studies and diffracted to 1.70 Å resolution. A Patterson search method is in progress using the structure of OYE from Pseudomonas putida as a starting model.« less

Three-dimensional characterization of the effective second-order nonlinearity in periodically poled crystals

NASA Astrophysics Data System (ADS)

Holmgren, Stefan J.; Pasiskevicius, Valdas; Wang, Shunhua; Laurell, Fredrik

2003-09-01

A novel technique for characterization of the second-order nonlinearity in nonlinear crystals is presented. It utilizes group-velocity walk-off between femtosecond pulses in type II SHG to achieve three-dimensional resolution of the nonlinearity. The longitudinal and transversal spatial resolution can be set independently. The technique is especially useful for characterizing quasi-phase-matched nonlinear crystals, and it is demonstrated in potassium titanyl phosphate.

Morphometry of the ear in Down's syndrome subjects. A three-dimensional computerized assessment.

PubMed

Sforza, C; Dellavia, C; Tartaglia, G M; Ferrario, V F

2005-07-01

The three-dimensional coordinates of 13 soft-tissue landmarks on the ears were obtained by a computerized digitizer in 28 subjects with Down's syndrome aged 12-45 years, and in 449 sex, age and ethnic group matched controls. From the landmarks, left and right linear distances (ear width and length), ratios (ear width-to-ear length), areas (ear area), angles (angle of the auricle versus the facial midplane) and the three-dimensional symmetry index were calculated. For both males and females, all linear dimensions and areas were significantly (Analysis of Variance, P < 0.001) larger in the reference subjects than in the subjects with Down's syndrome. All values significantly increased as a function of age (P < 0.05); the increment was larger in the reference subjects than in the subjects with Down's syndrome. On both sides of the face, the subjects with Down's syndrome had larger ear width-to-ear length ratios, and larger angles of the auricle versus the facial midplane than the reference subjects. The three-dimensional symmetry index was significantly larger in the reference subjects and in the older persons. In conclusion, ear dimensions, position and shape significantly differed in subjects with Down's syndrome when compared to sex, age and ethnic group matched controls. Some of the differences were sex and age related.

Corrosion in drinking water pipes: the importance of green rusts.

PubMed

Swietlik, Joanna; Raczyk-Stanisławiak, Urszula; Piszora, Paweł; Nawrocki, Jacek

2012-01-01

Complex crystallographic composition of the corrosion products is studied by diffraction methods and results obtained after different pre-treatment of samples are compared. The green rusts are found to be much more abundant in corrosion scales than it has been assumed so far. The characteristic and crystallographic composition of corrosion scales and deposits suspended in steady waters were analyzed by X-ray diffraction (XRD). The necessity of the examination of corrosion products in the wet conditions is indicated. The drying of the samples before analysis is shown to substantially change the crystallographic phases originally present in corrosion products. On sample drying the unstable green rusts is converted into more stable phases such as goethite and lepidocrocite, while the content of magnetite and siderite decreases. Three types of green rusts in wet materials sampled from tubercles are identified. Unexpectedly, in almost all corrosion scale samples significant amounts of the least stable green rust in chloride form was detected. Analysis of corrosion products suspended in steady water, which remained between tubercles and possibly in their interiors, revealed complex crystallographic composition of the sampled material. Goethite, lepidocrocite and magnetite as well as low amounts of siderite and quartz were present in all samples. Six different forms of green rusts were identified in the deposits separated from steady waters and the most abundant was carbonate green rust GR(CO(3)(2-))(I). Copyright © 2011 Elsevier Ltd. All rights reserved.

Assessment of pelvic floor by three-dimensional-ultrasound in primiparous women according to delivery mode: initial experience from a single reference service in Brazil.

PubMed

Araujo Júnior, Edward; de Freitas, Rogério Caixeta Moraes; Di Bella, Zsuzsanna Ilona Katalin de Jármy; Alexandre, Sandra Maria; Nakamura, Mary Uchiyama; Nardozza, Luciano Marcondes Machado; Moron, Antonio Fernandes

2013-03-01

To evaluate changes to the pelvic floor of primiparous women with different delivery modes, using three-dimensional ultrasound. A prospective cross-sectional study on 35 primiparae divided into groups according to the delivery mode: elective cesarean delivery (n=10), vaginal delivery (n=16), and forceps delivery (n=9). Three-dimensional ultrasound on the pelvic floor was performed on the second postpartum day with the patient in a resting position. A convex volumetric transducer (RAB4-8L) was used, in contact with the large labia, with the patient in the gynecological position. Biometric measurements of the urogenital hiatus were taken in the axial plane on images in the rendering mode, in order to assess the area, anteroposterior and transverse diameters, average thickness, and avulsion of the levator ani muscle. Differences between groups were evaluated by determining the mean differences and their respective 95% confidence intervals. The proportions of levator ani muscle avulsion were compared between elective cesarean section and vaginal birth using Fisher's exact test. The mean areas of the urogenital hiatus in the cases of vaginal and forceps deliveries were 17.0 and 20.1 cm(2), respectively, versus 12.4 cm(2) in the Control Group (elective cesarean). Avulsion of the levator ani muscle was observed in women who underwent vaginal delivery (3/25), however there was no statistically significant difference between cesarean section and vaginal delivery groups (p=0.5). Transperineal three-dimensional ultrasound was useful for assessing the pelvic floor of primiparous women, by allowing pelvic morphological changes to be differentiated according to the delivery mode.

Real time three dimensional sensing system

DOEpatents

Gordon, S.J.

1996-12-31

The invention is a three dimensional sensing system which utilizes two flexibly located cameras for receiving and recording visual information with respect to a sensed object illuminated by a series of light planes. Each pixel of each image is converted to a digital word and the words are grouped into stripes, each stripe comprising contiguous pixels. One pixel of each stripe in one image is selected and an epi-polar line of that point is drawn in the other image. The three dimensional coordinate of each selected point is determined by determining the point on said epi-polar line which also lies on a stripe in the second image and which is closest to a known light plane. 7 figs.

Real time three dimensional sensing system

DOEpatents

Gordon, Steven J.

1996-01-01

The invention is a three dimensional sensing system which utilizes two flexibly located cameras for receiving and recording visual information with respect to a sensed object illuminated by a series of light planes. Each pixel of each image is converted to a digital word and the words are grouped into stripes, each stripe comprising contiguous pixels. One pixel of each stripe in one image is selected and an epi-polar line of that point is drawn in the other image. The three dimensional coordinate of each selected point is determined by determining the point on said epi-polar line which also lies on a stripe in the second image and which is closest to a known light plane.

Dimensional Accuracy of Hydrophilic and Hydrophobic VPS Impression Materials Using Different Impression Techniques - An Invitro Study

PubMed Central

Pilla, Ajai; Pathipaka, Suman

2016-01-01

Introduction The dimensional stability of the impression material could have an influence on the accuracy of the final restoration. Vinyl Polysiloxane Impression materials (VPS) are most frequently used as the impression material in fixed prosthodontics. As VPS is hydrophobic when it is poured with gypsum products, manufacturers added intrinsic surfactants and marketed as hydrophilic VPS. These hydrophilic VPS have shown increased wettability with gypsum slurries. VPS are available in different viscosities ranging from very low to very high for usage under different impression techniques. Aim To compare the dimensional accuracy of hydrophilic VPS and hydrophobic VPS using monophase, one step and two step putty wash impression techniques. Materials and Methods To test the dimensional accuracy of the impression materials a stainless steel die was fabricated as prescribed by ADA specification no. 19 for elastomeric impression materials. A total of 60 impressions were made. The materials were divided into two groups, Group1 hydrophilic VPS (Aquasil) and Group 2 hydrophobic VPS (Variotime). These were further divided into three subgroups A, B, C for monophase, one-step and two-step putty wash technique with 10 samples in each subgroup. The dimensional accuracy of the impressions was evaluated after 24 hours using vertical profile projector with lens magnification range of 20X-125X illumination. The study was analyzed through one-way ANOVA, post-hoc Tukey HSD test and unpaired t-test for mean comparison between groups. Results Results showed that the three different impression techniques (monophase, 1-step, 2-step putty wash techniques) did cause significant change in dimensional accuracy between hydrophilic VPS and hydrophobic VPS impression materials. One-way ANOVA disclosed, mean dimensional change and SD for hydrophilic VPS varied between 0.56% and 0.16%, which were low, suggesting hydrophilic VPS was satisfactory with all three impression techniques. However, mean dimensional change and SD for hydrophobic VPS were much higher with monophase, mere increase for 1-step and 2-step, than the standard steel die (p<0.05). Unpaired t-test displayed that hydrophilic VPS judged satisfactory compared to hydrophobic VPS among 1-step and 2-step impression technique. Conclusion Within the limitations of this study, it can be concluded that hydrophilic Vinyl polysiloxane was more dimensionally accurate than hydrophobic Vinyl polysiloxane using monophase, one step and two step putty wash impression techniques under moist conditions. PMID:27042587

An X-ray crystallographic and density functional theory study of (3Z)-4-(5-ethylsulfonyl-2-hydroxyanilino)pent-3-en-2-one and (3Z)-4-(5-tert-butyl-2-hydroxyanilino)pent-3-en-2-one.

PubMed

Akerman, Kate J; Munro, Orde Q

2013-03-01

The Schiff base enaminones (3Z)-4-(5-ethylsulfonyl-2-hydroxyanilino)pent-3-en-2-one, C13H17NO4S, (I), and (3Z)-4-(5-tert-butyl-2-hydroxyanilino)pent-3-en-2-one, C15H21NO2, (II), were studied by X-ray crystallography and density functional theory (DFT). Although the keto tautomer of these compounds is dominant, the O=C-C=C-N bond lengths are consistent with some electron delocalization and partial enol character. Both (I) and (II) are nonplanar, with the amino-phenol group canted relative to the rest of the molecule; the twist about the N(enamine)-C(aryl) bond leads to dihedral angles of 40.5 (2) and -116.7 (1)° for (I) and (II), respectively. Compound (I) has a bifurcated intramolecular hydrogen bond between the N-H group and the flanking carbonyl and hydroxy O atoms, as well as an intermolecular hydrogen bond, leading to an infinite one-dimensional hydrogen-bonded chain. Compound (II) has one intramolecular hydrogen bond and one intermolecular C=O...H-O hydrogen bond, and consequently also forms a one-dimensional hydrogen-bonded chain. The DFT-calculated structures [in vacuo, B3LYP/6-311G(d,p) level] for the keto tautomers compare favourably with the X-ray crystal structures of (I) and (II), confirming the dominance of the keto tautomer. The simulations indicate that the keto tautomers are 20.55 and 18.86 kJ mol(-1) lower in energy than the enol tautomers for (I) and (II), respectively.

Three-dimensional cell groups with disordered nuclei and cellular discohesion (3DDD) are associated with high sensitivity and specificity for cystoscopic urine cytopathological diagnosis of low-grade urothelial neoplasia.

PubMed

Mai, Kien T; Ball, Christopher G; Kos, Zuzana; Belanger, Eric C; Islam, Shahidul; Sekhon, Harman

2014-07-01

Cystoscopic urine obtained before the resection of low-grade urothelial carcinoma (LGUC), with adequate cytological sampling of the tumor, frequently revealed the presence of three-dimensional cell groups with disordered nuclei and cellular discohesion (3DDD). 936 cystoscopic urine specimens were categorized into five groups: Group 1 (80 specimens) with biopsy-proven LGUC within 6 months of cytologic examination, Group 2 (23 specimens) with biopsy proven LGUC within 6 to 36 months of cytologic examination, Group 3 (527 specimens) with a history of LGUC but no tumor for a period of greater than 3 years, Group 4 (300 specimens) with no association with LGUC, and Group 5 (6 specimens) with urinary lithiasis. Specimens with scant cellularity accounted for 20% of those in Group 1. For 3DDD in detecting LGUC in adequate cystoscopic urine, the sensitivity was 70%, specificity was 94%. Two- or three-dimensional cell groups with ordered nuclei and/or cellular non-discohesion were often seen in specimens from Groups 4 or 5. The 3DDD was present in a significant number of cases with concurrent negative cystoscopic findings but also positive LGUC in ensuing follow-up. In these cases, 3DDD with or without tumor identified at concurrent cystoscopy were found to be morphologically similar. Furthermore, the presence of 3DDD in 8% of Group 3 likely represents urothelial dysplasia that is not cystoscopically detectable. The high specificity and sensitivity of 3DDD is demonstrated. These findings are consistent with the decreased cell adhesion and disordered nuclear arrangement of low grade urothelial neoplasia. © 2013 Wiley Periodicals, Inc.

A Structure-Function Study of RecA: The Structural Basis for ATP Specificity in the Strand Exchange Reaction

NASA Astrophysics Data System (ADS)

Gegner, Julie; Spruill, Natalie; Plesniak, Leigh A.

1999-11-01

The terms "structure" and "function" can assume a variety of meanings. In biochemistry, the "structure" of a protein can refer to its sequence of amino acids, the three-dimensional arrangement of atoms within a subunit, or the arrangement of subunits into a larger oligomeric or filamentous state. Likewise, the function of biological macromolecules can be examined at many levels. The function of a protein can be described by its role in an organism's survival or by a chemical reaction that it promotes. We have designed a three-part biochemical laboratory experiment that characterizes the structure and function of the Escherichia coli RecA protein. The first part examines the importance of RecA in the survival of bacteria that have been exposed to UV light. This is the broadest view of function of the enzyme. Second, the students use an in vitro assay of RecA whereby the protein promotes homologous recombination. Because RecA functions not catalytically, but rather stoichiometrically, in this recombination reaction, the oligomeric state of RecA in complex with DNA must also be discussed. Finally, through molecular modeling of X-ray crystallographic structures, students identify functionally important features of the ATP cofactor binding site of RecA.

Structure and thermodynamic stability of UTa 3O 10, aU(v)-bearing compound

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Xiaofeng; Lipp, Christian; Tiferet, Eitan

Heating a mixture of uranyl (VI) nitrate and tantalum (V) oxide in the molar ratio of 2 : 3 to 1400 °C resulted in the formation of a new compound, UTa 3O 10. The honey colored to yellow brown crystals of UTa 3O 10 crystallize in an orthorhombic structure with the space group Fddd (no. 70), lattice parameters a = 7.3947(1), b = 12.7599(2), c = 15.8156(2) Å, and Z = 8. Vertex sharing [TaO 6] 7– octahedra of two crystallographically distinct Ta cations form a three dimensional tantalate framework. Within this framework, six membered rings of [TaO 6] 7–more » octahedra are formed within the (001) plane. The center of these rings is occupied by the uranyl cations [UO 2]+, with an oxidation state of +5 for uranium. The pentavalence of U and Ta was confirmed by X-ray photoelectron spectroscopy and X-ray adsorption spectroscopy. The enthalpy of formation of UTa 3O 10 from Ta 2O 5, β-U 3O 7, and U3O8 has been determined to be 13.1 ± 18.1 kJ mol–1 using high temperature oxide melt solution calorimetry with sodium molybdate as the solvent at 700 °C. As a result, the close to zero enthalpy of formation of UTa 3O 10 can be explained by closely balanced structural stabilizing and destabilizing factors, which may also apply to other UM 3O 10 compounds.« less

Structure and thermodynamic stability of UTa 3O 10, aU(v)-bearing compound

DOE PAGES

Guo, Xiaofeng; Lipp, Christian; Tiferet, Eitan; ...

2016-09-09

Heating a mixture of uranyl (VI) nitrate and tantalum (V) oxide in the molar ratio of 2 : 3 to 1400 °C resulted in the formation of a new compound, UTa 3O 10. The honey colored to yellow brown crystals of UTa 3O 10 crystallize in an orthorhombic structure with the space group Fddd (no. 70), lattice parameters a = 7.3947(1), b = 12.7599(2), c = 15.8156(2) Å, and Z = 8. Vertex sharing [TaO 6] 7– octahedra of two crystallographically distinct Ta cations form a three dimensional tantalate framework. Within this framework, six membered rings of [TaO 6] 7–more » octahedra are formed within the (001) plane. The center of these rings is occupied by the uranyl cations [UO 2]+, with an oxidation state of +5 for uranium. The pentavalence of U and Ta was confirmed by X-ray photoelectron spectroscopy and X-ray adsorption spectroscopy. The enthalpy of formation of UTa 3O 10 from Ta 2O 5, β-U 3O 7, and U3O8 has been determined to be 13.1 ± 18.1 kJ mol–1 using high temperature oxide melt solution calorimetry with sodium molybdate as the solvent at 700 °C. As a result, the close to zero enthalpy of formation of UTa 3O 10 can be explained by closely balanced structural stabilizing and destabilizing factors, which may also apply to other UM 3O 10 compounds.« less

Process metallurgy simulation for metal drawing process optimization by using two-scale finite element method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakamachi, Eiji; Yoshida, Takashi; Yamaguchi, Toshihiko

2014-10-06

We developed two-scale FE analysis procedure based on the crystallographic homogenization method by considering the hierarchical structure of poly-crystal aluminium alloy metal. It can be characterized as the combination of two-scale structure, such as the microscopic polycrystal structure and the macroscopic elastic plastic continuum. Micro polycrystal structure can be modeled as a three dimensional representative volume element (RVE). RVE is featured as by 3×3×3 eight-nodes solid finite elements, which has 216 crystal orientations. This FE analysis code can predict the deformation, strain and stress evolutions in the wire drawing processes in the macro- scales, and further the crystal texture andmore » hardening evolutions in the micro-scale. In this study, we analyzed the texture evolution in the wire drawing processes by our two-scale FE analysis code under conditions of various drawing angles of dice. We evaluates the texture evolution in the surface and center regions of the wire cross section, and to clarify the effects of processing conditions on the texture evolution.« less

Triaqua-1κO,2κ2 O-bis­(2,2′-bipyridine)-1κ2 N,N′;2κ2 N,N′-chlorido-1κCl-μ-terephthalato-1:2κ2 O 1:O 4-dicopper(II) nitrate monohydrate

PubMed Central

Liu, Yang; Feng, Yong-Lan; Kuang, Dai-Zhi

2012-01-01

In the binuclear title compound, [Cu2(C8H4O4)Cl(C10H8N2)2(H2O)3]NO3·H2O, the two crystallographically independent CuII ions have similar coordination environments. One of the CuII ions has a square-pyramidal arrangement, which is defined by a water mol­ecule occupying the apical position, with the equatorial ligators consisting of two N atoms from a 2,2′-bipyridine mol­ecule, one carboxyl­ate O atom from a terephthalate ligand and one O atom from a water mol­ecule. The other CuII ion has a similar coordination environment, except that the apical position is occupied by a chloride ligand instead of a water mol­ecule. An O—H⋯O and O—H⋯Cl hydrogen-bonded three-dimensional network is formed between the components. PMID:22719307

Correlations among void shape distributions, dynamic damage mode, and loading kinetics [Correlations among spall void shape distributions, damage mode and shock loading kinetics

DOE PAGES

Brown, A. D.; Pham, Q.; Fortin, E. V.; ...

2016-11-10

Here, three-dimensional x-ray tomography (XRT) provides a nondestructive technique to characterize the size, shape, and location of damage in dynamically loaded metals. A shape-fitting method comprising the inertia tensors of individual damage sites was applied to study differences of spall damage development in face-centered-cubic (FCC) and hexagonal-closed-packed (HCP) multicrystals and for a suite of experiments on high-purity copper to examine the influence of loading kinetics on the spall damage process. Applying a volume-weighted average to the best-fit ellipsoidal aspect-ratios allows a quantitative assessment for determining the extent of damage coalescence present in a shocked metal. It was found that incipientmore » transgranular HCP spall damage nucleates in a lenticular shape and is heavily oriented along particular crystallographic slip directions. In polycrystalline materials, shape distributions indicate that a decrease in the tensile loading rate leads to a transition to coalesced damage dominance and that the plastic processes driving void growth are time dependent.« less

Electron delocalization and charge mobility as a function of reduction in a metal-organic framework.

PubMed

Aubrey, Michael L; Wiers, Brian M; Andrews, Sean C; Sakurai, Tsuneaki; Reyes-Lillo, Sebastian E; Hamed, Samia M; Yu, Chung-Jui; Darago, Lucy E; Mason, Jarad A; Baeg, Jin-Ook; Grandjean, Fernande; Long, Gary J; Seki, Shu; Neaton, Jeffrey B; Yang, Peidong; Long, Jeffrey R

2018-06-04

Conductive metal-organic frameworks are an emerging class of three-dimensional architectures with degrees of modularity, synthetic flexibility and structural predictability that are unprecedented in other porous materials. However, engendering long-range charge delocalization and establishing synthetic strategies that are broadly applicable to the diverse range of structures encountered for this class of materials remain challenging. Here, we report the synthesis of K x Fe 2 (BDP) 3 (0 ≤ x ≤ 2; BDP 2-  = 1,4-benzenedipyrazolate), which exhibits full charge delocalization within the parent framework and charge mobilities comparable to technologically relevant polymers and ceramics. Through a battery of spectroscopic methods, computational techniques and single-microcrystal field-effect transistor measurements, we demonstrate that fractional reduction of Fe 2 (BDP) 3 results in a metal-organic framework that displays a nearly 10,000-fold enhancement in conductivity along a single crystallographic axis. The attainment of such properties in a K x Fe 2 (BDP) 3 field-effect transistor represents the realization of a general synthetic strategy for the creation of new porous conductor-based devices.

Structural changes in the BH3 domain of SOUL protein upon interaction with the anti-apoptotic protein Bcl-xL

PubMed Central

Ambrosi, Emmanuele; Capaldi, Stefano; Bovi, Michele; Saccomani, Gianmaria; Perduca, Massimiliano; Monaco, Hugo L.

2011-01-01

The SOUL protein is known to induce apoptosis by provoking the mitochondrial permeability transition, and a sequence homologous with the BH3 (Bcl-2 homology 3) domains has recently been identified in the protein, thus making it a potential new member of the BH3-only protein family. In the present study, we provide NMR, SPR (surface plasmon resonance) and crystallographic evidence that a peptide spanning residues 147–172 in SOUL interacts with the anti-apoptotic protein Bcl-xL. We have crystallized SOUL alone and the complex of its BH3 domain peptide with Bcl-xL, and solved their three-dimensional structures. The SOUL monomer is a single domain organized as a distorted β-barrel with eight anti-parallel strands and two α-helices. The BH3 domain extends across 15 residues at the end of the second helix and eight amino acids in the chain following it. There are important structural differences in the BH3 domain in the intact SOUL molecule and the same sequence bound to Bcl-xL. PMID:21639858

Process metallurgy simulation for metal drawing process optimization by using two-scale finite element method

NASA Astrophysics Data System (ADS)

Nakamachi, Eiji; Yoshida, Takashi; Kuramae, Hiroyuki; Morimoto, Hideo; Yamaguchi, Toshihiko; Morita, Yusuke

2014-10-01

We developed two-scale FE analysis procedure based on the crystallographic homogenization method by considering the hierarchical structure of poly-crystal aluminium alloy metal. It can be characterized as the combination of two-scale structure, such as the microscopic polycrystal structure and the macroscopic elastic plastic continuum. Micro polycrystal structure can be modeled as a three dimensional representative volume element (RVE). RVE is featured as by 3×3×3 eight-nodes solid finite elements, which has 216 crystal orientations. This FE analysis code can predict the deformation, strain and stress evolutions in the wire drawing processes in the macro- scales, and further the crystal texture and hardening evolutions in the micro-scale. In this study, we analyzed the texture evolution in the wire drawing processes by our two-scale FE analysis code under conditions of various drawing angles of dice. We evaluates the texture evolution in the surface and center regions of the wire cross section, and to clarify the effects of processing conditions on the texture evolution.

