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Sample records for structural characterization magnetochemistry

  1. Heterobridged dinuclear, tetranuclear, dinuclear-based 1-d, and heptanuclear-based 1-D complexes of copper(II) derived from a dinucleating ligand: syntheses, structures, magnetochemistry, spectroscopy, and catecholase activity.

    PubMed

    Majumder, Samit; Sarkar, Sohini; Sasmal, Sujit; Sañudo, E Carolina; Mohanta, Sasankasekhar

    2011-08-15

    The work in this paper presents syntheses, characterization, crystal structures, variable-temperature/field magnetic properties, catecholase activity, and electrospray ionization mass spectroscopic (ESI-MS positive) study of five copper(II) complexes of composition [Cu(II)(2)L(μ(1,1)-NO(3))(H(2)O)(NO(3))](NO(3)) (1), [{Cu(II)(2)L(μ-OH)(H(2)O)}(μ-ClO(4))](n)(ClO(4))(n) (2), [{Cu(II)(2)L(NCS)(2)}(μ(1,3)-NCS)](n) (3), [{Cu(II)(2)L(μ(1,1)-N(3))(ClO(4))}(2)(μ(1,3)-N(3))(2)] (4), and [{Cu(II)(2)L(μ-OH)}{Cu(II)(2)L(μ(1,1)-N(3))}{Cu(II)(μ(1,1)-N(3))(4)(dmf)}{Cu(II)(2)(μ(1,1)-N(3))(2)(N(3))(4)}](n)·ndmf (5), derived from a new compartmental ligand 2,6-bis[N-(2-pyridylethyl)formidoyl]-4-ethylphenol, which is the 1:2 condensation product of 4-ethyl-2,6-diformylphenol and 2-(2-aminoethyl)pyridine. The title compounds are either of the following nuclearities/topologies: dinuclear (1), dinuclear-based one-dimensional (2 and 3), tetranuclear (4), and heptanuclear-based one-dimensional (5). The bridging moieties in 1-5 are as follows: μ-phenoxo-μ(1,1)-nitrate (1), μ-phenoxo-μ-hydroxo and μ-perchlorate (2), μ-phenoxo and μ(1,3)-thiocyanate (3), μ-phenoxo-μ(1,1)-azide and μ(1,3)-azide (4), μ-phenoxo-μ-hydroxo, μ-phenoxo-μ(1,1)-azide, and μ(1,1)-azide (5). All the five compounds exhibit overall antiferromagnetic interaction. The J values in 1-4 have been determined (-135 cm(-1) for 1, -298 cm(-1) for 2, -105 cm(-1) for 3, -119.5 cm(-1) for 4). The pairwise interactions in 5 have been evaluated qualitatively to result in S(T) = 3/2 spin ground state, which has been verified by magnetization experiment. Utilizing 3,5-di-tert-butyl catechol (3,5-DTBCH(2)) as the substrate, catecholase activity of all the five complexes have been checked. While 1 and 3 are inactive, complexes 2, 4, and 5 show catecholase activity with turn over numbers 39 h(-1) (for 2), 40 h(-1) (for 4), and 48 h(-1) (for 5) in dmf and 167 h(-1) (for 2) and 215 h(-1) (for 4) in acetonitrile

  2. Ultrasonic characterization of structural ceramics

    NASA Technical Reports Server (NTRS)

    Klima, S. J.; Baaklini, G. Y.

    1986-01-01

    Ultrasonic velocity and attenuation measurements were used to characterize density and microstructure in monolithic silicon nitride and silicon carbide. Research samples of these structural ceramics exhibited a wide range of density and microstructural variations. It was shown that bulk density variations correlate with and can be estimated by velocity measurements. Variations in microstructural features such as grain size or shape and pore morphology had a minor effect on velocity. However, these features had a pronounced effect on ultrasonic attenuation. The ultrasonic results are supplemented by low-energy radiography and scanning laser acoustic microscopy.

  3. Damping characterization in large structures

    NASA Technical Reports Server (NTRS)

    Eke, Fidelis O.; Eke, Estelle M.

    1991-01-01

    This research project has as its main goal the development of methods for selecting the damping characteristics of components of a large structure or multibody system, in such a way as to produce some desired system damping characteristics. The main need for such an analytical device is in the simulation of the dynamics of multibody systems consisting, at least partially, of flexible components. The reason for this need is that all existing simulation codes for multibody systems require component-by-component characterization of complex systems, whereas requirements (including damping) often appear at the overall system level. The main goal was met in large part by the development of a method that will in fact synthesize component damping matrices from a given system damping matrix. The restrictions to the method are that the desired system damping matrix must be diagonal (which is almost always the case) and that interbody connections must be by simple hinges. In addition to the technical outcome, this project contributed positively to the educational and research infrastructure of Tuskegee University - a Historically Black Institution.

  4. Automated Characterization Of Vibrations Of A Structure

    NASA Technical Reports Server (NTRS)

    Bayard, David S.; Yam, Yeung; Mettler, Edward; Hadaegh, Fred Y.; Milman, Mark H.; Scheid, Robert E.

    1992-01-01

    Automated method of characterizing dynamical properties of large flexible structure yields estimates of modal parameters used by robust control system to stabilize structure and minimize undesired motions. Based on extraction of desired modal and control-design data from responses of structure to known vibrational excitations. Applicable to terrestrial structures where vibrations are important - aircraft, buildings, bridges, cranes, and drill strings.

  5. Structural characterization of multimetallic nanoparticles

    NASA Astrophysics Data System (ADS)

    Mukundan, Vineetha

    Bimetallic and trimetallic alloy nanoparticles have enhanced catalytic activities due to their unique structural properties. Using in situ time-resolved synchrotron based x-ray diffraction, we investigated the structural properties of nanoscale catalysts undergoing various heat treatments. Thermal treatment brings about changes in particle size, morphology, dispersion of metals on support, alloying, surface electronic properties, etc. First, the mechanisms of coalescence and grain growth in PtNiCo nanoparticles supported on planar silica on silicon were examined in detail in the temperature range 400-900°C. The sintering process in PtNiCo nanoparticles was found to be accompanied by lattice contraction and L10 chemical ordering. The mass transport involved in sintering is attributed to grain boundary diffusion and its corresponding activation energy is estimated from the data analysis. Nanoscale alloying and phase transformations in physical mixtures of Pd and Cu ultrafine nanoparticles were also investigated in real time with in situ synchrotron based x-ray diffraction complemented by ex situ high-resolution transmission electron microscopy. PdCu nanoparticles are interesting because they are found to be more efficient as catalysts in ethanol oxidation reaction (EOR) than monometallic Pd catalysts. The combination of metal support interaction and reactive/non-reactive environment was found to determine the thermal evolution and ultimate structure of this binary system. The composition of the as prepared Pd:Cu mixture in this study was 34% Pd and 66% Cu. At 300°C, the nanoparticles supported on silica and carbon black intermix to form a chemically ordered CsCl-type (B2) alloy phase. The B2 phase transforms into a disordered fcc alloy at higher temperature (>450°C). The alloy nanoparticles supported on silica and carbon black are homogeneous in volume, but evidence was found of Pd surface enrichment. In sharp contrast, when supported on alumina, the two metals

  6. Health Monitoring for Airframe Structural Characterization

    NASA Technical Reports Server (NTRS)

    Munns, Thomas E.; Kent, Renee M.; Bartolini, Antony; Gause, Charles B.; Borinski, Jason W.; Dietz, Jason; Elster, Jennifer L.; Boyd, Clark; Vicari, Larry; Ray, Asok; Cooper, E. G. (Technical Monitor)

    2002-01-01

    This study established requirements for structural health monitoring systems, identified and characterized a prototype structural sensor system, developed sensor interpretation algorithms, and demonstrated the sensor systems on operationally realistic test articles. Fiber-optic corrosion sensors (i.e., moisture and metal ion sensors) and low-cycle fatigue sensors (i.e., strain and acoustic emission sensors) were evaluated to validate their suitability for monitoring aging degradation; characterize the sensor performance in aircraft environments; and demonstrate placement processes and multiplexing schemes. In addition, a unique micromachined multimeasure and sensor concept was developed and demonstrated. The results show that structural degradation of aircraft materials could be effectively detected and characterized using available and emerging sensors. A key component of the structural health monitoring capability is the ability to interpret the information provided by sensor system in order to characterize the structural condition. Novel deterministic and stochastic fatigue damage development and growth models were developed for this program. These models enable real time characterization and assessment of structural fatigue damage.

  7. Experiments In Characterizing Vibrations Of A Structure

    NASA Technical Reports Server (NTRS)

    Yam, Yeung; Hadaegh, Fred Y.; Bayard, David S.

    1993-01-01

    Report discusses experiments conducted to test methods of identification of vibrational and coupled rotational/vibrational modes of flexible structure. Report one in series that chronicle development of integrated system of methods, sensors, actuators, analog and digital signal-processing equipment, and algorithms to suppress vibrations in large, flexible structure even when dynamics of structure partly unknown and/or changing. Two prior articles describing aspects of research, "Autonomous Frequency-Domain Indentification" (NPO-18099), and "Automated Characterization Of Vibrations Of A Structure" (NPO-18141).

  8. Structural characterization of unusually stable polycyclic ozonides

    NASA Astrophysics Data System (ADS)

    Cusati, R. C.; Pereira, U. A.; Barbosa, L. C. A.; Maltha, C. R. A.; Carneiro, José W. M.; Corrêa, R. S.; Doriguetto, A. C.

    2015-02-01

    The single crystal structure of seven tri- and tetracyclic ozonides derived from 8-oxabicycle[3.2.1]oct-6-en-3-ones have been characterized by X-ray diffraction method. Five ozonides (4, 5, 6, 7 and 8) crystallize in the monoclinic crystal system with P21/c space group. Compound 3 crystallize in the unusual centrosymmetric space group R 3 bar m, which represents ∼0.04% of the total number of structures know. The supramolecular structure of 3 forms infinite channels in a hexagram fashion, resulting in a honeycomb-like structure. Semi-empirical (PM6) and density functional theory methods (DFT) with the B3LYP functional and the 6-31G(d) basis set were used to optimize the geometries and compute structural parameters (bond lengths, angles and dihedral angles) that could be compared to the refined crystal structure. The theoretical results show good agreements with the experimental structure.

  9. Electrochemical Characterization of Semiconductor Materials and Structures

    NASA Technical Reports Server (NTRS)

    1997-01-01

    The objective of this investigation was to demonstrate the applicability of electrochemical techniques for characterization of complex device structures based on InP and GaAs, Ge, InGaAs, InSb, InAs and InSb, including: (1) accurate EC-V net majority carrier concentration depth profiling, and (2) surface and bulk structural and electrical type defect densities. Our motivation for this R&D effort was as follows: Advanced space solar cells and thermophotovoltaic (TPV) cells are fabricated using a large variety of III-V materials based on InP and GaAs for solar cells and low bandgap materials such as Ge, InGaAs, InAs and InSb for TPV applications. At the present time for complex device structures using these materials, however, there is no simple way to assess the quality of these structures prior to device fabrication. Therefore, process optimization is a very time consuming and a costly endeavor. Completion of this R&D effort would have had unquestionable benefits for space solar cell and TPV cells, since electrochemical characterization of the above cell structures, if properly designed can provide many useful structural and electrical material information virtually at any depth inside various layers and at the interfaces. This, could have been applied for step-by-step process optimization, which could have been used for fabrication of new generation high efficiency, low cost space PV and TPV cells. The four projects were as follows: (1) Electrochemical characterization of Germanium Substrates and Structures for TPV and other Device applications; (2) Electrochemical characterization of InP and GaAs based structures grown on InP, GaAs, and Si of Ge substrates for space solar cell applications; (3) Electrochemical characterization of InGaAs based structures grown on Ge Substrates,using InP as a buffer layer for TPV applications; (4) Electrochemical characterization of InSb and InAs bases structures for TPV applications.

  10. Electrochemical characterization of InP structures

    NASA Technical Reports Server (NTRS)

    Faur, Maria; Faur, Mircea; Vargas-Aburto, Carlos; Wilt, David M.; Goradia, Manju

    1992-01-01

    Electrochemical (EC) techniques represent a simple and yet accurate method to characterize InP and related materials structures. With EC techniques, uncertainties in the measurements arising from factors such as surface effects, the composition and thickness of a front dead layer, the contacts, etc., can be significantly reduced when both a suitable electrolyte is used and the measuring conditions are carefully selected. In this work, the use of photoelectrochemical techniques with InP structures is reported. The work focuses on both the characterization and the optimization of structures grown by thermal diffusion and by epitaxial methods. Characterization of the structures is done by studying the variation in the density of surface states, number of defects, and net majority carrier concentration as a function of material removed. A step-by-step optimization process of n(sup +)p and p(sup+)n InP structures is also described. This involves the passivation and subsequent removal of damaged layers in order to extract the performance parameters of solar cells fabricated with these structures.

  11. Electrochemical Characterization of Semiconductor Materials and Structures

    NASA Technical Reports Server (NTRS)

    1997-01-01

    For a period covering October 1, 1995 through August 12, 1996, the research group at CSU has conducted theoretical and experimental research on "Electrochemical Characterization of Semiconductor Materials and Structures. " The objective of this investigation was to demonstrate the applicability of electrochemical techniques for characterization of complex device structures based on InP and GaAs, Ge, InGaAs, InSb, InAs and InSb, including: (1) accurate EC-V net majority carrier concentration depth profiling, and (2) surface and bulk structural and electrical type defect densities. Our motivation for this R&D effort was as follows: "Advanced space solar cells and ThermoPhotoVoltaic (TPV) cells are fabricated using a large variety of III-V materials based on InP and GaAs for solar cells and low bandgap materials such as Ge, InGaAs, InAs and InSb for TPV applications. At the present time for complex device structures using these materials, however, there is no simple way to assess the quality of these structures prior to device fabrication. Therefore, process optimization is a very time consuming and a costly endeavor". Completion of this R&D effort would have had unquestionable benefits for space solar cell and TPV cells, since electrochemical characterization of the above cell structures, if properly designed can provide many useful structural and electrical material information virtually at any depth inside various layers and at the interfaces. This, could have been applied for step-by-step process optimization, which could have been used for fabrication of new generation high efficiency, low cost space PV and TPV cells.

  12. Structure characterization of the 26S proteasome

    PubMed Central

    Kim, Ho Min; Yu, Yadong; Cheng, Yifan

    2010-01-01

    In all eukaryotic cells, 26S proteasome plays an essential role in the process of ATP-dependent protein degradation. In this review, we focus on structure characterization of the 26S proteasome. Although the progress towards a high-resolution structure of the 26S proteasome has been slow, the recently solved structures of various proteasomal subcomplexes have greatly enhanced our understanding of this large machinery. In addition to having an ATP-dependent proteolytic function, the 26S proteasome is also involved in many non-proteolytic cellular activities, which are often mediated by subunits in its 19S regulatory complex. Thus, we include a detailed discussion of the structures of 19S subunits, including proteasomal ATPases, ubiquitin receptors, deubiquitinating enzymes and subunits that contain PCI domain. PMID:20800708

  13. Structural Characterization of Sm(III)(EDTMP).

    PubMed

    Yang, Y; Pushie, M J; Cooper, D M L; Doschak, M R

    2015-11-01

    Samarium-153 ethylenediamine-N,N,N',N'-tetrakis(methylenephosphonic acid) ((153)Sm-EDTMP, or samarium lexidronam), also known by its registered trademark name Quadramet, is an approved therapeutic radiopharmaceutical used in the palliative treatment of painful bone metastases. Typically, patients with prostate, breast, or lung cancer are most likely to go on to require bone pain palliation treatment due to bone metastases. Sm(EDTMP) is a bone-seeking drug which accumulates on rapidly growing bone, thereby delivering a highly region-specific dose of radiation, chiefly through β particle emission. Even with its widespread clinical use, the structure of Sm(EDTMP) has not yet been characterized at atomic resolution, despite attempts to crystallize the complex. Herein, we prepared a 1:1 complex of the cold (stable isotope) of Sm(EDTMP) under alkaline conditions and then isolated and characterized the complex using conventional spectroscopic techniques, as well as with extended X-ray absorption fine structure (EXAFS) spectroscopy and density functional structure calculations, using natural abundance Sm. We present the atomic resolution structure of [Sm(III)(EDTMP)-8H](5-) for the first time, supported by the EXAFS data and complementary spectroscopic techniques, which demonstrate that the samarium coordination environment in solution is in agreement with the structure that has long been conjectured.

  14. Synthesis and structural characterization of CZTS nanoparticles

    SciTech Connect

    Lydia, R.; Reddy, P. Sreedhara

    2013-06-03

    The CZTS nanoparticles were successfully synthesized by Chemical co-precipitation method with different pH values in the range of 6 to 8. The synthesized nanoparticles were characterized by X-ray diffraction, scanning electron microscopy and energy dispersive spectroscopy. XRD studies revealed that the CZTS nanoparticles exhibited Kesterite Structure with preferential orientation along the (112) direction. Sample at pH value of 7 reached the nearly stoichiometric ratio.

  15. Diffractaic acid: Crystalline structure and physicochemical characterization

    NASA Astrophysics Data System (ADS)

    de Castro Fonseca, Jéssica; de Oliveira, Yara Santiago; Bezerra, Beatriz P.; Ellena, Javier; Honda, Neli Kika; Silva, Camilla V. N. S.; da Silva Santos, Noemia Pereira; Santos-Magalhães, Nereide Stela; Ayala, Alejandro Pedro

    2016-08-01

    Diffractaic acid (DA) is a secondary metabolite of lichens that belongs to the chemical class of depsides, and some relevant pharmacological properties are associated with this natural product, such as antioxidant, antiulcerogenic and gastroprotective effects. Considering the relevant biological activities and taking into account that the activities are intrinsically related to the structure, the main goal of this study was to elucidate the structure of diffractaic acid by single crystal X-ray diffraction as well to characterize its physicochemical properties by powder X-ray diffraction, thermal analysis and vibrational spectroscopy. It was observed that DA belongs to the monoclinic crystal system, crystallizing in the space group P21/c with the following cell parameters: a = 18.535(7) Å, b = 4.0439(18) Å, c = 23.964(6) Å, β = 91.55(3)°. The crystal packing is characterized by difractaic acid dimers, which are reflected in the vibrational spectrum. These observations were supported by quantum mechanical calculations.

  16. Thermomechanical characterization and modeling for TSV structures

    NASA Astrophysics Data System (ADS)

    Jiang, Tengfei; Ryu, Suk-Kyu; Zhao, Qiu; Im, Jay; Ho, Paul S.; Huang, Rui

    2014-06-01

    Continual scaling of devices and on-chip wiring has brought significant challenges for materials and processes beyond the 32-nm technology node in microelectronics. Recently, three-dimensional (3-D) integration with through-silicon vias (TSVs) has emerged as an effective solution to meet the future technology requirements. Among others, thermo-mechanical reliability is a key concern for the development of TSV structures used in die stacking as 3-D interconnects. This paper presents experimental measurements of the thermal stresses in TSV structures and analyses of interfacial reliability. The micro-Raman measurements were made to characterize the local distribution of the near-surface stresses in Si around TSVs. On the other hand, the precision wafer curvature technique was employed to measure the average stress and deformation in the TSV structures subject to thermal cycling. To understand the elastic and plastic behavior of TSVs, the microstructural evolution of the Cu vias was analyzed using focused ion beam (FIB) and electron backscattering diffraction (EBSD) techniques. Furthermore, the impact of thermal stresses on interfacial reliability of TSV structures was investigated by a shear-lag cohesive zone model that predicts the critical temperatures and critical via diameters.

  17. Thermomechanical characterization and modeling for TSV structures

    SciTech Connect

    Jiang, Tengfei; Zhao, Qiu; Im, Jay; Ho, Paul S.; Ryu, Suk-Kyu; Huang, Rui

    2014-06-19

    Continual scaling of devices and on-chip wiring has brought significant challenges for materials and processes beyond the 32-nm technology node in microelectronics. Recently, three-dimensional (3-D) integration with through-silicon vias (TSVs) has emerged as an effective solution to meet the future technology requirements. Among others, thermo-mechanical reliability is a key concern for the development of TSV structures used in die stacking as 3-D interconnects. This paper presents experimental measurements of the thermal stresses in TSV structures and analyses of interfacial reliability. The micro-Raman measurements were made to characterize the local distribution of the near-surface stresses in Si around TSVs. On the other hand, the precision wafer curvature technique was employed to measure the average stress and deformation in the TSV structures subject to thermal cycling. To understand the elastic and plastic behavior of TSVs, the microstructural evolution of the Cu vias was analyzed using focused ion beam (FIB) and electron backscattering diffraction (EBSD) techniques. Furthermore, the impact of thermal stresses on interfacial reliability of TSV structures was investigated by a shear-lag cohesive zone model that predicts the critical temperatures and critical via diameters.

  18. Structural characterization of the human proteome.

    PubMed

    Müller, Arne; MacCallum, Robert M; Sternberg, Michael J E

    2002-11-01

    This paper reports an analysis of the encoded proteins (the proteome) of the genomes of human, fly, worm, yeast, and representatives of bacteria and archaea in terms of the three-dimensional structures of their globular domains together with a general sequence-based study. We show that 39% of the human proteome can be assigned to known structures. We estimate that for 77% of the proteome, there is some functional annotation, but only 26% of the proteome can be assigned to standard sequence motifs that characterize function. Of the human protein sequences, 13% are transmembrane proteins, but only 3% of the residues in the proteome form membrane-spanning regions. There are substantial differences in the composition of globular domains of transmembrane proteins between the proteomes we have analyzed. Commonly occurring structural superfamilies are identified within the proteome. The frequencies of these superfamilies enable us to estimate that 98% of the human proteome evolved by domain duplication, with four of the 10 most duplicated superfamilies specific for multicellular organisms. The zinc-finger superfamily is massively duplicated in human compared to fly and worm, and occurrence of domains in repeats is more common in metazoa than in single cellular organisms. Structural superfamilies over- and underrepresented in human disease genes have been identified. Data and results can be downloaded and analyzed via web-based applications at http://www.sbg.bio.ic.ac.uk.

  19. Structural characterization of rotor blades through photogrammetry

    NASA Astrophysics Data System (ADS)

    Bernardini, Giovanni; Serafini, Jacopo; Enei, Claudio; Mattioni, Luca; Ficuciello, Corrado; Vezzari, Valerio

    2016-06-01

    This paper deals with the use of photogrammetry for the experimental identification of structural and inertial properties of helicopter rotor blades4. The identification procedure is based upon theoretical/numerical algorithms for the evaluation of mass and flexural stiffness distributions which are an extension of those proposed in the past by Larsen, whereas the torsional properties (stiffness and shear center position) are determined through the Euler-Bernoulli beam theory. The identification algorithms require the knowledge of the blade displacement field produced by known steady loads. These data are experimentally obtained through photogrammetric detection technique, which allows the identification of 3D coordinates of labeled points (markers) on the structure through the correlation of 2D digital photos. Indeed, the displacement field is simply evaluated by comparing the markers positions on the loaded configuration with those on the reference one. The proposed identification procedure, numerically and experimentally validated in the past by the authors, has been here applied to the structural characterization of two main rotor blades, designed for ultra-light helicopters. Strain gauges measurements have been used to assess the accuracy of the identified properties through natural frequencies comparison as well as to evaluate the blades damping characteristics.

  20. Structural characterization of rotor blades through photogrammetry

    NASA Astrophysics Data System (ADS)

    Bernardini, Giovanni; Serafini, Jacopo; Enei, Claudio; Mattioni, Luca; Ficuciello, Corrado; Vezzari, Valerio

    2016-06-01

    This paper deals with the use of photogrammetry for the experimental identification of structural and inertial properties of helicopter rotor blades4. The identification procedure is based upon theoretical/numerical algorithms for the evaluation of mass and flexural stiffness distributions which are an extension of those proposed in the past by Larsen, whereas the torsional properties (stiffness and shear center position) are determined through the Euler–Bernoulli beam theory. The identification algorithms require the knowledge of the blade displacement field produced by known steady loads. These data are experimentally obtained through photogrammetric detection technique, which allows the identification of 3D coordinates of labeled points (markers) on the structure through the correlation of 2D digital photos. Indeed, the displacement field is simply evaluated by comparing the markers positions on the loaded configuration with those on the reference one. The proposed identification procedure, numerically and experimentally validated in the past by the authors, has been here applied to the structural characterization of two main rotor blades, designed for ultra-light helicopters. Strain gauges measurements have been used to assess the accuracy of the identified properties through natural frequencies comparison as well as to evaluate the blades damping characteristics.

  1. Structural characterization of copolymer embedded magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Nedelcu, G. G.; Nastro, A.; Filippelli, L.; Cazacu, M.; Iacob, M.; Rossi, C. Oliviero; Popa, A.; Toloman, D.; Dobromir, M.; Iacomi, F.

    2015-10-01

    Small magnetic nanoparticles (Fe3O4) were synthesized by co-precipitation and coated by emulsion polymerization with poly(methyl methacrylate-co-acrylic acid) (PMMA-co-AAc) to create surface functional groups that can attach drug molecules and other biomolecules. The coated and uncoated magnetite nanoparticles were stored for two years in normal closed ships and than characterized by Fourier transform infrared spectroscopy, X-ray diffraction, transmission electron microscopy, vibrating sample magnetometry, and electron paramagnetic resonance spectroscopy. The solid phase transformation of magnetite to maghemite, as well as an increase in particle size were evidenced for the uncoated nanoparticles. The coated nanoparticles preserved their magnetite structure and magnetic properties. The influences of monomers and surfactant layers on interactions between the magnetic nanoparticles evidenced that the thickness of the polymer has a significant effect on magnetic properties.

  2. Structural characterization of submerged granular packings

    NASA Astrophysics Data System (ADS)

    Jakšić, Z. M.; Šćepanović, J. R.; Lončarević, I.; Budinski-Petković, Lj.; Vrhovac, S. B.; Belić, A.

    2014-12-01

    We consider the impact of the effective gravitational acceleration on microstructural properties of granular packings through experimental studies of spherical granular materials saturated within fluids of varying density. We characterize the local organization of spheres in terms of contact connectivity, distribution of the Delaunay free volumes, and the shape factor (parameter of nonsphericity) of the Voronoï polygons. The shape factor gives a clear physical picture of the competition between less and more ordered domains of particles in experimentally obtained packings. As the effective gravity increases, the probability distribution of the shape factor becomes narrower and more localized around the lowest values of the shape factor corresponding to regular hexagon. It is found that curves of the pore distributions are asymmetric with a long tail on the right-hand side, which progressively reduces while the effective gravity gets stronger for lower densities of interstitial fluid. We show that the distribution of local areas (Voronoï cells) broadens with decreasing value of the effective gravity due to the formation of lose structures such as large pores and chainlike structures (arches or bridges). Our results should be particularly helpful in testing the newly developed simulation techniques involving liquid-related forces associated with immersed granular particles.

  3. Structural Characterization of Bimetallic Nanocrystal Electrocatalysts

    SciTech Connect

    Cullen, David A

    2016-01-01

    Late transition metal nanocrystals find applications in heterogeneous catalysis such as plasmon-enhanced catalysis and as electrode materials for fuel cells, a zero-emission and sustainable energy technology. Their commercial viability for automotive transportation has steadily increased in recent years, almost exclusively due to the discovery of more efficient bimetallic nanocatalysts for the oxygen reduction reaction (ORR) at the cathode. Despite improvements to catalyst design, achieving high activity while maintaining durability is essential to further enhance their performance for this and other important applications in catalysis. Electronic effects arising from the generation of metal-metal interfaces, from plasmonic metals, and from lattice distortions, can vastly improve sorption properties at catalytic surfaces, while increasing durability.[1] Multimetallic lattice-strained nanoparticles are thus an interesting opportunity for fundamental research.[2,3] A colloidal synthesis approach is demonstrated to produce AuPd alloy and Pd@Au core-shell nanoicosahedra as catalysts for electro-oxidations. The nanoparticles are characterized using aberration-corrected scanning transmission electron microscopy (ac-STEM) and large solid angle energy dispersive X-ray spectroscopy (EDS) on an FEI Talos 4-detector STEM/EDS system. Figure 1 shows bright-field (BF) and high-angle annular dark-field (HAADF) ac-STEM images of the alloy and core-shell nanoicosahedra together with EDS line-scans and elemental maps. These structures are unique in that the presence of twin boundaries, alloying, and core-shell morphology could create highly strained surfaces and interfaces. The shell thickness of the core-shell structures observed in HAADF-STEM images is tuned by adjusting the ratio between metal precursors (Figure 2a-f) to produce shells ranging from a few to several monolayers. Specific activity was measured in ethanol electro-oxidation to examine the effect of shell thickness on

  4. Structural Characterization of Crystalline Ice Nanoclusters

    NASA Technical Reports Server (NTRS)

    Blake, David

    2000-01-01

    Water ice nanoclusters are useful analogs for studying a variety of processes that occur within icy grains in the extraterrestrial environment. The surface of ice nanoclusters prepared in the laboratory is similar to the surface of interstellar ice grains. In cold molecular clouds, the silicate cores of interstellar grains are typically approx. 100 nm in diameter and have a coating of impure amorphous water ice. Depositional, thermal and radiolytic processes leave the surface and subsurface molecules in a disordered state. In this state, structural defects become mobile and reactions of trapped gases and small molecules can occur. The large surface area of nanocluster deposits relative to their bulk allows for routine observation of such surface-mediated processes. Furthermore, the disordered surface and subsurface layers in nanocluster deposits mimic the structure of amorphous ice rinds found on interstellar dust grains. Transmission Electron Microscopy (TEM has been used tn characterize the crystallinity, growth mechanism, and size distribution of nanoclusters formed from a mixture of water vapor with an inert carrier gas that has been rapidly cooled to 77K. E M imaging reveals a Gaussian size distribution around a modal diameter that increases from approx. 15 to 30 nm as the percentage of water vapor within the mixture increases from 0.5 to 2.007, respectively . TEM bright and dark field imaging also reveals the crystalline nature of the clusters. h4any of the clusters show a mosaic structure in which crystalline domains originate at the center Other images show mirror planes that are separated by approx. 10 nm. Electron diffraction patterns of these clusters show that the clusters are composed of cubic ice with only a small hexagonal component. Further, the crystalline domain size is approximately the same as the modal diameter suggesting that the clusters are single crystals.

  5. Structural characterization of allomelanin from black oat.

    PubMed

    Varga, Mónika; Berkesi, Ottó; Darula, Zsuzsanna; May, Nóra Veronika; Palágyi, András

    2016-10-01

    The brown to black coloration found in plants is due to the melanins, which have been relatively poorly investigated among the plant pigments. The aim of this work was to study the dark pigment extracted from the black oat hull with respect to composition and structure. Ultraviolet-visible (UV-Vis) spectroscopy, electron paramagnetic resonance (EPR) spectroscopy, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) and Fourier transform infrared (FT-IR) spectroscopy were applied for the characterization of the pigment. UV-Vis spectroscopy revealed that the extracted material displays a broadband, structureless absorption profile a common feature of melanins. MALDI-TOF MS measurements demonstrated that oat melanin is a homopolymer built up from p-coumaric acid and consists mainly of low molecular weight (527-1499 Da) oligomers of 3-9 monomer units. The tetramer oligomer proved to be dominant. The results of the FT-IR analysis indicated that oat melanin is a fully conjugated aromatic system containing tetrasubstituted aromatic rings linked by CC coupling. The in vitro preparation of melanin from p-coumaric acid by horseradish peroxidase was performed for comparison. The resulting polymer consisted of oligomers of 4-9 monomer units similarly to those in oat melanin. However, the building blocks proved to be connected to each other via COC linkages in contrast with the CC linkages in oat melanin. PMID:27427433

  6. Structural characterization of human Uch37

    SciTech Connect

    Burgie, E. Sethe; Bingman, Craig A.; Soni, Ameet B.; Phillips, Jr., George N.

    2012-06-28

    Uch37 is a deubiquitylating enzyme (DUB) that is functionally linked with multiple protein complexes and signal transduction pathways. Uch37 associates with the 26S proteasome through Rpn13 where it serves to remove distal ubiquitin moeities from polyubiquitylated proteins. Uch37's proteasome associated activity was shown to liberate proteins from destruction. However, Uch37 may also specifically facilitate the destruction of inducible nitric oxide synthase and I{kappa}B-{alpha} at the proteasome. Wicks et al. established Uch37's potential to modulate the transforming growth factor-{beta}(TGF-{beta}) signaling cascade, through tis interaction with SMAD7. Yao et al. demonstrated that Uch37 also associates with the Ino80 chromatin-remodeling complex (Ino80 complex), which is involved in DNA repair and transcriptional regulation. Uch37's importance in metazoan development was underscored recently as Uch37 knockouts in mice result in prenatal lethality, where mutant embryos had severe defects in brain development. Protein ubiquitylation is an ATP-dependent post-translational modification that serves to signal a wide variety of cellular processes in eukaryotes. A protein cascade, generally comprising three enzymes, functions to activate, transport and specifically transfer ubiquitin to the targeted protein, culminating in an isopeptide linkage between the {epsilon}-amino group of a target protein's lysysl residue and the ubiquitin's terminal carboxylate. Monoubiquitination plays an important role in histone regulation, endocytosis, and viral budding. Further processing of the target protein may be accomplished by ubiquitylation of the protein on a different lysine, or through the formation of polyubiquitin chains, where the best-characterized outcome is destruction of the polyubiquitin-labeled protein in the proteasome. DUBs catalyze the removal of ubiquitin from proteins. This activity serves to reverse the effects of ubiquitination, permit ubiquitin recycling, or

  7. Structure-based characterization of multiprotein complexes.

    PubMed

    Wiederstein, Markus; Gruber, Markus; Frank, Karl; Melo, Francisco; Sippl, Manfred J

    2014-07-01

    Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies. PMID:24954616

  8. SDSL-ESR-based protein structure characterization.

    PubMed

    Strancar, Janez; Kavalenka, Aleh; Urbancic, Iztok; Ljubetic, Ajasja; Hemminga, Marcus A

    2010-03-01

    As proteins are key molecules in living cells, knowledge about their structure can provide important insights and applications in science, biotechnology, and medicine. However, many protein structures are still a big challenge for existing high-resolution structure-determination methods, as can be seen in the number of protein structures published in the Protein Data Bank. This is especially the case for less-ordered, more hydrophobic and more flexible protein systems. The lack of efficient methods for structure determination calls for urgent development of a new class of biophysical techniques. This work attempts to address this problem with a novel combination of site-directed spin labelling electron spin resonance spectroscopy (SDSL-ESR) and protein structure modelling, which is coupled by restriction of the conformational spaces of the amino acid side chains. Comparison of the application to four different protein systems enables us to generalize the new method and to establish a general procedure for determination of protein structure.

  9. Structural characterization of thin film photonic crystals

    SciTech Connect

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

    2001-06-15

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

  10. Characterization of Vapor Deposited Nano Structured Membranes

    SciTech Connect

    Jankowski, A; Cherepy, N; Ferreira, J; Hayes, J

    2004-03-25

    The vapor deposition methods of planar magnetron sputtering and electron-beam evaporation are used to synthesize materials with nano structured morphological features that have ultra-high surface areas with continuous open porosity at the nano scale. These nano structured membranes are used in a variety of fuel cells to provide electrode and catalytic functions. Specifically, stand alone and composite nickel electrodes for use in thin film solid-oxide, and molten carbonate fuel cells are formed by sputter deposition and electron bean evaporation, respectively. Also, a potentially high-performance catalyst material for the direct reformation of hydrocarbon fuels at low temperatures is deposited as a nano structure by the reactive sputtering of a copper-zinc alloy using a partial pressure of oxygen at an elevated substrate temperature.

  11. Structural and biochemical characterization of DSL ribozyme.

    PubMed

    Horie, Souta; Ikawa, Yoshiya; Inoue, Tan

    2006-01-01

    We recently reported on the molecular design and synthesis of a new RNA ligase ribozyme (DSL), whose active site was selected from a sequence library consisting of 30 random nucleotides set on a defined 3D structure of a designed RNA scaffold. In this study, we report on the structural and biochemical analyses of DSL. Structural analysis indicates that the active site, which consists of the selected sequence, attaches to the folded scaffold as designed. To see whether DSL resembles known ribozymes, a biochemical assay was performed. Metal-dependent kinetic studies suggest that the ligase requires Mg2+ ions. The replacement of Mg2+ with Co(NH3)6(3+) prohibits the reaction, indicating that DSL requires innersphere coordination of Mg2+ for a ligation reaction. The results show that DSL has requirements similar to those of previously reported catalytic RNAs.

  12. Large space structures control algorithm characterization

    NASA Technical Reports Server (NTRS)

    Fogel, E.

    1983-01-01

    Feedback control algorithms are developed for sensor/actuator pairs on large space systems. These algorithms have been sized in terms of (1) floating point operation (FLOP) demands; (2) storage for variables; and (3) input/output data flow. FLOP sizing (per control cycle) was done as a function of the number of control states and the number of sensor/actuator pairs. Storage for variables and I/O sizing was done for specific structure examples.

  13. Structural characterization of carangid fish myoglobins.

    PubMed

    Hasan, Muhammad Mehedi; Watabe, Shugo; Ochiai, Yoshihiro

    2012-10-01

    The primary structures of myoglobin (Mb) from the following five carangid species were determined: yellowtail Seriola quinqueradiata, greater amberjack Seriola dumerili, yellowtail kingfish Seriola lalandi, Japanese horse mackerel Trachurus japonicus, and silver trevally Pseudocaranx dentex. The sequences were of varying composition both in the coding and in the noncoding regions, but all contained the open reading frame of 444 nucleotides encoding 147 amino acids. Amino acid sequence identities of carangid Mbs were in the range of 81-99%. The similarity of the heme pocket and associated heme-binding residues of carangid Mbs were evidence of the conservative nature of Mbs. Similar to the other teleost Mbs, carangid Mbs did not contain a D helix and had mostly conserved A and E helices as well as E-F and G-H inter-helical segments. Hydropathy profiles of carangid Mbs showed species-specific variations where silver trevally Mb exhibited generally higher hydrophobicity. Phylogenetic analysis based on the primary structures was in agreement with conventional morphological taxonomy, establishing close proximity of carangid Mbs with those of cichlid and scombroid, the other members of the Perciformes order. PMID:22361749

  14. Structural characterization of nanowires and nanowire arrays

    NASA Astrophysics Data System (ADS)

    Becker, Catherine Rose

    Nanowires, which have diameter less than a few hundred nanometers and high aspect ratios, may have the same properties as their corresponding bulk materials, or may exhibit unique properties due to their confined dimensions and increased surface to volume ratios. They are a popular field of technological investigation in applications that depend on the transport of charge carriers, because of expectations that microcircuit miniaturization will lead to the next boom in the electronics industry. In this work, the high spatial resolution afforded by transmission electron microscopy (TEM) is used to study nanowires formed by electrochemical deposition into porous alumina templates. The goal is to determine the effect of the synthesis and subsequent processing on the microstructure and crystallinity of the wires. A thorough understanding of the microstructural features of a material is vital for optimizing its performance in a desired application. Two material systems were studied in this work. The first is bismuth telluride (Bi 2Te3), which is used in thermoelectric applications. The second is metallic copper, the electrochemical deposition of which is of interest for interconnects in semiconductor devices. The first part of this work utilized TEM to obtain a thorough characterization of the microstructural features of individual Bi2Te3 nanowires following release from the templates. As deposited, the nanowires are fine grained and exhibit significant lattice strain. Annealing increases the grain size and dislocations are created to accommodate the lattice strain. The degree of these microstructural changes depends on the thermal treatment. However, no differences were seen in the nanowire microstructure as a function of the synthetic parameters. The second part of this work utilized a modified dark field TEM technique in order to obtain a spatially resolved, semi-quantitative understanding of the evolution of preferred orientation as a function of the electrochemical

  15. C- V characterization of MOS capacitors in SOI structures

    NASA Astrophysics Data System (ADS)

    Rustagi, S. C.; Mohsen, Z. O.; Chandra, S.; Chand, A.

    1996-06-01

    The capacitance-voltage characterization of a MOS structure in the SOI film has been carried out and the results have been interpreted with the help of a numerical solution to the one-dimensional Laplace-Poisson's equation. Various parameters characterizing the SOI MOS structures have been extracted. It has been shown that the C- V data on a simple three-terminal SOI MOS capacitor structure can yield all the information such as the thickness of the gate oxide, buried-oxide as well as the SOI film, along with the doping density in the film and the substrate.

  16. Characterization of fluid transport in microscale structures

    SciTech Connect

    Paul, P.H.

    1998-01-01

    A new tool for imaging both scalar transport and velocity fields in liquid flows through microscale structures is described. The technique employs an ultraviolet laser pulse to write a pattern into the flow by uncaging a fluorescent dye. This is followed, at selected time delays, by flood illumination with a pulse of visible light which excites the uncaged dye. The resulting fluorescence image collected onto a sensitive CCD camera. The instrument is designed as an oil immersion microscope to minimize the beam steering effects. The caged fluorescent dye is seeded in trace quantities throughout the active fluid, thus images with high contrast and minimal distortion due to any molecular diffusion history can be obtained at any point within the microchannel by selectivity activating the dye in the immediate region of interest. The author reports images of pressure- and electrokinetically-driven steady flow within round cross section capillaries having micron scale inner diameters. The author also demonstrates the ability to recover the velocity profile from a time sequence of these scalar images by direct inversion of the conserved scalar advection-convection equation.

  17. Structural characterization of MAPLE deposited lipase biofilm

    NASA Astrophysics Data System (ADS)

    Aronne, Antonio; Ausanio, Giovanni; Bloisi, Francesco; Calabria, Raffaela; Califano, Valeria; Fanelli, Esther; Massoli, Patrizio; Vicari, Luciano R. M.

    2014-11-01

    Lipases (triacylglycerol ester hydrolases) are enzymes used in several industrial applications. Enzymes immobilization can be used to address key issues limiting widespread application at industrial level. Immobilization efficiency is related to the ability to preserve the native conformation of the enzyme. MAPLE (Matrix Assisted Pulsed Laser Evaporation) technique, a laser deposition procedure for treating organic/polymeric/biomaterials, was applied for the deposition of lipase enzyme in an ice matrix, using near infrared laser radiation. Microscopy analysis showed that the deposition occurred in micrometric and submicrometric clusters with a wide size distribution. AFM imaging showed that inter-cluster regions are uniformly covered with smaller aggregates of nanometric size. Fourier transform infrared spectroscopy was used for both recognizing the deposited material and analyzing its secondary structure. Results showed that the protein underwent reversible self-association during the deposition process. Actually, preliminary tests of MAPLE deposited lipase used for soybean oil transesterification with isopropyl alcohol followed by gas chromatography-mass spectrometry gave results consistent with undamaged deposition of lipase.

  18. Carbon nano structures: Production and characterization

    NASA Astrophysics Data System (ADS)

    Beig Agha, Rosa

    L'objectif de ce memoire est de preparer et de caracteriser des nanostructures de carbone (CNS -- Carbon Nanostructures, en licence a l'Institut de recherche sur l'hydrogene, Quebec, Canada), un carbone avec un plus grand degre de graphitisation et une meilleure porosite. Le Chapitre 1 est une description generale des PEMFCs (PEMFC -- Polymer Electrolyte Membrane Fuel Cell) et plus particulierement des CNS comme support de catalyseurs, leur synthese et purification. Le Chapitre 2 decrit plus en details la methode de synthese et la purification des CNS, la theorie de formation des nanostructures et les differentes techniques de caracterisation que nous avons utilises telles que la diffraction aux rayons-X (XRD -- X-ray diffraction), la microscopie electronique a transmission (TEM -- transmission electron microscope ), la spectroscopie Raman, les isothermes d'adsorption d'azote a 77 K (analyse BET, t-plot, DFT), l'intrusion au mercure, et l'analyse thermogravimetrique (TGA -- thermogravimetric analysis). Le Chapitre 3 presente les resultats obtenus a chaque etape de la synthese des CNS et avec des echantillons produits a l'aide d'un broyeur de type SPEXRTM (SPEX/CertiPrep 8000D) et d'un broyeur de type planetaire (Fritsch Pulverisette 5). La difference essentielle entre ces deux types de broyeur est la facon avec laquelle les materiaux sont broyes. Le broyeur de type SPEX secoue le creuset contenant les materiaux et des billes d'acier selon 3 axes produisant ainsi des impacts de tres grande energie. Le broyeur planetaire quant a lui fait tourner et deplace le creuset contenant les materiaux et des billes d'acier selon 2 axes (plan). Les materiaux sont donc broyes differemment et l'objectif est de voir si les CNS produits ont les memes structures et proprietes. Lors de nos travaux nous avons ete confrontes a un probleme majeur. Nous n'arrivions pas a reproduire les CNS dont la methode de synthese a originellement ete developpee dans les laboratoires de l'Institut de

  19. Characterization and Prediction of Protein Flexibility Based on Structural Alphabets

    PubMed Central

    Liu, Bin

    2016-01-01

    Motivation. To assist efforts in determining and exploring the functional properties of proteins, it is desirable to characterize and predict protein flexibilities. Results. In this study, the conformational entropy is used as an indicator of the protein flexibility. We first explore whether the conformational change can capture the protein flexibility. The well-defined decoy structures are converted into one-dimensional series of letters from a structural alphabet. Four different structure alphabets, including the secondary structure in 3-class and 8-class, the PB structure alphabet (16-letter), and the DW structure alphabet (28-letter), are investigated. The conformational entropy is then calculated from the structure alphabet letters. Some of the proteins show high correlation between the conformation entropy and the protein flexibility. We then predict the protein flexibility from basic amino acid sequence. The local structures are predicted by the dual-layer model and the conformational entropy of the predicted class distribution is then calculated. The results show that the conformational entropy is a good indicator of the protein flexibility, but false positives remain a problem. The DW structure alphabet performs the best, which means that more subtle local structures can be captured by large number of structure alphabet letters. Overall this study provides a simple and efficient method for the characterization and prediction of the protein flexibility. PMID:27660756

  20. Characterization and Prediction of Protein Flexibility Based on Structural Alphabets

    PubMed Central

    Liu, Bin

    2016-01-01

    Motivation. To assist efforts in determining and exploring the functional properties of proteins, it is desirable to characterize and predict protein flexibilities. Results. In this study, the conformational entropy is used as an indicator of the protein flexibility. We first explore whether the conformational change can capture the protein flexibility. The well-defined decoy structures are converted into one-dimensional series of letters from a structural alphabet. Four different structure alphabets, including the secondary structure in 3-class and 8-class, the PB structure alphabet (16-letter), and the DW structure alphabet (28-letter), are investigated. The conformational entropy is then calculated from the structure alphabet letters. Some of the proteins show high correlation between the conformation entropy and the protein flexibility. We then predict the protein flexibility from basic amino acid sequence. The local structures are predicted by the dual-layer model and the conformational entropy of the predicted class distribution is then calculated. The results show that the conformational entropy is a good indicator of the protein flexibility, but false positives remain a problem. The DW structure alphabet performs the best, which means that more subtle local structures can be captured by large number of structure alphabet letters. Overall this study provides a simple and efficient method for the characterization and prediction of the protein flexibility.

  1. Characterization of degradation processes in MOS VLSI structures

    NASA Astrophysics Data System (ADS)

    Brozek, Tomasz; Jakubowski, Andrzej; Majkusiak, Bogdan

    1992-08-01

    The detailed investigations of degradation processes, their characterization and understanding of mechanisms responsible for degradation is of great technological interest, both from the fabrication point of view, and as a long-term reliability concern. Some of the effects usually need investigation in the completed MOS transistor structure (hot carrier degradation, threshold voltage, and channel mobility deterioration), but others should be studied with the special test structures so that effects can be investigated independently (electromigration, radiation effects, oxide wear-out). The paper presents a review of problems related to reliability of VLSI ICs, degradation processes, and their characterization.

  2. Complexation of Actinides in Solution: Thermodynamic Measurementsand Structural Characterization

    SciTech Connect

    Rao, L.

    2007-02-01

    This paper presents a brief introduction of the studies of actinide complexation in solution at Lawrence Berkeley National Laboratory. An integrated approach of thermodynamic measurements and structural characterization is taken to obtain fundamental understanding of actinide complexation in solution that is of importance in predicting the behavior of actinides in separation processes and environmental transport.

  3. Characterizing Thematized Derivative Schema by the Underlying Emergent Structures

    ERIC Educational Resources Information Center

    Garcia, Mercedes; Llinares, Salvador; Sanchez-Matamoros, Gloria

    2011-01-01

    This paper reports on different underlying structures of the derivative schema of three undergraduate students that were considered to be at the trans level of development of the derivative schema (action-process-object-schema). The derivative schema is characterized in terms of the students' ability to explicitly transfer the relationship between…

  4. Faculty Perceptions of Students: Structure of Faculty Characterizations, Part III.

    ERIC Educational Resources Information Center

    Davis, Junius A.

    The structure of characterizations of college students by faculty members, particularly observable and significant dimensions or trait patterns, were investigated. Student ratings by faculty members on 80 bi-polar traits, together with Scholastic Aptitude Test (SAT) scores and high school and college freshman average grades, were obtained.…

  5. Fluorescence microscopy for the characterization of structural integrity

    NASA Technical Reports Server (NTRS)

    Street, Kenneth W.; Leonhardt, Todd A.

    1991-01-01

    The absorption characteristics of light and the optical technique of fluorescence microscopy for enhancing metallographic interpretation are presented. Characterization of thermally sprayed coatings by optical microscopy suffers because of the tendency for misidentification of the microstructure produced by metallographic preparation. Gray scale, in bright field microscopy, is frequently the only means of differentiating the actual structural details of porosity, cracking, and debonding of coatings. Fluorescence microscopy is a technique that helps to distinguish the artifacts of metallographic preparation (pullout, cracking, debonding) from the microstructure of the specimen by color contrasting structural differences. Alternative instrumentation and the use of other dye systems are also discussed. The combination of epoxy vacuum infiltration with fluorescence microscopy to verify microstructural defects is an effective means to characterize advanced materials and to assess structural integrity.

  6. Analysis, structural characterization, and bioactivity of oligosaccharides derived from lactose.

    PubMed

    Moreno, F Javier; Montilla, Antonia; Villamiel, Mar; Corzo, Nieves; Olano, Agustín

    2014-06-01

    The increasing interest for prebiotic carbohydrates as functional food ingredients has promoted the synthesis of galactooligosaccharides and new lactose derivatives. This review provides a comprehensive overview on the chromatographic analysis, structural characterization, and bioactivity studies of lactose-derived oligosaccharides. The most common chromatographic techniques used for the separation and structural characterization of this type of oligosaccharides, including GC and HPLC in different operational modes, coupled to various detectors are discussed. Insights on oligosaccharide MS fragmentation patterns, using different ionization sources and mass analyzers, as well as data on structural analysis by NMR spectroscopy are also described. Finally, this article deals with the bioactive effects of galacto oligosaccharides and oligosaccharides derived from lactulose on the gastrointestinal and immune systems, which support their consumption to provide significant health benefits.

  7. Structural characterization of adsorbed helical and beta-sheet peptides

    NASA Astrophysics Data System (ADS)

    Samuel, Newton Thangadurai

    Adsorbed peptides on surfaces have potential applications in the fields of biomaterials, tissue engineering, peptide microarrays and nanobiotechnology. The surface region, the "biomolecular interface" between a material and the biological environment, plays a crucial role in these applications. As a result, characterization of adsorbed peptide structure, especially with respect to identity, concentration, spatial distribution, conformation and orientation, is important. The present research employs NEXAFS (near-edge X-ray absorption fine structure spectroscopy) and SFG (sum frequency generation spectroscopy) to provide information about the adsorbed peptide structure. Soft X-ray NEXAFS is a synchrotron-based technique which typically utilizes polarized X-rays to interrogate surfaces under ultra-high vacuum conditions. SFG is a non-linear optical technique which utilizes a combination of a fixed visible and a tunable infrared laser beams to generate a surface-vibrational spectrum of surface species. SFG has the added advantage of being able to directly analyze the surface-structure at the solid-liquid interface. The main goals of the present research were twofold: characterize the structure of adsorbed peptides (1) ex situ using soft X-ray NEXAFS, and (2) in situ using non-linear laser spectroscopy (SFG). Achieving the former goal involved first developing a comprehensive characterization of the carbon, nitrogen and oxygen k-edge NEXAFS spectra for amino acids, and then using a series of helical and beta-sheet peptides to demonstrate the sensitivity of polarization-dependent NEXAFS to secondary structure of adsorbed peptides. Characterizing the structure of adsorbed peptides in situ using SFG involved developing a model system to probe the solid-liquid interface in situ; demonstrating the ability to probe the molecular interactions and adsorbed secondary structure; following the time-dependent ordering of the adsorbed peptides; and establishing the ability to obtain

  8. Thermodynamic and structural characterization of an antibody gel

    PubMed Central

    Esue, Osigwe; Xie, Anna X.; Kamerzell, Tim J.; Patapoff, Thomas W.

    2013-01-01

    Although extensively studied, protein–protein interactions remain highly elusive and are of increasing interest in drug development. We show the assembly of a monoclonal antibody, using multivalent carboxylate ions, into highly-ordered structures. While the presence and function of similar structures in vivo are not known, the results may present a possible unexplored area of antibody structure-function relationships. Using a variety of tools (e.g., mechanical rheology, electron microscopy, isothermal calorimetry, Fourier transform infrared spectroscopy), we characterized the physical, biochemical, and thermodynamic properties of these structures and found that citrate may interact directly with the amino acid residue histidine, after which the individual protein units assemble into a filamentous network gel exhibiting high elasticity and interfilament interactions. Citrate interacts exothermically with the monoclonal antibody with an association constant that is highly dependent on solution pH and temperature. Secondary structure analysis also reveals involvement of hydrophobic and aromatic residues. PMID:23425660

  9. Characterization of Coherent Structures in the Cardiovascular System

    PubMed Central

    Shadden, Shawn C.; Taylor, Charles A.

    2013-01-01

    Recent advances in blood flow modeling have provided highly resolved, four-dimensional data of fluid mechanics in large vessels. The motivation for such modeling is often to better understand how flow conditions relate to health and disease, or to evaluate interventions that affect, or are affected by, blood flow mechanics. Vessel geometry and the pulsatile pumping of blood leads to complex flow, which is often difficult to characterize. This article discusses a computational method to better characterize blood flow kinematics. In particular, we compute Lagrangian coherent structures (LCS) to study flow in large vessels. We demonstrate that LCS can be used to characterize flow stagnation, flow separation, partitioning of fluid to downstream vasculature, and mechanisms governing stirring and mixing in vascular models. This perspective allows valuable under-standing of flow features in large vessels beyond methods traditionally considered. PMID:18437573

  10. RF and structural characterization of new SRF films

    SciTech Connect

    A.-M. Valente-Feliciano,H. L. Phillips,C. E. Reece,X. Zhao,D. Gu,R. Lukaszew,B. Xiao,K. Seo

    2009-09-01

    In the past years, energetic vacuum deposition methods have been developed in different laboratories to improve Nb/Cu technology for superconducting cavities. Jefferson Lab is pursuing energetic condensation deposition via Electron Cyclotron Resonance. As part of this study, the influence of the deposition energy on the material and RF properties of the Nb thin film is investigated. The film surface and structure analyses are conducted with various techniques like X-ray diffraction, Transmission Electron Microscopy, Auger Electron Spectroscopy and RHEED. The microwave properties of the films are characterized on 50 mm disk samples with a 7.5 GHz surface impedance characterization system. This paper presents surface impedance measurements in correlation with surface and material characterization for Nb films produced on copper substrates with different bias voltages and also highlights emerging opportunities for developing multilayer SRF films with a new deposition system.

  11. Biophysical characterization of α-synuclein and its controversial structure

    PubMed Central

    Alderson, T Reid; Markley, John L

    2014-01-01

    α-synuclein, a presynaptic protein of poorly defined function, constitutes the main component of Parkinson disease-associated Lewy bodies. Extensive biophysical investigations have provided evidence that isolated α-synuclein is an intrinsically disordered protein (IDP) in vitro. Subsequently serving as a model IDP in numerous studies, α-synuclein has aided in the development of many technologies used to characterize IDPs and arguably represents the most thoroughly analyzed IDP to date. Recent reports, however, have challenged the disordered nature of α-synuclein inside cells and have instead proposed a physiologically relevant helical tetramer. Despite α-synuclein’s rich biophysical history, a single coherent picture has not yet emerged concerning its in vivo structure, dynamics, and physiological role(s). We present herein a review of the biophysical discoveries, developments, and models pertinent to the characterization of α-synuclein’s structure and analysis of the native tetramer controversy. PMID:24634806

  12. Characterizing Protein Structure, Dynamics and Conformation in Lyophilized Solids

    PubMed Central

    Moorthy, Balakrishnan S.; Iyer, Lavanya K.; Topp, Elizabeth M.

    2015-01-01

    The long-term stability of protein therapeutics in the solid-state depends on the preservation of native structure during lyophilization and in the lyophilized powder. Proteins can reversibly or irreversibly unfold upon lyophilization, acquiring conformations susceptible to degradation during storage. Therefore, characterizing proteins in the dried state is crucial for the design of safe and efficacious formulations. This review summarizes the basic principles and applications of the analytical techniques that are commonly used to characterize protein structure, dynamics and conformation in lyophilized solids. The review also discusses the applications of recently developed mass spectrometry based methods (solid-state hydrogen deuterium exchange mass spectrometry (ssHDX-MS) and solid-state photolytic labeling mass spectrometry (ssPL-MS)) and their ability to study proteins in the solid-state at high resolution. PMID:26446463

  13. Structural characterization of bimetallic Pd-Cu vapor derived catalysts

    NASA Astrophysics Data System (ADS)

    Balerna, Antonella; Evangelisti, Claudio; Psaro, Rinaldo; Fusini, Graziano; Carpita, Adriano

    2016-05-01

    Pd-Cu bimetallic Solvated Metal Atoms (SMA) were synthesized by metal vapor synthesis technique and supported on PVPy resin. Since the catalytic activity, of the Pd-Cu system turned out to be quite high also compared to the corresponding monometallic system, a structural characterization, using electron microscopy techniques and X-ray Absorption Fine Structure spectroscopy, was performed. HRTEM analysis showed the presence of Pd particles distributed in a narrow range with a mean diameter of about 2.5 nm while the XAFS analysis, confirmed the presence of the Pd nanoparticles but revealed also some alloying with Cu atoms.

  14. Characterization of seismic hazard and structural response by energy flux

    USGS Publications Warehouse

    Afak, E.

    2000-01-01

    Seismic safety of structures depends on the structure's ability to absorb the seismic energy that is transmitted from ground to structure. One parameter that can be used to characterize seismic energy is the energy flux. Energy flux is defined as the amount of energy transmitted per unit time through a cross-section of a medium, and is equal to kinetic energy multiplied by the propagation velocity of seismic waves. The peak or the integral of energy flux can be used to characterize ground motions. By definition, energy flux automatically accounts for site amplification. Energy flux in a structure can be studied by formulating the problem as a wave propagation problem. For buildings founded on layered soil media and subjected to vertically incident plane shear waves, energy flux equations are derived by modeling the buildings as an extension of the layered soil medium, and considering each story as another layer. The propagation of energy flux in the layers is described in terms of the upgoing and downgoing energy flux in each layer, and the energy reflection and transmission coefficients at each interface. The formulation results in a pair of simple finite-difference equations for each layer, which can be solved recursively starting from the bedrock. The upgoing and downgoing energy flux in the layers allows calculation of the energy demand and energy dissipation in each layer. The methodology is applicable to linear, as well as nonlinear structures. ?? 2000 Published by Elsevier Science Ltd.

  15. Optical fiber sensors for materials and structures characterization

    NASA Technical Reports Server (NTRS)

    Lindner, D. K.; Claus, R. O.

    1991-01-01

    The final technical report on Optical Fiber Sensors for Materials and Structures Characterization, covering the period August 1990 through August 1991 is presented. Research programs in the following technical areas are described; sapphire optical fiber sensors; vibration analysis using two-mode elliptical core fibers and sensors; extrinsic Fabry-Perot interferometer development; and coatings for fluorescent-based sensor. Research progress in each of these areas was substantial, as evidenced by the technical publications which are included as appendices.

  16. Characterization of mirror-based modulation-averaging structures.

    PubMed

    Komljenovic, Tin; Babić, Dubravko; Sipus, Zvonimir

    2013-05-10

    Modulation-averaging reflectors have recently been proposed as a means for improving the link margin in self-seeded wavelength-division multiplexing in passive optical networks. In this work, we describe simple methods for determining key parameters of such structures and use them to predict their averaging efficiency. We characterize several reflectors built by arraying fiber-Bragg gratings along a segment of an optical fiber and show very good agreement between experiments and theoretical models. PMID:23669835

  17. Characterization of electronic structure of periodically strained graphene

    SciTech Connect

    Aslani, Marjan; Garner, C. Michael Nishi, Yoshio; Kumar, Suhas; Nordlund, Dennis; Pianetta, Piero

    2015-11-02

    We induced periodic biaxial tensile strain in polycrystalline graphene by wrapping it over a substrate with repeating pillar-like structures with a periodicity of 600 nm. Using Raman spectroscopy, we determined to have introduced biaxial strains in graphene in the range of 0.4% to 0.7%. Its band structure was characterized using photoemission from valance bands, shifts in the secondary electron emission, and x-ray absorption from the carbon 1s levels to the unoccupied graphene conduction bands. It was observed that relative to unstrained graphene, strained graphene had a higher work function and higher density of states in the valence and conduction bands. We measured the conductivity of the strained and unstrained graphene in response to a gate voltage and correlated the changes in their behavior to the changes in the electronic structure. From these sets of data, we propose a simple band diagram representing graphene with periodic biaxial strain.

  18. Characterization of electronic structure of periodically strained graphene

    SciTech Connect

    Aslani, Marjan; Garner, C. Michael; Kumar, Suhas; Nordlund, Dennis; Pianetta, Piero; Nishi, Yoshio

    2015-11-03

    We induced periodic biaxial tensile strain in polycrystalline graphene by wrapping it over a substrate with repeating pillar-like structures with a periodicity of 600 nm. Using Raman spectroscopy, we determined to have introduced biaxial strains in graphene in the range of 0.4% to 0.7%. Its band structure was characterized using photoemission from valance bands, shifts in the secondary electron emission, and x-ray absorption from the carbon 1s levels to the unoccupied graphene conduction bands. It was observed that relative to unstrained graphene, strained graphene had a higher work function and higher density of states in the valence and conduction bands. Furthermore, we measured the conductivity of the strained and unstrained graphene in response to a gate voltage and correlated the changes in their behavior to the changes in the electronic structure. From these sets of data, we propose a simple band diagram representing graphene with periodic biaxial strain.

  19. Structural Characterization of Arabidopsis Leaf Arabinogalactan Polysaccharides1[W

    PubMed Central

    Tryfona, Theodora; Liang, Hui-Chung; Kotake, Toshihisa; Tsumuraya, Yoichi; Stephens, Elaine; Dupree, Paul

    2012-01-01

    Proteins decorated with arabinogalactan (AG) have important roles in cell wall structure and plant development, yet the structure and biosynthesis of this polysaccharide are poorly understood. To facilitate the analysis of biosynthetic mutants, water-extractable arabinogalactan proteins (AGPs) were isolated from the leaves of Arabidopsis (Arabidopsis thaliana) plants and the structure of the AG carbohydrate component was studied. Enzymes able to hydrolyze specifically AG were utilized to release AG oligosaccharides. The released oligosaccharides were characterized by high-energy matrix-assisted laser desorption ionization-collision-induced dissociation mass spectrometry and polysaccharide analysis by carbohydrate gel electrophoresis. The Arabidopsis AG is composed of a β-(1→3)-galactan backbone with β-(1→6)-d-galactan side chains. The β-(1→6)-galactan side chains vary in length from one to over 20 galactosyl residues, and they are partly substituted with single α-(1→3)-l-arabinofuranosyl residues. Additionally, a substantial proportion of the β-(1→6)-galactan side chain oligosaccharides are substituted at the nonreducing termini with single 4-O-methyl-glucuronosyl residues via β-(1→6)-linkages. The β-(1→6)-galactan side chains are occasionally substituted with α-l-fucosyl. In the fucose-deficient murus1 mutant, AGPs lack these fucose modifications. This work demonstrates that Arabidopsis mutants in AGP structure can be identified and characterized. The detailed structural elucidation of the AG polysaccharides from the leaves of Arabidopsis is essential for insights into the structure-function relationships of these molecules and will assist studies on their biosynthesis. PMID:22891237

  20. Characterization of photonic amorphous structures with different characteristic lengths

    NASA Astrophysics Data System (ADS)

    Wen, Cheng-Chi; Hung, Yu-Chueh

    2016-04-01

    Photonic amorphous structure (PAS) has attracted increasing research attention due to their interesting characteristics, such as noniridescent structural colors and isotropic photonic band gap. In this work, we present PAS with different characteristic lengths and analyze their structural and topological properties. First, a Fourier spectral method was used to solve Cahn-Hilliard equation and generate a spinodal binary phase structure. By changing the time of the evolution of phase field, mobility, and standard deviation, the characteristic length of amorphous structures can be adjusted. We present the numerical analysis based on finite-difference time-domain (FDTD) method to characterize the density of state (DOS) of PAS based on different time of the evolution of phase field. The corresponding spatial Fourier spectrum of PAS is calculated to examine the characteristic length, and the photonic band gap properties will be discussed in association with the characteristic length. These results are crucial for design of new optical materials display devices base on dielectric amorphous photonic structures.

  1. Massively parallel sequencing approaches for characterization of structural variation.

    PubMed

    Koboldt, Daniel C; Larson, David E; Chen, Ken; Ding, Li; Wilson, Richard K

    2012-01-01

    The emergence of next-generation sequencing (NGS) technologies offers an incredible opportunity to comprehensively study DNA sequence variation in human genomes. Commercially available platforms from Roche (454), Illumina (Genome Analyzer and Hiseq 2000), and Applied Biosystems (SOLiD) have the capability to completely sequence individual genomes to high levels of coverage. NGS data is particularly advantageous for the study of structural variation (SV) because it offers the sensitivity to detect variants of various sizes and types, as well as the precision to characterize their breakpoints at base pair resolution. In this chapter, we present methods and software algorithms that have been developed to detect SVs and copy number changes using massively parallel sequencing data. We describe visualization and de novo assembly strategies for characterizing SV breakpoints and removing false positives.

  2. Function discovery and structural characterization of a methylphosphonate esterase.

    PubMed

    Xiang, Dao Feng; Patskovsky, Yury; Nemmara, Venkatesh V; Toro, Rafael; Almo, Steven C; Raushel, Frank M

    2015-05-12

    Pmi1525, an enzyme of unknown function from Proteus mirabilis HI4320 and the amidohydrolase superfamily, was cloned, purified to homogeneity, and functionally characterized. The three-dimensional structure of Pmi1525 was determined with zinc and cacodylate bound in the active site (PDB id: 3RHG ). The structure was also determined with manganese and butyrate in the active site (PDB id: 4QSF ). Pmi1525 folds as a distorted (β/α)8-barrel that is typical for members of the amidohydrolase superfamily and cog1735. The substrate profile for Pmi1525 was determined via a strategy that marshaled the utilization of bioinformatics, structural characterization, and focused library screening. The protein was found to efficiently catalyze the hydrolysis of organophosphonate and carboxylate esters. The best substrates identified for Pmi1525 are ethyl 4-nitrophenylmethyl phosphonate (kcat and kcat/Km values of 580 s(-1) and 1.2 × 10(5) M(-1) s(-1), respectively) and 4-nitrophenyl butyrate (kcat and kcat/Km values of 140 s(-1) and 1.4 × 10(5) M(-1) s(-1), respectively). Pmi1525 is stereoselective for the hydrolysis of chiral methylphosphonate esters. The enzyme hydrolyzes the (SP)-enantiomer of isobutyl 4-nitrophenyl methylphosphonate 14 times faster than the corresponding (RP)-enantiomer. The catalytic properties of this enzyme make it an attractive template for the evolution of novel enzymes for the detection, destruction, and detoxification of organophosphonate nerve agents. PMID:25873441

  3. Characterization of the nanoscale structure of milk fat.

    PubMed

    Ramel, Pere Randy R; Peyronel, Fernanda; Marangoni, Alejandro G

    2016-07-15

    The nanoscale structure of milk fat (MF) crystal networks is extensively described for the first time through the characterization of milk fat-crystalline nanoplatelets (MF-CNPs). Removing oil by washing with cold isobutanol and breaking-down crystal aggregates by controlled homogenization allowed for the extraction and visualization of individual MF-CNPs that are mainly composed of high melting triacylglycerols (TAGs). By image analysis, the length and width of MF-CNPs were measured (600 nm × 200 nm-900 nm × 300 nm). Using small-angle X-ray scattering (SAXS), crystalline domain size, (i.e., thickness of MF-CNPs), was determined (27 nm (d001)). Through interpretation of ultra-small-angle X-ray scattering (USAXS) patterns of MF using Unified Fit and Guinier-Porod models, structural properties of MF-CNPs (smooth surfaces) and MF-CNP aggregations were characterized (RLCA aggregation of MF-CNPs to form larger structures that present diffused surfaces). Elucidation of MF-CNPs provides a new dimension of analysis for describing MF crystal networks and opens-up opportunities for modifying MF properties through nanoengineering.

  4. The impact of protein characterization in structural proteomics.

    PubMed

    Geerlof, Arie; Brown, J; Coutard, B; Egloff, M P; Enguita, F J; Fogg, M J; Gilbert, R J C; Groves, M R; Haouz, A; Nettleship, J E; Nordlund, P; Owens, R J; Ruff, M; Sainsbury, S; Svergun, D I; Wilmanns, Matthias

    2006-10-01

    Protein characterization plays a role in two key aspects of structural proteomics. The first is the quality assessment of the produced protein preparations. Obtaining well diffracting crystals is one of the major bottlenecks in the structure-determination pipeline. Often, this is caused by the poor quality of the protein preparation used for crystallization trials. Hence, it is essential to perform an extensive quality assessment of the protein preparations prior to crystallization and to use the results in the evaluation of the process. Here, a protein-production and crystallization strategy is proposed with threshold values for protein purity (95%) and monodispersity (85%) below which a further optimization of the protein-production process is strongly recommended. The second aspect is the determination of protein characteristics such as domains, oligomeric state, post-translational modifications and protein-protein and protein-ligand interactions. In this paper, applications and new developments of protein-characterization methods using MS, fluorescence spectroscopy, static light scattering, analytical ultracentrifugation and small-angle X-ray scattering within the EC Structural Proteomics in Europe contract are described. Examples of the application of the various methods are given. PMID:17001090

  5. Function Discovery and Structural Characterization of a Methylphosphonate Esterase

    PubMed Central

    Xiang, Dao Feng; Patskovsky, Yury; Nemmara, Venkatesh V.; Toro, Rafael; Almo, Steven C.; Raushel, Frank M.

    2015-01-01

    Pmi1525, an enzyme of unknown function from Proteus Mirabilis HI4320 and the amidohydrolase superfamily, was cloned, purified to homogeneity, and functionally characterized. The three-dimensional structure of Pmi1525 was determined with zinc and cacodylate bound in the active site (PDB id: 3RHG). The structure was also determined with manganese and butyrate in the active site (PDB id: 4QSF). Pmi1525 folds as a distorted (β/α)8-barrel that is typical for members of the amidohydrolase superfamily and cog1735. The substrate profile for Pmi1525 was determined via a strategy that marshaled the utilization of bioinformatics, structural characterization and focused library screening. The protein was found to efficiently catalyze the hydrolysis of organophosphonate and carboxylate esters. The best substrates identified for Pmi1525 are ethyl 4-nitrophenylmethyl phosphonate (kcat and kcat/Km values of 580 s−1 and 1.2 × 105 M−1 s−1, respectively) and 4-nitrophenyl butyrate (kcat and kcat/Km values of 140 s−1 and 1.4 × 105 M−1 s−1, respectively). Pmi1525 is stereoselective for the hydrolysis of chiral methylphosphonate esters. The enzyme hydrolyzes the (SP)-enantiomer of isobutyl 4-nitrophenyl methylphosphonate 14 times faster than the corresponding (RP)-enantiomer. The catalytic properties of this enzyme make it an attractive template for the evolution of novel enzymes for the detection, destruction, and detoxification of organophosphonate nerve agents. PMID:25873441

  6. Hierarchical structures of amorphous solids characterized by persistent homology.

    PubMed

    Hiraoka, Yasuaki; Nakamura, Takenobu; Hirata, Akihiko; Escolar, Emerson G; Matsue, Kaname; Nishiura, Yasumasa

    2016-06-28

    This article proposes a topological method that extracts hierarchical structures of various amorphous solids. The method is based on the persistence diagram (PD), a mathematical tool for capturing shapes of multiscale data. The input to the PDs is given by an atomic configuration and the output is expressed as 2D histograms. Then, specific distributions such as curves and islands in the PDs identify meaningful shape characteristics of the atomic configuration. Although the method can be applied to a wide variety of disordered systems, it is applied here to silica glass, the Lennard-Jones system, and Cu-Zr metallic glass as standard examples of continuous random network and random packing structures. In silica glass, the method classified the atomic rings as short-range and medium-range orders and unveiled hierarchical ring structures among them. These detailed geometric characterizations clarified a real space origin of the first sharp diffraction peak and also indicated that PDs contain information on elastic response. Even in the Lennard-Jones system and Cu-Zr metallic glass, the hierarchical structures in the atomic configurations were derived in a similar way using PDs, although the glass structures and properties substantially differ from silica glass. These results suggest that the PDs provide a unified method that extracts greater depth of geometric information in amorphous solids than conventional methods.

  7. Characterizing Englacial and Subglacial Temperature Structure Using Airborne Radar Sounding

    NASA Astrophysics Data System (ADS)

    Schroeder, D. M.; Seroussi, H. L.

    2015-12-01

    The temperature structure of ice sheet and glaciers is a fundamental control on ice flow, rheology, and stability. However, it is difficult to observationally constrain temperature structures at the catchment to ice-sheet scale. The englacial attenuation of radar sounding data is strongly dependent on the temperature structure of the ice sheets. Therefore, echo strength profiles from airborne radar sounding observation do contain temperature information. However, direct interpretation of englacial attenuation rates from radar sounding profiles is often difficult or impossible due to the ambiguous contribution the geometric and material properties of the bed to echo strength variations. To overcome this challenge, we presents techniques that treat radar sounding echo strength and ice thickness profiles as continuous signals, taking advantage of along-profile ice thickness and echo strength variations to constrain the spatial pattern of englacial attenuation and basal reflectivity. We then apply these techniques to an airborne radar sounding survey in order to characterize the englacial and subglacial temperature structure of the Thwaites Glacier catchment in West Antarctic. We then interpreted this structure in context of local ice sheet velocity, advection, force balance, and bed conditions using the ISSM ice sheet model.

  8. Hierarchical structures of amorphous solids characterized by persistent homology

    PubMed Central

    Hiraoka, Yasuaki; Nakamura, Takenobu; Hirata, Akihiko; Escolar, Emerson G.; Matsue, Kaname; Nishiura, Yasumasa

    2016-01-01

    This article proposes a topological method that extracts hierarchical structures of various amorphous solids. The method is based on the persistence diagram (PD), a mathematical tool for capturing shapes of multiscale data. The input to the PDs is given by an atomic configuration and the output is expressed as 2D histograms. Then, specific distributions such as curves and islands in the PDs identify meaningful shape characteristics of the atomic configuration. Although the method can be applied to a wide variety of disordered systems, it is applied here to silica glass, the Lennard-Jones system, and Cu-Zr metallic glass as standard examples of continuous random network and random packing structures. In silica glass, the method classified the atomic rings as short-range and medium-range orders and unveiled hierarchical ring structures among them. These detailed geometric characterizations clarified a real space origin of the first sharp diffraction peak and also indicated that PDs contain information on elastic response. Even in the Lennard-Jones system and Cu-Zr metallic glass, the hierarchical structures in the atomic configurations were derived in a similar way using PDs, although the glass structures and properties substantially differ from silica glass. These results suggest that the PDs provide a unified method that extracts greater depth of geometric information in amorphous solids than conventional methods. PMID:27298351

  9. Structural characterization of recombinant therapeutic proteins by circular dichroism.

    PubMed

    Bertucci, Carlo; Pistolozzi, Marco; De Simone, Angela

    2011-10-01

    Most of the protein therapeutics are now produced by recombinant DNA technology. The advantages of recombinant proteins are related to their higher specificity and to their safety as exposure to animal or human diseases. However, several problems are still present in development of recombinant proteins as therapeutics, such as low bioavailability, short serum half-life, and immune response. Their successful application hinges on the protein stereochemical stability, and on the folding and the tendency to aggregate induced by purification steps and storage. All these aspects determine the failure of many potential protein therapies, and limitations in the development of the formulation. The application of multiple analytical techniques is important in order to obtain a detailed product profile and to understand how manufacturing can influence product structure and activity. Surely the protein conformation is a key aspect to be assessed, because a specific conformation is often essential for the biological function of the protein. Thus, there is a growing need to perform structural studies under the conditions in which the proteins operate, and to monitor the structural changes of the protein. Circular dichroism has been increasingly recognised as a valuable and reliable technique to get this information. In particular, examples will be here reported on the use of circular dichroism spectroscopy in the structural characterization of free and formulated recombinant proteins, looking at the prediction of the secondary structure, propensity to conformational changes, stability, and tendency to aggregate.

  10. Rapid Characterization of Vegetation Structure with a Microsoft Kinect Sensor

    PubMed Central

    Azzari, George; Goulden, Michael L.; Rusu, Radu B.

    2013-01-01

    The importance of vegetation structure and biomass in controlling land-atmosphere exchange is widely recognized, but measurements of canopy structure are challenging, time consuming, and often rely on destructive methods. The Microsoft Kinect is an infrared sensor designed for video gaming that outputs synchronized color and depth images and that has the potential to allow rapid characterization of vegetation structure. We compared depth images from a Kinect sensor with manual measurements of plant structure and size for two species growing in a California grassland. The depth images agreed well with the horizontal and vertical measurements of plant size made manually. Similarly, the plant volumes calculated with a three-dimensional convex hulls approach was well related to plant biomass. The Kinect showed some limitations for ecological observation associated with a short measurement range and daytime light contamination. Nonetheless, the Kinect's light weight, fast acquisition time, low power requirement, and cost make it a promising tool for rapid field surveys of canopy structure, especially in small-statured vegetation. PMID:23435053

  11. Structural characterization of impurified zinc oxide thin films

    SciTech Connect

    Trinca, L. M.; Galca, A. C. Stancu, V. Chirila, C. Pintilie, L.

