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Sample records for probing structure property

  1. Scanning Probe Evaluation of Electronic, Mechanical and Structural Material Properties

    NASA Astrophysics Data System (ADS)

    Virwani, Kumar

    2011-03-01

    We present atomic force microscopy (AFM) studies of a range of properties from three different classes of materials: mixed ionic electronic conductors, low-k dielectrics, and polymer-coated magnetic nanoparticles. (1) Mixed ionic electronic conductors are being investigated as novel diodes to drive phase-change memory elements. Their current-voltage characteristics are measured with direct-current and pulsed-mode conductive AFM (C-AFM). The challenges to reliability of the C-AFM method include the electrical integrity of the probe, the sample and the contacts, and the minimization of path capacitance. The role of C-AFM in the optimization of these electro-active materials will be presented. (2) Low dielectric constant (low-k) materials are used in microprocessors as interlayer insulators, a role directly affected by their mechanical performance. The mechanical properties of nanoporous silicate low-k thin films are investigated in a comparative study of nanomechanics measured by AFM and by traditional nanoindentation. Both methods are still undergoing refinement as reliable analytical tools for determining nanomechanical properties. We will focus on AFM, the faster of the two methods, and its developmental challenges of probe shape, cantilever force constant, machine compliance and calibration standards. (3) Magnetic nanoparticles are being explored for their use in patterned media for magnetic storage. Current methods for visualizing the core-shell structure of polymer-coated magnetic nanoparticles include dye-staining the polymer shell to provide contrast in transmission electron microscopy. AFM-based fast force-volume measurements provide direct visualization of the hard metal oxide core within the soft polymer shell based on structural property differences. In particular, the monitoring of adhesion and deformation between the AFM tip and the nanoparticle, particle-by-particle, provides a reliable qualitative tool to visualize core-shell contrast without the use

  2. Probing Structure Property Relationships in Complex Engineering Silicones by 1H NMR

    SciTech Connect

    Chinn, S C; Gjersing, E L; Maxwell, R S; Eastwood, E; Bowen, D; Stephens, T

    2006-07-14

    It is generally accepted that the properties of polymeric materials are controlled by the network structure and the reactions by which they have been constructed. These properties include the bulk moduli at creation, but also the properties as a function of age during use. In order to interpret mechanical properties and predict the time dependent changes in these properties, detailed knowledge of the effect of structural changes must be obtained. The degree and type of crosslinking, the molecular weight between crosslinks, the number of elastically ineffective chains (loops, dangling chain ends, sol-fraction) must be characterized. A number of theoretical and experimental efforts have been reported in the last few years on model networks prepared by endlinking reactions and the relationships of those structures with the ultimate mechanical properties. A range of experimental methods have been used to investigate structure including rheometric, scattering, infrared, {sup 29}Si MAS and CPMAS, {sup 1}H relaxation measurements, and recently {sup 1}H multiple quantum methods. Characterization of the growth of multiple quantum coherences have recently been shown to provide detailed insight into silicone network structure by the ability to selective probe the individual components of the polymer network, such as the polymer-filler interface or network chains. We have employed recently developed MQ methods to investigate the structure-property relationships in a series of complex, endlinked filled-PDMS blends. Here, a systematic study of the relationship between the molecular formulation, as dictated by the amount and type of crosslinks present and by the remaining network chains, and the segmental dynamics as observed by MQ NMR was performed.

  3. Probing the band structure and local electronic properties of low-dimensional semiconductor structures

    NASA Astrophysics Data System (ADS)

    Walrath, Jenna Cherie

    Low-dimensional semiconductor structures are important for a wide variety of applications, and recent advances in nanoscale fabrication are paving the way for increasingly precise nano-engineering of a wide range of materials. It is therefore essential that the physics of materials at the nanoscale are thoroughly understood to unleash the full potential of nanotechnology, requiring the development of increasingly sophisticated instrumentation and modeling. Of particular interest is the relationship between the local density of states (LDOS) of low-dimensional structures and the band structure and local electronic properties. This dissertation presents the investigation of the band structure, LDOS, and local electronic properties of nanostructures ranging from zero-dimensional (0D) quantum dots (QDs) to two-dimensional (2D) thin films, synthesizing computational and experimental approaches including Poisson-Schrodinger band structure calculations, scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS), and scanning thermoelectric microscopy (SThEM). A method is presented for quantifying the local Seebeck coefficient (S) with SThEM, using a quasi-3D conversion matrix approach to directly convert temperature gradient-induced voltages S. For a GaAs p-n junction, the resulting S-profile is consistent with that computed using the free carrier concentration profile. This combined computational-experimental approach is expected to enable nanoscale measurements of S across a wide variety of heterostructure interfaces. The local carrier concentration, n, is profiled across epitaxial InAs/GaAs QDs, where SThEM is used to profile the temperature gradient-induced voltage, which is converted to a profile of the local S and finally to an n profile. The S profile is converted to a conduction band-edge profile and compared with Poisson-Schrodinger band-edge simulations. The combined computational-experimental approach suggests a reduced n in the QD center in

  4. A novel approach to study the structure-property relationships and applications in living systems of modular Cu2+ fluorescent probes

    NASA Astrophysics Data System (ADS)

    She, Mengyao; Yang, Zheng; Hao, Likai; Wang, Zhaohui; Luo, Tianyou; Obst, Martin; Liu, Ping; Shen, Yehua; Zhang, Shengyong; Li, Jianli

    2016-08-01

    A series of Cu2+ probe which contains 9 probes have been synthesized and established. All the probes were synthesized using Rhodamine B as the fluorophore, conjugated to various differently substituted cinnamyl aldehyde with C=N Schiff base structural motif as their core moiety. The structure-property relationships of these probes have been investigated. The change of optical properties, caused by different electronic effect and steric effect of the recognition group, has been analyzed systematically. DFT calculation simulation of the Ring-Close and Ring-Open form of all the probes have been employed to illuminate, summarize and confirm these correlations between optical properties and molecular structures. In addition, biological experiment demonstrated that all the probes have a high potential for both sensitive and selective detection, mapping of adsorbed Cu2+ both in vivo and environmental microbial systems. This approach provides a significant strategy for studying structure-property relationships and guiding the synthesis of probes with various optical properties.

  5. Probing structure-property relationships in perpendicularly magnetized Fe/Cu(001) using MXLD and XPD

    SciTech Connect

    Cummins, T.R.; Waddill, G.D.; Goodman, K.W.

    1997-04-01

    Magnetic X-ray Linear Dichroism (MXLD) in Photoelectron Spectroscopy and X-Ray Photoelectron Diffraction (XPD) of the Fe 3p core level have been used to probe the magnetic structure-property relationships of perpendicularly magnetized Fe/Cu(001), in an element-specific fashion. A strong MEXLD effect was observed in the high resolution photoelectron spectroscopy of the Fe 3p at {open_quotes}normal{close_quotes} emission and was used to follow the loss of perpendicular ferromagnetic ordering as the temperature was raised toward room temperature. In parallel with this, {open_quotes}Forward Focussing{close_quotes} in XPD was used as a direct measure of geometric structure in the overlayer. These results and the implications of their correlation will be discussed. Additionally, an investigation of the effect of Mn doping of the Fe/Cu(001) will be described. These measurements were performed at the Spectromicroscopy Facility (Beamline 7.0.1) of the Advanced Light Source.

  6. An integrated approach for probing the structure and mechanical properties of diatoms: Toward engineered nanotemplates.

