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Sample records for structural characterization magnetochemistry

  1. Synthesis, structural characterization and thermal properties of a new copper(II) one-dimensional coordination polymer based on bridging N,N'-bis(2-hydroxybenzylidene)-2,2-dimethylpropane-1,3-diamine and dicyanamide ligands.

    PubMed

    Hopa, Cigdem; Cokay, Ismail

    2016-02-01

    The design and synthesis of polymeric coordination compounds of 3d transition metals are of great interest in the search for functional materials. The coordination chemistry of the copper(II) ion is of interest currently due to potential applications in the areas of molecular biology and magnetochemistry. A novel coordination polymer of Cu(II) with bridging N,N'-bis(2-hydroxyphenyl)-2,2-dimethylpropane-1,3-diamine (H2L-DM) and dicyanamide (dca) ligands, catena-poly[[[μ2-2,2-dimethyl-N,N'-bis(2-oxidobenzylidene)propane-1,3-diamine-1:2κ(6)O,N,N',O':O,O']dicopper(II)]-di-μ-dicyanamido-1:2'κ(2)N(1):N(5);2:1'κ(2)N(1):N(5)], [Cu2(C19H20N2O2)(C2N3)2]n, has been synthesized and characterized by CHN elemental analysis, IR spectroscopy, thermal analysis and X-ray single-crystal diffraction analysis. Structural studies show that the Cu(II) centres in the dimeric asymmetric unit adopt distorted square-pyramidal geometries, as confirmed by the Addison parameter (τ) values. The chelating characteristics of the L-DM(2-) ligand results in the formation of a Cu(II) dimer with a double phenolate bridge in the asymmetric unit. In the crystal, the dimeric units are further linked to adjacent dimeric units through μ1,5-dca bridges to produce one-dimensional polymeric chains.

  2. Structural characterization of solid foams

    NASA Astrophysics Data System (ADS)

    Maire, Éric; Adrien, Jérôme; Petit, Clémence

    2014-10-01

    For being a useful contribution to the understanding of the properties of solid foams, the characterization of the structure of solid foams has to be performed at different scales. The microstructure of the solid part of the foams has to be analyzed. For this, standard SEM observations are often used. The most important aspect (and the most problematic) remains the characterization of the porous architecture of these materials. The methods introduced in this paper concern both scales and the article discusses the specificity of the experiments in the case of porous materials. X-ray tomography is described in more details because it becomes widely used for this purpose. The paper also shows how the obtained 3D images (sometimes obtained during deformation) can be processed to yield important morphological parameters describing the foams. xml:lang="fr"

  3. 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.

  4. Structural flyby characterization of nanoporosity

    NASA Astrophysics Data System (ADS)

    Rosa, R. R.; Ferreira da Silva, A.; Brito, R. C.; Roman, L. S.; Baroni, M. P. M. A.; Ramos, F. M.; Ahuja, R.; Persson, C.

    2004-08-01

    Recently, Ferreira da Silva et al. [3] have performed a gradient pattern analysis of a canonical sample set (CSS) of scanning force microscopy (SFM) images of p-Si. They applied the so-called Gradient Pattern Analysis to images of three typical p-Si samples distinguished by different absorption energy levels and aspect ratios. Taking into account the measures of spatial asymmetric fluctuations they interpreted the global porosity not only in terms of the amount of roughness, but rather in terms of the structural complexity (e.g., walls and fine structures as slots). This analysis has been adapted in order to operate in a OpenGL flyby environment (the StrFB code), whose application give the numerical characterization of the structure during the flyby real time. Using this analysis we compare the levels of asymmetric fragmentation of active porosity related to different materials as p-Si and "porous diamond-like" carbon. In summary we have shown that the gradient pattern analysis technique in a flyby environment is a reliable sensitive method to investigate, qualitatively and quantitatively, the complex morphology of active nanostructures.

  5. 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.

  6. 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.

  7. Structural Characterization of Schladitz Whiskers.

    DTIC Science & Technology

    1982-05-01

    and Eicke, 9 ,14 Lashmore ,16 and Newkirk and Wilsdorf. 1 7 7 I The ultimate tensile strength (UTS) of polycrystalline steel whiskers has been reported...have * Private communication by D. S. Lashmore , L. J. Swartzendruber and L. H. Bennett. 17 a combined with Fe to Fe 3 C. It was calculated that 18 + 2...by Lashmore (1977), and Schladitz (1968) reported values approach- ing 8 GPa. The structural details described in the previous chapter do not fit into

  8. 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.

  9. 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).

  10. 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.

  11. 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.

  12. Molecular and electronic structures of the members of the electron transfer series [Mn(bpy)3]n (n = 2+, 1+, 0, 1-) and [Mn(tpy)2]m (m = 4+, 3+, 2+, 1+, 0). An experimental and density functional theory study.

    PubMed

    Wang, Mei; England, Jason; Weyhermüller, Thomas; Wieghardt, Karl

    2014-02-17

    The members of the electron transfer series [Mn(bpy)3](n) (n = 2+, 1+, 0, 1-) and [Mn(tpy)2](m) (m = 2+, 1+, 0) have been investigated using a combination of magnetochemistry, electrochemistry, and UV-vis-NIR spectroscopy; and X-ray crystal structures of [Mn(II)((Me)bpy(•))2((Me)bpy(0))](0), [Li(THF)4][Mn(II)(bpy(•))3], and [Mn(II)(tpy(•))2](0) have been obtained (bpy = 2,2'-bipyridine; (Me)bpy = 4,4'-dimethyl-2,2'-bipyridine; tpy = 2,2':6,2″-terpyridine; THF = tetrahydrofuran). It is the first time that the latter complex has been isolated and characterized. Through these studies, the electronic structures of each member of both series of complexes have been elucidated, and their molecular and electronic structures further corroborated by broken symmetry (BS) density functional theoretical (DFT) calculations. It is shown that all one-electron reductions that comprise the aforementioned redox series are ligand-based. Hence, all species contain a central high-spin Mn(II) ion (SMn = 5/2). In contrast, the analogous series of Tc(II) and Re(II) complexes possess low-spin electron configurations.

  13. Characterization and Cure Monitoring of Structural Adhesives

    DTIC Science & Technology

    1989-02-01

    OX tiLE (OP? MTL TR 89-15 AD CHARACTERIZATION AND CURE MONITORING OF STRUCTURAL ADHESIVES CD WALTER X. ZUKAS, HOWARD H. WONG, DAVID A. DUNN, and...REPORT NUMB3ER 7. AUTHOR(s) 8. CONTRACT OR GRANT NUMBERs) Walter X. Zukas, Howard H. Wong, David A. Dunn, and Stanley E. Wentworth I. PERFORING...Technology, Gaithersburg, MD 20899 1 ATTN: B. Fanconi, Polymer Standards Division 1 D. Hunston, Polymer Standards Division 1 Dr. Stanley M. Barkin , Staff

  14. Instrumentation for the Characterization of Inflatable Structures

    NASA Technical Reports Server (NTRS)

    Swanson, Gregory T.; Cassell, Alan M.; Johnson, R. Keith

    2012-01-01

    Current entry, descent, and landing technologies are not practical for heavy payloads due to mass and volume constraints dictated by limitations imposed by launch vehicle fairings. Therefore, new technologies are now being explored to provide a mass- and volume-efficient solution for heavy payload capabilities, including Inflatable Aerodynamic Decelerators (IAD) [1]. Consideration of IADs for space applications has prompted the development of instrumentation systems for integration with flexible structures to characterize system response to flight-like environment testing. This development opportunity faces many challenges specific to inflatable structures in extreme environments, including but not limited to physical flexibility, packaging, temperature, structural integration and data acquisition [2]. In the spring of 2012, two large scale Hypersonic Inflatable Aerodynamic Decelerators (HIAD) will be tested in the National Full-Scale Aerodynamics Complex s 40 by 80 wind tunnel at NASA Ames Research Center. The test series will characterize the performance of a 3.0 m and 6.0 m HIAD at various angles of attack and levels of inflation during flight-like loading. To analyze the performance of these inflatable test articles as they undergo aerodynamic loading, many instrumentation systems have been researched and developed. These systems will utilize new experimental sensing systems developed by the HIAD ground test campaign instrumentation team, in addition to traditional wind tunnel sensing techniques in an effort to improve test article characterization and model validation. During the 2012 test series the instrumentation systems will target inflatable aeroshell static and dynamic deformation, structural strap loading, surface pressure distribution, localized skin deflection, and torus inflation pressure. This paper will offer an overview of inflatable structure instrumentation, and provide detail into the design and implementation of the sensors systems that will

  15. Structural characterization of dimeric murine aminoacylase III.

    PubMed

    Ryazantsev, Sergey; Abuladze, Natalia; Newman, Debra; Bondar, Galyna; Kurtz, Ira; Pushkin, Alexander

    2007-05-01

    Aminoacylase III (AAIII) plays an important role in deacetylation of acetylated amino acids and N-acetylated S-cysteine conjugates of halogenated alkenes and alkanes. AAIII, recently cloned from mouse kidney and partially characterized, is a mixture of tetramers and dimers. In the present work, AAIII dimers were purified and shown to be enzymatically active. Limited trypsinolysis showed two domains of approximately 9 and 25 kDa. The three-dimensional structure of the dimer was studied by electron microscopy of negative stained samples and by single-particle reconstruction. A 16A resolution model of the AAIII dimer was created. It has an unusual, cage-like, structure. A realistic AAIII tetramer model was built from two dimers.

  16. 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.

  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 thioether-bridged bacteriocins.

    PubMed

    Lohans, Christopher T; Vederas, John C

    2014-01-01

    Bacteriocins are a group of ribosomally synthesized antimicrobial peptides produced by bacteria, some of which are extensively post-translationally modified. Some bacteriocins, namely the lantibiotics and sactibiotics, contain one or more thioether bridges. However, these modifications complicate the structural elucidation of these bacteriocins using conventional techniques. This review will discuss the techniques and strategies that have been applied to determine the primary structures of lantibiotics and sactibiotics. A major challenge is to identify the topology of thioether bridges in these peptides (i.e., which amino-acid residues are involved in which bridges). Edman degradation, NMR spectroscopy and tandem MS have all been commonly applied to characterize these bacteriocins, but can be incompatible with the post-translational modifications present. Chemical modifications to the modified residues, such as desulfurization and reduction, make the treated bacteriocins more compatible to analysis by these standard peptide analytical techniques. Despite their differences in structure, similar strategies have proved useful to study the structures of both lantibiotics and sactibiotics.

  19. Macroscale and Microscale Structural Characterization of Cephalopod Chromatophores

    DTIC Science & Technology

    2011-04-01

    Macroscale and Microscale Structural Characterization of Cephalopod Chromatophores by Keith M. Kirkwood, Eric D. Wetzel, George Bell, Alan M...21005 ARL-RP-0318 April 2011 Macroscale and Microscale Structural Characterization of Cephalopod Chromatophores Keith M. Kirkwood and...Structural Characterization of Cephalopod Chromatophores 5a. CONTRACT NUMBER ORISE Contract 120-1120-99 (GHIORSE) 5b. GRANT NUMBER 5c. PROGRAM

  20. Beta environmental fine structure characterization of defects

    NASA Astrophysics Data System (ADS)

    Benedek, G.; Fiorini, E.; Giuliani, A.; Milani, P.; Monfardini, A.; Nucciotti, A.; Prandoni, M. L.; Sancrotti, M.

    1999-04-01

    The fine structure of beta emission (BEFS) due to the interference with the scattered waves from neighboring atoms, analogous to EXAFS, is known to produce oscillations in the Kurie plot. Here we suggest the use of BEFS for characterizing the lattice environment of β-emitting defects located at a distance from the crystal surface not exceeding the mean free path of β-electrons. Examples of defective structures in semiconductors whose atomic arrangement could be conveniently studied with BEFS are tritium-passivated dangling bonds, β-radioactive ions implanted in the crystal lattice or segregated at extended defects such as dislocations, grain boundaries or radiation damage. Also 14C-doped diamond-like materials and other exotic carbon forms, as well as the atomic environment of ions in metal alloys could be good candidate for BEFS. In this work we have calculated the fractional BEFS modulation for 187Re in its ordinary hcp crystal lattice for which experimental data by Cosulich et al. are available. The good correspondence between theory and experiment permits to conclude that BEFS experiments at low temperature are accessible to the present bolometric detection techniques and can provide an expedient method, as compared to EXAFS, for an accurate structural assessment of extended defects in solids.

  1. 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.

  2. Characterization of Imposed Ordered Structures in MDPX

    NASA Astrophysics Data System (ADS)

    Hall, Taylor; Thomas, Edward; Konopka, Uwe; Merlino, Robert; Rosenberg, Marlene

    2016-10-01

    It is well understood that the microparticles in complex, or dusty, plasmas will form self-consistent crystalline patterns at the proper plasma parameters. In the Magnetized Dusty Plasma Experiment (MDPX) device, studies have been made of imposed, ordered structuring of the dust particles to a two dimensional grid. At high magnetic field (B >1 Tesla), the dust particles are shown to become spatially oriented to the structure of a wire mesh embedded in an electrically floating, upper electrode while the particles are suspended in a plasma that is generated by the powered, lower electrode in the experiment. With even higher magnetic field (B >2 Tesla), the particles become strongly confined to the mesh pattern with the particles constrained to a quasi-discreet motion that closely follows the mesh pattern. This presentation characterizes the structure of the potential energy well in which the dust particles are trapped through observation of particle motion and measurement of the thermal properties of the particles. This work is supported by funding from the U. S. Department of Energy Grant Number DE - SC0010485 and the NASA/Jet Propulsion Laboratory, JPL-1543114.

  3. 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.

  4. Electro-mechanical characterization of structural supercapacitors

    NASA Astrophysics Data System (ADS)

    Gallagher, T.; LaMaster, D.; Ciocanel, C.; Browder, C.

    2012-04-01

    The paper presents electrical and mechanical properties of structural supercapacitors and discusses limitations associated with the approach taken for the electrical properties evaluation. The structural supercapacitors characterized in this work had the electrodes made of carbon fiber weave, separator made of several cellulose based products, and the solid electrolyte made as PEGDGE based polymer blend. The reported electrical properties include capacitance and leakage resistance; the former was measured using cyclic voltammetry. Mechanical properties have been evaluated thorough tensile and three point bending tests performed on structural supercapacitor coupons. The results indicate that the separator material plays an important role on the electrical as well as mechanical properties of the structural capacitor, and that Celgard 3501 used as separator leads to most benefits for both mechanical and electrical properties. Specific capacitance and leakage resistance as high as 1.4kF/m3 and 380kΩ, respectively, were achieved. Two types of solid polymer electrolytes were used in fabrication, with one leading to higher and more consistent leakage resistance values at the expense of a slight decrease in specific capacitance when compared to the other SPE formulation. The ultimate tensile strength and modulus of elasticity of the developed power storage composite were evaluated at 466MPa and 18.9MPa, respectively. These values are 58% and 69% of the tensile strength and modulus of elasticity values measured for a single layer composite material made with the same type of carbon fiber and with a West System 105 epoxy instead of solid polymer electrolyte.

  5. Structural characterization of submerged granular packings.

    PubMed

    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.

  6. 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.

  7. 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

  8. Detection and Characterization of R Loop Structures.

    PubMed

    Boque-Sastre, Raquel; Soler, Marta; Guil, Sonia

    2017-01-01

    R loops are special three stranded nucleic acid structures that comprise a nascent RNA hybridized with the DNA template strand, leaving a non-template DNA single-stranded. More specifically, R loops form in vivo as G-rich RNA transcripts invade the DNA duplex and anneal to the template strand to generate an RNA:DNA hybrid, leaving the non-template, G-rich DNA strand in a largely single-stranded conformation (Aguilera and Garcia-Muse, Mol Cell 46:115-124, 2012).DNA-RNA hybrids are a natural occurrence within eukaryotic cells, with levels of these hybrids increasing at sites with high transcriptional activity, such as during transcription initiation, repression, and elongation. RNA-DNA hybrids influence genomic instability, and growing evidence points to an important role for R loops in active gene expression regulation (Ginno et al., Mol Cell 45, 814-825, 2012; Sun et al., Science 340: 619-621, 2013; Bhatia et al., Nature 511, 362-365, 2014). Analysis of the occurrence of such structures is therefore of increasing relevance and herein we describe methods for the in vivo and in vitro identification and characterization of R loops in mammalian systems.R loops (DNA:RNA hybrids and the associated single-stranded DNA) have been traditionally associated with threats to genome integrity, making some regions of the genome more prone to DNA-damaging and mutagenic agents. Initially considered to be rare byproducts of transcription, over the last decade accumulating evidence has pointed to a new view in which R loops form more frequently than previously thought. The R loop field has become an increasingly expanded area of research, placing these structures as a major threat to genome stability but also as potential regulators of gene expression. Special interest has arisen as they have also been linked to a variety of diseases, including neurological disorders and cancer, positioning them as potential therapeutic targets [5].

  9. 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.

  10. Statistical characterization of phenolic-novolak structures

    NASA Technical Reports Server (NTRS)

    Parker, J. A.; Winkler, E. L.

    1971-01-01

    Three statistical methods of general validity are valuable for characterizing any polymer which results from chain polymerization of multifunctional branching monomers linked through bifunctional monomers.

  11. Structural characterization of soy protein nanoparticles from high shear microfluidization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soy protein nanoparticles were produced with a microfluidizer and characterized in terms of particle size, size distribution, morphology, rheological properties, and aggregate structure. Three stages of structure breakdown were observed when the soy protein dispersion was passed through the microflu...

  12. 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

  13. Structure-based characterization of multiprotein complexes.

    PubMed

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

    2014-07-08

    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.

  14. Development and Characterization of Multilayer Integrated Warhead Structure.

    DTIC Science & Technology

    1985-05-01

    the final concept. Steel castings ( 17 - 4PH ) were made and specimens were machined to characterize the structural properties of the concept. The pioperty...casting 17 - 4PH test specimens and characterizing these composite structures. It was anticipated that problem would occur in the transition . from...MULTILAYER Final Report INTEGRATED WARHEAD STRUCTURE 3/ 17 /83 to 9/30/84 G. PERFORMING ORG. REPORT NUMBER 7. AUTHOR(a) 0. CONTRACT OR GRANT NUMBER(s) D

  15. Synthesis and structural characterization of zinc titanates

    NASA Astrophysics Data System (ADS)

    Akgül, Güvenç

    2013-04-01

    The aim of this study is to accurately obtain of local atomic structures of zinc titanates (ZnTiO3 and Zn2TiO4). Samples have been synthesized by the ball milling method using mixture of high purity ZnO and TiO2 powders. X-ray diffraction (XRD), X-ray absorption near edge structure (XANES), and extended X-ray absorption fine structure (EXAFS) techniques have been used to probe crystal and local structures of the synthesized powders. They have been found to exhibit very high crystallinity. In addition, the EXAFS results have showed that the ball milling is a quite effective method to fabricate highly crystalline nanosized powders. The obtained results are presented in detail.

  16. AFM Structural Characterization of Drinking Water Biofilm ...

    EPA Pesticide Factsheets

    Due to the complexity of mixed culture drinking water biofilm, direct visual observation under in situ conditions has been challenging. In this study, atomic force microscopy (AFM) revealed the three dimensional morphology and arrangement of drinking water relevant biofilm in air and aqueous solution. Operating parameters were optimized to improve imaging of structural details for a mature biofilm in liquid. By using a soft cantilever (0.03 N/m) and slow scan rate (0.5 Hz), biofilm and individual bacterial cell’s structural topography were resolved and continuously imaged in liquid without loss of spatial resolution or sample damage. The developed methodology will allow future in situ investigations to temporally monitor mixed culture drinking water biofilm structural changes during disinfection treatments. Due to the complexity of mixed culture drinking water biofilm, direct visual observation under in situ conditions has been challenging. In this study, atomic force microscopy (AFM) revealed the three dimensional morphology and arrangement of drinking water relevant biofilm in air and aqueous solution. Operating parameters were optimized to improve imaging of structural details for a mature biofilm in liquid. By using a soft cantilever (0.03 N/m) and slow scan rate (0.5 Hz), biofilm and individual bacterial cell’s structural topography were resolved and continuously imaged in liquid without loss of spatial resolution or sample damage. The developed methodo

  17. 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.

  18. DNA Microarrays for Aptamer Identification and Structural Characterization

    DTIC Science & Technology

    2012-09-01

    AFRL-RH-WP-TR-2013-0130 DNA MICROARRAYS FOR APTAMER IDENTIFICATION AND STRUCTURAL CHARACTERIZATION Jennifer A. Martin National Research Council...Interim September 2010 to September 2012 4. TITLE AND SUBTITLE DNA Microarrays for Aptamer Identification and Structural Characterization 5a. CONTRACT... Aptamers are ideal recognition elements, but integrating aptamers onto a sensor platform has two main challenges: (1) aptamers are selected in

  19. Spectroscopic and structural characterization of pascoite

    NASA Astrophysics Data System (ADS)

    Reddy, G. Udayabhaskara; Reddy, R. Ramasubba; Reddy, S. Lakshmi; Frost, Ray L.; Endo, Tamio

    2011-09-01

    Pascoite mineral having yellow-orange colour of Colorado, USA origin has been characterized by EPR, optical and NIR spectroscopy. The colour dark red-orange to yellow-orange colour of the pascoite indicates that the mineral contain mixed valency of vanadium. The optical spectrum exhibits a number of electronic bands due to presence of VO(II) ions in the mineral. From EPR studies, the parameters of g, A are evaluated and the data confirm that the ion is in distorted octahedron. Optical absorption studies reveal that two sets of VO(II) is in distorted octahedron. The bands in NIR spectra are due to the overtones and combinations of water molecules.

  20. Structural Characterization of Bacterioferritin from Blastochloris viridis

    PubMed Central

    Wahlgren, Weixiao Y.; Omran, Hadil; von Stetten, David; Royant, Antoine; van der Post, Sjoerd; Katona, Gergely

    2012-01-01

    Iron storage and elimination of toxic ferrous iron are the responsibility of bacterioferritins in bacterial species. Bacterioferritins are capable of oxidizing iron using molecular oxygen and import iron ions into the large central cavity of the protein, where they are stored in a mineralized form. We isolated, crystallized bacterioferritin from the microaerophilic/anaerobic, purple non-sulfur bacterium Blastochloris viridis and determined its amino acid sequence and X-ray structure. The structure and sequence revealed similarity to other purple bacterial species with substantial differences in the pore regions. Static 3- and 4-fold pores do not allow the passage of iron ions even though structural dynamics may assist the iron gating. On the other hand the B-pore is open to water and larger ions in its native state. In order to study the mechanism of iron import, multiple soaking experiments were performed. Upon Fe(II) and urea treatment the ferroxidase site undergoes reorganization as seen in bacterioferritin from Escherichia coli and Pseudomonas aeruginosa. When soaking with Fe(II) only, a closely bound small molecular ligand is observed close to Fe1 and the coordination of Glu94 to Fe2 changes from bidentate to monodentate. DFT calculations indicate that the bound ligand is most likely a water or a hydroxide molecule representing a product complex. On the other hand the different soaking treatments did not modify the conformation of other pore regions. PMID:23056552

  1. Amplification and characterization of eukaryotic structural genes.

    PubMed

    Maniatis, T; Efstratiadis, A; Sim, G K; Kafatos, F

    1978-05-01

    An approach to the study of eukaryotic structural genes which are differentially expressed during development is described. This approach involves the isolation and amplification of mRNA sequences by in vitro conversion of mRNA to double-stranded cDNA followed by molecular cloning in bacterial plasmids. This procedure provides highly specific hybridization probes that can be used to identify genes and their contiguous DNA sequences in genomic DNA, and to detect specific RNA transcripts during development. The nature of the method allows the isolation of individual mRNA sequences from a complex population of molecules at different stages of development.

  2. Characterizing the Community Structure of Complex Networks

    PubMed Central

    Lancichinetti, Andrea; Kivelä, Mikko; Saramäki, Jari; Fortunato, Santo

    2010-01-01

    Background Community structure is one of the key properties of complex networks and plays a crucial role in their topology and function. While an impressive amount of work has been done on the issue of community detection, very little attention has been so far devoted to the investigation of communities in real networks. Methodology/Principal Findings We present a systematic empirical analysis of the statistical properties of communities in large information, communication, technological, biological, and social networks. We find that the mesoscopic organization of networks of the same category is remarkably similar. This is reflected in several characteristics of community structure, which can be used as “fingerprints” of specific network categories. While community size distributions are always broad, certain categories of networks consist mainly of tree-like communities, while others have denser modules. Average path lengths within communities initially grow logarithmically with community size, but the growth saturates or slows down for communities larger than a characteristic size. This behaviour is related to the presence of hubs within communities, whose roles differ across categories. Also the community embeddedness of nodes, measured in terms of the fraction of links within their communities, has a characteristic distribution for each category. Conclusions/Significance Our findings, verified by the use of two fundamentally different community detection methods, allow for a classification of real networks and pave the way to a realistic modelling of networks' evolution. PMID:20711338

  3. Structural Characterization of Methanol Substituted Lanthanum Halides

    PubMed Central

    Boyle, Timothy J.; Ottley, Leigh Anna M.; Alam, Todd M.; Rodriguez, Mark A.; Yang, Pin; Mcintyre, Sarah K.

    2010-01-01

    The first study into the alcohol solvation of lanthanum halide [LaX3] derivatives as a means to lower the processing temperature for the production of the LaBr3 scintillators was undertaken using methanol (MeOH). Initially the de-hydration of {[La(µ-Br)(H2O)7](Br)2}2 (1) was investigated through the simple room temperature dissolution of 1 in MeOH. The mixed solvate monomeric [La(H2O)7(MeOH)2](Br)3 (2) compound was isolated where the La metal center retains its original 9-coordination through the binding of two additional MeOH solvents but necessitates the transfer of the innersphere Br to the outersphere. In an attempt to in situ dry the reaction mixture of 1 in MeOH over CaH2, crystals of [Ca(MeOH)6](Br)2 (3) were isolated. Compound 1 dissolved in MeOH at reflux temperatures led to the isolation of an unusual arrangement identified as the salt derivative {[LaBr2.75•5.25(MeOH)]+0.25 [LaBr3.25•4.75(MeOH)]−0.25} (4). The fully substituted species was ultimately isolated through the dissolution of dried LaBr3 in MeOH forming the 8-coordinated [LaBr3(MeOH)5] (5) complex. It was determined that the concentration of the crystallization solution directed the structure isolated (4 concentrated; 5 dilute) The other LaX3 derivatives were isolated as [(MeOH)4(Cl)2La(µ-Cl)]2 (6) and [La(MeOH)9](I)3•MeOH (7). Beryllium Dome XRD analysis indicated that the bulk material for 5 appear to have multiple solvated species, 6 is consistent with the single crystal, and 7 was too broad to elucidate structural aspects. Multinuclear NMR (139La) indicated that these compounds do not retain their structure in MeOD. TGA/DTA data revealed that the de-solvation temperatures of the MeOH derivatives 4 – 6 were slightly higher in comparison to their hydrated counterparts. PMID:20514349

  4. 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

  5. Characterization of Fine Structure in Sprites

    NASA Astrophysics Data System (ADS)

    Gerken, E. A.; Inan, U. S.

    2001-12-01

    During the summer months of 1998-2000, Stanford University fielded campaigns to telescopically image sprites. The campaigns were conducted at Langmuir Laboratory (operated by New Mexico Institute of Mining and Technology) in Socorro NM and Yucca Ridge Observatory in Fort Collins CO. The experiment consisted of two intensified CCD cameras, two photometers, and crossed magnetic loop VLF antennas. One camera was mounted on a 16in diameter, 72in focal length Newtonian telescope with a field of view of 0.72x0.9 degrees and the other had a 50mm lens with a field of view of 9x12 degrees. Similarly one photometer was mounted on an 8in diameter, 1200mm focal length Newtonian telescope with a circular field of view of 1 degree and the second was red-filtered and had a wider field of view of 3x6 degrees. All four instruments were mounted on the same platform and were aligned. Video data was stored on VHS tapes with the photometer signals recorded on the audio channels. GPS video time-stamping and IRIG-B code were used for timing. Data from these campaigns reveal streamer structures within sprites ranging from 25m to 200m in width. Streamer morphologies are diverse ranging from single columns to multiply-forked structures to chains of beads. Faint downward branching is observed prior to some large sprite events. Streamers are seen to develop on time scales from less than 17ms to over 100ms. Streamer sizes and velocities are compared to existing models and charge moments for associated sferics are presented.

  6. Structure and characterization of AAT-1 isoforms.

    PubMed

    Matsuda, Eiko; Ishizaki, Ray; Taira, Takahiro; Iguchi-Ariga, Sanae M M; Ariga, Hiroyoshi

    2005-05-01

    A novel protein, AAT-1, was identified as a AMY-1-binding protein and three splicing variants of AAT-1, AAT-1alpha, -beta and -gamma were identified. The function of AAT-1 is thought to be related to spermatogenesis. In this study, we further identified other splicing isoforms of AAT-1, AAT-1L, AAT-1M and AAT-1S, consisting of 767, 603 and 252 amino acids, respectively. These isoforms were found to use a promoter different from that used by AAT-1alpha, -beta and -gamma in the aat-1 gene, which contains 20 exons. Only 60 amino acids in the C-terminal portion of AAT-1 derived from exons 15-17 are common among AAT-1L, AAT-1M, AAT-1S and AAT-1alpha. While AAT-1alpha is specifically expressed in the testis, AAT-1L, AAT-1M, AAT-1S were found to be differentially expressed in human tissues. All of the isoforms of AAT-1 were found to bind to and colocalized with AMY-1 in human cells. While AAT-1L and AAT-1M were found to be localized diffusely in the cytoplasm, AAT-1S, like AAT-1alpha, was found to be localized in the mitochondria-like structure, suggesting different roles of AAT-1 isoforms in cells.

  7. 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.

  8. Aromatase inhibitors: structural features and biochemical characterization.

    PubMed

    Hong, Yanyan; Chen, Shiuan

    2006-11-01

    Aromatase is the enzyme synthesizing estrogens from androgens. In estrogen-dependent breast tumors, estrogens induce the expression of growth factors responsible for cancer cell proliferation. In situ estrogen synthesis by aromatase "is thought to play a key role in the promotion of breast cancer growth. Aromatase inhibitors (AIs) provide new approaches for the prevention and treatment of breast cancer by inhibiting estrogen biosynthesis. Through reverse transcription polymerase chain reaction (RT-PCR) and immunohistochemical techniques, aromatase has been found to be expressed in many endocrine tissues and tumors originating from these tissues. Unexpectedly, this enzyme is now known to also be expressed in liver, lung, and colon cancers. Such findings suggest a potential role for endocrine manipulation of these types of cancer using AIs. Three Food and Drug Administration (FDA)-approved AIs, anastrozole (Arimidex), letrozole (Femara), and exemestane (Aromasin), effectively challenging tamoxifen, have been used as first-line drugs in the treatment of hormone-dependent breast cancer, and possibly other aromatase-expressing cancers. In addition, natural anti-aromatase chemicals, such as flavones and coumarins, have been identified. Efforts to develop new lines of AIs derived from these phytochemicals have been initiated in several laboratories. Finally, significant progress has been made in the understanding of the structure-function relationship of aromatase. Such information has helped the examination of binding characteristics of AIs, the evaluation of reaction mechanism of aromatase, and the explanation of the molecular basis for a low catalytic activity of the natural variant, M364T.

  9. Surface characterization of semiconductor photocathode structures

    NASA Astrophysics Data System (ADS)

    Liu, Zhi

    The need for a high performance photocathode in the electron beam lithography and microscopy is well established. Previous research demonstrated high brightness (1 x 108 A/cm2-sr at 3 KeV), and an energy spread as low as 50meV at room temperature for a GaAs based negative electron affinity (NEA) cathode in a sealed-off tube. However the GaAs cathodes suffer rapid decay in an open vacuum system. Achieving a clean, stoichiometric and repeatable GaAs(100) surface was the first step in this study. Based on the knowledge obtained from synchrotron radiation photoelectron spectroscopy, we successfully developed and optimized a reliable surface cleaning technique for our GaAs photocathodes. The fully activated photocathode and its decay under different vacuum conditions were investigated. The NEA activation layer is about 1 nm thick and was very vulnerable to oxygen in the system. A revised double dipole structural model was proposed to explain how the Cs/O co-deposition could produce a NEA surface. We found the chemical changes of oxygen species in the activation layer caused the initial quantum yield (QY) decay of the cathode. Further exposure to oxygen oxidized the substrate and permanently reduced the QY to zero. Energy distribution curve measurements of GaAs(100) and GaN(0001) NEA surfaces were performed under laser illumination. We found that the main contribution to the total emitted current of NEA GaAs and GaN surfaces was due to the electrons that were lost an average 140meV and 310 meV respectively in the near surface region prior to emission into vacuum. This energy loss is due not to the scattering through Cs or Cs/O layer; In GaN, it is probably due to a Gunn-like effect involving inter-valley phonon scattering within the band-bending region. We observed a highly directional emission profile from GaAs cathodes (electrons emitted within a semi-angle of 15° relative to the surface normal). In practice, it is expected that the highly directional photoemission

  10. Geophysical characterization of the Chicxulub impact structure

    NASA Astrophysics Data System (ADS)

    Gulick, S. P.; Christeson, G. L.; Barton, P. J.; Grieve, R. A.; Morgan, J. V.; Fucugauchi, J. U.

    2013-05-01

    The Chicxulub impact structure, conclusively linked to the 65.5 Ma mass extinction, includes three sets of inward dipping, ring faults, between 70 and 130 km radially with a topographically elevated inner rim, at the inner edge of these faults except in the northeast where such a rim is absent. Slump blocks offset by large faults result in a terrace zone, that steps down from the inner rim into the annular trough. The inner blocks underlie the peak ring --an internal topographic ring of topography that exhibits variable relief due to target asymmetries and bounds the coherent melt sheet within the central basin. Impact breccias lie within the annular trough above the slump blocks and proximal ejecta and within the central basin above the melt sheet. Beneath the melt sheet is the top of the central uplift, displaced by >10 km vertically, and an upwarped Moho, displaced by 1-2 km. These interpretations and hydrocode models support the following working hypothesis for the formation of Chicxulub: a 50 km radius transient cavity, lined with melt and impact breccia, formed within 10s of seconds of the 65.5 Ma impact and within minutes, weakened rebounding crust rose above kilometers above the surface, the transient crater rim underwent localized, brittle deformation and collapsed into large slump blocks resulting in a inner rim being preserved 70-85 km from crater center, and ring faults forming farther outwards. The overheightened central uplift of weakened crust collapsed outwards forming the peak ring, and buried the inner slump blocks. Most impact melt that lined the transient cavity was transported on top of the central uplift, ultimately emplaced as a coherent <3-km thick melt sheet that shallows within the inner regions of the peak ring. Smaller pockets of melt flowed into the annular trough. During and likely for sometime after these events, slope collapse, proximal ejecta, ground surge, and tsunami waves infilled the annular trough with sediments up to 3 km

  11. 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

  12. 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

  13. 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.

  14. Mathematical model for characterizing noise transmission into finite cylindrical structures

    NASA Astrophysics Data System (ADS)

    Li, Deyu; Vipperman, Jeffrey S.

    2005-02-01

    This work presents a theoretical study of the sound transmission into a finite cylinder under coupled structural and acoustic vibration. Particular attention of this study is focused on evaluating a dimensionless quantity, ``noise reduction,'' for characterizing noise transmission into a small cylindrical enclosure. An analytical expression of the exterior sound pressure resulting from an oblique plane wave impinging upon the cylindrical shell is first presented, which is approximated from the exterior sound pressure for an infinite cylindrical structure. Next, the analytical solution of the interior sound pressure is computed using modal-interaction theory for the coupled structural acoustic system. These results are then used to derive the analytical formula for the noise reduction. Finally, the model is used to predict and characterize the sound transmission into a ChamberCore cylindrical structure, and the results are compared with experimental data. The effects of incidence angle and internal acoustic damping on the sound transmission into the cylinder are also parametrically studied. .

  15. 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…

  16. 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.…

  17. 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.

  18. Preliminary Characterization and Classification Scheme for Tectonic Structures on Enceladus

    NASA Astrophysics Data System (ADS)

    Nahm, A.; Kattenhorn, S. A.

    2013-12-01

    The ice shell of Enceladus has experienced widespread and diverse tectonic deformation. Its leading and trailing hemispheres are pervasively fractured and these are separated by older cratered terrains on the sub- and anti-Saturnian hemispheres that exhibit relatively little tectonic deformation. The south polar terrain (SPT) is tectonically complex, geologically active, and is separated from the rest of Enceladus by the south polar dichotomy. The diversity of structures visible on the surface attests to a complicated and perhaps long-lived tectonic history. Currently, no fundamental classification scheme based on formation mechanisms exists for the tectonic structures on Enceladus, as does for Europa, which limits analysis and discussion of tectonic structures and the regional and global tectonic history. Characterization and classification of structures based on their formation mechanisms allows for the stress states (orientation, magnitude, and sense) responsible for their formation to be inferred. Thus, characterizing and classifying structures on Enceladus is a major first step in understanding its tectonic history. Here, we present a preliminary global classification scheme for tectonic structures on Enceladus. The basemap used for our preliminary structure classification was the global Imaging Science Subsystem (ISS) mosaic obtained from Ciclops (110 mpp; http://www.ciclops.org/view/7590/Map_of_Enceladus_-_December_2011?js=1). The structures observed on the surface have been divided into fifteen classes based on morphology. These classes represent the diversity of structure morphology on Enceladus and include the 'tiger stripes' in the SPT, the arcuate ridges that make up the south polar dichotomy, wide fracture complexes, several classes of narrow fractures, curvilinear subparallel fractures, rifts that extend north from the SPT boundary, terrain reminiscent of Ganymede's grooved terrain, and topographic ridges with multiple orientations. The preliminary

  19. 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.