Automation in biological crystallization.

PubMed

Stewart, Patrick Shaw; Mueller-Dieckmann, Jochen

2014-06-01

Crystallization remains the bottleneck in the crystallographic process leading from a gene to a three-dimensional model of the encoded protein or RNA. Automation of the individual steps of a crystallization experiment, from the preparation of crystallization cocktails for initial or optimization screens to the imaging of the experiments, has been the response to address this issue. Today, large high-throughput crystallization facilities, many of them open to the general user community, are capable of setting up thousands of crystallization trials per day. It is thus possible to test multiple constructs of each target for their ability to form crystals on a production-line basis. This has improved success rates and made crystallization much more convenient. High-throughput crystallization, however, cannot relieve users of the task of producing samples of high quality. Moreover, the time gained from eliminating manual preparations must now be invested in the careful evaluation of the increased number of experiments. The latter requires a sophisticated data and laboratory information-management system. A review of the current state of automation at the individual steps of crystallization with specific attention to the automation of optimization is given.

Automation in biological crystallization

PubMed Central

Shaw Stewart, Patrick; Mueller-Dieckmann, Jochen

2014-01-01

Crystallization remains the bottleneck in the crystallographic process leading from a gene to a three-dimensional model of the encoded protein or RNA. Automation of the individual steps of a crystallization experiment, from the preparation of crystallization cocktails for initial or optimization screens to the imaging of the experiments, has been the response to address this issue. Today, large high-throughput crystallization facilities, many of them open to the general user community, are capable of setting up thousands of crystallization trials per day. It is thus possible to test multiple constructs of each target for their ability to form crystals on a production-line basis. This has improved success rates and made crystallization much more convenient. High-throughput crystallization, however, cannot relieve users of the task of producing samples of high quality. Moreover, the time gained from eliminating manual preparations must now be invested in the careful evaluation of the increased number of experiments. The latter requires a sophisticated data and laboratory information-management system. A review of the current state of automation at the individual steps of crystallization with specific attention to the automation of optimization is given. PMID:24915074

3D DDD modelling of dislocation-precipitate interaction in a nickel-based single crystal superalloy under cyclic deformation

NASA Astrophysics Data System (ADS)

Lin, Bing; Huang, Minsheng; Zhao, Liguo; Roy, Anish; Silberschmidt, Vadim; Barnard, Nick; Whittaker, Mark; McColvin, Gordon

2018-06-01

Strain-controlled cyclic deformation of a nickel-based single crystal superalloy has been modelled using three-dimensional (3D) discrete dislocation dynamics (DDD) for both [0 0 1] and [1 1 1] orientations. The work focused on the interaction between dislocations and precipitates during cyclic plastic deformation at elevated temperature, which has not been well studied yet. A representative volume element with cubic γ‧-precipitates was chosen to represent the material, with enforced periodical boundary conditions. In particular, cutting of superdislocations into precipitates was simulated by a back-force method. The global cyclic stress-strain responses were captured well by the DDD model when compared to experimental data, particularly the effects of crystallographic orientation. Dislocation evolution showed that considerably high density of dislocations was produced for [1 1 1] orientation when compared to [0 0 1] orientation. Cutting of dislocations into the precipitates had a significant effect on the plastic deformation, leading to material softening. Contour plots of in-plane shear strain proved the development of heterogeneous strain field, resulting in the formation of shear-band embryos.

Primary combination of phase-field and discrete dislocation dynamics methods for investigating athermal plastic deformation in various realistic Ni-base single crystal superalloy microstructures

NASA Astrophysics Data System (ADS)

Gao, Siwen; Rajendran, Mohan Kumar; Fivel, Marc; Ma, Anxin; Shchyglo, Oleg; Hartmaier, Alexander; Steinbach, Ingo

2015-10-01

Three-dimensional discrete dislocation dynamics (DDD) simulations in combination with the phase-field method are performed to investigate the influence of different realistic Ni-base single crystal superalloy microstructures with the same volume fraction of {γ\\prime} precipitates on plastic deformation at room temperature. The phase-field method is used to generate realistic microstructures as the boundary conditions for DDD simulations in which a constant high uniaxial tensile load is applied along different crystallographic directions. In addition, the lattice mismatch between the γ and {γ\\prime} phases is taken into account as a source of internal stresses. Due to the high antiphase boundary energy and the rare formation of superdislocations, precipitate cutting is not observed in the present simulations. Therefore, the plastic deformation is mainly caused by dislocation motion in γ matrix channels. From a comparison of the macroscopic mechanical response and the dislocation evolution for different microstructures in each loading direction, we found that, for a given {γ\\prime} phase volume fraction, the optimal microstructure should possess narrow and homogeneous γ matrix channels.

Solo surgery--early results of robot-assisted three-dimensional laparoscopic hysterectomy.

PubMed

Tuschy, Benjamin; Berlit, Sebastian; Brade, Joachim; Sütterlin, Marc; Hornemann, Amadeus

2014-08-01

Report of our initial experience in laparoscopic hysterectomy by a solo surgeon using a robotic camera system with three-dimensional visualisation. This novel device (Einstein Vision®, B. Braun, Aesculap AG, Tuttlingen, Germany) (EV) was used for laparoscopic supracervical hysterectomy (LASH) performed by one surgeon. Demographic data, clinical and surgical parameters were evaluated. Our first 22 cases, performed between June and November 2012, were compared with a cohort of 22 age-matched controls who underwent two-dimensional LASH performed by the same surgeon with a second surgeon assisting. Compared to standard two-dimensional laparoscopic hysterectomy, there were no significant differences regarding duration of surgery, hospital stay, blood loss or incidence of complications. The number of trocars used was significantly higher in the control group (p <.0001). All hysterectomies in the treatment group were performed without assistance of a second physician. Robot-assisted solo surgery laparoscopic hysterectomy is a feasible and safe procedure. Duration of surgery, hospital stay, blood loss, and complication rates are comparable to a conventional laparoscopic hysterectomy.

Nanowire-templated lateral epitaxial growth of non-polar group III nitrides

DOEpatents

Wang, George T [Albuquerque, NM; Li, Qiming [Albuquerque, NM; Creighton, J Randall [Albuquerque, NM

2010-03-02

A method for growing high quality, nonpolar Group III nitrides using lateral growth from Group III nitride nanowires. The method of nanowire-templated lateral epitaxial growth (NTLEG) employs crystallographically aligned, substantially vertical Group III nitride nanowire arrays grown by metal-catalyzed metal-organic chemical vapor deposition (MOCVD) as templates for the lateral growth and coalescence of virtually crack-free Group III nitride films. This method requires no patterning or separate nitride growth step.

Verification of the Robin and Graham classification system of hip disease in cerebral palsy using three-dimensional computed tomography.

PubMed

Gose, Shinichi; Sakai, Takashi; Shibata, Toru; Akiyama, Keisuke; Yoshikawa, Hideki; Sugamoto, Kazuomi

2011-12-01

We evaluated the validity of the Robin and Graham classification system of hip disease in cerebral palsy (CP) using three-dimensional computed tomography in young people with CP. A total of 91 hips in 91 consecutive children with bilateral spastic CP (57 males, 34 females; nine classified at Gross Motor Function Classification System level II, 42 at level III, 32 at level IV, and eight at level V; mean age 5 y 2 mo, SD 11 mo; range 2-6 y) were investigated retrospectively using anteroposterior plain radiographs and three-dimensional computed tomography (3D-CT) of the hip. The migration percentage was calculated on plain radiographs and all participants were classified into four groups according to migration percentage: grade II, migration percentage ≥ 10% but ≤ 15%, (four hips), grade III, migration percentage >15% but ≤ 30%, (20 hips); grade IV, migration percentage >30% but <100%, (63 hips); and grade V, migration percentage ≥ 100%, (four hips). The lateral opening angle and the sagittal inclination angle of the acetabulum, the neck-shaft angle, and the femoral anteversion of the femur were measured on 3D-CT. The three-dimensional quantitative evaluation indicated that there were significant differences in the lateral opening angle and the neck-shaft angle between the four groups (Kruskal-Wallis test, p ≤ 0.001). This three-dimensional evaluation supports the validation of the Robin and Graham classification system for hip disease in 2- to 7-year-olds with CP. © The Authors. Developmental Medicine & Child Neurology © 2011 Mac Keith Press.

Three-dimensional organic Dirac-line materials due to nonsymmorphic symmetry: A data mining approach

NASA Astrophysics Data System (ADS)

Geilhufe, R. Matthias; Bouhon, Adrien; Borysov, Stanislav S.; Balatsky, Alexander V.

2017-01-01

A data mining study of electronic Kohn-Sham band structures was performed to identify Dirac materials within the Organic Materials Database. Out of that, the three-dimensional organic crystal 5,6-bis(trifluoromethyl)-2-methoxy-1 H -1,3-diazepine was found to host different Dirac-line nodes within the band structure. From a group theoretical analysis, it is possible to distinguish between Dirac-line nodes occurring due to twofold degenerate energy levels protected by the monoclinic crystalline symmetry and twofold degenerate accidental crossings protected by the topology of the electronic band structure. The obtained results can be generalized to all materials having the space group P 21/c (No. 14, C2h 5) by introducing three distinct topological classes.

Low-dimensional representations of the three component loop braid group

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bruillard, Paul; Chang, Liang; Hong, Seung-Moon

2015-11-01

Motivated by physical and topological applications, we study representations of the group LB3 o motions of 3 unlinked oriented circles in R3. Our point of view is to regard the three strand braid group B3 as a subgroup of LB3 and study the problem of extending B3 representations. We introduce the notion of a standard extension and characterize B3 represenations admiting such an extension. In particular we show, using a classification result of Tuba and Wenzl, that every irreducible B3 representation of dimension at most 5 has a (standard) extension. We show that this result is sharp by exhibiting anmore » irreducible 6-dimensional B3 representation that has no extension (standard or otherwise). We obtain complete classifications of (1) irreducible 2-dimensional LB3 representations (2) extensions of irreducible B3 representations and (3) irreducible LB3 representations whose restriction to B3 has abelian image.« less

Ca2Mg(NO3)6×12H2O-structural investigations on a new compound retrieved from chimney deposits of a combined heat and power plant

NASA Astrophysics Data System (ADS)

Kahlenberg, Volker; Tessadri, Richard; Tribus, Martina; Schmidmair, Daniela; Perfler, Lukas; Haefeker, Udo

2014-10-01

Phase analysis of incrustations retrieved from chimney deposits of a combined heat and power plant in Malchow/Germany by X-ray powder diffraction gave evidence for the existence of a previously unknown hydrous calcium magnesium nitrate. Optical investigations of the sample showed the presence of colorless platy crystals with a maximum diameter of about 250 μm embedded in a partly polycrystalline and partly glassy matrix. Aided by EDX-analysis and Raman spectroscopy, a single-crystal diffraction study performed at ambient conditions demonstrated that the material represents a phase with composition Ca2Mg(NO3)6×12H2O. Basic crystallographic data are as follows: trigonal symmetry, space group type R , a = 10.5583(5) Å, c = 19.5351(10) Å, V = 1885.97(16) Å3, Z = 3, ( R(| F|) = 0.0248). The magnesium ions are coordinated by water molecules to form distorted Mg(H2O)6-octahedra. The calcium atoms are surrounded by nine ligands. The resulting CaO9 tricapped trigonal prisms involve oxygen atoms from additional water moieties as well as from three different bidentate nitrate groups, respectively. Hydrogen bonds link one octahedron with two adjacent prisms into trimers. The trimers in turn are stacked in columns running parallel to [001]. Further hydrogen bonding between neighboring columns results in the formation of a three-dimensional network. To our best knowledge, Ca2Mg(NO3)6×12H2O represents a new structure type. However, column-like topologies with rods consisting of different types of polyhedra have been also observed in other trigonal hydrous nitrates. The structural relationships between these compounds are discussed. It is interesting to note that in previous phase equilibrium studies on the ternary system Ca(NO3)2-Mg(NO3)2-H2O no other hydrous double salt has been described. Finally, the results of the structure analysis allowed a qualitative and quantitative phase analysis of the crystalline part of the chimney deposit by the Rietveld method.

Ferroelectric properties of oxalate and phenanthroline based 1-D single chain molecular magnet [{FeII(Δ)FeII(Λ)}0.5{CrII(Δ)CrII(Λ)}0.5(ox)2(phen)2

NASA Astrophysics Data System (ADS)

Bhatt, Pramod; Mukadam, M. D.; Mandal, B. P.; Yusuf, S. M.

2018-04-01

The one-dimensional (1-D) single chain molecular magnet [{FeII(Δ)FeII(Λ)}0.5{CrII(Δ)CrII(Λ)}0.5(ox)2(phen)2] is hydrothermally synthesized using oxalate (ox) and phenanthroline (phen) ligands with transition metal ions (Fe and Cr). The compound is characterized using x-ray diffraction, dc magnetization measurements and P-E ferroelectric loop measurements. The diffraction analysis using Rietveld refinement confirms a single phase formation of the compound in monoclinic structure with space group of P21. The compound crystallizes in 1-D chain like structure containing two different crystallographic sites of metal ions (Δ- and Λ-), which are bridged by the ox ligand and Phen ligand. These two metals site are different in bond length and bond angles results lattice distortions. The lattice distortion induces ferroelectric behavior in the compound which is discussed in terms of lattice distortion induced dipole moments.

Three-dimensional accuracy of plastic transfer impression copings for three implant systems.

PubMed

Teo, Juin Wei; Tan, Keson B; Nicholls, Jack I; Wong, Keng Mun; Uy, Joanne

2014-01-01

The purpose of this study was to compare the three-dimensional accuracy of indirect plastic impression copings and direct implant-level impression copings from three implant systems (Nobel Biocare [NB], Biomet 3i [3i], and Straumann [STR]) at three interimplant buccolingual angulations (0, 8, and 15 degrees). Two-implant master models were used to simulate a three-unit implant fixed partial denture. Test models were made from Impregum impressions using direct implant-level impression copings (DR). Abutments were then connected to the master models for impressions using the plastic impression copings (INDR) at three different angulations for a total of 18 test groups (n = 5 in each group). A coordinate measuring machine was used to measure linear distortions, three-dimensional (3D) distortions, angular distortions, and absolute angular distortions between the master and test models. Three-way analysis of variance showed that the implant system had a significant effect on 3D distortions and absolute angular distortions in the x- and y-axes. Interimplant angulation had a significant effect on 3D distortions and absolute angular distortions in the y-axis. Impression technique had a significant effect on absolute angular distortions in the y-axis. With DR, the NB and 3i systems were not significantly different. With INDR, 3i appeared to have less distortion than the other systems. Interimplant angulations did not significantly affect the accuracy of NBDR, 3iINDR, and STRINDR. The accuracy of INDR and DR was comparable at all interimplant angulations for 3i and STR. For NB, INDR was comparable to DR at 0 and 8 degrees but was less accurate at 15 degrees. Three-dimensional accuracy of implant impressions varied with implant system, interimplant angulation, and impression technique.

Out-of-Bounds Hydrodynamics in Anisotropic Dirac Fluids

NASA Astrophysics Data System (ADS)

Link, Julia M.; Narozhny, Boris N.; Kiselev, Egor I.; Schmalian, Jörg

2018-05-01

We study hydrodynamic transport in two-dimensional, interacting electronic systems with merging Dirac points at charge neutrality. The dispersion along one crystallographic direction is Dirac-like, while it is Newtonian-like in the orthogonal direction. As a result, the electrical conductivity is metallic in one and insulating in the other direction. The shear viscosity tensor contains six independent components, which can be probed by measuring an anisotropic thermal flow. One of the viscosity components vanishes at zero temperature leading to a generalization of the previously conjectured lower bound for the shear viscosity to entropy density ratio.

Expression, limited proteolysis and preliminary crystallographic analysis of IpaD, a component of the Shigella flexneri type III secretion system

PubMed Central

Johnson, Steven; Roversi, Pietro; Espina, Marianela; Deane, Janet E.; Birket, Susan; Picking, William D.; Blocker, Ariel; Picking, Wendy L.; Lea, Susan M.

2006-01-01

IpaD, the putative needle-tip protein of the Shigella flexneri type III secretion system, has been overexpressed and purified. Crystals were grown of the native protein in space group P212121, with unit-cell parameters a = 55.9, b = 100.7, c = 112.0 Å, and data were collected to 2.9 Å resolution. Analysis of the native Patterson map revealed a peak at 50% of the origin on the Harker section v = 0.5, suggesting twofold non-crystallographic symmetry parallel to the b crystallographic axis. As attempts to derivatize or grow selenomethionine-labelled protein crystals failed, in-drop proteolysis was used to produce new crystal forms. A trace amount of subtilisin Carlsberg was added to IpaD before sparse-matrix screening, resulting in the production of several new crystal forms. This approach produced SeMet-labelled crystals and diffraction data were collected to 3.2 Å resolution. The SeMet crystals belong to space group C2, with unit-cell parameters a = 139.4, b = 45.0, c = 99.5 Å, β = 107.9°. An anomalous difference Patterson map revealed peaks on the Harker section v = 0, while the self-rotation function indicates the presence of a twofold noncrystallographic symmetry axis, which is consistent with two molecules per asymmetric unit. PMID:16946465

Expression, limited proteolysis and preliminary crystallographic analysis of IpaD, a component of the Shigella flexneri type III secretion system.

PubMed

Johnson, Steven; Roversi, Pietro; Espina, Marianela; Deane, Janet E; Birket, Susan; Picking, William D; Blocker, Ariel; Picking, Wendy L; Lea, Susan M

2006-09-01

IpaD, the putative needle-tip protein of the Shigella flexneri type III secretion system, has been overexpressed and purified. Crystals were grown of the native protein in space group P2(1)2(1)2(1), with unit-cell parameters a = 55.9, b = 100.7, c = 112.0 A, and data were collected to 2.9 A resolution. Analysis of the native Patterson map revealed a peak at 50% of the origin on the Harker section v = 0.5, suggesting twofold non-crystallographic symmetry parallel to the b crystallographic axis. As attempts to derivatize or grow selenomethionine-labelled protein crystals failed, in-drop proteolysis was used to produce new crystal forms. A trace amount of subtilisin Carlsberg was added to IpaD before sparse-matrix screening, resulting in the production of several new crystal forms. This approach produced SeMet-labelled crystals and diffraction data were collected to 3.2 A resolution. The SeMet crystals belong to space group C2, with unit-cell parameters a = 139.4, b = 45.0, c = 99.5 A, beta = 107.9 degrees . An anomalous difference Patterson map revealed peaks on the Harker section v = 0, while the self-rotation function indicates the presence of a twofold noncrystallographic symmetry axis, which is consistent with two molecules per asymmetric unit.

Fate of superconductivity in three-dimensional disordered Luttinger semimetals

NASA Astrophysics Data System (ADS)

Mandal, Ipsita

2018-05-01

Superconducting instability can occur in three-dimensional quadratic band crossing semimetals only at a finite coupling strength due to the vanishing of density of states at the quadratic band touching point. Since realistic materials are always disordered to some extent, we study the effect of short-ranged-correlated disorder on this superconducting quantum critical point using a controlled loop-expansion applying dimensional regularization. The renormalization group (RG) scheme allows us to determine the RG flows of the various interaction strengths and shows that disorder destroys the superconducting quantum critical point. In fact, the system exhibits a runaway flow to strong disorder.

Dimensional assessment of personality pathology in patients with eating disorders.

PubMed

Goldner, E M; Srikameswaran, S; Schroeder, M L; Livesley, W J; Birmingham, C L

1999-02-22

This study examined patients with eating disorders on personality pathology using a dimensional method. Female subjects who met DSM-IV diagnostic criteria for eating disorder (n = 136) were evaluated and compared to an age-controlled general population sample (n = 68). We assessed 18 features of personality disorder with the Dimensional Assessment of Personality Pathology - Basic Questionnaire (DAPP-BQ). Factor analysis and cluster analysis were used to derive three clusters of patients. A five-factor solution was obtained with limited intercorrelation between factors. Cluster analysis produced three clusters with the following characteristics: Cluster 1 members (constituting 49.3% of the sample and labelled 'rigid') had higher mean scores on factors denoting compulsivity and interpersonal difficulties; Cluster 2 (18.4% of the sample) showed highest scores in factors denoting psychopathy, neuroticism and impulsive features, and appeared to constitute a borderline psychopathology group; Cluster 3 (32.4% of the sample) was characterized by few differences in personality pathology in comparison to the normal population sample. Cluster membership was associated with DSM-IV diagnosis -- a large proportion of patients with anorexia nervosa were members of Cluster 1. An empirical classification of eating-disordered patients derived from dimensional assessment of personality pathology identified three groups with clinical relevance.

The 2.0-A resolution structure of soybean beta-amylase complexed with alpha-cyclodextrin.

PubMed

Mikami, B; Hehre, E J; Sato, M; Katsube, Y; Hirose, M; Morita, Y; Sacchettini, J C

1993-07-13

New crystallographic findings are presented which offer a deeper understanding of the structure and functioning of beta-amylase, the first known exo-type starch-hydrolyzing enzyme. A refined three-dimensional structure of soybean beta-amylase, complexed with the inhibitor alpha-cyclodextrin, has been determined at 2.0-A resolution with a conventional R-value of 17.5%. The model contains 491 amino acid residues, 319 water molecules, 1 sulfate ion, and 1 alpha-cyclodextrin molecule. The protein consists of a core with an (alpha/beta)8 supersecondary structure, plus a smaller globular region formed by long loops (L3, L4, and L5) extending from beta-strands beta 3, beta 4, and beta 5. Between the two regions is a cleft that opens into a pocket whose floor contains the postulated catalytic center near the carboxyl group of Glu 186. The annular alpha-cyclodextrin binds in (and partly projects from) the cleft with its glucosyl O-2/O-3 face abutting the (alpha/beta)8 side and with its alpha-D(1 --> 4) glucosidic linkage progression running clockwise as viewed from that side. The ligand does not bind deeply enough to interact with the carboxyl group of Glu 186. Rather, it occupies most of the cleft entrance, strongly suggesting that alpha-cyclodextrin inhibits catalysis by blocking substrate access to the more deeply located reaction center. Of the various alpha-cyclodextrin interactions with protein residues in loops L4, L5, L6, and L7, most notable is the shallow inclusion complex formed with Leu 383 (in L7, on the core side of the cleft) through contacts of its methyl groups with the C-3 atoms of four of the ligand's D-glucopyranosyl residues. All six residues of the bound alpha-cyclodextrin are of 4C1 conformation and are joined by alpha-1,4 linkages with similar torsional angles to form a nearly symmetrical torus as reported for crystalline inclusion complexes with alpha-cyclodextrin. We envision a significant role for the methyl groups of Leu 383 at the cleft entrance with respect to the productive binding of the outer chains of starch.