    PubMed

    Moreno, Miguel Diaz; Ma, Kaka; Schoenung, Julie; Dávila, Lilian P

    2015-10-01

    The wide variety of diatom frustule shapes and intricate architectures provide viable prototypes to guide the design and fabrication of nanodevices and nanostructured materials for applications ranging from sensors to nanotemplates. In this study, a combined experimental-simulation method was developed to probe the porous structure and mechanical behavior of two distinct marine diatom species, Coscinodiscus sp. (centric) and Synedra sp. (pennate), through ambient nanoindentation and finite element method analysis. These diatom frustule dimensions differed largely depending on diatom species with pore diameters d ranging from 0.3 to 3.0 μm. Young's modulus E and hardness H measurements of the diatom frustules were obtained via nanoindentation experiments. These values varied depending on diatom species (E between 1.1-10.6 GPa, H between 0.10-1.03 GPa for the Coscinodiscus sp.; and E between 13.7-18.6 GPa, H between 0.85-1.41 GPa for the Synedra sp.). Additionally, the mechanical response of diatom structures to uniform compression was examined. Predictive simulations were performed on the aforementioned diatom frustules, as well as another diatom structure (pennate Fragilariopsis kerguelensis), to correlate the mechanical response with specific morphology variables (e.g., pore or slit sizes). Results from calculated von Mises stress and displacement distributions unveil unique information on the effect that uniform loads have on these frustules, which can aid the design of tailored nanotemplates. A correlation between mechanical properties and porosity was established for selected frustules, and reported for the first time in this study.

  7. Structure, cell wall elasticity and polysaccharide properties of living yeast cells, as probed by AFM

    NASA Astrophysics Data System (ADS)

    Alsteens, David; Dupres, Vincent; McEvoy, Kevin; Wildling, Linda; Gruber, Hermann J.; Dufrêne, Yves F.

    2008-09-01

    Although the chemical composition of yeast cell walls is known, the organization, assembly, and interactions of the various macromolecules remain poorly understood. Here, we used in situ atomic force microscopy (AFM) in three different modes to probe the ultrastructure, cell wall elasticity and polymer properties of two brewing yeast strains, i.e. Saccharomyces carlsbergensis and S. cerevisiae. Topographic images of the two strains revealed smooth and homogeneous cell surfaces, and the presence of circular bud scars on dividing cells. Nanomechanical measurements demonstrated that the cell wall elasticity of S. carlsbergensis is homogeneous. By contrast, the bud scar of S. cerevisiae was found to be stiffer than the cell wall, presumably due to the accumulation of chitin. Notably, single molecule force spectroscopy with lectin-modified tips revealed major differences in polysaccharide properties of the two strains. Polysaccharides were clearly more extended on S. cerevisiae, suggesting that not only oligosaccharides, but also polypeptide chains of the mannoproteins were stretched. Consistent with earlier cell surface analyses, these findings may explain the very different aggregation properties of the two organisms. This study demonstrates the power of using multiple complementary AFM modalities for probing the organization and interactions of the various macromolecules of microbial cell walls.

  8. Local probing of structure and property in dimensionally confined amorphous and crystalline structures by S/TEM

    NASA Astrophysics Data System (ADS)

    Yan, Aiming

    The characterization of materials' microstructure has been brought up to a new level since the invention and broad application of transmission electron microscope (TEM) thanks to the high-energy electron beam source which guarantees an unsurpassable spatial resolution and theoretical study of interaction between electron and matter. The advent of nano-world has imposed an urgent request to characterize nano-assemblies in nano- or even sub-nano-scale and scanning transmission electron microscopy (STEM) which typically utilizes an electron probe with a size of 1nm or even smaller has found its unique advantage to unravel the local structure, chemical and physical properties of these emerging nanostructures. Dimensionally constrained nanostructures such as thin films and nanopatterned systems have attracted people's attention for decades due to their novel chemical and physical properties and popularity in energy storage, biological integration and etc. This dissertation focuses on the unique characterization capability of S/TEM to study the local order in amorphous transparent conducting oxide thin films, disordering in 2-D layered materials, localized surface plasmons in nanoporous gold patterns on 2-D layered structures and crystallization process in dimensionally and spatially constrained oxide nanopatterns observed by in-situ TEM. Electron diffraction and x-ray diffraction are commonly used techniques to study the crystallinity in a certain material - crystalline or amorphous. In amorphous materials which lack long-range order, normal electron diffraction and x-ray diffraction techniques won't be able to extract any useful information regarding the ordering or disordering in the materials. We have developed a unique set of electron diffraction methods in both TEM and STEM, combined with density functional theory molecular dynamics of liquid quench to study the short-range (< 1 nm) and medium-range order (between 1 nm and 3 nm) in amorphous transparent oxide films

  9. 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

  10. A theoretical probe of high-valence uranium and transuranium silylamides: Structural and redox properties

    NASA Astrophysics Data System (ADS)

    Zhong, Yu-Xi; Guo, Yuan-Ru; Pan, Qing-Jiang

    2016-02-01

    Relativistic density functional theory was used to explore the structural and redox properties of 18 prototypical actinyl silylamides including a variation of metals (U, Np and Pu), metal oxidation states (VI and V) and equatorial ligands. A theoretical approach associated with implicit solvation and spin-orbit/multiplet corrections was proved to be reliable. A marked shift of reduction potentials of actinyl silylamides caused by changes of equatorial coordination ligands and implicit solvation was elucidated by analyses of electronic structures and single-electron reduction mechanism.

  11. A novel approach to study the structure-property relationships and applications in living systems of modular Cu2+ fluorescent probes

    PubMed Central

    She, Mengyao; Yang, Zheng; Hao, Likai; Wang, Zhaohui; Luo, Tianyou; Obst, Martin; Liu, Ping; Shen, Yehua; Zhang, Shengyong; Li, Jianli

    2016-01-01

    A series of Cu2+ probe which contains 9 probes have been synthesized and established. All the probes were synthesized using Rhodamine B as the fluorophore, conjugated to various differently substituted cinnamyl aldehyde with C=N Schiff base structural motif as their core moiety. The structure-property relationships of these probes have been investigated. The change of optical properties, caused by different electronic effect and steric effect of the recognition group, has been analyzed systematically. DFT calculation simulation of the Ring-Close and Ring-Open form of all the probes have been employed to illuminate, summarize and confirm these correlations between optical properties and molecular structures. In addition, biological experiment demonstrated that all the probes have a high potential for both sensitive and selective detection, mapping of adsorbed Cu2+ both in vivo and environmental microbial systems. This approach provides a significant strategy for studying structure-property relationships and guiding the synthesis of probes with various optical properties. PMID:27485974

  12. Probing of field-induced structures and tunable rheological properties of surfactant capped magnetically polarizable nanofluids.

    PubMed

    Felicia, Leona J; Philip, John

    2013-01-08

    Oil-based nanofluid containing surfactant-capped magnetite nanoparticles are synthesized by a simple coprecipitation approach, and their magnetorheological properties are studied for different magnetic field strengths and volume fractions. We observe a distinct "plateau-like region" in the shear thinning viscosity curve, under an external magnetic field, possibly due to a peculiar alignment of the chains with respect to the field direction where the structure is stable against fragmentation. The observed plateau regime is reminiscent to that of kinetically arrested gel networks. Interestingly, such a plateau regime has been observed only above certain critical magnetic field when the dipolar interaction strength is much greater than the thermal energy where the aggregation becomes a nonequilibrium transport-limited process. The good collapse of specific viscosity data against Mason number for different magnetic field strengths onto a single curve suggests the dominance of hydrodynamic and magnetic forces on thermal force above a certain magnetic field strength. The observed increase in both static and dynamic yield stresses under the magnetic field confirms the formation of columnar structures that hinder the flow behavior. The hysteresis observed in the magnetic sweep experiments shows the inability of the chains to relax within the measurement time. The dynamic measurements confirm that the field-induced structures impart elastic behavior to the dispersion, which is found to increase with magnetic field and saturates at higher field strengths.