  20. Characterization of coherent structures in the cardiovascular system.

    PubMed

    Shadden, Shawn C; Taylor, Charles A

    2008-07-01

    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 understanding of flow features in large vessels beyond methods traditionally considered.

  1. Preparation, structural, and calorimetric characterization of bicomponent metallic photonic crystals

    NASA Astrophysics Data System (ADS)

    Kozlov, M. E.; Murthy, N. S.; Udod, I.; Khayrullin, I. I.; Baughman, R. H.; Zakhidov, A. A.

    2007-03-01

    We report preparation and characterization of novel bicomponent metal-based photonic crystals having submicron three-dimensional (3D) periodicity. Fabricated photonic crystals include SiO2 sphere lattices infiltrated interstitially with metals, carbon inverse lattices filled with metal or metal alloy spheres, Sb inverse lattices, and Sb inverse lattices filled with Bi spheres. Starting from a face centered SiO2 lattice template, these materials were obtained by sequences of either templating and template extraction or templating, template extraction, and retemplating. Surprising high fidelity was obtained for all templating and template extraction steps. Scanning electron microscopy (SEM), small angle X-ray scattering (SAXS) and differential scanning calorimetry (DSC) were used to characterize the structure and the effects of the structure on calorimetric properties. To the best of our knowledge, SAXS data on metallic photonic crystals were collected for first time.

  2. Structural and functional characterization of synapse-associated protein-97

    NASA Astrophysics Data System (ADS)

    Wang, Lei

    Synapse-associated protein-97 (SAP97) as a scaffold protein plays an important role in regulating neural signal transmission in the central nervous system by coupling with activated membrane receptors, ion channels, and downstream signaling proteins. SAP97 consists of six functional domains: L27, PDZ1, PDZ2, PDZ3, SH3, and GK. Each of these domains mediates the interactions of SAP97 with other proteins. Understanding the molecular mechanism of these interactions in neural signal transmission is a goal of this study. Here high-resolution nuclear magnetic resonance spectroscopy and fluorescence anisotropy are employed towards the goal of the structural and functional characterization of SAP97; specifically, we (a) characterize the binding of the PDZ domains of SAP97 with the C-terminus of NR2B, and determine the structure of the PDZ1-NR2B; (b) characterize the binding of the PDZ domains with the C-terminus of stargazin and multiple mutants, and identify the perturbed amino acids in PDZ2 upon the binding of stargazin; (c) characterize the binding specificity carried by the beta2/beta3 loop of the PDZ3 domain. These results provide insight into the molecular mechanism for the binding specificities of the PDZ domains of SAP97, thereby furthering the development of drugs that target these domains to treat neurological diseases.

  3. 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.

  4. 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.

  5. (abstract) Characterization of Structural Response for Systems with Loose Joints

    NASA Technical Reports Server (NTRS)

    Bruno, Robin J.

    1995-01-01

    This paper describes a technique to locate and characterize loose joints in a large truss structure to generate an accurate structural model. The joint looseness is modeled as a gap in the member that opens and closes depending on the loading. Arbitrarily placed actuators are used to prestress the structure to first linearize the response. Next the actuator displacements are systematically reduced while monitoring the displacement response. The gap locations are determined by comparing the measured displacements with sets of calculated displacements and the sizes are estimated by monitoring the gap member length changes using the appropriate linear force-displacement relationship for the load level. The effect of measurement error in the truss displacements and the actuator length changes are investigated.

  6. 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.

  7. 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.

  8. Characterization of graphene-nanoplatelets structure via thermogravimetry.

    PubMed

    Shtein, Michael; Pri-Bar, Ilan; Varenik, Maxim; Regev, Oren

    2015-04-21

    The rapid increase in graphene-based applications has been accompanied by novel top-down manufacturing methods for graphene and its derivatives (e.g., graphene nanoplatelets (GnPs)). The characterization of the bulk properties of these materials by imaging and surface techniques (e.g., electron microscopy and Raman spectroscopy) is only possible through laborious and time-consuming statistical analysis, which precludes simple and efficient quality control during GnP production. We report that thermogravimetry (TG) may be utilized, beyond its conventional applications (e.g., quantification of impurities or surfactants, or labile functional groups) to characterize bulk GnP properties. We characterize the structural parameters of GnP (i.e., defect density, mean lateral dimension, and polydispersity) by imaging and surface techniques, on one hand, and by a systematic TG, on the other. The combined data demonstrate that the combustion temperature of commercially available and laboratory-prepared GnPs is correlated with their mean lateral dimension and defect density, while the combustion temperature range is proportional to their polydispersity index. Mapping all these parameters allows one to evaluate the GnPs' structure following a simple thermogravimetric experiment (without necessitating further statistical analysis). Finally, TG is also used to detect and quantify different GnP constituents in powder and to conduct rapid quality-control tests during GnP production.

  9. Structural characterizations of the chloroplast translocon protein Tic110

    PubMed Central

    Tsai, Jia-Yin; Chu, Chiung-Chih; Yeh, Yi-Hung; Chen, Lih-Jen; Li, Hsou-min; Hsiao, Chwan-Deng

    2013-01-01

    Tic110 is a major component of the chloroplast protein import translocon. Two functions with mutually exclusive structures have been proposed for Tic110: a protein-conducting channel with six transmembrane domains and a scaffold with two N-terminal transmembrane domains followed by a large soluble domain for binding transit peptides and other stromal translocon components. To investigate the structure of Tic110, Tic110 from Cyanidioschyzon merolae (CmTic110) was characterized. We constructed three fragments, CmTic110A, CmTic110B and CmTic110C, with increasing N-terminal truncations, to perform small-angle X-ray scattering (SAXS) and X-ray crystallography analyses and Dali structural comparison. Here we report the molecular envelope of CmTic110B and CmTic110C determined by SAXS, and the crystal structure of CmTic110C at 4.2 Å. Our data indicate that the C-terminal half of CmTic110 possesses a rod-shaped helix-repeat structure that is too flattened and elongated to be a channel. The structure is most similar to the HEAT-repeat motif that functions as scaffolds for protein–protein interactions. PMID:23711301

  10. 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.

  11. Characterization of cuttlebone for a biomimetic design of cellular structures

    NASA Astrophysics Data System (ADS)

    Cadman, Joseph; Zhou, Shiwei; Chen, Yuhang; Li, Wei; Appleyard, Richard; Li, Qing

    2010-03-01

    Cuttlebone is a natural material possessing the multifunctional properties of high porosity, high flexural stiffness and compressive strength, making it a fine example of design optimization of cellular structures created by nature. Examination of cuttlebone using scanning electron microscopy (SEM) reveals an approximately periodic microstructure, appropriate for computational characterization using direct homogenization techniques. In this paper, volume fractions and stiffness tensors were determined based on two different unit cell models that were extracted from two different cuttlefish samples. These characterized results were then used as the target values in an inverse homogenization procedure aiming to re-generate microstructures with the same properties as cuttlebone. Unit cells with similar topologies to the original cuttlebone unit cells were achieved, attaining the same volume fraction (i.e. bulk density) and the same (or very close) stiffness tensor. In addition, a range of alternate unit cell topologies were achieved also attaining the target properties, revealing the non-unique nature of this inverse homogenization problem.

  12. Characterization of localized transverse structures in wide-aperture lasers

    NASA Astrophysics Data System (ADS)

    Rosanov, N. N.; Fedorov, A. V.; Fedorov, S. V.; Khodova, G. V.

    The problem of characterization of spatio-temporal patterns is discussed for the case of wide-aperture lasers with nonlinear losses where variety of such patterns is especially rich. Laser autosolitons (LASs)-localized transverse structures representing “islands of lasing” on a background of the nonlasing mode on the laser aperture-are studied. Existence of stable single LASs which are motionless or moving in the transverse direction with constant linear velocity is shown. Described are also LASs with regular wavefronts, those with screw dislocations (defects) of wavefronts with different topological indices, and those with axially symmetric and asymmetric intensity distributions rotating with constant angular velocity around the LAS center. An approach is given for qualitative and quantitative characterization of a single LAS by its linear and angular velocities and frequency shift, based on a combination of analytical methods and computer simulations. Results of investigations of weak and strong interactions among the LASs are presented.

  13. EDITORIAL: (Nano)characterization of semiconductor materials and structures (Nano)characterization of semiconductor materials and structures

    NASA Astrophysics Data System (ADS)

    Bonanni, Alberta

    2011-06-01

    The latest impressive advancements in the epitaxial fabrication of semiconductors and in the refinement of characterization techniques have the potential to allow insight into the deep relation between materials' structural properties and their physical and chemical functionalities. Furthermore, while the comprehensive (nano)characterization of semiconductor materials and structures is becoming more and more necessary, a compendium of the currently available techniques is lacking. We are positive that an overview of the hurdles related to the specific methods, often leading to deceptive interpretations, will be most informative for the broad community working on semiconductors, and will help in shining some light onto a plethora of controversial reports found in the literature. From this perspective, with this special issue we address and highlight the challenges and misinterpretations related to complementary local (nanoscale) and more global experimental methods for the characterization of semiconductors. The six topical reviews and the three invited papers by leading experts in the specific fields collected in here are intended to provide the required broad overview on the possibilities of actual (nano)characterization methods, from the microscopy of single quantum structures, over the synchrotron-based absorption and diffraction of nano-objects, to the contentious detection of tiny magnetic signals by quantum interference and resonance techniques. We are grateful to all the authors for their valuable contributions. Moreover, I would like to thank the Editorial Board of the journal for supporting the realization of this special issue and for inviting me to serve as Guest Editor. We greatly appreciate the work of the reviewers, of the editorial staff of Semiconductor Science and Technology and of IOP Publishing. In particular, the efforts of Alice Malhador in coordinating this special issue are acknowledged.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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

  19. Rapid characterization of vegetation structure with a Microsoft Kinect sensor.

    PubMed

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

    2013-02-11

    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.

  20. 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.

  1. Isolation and structural characterization of anthocyanin-furfuryl pigments.

    PubMed

    Sousa, André; Mateus, Nuno; Silva, Artur Manuel Soares; Vivas, Nicolas; Nonier, Marie-Françoise; Pianet, Isabelle; de Freitas, Victor

    2010-05-12

    Condensation reactions of malvidin-3-glucoside with two representative oak wood furanic aldehydes (furfural and methylfurfural) were conducted in wine-like model solutions. Methylfurfural led to the formation of malvidin-3-glucoside-methylfurfural (603 m/z), whereas furfural led to the formation of malvidin-3-glucoside-furfural (589 m/z). The latter was structurally characterized by 1D and 2D NMR, allowing an elucidation of the formation mechanism of these anthocyanin-furanic aldehyde adducts in the absence of flavanols.

  2. Use of thermal imaging in characterization of ceramic fiber structures

    NASA Astrophysics Data System (ADS)

    Järveläinen, Matti; Keskinen, Lassi; Levänen, Erkki

    2013-12-01

    Fibrous bodies that contain open porosity can have a very heterogeneous structure that is difficult to characterize in terms of local flow resistance changes within the same sample. This article presents a method that is applicable for a quick analysis of flow distribution even with large samples. In this first attempt to understand how our flow distribution thermal imaging works, we present how the measuring parameters and the results correlate with sample's thickness and density. The results indicate that our method can quickly make a distinction between areas that have different flow resistances because of variations in the sample's density or wall thickness.

  3. 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.

  4. Characterization of asphaltene structure using atomic force microscopy.

    PubMed

    Sabbaghi, S; Shariaty-Niassar, M; Ayatollahi, Sh; Jahanmiri, A

    2008-09-01

    In this study, at the first stage, asphaltene was extracted. The roughness of asphaltene coating at different rpm was studied using an image analysis confocal microscopy. The basics of quantum mechanics and statistical thermodynamics are used to predict the potential energy and the intermolecular forces of asphaltene molecules. The functional forms for the potential energy and intermolecular forces are evaluated. Our final goal is to be able to observe and determine the surface structures of asphaltene micelles with scanning probe microscopes. So, the focus of the work on these unusual molecules is to characterize their structure, dynamics and thermodynamics and to establish the relationship between these properties and petroleum fluid behaviour. The existence of various nanostructures of asphaltene in petroleum has been extensively discussed. A set of fitted data is used to check the validity of the calculated results. The good agreement between the proposed models and the data is promising.

  5. Structural characterization of carbon materials prepared at low temperature

    SciTech Connect

    Song, X.Y.; Chu, X.; Kinoshita, K.

    1995-12-31

    High-capacity carbon electrodes for rechargeable lithium-ion batteries were prepared by carbonization of thermosetting resins such as phenol-formaldehyde at temperatures between 500 C and 600 C. Their structures were characterized by high resolution transmission electron microscopy, in-situ transmission electron microscopy and x-ray diffraction analysis. These studies suggest that the carbons consist predominantly of disorganized (amorphous) phase. However evidence was found in carbon containing nickel cobalt oxide for the presence of organized graphite-like regions of parallel and curved layer planes. These graphitized structure usually appear as agglomerate particles which are composed of many smaller (100-nm diameter) particles. The high degree of graphitization is attributed to catalytic graphitization that occurs in the presence of the metal oxide.

  6. 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.

  7. 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.

  8. Structured light imaging system for structural and optical characterization of 3D tissue-simulating phantoms

    NASA Astrophysics Data System (ADS)

    Liu, Songde; Smith, Zach; Xu, Ronald X.

    2016-10-01

    There is a pressing need for a phantom standard to calibrate medical optical devices. However, 3D printing of tissue-simulating phantom standard is challenged by lacking of appropriate methods to characterize and reproduce surface topography and optical properties accurately. We have developed a structured light imaging system to characterize surface topography and optical properties (absorption coefficient and reduced scattering coefficient) of 3D tissue-simulating phantoms. The system consisted of a hyperspectral light source, a digital light projector (DLP), a CMOS camera, two polarizers, a rotational stage, a translation stage, a motion controller, and a personal computer. Tissue-simulating phantoms with different structural and optical properties were characterized by the proposed imaging system and validated by a standard integrating sphere system. The experimental results showed that the proposed system was able to achieve pixel-level optical properties with a percentage error of less than 11% for absorption coefficient and less than 7% for reduced scattering coefficient for phantoms without surface curvature. In the meanwhile, 3D topographic profile of the phantom can be effectively reconstructed with an accuracy of less than 1% deviation error. Our study demonstrated that the proposed structured light imaging system has the potential to characterize structural profile and optical properties of 3D tissue-simulating phantoms.

  9. 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.

  10. Characterizing rhodopsin signaling by EPR spectroscopy: from structure to dynamics.

    PubMed

    Van Eps, Ned; Caro, Lydia N; Morizumi, Takefumi; Ernst, Oliver P

    2015-09-26

    Electron paramagnetic resonance (EPR) spectroscopy, together with spin labeling techniques, has played a major role in the characterization of rhodopsin, the photoreceptor protein and G protein-coupled receptor (GPCR) in rod cells. Two decades ago, these biophysical tools were the first to identify transmembrane helical movements in rhodopsin upon photo-activation, a critical step in the study of GPCR signaling. EPR methods were employed to identify functional loop dynamics within rhodopsin, to measure light-induced millisecond timescale changes in rhodopsin conformation, to characterize the effects of partial agonists on the apoprotein opsin, and to study lipid interactions with rhodopsin. With the emergence of advanced pulsed EPR techniques, the stage was set to determine the amplitude of structural changes in rhodopsin and the dynamics in the rhodopsin signaling complexes. Work in this area has yielded invaluable information about mechanistic properties of GPCRs. Using EPR techniques, receptors are studied in native-like membrane environments and the effects of lipids on conformational equilibria can be explored. This perspective addresses the impact of EPR methods on rhodopsin and GPCR structural biology, highlighting historical discoveries made with spin labeling techniques, and outlining exciting new directions in the field.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Amyloid oligomer structure characterization from simulations: a general method.

    PubMed

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

    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 Aβ9-40, resulting from two atomistic molecular dynamics simulations in explicit solvent, each of 200 ns, starting from two distinct structures.

  16. 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.

  17. 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.

  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. Structural characterization of NETNES glycopeptide from Trypanosoma cruzi.

    PubMed

    Chiodi, Carla G; Verli, Hugo

    2013-05-24

    Trypanosoma cruzi is a protozoan, responsible for Chagas disease, that parasites triatomines and some vertebrates, mainly Homo sapiens. In 2010, nearly 10 million people in whole world, most from Latin America, had Chagas disease, which is an illness of high morbidity, low mortality, and serious problems of quality of life. The available treatment has high toxicity and low efficacy at chronic phase. Some of the protozoan antigenic or virulence factors include complex carbohydrate structures that, due to their uniqueness, may constitute potential selective targets for the development of new treatments. One example of such structures is NETNES, a low abundance T. cruzi glycopeptide, comprising 13 amino acid residues, one or two N-glycosylation chains, a GPI anchor and two P-glycosylations. In this context, the current work aims to obtain an atomic model for NETNES, including its glycan chains and membrane attachment, in order to contribute in the characterization of its structure and dynamics. Based on POPC and GPI models built in agreement with experimental data, our results indicate that, in the first third of the simulation, NETNES peptide is very flexible in solution, bending itself between asparagine residues and lying down on some carbohydrates and membrane, exposing amino acid residues and some other glycans, mainly terminal mannoses, to the extracellular medium, remaining in this position until the end of simulations.

  20. 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.

  1. Synthesis and characterization of carbon nanotube-polymer multilayer structures.

    PubMed

    Misra, Abha; Raney, Jordan R; De Nardo, Luigi; Craig, Anna E; Daraio, Chiara

    2011-10-25

    We develop lightweight, multilayer materials composed of alternating layers of poly dimethyl siloxane (PDMS) polymer and vertically aligned carbon nanotube (CNT) arrays, and characterize their mechanical response in compression. The CNT arrays used in the assembly are synthesized with graded mechanical properties along their thickness, and their use enables the creation of multilayer structures with low density (0.12-0.28 g/cm(3)). We test the mechanical response of structures composed of different numbers of CNT layers partially embedded in PDMS polymer, under quasi-static and dynamic loading. The resulting materials exhibit a hierarchical, fibrous structure with unique mechanical properties: They can sustain large compressive deformations (up to ∼0.8 strain) with a nearly complete recovery and present strain localization in selected sections of the materials. Energy absorption, as determined by the hysteresis observed in stress-strain curves, is found to be at least 3 orders of magnitude larger than that of natural and synthetic cellular materials of comparable density. Conductive bucky paper is included within the polymer interlayers. This allows the measurement of resistance variation as a function of applied stress, showing strong correlation with the observed strain localization in compression.

  2. Characterization of electronic structure of periodically strained graphene

    DOE PAGES

    Aslani, Marjan; Garner, C. Michael; Kumar, Suhas; ...

    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

  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. Tensile Characterization of FRP Rods for Reinforced Concrete Structures

    NASA Astrophysics Data System (ADS)

    Micelli, F.; Nanni, A.

    2003-07-01

    The application of FRP rods as an internal or external reinforcement in new or damaged concrete structures is based on the development of design equations that take into account the mechanical properties of FRP material systems.The measurement of mechanical characteristics of FRP requires a special anchoring and protocol, since it is well known that these characteristics depend on the direction and content of fibers. In this study, an effective tensile test method is described for the mechanical characterization of FRP rods. Twelve types of glass and carbon FRP specimens with different sizes and surface characteristics were tested to validate the procedure proposed. In all, 79 tensile tests were performed, and the results obtained are discussed in this paper. Recommendations are given for specimen preparation and test setup in order to facilitate the further investigation and standardization of the FRP rods used in civil engineering.

  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 and Crystal Structure of a Robust Cyclohexanone Monooxygenase.

    PubMed

    Romero, Elvira; Castellanos, J Rubén Gómez; Mattevi, Andrea; Fraaije, Marco W

    2016-12-19

    Cyclohexanone monooxygenase (CHMO) is a promising biocatalyst for industrial reactions owing to its broad substrate spectrum and excellent regio-, chemo-, and enantioselectivity. However, the low stability of many Baeyer-Villiger monooxygenases is an obstacle for their exploitation in industry. Characterization and crystal structure determination of a robust CHMO from Thermocrispum municipale is reported. The enzyme efficiently converts a variety of aliphatic, aromatic, and cyclic ketones, as well as prochiral sulfides. A compact substrate-binding cavity explains its preference for small rather than bulky substrates. Small-scale conversions with either purified enzyme or whole cells demonstrated the remarkable properties of this newly discovered CHMO. The exceptional solvent tolerance and thermostability make the enzyme very attractive for biotechnology.

  7. Characterization and Crystal Structure of a Robust Cyclohexanone Monooxygenase

    PubMed Central

    Romero, Elvira; Castellanos, J. Rubén Gómez

    2016-01-01

    Abstract Cyclohexanone monooxygenase (CHMO) is a promising biocatalyst for industrial reactions owing to its broad substrate spectrum and excellent regio‐, chemo‐, and enantioselectivity. However, the low stability of many Baeyer–Villiger monooxygenases is an obstacle for their exploitation in industry. Characterization and crystal structure determination of a robust CHMO from Thermocrispum municipale is reported. The enzyme efficiently converts a variety of aliphatic, aromatic, and cyclic ketones, as well as prochiral sulfides. A compact substrate‐binding cavity explains its preference for small rather than bulky substrates. Small‐scale conversions with either purified enzyme or whole cells demonstrated the remarkable properties of this newly discovered CHMO. The exceptional solvent tolerance and thermostability make the enzyme very attractive for biotechnology. PMID:27873437

  8. Structural Characterization of Core Region in Erwinia amylovora Lipopolysaccharide

    PubMed Central

    Casillo, Angela; Ziaco, Marcello; Lindner, Buko; Merino, Susana; Mendoza-Barberá, Elena; Tomás, Juan M.; Corsaro, Maria Michela

    2017-01-01

    Erwinia amylovora (E. amylovora) is the first bacterial plant pathogen described and demonstrated to cause fire blight, a devastating plant disease affecting a wide range of species including a wide variety of Rosaceae. In this study, we reported the lipopolysaccharide (LPS) core structure from E. amylovora strain CFBP1430, the first one for an E. amylovora highly pathogenic strain. The chemical characterization was performed on the mutants waaL (lacking only the O-antigen LPS with a complete LPS-core), wabH and wabG (outer-LPS core mutants). The LPSs were isolated from dry cells and analyzed by means of chemical and spectroscopic methods. In particular, they were subjected to a mild acid hydrolysis and/or a hydrazinolysis and investigated in detail by one and two dimensional Nuclear Magnetic Resonance (NMR) spectroscopy and ElectroSpray Ionization Fourier Transform-Ion Cyclotron Resonance (ESI FT-ICR) mass spectrometry. PMID:28273861

  9. 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.

  10. 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.

  11. Structural Characterization of Core Region in Erwinia amylovora Lipopolysaccharide.

    PubMed

    Casillo, Angela; Ziaco, Marcello; Lindner, Buko; Merino, Susana; Mendoza-Barberá, Elena; Tomás, Juan M; Corsaro, Maria Michela

    2017-03-04

    Erwinia amylovora (E. amylovora) is the first bacterial plant pathogen described and demonstrated to cause fire blight, a devastating plant disease affecting a wide range of species including a wide variety of Rosaceae. In this study, we reported the lipopolysaccharide (LPS) core structure from E. amylovora strain CFBP1430, the first one for an E. amylovora highly pathogenic strain. The chemical characterization was performed on the mutants waaL (lacking only the O-antigen LPS with a complete LPS-core), wabH and wabG (outer-LPS core mutants). The LPSs were isolated from dry cells and analyzed by means of chemical and spectroscopic methods. In particular, they were subjected to a mild acid hydrolysis and/or a hydrazinolysis and investigated in detail by one and two dimensional Nuclear Magnetic Resonance (NMR) spectroscopy and ElectroSpray Ionization Fourier Transform-Ion Cyclotron Resonance (ESI FT-ICR) mass spectrometry.

  12. Hexamethylenetetramine carboxyborane: synthesis, structural characterization and CO releasing properties.

    PubMed

    Ayudhya, T I; Raymond, C C; Dingra, N N

    2017-01-17

    Carbon monoxide, although widely known as a toxic gas, has received great attention in the past few decades due to its promising role as a medical gas. Several classes of carbon monoxide releasing molecules (CORMs) have been synthesised with many of them having pharmacological activities under physiological conditions. Herein, we report the synthesis and structural characterization of the first example of amine carboxyborane that releases CO under physiological conditions without the aid of inducers. A representative compound hexamethylenetetramine carboxyborane (HMTA-CB) described here has a half-life of 2.7 days and gradually releases CO with the rate constant of 3.0 × 10(-6) s(-1). Its ability to promote cell growth shows the beneficial effect of slow CO release to supplement CO in small amounts over time.

  13. 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

  14. Low tip damage AFM technique development for nano structures characterization

    NASA Astrophysics Data System (ADS)

    Liu, Biao; Wang, Charles C.; Huang, Po-Fu; Uritsky, Yuri

    2010-06-01

    Ambient dynamic mode (tapping mode or intermittent-contact mode) AFM imaging has been used extensively for the characterization of the topography of nano structures. However, the results are beset with artifacts, because hard tapping of the AFM tip on sample surface usually causes premature tip damage. Through careful study of the cantilever amplitude and phase signals as functions of tip-to-sample distance, principle of non-contact AFM operation was discovered to enable high resolution and low tip damage AFM image acquisition [1, 2]. However, current study discovers that the conventional way of acquiring amplitude and phase versus distance curves gives erroneous non-contact operating range, because the tip gets damaged during the data acquisition process. A new technique is developed to reliably map the operating parameters of an intact tip that ensures the AFM be operated with the correct non-contact settings. Two examples are given to illustrate the successful applications of this new technique. The first example involves the size characterization of polystyrene latex (PSL) nano particles used for light scattering tool calibration. The second example is the development of robust recipes for the measurement of the depth of phase-shift mask trenches.

  15. Perovskite oxide nanowires: synthesis, property and structural characterization.

    PubMed

    Zhu, Xinhua; Liu, Zhiguo; Ming, Naiben

    2010-07-01

    Perovskite oxide materials display a wide spectrum of functional properties, including switchable polarization, piezoelectricity, pyroelectricity, and non-linear dielectric behavior. These properties are indispensable for application in electronic devices such as non-volatile memories, sensors, microactuators, infrared detectors, microwave phase filters, and so on. Recent advances in science and technology of perovskite oxide materials have resulted in the feature sizes of perovskite oxides-based electronic devices entering into nanoscale dimensions. At nanoscale perovskite oxide materials exhibit a pronounced size effect manifesting itself in a significant deviation of the properties of low-dimensional structures from the bulk and film counterparts. In the last decade low-dimensional perovskite nanosized oxides have been received much attention because of their superior physical and chemical properties. Among them, perovskite oxide nanowires are especially attractive for nanoscience studies and nanotechnology applications. Compared to other low-dimensional perovskite oxide systems, perovskite oxide nanowires are not only used as the building blocks of future nanodevices, but also they offer fundamental scientific opportunities for investigating the intrinsic size effects of physical properties. In the recent years, much progress has been made both in synthesis and physical property testing of perovskite oxide nanowires, which have a profound impact on the nanoelectronics. In this work, an overview of the state of art in perovskite oxide nanowires is presented, which covers their synthesis, property, and structural characterization. In the first part, the recent literatures for fabricating perovskite oxide nanowires with promising features, are critically reviewed. The second part deals with the recent advances on the physical property testing of perovskite oxide nanowires. The third part summarizes the recent progress on microstructural characterizations of

  16. 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.

  17. 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

  18. 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

  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. Structural characterization of mesquite (Prosopis velutina) gum and its fractions.

    PubMed

    López-Franco, Yolanda L; de la Barca, Ana M Calderón; Valdez, Miguel A; Peter, Martin G; Rinaudo, Marguerite; Chambat, Gérard; Goycoolea, Francisco M

    2008-08-11

    Structural and physicochemical characteristics of mesquite gum (from Prosopis velutina) were investigated using FT-IR spectroscopic, mass spectrometric and chromatographic methods. Four fractions (F-I, F-IIa, F-IIb and F-III) were isolated by hydrophobic interaction chromatography. The samples were characterized and analyzed for their monosaccharide and oligomers composition by high performance anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD). L-Arabinose (L-Ara) and D-galactose (D-Gal) were found as the main carbohydrate constituent residues in the polysaccharides from mesquite gum and their ratio (L-Ara/D-Gal) varied within the range 2.54 to 3.06 among the various fractions. Small amounts of D-glucose (D-Glc), D-mannose (D-Man) and D-xylose (D-Xyl) were also detected, particularly in Fractions IIa, IIb and III. Infrared spectroscopy identified polysaccharides and protein in all the samples. Data from mass spectrometry (MALDI-TOF MS) was consistent with the idea that the structure corresponding to the periphereal chains of Fraction I is predominantly a chain of pentoses attached to uronic acid.

  1. 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.

  2. 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.

  3. 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.

  4. 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

    2015-03-05

    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.

  5. Structural characterization of phytotoxic terpenoids from Cestrum parqui.

    PubMed

    D'Abrosca, Brigida; Dellagreca, Marina; Fiorentino, Antonio; Monaco, Pietro; Natale, Angela; Oriano, Palma; Zarrelli, Armando

    2005-11-01

    Isolation, chemical characterization and phytotoxicity of nine polyhydroxylated terpenes (five C13nor-isoprenoids, two sesquiterpenes, a spirostane and a pseudosapogenin) from Cestrum parqui L'Herr are reported. In this work we completed the phytochemical investigation of the terpenic fraction of the plant and described the structural elucidation of polar isoprenoids using NMR methods. All the configurations of the compounds have been assigned by NOESY experiments. Four new structures have been identified as (3S,5R,6R,7E,9R)-5,6,9-trihydroxy-3-isopropyloxy-7-megastigmene, 5alpha-spirostan-3beta,12beta,15alpha-triol, and 26-O-(3'-isopentanoyl)-beta-d-glucopyranosyl-5alpha-furost-20(22)-ene-3beta,26-diol, and as an unusual tricyclic sesquiterpene. The compounds have been assayed for their phytotoxicity on lettuce at the concentrations ranging between 10(-4) and 10(-7)M. The activities of some compounds were similar to that of the herbicide pendimethalin.

  6. Mechanochemically synthesized cobalt monoselenide: structural characterization and optical properties

    NASA Astrophysics Data System (ADS)

    Achimovičová, Marcela; Daneu, Nina; Dutková, Erika; Zorkovská, Anna

    2017-03-01

    Chalcogenide semiconductor cobalt monoselenide, CoSe, was prepared from metallic cobalt and selenium powders in stoichiometric ratio by simple and fast mechanochemical synthesis after 120 min of milling in a planetary ball mill Pulverisette 6 (Fritsch, Germany) in an argon atmosphere. Crystal structure and morphology of the product were characterized by X-ray diffraction, specific surface area measurements, and transmission electron microscopy. X-ray diffraction analysis confirmed the hexagonal crystal structure of the product-CoSe (freboldite) with the average size of the crystallites 26 nm. Transmission electron microscopy analysis has revealed that CoSe nanostructures are composed of agglomerated and randomly oriented nanoparticles. The optical properties were studied using UV-Vis and photoluminescence spectroscopy. Mechanochemically synthesized CoSe nanostructures showed higher absorption in whole UV-Vis optical region and the determined band-gap energy 1.70 eV is blue-shifted relative to the bulk CoSe. Both UV-Vis and photoluminescence spectra indicate quantum size effect of CoSe nanocrystals.

  7. Structural characterization of nitrosomonas europaea cytochrome c-552 variants with marked differences in electronic structure.

    PubMed

    Can, Mehmet; Krucinska, Jolanta; Zoppellaro, Giorgio; Andersen, Niels H; Wedekind, Joseph E; Hersleth, Hans-Petter; Andersson, K Kristoffer; Bren, Kara L

    2013-09-23

    Nitrosomonas europaea cytochrome c-552 (Ne c-552) variants with the same His/Met axial ligand set but with different EPR spectra have been characterized structurally, to aid understanding of how molecular structure determines heme electronic structure. Visible light absorption, Raman, and resonance Raman spectroscopy of the protein crystals was performed along with structure determination. The structures solved are those of Ne c-552, which displays a "HALS" (or highly anisotropic low-spin) EPR spectrum, and of the deletion mutant Ne N64Δ, which has a rhombic EPR spectrum. Two X-ray crystal structures of wild-type Ne c-552 are reported; one is of the protein isolated from N. europaea cells (Ne c-552n, 2.35 Å resolution), and the other is of recombinant protein expressed in Escherichia coli (Ne c-552r, 1.63 Å resolution). Ne N64Δ crystallized in two different space groups, and two structures are reported [monoclinic (2.1 Å resolution) and hexagonal (2.3 Å resolution)]. Comparison of the structures of the wild-type and mutant proteins reveals that heme ruffling is increased in the mutant; increased ruffling is predicted to yield a more rhombic EPR spectrum. The 2.35 Å Ne c-552n structure shows 18 molecules in the asymmetric unit; analysis of the structure is consistent with population of more than one axial Met configuration, as seen previously by NMR. Finally, the mutation was shown to yield a more hydrophobic heme pocket and to expel water molecules from near the axial Met. These structures reveal that heme pocket residue 64 plays multiple roles in regulating the axial ligand orientation and the interaction of water with the heme. These results support the hypothesis that more ruffled hemes lead to more rhombic EPR signals in cytochromes c with His/Met axial ligation.

  8. 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

  9. Structural characterization of the DC-SIGN-Lewis(X) complex.

    PubMed

    Pederson, Kari; Mitchell, Daniel A; Prestegard, James H

    2014-09-09

    Dendritic cell-specific intracellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN) is a C-type lectin highly expressed on the surface of antigen-presenting dendritic cells. DC-SIGN mediates interactions among dendritic cells, pathogens, and a variety of epithelia, myeloid cells, and endothelia by binding to high mannose residues on pathogenic invaders or fucosylated residues on the membranes of other immune cells. Although these interactions are normally beneficial, they can also contribute to disease. The structural characterization of binding geometries is therefore of interest as a basis for the construction of mimetics that can mediate the effects of abnormal immune response. Here, we report the structural characteristics of the interaction of the DC-SIGN carbohydrate recognition domain (CRD) with a common fucosylated entity, the Lewis(X) trisaccharide (Le(X)), using NMR methods. Titration of the monomeric DC-SIGN CRD with Le(X) monitored by 2D NMR revealed significant perturbations of DC-SIGN cross-peak positions in (1)H-(15)N heteronuclear single quantum coherence (HSQC) spectra and identified residues near the binding site. Additionally, saturation transfer difference (STD) and transferred nuclear Overhauser effect (trNOE) NMR experiments, using a tetrameric form of DC-SIGN, identified binding epitopes and bound conformations of the Le(X) ligand. The restraints derived from these multiple experiments were used to generate models for the binding of Le(X) to the DC-SIGN CRD. Ranking of the models based on the fit of model-based simulations of the trNOE data and STD buildup curves suggested conformations distinct from those seen in previous crystal structures. The new conformations offer insight into how differences between binding of Lewis(X) and mannose-terminated saccharides may be propagated.

  10. Biochemical and structural characterization of Plasmodium falciparum glutamate dehydrogenase 2.

    PubMed

    Zocher, Kathleen; Fritz-Wolf, Karin; Kehr, Sebastian; Fischer, Marina; Rahlfs, Stefan; Becker, Katja

    2012-05-01

    Glutamate dehydrogenases (GDHs) play key roles in cellular redox, amino acid, and energy metabolism, thus representing potential targets for pharmacological interventions. Here we studied the functional network provided by the three known glutamate dehydrogenases of the malaria parasite Plasmodium falciparum. The recombinant production of the previously described PfGDH1 as hexahistidyl-tagged proteins was optimized. Additionally, PfGDH2 was cloned, recombinantly produced, and characterized. Like PfGDH1, PfGDH2 is an NADP(H)-dependent enzyme with a specific activity comparable to PfGDH1 but with slightly higher K(m) values for its substrates. The three-dimensional structure of hexameric PfGDH2 was solved to 3.1 Å resolution. The overall structure shows high similarity with PfGDH1 but with significant differences occurring at the subunit interface. As in mammalian GDH1, in PfGDH2 the subunit-subunit interactions are mainly assisted by hydrogen bonds and hydrophobic interactions, whereas in PfGDH1 these contacts are mediated by networks of salt bridges and hydrogen bonds. In accordance with this, the known bovine GDH inhibitors hexachlorophene, GW5074, and bithionol were more effective on PfGDH2 than on PfGDH1. Subcellular localization was determined for all three plasmodial GDHs by fusion with the green fluorescent protein. Based on our data, PfGDH1 and PfGDH3 are cytosolic proteins whereas PfGDH2 clearly localizes to the apicoplast, a plastid-like organelle specific for apicomplexan parasites. This study provides new insights into the structure and function of GDH isoenzymes of P. falciparum, which represent potential targets for the development of novel antimalarial drugs.