    2014-11-05

    Europium doped zinc oxide (Eu:ZnO) thin films have been obtained by pulsed laser deposition (PLD). 002 textured thin films were achieved on glass and silicon substrates, while hetero-epilayers and homo-epilayers have been attained on single crystal SrTiO{sub 3} and ZnO, respectively. X-ray Diffraction (XRD) was employed to characterize the Eu:ZnO thin films. Extended XRD studies confirmed the different thin film structural properties as function of chosen substrates.

  12. Complete structural characterization of foams using three-dimensional images

    NASA Astrophysics Data System (ADS)

    Montminy, Matthew Dennis

    Open-celled foams are three-dimensional networks of polymeric cells. The mechanical properties of a foam depend on the size and geometry of its cells. Since foams have a three-dimensional polyhedral structure, the two-dimensional imaging techniques currently used to characterize foams provide only limited accuracy. Magnetic resonance imaging (MRI) and x-ray computerized tomography (x-ray CT) methods offer opportunities for three-dimensional imaging of these polyhedral structures. This thesis involves the development of computer algorithms and software which can use digital three-dimensional images to determine structural parameters such as strut length distribution, window size distributions, and cell volume distributions. A novel set of algorithms has been designed specifically to analyze images of open-celled foams. The image processing approach uses conformal curvature flow (CCF) segmentation to find foam struts in the 3-D images. Once these struts have been detected, volume thinning is used to find the structural skeleton of the foam. This skeleton, which resembles a stick figure model of the foam, can used to determine many statistical characteristics of the foam, including strut length distributions, window size and shape distributions, and cell volume distributions. A Windows-based software package called FoamView was developed to facilitate 3D foam image processing using this specialized image analysis approach. FoamView includes a graphical user interface which allows the user to interact with visualizations of the foam structure, aiding the image analysis process. FoamView facilitates the analysis of relatively large foam samples containing 50 to 100 cells in relatively short times ranging from 1--3 hours. This software was used to analyze open-celled and closed-celled polyurethane foam samples obtained using x-ray computerized tomography. The structural schematics resulting from the analysis were used to compute strut length, interior angle, window size

  13. Characterization of iron-phosphate-silicate chemical garden structures.

    PubMed

    Barge, Laura M; Doloboff, Ivria J; White, Lauren M; Stucky, Galen D; Russell, Michael J; Kanik, Isik

    2012-02-28

    Chemical gardens form when ferrous chloride hydrate seed crystals are added or concentrated solutions are injected into solutions of sodium silicate and potassium phosphate. Various precipitation morphologies are observed depending on silicate and phosphate concentrations, including hollow plumes, bulbs, and tubes. The growth of precipitates is controlled by the internal osmotic pressure, fluid buoyancy, and membrane strength. Additionally, rapid bubble-led growth is observed when silicate concentrations are high. ESEM/EDX analysis confirms compositional gradients within the membranes, and voltage measurements across the membranes during growth show a final potential of around 150-200 mV, indicating that electrochemical gradients are maintained across the membranes as growth proceeds. The characterization of chemical gardens formed with iron, silicate, and phosphate, three important components of an early earth prebiotic hydrothermal system, can help us understand the properties of analogous structures that likely formed at submarine alkaline hydrothermal vents in the Hadean-structures offering themselves as the hatchery of life.

  14. Characterization of structure and thermophysical properties of three ESR slags

    NASA Astrophysics Data System (ADS)

    Plotkowski, A.; deBarbadillo, J.; Krane, Matthew J. M.

    2016-07-01

    The structure and properties of electroslag remelting (ESR) slags were characterized. Slags samples of three compositions were obtained from industrial remelting processes at Special Metals Corporation and from casting in a laboratory vacuum induction melter. The structure of the slag samples was observed using optical and electron microscopy, and phases were identified and their relative amounts quantified using X-ray diffraction. Laser flash thermal diffusivity, density, and differential scanning calorimetry measurements for specific heat were performed to determine the bulk thermal conductivity of the samples. Sample porosity was measured as a function of depth using a serial sectioning technique, and a onedimensional computational model was developed to estimate the thermal conductivity of the fully dense slags. These results are discussed in context with previous studies, and opportunities for future research are identified. AFRL Case Number: 88ABW-2015-1871.

  15. Structural and optical characterization of the propolis films

    NASA Astrophysics Data System (ADS)

    Drapak, S. I.; Bakhtinov, A. P.; Gavrylyuk, S. V.; Drapak, I. T.; Kovalyuk, Z. D.

    2006-10-01

    We have performed structural and optical characterizations of the propolis (an organic entity of biological nature) films grown on various non-organic substrates. The films were grown from a propolis melt or a propolis alcohol solution. The crystal structure has been observed in the films precipitated from the solution onto substrates such as an amorphous glass and sapphire or semiconductor indium monoselenide. For any growth method, the propolis film is a semiconductor with the bandgap of 3.07 eV at 300 K that is confirmed by a maximum in photoluminescence spectra at 2.86 eV. We argue that propolis films might be used in various optoelectronic device applications.

  16. Structural and Energetic Characterization of the Ankyrin Repeat Protein Family

    PubMed Central

    Parra, R. Gonzalo; Espada, Rocío; Verstraete, Nina; Ferreiro, Diego U.

    2015-01-01

    Ankyrin repeat containing proteins are one of the most abundant solenoid folds. Usually implicated in specific protein-protein interactions, these proteins are readily amenable for design, with promising biotechnological and biomedical applications. Studying repeat protein families presents technical challenges due to the high sequence divergence among the repeating units. We developed and applied a systematic method to consistently identify and annotate the structural repetitions over the members of the complete Ankyrin Repeat Protein Family, with increased sensitivity over previous studies. We statistically characterized the number of repeats, the folding of the repeat-arrays, their structural variations, insertions and deletions. An energetic analysis of the local frustration patterns reveal the basic features underlying fold stability and its relation to the functional binding regions. We found a strong linear correlation between the conservation of the energetic features in the repeat arrays and their sequence variations, and discuss new insights into the organization and function of these ubiquitous proteins. PMID:26691182

  17. Structural and functional characterization of two alpha-synuclein strains

    NASA Astrophysics Data System (ADS)

    Bousset, Luc; Pieri, Laura; Ruiz-Arlandis, Gemma; Gath, Julia; Jensen, Poul Henning; Habenstein, Birgit; Madiona, Karine; Olieric, Vincent; Böckmann, Anja; Meier, Beat H.; Melki, Ronald

    2013-10-01

    α-synuclein aggregation is implicated in a variety of diseases including Parkinson’s disease, dementia with Lewy bodies, pure autonomic failure and multiple system atrophy. The association of protein aggregates made of a single protein with a variety of clinical phenotypes has been explained for prion diseases by the existence of different strains that propagate through the infection pathway. Here we structurally and functionally characterize two polymorphs of α-synuclein. We present evidence that the two forms indeed fulfil the molecular criteria to be identified as two strains of α-synuclein. Specifically, we show that the two strains have different structures, levels of toxicity, and in vitro and in vivo seeding and propagation properties. Such strain differences may account for differences in disease progression in different individuals/cell types and/or types of synucleinopathies.

  18. Detecting tubular structures via direct vector field singularity characterization.

    PubMed

    Cabuk, Aytekin D; Alpay, Erdenay; Acar, Burak

    2010-01-01

    The initial step of vessel segmentation in 3D is the detection of vessel centerlines. The proposed methods in literature are either dependent on vessel radius and/or have low response at vessel bifurcations. In this paper we propose a 3D tubular structure detection method that removes these two drawbacks. The proposed method exploits the observations on the eigenvalues of the Hessian matrix as is done in literature, yet it employs a direct 3D vector field singularity characterization. The Gradient Vector Flow vector field is used and the eigenvalues of its Jacobian are exploited in computing a parameter free vesselness map. Results on phantom and real patient data exhibit robustness to scale, high response at vessel bifurcations, and good noise/non-vessel structure suppression.

  19. Sparse labeling of proteins: Structural characterization from long range constraints

    NASA Astrophysics Data System (ADS)

    Prestegard, James H.; Agard, David A.; Moremen, Kelley W.; Lavery, Laura A.; Morris, Laura C.; Pederson, Kari

    2014-04-01

    Structural characterization of biologically important proteins faces many challenges associated with degradation of resolution as molecular size increases and loss of resolution improving tools such as perdeuteration when non-bacterial hosts must be used for expression. In these cases, sparse isotopic labeling (single or small subsets of amino acids) combined with long range paramagnetic constraints and improved computational modeling offer an alternative. This perspective provides a brief overview of this approach and two discussions of potential applications; one involving a very large system (an Hsp90 homolog) in which perdeuteration is possible and methyl-TROSY sequences can potentially be used to improve resolution, and one involving ligand placement in a glycosylated protein where resolution is achieved by single amino acid labeling (the sialyltransferase, ST6Gal1). This is not intended as a comprehensive review, but as a discussion of future prospects that promise impact on important questions in the structural biology area.

  20. Integral structural-functional method for characterizing microbial populations

    NASA Astrophysics Data System (ADS)

    Yakushev, A. V.

    2015-04-01

    An original integral structural-functional method has been proposed for characterizing microbial communities. The novelty of the approach is the in situ study of microorganisms based on the growth kinetics of microbial associations in liquid nutrient broth media under selective conditions rather than on the level of taxa or large functional groups. The method involves the analysis of the integral growth model of a periodic culture. The kinetic parameters of such associations reflect their capacity of growing on different media, i.e., their physiological diversity, and the metabolic capacity of the microorganisms for growth on a nutrient medium. Therefore, the obtained parameters are determined by the features of the microbial ecological strategies. The inoculation of a dense medium from the original inoculate allows characterizing the taxonomic composition of the dominants in the soil community. The inoculation from the associations developed on selective media characterizes the composition of syntrophic groups, which fulfill a specific function in nature. This method is of greater information value than the classical methods of inoculation on selective media.

  1. Microscopic characterization of defect structure in RDX crystals.

    PubMed

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

    2013-12-01

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

  2. Characterization of the B/Si surface electronic structures

    SciTech Connect

    Cao, R.; Yang, X.; Pianetta, P.

    1992-11-01

    High resolution angle resolved core level and valence band photoelectron spectroscopy have been used to characterize the electronic structures of the B/Si(111)-({radical}3 x {radical}3) surfaces. The results have been compared with theoretic calculations and other group III metals and Si terminated Si(111) surfaces that share the same type of surface reconstruction. We have observed a structure evolution from B-T{sub 4} to B-S{sub 5} and finally to Si- T{sub 4} as deposited boron atoms diffuse into the substrate with increasing annealing temperature. The chemically shifted component appearing in the Si 2p core level spectrum is attributed to charge transfer from the top layer Si and Si adatoms to the sublayer B-S{sub 5} atoms. For the Si/Si(111)-({radical}3 {times} {radical}3) surface, a newly discovered chemically shifted component is associated with back bond formation between the Si adatoms and the underneath Si atoms. A new emission feature has been observed in the valence band spectra unique to the B/Si(111)-({radical}3 {times} {radical}3) surface with B-S{sub 5} configuration. Thin Ge layer growth on this structure has also been performed, and we found that no epitaxial growth could be achieved and the underneath structure was little disturbed.

  3. Characterization of the Streptococcus adjacens group antigen structure.

    PubMed Central

    Sieling, P A; Thomas, M J; van de Rijn, I

    1992-01-01

    Serological classification of bacteria requires the presence of an antigen unique to the organism of interest. Streptococci are serologically differentiated by group antigens, many of which are carbohydrates, although some are amphiphiles. This report describes the chemical characterization of the Streptococcus adjacens group antigen structure. Previous studies demonstrated that the amphiphile contained phosphorus, ribitol, galactose, galactosamine, alanine, and fatty acids. Phosphodiester bonds present in the purified group antigen were identified as part of a poly(ribitol phosphate), since ribitol phosphate was the only organic phosphate detected after acid hydrolysis. Hydrofluoric acid cleavage of the phosphodiester bonds generated oligosaccharide repeating units. Gas chromatography-mass spectrometric analysis of the methylated, acetylated oligosaccharide suggested that the repeating unit is a trisaccharide of Galp beta 1-3Galp beta 1-4GalNac with N-acetylgalactosamine attached in beta-linkage to either the number two or the number four carbon of ribitol. The lipid- and carbohydrate-substituted poly(ribitol phosphate) of the S. adjacens group antigen therefore is a unique amphiphile structure, differing in its repeating-unit structure from the polyglycerophosphate structure of the more common gram-positive amphiphile lipoteichoic acid. PMID:1309524

  4. Amyloid oligomer structure characterization from simulations: A general method

    SciTech Connect

    Nguyen, Phuong H.; Li, Mai Suan

    2014-03-07

    Amyloid oligomers and plaques are composed of multiple chemically identical proteins. Therefore, one of the first fundamental problems in the characterization of structures from simulations is the treatment of the degeneracy, i.e., the permutation of the molecules. Second, the intramolecular and intermolecular degrees of freedom of the various molecules must be taken into account. Currently, the well-known dihedral principal component analysis method only considers the intramolecular degrees of freedom, and other methods employing collective variables can only describe intermolecular degrees of freedom at the global level. With this in mind, we propose a general method that identifies all the structures accurately. The basis idea is that the intramolecular and intermolecular states are described in terms of combinations of single-molecule and double-molecule states, respectively, and the overall structures of oligomers are the product basis of the intramolecular and intermolecular states. This way, the degeneracy is automatically avoided. The method is illustrated on the conformational ensemble of the tetramer of the Alzheimer's peptide Aβ{sub 9−40}, resulting from two atomistic molecular dynamics simulations in explicit solvent, each of 200 ns, starting from two distinct structures.

  5. Cloning, expression, and preliminary structural characterization of RTN-1C

    SciTech Connect

    Fazi, Barbara; Melino, Sonia; Sano, Federica Di; Cicero, Daniel O.; Piacentini, Mauro . E-mail: mauro.piacentini@uniroma2.it; Paci, Maurizio

    2006-04-14

    Reticulons (RTNs) are endoplasmic reticulum-associated proteins widely distributed in plants, yeast, and animals. They are characterized by unique N-terminal parts and a common 200 amino acid C-terminal domain containing two long hydrophobic sequences. Despite their implication in many cellular processes, their molecular structure and function are still largely unknown. In this study, the reticulon family member RTN-1C has been expressed and purified in Escherichia coli and its molecular structure has been analysed by fluorescence and CD spectroscopy in different detergents in order to obtain a good solubility and a relative stability. The isotopically enriched protein has been also produced to perform structural studies by NMR spectroscopy. The preliminary results obtained showed that RTN-1C protein possesses helical transmembrane segments when a membrane-like environment is produced by detergents. Moreover, fluorescence experiments indicated the exposure of tryptophan side chains as predicted by structure prediction programs. We also produced the isotopically labelled protein and the procedure adopted allowed us to plan future NMR studies to investigate the biochemical behaviour of reticulon-1C and of its peptides spanning out from the membrane.

  6. Amyloid oligomer structure characterization from simulations: A general method

    NASA Astrophysics Data System (ADS)

    Nguyen, Phuong H.; Li, Mai Suan; Derreumaux, Philippe

    2014-03-01

    Amyloid oligomers and plaques are composed of multiple chemically identical proteins. Therefore, one of the first fundamental problems in the characterization of structures from simulations is the treatment of the degeneracy, i.e., the permutation of the molecules. Second, the intramolecular and intermolecular degrees of freedom of the various molecules must be taken into account. Currently, the well-known dihedral principal component analysis method only considers the intramolecular degrees of freedom, and other methods employing collective variables can only describe intermolecular degrees of freedom at the global level. With this in mind, we propose a general method that identifies all the structures accurately. The basis idea is that the intramolecular and intermolecular states are described in terms of combinations of single-molecule and double-molecule states, respectively, and the overall structures of oligomers are the product basis of the intramolecular and intermolecular states. This way, the degeneracy is automatically avoided. The method is illustrated on the conformational ensemble of the tetramer of the Alzheimer's peptide Aβ9-40, resulting from two atomistic molecular dynamics simulations in explicit solvent, each of 200 ns, starting from two distinct structures.

  7. Photogrammetric detection technique for rotor blades structural characterization

    NASA Astrophysics Data System (ADS)

    Enei, C.; Bernardini, G.; Serafini, J.; Mattioni, L.; Ficuciello, C.; Vezzari, V.

    2015-11-01

    This paper describes an innovative use of photogrammetric detection techniques to experimentally estimate structural/inertial properties of helicopter rotor blades. The identification algorithms for the evaluation of mass and flexural stiffness distributions are an extension of the ones proposed by Larsen, whereas the procedure for torsional properties determination (stiffness and shear center position) is based on the Euler-Prandtl beam theory. These algorithms rely on measurements performed through photogrammetric detection, which requires the collection of digital photos allowing the identification of 3D coordinates of labeled points (markers) on the structure through the correlation of 2D pictures. The displacements are evaluated by comparing the positions of markers in loaded and reference configuration. Being the applied loads known, the structural characteristics can be directly obtained from the measured displacements. The accuracy of the proposed identification algorithms has been firstly verified by comparison with numerical and experimental data, and then applied to the structural characterization of two main rotor blades, designed for ultra-light helicopter applications.

  8. Optical characterization of vitreous structure in health and disease

    NASA Astrophysics Data System (ADS)

    Sampathkumar, Ashwin; Khoshnevis, Matin; Ketterling, Jeffrey A.; Sebag, J.

    2015-03-01

    Patients with myopic vitreopathy (MV) and posterior vitreous detachment (PVD) see floaters, which often can degrade contrast sensitivity to a significant extent. The floaters are associated with irregularly shaped vitreous opacities. In contrast, asteroid hyalosis (AH), which is characterized by microscopic, spherical, white asteroid bodies (ABs) that move with vitreous displacement during eye movements, does not interfere significantly with vision. We hypothesize that the irregular surface of vitreous opacities associated with MV distinguish MV from AH and its smooth-surfaced ABs. A finite-element model was developed to characterize the light-scattering field of vitreous opacities in MV and AH. Vitreous opacities were modeled as spherical bodies and illuminated by a plane wave of light in the optical wavelength of 400-1000 nm. The model has provisions to add random perturbations to the spherical surfaces to vary light-scattering properties and mimic disturbances in vision from simple diffraction rings to more-complex patterns. Samples of ex vivo porcine vitreous (0.4-0.5 ml) were placed in a custom spectrophotometer and the static, light-scattering field of the sample was measured in the spectral range of 400-1000 nm with a resolution of 0.3 nm. Model solutions mimicking healthy vitreous and AH were experimentally validated using a laboratory optical apparatus. Model-based estimates of scattering cross-sections of calibrated gold nanoparticles were found to be in good agreement with experimental measurements. Simulation results potentially can complement experimental data to quantitatively characterize vitreous opacities and distinguish between structures that significantly impact vision, such as those due to myopic vitreopathy and aging, from those that have little impact, like ABs. Such techniques to determine the structural significance of vitreous opacification would be very useful in selecting patients for surgery as well as evaluating the efficacy of

  9. Characterization of adhesive from oysters: A structural and compositional study

    NASA Astrophysics Data System (ADS)

    Alberts, Erik

    The inability for man-made adhesives to set in wet or humid environments is an ongoing challenging the design of biomedical and marine adhesive materials. However, we see that nature has already overcome this challenge. Mussels, barnacles, oysters and sandcastle worms all have unique mechanisms by which they attach themselves to surfaces. By understanding what evolution has already spent millions of years perfecting, we can design novel adhesive materials inspired by nature's elegant designs. The well-studied mussel is currently the standard for design of marine inspired biomimetic polymers. In the work presented here, we aim to provide new insights into the adhesive produced by the eastern oyster, Crassostrea virginica. Unlike the mussel, which produces thread-like plaques comprised of DOPA containing-protein, the oyster secretes an organic-inorganic hybrid adhesive as it settles and grows onto a surface. This form of adhesion renders the oyster to be permanently fixed in place. Over time, hundreds of thousands of oyster grow and agglomerate to form extensive reef structures. These reefs are not only essential to survival of the oyster, but are also vital to intertidal ecosystems. While the shell of the oyster has been extensively studied, curiously, only a few conflicting insights have been made into the nature of the adhesive and contact zone between shell and substrate, and even lesfs information has been ascertained on organic and inorganic composition. In this work, we provide microscopy and histochemical studies to characterize the structure and composition of the adhesive, using oyster in the adult and juvenile stages of life. Preliminary work on extracting and characterizing organic components through collaborative help with solid-state NMR (SSNMR) and proteomics are also detailed here. We aim to provide a full, comprehensive characterization of oyster adhesive so that in the future, we may apply what we learn to the design of new materials.

  10. Structural and spectroscopic characterization of mixed planetary ices.

    PubMed

    Plattner, Nuria; Lee, Myung Won; Meuwly, Markus

    2010-01-01

    Mixed ices play a central role in characterizing the origin, evolution, stability and chemistry of planetary ice surfaces. Examples include the polar areas of Mars, the crust of the Jupiter moon Europa, or atmospheres of planets and their satellites, particularly in the outer solar system. Atomistic simulations using accurate representations of the interaction potentials have recently shown to be suitable to quantitatively describe both, the mid- and the far-infrared spectrum of mixed H2O/CO amorphous ices. In this work, molecular dynamics simulations are used to investigate structural and spectroscopic properties of mixed and crystalline ices containing H2O, CO and CO2. Particular findings include: (a) the sensitivity of the water bending mode to the local environment of the water molecules which, together with structural insights from MD simulations, provides a detailed picture for the relationship between spectroscopy and structure; and (b) the sensitivity of the low-frequency spectrum to the structure of the mixed CO2/H2O ice. Specifically, for mixed H2O/CO2 ices with low water contents isolated water molecules are found which give rise to a band shifted by only 12 cm(-1) from the gas-phase value whereas for increasing water concentration (for a 1 : 1 mixture) the band progressively shifts to higher frequency because water clusters can form. More generally it is found that changes in the ice structure due to the presence of CO2 are larger compared to changes induced by the presence of CO and that this difference is reflected in the shape of the water bending vibration. Thus, the water bending vibration appears to be a suitable diagnostic for structural and chemical aspects of mixed ices. PMID:21302549

  11. Characterization of the structure of heterogeneous materials and particle packings

    NASA Astrophysics Data System (ADS)

    Jiao, Yang

    In this dissertation, we present a combination of computational and theoretical results concerning the characterization of the microstructure of heterogeneous materials and hard-particle packings. An overview of the dissertation is provided in Chapter 1. In Part I of this dissertation, we focus on the characterization of multi-phase heterogeneous materials. In Chapter 2, we present a detailed discussion of the correlation functions that statistically characterize the microstructure of a heterogeneous material. Examples of such materials include composites, colloids, foams and biological media. In Chapter 3, we introduce a microstructure reconstruction/construction procedure developed by Yeong and Torquato and devise a powerful universal sampling scheme, called the lattice-point scheme, that enables one to incorporate the widest class of lower-order correlation functions known to date into the Yeong-Torquato procedure, which opens the door to many fruitful applications. In Chapter 4, we present two major applications of our lattice-point scheme including modelling heterogeneous materials via two-point correlation functions and identifying superior microstructure descriptors of random media. These developments suggest novel approach for material design and more accurate rigorous structure-property relations; they also have ramifications in atomic and molecular systems. In Part II of this dissertation, we focus on quantitatively describing the structure of hard-particle packings, which have been employed to model a wide spectrum of condensed matters such as simple liquid, disordered/crystalline solids and granular media as well as biological systems. In Chapter 5, we present two major numerical packing protocols, namely the Donev-Torquato-Stillinger (DTS) event-driven molecular dynamics (MD) algorithm for smooth convex particles and the adaptive-shrinking-cell (ASC) scheme for hard polyhedral particles. In Chapter 6, the DTS event-driven MD algorithm is employed to

  12. Pyroxene Spectroscopy: Remote Characterization of Composition, Structure and Thermal History

    NASA Astrophysics Data System (ADS)

    Klima, Rachel L.; Dyar, Darby; Glotch, Timothy; Lane, Melissa

    2014-11-01

    Pyroxene is one of the most commonly used minerals for remote analysis of mineralogy and composition of planetary bodies. This is in part due to the prevalence of pyroxene on the surfaces of objects in the inner solar system. Pyroxene also exhibits a distinctive spectrum that is highly sensitive to its specific composition, structure, and cation site occupancy. Cation ordering, which is partially a result of the cooling history of a pyroxene, affects the strengths of absorptions caused by Fe2+ in the M1 and M2 cation sites, which in turn affects the relative band 1 and band 2 areas. Terrestrial pyroxenes are generally quite well-ordered, as many have been exposed to and held for long times at temperatures warm enough to allow cations to exchange between the M1 and M2 sites. Extraterrestrial pyroxenes have been exposed to a vast array of cooling regimes, including flash heating and cooling in the protoplanetary disk, impact brecciation and melting, and more traditional igneous processes.To push pyroxene spectroscopy beyond simple mineral identification and develop it as a tool for characterizing the thermal history of a body, we have been working to characterize and document the crystal chemistry, structure, and site occupancies of a suite of 91 synthetic pyroxenes. This is accomplished by measuring single-crystal XRD, Attenuated Total Reflectance (ATR) and electron probe microanalysis (EMP), variable-temperature Mössbauer and Raman spectra. For each of the samples, visible-far IR spectra have also been collected. We will present the results of this integrated study, focusing on how the crystal structure, composition and site occupancy in pyroxenes is reflected in their visible-infrared spectra and how they can be used to evaluate the thermal history of asteroids and the Moon.

  13. Function Discovery and Structural Characterization of a Methylphosphonate Esterase

    SciTech Connect

    Xiang, Dao Feng; Patskovsky, Yury; Nemmara, Venkatesh V.; Toro, Rafael; Almo, Steven C.; Raushel, Frank M.

    2015-05-12

    Pmi1525, an enzyme of unknown function from Proteus mirabilis HI4320 and the amidohydrolase superfamily, was cloned, purified to homogeneity, and functionally characterized. The three-dimensional structure of Pmi1525 was determined with zinc and cacodylate bound in the active site (PDB id: 3RHG). We also determined the structure with manganese and butyrate in the active site (PDB id: 4QSF). Pmi1525 folds as a distorted (β/α)8-barrel that is typical for members of the amidohydrolase superfamily and cog1735. Moreover, the substrate profile for Pmi1525 was determined via a strategy that marshaled the utilization of bioinformatics, structural characterization, and focused library screening. The protein was found to efficiently catalyze the hydrolysis of organophosphonate and carboxylate esters. The best substrates identified for Pmi1525 are ethyl 4-nitrophenylmethyl phosphonate (kcat and kcat /Km values of 580 s–1 and 1.2 × 105 M–1 s–1, respectively) and 4-nitrophenyl butyrate (kcat and kcat /Km values of 140 s–1 and 1.4 × 105 M–1 s–1, respectively). Pmi1525 is stereoselective for the hydrolysis of chiral methylphosphonate esters. The enzyme hydrolyzes the (SP)-enantiomer of isobutyl 4-nitrophenyl methylphosphonate 14 times faster than the corresponding (RP)-enantiomer. The catalytic properties of this enzyme make it an attractive template for the evolution of novel enzymes for the detection, destruction, and detoxification of organophosphonate nerve agents.

  14. Characterization Of Spatial Heterogeneity and Structure at Landscape Scale

    NASA Astrophysics Data System (ADS)

    Garrigues, S.; Allard, D.; Baret, F.

    The monitoring of land surface dynamic processes at global scale, such as primary production, carbon and water fluxes, requires high temporal frequency remote sensing observations. Because of technological constraints, the sensors are characterized by coarse spatial resolution, i.e. a resolution from few hundred meters (MERIS/ENVISAT, MODIS/TERRA) up to one or few kilometres (VEGETATION/SPOT, SEVIRI/MSG). However, the scenes observed at this range of scales, present spatial heterogeneity which may have a great influence on land surface characteristic estimation from remotely sensed data. Therefore the characterisation of spatial heterogeneity is an important concern to scale non linear land surface processes. The aim of this study is to discuss a geostatistical approach based on two complementary tools to characterize spatial structure of remote sensing data at the landscape scale. The high spatial resolution NDVI (vegetation index) of SPOT/HRV images (20m resolution) is used to characterize the ground spatial structure of different landscapes. These NDVI images are then aggregated in order to describe the evolution of their structure with the spatial resolution. A classical method consists in describing the image spatial heterogeneity by a geostatistic tool: the variogram. The interest of the variogram is that it jointly allows to model the spatial distribution of a scene as well as to quantify the spatial heterogeneity as a function of the spatial resolution. A typology of spatial heterogeneity is derived from the variogram model parameters computed over several types of landscapes. To account for the availability of multiple wavebands, a multivariate description of the spatial heterogeneity could also be proposed. A first limit of the variogram approach is the assumption of spatial stationarity, necessary for modelling the variogram. Spatial stationarity can be checked by: Dividing the image into local windows and adjusting the corresponding variogram model

  15. Characterization of Spatial Heterogeneity and Structure at Landscape Scale

    NASA Astrophysics Data System (ADS)

    Garrigues, S.; Allard, D.; Baret, F.

    2004-05-01

    The monitoring of land surface dynamic processes at global scale, such as primary production, carbon and water fluxes, requires high temporal frequency remote sensing observations. Because of technological constraints, the sensors are characterized by coarse spatial resolution, i.e. a resolution from few hundred meters (MERIS/ENVISAT, MODIS/TERRA) up to one or few kilometres (VEGETATION/SPOT, SEVIRI/MSG). However, the scenes observed at this range of scales, present spatial heterogeneity which may have a great influence on land surface characteristic estimation from remotely sensed data. Therefore the characterisation of spatial heterogeneity is an important concern to scale non linear land surface processes. The aim of this study is to discuss a geostatistical approach based on two complementary tools to characterize spatial structure of remote sensing data at the landscape scale. The high spatial resolution NDVI (vegetation index) of SPOT/HRV images (20m resolution) is used to characterize the ground spatial structure of different landscapes. These NDVI images are then aggregated in order to describe the evolution of their structure with the spatial resolution. A classical method consists in describing the image spatial heterogeneity by a geostatistic tool: the variogram. The interest of the variogram is that it jointly allows to model the spatial distribution of a scene as well as to quantify the spatial heterogeneity as a function of the spatial resolution. A typology of spatial heterogeneity is derived from the variogram model parameters computed over several types of landscapes. To account for the availability of multiple wavebands, a multivariate description of the spatial heterogeneity could also be proposed. A first limit of the variogram approach is the assumption of spatial stationarity, necessary for modelling the variogram. Spatial stationarity can be checked by: - Dividing the image into local windows and adjusting the corresponding variogram model

  16. Structural, Mechanistic, and Antigenic Characterization of the Human Astrovirus Capsid

    PubMed Central

    York, Royce L.; Yousefi, Payam A.; Bogdanoff, Walter; Haile, Sara; Tripathi, Sarvind

    2015-01-01

    ABSTRACT Human astroviruses (HAstVs) are nonenveloped, positive-sense, single-stranded RNA viruses that are a leading cause of viral gastroenteritis. HAstV particles display T=3 icosahedral symmetry formed by 180 copies of the capsid protein (CP), which undergoes proteolytic maturation to generate infectious HAstV particles. Little is known about the molecular features that govern HAstV particle assembly, maturation, infectivity, and immunogenicity. Here we report the crystal structures of the two main structural domains of the HAstV CP: the core domain at 2.60-Å resolution and the spike domain at 0.95-Å resolution. Fitting of these structures into the previously determined 25-Å-resolution electron cryomicroscopy density maps of HAstV allowed us to characterize the molecular features on the surfaces of immature and mature T=3 HAstV particles. The highly electropositive inner surface of HAstV supports a model in which interaction of the HAstV CP core with viral RNA is a driving force in T=3 HAstV particle formation. Additionally, mapping of conserved residues onto the HAstV CP core and spike domains in the context of the immature and mature HAstV particles revealed dramatic changes to the exposure of conserved residues during virus maturation. Indeed, we show that antibodies raised against mature HAstV have reactivity to both the HAstV CP core and spike domains, revealing for the first time that the CP core domain is antigenic. Together, these data provide new molecular insights into HAstV that have practical applications for the development of vaccines and antiviral therapies. IMPORTANCE Astroviruses are a leading cause of viral diarrhea in young children, immunocompromised individuals, and the elderly. Despite the prevalence of astroviruses, little is known at the molecular level about how the astrovirus particle assembles and is converted into an infectious, mature virus. In this paper, we describe the high-resolution structures of the two main astrovirus

  17. Characterization of electronic structure of periodically strained graphene

    DOE PAGES

    Aslani, Marjan; Garner, C. Michael; Kumar, Suhas; Nordlund, Dennis; Pianetta, Piero; Nishi, Yoshio

    2015-11-03

    We induced periodic biaxial tensile strain in polycrystalline graphene by wrapping it over a substrate with repeating pillar-like structures with a periodicity of 600 nm. Using Raman spectroscopy, we determined to have introduced biaxial strains in graphene in the range of 0.4% to 0.7%. Its band structure was characterized using photoemission from valance bands, shifts in the secondary electron emission, and x-ray absorption from the carbon 1s levels to the unoccupied graphene conduction bands. It was observed that relative to unstrained graphene, strained graphene had a higher work function and higher density of states in the valence and conduction bands.more » Furthermore, we measured the conductivity of the strained and unstrained graphene in response to a gate voltage and correlated the changes in their behavior to the changes in the electronic structure. From these sets of data, we propose a simple band diagram representing graphene with periodic biaxial strain.« less

  18. A structural framework for anomalous change detection and characterization

    SciTech Connect

    Prasad, Lakshman; Theiler, James P

    2009-01-01

    We present a spatially adaptive scheme for automatically searching a pair of images of a scene for unusual and interesting changes. Our motivation is to bring into play structural aspects of image features alongside the spectral attributes used for anomalous change detection (ACD). We leverage a small but informative subset of pixels, namely edge pixels of the images, as anchor points of a Delaunay triangulation to jointly decompose the images into a set of triangular regions, called trixels, which are spectrally uniform. Such decomposition helps in image regularization by simple-function approximation on a feature-adaptive grid. Applying ACD to this trixel grid instead of pixels offers several advantages. It allows: (1) edge-preserving smoothing of images, (2) speed-up of spatial computations by significantly reducing the representation of the images, and (3) the easy recovery of structure of the detected anomalous changes by associating anomalous trixels with polygonal image features. The latter facility further enables the application of shape-theoretic criteria and algorithms to characterize the changes and recognize them as interesting or not. This incorporation of spatial information has the potential to filter out some spurious changes, such as due to parallax, shadows, and misregistration, by identifying and filtering out those that are structurally similar and spatially pervasive. Our framework supports the joint spatial and spectral analysis of images, potentially enabling the design of more robust ACD algorithms.

  19. Biochemical and structural characterization of Cryptosporidium parvum Lactate dehydrogenase.

    PubMed

    Cook, William J; Senkovich, Olga; Hernandez, Agustin; Speed, Haley; Chattopadhyay, Debasish

    2015-03-01

    The protozoan parasite Cryptosporidium parvum causes waterborne diseases worldwide. There is no effective therapy for C. parvum infection. The parasite depends mainly on glycolysis for energy production. Lactate dehydrogenase is a major regulator of glycolysis. This paper describes the biochemical characterization of C. parvum lactate dehydrogenase and high resolution crystal structures of the apo-enzyme and four ternary complexes. The ternary complexes capture the enzyme bound to NAD/NADH or its 3-acetylpyridine analog in the cofactor binding pocket, while the substrate binding site is occupied by one of the following ligands: lactate, pyruvate or oxamate. The results reveal distinctive features of the parasitic enzyme. For example, C. parvum lactate dehydrogenase prefers the acetylpyridine analog of NADH as a cofactor. Moreover, it is slightly less sensitive to gossypol inhibition compared with mammalian lactate dehydrogenases and not inhibited by excess pyruvate. The active site loop and the antigenic loop in C. parvum lactate dehydrogenase are considerably different from those in the human counterpart. Structural features and enzymatic properties of C. parvum lactate dehydrogenase are similar to enzymes from related parasites. Structural comparison with malate dehydrogenase supports a common ancestry for the two genes.

  20. Structural characterization studies on the natural mineral pyrophyllite

    NASA Astrophysics Data System (ADS)

    Reddy, T. Ravindra; Lakshmi Reddy, S.; Endo, Tamio

    2016-03-01

    A light-yellow-colored pyrophyllite (Al2O3.SiO2) mineral obtained from Vempalli, Cuddapah district, Andhra Pradesh, India, is investigated in the present work. Chemical analysis carried out using energy-dispersive spectroscopy (EDX) shows that Fe2O3 is present by about 1.56 wt%. Structural characterization was performed using X-ray diffraction (XRD). XRD results suggest that the unit cell is monoclinic with a = 5.16, b = 8.798, c = 9.347 Å and β = 100.46°. The ligands around the metal ion present in the structure are investigated using FTIR spectroscopy. EDX analysis indicates that iron and titanium are only two transition metals present in it. Morphology studied using scanning electron microscopy suggests that the unit cell consists of a dioctahedral layered structure. Fe3+ is present in the location of Al3+ in the unit cell of pyrophyllite. Electron paramagnetic resonance results indicate that the unit cell of the crystal contains Fe(III), and its g values are found to be 4.10 and 2.0. Infrared properties are due to the presence of silicate and hydroxyl anions as ligands. Nonlinear optical measurements carried out using Z-scan reveal the occurrence of strong nonlinear optical limiting in the material, indicating potential applications in laser safety devices.

  1. Characterization of ion-exchange membrane materials: properties vs structure.

    PubMed

    Berezina, N P; Kononenko, N A; Dyomina, O A; Gnusin, N P

    2008-06-22

    This review focuses on the preparation, structure and applications of ion-exchange membranes formed from various materials and exhibiting various functions (electrodialytic, perfluorinated sulphocation-exchange and novel laboratory-tested membranes). A number of experimental techniques for measuring electrotransport properties as well as the general procedure for membrane testing are also described. The review emphasizes the relationships between membrane structures, physical and chemical properties and mechanisms of electrochemical processes that occur in charged membrane materials. The water content in membranes is considered to be a key factor in the ion and water transfer and in polarization processes in electromembrane systems. We suggest the theoretical approach, which makes it possible to model and characterize the electrochemical properties of heterogeneous membranes using several transport-structural parameters. These parameters are extracted from the experimental dependences of specific electroconductivity and diffusion permeability on concentration. The review covers the most significant experimental and theoretical research on ion-exchange membranes that have been carried out in the Membrane Materials Laboratory of the Kuban State University. These results have been discussed at the conferences "Membrane Electrochemistry", Krasnodar, Russia for many years and were published mainly in Russian scientific sources.

  2. Biochemical and structural characterization of Cryptosporidium parvum Lactate dehydrogenase.

    PubMed

    Cook, William J; Senkovich, Olga; Hernandez, Agustin; Speed, Haley; Chattopadhyay, Debasish

    2015-03-01

    The protozoan parasite Cryptosporidium parvum causes waterborne diseases worldwide. There is no effective therapy for C. parvum infection. The parasite depends mainly on glycolysis for energy production. Lactate dehydrogenase is a major regulator of glycolysis. This paper describes the biochemical characterization of C. parvum lactate dehydrogenase and high resolution crystal structures of the apo-enzyme and four ternary complexes. The ternary complexes capture the enzyme bound to NAD/NADH or its 3-acetylpyridine analog in the cofactor binding pocket, while the substrate binding site is occupied by one of the following ligands: lactate, pyruvate or oxamate. The results reveal distinctive features of the parasitic enzyme. For example, C. parvum lactate dehydrogenase prefers the acetylpyridine analog of NADH as a cofactor. Moreover, it is slightly less sensitive to gossypol inhibition compared with mammalian lactate dehydrogenases and not inhibited by excess pyruvate. The active site loop and the antigenic loop in C. parvum lactate dehydrogenase are considerably different from those in the human counterpart. Structural features and enzymatic properties of C. parvum lactate dehydrogenase are similar to enzymes from related parasites. Structural comparison with malate dehydrogenase supports a common ancestry for the two genes. PMID:25542170

  3. Characterizing Fractured Rock with Geo-structural and Micro-structural Models

    NASA Astrophysics Data System (ADS)

    Dershowitz, William

    2015-04-01

    Fracture spatial structure and hydro-mechanical properties are key to the understanding of fractured rock geomechanical stability, hydrodynamics, and solute transport. This paper presents a quantitative approach to fracture characterization to provide information useful for stability and flow analysis, and for coupled flow/geomechanics. The approach presented is based on the concept of geo-structural, hydro-mechanical, and microstructural models. This approach is applicable for data collected from exposed surfaces (mapping, LiDAR, aero-magnetics), boreholes (core, optical images, and images based on resistivity and geophysical methods), and three dimensional imaging (seismic attributes and microseismics). Examples are presented comparing the results of conventional fracture characterization procedures and the recommended procedure. Fracture characterization for geo-structural fracture models is based on the idea that the geologically based fracture spatial pattern is the key, rather than individual fracture statistics. For example, while fracture intensity statistics can useful, the three dimensional fracture pattern for a bedded sedimentary rock can be better reproduced from the combination of a mechanical bedding model and a correlation between fracture spacing and bed height. In a fracture geo-structural model, the fracture spatial pattern, orientation, and intensity should be characterized in a combination of global and local coordinate systems. While some fracture sets may be oriented relative to the regional tectonics (the global coordinate system), other fracture sets are oriented relative to bedding (a local coordinate system). Fracture hydro-mechanical models define the combination of (a) conductive fractures, (b) flow-barrier fractures, (c) fractures which provide storage porosity, (d) fractures of significance for kinematic stability, and (e) fractures of significance for rock mass strength and deformability. The hydromechanical fractures are a subset of

  4. Characterization of multifunctional structural capacitors for embedded energy storage

    NASA Astrophysics Data System (ADS)

    Lin, Yirong; Sodano, Henry A.

    2009-12-01

    Multifunctional composites are a class of materials that combine structural and other functionalities such as sensing, actuation, energy harvesting, and vibration control in order to maximize structural performance while minimizing weight and complexity. Among all the multifunctional composites developed so far, piezoelectric composites have been widely studied due to the high coupling of energy between the electrical and mechanical domains and the inherently high dielectric constant. Several piezoelectric fiber composites have been developed for sensing and actuation applications; however, none of the previously studied composites fully embed all components of an energy storage device as load bearing members of the structure. A multifunctional fiber that can be embedded in a composite material to perform sensing and actuation has been recently developed [Y. Lin and H. A. Sodano, Adv. Funct. Mater. 18, 592 (2008)], in addition to providing load bearing functionality. The design was achieved by coating a common structural fiber, silicon carbide, with a barium titanate piezoelectric shell, and poling the active material radically by employing the structural fiber as one of the electrodes. The silicon carbide core fiber also carries external mechanical loading to protect the brittle barium titanate shell from fracture. The excellent piezoelectric and dielectric properties of the barium titanate material make the active structural fiber an outstanding candidate for converting and storing ambient mechanical energy into electrical energy to power other electric devices in the system. This paper focuses on the characterization of energy storage capability of the multifunctional fiber provided by the dielectric properties of the barium titanate shell. The capacitances of the multifunctional fibers with four different aspect ratios are tested and compared with the theoretical expressions for the cylindrical capacitor, while the breakdown voltages of the multifunctional

  5. Characterizing the structure of topological insulator thin films

    SciTech Connect

    Richardella, Anthony; Kandala, Abhinav; Lee, Joon Sue; Samarth, Nitin

    2015-08-01

    We describe the characterization of structural defects that occur during molecular beam epitaxy of topological insulator thin films on commonly used substrates. Twinned domains are ubiquitous but can be reduced by growth on smooth InP (111)A substrates, depending on details of the oxide desorption. Even with a low density of twins, the lattice mismatch between (Bi, Sb){sub 2}Te{sub 3} and InP can cause tilts in the film with respect to the substrate. We also briefly discuss transport in simultaneously top and back electrically gated devices using SrTiO{sub 3} and the use of capping layers to protect topological insulator films from oxidation and exposure.

  6. Characterization of Thermal and Mechanical Impact on Aluminum Honeycomb Structures

    NASA Technical Reports Server (NTRS)

    Robinson, Christen M.

    2013-01-01

    This study supports NASA Kennedy Space Center's research in the area of intelligent thermal management systems and multifunctional thermal systems. This project addresses the evaluation of the mechanical and thermal properties of metallic cellular solid (MCS) materials; those that are lightweight; high strength, tunable, multifunctional and affordable. A portion of the work includes understanding the mechanical properties of honeycomb structured cellular solids upon impact testing under ambient, water-immersed, liquid nitrogen-cooled, and liquid nitrogen-immersed conditions. Additionally, this study will address characterization techniques of the aluminum honeycomb's ability to resist multiple high-rate loadings or impacts in varying environmental conditions, using various techniques for the quantitative and qualitative determination for commercial applicability.

  7. Fabrication, characterization, and optical properties of gold nanobowl submonolayer structures.

    PubMed

    Ye, Jian; Van Dorpe, Pol; Van Roy, Willem; Borghs, Gustaaf; Maes, Guido

    2009-02-01

    We report on a versatile method to fabricate hollow gold nanobowls and complex gold nanobowls (with a core) based on an ion milling and a vapor HF etching technique. Two different sized hollow gold nanobowls are fabricated by milling and etching submonolayers of gold nanoshells deposited on a substrate, and their sizes and morphologies are characterized by scanning electron microscopy (SEM) and atomic force microscopy (AFM). Optical properties of hollow gold nanobowls with different sizes are investigated experimentally and theoretically, showing highly tunable plasmon resonance ranging from the visible to the near-infrared region. Additionally, finite difference time domain (FDTD) calculations show an enhanced localized electromagnetic field around hollow gold nanobowl structures, which indicates a potential application in surface-enhanced Raman scattering (SERS) spectroscopy for biomolecular detection. Finally, we demonstrate the fabrication of complex gold nanobowls with a gold nanoparticle core which offers the capability to create plasmon hybridized nanostructures. PMID:19125593

  8. Isolation and structural characterization of chondroitin sulfate from bony fishes.

    PubMed

    Maccari, Francesca; Galeotti, Fabio; Volpi, Nicola

    2015-09-20

    Chondroitin sulfate (CS) was purified from the bones of common fishes, monkfish, cod, spiny dogfish, salmon and tuna, and characterized in an effort to find alternative sources and new peculiar structures of this complex biomacromolecule utilized in the pharmaceutical and nutraceutical industry. Quantitative analyses yielded a CS content ranging from 0.011% for cod up to 0.34% for monkfish. The disaccharide pattern showed the presence of nonsulfated disaccharide, monosulfated species ΔDi6s and ΔDi4s, and disulfated disaccharides in different percentages. The disulfated species ΔDi2,6dis was present in all CS extracts in a range of 1.3-10.5%. The presence of these disulfated disaccharides may be a useful marker for the marine origin of CS. The newly identified sources would certainly enable the production of CS with unique disaccharide composition and properties.

  9. Structural and functional characterization of enamel pigmentation in shrews.

    PubMed

    Dumont, M; Tütken, T; Kostka, A; Duarte, M J; Borodin, S

    2014-04-01

    Pigmented tooth enamel occurs in several vertebrate clades, ranging from mammals to fish. Although an iron compound is associated with this orange to red colored pigmentation, its chemical and structural organization within the enamel is unknown. To determine the nature of the iron compound, we investigated heavily pigmented teeth of the northern short-tailed shrew Blarina brevicauda using combined characterization techniques such as scanning and transmission electron microscopy and synchrotron X-ray diffraction. We found that the pigmentation of the enamel with an iron content of around 8wt% results from a close to amorphous magnetite phase deposited around the nm-sized enamel crystals. Furthermore, the influence of the pigmentation on the enamel hardness was determined by nanoindentation measurements. Finally, the biomechanical function and biological context are discussed in light of the obtained results. PMID:24556576

  10. Fabrication, characterization, and application of microresonators and resonant structures

    NASA Astrophysics Data System (ADS)

    Cohoon, Gregory A.

    Optical resonators are structures that allow light to circulate and store energy for a duration of time. This work primarily looks at the fabrication, characterization, and application of whispering gallery mode microresonators and the analysis of organic photonic crystal-like structures and simulation of their resonant effects. Whispering gallery mode (WGM) microresonators are a class of cylindrically symmetric optical resonator which light circulates around the equator of the structure. These resonators are named after acoustic whispering galleries, where a whisper can be heard anywhere along the perimeter of a circular room. These optical structures are known for their ultra high Q-factor and their low mode volume. Q-factor describes the photon lifetime in the cavity and is responsible for the energy buildup within the cavity and sharp spectral characteristics of WGM resonators. The energy buildup is ideal for non-linear optics and the sharp spectral features are beneficial for sensing applications. Characterization of microbubble resonators is done by coupling light from a tunable laser source via tapered optical fiber into the cavity. The fabrication of quality tapered optical fiber on the order of 1--2 microm is critical to working on WGM resonators. The measurement of Q-factors up to 2x10 8 and mode spectra are possible with these resonators and experimental techniques. This work focuses on microdisk and microbubble WGM resonators. The microdisk resonators are fabricated by femtosecond laser micromachining. The micromachined resonators are fabricated by ablating rotating optical fiber to generate the disk shape and then heated to reflow the surface to improve optical quality. These resonators have a spares mode spectrum and display a Q factor as high a 2x106. The microbubble resonators are hollow microresonators fabricated by heating a pressurized capillary tube which forms a bubble in the area exposed to heat. These have a wall thickness of 2--5 microm and

  11. Characterization of natural photonic structures by means of optimization strategies

    NASA Astrophysics Data System (ADS)

    Macías, Demetrio; Vial, Alexandre; Luna, Ana; Skigin, Diana C.; Inchaussandague, Marina E.

    2015-03-01

    Natural photonic structures exhibit remarkable color effects such as metallic appearance and iridescence. A rigorous study of the electromagnetic response of such complex structures requires to accurately determine some of their relevant optical parameters, e.g. the dielectric constants of the materials involved. In a recent work, we have shown that heuristic optimization strategies are suitable tools for the retrieval of the complex refractive index of the materials comprising natural multilayer systems such as the Coleoptera's cuticle. Moreover, the numerical results obtained illustrate the great potential of this kind of algorithms not only for the study of natural photonic structures, but also for the design of biomimetic photonic devices for lightning, sensing or anti-counterfeiting applications. In a first stage, we assumed that the materials which comprise the layers are characterized by isotropic non-dispersive dielectric permittivities. However, it is well known that the cuticle of many Coleoptera exhibit anisotropy in their constituent materials, and also dispersion has been reported. In this contribution we improve our previous approach in order to have a more realistic and useful computational tool for the retrieval of the relevant parameters of biological structures. For this, we include, within the inversion algorithm, a dispersion model to describe the frequency-dependent dielectric permittivity of the layers' materials. Also, in order to guarantee the uniqueness of the solution and the convergence to the global optimum, we simultaneously include in the fitness function the information of several angles of incidence, as well as that of the p- and s-polarization states.

  12. Structural Characterization of Myotoxic Ecarpholin S From Echis carinatus Venom

    SciTech Connect

    Zhou, X.; Tan, T; Valiyaveettil, S; Go, M; Kini, R; Velazquez-Campoy, A; Sivaraman, J

    2008-01-01

    Phospholipase A2 (PLA2), a common toxic component of snake venom, has been implicated in various pharmacological effects. Ecarpholin S, isolated from the venom of the snake Echis carinatus sochureki, is a phospholipase A2 (PLA2) belonging to the Ser49-PLA2 subgroup. It has been characterized as having low enzymatic but potent myotoxic activities. The crystal structures of native ecarpholin S and its complexes with lauric acid, and its inhibitor suramin, were elucidated. This is the first report of the structure of a member of the Ser49-PLA2 subgroup. We also examined interactions of ecarpholin S with phosphatidylglycerol and lauric acid, using surface plasmon resonance, and of suramin with isothermal titration calorimetry. Most Ca2+-dependent PLA2 enzymes have Asp in position 49, which plays a crucial role in Ca2+ binding. The three-dimensional structure of ecarpholin S reveals a unique conformation of the Ca2+-binding loop that is not favorable for Ca2+ coordination. Furthermore, the endogenously bound fatty acid (lauric acid) in the hydrophobic channel may also interrupt the catalytic cycle. These two observations may account for the low enzymatic activity of ecarpholin S, despite full retention of the catalytic machinery. These observations may also be applicable to other non-Asp49-PLA2 enzymes. The interaction of suramin in its complex with ecarpholin S is quite different from that reported for the Lys49-PLA2/suramin complex, where the interfacial recognition face (i-face), C-terminal region, and N-terminal region of ecarpholin S play important roles. This study provides significant structural and functional insights into the myotoxic activity of ecarpholin S and, in general, of non-Asp49-PLA2 enzymes.

  13. Characterization of structural relaxation in inorganic glasses using length dilatometry

    NASA Astrophysics Data System (ADS)

    Koontz, Erick

    The processes that govern how a glass relaxes towards its thermodynamic quasi-equilibrium state are major factors in understanding glass behavior near the glass transition region, as characterized by the glass transition temperature (Tg). Intrinsic glass properties such as specific volume, enthalpy, entropy, density, etc. are used to map the behavior of the glass network below in and near the transition region. The question of whether a true thermodynamic second order phase transition takes place in the glass transition region is another pending question. Linking viscosity behavior to entropy, or viewing the glass configuration as an energy landscape are just a couple of the most prevalent methods used for attempting to understand the glass transition. The structural relaxation behavior of inorganic glasses is important for more than scientific reasons, many commercial glass processing operations including glass melting and certain forms of optical fabrication include significant time spent in the glass transition region. For this reason knowledge of structural relaxation processes can, at a minimum, provide information for annealing duration of melt-quenched glasses. The development of a predictive model for annealing time prescription has the potential to save glass manufacturers significant time and money as well as increasing volume throughput. In optical hot forming processes such as precision glass molding, molded optical components can significantly change in shape upon cooling through the glass transition. This change in shape is not scientifically predictable as of yet though manufacturers typically use empirical rules developed in house. The classification of glass behavior in the glass transition region would allow molds to be accurately designed and save money for the producers. The work discussed in this dissertation is comprised of the development of a dilatometric measurement and characterization method of structural relaxation. The measurement and

  14. Characterizing 3D Vegetation Structure from Space: Mission Requirements

    NASA Technical Reports Server (NTRS)

    Hall, Forrest G.; Bergen, Kathleen; Blair, James B.; Dubayah, Ralph; Houghton, Richard; Hurtt, George; Kellndorfer, Josef; Lefsky, Michael; Ranson, Jon; Saatchi, Sasan; Shugart, H. H.; Wickland, Diane

    2012-01-01

    Human and natural forces are rapidly modifying the global distribution and structure of terrestrial ecosystems on which all of life depends, altering the global carbon cycle, affecting our climate now and for the foreseeable future, causing steep reductions in species diversity, and endangering Earth s sustainability. To understand changes and trends in terrestrial ecosystems and their functioning as carbon sources and sinks, and to characterize the impact of their changes on climate, habitat and biodiversity, new space assets are urgently needed to produce high spatial resolution global maps of the three-dimensional (3D) structure of vegetation, its biomass above ground, the carbon stored within and the implications for atmospheric green house gas concentrations and climate. These needs were articulated in a 2007 National Research Council (NRC) report (NRC, 2007) recommending a new satellite mission, DESDynI, carrying an L-band Polarized Synthetic Aperture Radar (Pol-SAR) and a multi-beam lidar (Light RAnging And Detection) operating at 1064 nm. The objectives of this paper are to articulate the importance of these new, multi-year, 3D vegetation structure and biomass measurements, to briefly review the feasibility of radar and lidar remote sensing technology to meet these requirements, to define the data products and measurement requirements, and to consider implications of mission durations. The paper addresses these objectives by synthesizing research results and other input from a broad community of terrestrial ecology, carbon cycle, and remote sensing scientists and working groups. We conclude that: (1) current global biomass and 3-D vegetation structure information is unsuitable for both science and management and policy. The only existing global datasets of biomass are approximations based on combining land cover type and representative carbon values, instead of measurements of actual biomass. Current measurement attempts based on radar and multispectral

  15. Development of an in-situ soil structure characterization methodology

    NASA Astrophysics Data System (ADS)

    Debos, Endre; Kriston, Sandor

    2015-04-01

    The agricultural cultivation has several direct and indirect effects on the soil properties, among which the soil structure degradation is the best known and most detectable one. Soil structure degradation leads to several water and nutrient management problems, which reduce the efficiency of agricultural production. There are several innovative technological approaches aiming to reduce these negative impacts on the soil structure. The tests, validation and optimization of these methods require an adequate technology to measure the impacts on the complex soil system. This study aims to develop an in-situ soil structure and root development testing methodology, which can be used in field experiments and which allows one to follow the real time changes in the soil structure - evolution / degradation and its quantitative characterization. The method is adapted from remote sensing image processing technology. A specifically transformed A/4 size scanner is placed into the soil into a safe depth that cannot be reached by the agrotechnical treatments. Only the scanner USB cable comes to the surface to allow the image acquisition without any soil disturbance. Several images from the same place can be taken throughout the vegetation season to follow the soil consolidation and structure development after the last tillage treatment for the seedbed preparation. The scanned image of the soil profile is classified using supervised image classification, namely the maximum likelihood classification algorithm. The resulting image has two principal classes, soil matrix and pore space and other complementary classes to cover the occurring thematic classes, like roots, stones. The calculated data is calibrated with filed sampled porosity data. As the scanner is buried under the soil with no changes in light conditions, the image processing can be automated for better temporal comparison. Besides the total porosity each pore size fractions and their distributions can be calculated for

  16. Production and structural characterization of Lactobacillus helveticus derived biosurfactant.

    PubMed

    Sharma, Deepansh; Saharan, Baljeet Singh; Chauhan, Nikhil; Bansal, Anshul; Procha, Suresh

    2014-01-01

    A probiotic strain of lactobacilli was isolated from traditional soft Churpi cheese of Yak milk and found positive for biosurfactant production. Lactobacilli reduced the surface tension of phosphate buffer saline (PBS) from 72.0 to 39.5 mNm(-1) pH 7.2 and its critical micelle concentration (CMC) was found to be 2.5 mg mL(-1). Low cost production of Lactobacilli derived biosurfactant was carried out at lab scale fermenter which yields 0.8 mg mL(-1) biosurfactant. The biosurfactant was found least phytotoxic and cytotoxic as compared to the rhamnolipid and sodium dodecyl sulphate (SDS) at different concentration. Structural attributes of biosurfactant were determined by FTIR, NMR ((1)H and (13)C), UPLC-MS, and fatty acid analysis by GCMS which confirmed the presence of glycolipid type of biosurfactant closely similar to xylolipids. Biosurfactant is mainly constituted by lipid and sugar fractions. The present study outcomes provide valuable information on structural characterization of the biosurfactant produced by L. helveticus MRTL91. These findings are encouraging for the application of Lactobacilli derived biosurfactant as nontoxic surface active agents in the emerging field of biomedical applications. PMID:25506070

  17. Microstructural, Structural, and Thermal Characterization of Annealed Carbon Steels

    NASA Astrophysics Data System (ADS)

    Lara-Guevara, A.; Ortiz-Echeverri, C. J.; Rojas-Rodriguez, I.; Mosquera-Mosquera, J. C.; Ariza-Calderón, H.; Ayala-Garcia, I.; Rodriguez-García, M. E.

    2016-10-01

    As is well known, the metallurgical microstructure of carbon steel is formed by ferrite and pearlite after the annealing heat treatment. When the cooling rate increases, the diffusive process is interrupted causing a change in the metallurgical microstructure which will affect steel properties. The aim of this work was to study thermal, structural, and microstructural properties of annealed carbon steel samples with four different carbon contents. Crystalline structure and crystalline quality were studied by the X-ray diffraction technique, where the full width at half maximum analysis showed that as the carbon content increased, the crystalline quality decreased. The metallurgical microstructure morphology was studied by scanning electron microscopy. The thermal diffusivity and the heat capacity were determined by the photoacoustic technique and by the thermal relaxation method, respectively. The thermal diffusivity and the thermal conductivity decreased as the carbon content increased. The amplitude signal of photothermal radiometry increased as the carbon content increased, while the phase signal of photothermal radiometry did not show significant differences among studied carbon steel types. The photoacoustic technique represents an important alternative in the steel characterization field.

  18. Characterization of large structural genetic mosaicism in human autosomes.

    PubMed

    Machiela, Mitchell J; Zhou, Weiyin; Sampson, Joshua N; Dean, Michael C; Jacobs, Kevin B; Black, Amanda; Brinton, Louise A; Chang, I-Shou; Chen, Chu; Chen, Constance; Chen, Kexin; Cook, Linda S; Crous Bou, Marta; De Vivo, Immaculata; Doherty, Jennifer; Friedenreich, Christine M; Gaudet, Mia M; Haiman, Christopher A; Hankinson, Susan E; Hartge, Patricia; Henderson, Brian E; Hong, Yun-Chul; Hosgood, H Dean; Hsiung, Chao A; Hu, Wei; Hunter, David J; Jessop, Lea; Kim, Hee Nam; Kim, Yeul Hong; Kim, Young Tae; Klein, Robert; Kraft, Peter; Lan, Qing; Lin, Dongxin; Liu, Jianjun; Le Marchand, Loic; Liang, Xiaolin; Lissowska, Jolanta; Lu, Lingeng; Magliocco, Anthony M; Matsuo, Keitaro; Olson, Sara H; Orlow, Irene; Park, Jae Yong; Pooler, Loreall; Prescott, Jennifer; Rastogi, Radhai; Risch, Harvey A; Schumacher, Fredrick; Seow, Adeline; Setiawan, Veronica Wendy; Shen, Hongbing; Sheng, Xin; Shin, Min-Ho; Shu, Xiao-Ou; VanDen Berg, David; Wang, Jiu-Cun; Wentzensen, Nicolas; Wong, Maria Pik; Wu, Chen; Wu, Tangchun; Wu, Yi-Long; Xia, Lucy; Yang, Hannah P; Yang, Pan-Chyr; Zheng, Wei; Zhou, Baosen; Abnet, Christian C; Albanes, Demetrius; Aldrich, Melinda C; Amos, Christopher; Amundadottir, Laufey T; Berndt, Sonja I; Blot, William J; Bock, Cathryn H; Bracci, Paige M; Burdett, Laurie; Buring, Julie E; Butler, Mary A; Carreón, Tania; Chatterjee, Nilanjan; Chung, Charles C; Cook, Michael B; Cullen, Michael; Davis, Faith G; Ding, Ti; Duell, Eric J; Epstein, Caroline G; Fan, Jin-Hu; Figueroa, Jonine D; Fraumeni, Joseph F; Freedman, Neal D; Fuchs, Charles S; Gao, Yu-Tang; Gapstur, Susan M; Patiño-Garcia, Ana; Garcia-Closas, Montserrat; Gaziano, J Michael; Giles, Graham G; Gillanders, Elizabeth M; Giovannucci, Edward L; Goldin, Lynn; Goldstein, Alisa M; Greene, Mark H; Hallmans, Goran; Harris, Curtis C; Henriksson, Roger; Holly, Elizabeth A; Hoover, Robert N; Hu, Nan; Hutchinson, Amy; Jenab, Mazda; Johansen, Christoffer; Khaw, Kay-Tee; Koh, Woon-Puay; Kolonel, Laurence N; Kooperberg, Charles; Krogh, Vittorio; Kurtz, Robert C; LaCroix, Andrea; Landgren, Annelie; Landi, Maria Teresa; Li, Donghui; Liao, Linda M; Malats, Nuria; McGlynn, Katherine A; McNeill, Lorna H; McWilliams, Robert R; Melin, Beatrice S; Mirabello, Lisa; Peplonska, Beata; Peters, Ulrike; Petersen, Gloria M; Prokunina-Olsson, Ludmila; Purdue, Mark; Qiao, You-Lin; Rabe, Kari G; Rajaraman, Preetha; Real, Francisco X; Riboli, Elio; Rodríguez-Santiago, Benjamín; Rothman, Nathaniel; Ruder, Avima M; Savage, Sharon A; Schwartz, Ann G; Schwartz, Kendra L; Sesso, Howard D; Severi, Gianluca; Silverman, Debra T; Spitz, Margaret R; Stevens, Victoria L; Stolzenberg-Solomon, Rachael; Stram, Daniel; Tang, Ze-Zhong; Taylor, Philip R; Teras, Lauren R; Tobias, Geoffrey S; Viswanathan, Kala; Wacholder, Sholom; Wang, Zhaoming; Weinstein, Stephanie J; Wheeler, William; White, Emily; Wiencke, John K; Wolpin, Brian M; Wu, Xifeng; Wunder, Jay S; Yu, Kai; Zanetti, Krista A; Zeleniuch-Jacquotte, Anne; Ziegler, Regina G; de Andrade, Mariza; Barnes, Kathleen C; Beaty, Terri H; Bierut, Laura J; Desch, Karl C; Doheny, Kimberly F; Feenstra, Bjarke; Ginsburg, David; Heit, John A; Kang, Jae H; Laurie, Cecilia A; Li, Jun Z; Lowe, William L; Marazita, Mary L; Melbye, Mads; Mirel, Daniel B; Murray, Jeffrey C; Nelson, Sarah C; Pasquale, Louis R; Rice, Kenneth; Wiggs, Janey L; Wise, Anastasia; Tucker, Margaret; Pérez-Jurado, Luis A; Laurie, Cathy C; Caporaso, Neil E; Yeager, Meredith; Chanock, Stephen J

    2015-03-01

    Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a set of 24,849 genotyped individuals (total GWAS set II [TGSII]) in whom 341 large autosomal abnormalities were observed in 168 (0.68%) individuals. Merging data from the new TGSII set with data from two prior reports (the Gene-Environment Association Studies and the total GWAS set I) generated a large dataset of 127,179 individuals; we then conducted a meta-analysis to investigate the patterns of detectable autosomal mosaicism (n = 1,315 events in 925 [0.73%] individuals). Restricting to events >2 Mb in size, we observed an increase in event frequency as event size decreased. The combined results underscore that the rate of detectable mosaicism increases with age (p value = 5.5 × 10(-31)) and is higher in men (p value = 0.002) but lower in participants of African ancestry (p value = 0.003). In a subset of 47 individuals from whom serial samples were collected up to 6 years apart, complex changes were noted over time and showed an overall increase in the proportion of mosaic cells as age increased. Our large combined sample allowed for a unique ability to characterize detectable genetic mosaicism involving large structural events and strengthens the emerging evidence of non-random erosion of the genome in the aging population. PMID:25748358

  19. Production and Structural Characterization of Lactobacillus helveticus Derived Biosurfactant

    PubMed Central

    Sharma, Deepansh; Saharan, Baljeet Singh; Chauhan, Nikhil; Bansal, Anshul; Procha, Suresh

    2014-01-01

    A probiotic strain of lactobacilli was isolated from traditional soft Churpi cheese of Yak milk and found positive for biosurfactant production. Lactobacilli reduced the surface tension of phosphate buffer saline (PBS) from 72.0 to 39.5 mNm−1 pH 7.2 and its critical micelle concentration (CMC) was found to be 2.5 mg mL−1. Low cost production of Lactobacilli derived biosurfactant was carried out at lab scale fermenter which yields 0.8 mg mL−1 biosurfactant. The biosurfactant was found least phytotoxic and cytotoxic as compared to the rhamnolipid and sodium dodecyl sulphate (SDS) at different concentration. Structural attributes of biosurfactant were determined by FTIR, NMR (1H and 13C), UPLC-MS, and fatty acid analysis by GCMS which confirmed the presence of glycolipid type of biosurfactant closely similar to xylolipids. Biosurfactant is mainly constituted by lipid and sugar fractions. The present study outcomes provide valuable information on structural characterization of the biosurfactant produced by L. helveticus MRTL91. These findings are encouraging for the application of Lactobacilli derived biosurfactant as nontoxic surface active agents in the emerging field of biomedical applications. PMID:25506070

  20. Microstructural characterization and pore structure analysis of nuclear graphite

    NASA Astrophysics Data System (ADS)

    Kane, J.; Karthik, C.; Butt, D. P.; Windes, W. E.; Ubic, R.

    2011-08-01

    Graphite will be used as a structural and moderator material in next-generation nuclear reactors. While the overall nature of the production of nuclear graphite is well understood, the historic nuclear grades of graphite are no longer available. This paper reports the virgin microstructural characteristics of filler particles and macro-scale porosity in virgin nuclear graphite grades of interest to the Next Generation Nuclear Plant program. Optical microscopy was used to characterize filler particle size and shape as well as the arrangement of shrinkage cracks. Computer aided image analysis was applied to optical images to quantitatively determine the variation of pore structure, area, eccentricity, and orientation within and between grades. The overall porosity ranged between ˜14% and 21%. A few large pores constitute the majority of the overall porosity. The distribution of pore area in all grades was roughly logarithmic in nature. The average pore was best fit by an ellipse with aspect ratio of ˜2. An estimated 0.6-0.9% of observed porosity was attributed to shrinkage cracks in the filler particles. Finally, a preferred orientation of the porosity was observed in all grades.

  1. Microstructural Characterization and Pore Structure Analysis of Nuclear Graphite

    SciTech Connect

    J. Kane; C. Karthik; D. P. Butt; W. E. Windes; R. Ubic

    2011-08-01

    Graphite will be used as a structural and moderator material in next-generation nuclear reactors. While the overall nature of the production of nuclear graphite is well understood, the historic nuclear grades of graphite are no longer available. This paper reports the virgin microstructural characteristics of filler particles and macro-scale porosity in virgin nuclear graphite grades of interest to the Next Generation Nuclear Plant program. Optical microscopy was used to characterize filler particle size and shape as well as the arrangement of shrinkage cracks. Computer aided image analysis was applied to optical images to quantitatively determine the variation of pore structure, area, eccentricity, and orientation within and between grades. The overall porosity ranged between {approx}14% and 21%. A few large pores constitute the majority of the overall porosity. The distribution of pore area in all grades was roughly logarithmic in nature. The average pore was best fit by an ellipse with aspect ratio of {approx}2. An estimated 0.6-0.9% of observed porosity was attributed to shrinkage cracks in the filler particles. Finally, a preferred orientation of the porosity was observed in all grades.

  2. Characterization of large structural genetic mosaicism in human autosomes.

    PubMed

    Machiela, Mitchell J; Zhou, Weiyin; Sampson, Joshua N; Dean, Michael C; Jacobs, Kevin B; Black, Amanda; Brinton, Louise A; Chang, I-Shou; Chen, Chu; Chen, Constance; Chen, Kexin; Cook, Linda S; Crous Bou, Marta; De Vivo, Immaculata; Doherty, Jennifer; Friedenreich, Christine M; Gaudet, Mia M; Haiman, Christopher A; Hankinson, Susan E; Hartge, Patricia; Henderson, Brian E; Hong, Yun-Chul; Hosgood, H Dean; Hsiung, Chao A; Hu, Wei; Hunter, David J; Jessop, Lea; Kim, Hee Nam; Kim, Yeul Hong; Kim, Young Tae; Klein, Robert; Kraft, Peter; Lan, Qing; Lin, Dongxin; Liu, Jianjun; Le Marchand, Loic; Liang, Xiaolin; Lissowska, Jolanta; Lu, Lingeng; Magliocco, Anthony M; Matsuo, Keitaro; Olson, Sara H; Orlow, Irene; Park, Jae Yong; Pooler, Loreall; Prescott, Jennifer; Rastogi, Radhai; Risch, Harvey A; Schumacher, Fredrick; Seow, Adeline; Setiawan, Veronica Wendy; Shen, Hongbing; Sheng, Xin; Shin, Min-Ho; Shu, Xiao-Ou; VanDen Berg, David; Wang, Jiu-Cun; Wentzensen, Nicolas; Wong, Maria Pik; Wu, Chen; Wu, Tangchun; Wu, Yi-Long; Xia, Lucy; Yang, Hannah P; Yang, Pan-Chyr; Zheng, Wei; Zhou, Baosen; Abnet, Christian C; Albanes, Demetrius; Aldrich, Melinda C; Amos, Christopher; Amundadottir, Laufey T; Berndt, Sonja I; Blot, William J; Bock, Cathryn H; Bracci, Paige M; Burdett, Laurie; Buring, Julie E; Butler, Mary A; Carreón, Tania; Chatterjee, Nilanjan; Chung, Charles C; Cook, Michael B; Cullen, Michael; Davis, Faith G; Ding, Ti; Duell, Eric J; Epstein, Caroline G; Fan, Jin-Hu; Figueroa, Jonine D; Fraumeni, Joseph F; Freedman, Neal D; Fuchs, Charles S; Gao, Yu-Tang; Gapstur, Susan M; Patiño-Garcia, Ana; Garcia-Closas, Montserrat; Gaziano, J Michael; Giles, Graham G; Gillanders, Elizabeth M; Giovannucci, Edward L; Goldin, Lynn; Goldstein, Alisa M; Greene, Mark H; Hallmans, Goran; Harris, Curtis C; Henriksson, Roger; Holly, Elizabeth A; Hoover, Robert N; Hu, Nan; Hutchinson, Amy; Jenab, Mazda; Johansen, Christoffer; Khaw, Kay-Tee; Koh, Woon-Puay; Kolonel, Laurence N; Kooperberg, Charles; Krogh, Vittorio; Kurtz, Robert C; LaCroix, Andrea; Landgren, Annelie; Landi, Maria Teresa; Li, Donghui; Liao, Linda M; Malats, Nuria; McGlynn, Katherine A; McNeill, Lorna H; McWilliams, Robert R; Melin, Beatrice S; Mirabello, Lisa; Peplonska, Beata; Peters, Ulrike; Petersen, Gloria M; Prokunina-Olsson, Ludmila; Purdue, Mark; Qiao, You-Lin; Rabe, Kari G; Rajaraman, Preetha; Real, Francisco X; Riboli, Elio; Rodríguez-Santiago, Benjamín; Rothman, Nathaniel; Ruder, Avima M; Savage, Sharon A; Schwartz, Ann G; Schwartz, Kendra L; Sesso, Howard D; Severi, Gianluca; Silverman, Debra T; Spitz, Margaret R; Stevens, Victoria L; Stolzenberg-Solomon, Rachael; Stram, Daniel; Tang, Ze-Zhong; Taylor, Philip R; Teras, Lauren R; Tobias, Geoffrey S; Viswanathan, Kala; Wacholder, Sholom; Wang, Zhaoming; Weinstein, Stephanie J; Wheeler, William; White, Emily; Wiencke, John K; Wolpin, Brian M; Wu, Xifeng; Wunder, Jay S; Yu, Kai; Zanetti, Krista A; Zeleniuch-Jacquotte, Anne; Ziegler, Regina G; de Andrade, Mariza; Barnes, Kathleen C; Beaty, Terri H; Bierut, Laura J; Desch, Karl C; Doheny, Kimberly F; Feenstra, Bjarke; Ginsburg, David; Heit, John A; Kang, Jae H; Laurie, Cecilia A; Li, Jun Z; Lowe, William L; Marazita, Mary L; Melbye, Mads; Mirel, Daniel B; Murray, Jeffrey C; Nelson, Sarah C; Pasquale, Louis R; Rice, Kenneth; Wiggs, Janey L; Wise, Anastasia; Tucker, Margaret; Pérez-Jurado, Luis A; Laurie, Cathy C; Caporaso, Neil E; Yeager, Meredith; Chanock, Stephen J

    2015-03-01

    Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a set of 24,849 genotyped individuals (total GWAS set II [TGSII]) in whom 341 large autosomal abnormalities were observed in 168 (0.68%) individuals. Merging data from the new TGSII set with data from two prior reports (the Gene-Environment Association Studies and the total GWAS set I) generated a large dataset of 127,179 individuals; we then conducted a meta-analysis to investigate the patterns of detectable autosomal mosaicism (n = 1,315 events in 925 [0.73%] individuals). Restricting to events >2 Mb in size, we observed an increase in event frequency as event size decreased. The combined results underscore that the rate of detectable mosaicism increases with age (p value = 5.5 × 10(-31)) and is higher in men (p value = 0.002) but lower in participants of African ancestry (p value = 0.003). In a subset of 47 individuals from whom serial samples were collected up to 6 years apart, complex changes were noted over time and showed an overall increase in the proportion of mosaic cells as age increased. Our large combined sample allowed for a unique ability to characterize detectable genetic mosaicism involving large structural events and strengthens the emerging evidence of non-random erosion of the genome in the aging population.

  3. Characterization of Polyimide Foams for Ultra-Lightweight Space Structures

    NASA Technical Reports Server (NTRS)

    Meador, Michael (Technical Monitor); Hillman, Keithan; Veazie, David R.