Dimensional stability of two impression materials after a 6-month storage period.

PubMed

Martins, Francisco; Branco, Patrícia; Reis, José; Barbero Navarro, Ignacio; Maurício, Paulo

2017-01-01

Objective: Oral rehabilitation success is enhanced by an accurate and reproducible final impression. The purpose of this study is to evaluate the dimensional changes of a polyether and addition silicone subjected to disinfection and/or sterilization after a long storage period. Material and methods: Ninety samples were obtained from polyether Impregum TM Penta TM (3M ESPE TM , Seefeld, Germany) and 90 of addition silicone Imprint TM 4 Penta TM Putty (3M ESPE TM , Seefeld, Germany) according to ISO 4823:2000. The samples of each material were split to form three groups with 30 samples each: a control group, a hypochlorite group (disinfection) and an autoclave group (sterilization). Samples were stored in the Portuguese Institute for Quality for six months at 23 °C. Samples were measured by laser interferometry, according to the Michelson technique before calculating dimensional stability according ISO 4823:2000. A statistical analysis via a three-way mixed ANOVA was performed. Results: Significant shrinkage of Impregum TM Penta TM was 0.77 ± 0.17% in the control group, 0.42 ± 0.19% in the hypochlorite group and 0.52 ± 0.28% in the autoclave group. For Imprint TM 4 Penta TM Putty, the control group had a shrinkage of 0.42 ± 0.12%, the hypochlorite group 0.36 ± 0.09% and the autoclave group 0.59 ± 0.13%. Conclusions: The long-term storage of samples subjected to disinfection with 5.25% hypochlorite or autoclave sterilization can be used in a clinical setting as the dimensional changes are below the maximum permitted by the ISO 4823:2000, since there are no clinically significant changes in the dimension of the samples during the storage period.

Highly aligned vertical GaN nanowires using submonolayer metal catalysts

DOEpatents

Wang, George T [Albuquerque, NM; Li, Qiming [Albuquerque, NM; Creighton, J Randall [Albuquerque, NM

2010-06-29

A method for forming vertically oriented, crystallographically aligned nanowires (nanocolumns) using monolayer or submonolayer quantities of metal atoms to form uniformly sized metal islands that serve as catalysts for MOCVD growth of Group III nitride nanowires.

Three-Dimensional Model of Strengths: Examination of Invariance Across Gender, Age, Education Levels, and Marriage Status.

PubMed

Duan, Wenjie; Ho, Samuel Mun Yin

2017-02-01

Strengths are positive qualities that significantly contributed to well-being of individuals and community. Therefore, a reliable and valid measure of strengths for research and practice is needed. The Brief Strengths Scale (BSS) is a newly developed tool for measuring the three-dimensional strengths model (i.e., temperance, intellectual, and interpersonal strength). However, empirical support for the measurement invariance of the BSS has not been obtained. This study examined the three-factor structure of BSS across gender, age, education, and marriage groups in a community sample (n = 375) using multi-group confirmatory factor analysis. After removing one item of each subscale from the original version, the revised model provided a good fit to the data at different subgroups. The revised nine-item BSS indicated that measurement invariance across gender and age groups was achieved. In addition, the measurement was more influenced by social-cultural factors than biological factors.

In vitro three-dimensional coculturing poly3-hydroxybutyrate-co-3-hydroxyhexanoate with mouse-induced pluripotent stem cells for myocardial patch application.

PubMed

Shijun, Xu; Junsheng, Mu; Jianqun, Zhang; Ping, Bo

2016-03-01

Identifying a suitable polymeric biomaterial for myocardial patch repair following myocardial infarction, cerebral infarction, and cartilage injury is essential. This study aimed to investigate the effect of the novel polymer material, poly3-hydroxybutyrate-co-3-hydroxyhexanoate, on the adhesion, proliferation, and differentiation of mouse-induced pluripotent stem cells in vitro. Mouse-induced pluripotent stem cells were isolated, expanded, and cultured on either two-dimensional or three-dimensional poly3-hydroxybutyrate-co-3-hydroxyhexanoate films (membranes were perforated to imitate three-dimensional space). Following attachment onto the films, mouse-induced pluripotent stem cell morphology was visualized using scanning electron microscopy. Cell vitality was detected using the Cell Counting Kit-8 assay and cell proliferation was observed using fluorescent 4',6-diamidino-2-phenylindole (DAPI) staining. Mouse-induced pluripotent stem cells were induced into cardiomyocytes by differentiation medium containing vitamin C. A control group in the absence of an inducer was included. Mouse-induced pluripotent stem cell survival and differentiation were observed using immunofluorescence and flow cytometry, respectively. Mouse-induced pluripotent stem cells growth, proliferation, and differentiation were observed on both two-dimensional and three-dimensional poly3-hydroxybutyrate-co-3-hydroxyhexanoate films. Vitamin C markedly improved the efficiency of mouse-induced pluripotent stem cells differentiation into cardiomyocytes on poly3-hydroxybutyrate-co-3-hydroxyhexanoate films. Three-dimensional culture was better at promoting mouse-induced pluripotent stem cell proliferation and differentiation compared with two-dimensional culture. © The Author(s) 2016.

Magnetic Resonance Imaging of Three-Dimensional Cervical Anatomy in the Second and Third Trimester

PubMed Central

HOUSE, Michael; BHADELIA, Rafeeque A.; MYERS, Kristin; SOCRATE, Simona

2009-01-01

OBJECTIVE Although a short cervix is known to be associated with preterm birth, the patterns of three-dimensional, anatomic changes leading to a short cervix are unknown. Our objective was to 1) construct three-dimensional anatomic models during normal pregnancy and 2) use the models to compare cervical anatomy in the second and third trimester. STUDY DESIGN A cross sectional study was performed in a population of patients referred to magnetic resonance imaging (MRI) for a fetal indication. Using magnetic resonance images for guidance, three-dimensional solid models of the following anatomic structures were constructed: amniotic cavity, uterine wall, cervical stroma, cervical mucosa and anterior vaginal wall. To compare cervical anatomy in the second and third trimester, models were matched according the size of the bony pelvis. RESULTS Fourteen patients were imaged and divided into two groups according to gestational age: 20 – 24 weeks (n=7)) and 31 – 36 weeks (n=7). Compared to the second trimester, the third trimester was associated with significant descent of the amniotic sac. (p=.02). Descent of the amniotic sac was associated with modified anatomy of the uterocervical junction. These 3-dimensional changes were associated with a cervix that appeared shorter in the third trimester. CONCLUSION We report a technique for constructing MRI-based, three-dimensional anatomic models during pregnancy. Compared to the second trimester, the third trimester is associated with three-dimensional changes in the cervix and lower uterine segment. PMID:19297070

Expression, crystallization and preliminary crystallographic studies of a novel bifunctional N-­acetylglutamate synthase/kinase from Xanthomonas campestris homologous to vertebrate N-acetylglutamate synthase

PubMed Central

Shi, Dashuang; Caldovic, Ljubica; Jin, Zhongmin; Yu, Xiaolin; Qu, Qiuhao; Roth, Lauren; Morizono, Hiroki; Hathout, Yetrib; Allewell, Norma M.; Tuchman, Mendel

2006-01-01

A novel N-acetylglutamate synthase/kinase bifunctional enzyme of arginine biosynthesis that was homologous to vertebrate N-acetylglutamate synthases was identified in Xanthomonas campestris. The protein was overexpressed, purified and crystallized. The crystals belong to the hexagonal space group P6222, with unit-cell parameters a = b = 134.60, c = 192.11 Å, and diffract to about 3.0 Å resolution. Selenomethionine-substituted recombinant protein was produced and selenomethionine substitution was verified by mass spectroscopy. Multiple anomalous dispersion (MAD) data were collected at three wavelengths at SER-CAT, Advanced Photon Source, Argonne National Laboratory. Structure determination is under way using the MAD phasing method. PMID:17142901

Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of DHNA synthetase from Geobacillus kaustophilus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kanaujia, Shankar Prasad; Ranjani, Chellamuthu Vasuki; Jeyakanthan, Jeyaraman

2007-02-01

DHNA synthetase from G. kaustophilus has been cloned, expressed, purified and crystallized. The aerobic Gram-positive bacterium Geobacillus kaustophilus is a bacillus species that was isolated from deep-sea sediment from the Mariana Trench. 1,4-Dihydroxy-2-naphthoate (DHNA) synthetase plays a vital role in the biosynthesis of menaquinone (vitamin K{sub 2}) in this bacterium. DHNA synthetase from Geobacillus kaustophilus was crystallized in the orthorhombic space group C222{sub 1}, with unit-cell parameters a = 77.01, b = 130.66, c = 131.69 Å. The crystal diffracted to a resolution of 2.2 Å. Preliminary studies and molecular-replacement calculations reveal the presence of three monomers in the asymmetricmore » unit.« less

Matrix-assisted laser desorption ionization time-of-flight mass spectrometric analysis of degradation products after treatment of methylene blue aqueous solution with three-dimensionally integrated microsolution plasma

NASA Astrophysics Data System (ADS)

Shirafuji, Tatsuru; Nomura, Ayano; Hayashi, Yui; Tanaka, Kenji; Goto, Motonobu

2016-01-01

Methylene blue can be degraded in three-dimensionally integrated microsolution plasma. The degradation products have been analyzed by matrix-assisted laser desorption ionization time-of-flight (MALDI TOF) mass spectrometry to understand the degradation mechanisms. The results of MALDI TOF mass spectrometry have shown that sulfoxide is formed at the first stage of the oxidation. Then, partial oxidation proceeds on the methyl groups left on the sulfoxide. The sulfoxide is subsequently separated to two benzene derivatives. Finally, weak functional groups are removed from the benzene derivatives.

Crystal structures of hibiscus acid and hibiscus acid dimethyl ester isolated from Hibiscus sabdariffa (Malvaceae).

PubMed

Zheoat, Ahmed M; Gray, Alexander I; Igoli, John O; Kennedy, Alan R; Ferro, Valerie A

2017-09-01

The biologically active title compounds have been isolated from Hibiscus sabdariffa plants, hibiscus acid as a dimethyl sulfoxide monosolvate [systematic name: (2 S ,3 R )-3-hy-droxy-5-oxo-2,3,4,5-tetra-hydro-furan-2,3-di-carb-oxy-lic acid dimethyl sulfoxide monosolvate], C 6 H 6 O 7 ·C 2 H 6 OS, (I), and hibiscus acid dimethyl ester [systematic name: dimethyl (2 S ,3 R )-3-hy-droxy-5-oxo-2,3,4,5-tetra-hydro-furan-2,3-di-carboxyl-ate], C 8 H 10 O 7 , (II). Compound (I) forms a layered structure with alternating layers of lactone and solvent mol-ecules, that include a two-dimensional hydrogen-bonding construct. Compound (II) has two crystallographically independent and conformationally similar mol-ecules per asymmetric unit and forms a one-dimensional hydrogen-bonding construct. The known absolute configuration for both compounds has been confirmed.

Superconductivity in Ta3Pd3Te14 with quasi-one-dimensional PdTe2 chains.

PubMed

Jiao, Wen-He; He, Lan-Po; Liu, Yi; Xu, Xiao-Feng; Li, Yu-Ke; Zhang, Chu-Hang; Zhou, Nan; Xu, Zhu-An; Li, Shi-Yan; Cao, Guang-Han

2016-02-15

We report bulk superconductivity at 1.0 K in a low-dimensional ternary telluride Ta3Pd3Te14 containing edge-sharing PdTe2 chains along crystallographic b axis, similar to the recently discovered superconductor Ta4Pd3Te16. The electronic heat capacity data show an obvious anomaly at the transition temperature, which indicates bulk superconductivity. The specific-heat jump is ΔC/(γ(n)T(c)) ≈ 1.35, suggesting a weak coupling scenario. By measuring the low-temperature thermal conductivity, we conclude that Ta3Pd3Te14 is very likely a dirty s-wave superconductor. The emergence of superconductivity in Ta3Pd3Te14 with a lower T(c), compared to that of Ta4Pd3Te16, may be attributed to the lower density of states.

Dynamics of vacancies in two-dimensional Lennard-Jones crystals

NASA Astrophysics Data System (ADS)

Yao, Zhenwei; Olvera de La Cruz, Monica

2015-03-01

Vacancies represent an important class of crystallographic defects, and their behaviors can be strongly coupled with relevant material properties. We report the rich dynamics of vacancies in two-dimensional Lennard-Jones crystals in several thermodynamic states. Specifically, we numerically observe significantly faster diffusion of the 2-point vacancy with two missing particles in comparison with other types of vacancies; it opens the possibility of doping 2-point vacancies into atomic materials to enhance atomic migration. In addition, the resulting dislocations in the healing of a long vacancy suggest the intimate connection between vacancies and topological defects that may provide an extra dimension in the engineering of defects in extensive crystalline materials for desired properties. We thank the financial support from the U.S. Department of Commerce, National Institute of Standards and Technology, the Office of the Director of Defense Research and Engineering (DDR&E) and the Air Force Office of Scientific Research.

Effectiveness of three-dimensional digital animation in teaching human anatomy in an authentic classroom context.

PubMed

Hoyek, Nady; Collet, Christian; Di Rienzo, Franck; De Almeida, Mickael; Guillot, Aymeric

2014-01-01

Three-dimensional (3D) digital animations were used to teach the human musculoskeletal system to first year kinesiology students. The purpose of this study was to assess the effectiveness of this method by comparing two groups from two different academic years during two of their official required anatomy examinations (trunk and upper limb assessments). During the upper limb section, the teacher used two-dimensional (2D) drawings embedded into PowerPoint(®) slides and 3D digital animations for the first group (2D group) and the second (3D group), respectively. The same 3D digital animations were used for both groups during the trunk section. The only difference between the two was the multimedia used to present the information during the upper limb section. The 2D group surprisingly outperformed the 3D group on the trunk assessment. On the upper limb assessment no difference in the scores on the overall anatomy examination was found. However, the 3D group outperformed the 2D group in questions requiring spatial ability. Data supported that 3D digital animations were effective instructional multimedia material tools in teaching human anatomy especially in recalling anatomical knowledge requiring spatial ability. The importance of evaluating the effectiveness of a new instructional material outside laboratory environment (e.g., after a complete semester and on official examinations) was discussed. © 2014 American Association of Anatomists.

First-principles study of crystallographic slip modes in ω-Zr

DOE PAGES

Kumar, Anil; Kumar, M. Arul; Beyerlein, Irene Jane

2017-08-21

We use first-principles density functional theory to study the preferred modes of slip in the high-pressure ω phase of Zr. The generalized stacking fault energy surfaces associated with shearing on nine distinct crystallographic slip modes in the hexagonal ω-Zr crystal are calculated, from which characteristics such as ideal shear stress, the dislocation Burgers vector, and possible accompanying atomic shuffles, are extracted. Comparison of energy barriers and ideal shear stresses suggests that the favorable modes are prismatic < c >, prismatic-II <101¯0> and pyramidal-II < c+a >, which are distinct from the ground state hexagonal close packed α phase of Zr.more » Operation of these three modes can accommodate any deformation state. The relative preferences among the identified slip modes are examined using a mean-field crystal plasticity model and comparing the calculated deformation texture with the measurement. In conclusion, knowledge of the basic crystallographic modes of slip is critical to understanding and analyzing the plastic deformation behavior of ω-Zr or mixed α-ω phase-Zr.« less

Positive Charges on the Surface of Thaumatin Are Crucial for the Multi-Point Interaction with the Sweet Receptor.

PubMed

Masuda, Tetsuya; Kigo, Satomi; Mitsumoto, Mayuko; Ohta, Keisuke; Suzuki, Mamoru; Mikami, Bunzo; Kitabatake, Naofumi; Tani, Fumito

2018-01-01

Thaumatin, an intensely sweet-tasting protein, elicits sweet taste with a threshold of only 50 nM. Previous studies from our laboratory suggested that the complex model between the T1R2-T1R3 sweet receptor and thaumatin depends critically on the complementarity of electrostatic potentials. In order to further validate this model, we focused on three lysine residues (Lys78, Lys106, and Lys137), which were expected to be part of the interaction sites. Three thaumatin mutants (K78A, K106A, and K137A) were prepared and their threshold values of sweetness were examined. The results showed that the sweetness of K106A was reduced by about three times and those of K78A and K137A were reduced by about five times when compared to wild-type thaumatin. The three-dimensional structures of these mutants were also determined by X-ray crystallographic analyses at atomic resolutions. The overall structures of mutant proteins were similar to that of wild-type but the electrostatic potentials around the mutated sites became more negative. Since the three lysine residues are located in 20-40 Å apart each other on the surface of thaumatin molecule, these results suggest the positive charges on the surface of thaumatin play a crucial role in the interaction with the sweet receptor, and are consistent with a large surface is required for interaction with the sweet receptor, as proposed by the multipoint interaction model named wedge model.

Evaluation of engraftment of superparamagnetic iron oxide-labeled mesenchymal stem cells using three-dimensional reconstruction of magnetic resonance imaging in photothrombotic cerebral infarction models of rats.

PubMed

Shim, Jaehyun; Kwak, Byung Kook; Jung, Jisung; Park, Serah

2015-01-01

To evaluate engraftment by visualizing the location of human bone marrow-derived mesenchymal stem cells (hBM-MSCs) three-dimensionally in photothrombotic cerebral infarction (PTCI) models of rats. Magnetic resonance imaging (MRI) of an agarose block containing superparamagnetic iron oxide (SPIO)-labeled hBM-MSCs was performed using a 3.0-T MRI, T2-(T2WI), T2(*)-(T2(*)WI), and susceptibility-weighted images (SWI). PTCI was induced in 6 rats, and 2.5 × 10(5) SPIO-labeled hBM-MSCs were infused through the ipsilateral internal carotid artery (ICA group) or tail vein (IV group). MRI was performed on days 1, 3, 7, and 14 after stem cell injection. Dark signal regions were confirmed using histology. Three-dimensional MRI reconstruction was performed using the clinical workflow solution to evaluate the engraftment of hBM-MSCs. Volumetric analysis of the engraftment was also performed. The volumes of SPIO-labeled hBM-MSCs in the phantom MRI were 129.3, 68.4, and 25.9 µL using SWI, T2(*)WI, and T2WI, respectively. SPIO-labeled hBM-MSCs appeared on day 1 after injection, encircling the cerebral infarction from the ventral side. Dark signal regions matched iron positive cells and human origin (positive) cells. The volume of the engraftment was larger in the ICA group on days 1, 3, and 7, after stem cell injection (p < 0.05 on SWI). SWI was the most sensitive MRI pulse sequence (p < 0.05). The volume of infarction decreased until day 14. The engraftment of SPIO-labeled hBM-MSCs can be visualized and evaluated three-dimensionally in PTCI models of rats. The engraftment volume was larger in the ICA group than IV group on early stage within one week.

Band structure of the quasi two-dimensional purple molybdenum bronze

NASA Astrophysics Data System (ADS)

Guyot, H.; Balaska, H.; Perrier, P.; Marcus, J.

2006-09-01

The molybdenum purple bronze KMo 6O 17 is quasi two-dimensional (2D) metallic oxide that shows a Peierls transition towards a metallic charge density wave state. Since this specific transition is directly related to the electron properties of the normal state, we have investigated the electronic structure of this bronze at room temperature. The shape of the Mo K1s absorption edge reveals the presence of distorted MoO 6 octahedra in the crystallographic structure. Photoemission experiments evidence a large conduction band, with a bandwidth of 800 meV and confirm the metallic character of this bronze. A wide depleted zone separates the conduction band from the valence band that exhibits a fourfold structure, directly connected to the octahedral symmetry of the Mo sites. The band structure is determined by ARUPS in two main directions of the (0 0 1) Brillouin zone. It exhibits some unpredicted features but corroborates the earlier theoretical band structure and Fermi surface. It confirms the hidden one-dimensionality of KMo 6O 17 that has been proposed to explain the origin of the Peierls transition in this 2D compound.

3D laparoscopic surgery: a prospective clinical trial.

PubMed

Agrusa, Antonino; Di Buono, Giuseppe; Buscemi, Salvatore; Cucinella, Gaspare; Romano, Giorgio; Gulotta, Gaspare

2018-04-03

Since it's introduction, laparoscopic surgery represented a real revolution in clinical practice. The use of a new generation three-dimensional (3D) HD laparoscopic system can be considered a favorable "hybrid" made by combining two different elements: feasibility and diffusion of laparoscopy and improved quality of vision. In this study we report our clinical experience with use of three-dimensional (3D) HD vision system for laparoscopic surgery. Between 2013 and 2017 a prospective cohort study was conducted at the University Hospital of Palermo. We considered 163 patients underwent to laparoscopic three-dimensional (3D) HD surgery for various indications. This 3D-group was compared to a retrospective-prospective control group of patients who underwent the same surgical procedures. Considerating specific surgical procedures there is no significant difference in term of age and gender. The analysis of all the groups of diseases shows that the laparoscopic procedures performed with 3D technology have a shorter mean operative time than comparable 2D procedures when we consider surgery that require complex tasks. The use of 3D laparoscopic technology is an extraordinary innovation in clinical practice, but the instrumentation is still not widespread. Precisely for this reason the studies in literature are few and mainly limited to the evaluation of the surgical skills to the simulator. This study aims to evaluate the actual benefits of the 3D laparoscopic system integrating it in clinical practice. The three-dimensional view allows advanced performance in particular conditions, such as small and deep spaces and promotes performing complex surgical laparoscopic procedures.

The structure and mobility of the intervariant boundaries in 18R martensite in a Cu-Zn-Al alloy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, J.X.; Zheng, Y.F.; Zhao, L.C.