  13. Probing the structure, stability and hydrogen storage properties of calcium dodecahydro-closo-dodecaborate

    SciTech Connect

    Stavila, Vitalie; Her, Jae-Hyuk; Zhou Wei; Hwang, Son-Jong; Kim, Chul; Ottley, Leigh Anna M.; Udovic, Terrence J.

    2010-05-15

    Calcium borohydride can reversibly store up to 9.6 wt% hydrogen; however, the material displays poor cyclability, generally associated with the formation of stable intermediate species. In an effort to understand the role of such intermediates on the hydrogen storage properties of Ca(BH{sub 4}){sub 2}, calcium dodecahydro-closo-dodecaborate was isolated and characterized by diffraction and spectroscopic techniques. The crystal structure of CaB{sub 12}H{sub 12} was determined from powder XRD data and confirmed by DFT and neutron vibrational spectroscopy studies. Attempts to dehydrogenate/hydrogenate mixtures of CaB{sub 12}H{sub 12} and CaH{sub 2} were made under conditions known to favor partial reversibility in calcium borohydride. However, up to 670 K no notable formation of Ca(BH{sub 4}){sub 2} (during hydrogenation) or CaB{sub 6} (during dehydrogenation) occurred. It was demonstrated that the stability of CaB{sub 12}H{sub 12} can be significantly altered using CaH{sub 2} as a destabilizing agent to favor the hydrogen release. - Graphical abstract: Calcium dodecahydro-closo-dodecaborate, CaB{sub 12}H{sub 12} (1), was isolated by dehydration/desolvation of [Ca(H{sub 2}O){sub 7}][B{sub 12}H{sub 12}].H{sub 2}O (2) or [Ca(H{sub 2}O){sub 5}(MeCN){sub 2}][B{sub 12}H{sub 12}] (3). The crystal structure of 1 was determined by powder X-ray diffraction and confirmed by neutron vibrational spectroscopy and first-principles calculations. Hydrogen storage properties of 1 in the presence of calcium hydride were elucidated.

  14. A resonant structure designed for probing the elastic properties of suspension and adherent cells in liquid environments

    NASA Astrophysics Data System (ADS)

    Desmaële, D.; Boukallel, M.; Régnier, S.

    2012-11-01

    This paper presents a novel force sensitive structure exploiting a dynamic mode for probing the elastic properties of living cells. A key feature of this structure is the possibility of conducting measurements in liquid environments while keeping high dynamic performances. The structure indeed provides a steady area that can be adapted so that suspension or adherent cells can be placed in a culture medium. The steady area is also connected to two adjacent beam resonators. Because these resonators never need to be immersed into the culture medium during measurements, forces applied to cells can be estimated with a high sensitivity via frequency shifts. In this paper, we conduct an extensive theoretical analysis to investigate the nonlinear effects of large static pre-deflections on the dynamic behavior of the structure. As a proof of concept, we also report the fabrication, characterization and calibration of the first prototype intended to deal with suspension cells with a diameter ranging from 100 to 500 μm. This prototype currently offers a quality factor of 700 and a force sensitivity of ˜2.6 Hz mN-1. We also demonstrate that the prototype is capable of measuring the elastic modulus of biological samples in a rapid and sufficiently accurate manner without the need of a descriptive model.

  15. Probing metamaterials with structured light

    DOE PAGES

    Xu, Yun; Sun, Jingbo; Walasik, Wiktor; ...

    2016-11-03

    Photonic metamaterials and metasurfaces are nanostructured optical materials engineered to enable properties that have not been found in nature. Optical characterization of these structures is a challenging task. We report a reliable technique that is particularly useful for characterization of phase properties introduced by small and spatially inhomogeneous samples of metamaterials and metasurfaces. The proposed structured light, or vortex based interferometric method is used to directly visualize phase changes introduced by subwavelength-thick nanostructures. In order to demonstrate the efficiency of the proposed technique, we designed and fabricated several metasurface samples consisting of metal nano-antennas introducing different phase shifts and experimentallymore » measured phase shifts of the transmitted light. The experimental results are in good agreement with numerical simulations and with the designed properties of the antenna arrays. Finally, due to the presence of the singularity in the vortex beam, one of the potential applications of the proposed approach based on structured light is step-by-step probing of small fractions of the micro-scale samples or images.« less

  16. Probing metamaterials with structured light

    SciTech Connect

    Xu, Yun; Sun, Jingbo; Walasik, Wiktor; Litchinitser, Natalia M.

    2016-11-03

    Photonic metamaterials and metasurfaces are nanostructured optical materials engineered to enable properties that have not been found in nature. Optical characterization of these structures is a challenging task. We report a reliable technique that is particularly useful for characterization of phase properties introduced by small and spatially inhomogeneous samples of metamaterials and metasurfaces. The proposed structured light, or vortex based interferometric method is used to directly visualize phase changes introduced by subwavelength-thick nanostructures. In order to demonstrate the efficiency of the proposed technique, we designed and fabricated several metasurface samples consisting of metal nano-antennas introducing different phase shifts and experimentally measured phase shifts of the transmitted light. The experimental results are in good agreement with numerical simulations and with the designed properties of the antenna arrays. Finally, due to the presence of the singularity in the vortex beam, one of the potential applications of the proposed approach based on structured light is step-by-step probing of small fractions of the micro-scale samples or images.

  17. Coupled plasmon-waveguide resonators: a new spectroscopic tool for probing proteolipid film structure and properties.

    PubMed Central

    Salamon, Z; Macleod, H A; Tollin, G

    1997-01-01

    A variant of surface plasmon resonance (SPR) spectroscopy has been developed that involves a coupling of plasmon resonances in a thin metal film and waveguide modes in a dielectric overcoating. This new technique is referred to as coupled plasmon-waveguide resonance (CPWR) spectroscopy. It combines a greatly enhanced sensitivity (due to increased electromagnetic field intensities at the dielectric surface) and spectral resolution (due to decreased resonance linewidths), with the ability to directly measure anisotropies in refractive index and optical absorption coefficient in a dielectric film adsorbed onto the surface of the overcoating. Experimental data obtained with an egg phosphatidylcholine bilayer are presented to document these properties. PMID:9370473

  18. Wave tilt sounding of multilayered structures. [for probing of stratified planetary surface electrical properties and thickness

    NASA Technical Reports Server (NTRS)

    Warne, L.; Jaggard, D. L.; Elachi, C.

    1979-01-01

    The relationship between the wave tilt and the electrical parameters of a multilayered structure is investigated. Particular emphasis is placed on the inverse problem associated with the sounding planetary surfaces. An inversion technique, based on multifrequency wave tilt, is proposed and demonstrated with several computer models. It is determined that there is close agreement between the electrical parameters used in the models and those in the inversion values.