    2003-01-01

    Ultra-lightweight materials have played a significant role in nearly every area of human activity ranging from magnetic tapes and artificial organs to atmospheric balloons and space inflatables. The application range of ultra-lightweight materials in past decades has expanded dramatically due to their unsurpassed efficiency in terms of low weight and high compliance properties. A new generation of ultra-lightweight materials involving advanced polymeric materials, such as TEEK (TM) polyimide foams, is beginning to emerge to produce novel performance from ultra-lightweight systems for space applications. As a result, they require that special conditions be fulfilled to ensure adequate structural performance, shape retention, and thermal stability. It is therefore important and essential to develop methodologies for predicting the complex properties of ultra-lightweight foams. To support NASA programs such as the Reusable Launch Vehicle (RLV), Clark Atlanta University, along with SORDAL, Inc., has initiated projects for commercial process development of polyimide foams for the proposed cryogenic tank integrated structure (see figure 1). Fabrication and characterization of high temperature, advanced aerospace-grade polyimide foams and filled foam sandwich composites for specified lifetimes in NASA space applications, as well as quantifying the lifetime of components, are immensely attractive goals. In order to improve the development, durability, safety, and life cycle performance of ultra-lightweight polymeric foams, test methods for the properties are constant concerns in terms of timeliness, reliability, and cost. A major challenge is to identify the mechanisms of failures (i.e., core failure, interfacial debonding, and crack development) that are reflected in the measured properties. The long-term goal of the this research is to develop the tools and capabilities necessary to successfully engineer ultra-lightweight polymeric foams. The desire is to reduce density

  4. Characterization of structural relaxation in inorganic glasses using length dilatometry

    NASA Astrophysics Data System (ADS)

    Koontz, Erick

    The processes that govern how a glass relaxes towards its thermodynamic quasi-equilibrium state are major factors in understanding glass behavior near the glass transition region, as characterized by the glass transition temperature (Tg). Intrinsic glass properties such as specific volume, enthalpy, entropy, density, etc. are used to map the behavior of the glass network below in and near the transition region. The question of whether a true thermodynamic second order phase transition takes place in the glass transition region is another pending question. Linking viscosity behavior to entropy, or viewing the glass configuration as an energy landscape are just a couple of the most prevalent methods used for attempting to understand the glass transition. The structural relaxation behavior of inorganic glasses is important for more than scientific reasons, many commercial glass processing operations including glass melting and certain forms of optical fabrication include significant time spent in the glass transition region. For this reason knowledge of structural relaxation processes can, at a minimum, provide information for annealing duration of melt-quenched glasses. The development of a predictive model for annealing time prescription has the potential to save glass manufacturers significant time and money as well as increasing volume throughput. In optical hot forming processes such as precision glass molding, molded optical components can significantly change in shape upon cooling through the glass transition. This change in shape is not scientifically predictable as of yet though manufacturers typically use empirical rules developed in house. The classification of glass behavior in the glass transition region would allow molds to be accurately designed and save money for the producers. The work discussed in this dissertation is comprised of the development of a dilatometric measurement and characterization method of structural relaxation. The measurement and

  5. Structural characterization of the lignin from jute (Corchorus capsularis) fibers.

    PubMed

    del Río, José C; Rencoret, Jorge; Marques, Gisela; Li, Jiebing; Gellerstedt, Göran; Jiménez-Barbero, Jesús; Martínez, Angel T; Gutiérrez, Ana

    2009-11-11

    The structural characteristics of the lignin from jute (Corchorus capsularis ) fibers, which are used for high-quality paper pulp production, were studied. The lignin content (13.3% Klason lignin) was high compared to other nonwoody bast fibers used for pulp production. The lignin structure was characterized by pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS), 2D-NMR, and thioacidolysis. Upon Py-GC/MS, jute fibers released predominantly products from syringylpropanoid units with the S/G ratio being 2.1 and a H/G/S composition of 2:33:65. 2D-NMR of the milled wood lignin (MWL) isolated from jute fibers showed a predominance of beta-O-4' aryl ether linkages (72% of total side chains), followed by beta-beta' resinol-type linkages (16% of total side chains) and lower amounts of beta-5' phenylcoumaran (4%) and beta-1' spirodienone-type (4%) linkages and cinnamyl end groups (4%). The high predominance of the S-lignin units, together with the high proportion of beta-O-4' aryl ether linkages, which are easily cleaved during alkaline cooking, are advantageous for pulping. On the other hand, a small percentage (ca. 4%) of the lignin side chain was found to be acetylated at the gamma-carbon, predominantly over syringyl units. The analysis of desulphurated thioacidolysis dimers provided additional information on the relative abundances of the various carbon-carbon and diaryl ether bonds and the type of units (syringyl or guaiacyl) involved in each of the above linkage types. Interestingly, the major part of the beta-beta' dimers included two syringyl units, indicating that most of the beta-beta' substructures identified in the HSQC spectra were of the syringaresinol type (pinoresinol being absent), as already observed in the lignin of other angiosperms.

  6. Characterization of Large Structural Genetic Mosaicism in Human Autosomes

    PubMed Central

    Machiela, Mitchell J.; Zhou, Weiyin; Sampson, Joshua N.; Dean, Michael C.; Jacobs, Kevin B.; Black, Amanda; Brinton, Louise A.; Chang, I-Shou; Chen, Chu; Chen, Constance; Chen, Kexin; Cook, Linda S.; Crous Bou, Marta; De Vivo, Immaculata; Doherty, Jennifer; Friedenreich, Christine M.; Gaudet, Mia M.; Haiman, Christopher A.; Hankinson, Susan E.; Hartge, Patricia; Henderson, Brian E.; Hong, Yun-Chul; Hosgood, H. Dean; Hsiung, Chao A.; Hu, Wei; Hunter, David J.; Jessop, Lea; Kim, Hee Nam; Kim, Yeul Hong; Kim, Young Tae; Klein, Robert; Kraft, Peter; Lan, Qing; Lin, Dongxin; Liu, Jianjun; Le Marchand, Loic; Liang, Xiaolin; Lissowska, Jolanta; Lu, Lingeng; Magliocco, Anthony M.; Matsuo, Keitaro; Olson, Sara H.; Orlow, Irene; Park, Jae Yong; Pooler, Loreall; Prescott, Jennifer; Rastogi, Radhai; Risch, Harvey A.; Schumacher, Fredrick; Seow, Adeline; Setiawan, Veronica Wendy; Shen, Hongbing; Sheng, Xin; Shin, Min-Ho; Shu, Xiao-Ou; VanDen Berg, David; Wang, Jiu-Cun; Wentzensen, Nicolas; Wong, Maria Pik; Wu, Chen; Wu, Tangchun; Wu, Yi-Long; Xia, Lucy; Yang, Hannah P.; Yang, Pan-Chyr; Zheng, Wei; Zhou, Baosen; Abnet, Christian C.; Albanes, Demetrius; Aldrich, Melinda C.; Amos, Christopher; Amundadottir, Laufey T.; Berndt, Sonja I.; Blot, William J.; Bock, Cathryn H.; Bracci, Paige M.; Burdett, Laurie; Buring, Julie E.; Butler, Mary A.; Carreón, Tania; Chatterjee, Nilanjan; Chung, Charles C.; Cook, Michael B.; Cullen, Michael; Davis, Faith G.; Ding, Ti; Duell, Eric J.; Epstein, Caroline G.; Fan, Jin-Hu; Figueroa, Jonine D.; Fraumeni, Joseph F.; Freedman, Neal D.; Fuchs, Charles S.; Gao, Yu-Tang; Gapstur, Susan M.; Patiño-Garcia, Ana; Garcia-Closas, Montserrat; Gaziano, J. Michael; Giles, Graham G.; Gillanders, Elizabeth M.; Giovannucci, Edward L.; Goldin, Lynn; Goldstein, Alisa M.; Greene, Mark H.; Hallmans, Goran; Harris, Curtis C.; Henriksson, Roger; Holly, Elizabeth A.; Hoover, Robert N.; Hu, Nan; Hutchinson, Amy; Jenab, Mazda; Johansen, Christoffer; Khaw, Kay-Tee; Koh, Woon-Puay; Kolonel, Laurence N.; Kooperberg, Charles; Krogh, Vittorio; Kurtz, Robert C.; LaCroix, Andrea; Landgren, Annelie; Landi, Maria Teresa; Li, Donghui; Liao, Linda M.; Malats, Nuria; McGlynn, Katherine A.; McNeill, Lorna H.; McWilliams, Robert R.; Melin, Beatrice S.; Mirabello, Lisa; Peplonska, Beata; Peters, Ulrike; Petersen, Gloria M.; Prokunina-Olsson, Ludmila; Purdue, Mark; Qiao, You-Lin; Rabe, Kari G.; Rajaraman, Preetha; Real, Francisco X.; Riboli, Elio; Rodríguez-Santiago, Benjamín; Rothman, Nathaniel; Ruder, Avima M.; Savage, Sharon A.; Schwartz, Ann G.; Schwartz, Kendra L.; Sesso, Howard D.; Severi, Gianluca; Silverman, Debra T.; Spitz, Margaret R.; Stevens, Victoria L.; Stolzenberg-Solomon, Rachael; Stram, Daniel; Tang, Ze-Zhong; Taylor, Philip R.; Teras, Lauren R.; Tobias, Geoffrey S.; Viswanathan, Kala; Wacholder, Sholom; Wang, Zhaoming; Weinstein, Stephanie J.; Wheeler, William; White, Emily; Wiencke, John K.; Wolpin, Brian M.; Wu, Xifeng; Wunder, Jay S.; Yu, Kai; Zanetti, Krista A.; Zeleniuch-Jacquotte, Anne; Ziegler, Regina G.; de Andrade, Mariza; Barnes, Kathleen C.; Beaty, Terri H.; Bierut, Laura J.; Desch, Karl C.; Doheny, Kimberly F.; Feenstra, Bjarke; Ginsburg, David; Heit, John A.; Kang, Jae H.; Laurie, Cecilia A.; Li, Jun Z.; Lowe, William L.; Marazita, Mary L.; Melbye, Mads; Mirel, Daniel B.; Murray, Jeffrey C.; Nelson, Sarah C.; Pasquale, Louis R.; Rice, Kenneth; Wiggs, Janey L.; Wise, Anastasia; Tucker, Margaret; Pérez-Jurado, Luis A.; Laurie, Cathy C.; Caporaso, Neil E.; Yeager, Meredith; Chanock, Stephen J.

    2015-01-01

    Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a set of 24,849 genotyped individuals (total GWAS set II [TGSII]) in whom 341 large autosomal abnormalities were observed in 168 (0.68%) individuals. Merging data from the new TGSII set with data from two prior reports (the Gene-Environment Association Studies and the total GWAS set I) generated a large dataset of 127,179 individuals; we then conducted a meta-analysis to investigate the patterns of detectable autosomal mosaicism (n = 1,315 events in 925 [0.73%] individuals). Restricting to events >2 Mb in size, we observed an increase in event frequency as event size decreased. The combined results underscore that the rate of detectable mosaicism increases with age (p value = 5.5 × 10−31) and is higher in men (p value = 0.002) but lower in participants of African ancestry (p value = 0.003). In a subset of 47 individuals from whom serial samples were collected up to 6 years apart, complex changes were noted over time and showed an overall increase in the proportion of mosaic cells as age increased. Our large combined sample allowed for a unique ability to characterize detectable genetic mosaicism involving large structural events and strengthens the emerging evidence of non-random erosion of the genome in the aging population. PMID:25748358

  7. Characterizing unknown systematics in large scale structure surveys

    SciTech Connect

    Agarwal, Nishant; Ho, Shirley; Myers, Adam D.; Seo, Hee-Jong; Ross, Ashley J.; Bahcall, Neta; Brinkmann, Jonathan; Eisenstein, Daniel J.; Muna, Demitri; Palanque-Delabrouille, Nathalie; Yèche, Christophe; Petitjean, Patrick; Schneider, Donald P.; Streblyanska, Alina; Weaver, Benjamin A.

    2014-04-01

    Photometric large scale structure (LSS) surveys probe the largest volumes in the Universe, but are inevitably limited by systematic uncertainties. Imperfect photometric calibration leads to biases in our measurements of the density fields of LSS tracers such as galaxies and quasars, and as a result in cosmological parameter estimation. Earlier studies have proposed using cross-correlations between different redshift slices or cross-correlations between different surveys to reduce the effects of such systematics. In this paper we develop a method to characterize unknown systematics. We demonstrate that while we do not have sufficient information to correct for unknown systematics in the data, we can obtain an estimate of their magnitude. We define a parameter to estimate contamination from unknown systematics using cross-correlations between different redshift slices and propose discarding bins in the angular power spectrum that lie outside a certain contamination tolerance level. We show that this method improves estimates of the bias using simulated data and further apply it to photometric luminous red galaxies in the Sloan Digital Sky Survey as a case study.

  8. Crystal structure controlled synthesis and characterization of copper sulfide nanoparticles

    NASA Astrophysics Data System (ADS)

    Senthilkumar, M.; Babu, S. Moorthy

    2016-05-01

    Phase pure, controlled crystal structure of digenite (Cu9S5) copper sulfide nanoparticles were synthesized by hot injection method at the temperature of 180°C. The mixture of Oleylamine, 1-Octadecene and 1-Dodecanethiol were taken as solvent as well as capping agents. The effect of the mixture of solvents on the phase formation and morphology of the synthesized nanoparticles were analysed. The nanocrystals were characterized using X-Ray diffraction (XRD) which confirms the presence of single phase rhombohedral digenite Cu9S5 NPs, Morphological analysis clearly depicts the formation of hexagonal faceted Cu9S5 NPs, Energy dispersive X-ray absorption spectroscopy (EDS) reveals the stoichiometric ratio of 1.8:1 for synthesized NPs. From the UV-Vis absorption spectroscopy the bandgap value of Cu1.8S is found to be 1.71 eV. The presence of capping agents along the surface of the Cu9S5 NPs was confirmed from FTIR analysis.

  9. Synthesis, structure characterization and catalytic activity of nickel tungstate nanoparticles

    NASA Astrophysics Data System (ADS)

    Pourmortazavi, Seied Mahdi; Rahimi-Nasrabadi, Mehdi; Khalilian-Shalamzari, Morteza; Zahedi, Mir Mahdi; Hajimirsadeghi, Seiedeh Somayyeh; Omrani, Ismail

    2012-12-01

    Taguchi robust design was applied to optimize experimental parameters for controllable, simple and fast synthesis of nickel tungstate nanoparticles. NiWO4 nanoparticles were synthesized by precipitation reaction involving addition of nickel ion solution to the tungstate aqueous reagent and then formation of nickel tungstate nucleolus which are insoluble in aqueous media. Effects of various parameters such as nickel and tungstate concentrations, flow rate of reagent addition and reactor temperature on diameter of synthesized nickel tungstate nanoparticles were investigated experimentally by the aid of orthogonal array design. The results for analysis of variance (ANOVA) showed that particle size of nickel tungstate can be effectively tuned by controlling significant variables involving nickel and tungstate concentrations and flow rate; while, temperature of the reactor has a no considerable effect on the size of NiWO4 particles. The ANOVA results proposed the optimum conditions for synthesis of nickel tungstate nanoparticles via this technique. Also, under optimum condition nanoparticles of NiWO4 were prepared and their structure and chemical composition were characterized by means of EDAX, XRD, SEM, FT-IR spectroscopy, UV-vis spectroscopy, and photoluminescence. Finally, catalytic activity of the nanoparticles in a cycloaddition reaction was examined.

  10. Synthesis, single crystal structure and characterization of pentanitromonoformylhexaazaisowurtzitane.

    PubMed

    Chen, Huaxiong; Chen, Shusen; Li, Lijie; Jiao, Qingze; Wei, Tianyu; Jin, Shaohua

    2010-03-15

    Pentanitromonoformylhexaazaisowurtzitane (PNMFIW) was synthesized by the nitrolysis of tetraacetyldiformylhexaazaisowurtzitane (TADFIW) in mixed nitric and sulfuric acids and structurally characterized by element analysis, FT-IR, MS and (1)H NMR. Single crystals of PNMFIW were grown from aqueous solution employing the technique of controlled evaporation. PNMFIW belongs to the orthorhombic system having four molecules in the unit cell, with space group P2(1)2(1)2(1) and the lattice parameters a=8.8000(18)A, b=12.534(2)A, and c=12.829(3)A. The calculated density reaches 1.977 g/cm(3) at 93 K, while the experimental density is 1.946 g/cm(3) at 20 degrees C. The calculated detonation velocity and pressure of PNMFIW according to the experimental density are 9195.76 m/s and 39.68G Pa, respectively. PNMFIW is insensitive compared with epsilon-HNIW through drop hammer impact sensitivity test. PMID:19913358

  11. Characterization of Chitin and Chitosan Molecular Structure in Aqueous Solution

    SciTech Connect

    Franca, Eduardo D.; Lins, Roberto D.; Freitas, Luiz C.; Straatsma, t. P.

    2008-11-08

    Molecular dynamics simulations have been used to characterize the structure of chitin and chitosan fibers in aqueous solutions. Chitin fibers, whether isolated or in the form of a β-chitin nanoparticle, adopt the so-called 2-fold helix with Φ and φ values similar to its crystalline state. In solution, the intramolecular hydrogen bond HO3(n)•••O5(n+1) responsible for the 2-fold helical motif is stabilized by hydrogen bonds with water molecules in a well-defined orientation. On the other hand, chitosan can adopt five distinct helical motifs and its conformational equilibrium is highly dependent on pH. The hydrogen bond pattern and solvation around the O3 atom of insoluble chitosan (basic pH) are nearly identical to these quantities in chitin. Our findings suggest that the solubility and conformation of these polysaccharides are related to the stability of the intrachain HO3(n)•••O5(n+1) hydrogen bond, which is affect by the water exchange around the O3-HO3 hydroxyl group.

  12. Characterization of a rice bran oil structured lipid.

    PubMed

    Jennings, Brenda H; Akoh, Casimir C

    2009-04-22

    Rice bran oil (RBO) was enzymatically modified in a continuous packed bed bioreactor to incorporate caprylic acid with Lipozyme RM IM as biocatalyst. The reaction product was purified by short-path distillation. Rice bran oil structured lipid (RBOSL) contained 32.1 mol % caprylic acid. Positional analysis revealed 0.7 mol % caprylic acid at the sn-2 position and 47.8 mol % caprylic acid at the sn-1,3 positions. Composition of free fatty acids and smoke point of RBO and RBOSL were not significantly different. Saponification value, iodine value, and viscosity of RBO were significantly different from those of RBOSL. The color of RBOSL was darker, more yellow and less green than RBO. Volatile compounds in RBO and RBOSL were determined by GC-MS. Melting onset temperatures of RBO and RBOSL were not significantly different, while melting end point temperatures and melting enthalpies were significantly different. This characterization study results will help determine potential food applications of RBOSL. PMID:19284800

  13. Structure and characterization of RNase H3 from Aquifex aeolicus.

    PubMed

    Jongruja, Nujarin; You, Dong-Ju; Angkawidjaja, Clement; Kanaya, Eiko; Koga, Yuichi; Kanaya, Shigenori

    2012-08-01

    The crystal structure of ribonuclease H3 from Aquifex aeolicus (Aae-RNase H3) was determined at 2.0 Å resolution. Aae-RNase H3 consists of an N-terminal TATA box-binding protein (TBP)-like domain (N-domain) and a C-terminal RNase H domain (C-domain). The structure of the C-domain highly resembles that of Bacillus stearothermophilus RNase H3 (Bst-RNase H3), except that it contains three disulfide bonds, and the fourth conserved glutamate residue of the Asp-Glu-Asp-Glu active site motif (Glu198) is located far from the active site. These disulfide bonds were shown to contribute to hyper-stabilization of the protein. Non-conserved Glu194 was identified as the fourth active site residue. The structure of the N-domain without the C-domain also highly resembles that of Bst-RNase H3. However, the arrangement of the N-domain relative to the C-domain greatly varies for these proteins because of the difference in the linker size between the domains. The linker of Bst-RNase H3 is relatively long and flexible, while that of Aae-RNase H3 is short and assumes a helix formation. Biochemical characterizations of Aae-RNase H3 and its derivatives without the N- or C-domain or with a mutation in the N-domain indicate that the N-domain of Aae-RNase H3 is important for substrate binding, and uses the flat surface of the β-sheet for substrate binding. However, this surface is located far from the active site and on the opposite side to the active site. We propose that the N-domain of Aae-RNase H3 is required for initial contact with the substrate. The resulting complex may be rearranged such that only the C-domain forms a complex with the substrate. PMID:22686566

  14. Pore- and micro-structural characterization of a novel structural binder based on iron carbonation

    SciTech Connect

    Das, Sumanta; Stone, David; Convey, Diana; Neithalath, Narayanan

    2014-12-15

    The pore- and micro-structural features of a novel binding material based on the carbonation of waste metallic iron powder are reported in this paper. The binder contains metallic iron powder as the major ingredient, followed by additives containing silica and alumina to facilitate favorable reaction product formation. Compressive strengths sufficient for a majority of concrete applications are attained. The material pore structure is investigated primarily through mercury intrusion porosimetry whereas electron microscopy is used for microstructural characterization. Reduction in the overall porosity and the average pore size with an increase in carbonation duration from 1 day to 4 days is noticed. The pore structure features are used in predictive models for gas and moisture transport (water vapor diffusivity and moisture permeability) through the porous medium which dictates its long-term durability when used in structural applications. Comparisons of the pore structure with those of a Portland cement paste are also provided. The morphology of the reaction products in the iron-based binder, and the distribution of constituent elements in the microstructure are also reported. - Highlights: • Carbonation of iron produces a dense microstructure. • Pore volume in iron carbonate lower, critical size higher than those in OPC pastes • Reaction product contains iron, carbon, silicon, aluminum and calcium. • Power-law for porosity-moisture permeability relationship was established.

  15. Structural characterization and electronic structure of laser treated TiN thin film

    SciTech Connect

    Soni, Sheetal; Nair, K. G. M.; Phase, D. M.; Gupta, Ratnesh

    2012-06-05

    TiN thin films prepared by laser treatment using Kr-F excimer laser in the controlled atmosphere. The depth distribution and composition of nitrogen and contaminated oxygen have been determined by non-Rutherford proton backscattering using 1.7 MeV Tendetron accelerator. The electronic structure of TiN thin film have been characterized by resonant photoelectron spectroscopy using indus-I synchrotron radiation. Specifically, complex resonance profile that shows the enhancement at 45 eV which is consistent with the resonant photoemission of Ti 3d states involved in the Titanium nitride and oxide.

  16. Underground structure characterization using motor vehicles as passive seismic sources

    NASA Astrophysics Data System (ADS)

    Kuzma, H. A.; Liu, Y.; Zhao, Y.; Rector, J.; Vaidya, S.

    2009-12-01

    The ability to detect and characterize underground voids will be critical to the success of On-Site Inspections (OSI) as mandated by the nuclear Comprehensive Test Ban Treaty (CTBT). OSIs may be conducted in order to successfully locate the Ground Zero of underground tests as well as infrastructure related to testing. Recently, our team has shown the potential of a new technique to detect underground objects using the amplitude of seismic surface waves generated by motor vehicles. In an experiment conducted in June, 2009 we were able to detect an abandoned railroad tunnel by recognizing a clear pattern in the surface waves scattered by the tunnel, using a signal generated by driving a car on a dirt road across the tunnel. Synthetic experiments conducted using physically realistic wave-equation models further suggest that the technique can be readily applied to detecting underground features: it may be possible to image structures of importance to OSI simply by laying out an array of geophones (or using an array already in place for passive listening for event aftershocks) and driving vehicles around the site. We present evidence from a set of field experiments and from synthetic modeling and inversion studies to illustrate adaptations of the technique for OSI. Signature of an abandoned underground railroad tunnel at Donner Summit, CA. To produce this image, a line of geophones was placed along a dirt road perpendicular to the tunnel (black box) and a single car was driven along the road. A normalized mean power-spectrum is displayed on a log scale as a function of meters from the center of the tunnel. The top of the tunnel was 18m below ground surface. The tunnel anomaly is made up of a shadow (light) directly above the tunnel and amplitude build-up (dark) on either side of the tunnel. The size of the anomaly (6 orders of magnitude) suggests that the method can be extended to find deep structures at greater distances from the source and receivers.

  17. Synthesis, structure, and spectroscopic characterization of three uranyl phosphates with unique structural units

    SciTech Connect

    Wylie, Ernest M.; Dawes, Colleen M.; Burns, Peter C.

    2012-12-15

    Single crystals of Zn{sub 4}(OH){sub 2}[(UO{sub 2})(PO{sub 4}){sub 2}(OH){sub 2}(H{sub 2}O)] (UZnP), Cs[(UO{sub 2})(HPO{sub 4})NO{sub 3}] (UCsP), and In{sub 3}[(UO{sub 2}){sub 2}(PO{sub 4}){sub 4}OH(H{sub 2}O){sub 6}].2H{sub 2}O (UInP) were obtained from hydrothermal reactions and have been structurally and chemically characterized. UZnP crystallizes in space group Pbcn, a=8.8817(7), b=6.6109(5), c=19.569(1) A; UCsP crystallizes in P-1, a=7.015(2), b=7.441(1), c=9.393(2) A, {alpha}=72.974(2), {beta}=74.261(2), {gamma}=79.498(2); and UInP crystallizes in P-1, a=7.9856(5), b=9.159(1), c=9.2398(6) A {alpha}=101.289(1), {beta}=114.642(1), {gamma}=99.203(2). The U{sup 6+} cations are present as (UO{sub 2}){sup 2+} uranyl ions coordinated by five O atoms to give pentagonal bipyramids. The structural unit in UZnP is a finite cluster containing a uranyl pentagonal bipyramid that shares corners with two phosphate tetrahedra. The structural unit in UCsP is composed of uranyl pentagonal bipyramids with one chelating nitrate group that are linked into chains by three bridging hydrogen phosphate tetrahedra. In UInP, the structural unit contains pairs of edge-sharing uranyl pentagonal bipyramids with two chelating phosphate tetrahedra that are linked into chains through two bridging phosphate tetrahedra. Indium octahedra link these uranyl phosphate chains into a 3-dimensional framework. All three compounds exhibit unique structural units that deviate from the typical layered structures observed in uranyl phosphate solid-state chemistry. - Graphical abstract: Three new uranyl phosphates with unique structural units are reported. Black-Small-Square Highlights: Black-Right-Pointing-Pointer Three new uranyl phosphates have been synthesized hydrothermally. Black-Right-Pointing-Pointer Single crystal analyses reveal unique structural units. Black-Right-Pointing-Pointer The dimensionality of these compounds deviate from typical U{sup 6+} layered structures.

  18. Reflection spectra and magnetochemistry of iron oxides and natural surfaces

    NASA Technical Reports Server (NTRS)

    Wasilewski, P.

    1978-01-01

    The magnetic properties and spectral characteristics of iron oxides are distinctive. Diagnostic features in reflectance spectra (0.5 to 2.4 micron) for alpha Fe2O3, gamma Fe2O3, and FeOOH include location of Fe3(+) absorption features, intensity ratios at various wavelengths, and the curve shape between 1.2 micron and 2.4 micron. The reflection spectrum of natural rock surfaces are seldom those of the bulk rock because of weathering effects. Coatings are found to be dominated by iron oxides and clay. A simple macroscopic model of rock spectra (based on concepts of stains and coatings) is considered adequate for interpretation of LANDSAT data. The magnetic properties of materials associated with specific spectral types and systematic changes in both spectra and magnetic properties are considered.

  19. Characterizing 3D RNA structure by single molecule FRET.

    PubMed

    Stephenson, James D; Kenyon, Julia C; Symmons, Martyn F; Lever, Andrew M L

    2016-07-01

    The importance of elucidating the three dimensional structures of RNA molecules is becoming increasingly clear. However, traditional protein structural techniques such as NMR and X-ray crystallography have several important drawbacks when probing long RNA molecules. Single molecule Förster resonance energy transfer (smFRET) has emerged as a useful alternative as it allows native sequences to be probed in physiological conditions and allows multiple conformations to be probed simultaneously. This review serves to describe the method of generating a three dimensional RNA structure from smFRET data from the biochemical probing of the secondary structure to the computational refinement of the final model.

  20. Fabrication and Characterization of Woodpile Structures for Direct Laser Acceleration

    SciTech Connect

    McGuinness, C.; Colby, E.; England, R.J.; Ng, J.; Noble, R.J.; Peralta, E.; Soong, K.; Spencer, J.; Walz, D.; Byer, R.L.; /Stanford U., Ginzton Lab.

    2010-08-26

    An eight and nine layer three dimensional photonic crystal with a defect designed specifically for accelerator applications has been fabricated. The structures were fabricated using a combination of nanofabrication techniques, including low pressure chemical vapor deposition, optical lithography, and chemical mechanical polishing. Limits imposed by the optical lithography set the minimum feature size to 400 nm, corresponding to a structure with a bandgap centered at 4.26 {micro}m. Reflection spectroscopy reveal a peak in reflectivity about the predicted region, and good agreement with simulation is shown. The eight and nine layer structures will be aligned and bonded together to form the complete seventeen layer woodpile accelerator structure.

  1. AFM characterization of the shape of surface structures with localization factor.

    PubMed

    Bonyár, Attila

    2016-08-01

    Although with the use of scanning probe microscopy (SPM) methods the topographical imaging of surfaces is now widely available, the characterization of surface structures, especially their shape, and the processes which change these features is not trivial with the existing surface describing parameters. In this work the application of a parameter called localization factor is demonstrated for the quantitative characterization of surface structures and for processes which alter the shape of these structures. The theory and optimal operation range of this parameter are discussed with three application examples: microstructure characterization of gold thin films, characterization of the changes in the grain structure of these films during thermal annealing, and finally, characterization of the oxidation processes on a polished tin surface. PMID:27174696

  2. Structure characterization of protein fractions from lotus ( Nelumbo nucifera) seed

    NASA Astrophysics Data System (ADS)

    Zeng, Hong-Yan; Cai, Lian-Hui; Cai, Xi-Ling; Wang, Ya-Ju; Li, Yu-Qin

    2011-08-01

    Protein fractionation of lotus seed was carried out and the structures of the protein fractions were studied. Fourier transform infrared spectroscopy (FTIR) as well as ultraviolet visible spectroscopy (UV-vis) was used to investigate changes in molecular structures of the protein fractions. FTIR and UV-vis spectra showed the protein fractions had different protein molecular structures. FTIR spectra showed β-sheets and β-turns as the major secondary structures in the individual protein fractions, while the amounts of α-helix and random coil structures among the different fractions did not significantly change. The amounts of β-sheet structures of albumin and globulin were significantly higher than ones of prolamin and glutelin, implying albumin and globulin had high stabilities because of the high content in β-sheet structures. The observed similarity in the amounts of α-helix, random coil, β-sheet and β-turn structures shared by albumin and globulin indicated that their interior conformations were similar.

  3. NMR Methods for Characterization of RNA Secondary Structure.

    PubMed

    Kennedy, Scott D

    2016-01-01

    Knowledge of RNA secondary structure is often sufficient to identify relationships between the structure of RNA and processing pathways, and the design of therapeutics. Nuclear magnetic resonance (NMR) can identify types of nucleotide base pairs and the sequence, thus limiting possible secondary structures. Because NMR experiments, like chemical mapping, are performed in solution, not in single crystals, experiments can be initiated as soon as the biomolecule is expressed and purified. This chapter summarizes NMR methods that permit rapid identification of RNA secondary structure, information that can be used as supplements to chemical mapping, and/or as preliminary steps required for 3D structure determination. The primary aim is to provide guidelines to enable a researcher with minimal knowledge of NMR to quickly extract secondary structure information from basic datasets. Instrumental and sample considerations that can maximize data quality are discussed along with some details for optimal data acquisition and processing parameters. Approaches for identifying base pair types in both unlabeled and isotopically labeled RNA are covered. Common problems, such as missing signals and overlaps, and approaches to address them are considered. Programs under development for merging NMR data with structure prediction algorithms are briefly discussed. PMID:27665604

  4. Characterization of photodeposited selenium planar structures by scanning force microscopy

    NASA Astrophysics Data System (ADS)

    Peled, A.; Baranauskas, V.; Rodrigues, C.; Art-Weisman, D.; Grantman, L.; Friesem, A. A.

    1995-06-01

    This article describes the results of a surface morphology study of photodeposited thin film devices of Selenium by scanning force microscopy (SFM). First, the structures of the photodeposited films were investigated at device level dimensions of the order of visible wavelength. Specifically, ultrathin sinusoidal holographic gratings with spatial periods in the range 480-514 nm were visually identified from SFM nanograph images. Second, grain level structural investigation was performed using image processing techniques such as filtering and one- and two-dimensional Fourier transforms analysis. The variation of the surface grain structure was sampled across the Gaussian profiles of the laser photodeposited patterns. It was found that the random amorphous clustering at the perimeter of the deposited structures becomes progressively grainy towards the center, creating protrusions above the surface with trigonal Selenium (t-Se) crystalline features. Third, performing image enhancement analysis at high magnification—the nanometer level structure was investigated for amorphous Selenium (a-Se) and the laser thermally induced structural transformations of the a-Se films. It was found that the atomic solid-state structure of a-Se films, previously deduced only by indirect methods, consists mainly of a random mixture of Sex branched chains containing also a small concentration of imperfect ring structures characteristic of the α- and β-monoclinic phases. The triclinic crystalline phase (t-Se) was identified in the center of the laser overheated regions of the film Gaussian profile. The results enable us to conclude about the debate in the literature regarding the crystalline and amorphous structure of Selenium thin films.

  5. Structural Characterization of Layered Morphologies in Precise Copolymers

    NASA Astrophysics Data System (ADS)

    Trigg, Edward; Gaines, Taylor; Wagener, Kenneth; Winey, Karen

    2015-03-01

    Layered morphologies have been observed in precise polyethylene-based copolymers that contain acid, charged, or polar functional groups precisely spaced along a linear alkane chain. Sufficiently long alkane segments form structures resembling orthorhombic polyethylene crystals, while the functional groups form 2-D layers that disrupt the alkane crystal structure to varying degrees. Here, layered morphologies in precise copolymers containing acrylic acid, phosphonic acid, imidazolium bromide, and sulfone groups are studied via X-ray scattering. Specifically, the composition profiles of the layered structures are obtained by Fourier synthesis, and the coherence length is investigated using peak width analysis. This analysis indicates that the layers of functional groups are frequently bordered by two crystallites, which suggests different dynamics relative to layers bordered by one crystalline and one amorphous microdomain. Detailed understanding of the structure of the layered morphologies will allow for a systematic investigation of proton and ion conductivity mechanisms, which are expected to occur through the high-dielectric layers.

  6. Synthesis and structural characterization of polyaniline/cobalt chloride composites

    NASA Astrophysics Data System (ADS)

    Asha, Goyal, Sneh Lata; Kishore, Nawal

    2016-05-01

    Polyaniline (PANI) and PANI /cobalt chloride composites were synthesized by in situ chemical oxidative polymerization of aniline with CoCl2.6H2O using ammonium peroxidisulphate as an oxidant. These composites were characterized by X-ray diffraction (XRD) and Scanning electron microscopy (SEM). The XRD study reveals that both PANI and composites are amorphous. The XRD and SEM results confirm the presence of cobalt chloride in the composites.

  7. Characterization of flow-induced structures in carbon nanotube suspensions

    NASA Astrophysics Data System (ADS)

    Khalkhal, Fatemeh

    Carbon nanotubes (CNTs) are fibre-like nano-particles with many different applications. Due to their high specific surface area, high electric current density, thermal stability and excellent mechanical properties, they are used to reinforce physical properties of polymer matrices. The macroscopic properties of suspensions are inherited from their properties at micron and sub-micron scales. The suspensions structure can be easily influenced by many parameters such as the extent of external shear forces, the suspension concentration, temperature, the particles specifications, etc. This makes the study of the suspension structure a very challenging task and has been the subject of interest to many researchers. In this thesis, the structure of a model carbon nanotube suspension dispersed in an epoxy is studied by employing a set of rheological methods, scaling and fractal theories and a structural thixotropic model. The effect of flow history on linear viscoelastic properties of suspensions and the evolution of structure upon cessation of shear flow has been studied over a wide range of pre-shearing rates, concentration and temperature. The results of these analyses are as follows. The effect of flow history is more pronounced on the suspensions structure in dilute and semi-dilute concentration regimes. By pre-shearing at low rates, more inter-particle entanglements were induced, which resulted in reduction of rheological percolation thresholds. After cessation of shear flow, for dilute and semi-dilute suspensions, the formed metastable structures were distinguishable by different storage moduli, which were inversely related to the rate of pre-shearing. However, for the concentrated suspensions, the formed metastable structures had an approximately equal storage modulus regardless of the rate of the applied pre-shearing. It was shown that the rate of formation of these metastable structures was enhanced by increasing concentration. Furthermore, the rate of structure

  8. Structural characterization of lignin from grape stalks (Vitis vinifera L.).

    PubMed

    Prozil, Sónia O; Evtuguin, Dmitry V; Silva, Artur M S; Lopes, Luísa P C

    2014-06-18

    The chemical structure of lignin from grape stalks, an abundant waste of winemaking, has been studied. The dioxane lignin was isolated from extractive- and protein-free grape stalks (Vitis vinifera L.) by modified acidolytic procedure and submitted to a structural analysis by wet chemistry (nitrobenzene and permanganate oxidation (PO)) and spectroscopic techniques. The results obtained suggest that grape stalk lignin is an HGS type with molar proportions of p-hydroxyphenyl (H), guaiacyl (G) and syringyl (S) units of 3:71:26. Structural analysis by (1)H and (13)C NMR spectroscopy and PO indicates the predominance of β-O-4' structures (39% mol) in grape stalk lignin together with moderate amounts of β-5', β-β, β-1', 5-5', and 4-O-5' structures. NMR studies also revealed that grape lignin should be structurally associated with tannins. The condensation degree of grape stalks lignin is higher than that of conventional wood lignins and lignins from other agricultural residues.

  9. Synthesis and characterization of a new structure of gas hydrate

    SciTech Connect

    Tulk, Christopher A; Chakoumakos, Bryan C; Ehm, Lars; Klug, Dennis D; Parise, John B; Yang, Ling; Martin, Dave; Ripmeester, John; Moudrakovski, Igor; Ratcliffe, Chris

    2009-01-01

    Atoms and molecules 0.4 0.9 nm in diameter can be incorporated in the cages formed by hydrogen-bonded water molecules making up the crystalline solid clathrate hydrates. There are three structural families of these hydrates , known as sI, sII and sH, and the structure usually depends on the largest guest molecule in the hydrate. Species such as Ar, Kr, Xe and methane form sI or sII hydrate, sH is unique in that it requires both small and large cage guests for stability. All three structures, containing methane, other hydrocarbons, H2S and CO2, O2 and N2 have been found in the geosphere, with sI methane hydrate by far the most abundant. At high pressures (P > 0.7 kbar) small guests (Ar, Kr, Xe, methane) are also known to form sH hydrate with multiple occupancy of the largest cage in the hydrate. The high-pressure methane hydrate of sH has been proposed as playing a role in the outer solar system, including formation models for Titan , and yet another high pressure phase of methane has been reported , although its structure remains unknown. In this study, we report a new and unique hydrate structure that is derived from the high pressure sH hydrate of xenon. After quench recovery at ambient pressure and 77 K it shows considerable stability at low temperatures (T < 160 K) and is compositionally similar to the sI Xe clathrate starting material. This evidence of structural complexity in compositionally similar clathrate compounds indicates that thermodynamic pressure temperature conditions may not be the only important factor in structure determination, but also the reaction path may have an important effect.

  10. Characterization of crystalline structures in Opuntia ficus-indica.

    PubMed

    Contreras-Padilla, Margarita; Rivera-Muñoz, Eric M; Gutiérrez-Cortez, Elsa; del López, Alicia Real; Rodríguez-García, Mario Enrique

    2015-01-01

    This research studies the crystalline compounds present in nopal (Opuntia ficus-indica) cladodes. The identification of the crystalline structures was performed using X-ray diffraction, scanning electron microscopy, mass spectrometry, and Fourier transform infrared spectroscopy. The crystalline structures identified were calcium carbonate (calcite) [CaCO3], calcium-magnesium bicarbonate [CaMg(CO3)2], magnesium oxide [MgO], calcium oxalate monohydrate [Ca(C2O4)•(H2O)], potassium peroxydiphosphate [K4P2O8] and potassium chloride [KCl]. The SEM images indicate that calcite crystals grow to dipyramidal, octahedral-like, prismatic, and flower-like structures; meanwhile, calcium-magnesium bicarbonate structures show rhombohedral exfoliation and calcium oxalate monohydrate is present in a drusenoid morphology. These calcium carbonate compounds have a great importance for humans because their bioavailability. This is the first report about the identification and structural analysis of calcium carbonate and calcium-magnesium bicarbonate in nopal cladodes, as well as the presence of magnesium oxide, potassium peroxydiphosphate and potassium chloride in these plants. The significance of the study of the inorganic components of these cactus plants is related with the increasing interest in the potential use of Opuntia as a raw material of products for the food, pharmaceutical, and cosmetic industries. PMID:25465849

  11. Characterization of crystalline structures in Opuntia ficus-indica.

    PubMed

    Contreras-Padilla, Margarita; Rivera-Muñoz, Eric M; Gutiérrez-Cortez, Elsa; del López, Alicia Real; Rodríguez-García, Mario Enrique

    2015-01-01

    This research studies the crystalline compounds present in nopal (Opuntia ficus-indica) cladodes. The identification of the crystalline structures was performed using X-ray diffraction, scanning electron microscopy, mass spectrometry, and Fourier transform infrared spectroscopy. The crystalline structures identified were calcium carbonate (calcite) [CaCO3], calcium-magnesium bicarbonate [CaMg(CO3)2], magnesium oxide [MgO], calcium oxalate monohydrate [Ca(C2O4)•(H2O)], potassium peroxydiphosphate [K4P2O8] and potassium chloride [KCl]. The SEM images indicate that calcite crystals grow to dipyramidal, octahedral-like, prismatic, and flower-like structures; meanwhile, calcium-magnesium bicarbonate structures show rhombohedral exfoliation and calcium oxalate monohydrate is present in a drusenoid morphology. These calcium carbonate compounds have a great importance for humans because their bioavailability. This is the first report about the identification and structural analysis of calcium carbonate and calcium-magnesium bicarbonate in nopal cladodes, as well as the presence of magnesium oxide, potassium peroxydiphosphate and potassium chloride in these plants. The significance of the study of the inorganic components of these cactus plants is related with the increasing interest in the potential use of Opuntia as a raw material of products for the food, pharmaceutical, and cosmetic industries.

  12. Statistical models of video structure for content analysis and characterization.

    PubMed

    Vasconcelos, N; Lippman, A

    2000-01-01

    Content structure plays an important role in the understanding of video. In this paper, we argue that knowledge about structure can be used both as a means to improve the performance of content analysis and to extract features that convey semantic information about the content. We introduce statistical models for two important components of this structure, shot duration and activity, and demonstrate the usefulness of these models with two practical applications. First, we develop a Bayesian formulation for the shot segmentation problem that is shown to extend the standard thresholding model in an adaptive and intuitive way, leading to improved segmentation accuracy. Second, by applying the transformation into the shot duration/activity feature space to a database of movie clips, we also illustrate how the Bayesian model captures semantic properties of the content. We suggest ways in which these properties can be used as a basis for intuitive content-based access to movie libraries.

  13. Photoluminescence characterization of single heterojunction quantum well structures

    NASA Astrophysics Data System (ADS)

    Aina, O.; Mattingly, M.; Juan, F. Y.; Bhattacharya, P. K.

    1987-01-01

    A photoluminescence emission band at 830 nm has been detected in single heterojunction quantum well structures (modulation-doped structures) in the range of 250-400 K. This emission band is observed neither in heterojunction structures without a two-dimensional electron gas (2DEG), nor in n(+) AlGaAs and GaAs. The intensity of the emission band increases as the mobility of the samples with 2DEG and shows excitonic behavior in its variation with incident laser excitation intensity. This photoluminescence emission was observed in samples grown by both molecular beam epitaxy and by organometallic vapor phase epitaxy. This effect may be useful as a rough identification of high quality, modulation-doped heterostructures.

  14. Processing-structure characterization of rheocast IN-100 superalloy

    NASA Technical Reports Server (NTRS)

    Cheng, Jung-Jen Allen; Apelian, Diran; Doherty, Roger D.

    1986-01-01

    The rheocasting solidification process was applied in the production of IN-100 nickel base superalloy, and the effects of processing variables, such as stirring speed, isothermal stirring time, and volume fraction solid during isothermal stirring, on the resultant rheocast structure were investigated. Ingots that were furnace cooled at the same rate but without stirring were compared with the rheocast ingots. Rheocasting yielded fine-grained structures, where the extent of microsegregation, the variation in macrostructure, and the solidification-induced porosity and ingot cracking were found to be reduced in comparison to the unstirred ingots. The grain size and nonuniformity were reduced by increasing the stirring speed, isothermal stirring time, or the volume fraction solid during stirring; decreased microsegregation was achieved by an increase in the volume fraction solid. The structures of grain boundaries lent support to the grain boundary mechanism proposed by Vogel et al. (1977) for rheocasting.

  15. Raman scattering characterization of space solar cell structures

    NASA Technical Reports Server (NTRS)

    Mintairov, Alexander M.; Khvostikov, V. P.; Paleeva, E. V.; Sorokina, S. V.

    1995-01-01

    A contactless method for the determination of the free-carrier density and the composition distribution across the thickness of 3-5 multi-layer solar cell structures, using the Raman scattering method, is developed. The method includes a step analysis of Raman spectra from optical phonons and phonon-plasmon modes of different layers. The method provides simultaneous measurements of the element composition and the thickness of the structure's layers together with the free-carrier density. The results of measurements of the free-carrier density composition distributions of the liquid phase epitaxy grown AlGaAs/GaAs and GaSb solar cell structures are presented and discussed.

  16. Structural characterization of coatomer in its cytosolic state.

    PubMed

    Wang, Shengliu; Zhai, Yujia; Pang, Xiaoyun; Niu, Tongxin; Ding, Yue-He; Dong, Meng-Qiu; Hsu, Victor W; Sun, Zhe; Sun, Fei

    2016-08-01

    Studies on coat protein I (COPI) have contributed to a basic understanding of how coat proteins generate vesicles to initiate intracellular transport. The core component of the COPI complex is coatomer, which is a multimeric complex that needs to be recruited from the cytosol to membrane in order to function in membrane bending and cargo sorting. Previous structural studies on the clathrin adaptors have found that membrane recruitment induces a large conformational change in promoting their role in cargo sorting. Here, pursuing negative-stain electron microscopy coupled with single-particle analyses, and also performing CXMS (chemical cross-linking coupled with mass spectrometry) for validation, we have reconstructed the structure of coatomer in its soluble form. When compared to the previously elucidated structure of coatomer in its membrane-bound form we do not observe a large conformational change. Thus, the result uncovers a key difference between how COPI versus clathrin coats are regulated by membrane recruitment. PMID:27472951

  17. Dynamic characterization of thin-film inflatable structures

    NASA Astrophysics Data System (ADS)

    Slade, Kara Nicole

    Inflatable structures constructed from thin polyimide films form a key part of several technology development programs for solar thermal propulsion for satellites, as well as for other applications both in space and on earth. This project investigates the mechanical properties of several of these structures, focusing primarily on their dynamic behavior. The primary focus is the Shooting Star Experiment prototype developed by NASA, but a simpler cylindrical structure is also considered in order to provide an analytically tractable situation for the evaluation of testing and modeling techniques. The cylindrical strut is tested statically to determine its load-deflection characteristics both in linear and nonlinear regimes. The phenomenon of wrinkling is observed under large deflection conditions, particularly at lower pressure. Then, modal testing is used to determine the dynamic properties of the strut for comparison to numerical models. Modal testing is also conducted on Pathfinder 3, a prototype inflatable solar concentrator for the Shooting Star Experiment, both in vacuum and ambient atmospheric conditions. The orbital terminator crossing test is used to determine the dynamic susceptibility of the Pathfinder 3 structure to thermal shock, and it is found to undergo only quasistatic deformations. Finite element models of the cylinder and the Pathfinder 3 concentrator are then constructed using MSC NASTRAN. The inflatable cylinder may be modeled as a beam if only global bending is considered. This restriction leads to the development of a frequency-dependent modulus of elasticity in bending for the structure, developed from engineering beam theory. Both frequency-dependent beam models and shell models are constructed and evaluated for their efficacy. The results from the modeling of the strut are then applied to the inflatable concentrator, where it is found that the shell model captures more of the dynamic subtleties of the system than the beam model, but that both

  18. Preparation, characterization, and sequential transformation of dicarbide cluster compounds with permetalated ethyne, ethene, and ethane structures

    SciTech Connect

    Akita, Munetaka; Sugimoto, Shuichiro; Tanaka, Masako; Moro-oka, Yoshihiko

    1992-09-09

    The preparation, characterization and sequential transformation of dicarbide cluster compounds with permetalated ethyne, ethene and ethane structures is discussed. The group reporting has developed a preparative method for ethynediyldimetal complexes via deprotonation. 10 refs., 3 figs.

  19. Characterization of bacterial community structure on a weathered pegmatitic granite.

    PubMed

    Gleeson, Deirdre B; Kennedy, Nabla M; Clipson, Nicholas; Melville, Karrie; Gadd, Geoffrey M; McDermott, Frank P

    2006-05-01

    This study exploited the contrasting major element chemistry of a pegmatitic granite to investigate mineralogical influences on bacterial community structure. Intact crystals of variably weathered muscovite, plagioclase, K-feldspar, and quartz were extracted, together with whole-rock granite. Environmental scanning electron microscopy revealed a diversity of bacterial structures, with rods and cocci clearly visible on surfaces of all mineral types. Bacterial automated ribosomal intergenic spacer analysis was used to generate a ribotype profile for each mineral. A randomization test revealed that community fingerprints differed between different mineral types, whereas canonical correspondence analysis (CCA) showed that mineral chemistry affected individual bacterial ribotypes. CCA also revealed that Al, Si, and Ca had a significant impact on bacterial community structure within the system, which contrasts with the finding within fungal communities that although Al and Si also had a significant impact, K rather than Ca was important. The bacterial populations associated with different minerals were different. Members of each of these populations were found almost exclusively on a single mineral type, as was previously reported for fungal populations. These results show that bacterial community structure was driven by the chemical composition of minerals, indicating selective pressure by individual chemical elements on bacterial populations in situ.

  20. Structural characterization of nano-sized calcium deficient apatite powders.

    PubMed

    Liou, Sz-Chian; Chen, San-Yuan; Lee, Hsin-Yi; Bow, Jong-Shing

    2004-01-01

    Nano-sized calcium-deficient apatitic (CDHA) crystals with Ca/P ratios from 1.5 to 1.67 were synthesized using wet chemical method and of needle-like shape with 5-10 nm in diameter and 40-50 nm in length was observed. The structural environment of the Ca atoms in all the CDHA nano-crystals has been investigated using EXAFS, XANES and EELS. The results reveal that a maximum Fourier transform amplitude occurs at the apatite with a Ca/P ratio of 1.67 and the structural disorder increase following the sequence of 1.67>1.5>1.6>1.55. A similar phenomenon is also observed in both K-edge XANES and L(2,3)-edge ELNES in the Ca atom. The structural analysis further demonstrates that different chemical and biological properties among these CDHA nano-crystals with Ca/P ratio from 1.5 to 1.67 are primarily due to the effect of stoichiometry and non-stoichiometry as compared to the structural order-disorder.

  1. Structural and magnetic characterization of YIG particles prepared using microemulsions

    NASA Astrophysics Data System (ADS)

    Baldomir, D.; Teijeiro, A. G.; Rivas, J.; Vaqueiro, P.; Paz, S. B.; López Quintela, A.

    1995-02-01

    Yttrium-iron-garnet (YIG) particles have been synthesized using the microemulsion technique. A comparison of ferrite powders obtained by this method and those prepared by sol-gel and solid state reactions is reported. We have studied both the magnetic and structural properties and have found a dependence on annealing temperatures.

  2. Directed Evolution and Structural Characterization of a Simvastatin Synthase

    SciTech Connect

    Gao, Xue; Xie, Xinkai; Pashkov, Inna; Sawaya, Michael R.; Laidman, Janel; Zhang, Wenjun; Cacho, Ralph; Yeates, Todd O.; Tang, Yi; UCLA

    2010-02-02

    Enzymes from natural product biosynthetic pathways are attractive candidates for creating tailored biocatalysts to produce semisynthetic pharmaceutical compounds. LovD is an acyltransferase that converts the inactive monacolin J acid (MJA) into the cholesterol-lowering lovastatin. LovD can also synthesize the blockbuster drug simvastatin using MJA and a synthetic {alpha}-dimethylbutyryl thioester, albeit with suboptimal properties as a biocatalyst. Here we used directed evolution to improve the properties of LovD toward semisynthesis of simvastatin. Mutants with improved catalytic efficiency, solubility, and thermal stability were obtained, with the best mutant displaying an {approx}11-fold increase in an Escherichia coli-based biocatalytic platform. To understand the structural basis of LovD enzymology, seven X-ray crystal structures were determined, including the parent LovD, an improved mutant G5, and G5 cocrystallized with ligands. Comparisons between the structures reveal that beneficial mutations stabilize the structure of G5 in a more compact conformation that is favorable for catalysis.

  3. Characterization of fungal community structure on a weathered pegmatitic granite.

    PubMed

    Gleeson, Deirdre B; Clipson, Nicholas; Melville, Karrie; Gadd, Geoffrey M; McDermott, Frank P

    2005-10-01

    This study exploited the contrasting major element chemistry of adjacent, physically separable crystals of framework and sheet silicates in a pegmatitic granite to investigate the mineralogical influences of fungal community structure on mineral surfaces. Large intact crystals of variably weathered muscovite, plagioclase, K-feldspar, and quartz were individually extracted, together with whole-rock granite. Environmental scanning electron microscopy (ESEM) revealed a diversity of fungal structures, with microcolonial fungi and fungal hyphae clearly visible on surfaces of all mineral types. Fungal automated ribosomal intergenic spacer analysis (FARISA) was used to generate a ribotype profile for each mineral sample and a randomization test revealed that ribotype profiles, or community fingerprints, differed between different mineral types. Canonical correspondence analysis (CCA) revealed that mineral chemistry affected individual fungal ribotypes, and strong relationships were found between certain ribotypes and particular chemical elements. This finding was further supported by analysis of variance (ANOVA) of the 16 most abundant ribotypes within the community. Significantly, individual ribotypes were largely restricted to single mineral types and ribotypes clustered strongly on the basis of mineral type. CCA also revealed that Al, Si, and Ca had a significant impact on fungal community structure within this system. These results show that fungal community structure was driven by the chemical composition of mineral substrates, indicating selective pressure by individual chemical elements on fungal populations in situ.

  4. Structural and Mechanical Characterization of Thermally Treated Conch Shells

    NASA Astrophysics Data System (ADS)

    Li, Haoze; Jin, Dalai; Li, Rui; Li, Xiaodong

    2015-04-01

    Seashells are natural nanocomposite armors with an exceptional combination of strength and toughness. Conch shells have a crossed-lamellar structure constructed with aragonite and biopolymer. Thermal treatment uncovered a nanoscale hierarchical structure in shell's third-order lamellae. Individual third-order lamellae were found to consist of aragonite nanoparticles cemented with biopolymer. The biopolymer renders conch shells joint increase in strength, ductility and fracture energy, and especially the fracture energy increase is more remarkable. The shell's aragonite transformed to calcite at 407°C and lime at 607°C. The shell's biopolymer was burned out in the thermal treatment at 310°C, leading to 1.7% mass loss. The crossed-lamellar structure remained in the 500°C thermally treated shell. The 900°C heat treatment destroyed the crossed-lamellar architecture completely. Thermal treatment resulted in reduction in mechanical properties due to the joint effects—burning out of biopolymer, phase transformation, and destruction of structural integrity. The findings advance our understanding of conch shell's architecture and provide new guidelines for the design and manufacturing of bio-inspired materials.

  5. Production of C-Fe-Pd nanocomposites via Infra-red radiation and its structural characterization

    NASA Astrophysics Data System (ADS)

    Kovtun, A. V.; Dzidziguri, E. L.; Muratov, D. G.

    2016-08-01

    The objective of the present study is to produce C-Fe-Pd nanocomposites using pyrolyzed infrared (IR) radiation. The structural characterization was analyzed using X-ray diffraction (XRD), transmission electron microscopy (TEM) and X-ray fluorescence analysis. In addition, the size of metal nanocomposites as a function of the pyrolysis temperature, and its distribution within the carbon matrix is also characterized.

  6. Structural and Kinetic Characterization of Thymidine Kinase from Leishmania major

    PubMed Central

    Recio, Eliseo; Nettleship, Joanne E.; Rada, Heather; González-Pacanowska, Dolores; Wilson, Keith S.

    2015-01-01

    Leishmania spp. is a protozoan parasite and the causative agent of leishmaniasis. Thymidine kinase (TK) catalyses the transfer of the γ-phosphate of ATP to 2’-deoxythymidine (dThd) forming thymidine monophosphate (dTMP). L. major Type II TK (LmTK) has been previously shown to be important for infectivity of the parasite and therefore has potential as a drug target for anti-leishmanial therapy. In this study, we determined the enzymatic properties and the 3D structures of holo forms of the enzyme. LmTK efficiently phosphorylates dThd and dUrd and has high structural homology to TKs from other species. However, it significantly differs in its kinetic properties from Trypanosoma brucei TK since purines are not substrates of the enzyme and dNTPs such as dUTP inhibit LmTK. The enzyme had Km and kcat values for dThd of 1.1 μM and 2.62 s-1 and exhibits cooperative binding for ATP. Additionally, we show that the anti-retroviral prodrug zidovudine (3-azido-3-deoxythymidine, AZT) and 5’-modified dUrd can be readily phosphorylated by LmTK. The production of recombinant enzyme at a level suitable for structural studies was achieved by the construction of C-terminal truncated versions of the enzyme and the use of a baculoviral expression system. The structures of the catalytic core of LmTK in complex with dThd, the negative feedback regulator dTTP and the bi-substrate analogue AP5dT, were determined to 2.74, 3.00 and 2.40 Å, respectively, and provide the structural basis for exclusion of purines and dNTP inhibition. The results will aid the process of rational drug design with LmTK as a potential target for anti-leishmanial drugs. PMID:25978379

  7. Structural and Functional Characterization of Pseudomonas aeruginosa AlgX

    PubMed Central

    Riley, Laura M.; Weadge, Joel T.; Baker, Perrin; Robinson, Howard; Codée, Jeroen D. C.; Tipton, Peter A.; Ohman, Dennis E.; Howell, P. Lynne

    2013-01-01

    The exopolysaccharide alginate, produced by mucoid Pseudomonas aeruginosa in the lungs of cystic fibrosis patients, undergoes two different chemical modifications as it is synthesized that alter the properties of the polymer and hence the biofilm. One modification, acetylation, causes the cells in the biofilm to adhere better to lung epithelium, form microcolonies, and resist the effects of the host immune system and/or antibiotics. Alginate biosynthesis requires 12 proteins encoded by the algD operon, including AlgX, and although this protein is essential for polymer production, its exact role is unknown. In this study, we present the X-ray crystal structure of AlgX at 2.15 Å resolution. The structure reveals that AlgX is a two-domain protein, with an N-terminal domain with structural homology to members of the SGNH hydrolase superfamily and a C-terminal carbohydrate-binding module. A number of residues in the carbohydrate-binding module form a substrate recognition “pinch point” that we propose aids in alginate binding and orientation. Although the topology of the N-terminal domain deviates from canonical SGNH hydrolases, the residues that constitute the Ser-His-Asp catalytic triad characteristic of this family are structurally conserved. In vivo studies reveal that site-specific mutation of these residues results in non-acetylated alginate. This catalytic triad is also required for acetylesterase activity in vitro. Our data suggest that not only does AlgX protect the polymer as it passages through the periplasm but that it also plays a role in alginate acetylation. Our results provide the first structural insight for a wide group of closely related bacterial polysaccharide acetyltransferases. PMID:23779107

  8. Fabrication and characterization of nanometric SiOx/SiOy multilayer structures obtained by LPCVD

    SciTech Connect

    Román-López, S.; Aceves-Mijares, M.; Pedraza-Chávez, J.; Carrillo-López, J.

    2014-05-15

    This work presents the fabrication of nanometric multilayer structures and their characterization by Atomic Force Microscopy, Photoluminescence and Fourier Transform Infra Red spectroscopy. The structures were deposited by Low Pressure Chemical Vapor Deposition (LPCVD). Three types of multilayer structure were fabricated. After the deposition some samples were annealed in N{sub 2} ambient for three hours. It was found that the structures keep the characteristics of each layer.

  9. Material characterization of structural adhesives in the lap shear mode

    NASA Technical Reports Server (NTRS)

    Sancaktar, E.; Schenck, S. C.

    1983-01-01

    A general method for characterizing structual adhesives in the bonded lap shear mode is proposed. Two approaches in the form of semiempirical and theoretical approaches are used. The semiempirical approach includes Ludwik's and Zhurkov's equations to describe respectively, the failure stresses in the constant strain rate and constant stress loading modes with the inclusion of the temperature effects. The theoretical approach is used to describe adhesive shear stress-strain behavior with the use of viscoelastic or nonlinear elastic constitutive equations. Two different model adhesives are used in the single lap shear mode with titanium adherends. These adhesives (one of which was developed at NASA Langley Research Center) are currently considered by NASA for possible aerospace applications. Use of different model adhesives helps in assessment of the generality of the method.

  10. Structural characterization of pharmaceutical heparins prepared from different animal tissues.

    PubMed

    Fu, Li; Li, Guoyun; Yang, Bo; Onishi, Akihiro; Li, Lingyun; Sun, Peilong; Zhang, Fuming; Linhardt, Robert J

    2013-05-01

    Although most pharmaceutical heparin used today is obtained from porcine intestine, heparin has historically been prepared from bovine lung and ovine intestine. There is some regulatory concern about establishing the species origin of heparin. This concern began with the outbreak of mad cow disease in the 1990s and was exacerbated during the heparin shortage in the 2000s and the heparin contamination crisis of 2007-2008. Three heparins from porcine, ovine, and bovine were characterized through state-of-the-art carbohydrate analysis methods with a view profiling their physicochemical properties. Differences in molecular weight, monosaccharide and disaccharide composition, oligosaccharide sequence, and antithrombin III-binding affinity were observed. These data provide some insight into the variability of heparins obtained from these three species and suggest some analytical approaches that may be useful in confirming the species origin of a heparin active pharmaceutical ingredient. PMID:23526651

  11. Structural and Electrical Characterization of Protonic Acid Doped Polyaniline

    NASA Astrophysics Data System (ADS)

    Shaktawat, Vinodini; Saxena, Narendra S.; Sharma, Kananbala; Sharma, Thaneshwar P.

    2008-04-01

    Polyaniline doped with different protonic acids were chemically synthesized using ammonium persulfate (APS) as an oxidant. These samples were characterized through X-ray diffraction (XRD) and Fourier transform infrared (FTIR) spectroscopy, which confirms the amorphous nature and acid doping, respectively. Electrical conduction in these samples has been studied through the measurement of I-V characteristics at room temperature as well as in the temperature range from 313 K to 413 K. So obtained characteristic curves were found to be nonlinear. The conductivity of phosphoric acid doped polyaniline sample is higher as compared to HCl doped polyaniline and pure polyaniline. Temperature dependence of conductivity suggests a semiconducting nature with increase in temperature. Activation energies have been found to be 50.86, 25.74 and 21.05 meV for pure polyaniline (base), polyaniline doped with hydrochloric, phosphoric acid, respectively.

  12. Structural characterization of human heparanase reveals insights into substrate recognition

    PubMed Central

    Wu, Liang; Viola, Cristina M.; Brzozowski, Andrzej M.; Davies, Gideon J.

    2016-01-01

    Heparan Sulfate (HS) is a glycosaminoglycan (GAG) which forms a key component of the extracellular matrix (ECM). Breakdown of HS is carried out by heparanase (HPSE), an endo-β-glucuronidase of the glycoside hydrolase (GH)79 family. Overexpression of HPSE is strongly linked to cancer metastases - reflecting breakdown of extracellular HS and release of stored growth factors. Here we present crystal structures of human HPSE at 1.6-1.9 Å resolution reveal how an endo-acting binding cleft is exposed by proteolytic activation of latent proHPSE. Oligosaccharide complexes map the substrate-binding and sulfate recognition motifs. These data shed light on the structure and interactions for a key enzyme involved in ECM maintenance, and provide a starting point for design of HPSE inhibitors as biochemical tools and anti-cancer therapeutics. PMID:26575439

  13. Structural Characterization of Novel Gemini Non-viral DNA

    SciTech Connect

    Foldvari,M.; Badea, I.; Wettig, S.; Verrall, R.; Bagonluri, M.

    2006-01-01

    The structural and physicochemical properties of novel cationic lipid-based DNA complexes have been investigated for the purpose of designing micro/nano-scale self-assembling delivery systems for cutaneous gene therapy. DNA/gemini surfactant (spacer n = 3-16; chain m = 12 or 16) complexes (1 : 10 charge ratio), with or without dioleoylphosphatidyl-ethanolamine (DOPE), designed for cellular transfection, were generally in the range of 100-200 nm as demonstrated by atomic force microscopy and particle size analysis. Small-angle X-ray scattering measurements indicated that the DNA/gemini complexes lacked long-range order, whereas DNA/gemini/DOPE complexes exhibited lamellar and polymorphic phases other than hexagonal. Correlation studies using transfection efficiency data in PAM 212 keratinocytes and in vitro skin absorption indicated that formulations containing gemini surfactants having the ability to induce structures other than lamellar in the resulting complexes, generally exhibited greater transfection activity and cutaneous absorption.

  14. Quantitative structural characterization of InAs/GaSb superlattices

    SciTech Connect

    Liu Ge; Fruhberger, Bernd; Schuller, Ivan K.; Haugan, Heather J.; Brown, Gail J.

    2006-09-15

    Molecular beam epitaxy grown InAs/GaSb superlattices, containing InSb-like interfacial layers, were analyzed by a combination of x-ray diffraction (XRD) and structural refinement. The superlattice refinement from x rays (SUPREX) method determines with high accuracy the average thicknesses and d spacings of the individual InAs and GaSb layers in addition to standard structural parameters usually obtained by XRD, such as the modulation length (periodicity), average out-of-plane interplanar spacings, and total thickness. The combined SUPREX/XRD experiments show that the absence of certain odd order satellite features in the x-ray data is due to asymmetric and inhomogeneous lattice strain.

  15. Structural characterization of the packings of granular regular polygons

    NASA Astrophysics Data System (ADS)

    Wang, Chuncheng; Dong, Kejun; Yu, Aibing

    2015-12-01

    By using a recently developed method for discrete modeling of nonspherical particles, we simulate the random packings of granular regular polygons with three to 11 edges under gravity. The effects of shape and friction on the packing structures are investigated by various structural parameters, including packing fraction, the radial distribution function, coordination number, Voronoi tessellation, and bond-orientational order. We find that packing fraction is generally higher for geometrically nonfrustrated regular polygons, and can be increased by the increase of edge number and decrease of friction. The changes of packing fraction are linked with those of the microstructures, such as the variations of the translational and orientational orders and local configurations. In particular, the free areas of Voronoi tessellations (which are related to local packing fractions) can be described by log-normal distributions for all polygons. The quantitative analyses establish a clearer picture for the packings of regular polygons.

  16. Towards structural and functional characterization of photosynthetic and mitochondrial supercomplexes.

    PubMed

    Dudkina, Natalya V; Folea, I Mihaela; Boekema, Egbert J

    2015-05-01

    Bioenergetic reactions in chloroplasts and mitochondria are catalyzed by large multi-subunit membrane proteins. About two decades ago it became clear that several of these large membrane proteins further associate into supercomplexes and since then a number of new ones have been described. In this review we focus on supercomplexes involved in light harvesting and electron transfer in the primary reactions of oxygenic photosynthesis and on the mitochondrial supercomplexes that catalyze electron transfer and ATP synthesis in oxidative phosphorylation. Functional and structural aspects are overviewed. In addition, several relevant technical aspects are discussed, including membrane solubilization with suitable detergents and methods of purification. Some open questions are addressed, such as the lack of high-resolution structures, the outstanding gaps in the knowledge about supercomplexes involved in cyclic electron transport in photosynthesis and the unusual mitochondrial protein complexes of protists and in particular of ciliates.

  17. Characterization of GPR101 transcript structure and expression patterns.

    PubMed

    Trivellin, Giampaolo; Bjelobaba, Ivana; Daly, Adrian F; Larco, Darwin O; Palmeira, Leonor; Faucz, Fabio R; Thiry, Albert; Leal, Letícia F; Rostomyan, Liliya; Quezado, Martha; Schernthaner-Reiter, Marie Helene; Janjic, Marija M; Villa, Chiara; Wu, T John; Stojilkovic, Stanko S; Beckers, Albert; Feldman, Benjamin; Stratakis, Constantine A

    2016-08-01

    We recently showed that Xq26.3 microduplications cause X-linked acrogigantism (X-LAG). X-LAG patients mainly present with growth hormone and prolactin-secreting adenomas and share a minimal duplicated region containing at least four genes. GPR101 was the only gene highly expressed in their pituitary lesions, but little is known about its expression patterns. In this work, GPR101 transcripts were characterized in human tissues by 5'-Rapid Amplification of cDNA Ends (RACE) and RNAseq, while the putative promoter was bioinformatically predicted. We investigated GPR101 mRNA and protein expression by RT-quantitative PCR (qPCR), whole-mount in situ hybridization, and immunostaining, in human, rhesus monkey, rat and zebrafish. We identified four GPR101 isoforms characterized by different 5'-untranslated regions (UTRs) and a common 6.1kb long 3'UTR. GPR101 expression was very low or absent in almost all adult human tissues examined, except for specific brain regions. Strong GPR101 staining was observed in human fetal pituitary and during adolescence, whereas very weak/absent expression was detected during childhood and adult life. In contrast to humans, adult monkey and rat pituitaries expressed GPR101, but in different cell types. Gpr101 is expressed in the brain and pituitary during rat and zebrafish development; in rat pituitary, Gpr101 is expressed only after birth and shows sexual dimorphism. This study shows that different GPR101 transcripts exist and that the brain is the major site of GPR101 expression across different species, although divergent species- and temporal-specific expression patterns are evident. These findings suggest an important role for GPR101 in brain and pituitary development and likely reflect the very different growth, development and maturation patterns among species. PMID:27282544

  18. Structural characterization of dual ion implantation in silicon

    NASA Astrophysics Data System (ADS)

    Nunes, B.; Franco, N.; Botelho do Rego, A. M.; Alves, E.; Colaço, R.

    2015-12-01

    <1 0 0> Si wafers were dual implanted at room temperature with Fe + C and Ti + C with fluences of 2 × 1017 cm-2. The samples were annealed in vacuum at 800 °C and 1000 °C respectively, and characterized in scanning electron microscope (FEG-SEM), grazing incidence X-ray diffraction (GIXRD) and X-ray photoelectron spectroscopy (XPS). The scanning electron microscopy characterization showed that both annealings generated precipitates, with sizes within the range of 10-100 nm at 800 °C and 1-10 μm for the 1000 °C annealing. The GIXRD measurements revealed the presence of different silicides phases. For the Fe + C implantation β-FeSi2 was observed at 800 °C while at 1000 °C α-FeSi2 and SiC were found. The Ti + C sample at 800 °C showed simultaneously the presence of four different phases, both metastable C49 and stable C54 silicide TiSi2, poly-Si and SiC. At higher temperatures the metastable C49-TiSi2 silicide phase was no longer observed, all the others remaining. The XPS analysis confirmed the existence of the SiC at 1000 °C temperature, and showed that the initial carbon clusters get richer in Si with the increase of temperature to form SiC. It was also possible to see that among all present species, C was the one that oxidized the most with increasing temperature.

  19. Raman lidar characterization of PBL structure during COPS

    NASA Astrophysics Data System (ADS)

    Summa, D.; Di Girolamo, P.; Stelitano, D.; Di Iorio, T.

    2012-04-01

    The planetary boundary layer includes the portion of the atmosphere which is directly influenced by the presence of the Earth's surface. Aerosol particles trapped within the PBL can be used as tracers to study boundary-layer vertical structure and time variability. Aerosols can be dispersed out of the PBL during strong convection or temporary breaks of the capping temperature inversion. As a result of this, elastic backscatter signals collected by lidar systems can be used to determine the height and the internal structure of the PBL. Our analysis considers a method based on the first order derivative of the range-corrected elastic signal (RCS), which is a modified version of the method defined by Seibert et al. (2000) and Sicard et al. (2006). The analysis is focused on selected case studies collected by the Raman lidar system BASIL during the Convective and Orographically-induced Precipitation Study (COPS), held in Southern Germany and Eastern France in the period 01 June - 31 August 2007. Measurements were performed by the Raman lidar system BASIL, which was operational in Achern (Black Forest, Lat: 48.64 ° N, Long: 8.06 ° E, Elev.: 140 m). During COPS, BASIL collected more than 500 hours of measurements, distributed over 58 measurement days and 34 intensive observation periods (IOPs), covering both night-time and daytime and the transitions between the two. Therefore BASIL data during COPS represent a unique source of information for the study of the boundary layer structure and evolution. Potential temperature profiles obtained from the radiosonde data were used to get an additional estimate of the boundary layer height. Estimates of the PBL height and structure for specific case studies obtained from the lidar data and their comparison with estimates obtained from the radiosonde data will be illustrated and discussed at the Conference.

  20. Structural defect characterization of silicon dendritic web ribbons

    NASA Technical Reports Server (NTRS)

    Cheng, L. J.

    1985-01-01

    An EBIC study of the cross section of silicon dendritic web ribbon has revealed that recombination-active structural defects are mainly concentrated in the inner part of the ribbon, particularly at and near the twin plane, whereas the material near the surface has significantly fewer defects. An analysis of the distribution of etch pits due to slip dislocations created by shear stress indicates that a minimum in the dislocation density is frequently observed in the ribbon adjacent to the dendrite.

  1. Structural and Histone Binding Ability Characterizations of Human PWWP Domains

    SciTech Connect

    Wu, Hong; Zeng, Hong; Lam, Robert; Tempel, Wolfram; Amaya, Maria F.; Xu, Chao; Dombrovski, Ludmila; Qiu, Wei; Wang, Yanming; Min, Jinrong

    2013-09-25

    The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain 'Royal Family', which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently. The PWWP domain has been shown to be a DNA binding domain, but sequence analysis and previous structural studies show that the PWWP domain exhibits significant similarity to other 'Royal Family' members, implying that the PWWP domain has the potential to bind histones. In order to further explore the function of the PWWP domain, we used the protein family approach to determine the crystal structures of the PWWP domains from seven different human proteins. Our fluorescence polarization binding studies show that PWWP domains have weak histone binding ability, which is also confirmed by our NMR titration experiments. Furthermore, we determined the crystal structures of the BRPF1 PWWP domain in complex with H3K36me3, and HDGF2 PWWP domain in complex with H3K79me3 and H4K20me3. PWWP proteins constitute a new family of methyl lysine histone binders. The PWWP domain consists of three motifs: a canonical {beta}-barrel core, an insertion motif between the second and third {beta}-strands and a C-terminal {alpha}-helix bundle. Both the canonical {beta}-barrel core and the insertion motif are directly involved in histone binding. The PWWP domain has been previously shown to be a DNA binding domain. Therefore, the PWWP domain exhibits dual functions: binding both DNA and methyllysine histones.

  2. A structurally-characterized NbCl5-NHC adduct.

    PubMed

    Bortoluzzi, Marco; Ferretti, Eleonora; Marchetti, Fabio; Pampaloni, Guido; Zacchini, Stefano

    2014-05-01

    The selective reactions of niobium pentachloride with two bulky NHC carbenes afforded NbCl5(NHC) complexes, bearing the highest oxidation state ever found for a metal centre in a transition metal halide-NHC adduct. The X-ray structure of 2a is the first one reported for a monodentate NHC-niobium species, and exhibits an abnormally long Nb-C bond. PMID:24658260

  3. Pore structure characterization of catalyst supports via low field NMR

    SciTech Connect

    Smith, D.M.; Glaves, C.L.; Gallegos, D.P.; Brinker, C.J.

    1988-01-01

    In this paper, the application of low-field NMR to both surface area and pore structure analysis of catalyst supports will be presented. Low-field (20 MHz) spin-lattice relaxation (T/sub 1/) experiments are performed on fluids contained in alumina and silica catalyst supports. Pore size distributions (PSD) calculated from these NMR experiments are compared to those obtained from mercury porosimetry and nitrogen condensation. 18 refs., 4 figs., 2 tabs.

  4. Purification and structural characterization of herpes simplex virus glycoprotein C

    SciTech Connect

    Kikuchi, G.E.; Baker, S.A.; Merajver, S.D.; Coligan, J.E.; Levine, M.; Glorioso, J.C.; Nairn, R.

    1987-01-27

    Purification of herpes simplex virus glycoprotein C (gC) in microgram amounts yielded sufficient material for an analysis of its secondary structure. Purification was facilitated by using the mutant virus gC-3, which bears a point mutation that interrupts the putative hydrophobic membrane anchor sequence, causing the secretion of gC-3 protein into the cell culture medium. gC-3 protein was purified by size fractionation of concentrated culture medium from infected cells on a gel filtration column of Sephacryl S-200, followed by immunoaffinity chromatography on a column constructed of gC-specific monoclonal antibodies cross-linked to a protein A-Sepharose CL-4B matrix. Purified gC-3 had a molecular weight of 130,000 as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the size expected for gC, was reactive with gC-specific monoclonal antibodies in protein immunoblots, and contained amino acid sequences characteristic of gC as determined by radiochemical amino acid microsequence analyses. Polyclonal antisera obtained from a rabbit immunized with gC-3 reacted with wild-type gC in immunoprecipitation, enzyme immunoassay, and immunoelectroblot (western blot) assays. Deglycosylation by treatment with trifluoromethanesulfonic acid reduced the molecular weight of gC-3 by approximately 35%. Analyses of both native and deglycosylated gC-3 by Raman spectroscopy showed that the native molecule consists of about 17%..cap alpha..-helix, 24% ..beta..-sheet, and 60% disordered secondary structures, whereas deglycosylated gC-3 consists of about 8% ..cap alpha..-helix, 10% ..beta..-sheet, 81% disordered structures. These data were in good agreement with the 11% ..cap alpha..-helix, 18% ..beta..-sheet, 61% ..beta..-turn, and 9% disordered structures calculated from Chou-Fasman analysis of the primary sequence of gC-3.

  5. Structural characterization and vibrational spectroscopy of the arsenate mineral wendwilsonite.

    PubMed

    Frost, Ray L; Scholz, Ricardo; López, Andrés; Belotti, Fernanda Maria; Xi, Yunfei

    2014-01-24

    In this paper, we have investigated on the natural wendwilsonite mineral with the formulae Ca2(Mg,Co)(AsO4)2⋅2(H2O). Raman spectroscopy complimented with infrared spectroscopy has been used to determine the molecular structure of the wendwilsonite arsenate mineral. A comparison is made with the roselite mineral group with formula Ca2B(AsO4)2⋅2H2O (where B may be Co, Fe(2+), Mg, Mn, Ni, Zn). The Raman spectra of the arsenate related to tetrahedral arsenate clusters with stretching region shows strong differences between that of wendwilsonite and the roselite arsenate minerals which is attributed to the cation substitution for calcium in the structure. The Raman arsenate (AsO4)(3-) stretching region shows strong differences between that of wendwilsonite and the roselite arsenate minerals which is attributed to the cation substitution for calcium in the structure. In the infrared spectra complexity exists of multiple to tetrahedral (AsO4)(3-) clusters with antisymmetric stretching vibrations observed indicating a reduction of the tetrahedral symmetry. This loss of degeneracy is also reflected in the bending modes. Strong Raman bands around 450 cm(-1) are assigned to ν4 bending modes. Multiple bands in the 350-300 cm(-1) region assigned to ν2 bending modes provide evidence of symmetry reduction of the arsenate anion. Three broad bands for wendwilsonite found at 3332, 3119 and 3001 cm(-1) are assigned to OH stretching bands. By using a Libowitzky empirical equation, hydrogen bond distances of 2.65 and 2.75Å are estimated. Vibrational spectra enable the molecular structure of the wendwilsonite mineral to be determined and whilst similarities exist in the spectral patterns with the roselite mineral group, sufficient differences exist to be able to determine the identification of the minerals.