  11. Structural Characterization of the Fla2 Flagellum of Rhodobacter sphaeroides

    PubMed Central

    de la Mora, Javier; Uchida, Kaoru; del Campo, Ana Martínez; Camarena, Laura; Aizawa, Shin-Ichi

    2015-01-01

    ABSTRACT Rhodobacter sphaeroides is a free-living alphaproteobacterium that contains two clusters of functional flagellar genes in its genome: one acquired by horizontal gene transfer (fla1) and one that is endogenous (fla2). We have shown that the Fla2 system is normally quiescent and under certain conditions produces polar flagella, while the Fla1 system is always active and produces a single flagellum at a nonpolar position. In this work we purified and characterized the structure and analyzed the composition of the Fla2 flagellum. The number of polar filaments per cell is 4.6 on average. By comparison with the Fla1 flagellum, the prominent features of the ultra structure of the Fla2 HBB are the absence of an H ring, thick and long hooks, and a smoother zone at the hook-filament junction. The Fla2 helical filaments have a pitch of 2.64 μm and a diameter of 1.4 μm, which are smaller than those of the Fla1 filaments. Fla2 filaments undergo polymorphic transitions in vitro and showed two polymorphs: curly (right-handed) and coiled. However, in vivo in free-swimming cells, we observed only a bundle of filaments, which should probably be left-handed. Together, our results indicate that Fla2 cell produces multiple right-handed polar flagella, which are not conventional but exceptional. IMPORTANCE R. sphaeroides possesses two functional sets of flagellar genes. The fla1 genes are normally expressed in the laboratory and were acquired by horizontal transfer. The fla2 genes are endogenous and are expressed in a Fla1− mutant grown phototrophically and in the absence of organic acids. The Fla1 system produces a single lateral or subpolar flagellum, and the Fla2 system produces multiple polar flagella. The two kinds of flagella are never expressed simultaneously, and both are used for swimming in liquid media. The two sets of genes are certainly ready for responding to specific environmental conditions. The characterization of the Fla2 system will help us to understand

  12. Structural Characterization of the Ag/ybco Interface

    NASA Astrophysics Data System (ADS)

    Tidjani, Mohammed Elkhamis

    1990-01-01

    The present research is intended to characterize the interface microstructure and long term stability of the deposited silver metal in contact to the superconducting oxide YBa_2Cu_3O _{rm 7-x} (YBCO). High resolution transmission electron microscopy (HRTEM) observations of the interfacial regions reveal that Ag contacts to YBCO occurred without any intermediate phase formation at the interface. The Ag metal exhibits a preferred orientation relationship with YBCO, in which the densely packed planes and directions of the metal are parallel to those of the superconductor. The formation of (111) interfaces and facets during deposition indicates that these planes are associated with the lowest interfacial energy. The as-deposited Ag film exhibits a granular morphology, and the Ag grains are often twinned along the (111) plane while the surface of YBCO is mostly rough and structurally unstable. Annealing of the Ag/YBCO interface resulted in outdiffusion of yttrium and oxygen at regions where the surface of YBCO was rough. This diffusion, however, did not result in the formation of continuous layers at the Ag/YBCO interface but only to growth of Ag_2 Y and Ag_2O inclusions. Thus it is believed that the stability of the Ag/YBCO depends on the quality of the surface of YBCO, especially its structure. Treatment of the surface of YBCO by ion-bombardment yielded flat surfaces but damaged a layer of about 30A. Such a cleaning process improved the quality of the deposited Ag since the Ag grains were larger and contained low defects concentration. The same orientation relationships between Ag and YBCO were observed after cleaning the surface of YBCO which implied that the destruction of the structure at the surface is only partial. Deposition of Ag in the same chamber where YBCO was initially grown, to minimize the contamination of the surface of YBCO, also was not effective in enhancing the structure of the Ag/YBCO interface. The roughness of the surface of YBCO did not decrease

  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. Dynamic quasistatic characterization of finite elements for shell structures.

    SciTech Connect

    Thomas, Jesse David

    2010-11-01

    Finite elements for shell structures have been investigated extensively, with numerous formulations offered in the literature. These elements are vital in modern computational solid mechanics due to their computational efficiency and accuracy for thin and moderately thick shell structures, allowing larger and more comprehensive (e.g. multi-scale and multi-physics) simulations. Problems now of interest in the research and development community are routinely pushing our computational capabilities, and thus shell finite elements are being used to deliver efficient yet high quality computations. Much work in the literature is devoted to the formulation of shell elements and their numerical accuracy, but there is little published work on the computational characterization and comparison of shell elements for modern solid mechanics problems. The present study is a comparison of three disparate shell element formulations in the Sandia National Laboratories massively parallel Sierra Solid Mechanics code. A constant membrane and bending stress shell element (Key and Hoff, 1995), a thick shell hex element (Key et al., 2004) and a 7-parameter shell element (Buechter et al., 1994) are available in Sierra Solid Mechanics for explicit transient dynamic, implicit transient dynamic and quasistatic calculations. Herein these three elements are applied to a set of canonical dynamic and quasistatic problems, and their numerical accuracy, computational efficiency and scalability are investigated. The results show the trade-off between the relative inefficiency and improved accuracy of the latter two high quality element types when compared with the highly optimized and more widely used constant membrane and bending stress shell element.

  15. 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.

  16. 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

  17. Structural Characterization of Hydroxyl Radical Adducts in Aqueous Media

    NASA Astrophysics Data System (ADS)

    Janik, Ireneusz; Tripathi, G. N. R.

    2015-06-01

    The oxidation by the hydroxyl (OH) radical is one of the most widely studied reactions because of its central role in chemistry, biology, organic synthesis, and photocatalysis in aqueous environments, wastewater treatment, and numerous other chemical processes. Although the redox potential of OH is very high, direct electron transfer (ET) is rarely observed. If it happens, it mostly proceeds through the formation of elusive OH adduct intermediate which facilitates ET and formation of hydroxide anion. Using time resolved resonance Raman technique we structurally characterized variety of OH adducts to sulfur containing organic compounds, halide ions as well as some metal cations. The bond between oxygen of OH radical and the atom of oxidized molecule differs depending on the nature of solute that OH radical reacts with. For most of sulfur containing organics, as well as halide and pseudo-halide ions, our observation suggested that this bond has two-center three-electron character. For several metal aqua ions studied, the nature of the bond depends on type of the cation being oxidized. Discussion on spectral parameters of all studied hydroxyl radical adducts as well as the role solvent plays in their stabilization will be presented.

  18. 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.

  19. Structural Characterization of a Capillary Microfluidic Chip Using Microreflectance.

    PubMed

    Lastras-Martínez, Luis F; Balderas-Navarro, Raul E; Castro-García, Ricardo; Hernández-Vidales, Karen; Almendarez-Rodríguez, Juan; Herrera-Jasso, Rafael; Prinz, Adrian; Bergmair, Iris

    2016-10-18

    The structural characterization of capillary microfluidic chips is important for reliable applications. In particular, nondestructive diagnostic tools to assess geometrical dimensions and their correlations with control processes are of much importance, preferably if they are implemented in situ. Several techniques to accomplish this task have been reported; namely, optical coherence tomography (OCT) jointly with confocal fluorescence microscopy (CFM) to investigate internal features of lab-on-a-chip technologies. In this paper, we report on the use of a simple optical technique, based on near-normal incidence microreflectance, which allows mapping internal features of a microfluidic chip in a straightforward way. Our setup is based on a charge-coupled device camera that allows a lateral resolution of ∼2.5 µm and allows us to measure in the wavelength range of 640-750 nm. The technique takes advantage of the Fabry-Perot interferences features in the reflectance spectra, which are further analyzed by a discrete Fourier transform. In this way, the amplitude of the Fourier coefficients is modulated by the presence of a microfluidic channel.

  20. 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.

  1. 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.

  2. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-06-01

    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.

  4. 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.

  5. Structural and functional characterization of Delphinus delphis hemoglobin system.

    PubMed

    Manconi, Barbara; Messana, Irene; Maggiani, Federica; Olianas, Alessandra; Pellegrini, Mariagiuseppina; Crnjar, Roberto; Castagnola, Massimo; Giardina, Bruno; Sanna, Maria Teresa

    2009-11-01

    Structural analysis of the hemoglobin (Hb) system of Delphinus delphis revealed a high globin multiplicity: HPLC-electrospray ionization-mass spectrometry (ESI-MS) analysis evidenced three major beta (beta1 16,022 Da, beta2 16,036 Da, beta3 16,036 Da, labeled according to their progressive elution times) and two major alpha globins (alpha1 15,345 Da, alpha2 15,329 Da). ESI-tandem mass and nucleotide sequence analyses showed that beta2 globin differs from beta1 for the substitution Val126 --> Leu, while beta3 globin differs from beta2 for the isobaric substitution Lys65 --> Gln. The alpha2 globin differs from the alpha1 for the substitution Ser15 --> Ala. Anion-exchange chromatography allowed the separation of two Hb fractions and HPLC-ESI-MS analysis revealed that the fraction with higher pI (HbI) contained beta1, beta2 and both the alpha globins, and the fraction with lower pI (HbII) contained beta3 and both the alpha globins. Both D. delphis Hb fractions displayed a lower intrinsic oxygen affinity, a decreased effect of 2,3-BPG and a reduced cooperativity with respect to human HbA(0), with HbII showing the more pronounced differences. With respect to HbA(0), either the substitution Probeta5 --> Gly or the Probeta5 --> Ala is present in all the cetacean beta globins sequenced so far, and it has been hypothesized that position 5 of beta globins may have a role in the interaction with 2,3-BPG. Regarding the particularly lowered cooperativity of HbII, it is interesting to observe that the variant human HbA, characterized by the substitution Lysbeta65 --> Gln (HbJ-Cairo) has a decreased cooperativity with respect to HbA(0).

  6. 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.

  7. Molecular and electronic structures of six-coordinate "low-valent" [M((Me)bpy)3]0 (M = Ti, V, Cr, Mo) and [M(tpy)2]0 (M = Ti, V, Cr), and seven-coordinate [MoF((Me)bpy)3](PF6) and [MX(tpy)2](PF6) (M = Mo, X = Cl and M = W, X = F).

    PubMed

    Wang, Mei; Weyhermüller, Thomas; England, Jason; Wieghardt, Karl

    2013-11-04

    The electronic structures of a series of so-called "low-valent" transition metal complexes [M((Me)bpy)3](0) and [M(tpy)2](0) ((Me)bpy = 4,4'-dimethyl-2,2'-bipyridine and tpy = 2,2',6',2″-terpyridine) have been determined using a combination of X-ray crystallography, magnetochemistry, and UV-vis-NIR spectroscopy. More specifically, the crystal structures of the long-known complexes [Ti(IV)(tpy(2-))2](0) (S = 0, 6), [V(IV)(tpy(2-))2] (S = 1/2, 7), [Ti(III)((Me)bpy(•))3](0) (S = 0, 1), [V(II)((Me)bpy(•))2((Me)bpy(0))](0) (S = 1/2, 2), and [Mo(III)((Me)bpy(•))3](0) (S = 0, 4) have been determined for the first time. In all cases, the experimental results confirm the electronic structure assignments that we ourselves have recently proposed. Additionally, the six-coordinate complex [Mo(III)(bpy(0))2Cl2]Cl·2.5CH3OH (S = 3/2, 13), and seven-coordinate species [Mo(IV)F((Me)bpy(•))2((Me)bpy(0))](PF6) (S = 0, 5), [Mo(IV)Cl(tpy(•))2](PF6)·CH2Cl2 (S = 0, 11), and [W(V)F(tpy(•))(tpy(2-))](PF6)·CH2Cl2 (S = 0, 12) have been synthesized and, for the first time, crystallographically characterized. Using the resulting data, plus that from previously published high-resolution X-ray structures of analogous compounds, it is shown that there is a linear correlation between the average C(py)-C'(py) bond distances in these complexes and the total charge (n) of the ligands, {(bpy)3}(n) and {(tpy)2}(n). Hence, an assignment of the total charge of coordinated bpy or tpy ligands and, by extension, the oxidation state of the central metal ion can reliably be made on the basis of X-ray crystallography alone. In this study, the oxidation states of the metal ions range from +II to +V and in no case has an oxidation state of zero been validated. It is, therefore, highly misleading to use the term "low-valent" to describe any of the aforementioned neutral complexes.

  8. Methodology Using Inverse Methods for Pit Characterization in Multilayer Structures

    NASA Astrophysics Data System (ADS)

    Aldrin, John C.; Sabbagh, Harold A.; Sabbagh, Elias H.; Murphy, R. Kim; Concordia, Michael; Judd, David R.; Lindgren, Eric; Knopp, Jeremy

    2006-03-01

    This paper presents a methodology incorporating ultrasonic and eddy current data and NDE models to characterize pits in first and second layers. Approaches such as equivalent pit dimensions, approximate probe models, and iterative inversion schemes were designed to improve the reliability and speed of inverse methods for second layer pit characterization. A novel clutter removal algorithm was developed to compensate for coherent background noise. Validation was achieved using artificial and real pitting corrosion samples.

  9. Fabrication and characterization of metallic quasi-periodic structures.

    PubMed

    Wang, Yongjin

    2008-01-21

    A variety of intriguing interference patterns are generated as a template to create metallic quasi-periodic structures using our robust experimental setup. A combination of thermal evaporation and lift-off process, the 2D metallic quasi-periodic structures are generated, a twelve-fold symmetry structure can be clearly observed in fabricated structures with four exposures. The excitation of surface plasmon (SP) resonances, which are determined by the geometry of metallic structures, the incident angle alpha, and the refractive index n(d) of the adjacent dielectric medium, is demonstrated in the optical transmission experiments. The optical transmission of metallic quasi-periodic structures can be tuned by varying the refractive index n(d), changing the period a and altering the incident angle alpha. The experimental results agree well with the predication for SP resonances. It's the first step to investigate the interesting optical properties of metallic quasi-periodic structures.

  10. Fabrication, characterization, and simulation of photonic bandgap structures

    NASA Astrophysics Data System (ADS)

    Wang, Hao

    Photonic bandgap (PBG) structures are artificial materials which are featured with periodically changed refractive index having a periodicity in the range of optical wavelengths. The studies in PBG structures are making rapid progress. However, the investigations of three-dimensional (3-D) PBG structures are still challenging. In this work, laser-assisted fabrication of 3-D PBG structures based on self-assembled silica colloidal crystals was developed. 3-D PBG structures were fabricated by laser-assisted nano-imprinting and laser-assisted chemical vapor deposition (LCVD), based on the self-assembled silica colloidal crystals. Silica colloidal crystals were self-assembled on silicon substrates using isothermal heating evaporation-induced self-assembly. To infiltrate the silica colloidal crystals, the laser-assisted imprinting technique was used using a short pulse (23 ns pulse duration) of a KrF excimer laser. The nanosecond laser pulse instantaneously melted the silicon substrates, which infiltrated and solidified over the assembled silica particles on the substrates. By removing silica particles embedded in the silicon using hydrofluoric acid, inverseopal PBG structures were produced. In the LCVD technique, a continuous-wave Nd:YAG laser (1.064 mum wavelength) and a CO2 laser (10.6 mum wavelength) were used as the energy source. Silica-core-silicon-shell PBG structures were obtained. This technique is capable of fabricating structures with various PBGs by obtaining different silicon-shell thickness with different LCVD parameters. Both theoretical calculations and experimental measurements to investigate the optical properties of the PBG structures were carried out. Spectroscopic ellipsometry was used to identify PBGs. The plain-wave expansion (PWE) method was used to calculate the photonic-band diagrams of the structures, which agreed with the experimental results. The calculation also provided fitting results of the Si-shell thicknesses. To investigate the

  11. 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.

  12. Molecular characterization and population structure of Blueberry mosaic associated virus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Blueberry mosaic disease was first described in the 1950s but the causal agent has not been characterized to date. Next generation sequencing was employed in the identification of the causal agent and an undescribed ophiovirus, tentatively named as Blueberry mosaic associated virus (BlMaV), was dete...

  13. 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

  14. A Structurally Characterized Organometallic Plutonium(IV) Complex.

    PubMed

    Apostolidis, Christos; Walter, Olaf; Vogt, Jochen; Liebing, Phil; Maron, Laurent; Edelmann, Frank T

    2017-03-30

    The blood-red plutonocene complex Pu(1,3-COT'')(1,4-COT'') (4; COT''=η(8) -bis(trimethylsilyl)cyclooctatetraenyl) has been synthesized by oxidation of the anionic sandwich complex Li[Pu(1,4-COT'')2 ] (3) with anhydrous cobalt(II) chloride. The first crystal structure determination of an organoplutonium(IV) complex revealed an asymmetric sandwich structure for 4 where one COT'' ring is 1,3-substituted while the other retains the original 1,4-substitution pattern. The electronic structure of 4 has been elucidated by a computational study, revealing a probable cause for the unexpected silyl group migration.

  15. Structural and functional characterization of Staphylococcus aureus dihydrodipicolinate synthase.

    PubMed

    Girish, Tavarekere S; Sharma, Eshita; Gopal, B

    2008-08-20

    Lysine biosynthesis is crucial for cell-wall formation in bacteria. Enzymes involved in lysine biosynthesis are thus potential targets for anti-microbial therapeutics. Dihydrodipicolinate synthase (DHDPS) catalyzes the first step of this pathway. Unlike its homologues, Staphylococcus aureus DHDPS is a dimer both in solution and in the crystal and is not feedback inhibited by lysine. The crystal structure of S. aureus DHDPS in the free and substrate bound forms provides a structural rationale for its catalytic mechanism. The structure also reveals unique conformational features of the S. aureus enzyme that could be crucial for the design of specific non-competitive inhibitors.

  16. The role of structure-to-property-relationships in materials characterization

    SciTech Connect

    Morgner, W.

    2000-07-01

    The paper deals with questions concerning the material characterization for steels in the field of engineering and metallurgy. Based on the structure-to-property-relationships, a procedure is proposed to strengthen the systematical development of methods for nondestructive characterization of materials. The state of the nondestructive characterization of metals is reviewed and applications are described in which adequate macroscopic physical properties are measured in order to characterize the materials state and properties nondestructively. The materials characterization of ball bearing steel and cast iron using multiparametrical approaches is discussed in detail.

  17. 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.

  18. 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.

  19. 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.

  20. Secondary structure characterization of beta-lactamase inclusion bodies.

    PubMed

    Przybycien, T M; Dunn, J P; Valax, P; Georgiou, G

    1994-01-01

    The secondary structure of proteins in E. coli inclusion bodies was investigated via Raman spectroscopy. Inclusion bodies were purified from cells expressing different forms of RTEM beta-lactamase and grown at either 37 or 42 degrees C. All of the solid phase inclusion body samples examined gave amide I band spectra that were perturbed from that of the native, purified protein in both solution and powder forms; secondary structure estimates indicated significant decreases in alpha-helix and increases in beta-sheet contents in the inclusion body samples. The structure estimates for inclusion bodies isolated from 37 degrees C cultures were similar, regardless of aggregate localization in the E. coli cytoplasmic or periplasmic spaces or beta-lactamase precursor content. Inclusion bodies obtained from 42 degrees C cells exhibited a further reduction of alpha-helix and augmentation of beta-sheet contents relative to those from 37 degrees C cultures. These results are consistent with the paradigm for inclusion body formation via the self-association of intra-cellular folding intermediates having extensive secondary structure content. Further, the overall secondary structure content of inclusion bodies is not significantly affected by subcellular compartmentalization, but may be altered at increased temperatures.

  1. 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.

  2. A characterization of structural proteins expressed by Bombyx mori bidensovirus.

    PubMed

    Lü, Peng; Xing, Yali; Hu, Zhaoyang; Yang, Yanhua; Pan, Ye; Chen, Kangmin; Zhu, Feifei; Zhou, Yajing; Chen, Keping; Yao, Qin

    2017-03-01

    Bombyx mori bidensiovirus (BmBDV) is a species of Bidensovirus that has been was placed into a new genus within the new family Bidnaviridae by the International Committee on Taxonomy of Viruses. BmBDV causes fatal flacherie disease in silkworms, which causes large losses to the sericulture industry. BmBDV contains two sets of complementary linear single-stranded DNAs of approximately 6.5kb (viral DNA 1, VD1) and 6.0kb (viral DNA 2, VD2). VD1 and VD2 are encapsidated in separate icosahedral non-enveloped capsids, which are similar in size and shape. However, the strategies used to express BmBDV structural proteins remains unclear. In this work, a total of six structural proteins were separated by two-dimensional electrophoresis and shown to be encoded by the BmBDV VP gene via mass spectrometry. The transmission electron microscopy results showed that co-expression of the BmBDV VP and SP structural proteins in Spodoptera frugiperda sf9 cells resulted in the formation of 22-24nm virus-like particles. Furthermore, a mutation of the major structural protein-encoding VP gene, in which the second in-frame ATG codon was mutated to GCG, abrogated the production of several structural proteins, indicating that this strategy of expressing BmBDV VP is dependent on a leaky scanning translation mechanism.

  3. Q+: characterizing the structure of young star clusters

    NASA Astrophysics Data System (ADS)

    Jaffa, S. E.; Whitworth, A. P.; Lomax, O.

    2017-04-01

    Many young star clusters appear to be fractal, i.e. they appear to be concentrated in a nested hierarchy of clusters within clusters. We present a new algorithm for statistically analysing the distribution of stars to quantify the level of substructure. We suggest that, even at the simplest level, the internal structure of a fractal cluster requires the specification of three parameters. (i) The 3D fractal dimension, D, measures the extent to which the clusters on one level of the nested hierarchy fill the volume of their parent cluster. (ii) The number of levels, L, reflects the finite ratio between the linear size of the large root-cluster at the top of the hierarchy, and the smallest leaf-clusters at the bottom of the hierarchy. (iii) The volume-density scaling exponent, C = -d ln [δ n]/d ln [L] measures the factor by which the excess density, δn, in a structure of scale L, exceeds that of the background formed by larger structures; it is similar, but not exactly equivalent, to the exponent in Larson's scaling relation between density and size for molecular clouds. We describe an algorithm that can be used to constrain the values of (D,L,C) and apply this method to artificial and observed clusters. We show that this algorithm is able to reliably describe the three-dimensional structure of an artificial star cluster from the two-dimensional projection, and quantify the varied structures observed in real and simulated clusters.

  4. 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.

  5. Structural and micromechanical characterization of type I collagen gels.

    PubMed

    Latinovic, Olga; Hough, Lawrence A; Daniel Ou-Yang, H

    2010-02-10

    In this paper we report a study where we use a novel optical tweezers technique to measure the local viscoelastic properties of type I collagen solutions spanning the sol-to-gel transition. We use phase contrast optical microscopy to reveal dense and sparse regions of the rigid fibril networks, and find that the spatial variations in the mechanical properties of the collagen gels closely follow the structural properties. Within the dense phase of the connected network in the gel samples, there are regions that exhibit drastically different viscoelastic properties. Within the sparse regions of the gel samples, no evidence of elasticity is found. In type I collagen gels, we find a high degree of structural inhomogeneity. The inhomogeneity in the structural properties of collagen gels and the corresponding viscoelastic properties provide benchmark measurements for the behavior of desirable biological materials, or tissue equivalents.

  6. Structural Characterization of Carbohydrates by Fourier Transform Tandem Mass Spectrometry

    PubMed Central

    Zhou, Wen; Håkansson, Kristina

    2012-01-01

    Fourier transform tandem mass spectrometry (MS/MS) provides high mass accuracy, high sensitivity, and analytical versatility and has therefore emerged as an indispensable tool for structural elucidation of biomolecules. Glycosylation is one of the most common posttranslational modifications, occurring in ~50% of proteins. However, due to the structural diversity of carbohydrates, arising from non-template driven biosynthesis, achievement of detailed structural insight is highly challenging. This review briefly discusses carbohydrate sample preparation and ionization methods, and highlights recent developments in alternative high-resolution MS/MS strategies, including infrared multiphoton dissociation (IRMPD), electron capture dissociation (ECD), and electron detachment dissociation (EDD), for carbohydrates with a focus on glycans and proteoglycans from mammalian glycoproteins. PMID:22389641

  7. 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.

  8. Characterization of the structure and tectonic of South America

    NASA Technical Reports Server (NTRS)

    Keller, G. R.; Lidiak, E. G. (Principal Investigator)

    1981-01-01

    Geologic studies of the South American plate were undertaken. The Guayana shield is reasonably well studied, and although data are sparce, the central Brazilian shield appears similar. Both the Amazon and Parnaiba basins seem to be related to an aulocogen structure. The collection of crustal structure information and the generation of measurement of surface wave dispersion in the shield areascontinues. Long period seismograms are digitized and analyzed. Exisiting crusted and upper mantle studies were indexed. Both MAGSAT scaler and vector magnetic anomaly data were used with regional gravity anomaly data to investigate the regional tectonic features of the South American plate.

  9. Growth, characterization, and properties of metastable and modulated semiconductor structures - Prospects for future studies

    NASA Technical Reports Server (NTRS)

    Grunthaner, F. J.; Madhukar, A.

    1983-01-01

    The general field of preparation and study of metastable and modulated semiconductor structures has progressed rapidly in recent years. This short overview offers an assessment of the progress and current understanding in the areas of fabrication, characterization, and utilization of these new material systems. The discussion includes the more prominent growth techniques, theoretical and experimental analysis of growth kinetics, and an overview of structural, chemical, electronic, and optical characterization. The probable application of these structures for the technological development of new device structures and concepts is considered. The discussion particularly emphasizes the prospects for future studies in view of the specific current understanding.

  10. Enhanced dynamic range fringe projection for micro-structure characterization

    NASA Astrophysics Data System (ADS)

    Samara, Ayman Mohammad

    We present a solution for one of the main limitations in classical interferometry and fringe projection, which is the dynamic range limitation. The technique is based on real time inverse fringe projection to enhance the dynamic range and increase the vertical resolution without the need of prior information about the test object or the system parameters. The object's form optical path difference map is first measured, and then used to generate inverse fringes to optically filter the low spatial frequency form. The surface finish can then be measured without the impact of the form. A stereo microscope-based fringe projection system was designed, constructed, and used to illustrate the technique. The system was also used to characterize solder bumps with an uncertainty of approximately 10%. Individual solder bumps were also characterized using Zygo's NewView(TM) scanning white light interferometer (SWLI), and the results were compared to measurements on Intel's bump metrology tool. The results show that the SWLI has the lowest uncertainty and maximum repeatability but the lowest measurement speed. Intel's tool has a repeatability of approximately 1% and a measurement speed of about 10 minutes per 100,000 bumps, making it suitable for high volume process control.

  11. Label-free characterization of biomembranes: from structure to dynamics.

    PubMed

    Mashaghi, Alireza; Mashaghi, Samaneh; Reviakine, Ilya; Heeren, Ron M A; Sandoghdar, Vahid; Bonn, Mischa

    2014-02-07

    We review recent progress in the study of the structure and dynamics of phospholipid membranes and associated proteins, using novel label-free analytical tools. We describe these techniques and illustrate them with examples highlighting current capabilities and limitations. Recent advances in applying such techniques to biological and model membranes for biophysical studies and biosensing applications are presented, and future prospects are discussed.

  12. Surface-Bound Biomembranes Incorporating Receptors: Electrochemical and Structural Characterization.

    DTIC Science & Technology

    1991-06-06

    receptnr; (Darszon, 1983; Levitzki , 1985). Here it is used to form planar structures that are potentially more stable and reproducible than the...4, 90-96. Levitzki , A.(1985). Reconstitution of membrane receptor systems. Biochim. Biophys. Acta, 822, 127-153. 16 Heuser, J.E. & Salpeter, S.R

  13. Structural characterization of siliceous spicules from marine sponges.

    PubMed

    Croce, Gianluca; Frache, Alberto; Milanesio, Marco; Marchese, Leonardo; Causà, Mauro; Viterbo, Davide; Barbaglia, Alessia; Bolis, Vera; Bavestrello, Giorgio; Cerrano, Carlo; Benatti, Umberto; Pozzolini, Marina; Giovine, Marco; Amenitsch, Heinz

    2004-01-01

    Siliceous sponges, one of the few animal groups involved in a biosilicification process, deposit hydrated silica in discrete skeletal elements called spicules. A multidisciplinary analysis of the structural features of the protein axial filaments inside the spicules of a number of marine sponges, belonging to two different classes (Demospongiae and Hexactinellida), is presented, together with a preliminary analysis of the biosilicification process. The study was carried out by a unique combination of techniques: fiber diffraction using synchrotron radiation, scanning electron microscopy (SEM), thermogravimetric analysis (TGA), differential scanning calorimetric (DSC), Fourier transform infrared spectroscopy (FTIR), and molecular modeling. From a phylogenetic point of view, the main result is the structural difference between the dimension and packing of the protein units in the spicule filaments of the Demospongiae and the Hexactinellida species. Models of the protein organization in the spicule axial filaments, consistent with the various experimental evidences, are given. The three different species of demosponges analyzed have similar general structural features, but they differ in the degree of order. The structural information on the spicule axial filaments can help shed some light on the still unknown molecular mechanisms controlling biosilicification.

  14. 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.

  15. 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.

  16. Structural characterization of Zn-In-Se thin films

    NASA Astrophysics Data System (ADS)

    Güllü, H. H.; Parlak, M.

    2017-02-01

    In this study, structural properties of the Zn-In-Se (ZIS) thin films deposited by thermal evaporation method were investigated. The as-grown and annealed ZIS films were found in polycrystalline structure with the main orientation in (112) direction. The compositional analysis of the films showed that they were in Zn-rich behavior and there was a slight change in the elemental contribution to the structure with annealing process. Raman analysis was carried out to determine the crystalline structure and the different vibration modes of ZIS thin films. According to these measurements, the highest Raman intensity was in the LO mode which was directly proportional to the crystallinity of the samples. The atomic force microscopy (AFM) analyses were done in order to obtain detailed information about the morphology of the thin film surface. The surface of the films was observed as nearly-smooth and uniform in as-grown and annealed forms. X-ray photoelectron spectroscopy (XPS) measurements were analyzed to get detailed information about surface and near-surface characteristics of the films. The results from the surface and depth compositional analyses of the films showed quite good agreement with the energy dispersive X-ray spectroscopy (EDS) analysis.

  17. Structural characterization of polymorphs and molecular complexes of finasteride

    NASA Astrophysics Data System (ADS)

    Wawrzycka, Irena; Stȩpniak, Krystyna; Matyjaszczyk, Sławomir; Kozioł, Anna E.; Lis, Tadeusz; Abboud, Khalil A.

    1999-01-01

    The molecular structure of finasteride, 17 β-( N-tert-butylcarbamoyl)-4-aza-5 α-androst-1-en-3-one, and structures of three related crystalline forms have been determined by X-ray analysis. The rigid steroid skeleton of the molecule adopts a half-chair/chair/chair/half-chair conformation. Two peptide groups, one cyclic (lactam) in the ring A and a second being a part of the substituent at C17, are the main factors influencing intermolecular contacts. Different hydrogen-bond interactions of these hydrophilic groups are observed in the crystal structures. An infinite ribbon of finasteride molecules is formed between lactam groups in the orthorhombic homomolecular crystal ( 1) obtained from an ethanol solution. The linear molecular complex finasteride-acetic acid ( 1a) is connected by hydrogen bonds between the lactam of finasteride and the carboxyl group of acetic acid. The crystallization from an ethyl acetate solution gives a complex structure of bis-finasteride monohydrate ethyl acetate clathrate ( 1b) with guest molecule disordered in channels. Crystals of a second (monoclinic) finasteride polymorph ( 2) were obtained during thermal decomposition of 1a, and sublimation of 1, 1a and 1b. Two polymorphic forms show different IR spectra.

  18. 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

  19. Fabrication and characterization of micro- /nano structures for nanophotonic applications

    NASA Astrophysics Data System (ADS)

    Jee, Hongsub

    The objective of this thesis is finding and developing fabrication methods to provide background techniques for potential applications with nanomaterials. The inclined UV lithography has announced to make three-dimensional fabrication process. With a movable stage, complex structures were achieved but difference of the refractive index, design of the final structures were limited. Refractive index matching medium between the substrate and the light source could reduce the refractive indices between the polymer and the substrate successfully. Nanoporous structures fabricated by multibeam interference lithography shows limitation of the usage since its periodicity. By insertion of the lift off resist layer between the patterned layer and the substrate, final photonic crystal structures could be partially removed for its own purpose and it provide potential application in the future. Two-step processing, combining with reactive ion etching system, nanoporous structures were on various substrates such as silicon and Polydimethylsiloxane. Photonic crystal template anodic aluminum oxide process has been described too. Large optical activity at visible wavelengths are of great attention in photonics. Dramatic enhancement of the optical activity of chiral poly(fluorene-alt-benzothiadiazole) with photoresist was demonstrated and successive photo patterning of chiral polymer shows the potential usage of this material for the photonics applications. Two photon lithography also used to pattern a photoresist-chiral polymer mixture into planar shapes and enhanced chirality can be realized by tuning the wavelength-dependent chiral response at both the molecular and geometric level. Near infrared light induced photopolymerization in-situ was demonstrated which can be applied everywhere where ultraviolet-polymerization is employed such as dentistry, coating industry. Use of the ultraviolet upconverting nanoparticles doped into the polymer, we show that expensive femtosecond pulsed

  20. 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.

  1. Construction and characterization of amorphous-silicon test structures

    SciTech Connect

    Koppel, L.N.; Milgram, A.A.

    1987-08-01

    The central goal of the project was to qualify amorphous silicon, a newly developed semiconductor material, as the basis for economical large-area photoconductive detectors of penetrating radiation. The thrust of the project was to establish the feasibility of constructing photoconductive amorphous-silicon devices whose electronic properties supported the radiation detection application. This issue of feasibility was successfully resolved by construction and experimental characterization of amorphous-silicon test pieces representative of the existing state-of-the-art. The focus of this work was the measurement of material electronic properties known to affect the performance of solid-state radiation detectors, and the investigation of candidate junction-device architectures. The construction and experimental evaluation of prototype radiation detectors based on amorphous silicon was beyond the scope of the current effort, and will form the core of work to be accomplished within a Phase II continuation of the project.

  2. Construction and characterization of amorphous-silicon test structures

    SciTech Connect

    Koppel, L.N.; Milgram, A.A.

    1987-08-01

    Semiconductor device fabrication and characterization work indicates that construction of amorphous-Si photoconductive radiation detectors is feasible. Amorphous Si films are mechanically stable and adhere well to candidate electrode materials; form Schottky-type rectifying junctions with several electrode metals. Materials exist for forming ohmic contacts on amorphous-Si films. Fabrication facilities accessible to ARACOR produce material of nominal band-gap energy, dangling bond density, and dielectric constant. Modification of amorphous-Si conductivity is feasible and supports the construction of PIN devices. Significant photoconductive response is observed for both Schottky-type and PIN devices, with the latter providing superior performance. It is recommended that construction and experimental evaluation of prototype amorphous-Si radiation detectors be persued in Phase II.

  3. Spectroscopic studies of anthracyclines: Structural characterization and in vitro tracking

    NASA Astrophysics Data System (ADS)

    Szafraniec, Ewelina; Majzner, Katarzyna; Farhane, Zeineb; Byrne, Hugh J.; Lukawska, Malgorzata; Oszczapowicz, Irena; Chlopicki, Stefan; Baranska, Malgorzata

    2016-12-01

    A broad spectroscopic characterization, using ultraviolet-visible (UV-vis) and Fourier transform infrared absorption as well as Raman scattering, of two commonly used anthracyclines antibiotics (DOX) daunorubicin (DNR), their epimers (EDOX, EDNR) and ten selected analogs is presented. The paper serves as a comprehensive spectral library of UV-vis, IR and Raman spectra of anthracyclines in the solid state and in solution. The particular advantage of Raman spectroscopy for the measurement and analysis of individual antibiotics is demonstrated. Raman spectroscopy can be used to monitor the in vitro uptake and distribution of the drug in cells, using both 488 nm and 785 nm as source wavelengths, with submicrometer spatial resolution, although the cellular accumulation of the drug is different in each case. The high information content of Raman spectra allows studies of the drug-cell interactions, and so the method seems very suitable for monitoring drug uptake and mechanisms of interaction with cellular compartments at the subcellular level.

  4. Extraction and characterization of nanocellulose structures from raw cotton linter.

    PubMed

    Morais, João Paulo Saraiva; Rosa, Morsyleide de Freitas; de Souza Filho, Men de sá Moreira; Nascimento, Lidyane Dias; do Nascimento, Diego Magalhães; Cassales, Ana Ribeiro

    2013-01-02

    This study aimed to characterize nanocellulose extracted from cotton (Gossypium hirsutum) linters. The nanocellulose was subjected to electronic microscopy, thermal analysis, X-ray diffractometry, light scattering, and contact angle. The properties of the nanocellulose are considerably different from the linter. The acidic hydrolyses applied to extract the nanocrystals increased the crystallinity index and the hydrophilicity and decreased the thermal stability. On average, the nanocrystals were 177 nm long and 12 nm wide, with an aspect ratio of 19 when measured by microscopy. The light scattering results were coherent with the crystal dimensions. Cotton linter is a potential source of nanocellulose crystals, particularly to be used in the production of hydrophilic nanocomposites. Extraction of nanocellulose from raw cotton linter does not require pulping.

  5. Nanoscale structural and mechanical characterization of natural nanocomposites: Seashells

    NASA Astrophysics Data System (ADS)

    Li, Xiaodong

    2007-03-01

    Seashells are natural nanocomposites with superior mechanical strength and toughness. What is the secret recipe that Mother Nature uses to fabricate seashells? What roles do the nanoscale structures play in the inelasticity and toughening of seashells? Can we learn from this to produce seashell-like nanocomposites? The focus of this article is nacre (mother-of-pearl). The recent discovery of nanoparticles in nacre is summarized, and the role these nanoparticles play in nacre’s toughness is elucidated. It was found that rotation and deformation of aragonite nanoparticles are the two prominent mechanisms contributing to energy dissipation in nacre. The biopolymer spacing between nanoparticles facilitates the particle rotation process. This article also presents future challenges in the study of nacre’s nanoscale structure and mechanical properties.

  6. 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.

  7. Structural characterization of hair fiber by optical coherence tomography (OCT)

    NASA Astrophysics Data System (ADS)

    Freitas, Anderson Zanardi; Robes Velasco, Maria Valeria; Paulo Raele, Marcus; Kaneko, Telma Mary; Vieira, Nilson Dias, Jr.; Baby, Andre Rolim

    2008-09-01

    In this work we use the optical coherence tomography (OCT) technique to produce in vitro transversal section images of human hair. It was possible to identify in the A-scan protocol its principal structures: cuticle, cortex and medulla. The mean diameter of medulla was 29 +/- 7 μm and hair diameter was 122 +/- 16 μm in our samples of standard Afro-ethnic hair. We also compared the OCT signal before and after chemical treatment with 18% w/w ammonium thioglycolate solution. After chemical treatment, it was not possible to identify the main structures of hair fiber, due the index matching promoted by deleterious action of chemical agent. A tridimensional image was built starting from 601 cross-sectional images (slices). Each slice was taken in steps of 6.0 μm at 8 frames per second, and the whole 3D image was built in 60 seconds.