  19. Probing the structural and magnetic properties of transition metal-benzene anion complexes.

    PubMed

    Li, Hui-Fang; Kuang, Xiao-Yu; Wang, Huai-Qian

    2011-05-07

    Two types of transition metal-benzene anion complexes, (titanium)(n)(benzene)(m)⁻ and (cobalt)(n)(benzene)(m)⁻ (n ≤ 2, m ≤ 3) have been determined using density functional theory. The photoelectron spectra of Ti(n)Bz(m)⁻ and Co(n)Bz(m)⁻ (n ≤ 2, m ≤ 3) were discussed from the perspective of quantum chemical calculations of the vertical detachment energies (VDEs) of several low-energy isomers obtained by the structural optimization procedure. The binding of Ti and Co atoms to benzene molecules is accounted by 3d-π bonds, as revealed by the molecular orbitals. The topology of the electronic density has been analyzed, suggesting that the C-C bonds were weakened in the transition metal-benzene complexes in comparison to those in free benzene. Spin density distribution results show the spin densities for Ti(n)Bz(m)⁻ and Co(n)Bz(m)⁻ (n ≤ 2, m ≤ 3) reside mainly on the metal Ti and Co centers (70%-90%). A shift to lower magnetic moment with respect to the pure titanium/cobalt cluster anions indicates the solvent benzene molecule acts to demagnetize the bare titanium/cobalt cluster anions.

  20. Probing Electronic, Structural, and Charge Transfer Properties of Organic Semiconductor/Inorganic Oxide Interfaces Using Field-Effect Transistors

    NASA Astrophysics Data System (ADS)

    Spalenka, Josef Wade

    Interfaces between organic semiconductors and inorganic oxides provide the functionality for devices including field-effect transistors (FETs) and organic photovoltaics. Organic FETs are sensitive to the physical structure and electronic properties of the few molecular layers of material at the interface between the semiconducting channel and the gate dielectric, and provide quantitative information such as the field-effect mobility of charge carriers and the concentration of trapped charge. In this thesis, FET interfaces between organic small-molecule semiconductors and SiO2, and donor/acceptor interfaces between organic small-molecules and the wide bandgap semiconductor ZnO are studied using electrical measurements of field-effect transistor devices. Monolayer-scale films of dihexyl sexithiophene are shown to have higher hole mobility than other monolayer organic semiconductors, and the origin of the high mobility is discussed. Studies of the crystal structure of the monolayer using X-ray structural probes and atomic force microscopy reveal the crystal structure is different in the monolayer regime compared to thicker films and bulk crystals. Progress and remaining challenges are discussed for in situ X-ray diffraction studies of the dynamic changes in the local crystal structure in organic monolayers due to charge carriers generated during the application of electric fields from the gate electrode in working FETs. Studies were conducted of light sensitive organic/inorganic interfaces that are modified with organic molecules grafted to the surface of ZnO nanoparticles and thin films. These interfaces are models for donor/acceptor interfaces in photovoltaics. The process of exciton dissociation at the donor/acceptor interface was sensitive to the insulating or semiconducting molecules grafted to the ZnO, and the photoinduced charge transfer process is measured by the threshold voltage shift of FETs during illumination. Charge transfer between light sensitive donor

  1. Influence of the Electronic Structure and Optical Properties of CeO2 and UO2 for Characterization with UV-Laser Assisted Atom Probe Tomography

    SciTech Connect

    Billy Valderrama; H.B. Henderson; C. Yablinsky; J. Gan; T.R. Allen; M.V. Manuel

    2015-09-01

    Oxide materials are used in numerous applications such as thermal barrier coatings, nuclear fuels, and electrical conductors and sensors, all applications where nanometer-scale stoichiometric changes can affect functional properties. Atom probe tomography can be used to characterize the precise chemical distribution of individual species and spatially quantify the oxygen to metal ratio at the nanometer scale. However, atom probe analysis of oxides can be accompanied by measurement artifacts caused by laser-material interactions. In this investigation, two technologically relevant oxide materials with the same crystal structure and an anion to cation ratio of 2.00, pure cerium oxide (CeO2) and uranium oxide (UO2) are studied. It was determined that electronic structure, optical properties, heat transfer properties, and oxide stability strongly affect their evaporation behavior, thus altering their measured stoichiometry, with thermal conductance and thermodynamic stability being strong factors.

  2. Probing cell mechanical properties with microfluidic devices

    NASA Astrophysics Data System (ADS)

    Rowat, Amy

    2012-02-01

    Exploiting flow on the micron-scale is emerging as a method to probe cell mechanical properties with 10-1000x advances in throughput over existing technologies. The mechanical properties of cells and the cell nucleus are implicated in a wide range of biological contexts: for example, the ability of white blood cells to deform is central to immune response; and malignant cells show decreased stiffness compared to benign cells. We recently developed a microfluidic device to probe cell and nucleus mechanical properties: cells are forced to deform through a narrow constrictions in response to an applied pressure; flowing cells through a series of constrictions enables us to probe the ability of hundreds of cells to deform and relax during flow. By tuning the constriction width so it is narrower than the width of the cell nucleus, we can specifically probe the effects of nuclear physical properties on whole cell deformability. We show that the nucleus is the rate-limiting step in cell passage: inducing a change in its shape to a multilobed structure results in cells that transit more quickly; increased levels of lamin A, a nuclear protein that is key for nuclear shape and mechanical stability, impairs the passage of cells through constrictions. We are currently developing a new class of microfluidic devices to simultaneously probe the deformability of hundreds of cell samples in parallel. Using the same soft lithography techniques, membranes are fabricated to have well-defined pore distribution, width, length, and tortuosity. We design the membranes to interface with a multiwell plate, enabling simultaneous measurement of hundreds of different samples. Given the wide spectrum of diseases where altered cell and nucleus mechanical properties are implicated, such a platform has great potential, for example, to screen cells based on their mechanical phenotype against a library of drugs.

  3. Characterization of structure and properties of thin film crystals and ferroelectric BiFeO3: A coupled TEM, SPM, and optical probe approach

    NASA Astrophysics Data System (ADS)

    Jokisaari, Jacob Ragnar

    Correlating advanced microscopy methods including transmission electron microscopy, scanning probe microscopy, and optical spectroscopy on the same materials and even the same specimens allows complimentary measurements to be obtained, revealing new details about structure-property relationships measured on a nanometer scale. Combining measurements not only corroborates the information obtained from any particular method, but also compensates for deficiencies of any single technique. An array of microscopy techniques including high resolution transmission electron microscopy, scanning probe microscopy, and Raman spectroscopy were applied to address scientific and engineering questions concerning the structure and properties of domain patterns in BiFeO3 ferroelectric thin films and to examine novel TiO2(B) thin films suitable for Li-ion battery applications. In BiFeO3, application of these combined techniques allowed a relationship between epitaxial strain and domain width to be established, two cases of strained films with unique domain structures to be identified, transformation of domain structures from all 109° to mixed to all 71° based on differing film thicknesses of 100 and 200 nm to be observed, and to identify growth-induced defects that control domain structure over very long range, 100 nm or more, compared to many studies. In TiO2(B) films, a combination of advanced microscopy and first principals calculations were applied with Raman spectroscopy to produce a definitive reference for further investigation of the crystallinity, structure, composition, and properties of TiO2(B) materials with Raman spectroscopy. Finally to extend these studies of nanostructures and allow direct measurement of electronic and optical properties, the design, development, and construction of proof-of-concept prototypes of specimen rods for in-situ transmission electron microcopy combining electrical probe, scanning tunneling measurements, and optical excitation and

  4. Nanoscale structural and electronic properties of ultrathin blends of two polyaromatic molecules: a Kelvin probe force microscopy investigation.