  6. Structural and functional characterization of Mycobacterium tuberculosis triosephosphate isomerase

    SciTech Connect

    Connor, Sean E.; Capodagli, Glenn C.; Deaton, Michelle K.; Pegan, Scott D.

    2012-04-18

    Tuberculosis (TB) is a major infectious disease that accounts for over 1.7 million deaths every year. Mycobacterium tuberculosis, the causative agent of tuberculosis, enters the human host by the inhalation of infectious aerosols. Additionally, one third of the world's population is likely to be infected with latent TB. The incidence of TB is on the rise owing in part to the emergence of multidrug-resistant strains. As a result, there is a growing need to focus on novel M. tuberculosis enzyme targets. M. tuberculosis triosephosphate isomerase (MtTPI) is an essential enzyme for gluconeogenetic pathways, making it a potential target for future therapeutics. In order to determine its structure, the X-ray crystal structure of MtTPI has been determined, as well as that of MtTPI bound with a reaction-intermediate analog. As a result, two forms of the active site were revealed. In conjunction with the kinetic parameters obtained for the MtTPI-facilitated conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (D-GAP), this provides a greater structural and biochemical understanding of this enzyme. Additionally, isothermal titration calorimetry was used to determine the binding constant for a reaction-intermediate analog bound to the active site of MtTPI.

  7. Characterization of structural response to hypersonic boundary-layer transition

    DOE PAGES

    Riley, Zachary B.; Deshmukh, Rohit; Miller, Brent A.; McNamara, Jack J.; Casper, Katya M.

    2016-05-24

    The inherent relationship between boundary-layer stability, aerodynamic heating, and surface conditions makes the potential for interaction between the structural response and boundary-layer transition an important and challenging area of study in high-speed flows. This paper phenomenologically explores this interaction using a fundamental two-dimensional aerothermoelastic model under the assumption of an aluminum panel with simple supports. Specifically, an existing model is extended to examine the impact of transition onset location, transition length, and transitional overshoot in heat flux and fluctuating pressure on the structural response of surface panels. Transitional flow conditions are found to yield significantly increased thermal gradients, and theymore » can result in higher maximum panel temperatures compared to turbulent flow. Results indicate that overshoot in heat flux and fluctuating pressure reduces the flutter onset time and increases the strain energy accumulated in the panel. Furthermore, overshoot occurring near the midchord can yield average temperatures and peak displacements exceeding those experienced by the panel subject to turbulent flow. Lastly, these results suggest that fully turbulent flow does not always conservatively predict the thermo-structural response of surface panels.« less

  8. Chemical and structural characterization of copper adsorbed on mosses (Bryophyta).

    PubMed

    González, Aridane G; Jimenez-Villacorta, Felix; Beike, Anna K; Reski, Ralf; Adamo, Paola; Pokrovsky, Oleg S

    2016-05-01

    The adsorption of copper on passive biomonitors (devitalized mosses Hypnum sp., Sphagnum denticulatum, Pseudoscleropodium purum and Brachythecium rutabulum) was studied under different experimental conditions such as a function of pH and Cu concentration in solution. Cu assimilation by living Physcomitrella patents was also investigated. Molecular structure of surface adsorbed and incorporated Cu was studied by X-ray Absorption Spectroscopy (XAS). Devitalized mosses exhibited the universal adsorption pattern of Cu as a function of pH, with a total binding sites number 0.05-0.06 mmolg(dry)(-1) and a maximal adsorption capacity of 0.93-1.25 mmolg(dry)(-1) for these devitalized species. The Extended X-ray Absorption Fine Structure (EXAFS) fit of the first neighbor demonstrated that for all studied mosses there are ∼4.5 O/N atoms around Cu at ∼1.95 Å likely in a pseudo-square geometry. The X-ray Absorption Near Edge Structure (XANES) analysis demonstrated that Cu(II)-cellulose (representing carboxylate groups) and Cu(II)-phosphate are the main moss surface binding moieties, and the percentage of these sites varies as a function of solution pH. P. patens exposed during one month to Cu(2+) yielded ∼20% of Cu(I) in the form of Cu-S(CN) complexes, suggesting metabolically-controlled reduction of adsorbed and assimilated Cu(2+). PMID:26852210

  9. Structure and Biochemical Characterization of Protein Acetyltransferase from Sulfolobus solfataricus

    SciTech Connect

    Brent, Michael M.; Iwata, Ayaka; Carten, Juliana; Zhao, Kehao; Marmorstein, Ronen

    2009-09-02

    The Sulfolobus solfataricus protein acetyltransferase (PAT) acetylates ALBA, an abundant nonspecific DNA-binding protein, on Lys{sup 16} to reduce its DNA affinity, and the Sir2 deacetylase reverses the modification to cause transcriptional repression. This represents a 'primitive' model for chromatin regulation analogous to histone modification in eukaryotes. We report the 1.84-{angstrom} crystal structure of PAT in complex with coenzyme A. The structure reveals homology to both prokaryotic GNAT acetyltransferases and eukaryotic histone acetyltransferases (HATs), with an additional 'bent helix' proximal to the substrate binding site that might play an autoregulatory function. Investigation of active site mutants suggests that PAT does not use a single general base or acid residue for substrate deprotonation and product reprotonation, respectively, and that a diffusional step, such as substrate binding, may be rate-limiting. The catalytic efficiency of PAT toward ALBA is low relative to other acetyltransferases, suggesting that there may be better, unidentified substrates for PAT. The structural similarity of PAT to eukaryotic HATs combined with its conserved role in chromatin regulation suggests that PAT is evolutionarily related to the eukaryotic HATs.

  10. Characterization of the structure and composition of gecko adhesive setae.

    PubMed

    Rizzo, N W; Gardner, K H; Walls, D J; Keiper-Hrynko, N M; Ganzke, T S; Hallahan, D L

    2006-06-22

    The ability of certain reptiles to adhere to vertical (and hang from horizontal) surfaces has been attributed to the presence of specialized adhesive setae on their feet. Structural and compositional studies of such adhesive setae will contribute significantly towards the design of biomimetic fibrillar adhesive materials. The results of electron microscopy analyses of the structure of such setae are presented, indicating their formation from aggregates of proteinaceous fibrils held together by a matrix and potentially surrounded by a limiting proteinaceous sheath. Microbeam X-ray diffraction analysis has shown conclusively that the only ordered protein constituent in these structures exhibits a diffraction pattern characteristic of beta-keratin. Raman microscopy of individual setae, however, clearly shows the presence of additional protein constituents, some of which may be identified as alpha-keratins. Electrophoretic analysis of solubilized setal proteins supports these conclusions, indicating the presence of a group of low-molecular-weight beta-keratins (14-20 kDa), together with alpha-keratins, and this interpretation is supported by immunological analyses.

  11. Synthesis, structure, and magnetic characterization of Cr4US8

    NASA Astrophysics Data System (ADS)

    Ward, Matthew D.; Chan, Ian Y.; Malliakas, Christos D.; Lee, Minseong; Choi, Eun Sang; Ibers, James A.

    2016-01-01

    The compound Cr4US8 has been synthesized at 1073 K and its crystal structure has been determined at 100 K. The structure is modulated with a two-fold commensurate supercell. The subcell may be indexed in an orthorhombic cell but weak supercell reflections lead to the monoclinic superspace group P21/c(α0γ)0s with two Cr sites, one U site, and four S sites. The structure comprises a three-dimensional framework of CrS6 octahedra with channels that are partially occupied by U atoms. Each U atom in these channels is coordinated by eight S atoms in a bicapped trigonal-prismatic arrangement. The magnetic behavior of Cr4US8 is complex. At temperatures above ~120 K at all measured fields, there is little difference between field-cooled and zero field-cooled data and χ(T) decreases monotonously with temperature, which is reminiscent of the Curie-Weiss law. At lower temperatures, the temperature dependence of χ(T) is complex and strongly dependent on the magnetic field strength.

  12. The synthesis and structural characterization of novel transition metal fluorides

    SciTech Connect

    Casteel, W.J. Jr.

    1992-09-01

    High purity KMF[sub 6] and K[sub 2]MF[sub 6] salts (M = Mo,Re, Ru, Os, Ir, Pt) are obtained from reduction hexafluorides. A rhombohedral unit cell is observed for KReF[sub 6]. Fluoride ion capture by Lewis acids from the hexafluorometallate (IV) salts affords high purity tetrafluorides for M = Mo, Re, Ru, Os, and Pd. The structure of RuF[sub 4] is determined from X-ray synchrotron and neutron powder data. Unit cells based on theorthorhombic PdF[sub 4] type cell are derived from X-ray powder data for ReF[sub 4] and OsF[sub 4]. Fluoride ion capture from KAgF[sub 4] provides the thermally unstable trifluoride as a bright, red, diamagnetic solid. The structure solution of AgF[sub 3] and redetermination of the AuF[sub 3] structure from X-ray synchrotron and neutron powder data demonstrate that the two are isostnictural. Thermal decomposition product of AgF[sub 3] is the mixed valence compound Ag[sup II]Ag[sub 2][sup III]F[sub 8]. Several new salts containing the (Ag - F)[sub n][sup n+] chain cation are prepared. The first linear (Ag - F)[sub n][sup n+] chain is observed in AgF[sup +]BF[sub 4 [sup [minus

  13. [STRUCTURAL CHARACTERIZATION OF PLATELETS AND PLATELET-DERIVED MICROVESICLES].

    PubMed

    Ponomareva, A A; Nevzorova, T A; Mordakhanova, E R; Andrianova, I A; Litvinov, R I

    2016-01-01

    Platelets are the anucleated blood cells, wich together with the fibrin stop bleeding (hemostasis). Cellular microvesicles are membrane-surrounded microparticles released into extracellular space upon activation and/or apoptosis of various cells. Platelet-derived macrovesicles from the major population of circulating blood microparticles that play an important role in hemostasis and thrombosis. Despite numerous studies on the pathophysiology of platelet-derived macrovesicles, mechanisms of their formation and structural details remain poorly understood. Here we investigated the ultrastructure of parental platelets and platelet-derived microvesicles formed in vitro by quiescent cells as well as by cells stimulated with one of the following activators: arachidonic acid, ADP, thrombin, calcium ionophore A23187. Using transmission electron microscopy of human platelets and isolated microvesicles, we analyzed the intracellular origin, steps of formation, structural diversity, and size distributions of the subcellular particles. We have revealed that thrombin, unlike other stimuli, not only induced vesiculation of the plasma membrane but also caused break-up of the cells followed by formation of microparticles that are comparable with microvesicles by size. A fraction of these microparticles contained cellular organelles surrounded by a thin membrane. The size of platelet-derived macrovesicles varied from 30 nm to 500 nm, however, the size distributions depended on the nature of a cell-activating stimulus. The results obtained provide new information about the formation of platelet-derived macrovesicles and their structural diversity, wich is important to understand their multiple functions in normal and disease states. PMID:27228656

  14. Chemical and structural characterization of copper adsorbed on mosses (Bryophyta).

    PubMed

    González, Aridane G; Jimenez-Villacorta, Felix; Beike, Anna K; Reski, Ralf; Adamo, Paola; Pokrovsky, Oleg S

    2016-05-01

    The adsorption of copper on passive biomonitors (devitalized mosses Hypnum sp., Sphagnum denticulatum, Pseudoscleropodium purum and Brachythecium rutabulum) was studied under different experimental conditions such as a function of pH and Cu concentration in solution. Cu assimilation by living Physcomitrella patents was also investigated. Molecular structure of surface adsorbed and incorporated Cu was studied by X-ray Absorption Spectroscopy (XAS). Devitalized mosses exhibited the universal adsorption pattern of Cu as a function of pH, with a total binding sites number 0.05-0.06 mmolg(dry)(-1) and a maximal adsorption capacity of 0.93-1.25 mmolg(dry)(-1) for these devitalized species. The Extended X-ray Absorption Fine Structure (EXAFS) fit of the first neighbor demonstrated that for all studied mosses there are ∼4.5 O/N atoms around Cu at ∼1.95 Å likely in a pseudo-square geometry. The X-ray Absorption Near Edge Structure (XANES) analysis demonstrated that Cu(II)-cellulose (representing carboxylate groups) and Cu(II)-phosphate are the main moss surface binding moieties, and the percentage of these sites varies as a function of solution pH. P. patens exposed during one month to Cu(2+) yielded ∼20% of Cu(I) in the form of Cu-S(CN) complexes, suggesting metabolically-controlled reduction of adsorbed and assimilated Cu(2+).

  15. Isolation, Characterization, and Aggregation of a Structured Bacterial Matrix Precursor*

    PubMed Central

    Chai, Liraz; Romero, Diego; Kayatekin, Can; Akabayov, Barak; Vlamakis, Hera; Losick, Richard; Kolter, Roberto

    2013-01-01

    Biofilms are surface-associated groups of microbial cells that are embedded in an extracellular matrix (ECM). The ECM is a network of biopolymers, mainly polysaccharides, proteins, and nucleic acids. ECM proteins serve a variety of structural roles and often form amyloid-like fibers. Despite the extensive study of the formation of amyloid fibers from their constituent subunits in humans, much less is known about the assembly of bacterial functional amyloid-like precursors into fibers. Using dynamic light scattering, atomic force microscopy, circular dichroism, and infrared spectroscopy, we show that our unique purification method of a Bacillus subtilis major matrix protein component results in stable oligomers that retain their native α-helical structure. The stability of these oligomers enabled us to control the external conditions that triggered their aggregation. In particular, we show that stretched fibers are formed on a hydrophobic surface, whereas plaque-like aggregates are formed in solution under acidic pH conditions. TasA is also shown to change conformation upon aggregation and gain some β-sheet structure. Our studies of the aggregation of a bacterial matrix protein from its subunits shed new light on assembly processes of the ECM within bacterial biofilms. PMID:23632024

  16. Cryo-Electron Tomography for Structural Characterization of Macromolecular Complexes

    PubMed Central

    Cope, Julia; Heumann, John; Hoenger, Andreas

    2011-01-01

    Cryo-electron tomography (cryo-ET) is an emerging 3-D reconstruction technology that combines the principles of tomographic 3-D reconstruction with the unmatched structural preservation of biological material embedded in vitreous ice. Cryo-ET is particularly suited to investigating cell-biological samples and large macromolecular structures that are too polymorphic to be reconstructed by classical averaging-based 3-D reconstruction procedures. This unit aims to make cryo-ET accessible to newcomers and discusses the specialized equipment required, as well as the relevant advantages and hurdles associated with sample preparation by vitrification and cryo-ET. Protocols describe specimen preparation, data recording and 3-D data reconstruction for cryo-ET, with a special focus on macromolecular complexes. A step-by-step procedure for specimen vitrification by plunge freezing is provided, followed by the general practicalities of tilt-series acquisition for cryo-ET, including advice on how to select an area appropriate for acquiring a tilt series. A brief introduction to the underlying computational reconstruction principles applied in tomography is described, along with instructions for reconstructing a tomogram from cryo-tilt series data. Finally, a method is detailed for extracting small subvolumes containing identical macromolecular structures from tomograms for alignment and averaging as a means to increase the signal-to-noise ratio and eliminate missing wedge effects inherent in tomographic reconstructions. PMID:21842467

  17. Cryo-electron tomography for structural characterization of macromolecular complexes.

    PubMed

    Cope, Julia; Heumann, John; Hoenger, Andreas

    2011-08-01

    Cryo-electron tomography (cryo-ET) is an emerging 3-D reconstruction technology that combines the principles of tomographic 3-D reconstruction with the unmatched structural preservation of biological matter embedded in vitreous ice. Cryo-ET is particularly suited to investigating cell-biological samples and large macromolecular structures that are too polymorphic to be reconstructed by classical averaging-based 3-D reconstruction procedures. This unit aims to make cryo-ET accessible to newcomers and discusses the specialized equipment required, as well as relevant advantages and hurdles associated with sample preparation by vitrification and cryo-ET. Protocols describe specimen preparation, data recording and 3-D data reconstruction for cryo-ET, with a special focus on macromolecular complexes. A step-by-step procedure for specimen vitrification by plunge freezing is provided, followed by the general practicalities of tilt-series acquisition for cryo-ET, including advice on how to select an area appropriate for acquiring a tilt series. A brief introduction to the underlying computational reconstruction principles applied in tomography is described, along with instructions for reconstructing a tomogram from cryo-tilt series data. Finally, a method is detailed for extracting small subvolumes containing identical macromolecular structures from tomograms for alignment and averaging as a means to increase the signal-to-noise ratio and eliminate missing wedge effects inherent in tomographic reconstructions.

  18. Synthesis and characterization of JBW structure and its thermal transformation

    SciTech Connect

    Hegazy, Eman Z.; Kosa, Samia A.; Abd El Maksod, Islam Hamdy

    2012-12-15

    In this paper, JBW zeolite prepared from Egyptian kaolin was investigated by means of XRD, IR, SEM, EDX and ion exchange of some heavy metals. Adsorption isotherms were used to investigate the structure and properties of the prepared zeolite. XRD analysis showed that the JBW was a pure crystalline phase with orthorhombic crystal symmetry. Thermal treatment showed that the JBW transformed into the It-Carn phase at 1000 Degree-Sign C through an intermediate crystalline alumino silicate phase. SEM images showed that the JBW crystallised in a cylindrical shape. However, spherical agglomerates were observed at lower magnifications. The ion exchange isotherms with Cu{sup 2+}, Ni{sup 2+} and Co{sup 2+} were found to follow a Freundlich isotherm. In addition, it shows higher affinity towards Cu{sup 2+} than other ions. - Graphical abstract: JBW zeolite structure was prepared from Egyptian kaolin and characterised. XRD analysis showed that the JBW was a pure crystalline phase with orthorhombic crystal symmetry. Thermal treatment showed that the JBW transformed into the It-Carn phase at 1000 Degree-Sign C through an intermediate crystalline alumino silicate phase. Highlights: Black-Right-Pointing-Pointer Egyptian kaolin was successfully used to prepare pure phase of JBW Structure. Black-Right-Pointing-Pointer JBW is stable till <300 Degree-Sign C. Black-Right-Pointing-Pointer JBW phase crystallizes as cylindrical shape but agglomerates in a Nano spherical shape. Black-Right-Pointing-Pointer The ion exchange isotherms of Cu{sup 2+}, Ni{sup 2+}, and Co{sup 2+} followed up Freundlich isotherm. Black-Right-Pointing-Pointer Selectivity towards Cu{sup 2+} is much higher than Co{sup 2+} or Ni{sup 2+}.

  19. Enzymatic and structural characterization of an archaeal thiamin phosphate synthase.

    PubMed

    Hayashi, Maria; Kobayashi, Kazuya; Esaki, Hiroyoshi; Konno, Hiroyuki; Akaji, Kenichi; Tazuya, Keiko; Yamada, Kazuko; Nakabayashi, Toshikatsu; Nosaka, Kazuto

    2014-04-01

    Studies on thiamin biosynthesis have so far been achieved in eubacteria, yeast and plants, in which the thiamin structure is formed as thiamin phosphate from a thiazole and a pyrimidine moiety. This condensation reaction is catalyzed by thiamin phosphate synthase, which is encoded by the thiE gene or its orthologs. On the other hand, most archaea do not seem to have the thiE gene, but instead their thiD gene, coding for a 2-methyl-4-amino-5-hydroxymethylpyrimidine (HMP) kinase/HMP phosphate kinase, possesses an additional C-terminal domain designated thiN. These two proteins, ThiE and ThiN, do not share sequence similarity. In this study, using recombinant protein from the hyperthermophile archaea Pyrobaculum calidifontis, we demonstrated that the ThiN protein is an analog of the ThiE protein, catalyzing the formation of thiamin phosphate with the release of inorganic pyrophosphate from HMP pyrophosphate and 4-methyl-5-β-hydroxyethylthiazole phosphate (HET-P). In addition, we found that the ThiN protein can liberate an inorganic pyrophosphate from HMP pyrophosphate in the absence of HET-P. A structure model of the enzyme-product complex of P. calidifontis ThiN domain was proposed on the basis of the known three-dimensional structure of the ortholog of Pyrococcus furiosus. The significance of Arg320 and His341 residues for thiN-coded thiamin phosphate synthase activity was confirmed by site-directed mutagenesis. This is the first report of the experimental analysis of an archaeal thiamin synthesis enzyme.

  20. Structural characterization of the Salmonella typhimurium LT2 umu operon.

    PubMed Central

    Thomas, S M; Crowne, H M; Pidsley, S C; Sedgwick, S G

    1990-01-01

    The umuDC operon of Escherichia coli encodes functions required for mutagenesis induced by radiation and a wide variety of chemicals. The closely related organism Salmonella typhimurium is markedly less mutable than E. coli, but a umu homolog has recently been identified and cloned from the LT2 subline. In this study the nucleotide sequence and structure of the S. typhimurium LT2 umu operon have been determined and its gene products have been identified so that the molecular basis of umu activity might be understood more fully. S. typhimurium LT2 umu consists of a smaller 417-base-pair (bp) umuD gene ending 2 bp upstream of a larger 1,266-bp umuC gene. The only apparent structural difference between the two operons is the lack of gene overlap. An SOS box identical to that found in E. coli is present in the promoter region upstream of umuD. The calculated molecular masses of the umuD and umuC gene products were 15.3 and 47.8 kilodaltons, respectively, which agree with figures determined by transpositional disruption and maxicell analysis. The S. typhimurium and E. coli umuD sequences were 68% homologous and encoded products with 71% amino acid identity; the umuC sequences were 71% homologous and encoded products with 83% amino acid identity. Furthermore, the potential UmuD cleavage site and associated catalytic sites could be identified. Thus the very different mutagenic responses of S. typhimurium LT2 and E. coli cannot be accounted for by gross differences in operon structure or gene products. Rather, the ability of the cloned S. typhimurium umuD gene to give stronger complementation of E. coli umuD77 mutants in the absence of a functional umuC gene suggests that Salmonella UmuC protein normally constrains UmuD protein activity. Images PMID:2203737

  1. Structural characterization of a karstified limestone formation using GPR

    NASA Astrophysics Data System (ADS)

    Rousset, D.; Sénéchal, G.; Gaffet, S.

    2009-12-01

    The Laboratoire Souterrain à Bas Bruit (LSBB) at Rustrel - Pays d'Apt, France, is an Inter-disciplinary Underground Science and Technology Laboratory buried in a karstified limestone formation. A multidisciplinary program focused on water circulation monitoring is presently performed inside the tunnels. This program comprises the investigation of faults, fractures, karstification and stratigraphy ofthe limestone massif using GPR. We present the main results obtained from these data. The tunnel has been dug in lower cretaceous limestone which is characterized by a low clay content, high electrical resistivity which results in generally very low attenuation of electro-magnetic waves. 90% of the tunnels floor are made of concrete whereas other are made of bare limestone. This experimental site offers a unique opportunity of perfoming measurements within an unweathered limestone massif. The whole 3km long tunnel has been investigated using single offset shielded 250 MHz antennas in May 2009. Processing includes : DC and very low frequency removal, amplitude compensation preserving lateral variations, migration and time to depth conversion. When necessary predictive deconvolution has been applied to remove ringing effects. These data sets are characterized by good signal to noise ratio and a signal penetration down to 18 meters. These data allow us to accurately map the stratigraphy of the surrounding rocks across the concrete walls of the tunnel. Some 20 m deep vertical wells have been drilled inside the tunnel through observed reflectors. This is a strong validation of the GPR images. The estimated resolution is centimetric to decimetric and matches the required geologic accuracy. The GPR data set allows to extend previous geological results in depth, particularly in the concrete coated parts of the tunnel where conventional geological surveying is impossible. Thanks to the processing which preserves lateral amplitude variations, GPR sections exhibit prominent

  2. Nanosized Ni–Al layered double hydroxides—Structural characterization

    SciTech Connect

    Jitianu, Mihaela; Gunness, Darren C.; Aboagye, Doreen E.; Zaharescu, Maria; Jitianu, Andrei

    2013-05-15

    Highlights: ► The takovite anionic clays were obtained using the sol–gel method. ► The effect of samples’ composition on the structural and textural characteristics has been investigated. ► X-ray analysis. ► FTIR spectroscopy evidenced a disordered interlayer structure. ► FESEM and TEM analysis showed that the samples have high porosity. - Abstract: Takovite, a natural mineral with the formula Ni{sub 6}Al{sub 2}(OH){sub 6}CO{sub 3}·5H{sub 2}O belongs to the large class of layered double hydroxides (LDHs) and contains positively charged Ni(II) and Al(III) layers alternating with layers containing carbonate ions and water molecules. Mesoporous takovite-type layered double hydroxides (LDH) of the general formula [Ni{sub 1−x}Al{sub x}(OH){sub 2}]{sup x+}(CO{sub 3}{sup 2−}){sub x/2}·nH{sub 2}O with different Ni/Al molar ratios (1.9–2.8) have been successfully synthesized by the sol–gel method, followed by anionic exchange using nickel acetylacetonate and aluminum isopropylate as cation precursors. A single LDH phase and an anisotropic growth of very small crystallites (below 4 nm) have been evidenced by X-ray diffraction. The effect of samples’ composition on their structural and textural characteristics has been investigated. The BET surface area values are in the range of 100–122 m{sup 2}/g. BJH pore radius decreased with increase in the Al(III) content in the LDHs. FESEM micrographs show large aggregates of highly porous LDH particles, while TEM analysis reveals irregular agglomerates of crystallites, among which some of them displayed a developing hexagonal shape. The average particle size variation with the Al(III) content in the samples follows the same trend as the pore radius, the sample with the highest Ni/Al ratio displaying also the smallest particle size. This sample becomes even more interesting, since TEM analysis shows agglomerates with inside circular structures, feature not observed for the other Ni/Al ratios investigated.

  3. Electrical and Structural Characterization of Web Dendrite Crystals

    NASA Technical Reports Server (NTRS)

    Schwuttke, G. H.; Koliwad, K.; Dumas, K. A.

    1985-01-01

    Minority carrier lifetime distributions in silicon web dendrites are measured. Emphasis is placed on measuring areal homogeneity of lifetime, show its dependency on structural defects, and its unique change during hot processing. The internal gettering action of defect layers present in web crystals and their relation to minority carrier lifetime distributions is discussed. Minority carrier lifetime maps of web dendrites obtained before and after high temperature heat treatment are compared to similar maps obtained from 100 mm diameter Czochralski silicon wafers. Such maps indicate similar or superior areal homogeneity of minority carrier lifetime in webs.

  4. Electrochemical and structural characterization of ordered graphite electrodes

    SciTech Connect

    McDermott, M.T.

    1993-01-01

    Highly oriented pyrolytic graphite (HOPG) was utilized to examine the structure/reactivity relationships for carbon electrodes in a well-defined matter. The basal plane of HOPG is ideal for this type of study due to its well-ordered surface structure. The electrochemical reactivity of basal plane HOPG was determined in terms of adsorption of anthraquinone 2,6-desulfonate ([Gamma][sub 2,6-AQDS]), the heterogeneous electron transfer rate constant of the ferro/ferricyanide redox couple (k[degrees] for Fe(CN)[sup [minus]3/[minus]4][sub 6]) and electrode capacitance (C[degrees]). [Gamma][sub 2,6-AQDS] tracks defects at basal plane HOPG electrodes indicating that the adsorption of 2,6-AQDS is a good marker for defects on the surface of basal plane HOPG. When measured on the same basal plane surface, k[degrees] for Fe(CN)[sup [minus]3/[minus]4][sub 6] and C[degrees] correlate with [Gamma][sub 2,6-AQDS] indicating that all three electrochemical observables are controlled by the same surface variables. This illustrates the importance of surface defects on electrochemical activity at basal plane HOPG electrodes. The correlation between k[degrees] for Fe(CN)[sup [minus]3/[minus]4][sub 6], C[degrees] and [Gamma][sub 2,6-AQDS] enabled the evaluation of these parameters at near-perfect basal plane. The data indicate that basal plane HOPG exhibits anomalously low electrochemical reactivity. An investigation of basal plane HOPG electrodes with scanning tunneling microscopy (STM) revealed that defects, in the form of cleavage steps, cover 1% of the surface for the HOPG sample studied. Atomic scale STM images of step edges revealed that structural defects induce an electronic perturbation of the surface which occupies a significant area near the defect. [Gamma][sub 2,6-AQDS], k[degrees] for Fe(CN)[sup [minus]3/[minus]4][sub 6] and C[degrees] are influenced not only by the structural defect but also by the defect induced electronic perturbation.

  5. System and process for ultrasonic characterization of deformed structures

    DOEpatents

    Panetta, Paul D.; Morra, Marino; Johnson, Kenneth I.

    2011-11-22

    Generally speaking, the method of the present invention is performed by making various ultrasonic scans at preselected orientations along the length of a material being tested. Data from the scans are then plotted together with various calculated parameters that are calculated from this data. Lines or curves are then fitted to the respective plotted points. Review of these plotted curves allows the location and severity of defects within these sections to be determined and quantified. With this information various other decisions related to how, when or whether repair or replacement of a particular portion of a structure can be made.

  6. Structural and giant magnetoresistance characterization of Ag sbnd Co multilayers

    NASA Astrophysics Data System (ADS)

    Angelakeris, M.; Poulopoulos, P.; Valassiades, O.; Stoemenos, J.; Kalogirou, O.; Niarchos, D.; Flevaris, N. K.

    1997-01-01

    Ag sbnd Co multilayers were prepared on various substrates (Si, polyimide and glass) by e-beam evaporation under ultra high vacuum. X-ray diffraction and high resolution electron microscopy studies showed a deterioration of multilayer structure upon reducing the individual Co-layer thickness to 0.5 nm. Furthermore, the saturation field in the parallel field geometry increases, as SQUID magnetometry revealed, while magnetoresistance reaches 16% at room temperature and exceeds 30% at 30 K. Magnetoresistance values were found to depend strongly on individual layer thicknesses as well as on the total film thickness.

  7. Electrical and Structural Characterization of Web Dendrite Crystals

    NASA Technical Reports Server (NTRS)

    Schwuttke, G. H.

    1984-01-01

    Minority carrier lifetime distributions in silicon web dendrites are measured. Emphasis is placed on measuring areal homogeneity of lifetime, show its dependancy on structural defects, and its unique change during hot processing. The internal gettering action of defect layers present in web crystals and their relation to minority carrier lifetime distributions is discussed. Minority carrier lifetime maps of web dendrites obtained before and after high temperature heat treatment are compared to similar maps obtained from 100 mm diameter Czochralski silicon wafers. Such maps indicate similar or superior areal homogeneity of minority carrier lifetime in webs.

  8. Characterization of Nora Virus Structural Proteins via Western Blot Analysis

    PubMed Central

    Ericson, Brad L.; Carlson, Darby J.

    2016-01-01

    Nora virus is a single stranded RNA picorna-like virus with four open reading frames (ORFs). The coding potentials of the ORFs are not fully characterized, but ORF3 and ORF4 are believed to encode the capsid proteins (VP3, VP4a, VP4b, and VP4c) comprising the virion. To determine the polypeptide composition of Nora virus virions, polypeptides from purified virus were compared to polypeptides detected in Nora virus infected Drosophila melanogaster. Nora virus was purified from infected flies and used to challenge mice for the production of antisera. ORF3, ORF4a, ORF4b, and ORF4c were individually cloned and expressed in E. coli; resultant recombinant proteins purified and were used to make monospecific antisera. Antisera were evaluated via Western blot against whole virus particles and Nora virus infected fly lysates. Viral purification yielded two particle types with densities of ~1.31 g/mL (empty particles) and ~1.33 g/mL (complete virions). Comparison of purified virus polypeptide composition to Nora virus infected D. melanogaster lysate showed the number of proteins in infected cell lysates is less than purified virus. Our results suggest the virion is composed of 6 polypeptides, VP3, VP4a, two forms of VP4b, and two forms of VP4c. This polypeptide composition is similar to other small RNA insect viruses. PMID:27298753

  9. Synthesis, physicochemical, structural and rheological characterizations of carboxymethyl xanthan derivatives.

    PubMed

    Yahoum, Madiha M; Moulai-Mostefa, Nadji; Le Cerf, Didier

    2016-12-10

    The aim of this work was to synthesize a carboxymethylated xanthan (CMXG) via an etherification reaction between different ratios (2, 4, and 6) of xanthan gum (XG) and monochloroacetic acid (MCAA) using the Williamson synthesis method. The synthetized products were characterized in terms of their physico-chemical and rheological properties. Both FTIR and proton nuclear magnetic resonance (H(1) NMR) analyses confirmed the grafting of carboxymethyl groups on xanthan hydroxyl groups. The obtained results demonstrated that the degree of substitution was proportional to the chloroacetic acid and xanthan gum ratios. The obtained carboxymethyl derivatives presented greater hydrophilicity and lower molecular weights with increasing degrees of substitution than native xanthan gum. The rheological study revealed that the viscosity of the CMXG derivatives decreased with the degree of substitution and with the conservation of the shear-thinning and weak gel behaviours. The flow curves suggested the existence of two different populations of particles consisting of CMXG particles with a smaller average size and a second population formed by the residual fractions of native XG particles. It was also found that the elastic modulus of XG was largely higher than that of the CMXG derivatives and decreased with increasing DS. For the CMXG derivatives, two regions of viscoelastic behaviour were observed, which were separated by a crossover point corresponding to the critical frequency and relaxation time, i.e., the time required for stress relaxation.

  10. Structural characterization and thermal stability of Notothenia coriiceps metallothionein.

    PubMed Central

    D'Auria, S; Carginale, V; Scudiero, R; Crescenzi, O; Di Maro, D; Temussi, P A; Parisi, E; Capasso, C

    2001-01-01

    Fish and mammalian metallothioneins (MTs) differ in the amino acid residues placed between their conserved cysteines. We have expressed the MT of an Antarctic fish, Notothenia coriiceps, and characterized it by means of multinuclear NMR spectroscopy. Overall, the architecture of the fish MT is very similar to that of mammalian MTs. However, NMR spectroscopy shows that the dynamic behaviour of the two domains is markedly different. With the aid of absorption and CD spectroscopies, we studied the conformational and electronic features of fish and mouse recombinant Cd-MT and the changes produced in these proteins by heating. When the temperature was increased from 20 to 90 degrees C, the Cd-thiolate chromophore absorbance at 254 nm of mouse MT was not modified up to 60 degrees C, whereas the absorbance of fish MT decreased significantly starting from 30 degrees C. The CD spectra also changed quite considerably with temperature, with a gradual decrease of the positive band at 260 nm that was more pronounced for fish than for mouse MT. The differential effect of temperature on fish and mouse MTs may reflect a different stability of metal-thiolate clusters of the two proteins. Such a conclusion is also corroborated by results showing differences in metal mobility between fish and mouse Zn-MT. PMID:11171106

  11. Structural characterization and electrochemical properties of novel salicylidene phosphonate derivatives

    NASA Astrophysics Data System (ADS)

    Dolaz, Mustafa; McKee, Vickie; Köse, Muhammet; Gölcü, Ayşegül; Tümer, Mehmet

    2010-09-01

    In this study, three novel salicylidene phosphonate ligands, diethyl (4-{[(1 E)-(2-hydroxyphenyl)methylidene]amino}benzyl)phosphonate (HL 1), diethyl (4-{[(1 E)-(2-hydroxy-3-methoxyphenyl)methylidene]amino}benzyl)phosphonate (HL 2) and diethyl (4-{[(1 E)-(2,4-dihydroxyphenyl)methylidene]amino}benzyl)phosphonate (HL 3) were synthesized and characterized by the analytical and spectroscopic techniques. We obtained their single crystals from the ethanolic solution. There are intramolecular phenol-imine hydrogen bonds in all three compounds between O1 and N1 atoms. The ligand HL 3 contains a second phenol group and this is makes an intermolecular hydrogen bond with the phosphine oxide of a neighbouring molecule O2-O3 (under symmetry operation - x, 0.5 + y, 0.5 - z). In order to investigate the redox behaviours of the salicylidene phosphonate ligands (HL 1-HL 3), we were studied electrochemical properties of the ligands at the different pH and scan rates.

  12. Synthesis, physicochemical, structural and rheological characterizations of carboxymethyl xanthan derivatives.

    PubMed

    Yahoum, Madiha M; Moulai-Mostefa, Nadji; Le Cerf, Didier

    2016-12-10

    The aim of this work was to synthesize a carboxymethylated xanthan (CMXG) via an etherification reaction between different ratios (2, 4, and 6) of xanthan gum (XG) and monochloroacetic acid (MCAA) using the Williamson synthesis method. The synthetized products were characterized in terms of their physico-chemical and rheological properties. Both FTIR and proton nuclear magnetic resonance (H(1) NMR) analyses confirmed the grafting of carboxymethyl groups on xanthan hydroxyl groups. The obtained results demonstrated that the degree of substitution was proportional to the chloroacetic acid and xanthan gum ratios. The obtained carboxymethyl derivatives presented greater hydrophilicity and lower molecular weights with increasing degrees of substitution than native xanthan gum. The rheological study revealed that the viscosity of the CMXG derivatives decreased with the degree of substitution and with the conservation of the shear-thinning and weak gel behaviours. The flow curves suggested the existence of two different populations of particles consisting of CMXG particles with a smaller average size and a second population formed by the residual fractions of native XG particles. It was also found that the elastic modulus of XG was largely higher than that of the CMXG derivatives and decreased with increasing DS. For the CMXG derivatives, two regions of viscoelastic behaviour were observed, which were separated by a crossover point corresponding to the critical frequency and relaxation time, i.e., the time required for stress relaxation. PMID:27577918

  13. Membrane characterization by microscopic and scattering methods: multiscale structure.

    PubMed

    Tamime, Rahma; Wyart, Yvan; Siozade, Laure; Baudin, Isabelle; Deumie, Carole; Glucina, Karl; Moulin, Philippe

    2011-04-13

    Several microscopic and scattering techniques at different observation scales (from atomic to macroscopic) were used to characterize both surface and bulk properties of four new flat-sheet polyethersulfone (PES) membranes (10, 30, 100 and 300 kDa) and new 100 kDa hollow fibers (PVDF). Scanning Electron Microscopy (SEM) with "in lens" detection was used to obtain information on the pore sizes of the skin layers at the atomic scale. White Light Interferometry (WLI) and Atomic Force Microscopy (AFM) using different scales (for WLI: windows: 900 × 900 µm2 and 360 × 360 µm2; number of points: 1024; for AFM: windows: 50 × 50 µm2 and 5 × 5 µm2; number of points: 512) showed that the membrane roughness increases markedly with the observation scale and that there is a continuity between the different scan sizes for the determination of the RMS roughness. High angular resolution ellipsometric measurements were used to obtain the signature of each cut-off and the origin of the scattering was identified as coming from the membrane bulk.

  14. Structural characterization of the mitomycin 7-O-methyltransferase

    SciTech Connect

    Singh, Shanteri; Chang, Aram; Goff, Randal D.; Bingman, Craig A.; Grüschow, Sabine; Sherman, David H.; Phillips, Jr., George N.; Thorson, Jon S.

    2014-10-02

    Mitomycins are quinone-containing antibiotics, widely used as antitumor drugs in chemotherapy. Mitomycin-7-O-methyltransferase (MmcR), a key tailoring enzyme involved in the biosynthesis of mitomycin in Streptomyces lavendulae, catalyzes the 7-O-methylation of both C9{beta}- and C9{alpha}-configured 7-hydroxymitomycins. We have determined the crystal structures of the MmcR-S-adenosylhomocysteine (SAH) binary complex and MmcR-SAH-mitomycin A (MMA) ternary complex at resolutions of 1.9 and 2.3 {angstrom}, respectively. The study revealed MmcR to adopt a common S-adenosyl-L-methionine-dependent O-methyltransferase fold and the presence of a structurally conserved active site general acid-base pair is consistent with a proton-assisted methyltransfer common to most methyltransferases. Given the importance of C7 alkylation to modulate mitomycin redox potential, this study may also present a template toward the future engineering of catalysts to generate uniquely bioactive mitomycins.

  15. Optical fiber sensors for characterization of materials and structures

    NASA Astrophysics Data System (ADS)

    Claus, Richard O.; Murphy, Kent A.

    1994-08-01

    Optical fiber systems have been developed during the past twenty-five years for primary applications in the high speed digital communication of information. Using much of the same rapidly-developing technology optical fiber sensor systems have been developed during the past fifteen years for the measurement of a wide range of physical observables and applications in aerospace and hydrospace, civil structures and biomedical instrumentation systems. The major advantage of optical fiber sensor methods over conventional sensor systems is the all-dielectric nature of the fiber and the intrinsic avoidance of electromagnetic interference and ground loops that plague wire and metal-based sensing networks. For physical property measurements in smart materials where actuator elements and arrays are driven by high voltage electrical signals, such immunity is especially important. Another major advantage is the operation of fiber sensors above the temperatures at which most conventional sensor instrumentation will not operate. Such operation allows the use of properly designed fiber sensors in situ for the analysis of the fabrication conditions of smart materials, as well as their performance in high temperature environments. Sensor elements incorporated into the material during fabrication may in some cases be used for material evaluation post processing. This paper briefly suggests the use of such optical fiber sensor elements during the fabrication, inservice lifetimes and damage and degradation phases of smart material and structural systems.

  16. Pore structure characterization of catalyst supports via low field NMR

    SciTech Connect

    Smith, D.M.; Glaves, C.L.; Gallegos, D.P. )

    1988-09-01

    The pore structures of two types of catalyst support material were studied: {gamma}-alumina and silica aerogel. The alumina samples were commercial catalyst supports made in 1/8 inch diameter pellet form by Harshaw Chemical. Aerogels were prepared by forming a gel in a two-step, base-catalyzed process using TEOS, followed by supercritical drying to form the aerogel. Two different aerogels were made, one undergoing the drying process immediately after gel formation (non-aged), and the other being aged in the gel state for two weeks in a basic solution of 0.1 molar NH{sub 4}OH at 323 K before being supercritically dried (aged). The aging process is believed to alter the aerogel pore structure. The pore size distribution of the alumina material was determined via NMR and compared to results obtained by mercury intrusion and nitrogen adsorption/condensation techniques. The pore size distributions of the two aerogel samples were measured via NMR and nitrogen adsorption/condensation; the material was too compressible for porosimetry.

  17. Structure and functional characterization of the atypical human kinase haspin

    PubMed Central

    Eswaran, Jeyanthy; Patnaik, Debasis; Filippakopoulos, Panagis; Wang, Fangwei; Stein, Ross L.; Murray, James W.; Higgins, Jonathan M. G.; Knapp, Stefan

    2009-01-01

    The protein kinase haspin/Gsg2 plays an important role in mitosis, where it specifically phosphorylates Thr-3 in histone H3 (H3T3). Its protein sequence is only weakly homologous to other protein kinases and lacks the highly conserved motifs normally required for kinase activity. Here we report structures of human haspin in complex with ATP and the inhibitor iodotubercidin. These structures reveal a constitutively active kinase conformation, stabilized by haspin-specific inserts. Haspin also has a highly atypical activation segment well adapted for specific recognition of the basic histone tail. Despite the lack of a DFG motif, ATP binding to haspin is similar to that in classical kinases; however, the ATP γ-phosphate forms hydrogen bonds with the conserved catalytic loop residues Asp-649 and His-651, and a His651Ala haspin mutant is inactive, suggesting a direct role for the catalytic loop in ATP recognition. Enzyme kinetic data show that haspin phosphorylates substrate peptides through a rapid equilibrium random mechanism. A detailed analysis of histone modifications in the neighborhood of H3T3 reveals that increasing methylation at Lys-4 (H3K4) strongly decreases substrate recognition, suggesting a key role of H3K4 methylation in the regulation of haspin activity. PMID:19918057

  18. Structure and functional characterization of the atypical human kinase haspin.

    PubMed

    Eswaran, Jeyanthy; Patnaik, Debasis; Filippakopoulos, Panagis; Wang, Fangwei; Stein, Ross L; Murray, James W; Higgins, Jonathan M G; Knapp, Stefan

    2009-12-01

    The protein kinase haspin/Gsg2 plays an important role in mitosis, where it specifically phosphorylates Thr-3 in histone H3 (H3T3). Its protein sequence is only weakly homologous to other protein kinases and lacks the highly conserved motifs normally required for kinase activity. Here we report structures of human haspin in complex with ATP and the inhibitor iodotubercidin. These structures reveal a constitutively active kinase conformation, stabilized by haspin-specific inserts. Haspin also has a highly atypical activation segment well adapted for specific recognition of the basic histone tail. Despite the lack of a DFG motif, ATP binding to haspin is similar to that in classical kinases; however, the ATP gamma-phosphate forms hydrogen bonds with the conserved catalytic loop residues Asp-649 and His-651, and a His651Ala haspin mutant is inactive, suggesting a direct role for the catalytic loop in ATP recognition. Enzyme kinetic data show that haspin phosphorylates substrate peptides through a rapid equilibrium random mechanism. A detailed analysis of histone modifications in the neighborhood of H3T3 reveals that increasing methylation at Lys-4 (H3K4) strongly decreases substrate recognition, suggesting a key role of H3K4 methylation in the regulation of haspin activity. PMID:19918057

  19. Isomerism of Cyanomethanimine: Accurate Structural, Energetic, and Spectroscopic Characterization.

    PubMed

    Puzzarini, Cristina

    2015-11-25

    The structures, relative stabilities, and rotational and vibrational parameters of the Z-C-, E-C-, and N-cyanomethanimine isomers have been evaluated using state-of-the-art quantum-chemical approaches. Equilibrium geometries have been calculated by means of a composite scheme based on coupled-cluster calculations that accounts for the extrapolation to the complete basis set limit and core-correlation effects. The latter approach is proved to provide molecular structures with an accuracy of 0.001-0.002 Å and 0.05-0.1° for bond lengths and angles, respectively. Systematically extrapolated ab initio energies, accounting for electron correlation through coupled-cluster theory, including up to single, double, triple, and quadruple excitations, and corrected for core-electron correlation and anharmonic zero-point vibrational energy, have been used to accurately determine relative energies and the Z-E isomerization barrier with an accuracy of about 1 kJ/mol. Vibrational and rotational spectroscopic parameters have been investigated by means of hybrid schemes that allow us to obtain rotational constants accurate to about a few megahertz and vibrational frequencies with a mean absolute error of ∼1%. Where available, for all properties considered, a very good agreement with experimental data has been observed.

  20. Structure and Mixing Characterization of Variable Density Transverse Jet Flows

    NASA Astrophysics Data System (ADS)

    Gevorkyan, Levon

    This dissertation describes an experimental study of the structural and mixing characteristics of transverse jets, or jets in crossfiow (JICF). Hot-wire anemometry, stereo particle image velocimetry (PIV), and acetone planar laser-induced fiuorescence (PLIF) measurements were utilized to illuminate and quantify the wind-ward (upstream) jet shear layer instability characteristics and their relationship to the velocity field evolution, as well as the effect of the overall velocity field on the scalar field distribution and resulting mixing characteristics. Transverse jets of various jet-to-crossfiow momentum flux ratios in the range 41 ≥ J ≥ 2, and jet-to-crossfiow density ratios in the range 1.00 ≥ S ≥ 0.35, were generated using mixtures of helium and nitrogen in the jet fluid. Jets were injected from one of three different injectors explored: a convergent nozzle with circular geometry which was mounted flush with the wind tunnel floor, another convergent nozzle with circular geometry whose exit plane lies above the crossfiow boundary layer, and a flush-mounted straight pipe injector with a circular orifice. Jet Reynolds number was kept constant for the majority of the mixing and structural exploration experiments at Rej = 1900, except when the effect of Reynolds number on cross-sectional jet structure was explored. Previous hot-wire based measurements at UCLA suggest that the upstream jet shear layer transitions from convective instability to absolute instability, giving rise to self-excited nonlinear states, as either the momentum flux ratio is lowered below J ≈10, or the density ratio is lowered below S ≈ 0.45 for the JICF injected from the flush nozzle injector. A similar transition to absolute instability when lowering momentum flux ratio was found in this work for the flush-mounted pipe injector. Cross-sectional PLIF measurements in the present studies suggested clear correspondence between the formation of a symmetric counter-rotating vortex pair

  1. Structure Characterization and Properties of K-Containing Copper Hexacyanoferrate.

    PubMed

    Ojwang, Dickson O; Grins, Jekabs; Wardecki, Dariusz; Valvo, Mario; Renman, Viktor; Häggström, Lennart; Ericsson, Tore; Gustafsson, Torbjörn; Mahmoud, Abdelfattah; Hermann, Raphaël P; Svensson, Gunnar

    2016-06-20

    Copper hexacyanoferrate, Cu(II)[Fe(III)(CN)6]2/3·nH2O, was synthesized, and varied amounts of K(+) ions were inserted via reduction by K2S2O3 (aq). Ideally, the reaction can be written as Cu(II)[Fe(III)(CN)6]2/3·nH2O + 2x/3K(+) + 2x/3e(-) ↔ K2x/3Cu(II)[Fe(II)xFe(III)1-x(CN)6]2/3·nH2O. Infrared, Raman, and Mössbauer spectroscopy studies show that Fe(III) is continuously reduced to Fe(II) with increasing x, accompanied by a decrease of the a-axis of the cubic Fm3̅m unit cell. Elemental analysis of K by inductively coupled plasma shows that the insertion only begins when a significant fraction, ∼20% of the Fe(III), has already been reduced. Thermogravimetric analysis shows a fast exchange of water with ambient atmosphere and a total weight loss of ∼26 wt % upon heating to 180 °C, above which the structure starts to decompose. The crystal structures of Cu(II)[Fe(III)(CN)6]2/3·nH2O and K2/3Cu[Fe(CN)6]2/3·nH2O were refined using synchrotron X-ray powder diffraction data. In both, one-third of the Fe(CN)6 groups are vacant, and the octahedron around Cu(II) is completed by water molecules. In the two structures, difference Fourier maps reveal three additional zeolitic water sites (8c, 32f, and 48g) in the center of the cavities formed by the -Cu-N-C-Fe- framework. The K-containing compound shows an increased electron density at two of these sites (32f and 48g), indicating them to be the preferred positions for the K(+) ions. PMID:27258790

  2. Growth, structural, electronic and optical characterization of nitride semiconductors

    NASA Astrophysics Data System (ADS)

    Constantin, Costel

    This project investigates the growth, optical, electronic, surface, magnetic and bulk properties of scandium gallium nitride on Sapphire(0001), manganese scandium nitride on MgO(001), heterostructures of cubic gallium nitride and scandium nitride on Mg(001), and chromium nitride on MgO(001) grown by radio frequency molecular beam epitaxy. The growth of ScxGa1- xN films has been performed at a substrate temperature of 650°C. The diffraction and optical experiments confirm the existence of two main regimes of growth; for high Sc concentration (x ≥ 0.54), a rocksalt crystal structure is obtained. For low x ( x ≤ 0.17), a wurtzite-like crystal structure is observed with local lattice distortions at the sites where the Sc atoms incorporate substitutionally into the Ga sites. The growth of MnxSc1- xN films, with x = 0.03-0.05, has been performed at a substrate temperature of ˜500°C. A rocksalt structure is observed for the MnxSc1-xN films. Magnetic measurements preformed on the Mn0.03Sc0.97 N film show ferromagnetic with a TC ˜ 50 K. As the manganese concentration is increased to x = 0.05, the ferromagnetism is reduced. The growth of heterostructures c-GaN(001)/ScN(001)/MgO(001) and ScN(001)/c-GaN(001)/MgO(001) adopt a cubical symmetry of the MgO(001) substrate. The zincblend c-GaN grown atop of ScN(001) shows a smoother surface (predominantly 2D growth) as compared to the rocksalt ScN(001) grown on atop of c-GaN(001). The growth of stoichiometric CrN(001) films is performed at a substrate temperature of 450°C. A novel growth method of highly crystalline stoichiometric CrN(001) films has been proposed. The room temperature scanning tunneling microscopy together with resistivity versus temperature experiments reveal the electronic behavior of CrN(001) films to be metallic below T N ≃ 270 K, and semiconductor above TN.

  3. Structure Characterization and Properties of K-Containing Copper Hexacyanoferrate

    DOE PAGES

    Ojwang, Dickson O.; Grins, Jekabs; Wardecki, Dariusz; Valvo, Mario; Renman, Viktor; Häggström, Lennart; Ericsson, Tore; Gustafsson, Torbjörn; Mahmoud, Abdelfattah; Hermann, Raphaël P.; et al

    2016-06-03

    Copper hexacyanoferrate, CuII[FeIII(CN)6]2/3 nH2O, was synthesized, and varied amounts of K+ ions were inserted via reduction by K2S2O3 (aq). Ideally, the reaction can be written as CuII[FeIII(CN)6]2/3∙ nH2O + 2x/3K+ + 2x/3e⁻ ↔K2x/3CuII[FeIIxFeIII1- x(CN)6]2/3 nH2O. Infrared, Raman, and Mössbauer spectroscopy studies show that FeIII is continuously reduced to FeII with increasing x, accompanied by a decrease of the a-axis of the cubic Fmore » $$m\\bar{3}$$m unit cell. Elemental analysis of K by inductively coupled plasma shows that the insertion only begins when a significant fraction, ~20% of the FeIII, has already been reduced. Thermogravimetric analysis shows a fast exchange of water with ambient atmosphere and a total weight loss of ~26 wt % upon heating to 180 °C, above which the structure starts to decompose. The crystal structures of CuII[FeIII(CN)6]2/3∙ nH2O and K2/3Cu[Fe(CN)6]2/3∙ nH2O were refined using synchrotron X-ray powder diffraction data. In both, one-third of the Fe(CN)6 groups are vacant, and the octahedron around CuII is completed by water molecules. In the two structures, difference Fourier maps reveal three additional zeolitic water sites (8c, 32f, and 48g) in the center of the cavities formed by the Cu N C Fe framework. In conclusion, the K-containing compound shows an increased electron density at two of these sites (32f and 48g), indicating them to be the preferred positions for the K+ ions.« less

  4. The synthesis and structural characterization of novel transition metal fluorides

    SciTech Connect

    Casteel, W.J. Jr.

    1992-09-01

    High purity KMF{sub 6} and K{sub 2}MF{sub 6} salts (M = Mo,Re, Ru, Os, Ir, Pt) are obtained from reduction hexafluorides. A rhombohedral unit cell is observed for KReF{sub 6}. Fluoride ion capture by Lewis acids from the hexafluorometallate (IV) salts affords high purity tetrafluorides for M = Mo, Re, Ru, Os, and Pd. The structure of RuF{sub 4} is determined from X-ray synchrotron and neutron powder data. Unit cells based on theorthorhombic PdF{sub 4} type cell are derived from X-ray powder data for ReF{sub 4} and OsF{sub 4}. Fluoride ion capture from KAgF{sub 4} provides the thermally unstable trifluoride as a bright, red, diamagnetic solid. The structure solution of AgF{sub 3} and redetermination of the AuF{sub 3} structure from X-ray synchrotron and neutron powder data demonstrate that the two are isostnictural. Thermal decomposition product of AgF{sub 3} is the mixed valence compound Ag{sup II}Ag{sub 2}{sup III}F{sub 8}. Several new salts containing the (Ag - F){sub n}{sup n+} chain cation are prepared. The first linear (Ag - F){sub n}{sup n+} chain is observed in AgF{sup +}BF{sub 4 {sup {minus}}} which crystallizes in a tetragonal unit. AgFAuF{sub 4} has a triclinic unit cell and is isostructural with CuFAuF{sub 4}. AgFAuF{sub 6} has an orthorhombic unit cell and appears to be isostructural with AgFAsF{sub 6}. A second mixed valence silver fluoride, Ag{sup II}Ag{sup III}F{sub 5}, is prepared, which magnetic measurements indicate is probably an AgF{sup +} salt. Magnetic data for all of the AgF{sup +} salts exhibit low magnitude, temperature independent paramagnetism characteristic of metallic systems. Cationic AG(II) in acidic AHF solutions is a powerful oxidizer, capable of oxidizing Xe to Xe(II) and O{sub 2} to O{sub 2}{sup +}. Reactions with C{sub 6}F{sub 6} and C{sub 3}F{sub 6} suggest an electron capture mechanism for cationic AG(II) oxidations.

  5. Synthesis, Characterization, and Theory of [9]-, [12]-, and [18]Cycloparaphenylene: Carbon Nanohoop Structures

    PubMed Central

    2008-01-01

    The first synthesis and characterization of [9]-, [12]-, and [18]cycloparaphenylene was demonstrated utilizing a novel aromatization reaction. We refer to these fascinating structures as “carbon nanohoops” due to their structural similarity to carbon nanotubes. Additionally, we have utilized computational methods to understand the unique properties of these fully conjugated macrocycles. PMID:19055403

  6. Materials and characterization using acoustic nonlinearity parameters and harmonic generation - Effects of crystalline and amorphous structures

    NASA Technical Reports Server (NTRS)

    Cantrell, John H.; Yost, William T.

    1990-01-01

    The effects of material structure on the nonlinearity parameters are reviewed. Problems discussed include definition of nonlinearity parameters, square-law nonlinearity and collinear beam-mixing, structure dependence of the nonlinearity parameters, negative nonlinearity parameters, and implications for materials characterization.

  7. First total synthesis of (+/-)-3-hydroxy-11-norcytisine: structure confirmation and biological characterization.

    PubMed

    Yohannes, Daniel; Hansen, Camilla P; Akireddy, Srinivasa Rao; Hauser, Terry A; Kiser, Melanie N; Gurnon, Nicholas J; Day, Cynthia S; Bhatti, Balwinder; Caldwell, William S

    2008-12-01

    The first total synthesis of the natural product 3-hydroxy-11-norcytisine (1), structurally related to cytisine (2), a benchmark ligand at neuronal nicotinic acetylcholine receptors (NNRs), has been achieved. The synthesis permits the unambiguous confirmation of the structure originally proposed for 1 and has enabled initial biological characterization of 1 and its related compounds against NNRs.

  8. Characterization of porous media structure by non linear NMR methods.

    PubMed

    Capuani, S; Alesiani, M; Alessandri, F M; Maraviglia, B

    2001-01-01

    In this paper we discuss the possibility of modifying the multiple spin echoes existing theory, developed for a homogeneous system, to describe also an inhomogeneous system such as a porous medium. We report here the first experimental application of MSE methods to materials like travertine. The ratio A(2)/A(1) from water in travertine presents minima for characteristic values of the delay time tau, like what was previously observed in the trabecular bone. By a judicious choice of the delay time tau and of the G gradient strength, the MSE sequence can be made sensitive to a specific length-scale of the sample heterogeneity. Furthermore the MSE image shows a particular new contrast that makes the non linear NMR method very attractive for the assessment of variations of the porous structure in porous systems. PMID:11445306

  9. Genetic structure characterization of Chileans reflects historical immigration patterns.

    PubMed

    Eyheramendy, Susana; Martinez, Felipe I; Manevy, Federico; Vial, Cecilia; Repetto, Gabriela M

    2015-01-01

    Identifying the ancestral components of genomes of admixed individuals helps uncovering the genetic basis of diseases and understanding the demographic history of populations. We estimate local ancestry on 313 Chileans and assess the contribution from three continental populations. The distribution of ancestry block-length suggests an average admixing time around 10 generations ago. Sex-chromosome analyses confirm imbalanced contribution of European men and Native-American women. Previously known genes under selection contain SNPs showing large difference in allele frequencies. Furthermore, we show that assessing ancestry is harder at SNPs with higher recombination rates and easier at SNPs with large difference in allele frequencies at the ancestral populations. Two observations, that African ancestry proportions systematically decrease from North to South, and that European ancestry proportions are highest in central regions, show that the genetic structure of Chileans is under the influence of a diffusion process leading to an ancestry gradient related to geography. PMID:25778948

  10. Characterization of the interior structure of synthetic diamond particles

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  11. Genetic structure characterization of Chileans reflects historical immigration patterns.

    PubMed

    Eyheramendy, Susana; Martinez, Felipe I; Manevy, Federico; Vial, Cecilia; Repetto, Gabriela M

    2015-03-17

    Identifying the ancestral components of genomes of admixed individuals helps uncovering the genetic basis of diseases and understanding the demographic history of populations. We estimate local ancestry on 313 Chileans and assess the contribution from three continental populations. The distribution of ancestry block-length suggests an average admixing time around 10 generations ago. Sex-chromosome analyses confirm imbalanced contribution of European men and Native-American women. Previously known genes under selection contain SNPs showing large difference in allele frequencies. Furthermore, we show that assessing ancestry is harder at SNPs with higher recombination rates and easier at SNPs with large difference in allele frequencies at the ancestral populations. Two observations, that African ancestry proportions systematically decrease from North to South, and that European ancestry proportions are highest in central regions, show that the genetic structure of Chileans is under the influence of a diffusion process leading to an ancestry gradient related to geography.

  12. Synthesis and characterization of JBW structure and its thermal transformation

    NASA Astrophysics Data System (ADS)

    Hegazy, Eman Z.; Kosa, Samia A.; Abd El Maksod, Islam Hamdy

    2012-12-01

    In this paper, JBW zeolite prepared from Egyptian kaolin was investigated by means of XRD, IR, SEM, EDX and ion exchange of some heavy metals. Adsorption isotherms were used to investigate the structure and properties of the prepared zeolite. XRD analysis showed that the JBW was a pure crystalline phase with orthorhombic crystal symmetry. Thermal treatment showed that the JBW transformed into the It-Carn phase at 1000 °C through an intermediate crystalline alumino silicate phase. SEM images showed that the JBW crystallised in a cylindrical shape. However, spherical agglomerates were observed at lower magnifications. The ion exchange isotherms with Cu2+, Ni2+ and Co2+ were found to follow a Freundlich isotherm. In addition, it shows higher affinity towards Cu2+ than other ions.

  13. Genetic structure characterization of Chileans reflects historical immigration patterns

    PubMed Central

    Eyheramendy, Susana; Martinez, Felipe I.; Manevy, Federico; Vial, Cecilia; Repetto, Gabriela M.

    2015-01-01

    Identifying the ancestral components of genomes of admixed individuals helps uncovering the genetic basis of diseases and understanding the demographic history of populations. We estimate local ancestry on 313 Chileans and assess the contribution from three continental populations. The distribution of ancestry block-length suggests an average admixing time around 10 generations ago. Sex-chromosome analyses confirm imbalanced contribution of European men and Native-American women. Previously known genes under selection contain SNPs showing large difference in allele frequencies. Furthermore, we show that assessing ancestry is harder at SNPs with higher recombination rates and easier at SNPs with large difference in allele frequencies at the ancestral populations. Two observations, that African ancestry proportions systematically decrease from North to South, and that European ancestry proportions are highest in central regions, show that the genetic structure of Chileans is under the influence of a diffusion process leading to an ancestry gradient related to geography. PMID:25778948

  14. Performance characterization of structured light-based fingerprint scanner

    NASA Astrophysics Data System (ADS)

    Hassebrook, Laurence G.; Wang, Minghao; Daley, Raymond C.

    2013-05-01

    Our group believes that the evolution of fingerprint capture technology is in transition to include 3-D non-contact fingerprint capture. More specifically we believe that systems based on structured light illumination provide the highest level of depth measurement accuracy. However, for these new technologies to be fully accepted by the biometric community, they must be compliant with federal standards of performance. At present these standards do not exist for this new biometric technology. We propose and define a set of test procedures to be used to verify compliance with the Federal Bureau of Investigation's image quality specification for Personal Identity Verification single fingerprint capture devices. The proposed test procedures include: geometric accuracy, lateral resolution based on intensity or depth, gray level uniformity and flattened fingerprint image quality. Several 2-D contact analogies, performance tradeoffs and optimization dilemmas are evaluated and proposed solutions are presented.

  15. Features and characterization needs of rubber composite structures

    NASA Technical Reports Server (NTRS)

    Tabaddor, Farhad

    1989-01-01

    Some of the major unique features of rubber composite structures are outlined. The features covered are those related to the material properties, but the analytical features are also briefly discussed. It is essential to recognize these features at the planning stage of any long-range analytical, experimental, or application program. The development of a general and comprehensive program which fully accounts for all the important characteristics of tires, under all the relevant modes of operation, may present a prohibitively expensive and impractical task at the near future. There is therefore a need to develop application methodologies which can utilize the less general models, beyond their theoretical limitations and yet with reasonable reliability, by proper mix of analytical, experimental, and testing activities.

  16. Hierarchical manufacture and characterization of multifunctional nanocomposite structures

    NASA Astrophysics Data System (ADS)

    Veedu, Vinod P. V.

    The objective of this work is to develop multifunctional 3-D nanocomposite structures in an attempt to solve the shortcomings of the traditional composite materials. To achieve this goal, at first a detailed analysis of the properties of the basic nano reinforcement, carbon nanotube, was performed in terms of mechanical behavior, thermoelastic responses and thermal conductivity using an analytical technique, namely, asymptotic homogenization method. In our initial experimental works, different polymer resins were reinforced with nanotubes as well as nanoparticles and their mechanical performances were investigated. These experiments reveal that at higher weight percentage loading of the nanoparticles and nanotubes there are dominant issues such as alignment and dispersion, which would weaken the material. This led us to seek a novel approach to nanocomposites. In this report, two multifunctional nanocomposite structures are introduced: nanotube based brushes and hierarchical 3-D nanocomposite. The nanotube brushes were fabricated using chemical vapor deposition. Functions performed by these brushes such as mechanical and chemical cleaning, painting and electrical contacts will be discussed. Also, we unveil a novel approach to the 3-D composite challenge, without altering the existing 2-D stack design, based on the concept of interlaminar carbon nanotube forests that would provide enhanced multifunctional properties in the thickness direction. The nanotube coated fabric cloths serve as building blocks for the multi-layered 3-D composites with the nanotubes forests providing much needed interlaminar strength and toughness under various loading conditions. For the fabricated 3-D composites with nanotube forests, we demonstrate remarkable improvements in the interlaminar fracture toughness, delamination resistance, in-plane mechanical properties, damping, thermoelastic behavior, and thermal and electrical conductivities providing truly three-dimensional multifunctional

  17. Kinetic and structural characterization of spinach carbonic anhydrase.

    PubMed

    Rowlett, R S; Chance, M R; Wirt, M D; Sidelinger, D E; Royal, J R; Woodroffe, M; Wang, Y F; Saha, R P; Lam, M G

    1994-11-29

    We have carried out kinetics studies of spinach carbonic anhydrase (CA) using stopped-flow spectrophotometry at steady state and 13C-NMR exchange at chemical equilibrium. We found that the rate of CO2<-->HCO3- exchange catalyzed by spinach CA at pH 7.0 to be 3-5 times faster than the maximal kcat for either CO2 hydration or HCO3- dehydration at steady state, suggesting a rate-determining H+ transfer step in the catalytic mechanism. Correspondingly, we measured a pH-independent solvent deuterium isotope effect on kcat of approximately 2.0, and found that the rate of catalysis was significantly decreased at external buffer concentrations below 5 mM. Our results are consistent with a zinc-hydroxide mechanism of action with for spinach CA, similar to that of animal carbonic anhydrases. We have also collected X-ray absorption spectra of spinach CA. Analysis of the extended fine structure (EXAFS) suggests that the coordination sphere of Zn in spinach CA must have one or more sulfur ligands, in contrast to animal CAs which have only nitrogen and oxygen ligands. The models which best fit the data have average Zn-N(O) distances of 1.99-2.06 A, average Zn-S distances of 2.31--2.32 A, and a total coordination number of 4-6. We conclude that animal and spinach CAs are convergently evolved enzymes which are structurally quite different, but functionally equivalent. PMID:7947805

  18. Production and characterization of carbon structures derived from wood

    NASA Astrophysics Data System (ADS)

    Xie, Xinfeng

    The objective of this research was to produce structural carbon materials from wood, a renewable biomaterial, for advanced material application. A broad range of materials were produced for study including carbonized wood, resin infused carbon composites made from carbonized wood, and carbon nanotubes from wood fibers. The effect of slow heating on the properties of carbonized wood was studied and important carbonized wood properties were found to be produced over a range of heating rates and peak temperatures. Slow heating rates promoted the formation and growth of graphene sheets in turbostratic crystallites, which had a significant influence on the electrical resistivity and Young's modulus of the carbonized wood. A reduction in the rate of heating may be beneficial with respect to carbon properties and the prevention of crack production during the manufacture of large monolithic carbon specimens from wood and wood-based materials. Investigation of selected physical and mechanical properties of resin-infused porous carbon composites made from medium density fiberboard demonstrated that the infused material can be used in specific applications, where high mechanical strength is not required but high dimensional stability at elevated-use temperatures, fire safety, or static dissipation and shielding is required. A unique cyclic heating process has been developed to produce carbon nanotubes directly from wood fibers. Study on the oxidative behavior of carbons derived from cellulose and lignin showed that cellulose carbon ablates faster at a lower temperature in air than lignin carbon when they were prepared at temperatures lower than 500°C due to cellulose carbon's lower content of aromatic structures. It is hypothesized that the formation of carbon nanotubes during the cyclic heating process occurred via template synthesis, with the nanochannels formed from the ablation of cellulose fibrils functioning as a template. Evidence of formation of nanochannels has been

  19. Mechanical characterization and structural assessment of biocomposites for construction

    NASA Astrophysics Data System (ADS)

    Christian, Sarah Jane

    The objective of this dissertation is to assess whether or not two particular biocomposite materials, made from hemp fabric and cellulose acetate or polyhydroxybutyrate matrices, are capable of being used for structural and/or construction purposes within in the construction and building industry. The objective of this dissertation was addressed by conducting research to meet the following three goals: (1) to measure the basic mechanical properties of hemp/cellulose acetate and hemp/PHB biocomposites and evaluate if they suitable for use in construction applications, (2) to determine how quickly moisture diffuses into the biocomposite materials and how the moisture affects the mechanical behavior, and (3) to determine how well simple models can predict behavior of structural scale laminates in tension and flexure using biocomposite ply behavior. Compression molding was used to manufacturing the biocomposites from hemp fabric and the themoplastic matrices: cellulose acetate and polyhydroxybutyrate. Four methods for determining the fiber volume fraction were evaluated, and the dissolution method, using different solvents for each matrix type, was used to determine the fiber volume fraction for each composite plate manufactured. Both types of biocomposite were tested in tension, compression, shear, and flexure and the measured properties were compared to wood and engineered wood products to assess whether the biocomposite properties are suitable for use in the construction industry. The biocomposites were conditioned in a humid environment to determine the rate of moisture diffusion into the materials. Then saturated specimens and specimens that were saturated and then dried were tested in tension to evaluate how moisture absorption affects the mechanical behavior of the biocomposites. Finally, simple models of laminate behavior based on laminate plate theory were evaluated to determine if ply level behavior could be used to predict structural scale laminate behavior

  20. Characterization of Periodontal Structures of Enamelin-Null Mice

    PubMed Central

    Chan, Hsun-Liang; Giannobile, William V.; Eber, Robert M.; Simmer, James P.; Hu, Jan C.

    2014-01-01

    Background Enamelin-null (ENAM−/−) mice have no enamel. When characterizing ENAM−/− mice, alveolar bone height reduction was observed, and it was hypothesized that enamel defects combined with diet are associated with the periodontal changes of ENAM−/− mice. The aim of the present study is to compare the dimension of interradicular bone of ENAM−/− (knock-out [KO]) with wild-type (WT) mice, maintained on hard (HC) or soft (SC) chow. Methods A total of 100 animals divided into four groups were studied at 3, 8, and 24 weeks of age: 1) KO/HC; 2) KO/SC; 3) WT/HC; and 4) WT/SC. Microcomputed tomography was performed, and the following measurements were made between mandibular first (M1) and second (M2) molars: relative alveolar bone height (RBH), crestal bone width (CBW), bone volume (BV), bone mineral content (BMC), and bone mineral density (BMD). The position of M1 and M2 in relation to the inferior border of the mandible was also determined at 24 weeks. All variables were analyzed by one-way analysis of variance and Dunnett test for pairwise comparisons. Morphologic analyses were conducted on hematoxylin and eosin–stained sections. Results Radiographically, the enamel layer was absent in ENAM−/− mice. Interproximal open contacts were observed exclusively in ENAM−/− mice, and the prevalence decreased over time, suggesting that a shifting of tooth position had occurred. Additionally, in the two ENAM−/− groups, RBH was significantly lower at 8 and 24 weeks (P <0.02); CBW, BV, and BMC were significantly less (P <0.05) at 24 weeks. No differences in BMD were found among the four groups. The molars migrated to a more coronal position in ENAM−/− mice and mice on HC. Histologic findings were consistent with radiographic observations. After eruption, the junctional epithelium was less organized in ENAM−/− mice. Conclusion The interdental bone density was not affected in the absence of enamelin, but its volume was, which is likely a

  1. Optical and structural characterization of yttrium calcium borate glasses

    NASA Astrophysics Data System (ADS)

    Santos, Cristiane; Meneses, Domingos D. S.; Echegut, Patrick; Neuville, Daniel R.; Hernandes, Antonio C.; Ibanez, Alain

    2010-03-01

    Structural and optical properties of new stable glasses in the Y2O3 -- CaO -- B2O3 system, containing the same Y/Ca ratio as the YCa4O(BO3)3 (YCOB) crystal, were determined from Raman and reflectance infrared spectroscopy [1]. We have obtained the optical functions using a dielectric function model and their evolution with composition are associated with an increase in the number of non-bridging oxygen and to calcium/yttrium oxides content with the formation of pentaborate, metaborate, orthoborate and pyroborate groups. The orthoborate and pyroborate signatures increase with increasing the modifier cations. Refractive indexes values (from 1.597 to 1.627 at λ = 2 μm) are in good agreement with those of the YCOB crystal, an indication that these glasses are potential candidates for doping with rare-earth ions for optical applications. [4pt] [1] C. N. Santos, D.D.S. Meneses, P. Echegut, D. R. Neuville, A. C. Hernandes, A. Ibanez, Appl. Phys. Lett. 94, 151901(2009).

  2. Characterization of Ion Dynamics in Structures for Lossless Ion Manipulations

    SciTech Connect

    Tolmachev, Aleksey V.; Webb, Ian K.; Ibrahim, Yehia M.; Garimella, Venkata BS; Zhang, Xinyu; Anderson, Gordon A.; Smith, Richard D.

    2014-08-23

    Structures for Lossless Ion Manipulation (SLIM) represent a novel class of ion optical devices based upon electrodes patterned on planar surfaces, and relying on a combined action of radio frequency and DC electric fields and specific buffer gas density conditions. Initial experimental studies have demonstrated the feasibility of the SLIM concept. This report offers an in-depth consideration of key ion dynamics properties in such devices based upon ion optics theory and computational modeling. The SLIM devices investigated are formed by two surfaces, each having an array of radio frequency (RF) "rung" electrodes, bordered by DC "guard" electrodes. Ion motion is confined by the RF effective potential in the direction orthogonal to the boards, and limited or controlled in the transversal direction by the guard DC potentials. Ions can be efficiently trapped and stored in SLIM devices where the confinement of ions can be ‘soft’ in regard to the extent of collisional activation, similarly to RF-only multipole ion guides and traps. The segmentation of the RF rung electrodes and guards along the axis makes it possible to apply electric field profiles to stimulate ion transfer within a SLIM. In the case of a linear DC gradient applied to RF rungs and guards, a virtually uniform electric field can be created along the axis of the device, enabling ion mobility separations.

  3. Valuation of brewers spent yeast polysaccharides: a structural characterization approach.

    PubMed

    Pinto, Mariana; Coelho, Elisabete; Nunes, Alexandra; Brandão, Tiago; Coimbra, Manuel A

    2015-02-13

    Brewers spent yeast (BSY) is a by-product from beer industry that can be exploited as source of glucans and mannoproteins, with potential biological activities. In order to solubilize these carbohydrate-rich polymeric materials, a sequential extraction with hot water and alkaline solutions (0.1-8 M KOH) was performed. Mannoproteins were mainly (85%) extracted with 4 M KOH whereas glucans were extracted with 8 M KOH and in an amount that accounted only for 34% of total glucose. Final residue still accounted for 34% of the initial glucans and contained 98% of glucose. Cellulase and α-amylase treatments showed the presence of both α- and β-(1→4)-Glc linkages. To promote total solubilization of these insoluble glucans, the final residue was submitted to a partial acid hydrolysis. This work is the first report showing that the most abundant polysaccharides in BSY are polymers that contain structural features similar to cellulose, thus justifying their resistance to alkaline extractions, acid hydrolysis, and insolubility in water.

  4. Processing-structure characterization of rheocast IN-100 superalloy

    NASA Astrophysics Data System (ADS)

    Cheng, Jung-Jen Allen; Apelian, Diran; Doherty, Roger D.

    1986-11-01

    The rheocasting solidification process has been applied in the production of IN-100 nickel base superalloy. A high vacuum furnace for rheocasting superalloys was used to rheocast ingots under different processing conditions. Processing variables which were evaluated include stirring speed, isothermal stirring time, and volume fraction solid during isothermal stirring. Ingots, furnace cooled at the same rate but without stirring, were also examined for comparison with the rheocast ingots. A detailed microstructural examination was made of the resultant microstructure both on furnace cooling after stirring and on reheating to the isothermal stirring temperature followed by water quenching. Rheocasting yielded fine-grained structures, where the extent of microsegregatiori, the variation in macrostructure, and the solidification-induced porosity were found to be reduced in comparison to the unstirred ingot. The grain size and nonuniformity in the as-cast ingot were reduced by increasing the stirring speed, isothermal stirring time, or the volume fraction solid during stirring. The degree of the microsegregation decreased significantly with increasing volume fraction solid. Grain boundaries, both with and without solute enrichment, were found in the rosette-like solid particles after rheocasting, lending support to the Vogel-Cantor-Doherty model of rheocasting based on the formation of grain boundaries by strain-induced recrystallization and by sintering. It is clear from these results that the microstructure of this superalloy was significantly improved by rheocasting. Improved mechanical properties were also found and will be reported separately.