1999-05-28

Detailed crystallographic analysis was carried out on the martensitic transformation and the various variant combinations in 18R martensite in a Cu-Zn-Al alloy. The self-accommodation of martensitic shear strain is quite perfect within a variant group, but not effective or even does not exist for variant combinations which belong to different groups. Twenty-three unique variant combinations between 24 martensite variants can be divided into four groups, i.e. reflection twin, 180 rotation twin, 120 rotation twin and 90 rotation twin. TEM and HREM observations show that the A C boundary is straight, well-defined and perfectly coherent, the A B boundary is irrational,more » coherent and gradually curved, and the A D boundary is stepped. The A C and A B boundaries have obvious mobility, and the mobility is not effective for A D boundary. The interplate group boundaries are curved, blurred and immobile. The morphology, structure and mobility of interplate boundary are all related to the degree of self-accommodation and the misorientation of twin boundary.« less

A Three-Dimensional Finite Element Analysis of the Stress Distribution Generated by Splinted and Nonsplinted Prostheses in the Rehabilitation of Various Bony Ridges with Regular or Short Morse Taper Implants.

PubMed

Toniollo, Marcelo Bighetti; Macedo, Ana Paula; Rodrigues, Renata Cristina; Ribeiro, Ricardo Faria; de Mattos, Maria G

The aim of this study was to compare the biomechanical performance of splinted or nonsplinted prostheses over short- or regular-length Morse taper implants (5 mm and 11 mm, respectively) in the posterior area of the mandible using finite element analysis. Three-dimensional geometric models of regular implants (Ø 4 × 11 mm) and short implants (Ø 4 × 5 mm) were placed into a simulated model of the left posterior mandible that included the first premolar tooth; all teeth posterior to this tooth had been removed. The four experimental groups were as follows: regular group SP (three regular implants were rehabilitated with splinted prostheses), regular group NSP (three regular implants were rehabilitated with nonsplinted prostheses), short group SP (three short implants were rehabilitated with splinted prostheses), and short group NSP (three short implants were rehabilitated with nonsplinted prostheses). Oblique forces were simulated in molars (365 N) and premolars (200 N). Qualitative and quantitative analyses of the minimum principal stress in bone were performed using ANSYS Workbench software, version 10.0. The use of splinting in the short group reduced the stress to the bone surrounding the implants and tooth. The use of NSP or SP in the regular group resulted in similar stresses. The best indication when there are short implants is to use SP. Use of NSP is feasible only when regular implants are present.

Production, purification, crystallization and preliminary X-ray structural studies of adeno-associated virus serotype 5

DOE Office of Scientific and Technical Information (OSTI.GOV)

DiMattia, Michael; Govindasamy, Lakshmanan; Levy, Hazel C.

2005-10-01

The production, purification, crystallization and preliminary crystallographic analysis of empty adeno-associated virus serotype 5 capsids are reported. Adeno-associated virus serotype 5 (AAV5) is under development for gene-therapy applications for the treatment of cystic fibrosis. To elucidate the structural features of AAV5 that control its enhanced transduction of the apical surface of airway epithelia compared with other AAV serotypes, X-ray crystallographic studies of the viral capsid have been initiated. The production, purification, crystallization and preliminary crystallographic analysis of empty AAV5 viral capsids are reported. The crystals diffract X-rays to beyond 3.2 Å resolution using synchrotron radiation and belong to the orthorhombicmore » space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 264.7, b = 447.9, c = 629.7 Å. There is one complete T = 1 viral capsid per asymmetric unit. The orientation and position of the viral capsid in the asymmetric unit have been determined by rotation and translation functions, respectively, and the AAV5 structure determination is in progress.« less

Fine refinement of solid-state molecular structures of Leu- and Met-enkephalins by NMR crystallography.

PubMed

Pawlak, Tomasz; Potrzebowski, Marek J

2014-03-27

This paper presents a methodology that allows the fine refinement of the crystal and molecular structure for compounds for which the data deposited in the crystallographic bases are of poor quality. Such species belong to the group of samples with molecular disorder. In the Cambridge Crystallographic Data Center (CCDC), there are approximately 22,000 deposited structures with an R-factor over 10. The powerful methodology we present employs crystal data for Leu-enkephalin (two crystallographic forms) with R-factor values of 14.0 and 8.9 and for Met-enkephalin (one form) with an R-factor of 10.5. NMR crystallography was employed in testing the X-ray data and the quality of the structure refinement. The GIPAW (gauge invariant projector augmented wave) method was used to optimize the coordinates of the enkephalins and to compute NMR parameters. As we reveal, this complementary approach makes it possible to generate a reasonable set of new coordinates that better correlate to real samples. This methodology is general and can be employed in the study of each compound possessing magnetically active nuclei.

Deformation-induced crystallographic-preferred orientation of hcp-iron: An experimental study using a deformation-DIA apparatus

NASA Astrophysics Data System (ADS)

Nishihara, Yu; Ohuchi, Tomohiro; Kawazoe, Takaaki; Seto, Yusuke; Maruyama, Genta; Higo, Yuji; Funakoshi, Ken-ichi; Tange, Yoshinori; Irifune, Tetsuo

2018-05-01

Shear and uniaxial deformation experiments on hexagonal close-packed iron (hcp-Fe) was conducted using a deformation-DIA apparatus at a pressure of 13-17 GPa and a temperature of 723 K to determine its deformation-induced crystallographic-preferred orientation (CPO). Development of the CPO in the deforming sample is determined in-situ based on two-dimensional X-ray diffraction using monochromatic synchrotron X-rays. In the shear deformation geometry, the <0001> and < 11 2 bar 0 > axes gradually align to be sub-parallel to the shear plane normal and shear direction, respectively, from the initial random texture. In the uniaxial compression and tensile geometry, the <0001> and < 11 2 bar 0 > axes, respectively, gradually align along the direction of the uniaxial deformation axis. These results suggest that basal slip (0001) < 11 2 bar 0 > is the dominant slip system in hcp-Fe under the studied deformation conditions. The P-wave anisotropy for a shear deformed sample was calculated using elastic constants at the inner core condition by recent ab-initio calculations. Strength of the calculated anisotropy was comparable to or higher than axisymmetric anisotropy in Earth's inner core.

Influence of buffer-layer construction and substrate orientation on the electron mobilities in metamorphic In{sup 0.70}Al{sup 0.30}As/In{sup 0.76}Ga{sup 0.24}As/In{sup 0.70}Al{sup 0.30}As structures on GaAs substrates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kulbachinskii, V. A., E-mail: kulb@mig.phys.msu.ru; Oveshnikov, L. N.; Lunin, R. A.

The influence of construction of the buffer layer and misorientation of the substrate on the electrical properties of In{sup 0.70}Al{sup 0.30}As/In{sup 0.76}Ga{sup 0.24}As/In{sup 0.70}Al{sup 0.30}As quantum wells on a GaAs substrate is studied. The temperature dependences (in the temperature range of 4.2 K < T < 300 K) and field dependences (in magnetic fields as high as 6 T) of the sample resistances are measured. Anisotropy of the resistances in different crystallographic directions is detected; this anisotropy depends on the substrate orientation and construction of the metamorphic buffer layer. In addition, the Hall effect and the Shubnikov–de Haas effect aremore » studied. The Shubnikov–de Haas effect is used to determine the mobilities of electrons separately in several occupied dimensionally quantized subbands in different crystallographic directions. The calculated anisotropy of mobilities is in agreement with experimental data on the anisotropy of the resistances.« less

An Interdisciplinary Theme: Topographic Maps and Plate Tectonics

ERIC Educational Resources Information Center

Concannon, James P.; Aulgur, Linda

2011-01-01

This is an interdisciplinary lesson designed for middle school students studying landforms and geological processes. Students create a two-dimensional topographic map from a three-dimensional landform that they create using clay. Students then use other groups' topographic maps to re-create landforms. Following this, students explore some basic…

Lattice Rotation Patterns and Strain Gradient Effects in Face-Centered-Cubic Single Crystals Under Spherical Indentation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Y. F.; Larson, B. C.; Lee, J. H.

Strain gradient effects are commonly modeled as the origin of the size dependence of material strength, such as the dependence of indentation hardness on contact depth and spherical indenter radius. However, studies on the microstructural comparisons of experiments and theories are limited. First, we have extended a strain gradient Mises-plasticity model to its crystal plasticity version and implemented a finite element method to simulate the load-displacement response and the lattice rotation field of Cu single crystals under spherical indentation. The strain gradient simulations demonstrate that the forming of distinct sectors of positive and negative angles in the lattice rotation fieldmore » is governed primarily by the slip geometry and crystallographic orientations, depending only weakly on strain gradient effects, although hardness depends strongly on strain gradients. Second, the lattice rotation simulations are compared quantitatively with micron resolution, three-dimensional X-ray microscopy (3DXM) measurements of the lattice rotation fields under 100mN force, 100 mu m radius spherical indentations in < 111 >, < 110 >, and < 001 > oriented Cu single crystals. Third, noting the limitation of continuum strain gradient crystal plasticity models, two-dimensional discrete dislocation simulation results suggest that the hardness in the nanocontact regime is governed synergistically by a combination of strain gradients and source-limited plasticity. However, the lattice rotation field in the discrete dislocation simulations is found to be insensitive to these two factors but to depend critically on dislocation obstacle densities and strengths.« less

Roots and decompositions of three-dimensional topological objects

NASA Astrophysics Data System (ADS)

Matveev, Sergei V.

2012-06-01

In 1942 M.H.A. Newman formulated and proved a simple lemma of great importance for various fields of mathematics, including algebra and the theory of Gröbner-Shirshov bases. Later it was called the Diamond Lemma, since its key construction was illustrated by a diamond-shaped diagram. In 2005 the author suggested a new version of this lemma suitable for topological applications. This paper gives a survey of results on the existence and uniqueness of prime decompositions of various topological objects: three-dimensional manifolds, knots in thickened surfaces, knotted graphs, three-dimensional orbifolds, and knotted theta-curves in three-dimensional manifolds. As it turned out, all these topological objects admit a prime decomposition, although it is not unique in some cases (for example, in the case of orbifolds). For theta-curves and knots of geometric degree 1 in a thickened torus, the algebraic structure of the corresponding semigroups can be completely described. In both cases the semigroups are quotients of free groups by explicit commutation relations. Bibliography: 33 titles.

Multitasking a three-dimensional Navier-Stokes algorithm on the Cray-2

NASA Technical Reports Server (NTRS)

Swisshelm, Julie M.

1989-01-01

A three-dimensional computational aerodynamics algorithm has been multitasked for efficient parallel execution on the Cray-2. It provides a means for examining the multitasking performance of a complete CFD application code. An embedded zonal multigrid scheme is used to solve the Reynolds-averaged Navier-Stokes equations for an internal flow model problem. The explicit nature of each component of the method allows a spatial partitioning of the computational domain to achieve a well-balanced task load for MIMD computers with vector-processing capability. Experiments have been conducted with both two- and three-dimensional multitasked cases. The best speedup attained by an individual task group was 3.54 on four processors of the Cray-2, while the entire solver yielded a speedup of 2.67 on four processors for the three-dimensional case. The multiprocessing efficiency of various types of computational tasks is examined, performance on two Cray-2s with different memory access speeds is compared, and extrapolation to larger problems is discussed.

Hydrothermal synthesis and structural characterization of a novel three-dimensional supramolecular framework constructed by zinc salt and pyridine-2,5-dicarboxylate

NASA Astrophysics Data System (ADS)

Wang, Xinlong; Qin, Chao; Wang, Enbo; Hu, Changwen; Xu, Lin

2004-07-01

A novel metal-organic coordination polymer, [Zn(PDB)(H 2O) 2] 4 n (H 2PDB=pyridine-2,5-dicarboxylic acid), has been hydrothermally synthesized and characterized by elemental analysis, IR, TG and single crystal X-ray diffraction. Colorless crystals crystallized in the triclinic system, space group P-1, a=7.0562(14) Å, b=7.38526(15) Å, c=18.4611(4) Å, α=90.01(3)°, β=96.98(3)°, γ=115.67(3)°, V=859.1(3) Å 3, Z=1 and R=0.0334. The structure of the compound exhibits a novel three-dimensional supramolecular network, mainly based on multipoint hydrogen bonds originated from within and outside of a large 24-membered ring. Interestingly, the three-dimensional network consists of one-dimensional parallelogrammic channels in which coordinated water molecules point into the channel wall.

Investigation into three dimensional hip anatomy in anterior dislocation after THA. Influence of the position of the hip rotation centre.

PubMed

Sariali, Elhadi; Klouche, Shahnez; Mamoudy, Patrick

2012-07-01

The components position is a major factor under the surgeon's control in determining the risk of dislocation post total hip arthroplasty. The aim of this study was to investigate the proper three-dimensional components position including the centre of rotation in the case of anterior dislocation. Among 1764 consecutive patients who underwent total hip arthroplasty using a direct anterior approach, 27 experienced anterior dislocation. The three-dimensional hip anatomy was investigated in 12 patients who were paired with 12 patients from the same initial cohort who did not experience dislocation and also with 36 control patients with osteoarthritis. A pelvic Cartesian referential was defined to perform the acetabular analysis. The coordinates were expressed as percentages of the pelvic width, height and depth. The anteversion angles were measured. The hip centre of rotation was significantly shifted medially and posteriorly in the dislocation group when compared to the non-dislocation group and also to the control group. There was no significant difference in component angular position between the dislocation-group and the non-dislocation group. However, the stem anteversion in the dislocation group was increased in comparison to the mean natural femoral anteversion of the control group. A medial and posterior displacement of the hip rotation centre was found to correlate to anterior dislocation post total hip arthoplasty. These results suggest the importance of an accurate restoration of the centre of rotation, whilst avoiding an excessive acetabular reaming which may induce a medial and a posterior displacement. III comparative non randomised. Copyright © 2011 Elsevier Ltd. All rights reserved.

Expression, purification and preliminary X-ray diffraction studies of the transcriptional factor PyrR from Bacillus halodurans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arreola, Rodrigo; Vega-Miranda, Anita; Gómez-Puyou, Armando

The gene-regulation factor PyrR from B. halodurans has been crystallized in two crystal forms. Preliminary crystallographic analysis showed that the protein forms tetramers in both space groups. The PyrR transcriptional regulator is widely distributed in bacteria. This RNA-binding protein is involved in the control of genes involved in pyrimidine biosynthesis, in which uridyl and guanyl nucleotides function as effectors. Here, the crystallization and preliminary X-ray diffraction analysis of two crystal forms of Bacillus halodurans PyrR are reported. One of the forms belongs to the monoclinic space group P2{sub 1} with unit-cell parameters a = 59.7, b = 87.4, c =more » 72.1 Å, β = 104.4°, while the other form belongs to the orthorhombic space group P22{sub 1}2{sub 1} with unit-cell parameters a = 72.7, b = 95.9, c = 177.1 Å. Preliminary X-ray diffraction data analysis and molecular-replacement solution revealed the presence of four and six monomers per asymmetric unit; a crystallographic tetramer is formed in both forms.« less

Concurrent three-dimensional conformal radiotherapy and chemotherapy for postoperative recurrence of mediastinal lymph node metastases in patients with esophageal squamous cell carcinoma: a phase 2 single-institution study

PubMed Central

2014-01-01

Aim The aim of this study was to evaluate the effects of radiotherapy plus concurrent weekly cisplatin chemotherapy on the postoperative recurrence of mediastinal lymph node metastases in esophageal cancer patients. Methods Ninety-eight patients were randomly enrolled to receive either three-dimensional conformal radiotherapy alone (group A) or concurrent chemoradiotherapy (group B). A radiation dose of 62–70 Gy/31–35 fractions was delivered to the recurrent tumor. Furthermore, the patients in group B simultaneously received weekly doses of cisplatin (30 mg/m2), and the survival outcomes and toxic effects were compared. Results The response rate of group B (91.8%) was significantly greater than that of group A (73.5%) (χ2 = 5.765, P = 0.016). The 1- and 3-year survival rates of group B (85.7% and 46.9%, respectively) were also greater than those of group A (69.4% and 28.6%, respectively). However, there were no significant differences in the 5-year survival rates. The numbers of patients who died of distant metastases in groups A and B were 13 (26.5%) and 5 (10.2%), respectively (χ2 = 4.356, P = 0.036). Acute radiation-related esophagitis and granulocytopenia in group B was frequent. However, intergroup differences in terms of late toxicity were not significant. Conclusions Three-dimensional conformal radiotherapy (3DCRT) is a practical and feasible technique to treat the recurrence of mediastinal lymph node metastases of postoperative esophageal cancer. In addition, concurrent chemotherapy can increase local tumor control, decrease the distant metastasis rate, and increase the long-term survival rate. PMID:24438695

Concurrent three-dimensional conformal radiotherapy and chemotherapy for postoperative recurrence of mediastinal lymph node metastases in patients with esophageal squamous cell carcinoma: a phase 2 single-institution study.

PubMed

Ma, Dai-yuan; Tan, Bang-xian; Liu, Mi; Li, Xian-fu; Zhou, Ye-qin; Lu, You

2014-01-19

The aim of this study was to evaluate the effects of radiotherapy plus concurrent weekly cisplatin chemotherapy on the postoperative recurrence of mediastinal lymph node metastases in esophageal cancer patients. Ninety-eight patients were randomly enrolled to receive either three-dimensional conformal radiotherapy alone (group A) or concurrent chemoradiotherapy (group B). A radiation dose of 62-70 Gy/31-35 fractions was delivered to the recurrent tumor. Furthermore, the patients in group B simultaneously received weekly doses of cisplatin (30 mg/m(2)), and the survival outcomes and toxic effects were compared. The response rate of group B (91.8%) was significantly greater than that of group A (73.5%) (χ(2) = 5.765, P = 0.016). The 1- and 3-year survival rates of group B (85.7% and 46.9%, respectively) were also greater than those of group A (69.4% and 28.6%, respectively). However, there were no significant differences in the 5-year survival rates. The numbers of patients who died of distant metastases in groups A and B were 13 (26.5%) and 5 (10.2%), respectively (χ(2) = 4.356, P = 0.036). Acute radiation-related esophagitis and granulocytopenia in group B was frequent. However, intergroup differences in terms of late toxicity were not significant. Three-dimensional conformal radiotherapy (3DCRT) is a practical and feasible technique to treat the recurrence of mediastinal lymph node metastases of postoperative esophageal cancer. In addition, concurrent chemotherapy can increase local tumor control, decrease the distant metastasis rate, and increase the long-term survival rate.

First description of Phanerozoic radiaxial fibrous dolomite

NASA Astrophysics Data System (ADS)

Richter, D. K.; Heinrich, F.; Geske, A.; Neuser, R. D.; Gies, H.; Immenhauser, A.

2014-05-01

The petrographic analysis and crystallographic analysis of concretionary carbonate cements ("coal balls") from Carboniferous paralic swamp deposits reveal the presence of (length fast) radiaxial fibrous dolomite (RFD), a fabric not previously reported from the Phanerozoic. This finding is of significance as earlier reports of Phanerozoic radiaxial fibrous carbonates are exclusively of calcite mineralogy. Dolomite concretions described here formed beneath marine transgressive intervals within palustrine coal seams. This is of significance as seawater was arguably the main source of Mg2 + ions for dolomite formation. Here, data from optical microscopy, cathodoluminescence, electron backscattered diffraction, X-ray diffraction and geochemical analyses are presented to characterize three paragenetic dolomite phases and one calcite phase in these concretions. The main focus is on the earliest diagenetic, non-stoichiometric (degree of order: 0.41-0.46) phase I, characterized by botryoidal dolomite constructed of fibres up to 110 μm wide with a systematic undulatory extinction and converging crystal axes. Petrographic and crystallographic evidence clearly qualifies phase I dolomite as radiaxial fibrous. Conversely, fascicular optical fabrics were not found. Carbon-isotope ratios (δ13C) are depleted (between - 11.8 and - 22.1‰) as expected for carbonate precipitation from marine pore-fluids in organic-matter-rich, paralic sediment. Oxygen isotope (δ18O) ratios range between - 1.3 and - 6.0‰. The earliest diagenetic nature of these cements is documented by the presence of ubiquitous, non-compacted fossil plant remains encased in phase I dolomite as well as by the complex zoned luminescence patterns in the crystals and is supported by crystallographic and thermodynamic considerations. It is argued that organic matter, and specifically carboxyl groups, reduced thermodynamic barriers for dolomite formation and facilitated Mg/CaCO3 precipitation. The data shown here reveal a hitherto unknown level of complexity with respect to radiaxial fibrous carbonates and are of importance for those concerned with dolomite and carbonate petrography in general.

Mixed-metal uranium(VI) iodates: hydrothermal syntheses, structures, and reactivity of Rb[UO(2)(CrO(4))(IO(3))(H(2)O)], A(2)[UO(2)(CrO(4))(IO(3))(2)] (A = K, Rb, Cs), and K(2)[UO(2)(MoO(4))(IO(3))(2)].

PubMed

Sykora, Richard E; McDaniel, Steven M; Wells, Daniel M; Albrecht-Schmitt, Thomas E

2002-10-07

The reactions of the molecular transition metal iodates A[CrO(3)(IO(3))] (A = K, Rb, Cs) with UO(3) under mild hydrothermal conditions provide access to four new, one-dimensional, uranyl chromatoiodates, Rb[UO(2)(CrO(4))(IO(3))(H(2)O)] (1) and A(2)[UO(2)(CrO(4))(IO(3))(2)] (A = K (2), Rb (3), Cs (4)). Under basic conditions, MoO(3), UO(3), and KIO(4) can be reacted to form K(2)[UO(2)(MoO(4))(IO(3))(2)] (5), which is isostructural with 2 and 3. The structure of 1 consists of one-dimensional[UO(2)(CrO(4))(IO(3))(H(2)O)](-) ribbons that contain uranyl moieties bound by bridging chromate and iodate anions as well as a terminal water molecule to create [UO(7)] pentagonal bipyramidal environments around the U(VI) centers. These ribbons are separated from one another by Rb(+) cations. When the iodate content is increased in the hydrothermal reactions, the terminal water molecule is replaced by a monodentate iodate anion to yield 2-4. These ribbons can be further modified by replacing tetrahedral chromate anions with MoO(4)(2)(-) anions to yield isostructural, one-dimensional [UO(2)(MoO(4))(IO(3))(2)](2)(-) ribbons. Crystallographic data: 1, triclinic, space group P(-)1, a = 7.3133(5) A, b = 8.0561(6) A, c = 8.4870(6) A, alpha = 88.740(1) degrees, beta = 87.075(1) degrees, gamma = 71.672(1) degrees, Z = 2; 2, monoclinic, space group P2(1)/c, a = 11.1337(5) A, b = 7.2884(4) A, c = 15.5661(7) A, beta = 107.977(1) degrees, Z = 4; 3, monoclinic, space group P2(1)/c, a = 11.3463(6) A, b = 7.3263(4) A, c = 15.9332(8) A, beta = 108.173(1) degrees, Z = 4; 4, monoclinic, space group P2(1)/n, a = 7.3929(5) A, b = 8.1346(6) A, c = 22.126(2) A, beta = 90.647(1) degrees, Z = 4; 5, monoclinic, space group P2(1)/c, a = 11.3717(6) A, b = 7.2903(4) A, c = 15.7122(8) A, beta = 108.167(1) degrees, Z = 4.