    PubMed

    Palermo, Vincenzo; Morelli, Susanna; Palma, Matteo; Simpson, Christopher; Nolde, Fabian; Herrmann, Andreas; Müllen, Klaus; Samorì, Paolo

    2006-04-10

    We describe a Kelvin Probe Force Microscopy (KPFM) study on the morphological and electronic properties of complex mono and bi-molecular ultrathin films self-assembled on mica. These architectures are made up from an electron-donor (D), a synthetic all-benzenoid polycyclic aromatic hydrocarbon, and an electron-acceptor (A), perylene-bis-dicarboximide. The former molecule self-assembles into fibers in single component films, while the latter molecule forms discontinuous layers. Taking advantage of the different solubility and self-organizing properties of the A and D molecules, multicomponent ultrathin films characterized by nanoscale phase segregated fibers of D embedded in a discontinuous layer of A are formed. The direct estimation of the surface potential, and consequently the local workfunction from KPFM images allow a comparison of the local electronic properties of the blend with those of the monocomponent films. A change in the average workfunction values of the A and D nanostructures in the blend occurs which is primarily caused by the intimate contact between the two components and the molecular order within the nanostructure self-assembled at the surface. Additional roles can be ascribed to the molecular packing density, to the presence of defects in the film, to the different conformation of the aliphatic peripheral chains that might cover the conjugated core and to the long-range nature of the electrostatic interactions employed to map the surface by KPFM limiting the spatial and potential resolution. The local workfunction studies of heterojunctions can be of help to tune the electronic properties of active multicomponent films, which is crucial for the fabrication of efficient organic electronic devices as solar cells.

  5. Probing the structural and dynamical properties of liquid water with models including non-local electron correlation

    SciTech Connect

    Del Ben, Mauro Hutter, Jürg; VandeVondele, Joost

    2015-08-07

    Water is a ubiquitous liquid that displays a wide range of anomalous properties and has a delicate structure that challenges experiment and simulation alike. The various intermolecular interactions that play an important role, such as repulsion, polarization, hydrogen bonding, and van der Waals interactions, are often difficult to reproduce faithfully in atomistic models. Here, electronic structure theories including all these interactions at equal footing, which requires the inclusion of non-local electron correlation, are used to describe structure and dynamics of bulk liquid water. Isobaric-isothermal (NpT) ensemble simulations based on the Random Phase Approximation (RPA) yield excellent density (0.994 g/ml) and fair radial distribution functions, while various other density functional approximations produce scattered results (0.8-1.2 g/ml). Molecular dynamics simulation in the microcanonical (NVE) ensemble based on Møller-Plesset perturbation theory (MP2) yields dynamical properties in the condensed phase, namely, the infrared spectrum and diffusion constant. At the MP2 and RPA levels of theory, ice is correctly predicted to float on water, resolving one of the anomalies as resulting from a delicate balance between van der Waals and hydrogen bonding interactions. For several properties, obtaining quantitative agreement with experiment requires correction for nuclear quantum effects (NQEs), highlighting their importance, for structure, dynamics, and electronic properties. A computed NQE shift of 0.6 eV for the band gap and absorption spectrum illustrates the latter. Giving access to both structure and dynamics of condensed phase systems, non-local electron correlation will increasingly be used to study systems where weak interactions are of paramount importance.

  6. Probing the structure of cytoplasm

    PubMed Central

    1986-01-01

    We have used size-fractionated, fluorescent dextrans to probe the structure of the cytoplasmic ground substance of living Swiss 3T3 cells by fluorescence recovery after photobleaching and video image processing. The data indicate that the cytoplasm of living cells has a fluid phase viscosity four times greater than water and contains structural barriers that restrict free diffusion of dissolved macromolecules in a size-dependent manner. Assuming these structural barriers comprise a filamentous meshwork, the combined fluorescence recovery after photobleaching and imaging data suggest that the average pore size of the meshwork is in the range of 300 to 400 A, but may be as small as 200 A in some cytoplasmic domains. PMID:2423529

  7. Properties of electromagnetic field focusing probe.

    PubMed

    Yamanashi, W S; Yassa, N A; Hill, D L; Patil, A A; Lester, P D

    1988-11-01

    The electromagnetic field focusing (EFF) apparatus consists of a radio frequency generator, solenoidal coil, and a hand-held or catheter probe. Applications such as aneurysm treatment, angioplasty, and neurosurgery in various models have been reported. The probe is operated in the near field (within one wavelength of an electromagnetic field source) of a coil inducing eddy currents in biological tissues, producing maximal convergence of the induced current at the probe tip. The probe produces very high temperatures depending on the wattage selected for the given radio frequency of output power. The high temperature can be used in cutting, cauterizing, or vaporizing. The EFF probe is comparable to different types of lasers and to bipolar and monopolar cautery. The EFF probe can be used with catheters or endoscopes. Objectives of this study were to determine what the thermal properties of the EFF probe are and how instrument parameters can be varied to obtain different temperatures in the tissue near the probe tip. In this study an F2 catheter was used as an insulated sheath and the tip of the guide wire was used as the probe tip. Different powers, wave forms, coil-to-probe distances, and probe-tip lengths were tested on a phantom that simulates tissue electrical properties. Some of the experiments were conducted under normal saline to simulate treatment of tissue with body fluids such as blood vessels or brain tissue under normal physiologic conditions. It is concluded that the EFF probe has the advantages of easy manipulation, relative safety, cost effectiveness, and a high degree of spatial control.(ABSTRACT TRUNCATED AT 250 WORDS)

  8. A probe into compositional and structural dependence of optical properties of lanthanum fluoride films prepared by resistive heating

    NASA Astrophysics Data System (ADS)

    Rao, Pritty; Kumar, Sanjiv; Tokas, R. B.; Sahoo, N. K.

    2015-01-01

    The paper describes investigations into the correlation between the optical properties and the composition, structure and morphology of lanthanum fluoride films deposited at 373-473 K substrate temperatures by resistive heating of lanthanum fluoride powders. The composition of the films that includes depth profiling of fluorine has been determined non-destructively by ion beam analysis while their structure and morphology have been investigated by glancing incidence X-ray diffraction and atomic force microscopy respectively. The films are polycrystalline, exist in hexagonal phase and display substrate temperature dependent texturing. The substrate temperature has an important influence on composition as well. The films deposited at 373 K or 398 K substrate temperatures are deficient in fluorine but tend to acquire stoichiometric composition at 473 K. Possessing granular (∼100 nm) morphology, the films, in general, are UV transparent but their optical loss increases with texturing. Carbon and oxygen, present as impurities, lower the density and consequently the refractive index (1.47) of the films. Annealing in vacuum at 573 K brings about deterioration in the optical properties of the films which are related mainly to morphological changes and thermal stress.

  9. Two-photon polarity probes built from octupolar fluorophores: synthesis, structure-properties relationships, and use in cellular imaging.

    PubMed

    Le Droumaguet, Céline; Sourdon, Aude; Genin, Emilie; Mongin, Olivier; Blanchard-Desce, Mireille

    2013-12-01

    A series of octupolar fluorophores built from a triphenylamine (TPA) core connected to electron-withdrawing (EW) peripheral groups through conjugated spacers has been synthesized. Their photoluminescence, solvatochromism, and two-photon absorption (2PA) properties were systematically investigated to derive structure-property relationships. All derivatives exhibit two 2PA bands in the 700-1000 nm region: a first band at low energy correlated with a core-to-periphery intramolecular charge transfer that leads to an intense 1PA in the blue-visible range, and a second more intense band at higher energy due to an efficient coupling of the branches through the TPA core. Increasing the strength of the EW end groups or the length of the conjugated spacers and replacing triple-bond linkers with double bonds induces both enhancement and broadening of the 2PA responses, thereby leading to cross-sections up to 2100 GM at peak and higher than 1000 GM over the whole 700-900 nm range. All derivatives exhibit intense photoluminescence (PL) in low- to medium-polarity environments (with quantum yields in the 0.5-0.9 range) and display a strong positive solvatochromic behavior (with Lippert-Mataga specific shifts ranging from 15,000 to 27,500 cm(-1)), triple bonds, and phenyl moieties in the conjugated spacers, thereby leading to larger sensitivities than those of double bonds and thienyl moieties. More hydrophilic derivatives were also shown to be biocompatible, to retain their 2PA and PL properties in biological conditions, and finally to be suitable as polarity sensors for multiphoton cell imaging.