  8. 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.

  9. Structural and Biochemical Characterization of Cinnamoyl-CoA Reductases.

    PubMed

    Sattler, Steven A; Walker, Alexander M; Vermerris, Wilfred; Sattler, Scott E; Kang, ChulHee

    2017-02-01

    Cinnamoyl-coenzyme A reductase (CCR) catalyzes the reduction of hydroxycinnamoyl-coenzyme A (CoA) esters using NADPH to produce hydroxycinnamyl aldehyde precursors in lignin synthesis. The catalytic mechanism and substrate specificity of cinnamoyl-CoA reductases from sorghum (Sorghum bicolor), a strategic plant for bioenergy production, were deduced from crystal structures, site-directed mutagenesis, and kinetic and thermodynamic analyses. Although SbCCR1 displayed higher affinity for caffeoyl-CoA or p-coumaroyl-CoA than for feruloyl-CoA, the enzyme showed significantly higher activity for the latter substrate. Through molecular docking and comparisons between the crystal structures of the Vitis vinifera dihydroflavonol reductase and SbCCR1, residues threonine-154 and tyrosine-310 were pinpointed as being involved in binding CoA-conjugated phenylpropanoids. Threonine-154 of SbCCR1 and other CCRs likely confers strong substrate specificity for feruloyl-CoA over other cinnamoyl-CoA thioesters, and the T154Y mutation in SbCCR1 led to broader substrate specificity and faster turnover. Through data mining using our structural and biochemical information, four additional putative CCR genes were discovered from sorghum genomic data. One of these, SbCCR2, displayed greater activity toward p-coumaroyl-CoA than did SbCCR1, which could imply a role in the synthesis of defense-related lignin. Taken together, these findings provide knowledge about critical residues and substrate preference among CCRs and provide, to our knowledge, the first three-dimensional structure information for a CCR from a monocot species.

  10. 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.

  11. Structure Characterization of Semiconducting Tin and Tungsten Mixed Oxides

    NASA Astrophysics Data System (ADS)

    Solis, J. L.; Frantti, J.; Lantto, V.; Häggström, L.; Wikner, M.

    Mixed-oxide powders of tin and tungsten were made by heating various mixtures of SnO and WO3 powders, corresponding to the nominal formula SnxWO3+x with x between 0.5 and 2.0, in an argon atmosphere at 600°C for 15 hours. The α-SnWO4 phase was the result of heating of an equi-molar mixture of SnO and WO3 powders. In addition to 119Sn Mössbauer experiments, X-ray diffraction and Raman spectroscopy were used to study the phase structures of the mixed-oxide powders. Mössbauer spectra from all samples show a small peak at ∽0mm/s from phase(s) like rutile SnO2, and a larger peak doublet centred at ∽3.4mm/s from the α-SnWO4 phase, where tin is in the form Sn4+ and Sn2+, respectively. Another peak doublet centred at ∽3.0mm/s was needed to obtain reasonable fits for samples with x≥1.3. This doublet originates from an undocumented phase where tin is also in the divalent form Sn2+. 119Sn Mössbauer spectroscopy made it possible to reveal the relative amounts of the two valence states of tin in the mixed-oxide structures. Raman spectroscopy as the other probe for ``local'' structures was insensitive to reveal the changes in the phase structures between different mixed-oxide samples up to x=1.72, but an extra peak at ∽890cm-1 in the Raman spectrum from the sample with x=2.0 indicates also the presence of the undocumented phase.

  12. 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.

  13. 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.

  14. Structural Characterization of Novel Pseudomonas aeruginosa Type IV Pilins

    SciTech Connect

    Nguyen, Y.; Jackson, S; Aidoo, F; Junop, M; Burrows, L

    2010-01-01

    Pseudomonas aeruginosa type IV pili, composed of PilA subunits, are used for attachment and twitching motility on surfaces. P. aeruginosa strains express one of five phylogenetically distinct PilA proteins, four of which are associated with accessory proteins that are involved either in pilin posttranslational modification or in modulation of pilus retraction dynamics. Full understanding of pilin diversity is crucial for the development of a broadly protective pilus-based vaccine. Here, we report the 1.6-{angstrom} X-ray crystal structure of an N-terminally truncated form of the novel PilA from strain Pa110594 (group V), which represents the first non-group II pilin structure solved. Although it maintains the typical T4a pilin fold, with a long N-terminal {alpha}-helix and four-stranded antiparallel {beta}-sheet connected to the C-terminus by a disulfide-bonded loop, the presence of an extra helix in the {alpha}{beta}-loop and a disulfide-bonded loop with helical character gives the structure T4b pilin characteristics. Despite the presence of T4b features, the structure of PilA from strain Pa110594 is most similar to the Neisseria gonorrhoeae pilin and is also predicted to assemble into a fiber similar to the GC pilus, based on our comparative pilus modeling. Interactions between surface-exposed areas of the pilin are suggested to contribute to pilus fiber stability. The non-synonymous sequence changes between group III and V pilins are clustered in the same surface-exposed areas, possibly having an effect on accessory protein interactions. However, based on our high-confidence model of group III PilA{sub PA14}, compensatory changes allow for maintenance of a similar shape.

  15. 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.

  16. 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

  17. 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.

  18. [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.

  19. A specific antidote for dabigatran: functional and structural characterization.

    PubMed

    Schiele, Felix; van Ryn, Joanne; Canada, Keith; Newsome, Corey; Sepulveda, Eliud; Park, John; Nar, Herbert; Litzenburger, Tobias

    2013-05-02

    Dabigatran etexilate is a direct thrombin inhibitor and used widely as an anticoagulant for the prevention of stroke in patients with atrial fibrillation. However, anticoagulation therapy can be associated with an increased risk of bleeding. Here, we present data on the identification, humanization, and in vitro pharmacology of an antidote for dabigatran (aDabi-Fab). The X-ray crystal structure of dabigatran in complex with the antidote reveals many structural similarities of dabigatran recognition compared with thrombin. By a tighter network of interactions, the antidote achieves an affinity for dabigatran that is ~350 times stronger than its affinity for thrombin. Despite the structural similarities in the mode of dabigatran binding, the antidote does not bind known thrombin substrates and has no activity in coagulation tests or platelet aggregation. In addition we demonstrate that the antidote rapidly reversed the anticoagulant activity of dabigatran in vivo in a rat model of anticoagulation. This is the first report of a specific antidote for a next-generation anticoagulant that may become a valuable tool in patients who require emergency procedures.

  20. 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

    2016-05-05

    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+).

  1. 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.

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

    PubMed Central

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

    2005-01-01

    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 β-keratin. Raman microscopy of individual setae, however, clearly shows the presence of additional protein constituents, some of which may be identified as α-keratins. Electrophoretic analysis of solubilized setal proteins supports these conclusions, indicating the presence of a group of low-molecular-weight β-keratins (14–20 kDa), together with α-keratins, and this interpretation is supported by immunological analyses. PMID:16849272

  3. 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.

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

    DOE PAGES

    Riley, Zachary B.; Deshmukh, Rohit; Miller, Brent A.; ...

    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

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

    SciTech Connect

    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 they 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.

  6. The Electronically Steerable Flash Lidar Adaptability for Characterizing Forest Structure

    NASA Astrophysics Data System (ADS)

    Ramond, T.; Weimer, C. S.; Lefsky, M. A.; Ruppert, L.; Donley, B.; Delker, T.; Applegate, J.

    2010-12-01

    The Electronically Steerable Flash Lidar (ESFL) instrument developed at Ball Aerospace is one that provides unprecedented flexibility to adapt to the scene of the moment. For probing the structure of forests, ESFL provides several features that can be changed shot-to-shot, enabling real time adaptability. The number of beams transmitted to the scene can vary. The spacing of the beams can be changed from a contiguous configuration suited to probing smaller scale forest structure to a sparse configuration to sample larger scale variations over the maximum possible swath. Variation of the oscillator rate can provide multiple range sampling resolutions. Data will be presented illustrating these capabilities during flight from a Twin Otter aircraft. The poster will discuss how this instrument could be used to design studies intended to quantify exactly what is the minimum sampling structure needed to measure a given scientific parameter with the desired accuracy. Such a result could allow for maximum efficiency of precious observation time in the world of remote sensing from airplane or from space.

  7. 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.

  8. Detailed Structural Characterization of Unbound Protein Phosphatase 1 Inhibitors

    PubMed Central

    Dancheck, Barbara; Nairn, Angus C.; Peti, Wolfgang

    2009-01-01

    Protein Phosphatase 1 (PP1) is an essential and ubiquitous serine/threonine protein phosphatase that is regulated by more than 100 known inhibitor and targeting proteins. It is currently unclear how protein inhibitors distinctly and specifically regulate PP1 to enable rapid responses to cellular alterations. We demonstrate that two PP1 inhibitors, I-2 and DARPP-32, belong to the class of intrinsically unstructured proteins (IUPs). We show that both inhibitors have distinct preferences for transient local and long range structure. These preferences are likely their structural signature for their interaction with PP1. Furthermore, we show that upon phosphorylation of Thr34 in DARPP-32, which turns DARPP-32 into a potent inhibitor of PP1, neither local nor long range structure of DARPP-32 is altered. Therefore, our data suggests a role for these transient 3-dimensional topologies in binding mechanisms that enable extensive contacts with PP1's invariant surfaces. Together, these interactions enable potent and selective inhibition of PP1. PMID:18954090

  9. Characterization of power absorption response of periodic three-dimensional structures to partially coherent fields.

    PubMed

    Tihon, Denis; Withington, Stafford; Thomas, Christopher N; Craeye, Christophe

    2016-12-01

    In many applications of absorbing structures it is important to understand their spatial response to incident fields, for example in thermal solar panels, bolometric imaging, and controlling radiative heat transfer. In practice, the illuminating field often originates from thermal sources and is only partially spatially coherent when it reaches the absorbing device. In this paper, we present a method to fully characterize the way a structure can absorb such partially coherent fields. The method is presented for any three-dimensional material and accounts for the partial coherence and partial polarization of the incident light. This characterization can be achieved numerically using simulation results or experimentally using the energy absorption interferometry that has been described previously in the literature. The absorbing structure is characterized through a set of absorbing functions onto which any partially coherent field can be projected. This set is compact for any structure of finite extent, and the absorbing function is discrete for periodic structures.

  10. Synthesis and structural characterization of three-layer Aurivillius ceramics

    NASA Astrophysics Data System (ADS)

    Haluska, Michael Stephan

    2003-07-01

    The three layer Aurivillius crystal structure was investigated for use as an ionic conductor. Sample synthesis was investigated using high temperature x-ray diffraction (HTXRD) for a range of compounds, using solid state synthesis and the polymerized complex method. Isothermal Avrami type kinetics studies were performed on Bi4Ti3O12 using in situ HTXRD and quantitative analysis performed via Rietveld refinements using TOPAS. The kinetics analysis yielded Avrami exponents of approximately 0.54, which fell in the range of the diffusion controlled reaction mechanisms. The activation energy over a range of temperatures was calculated to be on the order of 140kJ/mol. Crystal structure refinements were performed on the Bi2Sr2-xAxNb2TiO12 (A = Ca,Ba, x = 0.5, 1) series using combined x-ray and neutron diffraction Rietveld refinements. Refinements indicated a static disorder between the Bi and A sites, and between the Nb and Ti sites. A-site lattice strain investigated via the bond valence method reveals a linear increase in strain with the size of the substituted alkaline earth cation. Furthermore, large isotropic thermal parameters for the O1 and O4 oxygen sites reveal possible oxygen vacancy formation as a result of unresolved strain between the A and Ti layers of the structure. Oxygen stoichiometry is found to decrease as the size of the a lattice parameter decreases. Synthesis of non-stoichiometric three-layer phases was accomplished by aliovalent substitution and via forced site-mixing. Neither method produced samples with conductivities greater than 10-3 Scm at 900°C. Non-stoichiometric compositions follow similar structural trends to those observed in the stoichiometric crystal structure refinements. Increased numbers of oxygen vacancies were recorded than anticipated from the dopants. The number of extra vacancies corresponds well with the amount shown in the stoichiometric compositions. Based on the conductivity and number of charge carriers, the mobilities of

  11. 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+}.

  12. Structural characterization of the Salmonella typhimurium LT2 umu operon

    SciTech Connect

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

    1990-09-01

    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.

  13. Characterization of structural proteins of hirame rhabdovirus, HRV

    USGS Publications Warehouse

    Nishizawa, Toyohiko; Yoshimizu, Mamoru; Winton, James; Ahne, Winfried; Kimura, Takahisa

    1991-01-01

    Structural proteins of hirame rhabdovirus (HRV) were analyzed by SDS-polyacrylarnide gel electrophoresis, western blotting, 2-dimensional gel electrophoresis, and Triton X-100 treatment. Purified HRV virions were composed of: polymerase (L), glycoprotein (G), nucleoprotein (N), and 2 matrix proteins (M1 and M2). Based upon their relative mobilities, the estimated molecular weights of the proteins were: L, 156 KDa; G, 68 KDa; N, 46.4 KDa; M1, 26.4 KDa; and M2, 19.9 KDa. The electrophorehc pattern formed by the structural proteins of HRV was clearly different from that formed by pike fry rhabdovirus, spring viremia of carp virus, eel virus of America, and eel virus European X which belong to the Vesiculovirus genus; however, it resembled the pattern formed by structural proteins of viral hemorrhagic septicemia virus (VHSV) and infectious hematopoietic necrosis virus (IHNV) which are members of the Lyssavirus genus. Among HRV, IHNV, and VHSV, differences were observed in the relative mobilities of the G, N, M1, and M2 proteins. Western blot analysis revealed that the G. N, and M2 proteins of HRV shared antigenic determinants with IHNV and VHSV, but not with any of the 4 fish vesiculoviruses tested. Cross-reactions between the M1 proteins of HRV, IHNV, or VHSV were not detected in this assay. Two-dimensional gel electrophoresis was used to show that HRV differed from IHNV or VHSV in the isoelectric point (PI) of the M1 and M2 proteins. In this system, 2 forms of the M1 protein of HRV and IHNV were observed.These subspecies of M1 had the same relative mobility but different p1 values. Treatment of purified virions with 2% Triton X-100 in Tris buffer containing NaCl removed the G, M1, and M2 proteins of IHNV, but HRV virions were more stable under these conditions.

  14. 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.

  15. System and process for ultrasonic characterization of deformed structures

    SciTech Connect

    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.

  16. Growth, Characterization, and Simulation of Novel Semiconductor Tunnel Structures.

    NASA Astrophysics Data System (ADS)

    Chow, David Hsingkuo

    This thesis presents investigations of novel semiconductor heterostructure devices based on quantum mechanical tunneling. Due to their small characteristic dimensions, these devices have extremely fast charge transport properties. Thus, it is expected that tunnel structure devices will be well -suited to high frequency and optoelectronic applications. In chapter 2, a theoretical model is developed to simulate tunneling currents in single barrier heterostructures. The model includes band bending effects and a two band treatment of electron attenuation coefficients in the barrier. It is proposed that certain material systems have the appropriate band alignments to realize a novel single barrier negative differential resistance (NDR) mechanism. A thorough theoretical analysis of these single barrier NDR structures is presented. The first experimental demonstration of the single barrier NDR mechanism is reported in chapter 3. The HgTe/CdTe material system was selected for the demonstration. In this material system, low temperatures (<20 K) are needed to observe the NDR effect. High temperature (190-300 K) current-voltage curves from the single barrier Hg_{1-x}Cd_ {x}Te heterostructures have also been investigated, leading to a direct electrical measurement of the controversial HgTe/CdTe valence band offset. In chapter 4, results are presented from several studies of III-V heterostructures grown by molecular beam epitaxy. A measurement of the GaAs/AlAs valence band offset by x-ray photoemmision spectroscopy yields a value of 0.46 +/- 0.07 eV, independent of growth sequence. Optical measurements of electron tunneling times in GaAs/AlAs double barrier heterostructures are performed by growing structures with very thin cap layers. Tunneling times as short as ~12 ps are measured. Triple barrier GaAs/AlAs tunnel structures are found to display strong NDR, indicating that the tunneling process is coherent (as opposed to sequential) in nature. Finally, a technique for

  17. Composition and Partial Structure Characterization of Tremella Polysaccharides

    PubMed Central

    2009-01-01

    Heteropolysaccharides isolated from liquid cultures of nine Tremella species contained 0.3 to 1.2% protein, 2.7 to 5% ash, 0.9 to 3.4% acetyl groups, 76.5 to 84.2% carbohydrates and trace amounts of starch. The polysaccharides in aqueous solution were slightly acidic (pH 5.1 to 5.6). They consisted of the following monomeric sugars: fucose, ribose, xylose, arabinose, mannose, galactose, glucose and glucuronic acid. The backbones of the polysaccharide structures consisted of α-(1→3)-links while the side chains were β-linked. PMID:23983549

  18. 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.

  19. Membrane Characterization by Microscopic and Scattering Methods: Multiscale Structure

    PubMed Central

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

    2011-01-01

    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. PMID:24957612

  20. 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.

  1. 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.

  2. Human seminal alpha inhibins: isolation, characterization, and structure.

    PubMed Central

    Li, C H; Hammonds, R G; Ramasharma, K; Chung, D

    1985-01-01

    Two additional peptides with inhibin-like activity have been isolated from human seminal plasma. One consists of 52 amino acids and the other, 92 amino acids. They are designated alpha-inhibin-52 and alpha-inhibin-92. Sequence analyses show that the NH2-terminal 31 amino acids of alpha-inhibin-52 are identical to the structure of the inhibin-like peptide previously reported [ILP-(1-31), now designated alpha-inhibin-31], and the COOH-terminal 52 amino acids of alpha-inhibin-92 are identical to the structure of alpha-inhibin-52. The amino acid sequence of alpha-inhibin-92 is: (sequence in text) Bioassay data in mouse pituitaries in vitro show that alpha-inhibin-52 is 3.4 times more active and alpha-inhibin-92 is greater than 40 times more active than alpha-inhibin-31 in suppressing follitropin-release. Radioimmunoassay data indicate that alpha-inhibin-52 and alpha-inhibin-92 have only 60% immunoreactivity. PMID:3889920

  3. Structural characterization of some sol-gel derived phosphosilicate glasses

    NASA Astrophysics Data System (ADS)

    Todan, L.; Anghel, E. M.; Osiceanu, P.; Turcu, R. V. F.; Atkinson, I.; Simon, S.; Zaharescu, M.

    2015-04-01

    A comparative study of three phosphosilicate gels of the 90SiO2-10P2O5 composition obtained from tetraethoxysilane and three phosphorous precursors: triethylphosphate (TEP), triethylphosphite (TEPI) and H3PO4 is performed. 29Si and 31P Magic Angle Spining NMR, X-ray Photoelectron, X-ray Fluorescence and Raman spectroscopies as well as TG analysis are used in order to establish phosphorous precursors and annealing influence on composition and structure of the outcome materials. Unlike the three dimensional silicate network made of Si(OSi)x(OH)4-x species, unreacted TEP (100% Q1 condensed phosphorous units) from TEP derived gel and a large amount of isolated phosphorous species (39.7% Q0) in the H3PO4 derived gel are identified. Annealing at 700 °C of the three gels give similar structure with the 90SiO2-10P2O5 glass, excepting the triethylphosphate derived glass that has a much lower P content. Thus, the H3PO4 derived glass at 700 and 1000 °C shows 1.89 and 1.94 times higher P2O5/SiO2 ratios than in the case of the TEP derived one.

  4. Structural characterization of anti-inflammatory immunoglobulin G Fc proteins.

    PubMed

    Ahmed, Alysia A; Giddens, John; Pincetic, Andrew; Lomino, Joseph V; Ravetch, Jeffrey V; Wang, Lai-Xi; Bjorkman, Pamela J

    2014-09-09

    Immunoglobulin G (IgG) is a central mediator of host defense due to its ability to recognize and eliminate pathogens. The recognition and effector responses are encoded on distinct regions of IgGs. The diversity of the antigen recognition Fab domains accounts for IgG's ability to bind with high specificity to essentially any antigen. Recent studies have indicated that the Fc effector domain also displays considerable heterogeneity, accounting for its complex effector functions of inflammation, modulation, and immune suppression. Therapeutic anti-tumor antibodies, for example, require the pro-inflammatory properties of the IgG Fc to eliminate tumor cells, while the anti-inflammatory activity of intravenous IgG requires specific Fc glycans for activity. In particular, the anti-inflammatory activity of intravenous IgG is ascribed to a small population of IgGs in which the Asn297-linked complex N-glycans attached to each Fc CH2 domain include terminal α2,6-linked sialic acids. We used chemoenzymatic glycoengineering to prepare fully disialylated IgG Fc and solved its crystal structure. Comparison of the structures of asialylated Fc, sialylated Fc, and F241A Fc, a mutant that displays increased glycan sialylation, suggests that increased conformational flexibility of the CH2 domain is associated with the switch from pro-inflammatory to anti-inflammatory activity of the Fc.

  5. Structural and functional characterization of a specific antidote for ticagrelor.

    PubMed

    Buchanan, Andrew; Newton, Philip; Pehrsson, Susanne; Inghardt, Tord; Antonsson, Thomas; Svensson, Peder; Sjögren, Tove; Öster, Linda; Janefeldt, Annika; Sandinge, Ann-Sofie; Keyes, Feenagh; Austin, Mark; Spooner, Jennifer; Gennemark, Peter; Penney, Mark; Howells, Garnet; Vaughan, Tristan; Nylander, Sven

    2015-05-28

    Ticagrelor is a direct-acting reversibly binding P2Y12 antagonist and is widely used as an antiplatelet therapy for the prevention of cardiovascular events in acute coronary syndrome patients. However, antiplatelet therapy can be associated with an increased risk of bleeding. Here, we present data on the identification and the in vitro and in vivo pharmacology of an antigen-binding fragment (Fab) antidote for ticagrelor. The Fab has a 20 pM affinity for ticagrelor, which is 100 times stronger than ticagrelor's affinity for its target, P2Y12. Despite ticagrelor's structural similarities to adenosine, the Fab is highly specific and does not bind to adenosine, adenosine triphosphate, adenosine 5'-diphosphate, or structurally related drugs. The antidote concentration-dependently neutralized the free fraction of ticagrelor and reversed its antiplatelet activity both in vitro in human platelet-rich plasma and in vivo in mice. Lastly, the antidote proved effective in normalizing ticagrelor-dependent bleeding in a mouse model of acute surgery. This specific antidote for ticagrelor may prove valuable as an agent for patients who require emergency procedures.

  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. 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.

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

    DOE PAGES

    Ojwang, Dickson O.; Grins, Jekabs; Wardecki, Dariusz; ...

    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

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

    SciTech Connect

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

    2016-06-03

    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 F$m\\bar{3}$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.

  10. Structure and Functional Characterization of Vibrio parahaemolyticus Thermostable Direct Hemolysin*

    PubMed Central

    Yanagihara, Itaru; Nakahira, Kumiko; Yamane, Tsutomu; Kaieda, Shuji; Mayanagi, Kouta; Hamada, Daizo; Fukui, Takashi; Ohnishi, Kiyouhisa; Kajiyama, Shin'ichiro; Shimizu, Toshiyuki; Sato, Mamoru; Ikegami, Takahisa; Ikeguchi, Mitsunori; Honda, Takeshi; Hashimoto, Hiroshi

    2010-01-01

    Thermostable direct hemolysin (TDH) is a major virulence factor of Vibrio parahaemolyticus that causes pandemic foodborne enterocolitis mediated by seafood. TDH exists as a tetramer in solution, and it possesses extreme hemolytic activity. Here, we present the crystal structure of the TDH tetramer at 1.5 Å resolution. The TDH tetramer forms a central pore with dimensions of 23 Å in diameter and ∼50 Å in depth. π-Cation interactions between protomers comprising the tetramer were indispensable for hemolytic activity of TDH. The N-terminal region was intrinsically disordered outside of the pore. Molecular dynamic simulations suggested that water molecules permeate freely through the central and side channel pores. Electron micrographs showed that tetrameric TDH attached to liposomes, and some of the tetramer associated with liposome via one protomer. These findings imply a novel membrane attachment mechanism by a soluble tetrameric pore-forming toxin. PMID:20335168

  11. Characterization of the Structural Features and Interactions of Sclerostin

    PubMed Central

    Veverka, Vaclav; Henry, Alistair J.; Slocombe, Patrick M.; Ventom, Andrew; Mulloy, Barbara; Muskett, Frederick W.; Muzylak, Mariusz; Greenslade, Kevin; Moore, Adrian; Zhang, Li; Gong, Jianhua; Qian, Xueming; Paszty, Chris; Taylor, Richard J.; Robinson, Martyn K.; Carr, Mark D.

    2009-01-01

    The secreted glycoprotein sclerostin has recently emerged as a key negative regulator of Wnt signaling in bone and has stimulated considerable interest as a potential target for therapeutics designed to treat conditions associated with low bone mass, such as osteoporosis. We have determined the structure of sclerostin, which resulted in the identification of a previously unknown binding site for heparin, suggestive of a functional role in localizing sclerostin to the surface of target cells. We have also mapped the interaction site for an antibody that blocks the inhibition of Wnt signaling by sclerostin. This shows minimal overlap with the heparin binding site and highlights a key role for this region of sclerostin in protein interactions associated with the inhibition of Wnt signaling. The conserved N- and C-terminal arms of sclerostin were found to be unstructured, highly flexible, and unaffected by heparin binding, which suggests a role in stabilizing interactions with target proteins. PMID:19208630

  12. 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.

  13. Growth, characterization and crystal structure analysis of rifapentine

    NASA Astrophysics Data System (ADS)

    Zhou, K.; Li, J.; Zheng, D. S.

    2010-11-01

    Single crystals of rifapentine have been grown by cooling technique. The crystal structure analysis and the molecular arrangement of these crystals have been determined using X-ray diffraction (XRD) method. From single-crystal XRD studies, it is found that the compound crystallizes in the monoclinic system with a space group P2 1, and the corresponding lattice parameters were calculated ( a = 12.278(3) Å, b = 19.768(4) Å, c = 12.473(3) Å, Z = 2, beta = 112.35(3)°). FT-IR spectra are recorded to identify the various functional groups present in the compound. The UV-Vis spectrum of rifapentine takes place at a wavelength of 236, 255, 334 and 474 nm, respectively. The thermal stability of the crystal is determined from TG/DTA curves.

  14. Structural characterization of Mumps virus fusion protein core

    SciTech Connect

    Liu Yueyong; Xu Yanhui; Lou Zhiyong; Zhu Jieqing; Hu Xuebo; Gao, George F.; Qiu Bingsheng . E-mail: Qiubs@sun.im.ac.cn; Rao Zihe . E-mail: raozh@xtal.tsinghua.edu.cn; Tien, Po . E-mail: tienpo@sun.im.ac.cn

    2006-09-29

    The fusion proteins of enveloped viruses mediating the fusion between the viral and cellular membranes comprise two discontinuous heptad repeat (HR) domains located at the ectodomain of the enveloped glycoproteins. The crystal structure of the fusion protein core of Mumps virus (MuV) was determined at 2.2 A resolution. The complex is a six-helix bundle in which three HR1 peptides form a central highly hydrophobic coiled-coil and three HR2 peptides pack against the hydrophobic grooves on the surface of central coiled-coil in an oblique antiparallel manner. Fusion core of MuV, like those of simian virus 5 and human respiratory syncytium virus, forms typical 3-4-4-4-3 spacing. The similar charecterization in HR1 regions, as well as the existence of O-X-O motif in extended regions of HR2 helix, suggests a basic rule for the formation of the fusion core of viral fusion proteins.

  15. Structure and functional characterization of Vibrio parahaemolyticus thermostable direct hemolysin.

    PubMed

    Yanagihara, Itaru; Nakahira, Kumiko; Yamane, Tsutomu; Kaieda, Shuji; Mayanagi, Kouta; Hamada, Daizo; Fukui, Takashi; Ohnishi, Kiyouhisa; Kajiyama, Shin'ichiro; Shimizu, Toshiyuki; Sato, Mamoru; Ikegami, Takahisa; Ikeguchi, Mitsunori; Honda, Takeshi; Hashimoto, Hiroshi

    2010-05-21

    Thermostable direct hemolysin (TDH) is a major virulence factor of Vibrio parahaemolyticus that causes pandemic foodborne enterocolitis mediated by seafood. TDH exists as a tetramer in solution, and it possesses extreme hemolytic activity. Here, we present the crystal structure of the TDH tetramer at 1.5 A resolution. The TDH tetramer forms a central pore with dimensions of 23 A in diameter and approximately 50 A in depth. Pi-cation interactions between protomers comprising the tetramer were indispensable for hemolytic activity of TDH. The N-terminal region was intrinsically disordered outside of the pore. Molecular dynamic simulations suggested that water molecules permeate freely through the central and side channel pores. Electron micrographs showed that tetrameric TDH attached to liposomes, and some of the tetramer associated with liposome via one protomer. These findings imply a novel membrane attachment mechanism by a soluble tetrameric pore-forming toxin.

  16. Characterization of the bending stiffness of large space structure joints

    NASA Technical Reports Server (NTRS)

    Wu, K. Chauncey

    1989-01-01

    A technique for estimating the bending stiffness of large space structure joints is developed and demonstrated for an erectable joint concept. Experimental load-deflection data from a three-point bending test was used as input to solve a closed-form expression for the joint bending stiffness which was derived from linear beam theory. Potential error sources in both the experimental and analytical procedures are identified and discussed. The bending stiffness of a mechanically preloaded erectable joint is studied at three applied moments and seven joint orientations. Using this technique, the joint bending stiffness was bounded between 6 and 17 percent of the bending stiffness of the graphite/epoxy strut member.

  17. Synthesis, characterization and structural aspects of 3-azidopropylsilatrane

    NASA Astrophysics Data System (ADS)

    Singh, Raghubir; Kishore Puri, Jugal; Pal Sharma, Raj; Kumar Malik, Ashok; Ferretti, Valeria

    2010-10-01

    Reaction of 3-chloropropyltriethoxysilane ( 1) with sodium azide ( 2) in the presence of phase transfer catalyst, tert-butylammonium bromide provided 3-azidopropyltriethoxysilane ( 3). This undergoes transesterification reaction with triethanolamine in the presence of KOH to form a new silatrane 3-azidopropylsilatrane ( 4). Multinuclear NMR ( 1H, 13C and 29Si), IR and elemental analyses support the structure of novel silatrane 4. 29Si NMR indicates the presence of penta-coordinated silicon atom, which is supported by X-ray studies. It revealed that Si is present in distorted trigonal bipyramidal environment with three O atoms in equatorial positions and N atom at one of the apical positions. The second axial position is occupied by long alkyl chain bearing azide moiety. The interaction of Si with N forms a transannular bond having 2.176 Å bond length.

  18. The characterization of widespread fatigue damage in fuselage structure

    NASA Technical Reports Server (NTRS)

    Piascik, Robert S.; Willard, Scott A.; Miller, Matthew

    1994-01-01

    The characteristics of widespread fatigue damage (WSFD) in fuselage riveted structure were established by detailed nondestructive and destructive examinations of fatigue damage contained in a full size fuselage test article. The objectives of this were to establish an experimental data base for validating emerging WSFD analytical prediction methodology and to identify first order effects that contribute to fatigue crack initiation and growth. Detailed examinations were performed on a test panel containing four bays of a riveted lap splice joint. The panel was removed from a full scale fuselage test article after receiving 60,000 full pressurization cycles. The results of in situ examinations document the progression of fuselage skin fatigue crack growth through crack linkup. Detailed tear down examinations and fractography of the lap splice joint region revealed fatigue crack initiation sites, crack morphology, and crack linkup geometry. From this large data base, distributions of crack size and locations are presented and discussions of operative damage mechanisms are offered.

  19. 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

  20. Au-Based Catalysts: Electrochemical Characterization for Structural Insights.

    PubMed

    Pifferi, Valentina; Chan-Thaw, Carine E; Campisi, Sebastiano; Testolin, Anna; Villa, Alberto; Falciola, Luigi; Prati, Laura

    2016-02-25

    Au-based catalysts are widely used in important processes because of their peculiar characteristics. The catalyst performance depends strongly on the nature and structure of the metal nanoparticles, especially in the case of bimetallic catalysts where synergistic effects between the two metals can be occasionally seen. In this paper, it is shown that electrochemical characterisation (cyclovoltammetry CV and electrochemical impedance spectroscopy EIS) of AuPd systems can be used to determine the presence of an electronic interaction between the two metals, thus providing a strong support in the determination of the nature of the synergy between Au and Pd in the liquid phase oxidation of alcohols. However, it seems likely that the strong difference in the catalytic behavior between the single metals and the bimetallic system is connected not only to the redox behaviour, but also to the energetic balance between the different elementary steps of the reaction.

  1. Structural characterization of casein micelles: shape changes during film formation

    NASA Astrophysics Data System (ADS)

    Gebhardt, R.; Vendrely, C.; Kulozik, U.

    2011-11-01

    The objective of this study was to determine the effect of size-fractionation by centrifugation on the film structure of casein micelles. Fractionated casein micelles in solution were asymmetrically distributed with a small distribution width as measured by dynamic light scattering. Films prepared from the size-fractionated samples showed a smooth surface in optical microscopy images and a homogeneous microstructure in atomic force micrographs. The nano- and microstructure of casein films was probed by micro-beam grazing incidence small angle x-ray scattering (μGISAXS). Compared to the solution measurements, the sizes determined in the film were larger and broadly distributed. The measured GISAXS patterns clearly deviate from those simulated for a sphere and suggest a deformation of the casein micelles in the film.

  2. 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.

  3. Structural characterization of highly branched glucan sheath from Ceriporiopsis subvermispora.

    PubMed

    Suzuki, Daisuke; Nishimura, Hiroshi; Yoshioka, Koichi; Kaida, Rumi; Hayashi, Takahisa; Takabe, Keiji; Watanabe, Takashi

    2017-02-01

    Wood rotting basidiomycetes produce extracellular mucilaginous sheaths interfacing fungal hyphae and plant biomass. While the versatility of these fungal sheaths has been addressed, sheaths generated by selective white-rot fungi remain poorly understood. To fill this gap, the sheath produced by the basidiomycete Ceriporiopsis subvermispora, which degrades lignin while inflicting limited cellulose damage, was analyzed in this study. Fluorescence and transmission electron microscopy revealed that the sheath formed three days after inoculation into a beech wood slice on an agar plate and was embedded at the interface between fungal hyphae and wood cell walls. The sheath's chemical structure was evaluated from fungus cultures in a liquid medium containing [U-(13)C6]-d-glucose and beech wood slices. Compositional analysis, methylation analysis, and (13)C NMR demonstrated that the sheath mainly consisted of a comb-like β-1,6-glucopyranose residue-branched β-1,3-glucan, which is advantageous to retain water and extracellular secondary metabolites.

  4. 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.

  5. Biosynthesis and structural characterization of silver nanoparticles from bacterial isolates

    SciTech Connect

    Zaki, Sahar; El Kady, M.F.; Abd-El-Haleem, Desouky

    2011-10-15

    Graphical abstract: In this study five bacterial isolates belong to different genera were found to be able to biosynthesize silver nanoparticles. Biosynthesis and spectral characterization are reported here. Highlights: {yields} About 300 bacterial isolates were screened for their ability to produce nanosilvers {yields} Five of them were potential candidates for synthesis of silver nanoparticles {yields} Production of silver nanoparticles was examined using UV-Vis, XRD, SEM and EDS. {yields} The presence of nanoparticles with all five bacterial isolates was confirmed. -- Abstract: This study aimed to develop a green process for biosynthesis of silver nanomaterials by some Egyptian bacterial isolates. This target was achieved by screening an in-house culture collection consists of 300 bacterial isolates for silver nanoparticle formation. Through screening process, it was observed that strains belonging to Escherichia coli (S30, S78), Bacillus megaterium (S52), Acinetobacter sp. (S7) and Stenotrophomonas maltophilia (S54) were potential candidates for synthesis of silver nanoparticles. The extracellular production of silver nanoparticles by positive isolates was investigated by UV-Vis spectroscopy, X-ray diffraction (XRD), transmission electron microscope (TEM), scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). The results demonstrated that UV-visible spectrum of the aqueous medium containing silver ion showed a peak at 420 nm corresponding to the plasmon absorbance of silver nanoparticles. Scanning electron microscopy micrograph showed formation of silver nanoparticles in the range of 15-50 nm. XRD-spectrum of the silver nanoparticles exhibited 2{theta} values corresponding to the silver nanocrystal that produce in hexagonal and cubic crystal configurations with different plane of orientation. In addition, the signals of the silver atoms were observed by EDS-spectrum analysis that confirms the presence of silver nanoparticles (Ag

  6. Structural Characterization of Oxidized Glycerophosphatidylserine: Evidence of Polar Head Oxidation

    NASA Astrophysics Data System (ADS)

    Maciel, Elisabete; da Silva, Raquel Nunes; Simões, Cláudia; Domingues, Pedro; Domingues, M. Rosário M.