Three-dimensional hydrogeologic framework model of the Rio Grande transboundary region of New Mexico and Texas, USA, and northern Chihuahua, Mexico

USGS Publications Warehouse

Sweetkind, Donald S.

2017-09-08

As part of a U.S. Geological Survey study in cooperation with the Bureau of Reclamation, a digital three-dimensional hydrogeologic framework model was constructed for the Rio Grande transboundary region of New Mexico and Texas, USA, and northern Chihuahua, Mexico. This model was constructed to define the aquifer system geometry and subsurface lithologic characteristics and distribution for use in a regional numerical hydrologic model. The model includes five hydrostratigraphic units: river channel alluvium, three informal subdivisions of Santa Fe Group basin fill, and an undivided pre-Santa Fe Group bedrock unit. Model input data were compiled from published cross sections, well data, structure contour maps, selected geophysical data, and contiguous compilations of surficial geology and structural features in the study area. These data were used to construct faulted surfaces that represent the upper and lower subsurface hydrostratigraphic unit boundaries. The digital three-dimensional hydrogeologic framework model is constructed through combining faults, the elevation of the tops of each hydrostratigraphic unit, and boundary lines depicting the subsurface extent of each hydrostratigraphic unit. The framework also compiles a digital representation of the distribution of sedimentary facies within each hydrostratigraphic unit. The digital three-dimensional hydrogeologic model reproduces with reasonable accuracy the previously published subsurface hydrogeologic conceptualization of the aquifer system and represents the large-scale geometry of the subsurface aquifers. The model is at a scale and resolution appropriate for use as the foundation for a numerical hydrologic model of the study area.

Syntheses and crystal structures of the rare-earth metal(III) bromide ortho-oxidotungstates(VI) with the formula REBr[WO4] (RE = Y, Gd-Yb)

NASA Astrophysics Data System (ADS)

Schustereit, Tanja; Schleid, Thomas; Hartenbach, Ingo

2015-10-01

The rare-earth metal(III) bromide ortho-oxidotungstates(VI) with the formula REBr[WO4] crystallize triclinically in space group P 1 bar (a = 689-693, b = 715-728, c = 1074-1107 pm, α = 103-106, β ≈ 108 and γ = 93-95°, Z = 4) for RE = Y, Gd-Yb. Their crystal structure is isotypic with the most examples of the formally analogous lanthanoid(III) bromide oxidomolybdates(VI) REBr[MoO4] with RE = Y, Pr, Nd, Sm, Gd-Lu. It contains two crystallographically different rare-earth metal(III) cations with coordination numbers of seven plus one for (RE1)3+ and seven for (RE2)3+. The (RE1)3+ cations are surrounded by three Br- and four plus one O2- anions forming distorted trigonal dodecahedra, while the (RE2)3+ cations exhibit a coordination environment of one Br- and six O2- anions in the shape of a monocapped trigonal prism. Furthermore, the structure contains two crystallographically independent, isolated tetrahedral [WO4]2- units. All these polyhedra are fused together to form 1 ∞ {REBr[WO4]} chains running along [012]. Since the title compounds, synthesized by solid-state reactions from the underlying binaries, emerge as pure phases according to X-ray powder diffractometry, spectroscopic and magnetic measurements were performed.

Nanocrystal assembly for bottom-up plasmonic materials

NASA Astrophysics Data System (ADS)

Tao, Andrea Rae

2007-12-01

Plasmonic materials are emerging as key platforms for applications that rely on the manipulation of light at small length scales. Materials that possess sub-wavelength metallic features support either localized or propagating surface plasmons that can induce huge local electromagnetic fields at the metal surface, facilitating a host of extraordinary optical phenomena. For many of the breakthrough photonic, spectroscopic, and optoelectronic applications of plasmonics, the bottom-up fabrication of these materials from low-dimensional structures has yet to be explored. Because colloidal metal nanostructures can be readily synthesized with controlled shapes and sizes, and because these structures also generate plasmon-mediated evanescent fields near their surfaces when irradiated with light, Ag nanocrystals and nanowires are ideal building blocks for rationally designed plasmonic materials. This dissertation addresses three major challenges: (1) the synthesis of Ag polyhedral nanocrystals and nanowires, (2) the bottom-up organization of these nanostructures into one-, two-, and three-dimensional assemblies, and (3) the application of these assemblies as spectroscopic sensing platforms. Faceted Ag colloids were synthesized in high yield and with remarkable monodispersity using the polyol process, where Ag+ is reduced in the presence of a polymer capping agent that serves to regulate nucleation and crystallographic growth direction. The resulting nanocrystals and nanowires are bound exclusively by {100} and {111} crystal planes, where nanowires possess pentagonal cross-sections and nanocrystals possess octahedral symmetry. Because allowed plasmon modes are explicitly dictated by geometric considerations, each shape exhibits a unique scattering spectrum in the optical wavelengths. These shaped colloidal building blocks were assembled into ordered groupings and superlattices to achieve controlled electromagnetic coupling between individual nanostructures. Of particular note is the use of Langmuir-Blodgett assembly for the construction of two-dimensional nanocrystal superlattices with continuously variable interparticle spacing and density. For the first time, we demonstrate the complete bottom-up fabrication of a macroscopic material with a tunable plasmonic response in the visible wavelengths. Lastly, we show that these nanoscale materials behave as exceptional substrates for surface-enhanced Raman spectroscopy (SERS). Assemblies of Ag nanowires and nanocrystals facilitate intense electromagnetic field enhancement due to charge localization near the sharp corners, edges, and junctions of the nanocrystals. We not only demonstrate that these assemblies can achieve high chemical sensitivity and specificity, but exhibit their utility as portable field sensors for toxins and explosives. For the first time, we demonstrate that SERS can be employed for the facile detection of low-level arsenic concentrations in ground water. In addition, we show the feasibility of integrating these Ag nanocrystals into microfluidic, multiplexed "lab-on-a-chip" devices, where SERS can be used for the in situ sensing of low-volume analytes.

Crystallization, structure and dynamics of the proton-translocating P-type ATPase.

PubMed

Scarborough, G A

2000-01-01

Large single three-dimensional crystals of the dodecylmaltoside complex of the Neurospora crassa plasma membrane H(+)-ATPase (H(+) P-ATPase) can be grown in polyethylene-glycol-containing solutions optimized for moderate supersaturation of both the protein surfaces and detergent micellar region. Large two-dimensional H(+) P-ATPase crystals also grow on the surface of such mixtures and on carbon films located at such surfaces. Electron crystallographic analysis of the two-dimensional crystals grown on carbon films has recently elucidated the structure of the H(+) P-ATPase at a resolution of 0.8 nm in the membrane plane. The two-dimensional crystals comprise two offset layers of ring-shaped ATPase hexamers with their exocytoplasmic surfaces face to face. Side-to-side interactions between the cytoplasmic regions of the hexamers in each layer can be seen, and an interaction between identical exocytoplasmic loops in opposing hexamer layers holds the two layers together. Detergent rings around the membrane-embedded region of the hexamers are clearly visible, and detergent-detergent interactions between the rings are also apparent. The crystal packing forces thus comprise both protein-protein and detergent-detergent interactions, supporting the validity of the original crystallization strategy. Ten transmembrane helices in each ATPase monomer are well-defined in the structure map. They are all relatively straight, closely packed, moderately tilted at various angles with respect to a plane normal to the membrane surface and average approximately 3.5 nm in length. The transmembrane helix region is connected in at least three places to the larger cytoplasmic region, which comprises several discrete domains separated by relatively wide, deep clefts. Previous work has shown that the H(+) P-ATPase undergoes substantial conformational changes during its catalytic cycle that are not changes in secondary structure. Importantly, the results of hydrogen/deuterium exchange experiments indicate that these conformational changes are probably rigid-body interdomain movements that lead to cleft closure. When interpreted within the framework of established principles of enzyme catalysis, this information on the structure and dynamics of the H(+) P-ATPase molecule provides the basis of a rational model for the sequence of events that occurs as the ATPase proceeds through its transport cycle. The forces that drive the sequence can also be clearly stipulated. However, an understanding of the molecular mechanism of ion transport catalyzed by the H(+) P-ATPase awaits an atomic resolution structure.

A Comparative Study of 3-Dimensional Titanium Versus 2-Dimensional Titanium Miniplates for Open Reduction and Fixation of Mandibular Parasymphysis Fracture.

PubMed

Mittal, Yogesh; Varghese, K George; Mohan, S; Jayakumar, N; Chhag, Somil

2016-03-01

Three dimensional titanium plating system was developed by Farmand in 1995 to meet the requirements of semi rigid fixation with lesser complication. The purpose of this in vivo prospective study was to evaluate and compare the clinical effectiveness of three dimensional and two dimensional Titanium miniplates for open reduction and fixation of mandibular parasymphysis fracture. Thirty patients with non-comminuted mandibular parasymphysis fractures were divided randomly into two equal groups and were treated with 2 mm 3D and 2D miniplate system respectively. All patients were systematically monitored at 1st, 2nd, 3rd, 6th week, 3rd and 6th month postoperatively. The outcome parameters recorded were severity of pain, infection, mobility, occlusion derangement, paresthesia and implant failure. The data so collected was analyzed using independent t test and Chi square test (α = .05). The results showed that one patient in each group had post-operative infection, occlusion derangement and mobility (p > .05). In Group A, one patient had paresthesia while in Group B, two patients had paresthesia (p > .05). None of the patients in both the groups had implant failure. There was no statistically significant difference between 3D and 2D miniplate system in all the recorded parameters at all the follow-ups (p > .05). 3D miniplates were found to be better than 2D miniplates in terms of cost, ease of surgery and operative time. However, 3D miniplates were unfavorable for cases where fracture line was oblique and in close proximity to mental foramen, where they were difficult to adapt and more chances for tooth-root damage and inadvertent injury to the mental nerve due to traction.

The Workshop on Conductive Polymers: Final Report

DOE R&D Accomplishments Database

1985-10-01

Reports are made by groups on: polyacetylene, polyphenylene, polyaniline, and related systems; molecular, crystallographic, and defect structures in conducting polymers; heterocyclic polymers; synthesis of new and improved conducting polymers; future applications possibilities for conducting polymers; and challenges for improved understanding of properties. (DLC)

Influence of opacifiers on dimensional stability and detail reproduction of maxillofacial silicone elastomer

PubMed Central

2010-01-01

Background We evaluated the influence of chemical disinfection and accelerated aging on the dimensional stability and detail reproduction of a silicone elastomer containing one of two opacifiers. Methods A total of 90 samples were fabricated from Silastic MDX 4-4210 silicone and divided into groups (n = 10) according to opacifier content (barium sulfate or titanium dioxide) and disinfectant solution (neutral soap, Efferdent, or 4% chlorhexidine). The specimens were disinfected 3 times per week during 60 days and then subjected to accelerated aging for 1008 hours. Dimensional stability and detail reproduction tests were performed after specimens' fabrication (baseline), chemical disinfection and periodically during accelerated aging (252, 504, and 1008 hours). The results were analyzed using 3-way repeated-measures ANOVA and the Tukey HSD test (α = 0.05). Results All groups exhibited dimensional changes over time. The opacifier (p = .314), period (p < .0001) and their interactions (p = .0041) affected the dimensional stability of the silicone. Statistical significant dimensional differences occurred between groups with (0.071) and without opacifiers (0.053). Accelerated aging influenced the dimensional stability of the samples. All groups scored 2 in the detail reproduction tests, which represents the fully reproducing of three test grooves with accurate angles. Conclusions Incorporation of opacifiers alters the dimensional stability of silicones used in facial prosthetics, but seems to have no influence on detail reproduction. Accelerated aging is responsible for most of the dimensional changes in Silastic MDX4 4210, but all dimensional changes measured in this study remained within the limits of stability necessary for this application. PMID:21162729

Usefulness of real-time three-dimensional ultrasonography in percutaneous nephrostomy: an animal study.

PubMed

Hongzhang, Hong; Xiaojuan, Qin; Shengwei, Zhang; Feixiang, Xiang; Yujie, Xu; Haibing, Xiao; Gallina, Kazobinka; Wen, Ju; Fuqing, Zeng; Xiaoping, Zhang; Mingyue, Ding; Huageng, Liang; Xuming, Zhang

2018-05-17

To evaluate the effect of real-time three-dimensional (3D) ultrasonography (US) in guiding percutaneous nephrostomy (PCN). A hydronephrosis model was devised in which the ureters of 16 beagles were obstructed. The beagles were divided equally into groups 1 and 2. In group 1, the PCN was performed using real-time 3D US guidance, while in group 2 the PCN was guided using two-dimensional (2D) US. Visualization of the needle tract, length of puncture time and number of puncture times were recorded for the two groups. In group 1, score for visualization of the needle tract, length of puncture time and number of puncture times were 3, 7.3 ± 3.1 s and one time, respectively. In group 2, the respective results were 1.4 ± 0.5, 21.4 ± 5.8 s and 2.1 ± 0.6 times. The visualization of needle tract in group 1 was superior to that in group 2, and length of puncture time and number of puncture times were both lower in group 1 than in group 2. Real-time 3D US-guided PCN is superior to 2D US-guided PCN in terms of visualization of needle tract and the targeted pelvicalyceal system, leading to quick puncture. Real-time 3D US-guided puncture of the kidney holds great promise for clinical implementation in PCN. © 2018 The Authors BJU International © 2018 BJU International Published by John Wiley & Sons Ltd.

Three isostructural one-dimensional Ln(III) chains with distorted cubane motifs showing dual fluorescence and slow magnetic relaxation/magnetocaloric effect.

PubMed

Li, Yan; Yu, Jia-Wen; Liu, Zhong-Yi; Yang, En-Cui; Zhao, Xiao-Jun

2015-01-05

Three new homometallic lanthanide complexes with mixed carboxylate-modified rigid ligands, [Ln(μ3-OH)(na)(pyzc)]n (na(-) = 1-naphtholate, pyzc(-) = 2-pyrazinecarboxylate, Ln = Dy (1), Yb (2), and Gd (3)), were solvothermally synthesized, and their structures and magnetic as well as photophysical properties were completely investigated. Complexes 1-3 are crystallographically isostructural, exhibiting linear chains with four bidentate bridging μ-COO(-) moieties encapsulated cubic {Ln4(μ3-OH)4}(8+) clusters repeatedly extended by 4-fold chelating-bridging-pyzc(-) connectors. Magnetically, the former two complexes with highly anisotropic Dy(III) and weak anisotropic Yb(III) ions in the distorted NO7 triangular dodecahedron coordination environment display field-induced slow relaxation of magnetization. Fitting the dynamic magnetic data to the Arrhenius law gives energy barrier ΔE/kB = 39.6 K and pre-exponential factor τo = 1.52 × 10(-8) s for 1 and ΔE/kB = 14.1 K and τo = 2.13 × 10(-7) s for 2. By contrast, complex 3 with isotropic Gd(III) ion and weak intracluster antiferromagnetic coupling shows a significant cryogenic magnetocaloric effect, with a maximum -ΔSm value of 30.0 J kg(-1) K(-1) at 2.5 K and 70 kOe. Additionally, the chromophoric na(-) and pyzc(-) ligands can serve as antenna groups, selectively sensitizing the Dy(III)- and Yb(III)-based luminescence of 1 and 2 in the UV-visible region by an intramolecular energy transfer process. Thus, complexes 1-3, incorporating field-induced slow magnetic magnetization and interesting luminescence together, can be used as composite magneto-optical materials. More importantly, these interesting results further demonstrate that the mixed-ligand system with rigid carboxylate-functionalized chromophores can be excellent candidates for the preparations of new bifunctional magneto-optical materials.

The X-ray Crystallographic Structure and Activity Analysis of a Pseudomonas-Specific Subfamily of the HAD Enzyme Superfamily Evidences a Novel Biochemical Function

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peisach,E.; Wang, L.; Burroughs, A.

2008-01-01

The haloacid dehalogenase (HAD) superfamily is a large family of proteins dominated by phosphotransferases. Thirty-three sequence families within the HAD superfamily (HADSF) have been identified to assist in function assignment. One such family includes the enzyme phosphoacetaldehyde hydrolase (phosphonatase). Phosphonatase possesses the conserved Rossmanniod core domain and a C1-type cap domain. Other members of this family do not possess a cap domain and because the cap domain of phosphonatase plays an important role in active site desolvation and catalysis, the function of the capless family members must be unique. A representative of the capless subfamily, PSPTO{_}2114, from the plant pathogenmore » Pseudomonas syringae, was targeted for catalytic activity and structure analyses. The X-ray structure of PSPTO{_}2114 reveals a capless homodimer that conserves some but not all of the intersubunit contacts contributed by the core domains of the phosphonatase homodimer. The region of the PSPTO{_}2114 that corresponds to the catalytic scaffold of phosphonatase (and other HAD phosphotransfereases) positions amino acid residues that are ill suited for Mg+2 cofactor binding and mediation of phosphoryl group transfer between donor and acceptor substrates. The absence of phosphotransferase activity in PSPTO{_}2114 was confirmed by kinetic assays. To explore PSPTO{_}2114 function, the conservation of sequence motifs extending outside of the HADSF catalytic scaffold was examined. The stringently conserved residues among PSPTO{_}2114 homologs were mapped onto the PSPTO{_}2114 three-dimensional structure to identify a surface region unique to the family members that do not possess a cap domain. The hypothesis that this region is used in protein-protein recognition is explored to define, for the first time, HADSF proteins which have acquired a function other than that of a catalyst. Proteins 2008.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kish, Kevin; McDonnell, Patricia A.; Goldfarb, Valentina

Protein tyrosine phosphatase {gamma} is a membrane-bound receptor and is designated RPTP{gamma}. RPTP{gamma} and two mutants, RPTP{gamma}(V948I, S970T) and RPTP{gamma}(C858S, S970T), were recombinantly expressed and purified for X-ray crystallographic studies. The purified enzymes were crystallized using the hanging-drop vapor-diffusion method. Crystallographic data were obtained from several different crystal forms in the absence and the presence of inhibitor. In this paper, a description is given of how three different crystal forms were obtained that were used with various ligands. An orthorhombic crystal form and a trigonal crystal form were obtained both with and without ligand, and a monoclinic crystal form wasmore » only obtained in the presence of a particularly elaborated inhibitor.« less

Two-dimensional Zn(II) and one-dimensional Co(II) coordination polymers based on benzene-1,4-dicarboxylate and pyridine ligands.

PubMed

Zhou, Li-Juan; Han, Chang-Bao; Wang, Yu-Ling

2016-02-01

Coordination polymers constructed from metal ions and organic ligands have attracted considerable attention owing to their diverse structural topologies and potential applications. Ligands containing carboxylate groups are among the most extensively studied because of their versatile coordination modes. Reactions of benzene-1,4-dicarboxylic acid (H2BDC) and pyridine (py) with Zn(II) or Co(II) yielded two new coordination polymers, namely, poly[(μ4-benzene-1,4-dicarboxylato-κ(4)O:O':O'':O''')(pyridine-κN)zinc(II)], [Zn(C8H4O2)(C5H5N)]n, (I), and catena-poly[aqua(μ3-benzene-1,4-dicarboxylato-κ(3)O:O':O'')bis(pyridine-κN)cobalt(II)], [Co(C8H4O2)(C5H5N)2(H2O)]n, (II). In compound (I), the Zn(II) cation is five-coordinated by four carboxylate O atoms from four BDC(2-) ligands and one pyridine N atom in a distorted square-pyramidal coordination geometry. Four carboxylate groups bridge two Zn(II) ions to form centrosymmetric paddle-wheel-like Zn2(μ2-COO)4 units, which are linked by the benzene rings of the BDC(2-) ligands to generate a two-dimensional layered structure. The two-dimensional layer is extended into a three-dimensional supramolecular structure with the help of π-π stacking interactions between the aromatic rings. Compound (II) has a one-dimensional double-chain structure based on Co2(μ2-COO)2 units. The Co(II) cations are bridged by BDC(2-) ligands and are octahedrally coordinated by three carboxylate O atoms from three BDC(2-) ligands, one water O atom and two pyridine N atoms. Interchain O-H...O hydrogen-bonding interactions link these chains to form a three-dimensional supramolecular architecture.

Data Mining for New Two- and One-Dimensional Weakly Bonded Solids and Lattice-Commensurate Heterostructures.

PubMed

Cheon, Gowoon; Duerloo, Karel-Alexander N; Sendek, Austin D; Porter, Chase; Chen, Yuan; Reed, Evan J

2017-03-08

Layered materials held together by weak interactions including van der Waals forces, such as graphite, have attracted interest for both technological applications and fundamental physics in their layered form and as an isolated single-layer. Only a few dozen single-layer van der Waals solids have been subject to considerable research focus, although there are likely to be many more that could have superior properties. To identify a broad spectrum of layered materials, we present a novel data mining algorithm that determines the dimensionality of weakly bonded subcomponents based on the atomic positions of bulk, three-dimensional crystal structures. By applying this algorithm to the Materials Project database of over 50,000 inorganic crystals, we identify 1173 two-dimensional layered materials and 487 materials that consist of weakly bonded one-dimensional molecular chains. This is an order of magnitude increase in the number of identified materials with most materials not known as two- or one-dimensional materials. Moreover, we discover 98 weakly bonded heterostructures of two-dimensional and one-dimensional subcomponents that are found within bulk materials, opening new possibilities for much-studied assembly of van der Waals heterostructures. Chemical families of materials, band gaps, and point groups for the materials identified in this work are presented. Point group and piezoelectricity in layered materials are also evaluated in single-layer forms. Three hundred and twenty-five of these materials are expected to have piezoelectric monolayers with a variety of forms of the piezoelectric tensor. This work significantly extends the scope of potential low-dimensional weakly bonded solids to be investigated.

Assessing multiple-group diagnostic problems with multi-dimensional receiver operating characteristic surfaces: Application to proton MR Spectroscopy (MRS) in HIV-related neurological injury

PubMed Central

Yiannoutsos, Constantin T.; Nakas, Christos T.; Navia, Bradford A.