  5. Structural characterization and Hirshfeld surface analysis of racemic baclofen

    NASA Astrophysics Data System (ADS)

    Maniukiewicz, Waldemar; Oracz, Monika; Sieroń, Lesław

    2016-11-01

    The crystal structure of baclofen, (R,S) [4-amino-3-(4-chlorophenyl)butanoic acid], (C10H12ClNO2, Mr = 213.66) has been determined by single crystal X-ray diffraction analysis. The title compound crystallizes in the orthorhombic space group Pbca (No. 61) with a = 9.2704(5), b = 7.0397(4), c = 30.4015(15) Å, V = 1984.0(2) Å3 and Z = 8. The molecules exist as zwitterions, adopting a gauche conformation with respect to the Cαsbnd Cβ bond, and held in a cross-linked chain arrangement by strong Nsbnd H⋯O hydrogen bonds and Csbnd Cl⋯π interactions. The electrostatic molecular potential as well as the intermolecular interactions of the title compound were analyzed by the Hirshfeld surfaces. The FT-IR spectrum is also reported. The DTA, TG and DTG results indicate that baclofen is stable up to 205 °C.

  6. Electronic structure characterization and bandgap engineeringofsolar hydrogen materials

    SciTech Connect

    Guo, Jinghua

    2007-11-01

    Bandgap, band edge positions as well as the overall band structure of semiconductors are of crucial importance in photoelectrochemical and photocatalytic applications. The energy position of the band edge level can be controlled by the electronegativity of the dopants, the pH of the solution (flatband potential variation of 60 mV per pH unit), as well as by quantum confinement effects. Accordingly, band edges and bandgap can be tailored to achieve specific electronic, optical or photocatalytic properties. Synchrotron radiation with photon energy at or below 1 keV is giving new insight into such areas as condensed matter physics and extreme ultraviolet optics technology. In the soft x-ray region, the question tends to be, what are the electrons doing as they migrated between the atoms. In this paper, I will present a number of soft x-ray spectroscopic study of nanostructured 3d metal compounds Fe{sub 2}O{sub 3} and ZnO.

  7. Characterization of ion dynamics in structures for lossless ion manipulations.

    PubMed

    Tolmachev, Aleksey V; Webb, Ian K; Ibrahim, Yehia M; Garimella, Sandilya V B; Zhang, Xinyu; Anderson, Gordon A; Smith, Richard D

    2014-09-16

    Structures for Lossless Ion Manipulation (SLIM) represent a novel class of ion optical devices based upon electrodes patterned on planar surfaces, and relying on a combined action of radiofrequency and DC electric fields and specific buffer gas density conditions. Initial experimental studies have demonstrated the feasibility of the SLIM concept. This report offers an in-depth consideration of key ion dynamics properties in such devices based upon ion optics theory and computational modeling. The SLIM devices investigated are formed by two surfaces, each having an array of radiofrequency (RF) "rung" electrodes, bordered by DC "guard" electrodes. Ion motion is confined by the RF effective potential in the direction orthogonal to the boards and limited or controlled in the transversal direction by the guard DC potentials. Ions can be efficiently trapped and stored in SLIM devices where the confinement of ions can be "soft" in regard to the extent of collisional activation, similarly to RF-only multipole ion guides and traps. The segmentation of the RF rung electrodes and guards along the axis makes it possible to apply static or transient electric field profiles to stimulate ion transfer within a SLIM. In the case of a linear DC gradient applied to RF rungs and guards, a virtually uniform electric field can be created along the axis of the device, enabling high quality ion mobility separations. PMID:25152178

  8. Structural characterization of particle systems using spherical harmonics

    SciTech Connect

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

    2015-08-15

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

  9. Characterizing Facesheet/Core Disbonding in Honeycomb Core Sandwich Structure

    NASA Technical Reports Server (NTRS)

    Rinker, Martin; Ratcliffe, James G.; Adams, Daniel O.; Krueger, Ronald

    2013-01-01

    Results are presented from an experimental investigation into facesheet core disbonding in carbon fiber reinforced plastic/Nomex honeycomb sandwich structures using a Single Cantilever Beam test. Specimens with three, six and twelve-ply facesheets were tested. Specimens with different honeycomb cores consisting of four different cell sizes were also tested, in addition to specimens with three different widths. Three different data reduction methods were employed for computing apparent fracture toughness values from the test data, namely an area method, a compliance calibration technique and a modified beam theory method. The compliance calibration and modified beam theory approaches yielded comparable apparent fracture toughness values, which were generally lower than those computed using the area method. Disbonding in the three-ply facesheet specimens took place at the facesheet/core interface and yielded the lowest apparent fracture toughness values. Disbonding in the six and twelve-ply facesheet specimens took place within the core, near to the facesheet/core interface. Specimen width was not found to have a significant effect on apparent fracture toughness. The amount of scatter in the apparent fracture toughness data was found to increase with honeycomb core cell size.

  10. Thermal and structural characterization of synthetic and natural nanocrystalline hydroxyapatite.

    PubMed

    Sofronia, Ancuta M; Baies, Radu; Anghel, Elena M; Marinescu, Cornelia A; Tanasescu, Speranta

    2014-10-01

    The aim of this work was to study the thermal stability on heating and to obtain the processing parameters of synthetic and bone-derived hydroxyapatite over temperatures between room temperature and 1400°C by thermal analysis (thermogravimetry (TG)/differential scanning calorimetry (DSC) and thermo-mechanical analysis-TMA). Structural and surface modifications related to samples origin and calcination temperature were investigated by Fourier transformed infrared (FTIR) and Raman spectroscopy, X-ray diffraction (XRD) and BET method. FTIR spectra indicated that the organic constituents and carbonate are no longer present in the natural sample calcined at 800°C. Raman spectra highlighted the decomposition products of the hydroxyapatite. The calcination treatment modifies the processes kinetics of the synthetic samples, being able to isolate lattice water desorption processes of decarbonization and the dehydroxylation processes. Shrinkage of calcined synthetic sample increases by 10% compared to uncalcined synthetic powder. From the TMA correlated with TG analysis and heat capacity data it can be concluded that sintering temperature of the synthetic samples should be chosen in the temperature range of the onset of dehydroxylation and the temperature at which oxyapatite decomposition begins.

  11. Characterization of 32nm node BEOL grating structures using scatterometry

    NASA Astrophysics Data System (ADS)

    Zangooie, Shahin; Sendelbach, Matthew; Angyal, Matthew; Archie, Charles; Vaid, Alok; Matthew, Itty; Herrera, Pedro

    2008-03-01

    Implementations of scatterometry in the back end of the line (BEOL) of the devices requires design of advanced measurement targets with attention to CMP ground rule constraints as well as model simplicity details. In this paper we outline basic design rules for scatterometry back end targets by stacking and staggering measurement pads to reduce metal pattern density in the horizontal plane of the device and to avoid progressive dishing problems along the vertical direction. Furthermore, important characteristics of the copper shapes in terms of their opaqueness and uniformity are discussed. It is shown that the M1 copper thicknesses larger than 100 nm are more than sufficient for accurate back end scatterometry implementations eliminating the need for modeling of contributions from the buried layers. AFM and ellipsometry line scans also show that the copper pads are sufficiently uniform with a sweet spot area of around 20 μm. Hence, accurate scatterometry can be done with negligible edge and/or dishing contributions if the measurement spot is placed any where within the sweet spot area. Reference metrology utilizing CD-SEM and CD-AFM techniques prove accuracy of the optical solutions for the develop inspect and final inspect grating structures. The total measurement uncertainty (TMU) values for the process of record line width are of the order of 0.77 nm and 0.35 nm at the develop inspect and final inspect levels, respectively.

  12. Characterization and estimation of permeability correlation structure from performance data

    SciTech Connect

    Ershaghi, I.; Al-Qahtani, M.

    1997-08-01

    In this study, the influence of permeability structure and correlation length on the system effective permeability and recovery factors of 2-D cross-sectional reservoir models, under waterflood, is investigated. Reservoirs with identical statistical representation of permeability attributes are shown to exhibit different system effective permeability and production characteristics which can be expressed by a mean and variance. The mean and variance are shown to be significantly influenced by the correlation length. Detailed quantification of the influence of horizontal and vertical correlation lengths for different permeability distributions is presented. The effect of capillary pressure, P{sub c1} on the production characteristics and saturation profiles at different correlation lengths is also investigated. It is observed that neglecting P{sub c} causes considerable error at large horizontal and short vertical correlation lengths. The effect of using constant as opposed to variable relative permeability attributes is also investigated at different correlation lengths. Next we studied the influence of correlation anisotropy in 2-D reservoir models. For a reservoir under five-spot waterflood pattern, it is shown that the ratios of breakthrough times and recovery factors of the wells in each direction of correlation are greatly influenced by the degree of anisotropy. In fully developed fields, performance data can aid in the recognition of reservoir anisotropy. Finally, a procedure for estimating the spatial correlation length from performance data is presented. Both the production performance data and the system`s effective permeability are required in estimating the correlation length.

  13. Multiaxial nonlinear viscoelastic characterization and modeling of a structural adhesive

    SciTech Connect

    Popelar, C.F.; Liechti, K.M.

    1997-07-01

    Many polymeric materials, including structural adhesives, exhibit a nonlinear viscoelastic response. The nonlinear free volume approach is based on the Doolittle concept that the free volume controls the mobility of polymer molecules and, thus, the inherent time scale of the material. It then follows that factors such as temperature and moisture, which change the free volume, will influence the time scale. Furthermore, stress-induced dilatation will also affect the free volume and, hence, the time scale. However, during this investigation dilatational effects alone were found to be insufficient in describing the response of near pure shear tests performed on a bisphenol A epoxy with an amido amine hardener. Thus, the free volume approach presented here has been modified to include distortional effects in the inherent time scale of the material. In addition to predicting the global response under a variety of multiaxial stress states, the modified free volume theory also accurately predicts the local displacement fields, including those associated with a localized region, as determined from geometric moire measurements at various stages of deformation.

  14. Structural and Electrochemical Characterization of Lithium Transition Metal Phosphates

    NASA Astrophysics Data System (ADS)

    Hashambhoy, Ayesha Maria

    The lithium ion battery has emerged as one of the most promising hybrid vehicle energy storage systems of the future. Of the potential cathode chemistries explored, lithium transition metal phosphates have generated a significant amount of interest due to their low-cost precursors, potential ease of synthesis, stability, and their environmentally friendly nature. This is in contrast to layered oxide systems such as LiCoO2, which have long been considered state of the art, but are now being reevaluated due to their structural instability at elevated temperatures, and higher cost. In particular, LiFePO4 has an operating potential comparable to those batteries available on the market (˜3.5V vs. Li/Li+), and higher theoretical specific capacity (170mAh/g vs. that of LiCoO2 which is 140mAh/g). The manganese analog to LiFePO4, LiMnPO4, exhibits a higher operating potential (˜4.1V v Li/Li+), and the same theoretical capacity, however Li-ion diffusion through this structure is much more rate limited and its theoretical capacity cannot be realized at rates suitable for commercial applications. The purpose of this work was threefold: 1) To explore the impact of Fe substitution on Mn sites in LiMnPO 4. 2) To examine the effects of alterations to the particle/electrolyte interface on rate capability. 3) To explore a novel fabrication route for LiMnPO4 using microwaves, and determine an optimal power and time combination for best performance. The coexistence of Fe and Mn on the transition metal site M, of LiMPO 4 resulted in an improved apparent Li-ion diffusivity in both Fe and Mn regimes as compared to that observed for LiFePO4 and LiMnPO 4 respectively. Calculations made from two different analysis methods, cyclic voltammetry (CV) and galvanostatic intermittent titration (GITT) drew this same conclusion. The signature characteristics observed from the CVs pertaining to single and dual phase reactions led to a delithiation model of LiFe0.5Mn0.5PO4 proposing the localization

  15. Dodder hyphae invade the host: a structural and immunocytochemical characterization.

    PubMed

    Vaughn, K C

    2003-03-01

    developing hyphae are unique in composition and structure and represent an induction of a wall type in the host that is not noted in surrounding walls.

  16. Stacking Pattern of Inner Structures Characterizing Tsunami Deposits

    NASA Astrophysics Data System (ADS)

    Fujiwara, O.; Kamataki, T.; Hirakawa, K.; Irizuki, T.; Hasegawa, S.; Sakai, T.; Haraguchi, T.

    2006-12-01

    Processes of sediment transport and deposition by tsunamis are not well known, though they strongly influence the reliability of paleo-tsunami studies. We provide some criteria for distinguishing the tsunami deposits from other events such as storms, based on the observations and literature reviews for various depositional conditions. Tsunami waves have one hundred times or more longer wavelengths (ca. 100 km) and wave periods (ca. 15-20 min.), compared with wind waves. They cause repeating and long lasting sediment flows on the coast, and print their waveforms within the deposits. We positively conclude that the single deposits with co-existence of following four characters were deposited from tsunami. Complete set of four characters is rare due to the erosion by succeeding waves. Each of characters may individually be made by other processes, such as storms or floods. Interpretation of tsunami deposits needs reference to the background environment of the depositional sites. 1. The deposits display scour and grading structure composed of stacked sub-layers, each of which indicates the deposition from waning sediment flows. Each sub-layer often exhibits spaced stratification and HCS, and is graded with muddy top. 2. Mud drape or suspension fallout covers each sub-layer indicating long stagnant period between depositions of each sub-layer. 3. Flow reversal in landward- and seaward- directions is often displayed by a pair of underlying and overlying sub-layers. 4. The stacked sub-layers show fining- and thinning-upward trend in the deposits and indicate that they were sequentially deposited from waning wave train through time The AD 1703 Kanto tsunami deposit [1] and Holocene tsunami deposits in eastern Japan [2] are good examples. The former, about 90 cm thick sand bed deposited on the beach, has at least eight to nine sub- layers showing up- and return-flows. The latter, up to 1 m thick sand and gravel beds laid on the 10-m deep bay floor, are the stack of 5 cycle

  17. Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads.

    PubMed

    Moncunill, Valentí; Gonzalez, Santi; Beà, Sílvia; Andrieux, Lise O; Salaverria, Itziar; Royo, Cristina; Martinez, Laura; Puiggròs, Montserrat; Segura-Wang, Maia; Stütz, Adrian M; Navarro, Alba; Royo, Romina; Gelpí, Josep L; Gut, Ivo G; López-Otín, Carlos; Orozco, Modesto; Korbel, Jan O; Campo, Elias; Puente, Xose S; Torrents, David

    2014-11-01

    The development of high-throughput sequencing technologies has advanced our understanding of cancer. However, characterizing somatic structural variants in tumor genomes is still challenging because current strategies depend on the initial alignment of reads to a reference genome. Here, we describe SMUFIN (somatic mutation finder), a single program that directly compares sequence reads from normal and tumor genomes to accurately identify and characterize a range of somatic sequence variation, from single-nucleotide variants (SNV) to large structural variants at base pair resolution. Performance tests on modeled tumor genomes showed average sensitivity of 92% and 74% for SNVs and structural variants, with specificities of 95% and 91%, respectively. Analyses of aggressive forms of solid and hematological tumors revealed that SMUFIN identifies breakpoints associated with chromothripsis and chromoplexy with high specificity. SMUFIN provides an integrated solution for the accurate, fast and comprehensive characterization of somatic sequence variation in cancer. PMID:25344728

  18. Analysis and characterizations of planar transmission structures and components for superconducting and monolithic integrated circuits

    NASA Technical Reports Server (NTRS)

    Itoh, Tatsuo

    1992-01-01

    The research effort was continued to design and characterize superconducting transmission line structures. The research during this period was concentrated on the implementation of a superconductor into coplanar waveguide structures. First, the superconducting coplanar waveguide was examined, and compared with a superconducting microstrip line in terms of loss characteristics and their design aspects. Then, the research was carried on the design and characterization of the coplanar waveguide family in the packaging environment. The transition between the coaxial line to the conductor backed coplanar waveguide was also designed for the measurement of the superconducting conductor backed coplanar waveguide.

  19. Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening

    PubMed Central

    Brylinski, Michal

    2010-01-01

    The growing interest in the identification of kinase inhibitors, promising therapeutics in the treatment of many diseases, has created a demand for the structural characterization of the entire human kinome. At the outset of the drug development process, the lead-finding stage, approaches that enrich the screening library with bioactive compounds are needed. Here, protein structure-based methods can play an important role, but despite structural genomics efforts, it is unlikely that the three-dimensional structures of the entire kinome will be available soon. Therefore, at the proteome level, structure-based approaches must rely on predicted models, with a key issue being their utility in virtual ligand screening. In this study, we employ the recently developed FINDSITE/Q-Dock Ligand Homology Modeling approach, which is well suited for proteome-scale applications using predicted structures, to provide extensive structural and functional characterization of the human kinome. Specifically, we construct structure models for the human kinome; these are subsequently subject to virtual screening against a library of more than 2 million compounds. To rank the compounds, we employ a hierarchical approach that combines ligand- and structure-based filters. Modeling accuracy is carefully validated using available experimental data with particularly encouraging results found for the ability to identify, without prior knowledge, specific kinase inhibitors. More generally, the modeling procedure results in a large number of predicted molecular interactions between kinases and small ligands that should be of practical use in the development of novel inhibitors. The dataset is freely available to the academic community a user-friendly web interface at http://cssb.biology.gatech.edu/kinomelhm/as well as the ZINC website (http://zinc.docking.org/applications/2010Apr/Brylinski-2010.tar.gz). PMID:20853887

  20. Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus

    PubMed Central

    Duong-ly, Krisna C.; Schoeffield, Andrew J.; Pizarro-Dupuy, Mario A.; Zarr, Melissa; Pineiro, Silvia A.; Amzel, L. Mario; Gabelli, Sandra B.

    2015-01-01

    Given the broad range of substrates hydrolyzed by Nudix (nucleoside diphosphate linked to X) enzymes, identification of sequence and structural elements that correctly predict a Nudix substrate or characterize a family is key to correctly annotate the myriad of Nudix enzymes. Here, we present the structure determination and characterization of Bd3179 –- a Nudix hydrolase from Bdellovibrio bacteriovorus–that we show localized in the periplasmic space of this obligate Gram-negative predator. We demonstrate that the enzyme is a nucleoside diphosphate sugar hydrolase (NDPSase) and has a high degree of sequence and structural similarity to a canonical ADP-ribose hydrolase and to a nucleoside diphosphate sugar hydrolase (1.4 and 1.3 Å Cα RMSD respectively). Examination of the structural elements conserved in both types of enzymes confirms that an aspartate-X-lysine motif on the C-terminal helix of the α-β-α NDPSase fold differentiates NDPSases from ADPRases. PMID:26524597

  1. Structural characterization of rotavirus-directed synthesis and assembly of metallic nanoparticle arrays.

    PubMed

    Plascencia-Villa, Germán; Medina, Ariosto; Palomares, Laura A; Ramírez, Octavio T; Ascencio, Jorge A

    2013-08-01

    Self-assembled structures derived of viral proteins display sophisticated structures that are difficult to obtain with even advanced synthesis methods and the use of protein nanotubes for synthesis and organization of inorganic nanoarrays into well-defined architectures are here reported. Nanoparticle arrays derived of rotavirus VP6 nanotubes were synthesized by in situ functionalization with silver and gold nanoparticles. The size and morphology of metal nanoparticles were characterized by transmission electron microscopy (TEM) and high resolution TEM (HR-TEM). Processing of micrographs to obtain fast Fourier transforms (FFT) patterns of nanoparticles shown that the preferred morphologies are fcc-like and multiple twinned ones. Micrographs were used to assign structure and orientation, and the elemental composition analysis was performed with energy dispersive spectroscopy (EDS). Structural characterization of functionalized rotavirus VP6 demonstrated its utility for directed construction of hybrid anisotropic nanomaterials formed by arrays of metallic nanoparticles.

  2. Electrochemical characterization of p(+)n and n(+)p diffused InP structures

    NASA Technical Reports Server (NTRS)

    Wilt, David M.; Faur, Maria; Faur, Mircea; Goradia, M.; Vargas-Aburto, Carlos

    1993-01-01

    The relatively well documented and widely used electrolytes for characterization and processing of Si and GaAs-related materials and structures by electrochemical methods are of little or no use with InP because the electrolytes presently used either dissolve the surface preferentially at the defect areas or form residual oxides and introduce a large density of surface states. Using an electrolyte which was newly developed for anodic dissolution of InP, and was named the 'FAP' electrolyte, accurate characterization of InP related structures including nature and density of surface states, defect density, and net majority carrier concentration, all as functions of depth was performed. A step-by-step optimization of n(+)p and p(+)n InP structures made by thermal diffusion was done using the electrochemical techniques, and resulted in high performance homojunction InP structures.

  3. Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq.

    PubMed

    Watters, Kyle E; Abbott, Timothy R; Lucks, Julius B

    2016-01-29

    Many non-coding RNAs form structures that interact with cellular machinery to control gene expression. A central goal of molecular and synthetic biology is to uncover design principles linking RNA structure to function to understand and engineer this relationship. Here we report a simple, high-throughput method called in-cell SHAPE-Seq that combines in-cell probing of RNA structure with a measurement of gene expression to simultaneously characterize RNA structure and function in bacterial cells. We use in-cell SHAPE-Seq to study the structure-function relationship of two RNA mechanisms that regulate translation in Escherichia coli. We find that nucleotides that participate in RNA-RNA interactions are highly accessible when their binding partner is absent and that changes in RNA structure due to RNA-RNA interactions can be quantitatively correlated to changes in gene expression. We also characterize the cellular structures of three endogenously expressed non-coding RNAs: 5S rRNA, RNase P and the btuB riboswitch. Finally, a comparison between in-cell and in vitro folded RNA structures revealed remarkable similarities for synthetic RNAs, but significant differences for RNAs that participate in complex cellular interactions. Thus, in-cell SHAPE-Seq represents an easily approachable tool for biologists and engineers to uncover relationships between sequence, structure and function of RNAs in the cell.

  4. Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq.

    PubMed

    Watters, Kyle E; Abbott, Timothy R; Lucks, Julius B

    2016-01-29

    Many non-coding RNAs form structures that interact with cellular machinery to control gene expression. A central goal of molecular and synthetic biology is to uncover design principles linking RNA structure to function to understand and engineer this relationship. Here we report a simple, high-throughput method called in-cell SHAPE-Seq that combines in-cell probing of RNA structure with a measurement of gene expression to simultaneously characterize RNA structure and function in bacterial cells. We use in-cell SHAPE-Seq to study the structure-function relationship of two RNA mechanisms that regulate translation in Escherichia coli. We find that nucleotides that participate in RNA-RNA interactions are highly accessible when their binding partner is absent and that changes in RNA structure due to RNA-RNA interactions can be quantitatively correlated to changes in gene expression. We also characterize the cellular structures of three endogenously expressed non-coding RNAs: 5S rRNA, RNase P and the btuB riboswitch. Finally, a comparison between in-cell and in vitro folded RNA structures revealed remarkable similarities for synthetic RNAs, but significant differences for RNAs that participate in complex cellular interactions. Thus, in-cell SHAPE-Seq represents an easily approachable tool for biologists and engineers to uncover relationships between sequence, structure and function of RNAs in the cell. PMID:26350218

  5. First structurally characterized mixed-halogen nickel(III) NCN-pincer complex

    NASA Astrophysics Data System (ADS)

    Kozhanov, Konstantin A.; Bubnov, Michael P.; Cherkasov, Vladimir K.; Fukin, Georgy K.; Vavilina, Nina N.; Efremova, Larisa Yu.; Abakumov, Gleb A.

    2009-03-01

    A square-pyramidal mixed-halogen nickel(III) NCN-pincer complex (PipeNCN)NiClBr (where PipeNCN = 2,6-bis(piperidinomethyl)phenyl) was structurally characterized. Bromine occupies apical position; pincer ligand and chlorine atom are in the basal plane. EPR detects that complex in solution exists as a mixture of two structural isomers with bromine or chlorine atoms in the top of pyramid.

  6. Characterization of small thermal structures in RFX-mod electron temperature profiles

    NASA Astrophysics Data System (ADS)

    Fassina, A.; Gobbin, M.; Spagnolo, S.; Franz, P.; Terranova, D.

    2016-05-01

    In the RFX-mod reverse field pinch (RFP) experiment, electron temperature profiles often feature structures and fluctuations at fine scale. The present work aims at characterizing their occurrence and their localization, in particular by linking them to underlying tearing modes magnetic islands. The confinement characteristics are discussed, identifying analogies with respect to high scale T e structures. Finally, high frequency magnetic activity (i.e. microtearing instabilities) is confirmed to be closely correlated to the presence and proximity of temperature gradients.

  7. A semi-automated system for the characterization of NLC accelerating structures

    SciTech Connect

    Hanna, S.M.; Bowden, G.B.; Hoag, H.A.; Loewen, R.; Vlieks, A.E.; Wang, J.W.

    1995-06-01

    *A system for characterizing the phase shift per cell of a long X-band accelerator structure is described. The fields within the structure are perturbed by a small cylindrical metal bead pulled along the axis. A computer controls the bead position and processes the data from a network analyzer connected to the accelerator section. Measurements made on prototype accelerator sections are described, and they are shown to be in good agreement with theory.

  8. X-ray diffraction characterization of suspended structures forMEMS applications

    SciTech Connect

    Goudeau, P.; Tamura, N.; Lavelle, B.; Rigo, S.; Masri, T.; Bosseboeuf, A.; Sarnet, T.; Petit, J.-A.; Desmarres, J.-M.

    2005-09-15

    Mechanical stress control is becoming one of the major challenges for the future of micro and nanotechnologies. Micro scanning X-ray diffraction is one of the promising techniques that allows stress characterization in such complex structures at sub micron scales. Two types of MEMS structure have been studied: a bilayer cantilever composed of a gold film deposited on poly-silicon and a boron doped silicon bridge. X-ray diffraction results are discussed in view of numerical simulation experiments.

  9. Mass Spectrometry Combinations for Structural Characterization of Sulfated-Steroid Metabolites

    NASA Astrophysics Data System (ADS)

    Yan, Yuetian; Rempel, Don L.; Holy, Timothy E.; Gross, Michael L.

    2014-05-01

    Steroid conjugates, which often occur as metabolites, are challenging to characterize. One application is female-mouse urine, where steroid conjugates serve as important ligands for the pheromone-sensing neurons. Although the two with the highest abundance in mouse urine were previously characterized with mass spectrometry (MS) and NMR to be sulfated steroids, many more exist but remain structurally unresolved. Given that their physical and chemical properties are similar, they are likely to have a sulfated steroid ring structure. Because these compounds occur in trace amounts in mouse urine and elsewhere, their characterization by NMR will be difficult. Thus, MS methods become the primary approach for determining structure. Here, we show that a combination of MS tools is effective for determining the structures of sulfated steroids. Using 4-pregnene analogs, we explored high-resolving power MS (HR-MS) to determine chemical formulae; HD exchange MS (HDX-MS) to determine number of active, exchangeable hydrogens (e.g., OH groups); methoxyamine hydrochloride (MOX) derivatization MS, or reactive desorption electrospray ionization with hydroxylamine to determine the number of carbonyl groups; and tandem MS (MSn), high-resolution tandem MS (HRMS/MS), and GC-MS to obtain structural details of the steroid ring. From the fragmentation studies, we deduced three major fragmentation rules for this class of sulfated steroids. We also show that a combined MS approach is effective for determining structure of steroid metabolites, with important implications for targeted metabolomics in general and for the study of mouse social communication in particular.

  10. 2D and 3D reconstruction and geomechanical characterization of kilometre-scale complex folded structures

    NASA Astrophysics Data System (ADS)

    Zanchi, Andrea; Agliardi, Federico; Crosta, Giovanni B.; Villa, Alberto; Bistacchi, Andrea; Iudica, Gaetano

    2015-04-01

    The geometrical, structural and geomechanical characterization of large-scale folded structures in sedimentary rocks is an important issue for different geological and geo-hazard applications (e.g. hydrocarbon and geothermal reservoir exploitation, natural rock slope stability, mining, and tunnelling). Fold geometry controls topography and the spatial distribution of rock types with different strength and permeability. Fold-related fracture systems condition the fracture intensity, degree of freedom, and overall strength of rock masses. Nevertheless, scale issues and limited accessibility or partial exposure of structures often hamper a complete characterization of these complex structures. During the last years, advances in remote survey techniques as terrestrial Lidar (TLS) allowed significant improvements in the geometrical and geological characterization of large or inaccessible outcrops. However, sound methods relating structures to rock mass geomechanical properties are yet to be developed. Here we present results obtained by integrating remote survey and field assessment techniques to characterize a folded sedimentary succession exposed in unreachable vertical rock walls. The study area is located in the frontal part of the Southern Alps near Bergamo, Italy. We analysed large-scale detachment folds developed in the Upper Triassic sedimentary cover in the Zu Limestone. Folds are parallel and disharmonic, with regular wavelengths and amplitudes of about 200-250 m. We used a Riegl VZ-1000 long-range laser scanner to obtain points clouds with nominal spacings between 5 cm and 20 cm from 9 scan positions characterized by range between 350 m and 1300 m. We fixed shadowing and occlusion effects related to fold structure exposure by filling point clouds with data collected by terrestrial digital photogrammetry (TDP). In addition, we carried out field surveys of fold-related brittle structures and their geomechanical attributes at key locations. We classified cloud

  11. Concept Definition Study for In-Space Structural Characterization of a Lightweight Solar Array

    NASA Technical Reports Server (NTRS)

    Woods-Vedeler, Jessica A.; Pappa, Richard S.; Jones, Thomas W.; Spellman, Regina; Scott, Willis; Mockensturm, Eric M.; Liddle, Donn; Oshel, Ed; Snyder, Michael

    2002-01-01

    A Concept Definition Study (CDS) was conducted to develop a proposed "Lightweight High-Voltage Stretched-Lens Concentrator Solar Array Experiment" under NASA's New Millennium Program Space Technology-6 (NMP ST-6) activity. As part of a multi-organizational team, NASA Langley Research Center's role in this proposed experiment was to lead Structural Characterization of the solar array during the flight experiment. In support of this role, NASA LaRC participated in the CDS to de.ne an experiment for static, dynamic, and deployment characterization of the array. In this study, NASA LaRC traded state-of-the-art measurement approaches appropriate for an in-space, STS-based flight experiment, provided initial analysis and testing of the lightweight solar array and lens elements, performed a lighting and photogrammetric simulation in conjunction with JSC, and produced an experiment concept definition to meet structural characterization requirements.

  12. Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq

    PubMed Central

    Watters, Kyle E.; Abbott, Timothy R.; Lucks, Julius B.

    2016-01-01

    Many non-coding RNAs form structures that interact with cellular machinery to control gene expression. A central goal of molecular and synthetic biology is to uncover design principles linking RNA structure to function to understand and engineer this relationship. Here we report a simple, high-throughput method called in-cell SHAPE-Seq that combines in-cell probing of RNA structure with a measurement of gene expression to simultaneously characterize RNA structure and function in bacterial cells. We use in-cell SHAPE-Seq to study the structure–function relationship of two RNA mechanisms that regulate translation in Escherichia coli. We find that nucleotides that participate in RNA–RNA interactions are highly accessible when their binding partner is absent and that changes in RNA structure due to RNA–RNA interactions can be quantitatively correlated to changes in gene expression. We also characterize the cellular structures of three endogenously expressed non-coding RNAs: 5S rRNA, RNase P and the btuB riboswitch. Finally, a comparison between in-cell and in vitro folded RNA structures revealed remarkable similarities for synthetic RNAs, but significant differences for RNAs that participate in complex cellular interactions. Thus, in-cell SHAPE-Seq represents an easily approachable tool for biologists and engineers to uncover relationships between sequence, structure and function of RNAs in the cell. PMID:26350218

  13. Characterization of the geometry of microscale periodic structures using acoustic microscopy.

    PubMed

    Shaw, Anurupa; Liu, Jingfei; Yoon, Suk Wang; Declercq, Nico F

    2016-08-01

    Periodic structures are very common in both scientific investigations and engineering applications. The geometry of the periodic structure is important for its designed functionality. Although the techniques such as optical and electron microscopy are capable of measuring the periodicity of microscale periodically-corrugated structures, they cannot be used to measure the height or depth of the corrugation. The technique of acoustic microscopy has been developed rapidly and it has been applied in the studies of steel integrated structures, ferro-elastic ceramics, human retina, semiconductors, composites, etc. In acoustic microscopy, V(z) curves have been used to investigate the visco-elastic parameters of thin sliced samples of composites, animal tissue, etc., while in this work it is applied in characterizing the geometry of periodically corrugated structures. The measurements of the geometry of periodic structures obtained using acoustic microscopy are compared with those obtained using optical microscopy, and the reliability of this acoustic technique is also examined. PMID:27259118

  14. Characterization of the geometry of microscale periodic structures using acoustic microscopy.

    PubMed

    Shaw, Anurupa; Liu, Jingfei; Yoon, Suk Wang; Declercq, Nico F

    2016-08-01

    Periodic structures are very common in both scientific investigations and engineering applications. The geometry of the periodic structure is important for its designed functionality. Although the techniques such as optical and electron microscopy are capable of measuring the periodicity of microscale periodically-corrugated structures, they cannot be used to measure the height or depth of the corrugation. The technique of acoustic microscopy has been developed rapidly and it has been applied in the studies of steel integrated structures, ferro-elastic ceramics, human retina, semiconductors, composites, etc. In acoustic microscopy, V(z) curves have been used to investigate the visco-elastic parameters of thin sliced samples of composites, animal tissue, etc., while in this work it is applied in characterizing the geometry of periodically corrugated structures. The measurements of the geometry of periodic structures obtained using acoustic microscopy are compared with those obtained using optical microscopy, and the reliability of this acoustic technique is also examined.

  15. Characterization of irregularly micro-structured surfaces related to their wetting properties

    NASA Astrophysics Data System (ADS)

    Li, Ping; Xie, Jin; Deng, Zhenjie

    2015-04-01

    It is difficult to control a surface wetting due to the random surface texture, but its fabrication is easy. Hence, the volume ratio is proposed through the 3D characterization of micro-structured surface in contrast to traditional roughness factor, fractal dimension and aspect ratio through 2D characterization. The objective is to investigate the wetting properties related to the characterization of irregularly micro-structured surface. First, the irregularly micro-structured Si surfaces with 0.22-3.58 μm in depth were machined by the rubbing, the polishing and the grinding with different diamond abrasive grain size and random abrasive grain shape, respectively; secondly, the surface wetting properties were investigated with regard to the characterized parameters of measured micro-topographic surfaces; finally, the irregular wetting model was constructed by using volume ratio on the base of non-composite wetting. It is shown that the contact angle increases with increasing roughness factor and aspect ratio and decreasing fractal dimension on the irregularly micro-structured surfaces, but it is different from the prediction of non-composite wetting model. Moreover, the irregularly micro-structured surfaces without anisotropic properties produce smaller contact angles than regularly micro-structured surfaces with anisotropic properties. The experimental results show that an increase in volume ratio leads to a decrease in contact angle. It is identical to the predictions of the proposed model. This is because the volume ratio precisely illustrates 3D contact information between the liquid and solid interfaces. It is confirmed that the volume ratio may be utilized to predict and control the wetting of irregularly micro-structured surface.

  16. Structural characterization of germanium-arsenic-sulfur chalcogenide glasses and understanding structural relaxation in oxide glasses

    NASA Astrophysics Data System (ADS)

    Soyer-Uzun, Sezen

    The structures of chalcogenide glasses in the GexAsx S100-2x system with 33.3 ≤ 100-2x ≤ 70.0 are investigated using neutron/x-ray diffraction. Ge and As atoms are primarily heteropolar bonded to S atoms in glasses near stoichiometry (x ≤ 18.2). Large scale three-dimensional structural models obtained from reverse Monte Carlo (RMC) simulations are used to investigate the nature of intermediate-range structural order in these ternary glasses. Heteropolar bonded mixed GeS2 and As2S3 network in glasses with compositions near stoichiometry is transformed into a heterogeneous glass with mixed GeS2 network and As-rich clusters with increasing S-deficiency. The latter structure is largely homogenized with further increase in metal content. Combined neutron/x-ray diffraction, Ge and As K-edge EXAFS and Raman spectroscopy are employed to study the compositional dependence of the short- and intermediate- range structures of As-rich GexAsyS 100-x-y glasses with x:y = 1:17.3. The structures of glasses with compositions near stoichiometry consist mainly of heteropolar-bonded As2S 3 network. However, increasing metal content (x+y = 55) results in a novel glass consisting predominantly of As4S3 molecules with near-zero connectivity and dimensionality. Formation of As-As homopolar bonded structural regions that coexist with As4S3 molecules is observed with further increase in metal content (60 ≤ x+y ≤ 65). Structural mechanisms of densification of a molecular chalcogenide glass of composition Ge2.5As51.25S46.25 are studied in situ in a panoramic cell equipped with Moissanite (SiC) anvils at pressures ranging from 1 atm to 11 GPa at ambient temperature as well as ex situ on a sample quenched from 12 GPa in a multi-anvil cell using high-energy x-ray diffraction. 11B MAS NMR spectroscopy is employed to monitor relaxation kinetics of boron coordination environments in a borosilicate glass in response to temperature jumps. The relaxation timescale of the BO4:BO 3 ratio is

  17. Electrical network method for the thermal or structural characterization of a conducting material sample or structure

    DOEpatents

    Ortiz, M.G.

    1993-06-08

    A method for modeling a conducting material sample or structure system, as an electrical network of resistances in which each resistance of the network is representative of a specific physical region of the system. The method encompasses measuring a resistance between two external leads and using this measurement in a series of equations describing the network to solve for the network resistances for a specified region and temperature. A calibration system is then developed using the calculated resistances at specified temperatures. This allows for the translation of the calculated resistances to a region temperature. The method can also be used to detect and quantify structural defects in the system.

  18. Electrical network method for the thermal or structural characterization of a conducting material sample or structure

    DOEpatents

    Ortiz, Marco G.

    1993-01-01

    A method for modeling a conducting material sample or structure system, as an electrical network of resistances in which each resistance of the network is representative of a specific physical region of the system. The method encompasses measuring a resistance between two external leads and using this measurement in a series of equations describing the network to solve for the network resistances for a specified region and temperature. A calibration system is then developed using the calculated resistances at specified temperatures. This allows for the translation of the calculated resistances to a region temperature. The method can also be used to detect and quantify structural defects in the system.

  19. Optoelectronic characterization of carrier extraction in a hot carrier photovoltaic cell structure

    NASA Astrophysics Data System (ADS)

    Dimmock, James A. R.; Kauer, Matthias; Smith, Katherine; Liu, Huiyun; Stavrinou, Paul N.; Ekins-Daukes, Nicholas J.

    2016-07-01

    A hot carrier photovoltaic cell requires extraction of electrons on a timescale faster than they can lose energy to the lattice. We optically and optoelectronically characterize two resonant tunneling structures, showing their compatability with hot carrier photovoltaic operation, demonstrating structural and carrier extraction properties necessary for such a device. In particular we use time resolved and temperature dependent photoluminescence to determine extraction timescales and energy levels in the structures and demonstrate fast carrier extraction by tunneling. We also show that such devices are capable of extracting photo-generated electrons at high carrier densities, with an open circuit voltage in excess of 1 V.

  20. Fabrication and Structure Characterization of Alumina-Aluminum Interpenetrating Phase Composites

    NASA Astrophysics Data System (ADS)

    Dolata, Anna J.

    2016-01-01

    Alumina-Aluminum composites with interpenetrating networks structure belong to advanced materials with potentially better properties when compared with composites reinforced by particles or fibers. The paper presents the experimental results of fabrication and structure characterization of Al matrix composites locally reinforced via Al2O3 ceramic foam. The composites were obtained using centrifugal infiltration of porous ceramics by liquid aluminum alloy. Both scanning electron microscopy (SEM + EDS) and x-ray tomography were used to determine the structure of foams and composites especially in reinforced areas. The quality of castings, degree of pore filling in ceramic foams by Al alloy, and microstructure in area of interface were assessed.

  1. Fabrication and Structure Characterization of Alumina-Aluminum Interpenetrating Phase Composites

    NASA Astrophysics Data System (ADS)

    Dolata, Anna J.

    2016-08-01

    Alumina-Aluminum composites with interpenetrating networks structure belong to advanced materials with potentially better properties when compared with composites reinforced by particles or fibers. The paper presents the experimental results of fabrication and structure characterization of Al matrix composites locally reinforced via Al2O3 ceramic foam. The composites were obtained using centrifugal infiltration of porous ceramics by liquid aluminum alloy. Both scanning electron microscopy (SEM + EDS) and x-ray tomography were used to determine the structure of foams and composites especially in reinforced areas. The quality of castings, degree of pore filling in ceramic foams by Al alloy, and microstructure in area of interface were assessed.

  2. Characterization and crystal structure determination of β-1,2-mannobiose phosphorylase from Listeria innocua.

    PubMed

    Tsuda, Tomohiro; Nihira, Takanori; Chiku, Kazuhiro; Suzuki, Erika; Arakawa, Takatoshi; Nishimoto, Mamoru; Kitaoka, Motomitsu; Nakai, Hiroyuki; Fushinobu, Shinya

    2015-12-21

    Glycoside hydrolase family 130 consists of phosphorylases and hydrolases for β-mannosides. Here, we characterized β-1,2-mannobiose phosphorylase from Listeria innocua (Lin0857) and determined its crystal structures complexed with β-1,2-linked mannooligosaccharides. β-1,2-Mannotriose was bound in a U-shape, interacting with a phosphate analog at both ends. Lin0857 has a unique dimer structure connected by a loop, and a significant open-close loop displacement was observed for substrate entry. A long loop, which is exclusively present in Lin0857, covers the active site to limit the pocket size. A structural basis for substrate recognition and phosphorolysis was provided.

  3. Recognition and characterization of hierarchical interstellar structure. II - Structure tree statistics

    NASA Technical Reports Server (NTRS)

    Houlahan, Padraig; Scalo, John

    1992-01-01

    A new method of image analysis is described, in which images partitioned into 'clouds' are represented by simplified skeleton images, called structure trees, that preserve the spatial relations of the component clouds while disregarding information concerning their sizes and shapes. The method can be used to discriminate between images of projected hierarchical (multiply nested) and random three-dimensional simulated collections of clouds constructed on the basis of observed interstellar properties, and even intermediate systems formed by combining random and hierarchical simulations. For a given structure type, the method can distinguish between different subclasses of models with different parameters and reliably estimate their hierarchical parameters: average number of children per parent, scale reduction factor per level of hierarchy, density contrast, and number of resolved levels. An application to a column density image of the Taurus complex constructed from IRAS data is given. Moderately strong evidence for a hierarchical structural component is found, and parameters of the hierarchy, as well as the average volume filling factor and mass efficiency of fragmentation per level of hierarchy, are estimated. The existence of nested structure contradicts models in which large molecular clouds are supposed to fragment, in a single stage, into roughly stellar-mass cores.

  4. Structural Characterization of GNNQQNY Amyloid Fibrils by Magic Angle Spinning NMR. †

    PubMed Central

    van der Wel, Patrick C.A.; Lewandowski, Józef R.; Griffin, Robert G.

    2010-01-01

    Several human diseases are associated with the formation of amyloid aggregates, but experimental characterization of these amyloid fibrils and their oligomeric precursors has remained challenging. Experimental and computational analysis of simpler model systems has therefore been necessary, for instance on the peptide fragment GNNQQNY7-13 of yeast prion protein Sup35p. Expanding on a previous publication, we report here a detailed structural characterization of GNNQQNY fibrils using magic angle spinning (MAS) NMR. Based on additional chemical shift assignments we confirm the coexistence of three distinct peptide conformations within the fibrillar samples, as reflected in substantial chemical shift differences. Backbone torsion angle measurements indicate that the basic structure of these co-existing conformers is an extended β-sheet. We structurally characterize a previously identified localized distortion of the β-strand backbone specific to one of the conformers. Intermolecular contacts are consistent with each of the conformers being present in its own parallel and in-register sheet. Overall the MAS NMR data indicate a substantial difference between the structure of the fibrillar and crystalline forms of these peptides, with a clear increased complexity in the GNNQQNY fibril structure. These experimental data can provide guidance for future work, both experimental and theoretical, and provide insights into the distinction between fibril growth and crystal formation. PMID:20695483

  5. Characterization of structure and properties of bone by spectral measure method.

    PubMed

    Cherkaev, Elena; Bonifasi-Lista, Carlos

    2011-01-11

    Novel mathematical method called spectral measure method (SMM) is developed for characterization of bone structure and indirect estimation of bone properties. The spectral measure method is based on an inverse homogenization technique which allows to derive information about the structure of composite material from measured effective electric or viscoelastic properties. The mechanical properties and ability to withstand fracture depend on the structural organization of bone as a hierarchical composite. Information about the bone structural parameters is contained in the spectral measure in the Stieltjes integral representation of the effective properties. The method is based on constructing the spectral measure either by calculating it directly from micro-CT images or using measurements of electric or viscoelastic properties over a frequency range. In the present paper, we generalize the Stieltjes representation to the viscoelastic case and show how bone microstructure, in particular, bone volume or porosity, can be characterized by the spectral function calculated using measurements of complex permittivity or viscoelastic modulus. For validation purposes, we numerically simulated measured data using micro-CT images of cancellous bone. Recovered values of bone porosity are in excellent agreement with true porosity estimated from the micro-CT images. We also discuss another application of this method, which allows to estimate properties difficult to measure directly. The spectral measure method based on the derived Stieltjes representation for viscoelastic composites, has a potential for non-invasive characterization of bone structure using electric or mechanical measurements. The method is applicable to sea ice, porous rock, and other composite materials.

  6. Structural characterization of PEGylated rHuG-CSF and location of PEG attachment sites.

    PubMed

    Cindrić, Mario; Cepo, Tina; Galić, Nives; Bukvić-Krajacić, Mirjana; Tomczyk, Nick; Vissers, Johaness P C; Bindila, Laura; Peter-Katalinić, Jasna

    2007-06-28

    Mass spectrometry structural characterization is an essential tool in validating the quality of PEG-rHu-proteins. However, in either case top-down or bottom-up fashion, the interference of high intensity PEG signals on MS detection or detrimental influence of PEG on protein structure, leads to incomplete structural characterization. We propose here a method that permits complete and reliable structural characterization of PEGylated recombinant human granulocyte-colony stimulating factor (rHuG-CSF). The approach includes on-column 2-methoxy-4,5-dihydro-1H-imidazole derivatization of digested PEG rHuG-CSF and subsequent LC/MS investigation. By comparing the LC/MS retention of derivatized and underivatized digested PEG rHuG-CSF, location of the PEG attachment within rHuG-CSF could be deduced. Besides, the protein sequence coverage and position of the disulfide bridges was fully deducible from the MS data interpretation. Additionally, ultra performance liquid chromatography-mass spectrometry-to-the-E (UPLC-MS(E)) was introduced for analysis of label-free digested PEG rHuG-CSF here to enable high resolution and mass accuracy of MS detection and facilitate deep structural insights of peptides.

  7. Structural characterization and DPPH· radical scavenging activity of a polysaccharide from Guara fruits.

    PubMed

    Hua, Dehong; Zhang, Dezhi; Huang, Bing; Yi, Pan; Yan, Chunyan

    2014-03-15

    The crude polysaccharides were extracted from fruits of Psidium guajava Linn. by hot water. After removal of proteins, isolation and purification by DEAE-52 Cellulose chromatography and Sephadex G-75 gel filtration, a polysaccharide (GP70-2) was obtained and structurally characterized. GP70-2 has a relative molecular weight of 74 kDa and was composed of D-galactose and L-arabinose in the ratio of 1:1, with a specific optical rotation of [a]D(25) = +101°. Structural characterization of this novel polysaccharide was carried out using infrared spectroscopy, methylation analyses, and NMR studies ((1)H, (13)C, (1)H-(1)H-COSY, HMQC, and HMBC). Based on the above data, the following structure was assigned to the repeated core unit of GP70-2: [Formula: see text]. This polysaccharide showed a concentration dependent DPPH· radical scavenging activity.

  8. Solid state NMR: The essential technology for helical membrane protein structural characterization

    NASA Astrophysics Data System (ADS)

    Cross, Timothy A.; Ekanayake, Vindana; Paulino, Joana; Wright, Anna

    2014-02-01

    NMR spectroscopy of helical membrane proteins has been very challenging on multiple fronts. The expression and purification of these proteins while maintaining functionality has consumed countless graduate student hours. Sample preparations have depended on whether solution or solid-state NMR spectroscopy was to be performed - neither have been easy. In recent years it has become increasingly apparent that membrane mimic environments influence the structural result. Indeed, in these recent years we have rediscovered that Nobel laureate, Christian Anfinsen, did not say that protein structure was exclusively dictated by the amino acid sequence, but rather by the sequence in a given environment (Anfinsen, 1973) [106]. The environment matters, molecular interactions with the membrane environment are significant and many examples of distorted, non-native membrane protein structures have recently been documented in the literature. However, solid-state NMR structures of helical membrane proteins in proteoliposomes and bilayers are proving to be native structures that permit a high resolution characterization of their functional states. Indeed, solid-state NMR is uniquely able to characterize helical membrane protein structures in lipid environments without detergents. Recent progress in expression, purification, reconstitution, sample preparation and in the solid-state NMR spectroscopy of both oriented samples and magic angle spinning samples has demonstrated that helical membrane protein structures can be achieved in a timely fashion. Indeed, this is a spectacular opportunity for the NMR community to have a major impact on biomedical research through the solid-state NMR spectroscopy of these proteins.

  9. Solid state NMR: The essential technology for helical membrane protein structural characterization.

    PubMed

    Cross, Timothy A; Ekanayake, Vindana; Paulino, Joana; Wright, Anna

    2014-02-01

    NMR spectroscopy of helical membrane proteins has been very challenging on multiple fronts. The expression and purification of these proteins while maintaining functionality has consumed countless graduate student hours. Sample preparations have depended on whether solution or solid-state NMR spectroscopy was to be performed - neither have been easy. In recent years it has become increasingly apparent that membrane mimic environments influence the structural result. Indeed, in these recent years we have rediscovered that Nobel laureate, Christian Anfinsen, did not say that protein structure was exclusively dictated by the amino acid sequence, but rather by the sequence in a given environment (Anfinsen, 1973) [106]. The environment matters, molecular interactions with the membrane environment are significant and many examples of distorted, non-native membrane protein structures have recently been documented in the literature. However, solid-state NMR structures of helical membrane proteins in proteoliposomes and bilayers are proving to be native structures that permit a high resolution characterization of their functional states. Indeed, solid-state NMR is uniquely able to characterize helical membrane protein structures in lipid environments without detergents. Recent progress in expression, purification, reconstitution, sample preparation and in the solid-state NMR spectroscopy of both oriented samples and magic angle spinning samples has demonstrated that helical membrane protein structures can be achieved in a timely fashion. Indeed, this is a spectacular opportunity for the NMR community to have a major impact on biomedical research through the solid-state NMR spectroscopy of these proteins.

  10. Identification, characterization and evolution of non-local quasi-Lagrangian structures in turbulence

    NASA Astrophysics Data System (ADS)

    Yang, Yue

    2016-06-01

    The recent progress on non-local Lagrangian and quasi-Lagrangian structures in turbulence is reviewed. The quasi-Lagrangian structures, e.g., vortex surfaces in viscous flow, gas-liquid interfaces in multi-phase flow, and flame fronts in premixed combustion, can show essential Lagrangian following properties, but they are able to have topological changes in the temporal evolution. In addition, they can represent or influence the turbulent flow field. The challenges for the investigation of the non-local structures include their identification, characterization, and evolution. The improving understanding of the quasi-Lagrangian structures is expected to be helpful to elucidate crucial dynamics and develop structure-based predictive models in turbulence.

  11. Test method development for structural characterization of fiber composites at high temperatures

    NASA Technical Reports Server (NTRS)

    Mandell, J. F.; Grande, D. H.; Edwards, B.

    1985-01-01

    Test methods used for structural characterization of polymer matrix composites can be applied to glass and ceramic matrix composites only at low temperatures. New test methods are required for tensile, compressive, and shear properties of fiber composites at high temperatures. A tensile test which should be useful to at least 1000 C has been developed and used to characterize the properties of a Nicalon/glass composite up to the matrix limiting temperature of 600 C. Longitudinal and transverse unidirectional composite data are presented and discussed.

  12. Synthesis and characterization of high temperature curable poly(arylene ether) structural adhesive and composite matrices

    SciTech Connect

    Mecham, S.J.; Jayaraman, S.; Bobbitt, M.M.

    1996-12-31

    Crosslinked poly(arylene ether) systems are projected to display many desirable properties suitable for aerospace structural adhesive and composite matrix applications. The synthesis and characterization of a series of processable high temperature curing poly(arylene ether) oligomers incorporating terminally reactive phenylethynyl endgroups will be discussed. Characterization of the oligomers includes NMR, intrinsic viscosity, parallel plate rheological behavior, TGA, and DSC. Curing of these oligomers was conducted at or above 380{degrees}C, providing a large processing window. Thermal stability is very good and the melt viscosity of the oligomers in the processing temperature range is exceptionally low.

  13. Undefined freeform surfaces having deterministic structure: issues of their characterization for functionality and manufacture

    NASA Astrophysics Data System (ADS)

    Whitehouse, David J.

    2016-09-01

    There is an increasing use of surfaces which have structure, an increase in the use of freeform surfaces, and most importantly an increase in the number of surfaces having both characteristics. These can be called multi-function surfaces, where more than one function is helped by the geometrical features: the structure can help one, the freeform another. Alternatively, they can be complementary to optimize a single function, but in all cases both geometries are involved. This paper examines some of the problems posed by having such disparate geometries on one surface; in particular, the methods of characterization needed to help understand the functionality and also to some extent their manufacture. This involves investigating ways of expressing how local and global geometric features of undefined freeform surfaces might influence function and how surface structure on top of or in series with the freeform affects the nature of the characterization. Some methods have been found of identifying possible strategies for tackling the characterization problem, based in part on the principles of least action and on the way that nature has solved the marriage of flexible freeform geometry and structure on surfaces.

  14. Raman and structural characterization of LuAlO{sub 3}

    SciTech Connect

    Casu, Alberto; Ricci, Pier Carlo

    2011-11-15

    The structural and vibrational properties of lutetium orthoaluminate perovskite (LuAlO{sub 3}) were investigated by means of Raman spectroscopy and EXAFS measurements. The analysis of Raman spectra taken in four different polarized configurations along the principal axes at 20 K and room temperature conditions permits to assign the principal vibrational modes in LuAP single crystals and to confirm the belonging to the D{sub 2h}{sup 16} space group. EXAFS measurements were performed at room temperature in order to obtain local structural informations on the first and next nearest neighbors around lutetium absorptions sites. Unit cell parameters and bond lengths were determined by the analysis of the EXAFS spectroscopy at the L{sub 3} absorption edge of lutetium. The informations thus gathered on this compound can offer a useful addition in the framework of a full structural characterization of LuAlO{sub 3}. - Graphical abstract: Raman active mode in LuAP crystal. Highlights: > Structural characterization of LuAlO{sub 3} is obtained by Raman and EXAFS spectroscopies. > Vibrational modes, temperature-dependent variations studied by Raman spectroscopy. > Cell parameters and local characterization obtained by EXAFS spectroscopy.

  15. Microfluidic-based fabrication, characterization and magnetic functionalization of microparticles with novel internal anisotropic structure

    PubMed Central

    Qiu, Yang; Wang, Fei; Liu, Ying-Mei; Wang, Wei; Chu, Liang-Yin; Wang, Hua-Lin

    2015-01-01

    Easy fabrication and independent control of the internal and external morphologies of core-shell microparticles still remain challenging. Core-shell microparticle comprised of a previously unknown internal anisotropic structure and a spherical shell was fabricated by microfluidic-based emulsificaiton and photopolymerization. The interfacial and spatial 3D morphology of the anisotropic structure were observed by SEM and micro-CT respectively. Meanwhile, a series of layer-by-layer scans of the anisotropic structure were obtained via the micro-CT, which enhanced the detail characterization and analysis of micro materials. The formation mechanism of the internal anisotropic structure may be attributed to solution-directed diffusion caused by the semipermeable membrane structure and chemical potential difference between inside and outside of the semipermeable membrane-like polymerized shell. The morphology evolution of the anisotropic structure was influenced and controlled by adjusting reaction parameters including polymerization degree, polymerization speed, and solute concentration difference. The potential applications of these microparticles in microrheological characterization and image enhancement were also proposed by embedding magnetic nanoparticles in the inner core. PMID:26268148

  16. Structure characterization of the non-crystalline complexes of copper salts with native cyclodextrins.

    PubMed

    Velasco, Manuel I; Krapacher, Claudio R; de Rossi, Rita H; Rossi, Laura I

    2016-06-28

    The characterization of non-crystalline complexes is particularly difficult when techniques like X-ray diffraction or NMR cannot be used. We propose a simple procedure to characterize the physicochemical properties of amorphous new coordination compounds between cyclodextrins (CD) and Cu(2+) salts, by means of the integration of the information provided by several techniques including elemental analysis, flame atomic absorption, TGA, UV-Vis diffuse reflectance, colorimetry, FT-IR and EPR. On the basis of these procedures, we suggest geometrical and structural approximations resulting in an octahedral or distorted octahedral geometry with diverse positions for the metallic centre. According to the EPR spectrum, only one of the complexes may have rhombic symmetry. We also analyzed enthalpy-entropy compensation and the isokinetic effect. In addition, general trends in thermal stability, spectroscopic properties and inclusion in the cavity were analysed. This complete characterization methodology becomes essential for their future application as catalysts. PMID:27272478

  17. Fabrication and Characterization of a-Si Micro and Nano-Gap Structure for Electrochemical Sensor

    NASA Astrophysics Data System (ADS)

    Dhahi, Th. S.; Hashim, U.; Ahmed, N. M.; Ali, Md. Eaqub

    2011-05-01

    The development and application of micro gap for electrochemical sensors and biomolecule detection are reviewed in this article. The preparation methods for micro- and nano-gaps and their properties are discussed along with their advantages in electrochemical sensors and biomolecule detection. Biology and medicine have seen great advances in biosensors and biochips capable of characterizing and quantifying electrochemical sensor. To understand the important relationship between sensibility and nano structure, we introduce the fabrication and characterization of micro- and nano-gap structures for electrochemical sensor. In this paper, two mask designs are proposed. The first is the lateral micro- and nano-gap with aluminum (Al) electrode, and the second mask is for pad Al electrode pattern. Lateral micro-gaps are introduced in the fabrication process using amorphous silicon (a-Si) and Al as an electrode. Conventional ultraviolet lithography technique and dry etching for a-Si layer with wet etching for Al surface processes are used to fabricate the micro- and nano-gaps based on the standard complementary metal-oxide-semiconductor technology and characterization of its conductivity. Electrical characterization is applied using Semiconductor Parameter Analyzer, Spectrum Analyzer, current-voltage (IV)-capacitance-voltage (CV) station for electrical characteristics. Conductivity, resistance, and capacitance tests are performed to characterize and verify the structure of the device, resulting in a small micro-gap as revealed by a further IV curve result showing a current in nano amps. The characteristics of the fabricated gap are close to those of a micro-gap, as verified by the literature.

  18. Mass spectrometry combinations for structural characterization of sulfated-steroid metabolites

    PubMed Central

    Yan, Yuetian; Rempel, Don; Holy, Timothy E.; Gross, Michael L.

    2015-01-01

    Steroid conjugates, which often occur as metabolites, are challenging to characterize. One application is female-mouse urine, where steroid conjugates serve as important ligands for the pheromone-sensing neurons. Although the two with the highest abundance in mouse urine were previously characterized with mass spectrometry (MS) and NMR to be sulfated steroids, many more exist but remain structurally unresolved. Given that their physical and chemical properties are similar, they are likely to have a sulfated steroid ring structure. Because these compounds occur in trace amounts in mouse urine and elsewhere, their characterization by NMR will be difficult. Thus, MS methods become the primary approach for determining structure. Here, we show that a combination of MS tools is effective for determining the structures of sulfated steroids. Using 4-pregnene analogs, we explored high-resolving power MS (HR-MS) to determine chemical formulae; HD exchange MS (HDX-MS) to determine number of active, exchangeable hydrogens (e.g., OH groups); methoxyamine hydrochloride (MOX) derivatization MS, or reactive desorption electrospray ionization with hydroxylamine to determine the number of carbonyl groups; and tandem MS (MSn), high-resolution tandem MS (HRMS/MS), and GC-MS to obtain structural details of the steroid ring. From the fragmentation studies, we deduced three major fragmentation rules for this class of sulfated steroids. We also show that a combined MS approach is effective for determining structure of steroid metabolites, with important implications for targeted metabolomics in general and for the study of mouse social communication in particular. PMID:24658800

  19. Photosystem II reconstitution into proteoliposomes and methodologies for structure-function characterization.

    PubMed

    Joly, David; Govindachary, Sridharan; Fragata, Mário

    2011-01-01

    This chapter discusses the photosystem II (PSII) reconstitution into proteoliposomes. In the first part of the chapter, protocols are outlined for the preparation of lipid bilayer vesicles (liposomes) constituted of individual thylakoid lipids or their mixtures, for the preparation of PSII particles, and for the incorporation of the PSII particles into the liposomes. In the second part of the chapter, methodologies are described for the structure-function characterization of the PSII-lipid complexes (proteoliposomes). This includes the sodium dodecylsulfate-polyacrylamide gel electrophoresis determination of the PSII proteins, the measurement of oxygen-evolving activity of PSII in the proteoliposomes, the study of structural changes of the PSII proteins upon their incorporation into the lipid bilayers by Fourier transform infrared (FT-IR) spectroscopy, and the characterization of the PSII activity by fluorescence induction.

  20. Nondestructive techniques for characterizing mechanical properties of structural materials: An overview

    NASA Technical Reports Server (NTRS)

    Vary, A.; Klima, S. J.

    1985-01-01

    An overview of nondestructive evaluation (NDE) is presented to indicate the availability and application potentials of techniques for quantitative characterization of the mechanical properties of structural materials. The purpose is to review NDE techniques that go beyond the usual emphasis on flaw detection and characterization. Discussed are current and emerging NDE techniques that can verify and monitor entrinsic properties (e.g., tensile, shear, and yield strengths; fracture toughness, hardness, ductility; elastic moduli) and underlying microstructural and morphological factors. Most of the techniques described are, at present, neither widely applied nor widely accepted in commerce and industry because they are still emerging from the laboratory. The limitations of the techniques may be overcome by advances in applications research and instrumentation technology and perhaps by accommodations for their use in the design of structural parts.

  1. Crystal structure and functional characterization of a light-driven chloride pump having an NTQ motif.

    PubMed

    Kim, Kuglae; Kwon, Soon-Kyeong; Jun, Sung-Hoon; Cha, Jeong Seok; Kim, Hoyoung; Lee, Weontae; Kim, Jihyun F; Cho, Hyun-Soo

    2016-01-01

    A novel light-driven chloride-pumping rhodopsin (ClR) containing an 'NTQ motif' in its putative ion conduction pathway has been discovered and functionally characterized in a genomic analysis study of a marine bacterium. Here we report the crystal structure of ClR from the flavobacterium Nonlabens marinus S1-08(T) determined under two conditions at 2.0 and 1.56 Å resolutions. The structures reveal two chloride-binding sites, one around the protonated Schiff base and the other on a cytoplasmic loop. We identify a '3 omega motif' formed by three non-consecutive aromatic amino acids that is correlated with the B-C loop orientation. Detailed ClR structural analyses with functional studies in E. coli reveal the chloride ion transduction pathway. Our results help understand the molecular mechanism and physiological role of ClR and provide a structural basis for optogenetic applications. PMID:27554809

  2. Characterization of Effect of Support Structures in Laser Additive Manufacturing of Stainless Steel

    NASA Astrophysics Data System (ADS)

    Järvinen, Jukka-Pekka; Matilainen, Ville; Li, Xiaoyun; Piili, Heidi; Salminen, Antti; Mäkelä, Ismo; Nyrhilä, Olli

    Laser additive manufacturing (LAM) of stainless steel is a layer wisetechnology for fabricating 3D parts from metal powder via selectively melting powder with laser beam. Support structures play a significant role in LAM process as they help to remove heat away from the process and on the other hand hold the work piece in its place. A successful design of support structures can help to achievea building process fast and inexpensive with high quality. Aimof this study was to characterize the usability of two types of support structures: web and tube supports. Purpose of this studywas also to analyze how suitable they are in two industrial application cases: case for dental application and case for jewelry application. It was concluded that the removability of web supports was much better than tube supports. It was noticed that support structures are an important part of LAM process and they strongly affect the manufacturability and the end quality of the part.

  3. Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola

    PubMed Central

    Dhakshnamoorthy, Balasundaresan; Rohaim, Ahmed; Rui, Huan; Blachowicz, Lydia; Roux, Benoît

    2016-01-01

    The selectivity filter is an essential functional element of K+ channels that is highly conserved both in terms of its primary sequence and its three-dimensional structure. Here, we investigate the properties of an ion channel from the Gram-positive bacterium Tsukamurella paurometabola with a selectivity filter formed by an uncommon proline-rich sequence. Electrophysiological recordings show that it is a non-selective cation channel and that its activity depends on Ca2+ concentration. In the crystal structure, the selectivity filter adopts a novel conformation with Ca2+ ions bound within the filter near the pore helix where they are coordinated by backbone oxygen atoms, a recurrent motif found in multiple proteins. The binding of Ca2+ ion in the selectivity filter controls the widening of the pore as shown in crystal structures and in molecular dynamics simulations. The structural, functional and computational data provide a characterization of this calcium-gated cationic channel. PMID:27678077

  4. Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola

    NASA Astrophysics Data System (ADS)

    Dhakshnamoorthy, Balasundaresan; Rohaim, Ahmed; Rui, Huan; Blachowicz, Lydia; Roux, Benoît

    2016-09-01

    The selectivity filter is an essential functional element of K+ channels that is highly conserved both in terms of its primary sequence and its three-dimensional structure. Here, we investigate the properties of an ion channel from the Gram-positive bacterium Tsukamurella paurometabola with a selectivity filter formed by an uncommon proline-rich sequence. Electrophysiological recordings show that it is a non-selective cation channel and that its activity depends on Ca2+ concentration. In the crystal structure, the selectivity filter adopts a novel conformation with Ca2+ ions bound within the filter near the pore helix where they are coordinated by backbone oxygen atoms, a recurrent motif found in multiple proteins. The binding of Ca2+ ion in the selectivity filter controls the widening of the pore as shown in crystal structures and in molecular dynamics simulations. The structural, functional and computational data provide a characterization of this calcium-gated cationic channel.

  5. Ultrasonic-assisted synthesis and structural characterization of two new nano-structured Hg(II) coordination polymers.

    PubMed

    Ghasempour, Hosein; Azhdari Tehrani, Alireza; Morsali, Ali

    2015-11-01

    Two new Hg(II) coordination polymers containing N,N'-Bis-pyridin-3-ylmethylene-naphtalene-1,5-diamine ligand were synthesized by conventional and sonochemical methods, characterized by spectroscopic techniques (FT-IR and elemental analysis), and their X-ray crystallographic structures were determined. The crystal packing and supramolecular features of these coordination polymers were studied using geometrical analysis and Hirshfeld surface analysis. The crystal structure analysis revealed that H⋯H contacts, C-H⋯π and C-H⋯X (X = Cl for 1 and X = Br for 2) hydrogen bonding interactions are strong enough to govern the supramolecular architecture. The BFDH analysis helps us to compare the predicted morphology to that obtained under ultrasonication. This study may provide further insight into discovering the role of weak intermolecular interactions in the context of nano-supramolecular assembly.

  6. Characterizing Molecular Structure by Combining Experimental Measurements with Density Functional Theory Computations

    NASA Astrophysics Data System (ADS)

    Lopez-Encarnacion, Juan M.

    2016-06-01

    In this talk, the power and synergy of combining experimental measurements with density functional theory computations as a single tool to unambiguously characterize the molecular structure of complex atomic systems is shown. Here, we bring three beautiful cases where the interaction between the experiment and theory is in very good agreement for both finite and extended systems: 1) Characterizing Metal Coordination Environments in Porous Organic Polymers: A Joint Density Functional Theory and Experimental Infrared Spectroscopy Study 2) Characterization of Rhenium Compounds Obtained by Electrochemical Synthesis After Aging Process and 3) Infrared Study of H(D)2 + Co4+ Chemical Reaction: Characterizing Molecular Structures. J.M. López-Encarnación, K.K. Tanabe, M.J.A. Johnson, J. Jellinek, Chemistry-A European Journal 19 (41), 13646-13651 A. Vargas-Uscategui, E. Mosquera, J.M. López-Encarnación, B. Chornik, R. S. Katiyar, L. Cifuentes, Journal of Solid State Chemistry 220, 17-21

  7. Unexpected structural complexity of supernumerary marker chromosomes characterized by microarray comparative genomic hybridization

    PubMed Central

    Tsuchiya, Karen D; Opheim, Kent E; Hannibal, Mark C; Hing, Anne V; Glass, Ian A; Raff, Michael L; Norwood, Thomas; Torchia, Beth A

    2008-01-01

    Background Supernumerary marker chromosomes (SMCs) are structurally abnormal extra chromosomes that cannot be unambiguously identified by conventional banding techniques. In the past, SMCs have been characterized using a variety of different molecular cytogenetic techniques. Although these techniques can sometimes identify the chromosome of origin of SMCs, they are cumbersome to perform and are not available in many clinical cytogenetic laboratories. Furthermore, they cannot precisely determine the region or breakpoints of the chromosome(s) involved. In this study, we describe four patients who possess one or more SMCs (a total of eight SMCs in all four patients) that were characterized by microarray comparative genomic hybridization (array CGH). Results In at least one SMC from all four patients, array CGH uncovered unexpected complexity, in the form of complex rearrangements, that could have gone undetected using other molecular cytogenetic techniques. Although array CGH accurately defined the chromosome content of all but two minute SMCs, fluorescence in situ hybridization was necessary to determine the structure of the markers. Conclusion The increasing use of array CGH in clinical cytogenetic laboratories will provide an efficient method for more comprehensive characterization of SMCs. Improved SMC characterization, facilitated by array CGH, will allow for more accurate SMC/phenotype correlation. PMID:18471320

  8. Cobalt Molybdenum Oxynitrides: Synthesis, Structural, Characterization, and Catalytic Activity for the Oxygen Reduction Reaction

    SciTech Connect

    Cao, Bingfei; Veith, Gabriel M; Diaz, Rosa; Liu, Jue; Stach, Eric; Adzic, Radoslav R.; Khalifah, P.

    2013-01-01

    Here, we report the synthesis and characterization of CoxMo1 xOyNz compounds supported on carbon black as potential cathode catalysts for ORR. They were prepared by a conventional impregnation method. Their ORR activities in both acid and alkaline electrolytes were evaluated via half-cell measurements. The synthesis temperature and sample composition both strongly impacted their physical and chemical properties. Factors influencing their crystal structures, morphologies and ORR activities will be discussed based on the results of structural and spectroscopic studies.

  9. Isolation and structural characterization of a mainly ligand-based dimetallic radical.

    PubMed

    Li, Shuyu; Wang, Xingyong; Zhang, Zaichao; Zhao, Yue; Wang, Xinping

    2015-12-14

    A radical cation of ruthenium was isolated and structurally characterized. The EPR spectrum and theoretical calculations indicate that the spin density mainly resides on ligands. The X-ray structure shows that the change in metal-metal bond lengths is negligible upon one-electron oxidation. sp(3) C-H bond activation was observed during the reaction of the parent molecule with the trityl cation, which possibly occurs via an oxidative EC mechanism: a thermodynamically favorable electron-transfer to give the radical cation intermediate, followed by the hydrogen atom abstraction to afford a cationic tetramethylfulvene complex with formation of a metal-carbon bond.

  10. Using the structure-function linkage database to characterize functional domains in enzymes.

    PubMed

    Brown, Shoshana; Babbitt, Patricia

    2014-12-12

    The Structure-Function Linkage Database (SFLD; http://sfld.rbvi.ucsf.edu/) is a Web-accessible database designed to link enzyme sequence, structure, and functional information. This unit describes the protocols by which a user may query the database to predict the function of uncharacterized enzymes and to correct misannotated functional assignments. The information in this unit is especially useful in helping a user discriminate functional capabilities of a sequence that is only distantly related to characterized sequences in publicly available databases.

  11. Growth and characterization of periodically polarity-inverted ZnO structures on sapphire substrates

    SciTech Connect

    Park, Jinsub; Yao, Takafumi

    2012-10-15

    We report on the fabrication and characterization of periodically polarity inverted (PPI) ZnO heterostructures on (0 0 0 1) Al{sub 2}O{sub 3} substrates. For the periodically inverted array of ZnO polarity, CrN and Cr{sub 2}O{sub 3} polarity selection buffer layers are used for the Zn- and O-polar ZnO films, respectively. The change of polarity and period in fabricated ZnO structures is evaluated by diffraction patterns and polarity sensitive piezo-response microscopy. Finally, PPI ZnO structures with subnanometer scale period are demonstrated by using holographic lithography and regrowth techniques.

  12. Efficiency of hit generation and structural characterization in fragment-based ligand discovery.

    PubMed

    Larsson, Andreas; Jansson, Anna; Åberg, Anders; Nordlund, Pär

    2011-08-01

    Fragment-based ligand discovery constitutes a useful strategy for the generation of high affinity ligands with suitable physico-chemical properties to serve as drug leads. There is an increasing number of generic biophysical screening strategies established with the potential for accelerating the generation of useful fragment hits. Crystal structures of these hits can subsequently be used as starting points for fragment evolution to high affinity ligands. Emerging understanding of the efficiency and operative aspects of hit generation and structural characterization in FBLD suggests that this method should be well suited for academic ligand development of chemical tools and experimental therapeutics.

  13. Characterization of Structural and Pigmentary Colors in Common Emigrant (Catopsilia Pomona) Butterfly

    SciTech Connect

    Ghate, Ekata; Kulkarni, G. R.; Bhoraskar, S. V.; Adhi, K. P.

    2011-10-20

    Study of structural colors in case of insects and butterflies is important for their biomimic and biophotonics applications. Structural color is the color which is produced by physical structures and their interaction with light while pigmentary color is produced by absorption of light by pigments. Common Emigrant butterfly is widely distributed in India. It is of moderate size with wing span of about 60-80 mm. The wings are broadly white with yellow or sulphur yellow coloration at places as well as few dark black patches. It belongs to family Pieridae. A study of structural color in case of Common Emigrant butterfly has been carried out in the present work. The characterization of wing color was performed using absorption spectroscopy. Scanning electron microscopic study of the wings of Common Emigrant butterfly showed that three different types of scales are present on the wing surface dorsally. Diffracting structures are present in certain parts of the surfaces of the various scales. Bead like structures are embedded in the intricate structures of the scales. Absorption spectra revealed that a strong absorption peak is seen in the UV-range. Crystalline structure of beads was confirmed by the X-ray diffraction analysis.

  14. Foam injection molding of thermoplastic elastomers: Blowing agents, foaming process and characterization of structural foams

    NASA Astrophysics Data System (ADS)

    Ries, S.; Spoerrer, A.; Altstaedt, V.

    2014-05-01

    Polymer foams play an important role caused by the steadily increasing demand to light weight design. In case of soft polymers, like thermoplastic elastomers (TPE), the haptic feeling of the surface is affected by the inner foam structure. Foam injection molding of TPEs leads to so called structural foam, consisting of two compact skin layers and a cellular core. The properties of soft structural foams like soft-touch, elastic and plastic behavior are affected by the resulting foam structure, e.g. thickness of the compact skins and the foam core or density. This inner structure can considerably be influenced by different processing parameters and the chosen blowing agent. This paper is focused on the selection and characterization of suitable blowing agents for foam injection molding of a TPE-blend. The aim was a high density reduction and a decent inner structure. Therefore DSC and TGA measurements were performed on different blowing agents to find out which one is appropriate for the used TPE. Moreover a new analyzing method for the description of processing characteristics by temperature dependent expansion measurements was developed. After choosing suitable blowing agents structural foams were molded with different types of blowing agents and combinations and with the breathing mold technology in order to get lower densities. The foam structure was analyzed to show the influence of the different blowing agents and combinations. Finally compression tests were performed to estimate the influence of the used blowing agent and the density reduction on the compression modulus.

  15. Synthesis, Structural Characterization of a Novel Ferrocene Derivative and Preliminarily Anticancer Activity.

    PubMed

    Yong, Jianping; Wu, Xiaoyuan; Liao, Jianzhen; Lu, Canzhong; Liu, Xiaolong

    2016-01-01

    A novel structure of ferrocene derivative 1 was synthesized with cyanuric chloride and ferrocenemethanol as starting materials. The synthesized compound was fully characterized using 1H NMR, 13C NMR, MS and XRD. Subsequently, the in vitro anticancer effect against A549, HCT116 and MCF-7 cell lines was preliminarily evaluated by the MTT method. The result showed that this compound exhibits good cytotoxic effect on A549, HCT116 and MCF-7 cell lines.

  16. Structural and Functional Characterization of a Caenorhabditis elegans Genetic Interaction Network within Pathways.

    PubMed

    Boucher, Benjamin; Lee, Anna Y; Hallett, Michael; Jenna, Sarah

    2016-02-01

    A genetic interaction (GI) is defined when the mutation of one gene modifies the phenotypic expression associated with the mutation of a second gene. Genome-wide efforts to map GIs in yeast revealed structural and functional properties of a GI network. This provided insights into the mechanisms underlying the robustness of yeast to genetic and environmental insults, and also into the link existing between genotype and phenotype. While a significant conservation of GIs and GI network structure has been reported between distant yeast species, such a conservation is not clear between unicellular and multicellular organisms. Structural and functional characterization of a GI network in these latter organisms is consequently of high interest. In this study, we present an in-depth characterization of ~1.5K GIs in the nematode Caenorhabditis elegans. We identify and characterize six distinct classes of GIs by examining a wide-range of structural and functional properties of genes and network, including co-expression, phenotypical manifestations, relationship with protein-protein interaction dense subnetworks (PDS) and pathways, molecular and biological functions, gene essentiality and pleiotropy. Our study shows that GI classes link genes within pathways and display distinctive properties, specifically towards PDS. It suggests a model in which pathways are composed of PDS-centric and PDS-independent GIs coordinating molecular machines through two specific classes of GIs involving pleiotropic and non-pleiotropic connectors. Our study provides the first in-depth characterization of a GI network within pathways of a multicellular organism. It also suggests a model to understand better how GIs control system robustness and evolution. PMID:26871911

  17. Structural and Functional Characterization of a Caenorhabditis elegans Genetic Interaction Network within Pathways

    PubMed Central

    Boucher, Benjamin; Lee, Anna Y.; Hallett, Michael; Jenna, Sarah

    2016-01-01

    A genetic interaction (GI) is defined when the mutation of one gene modifies the phenotypic expression associated with the mutation of a second gene. Genome-wide efforts to map GIs in yeast revealed structural and functional properties of a GI network. This provided insights into the mechanisms underlying the robustness of yeast to genetic and environmental insults, and also into the link existing between genotype and phenotype. While a significant conservation of GIs and GI network structure has been reported between distant yeast species, such a conservation is not clear between unicellular and multicellular organisms. Structural and functional characterization of a GI network in these latter organisms is consequently of high interest. In this study, we present an in-depth characterization of ~1.5K GIs in the nematode Caenorhabditis elegans. We identify and characterize six distinct classes of GIs by examining a wide-range of structural and functional properties of genes and network, including co-expression, phenotypical manifestations, relationship with protein-protein interaction dense subnetworks (PDS) and pathways, molecular and biological functions, gene essentiality and pleiotropy. Our study shows that GI classes link genes within pathways and display distinctive properties, specifically towards PDS. It suggests a model in which pathways are composed of PDS-centric and PDS-independent GIs coordinating molecular machines through two specific classes of GIs involving pleiotropic and non-pleiotropic connectors. Our study provides the first in-depth characterization of a GI network within pathways of a multicellular organism. It also suggests a model to understand better how GIs control system robustness and evolution. PMID:26871911

  18. Large-Scale Production and Structural and Biophysical Characterizations of the Human Hepatitis B Virus Polymerase

    PubMed Central

    Vörös, Judit; Urbanek, Annika; Rautureau, Gilles Jean Philippe; O'Connor, Maggie; Fisher, Henry C.; Ashcroft, Alison E.