  10. Probing the effect of intrinsic defects and dopants on the structural evolution and optical properties of ZnO nanocrystallites

    SciTech Connect

    Panda, N. R.; Sahu, D.; Acharya, B. S.; Nayak, P.

    2015-06-24

    Role of intrinsic defects and external impurities in modifying the structural and optical properties of ZnO nanostructures has been studied and discussed. ZnO nanocrystallites doped with B, N and S elements have been prepared by ultrasound assisted wet chemical method. Structural evolution of ZnO in presence of dopant ions has been studied by XRD and electron microscopic measurements. Elemental analysis like XPS has been carried out to ascertain the dopant configuration. A variation in crystallographic parameters and microstructure is found to be observed as impurity is incorporated into ZnO. This has been explained on the basis of the substitution of dopant at Zn{sup 2+} and O{sup −} sites rearranging the lattice. Optical absorption measurements and PL studies reflect a change in band gap of ZnO by impurity adsorption. Most of the cases, the band gap is found to be broadened which has been explained in the line of Moss-Burstein effect. The excitonic emission in ZnO is observed to blue shift supporting the above results and the defect emissions also get modified in terms of position and intensity. New PL bands observed have been assigned to the transitions related to the defect states present in the band gap of ZnO along with intrinsic defects.

  11. Probing the structural dependency of photoinduced properties of colloidal quantum dots using metal-oxide photo-active substrates

    NASA Astrophysics Data System (ADS)

    Patty, Kira; Sadeghi, Seyed M.; Campbell, Quinn; Hamilton, Nathan; West, Robert G.; Mao, Chuanbin

    2014-09-01

    We used photoactive substrates consisting of about 1 nm coating of a metal oxide on glass substrates to investigate the impact of the structures of colloidal quantum dots on their photophysical and photochemical properties. We showed during irradiation these substrates can interact uniquely with such quantum dots, inducing distinct forms of photo-induced processes when they have different cores, shells, or ligands. In particular, our results showed that for certain types of core-shell quantum dot structures an ultrathin layer of a metal oxide can reduce suppression of quantum efficiency of the quantum dots happening when they undergo extensive photo-oxidation. This suggests the possibility of shrinking the sizes of quantum dots without significant enhancement of their non-radiative decay rates. We show that such quantum dots are not influenced significantly by Coulomb blockade or photoionization, while those without a shell can undergo a large amount of photo-induced fluorescence enhancement via such blockade when they are in touch with the metal oxide.

  12. Probing the structural dependency of photoinduced properties of colloidal quantum dots using metal-oxide photo-active substrates

    SciTech Connect

    Patty, Kira; Campbell, Quinn; Hamilton, Nathan; West, Robert G.; Sadeghi, Seyed M.; Mao, Chuanbin

    2014-09-21

    We used photoactive substrates consisting of about 1 nm coating of a metal oxide on glass substrates to investigate the impact of the structures of colloidal quantum dots on their photophysical and photochemical properties. We showed during irradiation these substrates can interact uniquely with such quantum dots, inducing distinct forms of photo-induced processes when they have different cores, shells, or ligands. In particular, our results showed that for certain types of core-shell quantum dot structures an ultrathin layer of a metal oxide can reduce suppression of quantum efficiency of the quantum dots happening when they undergo extensive photo-oxidation. This suggests the possibility of shrinking the sizes of quantum dots without significant enhancement of their non-radiative decay rates. We show that such quantum dots are not influenced significantly by Coulomb blockade or photoionization, while those without a shell can undergo a large amount of photo-induced fluorescence enhancement via such blockade when they are in touch with the metal oxide.

  13. Probing the Crystal Structure, Composition-Dependent Absolute Energy Levels, and Electrocatalytic Properties of Silver Indium Sulfide Nanostructures.

    PubMed

    Saji, Pintu; Ganguli, Ashok K; Bhat, Mohsin A; Ingole, Pravin P

    2016-04-18

    The absolute electronic energy levels in silver indium sulfide (AIS) nanocrystals (NCs) with varying compositions and crystallographic phases have been determined by using cyclic voltammetry. Different crystallographic phases, that is, metastable cubic, orthorhombic, monoclinic, and a mixture of cubic and orthorhombic AIS NCs, were studied. The band gap values estimated from the cyclic voltammetry measurements match well with the band gap values calculated from the diffuse reflectance spectra measurements. The AIS nanostructures were found to show good electrocatalytic activity towards the hydrogen evolution reaction (HER). Our results clearly establish that the electronic and electrocatalytic properties of AIS NCs are strongly sensitive to the composition and crystal structure of AIS NCs. Monoclinic AIS was found to be the most active HER electrocatalyst, with electrocatalytic activity that is almost comparable to the MoS2 -based nanostructures reported in the literature, whereas cubic AIS was observed to be the least active of the studied crystallographic phases and compositions. In view of the HER activity and electronic band structure parameters observed herein, we hypothesize that the Fermi energy level of AIS NCs is an important factor that decides the electrocatalytic efficiency of these nanocomposites. The work presented herein, in addition to being the first of its kind regarding the composition and phase-dependence of electrochemical aspects of AIS NCs, also presents a simple solvothermal method for the synthesis of different crystallographic phases with various Ag/In molar ratios.

  14. Conformationally dynamic π-conjugation: probing structure-property relationships of fluorescent tris(N-salicylideneaniline)s.

    PubMed

    Vieweger, Mario; Jiang, Xuan; Lim, Young-Kwan; Jo, Junyong; Lee, Dongwhan; Dragnea, Bogdan

    2011-11-24

    We recently reported the design and synthesis of a series of conformationally dynamic chromophores that are built on the C(3)-symmetric tris(N-salicylideneaniline) platform. This system utilizes cooperative structural folding-unfolding motions for fluorescence switching, which is driven by the assembly and disassembly of hydrogen bonds between the rigid core and rotatable peripheral part of the molecule. Here, we report detailed time-resolved spectroscopic studies to investigate the structure-property relationships of a series of functionalized tris(N-salicylideneaniline)s. Time-resolved fluorescence decay spectroscopy was applied to determine the main relaxation mechanisms of these π-extended fluorophores, and to address the effects of hydrogen bonding, steric constraints, and extension of the π-conjugation on their relaxation dynamics. Our results agree well with the conformational switching model that was previously suggested from steady-state experiments. Notably, extension of the π-conjugation from peripheral aryl groups resulted in the stabilization of the excited states, as evidenced by longer lifetimes and lower nonradiative decay constants. As a consequence, an increase in the fluorescence quantum yields was observed, which could be explained by the suppression of the torsional motions about the C-N bonds from an overall increase in the quinoid character of the excited states. A combination of time-resolved and steady-state techniques also revealed intermolecular interactions through π-π stacking at higher concentrations, which provide additional de-excitation pathways that become more pronounced in solid samples.

  15. Propane-Water Mixtures Confined within Cylindrical Silica Nanopores: Structural and Dynamical Properties Probed by Molecular Dynamics.