    2011-10-01

    Non-oxidized phosphatidylserine (PS) is known to play a key role in apoptosis but there is considerable research evidence suggesting that oxidized PS also plays a role in this event, leading to the increasing interest in studying PS oxidative modifications. In this work, different PS (1-palmitoyl-2-linoleoyl-sn-glycero-3-phospho-L-serine (PLPS), 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine (POPS), and 1,2-dipalmitoyl-sn-glycero-3-phospho-L-serine (DPPS) were oxidized in vitro by hydroxyl radical, generated under Fenton reaction conditions, and the reactions were monitored by ESI-MS in negative mode. Oxidation products were then fractionated by thin layer chromatography (TLC) and characterized by tandem mass spectrometry (MS/MS). This approach allowed the identification of hydroxyl, peroxy, and keto derivatives due to oxidation of unsaturated fatty acyl chains. Oxidation products due to oxidation of serine polar head were also identified. These products, with lower molecular weight than the non-modified PS, were identified as [M - 29 - H]- (terminal acetic acid), [M - 30 - H]- (terminal acetamide), [M - 13 - H]- (terminal hydroperoxyacetaldehyde), and [M - 13 - H]- (terminal hydroxyacetaldehyde plus hydroxy fatty acyl chain). Phosphatidic acid was also formed in these conditions. These findings confirm the oxidation of the serine polar head induced by the hydroxyl radical. The identification of these modifications may be a valuable tool to evaluate phosphatidylserine alteration under physiopathologic conditions and also to help understand the biological role of phosphatidylserine oxidation in the apoptotic process and other biological functions.

  7. Structural characterization of oxidized glycerophosphatidylserine: evidence of polar head oxidation.

    PubMed

    Maciel, Elisabete; da Silva, Raquel Nunes; Simões, Cláudia; Domingues, Pedro; Domingues, M Rosário M

    2011-10-01

    Non-oxidized phosphatidylserine (PS) is known to play a key role in apoptosis but there is considerable research evidence suggesting that oxidized PS also plays a role in this event, leading to the increasing interest in studying PS oxidative modifications. In this work, different PS (1-palmitoyl-2-linoleoyl-sn-glycero-3-phospho-L-serine (PLPS), 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine (POPS), and 1,2-dipalmitoyl-sn-glycero-3-phospho-L-serine (DPPS) were oxidized in vitro by hydroxyl radical, generated under Fenton reaction conditions, and the reactions were monitored by ESI-MS in negative mode. Oxidation products were then fractionated by thin layer chromatography (TLC) and characterized by tandem mass spectrometry (MS/MS). This approach allowed the identification of hydroxyl, peroxy, and keto derivatives due to oxidation of unsaturated fatty acyl chains. Oxidation products due to oxidation of serine polar head were also identified. These products, with lower molecular weight than the non-modified PS, were identified as [M - 29 - H](-) (terminal acetic acid), [M - 30 - H](-) (terminal acetamide), [M - 13 - H](-) (terminal hydroperoxyacetaldehyde), and [M - 13 - H](-) (terminal hydroxyacetaldehyde plus hydroxy fatty acyl chain). Phosphatidic acid was also formed in these conditions. These findings confirm the oxidation of the serine polar head induced by the hydroxyl radical. The identification of these modifications may be a valuable tool to evaluate phosphatidylserine alteration under physiopathologic conditions and also to help understand the biological role of phosphatidylserine oxidation in the apoptotic process and other biological functions.

  8. Synthesis and Characterization of Elastomeric Heptablock Terpolymers Structured by Crystallization

    SciTech Connect

    Alfonzo, C.Guillermo; Fleury, Guillaume; Chaffin, Kimberly A.; Bates, Frank S.

    2010-12-07

    We report the synthesis and characterization of fully saturated hydrocarbon block copolymer thermoplastic elastomers with competitive mechanical properties and attractive processing features. Block copolymers containing glassy poly(cyclohexylethylene) (C), elastomeric poly(ethylene-alt-propylene) (P), and semicrystalline poly(ethylene) (E) were produced in a CEC-P-CEC heptablock architecture, denoted XPX, by anionic polymerization and catalytic hydrogenation. The X blocks contain equal volume fractions of C and E, totaling 40%-60% of the material overall. All the XPX polymers are disordered above the melt temperature for E (T{sub m,E} {approx_equal} 95 C) as evidenced by SAXS and dynamic mechanical spectroscopy measurements. Cooling below T{sub m,E} results in crystallization of the E blocks, which induces microphase segregation of E, C, and P into a complex morphology with a continuous rubbery domain and randomly arranged hard domains as shown by TEM. This mechanism of segregation decouples the processing temperature from the XPX molecular weight up to a limiting value. Tensile mechanical testing (simple extension and cyclic loading) demonstrates that the tensile strength (ca. 30 MPa) and strain at break (>500%) are comparable to the behavior of CPC triblock thermoplastic elastomers of similar molecular weight and glass content. However, in the CPC materials, processability is constrained by the order-disorder transition temperature, limiting the applications of these materials. Elastic recovery of the XPX materials following seven cycles of tensile deformation is correlated with the fraction of X in the heptablock copolymer, and the residual strain approaches that of CPC when the fraction of hard blocks f{sub X} {le} 0.39.

  9. Structural characterization of human general transcription factor TFIIF in solution

    PubMed Central

    Akashi, Satoko; Nagakura, Shinjiro; Yamamoto, Seiji; Okuda, Masahiko; Ohkuma, Yoshiaki; Nishimura, Yoshifumi

    2008-01-01

    Human general transcription factor IIF (TFIIF), a component of the transcription pre-initiation complex (PIC) associated with RNA polymerase II (Pol II), was characterized by size-exclusion chromatography (SEC), electrospray ionization mass spectrometry (ESI-MS), and chemical cross-linking. Recombinant TFIIF, composed of an equimolar ratio of α and β subunits, was bacterially expressed, purified to homogeneity, and found to have a transcription activity similar to a natural one in the human in vitro transcription system. SEC of purified TFIIF, as previously reported, suggested that this protein has a size >200 kDa. In contrast, ESI-MS of the purified sample gave a molecular size of 87 kDa, indicating that TFIIF is an αβ heterodimer, which was confirmed by matrix-assisted laser desorption/ionization (MALDI) MS of the cross-linked TFIIF components. Recent electron microscopy (EM) and photo-cross-linking studies showed that the yeast TFIIF homolog containing Tfg1 and Tfg2, corresponding to the human α and β subunits, exists as a heterodimer in the PIC, so the human TFIIF is also likely to exist as a heterodimer even in the PIC. In the yeast PIC, EM and photo-cross-linking studies showed different results for the mutual location of TFIIE and TFIIF along DNA. We have examined the direct interaction between human TFIIF and TFIIE by ESI-MS, SEC, and chemical cross-linking; however, no direct interaction was observed, at least in solution. This is consistent with the previous photo-cross-linking observation that TFIIF and TFIIE flank DNA separately on both sides of the Pol II central cleft in the yeast PIC. PMID:18218714

  10. Structural and tribometric characterization of biomimetically inspired synthetic "insect adhesives".

    PubMed

    Speidel, Matthias W; Kleemeier, Malte; Hartwig, Andreas; Rischka, Klaus; Ellermann, Angelika; Daniels, Rolf; Betz, Oliver

    2017-01-01

    Background: Based on previous chemical analyses of insect tarsal adhesives, we prepared 12 heterogeneous synthetic emulsions mimicking the polar/non-polar principle, analysed their microscopical structure and tested their adhesive, frictional, and rheological properties. Results: The prepared emulsions varied in their consistency from solid rubber-like, over soft elastic, to fluid (watery or oily). With droplet sizes >100 nm, all the emulsions belonged to the common type of macroemulsions. The emulsions of the first generation generally showed broader droplet-size ranges compared with the second generation, especially when less defined components such as petrolatum or waxes were present in the lipophilic fraction of the first generation of emulsions. Some of the prepared emulsions showed a yield point and were Bingham fluids. Tribometric adhesion was tested via probe tack tests. Compared with the "second generation" (containing less viscous components), the "first generation" emulsions were much more adhesive (31-93 mN), a finding attributable to their highly viscous components, i.e., wax, petrolatum, gelatin and poly(vinyl alcohol). In the second generation emulsions, we attained much lower adhesivenesses, ranging between 1-18 mN. The adhesive performance was drastically reduced in the emulsions that contained albumin as the protein component or that lacked protein. Tribometric shear tests were performed at moderate normal loads. Our measured friction forces (4-93 mN in the first and 0.1-5.8 mN in the second generation emulsions) were comparatively low. Differences in shear performance were related to the chemical composition and emulsion structure. Conclusion: By varying their chemical composition, synthetic heterogeneous adhesive emulsions can be adjusted to have diverse consistencies and are able to mimic certain rheological and tribological properties of natural tarsal insect adhesives.

  11. Statistical Characterization of the Flow Structure in the Rhine Valley

    NASA Astrophysics Data System (ADS)

    Philippe, Philippe; Debas, Alain M.; Haeberli, Christian; Flamant, Pierre H.

    The flow structure at the intersection between the Rhine and the Seez valleys nearthe Swiss city of Bad Ragaz has been documented by means of wind and pressuremeasurements collected from 9 September to 10 November 1999 during the MesoscaleAlpine Programme (MAP) experiment. To understand better the dynamics of theageostrophic winds that develop in this part of the Rhine valley, some key questionsare answered in this paper including the following: (i) How does air blow at theintersection of the Rhine and Seez valleys? and (ii) what are the dynamical processes(mechanical or thermal) driving the flow circulations in the valleys?Statistical analysis of the wind and pressure patterns at synoptic scale and at the scaleof the valley shows that five main flow patterns, SE/S, NW/W, NW/N, NW/S, SE/N(wind direction in the Seez valley/wind direction in the Rhine valley) prevail. The SE/S regime is the flow splitting situation. It is mainly driven by a strong pressure gradient across the Alps leading to foehn, even though some nocturnal cases are generated bylocal thermal gradients. The NW/W and NW/N regimes are mechanically forced bythe synoptic pressure gradient (as the flow splitting case). The difference between thetwo regimes is due to the synoptic flow direction [westerly (northerly) synoptic flowfor the NW/W (NW/N) regime], showing that the Rhine valley (particularly from BadRagaz to Lake Constance) is less efficient in channelling the flow than the Seez valley.The NW/S (occurring mainly during nighttime) and SE/N (occurring mainly duringdaytime) regimes are mainly katabatic flows. However, the SE/N regime is also partlyforced at the synoptic scale during the foehn case that occurred between 18 October and 20 October 1999, with a complex layered vertical structure.

  12. 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

  13. Purification and structural characterization of siderophore (corynebactin) from Corynebacterium diphtheriae.

    PubMed

    Zajdowicz, Sheryl; Haller, Jon C; Krafft, Amy E; Hunsucker, Steve W; Mant, Colin T; Duncan, Mark W; Hodges, Robert S; Jones, David N M; Holmes, Randall K

    2012-01-01

    During infection, Corynebacterium diphtheriae must compete with host iron-sequestering mechanisms for iron. C. diphtheriae can acquire iron by a siderophore-dependent iron-uptake pathway, by uptake and degradation of heme, or both. Previous studies showed that production of siderophore (corynebactin) by C. diphtheriae is repressed under high-iron growth conditions by the iron-activated diphtheria toxin repressor (DtxR) and that partially purified corynebactin fails to react in chemical assays for catecholate or hydroxamate compounds. In this study, we purified corynebactin from supernatants of low-iron cultures of the siderophore-overproducing, DtxR-negative mutant strain C. diphtheriae C7(β) ΔdtxR by sequential anion-exchange chromatography on AG1-X2 and Source 15Q resins, followed by reverse-phase high-performance liquid chromatography (RP-HPLC) on Zorbax C8 resin. The Chrome Azurol S (CAS) chemical assay for siderophores was used to detect and measure corynebactin during purification, and the biological activity of purified corynebactin was shown by its ability to promote growth and iron uptake in siderophore-deficient mutant strains of C. diphtheriae under iron-limiting conditions. Mass spectrometry and NMR analysis demonstrated that corynebactin has a novel structure, consisting of a central lysine residue linked through its α- and ε- amino groups by amide bonds to the terminal carboxyl groups of two different citrate residues. Corynebactin from C. diphtheriae is structurally related to staphyloferrin A from Staphylococcus aureus and rhizoferrin from Rhizopus microsporus in which d-ornithine or 1,4-diaminobutane, respectively, replaces the central lysine residue that is present in corynebactin.

  14. Structural and tribometric characterization of biomimetically inspired synthetic "insect adhesives"

    PubMed Central

    Speidel, Matthias W; Kleemeier, Malte; Hartwig, Andreas; Rischka, Klaus; Ellermann, Angelika; Daniels, Rolf

    2017-01-01

    Background: Based on previous chemical analyses of insect tarsal adhesives, we prepared 12 heterogeneous synthetic emulsions mimicking the polar/non-polar principle, analysed their microscopical structure and tested their adhesive, frictional, and rheological properties. Results: The prepared emulsions varied in their consistency from solid rubber-like, over soft elastic, to fluid (watery or oily). With droplet sizes >100 nm, all the emulsions belonged to the common type of macroemulsions. The emulsions of the first generation generally showed broader droplet-size ranges compared with the second generation, especially when less defined components such as petrolatum or waxes were present in the lipophilic fraction of the first generation of emulsions. Some of the prepared emulsions showed a yield point and were Bingham fluids. Tribometric adhesion was tested via probe tack tests. Compared with the "second generation" (containing less viscous components), the "first generation" emulsions were much more adhesive (31–93 mN), a finding attributable to their highly viscous components, i.e., wax, petrolatum, gelatin and poly(vinyl alcohol). In the second generation emulsions, we attained much lower adhesivenesses, ranging between 1–18 mN. The adhesive performance was drastically reduced in the emulsions that contained albumin as the protein component or that lacked protein. Tribometric shear tests were performed at moderate normal loads. Our measured friction forces (4–93 mN in the first and 0.1–5.8 mN in the second generation emulsions) were comparatively low. Differences in shear performance were related to the chemical composition and emulsion structure. Conclusion: By varying their chemical composition, synthetic heterogeneous adhesive emulsions can be adjusted to have diverse consistencies and are able to mimic certain rheological and tribological properties of natural tarsal insect adhesives. PMID:28144564

  15. Thiaminylated adenine nucleotides. Chemical synthesis, structural characterization and natural occurrence.

    PubMed

    Frédérich, Michel; Delvaux, David; Gigliobianco, Tiziana; Gangolf, Marjorie; Dive, Georges; Mazzucchelli, Gabriel; Elias, Benjamin; De Pauw, Edwin; Angenot, Luc; Wins, Pierre; Bettendorff, Lucien

    2009-06-01

    Thiamine and its three phosphorylated derivatives (mono-, di- and triphosphate) occur naturally in most cells. Recently, we reported the presence of a fourth thiamine derivative, adenosine thiamine triphosphate, produced in Escherichia coli in response to carbon starvation. Here, we show that the chemical synthesis of adenosine thiamine triphosphate leads to another new compound, adenosine thiamine diphosphate, as a side product. The structure of both compounds was confirmed by MS analysis and 1H-, 13C- and 31P-NMR, and some of their chemical properties were determined. Our results show an upfield shifting of the C-2 proton of the thiazolium ring in adenosine thiamine derivatives compared with conventional thiamine phosphate derivatives. This modification of the electronic environment of the C-2 proton might be explained by a through-space interaction with the adenosine moiety, suggesting U-shaped folding of adenosine thiamine derivatives. Such a structure in which the C-2 proton is embedded in a closed conformation can be located using molecular modeling as an energy minimum. In E. coli, adenosine thiamine triphosphate may account for 15% of the total thiamine under energy stress. It is less abundant in eukaryotic organisms, but is consistently found in mammalian tissues and some cell lines. Using HPLC, we show for the first time that adenosine thiamine diphosphate may also occur in small amounts in E. coli and in vertebrate liver. The discovery of two natural thiamine adenine compounds further highlights the complexity and diversity of thiamine biochemistry, which is not restricted to the cofactor role of thiamine diphosphate.

  16. Purification and Structural Characterization of Siderophore (Corynebactin) from Corynebacterium diphtheriae

    PubMed Central

    Zajdowicz, Sheryl; Haller, Jon C.; Krafft, Amy E.; Hunsucker, Steve W.; Mant, Colin T.; Duncan, Mark W.; Hodges, Robert S.; Jones, David N. M.; Holmes, Randall K.

    2012-01-01

    During infection, Corynebacterium diphtheriae must compete with host iron-sequestering mechanisms for iron. C. diphtheriae can acquire iron by a siderophore-dependent iron-uptake pathway, by uptake and degradation of heme, or both. Previous studies showed that production of siderophore (corynebactin) by C. diphtheriae is repressed under high-iron growth conditions by the iron-activated diphtheria toxin repressor (DtxR) and that partially purified corynebactin fails to react in chemical assays for catecholate or hydroxamate compounds. In this study, we purified corynebactin from supernatants of low-iron cultures of the siderophore-overproducing, DtxR-negative mutant strain C. diphtheriae C7(β) ΔdtxR by sequential anion-exchange chromatography on AG1-X2 and Source 15Q resins, followed by reverse-phase high-performance liquid chromatography (RP-HPLC) on Zorbax C8 resin. The Chrome Azurol S (CAS) chemical assay for siderophores was used to detect and measure corynebactin during purification, and the biological activity of purified corynebactin was shown by its ability to promote growth and iron uptake in siderophore-deficient mutant strains of C. diphtheriae under iron-limiting conditions. Mass spectrometry and NMR analysis demonstrated that corynebactin has a novel structure, consisting of a central lysine residue linked through its α- and ε- amino groups by amide bonds to the terminal carboxyl groups of two different citrate residues. Corynebactin from C. diphtheriae is structurally related to staphyloferrin A from Staphylococcus aureus and rhizoferrin from Rhizopus microsporus in which d-ornithine or 1,4-diaminobutane, respectively, replaces the central lysine residue that is present in corynebactin. PMID:22514641

  17. Higher order structure characterization of protein therapeutics by hydrogen/deuterium exchange mass spectrometry.

    PubMed

    Huang, Richard Y-C; Chen, Guodong

    2014-10-01

    Characterization of therapeutic drugs is a crucial step in drug development in the biopharmaceutical industry. Analysis of protein therapeutics is a challenging task because of the complexities associated with large molecular size and 3D structures. Recent advances in hydrogen/deuterium-exchange mass spectrometry (HDX-MS) have provided a means to assess higher-order structure of protein therapeutics in solution. In this review, the principles and procedures of HDX-MS for protein therapeutics characterization are presented, focusing on specific applications of epitope mapping for protein-protein interactions and higher-order structure comparison studies for conformational dynamics of protein therapeutics.

  18. 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

  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. Research Advances on Structural Characterization of Resistant Starch and Its Structure-Physiological Function Relationship: A Review.

    PubMed

    Ma, Zhen; Boye, Joyce I

    2016-09-19

    Resistant starch (RS) is defined as the fraction of starch that escapes digestion in the small intestine due to either difficult enzyme/starch contact or to the strength of the crystalline regions formed both in native starch and in those retrograded starch. RS occurs naturally in some foods, and some may be generated in others as the results of several processing conditions. A variety of techniques have been employed to obtain structural characteristics of resistant starch such as their crystallinity, structural order, chain length distribution and conformation, helicity, and double helical structures. These structure plays an important role in determining the physiological properties of RS such as their prebiotic and hypoglycaemic properties. However, such topic on structural characterization of RS and their structure-physiological function relationship have not been reviewed in previous literatures. Therefore, this review focuses on the past and current achievements of research on structural characterizations of a range of resistant starch prepared from different sources of native starches as a result of a variety of processing conditions. The potential relationships between the structure and the physiological properties of RS which is of paramount importance for the furtherance understanding and application of RS are also reviewed in this study.

  1. Structural And Functional Characterization of CC Chemokine CCL14

    SciTech Connect

    Blain, K.Y.; Kwiatkowski, W.; Zhao, Q.; Fleur, D.La; Naik, C.; Chun, T.-W.; Tsareva, T.; Kanakaraj, P.; Laird, M.W.; Shah, R.; George, L.; Sanyal, I.; Moore, P.A.; Demeler, B.; Choe, S.

    2009-06-02

    CC chemokine ligand 14, CCL14, is a human CC chemokine that is of recent interest because of its natural ability, upon proteolytic processing of the first eight NH{sub 2}-terminal residues, to bind to and signal through the human immunodeficiency virus type-1 (HIV-1) co-receptor, CC chemokine receptor 5 (CCR5). We report X-ray crystallographic structures of both full-length CCL14 and signaling-active, truncated CCL14 [9-74] determined at 2.23 and 1.8 {angstrom}, respectively. Although CCL14 and CCL14 [9-74] differ in their ability to bind CCR5 for biological signaling, we find that the NH{sub 2}-terminal eight amino acids (residues 1 through 8) are completely disordered in CCL14 and both show the identical mode of the dimeric assembly characteristic of the CC type chemokine structures. However, analytical ultracentrifugation studies reveal that the CCL14 is stable as a dimer at a concentration as low as 100 nM, whereas CCL14 [9-74] is fully monomeric at the same concentration. By the same method, the equilibrium between monomers of CCL14 [9-74] and higher order oligomers is estimated to be of EC{sub 1,4} = 4.98 {mu}M for monomer-tetramer conversion. The relative instability of CCL14 [9-74] oligomers as compared to CCL14 is also reflected in the K{sub d}'s that are estimated by the surface plasmon resonance method to be {approx}9.84 and 667 nM for CCL14 and CCL14 [9-74], respectively. This {approx}60-fold difference in stability at a physiologically relevant concentration can potentially account for their different signaling ability. Functional data from the activity assays by intracellular calcium flux and inhibition of CCR5-mediated HIV-1 entry show that only CCL14 [9-74] is fully active at these near-physiological concentrations where CCL14 [9-74] is monomeric and CCL14 is dimeric. These results together suggest that the ability of CCL14 [9-74] to monomerize can play a role for cellular activation.

  2. 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.

  3. Structural Characterization of Glucooligosaccharide Oxidase from Acremonium strictum

    PubMed Central

    Lee, Meng-Hwan; Lai, Wen-Lin; Lin, Shuen-Fuh; Hsu, Cheng-Sheng; Liaw, Shwu-Huey; Tsai, Ying-Chieh

    2005-01-01

    Glucooligosaccharide oxidase from Acremonium strictum was screened for potential applications in oligosaccharide acid production and carbohydrate detection. This protein is a unique covalent flavoenzyme which catalyzes the oxidation of a variety of carbohydrates with high selectivity for cello- and maltooligosaccharides. Kinetic measurements suggested that this enzyme possesses an open carbohydrate-binding groove, which is mainly composed of two glucosyl-binding subsites. The encoding gene was subsequently cloned, and one intron was detected in the genomic DNA. Large amounts of active enzymes were expressed in Pichia pastoris, with a yield of 300 mg per liter medium. The protein was predicted to share structural homology with plant cytokinin dehydrogenase and related flavoproteins that share a conserved flavin adenine dinucleotide (FAD)-binding domain. The closest sequence matches are those of plant berberine bridge enzyme-like proteins, particularly the characteristic flavinylation site. Unexpectedly, mutation of the putative FAD-attaching residue, H70, to alanine, serine, cysteine, and tyrosine did not abolish the covalent FAD linkage and had little effect on the Km. Instead, the variants displayed kcat values that were 50- to 600-fold lower, indicating that H70 is crucial for efficient redox catalysis, perhaps through modulation of the oxidative power of the flavin. PMID:16332885

  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. 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).

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

    PubMed Central

    2015-01-01

    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

  7. 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.

  8. 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.

  9. Structural and functional characterization of human NAD kinase.

    PubMed

    Lerner, F; Niere, M; Ludwig, A; Ziegler, M

    2001-10-19

    NADP is essential for biosynthetic pathways, energy, and signal transduction. Its synthesis is catalyzed by NAD kinase. Very little is known about the structure, function, and regulation of this enzyme from multicellular organisms. We identified a human NAD kinase cDNA and the corresponding gene using available database information. A cDNA was amplified from a human fibroblast cDNA library and functionally overexpressed in Escherichia coli. The obtained cDNA, slightly different from that deposited in the database, encodes a protein of 49 kDa. The gene is expressed in most human tissues, but not in skeletal muscle. Human NAD kinase differs considerably from that of prokaryotes by subunit molecular mass (49 kDa vs 30-35 kDa). The catalytically active homotetramer is highly selective for its substrates, NAD and ATP. It did not phosphorylate the nicotinic acid derivative of NAD (NAAD) suggesting that the potent calcium-mobilizing pyridine nucleotide NAADP is synthesized by an alternative route.

  10. Structural characterization of a serendipitously discovered bioactive macromolecule, lignin sulfate.

    PubMed

    Raghuraman, Arjun; Tiwari, Vaibhav; Thakkar, Jay N; Gunnarsson, Gunnar T; Shukla, Deepak; Hindle, Michael; Desai, Umesh R

    2005-01-01

    The herpes simplex virus-1 (HSV-1) utilizes cell-surface glycosaminoglycan, heparan sulfate, to gain entry into cells and cause infection. In a search for synthetic mimics of heparan sulfate to prevent HSV infection, we discovered potent inhibitory activity arising from sulfation of a monomeric flavonoid. Yet, detailed screening indicated that the sulfated flavonoid was completely inactive and the potent inhibitory activity arose from a macromolecular substance present in the parent flavonoid. The active principle was identified through a battery of biophysical and chemical analyses as a sulfated form of lignin, a three-dimensional network polymer composed of substituted phenylpropanoid monomers. Mass spectral analysis of the parent lignin and its sulfated derivative indicates the presence of p-coumaryl monomers interconnected through uncondensed beta-O-4-linkages. Elemental analysis of lignin sulfate correlates primarily with a polymer of p-coumaryl alcohol containing one sulfate group. High-performance size exclusion chromatography shows a wide molecular weight distribution from 1.5 to 40 kDa suggesting significant polydispersity. Polyacrylamide gel electrophoresis (PAGE) analysis indicates a highly networked polymer that differs significantly from linear charged polymers with respect to its electrophoretic mobility. Overall, macromolecular lignin sulfate presents a multitude of substructures that can interact with biomolecules, including viral glycoproteins, using hydrophobic, hydrogen-bonding, and ionic forces. Thus, lignin sulfate represents a large number of interesting structures with potential medicinal benefits.

  11. 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.

  12. 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.

  13. 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.

  14. Structural characterization of glycosaminoglycans from zebrafish in different ages

    PubMed Central

    Zhang, Fuming; Zhang, Zhenqing; Thistle, Robert; McKeen, Lindsey; Hosoyama, Saori; Toida, Toshihiko

    2009-01-01

    The zebrafish (Danio rerio) is a popular model organism for the study of developmental biology, disease mechanisms, and drug discovery. Glycosaminoglycans (GAGs), located on animal cell membranes and in the extracellular matrix, are important molecules in cellular communication during development, in normal physiology and pathophysiology. Vertebrates commonly contain a variety of GAGs including chondroitin/dermatan sulfates, heparin/heparan sulfate, hyaluronan and keratan sulfate. Zebrafish might represent an excellent experimental organism to study the biological roles of GAGs. A recent study showing the absence of heparan sulfate in adult zebrafish, suggested a more detailed evaluation of the GAGs present in this important model organism needed to be undertaken. This report aimed at examining the structural alterations of different GAGs at the molecular level at different developmental stages. GAGs were isolated and purified from zebrafish in different stages in development ranging from 0.5 days to adult. The content and disaccharide composition of chondroitin sulfate and heparan sulfate were determined using chemical assays, liquid chromotography and mass spectrometry. The presence of HS in adult fish was also confirmed using 1H-NMR. PMID:18777207

  15. 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

  16. Micromechanical properties and structural characterization of modern inarticulated brachiopod shells

    NASA Astrophysics Data System (ADS)

    Merkel, C.; Griesshaber, E.; Kelm, K.; Neuser, R.; Jordan, G.; Logan, A.; Mader, W.; Schmahl, W. W.

    2007-06-01

    brittleness of apatite. Second, there is a hierarchical structuring from the nanometer to a micrometer level. We could identify at least seven levels of hierarchy within the shells.

  17. Static and dynamic structural characterization of nanomaterial catalysts

    NASA Astrophysics Data System (ADS)

    Masiel, Daniel Joseph

    Heterogeneous catalysts systems are pervasive in industry, technology and academia. These systems often involve nanostructured transition metal particles that have crucial interfaces with either their supports or solid products. Understanding the nature of these interfaces as well as the structure of the catalysts and support materials themselves is crucial for the advancement of catalysis in general. Recent developments in the field of transmission electron microscopy (TEM) including dynamic transmission electron microscopy (DTEM), electron tomography, and in situ techniques stand poised to provide fresh insight into nanostructured catalyst systems. Several electron microscopy techniques are applied in this study to elucidate the mechanism of silica nanocoil growth and to discern the role of the support material and catalyst size in carbon dioxide and steam reforming of methane. The growth of silica nanocoils by faceted cobalt nanoparticles is a process that was initially believed to take place via a vapor-liquid-solid growth mechanism similar to other nanowire growth techniques. The extensive TEM work described here suggests that the process may instead occur via transport of silicate and silica species over the nanoparticle surface. Electron tomography studies of the interface between the catalyst particles and the wire indicate that they grow from edges between facets. Studies on reduction of the Co 3O4 nanoparticle precursors to the faceted pure cobalt catalysts were carried out using DTEM and in situ heating. Supported catalyst systems for methane reforming were studied using dark field scanning TEM to better understand sintering effects and the increased activity of Ni/Co catalysts supported by carbon nanotubes. Several novel electron microscopy techniques are described including annular dark field DTEM and a metaheuristic algorithm for solving the phase problem of coherent diffractive imaging. By inserting an annular dark field aperture into the back focal

  18. 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

  19. The Many Faces of Structure-Based Potentials: From Protein Folding Landscapes to Structural Characterization of Complex Biomolecules

    NASA Astrophysics Data System (ADS)

    Noel, Jeffrey K.; Onuchic, José N.

    Structural biology techniques, such as nuclear magnetic resonance (NMR), x-ray crystallography, and cryogenic electron microscopy (cryo-EM), have provided extraordinary insights into the details of the functional configurations of biomolecular systems. Recent advances in x-ray crystallography and cryo-EM have allowed for structural characterization of large molecular machines such as the ribosome, proteasome, and spliceosome. This deluge of structural data has been complemented by experimental techniques capable of probing dynamic information, such as Förster resonance energy transfer (FRET) and stopped flow spectrometry. While these experimental studies have provided tremendous insights into the dynamics of biomolecular systems, it is often difficult to combine the low resolution dynamical data with the high-resolution structural data into a consistent picture. Computer simulation of these biomolecular systems bridges static structural data with dynamic experiments at atomic resolution (Fig. 1).

  20. 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.

  1. 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

  2. Modeling and characterization of 2-D and 3-D textile structural composites

    SciTech Connect

    Yang, J.M.

    1986-01-01

    This dissertation studies the analytical modeling and experimental characterization of various two-dimensional and three-dimensional textile structure composites. In the analytical approach, various theoretical models were established to predict the stiffness, strength, nonlinear deformation, and failure behavior of triaxial woven-fabric composites, 3-D braided composites, and multilayer multidirectional warp knit fabric composites in polymer and metal matrices. The structure performance maps of various textile structural composites were also established, based upon these analytical methods. In the experimental approach, extensive mechanical testing and microstructural characterization were performed to investigate the thermomechanical properties and failure behavior of 3-D braided FP/Al composites. Results of this research will serve as the basis for assessing the potential of textile composites for structural applications.

  3. 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.

  4. 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.

  5. Potential and Limitations of the Modal Characterization of a Spacecraft Bus Structure by Means of Active Structure Elements

    NASA Technical Reports Server (NTRS)

    Grillenbeck, Anton M.; Dillinger, Stephan A.; Elliott, Kenny B.

    1998-01-01

    Theoretical and experimental studies have been performed to investigate the potential and limitations of the modal characterization of a typical spacecraft bus structure by means of active structure elements. The aim of these studies has been test and advance tools for performing an accurate on-orbit modal identification which may be characterized by the availability of a generally very limited test instrumentation, autonomous excitation capabilities by active structure elements and a zero-g environment. The NASA LARC CSI Evolutionary Testbed provided an excellent object for the experimental part of this study program. The main subjects of investigation were: (1) the selection of optimum excitation and measurement to unambiguously identify modes of interest; (2) the applicability of different types of excitation means with focus on active structure elements; and (3) the assessment of the modal identification potential of different types of excitation functions and modal analysis tools. Conventional as well as dedicated modal analysis tools were applied to determine modal parameters and mode shapes. The results will be presented and discussed based on orthogonality checks as well as on suitable indicators for the quality of the acquired modes with respect to modal purity. In particular, the suitability for modal analysis of the acquired frequency response functions as obtained by excitation with active structure elements will be demonstrated with the help of reciprocity checks. Finally, the results will be summarized in a procedure to perform an on-orbit modal identification, including an indication of limitation to be observed.

  6. Using the Structure-Function Linkage Database to Characterize Functional Domains in Enzymes

    PubMed Central

    Brown, Shoshana; Babbitt, Patricia

    2015-01-01

    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 protocol by which a user may query the database to predict the function of uncharacterized enzymes and to correct misannotated functional assignments. It 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. PMID:25501940

  7. 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.

  8. 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

  9. 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.

  10. Multiscale Structure of UXO Site Characterization: Spatial Estimation and Uncertainty Quantification

    SciTech Connect

    Ostrouchov, George; Doll, William E.; Beard, Les P.; Morris, Max D.; Wolf, Dennis A

    2009-01-01

    Unexploded ordnance (UXO) site characterization must consider both how the contamination is generated and how we observe that contamination. Within the generation and observation processes, dependence structures can be exploited at multiple scales. We describe a conceptual site characterization process, the dependence structures available at several scales, and consider their statistical estimation aspects. It is evident that most of the statistical methods that are needed to address the estimation problems are known but their application-specific implementation may not be available. We demonstrate estimation at one scale and propose a representation for site contamination intensity that takes full account of uncertainty, is flexible enough to answer regulatory requirements, and is a practical tool for managing detailed spatial site characterization and remediation. The representation is based on point process spatial estimation methods that require modern computational resources for practical application. These methods have provisions for including prior and covariate information.

  11. The impact of powder diffraction on the structural characterization of organic crystalline materials.

    PubMed

    Tremayne, Maryjane

    2004-12-15

    The bulk properties of organic crystalline materials depend on their molecular and crystal structures but, as many of these materials cannot be prepared in a suitable form for conventional single-crystal diffraction studies, structural characterization and rationalization of these properties must be obtained from powder diffraction data. The recent development of direct-space structure solution methods has enabled the study of a wide range of organic materials using powder diffraction data, many of structural complexity only made tractable by these advances in methodology. These direct-space methods are based on a number of global optimization techniques including Monte Carlo, simulated annealing, genetic algorithm and differential evolution approaches. In this article, the implementation and relative efficiency and reliability of these methods are discussed, and their impact on the structural study of organic materials is illustrated by examples of polymorphic systems, pharmaceutical, pigment and polypeptide structures and compounds used in the study of intermolecular networks.

  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. 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.

  14. 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.

  15. 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.

  16. Characterization of misfit dislocations in Si quantum well structures enabled by STEM based aberration correction.

    PubMed

    Batson, Philip E; Lagos, Maureen J

    2017-03-02

    The success of aberration correction techniques at the end of the 20th century came at a time of increasing need for atomic resolution imaging to better understand known structural defects that influence semiconductor device operation, and to advance the search for new structures and behavior that will form the basis for devices in the future. With this in mind, it is a pleasure to recognize the contributions of Ondrej Krivanek to the success of aberration correction techniques, and his extension of aberration techniques to EELS equipment that further promises to unite structural studies with characterization of behavior from meV to keV energies in the STEM.

  17. Scanning tunneling microscopy characterization of the geometric and electronic structure of hydrogen-terminated silicon surfaces

    NASA Technical Reports Server (NTRS)

    Kaiser, W. J.; Bell, L. D.; Hecht, M. H.; Grunthaner, F. J.

    1988-01-01

    Scanning tunneling microscopy (STM) methods are used to characterize hydrogen-terminated Si surfaces prepared by a novel method. The surface preparation method is used to expose the Si-SiO2 interface. STM images directly reveal the topographic structure of the Si-SiO2 interface. The dependence of interface topography on oxide preparation conditions observed by STM is compared to the results of conventional surface characterization methods. Also, the electronic structure of the hydrogen-terminated surface is studied by STM spectroscopy. The near-ideal electronic structure of this surface enables direct tunnel spectroscopy measurements of Schottky barrier phenomena. In addition, this method enables probing of semiconductor subsurface properties by STM.

  18. 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.

  19. 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.

  20. Characterization of Slosh Damping for Ortho-Grid and Iso-Grid Internal Tank Structures

    NASA Technical Reports Server (NTRS)

    Westra, Douglas G.; Sansone, Marco D.; Eberhart, Chad J.; West, Jeffrey S.

    2016-01-01

    Grid stiffened tank structures such as Ortho-Grid and Iso-Grid are widely used in cryogenic tanks for providing stiffening to the tank while reducing mass, compared to tank walls of constant cross-section. If the structure is internal to the tank, it will positively affect the fluid dynamic behavior of the liquid propellant, in regard to fluid slosh damping. As NASA and commercial companies endeavor to explore the solar system, vehicles will by necessity become more mass efficient, and design margin will be reduced where possible. Therefore, if the damping characteristics of the Ortho-Grid and Iso-Grid structure is understood, their positive damping effect can be taken into account in the systems design process. Historically, damping by internal structures has been characterized by rules of thumb and for Ortho-Grid, empirical design tools intended for slosh baffles of much larger cross-section have been used. There is little or no information available to characterize the slosh behavior of Iso-Grid internal structure. Therefore, to take advantage of these structures for their positive damping effects, there is much need for obtaining additional data and tools to characterize them. Recently, the NASA Marshall Space Flight Center conducted both sub-scale testing and computational fluid dynamics (CFD) simulations of slosh damping for Ortho-Grid and Iso-Grid tanks for cylindrical tanks containing water. Enhanced grid meshing techniques were applied to the geometrically detailed and complex Ortho-Grid and Iso-Grid structures. The Loci-STREAM CFD program with the Volume of Fluid Method module for tracking and locating the water-air fluid interface was used to conduct the simulations. The CFD simulations were validated with the test data and new empirical models for predicting damping and frequency of Ortho-Grid and Iso-Grid structures were generated.