    2014-01-01

    ABSTRACT Hepatitis B virus (HBV) is a major human pathogen that causes serious liver disease and 600,000 deaths annually. Approved therapies for treating chronic HBV infections usually target the multifunctional viral polymerase (hPOL). Unfortunately, these therapies—broad-spectrum antivirals—are not general cures, have side effects, and cause viral resistance. While hPOL remains an attractive therapeutic target, it is notoriously difficult to express and purify in a soluble form at yields appropriate for structural studies. Thus, no empirical structural data exist for hPOL, and this impedes medicinal chemistry and rational lead discovery efforts targeting HBV. Here, we present an efficient strategy to overexpress recombinant hPOL domains in Escherichia coli, purifying them at high yield and solving their known aggregation tendencies. This allowed us to perform the first structural and biophysical characterizations of hPOL domains. Apo-hPOL domains adopt mainly α-helical structures with small amounts of β-sheet structures. Our recombinant material exhibited metal-dependent, reverse transcriptase activity in vitro, with metal binding modulating the hPOL structure. Calcomine orange 2RS, a small molecule that inhibits duck HBV POL activity, also inhibited the in vitro priming activity of recombinant hPOL. Our work paves the way for structural and biophysical characterizations of hPOL and should facilitate high-throughput lead discovery for HBV. IMPORTANCE The viral polymerase from human hepatitis B virus (hPOL) is a well-validated therapeutic target. However, recombinant hPOL has a well-deserved reputation for being extremely difficult to express in a soluble, active form in yields appropriate to the structural studies that usually play an important role in drug discovery programs. This has hindered the development of much-needed new antivirals for HBV. However, we have solved this problem and report here procedures for expressing recombinant hPOL domains in

  19. Dispersed metal cluster catalysts by design. Synthesis, characterization, structure, and performance

    SciTech Connect

    Arslan, Ilke; Dixon, David A.; Gates, Bruce C.; Katz, Alexander

    2015-09-30

    To understand the class of metal cluster catalysts better and to lay a foundation for the prediction of properties leading to improved catalysts, we have synthesized metal catalysts with well-defined structures and varied the cluster structures and compositions systematically—including the ligands bonded to the metals. These ligands include supports and bulky organics that are being tuned to control both the electron transfer to or from the metal and the accessibility of reactants to influence catalytic properties. We have developed novel syntheses to prepare these well-defined catalysts with atomic-scale control the environment by choice and placement of ligands and applied state-of-the art spectroscopic, microscopic, and computational methods to determine their structures, reactivities, and catalytic properties. The ligands range from nearly flat MgO surfaces to enveloping zeolites to bulky calixarenes to provide controlled coverages of the metal clusters, while also enforcing unprecedented degrees of coordinative unsaturation at the metal site—thereby facilitating bonding and catalysis events at exposed metal atoms. With this wide range of ligand properties and our arsenal of characterization tools, we worked to achieve a deep, fundamental understanding of how to synthesize robust supported and ligand-modified metal clusters with controlled catalytic properties, thereby bridging the gap between active site structure and function in unsupported and supported metal catalysts. We used methods of organometallic and inorganic chemistry combined with surface chemistry for the precise synthesis of metal clusters and nanoparticles, characterizing them at various stages of preparation and under various conditions (including catalytic reaction conditions) and determining their structures and reactivities and how their catalytic properties depend on their compositions and structures. Key characterization methods included IR, NMR, and EXAFS spectroscopies to identify

  20. Synthesis, spectroscopic characterizations, crystal structures and DFT studies of nalidixic acid carbonyl hydrazones derivatives

    NASA Astrophysics Data System (ADS)

    Bergamini, F. R. G.; Ribeiro, M. A.; Lancellotti, M.; Machado, D.; Miranda, P. C. M. L.; Cuin, A.; Formiga, A. L. B.; Corbi, P. P.

    2016-09-01

    This article describes the synthesis and characterization of the 1-ethyl-7-methyl-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carbohydrazide (hzd) and six carbonyl hydrazones derivatives of the nalidixic with 1H-pyrrol-2-ylmethylidene (hpyrr), 1H-imidazol-2-ylmethylidene (h2imi), pyridin-2-ylmethylidene (h2py), pyridin-3-ylmethylidene (h3py), pyridin-4-ylmethylidene(h4py) and (2-hydroxyphenyl)methylidene (hsali). The carbonyl hydrazones were characterized by elemental and ESI-QTOF-MS analyses, IR and detailed NMR spectroscopic measurements. The 2D NMR experiments allowed the unambiguous assignment of the hydrogen, carbon and nitrogen atoms, which have not been reported for nalidixic acid carbonyl hydrazone derivatives so far. Crystal structures of hzd and the new carbonyl hydrazones h2imi, hpyrr and h3py were determined by X-ray diffraction studies. Although the synthesis of hzd was reported decades ago, the hzd crystal structure have not been reported yet. Geometric optimizations of all the characterized structures were performed with the aid of DFT studies. Despite the fact that the hydrazones with 2-pyridine carboxylic acid (h2py) and salicyl aldehyde (hsali) were already reported by literature, a detailed spectroscopic study followed by DFT studies are also reported for such compounds in this manuscript. Antimicrobial studies of the compounds are also presented.

  1. Structures and characterizations of bundles of collapsed double-walled carbon nanotubes.

    PubMed

    Zhong, X H; Wang, R; Liu, L B; Kang, M; Wen, Y Y; Hou, F; Feng, J M; Li, Y L

    2012-12-21

    The performance of carbon nanotube fibers (CNTFs) significantly depends on the packing styles of carbon nanotube (CNT) bundles. Revealing the structures and characterizations of CNT bundles is contributive to understanding the structures, properties and even the formation of CNTFs during chemical vapor deposition (CVD) processing. In this paper, bundles consisting of collapsed double-walled carbon nanotubes (CDWNT) in continuous CNTFs fabricated from CVD processing were characterized and analyzed by transmission electronic microscopy (TEM) and x-ray diffraction (XRD). TEM observations show that the continuous CNTFs are composed of CDWNT-bundle units. CDWNT-bundle units of 10-20 nm in thickness contain near numbers of collapsed tubes. The degree of collapse of the CDWNTs varies with their location in the bundle and their own diameter. CDWNT-bundle units pack side by side or face to face, assembling into super-bundles with diameters of 200-300 nm. XRD patterns show that three novel and strong peaks appear at 10°-15°, 21.3° and 23.7°, respectively, corresponding to CDWNT two side pores (10°-15°) and CDWNT layers (21.3° and 23.7°), which indicates the collapsed tube structures in CNTFs are common characterizations. Finally, a collapse mechanism is discussed from the observation and analysis. PMID:23196759

  2. Characterization of a Novel Water Pocket Inside the Human Cx26 Hemichannel Structure

    PubMed Central

    Araya-Secchi, Raul; Perez-Acle, Tomas; Kang, Seung-gu; Huynh, Tien; Bernardin, Alejandro; Escalona, Yerko; Garate, Jose-Antonio; Martínez, Agustin D.; García, Isaac E.; Sáez, Juan C.; Zhou, Ruhong

    2014-01-01

    Connexins (Cxs) are a family of vertebrate proteins constituents of gap junction channels (GJCs) that connect the cytoplasm of adjacent cells by the end-to-end docking of two Cx hemichannels. The intercellular transfer through GJCs occurs by passive diffusion allowing the exchange of water, ions, and small molecules. Despite the broad interest to understand, at the molecular level, the functional state of Cx-based channels, there are still many unanswered questions regarding structure-function relationships, perm-selectivity, and gating mechanisms. In particular, the ordering, structure, and dynamics of water inside Cx GJCs and hemichannels remains largely unexplored. In this work, we describe the identification and characterization of a believed novel water pocket—termed the IC pocket—located in-between the four transmembrane helices of each human Cx26 (hCx26) monomer at the intracellular (IC) side. Using molecular dynamics (MD) simulations to characterize hCx26 internal water structure and dynamics, six IC pockets were identified per hemichannel. A detailed characterization of the dynamics and ordering of water including conformational variability of residues forming the IC pockets, together with multiple sequence alignments, allowed us to propose a functional role for this cavity. An in vitro assessment of tracer uptake suggests that the IC pocket residue Arg-143 plays an essential role on the modulation of the hCx26 hemichannel permeability. PMID:25099799

  3. Structural characterization of a first-generation articulated-truss joint for space crane application

    NASA Technical Reports Server (NTRS)

    Sutter, Thomas R.; Wu, K. Chauncey; Riutort, Kevin T.; Laufer, Joseph B.; Phelps, James E.

    1992-01-01

    A first-generation space crane articulated-truss joint was statically and dynamically characterized in a configuration that approximated an operational environment. The articulated-truss joint was integrated into a test-bed for structural characterization. Static characterization was performed by applying known loads and measuring the corresponding deflections to obtain load-deflection curves. Dynamic characterization was performed using modal testing to experimentally determine the first six mode shapes, frequencies, and modal damping values. Static and dynamic characteristics were also determined for a reference truss that served as a characterization baseline. Load-deflection curves and experimental frequency response functions are presented for the reference truss and the articulated-truss joint mounted in the test-bed. The static and dynamic experimental results are compared with analytical predictions obtained from finite element analyses. Load-deflection response is also presented for one of the linear actuators used in the articulated-truss joint. Finally, an assessment is presented for the predictability of the truss hardware used in the reference truss and articulated-truss joint based upon hardware stiffness properties that were previously obtained during the Precision Segmented Reflector (PSR) Technology Development Program.

  4. Structure of dehaloperoxidase B at 1.58 Å resolution and structural characterization of the AB dimer from Amphitrite ornata

    SciTech Connect

    de Serrano, Vesna; D; Antonio, Jennifer; Franzen, Stefan; Ghiladi, Reza A.

    2012-04-18

    As members of the globin superfamily, dehaloperoxidase (DHP) isoenzymes A and B from the marine annelid Amphitrite ornata possess hemoglobin function, but they also exhibit a biologically relevant peroxidase activity that is capable of converting 2,4,6-trihalophenols to the corresponding 2,6-dihaloquinones in the presence of hydrogen peroxide. Here, a comprehensive structural study of recombinant DHP B, both by itself and cocrystallized with isoenzyme A, using X-ray diffraction is presented. The structure of DHP B refined to 1.58 {angstrom} resolution exhibits the same distal histidine (His55) conformational flexibility as that observed in isoenzyme A, as well as additional changes to the distal and proximal hydrogen-bonding networks. Furthermore, preliminary characterization of the DHP AB heterodimer is presented, which exhibits differences in the AB interface that are not observed in the A-only or B-only homodimers. These structural investigations of DHP B provide insights that may relate to the mechanistic details of the H{sub 2}O{sub 2}-dependent oxidative dehalogenation reaction catalyzed by dehaloperoxidase, present a clearer description of the function of specific residues in DHP at the molecular level and lead to a better understanding of the paradigms of globin structure-function relationships.

  5. Structure of dehaloperoxidase B at 1.58 Å resolution and structural characterization of the AB dimer from Amphitrite ornata

    SciTech Connect

    Serrano, Vesna de; D’Antonio, Jennifer; Franzen, Stefan; Ghiladi, Reza A.

    2010-05-01

    The crystal structure of dehaloperoxidase (DHP) isoenzyme B from the terebellid polychaete A. ornata, which exhibits both hemoglobin and peroxidase functions, has been determined at 1.58 Å resolution. As members of the globin superfamily, dehaloperoxidase (DHP) isoenzymes A and B from the marine annelid Amphitrite ornata possess hemoglobin function, but they also exhibit a biologically relevant peroxidase activity that is capable of converting 2,4,6-trihalophenols to the corresponding 2,6-dihaloquinones in the presence of hydrogen peroxide. Here, a comprehensive structural study of recombinant DHP B, both by itself and cocrystallized with isoenzyme A, using X-ray diffraction is presented. The structure of DHP B refined to 1.58 Å resolution exhibits the same distal histidine (His55) conformational flexibility as that observed in isoenzyme A, as well as additional changes to the distal and proximal hydrogen-bonding networks. Furthermore, preliminary characterization of the DHP AB heterodimer is presented, which exhibits differences in the AB interface that are not observed in the A-only or B-only homodimers. These structural investigations of DHP B provide insights that may relate to the mechanistic details of the H{sub 2}O{sub 2}-dependent oxidative dehalogenation reaction catalyzed by dehaloperoxidase, present a clearer description of the function of specific residues in DHP at the molecular level and lead to a better understanding of the paradigms of globin structure–function relationships.

  6. PREFACE: Symposium 1: Advanced Structure Analysis and Characterization of Ceramic Materials

    NASA Astrophysics Data System (ADS)

    Yashima, Masatomo

    2011-05-01

    Preface to Symposium 1 (Advanced Structure Analysis and Characterization of Ceramic Materials) of the International Congress of Ceramics III, held 14-18 November 2010 in Osaka, Japan Remarkable developments have been made recently in the structural analysis and characterization of inorganic crystalline and amorphous materials, such as x-ray, neutron, synchrotron and electron diffraction, x-ray/neutron scattering, IR/Raman scattering, NMR, XAFS, first-principle calculations, computer simulations, Rietveld analysis, the maximum-entropy method, in situ measurements at high temperatures/pressures and electron/nuclear density analysis. These techniques enable scientists to study not only static and long-range periodic structures but also dynamic and short-/intermediate-range structures. Multi-scale characterization from the electron to micrometer levels is becoming increasingly important as a means of understanding phenomena at the interfaces, grain boundaries and surfaces of ceramic materials. This symposium has discussed the structures and structure/property relationships of various ceramic materials (electro, magnetic and optical ceramics; energy and environment related ceramics; bio-ceramics; ceramics for reliability secure society; traditional ceramics) through 38 oral presentations including 8 invited lectures and 49 posters. Best poster awards were given to six excellent poster presentations (Y-C Chen, Tokyo Institute of Technology; C-Y Chung, Tohoku University; T Stawski, University of Twente; Y Hirano, Nagoya Institute of Technology; B Bittova, Charles University Prague; Y Onodera, Kyoto University). I have enjoyed working with my friends in the ICC3 conference. I would like to express special thanks to other organizers: Professor Scott T Misture, Alfred University, USA, Professor Xiaolong Chen, Institute of Physics, CAS, China, Professor Takashi Ida, Nagoya Institute of Technology, Japan, Professor Isao Tanaka, Kyoto University, Japan. I also acknowledge the

  7. Structural characterization of wind-sheared turbulent flow using self-organized mapping

    NASA Astrophysics Data System (ADS)

    Scott, Nicholas V.; Handler, Robert A.

    2016-05-01

    A nonlinear cluster analysis algorithm is used to characterize the spatial structure of a wind-sheared turbulent flow obtained from the direct numerical simulation (DNS) of the three-dimensional temperature and momentum fields. The application of self-organizing mapping to DNS data for data reduction is utilized because of the dimensional similitude in structure between DNS data and remotely sensed hyperspectral and multispectral data where the technique has been used extensively. For the three Reynolds numbers of 150, 180, and 220 used in the DNS, self-organized mapping is successful in the extraction of boundary layer streaky structures from the turbulent temperature and momentum fields. In addition, it preserves the cross-wind scale structure of the streaks exhibited in both fields which loosely scale with the inverse of the Reynolds number. Self-organizing mapping of the along wind component of the helicity density shows a layer of the turbulence field which is spotty suggesting significant direct coupling between the large and small-scale turbulent structures. The spatial correlation of the temperature and momentum fields allows for the possibility of the remote extrapolation of the momentum structure from thermal structure.

  8. Quantitative characterization of the atomic-scale structure of oxyhydroxides in rusts formed on steel surfaces

    SciTech Connect

    Saito, M.; Suzuki, S. . E-mail: ssuzuki@tagen.tohoku.ac.jp; Kimura, M.; Suzuki, T.; Kihira, H.; Waseda, Y.

    2005-11-15

    Quantitative X-ray structural analysis coupled with anomalous X-ray scattering has been used for characterizing the atomic-scale structure of rust formed on steel surfaces. Samples were prepared from rust layers formed on the surfaces of two commercial steels. X-ray scattered intensity profiles of the two samples showed that the rusts consisted mainly of two types of ferric oxyhydroxide, {alpha}-FeOOH and {gamma}-FeOOH. The amounts of these rust components and the realistic atomic arrangements in the components were estimated by fitting both the ordinary and the environmental interference functions with a model structure calculated using the reverse Monte Carlo simulation technique. The two rust components were found to be the network structure formed by FeO{sub 6} octahedral units, the network structure itself deviating from the ideal case. The present results also suggest that the structural analysis method using anomalous X-ray scattering and the reverse Monte Carlo technique is very successful in determining the atomic-scale structure of rusts formed on the steel surfaces.

  9. Comparative metabolomics and structural characterizations illuminate colibactin pathway-dependent small molecules.

    PubMed

    Vizcaino, Maria I; Engel, Philipp; Trautman, Eric; Crawford, Jason M

    2014-07-01

    The gene cluster responsible for synthesis of the unknown molecule "colibactin" has been identified in mutualistic and pathogenic Escherichia coli. The pathway endows its producer with a long-term persistence phenotype in the human bowel, a probiotic activity used in the treatment of ulcerative colitis, and a carcinogenic activity under host inflammatory conditions. To date, functional small molecules from this pathway have not been reported. Here we implemented a comparative metabolomics and targeted structural network analyses approach to identify a catalog of small molecules dependent on the colibactin pathway from the meningitis isolate E. coli IHE3034 and the probiotic E. coli Nissle 1917. The structures of 10 pathway-dependent small molecules are proposed based on structural characterizations and network relationships. The network will provide a roadmap for the structural and functional elucidation of a variety of other small molecules encoded by the pathway. From the characterized small molecule set, in vitro bacterial growth inhibitory and mammalian CNS receptor antagonist activities are presented. PMID:24932672

  10. Structural and Enzymatic Characterization of the Phosphotriesterase OPHC2 from Pseudomonas pseudoalcaligenes

    PubMed Central

    Gonzalez, Daniel; Elias, Mikael; Chabriere, Eric

    2013-01-01

    Background Organophosphates (OPs) are neurotoxic compounds for which current methods of elimination are unsatisfactory; thus bio-remediation is considered as a promising alternative. Here we provide the structural and enzymatic characterization of the recently identified enzyme isolated from Pseudomonas pseudoalcaligenes dubbed OPHC2. OPHC2 belongs to the metallo-β-lactamase superfamily and exhibits an unusual thermal resistance and some OP degrading abilities. Principal findings The X-ray structure of OPHC2 has been solved at 2.1 Å resolution. The enzyme is roughly globular exhibiting a αβ/βα topology typical of the metallo-β-lactamase superfamily. Several structural determinants, such as an extended dimerization surface and an intramolecular disulfide bridge, common features in thermostable enzymes, are consistent with its high Tm (97.8°C). Additionally, we provide the enzymatic characterization of OPHC2 against a wide range of OPs, esters and lactones. Significance OPHC2 possesses a broad substrate activity spectrum, since it hydrolyzes various phosphotriesters, esters, and a lactone. Because of its organophosphorus hydrolase activity, and given its intrinsic thermostability, OPHC2 is an interesting candidate for the development of an OPs bio-decontaminant. Its X-ray structure shed light on its active site, and provides key information for the understanding of the substrate binding mode and catalysis. PMID:24223749

  11. Structural and dynamic characterization of eukaryotic gene regulatory protein domains in solution

    SciTech Connect

    Lee, A L

    1996-05-01

    Solution NMR was primarily used to characterize structure and dynamics in two different eukaryotic protein systems: the {delta}-Al-{var_epsilon} activation domain from c-jun and the Drosophila RNA-binding protein Sex-lethal. The second system is the Drosophila Sex-lethal (Sxl) protein, an RNA-binding protein which is the ``master switch`` in sex determination. Sxl contains two adjacent RNA-binding domains (RBDs) of the RNP consensus-type. The NMR spectrum of the second RBD (Sxl-RBD2) was assigned using multidimensional heteronuclear NMR, and an intermediate-resolution family of structures was calculated from primarily NOE distance restraints. The overall fold was determined to be similar to other RBDs: a {beta}{alpha}{beta}-{beta}{alpha}{beta} pattern of secondary structure, with the two helices packed against a 4-stranded anti-parallel {beta}-sheet. In addition {sup 15}N T{sub 1}, T{sub 2}, and {sup 15}N/{sup 1}H NOE relaxation measurements were carried out to characterize the backbone dynamics of Sxl-RBD2 in solution. RNA corresponding to the polypyrimidine tract of transformer pre-mRNA was generated and titrated into 3 different Sxl-RBD protein constructs. Combining Sxl-RBD1+2 (bht RBDs) with this RNA formed a specific, high affinity protein/RNA complex that is amenable to further NMR characterization. The backbone {sup 1}H, {sup 13}C, and {sup 15}N resonances of Sxl-RBD1+2 were assigned using a triple-resonance approach, and {sup 15}N relaxation experiments were carried out to characterize the backbone dynamics of this complex. The changes in chemical shift in Sxl-RBD1+2 upon binding RNA are observed using Sxl-RBD2 as a substitute for unbound Sxl-RBD1+2. This allowed the binding interface to be qualitatively mapped for the second domain.

  12. Characterization and crystal structure of lysine insensitive Corynebacterium glutamicum dihydrodipicolinate synthase (cDHDPS) protein

    SciTech Connect

    Rice, E.A.; Bannon, G.A.; Glenn, K.C.; Jeong, S.S.; Sturman, E.J.; Rydel, T.J.

    2008-11-21

    The lysine insensitive Corynebacterium glutamicum dihydrodipicolinate synthase enzyme (cDHDPS) was recently successfully introduced into maize plants to enhance the level of lysine in the grain. To better understand lysine insensitivity of the cDHDPS, we expressed, purified, kinetically characterized the protein, and solved its X-ray crystal structure. The cDHDPS enzyme has a fold and overall structure that is highly similar to other DHDPS proteins. A noteworthy feature of the active site is the evidence that the catalytic lysine residue forms a Schiff base adduct with pyruvate. Analyses of the cDHDPS structure in the vicinity of the putative binding site for S-lysine revealed that the allosteric binding site in the Escherichia coli DHDPS protein does not exist in cDHDPS due to three non-conservative amino acids substitutions, and this is likely why cDHDPS is not feedback inhibited by lysine.

  13. Solution-based growth and structural characterization of homo- and heterobranched semiconductor nanowires.

    PubMed

    Dong, Angang; Tang, Rui; Buhro, William E

    2007-10-10

    Colloidal homobranched ZnSe nanowires (NWs) and heterobranched CdSe-ZnSe NWs are successfully synthesized by combining a sequential seeding strategy with the solution-liquid-solid (SLS) growth process. We have developed an efficient approach to deposit secondary bismuth nanoparticles onto the NW backbone to induce the subsequent SLS branch growth. The density, length, and diameter of branches are rationally controlled by varying reaction conditions. Structural characterization reveals that crystalline branches grow epitaxially from the backbone in both homo- and heterobranched NWs. Two different branching structures are observed in the CdSe-ZnSe heterobranched NWs, owing to the phase admixture, i.e., cubic and hexagonal crystal structures, coexisting in the CdSe NW backbones. These branched NWs with well-designed architectures are expected to have potential as three-dimensional building blocks in the fabrication of nanoscale electronics and photonics.

  14. Novel aldehyde and thiosemicarbazone derivatives: Synthesis, spectroscopic characterization, structural studies and molecular docking studies

    NASA Astrophysics Data System (ADS)

    Karakurt, Tuncay; Tahtaci, Hakan; Subasi, Nuriye Tuna; Er, Mustafa; Ağar, Erbil

    2016-12-01

    In this study our purpose is that, synthesis and characterization of compounds containing the aldehyde and thiosemicarbazone groups and comparison of the theoretical results with the experimental results. The structures of all synthesized compounds were elucidated by IR, 1H NMR, 13C NMR, elemental analyses techniques. The structure of compound (4) (C9H8N4O2S) was also elucidated by X-ray diffraction analysis. In addition, the theoretical IR spectrum, 1H NMR and 13C NMR chemical shift values, frontier molecular orbital values (FMO) of these molecules were analyzed by using Becke-3- Lee-Yang-Parr (B3LYP) method with LanL2DZ basis set. Finally, molecular docking studies were performed on synthesized compounds using the 4DKI beta-lactam protein structure to determine the potential binding mode of inhibitors.

  15. Biochemical characterization and structural analysis of a bifunctional cellulase/xylanase from Clostridium thermocellum.

    PubMed

    Yuan, Shuo-Fu; Wu, Tzu-Hui; Lee, Hsiao-Lin; Hsieh, Han-Yu; Lin, Wen-Ling; Yang, Barbara; Chang, Chih-Kang; Li, Qian; Gao, Jian; Huang, Chun-Hsiang; Ho, Meng-Chiao; Guo, Rey-Ting; Liang, Po-Huang

    2015-02-27

    We expressed an active form of CtCel5E (a bifunctional cellulase/xylanase from Clostridium thermocellum), performed biochemical characterization, and determined its apo- and ligand-bound crystal structures. From the structures, Asn-93, His-168, His-169, Asn-208, Trp-347, and Asn-349 were shown to provide hydrogen-bonding/hydrophobic interactions with both ligands. Compared with the structures of TmCel5A, a bifunctional cellulase/mannanase homolog from Thermotoga maritima, a flexible loop region in CtCel5E is the key for discriminating substrates. Moreover, site-directed mutagenesis data confirmed that His-168 is essential for xylanase activity, and His-169 is more important for xylanase activity, whereas Asn-93, Asn-208, Tyr-270, Trp-347, and Asn-349 are critical for both activities. In contrast, F267A improves enzyme activities.

  16. Inflight Characterization of the Cassini Spacecraft Propellant Slosh and Structural Frequencies

    NASA Technical Reports Server (NTRS)

    Lee, Allan Y.; Stupik, Joan

    2015-01-01

    While there has been extensive theoretical and analytical research regarding the characterization of spacecraft propellant slosh and structural frequencies, there have been limited studies to compare the analytical predictions with measured flight data. This paper uses flight telemetry from the Cassini spacecraft to get estimates of high-g propellant slosh frequencies and the magnetometer boom frequency characteristics, and compares these values with those predicted by theoretical works. Most Cassini attitude control data are available at a telemetry frequency of 0.5 Hz. Moreover, liquid sloshing is attenuated by propellant management device and attitude controllers. Identification of slosh and structural frequency are made on a best-effort basis. This paper reviews the analytical approaches that were used to predict the Cassini propellant slosh frequencies. The predicted frequencies are then compared with those estimated using telemetry from selected Cassini burns where propellant sloshing was observed (such as the Saturn Orbit Insertion burn). Determination of the magnetometer boom structural frequency is also discussed.

  17. Biochemical Characterization and Structural Analysis of a Bifunctional Cellulase/Xylanase from Clostridium thermocellum*

    PubMed Central

    Yuan, Shuo-Fu; Wu, Tzu-Hui; Lee, Hsiao-Lin; Hsieh, Han-Yu; Lin, Wen-Ling; Yang, Barbara; Chang, Chih-Kang; Li, Qian; Gao, Jian; Huang, Chun-Hsiang; Ho, Meng-Chiao; Guo, Rey-Ting; Liang, Po-Huang

    2015-01-01

    We expressed an active form of CtCel5E (a bifunctional cellulase/xylanase from Clostridium thermocellum), performed biochemical characterization, and determined its apo- and ligand-bound crystal structures. From the structures, Asn-93, His-168, His-169, Asn-208, Trp-347, and Asn-349 were shown to provide hydrogen-bonding/hydrophobic interactions with both ligands. Compared with the structures of TmCel5A, a bifunctional cellulase/mannanase homolog from Thermotoga maritima, a flexible loop region in CtCel5E is the key for discriminating substrates. Moreover, site-directed mutagenesis data confirmed that His-168 is essential for xylanase activity, and His-169 is more important for xylanase activity, whereas Asn-93, Asn-208, Tyr-270, Trp-347, and Asn-349 are critical for both activities. In contrast, F267A improves enzyme activities. PMID:25575592

  18. Silicon dioxide hollow microspheres with porous composite structure: synthesis and characterization.

    PubMed

    Yan, Xiuli; Lei, Zhongli

    2011-10-15

    In this paper, a strategy for hollow porous silica microspheres with ideally flower structure is presented. SiO(2)/PAM hybrid composite microspheres with porous were synthesized by the reaction that the porous polyacrylamide (PAM) micro-gels immersed in tetraethoxysilane (TEOS) anhydrous alcohol solution and water in a moist atmosphere, with ammonium hydroxide as a catalyst. The SiO(2) hollow microspheres with porous were obtained after calcination of the composite microspheres at 550 °C for 4 h. The morphology, composition, and crystalline structure of the microspheres were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), thermo-gravimetric analysis (TGA), Fourier transform infrared spectroscopy (FI-IR), and X-ray diffraction (XRD), N(2) absorption analysis, respectively. The results indicated that the obtained hollow porous SiO(2) microspheres were a perfect flower structure.

  19. Raman spectroscopic characterization of the core-rim structure in reaction bonded boron carbide ceramics

    SciTech Connect

    Jannotti, Phillip; Subhash, Ghatu; Zheng, James Q.; Halls, Virginia; Karandikar, Prashant G.; Salamone, S.; Aghajanian, Michael K.

    2015-01-26

    Raman spectroscopy was used to characterize the microstructure of reaction bonded boron carbide ceramics. Compositional and structural gradation in the silicon-doped boron carbide phase (rim), which develops around the parent boron carbide region (core) due to the reaction between silicon and boron carbide, was evaluated using changes in Raman peak position and intensity. Peak shifting and intensity variation from the core to the rim region was attributed to changes in the boron carbide crystal structure based on experimental Raman observations and ab initio calculations reported in literature. The results were consistent with compositional analysis determined by energy dispersive spectroscopy. The Raman analysis revealed the substitution of silicon atoms first into the linear 3-atom chain, and then into icosahedral units of the boron carbide structure. Thus, micro-Raman spectroscopy provided a non-destructive means of identifying the preferential positions of Si atoms in the boron carbide lattice.

  20. Metal-organic frameworks: structure, properties, methods of synthesis and characterization

    NASA Astrophysics Data System (ADS)

    Butova, V. V.; Soldatov, M. A.; Guda, A. A.; Lomachenko, K. A.; Lamberti, C.

    2016-03-01

    This review deals with key methods of synthesis and characterization of metal-organic frameworks (MOFs). The modular structure affords a wide variety of MOFs with different active metal sites and organic linkers. These compounds represent a new stage of development of porous materials in which the pore size and the active site structure can be modified within wide limits. The set of experimental methods considered in this review is sufficient for studying the short-range and long-range order of the MOF crystal structure, determining the morphology of samples and elucidating the processes that occur at the active metal site in the course of chemical reactions. The interest in metal-organic frameworks results, first of all, from their numerous possible applications, ranging from gas separation and storage to chemical reactions within the pores. The bibliography includes 362 references.

  1. Structural characterization, electrochemical, photoluminescence and thermal properties of potassium ion-mediated coordination polymer.

    PubMed

    Ceyhan, Gökhan; Köse, Muhammet; Tümer, Mehmet; Dal, Hakan

    2015-05-01

    A polymeric potassium complex of p-nitrophenol was synthesized and characterized by analytical and spectroscopic techniques. Molecular structure of the complex was determined by single crystal X-ray diffraction study. X-ray structural data show that crystals contain polymeric K(+) complex of p-nitrophenol. Asymmetric unit consists of one p-nitrophenolate, one K(+) ion and one water molecule. All bond lengths and angles in the phenyl rings have normal Csp2-Csp2 values and are in the expected ranges. The p-nitrophenolate is close to planar with small distortions by some atoms. Each potassium ion in the polymeric structure is identical and eight-coordinate, bonded to four nitro, two phenolate oxygen atoms from five p-nitrophenolate ligands and two oxygen atoms from two water molecules. Electronic, electrochemical, photoluminescence and thermal properties of the complex were also investigated.

  2. Structural and Biochemical Characterization of AidC, a Quorum-Quenching Lactonase With Atypical Selectivity

    PubMed Central

    Mascarenhas, Romila; Thomas, Pei W.; Wu, Chun-Xiang; Nocek, Boguslaw P.; Hoang, Quyen Q.; Liu, Dali; Fast, Walter

    2015-01-01

    Quorum-quenching catalysts are of interest for potential application as biochemical tools to interrogate interbacterial communication pathways, as anti-biofouling agents, and as anti-infective agents in plants and animals. Herein, the structure and function of AidC, an N-acyl-L-homoserine (AHL) lactonase from Chryseobacterium, is characterized. Steady-state kinetics show that zinc-supplemented AidC is one of the most efficient wild-type quorum-quenching enzymes characterized to date, with a kcat/KM value of approximately 2 × 106 M−1s−1 for N-heptanoyl-L-homoserine lactone. The enzyme has stricter substrate selectivity and significantly lower KM values (ca. 50 μM for preferred substrates) than typical AHL lactonases (ca. > 1 mM). X-ray crystal structures of AidC alone, and with the product N-hexanoyl-L-homoserine were determined at resolutions of 1.09 and 1.67 Å, respectively. Each structure displays as a dimer, and dimeric oligiomerization was also observed in solution by size-exclusion chromatography coupled with multi-angle light scattering. The structures reveal two atypical features as compared to previously characterized AHL lactonases: a ‘kinked’ α-helix that forms part of a closed binding pocket which provides affinity and enforces selectivity for AHL substrates, and an active-site His substitution that is usually found in a homologous family of phosphodiesterases. Implications for the catalytic mechanism of AHL lactonases are discussed. PMID:26115006

  3. Structural and biochemical characterization of AidC, a quorum-quenching lactonase with atypical selectivity

    DOE PAGES

    Mascarenhas, Romila; Thomas, Pei W.; Wu, Chun -Xiang; Nocek, Boguslaw P.; Hoang, Quyen Q.; Liu, Dali; Fast, Walter

    2015-06-26

    Quorum-quenching catalysts are of interest for potential application as biochemical tools for interrogating interbacterial communication pathways, as antibiofouling agents, and as anti-infective agents in plants and animals. Herein, the structure and function of AidC, an N-acyl-l-homoserine lactone (AHL) lactonase from Chryseobacterium, is characterized. Steady-state kinetics show that zinc-supplemented AidC is the most efficient wild-type quorum-quenching enzymes characterized to date, with a kcat/KM value of approximately 2 × 106 M-1 s-1 for N-heptanoyl-l-homoserine lactone. The enzyme has stricter substrate selectivity and significantly lower KM values (ca. 50 μM for preferred substrates) compared to those of typical AHL lactonases (ca. >1 mM).more » X-ray crystal structures of AidC alone and with the product N-hexanoyl-l-homoserine were determined at resolutions of 1.09 and 1.67 Å, respectively. Each structure displays as a dimer, and dimeric oligiomerization was also observed in solution by size-exclusion chromatography coupled with multiangle light scattering. Lastly, the structures reveal two atypical features as compared to previously characterized AHL lactonases: a "kinked" α-helix that forms part of a closed binding pocket that provides affinity and enforces selectivity for AHL substrates and an active-site His substitution that is usually found in a homologous family of phosphodiesterases. We discuss implications for the catalytic mechanism of AHL lactonases.« less

  4. Structural and biochemical characterization of AidC, a quorum-quenching lactonase with atypical selectivity

    SciTech Connect

    Mascarenhas, Romila; Thomas, Pei W.; Wu, Chun -Xiang; Nocek, Boguslaw P.; Hoang, Quyen Q.; Liu, Dali; Fast, Walter

    2015-06-26

    Quorum-quenching catalysts are of interest for potential application as biochemical tools for interrogating interbacterial communication pathways, as antibiofouling agents, and as anti-infective agents in plants and animals. Herein, the structure and function of AidC, an N-acyl-l-homoserine lactone (AHL) lactonase from Chryseobacterium, is characterized. Steady-state kinetics show that zinc-supplemented AidC is the most efficient wild-type quorum-quenching enzymes characterized to date, with a kcat/KM value of approximately 2 × 106 M-1 s-1 for N-heptanoyl-l-homoserine lactone. The enzyme has stricter substrate selectivity and significantly lower KM values (ca. 50 μM for preferred substrates) compared to those of typical AHL lactonases (ca. >1 mM). X-ray crystal structures of AidC alone and with the product N-hexanoyl-l-homoserine were determined at resolutions of 1.09 and 1.67 Å, respectively. Each structure displays as a dimer, and dimeric oligiomerization was also observed in solution by size-exclusion chromatography coupled with multiangle light scattering. Lastly, the structures reveal two atypical features as compared to previously characterized AHL lactonases: a "kinked" α-helix that forms part of a closed binding pocket that provides affinity and enforces selectivity for AHL substrates and an active-site His substitution that is usually found in a homologous family of phosphodiesterases. We discuss implications for the catalytic mechanism of AHL lactonases.

  5. Structural characterization of the N-linked oligosaccharides from tomato fruit.

    PubMed

    Zeleny, R; Altmann, F; Praznik, W

    1999-05-01

    The primary structures of the N-linked oligosaccharides from tomato fruit (Lycopersicon esculentum) have been elucidated. For the isolation of the protein fraction, two procedures were employed alternatively: a low temperature acetone powder method and ammonium sulfate precipitation of the tomato extract. After peptic digestion, the glycopeptides were purified by cation-exchange chromatography; the oligosaccharides were released by N-glycosidase A and fluorescently labelled with 2-aminopyridine. Structural characterization was accomplished by means of two-dimensional HPLC in combination with exoglycosidase digestions and MALDI-TOF mass spectrometry. Two varieties as well as two stages of ripening were investigated. In all the samples, the same sixteen N-glycosidic structures were detected; the two most abundant glycans showed identical properties to those of the major N-linked oligosaccharides of horseradish peroxidase and pineapple stem bromelain, respectively and accounted for about 65-78% of the total glycan amount; oligomannosidic glycans occurred only in small quantities (3-9%). The majority of the N-glycans were beta 1,2-xylosylated and carried an alpha 1,3-fucose residue linked to the terminal N-acetylglucosamine. This structural element contributes to cross-reactions among non-related glycoproteins and has been shown to be an IgE-reactive determinant (Tretter, Altmann, Kubelka, März, & Becker, 1993). The presented study gives a possible structural explanation for reported immunological cross-reactivities between tomato and grass pollen extracts due to carbohydrate IgE epitopes (Petersen, Vieths, Aulepp, Schlaak, & Becker, 1996), thereby demonstrating the importance of the structural characterization of plant N-glycans for a more reliable interpretation of immunological data. PMID:10365448

  6. A new method for the characterization of micro-/nano-periodic structures based on microscopic Moiré fringes.

    PubMed

    Wu, Dan; Xie, Huimin; Tang, Minjin; Hu, Zhenxing

    2014-01-01

    Linewidth and opening ratio (ratio of linewidth to period) are important parameters in characterizing micro-/nano-periodic and quasi-periodic structures. Periodic structures are conventionally characterized by the direct observation of specimens under a microscope. However, the field of view is relatively small, and only certain details can be acquired under a microscope. Moreover, the non-uniformity of the linewidth in quasi-periodic structures cannot be detected. This paper proposes a new characterization method for determining the linewidth and opening ratio of periodic structures based on Moiré fringe analysis. This method has the advantage of full-field characterization of the linewidth of micro-/nano-structures over a larger area than that afforded by direct observation. To validate the method, the linewidth of scanning electron microscope (SEM) scan lines was first calibrated with a standard grating. Next, a microperiodic structure with known geometry was characterized using this calibrated SEM system. The results indicate that the proposed method is simple and effective, indicating a potential approach for the characterization of gratings over large areas. This technique can be extended to various high-power scanning microscopes to characterize micro-/nano-structures.

  7. Structural characterization of new Schiff bases of sulfamethoxazole and sulfathiazole, their antibacterial activity and docking computation with DHPS protein structure.

    PubMed

    Mondal, Sudipa; Mandal, Santi M; Mondal, Tapan Kumar; Sinha, Chittaranjan

    2015-01-01

    New Schiff bases (1, 2) of substituted salicylaldehydes and sulfamethoxazole (SMX)/sulfathiazole (STZ) are synthesized and characterized by elemental analysis and spectroscopic data. Single crystal X-ray structure of one of the compounds (E)-4-((3,5-dichloro-2-hydroxybenzylidene)amino)-N-(5-methylisoxazol-3-yl)benzenesulfonamide (1c) has been determined. Antimicrobial activities of the Schiff bases and parent sulfonamides (SMX, STZ) have been examined against several Gram-positive and Gram-negative bacteria and sulfonamide resistant pathogens; the lowest MIC is observed for (E)-4-((3,5-dichloro-2-hydroxybenzylidene)amino)-N-(thiazol-2-yl)benzene sulfonamide (2c) (8.0 μg mL(-1)) and (E)-4-((3,5-dichloro-2-hydroxybenzylidene)amino)-N-(5-methylisoxazol-3-yl)benzene sulfonamide (1c) (16.0 μg mL(-1)) against sulfonamide resistant pathogens. DFT optimized structures of the Schiff bases have been used to carry out molecular docking studies with DHPS (dihydropteroate synthase) protein structure (downloaded from Protein Data Bank) using Discovery Studio 3.5 to find the most preferred binding mode of the ligand inside the protein cavity. The theoretical data have been well correlated with the experimental results. Cell viability assay and ADMET studies predict that 1c and 2c have good drug like characters. PMID:26056977

  8. Structural characterization of new Schiff bases of sulfamethoxazole and sulfathiazole, their antibacterial activity and docking computation with DHPS protein structure.

    PubMed

    Mondal, Sudipa; Mandal, Santi M; Mondal, Tapan Kumar; Sinha, Chittaranjan

    2015-01-01

    New Schiff bases (1, 2) of substituted salicylaldehydes and sulfamethoxazole (SMX)/sulfathiazole (STZ) are synthesized and characterized by elemental analysis and spectroscopic data. Single crystal X-ray structure of one of the compounds (E)-4-((3,5-dichloro-2-hydroxybenzylidene)amino)-N-(5-methylisoxazol-3-yl)benzenesulfonamide (1c) has been determined. Antimicrobial activities of the Schiff bases and parent sulfonamides (SMX, STZ) have been examined against several Gram-positive and Gram-negative bacteria and sulfonamide resistant pathogens; the lowest MIC is observed for (E)-4-((3,5-dichloro-2-hydroxybenzylidene)amino)-N-(thiazol-2-yl)benzene sulfonamide (2c) (8.0 μg mL(-1)) and (E)-4-((3,5-dichloro-2-hydroxybenzylidene)amino)-N-(5-methylisoxazol-3-yl)benzene sulfonamide (1c) (16.0 μg mL(-1)) against sulfonamide resistant pathogens. DFT optimized structures of the Schiff bases have been used to carry out molecular docking studies with DHPS (dihydropteroate synthase) protein structure (downloaded from Protein Data Bank) using Discovery Studio 3.5 to find the most preferred binding mode of the ligand inside the protein cavity. The theoretical data have been well correlated with the experimental results. Cell viability assay and ADMET studies predict that 1c and 2c have good drug like characters.

  9. Predicting X-ray absorption spectra of semiconducting polymers for electronic structure and morphology characterization

    NASA Astrophysics Data System (ADS)

    Su, Gregory; Patel, Shrayesh; Pemmaraju, C. Das; Kramer, Edward; Prendergast, David; Chabinyc, Michael

    2015-03-01

    Core-level X-ray absorption spectroscopy (XAS) reveals important information on the electronic structure of materials and plays a key role in morphology characterization. Semiconducting polymers are the active component in many organic electronics. Their electronic properties are critically linked to device performance, and a proper understanding of semiconducting polymer XAS is crucial. Techniques such as resonant X-ray scattering rely on core-level transitions to gain materials contrast and probe orientational order. However, it is difficult to identify these transitions based on experiments alone, and complementary simulations are required. We show that first-principles calculations can capture the essential features of experimental XAS of semiconducting polymers, and provide insight into which molecular model, such as oligomers or periodic boundary conditions, are best suited for XAS calculations. Simulated XAS can reveal contributions from individual atoms and be used to visualize molecular orbitals. This allows for improved characterization of molecular orientation and scattering analysis. These predictions lay the groundwork for understanding how chemical makeup is linked to electronic structure, and to properly utilize experiments to characterize semiconducting polymers.

  10. Structural Characterization of Melanin Pigments from Commercial Preparations of the Edible Mushroom Auricularia auricula.

    PubMed

    Prados-Rosales, Rafael; Toriola, Stacy; Nakouzi, Antonio; Chatterjee, Subhasish; Stark, Ruth; Gerfen, Gary; Tumpowsky, Paul; Dadachova, Ekaterina; Casadevall, Arturo

    2015-08-26

    Many of the most widely consumed edible mushrooms are pigmented, and these have been associated with some beneficial health effects. Nevertheless, the majority of the reported compounds associated with these desirable properties are non-pigmented. We have previously reported that melanin pigment from the edible mushroom Auricularia auricula can protect mice against ionizing radiation, although no physicochemical characterization was reported. Consequently, in this study we have characterized commercial A. auricula mushroom preparations for melanin content and carried out structural characterization of isolated insoluble melanin materials using a panel of sophisticated spectroscopic and physical/imaging techniques. Our results show that approximately 10% of the dry mass of A. auricula is melanin and that the pigment has physicochemical properties consistent with those of eumelanins, including hosting a stable free radical population. Electron microscopy studies show that melanin is associated with the mushroom cell wall in a manner similar to that of melanin from the model fungus C. neoformans. Elemental analysis of melanin indicated C, H, and N ratios consistent with 5,6-dihydroxyindole-2-carboxylic acid/5,6-dihydroxyindole and 1,8-dihydroxynaphthalene eumelanin. Validation of the identity of the isolated product as melanin was achieved by EPR analysis. A. auricula melanin manifested structural differences, relative to the C. neoformans melanin, with regard to the variable proportions of alkyl chains or oxygenated carbons. Given the necessity for new oral and inexpensive radioprotective materials coupled with the commercial availability of A. auricula mushrooms, this product may represent an excellent source of edible melanin.

  11. Structural Characterization of the ATPase Reaction Cycle of Endosomal AAA Protein Vps4

    SciTech Connect

    Xiao, Junyu; Xia, Hengchuan; Yoshino-Koh, Kae; Zhou, Jiahai; Xu, Zhaohui

    2008-12-12

    The multivesicular body (MVB) pathway functions in multiple cellular processes including cell surface receptor down-regulation and viral budding from host cells. An important step in the MVB pathway is the correct sorting of cargo molecules, which requires the assembly and disassembly of endosomal sorting complexes required for transport (ESCRTs) on the endosomal membrane. Disassembly of the ESCRTs is catalyzed by ATPase associated with various cellular activities (AAA) protein Vps4. Vps4 contains a single AAA domain and undergoes ATP-dependent quaternary structural change to disassemble the ESCRTs. Structural and biochemical analyses of the Vps4 ATPase reaction cycle are reported here. Crystal structures of Saccharomyces cerevisiae Vps4 in both the nucleotide-free form and the ADP-bound form provide the first structural view illustrating how nucleotide binding might induce conformational changes within Vps4 that lead to oligomerization and binding to its substrate ESCRT-III subunits. In contrast to previous models, characterization of the Vps4 structure now supports a model where the ground state of Vps4 in the ATPase reaction cycle is predominantly a monomer and the activated state is a dodecamer. Comparison with a previously reported human VPS4B structure suggests that Vps4 functions in the MVB pathway via a highly conserved mechanism supported by similar protein-protein interactions during its ATPase reaction cycle.

  12. Hierarchical structure observation and nanoindentation size effect characterization for a limnetic shell

    NASA Astrophysics Data System (ADS)

    Song, Jingru; Fan, Cuncai; Ma, Hansong; Wei, Yueguang

    2015-06-01

    In the present research, hierarchical structure observation and mechanical property characterization for a type of biomaterial are carried out. The investigated biomaterial is Hyriopsis cumingii, a typical limnetic shell, which consists of two different structural layers, a prismatic "pillar" structure and a nacreous "brick and mortar" structure. The prismatic layer looks like a "pillar forest" with variation-section pillars sized on the order of several tens of microns. The nacreous material looks like a "brick wall" with bricks sized on the order of several microns. Both pillars and bricks are composed of nanoparticles. The mechanical properties of the hierarchical biomaterial are measured by using the nanoindentation test. Hardness and modulus are measured for both the nacre layer and the prismatic layer, respectively. The nanoindentation size effects for the hierarchical structural materials are investigated experimentally. The results show that the prismatic nanostructured material has a higher stiffness and hardness than the nacre nanostructured material. In addition, the nanoindentation size effects for the hierarchical structural materials are described theoretically, by using the trans-scale mechanics theory considering both strain gradient effect and the surface/interface effect. The modeling results are consistent with experimental ones.

  13. Mass spectrometric peptide mapping analysis and structural characterization of dihydrodiol dehydrogenase isoenzymes.

    PubMed Central

    Gauss, C; Klein, J; Post, K; Suckau, D; Schneider, K; Thomas, H; Oesch, F; Przybylski, M

    1990-01-01

    The direct molecular weight determination and structural analysis of polypeptides and peptide mixtures have become amenable by the recent development of fast atom bombardment (FABMS) and 252Cf-plasma desorption (PDMS) mass spectrometry. FABMS and PDMS peptide mapping, i.e., the direct analysis of peptide mixtures resulting from proteolytic digestion, have been developed as powerful methods for the structural characterization of epoxide-metabolizing isoenzymes. The major advantage of this approach is provided by the selectivity of the endoproteolytic cleavage, combined with the specific and accurate molecular weight determination of complex digest mixtures containing peptides up to several thousands daltons in size. Furthermore, the mass spectrometric peptide mapping analysis can be combined with a range of protein-chemical modification reactions and with sequential degradation such as by carboxypeptidases. Both FABMS and PDMS peptide mapping have already been successfully applied to the structural differentiation of glutathione transferase and epoxide hydrolase isoenzymes in cases where references sequence data for at least one isoenzyme form was available. In the application described here, for a series of dihydrodiol dehydrogenase (DDH) isoenzymes with hitherto undetermined primary structures, a direct correlation between the structural differentiation from peptide mapping data and differences in their substrate specificities could be demonstrated. The mass spectrometric peptide mapping analysis of isoenzymes proved to be an efficient basis for the elucidation of the structure of one major DDH isoenzyme form; partial sequence data for this protein are reported. PMID:2272334

  14. Non-destructive testing for the structures and civil infrastructures characterization

    NASA Astrophysics Data System (ADS)

    Capozzoli, L.; Rizzo, E.

    2012-04-01

    This work evaluates the ability of non-conventional NDT techniques such as GPR, geoelectrical method and conventional ones such as infrared thermography (IRT) and sonic test for the characterization of building structures in laboratory and in-situ. Moreover, the integration of the different techniques were evaluated in order to reduce the degree of uncertainties associated. The presence of electromagnetic, resistivity or thermal anomalies in the behavior may be related to the presence of defects, crack, decay or moisture. The research was conducted in two phases: the first phase was performed in laboratory and the second one mainly in the field work. The laboratory experiments proceeded to calibrate the geophysical techniques GPR and geoelectrical method on building structures. A multi-layer structure was reconstructed in laboratory, in order to simulate a back-bridge: asphalt, reinforced concrete, sand and gravel layers. In the deep sandy layer, PVC, aluminum and steel pipes were introduced. This structure has also been brought to crack in a predetermined area and hidden internal fractures were investigated. GPR has allowed to characterize the panel in a non-invasive mode; radar maps were developed using various algorithms during post-process about 2D maps and 3D models with aerial acquisition of 400 MHz, 900MHz, 1500MHz, 2000MHz. Geoelectrical testing was performed with a network of 25 electrodes spaced at mutual distance of 5 cm. Two different configurations were used dipole-dipole and pole-dipole approaches. In the second phase, we proceeded to the analysis of pre-tensioned concrete in order to detect the possible presence of criticality in the structure. For this purpose by GPR 2GHz antenna, a '70 years precast bridge characterized by a high state of decay was studied; then were also analyzed a pillar and a beam of recent production directly into the processing plant. Moreover, results obtained using GPR were compared with those obtained through the use of

  15. Integrating structural and functional connectivity to characterize sediment dynamics in a small Alpine catchment

    NASA Astrophysics Data System (ADS)

    Cavalli, Marco; Crema, Stefano; Blok, Michiel; Lucía, Ana; Comiti, Francesco; Marchi, Lorenzo; Keesstra, Saskia

    2016-04-01

    Sediment connectivity can be regarded as a descriptor of the internal linkages between different landscape components within a catchment. The recent focus of the scientific community on connectivity related topics, both concerning hydrological and sediment connectivity, stresses the importance of understanding the main active pathways for a better estimation of energy and matter transfer at catchment scale. This task can be addressed using topography-based indices that analyse the linkages between landscape units. This approach to characterize connectivity is known as structural connectivity. The main limitation of structural connectivity is that it does not account for the processes driving sediment and energy fluxes (i.e., functional connectivity). In this work the integration between structural and functional approaches is proposed for characterizing sediment connectivity in mountain catchments. The structural approach, based on a topography-based sediment connectivity index, was used for assessing hillslope-to-channel connectivity. Since field data on processes driving sediment transport along the channel network are available, a functional approach has been devised to estimate within-channel connectivity. An index of unit stream power computed from the hydraulic properties of the channel (i.e., discharge, slope and channel width) has been compared with the critical unit stream power computed from incipient motion thresholds derived from field data to identify the cells of the Digital Terrain Model (DTM) in which sediment can be mobilized under near-bankfull conditions. The index expressing the within-channel connectivity is given by the length of the reaches consisting of contiguous cells that exceed the critical unit stream power. During high-magnitude floods, when unit stream power values exceed the threshold for incipient motion, channels experience an increase in both hydrological and sediment connectivity. The proposed index characterizes those sections

  16. Joint application of non-invasive techniques to characterize the dynamic behaviuor of engineering structures

    NASA Astrophysics Data System (ADS)

    Gallipoli, M. R.; Perrone, A.; Stabile, T. A.; Ponzo, F. C.; Ditommaso, R.

    2012-04-01

    The systematic monitoring of strategic civil infrastructures such as bridges, large dams or high-rise buildings in order to ensure their structural stability is a strategic issue particularly in earthquake-prone regions. Nevertheless, in areas less exposed to seismic hazard, the monitoring is also an important tool for civil engineers, for instance if they have to deal with structures exposed to heavy operational demands for extended periods of time and whose structural integrity might be in question or at risk. A continuous monitoring of such structures allows the identification of their fundamental response characteristics and the changes of these over time, the latter representing indicators for potential structural degradation. The aim of this paper is the estimation of fundamental dynamic parameters of some civil infrastructures by the joint application of fast executable, non-invasive techniques such as the Ambient Noise Standard Spectral Ratio, and Ground-Based microwave Radar Interferometer techniques. The joint approach combine conventional, non-conventional and innovative techniques in order to set up a non destructive evaluation procedure allowing for a multi-sensing monitoring at a multi-scale and multi-depth levels (i.e. with different degrees of spatial resolution and different subsurface depths). In particular, techniques based on ambient vibration recordings have become a popular tool for characterizing the seismic response and state-of-health of strategic civil infrastructure. The primary advantage of these approaches lies in the fact that no transient earthquake signals or even active excitation of the structure under investigation are required. The microwave interferometry radar technology, it has proven to be a powerful remote sensing tool for vibration measurement of structures, such as bridge, heritage architectural structures, vibrating stay cables, and engineering structures. The main advantage of this radar technique is the possibility to

  17. Characterizing conserved structural contacts by pair-wise relative contacts and relative packing groups.

    PubMed

    Holmes, J Bradley; Tsai, Jerry

    2005-12-01

    To adequately deal with the inherent complexity of interactions between protein side-chains, we develop and describe here a novel method for characterizing protein packing within a fold family. Instead of approaching side-chain interactions absolutely from one residue to another, we instead consider the relative interactions of contacting residue pairs. The basic element, the pair-wise relative contact, is constructed from a sequence alignment and contact analysis of a set of structures and consists of a cluster of similarly oriented, interacting, side-chain pairs. To demonstrate this construct's usefulness in analyzing protein structure, we used the pair-wise relative contacts to analyze two sets of protein structures as defined by SCOP: the diverse globin-like superfamily (126 structures) and the more uniform heme binding globin family (a 94 structure subset of the globin-like superfamily). The superfamily structure set produced 1266 unique pair-wise relative contacts, whereas the family structure subset gave 1001 unique pair-wise relative contacts. For both sets, we show that these constructs can be used to accurately and automatically differentiate between fold classes. Furthermore, these pair-wise relative contacts correlate well with sequence identity and thus provide a direct relationship between changes in sequence and changes in structure. To capture the complexity of protein packing, these pair-wise relative contacts can be superimposed around a single residue to create a multi-body construct called a relative packing group. Construction of convex hulls around the individual packing groups provides a measure of the variation in packing around a residue and defines an approximate volume of space occupied by the groups interacting with a residue. We find that these relative packing groups are useful in understanding the structural quality of sequence or structure alignments. Moreover, they provide context to calculate a value for structural randomness

  18. Benzocyclobutene as Substrate Material for Planar Millimeter-Wave Structures: Dielectric Characterization and Application

    NASA Astrophysics Data System (ADS)

    Costanzo, Sandra; Venneri, Ignazio; di Massa, Giuseppe; Borgia, Antonio

    2010-01-01

    The application of benzocyclobutene (BCB) polymer as dielectric substrate material for millimeter-wave microstrip structures is investigated in this paper to face the problem of large losses due to standard dielectrics in the high microwave range. Dielectric properties of BCB are characterized from S-parameter measurements on a conductor-backed coplanar waveguide (CBCPW) using the polymer as substrate material. Excellent features, with a low loss tangent and a stable dielectric constant, are demonstrated within the measurement range from 11 GHz to 65 GHz. As a validation of BCB high frequency performances, the design and experimental characterization of a V-band array on BCB substrate is presented. Measurement results on both matching and radiation characteristics of the millimeter-wave array are discussed.

  19. The Preparation and Structural Characterization of Three Structural Types of Gallium Compounds Derived from Gallium (II) Chloride

    NASA Technical Reports Server (NTRS)

    Gordon, Edward M.; Hepp, Aloysius F.; Duraj. Stan A.; Habash, Tuhfeh S.; Fanwick, Phillip E.; Schupp, John D.; Eckles, William E.; Long, Shawn

    1997-01-01

    The three compounds Ga2Cl4(4-mepy)2 (1),[GaCl2(4-mepy)4]GaCl4x1/2(4-mepy); (2) and GaCl2(4-mepy)2(S2CNEt2); (3) (4-mepy= 4-methylpyridine) have been prepared from reactions of gallium (II) chloride in 4-methylpyridine and characterized by single-crystal X-ray analysis. Small variations in the reaction conditions for gallium(II) chloride can produce crystals with substantially different structural properties. The three compounds described here encompass a neutral gallium(II) dimer in which each gallium is four-coordinate, an ionic compound containing both anionic and cationic gallium complex ions with different coordination numbers and a neutral six-coordinate heteroleptic

  20. Advanced analysis of complex seismic waveforms to characterize the subsurface Earth structure

    NASA Astrophysics Data System (ADS)

    Jia, Tianxia

    2011-12-01

    This thesis includes three major parts, (1) Body wave analysis of mantle structure under the Calabria slab, (2) Spatial Average Coherency (SPAC) analysis of microtremor to characterize the subsurface structure in urban areas, and (3) Surface wave dispersion inversion for shear wave velocity structure. Although these three projects apply different techniques and investigate different parts of the Earth, their aims are the same, which is to better understand and characterize the subsurface Earth structure by analyzing complex seismic waveforms that are recorded on the Earth surface. My first project is body wave analysis of mantle structure under the Calabria slab. Its aim is to better understand the subduction structure of the Calabria slab by analyzing seismograms generated by natural earthquakes. The rollback and subduction of the Calabrian Arc beneath the southern Tyrrhenian Sea is a case study of slab morphology and slab-mantle interactions at short spatial scale. I analyzed the seismograms traversing the Calabrian slab and upper mantle wedge under the southern Tyrrhenian Sea through body wave dispersion, scattering and attenuation, which are recorded during the PASSCAL CAT/SCAN experiment. Compressional body waves exhibit dispersion correlating with slab paths, which is high-frequency components arrivals being delayed relative to low-frequency components. Body wave scattering and attenuation are also spatially correlated with slab paths. I used this correlation to estimate the positions of slab boundaries, and further suggested that the observed spatial variation in near-slab attenuation could be ascribed to mantle flow patterns around the slab. My second project is Spatial Average Coherency (SPAC) analysis of microtremors for subsurface structure characterization. Shear-wave velocity (Vs) information in soil and rock has been recognized as a critical parameter for site-specific ground motion prediction study, which is highly necessary for urban areas located

  1. Mechanical and structural characterizations of gamma- and alpha-alumina nanofibers

    SciTech Connect

    Vahtrus, Mikk; Umalas, Madis; Polyakov, Boris; Dorogin, Leonid; Saar, Rando; Tamme, Maret; Saal, Kristjan; Lõhmus, Rünno; Vlassov, Sergei

    2015-09-15

    We investigate the applicability of alumina nanofibers as a potential reinforcement material in ceramic matrix compounds by comparing the mechanical properties of individual nanofibers before and after annealing at 1400 °C. Mechanical testing is performed inside a scanning electron microscope (SEM), which enables observation in real time of the deformation and fracture of the fibers under loading, thereby providing a close-up inspection of the freshly fractured area in vacuum. Improvement of both the Young's modulus and the breaking strength for annealed nanofibers is demonstrated. Mechanical testing is supplemented with the structural characterization of the fibers before and after annealing using SEM, transmission electron microscopy and X-ray diffraction methods. - Highlights: • Mechanical properties of individual alumina nanofibers were measured using in situ SEM cantilevered beam bending technique. • Improvement of mechanical properties of the alumina fibers after annealing at 1400 °C is demonstrated. • Formation of branched structures is demonstrated and their mechanical properties are studied. • XRD and electron microscopy were used for structural characterization of untreated and annealed nanofibers.

  2. Ion beam-based characterization of multicomponent oxide thin films and thin film layered structures

    SciTech Connect

    Krauss, A.R.; Rangaswamy, M.; Lin, Yuping; Gruen, D.M. ); Schultz, J.A. ); Schmidt, H.K. ); Chang, R.P.H. . Dept. of Materials Science)

    1992-01-01

    Fabrication of thin film layered structures of multi-component materials such as high temperature superconductors, ferroelectric and electro-optic materials, and alloy semiconductors, and the development of hybrid materials requires understanding of film growth and interface properties. For High Temperature Superconductors, the superconducting coherence length is extremely short (5--15 [Angstrom]), and fabrication of reliable devices will require control of film properties at extremely sharp interfaces; it will be necessary to verify the integrity of thin layers and layered structure devices over thicknesses comparable to the atomic layer spacing. Analytical techniques which probe the first 1--2 atomic layers are therefore necessary for in-situ characterization of relevant thin film growth processes. However, most surface-analytical techniques are sensitive to a region within 10--40 [Angstrom] of the surface and are physically incompatible with thin film deposition and are typically restricted to ultra high vacuum conditions. A review of ion beam-based analytical methods for the characterization of thin film and multi-layered thin film structures incorporating layers of multicomponent oxides is presented. Particular attention will be paid to the use of time-of-flight techniques based on the use of 1- 15 key ion beams which show potential for use as nondestructive, real-time, in-situ surface diagnostics for the growth of multicomponent metal and metal oxide thin films.

  3. Ion beam-based characterization of multicomponent oxide thin films and thin film layered structures

    SciTech Connect

    Krauss, A.R.; Rangaswamy, M.; Lin, Yuping; Gruen, D.M.; Schultz, J.A.; Schmidt, H.K.; Chang, R.P.H.

    1992-11-01

    Fabrication of thin film layered structures of multi-component materials such as high temperature superconductors, ferroelectric and electro-optic materials, and alloy semiconductors, and the development of hybrid materials requires understanding of film growth and interface properties. For High Temperature Superconductors, the superconducting coherence length is extremely short (5--15 {Angstrom}), and fabrication of reliable devices will require control of film properties at extremely sharp interfaces; it will be necessary to verify the integrity of thin layers and layered structure devices over thicknesses comparable to the atomic layer spacing. Analytical techniques which probe the first 1--2 atomic layers are therefore necessary for in-situ characterization of relevant thin film growth processes. However, most surface-analytical techniques are sensitive to a region within 10--40 {Angstrom} of the surface and are physically incompatible with thin film deposition and are typically restricted to ultra high vacuum conditions. A review of ion beam-based analytical methods for the characterization of thin film and multi-layered thin film structures incorporating layers of multicomponent oxides is presented. Particular attention will be paid to the use of time-of-flight techniques based on the use of 1- 15 key ion beams which show potential for use as nondestructive, real-time, in-situ surface diagnostics for the growth of multicomponent metal and metal oxide thin films.

  4. Layered rare earth hydroxides (LREHs): synthesis and structure characterization towards multifunctionality.

    PubMed

    Liang, Jianbo; Ma, Renzhi; Sasaki, Takayoshi

    2014-07-21

    Layered rare earth hydroxides (LREHs) represent a new family of layered host compounds that integrate attractive physicochemical properties of rare earth elements with the wide tunability of guest anions. The compounds have attracted significant research attention, and potential applications have been found in various fields such as optics, catalysis, bio-medicine and so on. In this perspective, we describe our recent progress in the synthesis, structure characterization, and development of functionalities of the LREH compounds. A unique homogeneous alkalization method, in which RE ions are precipitated from a solution containing RE salt, concentrated target anions and hexamethylenetetramine, has been employed to effectively produce highly crystalline LREH samples. A range of anionic forms including chloride-, nitrate-, sulfate- and organodisulfonate-series, have been synthesized and structurally characterized. Two types of cationic rare earth hydroxide layers, {[RE2(OH)5(H2O)2](+)}∞ for the chloride- and nitrate-series and {[RE(OH)2(H2O)](+)}∞ for the sulfate- and organodisulfonate-series, are classified. Unique dehydration/rehydration behaviors or thermal phase evolution of the LREH compounds have been revealed and discussed in relation to the crystal structures. An outlook for potential applications of LREH compounds as anion exchangers, precursors to unique functional oxides, and optical phosphors is described. PMID:24824303

  5. Biochemical and Structural Characterization of the Human TL1A Ectodomain

    SciTech Connect

    Zhan, C.; Yan, Q; Patskovsky, Y; Li, Z; Toro, R; Meyer, A; Cheng, H; Brenowitz, M; Nathenson, S; Almo, S

    2009-01-01

    TNF-like 1A (TL1A) is a newly described member of the TNF superfamily that is directly implicated in the pathogenesis of autoimmune diseases, including inflammatory bowel disease, atherosclerosis, and rheumatoid arthritis. We report the crystal structure of the human TL1A extracellular domain at a resolution of 2.5 {angstrom}, which reveals a jelly-roll fold typical of the TNF superfamily. This structural information, in combination with complementary mutagenesis and biochemical characterization, provides insights into the binding interface and the specificity of the interactions between TL1A and the DcR3 and DR3 receptors. These studies suggest that the mode of interaction between TL1A and DcR3 differs from other characterized TNF ligand/receptor complexes. In addition, we have generated functional TL1A mutants with altered disulfide bonding capability that exhibit enhanced solution properties, which will facilitate the production of materials for future cell-based and whole animal studies. In summary, these studies provide insights into the structure and function of TL1A and provide the basis for the rational manipulation of its interactions with cognate receptors.

  6. Structural characterization and aging of glassy pharmaceuticals made using acoustic levitation.

    PubMed

    Benmore, Chris J; Weber, J K R; Tailor, Amit N; Cherry, Brian R; Yarger, Jeffery L; Mou, Qiushi; Weber, Warner; Neuefeind, Joerg; Byrn, Stephen R

    2013-04-01

    Here, we report the structural characterization of several amorphous drugs made using the method of quenching molten droplets suspended in an acoustic levitator. (13) C NMR, X-ray, and neutron diffraction results are discussed for glassy cinnarizine, carbamazepine, miconazole nitrate, probucol, and clotrimazole. The (13) C NMR results did not find any change in chemical bonding induced by the amorphization process. High-energy X-ray diffraction results were used to characterize the ratio of crystalline to amorphous material present in the glasses over a period of 8 months. All the glasses were stable for at least 6 months except carbamazepine, which has a strong tendency to crystallize within a few months. Neutron and X-ray pair distribution function analyses were applied to the glassy materials, and the results were compared with their crystalline counterparts. The two diffraction techniques yielded similar results in most cases and identified distinct intramolecular and intermolecular correlations. The intramolecular scattering was calculated based on the crystal structure and fit to the measured X-ray structure factor. The resulting intermolecular pair distribution functions revealed broad-nearest and next-nearest neighbor molecule-molecule correlations. © 2013 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 102:1290-1300, 2013. PMID:23381910

  7. Detailed structural and biochemical characterization of the nexin-dynein regulatory complex

    PubMed Central

    Oda, Toshiyuki; Yanagisawa, Haruaki; Kikkawa, Masahide

    2015-01-01

    The nexin-dynein regulatory complex (N-DRC) forms a cross-bridge between the outer doublet microtubules of the axoneme and regulates dynein motor activity in cilia/flagella. Although the molecular composition and the three-dimensional structure of N-DRC have been studied using mutant strains lacking N-DRC subunits, more accurate approaches are necessary to characterize the structure and function of N-DRC. In this study, we precisely localized DRC1, DRC2, and DRC4 using cryo–electron tomography and structural labeling. All three N-DRC subunits had elongated conformations and spanned the length of N-DRC. Furthermore, we purified N-DRC and characterized its microtubule-binding properties. Purified N-DRC bound to the microtubule and partially inhibited microtubule sliding driven by the outer dynein arms (ODAs). Of interest, microtubule sliding was observed even in the presence of fourfold molar excess of N-DRC relative to ODA. These results provide insights into the role of N-DRC in generating the beating motions of cilia/flagella. PMID:25411337

  8. Structure activity characterization of Bordetella petrii lipid A, from environment to human isolates.

    PubMed

    Basheer, Soorej M; Bouchez, Valerie; Novikov, Alexey; Augusto, Luis A; Guiso, Nicole; Caroff, Martine

    2016-01-01

    Bordetella petrii, a facultative anaerobic species, is the only known member of the Bordetella genus with environmental origin. However it was also recently isolated from humans. The structures of the B. petrii lipid A moieties of the endotoxins were characterized here for the first time for an environmental strain and compared to that of human isolates. Characterization was achieved using chemical analyses, gas chromatography-mass spectrometry, and Matrix Assisted Laser Desorption Ionisation mass spectrometry. The analyses revealed that the different lipid A structures contain a common bisphosphorylated β-(1→6)-linked d-glucosamine disaccharide with hydroxytetradecanoic acid in amide as well at the C-3' in ester linkages. Similar to Bordetella pertussis and Bordetella bronchiseptica lipids A, the hydroxytetradecanoic acid at the C-2' position was substituted by tetradecanoic acid. Unlike B. pertussis, the hydroxytetradecanoic acid at the C-2 position was substituted with either 12:0 or 14:0 and/or their 2-OH forms. Depending on the environmental or human origin the structures differed in the length and degree of fatty acid acylation and impacted the IL-6 and TNF-α inflammatory responses tested. In one isolate we showed the presence at the C-3 position of the short-chain 10:0(3-OH), which according to our previous analyses is more characteristic of the human pathogens in the genus like B. pertussis and Bordetella parapertussis. PMID:26164553

  9. Structure activity characterization of Bordetella petrii lipid A, from environment to human isolates.

    PubMed

    Basheer, Soorej M; Bouchez, Valerie; Novikov, Alexey; Augusto, Luis A; Guiso, Nicole; Caroff, Martine

    2016-01-01

    Bordetella petrii, a facultative anaerobic species, is the only known member of the Bordetella genus with environmental origin. However it was also recently isolated from humans. The structures of the B. petrii lipid A moieties of the endotoxins were characterized here for the first time for an environmental strain and compared to that of human isolates. Characterization was achieved using chemical analyses, gas chromatography-mass spectrometry, and Matrix Assisted Laser Desorption Ionisation mass spectrometry. The analyses revealed that the different lipid A structures contain a common bisphosphorylated β-(1→6)-linked d-glucosamine disaccharide with hydroxytetradecanoic acid in amide as well at the C-3' in ester linkages. Similar to Bordetella pertussis and Bordetella bronchiseptica lipids A, the hydroxytetradecanoic acid at the C-2' position was substituted by tetradecanoic acid. Unlike B. pertussis, the hydroxytetradecanoic acid at the C-2 position was substituted with either 12:0 or 14:0 and/or their 2-OH forms. Depending on the environmental or human origin the structures differed in the length and degree of fatty acid acylation and impacted the IL-6 and TNF-α inflammatory responses tested. In one isolate we showed the presence at the C-3 position of the short-chain 10:0(3-OH), which according to our previous analyses is more characteristic of the human pathogens in the genus like B. pertussis and Bordetella parapertussis.

  10. [Spectrum characterization and fine structure of copper phthalocyanine-doped TiO2 microcavities].

    PubMed

    Liu, Cheng-lin; Zhang, Xin-yi; Zhong, Ju-hua; Zhu, Yi-hua; He, Bo; Wei, Shi-qiang

    2007-10-01

    Copper phthalocyanine-doped TiO2 microcavities were fabricated by chemistry method. Their spectrum characterization was studied by Fourier transform infrared (FTIR) and Raman spectroscopy, and their fine structure was analyzed by X-ray absorption fine structure (XAFS). The results show that there is interaction of copper phthalocyanine (CuPc) and TiO2 microcavities after TiO2 microcavities was doped with CuPc. For example, there is absorption at 900.76 cm(-1) in FTIR spectra, and the "red shift" of both OH vibration at 3392.75 cm(-1) and CH vibration at 2848.83 cm(-1). There exist definite peak shifts and intensity changes in infrared absorption in the C-C or C-N vibration in the planar phthalocyanine ring, the winding vibration of C-H inside and C-N outside plane of benzene ring. In Raman spectrum, there are 403.4, 592.1 and 679.1 cm(-1) characterized peaks of TiO2 in CuPc-doped TiO2 microcavities, but their wave-numbers show shifts to anatase TiO2. The vibration peaks at 1586.8 and 1525.6 cm(-1) show that there exists the composite material of CuPc and TiO2. These changes are related to the plane tropism of the molecule structure of copper phthalocyanine. XAFS showed tetrahedron TiO4 structure of Ti in TiO2 microcavities doped with copper phthalocyanine, and the changes of inner "medial distances" and the surface structure of TiO2 microcavities.

  11. Biochemical and structural characterization of polyphosphate kinase 2 from the intracellular pathogen Francisella tularensis

    PubMed Central

    Batten, Laura E.; Parnell, Alice E.; Wells, Neil J.; Murch, Amber L.; Oyston, Petra C. F.; Roach, Peter L.