    PubMed

    Le, Tran Thi Bao; Striolo, Alberto; Gautam, Siddharth S; Cole, David R

    2017-09-27

    Despite the multiple length and time scales over which fluid-mineral interactions occur, interfacial phenomena control the exchange of matter and impact the nature of multiphase flow, as well as the reactivity of C-O-H fluids in geologic systems. In general, the properties of confined fluids, and their influence on porous geologic phenomena are much less well understood compared to those of bulk fluids. We used equilibrium molecular dynamics simulations to study fluid systems composed of propane and water, at different compositions, confined within cylindrical pores of diameter ∼16 Å carved out of amorphous silica. The simulations are conducted within a single cylindrical pore. In the simulated system all the dangling silicon and oxygen atoms were saturated with hydroxyl groups and hydrogen atoms, respectively, yielding a total surface density of 3.8 -OH/nm(2). Simulations were performed at 300 K, at different bulk propane pressures, and varying the composition of the system. The structure of the confined fluids was quantified in terms of the molecular distribution of the various molecules within the pore as well as their orientation. This allowed us to quantify the hydrogen bond network and to observe the segregation of propane near the pore center. Transport properties were quantified in terms of the mean square displacement in the direction parallel to the pore axis, which allows us to extract self-diffusion coefficients. The diffusivity of propane in the cylindrical pore was found to depend on pressure, as well as on the amount of water present. It was found that the propane self-diffusion coefficient decreases with increasing water loading because of the formation of water bridges across the silica pores, at sufficiently high water content, which hinder propane transport. The rotational diffusion, the lifespan of hydrogen bonds, and the residence time of water molecules at contact with the silica substrate were quantified from the simulated trajectories

  16. Outer planet probe engineering model structural tests

    NASA Technical Reports Server (NTRS)

    Smittkamp, J. A.; Gustin, W. H.; Griffin, M. W.

    1977-01-01

    A series of proof of concept structural tests was performed on an engineering model of the Outer Planets Atmospheric Entry Probe. The tests consisted of pyrotechnic shock, dynamic and static loadings. The tests partially verified the structural concept.

  17. Modulation of the aggregation properties of sodium deoxycholate in presence of hydrophilic imidazolium based ionic liquid: water dynamics study to probe the structural alteration of the aggregates.

    PubMed

    Kundu, Niloy; Banik, Debasis; Roy, Arpita; Kuchlyan, Jagannath; Sarkar, Nilmoni

    2015-10-14

    In this article, we have investigated the effect of a hydrophilic ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim]-BF4), on the aggregation properties of a biological surfactant, sodium deoxycholate (NaDC), in water. In solution, unlike conventional surfactants it shows stepwise aggregation and the effect of the conventional ionic liquid on the aggregation properties is rather interesting. We have observed concentration dependent dual role of the ionic liquid; at their low concentration, the aggregated structure of NaDC reorganizes itself into an elongated rod like structure. However, the aggregated network is disintegrated into small aggregates upon further addition of ionic liquid. TEM (Transmission Electron Microscopy), SEM (Scanning Electron Microscopy) and FLIM (Fluorescence Lifetime Imaging Microscopy) images also confirmed the structural alteration of NaDC upon varying the concentration of the ionic liquid. The proton NMR data indicate that hydrophobic as well as electrostatic interaction is solely responsible for such structural adaptation of NaDC in the presence of an ionic liquid. The host-guest interaction inside the aggregates is monitored using Coumarin-153 (C-153) and the location of C-153 is probed by varying the excitation wavelength from 375 nm to 440 nm and the two binding sites of the aggregates are affected in a different fashion in the presence of ionic liquid. Excitation in the blue region selects the fluorophores which preferably bind to the buried region of the aggregates, whereas 440 nm excitation corresponds to the guest molecules which are exposed to the solvent molecules. The average solvation time of C-153 is increased in the presence of 1.68 wt% [bmim]-BF4 at λexc = 440 nm i.e. the probe molecules relocate themselves to a more restricted region. However, the average solvation time became 2.6 times faster in the presence of 11.2 wt% [bmim]-BF4, which corresponds to a more polar and exposed region. The time resolved

  18. Nuclear structure and weak probes

    NASA Astrophysics Data System (ADS)

    Horoi, Mihai

    2017-06-01

    Weak interaction in nuclei represents a well-known venue for testing many of the fundamental symmetries of the Standard Model. Analysis of these processes requires nuclear structure information, including nuclear data, and some theoretical approaches to describe it. Here we make an introduction into basic nuclear structure concepts, using the existing nuclear data and some simple mean-field and shell model approaches. Some applications to beta decays and double beta decays are presented.

  19. Probing the structure and nano-scale mechanical properties of polymer surfaces with scanning force microscopy and sum frequency vibrational spectroscopy

    SciTech Connect

    Gracias, David Hugo

    1999-05-01

    Scanning Force Microscopy (SFM) has been used to quantitatively measure the elastic modulus, friction and hardness of polymer surfaces with special emphasis on polyethylene and polypropylene. In the experiments, tips of different radii of curvature ranging from 20 nm to 1000 nm have been used and the high pressure applied by the SFM have been observed to affect the values obtained in the measurements. The contact of the SFM tip with the polymer surface is explained by fitting the experimental curves to theoretical predictions of contact mechanics. Sum Frequency Generation (SFG) Vibrational Spectroscopy has been used to measure vibrational spectra of polymer surfaces in the vibrational range of 2700 to 3100 cm-1. Strong correlations are established between surface chemistry and surface structure as probed by SFG and mechanical properties measured by SFM on the surfaces. In these studies segregation of low surface energy moieties, from the bulk of the polymer to the surface have been studied. It was found that surface segregation occurs in miscible polymer blends and a small concentration of surface active polymer can be used to totally modify the surface properties of the blend. A novel high vacuum SFM was built to do temperature dependent measurements of mechanical changes occurring at the surface of polypropylene during the glass transition of the polymer. Using this instrument the modulus and friction of polypropylene was measured in the range of room temperature to ˜-60°C. An increase in the ordering of the backbone of the polymer chains below the glass transition measured by SFG correlates well with the increase in modulus measured on the same surface with SFM. Friction measurements have been done on polyethylene with three different instruments by applying loads ranging from nN to sub newton i.e. over eight orders of magnitude. Pressure and contact area effects were observed to play a significant role in determining the frictional response of the polymer

  20. A Visual Recall Probe of Cognitive Structure

    ERIC Educational Resources Information Center

    Murray, Darrell L.

    1978-01-01

    Presents findings of a study on the visual perceptual dimension of cognitive structure as it relates to achievement in college biology. Results indicate a possibility of using visual recall probes for the early detection of learning differences related to achievement. (SL)

  1. Insight into Amyloid Structure Using Chemical Probes

    PubMed Central

    Reinke, Ashley A.; Gestwicki, Jason E.

    2011-01-01

    Alzheimer’s disease (AD) is a common neurodegenerative disorder characterized by the deposition of amyloids in the brain. One prominent form of amyloid is composed of repeating units of the amyloid-β (Aβ) peptide. Over the past decade, it has become clear that these Aβ amyloids are not homogeneous; rather, they are composed of a series of structures varying in their overall size and shape and the number of Aβ peptides they contain. Recent theories suggest that these different amyloid conformations may play distinct roles in disease, although their relative contributions are still being discovered. Here, we review how chemical probes, such as congo red, thioflavin T and their derivatives, have been powerful tools for better understanding amyloid structure and function. Moreover, we discuss how design and deployment of conformationally selective probes might be used to test emerging models of AD. PMID:21457473

  2. Probing microscopic mechanical properties of hard tissues with Brillouin spectroscopy

    NASA Astrophysics Data System (ADS)

    Meng, Zhaokai; Yakovlev, Vladislav V.

    2015-02-01

    Mechanical properties of hard tissues play an important role in understanding underlying biological structures, as well as assessing the quality of artificial bone replacement materials. In this study, we employed Brillouin spectroscopy as a non-invasive approach to probe the microscopic elasticity of hard tissues, such as bones. Brillouin spectra were collected using a background free virtually imaged phased array spectrometer. As a reference, Raman spectra were also acquired for each imaging point. Experimental results reveal a positive correlation between the local concentration of the mineral content and the corresponding tissue stiffness, assessed through a Brillouin shift.