  1. Characterization of long-gauge fiber optic sensors for structural identification

    NASA Astrophysics Data System (ADS)

    Li, Suzhen; Wu, Zhishen

    2005-05-01

    To monitor structural behavior of large-scale civil infrastructures such as long-span bridges, it requires direct and accurate measurement of "macroscopic" strains which are more representative of the deformation of entire structural element. On the other hand, quasi-distributed measurements are also supposed to serve the purpose to catch the characters of whole structure. In this regard, a novel packaging method for practical adaptation of long-gage FBG strain sensor in civil structures is proposed. After a series of tests including uniaxial tension and compression, bending, free-vibration and shaking table tests, the ability of the packaged FBG sensors fixed on different specimen for macro-strain measurements has been characterized by comparing with conventional foil strain gauges in both static and dynamic cases. Combined with the parametric identification method based on macro-stains, the applicability of quasi-distributed long-gage FBG sensors in structural parameter estimation and damage detection is discussed.

  2. Revised domain structure of ulvan lyase and characterization of the first ulvan binding domain

    PubMed Central

    Melcher, Rebecca L. J.; Neumann, Marten; Fuenzalida Werner, Juan Pablo; Gröhn, Franziska; Moerschbacher, Bruno M.

    2017-01-01

    Biomass waste products from green algae have recently been given new life, as these polysaccharides have potential applications in industry, agriculture, and medicine. One such polysaccharide group called ulvans displays many different, potentially useful properties that arise from their structural versatility. Hence, performing structural analyses on ulvan is crucial for future applications. However, chemical reaction–based analysis methods cannot fully characterize ulvan and tend to alter its structure. Thus, better methods require well-characterized ulvan-degrading enzymes. Therefore, we analysed a previously sequenced ulvan lyase (GenebankTM reference number JN104480) and characterized its domains. We suggest that the enzyme consists of a shorter than previously described catalytic domain, a newly identified substrate binding domain, and a C-terminal type 9 secretion system signal peptide. By separately expressing the two domains in E. coli, we confirmed that the binding domain is ulvan specific, having higher affinity for ulvan than most lectins for their ligands (affinity constant: 105 M−1). To our knowledge, this is the first description of an ulvan-binding domain. Overall, identifying this new binding domain is one step towards engineering ulvan enzymes that can be used to characterize ulvan, e.g. through enzymatic/mass spectrometric fingerprinting analyses, and help unlock its full potential. PMID:28327560

  3. New bismuth calcium oxysilicate with apatite structure: Synthesis and structural characterization

    SciTech Connect

    Uvarov, Vladimir; Shenawi-Khalil, Sanaa; Popov, Inna

    2010-07-15

    New bismuth calcium silicon oxide Ca{sub 4}Bi{sub 4.3}(SiO{sub 4})(HSiO{sub 4}){sub 5}O{sub 0.95}, with apatite structure has been synthesized. The structure was refined from powder X-ray diffraction data. The refinement revealed that the phase has P6{sub 3}/m (176) space group with unit cell parameters a=b=9.6090(7) A, c=7.0521(7) A, V=563.9 A{sup 3} and c/a=0.734. The R{sub wp} factor at Rietveld refinement was equal to 0.082. The synthesized phase has an unusual quantity of cation vacancies in a crystal lattice. Mechanisms of compensation of the excess charge of a lattice are considered and checked experimentally using the FT-IR spectroscopy, the thermal analysis and the XPS analysis. - Graphical abstract: The fragment Ca{sub 4}Bi{sub 4.3}(SiO{sub 4})(HSiO{sub 4}){sub 5}O{sub 0.95} structure along c-axis in polygonal mode.

  4. 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.

  5. 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.

  6. Relations between structural parameters and adsorption characterization of templated nanoporous materials with cubic symmetry

    SciTech Connect

    Ravikovitch, P.I.; Neimark, A.V.

    2000-03-21

    A systematic approach is proposed to structural characterization of templated nanoporous materials with cubic symmetry by gas adsorption. The authors hypothesize that regular structures of these materials can be described in terms of triply periodic minimal surfaces (TPMS), similarly to bicontinuous mesophases observed in oil-water, lipid, block copolymer, and other amphiphilic systems. The authors relate topological characteristics of TPMS to the pore structure parameters evaluated from adsorption measurements, such as the specific surface area, pore volume, mean pore size, and also pore wall thickness. The relations obtained can be used for discrimination of possible TPMS morphologies. The method developed is used for characterization of newly synthesized MCM-48 mesoporous materials by low-temperature nitrogen adsorption. They show that adsorption data fully support the minimal gyroid model of MCM-48 structure (Ia3d space group) established earlier by the X-ray diffraction (XRD) and transmission electron microscopy studies. The mean pore size of MCM-48 can be accurately described by the hydraulic diameter calculated from the capillary condensation region of nitrogen adsorption isotherms by the nonlocal density functional theory method. Moreover, the adsorption method allows one to estimate the pore wall thickness, which cannot be done by XRD. For a series of high-quality MCM-48 materials reported recently in the literature, the calculated mean wall thickness varied from 0.8 to 1.2 nm. The adsorption method developed is recommended as a complement to X-ray diffraction and electron microscopy techniques for characterization of nanoporous materials.

  7. 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.

  8. Structural and Biochemical Characterization of AidC, a Quorum-Quenching Lactonase with Atypical Selectivity.

    PubMed

    Mascarenhas, Romila; Thomas, Pei W; Wu, Chun-Xiang; Nocek, Boguslaw P; Hoang, Quyen Q; Liu, Dali; Fast, Walter

    2015-07-21

    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 × 10(6) 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. 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. Implications for the catalytic mechanism of AHL lactonases are discussed.

  9. Structural and functional characterization of the monomeric U-box domain from E4B†

    PubMed Central

    Nordquist, Kyle A.; Dimitrova, Yoana N.; Brzovic, Peter S.; Ridenour, Whitney B.; Munro, Kim A.; Soss, Sarah E.; Caprioli, Richard M.; Klevit, Rachel E.; Chazin, Walter J.

    2009-01-01

    Substantial evidence has accumulated indicating a significant role for oligomerization in the function of E3 ubiquitin ligases. Among the many characterized E3 ligases, the yeast U-box protein Ufd2 and its mammalian homolog E4B appear to be unique in functioning as monomers. An E4B U-box domain construct (E4BU) has been sub-cloned, over-expressed in E. Coli and purified, which enabled determination of a high resolution NMR solution structure and detailed biophysical analysis. E4BU is a stable monomeric protein that folds into the same structure observed for other structurally characterized U-box domains, all of which are homodimers. Multiple sequence alignment combined with comparative structural analysis reveals substitutions in the sequence that inhibit dimerization. The interaction between E4BU and the E2 conjugating enzyme UbcH5c has been mapped using NMR and this data has been used to generate a structural model for the complex. The E2 binding site is found to be similar to that observed for dimeric U-box and RING domain E3 ligases. Despite the inability to dimerize, E4BU was found to be active in a standard autoubiquitination assay. The structure of E4BU and its ability to function as a monomer are discussed in light of the ubiquitous observation of U-box and RING domain oligomerization. PMID:20017557

  10. Partitioning and characterization of high speed adder structures in deep-submicron technologies

    NASA Astrophysics Data System (ADS)

    Estrada, Adrián; Sassaw, Gashaw; Jiménez, Carlos J.; Valencia, Manuel

    2007-05-01

    The availability of higher performance (in area, time and power consumption) and greater precision binary adders is a constant requirement in digital systems. Consequently, the design and characterization of adders and, most of all, their adaptation to the requisites of present-day deep-submicron technologies, are today still issues of concern. The binary adder structures in deep-submicron technologies must be revised to achieve the best balance between the number of bits in the adder and its delay, area and power consumption. It is therefore very important to make an effort to carefully optimize adder structures, thus obtaining improvements in digital systems. This communication presents the optimization of adder structures for implementations in deep-submicron technologies through their partitioning into blocks. This partitioning consists of dividing the number of input bits to the adder into several subsets of bits that will constitute the inputs to several adder structures of the same or of different types. The structures used to accomplish this study range from the more traditional types, such as the carry look ahead adder, the ripple carry adder or the carry select adder, to more innovative kinds, like the parallel prefix adders of the type proposed by Brent-Kung, Han-Carlson, Kogge-Stone or Ladner-Fischer. The analyses carried out allow the characterization of structures implemented in deep-submicron technologies for area, delay and power consumption parameters.

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

    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.

  12. Structural characterization of nonactive site, TrkA-selective kinase inhibitors

    SciTech Connect

    Su, Hua-Poo; Rickert, Keith; Burlein, Christine; Narayan, Kartik; Bukhtiyarova, Marina; Hurzy, Danielle M.; Stump, Craig A.; Zhang, Xufang; Reid, John; Krasowska-Zoladek, Alicja; Tummala, Srivanya; Shipman, Jennifer M.; Kornienko, Maria; Lemaire, Peter A.; Krosky, Daniel; Heller, Amanda; Achab, Abdelghani; Chamberlin, Chad; Saradjian, Peter; Sauvagnat, Berengere; Yang, Xianshu; Ziebell, Michael R.; Nickbarg, Elliott; Sanders, John M.; Bilodeau, Mark T.; Carroll, Steven S.; Lumb, Kevin J.; Soisson, Stephen M.; Henze, Darrell A.; Cooke, Andrew J.

    2016-12-30

    Current therapies for chronic pain can have insufficient efficacy and lead to side effects, necessitating research of novel targets against pain. Although originally identified as an oncogene, Tropomyosin-related kinase A (TrkA) is linked to pain and elevated levels of NGF (the ligand for TrkA) are associated with chronic pain. Antibodies that block TrkA interaction with its ligand, NGF, are in clinical trials for pain relief. Here, we describe the identification of TrkA-specific inhibitors and the structural basis for their selectivity over other Trk family kinases. The X-ray structures reveal a binding site outside the kinase active site that uses residues from the kinase domain and the juxtamembrane region. Three modes of binding with the juxtamembrane region are characterized through a series of ligand-bound complexes. The structures indicate a critical pharmacophore on the compounds that leads to the distinct binding modes. The mode of interaction can allow TrkA selectivity over TrkB and TrkC or promiscuous, pan-Trk inhibition. This finding highlights the difficulty in characterizing the structure-activity relationship of a chemical series in the absence of structural information because of substantial differences in the interacting residues. These structures illustrate the flexibility of binding to sequences outside of—but adjacent to—the kinase domain of TrkA. This knowledge allows development of compounds with specificity for TrkA or the family of Trk proteins.

  13. 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

  14. Characterization, Modeling, and Failure Analysis of Composite Structure Materials under Static and Dynamic Loading

    NASA Astrophysics Data System (ADS)

    Werner, Brian Thomas

    Composite structures have long been used in many industries where it is advantageous to reduce weight while maintaining high stiffness and strength. Composites can now be found in an ever broadening range of applications: sporting equipment, automobiles, marine and aerospace structures, and energy production. These structures are typically sandwich panels composed of fiber reinforced polymer composite (FRPC) facesheets which provide the stiffness and the strength and a low density polymeric foam core that adds bending rigidity with little additional weight. The expanding use of composite structures exposes them to high energy, high velocity dynamic loadings which produce multi-axial dynamic states of stress. This circumstance can present quite a challenge to designers, as composite structures are highly anisotropic and display properties that are sensitive to loading rates. Computer codes are continually in development to assist designers in the creation of safe, efficient structures. While the design of an optimal composite structure is more complex, engineers can take advantage of the effect of enhanced energy dissipation displayed by a composite when loaded at high strain rates. In order to build and verify effective computer codes, the underlying assumptions must be verified by laboratory experiments. Many of these codes look to use a micromechanical approach to determine the response of the structure. For this, the material properties of the constituent materials must be verified, three-dimensional constitutive laws must be developed, and failure of these materials must be investigated under static and dynamic loading conditions. In this study, simple models are sought not only to ease their implementation into such codes, but to allow for efficient characterization of new materials that may be developed. Characterization of composite materials and sandwich structures is a costly, time intensive process. A constituent based design approach evaluates potential

  15. 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.

  16. Complex layered materials and periodic electromagnetic band-gap structures: Concepts, characterizations, and applications

    NASA Astrophysics Data System (ADS)

    Mosallaei, Hossein

    The main objective of this dissertation is to characterize and create insight into the electromagnetic performances of two classes of composite structures, namely, complex multi-layered media and periodic Electromagnetic Band-Gap (EBG) structures. The advanced and diversified computational techniques are applied to obtain their unique propagation characteristics and integrate the results into some novel applications. In the first part of this dissertation, the vector wave solution of Maxwell's equations is integrated with the Genetic Algorithm (GA) optimization method to provide a powerful technique for characterizing multi-layered materials, and obtaining their optimal designs. The developed method is successfully applied to determine the optimal composite coatings for Radar Cross Section (RCS) reduction of canonical structures. Both monostatic and bistatic scatterings are explored. A GA with hybrid planar/curved surface implementation is also introduced to efficiently obtain the optimal absorbing materials for curved structures. Furthermore, design optimization of the non-uniform Luneburg and 2-shell spherical lens antennas utilizing modal solution/GA-adaptive-cost function is presented. The lens antennas are effectively optimized for both high gain and suppressed grating lobes. The second part demonstrates the development of an advanced computational engine, which accurately computes the broadband characteristics of challenging periodic electromagnetic band-gap structures. This method utilizes the Finite Difference Time Domain (FDTD) technique with Periodic Boundary Condition/Perfectly Matched Layer (PBC/PML), which is efficiently integrated with the Prony scheme. The computational technique is successfully applied to characterize and present the unique propagation performances of different classes of periodic structures such as Frequency Selective Surfaces (FSS), Photonic Band-Gap (PBG) materials, and Left-Handed (LH) composite media. The results are

  17. Synthesis and structural characterization of hydrolysis products within the uranyl iminodiacetate and malate systems.

    PubMed

    Unruh, Daniel K; Gojdas, Kyle; Flores, Erin; Libo, Anna; Forbes, Tori Z

    2013-09-03

    The interplay of hydrolysis and chelation by organic ligands results in the formation of novel uranium species in aqueous solutions. Many of these molecular complexes have been identified by spectroscopic and potentiometric techniques, but a detailed structural understanding of these species is lacking. Identification of possible uranyl hydrolysis products in the presence of organic functional groups has been achieved by the crystallization of molecular species into a solid-state compound, followed by structural and chemical characterization of the material. The structures of three novel molecular complexes containing either iminodiacetate (ida) (Na3[(UO2)3(OH)3(ida)3]·8H2O (1)) or malate (mal) (K(pip)2[(UO2)3O(mal)3]·6H2O (2a) (pip = C4N2H12), (2b) (pip)3[(UO2)3O(mal)3]·H2O, and (pip)6[(UO2)11(O)4(OH)4(mal)6(CO3)2]·23H2O (3)) ligands have been determined by single-crystal X-ray diffraction and have been chemically characterized by IR, Raman, and NMR spectroscopies. A major structural component in compounds 1 and 2 is a trimeric 3:3 uranyl ida or mal species, but different bridging groups between the metal centers create variations in the structural topologies of the molecular units. Compound 3 contains a large polynuclear cluster with 11 U atoms, which is composed of trimeric and pentameric building units chelated by mal ligands and linked through hydroxyl groups and carbonate anions. The characterized compounds represent novel structural topologies for U(6+) hydrolysis products that may be important molecular species in near-neutral aqueous systems.

  18. 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.

  19. Electrodeposition and Characterization of Nickel, Iron, Copper Thin Films and the Creation of Nanoporous Structures

    NASA Astrophysics Data System (ADS)

    Yarranton, Jonathan; Hampton, Jennifer

    2013-03-01

    There has been much research in creating nanoporous platinum or gold thin films for catalysis, but there has not been as much work done with other, less noble metals. This research explored the deposition of nickel, iron, and copper ternary alloys using controlled potential electrolysis (CPE) and the selective removal of the copper with DC potential amperometry (DCPA) and linear sweep voltammetry (LSV) to create nanoporous structures. These structures have the advantage of increased surface area creating more efficient catalysts. All films were characterized before and after dealloying using scanning electron microscopy (SEM) and energy dispersive x-ray spectroscopy (EDS) for composition. The roughness of each of the films was characterized by the capacitance of the film, with higher capacitances indicating a higher electrochemical surface area. This material is based upon work supported by the National Science Foundation under RUI Grant DMR-1104725, MRI Grant CHE-0959282, and ARI grant PHY-0963317.

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

    NASA Technical Reports Server (NTRS)

    Vary, A.; Klima, S. J.

    1986-01-01

    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 flow 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. Synthesis, structural and electrochemical characterization of benzimidazole compounds exhibiting a smectic C liquid crystal phase

    NASA Astrophysics Data System (ADS)

    Wei, Bingzhuo; Tan, Shuai; Liang, Ting; Cao, Siyu; Wu, Yong

    2017-04-01

    Mesomorphic benzimidazole compounds were prepared from a biphenyl benzoate based precursor by substitution reaction of alkyl bromide with 2-mercaptobenzimidazole. Molecular structures of the benzimidazole compounds were characterized by nuclear magnetic resonance (NMR), Fourier transform infrared (FT-IR) spectroscopy and elemental analysis. Differential scanning calorimetry (DSC) measurements and polarizing optical microscopic (POM) observations revealed that the benzimidazole compounds exhibited a thermotropic smectic C (SC) phase. Temperature dependent X-ray diffraction (XRD) patterns suggested a tilted bilayer smectic structure in which intermolecular hydrogen bonds between benzimidazole moieties formed lamellar arrangement. Electrochemical impedance spectroscopy (EIS) characterization suggested that the SC phase favored anhydrous proton conduction of the benzimidazole compounds and the proton conductivities showed an Arrhenius temperature dependence.

  2. Electrical and structural characterization of Fe implanted GaInP

    NASA Astrophysics Data System (ADS)

    Fraboni, B.; Cesca, T.; Gasparotto, A.; Mattei, G.; Boscherini, F.; Impellizzeri, G.; Priolo, F.; Jakomin, R.; Longo, M.; Tarricone, L.

    2007-12-01

    We have investigated the structural and electrical properties of GaInP/GaAs epilayers that we have implanted with Fe atoms (190 keV) to produce a shallow high resistivity layer. SIMS, PIXE-channeling and EXAFS were used to provide a structural characterization. Current-voltage analyses as a function of temperature indicate the activation of an efficient and stable electrical compensation process, that we have ascribed to the interplay between a deep donor and a deep acceptor, located at EC-0.50 eV and EV+0.74 eV, respectively. We have focused our attention on the latter deep level, attributed to the Fe 2+/3+ related acceptor trap, that we have directly identified and characterized by spectral photocurrent analyses and by capacitance transient spectroscopy carried out under below band gap illumination that stimulated the direct emission/trapping of carriers from the deep trap.

  3. 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.

  4. 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

  5. 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.

  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. Structural Characterization of a Mo/Ru/Si Extreme Ultraviolet (EUV) Reflector by Optical Modeling

    NASA Astrophysics Data System (ADS)

    Kang, In-Yong; Kim, Tae Geun; Lee, Seung Yoon; Ahn, Jinho; Chung, Yong-Chae

    2004-06-01

    The performance of a multilayer extreme ultraviolet (EUV) reflector has a direct bearing on process throughput and the cost of new technology. Using measured data from an experimentally manufactured reflector, we intend, in this work, to show that the reflectivity of the Bragg reflector can be characterized by using structural parameters such as the d-spacing, density, thicknesses of the interdiffusion layers and oxidation layer. This quantitative analysis of the reflectivity derived from the structural parameters can be utilized to optimize the optical properties of the existing Mo/Ru/Si system and to provide fundamental insights into the science involved in a Bragg EUV reflector.

  8. 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.

  9. Using the Structure-function Linkage Database to characterize functional domains in enzymes.

    PubMed

    Brown, Shoshana; Babbitt, Patricia

    2006-03-01

    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 newly sequenced enzymes and to correct misannotated functional assignments for enzymes currently in public databases. It 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.

  10. 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.

  11. 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.

  12. 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.

  13. Fabrication and characterization of materials and structures for hybrid organic-inorganic photonics

    NASA Astrophysics Data System (ADS)

    Haško, Daniel; Chovan, Jozef; Uherek, František

    2017-03-01

    Hybrid organic-inorganic integrated photonics integrate the organic material, as a part of active layer, with inorganic structure, and it is the organic component that extends the functionalities as compared to inorganic photonics. This paper presents the results of fabrication and characterization of inorganic and organic layers, as well as of hybrid organic-inorganic structures. Inorganic oxide and nitride materials and structures were grown using plasma enhanced chemical vapor deposition. As a substrate for tested organic layers and for preparation of multilayer structures, commercially available SiO2 created by thermal oxidation on Si was used. The hybrid organic-inorganic structures were prepared by spin coating of organic materials on SiO2/Si inorganic structures. As the basic photonics devices, the testing strip inorganic and organic waveguides were fabricated using reactive ion etching. The shape of fabricated testing waveguides was trapezoidal and etched structures were able to guide the radiation. The presented technology enabled to prepare hybrid organic-inorganic structures of comparable dimensions and shape. The fabricated waveguides dimensions and shape will be used for optimisation and design of new lithographic mask to prepare photonic components with required characteristics.

  14. Multi-Site Fatigue Testing and Characterization of Fuselage Panels from Aging Aircraft Structure

    DTIC Science & Technology

    2013-06-07

    Multi-site fatigue damage is a common problem in the riveted lap joint structure of aging aircraft. Modeling and characterization of such damage is...an especially daunting task. In this effort we present the results from fatigue tests which were performed on fuselage lap joints extracted from...in the lap joint . Some spot welded lap joint panels were also tested during the larger program; however, only the results from mechanically fastened

  15. Determination of transport properties in chromium disilicide nanowires via combined thermoelectric and structural characterizations.

    PubMed

    Zhou, Feng; Szczech, Jeannine; Pettes, Michael T; Moore, Arden L; Jin, Song; Shi, Li

    2007-06-01

    The Seebeck coefficient, electrical conductivity, and thermal conductivity of individual chromium disilicide nanowires were characterized using a suspended microdevice and correlated with the crystal structure and growth direction obtained by transmission electron microscopy on the same nanowires. The obtained thermoelectric figure of merit of the nanowires was comparable to the bulk values. We show that combined Seebeck coefficient and electrical conductivity measurements provide an effective approach to probing the Fermi Level, carrier concentration and mobility in nanowires.

  16. 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

  17. 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

  18. 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

  19. 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.

  20. Quantitative Characterization of Local Protein Solvation To Predict Solvent Effects on Protein Structure

    PubMed Central

    Vagenende, Vincent; Trout, Bernhardt L.

    2012-01-01

    Characterization of solvent preferences of proteins is essential to the understanding of solvent effects on protein structure and stability. Although it is generally believed that solvent preferences at distinct loci of a protein surface may differ, quantitative characterization of local protein solvation has remained elusive. In this study, we show that local solvation preferences can be quantified over the entire protein surface from extended molecular dynamics simulations. By subjecting microsecond trajectories of two proteins (lysozyme and antibody fragment D1.3) in 4 M glycerol to rigorous statistical analyses, solvent preferences of individual protein residues are quantified by local preferential interaction coefficients. Local solvent preferences for glycerol vary widely from residue to residue and may change as a result of protein side-chain motions that are slower than the longest intrinsic solvation timescale of ∼10 ns. Differences of local solvent preferences between distinct protein side-chain conformations predict solvent effects on local protein structure in good agreement with experiment. This study extends the application scope of preferential interaction theory and enables molecular understanding of solvent effects on protein structure through comprehensive characterization of local protein solvation. PMID:22995508

  1. 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

  2. The new metal complex templated polyoxoborate(s) (POB(s)) structures. Synthesis, structural characterization, and hydrogen storage capacities

    NASA Astrophysics Data System (ADS)

    Ali Köse, Dursun; Yurdakul, Ömer; Şahin, Onur; Öztürk, Zeynel

    2017-04-01

    The polyoxoborate(s) (POB(s)) structures, including a neutral ligand-metal complex compound as a template, were synthesized and the structural characterizations were performed via single crystal X-ray diffraction, FTIR, 11B-NMR, solid state UV-Vis spectroscopy, SEM and elemental analysis methods. Moreover, the stabilization features were determined via TGA/DTA method. In addition, nitrogen and hydrogen adsorption measurements provided the realization to determine the pore size distribution, BET surface area, and hydrogen storage capacities. The molecular formulas of compounds were estimated as [Cu(C12H8N2)2(C2H3O2)][B5O6(OH)4]·2H3BO3·H2O (I) and [Ni(C12H8N2)2(H2O)2]·(B7O9(OH)5)·5H2O (II) and the existence of two different POB(s) structures as pentaborate (B5O6(OH)4) and heptaborate (B7O9(OH)5) within the compounds were observed. At last, it was found that the both structures have micro and mesoporosity with 0.407 and 1.480 m2/g BET surface areas, for the compound I and II, respectively. Moreover, within the same conditions, compound II could uptake 0.19 wt% hydrogen at 77 K and at the relative pressure of 1 while compound II uptakes 0.035 wt% hydrogen.

  3. 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.

  4. 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.

  5. 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

  6. Native top-down mass spectrometry for the structural characterization of human hemoglobin

    SciTech Connect

    Zhang, Jiang; Malmirchegini, G. Reza; Clubb, Robert T.; Loo, Joseph A.

    2015-06-09

    Native mass spectrometry (MS) has become an invaluable tool for the characterization of proteins and non-covalent protein complexes under near physiological solution conditions. Here we report the structural characterization of human hemoglobin (Hb), a 64 kDa oxygen-transporting protein complex, by high resolution native top-down mass spectrometry using electrospray ionization (ESI) and a 15-Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Native MS preserves the non-covalent interactions between the globin subunits, and electron capture dissociation (ECD) produces fragments directly from the intact Hb complex without dissociating the subunits. Using activated ion ECD, we observe the gradual unfolding process of the Hb complex in the gas phase. Without protein ion activation, the native Hb shows very limited ECD fragmentation from the N-termini, suggesting a tightly packed structure of the native complex and therefore low fragmentation efficiency. Precursor ion activation allows steady increase of N-terminal fragment ions, while the C-terminal fragments remain limited (38 c ions and 4 z ions on the α chain; 36 c ions and 2 z ions on the β chain). This ECD fragmentation pattern suggests that upon activation, the Hb complex starts to unfold from the N-termini of both subunits, whereas the C-terminal regions and therefore the potential regions involved in the subunit binding interactions remain intact. ECD-MS of the Hb dimer show similar fragmentation patterns as the Hb tetramer, providing further evidence for the hypothesized unfolding process of the Hb complex in the gas phase. Native top-down ECD-MS allows efficient probing of the Hb complex structure and the subunit binding interactions in the gas phase. Finally, it may provide a fast and effective means to probe the structure of novel protein complexes that are intractable to traditional structural characterization tools.

  7. Native top-down mass spectrometry for the structural characterization of human hemoglobin

    DOE PAGES

    Zhang, Jiang; Malmirchegini, G. Reza; Clubb, Robert T.; ...

    2015-06-09

    Native mass spectrometry (MS) has become an invaluable tool for the characterization of proteins and non-covalent protein complexes under near physiological solution conditions. Here we report the structural characterization of human hemoglobin (Hb), a 64 kDa oxygen-transporting protein complex, by high resolution native top-down mass spectrometry using electrospray ionization (ESI) and a 15-Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Native MS preserves the non-covalent interactions between the globin subunits, and electron capture dissociation (ECD) produces fragments directly from the intact Hb complex without dissociating the subunits. Using activated ion ECD, we observe the gradual unfolding process of themore » Hb complex in the gas phase. Without protein ion activation, the native Hb shows very limited ECD fragmentation from the N-termini, suggesting a tightly packed structure of the native complex and therefore low fragmentation efficiency. Precursor ion activation allows steady increase of N-terminal fragment ions, while the C-terminal fragments remain limited (38 c ions and 4 z ions on the α chain; 36 c ions and 2 z ions on the β chain). This ECD fragmentation pattern suggests that upon activation, the Hb complex starts to unfold from the N-termini of both subunits, whereas the C-terminal regions and therefore the potential regions involved in the subunit binding interactions remain intact. ECD-MS of the Hb dimer show similar fragmentation patterns as the Hb tetramer, providing further evidence for the hypothesized unfolding process of the Hb complex in the gas phase. Native top-down ECD-MS allows efficient probing of the Hb complex structure and the subunit binding interactions in the gas phase. Finally, it may provide a fast and effective means to probe the structure of novel protein complexes that are intractable to traditional structural characterization tools.« less

  8. Structural Characterization of Native Proteins and Protein Complexes by Electron Ionization Dissociation-Mass Spectrometry.

    PubMed

    Li, Huilin; Sheng, Yuewei; McGee, William; Cammarata, Michael; Holden, Dustin; Loo, Joseph A

    2017-03-07

    Mass spectrometry (MS) has played an increasingly important role in the identification and structural and functional characterization of proteins. In particular, the use of tandem mass spectrometry has afforded one of the most versatile methods to acquire structural information for proteins and protein complexes. The unique nature of electron capture dissociation (ECD) for cleaving protein backbone bonds while preserving noncovalent interactions has made it especially suitable for the study of native protein structures. However, the intra- and intermolecular interactions stabilized by hydrogen bonds and salt bridges can hinder the separation of fragments even with preactivation, which has become particularly problematic for the study of large macromolecular proteins and protein complexes. Here, we describe the capabilities of another activation method, 30 eV electron ionization dissociation (EID), for the top-down MS characterization of native protein-ligand and protein-protein complexes. Rich structural information that cannot be delivered by ECD can be generated by EID. EID allowed for the comparison of the gas-phase and the solution-phase structural stability and unfolding process of human carbonic anhydrase I (HCA-I). In addition, the EID fragmentation patterns reflect the structural similarities and differences among apo-, Zn-, and Cu,Zn-superoxide dismutase (SOD1) dimers. In particular, the structural changes due to Cu-binding and a point mutation (G41D) were revealed by EID-MS. The performance of EID was also compared to that of 193 nm ultraviolet photodissociation (UVPD), which allowed us to explore their qualitative similarities and differences as potential valuable tools for the MS study of native proteins and protein complexes.

  9. Structural and biochemical characterizations of an intramolecular tandem coiled coil protein.

    PubMed

    Shin, Donghyuk; Kim, Gwanho; Kim, Gyuhee; Zheng, Xu; Kim, Yang-Gyun; Lee, Sangho

    2014-12-12

    Coiled coil has served as an excellent model system for studying protein folding and developing protein-based biomaterials. Most designed coiled coils function as oligomers, namely intermolecular coiled coils. However, less is known about structural and biochemical behavior of intramolecular coiled coils where coiled coil domains are covalently linked in one polypeptide. Here we prepare a protein which harbors three coiled coil domains with two short linkers, termed intramolecular tandem coiled coil (ITCC) and characterize its structural and biochemical behavior in solution. ITCC consists of three coiled coil domains whose sequences are derived from Coil-Ser and its domain swapped dimer. Modifications include positioning E (Glu) residue at "e" and K (Lys) at "g" positions throughout heptad repeats to enhance ionic interaction among its constituent coiled coil domains. Molecular modeling of ITCC suggests a compact triple helical bundle structure with the second and the third coiled coil domains forming a canonical coiled coil. ITCC exists as a mixture of monomeric and dimeric species in solution. Small-angle X-ray scattering reveals ellipsoidal molecular envelopes for both dimeric and monomeric ITCC in solution. The theoretically modeled structures of ITCC dock well into the envelopes of both species. Higher ionic strength shifts the equilibrium into monomer with apparently more compact structure while secondary structure remains unchanged. Taken together, our results suggest that our designed ITCC is predominantly monomeric structure through the enhanced ionic interactions, and its conformation is affected by the concentration of ionic species in the buffer.

  10. 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.

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

    PubMed

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

    2014-07-02

    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.

  12. 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

  13. Structural and biochemical characterization of engineered tissue using FTIR spectroscopic imaging: melanoma progression as an example

    NASA Astrophysics Data System (ADS)

    Bhargava, Rohit; Kong, Rong

    2008-02-01

    Engineered tissue represents a convenient path to providing models for imaging and disease progression. The use of these models or phantoms is becoming increasingly prevalent. While structural characterization of these systems is well-documented, a combination of biochemical and structural knowledge is often helpful. Fourier transform infrared (FTIR) spectroscopic imaging is a rapidly emerging technique that combines the molecular selectivity of spectroscopy with the spatial specificity of optical microscopy. Here, we report on the application of FTIR spectroscopic for analysis of a melanoma model in engineered skin. We first characterize the biochemical properties, consistency and spectral changes in different layers of growing skin. Results provide simple indices for monitoring tissue consistency and reproducibility as a function of time. Second, we introduce malignant melanocytes to simulate tumor formation and growth. Both cellular changes associated with tumor formation and growth can be observed. FTIR images indicate holistic chemical changes during the tumor growth, allowing for the development of automated pathology protocols. FTIR imaging being non-destructive, further, samples remain entirely compatible with downstream tissue processing or staining. We specifically examined the correlation of structural changes, molecular content and reproducibility of the model systems. The development of analysis, integrating spectroscopy, imaging and computation will allow for quality control and standardization of both the structural and biochemical properties of tissue phantoms.

  14. Biophysical characterization of recombinant proteins: A key to higher structural genomics success

    PubMed Central

    Vedadi, Masoud; Arrowsmith, Cheryl H.; Allali-Hassani, Abdellah; Senisterra, Guillermo; Wasney, Gregory A.

    2010-01-01

    Hundreds of genomes have been successfully sequenced to date, and the data are publicly available. At the same time, the advances in large-scale expression and purification of recombinant proteins have paved the way for structural genomics efforts. Frequently, however, little is known about newly expressed proteins calling for large-scale protein characterization to better understand their biochemical roles and to enable structure–function relationship studies. In the Structural Genomics Consortium (SGC), we have established a platform to characterize large numbers of purified proteins. This includes screening for ligands, enzyme assays, peptide arrays and peptide displacement in a 384-well format. In this review, we describe this platform in more detail and report on how our approach significantly increases the success rate for structure determination. Coupled with high-resolution X-ray crystallography and structure-guided methods, this platform can also be used toward the development of chemical probes through screening families of proteins against a variety of chemical series and focused chemical libraries. PMID:20466062

  15. 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.

  16. Structural characterization, sulfation and antitumor activity of a polysaccharide fraction from Cyclina sinensis.

    PubMed

    Jiang, Changxing; Xiong, Qingping; Li, Songlin; Zhao, Xirong; Zeng, Xiaoxiong

    2015-01-22

    In the present study, we investigated the preliminary structure, sulfation and antitumor activity of a polysaccharide fraction from Cyclina sinensis (CSPS-1). Results of structural characterization showed that the backbone chain of CSPS-1 was composed of glucose linked by α-(1→4) glycosidic bond, and the branch chain was attached to backbone chain by (1→6) glycosidic bond. CSPS-1 was sulfated by chlorosulfonic acid-pyridine method under different modification conditions according to the orthogonal test L9(3(4)), affording nine sulfated polysaccharides (CSPS-1-S). The optimal sulfation conditions for CSPS-1 were reaction temperature of 65°C, reaction time of 2h and chlorosulfonic acid-pyridine ratio of 1:4. Structural analysis revealed that sulfation had occurred at position of C-6 in CSPS-1. In addition, CSPS-1-S exhibited significantly higher inhibitory activity in vitro against human gastric cancer BGC-823 cells.

  17. 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.

  18. Recent advances in endophytic exopolysaccharides: Production, structural characterization, physiological role and biological activity.

    PubMed

    Liu, Jun; Wang, Xingchi; Pu, Huimin; Liu, Shuang; Kan, Juan; Jin, Changhai

    2017-02-10

    Endophytes are microorganisms that colonize living, internal tissues of plants without causing any immediate, overt negative effects. In recent years, both endophytic bacteria and fungi have been demonstrated to be excellent exopolysaccharides (EPS) producers. This review focuses on the recent advances in EPS produced by endophytes, including its production, isolation and purification, structural characterization, physiological role and biological activity. In general, EPS production is influenced by media components and cultivation conditions. The structures of purified EPS range from linear homopolysaccharides to highly branched heteropolysaccharides. These structurally novel EPS not only play important roles in plant-endophyte interactions; but also exhibit several biological functions, such as antioxidant, antitumor, anti-inflammatory, anti-allergic and prebiotic activities. In order to utilize endophytic EPS on an industrial scale, both yield and productivity enhancement strategies are required at several levels. Besides, the exact mechanisms on the physiological roles and biological functions of EPS should be elucidated in future.

  19. Structural characterization of poly(amino)ester dendrimers and related impurities by electrospray tandem mass spectrometry.

    PubMed

    Tintaru, Aura; Monnier, Valérie; Bouillon, Camille; Giordanengo, Rémi; Quéléver, Gilles; Peng, Ling; Charles, Laurence

    2010-08-15

    An acid-terminated poly(amino)ester dendrimer was studied by electrospray ionization tandem mass spectrometry to establish its fragmentation pathways, with the aim of using them to investigate the structure of any defective molecules generated during the dendrimer synthesis. This poly(amino)ester dendrimer could be ionized in both polarities but the most structurally relevant dissociation pathways were found from the deprotonated molecule in negative ion mode. The dissociation pattern of this dendrimer is fully described and supported by accurate mass measurements. The main dissociation reactions of the negatively charged polyacidic dendrimer were shown to consist of (i) the release of carbon dioxide and ethene within a branch, which proceeds as many times as intact neutral branches are available; and (ii) the elimination of an entire dendrimer arm. Monitoring the occurrence of these reactions together with any deviation from these two main routes allowed six major dendritic impurities to be structurally characterized.

  20. 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.

  1. 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.

  2. 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.