    2015-01-01

    The metabolism of polyphosphate is important for the virulence of a wide range of pathogenic bacteria and the enzymes of polyphosphate metabolism have been proposed as an anti-bacterial target. In the intracellular pathogen Francisella tularensis, the product of the gene FTT1564 has been identified as a polyphosphate kinase from the polyphosphate kinase 2 (PPK2) family. The isogenic deletion mutant was defective for intracellular growth in macrophages and was attenuated in mice, indicating an important role for polyphosphate in the virulence of Francisella. Herein, we report the biochemical and structural characterization of F. tularensis polyphosphate kinase (FtPPK2) with a view to characterizing the enzyme as a novel target for inhibitors. Using an HPLC-based activity assay, the substrate specificity of FtPPK2 was found to include purine but not pyrimidine nts. The activity was also measured using 31P-NMR. FtPPK2 has been crystallized and the structure determined to 2.23 Å (1 Å=0.1 nm) resolution. The structure consists of a six-stranded parallel β-sheet surrounded by 12 α-helices, with a high degree of similarity to other members of the PPK2 family and the thymidylate kinase superfamily. Residues proposed to be important for substrate binding and catalysis have been identified in the structure, including a lid-loop and the conserved Walker A and B motifs. The ΔFTT1564 strain showed significantly increased sensitivity to a range of antibiotics in a manner independent of the mode of action of the antibiotic. This combination of biochemical, structural and microbiological data provide a sound foundation for future studies targeting the development of PPK2 small molecule inhibitors. PMID:26582818

  12. Structural and functional characterization of a plant S-nitrosoglutathione reductase from Solanum lycopersicum.

    PubMed

    Kubienová, Lucie; Kopečný, David; Tylichová, Martina; Briozzo, Pierre; Skopalová, Jana; Šebela, Marek; Navrátil, Milan; Tâche, Roselyne; Luhová, Lenka; Barroso, Juan B; Petřivalský, Marek

    2013-04-01

    S-nitrosoglutathione reductase (GSNOR), also known as S-(hydroxymethyl)glutathione (HMGSH) dehydrogenase, belongs to the large alcohol dehydrogenase superfamily, namely to the class III ADHs. GSNOR catalyses the oxidation of HMGSH to S-formylglutathione using a catalytic zinc and NAD(+) as a coenzyme. The enzyme also catalyses the NADH-dependent reduction of S-nitrosoglutathione (GSNO). In plants, GSNO has been suggested to serve as a nitric oxide (NO) reservoir locally or possibly as NO donor in distant cells and tissues. NO and NO-related molecules such as S-nitrosothiols (S-NOs) play a central role in the regulation of normal plant physiological processes and host defence. The enzyme thus participates in the cellular homeostasis of S-NOs and in the metabolism of reactive nitrogen species. Although GSNOR has recently been characterized from several organisms, this study represents the first detailed biochemical and structural characterization of a plant GSNOR, that from tomato (Solanum lycopersicum). SlGSNOR gene expression is higher in roots and stems compared to leaves of young plants. It is highly expressed in the pistil and stamens and in fruits during ripening. The enzyme is a dimer and preferentially catalyses reduction of GSNO while glutathione and S-methylglutathione behave as non-competitive inhibitors. Using NAD(+), the enzyme oxidizes HMGSH and other alcohols such as cinnamylalcohol, geraniol and ω-hydroxyfatty acids. The crystal structures of the apoenzyme, of the enzyme in complex with NAD(+) and in complex with NADH, solved up to 1.9 Å resolution, represent the first structures of a plant GSNOR. They confirm that the binding of the coenzyme is associated with the active site zinc movement and changes in its coordination. In comparison to the well characterized human GSNOR, plant GSNORs exhibit a difference in the composition of the anion-binding pocket, which negatively influences the affinity for the carboxyl group of ω-hydroxyfatty acids. PMID

  13. Genome-wide characterization of genetic diversity and population structure in Secale

    PubMed Central

    2014-01-01

    Background Numerous rye accessions are stored in ex situ genebanks worldwide. Little is known about the extent of genetic diversity contained in any of them and its relation to contemporary varieties, since to date rye genetic diversity studies had a very limited scope, analyzing few loci and/ or few accessions. Development of high throughput genotyping methods for rye opened the possibility for genome wide characterizations of large accessions sets. In this study we used 1054 Diversity Array Technology (DArT) markers with defined chromosomal location to characterize genetic diversity and population structure in a collection of 379 rye accessions including wild species, landraces, cultivated materials, historical and contemporary rye varieties. Results Average genetic similarity (GS) coefficients and average polymorphic information content (PIC) values varied among chromosomes. Comparison of chromosome specific average GS within and between germplasm sub-groups indicated regions of chromosomes 1R and 4R as being targeted by selection in current breeding programs. Bayesian clustering, principal coordinate analysis and Neighbor Joining clustering demonstrated that source and improvement status contributed significantly to the structure observed in the analyzed set of Secale germplasm. We revealed a relatively limited diversity in improved rye accessions, both historical and contemporary, as well as lack of correlation between clustering of improved accessions and geographic origin, suggesting common genetic background of rye accessions from diverse geographic regions and extensive germplasm exchange. Moreover, contemporary varieties were distinct from the remaining accessions. Conclusions Our results point to an influence of reproduction methods on the observed diversity patterns and indicate potential of ex situ collections for broadening the genetic diversity in rye breeding programs. Obtained data show that DArT markers provide a realistic picture of the genetic

  14. Synthesis, structure, characterization and fluorescent properties of Ag+ complexes with extended π⋯π interactions

    NASA Astrophysics Data System (ADS)

    Huang, Ting-Hong; Yan, Jie; Yang, Hu; Qiang, Liu; Du, Huai-Ming

    2015-12-01

    Two mixed-ligand Ag (I) complexes, [Ag2(Phterpy)2(NO3)2(dppe)]·CH3CN (1) and [Ag4(Phterpy)2(NO3)2(dppp)2](NO3)2·6H2O (2) (dppe = 1, 2-bis (diphenylphosphino) ethane, dppp = 1, 3-bis (diphenylphosphino) propane, Phterpy = 4‧-phenyl-2, 2‧:6‧, 2″-terpyridine), have been synthesized and structurally characterized by IR, 1H-NMR, 31P-NMR, elemental analysis and X-ray crystal structure analysis. Structural analysis reveals that the change of bridging ligands from dppe to dppp lead to the formation of centrosymmetric cations [Ag2(Phterpy)2(NO3)2(dppe)] and [Ag4(Phterpy)2 (NO3)2(dppp)2]2+, especially complex 2 containing two independent centrosymmetric tetramers with the central (obligate) Ag2O2 planes. Complexes 1 and 2 consist of the 1D infinite chains, with different variations in π-stacking patterns. Crystal structure of 1 contains 1D infinite chains constructed by π⋯π interactions between Phterpy, while 2 is built by π⋯π interaction of phenylene rings from dppp. All these reveal that the change of phosphine ligands might be the key of construction of different types of polynuclear structures and 1D π-stacking chain. Moreover, the solid-state emission spectra of complexes 1 and 2 display broad emission bands at 420-600 nm.

  15. Characterization of the Local Structure in Liquid Water by Various Order Parameters

    PubMed Central

    2015-01-01

    A wide range of geometric order parameters have been suggested to characterize the local structure of liquid water and its tetrahedral arrangement, but their respective merits have remained elusive. Here, we consider a series of popular order parameters and analyze molecular dynamics simulations of water, in the bulk and in the hydration shell of a hydrophobic solute, at 298 and 260 K. We show that these parameters are weakly correlated and probe different distortions, for example the angular versus radial disorders. We first combine these complementary descriptions to analyze the structural rearrangements leading to the density maximum in liquid water. Our results reveal no sign of a heterogeneous mixture and show that the density maximum arises from the depletion in interstitial water molecules upon cooling. In the hydration shell of the hydrophobic moiety of propanol, the order parameters suggest that the water local structure is similar to that in the bulk, with only a very weak depletion in ordered configurations, thus confirming the absence of any iceberg-type structure. Finally, we show that the main structural fluctuations that affect water reorientation dynamics in the bulk are angular distortions, which we explain by the jump hydrogen-bond exchange mechanism. PMID:26054933

  16. Comprehensive comparison of the chemical and structural characterization of landfill leachate and leonardite humic fractions.

    PubMed

    Tahiri, Abdelghani; Richel, Aurore; Destain, Jacqueline; Druart, Philippe; Thonart, Philippe; Ongena, Marc

    2016-03-01

    Humic substances (HS) are complex and heterogeneous mixtures of organic compounds that occur everywhere in the environment. They represent most of the dissolved organic matter in soils, sediments (fossil), water, and landfills. The exact structure of HS macromolecules has not yet been determined because of their complexity and heterogeneity. Various descriptions of HS are used depending on specific environments of origin and research interests. In order to improve the understanding of the structure of HS extracted from landfill leachate (LHS) and commercial HS from leonardite (HHS), this study sought to compare the composition and characterization of the structure of LHS and HHS using elemental composition, chromatographic (high-performance liquid chromatography (HPLC)), and spectroscopic techniques (UV-vis, FTIR, NMR, and MALDI-TOF). The results showed that LHS molecules have a lower molecular weight and less aromatic structure than HHS molecules. The characteristics of functional groups of both LHS and HHS, however, were basically similar, but there was some differences in absorbance intensity. There were also less aliphatic and acidic functional groups and more aromatic and polyphenolic compounds in the humic acid (HA) fraction than in the fulvic acid (FA) and other molecules (OM) fractions of both origins. The differences between LHS and HHS might be due to the time course of humification. Combining the results obtained from these analytical techniques cold improve our understanding of the structure of HS of different origins and thus enhance their potential use.

  17. Structural characterization of metal binding to a cold-adapted frataxin.

    PubMed

    Noguera, Martín E; Roman, Ernesto A; Rigal, Juan B; Cousido-Siah, Alexandra; Mitschler, André; Podjarny, Alberto; Santos, Javier

    2015-06-01

    Frataxin is an evolutionary conserved protein that participates in iron metabolism. Deficiency of this small protein in humans causes a severe neurodegenerative disease known as Friedreich's ataxia. A number of studies indicate that frataxin binds iron and regulates Fe-S cluster biosynthesis. Previous structural studies showed that metal binding occurs mainly in a region of high density of negative charge. However, a comprehensive characterization of the binding sites is required to gain further insights into the mechanistic details of frataxin function. In this work, we have solved the X-ray crystal structures of a cold-adapted frataxin from a psychrophilic bacterium in the presence of cobalt or europium ions. We have identified a number of metal-binding sites, mainly solvent exposed, several of which had not been observed in previous studies on mesophilic homologues. No major structural changes were detected upon metal binding, although the structures exhibit significant changes in crystallographic B-factors. The analysis of these B-factors, in combination with crystal packing and RMSD among structures, suggests the existence of localized changes in the internal motions. Based on these results, we propose that bacterial frataxins possess binding sites of moderate affinity for a quick capture and transfer of iron to other proteins and for the regulation of Fe-S cluster biosynthesis, modulating interactions with partner proteins.

  18. First structural characterization of a protactinium(V) single oxo bond in aqueous media.

    PubMed

    Le Naour, Claire; Trubert, Didier; Di Giandomenico, Maria V; Fillaux, Clara; Den Auwer, Christophe; Moisy, Philippe; Hennig, Christoph

    2005-12-12

    The present work describes the first structural studies of protactinium(V) in sulfuric and hydrofluoric acid media using X-ray absorption spectroscopy. The results show unambiguously the absence of the trans-dioxo bond that characterizes the other early actinide elements such as U and Np. In concentrated sulfuric acid (13 M), Pa(V) is proved to exhibit a single oxo bond as postulated in the literature for species in more dilute media. In a 0.5 M HF medium, XANES and EXAFS spectra indicate the absence of any oxo bond: Pa(V) exists in the form of a pure fluoro complex.

  19. First structural characterization of a protactinium(V) single oxo bond in aqueous media.

    PubMed

    Le Naour, Claire; Trubert, Didier; Di Giandomenico, Maria V; Fillaux, Clara; Den Auwer, Christophe; Moisy, Philippe; Hennig, Christoph

    2005-12-12

    The present work describes the first structural studies of protactinium(V) in sulfuric and hydrofluoric acid media using X-ray absorption spectroscopy. The results show unambiguously the absence of the trans-dioxo bond that characterizes the other early actinide elements such as U and Np. In concentrated sulfuric acid (13 M), Pa(V) is proved to exhibit a single oxo bond as postulated in the literature for species in more dilute media. In a 0.5 M HF medium, XANES and EXAFS spectra indicate the absence of any oxo bond: Pa(V) exists in the form of a pure fluoro complex. PMID:16323942

  20. Thermodynamic and structural characterization of the UFeO4 compound

    NASA Astrophysics Data System (ADS)

    Labroche, D.; Rogez, J.; Dugne, O.; Laval, J. P.

    2000-07-01

    In order to establish the whole ternary phase diagram (U-Fe-O), which is one of the main systems in the nuclear safety and enrichment programs, the UFeO4 ternary compound must be characterized with more precision. Indeed, the knowledge of this compound is essential because an experimental determination of the isothermal section at 1300 K shows that UFeO4 is involved in three-phase equilibria. The purpose of this work is to obtain thermodynamic data and new structural information on this ternary oxide.

  1. Purification, characterization and structural analysis of an abundant beta-1,3-glucanase from banana fruit.

    PubMed

    Peumans, W J; Barre, A; Derycke, V; Rougé, P; Zhang, W; May, G D; Delcour, J A; Van Leuven, F; Van Damme, E J

    2000-02-01

    An abundant, catalytically active beta-1,3-endoglucanase (EC 3.2.1. 39) has been isolated from the pulp of ripe bananas. Biochemical analysis of the purified protein, molecular modelling, and molecular cloning of the corresponding gene indicate that this banana enzyme closely resembles previously characterized plant beta-glucanases with respect to its amino-acid sequence, structure and biological activity. The results described in this paper demonstrate both the occurrence of an abundant active beta-1,3-endoglucanases in fruits and also readdress the question of the possible involvement of these enzymes in the ripening and/or softening process.

  2. Synthesis and structural characterization of vertical ferromagnetic MnAs/semiconducting InAs heterojunction nanowires

    NASA Astrophysics Data System (ADS)

    Kodaira, Ryutaro; Hara, Shinjiro; Kabamoto, Kyohei; Fujimagari, Hiromu

    2016-07-01

    The purpose of this study is to synthesize vertical ferromagnetic/semiconducting heterojunction nanowires by combing the catalyst-free selective-area growth of InAs nanowires and the endotaxial nanoclustering of MnAs and to structurally and magnetically characterize them. MnAs penetrates the InAs nanowires to form nanoclusters. The surface migration length of manganese adatoms on the nanowires, which is estimated to be 600 nm at 580 °C, is a key to the successful fabrication of vertical MnAs/InAs heterojunction nanowires with atomically abrupt heterointerfaces.

  3. Uranyl Sequestration: Synthesis and Structural Characterization of Uranyl Complexes with a Tetradentate Methylterephthalamide Ligand

    SciTech Connect

    Ni, Chengbao; Shuh, David; Raymond, Kenneth

    2011-03-07

    Uranyl complexes of a bis(methylterephthalamide) ligand (LH{sub 4}) have been synthesized and characterized by X-ray crystallography. The structure is an unexpected [Me{sub 4}N]{sub 8}[L(UO{sub 2})]{sub 4} tetramer, formed via coordination of the two MeTAM units of L to two uranyl moieties. Addition of KOH to the tetramer gave the corresponding monomeric uranyl methoxide species [Me{sub 4}N]K{sub 2}[LUO{sub 2}(OMe)].

  4. Structural characterization and dehydration kinetics of Kirka inderite mineral: Application of non-isothermal models

    SciTech Connect

    Figen, Aysel Kantuerk; Yilmaz, Muege Sari; Piskin, Sabriye

    2010-06-15

    Coats-Redfern, Arrhenius, Ozawa, Kissinger, and Doyle non-isothermal kinetic models were used to calculate the dynamic kinetic parameters for dehydration reaction of Mg-borate mineral, inderite (Kirka - Turkey) based on thermogravimetric analysis, derivative thermogravimetric analysis and differential thermal analysis. Dehydration experiments were carried out at different heating rates of 2, 5, 10, 15, and 20 deg. C/min in a pure nitrogen atmosphere. Structural and morphological properties have been characterized by X-Ray diffraction, Fourier transform-infrared spectroscopy, Scanning electron microscopy-energy dispersive spectroscopy, and Inductively coupled plasma-optical emission spectroscopy techniques.

  5. Characterization of properties and structural heterogeneity of crosslinked polymers formed by living radical photopolymerizations

    NASA Astrophysics Data System (ADS)

    Kannurpatti, Anandkumar R.

    Polymer networks formed by radical photopolymerizations of multifunctional monomers are finding use in an increasing number of applications. To meet this increasing demand, it is important to tailor these materials and their properties to suit the application requirements. However, to achieve this goal, an understanding of the underlying polymerization-structure-property relationships of these networks is necessary. This work focuses on understanding the effect of polymerization conditions and the evolution of material properties and structural heterogeneity in crosslinked polymers. While photopolymerizing these multifunctional monomers, microgels, unreacted double bonds (monomeric and pendant), and trapped radicals are features that have been observed by several researchers. Also, the resultant structure of the crosslinked polymers is extremely heterogeneous. Previously, examining the material properties of such networks as a function of temperature has been very difficult because the unreacted double bonds and trapped radicals continue to react as the temperature approaches the glass transition temperature of the material. Therefore, while studying the properties of the sample, the structure and properties are altered. In this work, "living" radical polymerizations are used to avoid radical trapping. As a result, for the first time the properties and structural heterogeneity of the polymers are studied as a function of temperature at various double bond conversions and crosslinking densities. To enable the use of "living" radical photopolymerizations in the characterization of polymer networks, it was important to understand the mechanism of the "living" radical polymerizations. Therefore, a study of the kinetics and mechanisms of the "living" radical polymerizations was also undertaken. Experimental and modeling studies were performed to understand the mechanism of these reactions. By performing dynamic mechanical and dielectric measurements on the polymer

  6. Ipolamiide and fulvoipolamiide from Stachytarpheta glabra (Verbenaceae): A structural and spectroscopic characterization

    NASA Astrophysics Data System (ADS)

    Viccini, Lyderson F.; Silva, Pâmela S.; Almeida, Mauro V. de; Saraiva, Maurício F.; Peixoto, Paulo Henrique P.; Salimena, Fátima Regina G.; Diniz, Renata; Rodrigues, Bernardo L.; Scowen, Ian; Edwards, Howell G. M.; Oliveira, Luiz F. C. de

    2008-03-01

    The phenylethanoid glycoside acteoside and the iridoids ipolamiide and 4-methoxycarbonyl-7-methylcyclopenta[ c]pyran (fulvoipolamiide) were isolated from the leaves of Stachytarpheta glabra. The solid state structure of fulvoipolamiide was confirmed by X-ray diffraction studies. The molecules of fulvoipolamiide are displayed in layers parallel to the crystallographic axis a. This molecule is planar with electron delocalization in the fused ring system and the pyran rings of adjacent layers in the solid state structure are involved in a π-π stacking interaction. Raman spectroscopy has also been used to characterize the most important bands present in the spectra of fulvoipolamiide and ipolamiide, and comparison made with literature allows the assignment of some key markers, specially the bands in the 1600-1700 cm -1 range.

  7. Structural characterization and anti-fatigue activity of polysaccharides from the roots of Morinda officinalis.

    PubMed

    Zhang, Hua-Lin; Li, Jun; Li, George; Wang, Dong-mei; Zhu, Long-ping; Yang, De-po

    2009-04-01

    Three polysaccharides MP-1, MP-2, and MP-3 were isolated from hot water extract of Chinese medicine Morinda officinalis through 95% ethanol precipitation and gel-filtration chromatography (DEAE-Sepharose CL-6B column and Sephadex G-75 or G-100 column). MP-1 was identified as an inulin-type fructan with simple linear (2-->1)-linked structure. Both MP-2 and MP-3 were acidic polysaccharides which consisted predominantly of galacturonic acid, arabinose and galactose. Partial structure characterization of MP-3 was carried out by partial acid hydrolysis and periodate oxidation. The total polysaccharides of the herb were tested in mice weight-loaded swimming model and were found to have anti-fatigue activity. PMID:19150459

  8. Structural Characterization of Bimetallic Nanomaterials with Overlapping X-ray Absorption Edges

    SciTech Connect

    Menard, L.; Wang, Q; Kang, J; Sealey, A; Girolami, G; Teng, X; Frenkel, A; Nuzzo, R

    2009-01-01

    We describe a data analysis method for extended x-ray absorption fine structure spectroscopy suitable for use with compounds of diverse form that contain overlapping absorption edges. This method employs direct concurrent analysis of the data-demonstrated here for cases involving two interfering metal edges-and does not utilize subtractive or data filtering strategies that have been previously used to address this challenge. Its generality and precision are demonstrated in analyses made on two model nanoscale samples: (1) a Ir-Pt nanoparticle system supported on ?-Al2O3 and (2) a hybrid system of Pt nanowires on which Au nanoparticles have been nucleated and grown at the nanowire tips, stacking faults, and twinning boundaries. The results obtained demonstrate the unique compositional and structural qualities of these two systems as well as the broader utility of the new x-ray absorption spectroscopy based protocol used to characterize them.

  9. Characterizing pore sizes and water structure in stimuli-responsive hydrogels

    SciTech Connect

    Hoffman, A.S.; Antonsen, K.P.; Ashida, T.; Bohnert, J.L.; Dong, L.C.; Nabeshima, Y.; Nagamatsu, S.; Park, T.G.; Sheu, M.S.; Wu, X.S.; Yan, Q.

    1993-12-31

    Hydrogels have been extensively investigated as potential matrices for drug delivery. In particular, hydrogels responsive to pH and temperature changes have been of greatest interest most recently. Proteins and peptide drugs are especially relevant for delivery from such hydrogel matrices due to the relatively {open_quotes}passive{close_quotes} and biocompatible microenvironment which should exist within the hydrogel aqueous pores. The large molecular size of many proteins requires an interconnected large pore structure. Furthermore, the gel pore {open_quotes}walls{close_quotes} should not provide hydrophobic sites for strong interactions with proteins. In the special case of ion exchange release the protein would be attracted by opposite charges on the polymer backbones. Therefore, it is important both to control and to characterize the pore structure and the water character within a hydrogel to be used or protein or peptide drug delivery. This talk will critically review techniques for estimating these two key parameters in hydrogels.

  10. Synthesis and characterization of DC magnetron sputtered nano structured molybdenum thin films

    NASA Astrophysics Data System (ADS)

    Rondiya, S. R.; Rokade, A. V.; Jadhavar, A. A.; Pandharkar, S. M.; Kulkarni, R. R.; Karpe, S. D.; Diwate, K. D.; Jadkar, S. R.

    2016-04-01

    Molybdenum (Mo) thin films were deposited on corning glass (#7059) substrates using DC magnetron sputtering system. The effect of substrate temperature on the structural, morphology and topological properties have been investigated. Films were characterized by variety of techniques such as low angle x-ray diffraction (low angle XRD), field emission scanning electron microscopy (FE-SEM), atomic force microscopy (AFM). The low angle XRD analysis revealed that the synthesized Mo films are nanocrystalline having cubic crystal structure with (110) preferential orientation. The microstructure of the deposited Mo thin films observed with FE-SEM images indicated that films are homogeneous and uniform with randomly oriented leaf shape morphology. The AFM analysis shows that with increase in substrate temperature the rms roughness of Mo films increases. The obtained results suggest that the synthesized nanostructured Mo thin films have potential application as a back contact material for high efficiency solar cells like CdTe, CIGS, CZTS etc.

  11. Structural characterization of P1'-diversified urea-based inhibitors of glutamate carboxypeptidase II.

    PubMed

    Pavlicek, Jiri; Ptacek, Jakub; Cerny, Jiri; Byun, Youngjoo; Skultetyova, Lubica; Pomper, Martin G; Lubkowski, Jacek; Barinka, Cyril

    2014-05-15

    Urea-based inhibitors of human glutamate carboxypeptidase II (GCPII) have advanced into clinical trials for imaging metastatic prostate cancer. In parallel efforts, agents with increased lipophilicity have been designed and evaluated for targeting GCPII residing within the neuraxis. Here we report the structural and computational characterization of six complexes between GCPII and P1'-diversified urea-based inhibitors that have the C-terminal glutamate replaced by more hydrophobic moieties. The X-ray structures are complemented by quantum mechanics calculations that provide a quantitative insight into the GCPII/inhibitor interactions. These data can be used for the rational design of novel glutamate-free GCPII inhibitors with tailored physicochemical properties.

  12. Structural and compositional characterization of the adhesive produced by reef building oysters.

    PubMed

    Alberts, Erik M; Taylor, Stephen D; Edwards, Stephanie L; Sherman, Debra M; Huang, Chia-Ping; Kenny, Paul; Wilker, Jonathan J

    2015-04-29

    Oysters have an impressive ability to overcome difficulties of life within the stressful intertidal zone. These shellfish produce an adhesive for attaching to each other and building protective reef communities. With their reefs often exceeding kilometers in length, oysters play a major role in balancing the health of coastal marine ecosystems. Few details are available to describe oyster adhesive composition or structure. Here several characterization methods were applied to describe the nature of this material. Microscopy studies indicated that the glue is comprised of organic fiber-like and sheet-like structures surrounded by an inorganic matrix. Phospholipids, cross-linking chemistry, and conjugated organics were found to differentiate this adhesive from the shell. Symbiosis in material synthesis could also be present, with oysters incorporating bacterial polysaccharides into their adhesive. Oyster glue shows that an organic-inorganic composite material can provide adhesion, a property especially important when constructing a marine ecosystem. PMID:25843147

  13. Structural characterization of selenosubtilisin by sup 77 Se-NMR spectroscopy

    SciTech Connect

    House, K.L.; Dunlap, R.B.; Odom, J.D.; Wu, Z.P.; Hilvert. D. Research Inst. of Scripps Clinic, La Jolla, CA )

    1991-03-15

    Selenosubtilisin is an artificial enzyme containing an active site selenocysteine residue. In this environment the selenium atom is a valuable probe of structure-function relationships and also confers novel redox and hydrolytic properties to the original protease template. The authors have used {sup 77}Se NMR spectroscopy to characterize different oxidation states of {sup 77}Se isotopically enriched selenosubtilisin. The oxidized form of the enzyme exhibits a {sup 77}Se resonance at 1,189 ppm. This is in good agreement with the {sup 77}Se chemical shifts for model seleninic acids, confirming that the prosthetic group is in the seleninic acid oxidation state. On treatment of the oxidized enzyme with three equivalents of 3-carboxy-4-nitrobenzenethiol at pH 5.0, they observe the enzyme bound selenenyl sulfide at 388.5 ppm. This work demonstrates the utility of {sup 77}Se NMR spectroscopy for examining structure-function relationships of selenium containing proteins.

  14. Inflight Characterization of the Cassini Spacecraft Propellant Slosh and Structural Frequencies

    NASA Technical Reports Server (NTRS)

    Lee, Allan Y.; Stupik, Joan

    2015-01-01

    While there has been extensive theoretical and analytical research regarding the characterization of spacecraft propellant slosh and structural frequencies, there have been limited studies to compare the analytical predictions with measured flight data. This paper uses flight telemetry from the Cassini spacecraft to get estimates of high-g propellant slosh frequencies and the magnetometer boom frequency characteristics, and compares these values with those predicted by theoretical works. Most Cassini attitude control data are available at a telemetry frequency of 0.5 Hz. Moreover, liquid sloshing is attenuated by propellant management device and attitude controllers. Identification of slosh and structural frequency are made on a best-effort basis. This paper reviews the analytical approaches that were used to predict the Cassini propellant slosh frequencies. The predicted frequencies are then compared with those estimated using telemetry from selected Cassini burns where propellant sloshing was observed (such as the Saturn Orbit Insertion burn).

  15. Structure and biochemical characterization of proliferating cellular nuclear antigen from a parasitic protozoon

    SciTech Connect

    Cardona-Felix, Cesar S.; Lara-Gonzalez, Samuel; Brieba, Luis G.

    2012-02-08

    Proliferating cellular nuclear antigen (PCNA) is a toroidal-shaped protein that is involved in cell-cycle control, DNA replication and DNA repair. Parasitic protozoa are early-diverged eukaryotes that are responsible for neglected diseases. In this work, a PCNA from a parasitic protozoon was identified, cloned and biochemically characterized and its crystal structure was determined. Structural and biochemical studies demonstrate that PCNA from Entamoeba histolytica assembles as a homotrimer that is able to interact with and stimulate the activity of a PCNA-interacting peptide-motif protein from E. histolytica, EhDNAligI. The data indicate a conservation of the biochemical mechanisms of PCNA-mediated interactions between metazoa, yeast and parasitic protozoa.

  16. Structural characterization of encapsulated ferritin provides insight into iron storage in bacterial nanocompartments.

    PubMed

    He, Didi; Hughes, Sam; Vanden-Hehir, Sally; Georgiev, Atanas; Altenbach, Kirsten; Tarrant, Emma; Mackay, C Logan; Waldron, Kevin J; Clarke, David J; Marles-Wright, Jon

    2016-01-01

    Ferritins are ubiquitous proteins that oxidise and store iron within a protein shell to protect cells from oxidative damage. We have characterized the structure and function of a new member of the ferritin superfamily that is sequestered within an encapsulin capsid. We show that this encapsulated ferritin (EncFtn) has two main alpha helices, which assemble in a metal dependent manner to form a ferroxidase center at a dimer interface. EncFtn adopts an open decameric structure that is topologically distinct from other ferritins. While EncFtn acts as a ferroxidase, it cannot mineralize iron. Conversely, the encapsulin shell associates with iron, but is not enzymatically active, and we demonstrate that EncFtn must be housed within the encapsulin for iron storage. This encapsulin nanocompartment is widely distributed in bacteria and archaea and represents a distinct class of iron storage system, where the oxidation and mineralization of iron are distributed between two proteins. PMID:27529188

  17. Synthesis, molecular modeling and structural characterization of vanillin derivatives as antimicrobial agents

    NASA Astrophysics Data System (ADS)

    Sun, Juan; Yin, Yong; Sheng, Gui-Hua; Yang, Zhi-Bo; Zhu, Hai-Liang

    2013-05-01

    Two vanillin derivatives have been designed and synthesized and their biological activities were also evaluated for antimicrobial activity. Their chemical structures are characterized by single crystal X-ray diffraction studies, 1H NMR, MS, and elemental analysis. Structural stabilization of them followed by intramolecular as well as intermolecular H-bonds makes these molecules as perfect examples in molecular recognition with self-complementary donor and acceptor units within a single molecule. Docking simulations have been performed to position compounds into the FtsZ active site to determine their probable binding model. Compound 3a shows the most potent biological activity, which may be a promising antimicrobial leading compound for the further research.

  18. Phenanthro[4,5-fgh]quinoxaline-Fused Subphthalocyanines: Synthesis, Structure, and Spectroscopic Characterization.

    PubMed

    Pan, Houhe; Liu, Wenbo; Wang, Chiming; Wang, Kang; Jiang, Jianzhuang

    2016-07-01

    A series of four phenanthro[4,5-fgh]quinoxaline-fused subphthalocyanine derivatives 0-3 containing zero, one, two, and three phenanthro[4,5-fgh]quinoxaline moieties, respectively, were isolated from the mixed cyclotrimerization reaction of 2,9-di-tert-butylphenanthro[4,5-fgh]quinoxaline-5,6-dicarbonitrile with 4,5-bis(2,6-diisopropylphenoxy)phthalonitrile and characterized by a series of spectroscopic methods including MALDI-TOF mass, (1) H NMR, electronic absorption, magnetic circular dichroism (MCD), and fluorescence spectroscopy. The molecular structures for the compounds 0 and 2 were clearly revealed on the basis of single-crystal X-ray diffraction analysis. Their electrochemical properties were also studied by cyclic voltammetry. In particular, theoretical calculations in combination with the electronic absorption and electrochemical analyses revealed the significant influence of the fused-phenanthro[4,5-fgh]quinoxaline units on the electronic structures.

  19. Characterization of Microgravity Effects on Bone Structure and Strength Using Fractal Analysis

    NASA Technical Reports Server (NTRS)

    Acharya, Raj S.; Shackelford, Linda

    1996-01-01

    Protecting humans against extreme environmental conditions requires a thorough understanding of the pathophysiological changes resulting from the exposure to those extreme conditions. Knowledge of the degree of medical risk associated with the exposure is of paramount importance in the design of effective prophylactic and therapeutic measures for space exploration. Major health hazards due o musculoskeletal systems include the signs and symptoms of hypercalciuria, lengthy recovery of lost bone tissue after flight, the possibility of irreversible trabecular bone loss, the possible effect of calcification in the soft tissues, and the possible increase in fracture potential. In this research, we characterize the trabecular structure with the aid of fractal analysis. Our research to relate local trabecular structural information to microgravity conditions is an important initial step in understanding the effect of microgravity and countermeasures on bone condition and strength. The proposed research is also closely linked with Osteoporosis and will benefit the general population.

  20. Functional and Structural Characterization of the Antiphagocytic Properties of a Novel Transglutaminase from Streptococcus suis*

    PubMed Central

    Yu, Jie; Pian, Yaya; Ge, Jingpeng; Guo, Jie; Zheng, Yuling; Jiang, Hua; Hao, Huaijie; Yuan, Yuan; Jiang, Yongqiang; Yang, Maojun

    2015-01-01

    Streptococcus suis serotype 2 (Ss2) is an important swine and human zoonotic pathogen. In the present study, we identified a novel secreted immunogenic protein, SsTGase, containing a highly conserved eukaryotic-like transglutaminase (TGase) domain at the N terminus. We found that inactivation of SsTGase significantly reduced the virulence of Ss2 in a pig infection model and impaired its antiphagocytosis in human blood. We further solved the crystal structure of the N-terminal portion of the protein in homodimer form at 2.1 Å. Structure-based mutagenesis and biochemical studies suggested that disruption of the homodimer directly resulted in the loss of its TGase activity and antiphagocytic ability. Characterization of SsTGase as a novel virulence factor of Ss2 by acting as a TGase would be beneficial for developing new therapeutic agents against Ss2 infections. PMID:26085092

  1. Structural Characterization of the Catalytic Subunit of a Novel RNA Splicing Endonuclease

    SciTech Connect

    Calvin, Kate; Hall, Michelle D.; Xu, Fangmin; Xue, Song; Li, Hong

    2010-07-13

    The RNA splicing endonuclease is responsible for recognition and excision of nuclear tRNA and all archaeal introns. Despite the conserved RNA cleavage chemistry and a similar enzyme assembly, currently known splicing endonuclease families have limited RNA specificity. Different from previously characterized splicing endonucleases in Archaea, the splicing endonuclease from archaeum Sulfolobus solfataricus was found to contain two different subunits and accept a broader range of substrates. Here, we report a crystal structure of the catalytic subunit of the S. solfataricus endonuclease at 3.1 {angstrom} resolution. The structure, together with analytical ultracentrifugation analysis, identifies the catalytic subunit as an inactive but stable homodimer, thus suggesting the possibility of two modes of functional assembly for the active enzyme.

  2. Structural and compositional characterization of the adhesive produced by reef building oysters.

    PubMed

    Alberts, Erik M; Taylor, Stephen D; Edwards, Stephanie L; Sherman, Debra M; Huang, Chia-Ping; Kenny, Paul; Wilker, Jonathan J

    2015-04-29

    Oysters have an impressive ability to overcome difficulties of life within the stressful intertidal zone. These shellfish produce an adhesive for attaching to each other and building protective reef communities. With their reefs often exceeding kilometers in length, oysters play a major role in balancing the health of coastal marine ecosystems. Few details are available to describe oyster adhesive composition or structure. Here several characterization methods were applied to describe the nature of this material. Microscopy studies indicated that the glue is comprised of organic fiber-like and sheet-like structures surrounded by an inorganic matrix. Phospholipids, cross-linking chemistry, and conjugated organics were found to differentiate this adhesive from the shell. Symbiosis in material synthesis could also be present, with oysters incorporating bacterial polysaccharides into their adhesive. Oyster glue shows that an organic-inorganic composite material can provide adhesion, a property especially important when constructing a marine ecosystem.

  3. Structural and Catalytic Characterization of a Fungal Baeyer-Villiger Monooxygenase

    PubMed Central

    Ferroni, Felix Martin; Tolmie, Carmien; Smit, Martha Sophia; Opperman, Diederik Johannes

    2016-01-01

    Baeyer-Villiger monooxygenases (BVMOs) are biocatalysts that convert ketones to esters. Due to their high regio-, stereo- and enantioselectivity and ability to catalyse these reactions under mild conditions, they have gained interest as alternatives to chemical Baeyer-Villiger catalysts. Despite their widespread occurrence within the fungal kingdom, most of the currently characterized BVMOs are from bacterial origin. Here we report the catalytic and structural characterization of BVMOAFL838 from Aspergillus flavus. BVMOAFL838 converts linear and aryl ketones with high regioselectivity. Steady-state kinetics revealed BVMOAFL838 to show significant substrate inhibition with phenylacetone, which was more pronounced at low pH, enzyme and buffer concentrations. Para substitutions on the phenyl group significantly improved substrate affinity and increased turnover frequencies. Steady-state kinetics revealed BVMOAFL838 to preferentially oxidize aliphatic ketones and aryl ketones when the phenyl group are separated by at least two carbons from the carbonyl group. The X-ray crystal structure, the first of a fungal BVMO, was determined at 1.9 Å and revealed the typical overall fold seen in type I bacterial BVMOs. The active site Arg and Asp are conserved, with the Arg found in the “in” position. Similar to phenylacetone monooxygenase (PAMO), a two residue insert relative to cyclohexanone monooxygenase (CHMO) forms a bulge within the active site. Approximately half of the “variable” loop is folded into a short α-helix and covers part of the active site entry channel in the non-NADPH bound structure. This study adds to the current efforts to rationalize the substrate scope of BVMOs through comparative catalytic and structural investigation of different BVMOs. PMID:27472055

  4. Structural and Catalytic Characterization of a Fungal Baeyer-Villiger Monooxygenase.

    PubMed

    Ferroni, Felix Martin; Tolmie, Carmien; Smit, Martha Sophia; Opperman, Diederik Johannes

    2016-01-01

    Baeyer-Villiger monooxygenases (BVMOs) are biocatalysts that convert ketones to esters. Due to their high regio-, stereo- and enantioselectivity and ability to catalyse these reactions under mild conditions, they have gained interest as alternatives to chemical Baeyer-Villiger catalysts. Despite their widespread occurrence within the fungal kingdom, most of the currently characterized BVMOs are from bacterial origin. Here we report the catalytic and structural characterization of BVMOAFL838 from Aspergillus flavus. BVMOAFL838 converts linear and aryl ketones with high regioselectivity. Steady-state kinetics revealed BVMOAFL838 to show significant substrate inhibition with phenylacetone, which was more pronounced at low pH, enzyme and buffer concentrations. Para substitutions on the phenyl group significantly improved substrate affinity and increased turnover frequencies. Steady-state kinetics revealed BVMOAFL838 to preferentially oxidize aliphatic ketones and aryl ketones when the phenyl group are separated by at least two carbons from the carbonyl group. The X-ray crystal structure, the first of a fungal BVMO, was determined at 1.9 Å and revealed the typical overall fold seen in type I bacterial BVMOs. The active site Arg and Asp are conserved, with the Arg found in the "in" position. Similar to phenylacetone monooxygenase (PAMO), a two residue insert relative to cyclohexanone monooxygenase (CHMO) forms a bulge within the active site. Approximately half of the "variable" loop is folded into a short α-helix and covers part of the active site entry channel in the non-NADPH bound structure. This study adds to the current efforts to rationalize the substrate scope of BVMOs through comparative catalytic and structural investigation of different BVMOs. PMID:27472055

  5. Monodentate Schiff base ligands: their structural characterization, photoluminescence, anticancer, electrochemical and sensor properties.

    PubMed

    Köse, Muhammet; Ceyhan, Gökhan; Tümer, Mehmet; Demirtaş, Ibrahim; Gönül, İlyas; McKee, Vickie

    2015-02-25

    Two Schiff base compounds, N,N'-bis(2-methoxy phenylidene)-1,5-diamino naphthalene (L(1)) and N,N'-bis(3,4,5-trimethoxy phenylidene)-1,5-diamino naphthalene (L(2)) were synthesized and characterized by the analytical and spectroscopic methods. The electrochemical and photoluminescence properties of the Schiff bases were investigated in the different conditions. The compounds L(1) and L(2) show the reversible redox processes at some potentials. The sensor properties of the Schiff bases were examined and color changes were observed upon addition of the metal cations, such as Hg(II), Cu(II), Co(II) and Al(III). The Schiff base compounds show the bathochromic shift from 545 to 585 nm. The single crystals of the compounds (L(1)) and (L(2)) were obtained from the methanol solution and characterized structurally by the X-ray crystallography technique. The molecule L(2) is centrosymmetric whereas the L(1) has no crystallographically imposed molecular symmetry. However, the molecular structures for these compounds are quite similar, differing principally in the conformation about methoxy groups and the dihedral angle between the two aromatic rings and diamine naphthalene.

  6. Structural characterization of nanoscale intermetallic precipitates in highly neutron irradiated reactor pressure vessel steels

    DOE PAGES

    Sprouster, D. J.; Sinsheimer, J.; Dooryhee, E.; Ghose, S.; Wells, P.; Stan, T.; Almirall, N.; Odette, G. R.; Ecker, L. E.

    2015-10-21

    Here, massive, thick-walled pressure vessels are permanent nuclear reactor structures that are exposed to a damaging flux of neutrons from the adjacent core. The neutrons cause embrittlement of the vessel steel that increases with dose (fluence or service time), as manifested by an increasing temperature transition from ductile-to-brittle fracture. Moreover, extending reactor life requires demonstrating that large safety margins against brittle fracture are maintained at the higher neutron fluence associated with 60 to 80 years of service. Here synchrotron-based x-ray diffraction and small angle x-ray scattering measurements are used to characterize a new class of highly embrittling nm-scale Mn-Ni-Si precipitatesmore » that develop in the irradiated steels at high fluence. Furthermore, these precipitates can lead to severe embrittlement that is not accounted for in current regulatory models. Application of the complementarity techniques has, for the very first time, successfully characterized the crystal structures of the nanoprecipitates, while also yielding self-consistent compositions, volume fractions and size distributions.« less

  7. Characterization by XDR of amorphous SiCx/c-Si structures at high temperatures

    NASA Astrophysics Data System (ADS)

    Torres, I.

    2011-09-01

    By annealing thin hydrogenated amorphous silicon carbide (a-SiCx:H) films deposited by Plasma Enhanced Chemical Vapor Deposition (PECVD) on crystalline silicon (c-Si) wafers, pn-junctions with very low inverse saturation current can be formed. This has been shown in heterojunction bipolar transistors and solar cells with +/- 400°C for this process. The characterization of these structures indicates that a-SiCx:H films partially re-crystallize during the annealing process forming Si-nanocrystals embedded in the amorphous film. Understanding this process and further improving the pn-junction the study of the re-crystallization process by X-Ray Diffraction (XRD) measurements has been done. This paper deals with the characterization of amorphous SiCx/c-Si structures with 100 and 300 nm thickness measured by XRD with the temperature chamber with an annealing process at 900°C. Both intrinsic and phosphorus-doped a-SiCx:H films were deposited on a c-Si substrate p-type of 300um-thickness with crystallographic orientation <100> using the PECVD reactor. From the in-situ measurements using the XDR, the crystallization phase was obtained; this was done by taking the maximum value of intensity at the dominant peak in the orientation <111> and normalization. Fitting this with the Avrami-Mehl-Johnson Theory the incubation as well as the crystallization time were obtained to study the thermally activated process.

  8. Structural characterization of nanoscale intermetallic precipitates in highly neutron irradiated reactor pressure vessel steels

    SciTech Connect

    Sprouster, D. J.; Sinsheimer, J.; Dooryhee, E.; Ghose, S.; Wells, P.; Stan, T.; Almirall, N.; Odette, G. R.; Ecker, L. E.

    2015-10-21

    Here, massive, thick-walled pressure vessels are permanent nuclear reactor structures that are exposed to a damaging flux of neutrons from the adjacent core. The neutrons cause embrittlement of the vessel steel that increases with dose (fluence or service time), as manifested by an increasing temperature transition from ductile-to-brittle fracture. Moreover, extending reactor life requires demonstrating that large safety margins against brittle fracture are maintained at the higher neutron fluence associated with 60 to 80 years of service. Here synchrotron-based x-ray diffraction and small angle x-ray scattering measurements are used to characterize a new class of highly embrittling nm-scale Mn-Ni-Si precipitates that develop in the irradiated steels at high fluence. Furthermore, these precipitates can lead to severe embrittlement that is not accounted for in current regulatory models. Application of the complementarity techniques has, for the very first time, successfully characterized the crystal structures of the nanoprecipitates, while also yielding self-consistent compositions, volume fractions and size distributions.

  9. Structure Characterization and Properties of Metal-Surfactant Complexes Dispersed in Organic Solvents.

    PubMed

    de la Iglesia, Pablo; Jaeger, Vance W; Xi, Yuyin; Pfaendtner, Jim; Pozzo, Lilo D

    2015-08-25

    This work describes the synthesis and characterization of metal-surfactant complexes. Dioctyl sulfosuccinate and dodecylbenzenesulfonate are associated with multivalent aluminum, iron, and vanadium ions using an ion exchange reaction. The metal complexes are dispersible in various organic solvents. In solvents with low polarity, the complexes form "inverse" macromolecular structures with multiple metal ions. In contrast, in alcohols, the complex size is reduced, showing a more disperse conformation. The metal and surfactant ions are still strongly bonded to each other in all the solvents probed. Small-angle X-ray and neutron scattering (SAXS and SANS) are used to characterize the structures. Simultaneous fitting of neutron and X-ray scattering spectra is performed in order to obtain an accurate description of the system. Scattering results are also validated by performing molecular dynamics (MD) simulations. The conductive and electrochemical properties of the complexes in solution are also evaluated. The dispersion of metal-organic complexes significantly increases electric conductivity, and some metal ions in the core of the complexes are shown to be electrochemically active in apolar solvents.

  10. Streptococcus pneumoniae TIGR4 Flavodoxin: Structural and Biophysical Characterization of a Novel Drug Target

    PubMed Central

    Rodríguez-Cárdenas, Ángela; Rojas, Adriana L.; Conde-Giménez, María; Velázquez-Campoy, Adrián; Hurtado-Guerrero, Ramón; Sancho, Javier

    2016-01-01

    Streptococcus pneumoniae (Sp) strain TIGR4 is a virulent, encapsulated serotype that causes bacteremia, otitis media, meningitis and pneumonia. Increased bacterial resistance and limited efficacy of the available vaccine to some serotypes complicate the treatment of diseases associated to this microorganism. Flavodoxins are bacterial proteins involved in several important metabolic pathways. The Sp flavodoxin (Spfld) gene was recently reported to be essential for the establishment of meningitis in a rat model, which makes SpFld a potential drug target. To facilitate future pharmacological studies, we have cloned and expressed SpFld in E. coli and we have performed an extensive structural and biochemical characterization of both the apo form and its active complex with the FMN cofactor. SpFld is a short-chain flavodoxin containing 146 residues. Unlike the well-characterized long-chain apoflavodoxins, the Sp apoprotein displays a simple two-state thermal unfolding equilibrium and binds FMN with moderate affinity. The X-ray structures of the apo and holo forms of SpFld differ at the FMN binding site, where substantial rearrangement of residues at the 91–100 loop occurs to permit cofactor binding. This work will set up the basis for future studies aiming at discovering new potential drugs to treat S. pneumoniae diseases through the inhibition of SpFld. PMID:27649488

  11. Solvate Structures and Computational/Spectroscopic Characterization of LiBF4 Electrolytes

    SciTech Connect

    Seo, D. M.; Boyle, Paul D.; Allen, Joshua L.; Han, Sang D.; Jonsson, Erlendur; Johansson, Patrik; Henderson, Wesley A.

    2014-07-21

    Crystal structures have been determined for both LiBF4 and HBF4 solvates—(acetonitrile)2:LiBF4, (ethylene glycol diethyl ether)1:LiBF4, (diethylene glycol diethyl ether)1:LiBF4, (tetrahydrofuran)1:LiBF4, (methyl methoxyacetate)1:LiBF4, (suc-cinonitrile)1:LiBF4, (N,N,N',N",N"-pentamethyldiethylenetriamine)1:HBF4, (N,N,N',N'-tetramethylethylenediamine)3/2:HBF4 and (phenanthroline)2:HBF4. These, as well as other known LiBF4 solvate structures, have been characterized by Raman vibrational spectroscopy to unambiguously assign the anion Raman band positions to specific forms of BF4-...Li+ cation coordination. In addition, complementary DFT calculations of BF4-...Li+ cation complexes have provided additional insight into the challenges associated with accurately interpreting the anion interactions from experimental Raman spectra. This information provides a crucial tool for the characterization of the ionic association interactions within electrolytes.

  12. Streptococcus pneumoniae TIGR4 Flavodoxin: Structural and Biophysical Characterization of a Novel Drug Target.

    PubMed

    Rodríguez-Cárdenas, Ángela; Rojas, Adriana L; Conde-Giménez, María; Velázquez-Campoy, Adrián; Hurtado-Guerrero, Ramón; Sancho, Javier

    2016-01-01

    Streptococcus pneumoniae (Sp) strain TIGR4 is a virulent, encapsulated serotype that causes bacteremia, otitis media, meningitis and pneumonia. Increased bacterial resistance and limited efficacy of the available vaccine to some serotypes complicate the treatment of diseases associated to this microorganism. Flavodoxins are bacterial proteins involved in several important metabolic pathways. The Sp flavodoxin (Spfld) gene was recently reported to be essential for the establishment of meningitis in a rat model, which makes SpFld a potential drug target. To facilitate future pharmacological studies, we have cloned and expressed SpFld in E. coli and we have performed an extensive structural and biochemical characterization of both the apo form and its active complex with the FMN cofactor. SpFld is a short-chain flavodoxin containing 146 residues. Unlike the well-characterized long-chain apoflavodoxins, the Sp apoprotein displays a simple two-state thermal unfolding equilibrium and binds FMN with moderate affinity. The X-ray structures of the apo and holo forms of SpFld differ at the FMN binding site, where substantial rearrangement of residues at the 91-100 loop occurs to permit cofactor binding. This work will set up the basis for future studies aiming at discovering new potential drugs to treat S. pneumoniae diseases through the inhibition of SpFld. PMID:27649488

  13. Monodentate Schiff base ligands: Their structural characterization, photoluminescence, anticancer, electrochemical and sensor properties

    NASA Astrophysics Data System (ADS)

    Köse, Muhammet; Ceyhan, Gökhan; Tümer, Mehmet; Demirtaş, İbrahim; Gönül, İlyas; McKee, Vickie

    2015-02-01

    Two Schiff base compounds, N,N‧-bis(2-methoxy phenylidene)-1,5-diamino naphthalene (L1) and N,N‧-bis(3,4,5-trimethoxy phenylidene)-1,5-diamino naphthalene (L2) were synthesized and characterized by the analytical and spectroscopic methods. The electrochemical and photoluminescence properties of the Schiff bases were investigated in the different conditions. The compounds L1 and L2 show the reversible redox processes at some potentials. The sensor properties of the Schiff bases were examined and color changes were observed upon addition of the metal cations, such as Hg(II), Cu(II), Co(II) and Al(III). The Schiff base compounds show the bathochromic shift from 545 to 585 nm. The single crystals of the compounds (L1) and (L2) were obtained from the methanol solution and characterized structurally by the X-ray crystallography technique. The molecule L2 is centrosymmetric whereas the L1 has no crystallographically imposed molecular symmetry. However, the molecular structures for these compounds are quite similar, differing principally in the conformation about methoxy groups and the dihedral angle between the two aromatic rings and diamine naphthalene.

  14. Syntheses and structural characterization of two new nanostructured Bi(III) supramolecular polymers via sonochemical method.

    PubMed

    Yan, Xiao-Wei; Haji-Hasani, Ensieh; Morsali, Ali

    2016-07-01

    Two new bismuth(III) coordination supramolecular polymers, {[Bi2(Hbpp)(bpp)(μ-I)2I6](Hbpp)·MeOH}n (1) and [Bi(Hbpp)(Br4)] (2), (bpp=1,3-di(pyridin-4-yl)propane) were prepared and were structurally characterized by single crystal X-ray diffraction. Single crystalline one-dimensional materials were prepared using a heat gradient applied a solution of the reagents using the branched tube method. The structural determination by single crystal X-ray crystallography shows that compounds 1 and 2 form monoclinic polymers with symmetry space group P21 in the solid state. These new nanostructured Bi(III) supramolecular compounds, {[Bi2(Hbpp)(bpp)(μ-I)2I6](Hbpp)·MeOH} (1) and [Bi(Hbpp)(Br4)] (2), were also synthesized by sonochemical method. The nanostructures were characterized by Field Emission-scanning electron microscopy (FE-SEM), powder X-ray diffraction (PXRD) and IR spectroscopy. PMID:26964932

  15. Human exonuclease 1 (EXO1) activity characterization and its function on flap structures

    PubMed Central

    Keijzers, Guido; Bohr, Vilhelm A.; Rasmussen, Lene Juel

    2015-01-01

    Human exonuclease 1 (EXO1) is involved in multiple DNA metabolism processes, including DNA repair and replication. Most of the fundamental roles of EXO1 have been described in yeast. Here, we report a biochemical characterization of human full-length EXO1. Prior to assay EXO1 on different DNA flap structures, we determined factors essential for the thermodynamic stability of EXO1. We show that enzymatic activity and stability of EXO1 on DNA is modulated by temperature. By characterization of EXO1 flap activity using various DNA flap substrates, we show that EXO1 has a strong capacity for degrading double stranded DNA and has a modest endonuclease or 5′ flap activity. Furthermore, we report novel mechanistic insights into the processing of flap structures, showing that EXO1 preferentially cleaves one nucleotide inwards in a double stranded region of a forked and nicked DNA flap substrates, suggesting a possible role of EXO1 in strand displacement. PMID:26182368

  16. Structural Characterization of Serum N-Glycans by Methylamidation, Fluorescent Labeling, and Analysis by Microchip Electrophoresis.

    PubMed

    Mitra, Indranil; Snyder, Christa M; Zhou, Xiaomei; Campos, Margit I; Alley, William R; Novotny, Milos V; Jacobson, Stephen C

    2016-09-20

    To characterize the structures of N-glycans derived from human serum, we report a strategy that combines microchip electrophoresis, standard addition, enzymatic digestion, and matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS). We compared (i) electrophoretic mobilities of known N-glycans from well-characterized (standard) glycoproteins through standard addition, (ii) the electrophoretic mobilities of N-glycans with their molecular weights determined by MALDI-MS, and (iii) electrophoretic profiles of N-glycans enzymatically treated with fucosidase. The key step to identify the sialylated N-glycans was to quantitatively neutralize the negative charge on both α2,3- and α2,6-linked sialic acids by covalent derivatization with methylamine. Both neutralized and nonsialylated N-glycans from these samples were then reacted with 8-aminopyrene-1,3,6-trisulfonic acid (APTS) to provide a fluorescent label and a triple-negative charge, separated by microchip electrophoresis, and detected by laser-induced fluorescence. The methylamidation step leads to a 24% increase in the peak capacity of the separation and direct correlation of electrophoretic and MALDI-MS results. In total, 37 unique N-glycan structures were assigned to 52 different peaks recorded in the electropherograms of the serum samples. This strategy ensures the needed separation efficiency and detectability, easily resolves linkage and positional glycan isomers, and is highly reproducible.

  17. Structural and Functional Characterization of Recombinant Interleukin-10 from Indian Major Carp Labeo rohita

    PubMed Central

    Karan, Sweta; Dash, Pujarini; Kaushik, Himani; Sahoo, Pramoda K.; Garg, Lalit C.

    2016-01-01

    Interleukin-10, an important regulator of both the innate and adaptive immune systems, is a multifunctional major cytokine. Though it is one of the major cytokines, IL-10 from the Indian major carp, Labeo rohita, has not yet been characterized. In the present study, we report large scale production and purification of biologically active recombinant IL-10 of L. rohita (rLrIL-10) using a heterologous expression system and its biophysical and functional characterization. High yield (~70 mg/L) of soluble rLrIL-10 was obtained at shake flask level. The rLrIL-10 was found to exist as a dimer. Far-UV CD spectroscopy showed presence of predominantly alpha helices. The tertiary structure of the purified rLrIL-10 was verified by fluorescence spectroscopy. Two-dimensional gel analysis revealed the presence of six isoforms of the rLrIL-10. The rLrIL-10 was biologically active and its administration significantly reduced serum proinflammatory cytokines, namely, interleukin 1β, TNFα, and IL-8, and augmented the NKEF transcript levels in spleen of L. rohita. Anti-inflammatory role of the rLrIL-10 was further established by inhibition of phagocytosis using NBT reduction assay in vitro. The data indicate that the dimeric alpha helical structure and function of IL-10 of L. rohita as a key regulator of anti-inflammatory response have remained conserved during evolution. PMID:27689097

  18. Isolation and structural characterization of a polysaccharide LRP4-A from Lycium ruthenicum Murr.

    PubMed

    Lv, Xiaopeng; Wang, Chengjian; Cheng, Yang; Huang, Linjuan; Wang, Zhongfu

    2013-01-10

    A complex polysaccharide, termed LRP4-A, was isolated from the fruit of Lycium ruthenicum Murr. and its structure was characterized. The crude polysaccharide LRP was obtained from the fruit of L. ruthenicum Murr. using hot water extraction followed by ethanol precipitation. The water-soluble polysaccharide LRP4-A was purified from LRP by anion-exchange chromatography and gel filtration chromatography. Its molecular weight was 1.05×10(5) Da. Monosaccharide composition analysis revealed that LRP4-A mainly consisted of rhamnose, arabinose, glucose, and galactose in the molar ratio of 1:7.6:0.5:8.6, with a trace of xylose. Structure of the polysaccharide LRP4-A was characterized using a series of analytical techniques, including methylation analysis, partial acid hydrolysis, IR, NMR, and ESI-MS. LRP4-A was identified to be a highly branching polysaccharide with a backbone of β-(1→6)-linked galactose partially substituted at O-3 position. The branches were composed of (1→3)-linked-Gal, (1→3)-linked-Ara, (1→5)-linked-Ara, and (1→2,4)-linked-Rha. Arabinose, galactose, and glucose were located at the termini of the branches.

  19. Synthesis and structural characterization of pincer type bicyclic diacyloxy- and diazaselenuranes.

    PubMed

    Selvakumar, K; Singh, Harkesh B; Goel, Nidhi; Singh, Udai P; Butcher, Ray J

    2011-10-14

    Synthesis and structural characterization of a new class of pincer type bicyclic diacyloxy- and diazaselenuranes is reported. The reaction of dimethyl 2-bromo-5-tert-butylisophthalate (28) with sodium benzeneselenolate affords the corresponding monoselenide, dimethyl 5-tert-butyl-2-(phenylselanyl)isophthalate (29). Reduction of 29 with LiAlH(4) provides 5-tert-butyl-2-(phenylselanyl)-1,3-phenylene)dimethanol 31. Oxidation of 29 or its hydrolyzed derivative, 5-tert-butyl-2-(phenylselanyl)isophthalic acid (30), with H(2)O(2) results in the formation of bicyclic diacyloxyselenurane (25). The reaction of 30 with aniline using the DCC coupling reaction gives 5-tert-butyl-N(1),N(3)-diphenyl-2-(phenylselanyl)isophthalamide (38). Reaction of 38 with H(2)O(2) leads to the formation of the corresponding bicyclic diazaselenurane (27) via selenoxide intermediate 39. Compounds 25, 27, 29 and 31 were characterized by single crystal X-ray crystallography. The structural aspects of the pincer type bicyclic chalcogenuranes are investigated using experimental and computational studies and compared with the related systems. PMID:21850325

  20. [Characterizing methods of structure and character for silane film on metal surface].

    PubMed

    Xu, Yi; Tang, Shou-yuan; Zhang, Xiao-feng

    2004-04-01

    Surface analysis methods for structure and characters of silane film on metal surface were reviewed in this paper. Many instrumental methods, such as XPS, ATR-FTIR, RA-FTIR, SIMS, ellipsometry, EIS and so on, were applied to characterizing different silane films on different metal base surfaces. According to the research on silane film formation mechanism, silane film state, silane film structure, silane film thickness, silane film corrosion resistance and so on, factors which affect silane film properties were discussed. Various parameters were proposed for characterizing silane film. Merits and defects of various surface analysis methods were expressed. In order to acquire more chemical information, different surface analysis methods can be combined for detection at the same time. Regarding the results from these detection and analysis, new silane treatment technique for metal surface can be optimized and improved greatly. Some other kinds of surface analysis methods were also mentioned in this paper. More advanced researches in the field of silane film analysis on metal surface were prospected. PMID:15766167

  1. Dynamic characterization of contact interactions of micro-robotic leg structures

    NASA Astrophysics Data System (ADS)

    Ryou, Jeong Hoon; Oldham, Kenn Richard

    2014-05-01

    Contact dynamics of microelectromechanical systems (MEMS) are typically complicated and it is consequently difficult to model all dynamic characteristics observed in time-domain responses involving impact. This issue becomes worse when a device, such as a mobile micro-robot, is not clamped to a substrate and has a complex mechanical structure. To characterize such a contact interaction situation, two walking micro-robot prototypes are tested having intentionally simple structures with different dimensions (21.2 mm × 16.3 mm × 0.75 mm and 32 mm × 25.4 mm × 4.1 mm) and weights (0.16 and 2.7 g). Contact interaction behaviors are characterized by analyzing experimental data under various excitation signals. A numerical approach was used to derive a novel contact model consisting of a coefficient of restitution matrix that uses modal vibration information. Experimental validation of the simulation model shows that it captures various dynamic features of the contact interaction when simulating leg behavior more accurately than previous contact models, such as single-point coefficient of restitution or compliant ground models. In addition, this paper shows that small-scale forces can be added to the simulation to improve model accuracy, resulting in average errors across driving conditions on the order of 2-6% for bounce frequency, maximum foot height, and average foot height, although there is substantial variation from case to case.

  2. Structural and Functional Characterization of Recombinant Interleukin-10 from Indian Major Carp Labeo rohita

    PubMed Central

    Karan, Sweta; Dash, Pujarini; Kaushik, Himani; Sahoo, Pramoda K.; Garg, Lalit C.

    2016-01-01

    Interleukin-10, an important regulator of both the innate and adaptive immune systems, is a multifunctional major cytokine. Though it is one of the major cytokines, IL-10 from the Indian major carp, Labeo rohita, has not yet been characterized. In the present study, we report large scale production and purification of biologically active recombinant IL-10 of L. rohita (rLrIL-10) using a heterologous expression system and its biophysical and functional characterization. High yield (~70 mg/L) of soluble rLrIL-10 was obtained at shake flask level. The rLrIL-10 was found to exist as a dimer. Far-UV CD spectroscopy showed presence of predominantly alpha helices. The tertiary structure of the purified rLrIL-10 was verified by fluorescence spectroscopy. Two-dimensional gel analysis revealed the presence of six isoforms of the rLrIL-10. The rLrIL-10 was biologically active and its administration significantly reduced serum proinflammatory cytokines, namely, interleukin 1β, TNFα, and IL-8, and augmented the NKEF transcript levels in spleen of L. rohita. Anti-inflammatory role of the rLrIL-10 was further established by inhibition of phagocytosis using NBT reduction assay in vitro. The data indicate that the dimeric alpha helical structure and function of IL-10 of L. rohita as a key regulator of anti-inflammatory response have remained conserved during evolution.

  3. Characterization of the solution structure of a neuroligin/beta-neurexin complex.

    PubMed

    Comoletti, Davide; Grishaev, Alexander; Whitten, Andrew E; Taylor, Palmer; Trewhella, Jill

    2008-09-25

    Neuroligins are post-synaptic cell adhesion molecules that promote synaptic maturation and stabilization upon binding with pre-synaptic partners, the alpha- and beta-neurexins. Using a combination of analytical ultracentrifugation, small angle X-ray, and neutron scattering, we have characterized the low-resolution three-dimensional structure of the extracellular domain of the neuroligins, free in solution, and in complex with beta-neurexin. The globular extracellular domain of the neuroligins forms stable homodimers through a four-helix bundle typical of the cholinesterases and other members of the alpha/beta-hydrolase fold family. The presence of the stalk region adds to the extracellular domain of neuroligin-1 an elongated structure, suggesting a rod-like nature of the stalk domain. Sedimentation equilibrium coupled with solution scattering data of the beta-neurexin/neuroligin-1 complex indicated a 2:2 stoichiometry where two beta-neurexin molecules bind to a neuroligin-1 dimer. Deuteration of neurexin allowed us to collect neutron scattering data that, in combination with other biochemical techniques, provide a basis for optimizing the positioning of each component in a detailed computational model of the neuroligin/neurexin complex. As several mutations of both neurexin and neuroligin genes have been linked to autism spectrum disorders and mental retardation, these new structures provide an important framework for the study of altered structure and function of these synaptic proteins.

  4. Structural, Nanomechanical and Nanotribological Characterization of Human Hair Using Atomic Force Microscopy and Nanoindentation

    NASA Astrophysics Data System (ADS)

    Bhushan, Bharat; Latorre, Carmen; Wei, Guohua

    Human hair is a nanocomposite biological fiber. Healthy, soft hair with good feel, shine, color and overall aesthetics is generally highly desirable. It is important to study hair care products such as shampoos and conditioners as well as damaging processes such as chemical dyeing and permanent wave treatments because they affect the maintenance and grooming process and therefore alter many hair properties. Nanoscale characterization of the cellular structure, the mechanical properties, as well as the morphological, frictional and adhesive properties (tribological properties) of hair is essential if we wish to evaluate and develop better cosmetic products, and crucial to advancing the understanding of biological and cosmetic science. The atomic/friction force microscope (AFM/FFM) and nanoindenter have recently become important tools for studying the micro/nanoscale properties of human hair. In this chapter, we present a comprehensive review of structural, mechanical, and tribological properties of various hair and skin as a function of ethnicity, damage, conditioning treatment, and various environments. Various cellular structures of human hair and fine sublamellar structures of the cuticle are identified and studied. Nanomechanical properties such as hardness, elastic modulus, creep and scratch resistance are discussed. Nanotribological properties such as roughness, friction, and adhesion are presented, as well as investigations of conditioner distribution, thickness and binding interactions.

  5. The design and structural characterization of a synthetic pentatricopeptide repeat protein.

    PubMed

    Gully, Benjamin S; Shah, Kunal R; Lee, Mihwa; Shearston, Kate; Smith, Nicole M; Sadowska, Agata; Blythe, Amanda J; Bernath-Levin, Kalia; Stanley, Will A; Small, Ian D; Bond, Charles S

    2015-02-01

    Proteins of the pentatricopeptide repeat (PPR) superfamily are characterized by tandem arrays of a degenerate 35-amino-acid α-hairpin motif. PPR proteins are typically single-stranded RNA-binding proteins with essential roles in organelle biogenesis, RNA editing and mRNA maturation. A modular, predictable code for sequence-specific binding of RNA by PPR proteins has recently been revealed, which opens the door to the de novo design of bespoke proteins with specific RNA targets, with widespread biotechnological potential. Here, the design and production of a synthetic PPR protein based on a consensus sequence and the determination of its crystal structure to 2.2 Å resolution are described. The crystal structure displays helical disorder, resulting in electron density representing an infinite superhelical PPR protein. A structural comparison with related tetratricopeptide repeat (TPR) proteins, and with native PPR proteins, reveals key roles for conserved residues in directing the structure and function of PPR proteins. The designed proteins have high solubility and thermal stability, and can form long tracts of PPR repeats. Thus, consensus-sequence synthetic PPR proteins could provide a suitable backbone for the design of bespoke RNA-binding proteins with the potential for high specificity.

  6. Structural and Enzymatic characterization of the lactonase SisLac from Sulfolobus islandicus

    PubMed Central

    Chabriere, Eric; Elias, Mikael

    2012-01-01

    Background A new member of the Phosphotriesterase-Like Lactonases (PLL) family from the hyperthermophilic archeon Sulfolobus islandicus (SisLac) has been characterized. SisLac is a native lactonase that exhibits a high promiscuous phosphotriesterase activity. SisLac thus represents a promising target for engineering studies, exhibiting both detoxification and bacterial quorum quenching abilities, including human pathogens such as Pseudomonas aeruginosa. Methodology/Principal Findings Here, we describe the substrate specificity of SisLac, providing extensive kinetic studies performed with various phosphotriesters, esters, N-acyl-homoserine lactones (AHLs) and other lactones as substrates. Moreover, we solved the X-ray structure of SisLac and structural comparisons with the closely related SsoPox structure highlighted differences in the surface salt bridge network and the dimerization interface. SisLac and SsoPox being close homologues (91% sequence identity), we undertook a mutational study to decipher these structural differences and their putative consequences on the stability and the catalytic properties of these proteins. Conclusions/Significance We show that SisLac is a very proficient lactonase against aroma lactones and AHLs as substrates. Hence, data herein emphasize the potential role of SisLac as quorum quenching agent in Sulfolobus. Moreover, despite the very high sequence homology with SsoPox, we highlight key epistatic substitutions that influence the enzyme stability and activity. PMID:23071703

  7. Near-complete structural characterization of phosphatidylcholines using electron impact excitation of ions from organics.

    PubMed

    Campbell, J Larry; Baba, Takashi

    2015-06-01

    Although lipids are critical components of many cellular assemblies and biological pathways, accurate descriptions of their molecular structures remain difficult to obtain. Many benchtop characterization methods require arduous and time-consuming procedures, and multiple assays are required whenever a new structural feature is probed. Here, we describe a new mass-spectrometry-based workflow for enhanced structural lipidomics that, in a single experiment, can yield almost complete structural information for a given glycerophospholipid (GPL) species. This includes the lipid's sum (Brutto) composition from the accurate mass measured for the intact lipid ion and the characteristic headgroup fragment, the regioisomer composition from fragment ions unique to the sn-1 and sn-2 positions, and the positions of carbon-carbon double bonds in the lipid acyl chains. Here, lipid ions are fragmented using electron impact excitation of ions from organics (EIEIO)--a technique where the singly charged lipid ions are irradiated by an electron beam, producing diagnostic product ions. We have evaluated this methodology on various lipid standards, as well as on a biological extract, to demonstrate this new method's utility.

  8. Structural characterization of Turtle Mountain anticline (Alberta, Canada) and impact on rock slope failure

    NASA Astrophysics Data System (ADS)

    Humair, Florian; Pedrazzini, Andrea; Epard, Jean-Luc; Froese, Corey R.; Jaboyedoff, Michel

    2013-10-01

    This paper proposes a structural investigation of the Turtle Mountain anticline (Alberta, Canada) to better understand the role of the different tectonic features on the development of both local and large scale rock slope instabilities occurring in Turtle Mountain. The study area is investigated by combining remote methods with detailed field surveys. In particular, the benefit of Terrestrial Laser Scanning for ductile and brittle tectonic structure interpretations is illustrated. The proposed tectonic interpretation allows the characterization of the fracturing pattern, the fold geometry and the role of these tectonic features in rock slope instability development. Ten discontinuity sets are identified in the study area, their local variations permitting the differentiation of the study zone into 20 homogenous structural domains. The anticline is described as an eastern verging fold that displays considerable geometry differences along its axis and developed by both flexural slip and tangential longitudinal strain folding mechanisms. Moreover, the origins of the discontinuity sets are determined according to the tectonic phases affecting the region (pre-folding, folding, post-folding). The localization and interpretation of kinematics of the different instabilities revealed the importance of considering the discrete brittle planes of weakness, which largely control the kinematic release of the local instabilities, and also the rock mass damage induced by large tectonic structures (fold hinge, thrust).

  9. A hirshfeld surface analysis, crystal structure and physicochemical characterization of 1-ethylpiperazinium trichlorocadmate(II)

    NASA Astrophysics Data System (ADS)

    Soudani, S.; Jeanneau, E.; Jelsch, C.; Lefebvre, F.; Ben Nasr, C.

    2016-07-01

    A novel organic-inorganic hybrid material, C6H15N2CdCl3.H2O, was synthesized, and its structure was determined at room temperature in the monoclinic space group P21/n with the following parameters: a = 10.3829 (17), b = 7.7459 (12), c = 14.905 (2) Å, β = 98.801 (15), and Z = 4. Its crystal structure is characterized by one-dimensional polymeric chains of edge-sharing CdCl5N distorted octahedra. These chains are linked to the water molecules via Osbnd H … Cl hydrogen bonds to form layers parallel to the (b, a + c) plane. The crystal structure was stabilized by an extensive network of Nsbnd H … Cl, Osbnd H … Cl and Nsbnd H … O hydrogen bonds. The differential scanning calorimetry (DSC) reveals that the title compound is stable until 101.6 °C. The optimized geometry parameters, normal mode frequencies, and corresponding vibrational assignments of the present compound were theoretically examined by DFT/B3LYP method with the Lanl2dz basis set. The FT-IR spectrum of the polycrystalline sample was examined and compared to the calculated spectrum. The calculated results showed that the optimized geometry could well reproduce the crystal structure and that the theoretical vibrational frequency values were in good agreement with their experimental counterparts.

  10. Amino-Functionalized Layered Crystalline Zirconium Phosphonates: Synthesis, Crystal Structure, and Spectroscopic Characterization.

    PubMed

    Taddei, Marco; Sassi, Paola; Costantino, Ferdinando; Vivani, Riccardo

    2016-06-20

    Two new layered zirconium phosphonates functionalized with amino groups were synthesized starting from aminomethylphosphonic acid in the presence of different mineralizers, and their structures were solved from powder X-ray diffraction data. Their topologies are unprecedented in zirconium phosphonate chemistry: the first, of formula ZrH[F3(O3PCH2NH2)], prepared in the presence of hydrofluoric acid, features uncommon ZrO2F4 units and a remarkable thermal stability; the second, of formula Zr2H2[(C2O4)3(O3PCH2NH2)2]·2H2O, prepared in the presence of oxalic acid, is based on ZrO7 units with oxalate anions coordinated to the metal atom, which were never observed before in any zirconium phosphonate. In addition, the structure of another compound based on (2-aminoethyl)phosphonic acid is reported, which was the object of a previously published study. This compound has layered α-type structure with -NH3(+) groups located in the interlayer space. All of the reported compounds were further characterized by means of vibrational spectroscopy, which provided important information on fine structural details that cannot be deduced from the powder X-ray diffraction data. PMID:27254781

  11. Characterization of multiscroll attractors using Lyapunov exponents and Lagrangian coherent structures.

    PubMed

    Fazanaro, Filipe I; Soriano, Diogo C; Suyama, Ricardo; Attux, Romis; Madrid, Marconi K; de Oliveira, José Raimundo

    2013-06-01

    The present work aims to apply a recently proposed method for estimating Lyapunov exponents to characterize-with the aid of the metric entropy and the fractal dimension-the degree of information and the topological structure associated with multiscroll attractors. In particular, the employed methodology offers the possibility of obtaining the whole Lyapunov spectrum directly from the state equations without employing any linearization procedure or time series-based analysis. As a main result, the predictability and the complexity associated with the phase trajectory were quantified as the number of scrolls are progressively increased for a particular piecewise linear model. In general, it is shown here that the trajectory tends to increase its complexity and unpredictability following an exponential behaviour with the addition of scrolls towards to an upper bound limit, except for some degenerated situations where a non-uniform grid of scrolls is attained. Moreover, the approach employed here also provides an easy way for estimating the finite time Lyapunov exponents of the dynamics and, consequently, the Lagrangian coherent structures for the vector field. These structures are particularly important to understand the stretching/folding behaviour underlying the chaotic multiscroll structure and can provide a better insight of phase space partition and exploration as new scrolls are progressively added to the attractor.

  12. Crystal structure and functional characterization of a light-driven chloride pump having an NTQ motif

    PubMed Central

    Kim, Kuglae; Kwon, Soon-Kyeong; Jun, Sung-Hoon; Cha, Jeong Seok; Kim, Hoyoung; Lee, Weontae; Kim, Jihyun F.; Cho, Hyun-Soo

    2016-01-01

    A novel light-driven chloride-pumping rhodopsin (ClR) containing an ‘NTQ motif' in its putative ion conduction pathway has been discovered and functionally characterized in a genomic analysis study of a marine bacterium. Here we report the crystal structure of ClR from the flavobacterium Nonlabens marinus S1-08T determined under two conditions at 2.0 and 1.56 Å resolutions. The structures reveal two chloride-binding sites, one around the protonated Schiff base and the other on a cytoplasmic loop. We identify a ‘3 omega motif' formed by three non-consecutive aromatic amino acids that is correlated with the B–C loop orientation. Detailed ClR structural analyses with functional studies in E. coli reveal the chloride ion transduction pathway. Our results help understand the molecular mechanism and physiological role of ClR and provide a structural basis for optogenetic applications. PMID:27554809

  13. Characterizing changes in soil bacterial community structure in response to short-term warming.

    PubMed

    Xiong, Jinbo; Sun, Huaibo; Peng, Fei; Zhang, Huayong; Xue, Xian; Gibbons, Sean M; Gilbert, Jack A; Chu, Haiyan

    2014-08-01

    High altitude alpine meadows are experiencing considerably greater than average increases in soil surface temperature, potentially as a result of ongoing climate change. The effects of warming on plant productivity and soil edaphic variables have been established previously, but the influence of warming on soil microbial community structure has not been well characterized. Here, the impact of 15 months of soil warming (both +1 and +2 °C) on bacterial community structure was examined in a field experiment on a Tibetan plateau alpine meadow using bar-coded pyrosequencing. Warming significantly changed (P < 0.05) the structure of the soil bacterial community, but the alpha diversity was not dramatically affected. Changes in the abundance of the Actinobacteria and Alphaproteobacteria were found to contribute the most to differences between ambient (AT) and artificially warmed conditions. A variance partitioning analysis (VPA) showed that warming directly explained 7.15% variation in bacterial community structure, while warming-induced changes in soil edaphic and plant phenotypic properties indirectly accounted for 28.3% and 20.6% of the community variance, respectively. Interestingly, certain taxa showed an inconsistent response to the two warming treatments, for example Deltaproteobacteria showed a decreased relative abundance at +1 °C, but a return to AT control relative abundance at +2 °C. This suggests complex microbial dynamics that could result from conditional dependencies between bacterial taxa.

  14. Structural and Biochemical Characterization of Compounds Inhibiting Mycobacterium tuberculosis Pantothenate Kinase*

    PubMed Central

    Björkelid, Christofer; Bergfors, Terese; Raichurkar, Anand Kumar V.; Mukherjee, Kakoli; Malolanarasimhan, Krishnan; Bandodkar, Balachandra; Jones, T. Alwyn

    2013-01-01

    Mycobacterium tuberculosis, the bacterial causative agent of tuberculosis, currently affects millions of people. The emergence of drug-resistant strains makes development of new antibiotics targeting the bacterium a global health priority. Pantothenate kinase, a key enzyme in the universal biosynthesis of the essential cofactor CoA, was targeted in this study to find new tuberculosis drugs. The biochemical characterizations of two new classes of compounds that inhibit pantothenate kinase from M. tuberculosis are described, along with crystal structures of their enzyme-inhibitor complexes. These represent the first crystal structures of this enzyme with engineered inhibitors. Both classes of compounds bind in the active site of the enzyme, overlapping with the binding sites of the natural substrate and product, pantothenate and phosphopantothenate, respectively. One class of compounds also interferes with binding of the cofactor ATP. The complexes were crystallized in two crystal forms, one of which is in a new space group for this enzyme and diffracts to the highest resolution reported for any pantothenate kinase structure. These two crystal forms allowed, for the first time, modeling of the cofactor-binding loop in both open and closed conformations. The structures also show a binding mode of ATP different from that previously reported for the M. tuberculosis enzyme but similar to that in the pantothenate kinases of other organisms. PMID:23661699

  15. Structural characterization of Spinacia oleracea trypsin inhibitor III (SOTI-III).

    PubMed

    Glotzbach, Bernhard; Schmelz, Stefan; Reinwarth, Michael; Christmann, Andreas; Heinz, Dirk W; Kolmar, Harald

    2013-01-01

    In recent decades, several canonical serine protease inhibitor families have been classified and characterized. In contrast to most trypsin inhibitors, those from garden four o'clock (Mirabilis jalapa) and spinach (Spinacia oleracea) do not share sequence similarity and have been proposed to form the new Mirabilis serine protease inhibitor family. These 30-40-amino-acid inhibitors possess a defined disulfide-bridge topology and belong to the cystine-knot miniproteins (knottins). To date, no atomic structure of this inhibitor family has been solved. Here, the first structure of S. oleracea trypsin inhibitor III (SOTI-III), in complex with bovine pancreatic trypsin, is reported. The inhibitor was synthesized by solid-phase peptide synthesis on a multi-milligram scale and was assayed to test its inhibitory activity and binding properties. The structure confirmed the proposed cystine-bridge topology. The structural features of SOTI-III suggest that it belongs to a new canonical serine protease inhibitor family with promising properties for use in protein-engineering and medical applications.