2013-01-01

We present the multi-dimensional Receiver Operating Characteristic (ROC) surface, a plot of the true classification rates of tests based on levels of biological markers, for multi-group discrimination, as an extension of the ROC curve, commonly used in two-group diagnostic testing. The volume under this surface (VUS) is a global accuracy measure of a test to classify subjects in multiple groups and useful to detect trends in marker measurements. We used three-dimensional ROC surfaces, and associated VUS, to discriminate between HIV-negative (NEG), HIV-positive neurologically asymptomatic (NAS) subjects and patients with AIDS demential complex (ADC), using brain metabolites measured by proton MRS. These were ratios of markers of inflammation, Choline (Cho) and myoinositol (MI), and brain injury, N-acetyl aspartate (NAA), divided by Creatine (Cr), measured in the basal ganglia and the frontal white matter. Statistically significant trends were observed in the three groups with respect to MI/Cr (VUS=0.43; 95% confidence interval (CI) 0.33-0.53), Cho/Cr (0.36; 0.27-0.45) in the basal ganglia and NAA/Cr in the frontal white matter (FWM) (0.29; 0.20-0.38), suggesting a continuum of injury during the neurologically asymptomatic stage of HIV infection, particularly with respect to brain inflammation. Adjusting for age increased the combined classification accuracy of age and NAA/Cr (p=0.053). Pairwise comparisons suggested that neuronal damage associated with NAA/Cr decreases was mainly observed in individuals with ADC, raising issues of synergism between HIV infection and age and possible acceleration of neurological deterioration in an aging HIV-positive population. The three-dimensional ROC surface and its associated VUS are useful for assessing marker accuracy, detecting data trends and offering insight in disease processes affecting multiple groups. PMID:18191586

Diorganotin-based coordination polymers derived from sulfonate/phosphonate/phosphonocarboxylate ligands.

PubMed

Shankar, Ravi; Jain, Archana; Kociok-Köhn, Gabriele; Molloy, Kieran C

2011-02-21

The reactions of diorganotin precursors [R(2)Sn(OR(1))(OSO(2)R(1))](n) [R = R(1) = Me (1); R = Me, R(1) = Et (2)] with an equimolar amount of t-butylphosphonic acid (RT, 8-10 h) in methanol result in the formation of identical products, of composition [(Me(2)Sn)(3)(O(3)PBu(t))(2)(O(2)P(OH)Bu(t))(2)](n) (3). On the other hand, a similar reaction of 2, when carried out in dichloromethane, affords [(Me(2)Sn)(3)(O(3)PBu(t))(2)(OSO(2)Et)(2)·MeOH](n) (4). A plausible mechanism implicating the role of solvent in the formation of these compounds has been put forward. In addition, the synthesis of [(Me(2)Sn)(3)(O(3)PCH(2)CH(2)COOMe)(2)(OSO(2)Me)(2)](n) (5) and [R(2)Sn(O(2)P(OH)CH(2)CH(2)COOMe)(OSO(2)R(1))](n) [R = Et, R(1) = Me (6); R = (n)Bu, R(1) = Et (7)] has been achieved by reacting 1 and related diorganotin(alkoxy)alkanesulfonates with 3-phosphonopropionic acid in methanol. The formation of a methylpropionate functionality on the phosphorus center in these structural frameworks results from in situ esterification of the carboxylic group. X-ray crystallographic studies of 1-7 are presented. The structures of 1 and 2 represent one-dimensional (1D) coordination polymers composed of alternate [Sn-O](2) and [Sn-O-S-O](2) cyclic rings formed by μ(2)-alkoxo and sulfonate ligands, respectively. For 3-5 and 7, variable bonding modes of phosphonate and/or sulfonate ligands afford the construction of two- and three-dimensional self-assemblies that are comprised of trinuclear tin entities with an Sn(3)P(2)O(6) core as well as [Sn-O-P-O](2) and/or [Sn-O-S-O](2) rings. The formation of a 1D coordination polymer in 6 is unique in terms of repeating eight-membered cyclic rings containing Sn, O, P, and S heteroatoms. The contribution from hydrogen-bonding interactions is also found to be significant in these structures.

Crystallographic identification of an unexpected by-product in an Ullman's reaction toward biphenyls: 1-(4-hexyloxy-3-hydroxyphenyl)ethanone.

PubMed

Manzano, Veronica E; Baggio, Ricardo; Cukiernik, Fabio D

2015-11-01

The synthesis of 3,3'-diacetoxy-4,4'-bis(hexyloxy)biphenyl following the nickel-modified Ullmann reaction yielded a by-product which was identified successfully by crystallographic analysis as 1-(4-hexyloxy-3-hydroxyphenyl)ethanone, C14H20O3. This unexpected nonbiphenyl by-product exhibited IR, (1)H NMR, (13)C NMR and COSY (correlation spectroscopy) spectra fully consistent with the proposed structure. The compound crystallized in the orthorombic Pbca space group, with two independent formula units in the asymmetric unit (one of which was slightly disordered), and showed a supramolecular architecture in which molecules linked by hydroxy-ethanone O-H···O interactions are organized in columns separated by the aliphatic tails.

The factorial validity of the Maslach Burnout Inventory-Student Survey in China.

PubMed

Hu, Qiao; Schaufeli, Wilmar B

2009-10-01

The dimensional structure of the Maslach Burnout Inventory-Student Survey (MBI-SS) was investigated using data collected from three samples of Chinese students in two high schools, a university, and a nursing school, respectively (total N = 1,499; 36% males, 64% females; M age 19.0 yr., SD = 1.3). Single group Confirmatory Factor Analyses corroborated the hypothesized three-factor model for the composite sample as well as for the three independent samples. Subsequent multigroup analyses revealed that the three-dimensional structure of the MBI-SS is partially invariant across three samples. It is concluded that the MBI-SS can be used to assess burnout in Chinese students.

Comparison in three dimensional gait kinematics between young and older adults on land and in shallow water.

PubMed

Abdul Jabbar, Khalid; Kudo, Shigetada; Goh, Kee Wee; Goh, Ming Rong

2017-09-01

This study investigated in three-dimensional space, firstly whether the aquatic medium and secondly ageing, had any effect on the lower limb's joint angles during aquatic-based gait. Three-dimensional joint kinematics of the lower limb of 51 healthy male participants [25 young group (24.6±4.9 years, 172.1±5.5cm, 69.8±10.3kg) and 26 older group (58.5±5.1 years, 167.9±5.1cm, 70.8±12.1kg)] were quantified during land and shallow water walking. Participants walked at their self-selected comfortable speed in both mediums. The results suggested that the properties of water - hydrodynamic drag, and buoyancy - affected the gait kinematics for both groups. Both age groups used more of their hip flexion in the aquatic environment to help them propel forward instead of using the ankle plantarflexion. The effect of age during the aquatic-based gait was identified in ankle adduction angle and knee abduction/adduction angle at initial contact. Only the older group elicited a significantly smaller ankle adduction angle during the aquatic-based gait when compared to the land-based gait. Only the young group elicited a significantly larger knee abduction/adduction angle at initial contact during the aquatic-based gait when compared to the land-based gait. These findings can facilitate professionals in the area of aquatic rehabilitation to better customise aquatic-based walking exercise programmes to suit their client's specific needs. Copyright © 2017 Elsevier B.V. All rights reserved.

Virtual reality anatomy: is it comparable with traditional methods in the teaching of human forearm musculoskeletal anatomy?

PubMed

Codd, Anthony M; Choudhury, Bipasha

2011-01-01

The use of cadavers to teach anatomy is well established, but limitations with this approach have led to the introduction of alternative teaching methods. One such method is the use of three-dimensional virtual reality computer models. An interactive, three-dimensional computer model of human forearm anterior compartment musculoskeletal anatomy was produced using the open source 3D imaging program "Blender." The aim was to evaluate the use of 3D virtual reality when compared with traditional anatomy teaching methods. Three groups were identified from the University of Manchester second year Human Anatomy Research Skills Module class: a "control" group (no prior knowledge of forearm anatomy), a "traditional methods" group (taught using dissection and textbooks), and a "model" group (taught solely using e-resource). The groups were assessed on anatomy of the forearm by a ten question practical examination. ANOVA analysis showed the model group mean test score to be significantly higher than the control group (mean 7.25 vs. 1.46, P < 0.001) and not significantly different to the traditional methods group (mean 6.87, P > 0.5). Feedback from all users of the e-resource was positive. Virtual reality anatomy learning can be used to compliment traditional teaching methods effectively. Copyright © 2011 American Association of Anatomists.

[Significance of three-dimensional reconstruction as a method of preoperative planning of laparoscopic radiofrequency ablation].

PubMed

Zhang, W W; Wang, H G; Shi, X J; Chen, M Y; Lu, S C

2016-09-01

To discuss the significance of three-dimensional reconstruction as a method of preoperative planning of laparoscopic radiofrequency ablation(LRFA). Thirty-two cases of LRFA admitted from January 2014 to December 2015 in Department of Hepatobiliary Surgery, Chinese People's Liberation Army General Hospital were analyzed(3D-LRFA group). Three-dimensional(3D) reconstruction were taken as a method of preoperative planning in 3D-LRFA group.Other 64 LRFA cases were paired over the same period without three-dimensional reconstruction before the operation (LRFA group). Hepatobiliary system contrast enhanced CT scan of 3D-RFA patients were taken by multi-slice spiral computed tomography(MSCT), and the DICOM data were processed by IQQA(®)-Liver and IQQA(®)-guide to make 3D reconstruction.Using 3D reconstruction model, diameter and scope of tumor were measured, suitable size (length and radiofrequency length) and number of RFA electrode were chosen, scope and effect of radiofrequency were simulated, reasonable needle track(s) was planed, position and angle of laparoscopic ultrasound (LUS) probe was designed and LUS image was simulated.Data of operation and recovery were collected and analyzed. Data between two sets of measurement data were compared with t test or rank sum test, and count data with χ(2) test or Fisher exact probability test.Tumor recurrence rate was analyzed with the Kaplan-Meier survival curve and Log-rank (Mantel-Cox) test. Compared with LRFA group ((216.8±66.2) minutes, (389.1±183.4) s), 3D-LRFA group ((173.3±59.4) minutes, (242.2±90.8) s) has shorter operation time(t=-3.138, P=0.002) and shorter mean puncture time(t=-2.340, P=0.021). There was no significant difference of blood loss(P=0.170), ablation rate (P=0.871) and incidence of complications(P=1.000). Compared with LRFA group ((6.3±3.9)days, (330±102)U/L, (167±64)ng/L), 3D-LRFA group ((4.3±3.1) days, (285±102) U/L, (139±43) ng/L) had shorter post-operative stay(t=-2.527, P=0.016), less post-operation ALT changes (t=-2.038, P=0.048) and post-operative TNF-α changes(t=-2.233, P=0.027). Disease-free survival between two groups was significantly different (χ(2)=4.049, P=0.046). Disease-free survival of 12 months survival rates were 77.6% and 65.7% in 3D-LRFA group and LRFA group, respectively.The median disease-free survival was 16.0 months in LRFA group and over 24.0 months in 3D-LRFA group. Three-dimensional model of liver reconstruction based on image information is a powerful tool in liver surgery planning.It helps to simulate tumor location and vital tubular structure, make plan for interventional treatment, and therefore mean puncture time and operation time is shortened, influence on liver function is reduced, hospital stay is decreased and DFS is prolonged.

Uncalibrated Three-Dimensional Microrobot Control

DTIC Science & Technology

2016-05-11

environment is essential. While many groups have already demonstrated the ability to control a microrobot in three dimensions through magnetically...or “uncalibrated”) controller which can dynamically adjust to changes in the operation environment is essential. While many groups have already...error squared and drive the microrobot to the desired position, [2]. The control signal is computed via a quasi -Newton method operating an

Studies of the structure-activity relationships of peptides and proteins involved in growth and development based on their three-dimensional structures.

PubMed

Nagata, Koji

2010-01-01

Peptides and proteins with similar amino acid sequences can have different biological functions. Knowledge of their three-dimensional molecular structures is critically important in identifying their functional determinants. In this review, I describe the results of our and other groups' structure-based functional characterization of insect insulin-like peptides, a crustacean hyperglycemic hormone-family peptide, a mammalian epidermal growth factor-family protein, and an intracellular signaling domain that recognizes proline-rich sequence.

Macroscopic response in active nonlinear photonic crystals.

PubMed

Alagappan, Gandhi; John, Sajeev; Li, Er Ping

2013-09-15

We derive macroscopic equations of motion for the slowly varying electric field amplitude in three-dimensional active nonlinear optical nanostructures. We show that the microscopic Maxwell equations and polarization dynamics can be simplified to a macroscopic one-dimensional problem in the direction of group velocity. For a three-level active material, we derive the steady-state equations for normal mode frequency, threshold pumping, nonlinear Bloch mode amplitude, and lasing in photonic crystals. Our analytical results accurately recapture the results of exact numerical methods.

Polymers functionalized with bronsted acid groups

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Humbeck, Jeffrey; Long, Jeffrey R.; McDonald, Thomas M.

Porous aromatic framework polymers functionalized with Bronsted acid moieties are prepared by polymerization of a three-dimensional organic aryl or heteroaryl monomer and its copolymerization with a second aryl or heteroaryl monomer functionalized with one or more Bronsted acid moiety. The polymers are characterized by a stable three-dimensional structure, which, in exemplary embodiments, includes interpenetrating subunits within one or more domain of the bulk polymer structure. The polymers are of use in methods of adsorbing ammonia and amines and in devices and systems configured for this purpose.

Y-TZP zirconia regeneration firing: Microstructural and crystallographic changes after grinding.

PubMed

Ryan, Daniel Patrick Obelenis; Fais, Laiza Maria Grassi; Antonio, Selma Gutierrez; Hatanaka, Gabriel Rodrigues; Candido, Lucas Miguel; Pinelli, Ligia Antunes Pereira

2017-07-26

This study evaluated microstructural and crystallographic phase changes after grinding (G) and regeneration firing/anneling (R) of Y-TZP ceramics. Thirty five bars (Lava TM and Ice Zirkon) were divided: Y-TZP pre-sintered, control (C), regeneration firing (R), dry grinding (DG), dry grinding+regeneration firing (DGR), wet grinding (WG) and wet grinding+regeneration firing (WGR). Grinding was conducted using a diamond bur and annealing at 1,000°C. The microstructure was analyzed by SEM and the crystalline phases by X-ray diffraction (XRD). XRD showed that pre-sintered specimens contained tetragonal and monoclinic phases, while groups C and R showed tetragonal, cubic and monoclinic phases. After grinding, the cubic phase was eliminated in all groups. Annealing (DGR and WGR) resulted in only tetragonal phase. SEM showed semi-circular cracks after grinding and homogenization of particles after annealing. After grinding, surfaces show tetragonal and monoclinic phases and R can be assumed to be necessary prior to porcelain layering when grinding is performed.

Screening of matrix metalloproteinases available from the protein data bank: insights into biological functions, domain organization, and zinc binding groups.

PubMed

Nicolotti, Orazio; Miscioscia, Teresa Fabiola; Leonetti, Francesco; Muncipinto, Giovanni; Carotti, Angelo

2007-01-01

A total of 142 matrix metalloproteinase (MMP) X-ray crystallographic structures were retrieved from the Protein Data Bank (PDB) and analyzed by an automated and efficient routine, developed in-house, with a series of bioinformatic tools. Highly informative heat maps and hierarchical clusterograms provided a reliable and comprehensive representation of the relationships existing among MMPs, enlarging and complementing the current knowledge in the field. Multiple sequence and structural alignments permitted better location and display of key MMP motifs and quantification of the residue consensus at each amino acid position in the most critical binding subsites of MMPs. The MMP active site consensus sequences, the C-alpha root-mean-square deviation (RMSd) analysis of diverse enzymatic subsites, and the examination of the chemical nature, binding topologies, and zinc binding groups (ZBGs) of ligands extracted from crystallographic complexes provided useful insights on the structural arrangements of the most potent MMP inhibitors.

Cloning, purification, crystallization and preliminary crystallographic analysis of a penicillin-binding protein homologue from Pyrococcus abyssi

DOE Office of Scientific and Technical Information (OSTI.GOV)

Delfosse, Vanessa; Hugonnet, Jean-Emmanuel; Sougakoff, Wladimir

The crystallization of a hypothetical penicillin-binding protein from the archaeon P. abyssi in space group C2 by hanging-drop vapour diffusion is reported. The genome of the hyperthermophilic archaeon Pyrococcus abyssi contains a gene (pab0087) encoding a penicillin-binding protein (PBP) homologue. This sequence consists of 447 residues and shows significant sequence similarity to low-molecular-weight PBPs and class C β-lactamases. The Pab0087 protein was overexpressed, purified and crystallized. Diffraction data from two different crystal forms were collected to 2.7 and 2.0 Å resolution. Both crystals belong to space group C2, with unit-cell parameters a = 160.59, b = 135.74, c = 113.02more » Å, β = 117.36° and a = 166.97, b = 131.25, c = 189.39 Å, β = 113.81°, respectively. The asymmetric unit contains four and eight molecules, respectively, with fourfold non-crystallographic symmetry.« less

Three-dimensional geologic mapping of the Cenozoic basin fill, Amargosa Desert basin, Nevada and California

USGS Publications Warehouse

Taylor, Emily M.; Sweetkind, Donald S.

2014-01-01

Understanding the subsurface geologic framework of the Cenozoic basin fill that underlies the Amargosa Desert in southern Nevada and southeastern California has been improved by using borehole data to construct three-dimensional lithologic and interpreted facies models. Lithologic data from 210 boreholes from a 20-kilometer (km) by 90-km area were reduced to a limited suite of descriptors based on geologic knowledge of the basin and distributed in three-dimensional space using interpolation methods. The resulting lithologic model of the Amargosa Desert basin portrays a complex system of interfingered coarse- to fine-grained alluvium, playa and palustrine deposits, eolian sands, and interbedded volcanic units. Lithologic units could not be represented in the model as a stacked stratigraphic sequence due to the complex interfingering of lithologic units and the absence of available time-stratigraphic markers. Instead, lithologic units were grouped into interpreted genetic classes, such as playa or alluvial fan, to create a three-dimensional model of the interpreted facies data. Three-dimensional facies models computed from these data portray the alluvial infilling of a tectonically formed basin with intermittent internal drainage and localized regional groundwater discharge. The lithologic and interpreted facies models compare favorably to resistivity, aeromagnetic, and geologic map data, lending confidence to the interpretation.

Multiscale structural changes of atomic order in severely deformed industrial aluminum

NASA Astrophysics Data System (ADS)

Samoilenko, Z. A.; Ivakhnenko, N. N.; Pushenko, E. I.; Pashinskaya, E. G.; Varyukhin, V. N.

2016-02-01

The regularities of multiscale structural changes in the atomic order of the aluminum alloy AD-1 after a severe cold plastic deformation by conventional rolling in smooth rolls or in rolls with relief recesses favorable for shear deformation have been investigated. It has been found that there are four types of structural fractions that differ in scale and perfection of atomic order: crystallographic planes with a long-range order; nanoscale fragments of the planes ( D = 100-300 Å) with an incipient long-range order; smaller groups of atoms ( D = 20-30 Å) of amorphized structure; and the least ordered structural fraction of intercluster medium, keeping only a short-range atomic order (2-3 interatomic distances, 10 Å). The presence of diffuse halo bands in the region of intense Debye lines indicates phase transitions of the order → disorder type with the formation of one to three groups of amorphous clusters with the dominance, in the nanometer scale, of the atomic order characteristic of the family of planes (111), (220), and (311) of crystalline aluminum. We have found a dynamic phase transition with the changing crystallographic order of aluminum, with the matrix structure of a face-centered cubic (FCC) lattice, in the form of nanosized local groups of atoms, that is, the deformation clusters of aluminum with a simple cubic K6 lattice. In the case of conventional rolling, the development of large clusters 50-500 Å in size is observed; however, in the use of rolls with relief recesses, the difference in the sizes of the clusters is one half as much: 50-250 Å. Based on the analysis of the integrated intensity of incoherent X-ray scattering by the samples, we have elucidated the nature of the lowest measured density for the sample subjected to conventional rolling, which consists in the volume concentration of disorderly arranged atoms, the highest of the compared structures, which indicates the formation therein of the greatest amount of fluctuation "voids."

Breaking the GaN material limits with nanoscale vertical polarisation super junction structures: A simulation analysis

NASA Astrophysics Data System (ADS)

Unni, Vineet; Sankara Narayanan, E. M.

2017-04-01

This is the first report on the numerical analysis of the performance of nanoscale vertical superjunction structures based on impurity doping and an innovative approach that utilizes the polarisation properties inherent in III-V nitride semiconductors. Such nanoscale vertical polarisation super junction structures can be realized by employing a combination of epitaxial growth along the non-polar crystallographic axes of Wurtzite GaN and nanolithography-based processing techniques. Detailed numerical simulations clearly highlight the limitations of a doping based approach and the advantages of the proposed solution for breaking the unipolar one-dimensional material limits of GaN by orders of magnitude.

Research Update: Emerging chalcostibite absorbers for thin-film solar cells

DOE PAGES

de Souza Lucas, Francisco Willian; Zakutayev, Andriy

2018-06-04

Copper antimony chalcogenides CuSbCh 2 (Ch=S, Se) are an emerging family of absorbers studied for thin-film solar cells. These non-toxic and Earth-abundant materials show a layered low-dimensional chalcostibite crystal structure, leading to interesting optoelectronic properties for applications in photovoltaic (PV) devices. This research update describes the CuSbCh 2 crystallographic structures, synthesis methods, competing phases, band structures, optoelectronic properties, point defects, carrier dynamics, and interface band offsets, based on experimental and theoretical data. Correlations between these absorber properties and PV device performance are discussed, and opportunities for further increase in the efficiency of the chalcostibite PV devices are highlighted.

Research Update: Emerging chalcostibite absorbers for thin-film solar cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

de Souza Lucas, Francisco Willian; Zakutayev, Andriy

Copper antimony chalcogenides CuSbCh 2 (Ch=S, Se) are an emerging family of absorbers studied for thin-film solar cells. These non-toxic and Earth-abundant materials show a layered low-dimensional chalcostibite crystal structure, leading to interesting optoelectronic properties for applications in photovoltaic (PV) devices. This research update describes the CuSbCh 2 crystallographic structures, synthesis methods, competing phases, band structures, optoelectronic properties, point defects, carrier dynamics, and interface band offsets, based on experimental and theoretical data. Correlations between these absorber properties and PV device performance are discussed, and opportunities for further increase in the efficiency of the chalcostibite PV devices are highlighted.

Statistical crystallography of surface micelle spacing

NASA Technical Reports Server (NTRS)

Noever, David A.

1992-01-01

The aggregation of the recently reported surface micelles of block polyelectrolytes is analyzed using techniques of statistical crystallography. A polygonal lattice (Voronoi mosaic) connects center-to-center points, yielding statistical agreement with crystallographic predictions; Aboav-Weaire's law and Lewis's law are verified. This protocol supplements the standard analysis of surface micelles leading to aggregation number determination and, when compared to numerical simulations, allows further insight into the random partitioning of surface films. In particular, agreement with Lewis's law has been linked to the geometric packing requirements of filling two-dimensional space which compete with (or balance) physical forces such as interfacial tension, electrostatic repulsion, and van der Waals attraction.