  3. Characterization of the crystalline structure of cellulose using static and dynamic FT-IR spectroscopy.

    PubMed

    Akerholm, Margaretha; Hinterstoisser, Barbara; Salmén, Lennart

    2004-02-25

    The cellulose structure is a factor of major importance for the strength properties of wood pulp fibers. The ability to characterize small differences in the crystalline structures of cellulose from fibers of different origins is thus highly important. In this work, dynamic FT-IR spectroscopy has been further explored as a method sensitive to cellulose structure variations. Using a model system of two different celluloses, the relation between spectral information and the relative cellulose Ialpha content was investigated. This relation was then used to determine the relative cellulose Ialpha content in different pulps. The estimated cellulose I allomorph compositions were found to be reasonable for both unbleached and bleached chemical pulps. In addition, it was found that the dynamic FT-IR spectroscopy technique had the potential to indicate possible correlation field splitting peaks of cellulose Ibeta.

  4. Synthesis, structural characterization and magnetic behaviour of a family of [CoLn] butterfly compounds.

    PubMed

    Funes, Alejandro V; Carrella, Luca; Rechkemmer, Yvonne; van Slageren, Joris; Rentschler, Eva; Alborés, Pablo

    2017-03-07

    We have successfully prepared and structurally characterized a family of butterfly-like [CoLn] complexes where all magnetic properties are due to the Ln(iii) ions. The complexes with Ln = Tb(1), Dy(2), Ho(3), Er(4) and Yb(5) are iso-structural. An exception is the complex with Ln = Gd(6) which strings in a one dimensional chain. The structural similarity together with the high tendency of the crystallites to align under an applied magnetic field allowed an overall DC magnetic data treatment to extract phenomenological crystal field parameters and hence to determine the ground state multiplet energy level splitting. The Dy(iii) member is the only one showing slow relaxation of magnetization under zero DC applied field, while all the others need a small DC applied field.

  5. 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

  6. 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.

  7. Structural and biochemical characterization of AidC, a quorum-quenching lactonase with atypical selectivity

    DOE PAGES

    Mascarenhas, Romila; Thomas, Pei W.; Wu, Chun -Xiang; ...

    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

  8. 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.

  9. 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.

  10. 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.

  11. Structural Characterization of Phase Separation in Fe-Cr: A Current Comparison of Experimental Methods

    NASA Astrophysics Data System (ADS)

    Xu, Xin; Odqvist, Joakim; Colliander, Magnus Hörnqvist; Thuvander, Mattias; Steuwer, Axel; Westraadt, Johan E.; King, Stephen; Hedström, Peter

    2016-12-01

    Self-assembly due to phase separation within a miscibility gap is important in numerous material systems and applications. A system of particular interest is the binary alloy system Fe-Cr, since it is both a suitable model material and the base system for the stainless steel alloy category, suffering from low-temperature embrittlement due to phase separation. Structural characterization of the minute nano-scale concentration fluctuations during early phase separation has for a long time been considered a major challenge within material characterization. However, recent developments present new opportunities in this field. Here, we present an overview of the current capabilities and limitations of different techniques. A set of Fe-Cr alloys were investigated using small-angle neutron scattering (SANS), atom probe tomography, and analytical transmission electron microscopy. The complementarity of the characterization techniques is clear, and combinatorial studies can provide complete quantitative structure information during phase separation in Fe-Cr alloys. Furthermore, we argue that SANS provides a unique in-situ access to the nanostructure, and that direct comparisons between SANS and phase-field modeling, solving the non-linear Cahn Hilliard equation with proper physical input, should be pursued.

  12. 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.

  13. Systematic structural characterization of metabolites in Arabidopsis via candidate substrate-product pair networks.

    PubMed

    Morreel, Kris; Saeys, Yvan; Dima, Oana; Lu, Fachuang; Van de Peer, Yves; Vanholme, Ruben; Ralph, John; Vanholme, Bartel; Boerjan, Wout

    2014-03-01

    Plant metabolomics is increasingly used for pathway discovery and to elucidate gene function. However, the main bottleneck is the identification of the detected compounds. This is more pronounced for secondary metabolites as many of their pathways are still underexplored. Here, an algorithm is presented in which liquid chromatography-mass spectrometry profiles are searched for pairs of peaks that have mass and retention time differences corresponding with those of substrates and products from well-known enzymatic reactions. Concatenating the latter peak pairs, called candidate substrate-product pairs (CSPP), into a network displays tentative (bio)synthetic routes. Starting from known peaks, propagating the network along these routes allows the characterization of adjacent peaks leading to their structure prediction. As a proof-of-principle, this high-throughput cheminformatics procedure was applied to the Arabidopsis thaliana leaf metabolome where it allowed the characterization of the structures of 60% of the profiled compounds. Moreover, based on searches in the Chemical Abstract Service database, the algorithm led to the characterization of 61 compounds that had never been described in plants before. The CSPP-based annotation was confirmed by independent MS(n) experiments. In addition to being high throughput, this method allows the annotation of low-abundance compounds that are otherwise not amenable to isolation and purification. This method will greatly advance the value of metabolomics in systems biology.

  14. Ostrich crystallins. Structural characterization of delta-crystallin with enzymic activity.

    PubMed Central

    Chiou, S H; Lo, C H; Chang, C Y; Itoh, T; Kaji, H; Samejima, T

    1991-01-01

    Lens crystallins from the African ostrich (Struthio camelus) were isolated and characterized. Four crystallin fractions corresponding to alpha-, delta/beta- and beta-crystallins similar to those of duck crystallins were isolated, but epsilon-crystallin was found to be absent. The native molecular masses and subunit structures of the purified fractions were analysed by gel filtration. SDS/PAGE and isoelectric focusing, revealing various extents of heterogeneity in each orthologous crystallin class. An ion-exchange chromatographic method was used for the large-scale preparation of delta-crystallin suitable for structural and enzymic studies. It was unexpectedly found that the purified native delta-crystallin of ostrich lens possessed high argininosuccinate lyase activity, in contrast with chicken delta-crystallin. The c.d. spectra indicated a predominant beta-sheet structure in alpha- and beta-crystallins, and a significant contribution of alpha-helical structure in the delta-crystallin fraction. The estimate of secondary structures from c.d. spectroscopy for each crystallin class bears a resemblance to that of duck crystallins, except that ostrich delta-crystallin possesses much less helical content than duck delta-crystallin. Comparison of crystallin compositions and structures from aquatic and terrestrial birds revealed distinct differences. Images Fig. 1. Fig. 2. Fig. 3. PMID:1991029

  15. 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.

  16. 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.

  17. Detection, characterization and evolution of internal repeats in Chitinases of known 3-D structure.

    PubMed

    Sivaji, Manigandan; Sadasivam, Vinoth; Narayanasamy, Jayabalan; Samuel, Selvaraj; Fan, Chuanzhu

    2014-01-01

    Chitinase proteins have evolved and diversified almost in all organisms ranging from prokaryotes to eukaryotes. During evolution, internal repeats may appear in amino acid sequences of proteins which alter the structural and functional features. Here we deciphered the internal repeats from Chitinase and characterized the structural similarities between them. Out of 24 diverse Chitinase sequences selected, six sequences (2CJL, 2DSK, 2XVP, 2Z37, 3EBV and 3HBE) did not contain any internal repeats of amino acid sequences. Ten sequences contained repeats of length <50, and the remaining 8 sequences contained repeat length between 50 and 100 residues. Two Chitinase sequences, 1ITX and 3SIM, were found to be structurally similar when analyzed using secondary structure of Chitinase from secondary and 3-Dimensional structure database of Protein Data Bank. Internal repeats of 3N17 and 1O6I were also involved in the ligand-binding site of those Chitinase proteins, respectively. Our analyses enhance our understanding towards the identification of structural characteristics of internal repeats in Chitinase proteins.

  18. Characterization of dermal plates from armored catfish Pterygoplichthys pardalis reveals sandwich-like nanocomposite structure.

    PubMed

    Ebenstein, Donna; Calderon, Carlos; Troncoso, Omar P; Torres, Fernando G

    2015-05-01

    Dermal plates from armored catfish are bony structures that cover their body. In this paper we characterized structural, chemical, and nanomechanical properties of the dermal plates from the Amazonian fish Pterygoplichthys pardalis. Analysis of the morphology of the plates using scanning electron microscopy (SEM) revealed that the dermal plates have a sandwich-like structure composed of an inner porous matrix surrounded by two external dense layers. This is different from the plywood-like laminated structure of elasmoid fish scales but similar to the structure of osteoderms found in the dermal armour of some reptiles and mammals. Chemical analysis performed using Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC) and X-ray diffraction (XRD) results revealed similarities between the composition of P. pardalis plates and the elasmoid fish scales of Arapaima gigas. Reduced moduli of P. pardalis plates measured using nanoindentation were also consistent with reported values for A. gigas scales, but further revealed that the dermal plate is an anisotropic and heterogeneous material, similar to many other fish scales and osteoderms. It is postulated that the sandwich-like structure of the dermal plates provides a lightweight and tough protective layer.

  19. The Structural and Functional Characterization of Mammalian ADP-dependent Glucokinase*

    PubMed Central

    Richter, Jan P.; Goroncy, Alexander K.; Ronimus, Ron S.; Sutherland-Smith, Andrew J.

    2016-01-01

    The enzyme-catalyzed phosphorylation of glucose to glucose-6-phosphate is a reaction central to the metabolism of all life. ADP-dependent glucokinase (ADPGK) catalyzes glucose-6-phosphate production, utilizing ADP as a phosphoryl donor in contrast to the more well characterized ATP-requiring hexokinases. ADPGK is found in Archaea and metazoa; in Archaea, ADPGK participates in a glycolytic role, but a function in most eukaryotic cell types remains unknown. We have determined structures of the eukaryotic ADPGK revealing a ribokinase-like tertiary fold similar to archaeal orthologues but with significant differences in some secondary structural elements. Both the unliganded and the AMP-bound ADPGK structures are in the “open” conformation. The structures reveal the presence of a disulfide bond between conserved cysteines that is positioned at the nucleotide-binding loop of eukaryotic ADPGK. The AMP-bound ADPGK structure defines the nucleotide-binding site with one of the disulfide bond cysteines coordinating the AMP with its main chain atoms, a nucleotide-binding motif that appears unique to eukaryotic ADPGKs. Key amino acids at the active site are structurally conserved between mammalian and archaeal ADPGK, and site-directed mutagenesis has confirmed residues essential for enzymatic activity. ADPGK is substrate inhibited by high glucose concentration and shows high specificity for glucose, with no activity for other sugars, as determined by NMR spectroscopy, including 2-deoxyglucose, the glucose analogue used for tumor detection by positron emission tomography. PMID:26555263

  20. A comparative study of theoretical graph models for characterizing structural networks of human brain.

    PubMed

    Li, Xiaojin; Hu, Xintao; Jin, Changfeng; Han, Junwei; Liu, Tianming; Guo, Lei; Hao, Wei; Li, Lingjiang

    2013-01-01

    Previous studies have investigated both structural and functional brain networks via graph-theoretical methods. However, there is an important issue that has not been adequately discussed before: what is the optimal theoretical graph model for describing the structural networks of human brain? In this paper, we perform a comparative study to address this problem. Firstly, large-scale cortical regions of interest (ROIs) are localized by recently developed and validated brain reference system named Dense Individualized Common Connectivity-based Cortical Landmarks (DICCCOL) to address the limitations in the identification of the brain network ROIs in previous studies. Then, we construct structural brain networks based on diffusion tensor imaging (DTI) data. Afterwards, the global and local graph properties of the constructed structural brain networks are measured using the state-of-the-art graph analysis algorithms and tools and are further compared with seven popular theoretical graph models. In addition, we compare the topological properties between two graph models, namely, stickiness-index-based model (STICKY) and scale-free gene duplication model (SF-GD), that have higher similarity with the real structural brain networks in terms of global and local graph properties. Our experimental results suggest that among the seven theoretical graph models compared in this study, STICKY and SF-GD models have better performances in characterizing the structural human brain network.

  1. 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

  2. Structure prediction and functional characterization of secondary metabolite proteins of Ocimum

    PubMed Central

    Roy, Sudeep; Maheshwari, Nidhi; Chauhan, Rashi; Sen, Naresh Kumar; Sharma, Ashok

    2011-01-01

    Various species of Ocimum have acquired special attention due to their medicinal properties. Different parts of the plant (root, stem, flower, leaves) are used in the treatment of a wide range of disorders from centuries. Experimental structures (X-ray and NMR) of proteins from different Ocimum species, are not yet available in the Protein Databank (PDB). These proteins play a key role in various metabolic pathways in Ocimum. 3D structures of the proteins are essential to determine most of their functions. Homology modeling approach was employed in order to derive structures for these proteins. A program meant for comparative modeling- Modeller 9v7 was utilized for the purpose. The modeled proteins were further validated by Prochek and Verify-3d and Errat servers. Amino acid composition and polarity of these proteins was determined by CLC-Protein Workbench tool. Expasy's Prot-param server and Cys_rec tool were used for physico-chemical and functional characterization of these proteins. Studies of secondary structure of these proteins were carried out by computational program, Profunc. Swiss-pdb viewer was used to visualize and analyze these homology derived structures. The structures are finally submitted in Protein Model Database, PMDB so that they become accessible to other users for further studies. PMID:21769194

  3. Stimulus-responsive hydrogels made from biosynthetic fibrinogen conjugates for tissue engineering: structural characterization.

    PubMed

    Frisman, Ilya; Shachaf, Yonatan; Seliktar, Dror; Bianco-Peled, Havazelet

    2011-06-07

    Nanostructured hydrogels based on "smart" polymer conjugates of poloxamers and protein molecules were developed in order to form stimulus-responsive materials with bioactive properties for 3-D cell culture. Functionalized Pluronic F127 was covalently attached to a fibrinopeptide backbone and cross-linked into a structurally versatile and mechanically stable polymer network endowed with bioactivity and temperature-responsive structural features. Small angle X-ray scattering and transmission electron microscopy combined with rheology were used to characterize the structural and mechanical features of this biosynthetic conjugate, both in solution and in hydrogel form. The temperature at which the chemical cross-linking of F127-fibrinopeptide conjugates was initiated had a profound influence on the mechanical properties of the thermo-responsive hydrogel. The analysis of the scattering data revealed modification in the structure of the protein backbone resulting from increases in ambient temperature, whereas the structure of the polymer was not affected by ambient temperature. The hydrogel cross-linking temperature also had a major influence on the modulus of the hydrogel, which was rationally correlated to the molecular structure of the polymer network. The hydrogel structure exhibited a small mesh size when cross-linked at low temperatures and a larger mesh size when cross-linked at higher temperatures. The mesh size was nicely correlated to the mechanical properties of the hydrogels at the respective cross-linking temperatures. The schematic charts that model this material's behavior help to illustrate the relationship that exists between the molecular structure, the cross-linking temperature, and the temperature-responsive features for this class of protein-polymer conjugates. The precise control over structural and mechanical properties that can be achieved with this bioactive hydrogel material is essential in designing a tissue-engineering scaffold for clinical

  4. 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

  5. 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

  6. Wafer scale imprint uniformity evaluated by LSPR spectroscopy: a high volume characterization method for nanometer scale structures.

    PubMed

    Jeppesen, Claus; Lindstedt, Daniel Nilsson; Vig, Asger Laurberg; Kristensen, Anders; Mortensen, N Asger

    2012-09-28

    We exploit the localized surface-plasmon resonance (LSPR) of terahertz gold gammadion structures for wafer scale critical dimension metrology of nanostructures. The proposed characterization method, LSPR spectroscopy, is based on optical transmission measurements and is benchmarked against numerical simulations of imprinted structures characterized by atomic force microscopy. There is a fair agreement between the two methods and the simulations enable the translation of optical spectra to critical dimensions of the physical structures, a concept known from scatterometry. The results demonstrate the potential of LSPR spectroscopy as an alternative characterization method to scanning electron microscopy, atomic force microscopy and scatterometry.

  7. 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

  8. Statistical characterizations of rainfall structure over two tropical stations in southern India for microwave communication

    NASA Astrophysics Data System (ADS)

    Ojo, J. S.; Ajewole, M. O.; Sarkar, S. K.

    2010-08-01

    Statistical characterizations of rainfall structure over two tropical stations in southern India are reported in this paper based on the 2-year rainfall data. The statistical characterizations has been based on cumulative distribution function, exceedance of threshold values, dependence of the intensity of rainfall on the event duration, seasonal variability, and worst months concept as well as diurnal variability. These results are needed to give the detailed insights to the system designers for the development of communication gadgets needed for better service, serve as a vital tool to estimate signal outages in a year over the region and for proper planning of radio communication in the region. Finally, the study shows that the recent International Telecommunications Union Recommendations (ITU-R) value underestimated rain rate for 0.01% exceedance for the two locations.

  9. 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

  10. 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

  11. 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.

  12. Nonlinear characterization of a bolted, industrial structure using a modal framework

    NASA Astrophysics Data System (ADS)

    Roettgen, Daniel R.; Allen, Matthew S.

    2017-02-01

    This article presents measurements from a sub assembly of an off-the-shelf automotive exhaust system containing a bolted-flange connection and uses a recently proposed modal framework to develop a nonlinear dynamic model for the structure. The nonlinear identification and characterization methods used are reviewed to highlight the strengths of the current approach and the areas where further development is needed. This marks the first use of these new testing and nonlinear identification tools, and the associated modal framework, on production hardware with a realistic joint and realistic torque levels. To screen the measurements for nonlinearities, we make use of a time frequency analysis routine designed for transient responses called the zeroed early-time fast Fourier transform (ZEFFT). This tool typically reveals the small frequency shifts and distortions that tend to occur near each mode that is affected by the nonlinearity. The damping in this structure is found to be significantly nonlinear and a Hilbert transform is used to characterize the damping versus amplitude behavior. A model is presented that captures these effects for each mode individually (e.g. assuming negligible nonlinear coupling between modes), treating each mode as a single degree-of-freedom oscillator with a spring and viscous damping element in parallel with a four parameter Iwan model. The parameters of this model are identified for each of the structure's modes that exhibited nonlinearity and the resulting nonlinear model is shown to capture the stiffness and damping accurately over a large range of response amplitudes.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Size-separation characterization of starch and glycogen for biosynthesis-structure-property relationships.

    PubMed

    Gilbert, Robert G

    2011-02-01

    Starch and glycogen are highly branched polymers of glucose of great importance to humans in managing and mitigating nutrition-related diseases, especially diabetes and obesity, and in industrial uses, for example in food and paper-making. Size-separation characterization using multiple-detection size-exclusion chromatography (SEC, also known as gel-permeation chromatography, GPC) is able to furnish substantial amounts of information on the relationships between the biosynthesis, processing, structure, and properties of these biopolymers, and achieves superior characterization for use in industrial product and process improvements. Multi-detector SEC is able to give much more information about structure than simple averages such as total molecular weight or size; the detailed information yielded by this technique has already given new information on important biosynthesis-structure-property reactions, and has considerable potential in this field in the future. However, it must be used with care to avoid artifacts arising from incomplete dissolution of the substrate and shear scission during separation. It is also essential in interpreting data to appreciate that this size-separation technique can only ever give size distributions, never true molecular weight distributions. Other size-separation techniques, particularly field-flow fractionation, require substantial technical development to be used on undegraded native starches.

  18. Fabrication and characterization of WS2 based photonic structures(Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Pedrini, Jacopo; Calafiore, Giuseppe; Chen, Christopher; Kastl, Christoph; Meinardi, Francesco; Cabrini, Stefano; Schwartzberg, Adam M.

    2016-09-01

    Transition metal dichalcogenides (TMDs) are gaining momentum as powerful and versatile materials thanks to the outstanding physical properties that arise when they are reduced to monolayers. TMDs are also interesting for applications in photonics because of the high refractive index through the visible and near-infrared spectrum. However, the extremely complex fabrication process due to the difficult production of large area, homogeneous and high quality samples hinders the development of TMD-based photonic structures. Moreover, the complex chemistry makes high-resolution etching of the TMD film extremely difficult. In this work we characterized the fundamental optical properties of a thick, bulk-like film of tungsten sulphide (WS2). We deposited a tungsten oxide film with atomic layer deposition (ALD) and then annealed it in presence of H2S. ALD allows the conformal growth of large area, uniform and high quality films. Spectroscopic ellipsometry measurements of the optical constants show that the refractive index is higher than 3 on the entire visible and near-infrared spectrum, even where the extinction coefficient is negligible. Motivated by this remarkable result, we fabricated and characterized a photonic structure by etching the oxide before the conversion, overcoming the fabrication limits posed by chemistry. Therefore, we demonstrated that a thick WS2 layer can be exploited to modulate the optical properties of photonic structures. The combination of high refractive index with low extinction coefficient over a large portion of the electromagnetic spectrum validates the importance of TMDs and endorses their application to photonic devices.

  19. Structural characterization of ANGPTL8 (betatrophin) with its interacting partner lipoprotein lipase.

    PubMed

    Siddiqa, Amnah; Ahmad, Jamil; Ali, Amjad; Paracha, Rehan Zafar; Bibi, Zurah; Aslam, Babar

    2016-04-01

    Angiopoietin-like protein 8 (ANGPTL8) (also known as betatrophin) is a newly identified secretory protein with a potential role in autophagy, lipid metabolism and pancreatic beta-cell proliferation. Its structural characterization is required to enhance our current understanding of its mechanism of action which could help in identifying its receptor and/or other binding partners. Based on the physiological significance and necessity of exploring structural features of ANGPTL8, the present study is conducted with a specific aim to model the structure of ANGPTL8 and study its possible interactions with Lipoprotein Lipase (LPL). To the best of our knowledge, this is the first attempt to predict 3-dimensional (3D) structure of ANGPTL8. Three different approaches were used for modeling of ANGPTL8 including homology modeling, de-novo structure prediction and their amalgam which is then proceeded by structure verification using ERRATT, PROSA, Qmean and Ramachandran plot scores. The selected models of ANGPTL8 were further evaluated for protein-protein interaction (PPI) analysis with LPL using CPORT and HADDOCK server. Our results have shown that the crystal structure of iSH2 domain of Phosphatidylinositol 3-kinase (PI3K) p85β subunit (PDB entry: 3mtt) is a good candidate for homology modeling of ANGPTL8. Analysis of inter-molecular interactions between the structure of ANGPTL8 and LPL revealed existence of several non-covalent interactions. The residues of LPL involved in these interactions belong from its lid region, thrombospondin (TSP) region and heparin binding site which is suggestive of a possible role of ANGPTL8 in regulating the proteolysis, motility and localization of LPL. Besides, the conserved residues of SE1 region of ANGPTL8 formed interactions with the residues around the hinge region of LPL. Overall, our results support a model of inhibition of LPL by ANGPTL8 through the steric block of its catalytic site which will be further explored using wet lab

  20. Structural and functional characterization of a cold adapted TPM-domain with ATPase/ADPase activity.

    PubMed

    Cerutti, María L; Otero, Lisandro H; Smal, Clara; Pellizza, Leonardo; Goldbaum, Fernando A; Klinke, Sebastián; Aran, Martín

    2016-11-01

    The Pfam PF04536 TPM_phosphatase family is a broadly conserved family of domains found across prokaryotes, plants and invertebrates. Despite having a similar protein fold, members of this family have been implicated in diverse cellular processes and found in varied subcellular localizations. Very recently, the biochemical characterization of two evolutionary divergent TPM domains has shown that they are able to hydrolyze phosphate groups from different substrates. However, there are still incorrect functional annotations and uncertain relationships between the structure and function of this family of domains. BA41 is an uncharacterized single-pass transmembrane protein from the Antarctic psychrotolerant bacterium Bizionia argentinensis with a predicted compact extracytoplasmic TPM domain and a C-terminal cytoplasmic low complexity region. To shed light on the structural properties that enable TPM domains to adopt divergent roles, we here accomplish a comprehensive structural and functional characterization of the central TPM domain of BA41 (BA41-TPM). Contrary to its predicted function as a beta-propeller methanol dehydrogenase, light scattering and crystallographic studies showed that BA41-TPM behaves as a globular monomeric protein and adopts a conserved Rossmann fold, typically observed in other TPM domain structures. Although the crystal structure reveals the conservation of residues involved in substrate binding, no putative catalytic or intramolecular metal ions were detected. Most important, however, extensive biochemical studies demonstrated that BA41-TPM has hydrolase activity against ADP, ATP, and other di- and triphosphate nucleotides and shares properties of cold-adapted enzymes. The role of BA41 in extracellular ATP-mediated signaling pathways and its occurrence in environmental and pathogenic microorganisms is discussed.

  1. [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.

  2. A novel characterization of organic molecular crystal structures for the purpose of crystal engineering.

    PubMed

    Thomas, Noel W

    2015-08-01

    A novel analytical approach is proposed for the characterization of organic molecular crystal structures where close packing is an important factor. It requires the identification of a unique reference axis within the crystal, along which three-dimensional space is divided into close-packed blocks (CPB) and junction zones (JZ). The degree of close packing along the reference axis is quantified by a two-dimensional packing function, ϕ2D, of symmetry determined by the space group. Values of ϕ2D reflect the degree of area-filling in planes perpendicular to this axis. The requirement of close packing within CPB allows the planar structures perpendicular to the reference axis to be analysed as tessellations of area-filling molecular-based cells (MBC), which are generally hexagonal. The form of these cells reflects the molecular shape in the cross-section, since their vertices are given by the centres of the voids between molecules. There are two basic types of MBC, Type 1, of glide or pseudo-glide symmetry, and Type 2, which is formed by lattice translations alone and generally requires a short unit-cell axis. MBC at layers of special symmetry are used to characterize the structures in terms of equivalent ellipses with parameters aell, bell and χell. The ratio aell/bell allows the established α, β, γ classification to be integrated into the current framework. The values of parameters aell and bell arising from all the structures considered, polynuclear aromatic hydrocarbons (PAH), substituted anthracenes and anthraquinones (SAA) and 2-benzyl-5-benzylidene (BBCP) are mapped onto a universal curve. The division of three-dimensional space into CPB and JZ is fundamentally useful for crystal engineering, since the structural perturbations brought about by substitution at hydrogen positions located within JZ are minimal. A contribution is also made to ongoing debate concerning the adoption of polar space groups, isomorphism and polymorphism.

  3. Characterization of mechanical properties of lamellar structure of the aortic wall: Effect of aging.

    PubMed

    Taghizadeh, Hadi; Tafazzoli-Shadpour, Mohammad

    2017-01-01

    Arterial wall tissues are sensitive to their mechanical surroundings and remodel their structure and mechanical properties when subjected to mechanical stimuli such as increased arterial pressure. Such remodeling is evident in hypertension and aging. Aging is characterized by stiffening of the artery wall which is assigned to disturbed elastin function and increased collagen content. To better understand and provide new insight on microstructural changes induced by aging, the lamellar model of the aortic media was utilized to characterize and compare wall structure and mechanical behavior of the young and old human thoracic aortic samples. Such model regards arterial media as two sets of alternating concentric layers, namely sheets of elastin and interlamellar layers. Histological and biaxial tests were performed and microstructural features and stress-strain curves of media were evaluated in young and old age groups. Then using optimization algorithms and hyperelastic constitutive equations the stress-strain curves of layers were evaluated for both age groups. Results indicated slight elevation in the volume fraction of interlamellar layer among old subjects most probably due to age related collagen deposition. Aging indicated substantial stiffening of interlamellar layers accompanied by noticeable softening of elastic lamellae. The general significant stiffening of old samples were attributed to both increase of volume fraction of interlamellar layers and earlier recruitment of collagen fibers during load bearing due to functional loss of elastin within wall lamellae. Mechanical characterization of lamellar structure of wall media is beneficial in study of arterial remodeling in response to alternated mechanical environment in aging and clinical conditions through coupling of wall microstructure and mechanical behavior.

  4. Using LiDAR Metrics to Characterize Forest Structural Complexity at Multiple Scales

    NASA Astrophysics Data System (ADS)

    Kane, V. R.; McGaughey, R. J.; Gersonde, R.; Franklin, J. F.

    2007-12-01

    Forest structure - the size and arrangement of trees and foliage - reflects a stand's history of initiation, growth, disturbance, and mortality. Because of this, studying the structure of forests can provide key insights into ecological processes, guides to silvicultural prescriptions to improve habitat, and assessments of forested landscapes. This study tested LiDAR metrics to characterize stands based on canopy structure. The study site was the 34,591 ha of forests in the Cedar River Watershed in western Washington State, USA. Stands ranged in age from <25 years old to >350 years old (including old-growth). Study sites spanned the western hemlock- Douglas fir (Tsuga heterophylla-Pseudotsuga menziesii), Pacific silver fir (Abies amabilis), and mountain hemlock (Tsuga mertansiana) forest zones. Eighty sample plots were used to ground truth the LiDAR data. A variety of structural indices were used to study canopy structural variations at the plot, stand, and landscape scales. The two most successful indices used the exposed geometry of the canopy surface: (1) the ratio of the canopy surface area to ground surface area (rumple index), and (2) the ratio of the volume beneath the canopy surface to maximum volume beneath the 95th percentile height (modified canopy volume method). These two indices integrated the spatial effects of tree heights, foliage distribution, and tree arrangement within 15m pixels. Variation between pixels revealed structural complexity at larger scales. Results: At the plot scale (~4 pixels), correlations with standard plot metrics (e.g., diameter at breast height) were similar to those reported by other studies. Comparison of structural complexity with age and height revealed a diversity of development pathways. The relationship between height and complexity allowed stands to be classified by the degree to which they have achieved their potential structural complexity, a new way to examine forest development. At the stand scale, the indices

  5. 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.

  6. Synthesis and characterization of three new beryllium phosphate/phosphites with different structure-directing agents

    NASA Astrophysics Data System (ADS)

    Pan, Jie; Xue, Zhen-Zhen; Li, Jin-Hua; Wei, Li; Wang, Guo-Ming

    2017-03-01

    Three new organically templated beryllium phosphate and phosphites, [C2H8N][Be2(PO4) (HPO4) (H2O)]·(H2O)0.5 (1), [C3H12N2][Be3(HPO3)4] (2) and [C6H18N2][Be3(HPO3)4] (3), have been synthesized and structurally characterized by single-crystal X-ray diffraction analyses. The structure of 1 consists of BeO4 and PO4 tetrahedra, displaying a double-layered structure with [Be4(PO4)2(HPO4)2(H2O)2] D4R-analogue as SBUs. Compound 2 presents a three-dimensional (3D) interrupted open-framework, constructed from two-dimensional layers pillared by phosphite nodes. Left- and right-handed helical channels occurred along the [010] direction in 2. For 3, adjacent sheets arrange in an -ABAB- staggered stacking mode to give a (3,4)-connected 3D structure with zigzag 12-ring channels. In 1-3, different protonated amine templates reside in the voids of structures and interact with the inorganic frameworks through hydrogen-bonds.

  7. Quantitative characterization of pore structure of several biochars with 3D imaging.

    PubMed

    Hyväluoma, Jari; Kulju, Sampo; Hannula, Markus; Wikberg, Hanne; Källi, Anssi; Rasa, Kimmo

    2017-03-24

    Pore space characteristics of biochars may vary depending on the used raw material and processing technology. Pore structure has significant effects on the water retention properties of biochar amended soils. In this work, several biochars were characterized with three-dimensional imaging and image analysis. X-ray computed microtomography was used to image biochars at resolution of 1.14 μm and the obtained images were analysed for porosity, pore size distribution, specific surface area and structural anisotropy. In addition, random walk simulations were used to relate structural anisotropy to diffusive transport. Image analysis showed that considerable part of the biochar volume consist of pores in size range relevant to hydrological processes and storage of plant available water. Porosity and pore size distribution were found to depend on the biochar type and the structural anisotopy analysis showed that used raw material considerably affects the pore characteristics at micrometre scale. Therefore, attention should be paid to raw material selection and quality in applications requiring optimized pore structure.

  8. Multistep Aggregation Pathway of Human Interleukin-1 Receptor Antagonist: Kinetic, Structural, and Morphological Characterization

    PubMed Central

    Krishnan, Sampathkumar; Raibekas, Andrei A.

    2009-01-01

    Abstract The complex, multistep aggregation kinetic and structural behavior of human recombinant interleukin-1 receptor antagonist (IL-1ra) was revealed and characterized by spectral probes and techniques. At a certain range of protein concentration (12–27 mg/mL) and temperature (44–48°C), two sequential aggregation kinetic transitions emerge, where the second transition is preceded by a lag phase and is associated with the main portion of the aggregated protein. Each kinetic transition is linked to a different type of aggregate population, referred to as type I and type II. The aggregate populations, isolated at a series of time points and analyzed by Fourier-transform infrared spectroscopy, show consecutive protein structural changes, from intramolecular (type I) to intermolecular (type II) β-sheet formation. The early type I protein spectral change resembles that seen for IL-1ra in the crystalline state. Moreover, Fourier-transform infrared data demonstrate that type I protein assembly alone can undergo a structural rearrangement and, consequently, convert to the type II aggregate. The aggregated protein structural changes are accompanied by the aggregate morphological changes, leading to a well-defined population of interacting spheres, as detected by scanning electron microscopy. A nucleation-driven IL-1ra aggregation pathway is proposed, and assumes two major activation energy barriers, where the second barrier is associated with the type I → type II aggregate structural rearrangement that, in turn, serves as a pseudonucleus triggering the second kinetic event. PMID:19134476

  9. Characterizing of functional human coding RNA editing from evolutionary, structural, and dynamic perspectives.

    PubMed

    Solomon, Oz; Bazak, Lily; Levanon, Erez Y; Amariglio, Ninette; Unger, Ron; Rechavi, Gideon; Eyal, Eran

    2014-11-01

    A-to-I RNA editing has been recently shown to be a widespread phenomenon with millions of sites spread in the human transcriptome. However, only few are known to be located in coding sequences and modify the amino acid sequence of the protein product. Here, we used high-throughput data, variant prediction tools, and protein structural information in order to find structural and functional preferences for coding RNA editing. We show that RNA editing has a unique pattern of amino acid changes characterized by enriched stop-to-tryptophan changes, positive-to-neutral and neutral-to-positive charge changes. RNA editing tends to have stronger structural effect than equivalent A-to-G SNPs but weaker effect than random A-to-G mutagenesis events. Sites edited at low level tend to be located at conserved positions with stronger predicted deleterious effect on proteins comparing to sites edited at high frequencies. Lowly edited sites tend to destabilize the protein structure and affect amino acids with larger number of intra-molecular contacts. Still, some highly edited sites are predicted also to prominently affect structure and tend to be located at critical positions of the protein matrix and are likely to be functionally important. Using our pipeline, we identify and discuss several novel putative functional coding changing editing sites in the genes COPA (I164V), GIPC1 (T62A), ZN358 (K382R), and CCNI (R75G).

  10. [Structural characterization of copper-phthalocyanine thin solid films by FTIR spectroscopy].

    PubMed

    Ding, H; Zhang, Y; Chen, W; Xi, S

    1997-04-01

    The structure of tris- (2, 4-di-t-amylpheoxy) - (8-quinolinoxy) copper phthalocyanine (CuPc) thin solid films has been characterized by Fourier transform infrared (FTIR) transmission, polarized transmission and reflection absorption (RA) spectroscopy. The following conclusions can be obtained from the above measurements: (1)in LB films, the hydrocarbon chains of CuPc are in hexagonal or pseudohexagonal subcell packing, the CH2 asymmetric vibrational vector is oriented with respect to the substrate surface and the RA spectroscopy can distinguish the two CH2 streching modes of benzene cycle; (2)in sublimed films, the molecules of CuPc are out of order.

  11. Synthesis, crystal structures and spectral characterization of chiral 4-R-1,2,4-triazoles

    NASA Astrophysics Data System (ADS)

    Gural'skiy, Il'ya A.; Reshetnikov, Viktor A.; Omelchenko, Irina V.; Szebesczyk, Agnieszka; Gumienna-Kontecka, Elzbieta; Fritsky, Igor O.

    2017-01-01

    1,2,4-triazoles attract attention as actively used medications and ligands for constructing coordination architectures. In this paper we describe four optically active 4-substituted 1,2,4-triazoles that have been prepared by Bayer's synthesis from the corresponding aliphatic chiral amines. This approach tends to be universal towards different triazoles and permits to conserve a homochirality of substrates. Novel asymmetric molecules have been characterized by spectroscopic techniques and their structures have been retrieved from the single crystal X-ray analysis. Chiro-optical studies of these heterocycles have been made by means of circular dichroism spectroscopy.

  12. Flexible and Asymmetric Ligand in Constructing Coordinated Complexes: Synthesis, Crystal Structures and Fluorescent Characterization

    PubMed Central

    Chen, Peng; Lin, Jianhua

    2011-01-01

    Flexible and asymmetric ligand L [L = 1-((pyridin-3-yl)methyl)-1H-benzotriazole], is used as a basic backbone to construct complicated metal-organic frameworks. Two new polymers, namely, [Ag2(L)2(NO3)2]n (1) and [Ag(L)(ClO4)]n (2), were synthesized and characterized by X-ray structure analysis and fluorescent spectroscopy. The complex 1 gives an “S” type double helical conformation, whereas complex 2 exhibits a 1D zigzag configuration. Different anions affect the silver coordination geometry and crystal packing topology. PMID:21339976

  13. 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.

  14. Characterization of coherent structures in a turbulent mixing layer by digital image analysis

    NASA Technical Reports Server (NTRS)

    Bernal, L. P.; Hernan, M. A.; Sarohia, V.

    1985-01-01

    Digital image analysis has been applied to a shadowgraph motion picture of a helium nitrogen mixing layer in order to characterize the coherent vortex structures in the flow. Both the primary spanwise coherent vortices and secondary streamwise vortices are considered. Pattern recognition algorithms were designed to take advantage of the more pronounced features of the vortices and of their temporal coherence to isolate them and to measure their characteristics. The resulting data base permits a deterministic description of the evolution of primary and seconary vortices.

  15. Quantitative void characterization in structural ceramics using scanning laser acoustic microscopy

    NASA Technical Reports Server (NTRS)

    Roth, D. J.; Generazio, E. R.; Baaklini, G. Y.