  16. Characterizing the nonlinear growth of large-scale structure in the Universe

    PubMed

    Coles; Chiang

    2000-07-27

    The local Universe displays a rich hierarchical pattern of galaxy clusters and superclusters. The early Universe, however, was almost smooth, with only slight 'ripples' as seen in the cosmic microwave background radiation. Models of the evolution of cosmic structure link these observations through the effect of gravity, because the small initially overdense fluctuations are predicted to attract additional mass as the Universe expands. During the early stages of this expansion, the ripples evolve independently, like linear waves on the surface of deep water. As the structures grow in mass, they interact with each other in nonlinear ways, more like waves breaking in shallow water. We have recently shown how cosmic structure can be characterized by phase correlations associated with these nonlinear interactions, but it was not clear how to use that information to obtain quantitative insights into the growth of structures. Here we report a method of revealing phase information, and show quantitatively how this relates to the formation of filaments, sheets and clusters of galaxies by nonlinear collapse. We develop a statistical method based on information entropy to separate linear from nonlinear effects, and thereby are able to disentangle those aspects of galaxy clustering that arise from initial conditions (the ripples) from the subsequent dynamical evolution.

  17. Fabrication, polarization, and characterization of PVDF matrix composites for integrated structural load sensing

    NASA Astrophysics Data System (ADS)

    Haghiashtiani, Ghazaleh; Greminger, Michael A.

    2015-04-01

    The focus of this work is to evaluate a new carbon fiber reinforced composite structure with integrated sensing capabilities. In this composite structure, the typical matrix material used for carbon fiber reinforced composites is replaced with the thermoplastic polyvinylidene difluoride (PVDF). Since PVDF has piezoelectric properties, it enables the structure to be used for integrated load sensing. In addition, the electrical conductivity property of the carbon fabric is harnessed to form the electrodes of the integrated sensor. In order to prevent the carbon fiber electrodes from shorting to each other, a thin Kevlar fabric layer is placed between the two carbon fiber electrode layers as a dielectric. The optimal polarization parameters were determined using a design of experiments approach. Once polarized, the samples were then used in compression and tensile tests to determine the effective d33 and d31 piezoelectric coefficients. The degree of polarization of the PVDF material was determined by relating the effective d33 coefficient of the composite to the achieved d33 of the PVDF component of the composite using a closed form expression. Using this approach, it was shown that optimal polarization of the composite material results in a PVDF component d33 of 3.2 pC N-1. Moreover, the Young’s modulus of the composite structure has been characterized.

  18. Deployment, Foam Rigidization, and Structural Characterization of Inflatable Thin-Film Booms

    NASA Technical Reports Server (NTRS)

    Schnell, Andrew R.; Leigh, Larry M., Jr.; Tinker, Michael L.; McConnaughey, Paul R. (Technical Monitor)

    2002-01-01

    Detailed investigation of the construction, packaging/deployment, foam rigidization, and structural characterization of polyimide film inflatable booms is described. These structures have considerable potential for use in space with solar concentrators, solar sails, space power systems including solar arrays, and other future missions. Numerous thin-film booms or struts were successfully constructed, inflated, injected with foam, and rigidized. Both solid-section and annular test articles were fabricated, using Kapton polyimide film, various adhesives, Styrofoam end plugs, and polyurethane pressurized foam. Numerous inflation/deployment experiments were conducted and compared to computer simulations using the MSC/DYTRAN code. Finite element models were developed for several foam-rigidized struts and compared to model test results. Several problems encountered in the construction, deployment, and foam injection/rigidization process are described. Areas of difficulty included inadequate adhesive strength, cracking of the film arid leakage, excessive bending of the structure during deployment, problems with foam distribution and curing properties, and control of foam leakage following injection into the structure. Many of these problems were overcome in the course of the research.

  19. Low-resolution characterization of the 3D structure of the Euglena gracilis photoreceptor

    SciTech Connect

    Barsanti, Laura; Coltelli, Primo; Evangelista, Valtere; Passarelli, Vincenzo; Frassanito, Anna Maria; Vesentini, Nicoletta; Gualtieri, Paolo

    2008-10-24

    This paper deals with the first characterization of the structure of the photoreceptive organelle of the unicellular alga Euglena gracilis (Euglenophyta). This organelle has a three-dimensional organization consisting of up to 50 closely stacked membrane lamellae. Ionically induced unstacking of the photoreceptor lamellae revealed ordered arrays well suited to structural analysis by electron microscopy and image analysis, which ultimately yielded a low-resolution picture of the structure. Each lamella is formed by the photoreceptive membrane protein of the cell assembled within the membrane layer in a hexagonal lattice. The first order diffraction spots in the calculated Fourier transform reveals the presence of 6-fold symmetrized topography (better resolution about 90 A). The 2D and 3D structural data are very similar with those recently published on proteorodopsin, a membrane protein used by marine bacterio-plankton as light-driven proton pump. In our opinion these similarity indicate that a photoreceptive protein belonging to the same superfamily of proteorodopsin could form the Euglena photoreceptor.

  20. Evaluation of water sampling methodologies for amplicon-based characterization of bacterial community structure.

    PubMed

    Staley, Christopher; Gould, Trevor J; Wang, Ping; Phillips, Jane; Cotner, James B; Sadowsky, Michael J

    2015-07-01

    Reduction in costs of next-generation sequencing technologies has allowed unprecedented characterization of bacterial communities from environmental samples including aquatic ecosystems. However, the extent to which extrinsic factors including sampling volume, sample replication, DNA extraction kits, and sequencing target affect the community structure inferred are poorly explored. Here, triplicate 1, 2, and 6L volume water samples from the Upper Mississippi River were processed to determine variation among replicates and sample volumes. Replicate variability significantly influenced differences in the community α-diversity (P=0.046), while volume significantly changed β-diversity (P=0.037). Differences in phylogenetic and taxonomic community structure differed both among triplicate samples and among the volumes filtered. Communities from 2L and 6L water samples showed similar clustering via discriminant analysis. To assess variation due to DNA extraction method, DNA was extracted from triplicate cell pellets from four sites along the Upper Mississippi River using the Epicentre Metagenomic DNA Isolation Kit for Water and MoBio PowerSoil kit. Operational taxonomic units representing ≤14% of sequence reads differed significantly among all sites and extraction kits used, although differences in diversity and community coverage were not significant (P≥0.057). Samples characterized using only the V6 region had significantly higher coverage and lower richness and α-diversity than those characterized using V4-V6 regions (P<0.001). Triplicate sampling of at least 2L of water provides robust representation of community variability, and these results indicate that DNA extraction kit and sequencing target displayed taxonomic biases that did not affect the overall biological conclusions drawn. PMID:25956022

  1. Structural Characterization of Melanin Pigments from Commercial Preparations of the Edible Mushroom Auricularia auricula

    PubMed Central

    Prados-Rosales, Rafael; Toriola, Stacy; Nakouzi, Antonio; Chatterjee, Subhasish; Stark, Ruth; Gerfen, Gary; Tumpowsky, Paul; Dadachova, Ekaterina; Casadevall, Arturo

    2016-01-01

    Many of the most widely consumed edible mushrooms are pigmented, and these have been associated with some beneficial health effects. Nevertheless, the majority of the reported compounds associated with these desirable properties are non-pigmented. We have previously reported that melanin pigment from the edible mushroom Auricularia auricula can protect mice against ionizing radiation, although no physicochemical characterization was reported. Consequently, in this study we have characterized commercial A. auricula mushroom preparations for melanin content and carried out structural characterization of isolated insoluble melanin materials using a panel of sophisticated spectroscopic and physical/imaging techniques. Our results show that approximately 10% of the dry mass of A. auricula is melanin and that the pigment has physicochemical properties consistent with those of eumelanins, including hosting a stable free radical population. Electron microscopy studies show that melanin is associated with the mushroom cell wall in a manner similar to that of melanin from the model fungus C. neoformans. Elemental analysis of melanin indicated C, H, and N ratios consistent with 5,6-dihydroxyindole-2-carboxylic acid/5,6-dihydroxyindole and 1,8-dihydroxynaphthalene eumelanin. Validation of the identity of the isolated product as melanin was achieved by EPR analysis. A. auricula melanin manifested structural differences, relative to the C. neoformans melanin, with regard to the variable proportions of alkyl chains or oxygenated carbons. Given the necessity for new oral and inexpensive radioprotective materials coupled with the commercial availability of A. auricula mushrooms, this product may represent an excellent source of edible melanin. PMID:26244793

  2. Structural characterization and DFT study of V(IV)O(acac)2 in imidazolium ionic liquids.

    PubMed

    Mota, Andreia; Hallett, Jason P; Kuznetsov, Maxim L; Correia, Isabel

    2011-09-01

    We report the structural characterization of vanadyl acetylacetonate in imidazolium room temperature ionic liquids--bbimNTf(2), bmimNTf(2), C(3)OmimNTf(2), bm(2)imNTf(2), bmimPF(6), bmimOTf, bmimBF(4), bmimMeCO(2), bmimMeSO(4), bmimMe(2)PO(4) and bmimN(CN)(2)--and organic solvents. The complex was characterized by visible electronic (Vis) and EPR spectroscopies. VO(acac)(2) shows solvatochromism in the selected ionic liquids and behaves as in organic solvents, evidencing coordination of the ionic liquid anion in the solvents with higher coordinating ability. The Lewis basicity order obtained for the IL anions was: PF(6)(-) < NTf(2)(-) < OTf(-)≈ MeCO(2)(-) < MeSO(4)(-) < BF(4)(-)≈ N(CN)(2)(-) < Me(2)PO(4)(-). The solvent effect on the spectroscopic data was tentatively examined using linear solvation energy relationships based on the Kamlet-Taft solvent scale (α, β and π*), however no suitable correlation was found with all data. The EPR characterization showed the presence of two isomers in bmimOTf, bmimMeCO(2) and bmimMe(2)PO(4), suggesting coordination of the ionic liquid anions in both equatorial and axial positions. The full geometry optimization of cis-/trans-VO(acac)(2)(OTf)(-) and cis-/trans-VO(acac)(2)(OTf)(mmim) structures was done at the B3P86/6-31G* level of theory. The calculations confirm that the anion OTf(-) is able to coordinate to VO(acac)(2) with the trans isomer being more stable than the cis by 4.8 kcal mol(-1). PMID:21789301

  3. Structural Characterization of HIV gp41 with the Membrane-proximal External Region

    SciTech Connect

    Shi, W.; Bohon, J; Han, D; Habte, H; Qin, Y; Cho, M; Chance, M

    2010-01-01

    Human immunodeficiency virus, type 1 (HIV-1) envelope glycoprotein (gp120/gp41) plays a critical role in virus infection and pathogenesis. Three of the six monoclonal antibodies considered to have broadly neutralizing activities (2F5, 4E10, and Z13e1) bind to the membrane-proximal external region (MPER) of gp41. This makes the MPER a desirable template for developing immunogens that can elicit antibodies with properties similar to these monoclonal antibodies, with a long term goal of developing antigens that could serve as novel HIV vaccines. In order to provide a structural basis for rational antigen design, an MPER construct, HR1-54Q, was generated for x-ray crystallographic and x-ray footprinting studies to provide both high resolution atomic coordinates and verification of the solution state of the antigen, respectively. The crystal structure of HR1-54Q reveals a trimeric, coiled-coil six-helical bundle, which probably represents a postfusion form of gp41. The MPER portion extends from HR2 in continuation of a slightly bent long helix and is relatively flexible. The structures observed for the 2F5 and 4E10 epitopes agree well with existing structural data, and enzyme-linked immunosorbent assays indicate that the antigen binds well to antibodies that recognize the above epitopes. Hydroxyl radical-mediated protein footprinting of the antigen in solution reveals specifically protected and accessible regions consistent with the predictions based on the trimeric structure from the crystallographic data. Overall, the HR1-54Q antigen, as characterized by crystallography and footprinting, represents a postfusion, trimeric form of HIV gp41, and its structure provides a rational basis for gp41 antigen design suitable for HIV vaccine development.

  4. Structural characterization of HIV gp41 with the membrane-proximal external region.

    PubMed

    Shi, Wuxian; Bohon, Jen; Han, Dong P; Habte, Habtom; Qin, Yali; Cho, Michael W; Chance, Mark R

    2010-07-30

    Human immunodeficiency virus, type 1 (HIV-1) envelope glycoprotein (gp120/gp41) plays a critical role in virus infection and pathogenesis. Three of the six monoclonal antibodies considered to have broadly neutralizing activities (2F5, 4E10, and Z13e1) bind to the membrane-proximal external region (MPER) of gp41. This makes the MPER a desirable template for developing immunogens that can elicit antibodies with properties similar to these monoclonal antibodies, with a long term goal of developing antigens that could serve as novel HIV vaccines. In order to provide a structural basis for rational antigen design, an MPER construct, HR1-54Q, was generated for x-ray crystallographic and x-ray footprinting studies to provide both high resolution atomic coordinates and verification of the solution state of the antigen, respectively. The crystal structure of HR1-54Q reveals a trimeric, coiled-coil six-helical bundle, which probably represents a postfusion form of gp41. The MPER portion extends from HR2 in continuation of a slightly bent long helix and is relatively flexible. The structures observed for the 2F5 and 4E10 epitopes agree well with existing structural data, and enzyme-linked immunosorbent assays indicate that the antigen binds well to antibodies that recognize the above epitopes. Hydroxyl radical-mediated protein footprinting of the antigen in solution reveals specifically protected and accessible regions consistent with the predictions based on the trimeric structure from the crystallographic data. Overall, the HR1-54Q antigen, as characterized by crystallography and footprinting, represents a postfusion, trimeric form of HIV gp41, and its structure provides a rational basis for gp41 antigen design suitable for HIV vaccine development. PMID:20525690

  5. Structural Characterization of HIV gp41 with the Membrane-proximal External Region*

    PubMed Central

    Shi, Wuxian; Bohon, Jen; Han, Dong P.; Habte, Habtom; Qin, Yali; Cho, Michael W.; Chance, Mark R.

    2010-01-01

    Human immunodeficiency virus, type 1 (HIV-1) envelope glycoprotein (gp120/gp41) plays a critical role in virus infection and pathogenesis. Three of the six monoclonal antibodies considered to have broadly neutralizing activities (2F5, 4E10, and Z13e1) bind to the membrane-proximal external region (MPER) of gp41. This makes the MPER a desirable template for developing immunogens that can elicit antibodies with properties similar to these monoclonal antibodies, with a long term goal of developing antigens that could serve as novel HIV vaccines. In order to provide a structural basis for rational antigen design, an MPER construct, HR1-54Q, was generated for x-ray crystallographic and x-ray footprinting studies to provide both high resolution atomic coordinates and verification of the solution state of the antigen, respectively. The crystal structure of HR1-54Q reveals a trimeric, coiled-coil six-helical bundle, which probably represents a postfusion form of gp41. The MPER portion extends from HR2 in continuation of a slightly bent long helix and is relatively flexible. The structures observed for the 2F5 and 4E10 epitopes agree well with existing structural data, and enzyme-linked immunosorbent assays indicate that the antigen binds well to antibodies that recognize the above epitopes. Hydroxyl radical-mediated protein footprinting of the antigen in solution reveals specifically protected and accessible regions consistent with the predictions based on the trimeric structure from the crystallographic data. Overall, the HR1-54Q antigen, as characterized by crystallography and footprinting, represents a postfusion, trimeric form of HIV gp41, and its structure provides a rational basis for gp41 antigen design suitable for HIV vaccine development. PMID:20525690

  6. Mechanical characterization and structural analysis of recycled fiber-reinforced-polymer resin-transfer-molded beams

    NASA Astrophysics Data System (ADS)

    Tan, Eugene Wie Loon

    1999-09-01

    The present investigation was focussed on the mechanical characterization and structural analysis of resin-transfer-molded beams containing recycled fiber-reinforced polymers. The beams were structurally reinforced with continuous unidirectional glass fibers. The reinforcing filler materials consisted entirely of recycled fiber-reinforced polymer wastes (trim and overspray). The principal resin was a 100-percent dicyclo-pentadiene unsaturated polyester specially formulated with very low viscosity for resin transfer molding. Variations of the resin transfer molding technique were employed to produce specimens for material characterization. The basic materials that constituted the structural beams, continuous-glass-fiber-reinforced, recycled-trim-filled and recycled-overspray-filled unsaturated polyesters, were fully characterized in axial and transverse compression and tension, and inplane and interlaminar shear, to ascertain their strengths, ultimate strains, elastic moduli and Poisson's ratios. Experimentally determined mechanical properties of the recycled-trim-filled and recycled-overspray-filled materials from the present investigation were superior to those of unsaturated polyester polymer concretes and Portland cement concretes. Mechanical testing and finite element analyses of flexure (1 x 1 x 20 in) and beam (2 x 4 x 40 in) specimens were conducted. These structurally-reinforced specimens were tested and analyzed in four-point, third-point flexure to determine their ultimate loads, maximum fiber stresses and mid-span deflections. The experimentally determined load capacities of these specimens were compared to those of equivalent steel-reinforced Portland cement concrete beams computed using reinforced concrete theory. Mechanics of materials beam theory was utilized to predict the ultimate loads and mid-span deflections of the flexure and beam specimens. However, these predictions proved to be severely inadequate. Finite element (fracture propagation

  7. Structural, mechanical and in vitro characterization of individually structured Ti-6Al-4V produced by direct laser forming.

    PubMed

    Hollander, Dirk A; von Walter, Matthias; Wirtz, Tobias; Sellei, Richard; Schmidt-Rohlfing, Bernhard; Paar, Othmar; Erli, Hans-Josef

    2006-03-01

    Direct laser forming (DLF) is a rapid prototyping technique which enables prompt modelling of metal parts with high bulk density on the base of individual three-dimensional data, including computer tomography models of anatomical structures. In our project, we tested DLF-produced material on the basis of the titanium alloy Ti-6Al-4V for its applicability as hard tissue biomaterial. To this end, we investigated mechanical and structural properties of DLF-Ti-6Al-4V. While the tensile and yield strengths of untreated DLF alloy ranged beyond 1000 MPa, a breaking elongation of 6.5+/-0.6% was determined for this material. After an additional post-DLF annealing treatment, this parameter was increased two-fold to 13.0+/-0.6%, while tensile and yield strengths were reduced by approx. 8%. A Young's modulus of 118.000+/-2.300 MPa was determined for post-DLF annealed Ti-6Al-4V. All data gained from tensile testing of post-DLF annealed Ti-6Al-4V matched American Society of Testing and Materials (ASTM) specifications for the usage of this alloy as medical material. Rotating bending tests revealed that the fatigue profile of post-DLF annealed Ti-6Al-4V was comparable to casted/hot isostatic pressed alloy. We characterized the structure of non-finished DLF-Ti-6Al-4V by scanning electron microscopy and observed a surface-associated layer of particles, which was removable by sandblasting as a finishing step. We manufactured porous specimens with nominal pore diameters of 500, 700 and 1000 microm. The diameters were reduced by the used DLF processing by approx. 300 microm. In an in vitro investigation, we cultured human osteoblasts on non-porous and porous blasted DLF-Ti-6Al-4V specimens to study morphology, vitality, proliferation and differentiation of the cells. The cells spreaded and proliferated on DLF-Ti-6Al-4V over a culture time of 14 days. On porous specimens, osteoblasts grew along the rims of the pores and formed circle-shaped structures, as visualized by live

  8. Characterization of Hertzian rolling microslip in precision revolute joints for deployable space structures

    NASA Astrophysics Data System (ADS)

    Jeon, Sungeun Ki

    2009-09-01

    The capabilities of space-born telescopes are primarily limited by their launch systems, dictating both light-gathering power and resolution, by constricting aperture size. Precision deployable space structure technology enables smaller stowed configurations for launch and a larger deployed operational state in space. The primary engineering difficulties arise from the accuracy and repeatability requirements of the deployed system, where an optical system requires tens of nanometers RMS surface displacement. Recent studies identify that instabilities and errors in a deployable space structure are primarily caused by the stick-slip friction between the contact interfaces of the latches and joints. The intent of this research is to model and characterize the nonlinearities of contact of a precision revolute joint for deployable space structures. The joint is a modified pin-clevis joint, where the deployment mechanism, load-path, and sources of instability are relegated to the contact interfaces of pair of angular contact bearings. This research presents a nonlinear lumped-parameter finite element modeling the nonlinear mechanics of contact to characterize the microdynamic behavior of the angular contact bearings for a precision revolute hinge. The mechanics of contact are based on Hertz contact theory and a numerical simulation subproblem based on the influence function method. The numerical simulation is rigorously validated and is shown to efficiently and effectively model transient rolling contact with varying normal contact forces, where current literature and numerical modeling techniques fail. The in uence of surface roughness and stochastic variations due to manufacturing and assembly are studied in regards to stiffness performance metrics. Rolling hysteresis is identified for various conditions, and a zero-loss rolling mechanism is discovered and investigated. Design implications, capabilities, recommendations, and optimal improvements for the precision hinge

  9. Structural and biochemical characterization of a novel aminopeptidase from human intestine.

    PubMed

    Tykvart, Jan; Bařinka, Cyril; Svoboda, Michal; Navrátil, Václav; Souček, Radko; Hubálek, Martin; Hradilek, Martin; Šácha, Pavel; Lubkowski, Jacek; Konvalinka, Jan

    2015-05-01

    N-acetylated α-linked acidic dipeptidase-like protein (NAALADase L), encoded by the NAALADL1 gene, is a close homolog of glutamate carboxypeptidase II, a metallopeptidase that has been intensively studied as a target for imaging and therapy of solid malignancies and neuropathologies. However, neither the physiological functions nor structural features of NAALADase L are known at present. Here, we report a thorough characterization of the protein product of the human NAALADL1 gene, including heterologous overexpression and purification, structural and biochemical characterization, and analysis of its expression profile. By solving the NAALADase L x-ray structure, we provide the first experimental evidence that it is a zinc-dependent metallopeptidase with a catalytic mechanism similar to that of glutamate carboxypeptidase II yet distinct substrate specificity. A proteome-based assay revealed that the NAALADL1 gene product possesses previously unrecognized aminopeptidase activity but no carboxy- or endopeptidase activity. These findings were corroborated by site-directed mutagenesis and identification of bestatin as a potent inhibitor of the enzyme. Analysis of NAALADL1 gene expression at both the mRNA and protein levels revealed the small intestine as the major site of protein expression and points toward extensive alternative splicing of the NAALADL1 gene transcript. Taken together, our data imply that the NAALADL1 gene product's primary physiological function is associated with the final stages of protein/peptide digestion and absorption in the human digestive system. Based on these results, we suggest a new name for this enzyme: human ileal aminopeptidase (HILAP). PMID:25752612

  10. Syntheses, Structural Characterization and Thermoanalysis of Transition-Metal Compounds Derived from 3,5-Dinitropyridone

    PubMed Central

    Fan, Rong; Zhou, Qiu-Ping; Zhang, Guo-Fang; Cai, Mei-Yu; Li, Ping; Gan, Li-Hua; Zhao, Feng-Qi; Li, Ji-Zhen; Fan, Xue-Zhong; Ng, Seik Weng

    2010-01-01

    Nine metal compounds of Mn(II), Zn(II) and Cd(II) derived from dinitropyridone ligands (3,5-dinitro-pyrid-2-one, 2HDNP; 3,5-dinitropyrid-4-one, 4HDNP and 3,5-dinitropyrid-4-one-N- hydroxide, 4HDNPO) were characterized by elemental analysis, FT-IR and partly by TG-DSC. Three of which were further structurally characterized by X-ray single-crystal diffraction analysis. The structures of the three compounds, Mn(4DNP)2(H2O)4, 4, Zn(4DNPO)2(H2O)4, 8, and Cd(4DNPO)2(H2O)4, 9, crystallize in the monoclinic space group P2(1)/n and Z = 2, with a = 8.9281(9), b = 9.1053(9), c = 10.6881(11) Å, β = 97.9840(10)° for 4; a = 8.4154(7), b = 9.9806(8), c = 10.5695(8) Å, β = 97.3500(10)° for 8; a = 8.5072(7), b = 10.2254(8), c = 10.5075(8) Å, β 96.6500(10)° for 9. All three complexes are octahedral consisting of four equatorial water molecules, and two nitrogen or oxygen donor ligands (DNP or DNPO). The abundant hydrogen-bonding and π-π stacking interactions seem to contribute to stabilization of the crystal structures of the compounds. The TG-DTG results revealed that the complexes showed a weight loss sequence corresponding to all coordinated water molecules, nitro groups, the breaking of the pyridine rings and finally the formation of metal oxides. PMID:20526459

  11. Silver sulfadoxinate: Synthesis, structural and spectroscopic characterizations, and preliminary antibacterial assays in vitro

    NASA Astrophysics Data System (ADS)

    Zanvettor, Nina T.; Abbehausen, Camilla; Lustri, Wilton R.; Cuin, Alexandre; Masciocchi, Norberto; Corbi, Pedro P.

    2015-02-01

    The sulfa drug sulfadoxine (SFX) reacted with Ag+ ions in aqueous solution, affording a new silver(I) complex (AgSFX), which was fully characterized by chemical, spectroscopic and structural methods. Elemental, ESI-TOF mass spectrometric and thermal analyses of AgSFX suggested a [Ag(C12H13N4O2S)] empirical formula. Infrared spectroscopic measurements indicated ligand coordination to Ag(I) through the nitrogen atoms of the (deprotonated) sulfonamide group and by the pyrimidine ring, as well as through oxygen atom(s) of the sulfonamide group. These hypotheses were corroborated by 13C and 15N SS-NMR spectroscopy and by an unconventional structural characterization based on X-ray powder diffraction data. The latter showed that AgSFX crystallizes as centrosymmetric dimers with a strong Ag⋯Ag interaction of 2.7435(6) Å, induced by the presence of exo-bidentate N,N‧ bridging ligands and the formation of an eight-membered ring of [AgNCN]2 sequence, nearly planar. Participation of oxygen atoms of the sulfonamide residues generates in the crystal a 1D coordination polymer, likely responsible for its very limited solubility in all common solvents. Besides the analytical, spectroscopic and structural description, the antibacterial properties of AgSFX were assayed using disc diffusion methods against Escherichia coli and Pseudomonas aeruginosa (Gram-negative), and Staphylococcus aureus (Gram-positive) bacterial strains. The AgSFX complex showed to be active against Gram-positive and Gram-negative bacterial strains, being comparable to the activities of silver sulfadiazine.

  12. Smart Fluids in Hydrology: Use of Non-Newtonian Fluids for Pore Structure Characterization

    NASA Astrophysics Data System (ADS)

    Abou Najm, M. R.; Atallah, N. M.; Selker, J. S.; Roques, C.; Stewart, R. D.; Rupp, D. E.; Saad, G.; El-Fadel, M.

    2015-12-01

    Classic porous media characterization relies on typical infiltration experiments with Newtonian fluids (i.e., water) to estimate hydraulic conductivity. However, such experiments are generally not able to discern important characteristics such as pore size distribution or pore structure. We show that introducing non-Newtonian fluids provides additional unique flow signatures that can be used for improved pore structure characterization while still representing the functional hydraulic behavior of real porous media. We present a new method for experimentally estimating the pore structure of porous media using a combination of Newtonian and non-Newtonian fluids. The proposed method transforms results of N infiltration experiments using water and N-1 non-Newtonian solutions into a system of equations that yields N representative radii (Ri) and their corresponding percent contribution to flow (wi). This method allows for estimating the soil retention curve using only saturated experiments. Experimental and numerical validation comparing the functional flow behavior of different soils to their modeled flow with N representative radii revealed the ability of the proposed method to represent the water retention and infiltration behavior of real soils. The experimental results showed the ability of such fluids to outsmart Newtonian fluids and infer pore size distribution and unsaturated behavior using simple saturated experiments. Specifically, we demonstrate using synthetic porous media that the use of different non-Newtonian fluids enables the definition of the radii and corresponding percent contribution to flow of multiple representative pores, thus improving the ability of pore-scale models to mimic the functional behavior of real porous media in terms of flow and porosity. The results advance the knowledge towards conceptualizing the complexity of porous media and can potentially impact applications in fields like irrigation efficiencies, vadose zone hydrology, soil

  13. Smart Fluids in Hydrology: Use of Non-Newtonian Fluids for Pore Structure Characterization

    NASA Astrophysics Data System (ADS)

    Abou Najm, Majdi; Atallah, Nabil; Selker, John; Roques, Clément; Stewart, Ryan; Rupp, David; Saad, George; El-Fadel, Mutasem

    2016-04-01

    Classic porous media characterization relies on typical infiltration experiments with Newtonian fluids (i.e., water) to estimate hydraulic conductivity. However, such experiments are generally not able to discern important characteristics such as pore size distribution or pore structure. We show that introducing non-Newtonian fluids provides additional unique flow signatures that can be used for improved pore structure characterization. We present a new method that transforms results of N infiltration experiments using water and N-1 non-Newtonian solutions into a system of equations that yields N representative radii (Ri) and their corresponding percent contribution to flow (wi). Those radii and weights are optimized in terms of flow and porosity to represent the functional hydraulic behavior of real porous media. The method also allows for estimating the soil retention curve using only saturated experiments. Experimental and numerical validation revealed the ability of the proposed method to represent the water retention and functional infiltration behavior of real soils. The experimental results showed the ability of such fluids to outsmart Newtonian fluids and infer pore size distribution and unsaturated behavior using simple saturated experiments. Specifically, we demonstrate using synthetic porous media composed of different combinations of sizes and numbers of capillary tubes that the use of different non-Newtonian fluids enables the prediction of the pore structure. The results advance the knowledge towards conceptualizing the complexity of porous media and can potentially impact applications in fields like irrigation efficiencies, vadose zone hydrology, soil-root-plant continuum, carbon sequestration into geologic formations, soil remediation, petroleum reservoir engineering, oil exploration and groundwater modeling.

  14. Structural and biochemical characterization of a novel aminopeptidase from human intestine.

    PubMed

    Tykvart, Jan; Bařinka, Cyril; Svoboda, Michal; Navrátil, Václav; Souček, Radko; Hubálek, Martin; Hradilek, Martin; Šácha, Pavel; Lubkowski, Jacek; Konvalinka, Jan

    2015-05-01

    N-acetylated α-linked acidic dipeptidase-like protein (NAALADase L), encoded by the NAALADL1 gene, is a close homolog of glutamate carboxypeptidase II, a metallopeptidase that has been intensively studied as a target for imaging and therapy of solid malignancies and neuropathologies. However, neither the physiological functions nor structural features of NAALADase L are known at present. Here, we report a thorough characterization of the protein product of the human NAALADL1 gene, including heterologous overexpression and purification, structural and biochemical characterization, and analysis of its expression profile. By solving the NAALADase L x-ray structure, we provide the first experimental evidence that it is a zinc-dependent metallopeptidase with a catalytic mechanism similar to that of glutamate carboxypeptidase II yet distinct substrate specificity. A proteome-based assay revealed that the NAALADL1 gene product possesses previously unrecognized aminopeptidase activity but no carboxy- or endopeptidase activity. These findings were corroborated by site-directed mutagenesis and identification of bestatin as a potent inhibitor of the enzyme. Analysis of NAALADL1 gene expression at both the mRNA and protein levels revealed the small intestine as the major site of protein expression and points toward extensive alternative splicing of the NAALADL1 gene transcript. Taken together, our data imply that the NAALADL1 gene product's primary physiological function is associated with the final stages of protein/peptide digestion and absorption in the human digestive system. Based on these results, we suggest a new name for this enzyme: human ileal aminopeptidase (HILAP).

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

    SciTech Connect

    Mosivand, Saba; Kazeminezhad, Iraj

    2015-10-15

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

  16. Characterizing spatial structure of sediment E. coli populations to inform sampling design.

    PubMed

    Piorkowski, Gregory S; Jamieson, Rob C; Hansen, Lisbeth Truelstrup; Bezanson, Greg S; Yost, Chris K

    2014-01-01

    Escherichia coli can persist in streambed sediments and influence water quality monitoring programs through their resuspension into overlying waters. This study examined the spatial patterns in E. coli concentration and population structure within streambed morphological features during baseflow and following stormflow to inform sampling strategies for representative characterization of E. coli populations within a stream reach. E. coli concentrations in bed sediments were significantly different (p = 0.002) among monitoring sites during baseflow, and significant interactive effects (p = 0.002) occurred among monitoring sites and morphological features following stormflow. Least absolute shrinkage and selection operator (LASSO) regression revealed that water velocity and effective particle size (D 10) explained E. coli concentration during baseflow, whereas sediment organic carbon, water velocity and median particle diameter (D 50) were important explanatory variables following stormflow. Principle Coordinate Analysis illustrated the site-scale differences in sediment E. coli populations between disconnected stream segments. Also, E. coli populations were similar among depositional features within a reach, but differed in relation to high velocity features (e.g., riffles). Canonical correspondence analysis resolved that E. coli population structure was primarily explained by spatial (26.9–31.7 %) over environmental variables (9.2–13.1 %). Spatial autocorrelation existed among monitoring sites and morphological features for both sampling events, and gradients in mean particle diameter and water velocity influenced E. coli population structure for the baseflow and stormflow sampling events, respectively. Representative characterization of streambed E. coli requires sampling of depositional and high velocity environments to accommodate strain selectivity among these features owing to sediment and water velocity heterogeneity.

  17. Structural characterization of tartrate dehydrogenase: a versatile enzyme catalyzing multiple reactions

    SciTech Connect

    Malik, Radhika; Viola, Ronald E.

    2010-10-28

    The first structure of an NAD-dependent tartrate dehydrogenase (TDH) has been solved to 2 {angstrom} resolution by single anomalous diffraction (SAD) phasing as a complex with the intermediate analog oxalate, Mg{sup 2+} and NADH. This TDH structure from Pseudomonas putida has a similar overall fold and domain organization to other structurally characterized members of the hydroxy-acid dehydrogenase family. However, there are considerable differences between TDH and these functionally related enzymes in the regions connecting the core secondary structure and in the relative positioning of important loops and helices. The active site in these complexes is highly ordered, allowing the identification of the substrate-binding and cofactor-binding groups and the ligands to the metal ions. Residues from the adjacent subunit are involved in both the substrate and divalent metal ion binding sites, establishing a dimer as the functional unit and providing structural support for an alternating-site reaction mechanism. The divalent metal ion plays a prominent role in substrate binding and orientation, together with several active-site arginines. Functional groups from both subunits form the cofactor-binding site and the ammonium ion aids in the orientation of the nicotinamide ring of the cofactor. A lysyl amino group (Lys192) is the base responsible for the water-mediated proton abstraction from the C2 hydroxyl group of the substrate that begins the catalytic reaction, followed by hydride transfer to NAD. A tyrosyl hydroxyl group (Tyr141) functions as a general acid to protonate the enolate intermediate. Each substrate undergoes the initial hydride transfer, but differences in substrate orientation are proposed to account for the different reactions catalyzed by TDH.

  18. Structural Characterization of a Therapeutic Anti-Methamphetamine Antibody Fragment: Oligomerization and Binding of Active Metabolites

    PubMed Central

    Gokulan, Kuppan; Varughese, Kottayil I.

    2013-01-01

    Vaccines and monoclonal antibodies (mAb) for treatment of (+)-methamphetamine (METH) abuse are in late stage preclinical and early clinical trial phases, respectively. These immunotherapies work as pharmacokinetic antagonists, sequestering METH and its metabolites away from sites of action in the brain and reduce the rewarding and toxic effects of the drug. A key aspect of these immunotherapy strategies is the understanding of the subtle molecular interactions important for generating antibodies with high affinity and specificity for METH. We previously determined crystal structures of a high affinity anti-METH therapeutic single chain antibody fragment (scFv6H4, KD = 10 nM) in complex with METH and the (+) stereoisomer of 3,4-methylenedioxymethamphetamine (MDMA, or “ecstasy”). Here we report the crystal structure of scFv6H4 in homo-trimeric unbound (apo) form (2.60Å), as well as monomeric forms in complex with two active metabolites; (+)-amphetamine (AMP, 2.38Å) and (+)-4-hydroxy methamphetamine (p-OH-METH, 2.33Å). The apo structure forms a trimer in the crystal lattice and it results in the formation of an intermolecular composite beta-sheet with a three-fold symmetry. We were also able to structurally characterize the coordination of the His-tags with Ni2+. Two of the histidine residues of each C-terminal His-tag interact with Ni2+ in an octahedral geometry. In the apo state the CDR loops of scFv6H4 form an open conformation of the binding pocket. Upon ligand binding, the CDR loops adopt a closed formation, encasing the drug almost completely. The structural information reported here elucidates key molecular interactions important in anti-methamphetamine abuse immunotherapy. PMID:24349338

  19. Structural characterization of terrestrial microbial Mn oxides from Pinal Creek, AZ

    SciTech Connect

    Bargar, John; Fuller, Christopher; Marcus, Matthew A.; Brearley, Adrian J.; Perez De la Rosa, M.; Webb, Samuel M.; Caldwell, Wendel A.

    2008-03-19

    The microbial catalysis of Mn(II) oxidation is believed to be a dominant source of abundant sorption- and redox-active Mn oxides in marine, freshwater, and subsurface aquatic environments. In spite of their importance, environmental oxides of known biogenic origin have generally not been characterized in detail from a structural perspective. Hyporheic zone Mn oxide grain coatings at Pinal Creek, Arizona, a metals-contaminated stream, have been identified as being dominantly microbial in origin and are well studied from bulk chemistry and contaminant hydrology perspectives. This site thus presents an excellent opportunity to study the structures of terrestrial microbial Mn oxides in detail. XRD and EXAFS measurements performed in this study indicate that the hydrated Pinal Creek Mn oxide grain coatings are layer-type Mn oxides with dominantly hexagonal or pseudo-hexagonal layer symmetry. XRD and TEM measurements suggest the oxides to be nanoparticulate plates with average dimensions on the order of 11 nm thick x 35 nm diameter, but with individual particles exhibiting thickness as small as a single layer and sheets as wide as 500 nm. The hydrated oxides exhibit a 10-A basal-plane spacing and turbostratic disorder. EXAFS analyses suggest the oxides contain layer Mn(IV) site vacancy defects, and layer Mn(III) is inferred to be present, as deduced from Jahn-Teller distortion of the local structure. The physical geometry and structural details of the coatings suggest formation within microbial biofilms. The biogenic Mnoxides are stable with respect to transformation into thermodynamically more stable phases over a time scale of at least 5 months. The nanoparticulate layered structural motif, also observed in pure culture laboratory studies, appears to be characteristic of biogenic Mn oxides and may explain the common occurrence of this mineral habit in soils and sediments.

  20. Automated metric characterization of urban structure using building decomposition from very high resolution imagery

    NASA Astrophysics Data System (ADS)

    Heinzel, Johannes; Kemper, Thomas

    2015-03-01

    Classification approaches for urban areas are mostly of qualitative and semantic nature. They produce interpreted classes similar to those from land cover and land use classifications. As a complement to those classes, quantitative measures directly derived from the image could lead to a metric characterization of the urban area. While these metrics lack of qualitative interpretation they are able to provide objective measure of the urban structures. Such quantitative measures are especially important in rapidly growing cities since, beside of the growth in area, they can provide structural information for specific areas and detect changes. Rustenburg, which serves as test area for the present study, is amongst the fastest growing cities in South Africa. It reveals a heterogeneous face of housing and building structures reflecting social and/or economic differences often linked to the spatial distribution of industrial and local mining sites. Up to date coverage with aerial photographs is provided by aerial surveys in regular intervals. Also recent satellite systems provide imagery with suitable resolution. Using such set of very high resolution images a fully automated algorithm has been developed which outputs metric classes by systematically combining important measures of building structure. The measurements are gained by decomposition of buildings directly from the imagery and by using methods from mathematical morphology. The decomposed building objects serve as basis for the computation of grid statistics. Finally a systematic combination of the single features leads to combined metrical classes. For the dominant urban structures verification results indicate an overall accuracy of at least 80% on the single feature level and 70% for the combined classes.

  1. Structural characterization of a neuroblast-specific phosphorylated region of MARCKS.

    PubMed

    Tinoco, Luzineide W; Fraga, Jully L; Anobom, Cristiane D; Zolessi, Flavio R; Obal, Gonzalo; Toledo, Andrea; Pritsch, Otto; Arruti, Cristina

    2014-04-01

    MARCKS (Myristoylated Alanine-Rich C Kinase substrate) is a natively unfolded protein that interacts with actin, Ca(2+)-Calmodulin, and some plasma membrane lipids. Such interactions occur at a highly conserved region that is specifically phosphorylated by PKC: the Effector Domain. There are two other conserved domains, MH1 (including a myristoylation site) and MH2, also located in the amino terminal region and whose structure and putative protein binding capabilities are currently unknown. MH2 sequence contains a serine that we described as being phosphorylated only in differentiating neurons (S25 in chick). Here, Circular Dichroism (CD) and Nuclear Magnetic Resonance (NMR) spectroscopy were used to characterize the phosphorylated and unphosphorylated forms of a peptide with the MARCKS sequence surrounding S25. The peptide phosphorylated at this residue is recognized by monoclonal antibody 3C3 (mAb 3C3). CD and NMR data indicated that S25 phosphorylation does not cause extensive modifications in the peptide structure. However, the sharper lines, the absence of multiple spin systems and relaxation dispersion data observed for the phosphorylated peptide suggested a more ordered structure. Surface Plasmon Resonance was employed to compare the binding properties of mAb 3C3 to MARCKS protein and peptide. SPR showed that mAb 3C3 binds to the whole protein and the peptide with a similar affinity, albeit different kinetics. The slightly ordered structure of the phosphorylated peptide might be at the origin of its ability to interact with mAb 3C3 antibody, but this binding did not noticeably modify the peptide structure.

  2. Structural characterization of a neuroblast-specific phosphorylated region of MARCKS.

    PubMed

    Tinoco, Luzineide W; Fraga, Jully L; Anobom, Cristiane D; Zolessi, Flavio R; Obal, Gonzalo; Toledo, Andrea; Pritsch, Otto; Arruti, Cristina

    2014-04-01

    MARCKS (Myristoylated Alanine-Rich C Kinase substrate) is a natively unfolded protein that interacts with actin, Ca(2+)-Calmodulin, and some plasma membrane lipids. Such interactions occur at a highly conserved region that is specifically phosphorylated by PKC: the Effector Domain. There are two other conserved domains, MH1 (including a myristoylation site) and MH2, also located in the amino terminal region and whose structure and putative protein binding capabilities are currently unknown. MH2 sequence contains a serine that we described as being phosphorylated only in differentiating neurons (S25 in chick). Here, Circular Dichroism (CD) and Nuclear Magnetic Resonance (NMR) spectroscopy were used to characterize the phosphorylated and unphosphorylated forms of a peptide with the MARCKS sequence surrounding S25. The peptide phosphorylated at this residue is recognized by monoclonal antibody 3C3 (mAb 3C3). CD and NMR data indicated that S25 phosphorylation does not cause extensive modifications in the peptide structure. However, the sharper lines, the absence of multiple spin systems and relaxation dispersion data observed for the phosphorylated peptide suggested a more ordered structure. Surface Plasmon Resonance was employed to compare the binding properties of mAb 3C3 to MARCKS protein and peptide. SPR showed that mAb 3C3 binds to the whole protein and the peptide with a similar affinity, albeit different kinetics. The slightly ordered structure of the phosphorylated peptide might be at the origin of its ability to interact with mAb 3C3 antibody, but this binding did not noticeably modify the peptide structure. PMID:24590112

  3. Structural characterization of terrestrial microbial Mn oxides from Pinal Creek, AZ

    NASA Astrophysics Data System (ADS)

    Bargar, John R.; Fuller, Christopher C.; Marcus, Matthew A.; Brearley, Adrian J.; Perez De la Rosa, M.; Webb, Samuel M.; Caldwell, Wendel A.

    2009-02-01

    The microbial catalysis of Mn(II) oxidation is believed to be a dominant source of abundant sorption- and redox-active Mn oxides in marine, freshwater, and subsurface aquatic environments. In spite of their importance, environmental oxides of known biogenic origin have generally not been characterized in detail from a structural perspective. Hyporheic zone Mn oxide grain coatings at Pinal Creek, Arizona, a metals-contaminated stream, have been identified as being dominantly microbial in origin and are well studied from bulk chemistry and contaminant hydrology perspectives. This site thus presents an excellent opportunity to study the structures of terrestrial microbial Mn oxides in detail. XRD and EXAFS measurements performed in this study indicate that the hydrated Pinal Creek Mn oxide grain coatings are layer-type Mn oxides with dominantly hexagonal or pseudo-hexagonal layer symmetry. XRD and TEM measurements suggest the oxides to be nanoparticulate plates with average dimensions on the order of 11 nm thick × 35 nm diameter, but with individual particles exhibiting thickness as small as a single layer and sheets as wide as 500 nm. The hydrated oxides exhibit a 10-Å basal-plane spacing and turbostratic disorder. EXAFS analyses suggest the oxides contain layer Mn(IV) site vacancy defects, and layer Mn(III) is inferred to be present, as deduced from Jahn-Teller distortion of the local structure. The physical geometry and structural details of the coatings suggest formation within microbial biofilms. The biogenic Mn oxides are stable with respect to transformation into thermodynamically more stable phases over a time scale of at least 5 months. The nanoparticulate layered structural motif, also observed in pure culture laboratory studies, appears to be characteristic of biogenic Mn oxides and may explain the common occurrence of this mineral habit in soils and sediments.

  4. Structural characterization of terrestrial microbial Mn oxides from Pinal Creek, AZ

    USGS Publications Warehouse

    Bargar, J.R.; Fuller, C.C.; Marcus, M.A.; Brearley, A.J.; Perez De la Rosa, M.; Webb, S.M.; Caldwell, W.A.

    2009-01-01

    The microbial catalysis of Mn(II) oxidation is believed to be a dominant source of abundant sorption- and redox-active Mn oxides in marine, freshwater, and subsurface aquatic environments. In spite of their importance, environmental oxides of known biogenic origin have generally not been characterized in detail from a structural perspective. Hyporheic zone Mn oxide grain coatings at Pinal Creek, Arizona, a metals-contaminated stream, have been identified as being dominantly microbial in origin and are well studied from bulk chemistry and contaminant hydrology perspectives. This site thus presents an excellent opportunity to study the structures of terrestrial microbial Mn oxides in detail. XRD and EXAFS measurements performed in this study indicate that the hydrated Pinal Creek Mn oxide grain coatings are layer-type Mn oxides with dominantly hexagonal or pseudo-hexagonal layer symmetry. XRD and TEM measurements suggest the oxides to be nanoparticulate plates with average dimensions on the order of 11 nm thick ?? 35 nm diameter, but with individual particles exhibiting thickness as small as a single layer and sheets as wide as 500 nm. The hydrated oxides exhibit a 10-?? basal-plane spacing and turbostratic disorder. EXAFS analyses suggest the oxides contain layer Mn(IV) site vacancy defects, and layer Mn(III) is inferred to be present, as deduced from Jahn-Teller distortion of the local structure. The physical geometry and structural details of the coatings suggest formation within microbial biofilms. The biogenic Mn oxides are stable with respect to transformation into thermodynamically more stable phases over a time scale of at least 5 months. The nanoparticulate layered structural motif, also observed in pure culture laboratory studies, appears to be characteristic of biogenic Mn oxides and may explain the common occurrence of this mineral habit in soils and sediments. ?? 2008 Elsevier Ltd.

  5. Structural characterization and comparison of three acyl-carrier-protein synthases from pathogenic bacteria

    SciTech Connect

    Halavaty, Andrei S.; Kim, Youngchang; Minasov, George; Shuvalova, Ludmilla; Dubrovska, Ievgeniia; Winsor, James; Zhou, Min; Onopriyenko, Olena; Skarina, Tatiana; Papazisi, Leka; Kwon, Keehwan; Peterson, Scott N.; Joachimiak, Andrzej; Savchenko, Alexei; Anderson, Wayne F.

    2012-10-01

    The structural characterization of acyl-carrier-protein synthase (AcpS) from three different pathogenic microorganisms is reported. One interesting finding of the present work is a crystal artifact related to the activity of the enzyme, which fortuitously represents an opportunity for a strategy to design a potential inhibitor of a pathogenic AcpS. Some bacterial type II fatty-acid synthesis (FAS II) enzymes have been shown to be important candidates for drug discovery. The scientific and medical quest for new FAS II protein targets continues to stimulate research in this field. One of the possible additional candidates is the acyl-carrier-protein synthase (AcpS) enzyme. Its holo form post-translationally modifies the apo form of an acyl carrier protein (ACP), which assures the constant delivery of thioester intermediates to the discrete enzymes of FAS II. At the Center for Structural Genomics of Infectious Diseases (CSGID), AcpSs from Staphylococcus aureus (AcpS{sub SA}), Vibrio cholerae (AcpS{sub VC}) and Bacillus anthracis (AcpS{sub BA}) have been structurally characterized in their apo, holo and product-bound forms, respectively. The structure of AcpS{sub BA} is emphasized because of the two 3′, 5′-adenosine diphosphate (3′, 5′-ADP) product molecules that are found in each of the three coenzyme A (CoA) binding sites of the trimeric protein. One 3′, 5′-ADP is bound as the 3′, 5′-ADP part of CoA in the known structures of the CoA–AcpS and 3′, 5′-ADP–AcpS binary complexes. The position of the second 3′, 5′-ADP has never been described before. It is in close proximity to the first 3′, 5′-ADP and the ACP-binding site. The coordination of two ADPs in AcpS{sub BA} may possibly be exploited for the design of AcpS inhibitors that can block binding of both CoA and ACP.

  6. Active and passive infrared thermography applied to the detection and characterization of hidden defects in structure

    NASA Astrophysics Data System (ADS)

    Dumoulin, Jean

    2013-04-01

    Infrared thermography for Non Destructive Testing (NDT) has encountered a wide spreading this last 2 decades, in particular thanks to emergence on the market of low cost uncooled infrared camera. So, infrared thermography is not anymore a measurement technique limited to laboratory application. It has been more and more involved in civil engineering and cultural heritage applications, but also in many other domains, as indicated by numerous papers in the literature. Nevertheless, laboratory, measurements are done as much as possible in quite ideal conditions (good atmosphere conditions, known properties of materials, etc.), while measurement on real site requires to consider the influence of not controlled environmental parameters and additional unknown thermal properties. So, dedicated protocol and additional sensors are required for measurement data correction. Furthermore, thermal excitation is required to enhance the signature of defects in materials. Post-processing of data requires to take into account the protocol used for the thermal excitation and sometimes its nature to avoid false detection. This analysis step is based on signal and image processing tool and allows to carry out the detection. Characterization of anomalies detected at the previous step can be done by additional signal processing in particular for manufactured objects. The use of thermal modelling and inverse method allows to determine properties of the defective area. The present paper will first address a review of some protocols currently in use for field measurement with passive and/or active infrared measurements. Illustrations in various experiments carried out on civil engineering structure will be shown and discussed. In a second part, different post-processing approaches will be presented and discussed. In particular, a review of the most standard processing methods like Fast Fourier Analysis, Principal Components Analysis, Polynomial Decomposition, defect characterization using

  7. 1H and 13C NMR characterization and secondary structure of the K2 polysaccharide of Klebsiella pneumoniae strain 52145.

    PubMed

    Corsaro, Maria Michela; De Castro, Cristina; Naldi, Teresa; Parrilli, Michelangelo; Tomás, Juan M; Regué, Miguel

    2005-09-26

    The complete (1)H and (13)C NMR characterization of the tetrasaccharide repeating unit from the K2 polysaccharide of Klebsiella pneumoniae strain 52145 is reported. [chemical structure] In addition a model for its secondary structure was suggested on the basis of dynamic and molecular calculations.

  8. Characterization of capture cross sections of interface states in dielectric/III-nitride heterojunction structures

    NASA Astrophysics Data System (ADS)

    Matys, M.; Stoklas, R.; Kuzmik, J.; Adamowicz, B.; Yatabe, Z.; Hashizume, T.

    2016-05-01

    We performed, for the first time, quantitative characterization of electron capture cross sections σ of the interface states at dielectric/III-N heterojunction interfaces. We developed a new method, which is based on the photo-assisted capacitance-voltage measurements using photon energies below the semiconductor band gap. The analysis was carried out for AlGaN/GaN metal-insulator-semiconductor heterojunction (MISH) structures with Al2O3, SiO2, or SiN films as insulator deposited on the AlGaN layers with Al content (x) varying over a wide range of values. Additionally, we also investigated an Al2O3/InAlN/GaN MISH structure. Prior to insulator deposition, the AlGaN and InAlN surfaces were subjected to different treatments. We found that σ for all these structures lies in the range between 5 × 10 - 19 and 10 - 16 cm2. Furthermore, we revealed that σ for dielectric/AlxGa1-xN interfaces increases with increasing x. We showed that both the multiphonon-emission and cascade processes can explain the obtained results.

  9. Biochemical and structural characterization of mouse mitochondrial aspartate aminotransferase, a newly identified kynurenine aminotransferase-IV

    SciTech Connect

    Han, Q.; Robinson, H.; Cai, T.; Tagle, D. A.; Li, J.

    2011-10-01

    Mammalian mAspAT (mitochondrial aspartate aminotransferase) is recently reported to have KAT (kynurenine aminotransferase) activity and plays a role in the biosynthesis of KYNA (kynurenic acid) in rat, mouse and human brains. This study concerns the biochemical and structural characterization of mouse mAspAT. In this study, mouse mAspAT cDNA was amplified from mouse brain first stand cDNA and its recombinant protein was expressed in an Escherichia coli expression system. Sixteen oxo acids were tested for the co-substrate specificity of mouse mAspAT and 14 of them were shown to be capable of serving as co-substrates for the enzyme. Structural analysis of mAspAT by macromolecular crystallography revealed that the cofactor-binding residues of mAspAT are similar to those of other KATs. The substrate-binding residues of mAspAT are slightly different from those of other KATs. Our results provide a biochemical and structural basis towards understanding the overall physiological role of mAspAT in vivo and insight into controlling the levels of endogenous KYNA through modulation of the enzyme in the mouse brain.

  10. Structural characterization of inhibitors with selectivity against members of a homologous enzyme family.

    PubMed

    Pavlovsky, Alexander G; Liu, Xuying; Faehnle, Christopher R; Potente, Nina; Viola, Ronald E

    2012-01-01

    The aspartate biosynthetic pathway provides essential metabolites for many important biological functions, including the production of four essential amino acids. As this critical pathway is only present in plants and microbes, any disruptions will be fatal to these organisms. An early pathway enzyme, l-aspartate-β-semialdehyde dehydrogenase, produces a key intermediate at the first branch point of this pathway. Developing potent and selective inhibitors against several orthologs in the l-aspartate-β-semialdehyde dehydrogenase family can serve as lead compounds for antibiotic development. Kinetic studies of two small molecule fragment libraries have identified inhibitors that show good selectivity against l-aspartate-β-semialdehyde dehydrogenases from two different bacterial species, Streptococcus pneumoniae and Vibrio cholerae, despite the presence of an identical constellation of active site amino acids in this homologous enzyme family. Structural characterization of enzyme-inhibitor complexes have elucidated different modes of binding between these structurally related enzymes. This information provides the basis for a structure-guided approach to the development of more potent and more selective inhibitors.

  11. Characterizing HII regions in High-z ULIRGs with far infrared fine structure lines

    NASA Astrophysics Data System (ADS)

    Brisbin, Drew; Ferkinhoff, Carl; Stacey, Gordon J.; Parshley, Stephen; Hailey-Dunsheath, Steve; Lamarche, Cody

    2015-01-01

    The nature of star-forming ULIRGs in the early Universe remains mysterious. Is their star formation fueled predominantly through cold flow accretion, or through major mergers? What fraction of the sources have AGN, and what is the stellar mass function powering the HII regions? Of particular importance to these questions is the characterization of the ionized gas properties, and the coupling with the cooler photodissociation region (PDR) gas. To address these issues we have undertaken a mini-survey of several z~1-2 luminous galaxies observed in multiple ionized oxygen far infrared fine structure lines. These fine structure lines allow us to constrain the density and radiation field of the ionized gas and test for the presence of harder AGN powered radiation. Coupled with previous data including the [CII] and [OI] fine structure lines emanating from PDR gas, we will also test the ability to simultaneously model both PDR and HII gas components. This survey, modest in extent, offers an illustrative snapshot of the diversity of systems in the early Universe.

  12. Structure and Mechanical Characterization of DNA i-Motif Nanowires by Molecular Dynamics Simulation

    PubMed Central

    Singh, Raghvendra Pratap; Blossey, Ralf; Cleri, Fabrizio

    2013-01-01

    We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm-long nanowires, based on a repeated TC5 sequence from crystallographic data, fully relaxed and equilibrated in water. The unusual C⋅C+ stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression, and bending deformations with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young’s and bending moduli of the nanowire, as well as estimates for the tensile strength and persistence length. According to our results, the i-motif nanowire shares similarities with structural proteins, as far as its tensile stiffness, but is closer to nucleic acids and flexible proteins, as far as its bending rigidity is concerned. Furthermore, thanks to its very thin cross section, the apparent tensile toughness is close to that of a metal. Besides their yet to be clarified biological significance, i-motif nanowires may qualify as interesting candidates for nanotechnology templates, due to such outstanding mechanical properties. PMID:24359754

  13. Crystal structure, spectroscopic characterization and antibacterial activities of a silver complex with sulfameter

    NASA Astrophysics Data System (ADS)

    Nakahata, Douglas H.; Lustri, Wilton R.; Cuin, Alexandre; Corbi, Pedro P.

    2016-12-01

    A silver complex with the sulfonamide sulfameter, also known as sulfamethoxydiazine (SMTR), was prepared and characterized. Chemical analyses were consistent with the [Ag(C11H11N4O3S)] composition (AgSMTR), while conductivity measurements in DMSO indicated a non-electrolyte behavior of the complex in this solvent. High-resolution ESI(+)-QTOF mass spectrometric experiments revealed the presence of the [Ag(C11H11N4O3S)+H]+ and [Ag2(C11H11N4O3S)2+H]+ species in solution. Infrared and NMR spectroscopies indicated coordination of the ligand to the metal by the nitrogen atoms of the sulfonamide group and of the pyrimidine ring. The structure of AgSMTR was solved by powder X-ray diffraction technique using the Rietveld method. The solved structure confirms the formation of a dimer, where each silver ion is coordinated by one of the nitrogen atoms of the pyrimidine ring, the nitrogen of the sulfonamide group and by an oxygen atom from the sulfonyl group. An argentophilic interaction of 2.901(1) Å is present in this dimeric structure. The AgSMTR complex was assayed over Gram-positive (Staphylococcus aureus) and Gram-negative (Pseudomonas aeruginosa and Escherichia coli) bacterial strains, and it was found that the compound is 8 times more active over the Gram-negative bacteria in DMSO solution, with MIC values in the micromolar range.

  14. Structural and functional characterization of aspartate racemase from the acidothermophilic archaeon Picrophilus torridus.

    PubMed

    Aihara, Takayuki; Ito, Toshiya; Yamanaka, Yasuaki; Noguchi, Keiichi; Odaka, Masafumi; Sekine, Masae; Homma, Hiroshi; Yohda, Masafumi

    2016-07-01

    Functional and structural characterizations of pyridoxal 5'-phosphate-independent aspartate racemase of the acidothermophilic archaeon Picrophilus torridus were performed. Picrophilus aspartate racemase exhibited high substrate specificity to aspartic acid. The optimal reaction temperature was 60 °C, which is almost the same as the optimal growth temperature. Reflecting the low pH in the cytosol, the optimal reaction pH of Picrophilus aspartate racemase was approximately 5.5. However, the activity at the putative cytosolic pH of 4.6 was approximately 6 times lower than that at the optimal pH of 5.5. The crystal structure of Picrophilus aspartate racemase was almost the same as that of other pyridoxal 5'-phosphate -independent aspartate racemases. In two molecules of the dimer, one molecule contained a tartaric acid molecule in the catalytic site; the structure of the other molecule was relatively flexible. Finally, we examined the intracellular existence of D-amino acids. Unexpectedly, the proportion of D-aspartate to total aspartate was not very high. In contrast, both D-proline and D-alanine were observed. Because Picrophilus aspartate racemase is highly specific to aspartate, other amino acid racemases might exist in Picrophilus torridus. PMID:27094682

  15. Structural and functional characterization of the nitrite channel NirC from Salmonella typhimurium

    PubMed Central

    Lü, Wei; Schwarzer, Nikola J.; Du, Juan; Gerbig-Smentek, Elke; Andrade, Susana L. A.; Einsle, Oliver

    2012-01-01

    Nitrite (NO2−) is a central intermediate in the nitrogen metabolism of microorganisms and plants, and is used as a cytotoxin by macrophages as part of the innate immune response. The bacterial membrane protein NirC acts as a specific channel to facilitate the transport of nitrite anions across lipid bilayers for cytoplasmic detoxification. Despite NirC’s importance in nitrogen metabolism and in the pathogenicity of enteric bacteria, available biochemical data are scarce. Here we present a functional and structural characterization of NirC from Salmonella typhimurium by lipid bilayer electrophysiology and X-ray crystallography. NirC is a pentameric member of the formate/nitrite transporter family of membrane proteins that operates as a channel with high conductance. Single-channel measurements reveal fast and slow gating events but, in contrast to the related FocA formate channel, no pH-dependent gating. A 2.4Å crystal structure of NirC at pH 5 shows similarity to FocA and aquaporins, but lacks the structural asymmetry observed in the formate channel at similarly low pH. Resolved water molecules in the protomers suggest a transport mechanism that also permits a facultative NO2−/H+ symport. PMID:23090993

  16. Characterization of tumor microvascular structure and permeability: comparison between magnetic resonance imaging and intravital confocal imaging

    PubMed Central

    Reitan, Nina Kristine; Thuen, Marte; Goa, Pål Erik; de Lange Davies, Catharina

    2010-01-01

    Solid tumors are characterized by abnormal blood vessel organization, structure, and function. These abnormalities give rise to enhanced vascular permeability and may predict therapeutic responses. The permeability and architecture of the microvasculature in human osteosarcoma tumors growing in dorsal window chambers in athymic mice were measured by confocal laser scanning microscopy (CLSM) and dynamic contrast enhanced magnetic resonance imaging (DCE-MRI). Dextran (40 kDa) and Gadomer were used as molecular tracers for CLSM and DCE-MRI, respectively. A significant correlation was found between permeability indicators. The extravasation rate Ki as measured by CLSM correlated positively with DCE-MRI parameters, such as the volume transfer constant Ktrans and the initial slope of the contrast agent concentration-time curve. This demonstrates that these two techniques give complementary information. Extravasation was further related to microvascular structure and was found to correlate with the fractal dimension and vascular density. The structural parameter values that were obtained from CLSM images were higher for abnormal tumor vasculature than for normal vessels. PMID:20615006

  17. Characterizing the spatial structure of endangered species habitat using geostatistical analysis of IKONOS imagery

    USGS Publications Warehouse

    Wallace, C.S.A.; Marsh, S.E.

    2005-01-01

    Our study used geostatistics to extract measures that characterize the spatial structure of vegetated landscapes from satellite imagery for mapping endangered Sonoran pronghorn habitat. Fine spatial resolution IKONOS data provided information at the scale of individual trees or shrubs that permitted analysis of vegetation structure and pattern. We derived images of landscape structure by calculating local estimates of the nugget, sill, and range variogram parameters within 25 ?? 25-m image windows. These variogram parameters, which describe the spatial autocorrelation of the 1-m image pixels, are shown in previous studies to discriminate between different species-specific vegetation associations. We constructed two independent models of pronghorn landscape preference by coupling the derived measures with Sonoran pronghorn sighting data: a distribution-based model and a cluster-based model. The distribution-based model used the descriptive statistics for variogram measures at pronghorn sightings, whereas the cluster-based model used the distribution of pronghorn sightings within clusters of an unsupervised classification of derived images. Both models define similar landscapes, and validation results confirm they effectively predict the locations of an independent set of pronghorn sightings. Such information, although not a substitute for field-based knowledge of the landscape and associated ecological processes, can provide valuable reconnaissance information to guide natural resource management efforts. ?? 2005 Taylor & Francis Group Ltd.

  18. Biochemical and structural characterization of mouse mitochondrial aspartate aminotransferase, a newly identified kynurenine aminotransferase-IV

    PubMed Central

    Han, Qian; Robinson, Howard; Cai, Tao; Tagle, Danilo A.; Li, Jianyong

    2010-01-01

    Synopsis Mammalian mitochondrial aspartate aminotransferase (mAspAT) is recently reported to have kynurenine aminotransferase (KAT) activity and plays a role in the biosynthesis of kynurenic acid (KYNA) in rat, mouse and human brains. This study concerns the biochemical and structural characterization of mouse mAspAT. In this study, mouse mAspAT cDNA was amplified from mouse brain first stand cDNA and its recombinant protein was expressed in an Escherichia coli expression system. Sixteen keto acids were tested for the co-substrate specificity of mouse mAspAT and fourteen of them were shown to be capable of serving as co-substrates for the enzyme. Structural analysis of mAspAT by macromolecular crystallography revealed that the cofactor binding residues of mAspAT are similar to those of other KATs. The substrate binding residues of mAspAT are slightly different from those of other KATs. Our data provide a biochemical and structural basis towards understanding the overall physiological role of mAspAT in vivo and insight into controlling the levels of endogenous KYNA through modulation of the enzyme in the mouse brain. PMID:20977429

  19. Structural characterization, α-glucosidase inhibitory and DPPH scavenging activities of polysaccharides from guava.

    PubMed

    Zhang, Ziling; Kong, Fansheng; Ni, Hui; Mo, Zhixian; Wan, Jian-Bo; Hua, Dehong; Yan, Chunyan

    2016-06-25

    To explore the chemicals responsible for the health benefits of guava, water-soluble polysaccharides were extracted including GP90 and P90. They exhibited excellent α-glucosidase inhibition activity with an EC50 of 2.27μg/mL and 0.18mg/mL. This suggests that their activities were 1379- and 17-fold higher than the positive control. The DPPH scavenging activities of GP90 was even higher than Vc at some concentrations. Upon further isolation, a novel polysaccharide termed GB90-1B was obtained. Monosaccharide analysis, methylation analysis, and NMR were used to analyze the structural characterization of GB90-1B. Structural analysis revealed that its backbone consisted of (1→5)-linked-α-l-arabinose, (1→2,3,5)-linked-α-l-arabinose and (1→3)-linked-α-l-arabinose. Branch linkages included (1→6)-linked-α-d-glucose, (1→)-linked-α-d-glucose and (1→)-linked-α-l-arabinose. The structure of the repeating unit of GP90-1B was predicted. PMID:27083799

  20. Structural characterization and functional properties of antihypertensive Cymodocea nodosa sulfated polysaccharide.

    PubMed

    Kolsi, Rihab Ben Abdallah; Fakhfakh, Jawhar; Krichen, Fatma; Jribi, Imed; Chiarore, Antonia; Patti, Francesco Paolo; Blecker, Christophe; Allouche, Noureddine; Belghith, Hafedh; Belghith, Karima

    2016-10-20

    A sulfated polysaccharide was successfully isolated from Cymodocea nodosa (CNSP). This is the first report that indicates the chemical composition, structural characterization, functional and antihypertensive properties of this polysaccharide. The CNSP consisted mainly of sulfate (23.17%), total sugars (54.90%), galactose (44.89%), mannose (17.30%), arabinose (12.05%), xylose (9.18%), maltose (1.07%) and uronic acid (11.03%) with low water activity (0.49). CNSP had an XRD pattern that was typical for a semi-crystalline polymer with homogeneous structure. It also displayed an important anti-hypertensive activity (IC50=0.43mgml) with a dose-dependent manner using a synthetic substrate, N-hippuryl-His-Leu hydrate salt (HHL). Overall, the results indicate that CNSP have attractive chemical, functional and biological properties, with a preliminary structural may have a backbone of branched 6-O-sulfated (1→4) galactosidic linkages, which can be considered in the future as alternative additive in various foods, cosmetic and pharmaceutical preparations.

  1. Structural characterization and functional properties of antihypertensive Cymodocea nodosa sulfated polysaccharide.

    PubMed

    Kolsi, Rihab Ben Abdallah; Fakhfakh, Jawhar; Krichen, Fatma; Jribi, Imed; Chiarore, Antonia; Patti, Francesco Paolo; Blecker, Christophe; Allouche, Noureddine; Belghith, Hafedh; Belghith, Karima

    2016-10-20

    A sulfated polysaccharide was successfully isolated from Cymodocea nodosa (CNSP). This is the first report that indicates the chemical composition, structural characterization, functional and antihypertensive properties of this polysaccharide. The CNSP consisted mainly of sulfate (23.17%), total sugars (54.90%), galactose (44.89%), mannose (17.30%), arabinose (12.05%), xylose (9.18%), maltose (1.07%) and uronic acid (11.03%) with low water activity (0.49). CNSP had an XRD pattern that was typical for a semi-crystalline polymer with homogeneous structure. It also displayed an important anti-hypertensive activity (IC50=0.43mgml) with a dose-dependent manner using a synthetic substrate, N-hippuryl-His-Leu hydrate salt (HHL). Overall, the results indicate that CNSP have attractive chemical, functional and biological properties, with a preliminary structural may have a backbone of branched 6-O-sulfated (1→4) galactosidic linkages, which can be considered in the future as alternative additive in various foods, cosmetic and pharmaceutical preparations. PMID:27474595

  2. Structural and Immunological Activity Characterization of a Polysaccharide Isolated from Meretrix meretrix Linnaeus

    PubMed Central

    Li, Li; Li, Heng; Qian, Jianying; He, Yongfeng; Zheng, Jialin; Lu, Zhenming; Xu, Zhenghong; Shi, Jinsong

    2015-01-01

    Polysaccharides from marine clams perform various biological activities, whereas information on structure is scarce. Here, a water-soluble polysaccharide MMPX-B2 was isolated from Meretrix meretrix Linnaeus. The proposed structure was deduced through characterization and its immunological activity was investigated. MMPX-B2 consisted of d-glucose and d-galctose residues at a molar ratio of 3.51:1.00. The average molecular weight of MMPX-B2 was 510 kDa. This polysaccharide possessed a main chain of (1→4)-linked-α-d-glucopyranosyl residues, partially substituted at the C-6 position by a few terminal β-d-galactose residues or branched chains consisting of (1→3)-linked β-d-galactose residues. Preliminary immunological tests in vitro showed that MMPX-B2 could stimulate the murine macrophages to release various cytokines, and the structure-activity relationship was then established. The present study demonstrated the potential immunological activity of MMPX-B2, and provided references for studying the active ingredients in M. meretrix. PMID:26729136

  3. Optimized method for TAG protein homology modeling: In silico and experimental structural characterization.

    PubMed

    Tomar, Jyoti Singh; Peddinti, Rama Krishna

    2016-07-01

    The DNA glycosylases cleave CN glycosyl bond to release a free base and generate abasic sites concurrently. Function and structure of these enzymes in the pathogenic bacterium Acinetobacter baumannii and its closely related species are not well characterized. Inhibition of TAG enzyme is a promising drug design strategy against A. baumannii. Here optimized molecular modeling approaches were used to provide a structural scaffold of TAG. The recombinant TAG protein was expressed and purified to determine oligomeric state using size exclusion chromatography, which showed the existence of TAG protein as monomer (mwt ∼21kDa). Secondary structure and substrate binding were analyzed using CD are in good agreement with the in silico predictions. Near UV-CD spectrum shows the involvement of Tyr residues in substrate recognition. Molecular docking studies were performed to understand the molecular recognition interactions and this knowledge was used to identify the potent inhibitors using virtual screening. Residues crucial for DNA holding and enzyme catalysis are reconfirmed by the in silico mutational studies. PMID:27017978

  4. Structural characterization, α-glucosidase inhibitory and DPPH scavenging activities of polysaccharides from guava.

    PubMed

    Zhang, Ziling; Kong, Fansheng; Ni, Hui; Mo, Zhixian; Wan, Jian-Bo; Hua, Dehong; Yan, Chunyan

    2016-06-25

    To explore the chemicals responsible for the health benefits of guava, water-soluble polysaccharides were extracted including GP90 and P90. They exhibited excellent α-glucosidase inhibition activity with an EC50 of 2.27μg/mL and 0.18mg/mL. This suggests that their activities were 1379- and 17-fold higher than the positive control. The DPPH scavenging activities of GP90 was even higher than Vc at some concentrations. Upon further isolation, a novel polysaccharide termed GB90-1B was obtained. Monosaccharide analysis, methylation analysis, and NMR were used to analyze the structural characterization of GB90-1B. Structural analysis revealed that its backbone consisted of (1→5)-linked-α-l-arabinose, (1→2,3,5)-linked-α-l-arabinose and (1→3)-linked-α-l-arabinose. Branch linkages included (1→6)-linked-α-d-glucose, (1→)-linked-α-d-glucose and (1→)-linked-α-l-arabinose. The structure of the repeating unit of GP90-1B was predicted.

  5. In situ hydrodynamic spectroscopy for structure characterization of porous energy storage electrodes

    NASA Astrophysics Data System (ADS)

    Shpigel, Netanel; Levi, Mikhael D.; Sigalov, Sergey; Girshevitz, Olga; Aurbach, Doron; Daikhin, Leonid; Pikma, Piret; Marandi, Margus; Jänes, Alar; Lust, Enn; Jäckel, Nicolas; Presser, Volker

    2016-05-01

    A primary atomic-scale effect accompanying Li-ion insertion into rechargeable battery electrodes is a significant intercalation-induced change of the unit cell volume of the crystalline material. This generates a variety of secondary multiscale dimensional changes and causes a deterioration in the energy storage performance stability. Although traditional in situ height-sensing techniques (atomic force microscopy or electrochemical dilatometry) are able to sense electrode thickness changes at a nanometre scale, they are much less informative concerning intercalation-induced changes of the porous electrode structure at a mesoscopic scale. Based on a electrochemical quartz-crystal microbalance with dissipation monitoring on multiple overtone orders, herein we introduce an in situ hydrodynamic spectroscopic method for porous electrode structure characterization. This new method will enable future developments and applications in the fields of battery and supercapacitor research, especially for diagnostics of viscoelastic properties of binders for composite electrodes and probing the micromechanical stability of their internal electrode porous structure and interfaces.

  6. Structural Characterization of Inhibitors with Selectivity against Members of a Homologous Enzyme Family

    SciTech Connect

    Pavlovsky, Alexander G.; Liu, Xuying; Faehnle, Christopher R.; Potente, Nina; Viola, Ronald E.

    2013-01-31

    The aspartate biosynthetic pathway provides essential metabolites for many important biological functions, including the production of four essential amino acids. As this critical pathway is only present in plants and microbes, any disruptions will be fatal to these organisms. An early pathway enzyme, L-aspartate-{beta}-semialdehyde dehydrogenase, produces a key intermediate at the first branch point of this pathway. Developing potent and selective inhibitors against several orthologs in the L-aspartate-{beta}-semialdehyde dehydrogenase family can serve as lead compounds for antibiotic development. Kinetic studies of two small molecule fragment libraries have identified inhibitors that show good selectivity against L-aspartate-{beta}-semialdehyde dehydrogenases from two different bacterial species, Streptococcus pneumoniae and Vibrio cholerae, despite the presence of an identical constellation of active site amino acids in this homologous enzyme family. Structural characterization of enzyme-inhibitor complexes have elucidated different modes of binding between these structurally related enzymes. This information provides the basis for a structure-guided approach to the development of more potent and more selective inhibitors.

  7. Structural Characterization of Edematous Corneas by Forward and Backward Second Harmonic Generation Imaging

    PubMed Central

    Hsueh, Chiu-Mei; Lo, Wen; Chen, Wei-Liang; Hovhannisyan, Vladimir A.; Liu, Guang-Yu; Wang, Sheng-Shun; Tan, Hsin-Yuan; Dong, Chen-Yuan

    2009-01-01

    Abstract The purpose of this study was to image and quantify the structural changes of corneal edema by second harmonic generation (SHG) microscopy. Bovine cornea was used as an experimental model to characterize structural alterations in edematous corneas. Forward SHG and backward SHG signals were simultaneously collected from normal and edematous bovine corneas to reveal the morphological differences between them. In edematous cornea, both an uneven expansion in the lamellar interspacing and an increased lamellar thickness in the posterior stroma (depth > 200 μm) were identified, whereas the anterior stroma, composed of interwoven collagen architecture, remained unaffected. Our findings of heterogeneous structural alteration at the microscopic scale in edematous corneas suggest that the strength of collagen cross-linking is heterogeneous in the corneal stroma. In addition, we found that qualitative backward SHG collagen fiber imaging and depth-dependent signal decay can be used to detect and diagnose corneal edema. Our work demonstrates that SHG imaging can provide morphological information for the investigation of corneal edema biophysics, and may be applied in the evaluation of advancing corneal edema in vivo. PMID:19686668

  8. Geoelectrical Characterization of the Punta Banda System: A Possible Structural Control for the Geothermal Anomalies

    NASA Astrophysics Data System (ADS)

    Arango-Galvan, C.; Flores-Marquez, E.; Prol-Ledesma, R.; Working Group, I.

    2007-05-01

    The lack of sufficient drinking water in México has become a very serious problem, especially in the northern desert regions of the country. In order to give a real solution to this phenomenon the IMPULSA research program has been created to develope novel technologies based on desalination of sea and brackish water using renewable sources of energy to face the problem. The Punta Banda geothermal anomaly is located towards the northern part of Baja California Peninsula (Mexico). High water temperatures in some wells along the coast depicted a geothermal anomaly. An audiomagnetotelluric survey was carried out in the area as a preliminary study, both to understand the process generating these anomalous temperatures and to assess its potential exploitation to supply hot water to desalination plants. Among the electromagnetic methods, the audiomagnetotellurics (AMT) method is appropriated for deep groundwater and geothermal studies. The survey consisted of 27 AMT stations covering a 5 km profile along the Agua Blanca Fault. The employed array allowed us to characte