Accuracy of Cup Positioning With the Computed Tomography-Based Two-dimensional to Three-Dimensional Matched Navigation System: A Prospective, Randomized Controlled Study.

PubMed

Yamada, Kazuki; Endo, Hirosuke; Tetsunaga, Tomonori; Miyake, Takamasa; Sanki, Tomoaki; Ozaki, Toshifumi

2018-01-01

The accuracy of various navigation systems used for total hip arthroplasty has been described, but no publications reported the accuracy of cup orientation in computed tomography (CT)-based 2D-3D (two-dimensional to three-dimensional) matched navigation. In a prospective, randomized controlled study, 80 hips including 44 with developmental dysplasia of the hips were divided into a CT-based 2D-3D matched navigation group (2D-3D group) and a paired-point matched navigation group (PPM group). The accuracy of cup orientation (absolute difference between the intraoperative record and the postoperative measurement) was compared between groups. Additionally, multiple logistic regression analysis was performed to evaluate patient factors affecting the accuracy of cup orientation in each navigation. The accuracy of cup inclination was 2.5° ± 2.2° in the 2D-3D group and 4.6° ± 3.3° in the PPM group (P = .0016). The accuracy of cup anteversion was 2.3° ± 1.7° in the 2D-3D group and 4.4° ± 3.3° in the PPM group (P = .0009). In the PPM group, the presence of roof osteophytes decreased the accuracy of cup inclination (odds ratio 8.27, P = .0140) and the absolute value of pelvic tilt had a negative influence on the accuracy of cup anteversion (odds ratio 1.27, P = .0222). In the 2D-3D group, patient factors had no effect on the accuracy of cup orientation. The accuracy of cup positioning in CT-based 2D-3D matched navigation was better than in paired-point matched navigation, and was not affected by patient factors. It is a useful system for even severely deformed pelvises such as developmental dysplasia of the hips. Copyright © 2017 Elsevier Inc. All rights reserved.

Discrete cosine and sine transforms generalized to honeycomb lattice

NASA Astrophysics Data System (ADS)

Hrivnák, Jiří; Motlochová, Lenka

2018-06-01

The discrete cosine and sine transforms are generalized to a triangular fragment of the honeycomb lattice. The honeycomb point sets are constructed by subtracting the root lattice from the weight lattice points of the crystallographic root system A2. The two-variable orbit functions of the Weyl group of A2, discretized simultaneously on the weight and root lattices, induce a novel parametric family of extended Weyl orbit functions. The periodicity and von Neumann and Dirichlet boundary properties of the extended Weyl orbit functions are detailed. Three types of discrete complex Fourier-Weyl transforms and real-valued Hartley-Weyl transforms are described. Unitary transform matrices and interpolating behavior of the discrete transforms are exemplified. Consequences of the developed discrete transforms for transversal eigenvibrations of the mechanical graphene model are discussed.

Evaluation of changes in left ventricular structure and function in hypertensive patients with coronary artery disease after PCI using real-time three-dimensional echocardiography.

PubMed

Meng, Yanhong; Zong, Ling; Zhang, Ziteng; Han, Youdong; Wang, Yanhui

2018-02-01

We aimed to evaluate the changes in left ventricular structure and function in hypertensive patients with coronary artery disease before and after percutaneous coronary intervention (PCI) using real-time three-dimensional echocardiography. Two hundred and eighty hypertensive patients with coronary artery disease undergoing PCI and 120 cases who did not receive PCI in our hospital were selected as the subjects of our study. All patients were administered with routine antiplatelet, anticoagulant, lipid-lowering, antihypertensive, dilating coronary artery and other medications. The left ventricular systolic function and systolic synchrony index changes before and after subjects were treated by PCI were analyzed using three-dimensional echocardiography. At 2 days before surgery, there were no significant differences in the left ventricular end-diastolic volume, left ventricular end-systolic volume (LVESV) and ejection fraction (EF) between the two patient groups (P>0.05). At 3 months and 9 months, the two key time points after PCI, the LVESV level in the PCI group was distinctly decreased, while EF was significantly increased (P<0.05). In addition, before treatment, there were no significant differences in the parameters of time from the corresponding segment of the myocardium to the minimal systolic volume in two patient groups, such as Tmsv-16SD, Tmsv-16Dif, Tmsv-12SD, Tmsv-12Dif, Tmsv-6SD and Tmsv-6Dif (P>0.05); however, the parameters of time from the corresponding segment of the myocardium to the minimal systolic volume in patients in the PCI group were significantly reduced at 3 and 9 months after surgery (P<0.05). Three-dimensional echocardiography can evaluate the critical parameters in the prognosis of hypertensive patients with coronary artery disease after PCI accurately and in real-time, which may play a significant role.

Investigation of Three-Dimensional Stress Fields and Slip Systems for FCC Single Crystal Superalloy Notched Specimens

NASA Technical Reports Server (NTRS)

Arakere, Nagaraj K.; Magnan, Shannon; Ebrahimi, Fereshteh; Ferroro, Luis

2004-01-01

Metals and their alloys, except for a few intermetallics, are inherently ductile, i.e. plastic deformation precedes fracture in these materials. Therefore, resistance to fracture is directly related to the development of the plastic zone at the crack tip. Recent studies indicate that the fracture toughness of single crystals depends on the crystallographic orientation of the notch as well as the loading direction. In general, the dependence of crack propagation resistance on crystallographic orientation arises from the anisotropy of (i) elastic constants, (ii) plastic deformation (or slip), and (iii) the weakest fracture planes (e.g. cleavage planes). Because of the triaxial stress state at the notch tips, many slip systems that otherwise would not be activated during uniaxial testing, become operational. The plastic zone formation in single crystals has been tackled theoretically by Rice and his co-workers and only limited experimental work has been conducted in this area. The study of the stresses and strains in the vicinity of a FCC single crystal notch tip is of relatively recent origin. We present experimental and numerical investigation of 3D stress fields and evolution of slip sector boundaries near notches in FCC single crystal tension test specimens, and demonstrate that a 3D linear elastic finite element model that includes the effect of material anisotropy is shown to predict active slip planes and sectors accurately. The slip sector boundaries are shown to have complex curved shapes with several slip systems active simultaneously near the notch. Results are presented for surface and mid-plane of the specimens. The results demonstrate that accounting for 3D elastic anisotropy is very important for accurate prediction of slip activation near FCC single crystal notches loaded in tension. Results from the study will help establish guidelines for fatigue damage near single crystal notches.

A three-dimensional visualization preoperative treatment planning system for microwave ablation in liver cancer: a simulated experimental study.

PubMed

Liu, Fangyi; Cheng, Zhigang; Han, Zhiyu; Yu, Xiaoling; Yu, Mingan; Liang, Ping

2017-06-01

To evaluate the application value of three-dimensional (3D) visualization preoperative treatment planning system (VPTPS) for microwave ablation (MWA) in liver cancer. The study was a simulated experimental study using the CT imaging data of patients in DICOM format in a model. Three students (who learn to interventional ultrasound for less than 1 year) and three experts (who have more than 5 years of experience in ablation techniques) in MWA performed the preoperative planning for 39 lesions (mean diameter 3.75 ± 1.73 cm) of 32 patients using two-dimensional (2D) image planning method and 3D VPTPS, respectively. The number of planning insertions, planning ablation rate, and damage rate to surrounding structures were compared between2D image planning group and 3D VPTPS group. There were fewer planning insertions, lower ablation rate and higher damage rate to surrounding structures in 2D image planning group than 3D VPTPS group for both students and experts. When using the 2D ultrasound planning method, students could carry out fewer planning insertions and had a lower ablation rate than the experts (p < 0.001). However, there was no significant difference in planning insertions, the ablation rate, and the incidence of damage to the surrounding structures between students and experts using 3D VPTPS. 3DVPTPS enables inexperienced physicians to have similar preoperative planning results to experts, and enhances students' preoperative planning capacity, which may improve the therapeutic efficacy and reduce the complication of MWA.

Influence of age on clinical outcomes of three-dimensional transfer of the tibial tuberosity for patellar instability with patella alta.

PubMed

Otsuki, Shuhei; Nakajima, Mikio; Fujiwara, Kenta; Okamoto, Yoshinori; Iida, Go; Murakami, Tomohiko; Neo, Masashi

2017-08-01

To evaluate the clinical outcomes of three-dimensional (3D) transfer of the tibial tuberosity for patellar instability with patella alta, with a focus on the influence of age at initial surgery. Three-dimensional surgery was performed on 28 knees with a mean follow-up of 46 months. Patients were separated into three groups based on the age at initial surgery: group A, 10 knees and an average age of 16.3 ± 1.8 (14-19) years; group B, 10 knees and an average age of 22.1 ± 2.5 (20-28) years; and group C, eight knees and an average age of 44.0 ± 2.2 (40-46) years. Patellofemoral geometry improvement focused on patella alta by determining the Insall-Salvati ratio and Caton-Deschamps index, rotational malalignment by measuring the tibial tubercle-trochlear groove (TT-TG) distance, and lateral patellar subluxation by measuring the patellar tilt. Clinical outcomes were evaluated by the Lysholm and Kujala scores, which were compared before and after surgery. Cartilage degeneration was evaluated by the International Cartilage Repair Society grading system at initial arthroscopy. The patellar height, TT-TG, and patellar tilt significantly improved in all groups postoperatively (p < 0.05). The Lysholm and Kujala scores also significantly improved postoperatively; however, both scores were lower in group C than in the other groups (p < 0.05). Particularly, pain scores were more severe in group C than in the other groups, and the severity of cartilage degeneration correlated with the pain scores (p < 0.05). Cartilage damage differed significantly between the groups at initial arthroscopy; particularly, group C included grades III and IV cartilage degeneration (p < 0.05). Age at initial surgery may be the predicting factor for poor clinical outcomes of 3D transfer surgery. The clinical outcome may depend on the age at surgery, which correlated with cartilage damage; thus, surgeons should be given this information when patients are considered undergoing patella surgery. Therapeutic case series, Level IV.

Modeling the characteristic etch morphologies along specific crystallographic orientations by anisotropic chemical etching

NASA Astrophysics Data System (ADS)

Li, Kun-Dar; Miao, Jin-Ru

2018-02-01

To improve the advanced manufacturing technology for functional materials, a sophisticated control of chemical etching process is highly demanded, especially in the fields of environment and energy related applications. In this study, a phase-field-based model is utilized to investigate the etch morphologies influenced by the crystallographic characters during anisotropic chemical etching. Three types of etching modes are inspected theoretically, including the isotropic, <100> and <111> preferred oriented etchings. Owing to the specific etching behavior along the crystallographic directions, different characteristic surface structures are presented in the simulations, such as the pimple-like, pyramidal hillock and ridge-like morphologies. In addition, the processing parameters affecting the surface morphological formation and evolution are also examined systematically. According to the numerical results, the growth mechanism of surface morphology in a chemical etching is revealed distinctly. While the etching dynamics plays a dominant role on the surface formation, the characteristic surface morphologies corresponding to the preferred etching direction become more apparent. As the atomic diffusion turned into a determinative factor, a smoothened surface would appear, even under the anisotropic etching conditions. These simulation results provide fundamental information to enhance the development and application of anisotropic chemical etching techniques.

Acquiring basic and advanced laparoscopic skills in novices using two-dimensional (2D), three-dimensional (3D) and ultra-high definition (4K) vision systems: A randomized control study.

PubMed

Abdelrahman, M; Belramman, A; Salem, R; Patel, B

2018-05-01

To compare the performance of novices in laparoscopic peg transfer and intra-corporeal suturing tasks in two-dimensional (2D), three-dimensional (3D) and ultra-high definition (4K) vision systems. Twenty-four novices were randomly assigned to 2D, 3D and 4K groups, eight in each group. All participants performed the two tasks on a box trainer until reaching proficiency. Their performance was assessed based on completion time, number of errors and number of repetitions using the validated FLS proficiency criteria. Eight candidates in each group completed the training curriculum. The mean performance time (in minutes) for the 2D group was 558.3, which was more than that of the 3D and 4K groups of 316.7 and 310.4 min respectively (P < 0.0001). The mean number of repetitions was lower for the 3D and 4K groups versus the 2D group: 125.9 and 127.4 respectively versus 152.1 (P < 0.0001). The mean number of errors was lower for the 4K group versus the 3D and 2D groups: 1.2 versus 26.1 and 50.2 respectively (P < 0.0001). The 4K vision system improved accuracy in acquiring laparoscopic skills for novices in complex tasks, which was shown in significant reduction in number of errors compared to the 3D and the 2D vision systems. The 3D and the 4K vision systems significantly improved speed and accuracy when compared to the 2D vision system based on shorter performance time, fewer errors and lesser number of repetitions. Copyright © 2018 IJS Publishing Group Ltd. Published by Elsevier Ltd. All rights reserved.

The holographic display of three-dimensional medical objects through the usage of a shiftable cylindrical lens

NASA Astrophysics Data System (ADS)

Teng, Dongdong; Liu, Lilin; Zhang, Yueli; Pang, Zhiyong; Wang, Biao

2014-09-01

Through the creative usage of a shiftable cylindrical lens, a wide-view-angle holographic display system is developed for medical object display in real three-dimensional (3D) space based on a time-multiplexing method. The two-dimensional (2D) source images for all computer generated holograms (CGHs) needed by the display system are only one group of computerized tomography (CT) or magnetic resonance imaging (MRI) slices from the scanning device. Complicated 3D message reconstruction on the computer is not necessary. A pelvis is taken as the target medical object to demonstrate this method and the obtained horizontal viewing angle reaches 28°.

The complex metal-rich boride Ti1+xRh2-x+yIr3-yB3 (x=0.68, y=1.06) with a new structure type containing B4 zigzag fragments: Synthesis, crystal chemistry and theoretical calculations

NASA Astrophysics Data System (ADS)

Goerens, Christian; Fokwa, Boniface P. T.

2012-08-01

Polycrystalline samples and single crystals of the new complex boride Ti1+xRh2-x+yIr3-yB3 (x=0.68; y=1.06) were synthesized by arc-melting the elements in a water-cooled copper crucible under an argon atmosphere and characterized by X-Ray diffraction as well as EDX measurements. The crystal structure was refined on the basis of single crystal data. The new phase, which represents a new structure type containing trans zigzag B4 fragments as well as isolated boron atoms crystallizes in the orthorhombic space group Pbam (Nr. 55) with the lattice parameters a=8.620(1) Å, b=14.995(2) Å and c=3.234(1) Å. First-principles density functional theory calculations using the Vienna ab-initio simulation package (VASP) were performed on an appropriate structural model (using a supercell approach) and the experimental crystallographic data could be reproduced accurately. Based on this model, the density of states and crystal orbital Hamilton population (for bonding analysis) were calculated, using the linear muffin-tin orbital atomic sphere approximation (LMTO-ASA) method. According to these calculations, this metal-rich compound should be metallic, as expected. Furthermore, very strong boron-boron interactions are observed in the trans zigzag B4 fragment, which induce a clear differentiation of two types of metal-boron contacts with different strength. The observed three-dimensional metal-metal interaction is in good agreement with the predicted metallic behavior.

Structure-property relationship of 3-(4-substituted benzyl)-1,3-diazaspiro[4.4]nonane-2,4-diones as new potentional anticonvulsant agents. An experimental and theoretical study

NASA Astrophysics Data System (ADS)

Lazić, Anita M.; Božić, Bojan Đ.; Vitnik, Vesna D.; Vitnik, Željko J.; Rogan, Jelena R.; Radovanović, Lidija D.; Valentić, Nataša V.; Ušćumlić, Gordana S.

2017-01-01

The structure-property relationship of newly synthesized 3-(4-substituted benzyl)-1,3-diazaspiro [4.4]nonane-2,4-diones was studied by experimental and calculated methods. The prepared compounds were characterized by UV-Vis, FT-IR, 1H NMR and 13C NMR spectroscopy and elemental analysis. The crystal structure was elucidated by single-crystal X-ray diffraction. The 3-benzyl-1,3-diazaspiro[4.4]nonane-2,4-dione crystallizes in triclinic P-1 space group, with two crystallographically independent molecules in the asymmetric unit. Cyclopentane ring adopts an envelope conformation. A three-dimensional crystal packing is governed by hydrogen N-H⋯O bonds, numerous C-H⋯O/N and C-H … π interactions between neighboring molecules. Density functional theory (DFT) calculations with B3LYP and M06-2X methods using 6-311++G(d,p) basis set were performed to provide structural and spectroscopic information. Comparisons between experimental and calculated UV-Vis spectral properties suggest that the monomeric form of the investigated spirohydantoins is dominant in all used solvents. The effects of substituents on the absorption spectra of spirohydantoins are interpreted by correlation of absorption frequencies with Hammett equation. The lipophilicities of the investigated molecules were estimated by calculation of their log P values. Some of the spirohydantoins synthesized in this work, exhibit the lipophilicities comparable to the standard medicine anticonvulsant drug Phenytoin. The results obtained in this investigation afford guidelines for the preparation of new derivatives of spirohydantoin as potential anticonvulsant agents and for better understanding the structure-activity relationship.

Expanding the remarkable structural diversity of uranyl tellurites: hydrothermal preparation and structures of K[UO(2)Te(2)O(5)(OH)], Tl(3)[(UO(2))(2)[Te(2)O(5)(OH)](Te(2)O(6))].2H(2)O, beta-Tl(2)[UO(2)(TeO(3))(2)], and Sr(3)[UO(2)(TeO(3))(2)](TeO(3))(2).

PubMed

Almond, Philip M; Albrecht-Schmitt, Thomas E

2002-10-21

The reactions of UO(2)(C(2)H(3)O(2))(2).2H(2)O with K(2)TeO(3).H(2)O, Na(2)TeO(3) and TlCl, or Na(2)TeO(3) and Sr(OH)(2).8H(2)O under mild hydrothermal conditions yield K[UO(2)Te(2)O(5)(OH)] (1), Tl(3)[(UO(2))(2)[Te(2)O(5)(OH)](Te(2)O(6))].2H(2)O (2) and beta-Tl(2)[UO(2)(TeO(3))(2)] (3), or Sr(3)[UO(2)(TeO(3))(2)](TeO(3))(2) (4), respectively. The structure of 1 consists of tetragonal bipyramidal U(VI) centers that are bound by terminal oxo groups and tellurite anions. These UO(6) units span between one-dimensional chains of corner-sharing, square pyramidal TeO(4) polyhedra to create two-dimensional layers. Alternating corner-shared oxygen atoms in the tellurium oxide chains are protonated to create short/long bonding patterns. The one-dimensional chains of corner-sharing TeO(4) units found in 1 are also present in 2. However, in 2 there are two distinct chains present, one where alternating corner-shared oxygen atoms are protonated, and one where the chains are unprotonated. The uranyl moieties in 2 are bound by five oxygen atoms from the tellurite chains to create seven-coordinate pentagonal bipyramidal U(VI). The structures of 3 and 4 both contain one-dimensional [UO(2)(TeO(3))(2)](2-) chains constructed from tetragonal bipyramidal U(VI) centers that are bridged by tellurite anions. The chains differ between 3 and 4 in that all of the pyramidal tellurite anions in 3 have the same orientation, whereas the tellurite anions in 4 have opposite orientations on each side of the chain. In 4, there are also additional isolated TeO(3)(2-) anions present. Crystallographic data: 1, orthorhombic, space group Cmcm, a = 7.9993(5) A, b = 8.7416(6) A, c = 11.4413(8) A, Z = 4; 2, orthorhombic, space group Pbam, a = 10.0623(8) A, b = 23.024(2) A, c = 7.9389(6) A, Z = 4; 3, monoclinic, space group P2(1)/n, a = 5.4766(4) A, b = 8.2348(6) A, c = 20.849(3) A, beta = 92.329(1) degrees, Z = 4; 4, monoclinic, space group C2/c, a = 20.546(1) A, b = 5.6571(3) A, c = 13.0979(8) A, beta = 94.416(1) degrees, Z = 4.

The role of three-dimensional printed models of skull in anatomy education: a randomized controlled trail.

PubMed

Chen, Shi; Pan, Zhouxian; Wu, Yanyan; Gu, Zhaoqi; Li, Man; Liang, Ze; Zhu, Huijuan; Yao, Yong; Shui, Wuyang; Shen, Zhen; Zhao, Jun; Pan, Hui

2017-04-03

Three-dimensional (3D) printed models represent educational tools of high quality compared with traditional teaching aids. Colored skull models were produced by 3D printing technology. A randomized controlled trial (RCT) was conducted to compare the learning efficiency of 3D printed skulls with that of cadaveric skulls and atlas. Seventy-nine medical students, who never studied anatomy, were randomized into three groups by drawing lots, using 3D printed skulls, cadaveric skulls, and atlas, respectively, to study the anatomical structures in skull through an introductory lecture and small group discussions. All students completed identical tests, which composed of a theory test and a lab test, before and after a lecture. Pre-test scores showed no differences between the three groups. In post-test, the 3D group was better than the other two groups in total score (cadaver: 29.5 [IQR: 25-33], 3D: 31.5 [IQR: 29-36], atlas: 27.75 [IQR: 24.125-32]; p = 0.044) and scores of lab test (cadaver: 14 [IQR: 10.5-18], 3D: 16.5 [IQR: 14.375-21.625], atlas: 14.5 [IQR: 10-18.125]; p = 0.049). Scores involving theory test, however, showed no difference between the three groups. In this RCT, an inexpensive, precise and rapidly-produced skull model had advantages in assisting anatomy study, especially in structure recognition, compared with traditional education materials.