    1986-01-01

    The ability of scanning laser acoustic microscopy (SLAM) to characterize artificially seeded voids in sintered silicon nitride structural ceramic specimens was investigated. Using trigonometric relationships and Airy's diffraction theory, predictions of internal void depth and size were obtained from acoustic diffraction patterns produced by the voids. Agreement was observed between actual and predicted void depths. However, predicted void diameters were generally much greater than actual diameters. Precise diameter predictions are difficult to obtain due to measurement uncertainty and the limitations of 100 MHz SLAM applied to typical ceramic specimens.

  16. 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)].

  17. Synthesis, structural and morphological characterization of the perovskite LaYbO3

    NASA Astrophysics Data System (ADS)

    Cabrera Ramírez, A.; Charry Pastrana, F. E.; Roa Rojas, J.; Landinez Tellez, D. A.; Fajardo, F.

    2016-02-01

    In this work we report synthesis of the LaYbO3 ceramics material by the solid state reaction technique and its structural and morphological characterization from X-ray diffraction and Scanning Electron Microscopy experiments. Rietveld refinement of the diffraction patterns reveals that this material crystallizes in an orthorhombic perovskite, Pnma space group (#62) with lattice parameters a=6.0233Å, b=8.2080Å and c=5.7203Å. Systematic monitoring of the synthesis process is carried out through analysis of results of X-ray diffraction. The surface morphology of the samples was qualitatively analysed as a function of the sintering process.

  18. Structural characterization of the enzymes composing the arginine deiminase pathway in Mycoplasma penetrans.

    PubMed

    Gallego, Pablo; Planell, Raquel; Benach, Jordi; Querol, Enrique; Perez-Pons, Josep A; Reverter, David

    2012-01-01

    The metabolism of arginine towards ATP synthesis has been considered a major source of energy for microorganisms such as Mycoplasma penetrans in anaerobic conditions. Additionally, this pathway has also been implicated in pathogenic and virulence mechanism of certain microorganisms, i.e. protection from acidic stress during infection. In this work we present the crystal structures of the three enzymes composing the gene cluster of the arginine deiminase pathway from M. penetrans: arginine deiminase (ADI), ornithine carbamoyltransferase (OTC) and carbamate kinase (CK). The arginine deiminase (ADI) structure has been refined to 2.3 Å resolution in its apo-form, displaying an "open" conformation of the active site of the enzyme in comparison to previous complex structures with substrate intermediates. The active site pocket of ADI is empty, with some of the catalytic and binding residues far from their active positions, suggesting major conformational changes upon substrate binding. Ornithine carbamoyltransferase (OTC) has been refined in two crystal forms at 2.5 Å and 2.6 Å resolution, respectively, both displaying an identical dodecameric structure with a 23-point symmetry. The dodecameric structure of OTC represents the highest level of organization in this protein family and in M.penetrans it is constituted by a novel interface between the four catalytic homotrimers. Carbamate kinase (CK) has been refined to 2.5 Å resolution and its structure is characterized by the presence of two ion sulfates in the active site, one in the carbamoyl phosphate binding site and the other in the β-phosphate ADP binding pocket of the enzyme. The CK structure also shows variations in some of the elements that regulate the catalytic activity of the enzyme. The relatively low number of metabolic pathways and the relevance in human pathogenesis of Mycoplasma penetrans places the arginine deiminase pathway enzymes as potential targets to design specific inhibitors against this human

  19. Design considerations for an astronaut monorail system for large space structures and the structural characterization of its positioning arm

    NASA Astrophysics Data System (ADS)

    Watson, Judith J.

    1992-08-01

    An astronaut monorail system (AMS) is presented as a vehicle to transport and position EVA astronauts along large space truss structures. The AMS is proposed specifically as an alternative to the crew and equipment transfer aid for Space Station Freedom. Design considerations for the AMS were discussed and a reference configuration was selected for the study. Equations were developed to characterize the stiffness and frequency behavior of the AMS positioning arm. Experimental data showed that these equations gave a fairly accurate representation of the stiffness and frequency behavior of the arm. A study was presented to show trends for the arm behavior based on varying parameters of the stiffness and frequency equations. An ergonomics study was conducted to provide boundary conditions for tolerable frequency and deflection to be used in developing a design concept for the positioning arm. The feasibility of the AMS positioning arm was examined using equations and working curves developed in this study. It was found that a positioning arm of a length to reach all interior points of the space station truss structure could not be designed to satisfy frequency and deflection constraints. By relaxing the design requirements and the ergonomic boundaries, an arm could be designed which would provide a stable work platform for the EVA astronaut and give him access to over 75 percent of the truss interior.

  20. Structural characterization of purine nucleoside phosphorylase from human pathogen Helicobacter pylori.

    PubMed

    Štefanić, Zoran; Mikleušević, Goran; Luić, Marija; Bzowska, Agnieszka; Ašler, Ivana Leščić

    2017-03-20

    Microaerophilic bacterium Helicobacer pylori is a well known human pathogen involved in the development of many diseases. Due to the evergrowing infection rate and increase of H. pylori antibiotic resistence, it is of utmost importance to find a new way to attack and eradicate H. pylori. The purine metabolism in H. pylori is solely dependant on the salvage pathway and one of the key enzymes in this pathway is purine nucleoside phosphorylase (PNP). In this timely context, we report here the basic biochemical and structural characterization of recombinant PNP from the H. pylori clinical isolate expressed in Escherichia coli. Structure of H. pylori PNP is typical for high molecular mass PNPs. However, its activity towards adenosine is very low, thus resembling more that of low molecular mass PNPs. Understanding the molecular mechanism of this key enzyme may lead to the development of new drug strategies and help in the eradication of H. pylori.

  1. 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.

  2. 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.

  3. Laser annealing of Al implanted silicon carbide: Structural and optical characterization

    NASA Astrophysics Data System (ADS)

    Boutopoulos, C.; Terzis, P.; Zergioti, I.; Kontos, A. G.; Zekentes, K.; Giannakopoulos, K.; Raptis, Y. S.

    2007-07-01

    Pulsed-laser-based methods have been applied for post-implant annealing of p-type Al-doped 4H-SiC wafers in order to restore the crystal structure and to electrically activate the doping species. The annealing was performed with the third harmonic (355 nm) of a Nd:YAG laser at 4 ns pulse duration. The epilayers were characterized by micro-Raman spectroscopy under surface and cross-sectional backscattering. Changes in the phonon mode-intensity were related to the laser annealing induced recrystallization of the implanted material. The results were compared with changes in the infrared reflectivity across the Reststrahlen band. Transmission electron microscopy analysis showed the formation of columnar polycrystalline structure after the laser annealing process.

  4. 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.

  5. 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.

  6. 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.

  7. Complex salts formed by anionic copolymers with hexadecyltrimethylammonium: Phase equilibrium and structural characterization using SAXS.

    NASA Astrophysics Data System (ADS)

    Percebom, Ana Maria; Bernardes, Juliana S.; Loh, Watson

    2009-01-01

    Extending earlier studies conducted by this research group about the hexadecyltrimethylammonium (CTA+) and other poly-anions in water, this study aims at analyzing the phase equilibrium and characterizing structures of mesophases formed by mixtures of oppositely charged surfactants and polymers. Its specific objective is to verify the effect of the charge density along the poly-electrolyte. Poly(4-styrenesulfonic acid-co-maleic acid), P(SS-AM), was used because this copolymer has three acid groups with different pKa values, enabling to obtain negative charges in all groups or only in a few. The self-assembly of the complex salt (anionic copolymer+cationic surfactant) was investigated in binary (+water) and ternary systems (+water+1-decanol), determining their phase diagrams and analyzing the structures of mesophases formed by SAXS.

  8. Identification of inks and structural characterization of contemporary artistic prints by laser-induced breakdown spectroscopy

    NASA Astrophysics Data System (ADS)

    Oujja, M.; Vila, A.; Rebollar, E.; García, J. F.; Castillejo, M.

    2005-08-01

    Identification of the inks used in artistic prints and the order in which different ink layers have been applied on a paper substrate are important factors to complement the classical stylistic aspects for the authentication of this type of objects. Laser-induced breakdown spectroscopy (LIBS) is investigated to determine the chemical composition and structural distribution of the constituent materials of model prints made by applying one or two layers of several blue and black inks on an Arches paper substrate. By using suitable laser excitation conditions, identification of the inks was possible by virtue of emissions from key elements present in their composition. Analysis of successive spectra on the same spot allowed the identification of the order in which the inks were applied on the paper. The results show the potential of laser-induced breakdown spectroscopy for the chemical and structural characterization of artistic prints.

  9. Magnetic and structural characterizations of Heusler Ni2FeGa nanoparticles

    NASA Astrophysics Data System (ADS)

    Xu, Yunli; Liu, Min; Huang, Xiufeng; Dai, Zhiwen; Qiu, Hongmei; Yu, Guanghua; Pan, Liqing

    2016-11-01

    This work describes the chemical preparation, structural characterization and magnetic properties of Heusler Ni2FeGa nanoparticles. The nanoparticles were synthesized by reducing a methanol solution mixture of NiCl2 · 6H2O, Fe(NO3)3 · 9H2O and Ga(NO3) · xH2O, and using SBA-15 as template. The obtained nanoparticles were investigated by means of x-ray diffraction, transmission electron microscopy, and vibrating sample magnetometer. The structure of the prepared nanoparticles is Heusler L21 phase with a second γ phase, and the ratio of the two components could be adjusted by the concentration of SBA in the precursor solution. The prepared nanoscale Ni2FeGa heusler alloys with a tensile strain of 0.56% present ferromagnetism at room-temperature and its Curie temperature exceeds 340 K.

  10. 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.

  11. 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).

  12. Computational characterization of the molecular structure and properties of Dye 7 for organic photovoltaics.

    PubMed

    Baldenebro-López, Jesús; Castorena-González, José; Flores-Holguin, Norma; Calderón-Guillén, Joel; Glossman-Mitnik, Daniel

    2012-03-01

    Organic dyes have great potential for its use in solar cells. In this recent work, the molecular structure and properties of Dye 7 were obtained using density functional theory (DFT) and different levels of calculation. Upon comparing the molecular structure and the ultraviolet visible spectrum with experimental data reported in the literature, it was found that the M05-2X/6-31G(d) level of calculation gave the best approximation. Once the appropriate methodology had been obtained, the molecule was characterized by obtaining the infrared spectrum, dipole moment, total energy, isotropic polarizability, molecular orbital energies, free energy of solvation in different solvents, and the chemical reactivity sites using the condensed Fukui functions.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. The early stages of amyloid formation: biophysical and structural characterization of human calcitonin pre-fibrillar assemblies.

    PubMed

    Avidan-Shpalter, Carmit; Gazit, Ehud

    2006-12-01

    Amyloid fibril formation is a nucleation dependent process characterized by a lag-phase prior to the appearance of detectable amyloid fibrils. While the three-dimensional structure of amyloid fibrils at atomic resolution is just beginning to be elucidated, the early process of monomers assembly into oligomers is less understood. Understanding the dynamic processes that lead to the formation of these intermediates is highly important as these assemblies might be the most pathological ones. Here, we investigated the biophysical and structural features characterizing the early stage assemblies formed by the human hormone calcitonin. We calculated the initial nucleus size by experimentally determining the dependence between the lag-time length and the hCT concentrations. We used size exclusion chromatography and dynamic light scattering in order to characterize the dynamic growth process of preliminary intermediates transformed into larger structures. The early structures were visualized using high-resolution transmission electron microscopy. Annular pore-like structures were observed along with protofibrilar structures. This observed morphology is similar to structures revealed during the fibrillization processes of beta-amyloid, alpha-synuclein, and islet amyloid polypeptide, suggesting that these intermediates represent a generic early structure conformation. The results introduced here imply that a variety of intermediate assemblies are formed during the early stages of amyloid fibril formation. The characterizing of their structural features and assembly kinetics will contribute to the rational design of inhibitors directed towards early structure assemblies.

  18. Need for Standardization of EBSD Measurements for Microstructural Characterization of Thin Film Structures

    SciTech Connect

    Geiss, Roy H.; Read, David T.

    2007-09-26

    Microstructural characterization of metal thin films includes measurement of grain size, crystallographic texture and misorientation angle across grain boundaries. All of these measurements can be made simultaneously by the use of electron backscatter diffraction (EBSD) in the scanning electron microscope. The use of EBSD measurements to characterize microstructure requires the collection and analysis of thousands of individual diffraction patterns, and the extraction of statistical quantities of interest from the data set. The results depend on the particular analytical procedures used. Since the grains in interconnect structures are often much smaller than those in bulk materials, the measurement and reporting protocols require adaptation of procedures developed for bulk materials. Here we demonstrate results from a specific procedure for collecting and analyzing EBSD data on electrodeposited copper films. We show that without careful controls, the apparent grain size can vary by a factor of two or more, and the time required to acquire the data can differ by hours. The demonstrated practical advantages of EBSD over previously available techniques and the severe effect of experimental parameters on the results support the need for standardization of the methods used for microstructural characterization by use of EBSD.

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

    SciTech Connect

    Lee, Andrew Loyd

    1996-05-01

    Solution NMR was primarily used to characterize structure and dynamics in two different eukaryotic protein systems: the δ-Al-ε 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 βαβ-βαβ pattern of secondary structure, with the two helices packed against a 4-stranded anti-parallel β-sheet. In addition 15N T1, T2, and 15N/1H 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 1H, 13C, and 15N resonances of Sxl-RBD1+2 were assigned using a triple-resonance approach, and 15N 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.

  20. Structural and kinetic characterization of two 4-oxalocrotonate tautomerases in Methylibium petroleiphilum strain PM1

    PubMed Central

    Terrell, Cassidy R.; Burks, Elizabeth A.; Whitman, Christian P.; Hoffman, David W.

    2013-01-01

    Methylibium petroleiphilumstrain PM1 uses various petroleum products including the fuel additive methyl tert-butyl ether and straight chain and aromatic hydrocarbons as sole carbon and energy sources. It has two operons, dmpI and dmpII, that code for the enzymes in a pair of parallel meta-fission pathways. In order to understand the roles of the pathways, the 4-oxalocrotonate tautomerase (4-OT) isozyme from each pathway was characterized. Tautomerase I and tautomerase II have the lowest pairwise sequence identity (35%) among the isozyme pairs in the parallel pathways, and could offer insight into substrate preferences and pathway functions. The kinetic parameters of tautomerase I and tautomerase II were determined using 2-hydroxymuconate and 5-(methyl)-2-hydroxymuconate. Both tautomerase I and tautomerase II process the substrates, but with different efficiencies. Crystal structures were determined for both tautomerase I and tautomerase II, at 1.57 and 1.64 Å resolution, respectively. The backbones of tautomerase I and tautomerase II are highly similar, but have distinct active site environments. The results, in combination with those for other structurally and kinetically characterized 4-OT isozymes, suggest that tautomerase I catalyzes the tautomerization of both 2-hydroxymuconate and alkyl derivatives, whereas tautomerase II might specialize in other aromatic hydrocarbon metabolites. PMID:23831510

  1. The Baryonic Structure Probe: An Origins Probe to Characterize the Cosmic Web

    NASA Astrophysics Data System (ADS)

    Sembach, K. R.; Cen, R.; Dave, R.; Cook, T.; Donahue, M.; Ebbets, D. C.; Green, J. C.; Jenkins, E. B.; Oegerle, W. R.; Ostriker, J. P.; Prochaska, J. X.; Savage, B. D.; Shull, J. M.; Stahl, H. P.; Tripp, T. M.; Oppenheimer, B. D.; Furlanetto, S. R.; Fang, T.

    2005-12-01

    This concept study defines the scientific requirements and instrumental performance needed for a space mission to detect and characterize the cosmic web of matter, the processes that produce and govern its structure, and its influence on the formation and evolution of galaxies. Our new numerical simulations explicitly track the observational signatures of the web gas as a function of time (redshift) up to the present day. The simulations include prescriptions for feedback interactions between galaxies and the intergalactic medium, and demonstrate that the ultraviolet O VI lines and the H I Lyman alpha line are premier diagnostics of low-density cosmic web regions. We define the field of view, angular resolution, and sensitivity needed to detect the web filaments in emission and absorption, and the spectral resolution needed to separate the gas signatures from foreground signals. These results define the driving science requirements for the Baryonic Structure Probe and any other future missions seeking to characterize the cosmic web. The science requirements can be met with a dedicated observatory in an L2 orbit capable of simultaneously observing both the faint emissions and weak absorption lines from the cosmic web. Our mission concept baselines a low risk 5-year core science mission with a 10-year design lifetime. Technological investments that would improve performance include the development of high quantum efficiency ultraviolet detectors, large format diffraction gratings, and improved optical coatings.

  2. Structural and optical characterizations of chemically deposited cadmium selenide thin films

    SciTech Connect

    Khomane, A.S.

    2011-10-15

    Highlights: {yields} CdSe thin films deposited first time using formic acid as a complexing agent. {yields} The deposited thin films were characterized by XRD, SEM, UV-vis-NIR and electrical techniques. {yields} X-ray diffraction analysis shows presence of zinc blende crystal structure. -- Abstract: Synthesis of cadmium selenide thin films by CBD method has been presented. The deposited film samples were subjected to XRD, SEM, UV-vis-NIR and TEP characterization. X-ray diffraction analysis showed that CdSe film sample crystallized in zinc blende or cubic phase structure. SEM studies reveal that the grains are spherical in shape and uniformly distributed all over the surface of the substrates. The optical band gap energy of as deposited film sample was found to be in the order of 1.8 eV. The electrical conductivity of the film sample was found to be 10{sup -6} ({Omega} cm){sup -1} with n-type of conduction mechanism.

  3. 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.

  4. 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.

  5. Solid freeform fabrication and characterization of porous calcium polyphosphate structures for tissue engineering purposes.

    PubMed

    Shanjani, Yaser; De Croos, J N Amritha; Pilliar, Robert M; Kandel, Rita A; Toyserkani, Ehsan

    2010-05-01

    Solid freeform fabrication (SFF) enables the fabrication of anatomically shaped porous components required for formation of tissue engineered implants. This article reports on the characterization of a three-dimensional-printing method, as a powder-based SFF technique, to create reproducible porous structures composed of calcium polyphosphate (CPP). CPP powder of 75-150 microm was mixed with 10 wt % polyvinyl alcohol (PVA) polymeric binder, and used in the SFF machine with appropriate settings for powder mesh size. The PVA binder was eliminated during the annealing procedure used to sinter the CPP particles. The porous SFF fabricated components were characterized using scanning electron microscopy, micro-CT scanning, X-ray diffraction, and mercury intrusion porosimetry. In addition, mechanical testing was conducted to determine the compressive strength of the CPP cylinders. The 35 vol % porous structures displayed compressive strength on average of 33.86 MPa, a value 57% higher than CPP of equivalent volume percent porosity made through conventional gravity sintering. Dimensional deviation and shrinkage analysis was conducted to identify anisotropic factors required for dimensional compensation during SFF sample formation and subsequent sintering. Cell culture studies showed that the substrate supported cartilage formation in vitro, which was integrated with the top surface of the porous CPP similar to that observed when chondrocytes were grown on CPP formed by conventional gravity sintering methods as determined histologically and biochemically.

  6. Synthesis, structural characterization and formation mechanism of ferroelectric bismuth vanadate nanotubes.

    PubMed

    Singh, Satyendra; Kumari, Neelam; Varma, K B R; Krupanidhi, S B

    2009-11-01

    We report the synthesis and structural characterization of ferroelectric bismuth vanadate (Bi2VO5.5) (BVO) nanotubes within the nanoporous anodic aluminum oxide (AAO) templates via sol-gel method. The as-prepared BVO nanotubes were characterized by X-ray powder diffraction (XRD), Scanning Electron Microscope (SEM), High-Resolution Transmission Electron Microscope (HRTEM) and the stoichiometry of the nanotubes was established by energy-dispersive X-ray spectroscopy (EDX). Postannealed (675 degrees C for 1 h), BVO nanotubes were a polycrystalline and the XRD studies confirmed the crystal structure to be orthorhombic. The uniformity in diameter and length of the nanotubes as reveled by the TEM and SEM suggested that these were influenced to a guest extent by the thickness and pore diameter of the nanoporous AAO template. EDX analysis demonstrated the formation of stoichiometric Bi2VO5.5 phase. HRTEM confirmed that the obtained BVO nanotubes were made up of nanoparticles of 5-9 nm range. The possible formation mechanism of nanotubes was elucidated.

  7. 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

  8. Synthesis and structural characterization of 9-azido-9-borafluorene: monomer and cyclotrimer of a borole azide.

    PubMed

    Biswas, Sunanda; Oppel, Iris M; Bettinger, Holger F

    2010-05-17

    The reaction of 2,2'-dilithiobiphenyl, generated from 2,2'-dibromobiphenyl and n-BuLi, with BCl(3) using n-hexane as solvent provides a high-yielding, simple preparative route to 9-chloro-9-borafluorene 1a. This in turn can be reacted with trimethylsilyl azide to yield 9-azido-9-borafluorene 2. Compound 2 exists as a cyclic trimer in the solid state, but in dichloromethane solution the monomer can coexist with the trimer. Azide 2 is rather unstable both in the solid state and in solution, and it transforms with trace amounts of water and oxygen to the 1,3,5-tris(2-biphenylyl)cyclotriboroxane that was characterized by X-ray diffraction analysis. Addition of pyridine and t-butyl pyridine to azide 2 afford the corresponding pyridine adducts. Compound 1a as well as the Lewis base adducts of 2 have been characterized by multinuclear NMR spectroscopy, and the structures were confirmed by X-ray diffraction analysis. The structural features of azide 2 and the strong Lewis acidity of its boron center have also been investigated by computational chemistry techniques at the MP2 level of theory.

  9. 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.

  10. Characterizing the structure and content of nurse handoffs: A Sequential Conversational Analysis approach.

    PubMed

    Abraham, Joanna; Kannampallil, Thomas; Brenner, Corinne; Lopez, Karen D; Almoosa, Khalid F; Patel, Bela; Patel, Vimla L

    2016-02-01

    Effective communication during nurse handoffs is instrumental in ensuring safe and quality patient care. Much of the prior research on nurse handoffs has utilized retrospective methods such as interviews, surveys and questionnaires. While extremely useful, an in-depth understanding of the structure and content of conversations, and the inherent relationships within the content is paramount to designing effective nurse handoff interventions. In this paper, we present a methodological framework-Sequential Conversational Analysis (SCA)-a mixed-method approach that integrates qualitative conversational analysis with quantitative sequential pattern analysis. We describe the SCA approach and provide a detailed example as a proof of concept of its use for the analysis of nurse handoff communication in a medical intensive care unit. This novel approach allows us to characterize the conversational structure, clinical content, disruptions in the conversation, and the inherently phasic nature of nurse handoff communication. The characterization of communication patterns highlights the relationships underlying the verbal content of nurse handoffs with specific emphasis on: the interactive nature of conversation, relevance of role-based (incoming, outgoing) communication requirements, clinical content focus on critical patient-related events, and discussion of pending patient management tasks. We also discuss the applicability of the SCA approach as a method for providing in-depth understanding of the dynamics of communication in other settings and domains.

  11. Structural characterization of nanoscale intermetallic precipitates in highly neutron irradiated reactor pressure vessel steels

    DOE PAGES

    Sprouster, D. J.; Sinsheimer, J.; Dooryhee, 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

  12. Characterization of the vertical structure of tropospheric water vapor over the Island of Tahiti

    NASA Astrophysics Data System (ADS)

    Serafini, Jonathan

    2014-05-01

    We study the vertical variability of tropospheric water vapor over the island of Tahiti from radiosondes made every 12 hours from 2003 to 2011. In particular, we present the characteristic profiles associated with the trade winds and those associated with the presence of deep convection. The vertical profiles associated with trade winds are usually strongly influenced by a temperature inversion layer about 400 meters thick. It is typically located 3 km altitude. This inversion area generally bounds the lower troposphere wetted by the ocean and the free tropophere dried by subsidence. The vertical structure of the water vapor is marked by a sudden decrease in the inversion layer. Conversely, when the convection is deep enough, it enhances mixing between the different layers of the troposphere and the profiles are more continuous. To characterize the vertical structure of the water vapor, we define a model whose objective is to identify the presence of this inversion layer (obstruction of deep convection), its altitude and its thickness. These two parameters, coupled with other weather index are used to characterize tropical rainfall.

  13. 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

  14. Tunable mechanical monolithic sensors for large band low frequency monitoring and characterization of sites and structures

    NASA Astrophysics Data System (ADS)

    Barone, F.; Giordano, G.; Acernese, F.; Romano, R.

    2016-10-01

    Among the different mechanical architectures present in literature, the Watts linkage is one of the most promising ones for the implementation of a new class of mechanical accelerometers (horizontal, vertical and angular). In this paper, we present monolithic implementations of uniaxial and triaxial mechanical seismometers and accelerometers based on the UNISA Folded Pendulum mechanical configuration, optimized for low frequency characterization of sites (including underground sites) and structures as inertial sensor (seismometer). This mechanical architecture allows the design and implementation of very large band monolithic sensors (10-7Hz 102 Hz), whose sensitivities for the most common applications are defined by the noise introduced by their readouts (e.g. ¡ 10-12 m/sqrt(Hz) with classical LVDT readouts). These unique features, coupled other relevant properties like scalability, compactness, lightness, high directivity, frequency tunability (typical resonance frequencies in the band 10-1 Hz 102 Hz), very high immunity to environmental noises and low cost make this class of sensors very effective for the implementation of uniaxial (horizontal and/or vertical) and triaxial seismometers and accelerometers for ground, space and underwater applications, including UHV and cryogenics ones. Typical applications of this class of monolithic sensors are in the field of earthquake engineering, seismology, geophysics, civil engineering, characterization of sites (including underground sites), structures (e.g. buildings, bridges, historical monuments), and, in general, in all applications requiring large band-low frequency performances coupled with high sensitivities and compactness.

  15. Near-complete structural characterization of phosphatidylcholines using electron impact excitation of ions from organics.

    PubMed

    Campbell, J Larry; Baba, Takashi

    2015-06-02

    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.

  16. Characterization of carbonized polydopamine nanoparticles suggests ordered supramolecular structure of polydopamine.

    PubMed

    Yu, Xiang; Fan, Hailong; Liu, Yang; Shi, Zujin; Jin, Zhaoxia

    2014-05-20

    Polydopamine is not only a multifunctional biopolymer with promising optoelectronic properties but it is also a versatile coating platform for different surfaces. The structure and formation of polydopamine is an active area of research. Some studies have supposed that polydopamine is composed of covalently bonded dihydroxyindole, indoledione, and dopamine units, but others proposed that noncovalent self-assembly contributes to polydopamine formation as well. However, it is difficult to directly find the details of supramolecular structure of polydopamine via self-assembly. In this study, we first report the graphite-like nanostructure observed in the carbonized polydopamine nanoparticles in nitrogen (or argon) environment at 800 °C. Raman characterization, which presents the typical D band and G band, confirmed the existence of graphite-like nanostructures. Our observation provides clear evidence for a layered-stacking supramolecular structure of polydopamine. Particularly, the size of graphite-like domains is similar to that of disk-shaped aggregates hypothesized in previous study about the polymerization of 5,6-dihydroxyindole [ Biomacromolecules 2012 , 13 , 2379 ]. Analysis of the hierarchical structure of polydopamine helps us understand its formation.

  17. Analytical and Experimental Characterization of Gravity Induced Deformations In Subscale Gossamer Structures

    NASA Technical Reports Server (NTRS)

    Johnston, John D.; Blandino, Joseph R.; McEvoy, Kiley C.

    2004-01-01

    The development of gossamer space structures such as solar sails and sunshields presents many challenges due to their large size and extreme flexibility. The post-deployment structural geometry exhibited during ground testing may significantly depart from the in-space configuration due to the presence of gravity-induced deformations (gravity sag) of lightly preloaded membranes. This paper describes a study carried out to characterize gravity sag in two subscale gossamer structures: a single quadrant from a 2 m, 4 quadrant square solar sail and a 1.7 m membrane layer from a multi-layer sunshield The behavior of the test articles was studied over a range of preloads and in several orientations with respect to gravity. An experimental study was carried out to measure the global surface profiles using photogrammetry, and nonlinear finite element analysis was used to predict the behavior of the test articles. Comparison of measured and predicted surface profiles shows that the finite dement analysis qualitatively predicts deformed shapes comparable to those observed in the laboratory. Quantitatively, finite element analysis predictions for peak gravity-induced deformations in both test articles were within 10% of measured values. Results from this study provide increased insight into gravity sag behavior in gossamer structures, and demonstrates the potential to analytically predict gravity-induced deformations to within reasonable accuracy.

  18. Biochemical and structural characterization of a novel bacterial manganese-dependent hydroxynitrile lyase.

    PubMed

    Hajnal, Ivan; Lyskowski, Andrzej; Hanefeld, Ulf; Gruber, Karl; Schwab, Helmut; Steiner, Kerstin

    2013-11-01

    Hydroxynitrile lyases (HNLs), which catalyse the decomposition of cyanohydrins, are found mainly in plants. In vitro, they are able to catalyse the synthesis of enantiopure cyanohydrins, which are versatile building blocks in the chemical industry. Recently, HNLs have also been discovered in bacteria. Here, we report on the detailed biochemical and structural characterization of a hydroxynitrile lyase from Granulicella tundricola (GtHNL), which was successfully heterologously expressed in Escherichia coli. The crystal structure was solved at a crystallographic resolution of 2.5 Å and exhibits a cupin fold. As GtHNL does not show any sequence or structural similarity to any other HNL and does not contain conserved motifs typical of HNLs, cupins represent a new class of HNLs. GtHNL is metal-dependent, as confirmed by inductively coupled plasma/optical emission spectroscopy, and in the crystal structure, manganese is bound to three histidine and one glutamine residue. GtHNL displayed a specific activity of 1.74 U·mg(-1) at pH 6 with (R)-mandelonitrile, and synthesized (R)-mandelonitrile with 90% enantiomeric excess at 80% conversion using 0.5 m benzaldehyde in a biphasic reaction system with methyl tertiary butyl ether.

  19. 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.

  20. Characterization of vertical-cavity surface-emitting laser structures by modulation spectroscopy: A status report

    NASA Astrophysics Data System (ADS)

    Klar, P. J.; Karcher, C.; Metzger, B.; Hosea, T. J. C.

    2005-05-01

    The present issue of physica status solidi (a) contains contributions from the International Workshop on Modulation Spectroscopy of Semiconductor Structures (MS3), held in Wrocaw, Poland, 1-3 July 2004.Editor's Choice is the article by P. J. Klar et al. [1] in which the advantages of these techniques are used to characterize optoelectronic devices. For a vertical-cavity surface-emitting laser structure (shown schematically in the lower part) to operate, the emission wavelength qw of its active region and the cavity mode at cav of its resonator structure need to coincide. The photomodulated reflectance spectrum (upper left part, bottom) shows clear features at both wavelengths whereas a feature at qw cannot be distinguished in the corresponding reflectance spectrum (top) due to its complicated photonic nature.The first author, Peter J. Klar is currently a lecturer of Physics at the Philipps-University of Marburg, Germany. His research interests include the physics of magnetic semiconductors and hybrids for spintronics, of III-N-V semiconductor structures for optoelectronics, and of novel nanostructures ranging from nanomagnetism to applications in catalysis.

  1. 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.

  2. 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.

  3. Surface-enhanced resonance Raman spectroscopic characterization of the protein native structure.

    PubMed

    Feng, Manliang; Tachikawa, Hiroyasu

    2008-06-11

    Surface-enhanced resonance Raman scattering (SERRS) spectra of biological species are often different from their resonance Raman (RR) spectra. A home-designed Raman flow system is used to determine the factors that contribute to the difference between the SERRS and RR of met-myoglobin (metMb). The results indicate that both the degree of protein-nanoparticles interaction and the laser irradiation contribute to the structural changes and are responsible for the observed differences between the SERRS and RR spectra of metMb. The prolonged adsorption of the protein molecules on the nanoparticle surface, which is the condition normally used for the conventional SERRS experiments, disturbs the heme pocket structure and facilitates the charge transfer process and the photoinduced transformation of proteins. The disruption of the heme pocket results in the loss of the distal water molecule, and the resulting SERRS spectrum of metMb shows a 5-coordinated high-spin heme. The flow system, when operated at a moderately high flow rate, can basically eliminate the factors that disturb the protein structure while maintaining a high enhancement factor. The SERRS spectrum obtained from a 1 x 10 (-7) M metMb solution using this flow system is basically identical to the RR spectrum of a 5 x 10 (-4) M metMb solution. Therefore, the Raman flow system reported here should be useful for characterizing the protein-nanoparticles interaction and the native structure of proteins using SERRS spectroscopy.

  4. 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).

  5. Interface mobilities for characterization of structure-borne sound sources resiliently mounted via multiple contact points

    NASA Astrophysics Data System (ADS)

    Mathiowetz, S.; Bonhoff, H. A.

    2013-10-01

    This paper introduces an expansion of the interface mobility method for structure-borne sound sources that are resiliently mounted to a receiving structure at multiple discrete contact points. Subsystems of source, receiver and isolators are represented by Fourier transforms of their mobility matrices. Along with the source activity, a formulation for the transmitted power fed into the receiver is obtained. Furthermore, the source descriptor and a coupling function for resiliently mounted multi-point sources are obtained which both form recognized concepts for structure-borne sound source characterization. The method is based on a neglection of cross-order terms which describe a coupling between Fourier coefficients of different order. With regard to a subsystem of discretely placed isolators, cross-order terms were found to account for variations of isolator parameters along the contact points. In a set of numerical studies it was shown that errors introduced by neglecting cross-order terms are most pronounced in the higher frequency region where isolators show resonant behavior due to internal wave effects. A subsystem of identical isolators is completely described by equal-order terms, therefore no error is introduced considering such cases. Moreover, errors inherent in the rigidly mounted case due to cross-order source or receiver mobilities are reduced significantly when isolator mobilities are large compared to those from source and receiver. Findings from theoretical studies were validated in practical settings considering structure-borne sound transmission from a ship diesel engine and a magnetic resonance imaging (MRI) device.

  6. 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.

  7. Low-resolution characterization of the 3D structure of the Euglena gracilis photoreceptor.

    PubMed

    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 90A). 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. Synthesis and characterization of crystalline structures based on phenylboronate ligands bound to alkaline earth cations.

    PubMed

    Reinholdt, Marc; Croissant, Jonas; Di Carlo, Lidia; Granier, Dominique; Gaveau, Philippe; Bégu, Sylvie; Devoisselle, Jean-Marie; Mutin, P Hubert; Smith, Mark E; Bonhomme, Christian; Gervais, Christel; van der Lee, Arie; Laurencin, Danielle

    2011-08-15

    We describe the preparation of the first crystalline compounds based on arylboronate ligands PhB(OH)(3)(-) coordinated to metal cations: [Ca(PhB(OH)(3))(2)], [Sr(PhB(OH)(3))(2)]·H(2)O, and [Ba(PhB(OH)(3))(2)]. The calcium and strontium structures were solved using powder and single-crystal X-ray diffraction, respectively. In both cases, the structures are composed of chains of cations connected through phenylboronate ligands, which interact one with each other to form a 2D lamellar structure. The temperature and pH conditions necessary for the formation of phase-pure compounds were investigated: changes in temperature were found to mainly affect the morphology of the crystallites, whereas strong variations in pH were found to affect the formation of pure phases. All three compounds were characterized using a wide range of analytical techniques (TGA, IR, Raman, XRD, and high resolution (1)H, (11)B, and (13)C solid-state NMR), and the different coordination modes of phenylboronate ligands were analyzed. Two different kinds of hydroxyl groups were identified in the structures: those involved in hydrogen bonds, and those that are effectively "free" and not involved in hydrogen bonds of any significant strength. To position precisely the OH protons within the structures, an NMR-crystallography approach was used: the comparison of experimental and calculated NMR parameters (determined using the Gauge Including Projector Augmented Wave method, GIPAW) allowed the most accurate positions to be identified. In the case of the calcium compound, it was found that it is the (43)Ca NMR data that are critical to help identify the best model of the structure.

  14. 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.

  15. 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

  16. Characterization of structural and electronic properties of nanoscale semiconductor device structures using cross-sectional scanning probe microscopy

    NASA Astrophysics Data System (ADS)

    Rosenthal, Paul Arthur

    Scanning probe microscopy (SPM) offers numerous advantages over metrology tools traditionally used for semiconductor materials and device characterization including high lateral spatial resolution, and relative ease of use. Cross-sectional SPM allows material and device measurements including layer thickness metrology and p-n junction delineation on actual nanoscale device structures. Site-specific SPM allows measurements to be performed on modern devices with real, non-arbitrary geometries including deep-submicron Si device structures. In Chapter II we present theoretical analysis and experimental results of capacitive force microscopy studies of AlxGa1-xAs/GaAs heterojunction bipolar transistor structures. The contrast obtained yields clear delineation of individual device layers based on doping, and enables a precise determination of the difference in basewidth between the two HBT samples examined. We experimentally determine a charged surface state density on the GaAs {110} surface that is consistent with published values. In Chapter III we present cross-sectional scanning capacitance microscopy (SCM) of nanoscale group IV Si device structures. Sample preparation techniques are discussed in context with recent experimental results from the literature. We then presented a theoretical calculation of the flat-band and threshold voltage of Si-MOSFETs as a function of doping including error analysis due to oxide thickness variations. Application to nanoscale FIB implanted Si is presented. The SCM contrast evolves as a function of applied bias as expected based on theoretical modeling of the tip-sample system as an MOS-capacitor. In Chapter IV we apply cross-sectional SCM to directly measure the electronic properties of a 120 nm gate length p-MOSFET including super-halo implants. Bias-dependent SCM images allow us to delineate the individual device regions and image the n+ super-halo implants. We have demonstrated the specific SCM bias conditions necessary for

  17. 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.

  18. Smart Fluids in Hydrology: Use of Non-Newtonian Fluids for Pore Structure Characterization