Effects of Laboratory Disinfecting Agents on Dimensional Stability of Three Commercially Available Heat-Cured Denture Acrylic Resins in India: An In-Vitro Study

PubMed Central

Jujare, Ravikanth Haridas; Varghese, Rana Kalappattil; Singh, Vishwa Deepak; Gaurav, Amit

2016-01-01

Introduction Dental professionals are exposed to a wide variety of microorganisms which calls for use of effective infection control procedures in the dental office and laboratories that can prevent cross-contamination that could extend to dentists, dental office staff, dental technicians as well as patients. This concern has led to a renewed interest in denture sterilization and disinfection. Heat polymerized dentures exhibit dimensional change during disinfection procedure. Aim The purpose of this study was to determine the influence of different types of widely used laboratory disinfecting agents on the dimensional stability of heat-cured denture acrylic resins and to compare the dimensional stability of three commercially available heat-cured denture acrylic resins in India. Materials and Methods Twelve specimens of uniform dimension each of three different brands namely Stellon, Trevalon and Acralyn-H were prepared using circular metal disc. Chemical disinfectants namely 2% alkaline glutaraldehyde, 1% povidone-iodine, 0.5% sodium hypochlorite and water as control group were used. Diameter of each specimen was measured before immersion and after immersion with time interval of 1 hour and 12 hours. The data was evaluated statistically using one way analysis of variance. Results All the specimens in three disinfectants and in water exhibited very small amount of linear expansion. Among three disinfectants, specimens in 2% alkaline glutaraldehyde exhibited least(0.005mm) and water showed highest (0.009mm) amount of dimensional change. Among resins, Trevalon showed least (0.067mm) and Acralyn-H exhibited highest (0.110mm) amount of dimensional change. Conclusion Although, all the specimens of three different brands of heat-cured denture acrylic resins exhibited increase in linear dimensional change in all the disinfectants and water, they were found to be statistically insignificant. PMID:27134996

Method for removing atomic-model bias in macromolecular crystallography

DOEpatents

Terwilliger, Thomas C [Santa Fe, NM

2006-08-01

Structure factor bias in an electron density map for an unknown crystallographic structure is minimized by using information in a first electron density map to elicit expected structure factor information. Observed structure factor amplitudes are combined with a starting set of crystallographic phases to form a first set of structure factors. A first electron density map is then derived and features of the first electron density map are identified to obtain expected distributions of electron density. Crystallographic phase probability distributions are established for possible crystallographic phases of reflection k, and the process is repeated as k is indexed through all of the plurality of reflections. An updated electron density map is derived from the crystallographic phase probability distributions for each one of the reflections. The entire process is then iterated to obtain a final set of crystallographic phases with minimum bias from known electron density maps.

Syntheses, structures and properties of four Cd(II) coordination polymers induced by the pH regulator

NASA Astrophysics Data System (ADS)

Xu, Yun; Ding, Fang; Liu, Dong; Yang, Pei-Pei; Zhu, Li-Li

2018-03-01

Four new coordination polymers [Cd2(CHDC)2(APYZ)(H2O)2](H2O) (1), [Cd(HCHDC)2(APYZ) (H2O)] (2), [Cd2(CHDC)2(PYZ)(H2O)2](H2O) (3), and [Cd(HCHDC)2(PYZ)(H2O)] (4) (H2CHDC = 1,4-cyclohexanedicarboxylic acid, APYZ = 2-aminopyrazine, PYZ = pyrazine) have been synthesized under the hydrothermal conditions by changing the pH regulator and the N-containing ligands. The pH regulator impacted on the degree of deprotonation of the 1,4-cyclohexanedicarboxylic acid ligand and resulted in the formation of the two pairs of different networks. Polymers 1 and 3 crystallize in monoclinic, space group P21/c, exhibit two dimensional 63 net, which further formed three-dimensional supramolecular structure by the Csbnd H⋯O hydrogen bond interactions. While polymers 2 and 4 possess one dimensional chain structures and further link into two dimensional layered supramolecular structures by intermolecular hydrogen bonding interactions. From all three conformers of H2CHDC, e,a-cis is consistently present in the Cd coordination polymers. Furthermore, photoluminescence properties of four polymers are also investigated, the luminescent intensity of polymer 1 (or 2) with amino group in pyrazine is dramatically stronger than that of the similar structure of polymer 3 (or 4) without amino group in pyrazine, the results shown that the presence of the amino group from 2-aminopyrazine play a key role in increasing the luminescence properties.

g-Tensor determination from single-crystal ESR data

NASA Astrophysics Data System (ADS)

Byrn, Marianne P.; Strouse, Charles E.

A general method is presented for extraction of the g tensor from single-crystal electron spin resonance data. This method does not depend on knowledge of crystal morphology or on the presence of crystallographic symmetry. The g values are obtained from rotations around three arbitrarily chosen but accurately known axes.

Crystallographically Anisotropic Shape of Forsterite: New Probe for Evaluating Dust Formation History from Infrared Spectroscopy

NASA Astrophysics Data System (ADS)

Takigawa, Aki; Tachibana, Shogo

2012-05-01

Crystalline dust has been observed by infrared spectroscopy around dust-enshrouded asymptotic giant branch stars, in protoplanetary disks, and from some comets. Crystalline materials often have a specific shape related to a specific crystallographic orientation (crystallographically anisotropic shape), which reflects the anisotropic nature of crystals, and their infrared spectral features depend on crystallographically anisotropic shapes. The crystallographically anisotropic shape is thus a potentially powerful probe to evaluate circumstellar dust-forming conditions quantitatively. In order to assess the possibility to determine the crystallographically anisotropic shape from infrared spectra, we calculated mass absorption coefficients for ellipsoidal forsterite particles, the most abundant circumstellar crystalline silicate, elongated and flattened along the crystallographic a-, b-, and c-axes with various aspect ratios in the wavelength range of 9-70 μm. It was found that differences in infrared features caused by various crystallographicaly anisotropic shapes are distinguishable from each other irrespective of the effects of temperature, size, chemical composition, and grain edges of forsterite in the range of 9-12 μm and 15-20 μm. We thus concluded that the crystallographically anisotropic shape of forsterite can be deduced from peak features in infrared spectra. We also showed that the crystallographically anisotropic shapes formed by evaporation and condensation of forsterite can be distinguished from each other and the temperature condition for evaporation can be evaluated from the peak features. We applied the present results to the infrared spectrum of a protoplanetary disk HD100546 and found that a certain fraction (~25%) of forsterite dust may have experienced high-temperature evaporation (>1600 K).

Three-dimensional comparison of facial morphology in white populations in Budapest, Hungary, and Houston, Texas.

PubMed

Gor, Troy; Kau, Chung How; English, Jeryl D; Lee, Robert P; Borbely, Peter

2010-03-01

The aim of this study was to assess the use of 3-dimensional facial averages in determining facial morphologic differences in 2 white population groups. Three-dimensional images were obtained in a reproducible and controlled environment from a commercially available stereo-photogrammetric camera capture system. The 3dMDface system (3dMD, Atlanta, Ga) photographed 200 subjects from 2 population groups (Budapest, Hungary, and Houston, Tex); each group included 50 men and 50 women, aged 18 to 30 years. Each face was obtained as a facial mesh and orientated along a triangulated axis. All faces were overlaid, one on top of the other, and a complex mathematical algorithm was used until an average composite face of 1 man and 1 woman was obtained for each subgroup (Hungarian men, Hungarian women, Texas men, and Texas women). These average facial composites were superimposed (men and women) based on a previously validated superimposition method, and the facial differences were quantified. Distinct facial differences were observed between the population groups. These differences could be seen in the nasal, malar, lips, and lower facial regions. In general, the mean facial differences were 0.55 +/- 0.60 mm between the Hungarian and Texas women, and 0.44 +/- 0.42 mm between the Hungarian and Texas men. The ranges of differences were -2.02 to 3.77 and -2.05 to 1.94 mm for the female and male pairings, respectively. Three-dimensional facial averages representing the facial soft-tissue morphology of adults can be used to assess diagnostic and treatment regimens for patients by population. Each population is different with respect to their soft-tissue structures, and traditional soft-tissue normative data (eg, white norms) should be altered and used for specific groups. American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

Structure of an LiKSO 4 single crystal studied by 7Li and 39K NMR at low temperature

NASA Astrophysics Data System (ADS)

Lim, A. R.; Jeong, S.-Y.

2000-09-01

The 7Li and 39K nuclear magnetic resonances in an LiKSO 4 single crystal grown by the slow evaporation method have been investigated using a Bruker FT nuclear magnetic resonance (NMR) spectrometer. From the experimental data, the quadrapole coupling constant and asymmetry parameter were determined at room temperature and low temperature, respectively. Unlike the case at 300 K, the 7Li NMR line consists of three sets at 180 K, while 39K nucleus exhibits six sets for the rotation around the three crystallographic axes. The three resonance lines of 7Li and 39K at low temperature can be explained by the existence of three kinds of twin domain, rotated with respect to each other by 120° around the c-axis. The three resonance lines are also related to the crystallographic mirror plane. Structure of ferroelastic LiKSO 4 crystals at 180 K can be directly inferred from the domain pattern obtained by 7Li and 39K NMR. The above results show that the equations of the twin boundaries belong to the mm2 F6 mm ferroelastic species. Therefore, the symmetry of phases III and II is given by orthorhombic structure with Cmc2 1 ( mm2) and hexagonal structural with P6 3mc (6 mm), respectively.

Crystallized N-terminal domain of influenza virus matrix protein M1 and method of determining and using same

NASA Technical Reports Server (NTRS)

Luo, Ming (Inventor); Sha, Bingdong (Inventor)

2000-01-01

The matrix protein, M1, of influenza virus strain A/PR/8/34 has been purified from virions and crystallized. The crystals consist of a stable fragment (18 Kd) of the M1 protein. X-ray diffraction studies indicated that the crystals have a space group of P3.sub.t 21 or P3.sub.2 21. Vm calculations showed that there are two monomers in an asymmetric unit. A crystallized N-terminal domain of M1, wherein the N-terminal domain of M1 is crystallized such that the three dimensional structure of the crystallized N-terminal domain of M1 can be determined to a resolution of about 2.1 .ANG. or better, and wherein the three dimensional structure of the uncrystallized N-terminal domain of M1 cannot be determined to a resolution of about 2.1 .ANG. or better. A method of purifying M1 and a method of crystallizing M1. A method of using the three-dimensional crystal structure of M1 to screen for antiviral, influenza virus treating or preventing compounds. A method of using the three-dimensional crystal structure of M1 to screen for improved binding to or inhibition of influenza virus M1. The use of the three-dimensional crystal structure of the M1 protein of influenza virus in the manufacture of an inhibitor of influenza virus M1. The use of the three-dimensional crystal structure of the M1 protein of influenza virus in the screening of candidates for inhibition of influenza virus M1.

Crystal Data

National Institute of Standards and Technology Data Gateway

SRD 3 NIST Crystal Data (PC database for purchase)   NIST Crystal Data contains chemical, physical, and crystallographic information useful to characterize more than 237,671 inorganic and organic crystalline materials. The data include the standard cell parameters, cell volume, space group number and symbol, calculated density, chemical formula, chemical name, and classification by chemical type.

Pacific oyster polyamine oxidase: a protein missing link in invertebrate evolution.

PubMed

Cervelli, Manuela; Polticelli, Fabio; Angelucci, Emanuela; Di Muzio, Elena; Stano, Pasquale; Mariottini, Paolo

2015-05-01

Polyamine oxidases catalyse the oxidation of polyamines and acetylpolyamines and are responsible for the polyamine interconversion metabolism in animal cells. Polyamine oxidases from yeast can oxidize spermine, N(1)-acetylspermine, and N(1)-acetylspermidine, while in vertebrates two different enzymes, namely spermine oxidase and acetylpolyamine oxidase, specifically catalyse the oxidation of spermine, and N(1)-acetylspermine/N(1)-acetylspermidine, respectively. In this work we proved that the specialized vertebrate spermine and acetylpolyamine oxidases have arisen from an ancestor invertebrate polyamine oxidase with lower specificity for polyamine substrates, as demonstrated by the enzymatic activity of the mollusc polyamine oxidase characterized here. This is the first report of an invertebrate polyamine oxidase, the Pacific oyster Crassostrea gigas (CgiPAO), overexpressed as a recombinant protein. This enzyme was biochemically characterized and demonstrated to be able to oxidase both N(1)-acetylspermine and spermine, albeit with different efficiency. Circular dichroism analysis gave an estimation of the secondary structure content and modelling of the three-dimensional structure of this protein and docking studies highlighted active site features. The availability of this pluripotent enzyme can have applications in crystallographic studies and pharmaceutical biotechnologies, including anticancer therapy as a source of hydrogen peroxide able to induce cancer cell death.

Thyroxine revisited.

PubMed

Katrusiak, Andrzej; Katrusiak, Anna

2004-12-01

The crystal structure of the common therapeutic agent, the pentahydrated sodium salt of L-thyroxine hormone (3-[4-(4-hydroxy-3,5-diiodophenoxy)-3,5-diiodophenyl]-L-alanine), has been determined and discussed in relation to the drug's stability. The stoichiometry and absolute configuration (-)-C(8)S-[C15H10I4NO4]-.Na+.5H2O have been confirmed. The crystals are built of a three-dimensional supramolecular network with two symmetry-independent L-thyroxine anions, in two distinct conformations not previously reported, linked by strong NH-O hydrogen bonds into dimers. Two independent sodium cations are fivefold and sixfold coordinated. The cations and two independent water molecules not involved in coordinating the Na cations form sheets along the crystallographic (001) planes. The presence of differently coordinated cations and non-coordinating water molecules may be responsible for water transport and loss, for decay of the crystals, and subsequent low stability of the drug. Only a conglomerate could be obtained when racemic sodium thyroxine was crystallized from ethanol and methanol solutions by evaporation, which explains the equal penta-hydration of the sodium salts of enantiomorphic and racemic thyroxine, and the fact that there are no apparent differences in their stability. (c) 2004 Wiley-Liss, Inc. and the American Pharmacists Association

Effects of surface stability on the morphological transformation of metals and metal oxides as investigated by first-principles calculations.

PubMed

Andrés, Juan; Gracia, Lourdes; Gouveia, Amanda Fernandes; Ferrer, Mateus Meneghetti; Longo, Elson

2015-10-09

Morphology is a key property of materials. Owing to their precise structure and morphology, crystals and nanocrystals provide excellent model systems for joint experimental and theoretical investigations into surface-related properties. Faceted polyhedral crystals and nanocrystals expose well-defined crystallographic planes depending on the synthesis method, which allow for thoughtful investigations into structure-reactivity relationships under practical conditions. This feature article introduces recent work, based on the combined use of experimental findings and first-principles calculations, to provide deeper knowledge of the electronic, structural, and energetic properties controlling the morphology and the transformation mechanisms of different metals and metal oxides: Ag, anatase TiO2, BaZrO3, and α-Ag2WO4. According to the Wulff theorem, the equilibrium shapes of these systems are obtained from the values of their respective surface energies. These investigations are useful to gain further understanding of how to achieve morphological control of complex three-dimensional crystals by tuning the ratio of the surface energy values of the different facets. This strategy allows the prediction of possible morphologies for a crystal and/or nanocrystal by controlling the relative values of surface energies.

NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores.

PubMed

Ryu, Hyojung; Lim, GyuTae; Sung, Bong Hyun; Lee, Jinhyuk

2016-02-15

Protein structure refinement is a necessary step for the study of protein function. In particular, some nuclear magnetic resonance (NMR) structures are of lower quality than X-ray crystallographic structures. Here, we present NMRe, a web-based server for NMR structure refinement. The previously developed knowledge-based energy function STAP (Statistical Torsion Angle Potential) was used for NMRe refinement. With STAP, NMRe provides two refinement protocols using two types of distance restraints. If a user provides NOE (Nuclear Overhauser Effect) data, the refinement is performed with the NOE distance restraints as a conventional NMR structure refinement. Additionally, NMRe generates NOE-like distance restraints based on the inter-hydrogen distances derived from the input structure. The efficiency of NMRe refinement was validated on 20 NMR structures. Most of the quality assessment scores of the refined NMR structures were better than those of the original structures. The refinement results are provided as a three-dimensional structure view, a secondary structure scheme, and numerical and graphical structure validation scores. NMRe is available at http://psb.kobic.re.kr/nmre/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Ternary germanides RERhGe2 (RE = Y, Gd-Ho) - New representatives of the YIrGe2 type

NASA Astrophysics Data System (ADS)

Voßwinkel, Daniel; Heletta, Lukas; Hoffmann, Rolf-Dieter; Pöttgen, Rainer

2016-11-01

The YIrGe2 type ternary germanides RERhGe2 (RE = Y, Gd-Ho) were synthesized from the elements by arc-melting and characterized by powder X-ray diffraction. The structure of DyRhGe2 was refined from single crystal X-ray diffractometer data: Immm, a = 426.49(9), b = 885.0(2), c = 1577.4(3) pm, wR2 = 0.0533, 637 F2 values, 30 variables (300 K data). The structure contains two crystallographically independent dysprosium atoms in pentagonal prismatic and hexagonal prismatic coordination. The three-dimensional [RhGe2] polyanion is stabilized through covalent Rh-Ge (243-261 pm) and Ge-Ge (245-251 pm) bonding. The close structural relationship with the slightly rhodium-poorer germanides RE5Rh4Ge10 (≡ RERh0.8Ge2) is discussed. Temperature-dependent magnetic susceptibility measurements reveal Pauli paramagnetism for YRhGe2 and Curie-Weiss paramagnetism for RERhGe2 with RE = Gd, Tb, Dy and Ho. These germanides order antiferromagnetically at TN = 7.2(5), 10.6(5), 8.1(5), and 6.4(5) K, respectively.

Model of a ternary complex between activated factor VII, tissue factor and factor IX.

PubMed

Chen, Shu-wen W; Pellequer, Jean-Luc; Schved, Jean-François; Giansily-Blaizot, Muriel

2002-07-01

Upon binding to tissue factor, FVIIa triggers coagulation by activating vitamin K-dependent zymogens, factor IX (FIX) and factor X (FX). To understand recognition mechanisms in the initiation step of the coagulation cascade, we present a three-dimensional model of the ternary complex between FVIIa:TF:FIX. This model was built using a full-space search algorithm in combination with computational graphics. With the known crystallographic complex FVIIa:TF kept fixed, the FIX docking was performed first with FIX Gla-EGF1 domains, followed by the FIX protease/EGF2 domains. Because the FIXa crystal structure lacks electron density for the Gla domain, we constructed a chimeric FIX molecule that contains the Gla-EGF1 domains of FVIIa and the EGF2-protease domains of FIXa. The FVIIa:TF:FIX complex has been extensively challenged against experimental data including site-directed mutagenesis, inhibitory peptide data, haemophilia B database mutations, inhibitor antibodies and a novel exosite binding inhibitor peptide. This FVIIa:TF:FIX complex provides a powerful tool to study the regulation of FVIIa production and presents new avenues for developing therapeutic inhibitory compounds of FVIIa:TF:substrate complex.

Adsorption and photocatalytic properties of transition metal Zinc(II) complex based on 5-(4-(tetrazol-5-yl)phenyl)isophthalic acid

NASA Astrophysics Data System (ADS)

Qiao, Yu; Ren, Shan-Shan; Liu, Li-Hui; Guan, Wei-Sheng; Li, Zhi-Min; Che, Guang-Bo; Liu, Chun-Bo; Wang, Yan-Yan; Wang, Qing-Wei; Li, Xiu-Ying; Zhu, En-Wei

2018-06-01

A new coordination polymeric zinc(II) complex, namely, [Zn2(L)(H2O)3]n·nNO3(1), (H3L = 5-(4-(tetrazol-5-yl)phenyl)isophthalic acid) has been synthesized under solvothermal conditions and structurally characterized by elemental analysis, IR spectroscopy, single-crystal X-ray diffraction analysis and powder X-ray diffraction. Complex 1 exhibits a three-dimensional structure with a Schläfli symbol of 44•69•82 topologies, constructed from two crystallographically independent five and six coordinated mode with metal center and connected H3L ligands. The complex has good thermal stability and excellent photoluminescent property. Furthermore, by comparing the photoluminescent and photocatalytic mutation results induced by interconversion of metal ions, we confirm that the properties mutation induced by metal ions is much controllable and obvious. In addition, the complex exhibits significantly enhanced photocatalytic activity for methylene blue (MB) under UV light irradiation (λ < 400 nm), and the degradation rate could reach 75% in 80 min. Meanwhile trapping experiments indicated that the •O2- and h+ are the main activated species.

X-ray structure determination and deuteration of nattokinase.

PubMed

Yanagisawa, Yasuhide; Chatake, Toshiyuki; Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki; Kawaguchi, Akio; Chiba-Kamosida, Kaori; Ogawa, Megumi; Adachi, Tatsumi; Morimoto, Yukio

2013-11-01

Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D2O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D2O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis.

X-ray structure determination and deuteration of nattokinase

PubMed Central

Yanagisawa, Yasuhide; Chatake, Toshiyuki; Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki; Kawaguchi, Akio; Chiba-Kamosida, Kaori; Ogawa, Megumi; Adachi, Tatsumi; Morimoto, Yukio

2013-01-01

Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D2O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D2O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis. PMID:24121331

Effect of Crystal Orientation on Analysis of Single-Crystal, Nickel-Based Turbine Blade Superalloys

NASA Technical Reports Server (NTRS)

Swanson, G. R.; Arakere, N. K.

2000-01-01

High-cycle fatigue-induced failures in turbine and turbopump blades is a pervasive problem. Single-crystal nickel turbine blades are used because of their superior creep, stress rupture, melt resistance, and thermomechanical fatigue capabilities. Single-crystal materials have highly orthotropic properties making the position of the crystal lattice relative to the part geometry a significant and complicating factor. A fatigue failure criterion based on the maximum shear stress amplitude on the 24 octahedral and 6 cube slip systems is presented for single-crystal nickel superalloys (FCC crystal). This criterion greatly reduces the scatter in uniaxial fatigue data for PWA 1493 at 1,200 F in air. Additionally, single-crystal turbine blades used in the Space Shuttle main engine high pressure fuel turbopump/alternate turbopump are modeled using a three-dimensional finite element (FE) model. This model accounts for material orthotrophy and crystal orientation. Fatigue life of the blade tip is computed using FE stress results and the failure criterion that was developed. Stress analysis results in the blade attachment region are also presented. Results demonstrate that control of crystallographic orientation has the potential to significantly increase a component's resistance to fatigue crack growth without adding additional weight or cost.

Atomic Force Microscopy Based Cell Shape Index

NASA Astrophysics Data System (ADS)

Adia-Nimuwa, Usienemfon; Mujdat Tiryaki, Volkan; Hartz, Steven; Xie, Kan; Ayres, Virginia

2013-03-01

Stellation is a measure of cell physiology and pathology for several cell groups including neural, liver and pancreatic cells. In the present work, we compare the results of a conventional two-dimensional shape index study of both atomic force microscopy (AFM) and fluorescent microscopy images with the results obtained using a new three-dimensional AFM-based shape index similar to sphericity index. The stellation of astrocytes is investigated on nanofibrillar scaffolds composed of electrospun polyamide nanofibers that has demonstrated promise for central nervous system (CNS) repair. Recent work by our group has given us the ability to clearly segment the cells from nanofibrillar scaffolds in AFM images. The clear-featured AFM images indicated that the astrocyte processes were longer than previously identified at 24h. It was furthermore shown that cell spreading could vary significantly as a function of environmental parameters, and that AFM images could record these variations. The new three-dimensional AFM-based shape index incorporates the new information: longer stellate processes and cell spreading. The support of NSF PHY-095776 is acknowledged.