  3. Interplay of stereoelectronic and enviromental effects in tuning the structural and magnetic properties of a prototypical spin probe: further insights from a first principle dynamical approach.

    PubMed

    Pavone, Michele; Cimino, Paola; De Angelis, Filippo; Barone, Vincenzo

    2006-04-05

    The nitrogen isotropic hyperfine coupling constant (hcc) and the g tensor of a prototypical spin probe (di-tert-butyl nitroxide, DTBN) in aqueous solution have been investigated by means of an integrated computational approach including Car-Parrinello molecular dynamics and quantum mechanical calculations involving a discrete-continuum embedding. The quantitative agreement between computed and experimental parameters fully validates our integrated approach. Decoupling of the structural, dynamical, and environmental contributions acting onto the spectral observables allows an unbiased judgment of the role played by different effects in determining the overall experimental observables and highlights the importance of finite-temperature vibrational averaging. Together with their intrinsic interest, our results pave the route toward more reliable interpretations of EPR parameters of complex systems of biological and technological relevance.

  4. Local structure probes of nanoscale heterogeneity in crystalline materials.

    PubMed

    Conradson, S; Espinosa, F; Villella, P

    2001-03-01

    In the conventional model of condensed matter increasing numbers of defects break down the order and ultimately convert perfect periodic crystals into aperiodic glasses. Local structure probes of a variety of materials with non-stoichiometric compositions, multiple degenerate ordering modes, or other symmetry breaking factors identify multiple ordered arrangements of atoms that render the materials heterogeneous on the nanometer scale. While exerting apparently negligible effects on bulk properties, this heterogeneity or phase separation does influence correlated or collective properties such as magnetism and phase stability.

  5. Ionization probes of molecular structure and chemistry

    SciTech Connect

    Johnson, P.M.

    1993-12-01

    Various photoionization processes provide very sensitive probes for the detection and understanding of the spectra of molecules relevant to combustion processes. The detection of ionization can be selective by using resonant multiphoton ionization or by exploiting the fact that different molecules have different sets of ionization potentials. Therefore, the structure and dynamics of individual molecules can be studied even in a mixed sample. The authors are continuing to develop methods for the selective spectroscopic detection of molecules by ionization, and to use these methods for the study of some molecules of combustion interest.

  6. Rheology and confocal reflectance microscopy as probes of mechanical properties and structure during collagen and collagen/hyaluronan self-assembly.

    PubMed

    Yang, Ya-li; Kaufman, Laura J

    2009-02-18

    In this work, the gelation of three-dimensional collagen and collagen/hyaluronan (HA) composites is studied by time sweep rheology and time lapse confocal reflectance microscopy (CRM). To investigate the complementary nature of these techniques, first collagen gel formation is investigated at concentrations of 0.5, 1.0, and 1.5 mg/mL at 37 degrees C and 32 degrees C. The following parameters are used to describe the self-assembly process in all gels: the crossover time (t(c)), the slope of the growth phase (k(g)), and the arrest time (t(a)). The first two measures are determined by rheology, and the third by CRM. A frequency-independent rheological measure of gelation, t(g), is also measured at 37 degrees C. However, this quantity cannot be straightforwardly determined for gels formed at 32 degrees C, indicating that percolation theory does not fully capture the dynamics of collagen network formation. The effects of collagen concentration and gelation temperature on k(g), t(c), and t(a) as well as on the mechanical properties and structure of these gels both during gelation and at equilibrium are elucidated. Composite collagen/HA gels are also prepared, and their properties are monitored at equilibrium and during gelation at 37 degrees C and 32 degrees C. We show that addition of HA subtly alters mechanical properties and structure of these systems both during the gelation process and at equilibrium. This occurs in a temperature-dependent manner, with the ratio of HA deposited on collagen fibers versus that distributed homogeneously between fibers increasing with decreasing gelation temperature. In addition to providing information on collagen and collagen/HA structure and mechanical properties during gelation, this work shows new ways in which rheology and microscopy can be used complementarily to reveal details of gelation processes.

  7. Rheology and Confocal Reflectance Microscopy as Probes of Mechanical Properties and Structure during Collagen and Collagen/Hyaluronan Self-Assembly

    PubMed Central

    Yang, Ya-li; Kaufman, Laura J.

    2009-01-01

    In this work, the gelation of three-dimensional collagen and collagen/hyaluronan (HA) composites is studied by time sweep rheology and time lapse confocal reflectance microscopy (CRM). To investigate the complementary nature of these techniques, first collagen gel formation is investigated at concentrations of 0.5, 1.0, and 1.5 mg/mL at 37°C and 32°C. The following parameters are used to describe the self-assembly process in all gels: the crossover time (tc), the slope of the growth phase (kg), and the arrest time (ta). The first two measures are determined by rheology, and the third by CRM. A frequency-independent rheological measure of gelation, tg, is also measured at 37°C. However, this quantity cannot be straightforwardly determined for gels formed at 32°C, indicating that percolation theory does not fully capture the dynamics of collagen network formation. The effects of collagen concentration and gelation temperature on kg, tc, and ta as well as on the mechanical properties and structure of these gels both during gelation and at equilibrium are elucidated. Composite collagen/HA gels are also prepared, and their properties are monitored at equilibrium and during gelation at 37°C and 32°C. We show that addition of HA subtly alters mechanical properties and structure of these systems both during the gelation process and at equilibrium. This occurs in a temperature-dependent manner, with the ratio of HA deposited on collagen fibers versus that distributed homogeneously between fibers increasing with decreasing gelation temperature. In addition to providing information on collagen and collagen/HA structure and mechanical properties during gelation, this work shows new ways in which rheology and microscopy can be used complementarily to reveal details of gelation processes. PMID:19217873

  8. Probing the Structures and Electronic Properties of Dual-Phosphorus-Doped Gold Cluster Anions (AunP-2, n = 1–8): A Density functional Theory Investigation

    SciTech Connect

    Xu, Kang-Ming; Huang, Teng; Liu, Yi-Rong; Jiang, Shuai; Zhang, Yang; Lv, Yu-Zhou; Gai, Yan-Bo; Huang, Wei

    2015-07-29

    The geometries of gold clusters doped with two phosphorus atoms, (AunP-2, n = 1–8) were investigated using density functional theory (DFT) methods. Various two-dimensional (2D) and three-dimensional (3D) structures of the doped clusters were studied. The results indicate that the structures of dual-phosphorus-doped gold clusters exhibit large differences from those of pure gold clusters with small cluster sizes. In our study, as for Au6P-2, two cis–trans isomers were found. The global minimum of Au8P-2 presents a similar configuration to that of Au-20, a pyramid-shaped unit, and the potential novel optical and catalytic properties of this structure warrant further attention. The higher stability of AunP-2 clusters relative to Au-n+2 (n = 1–8) clusters was verified based on various energy parameters, and the results indicate that the phosphorus atom can improve the stabilities of the gold clusters. We then explored the evolutionary path of (n = 1–8) clusters. We found that AunP-2 clusters exhibit the 2D–3D structural transition at n = 6, which is much clearer and faster than that of pure gold clusters and single-phosphorus-doped clusters. The electronic properties of AunP-2 (n = 1–8) were then investigated. The photoelectron spectra provide additional fundamental information on the structures and molecular orbitals shed light on the evolution of AunP-2 (n = 1–8). Natural bond orbital (NBO) described the charge distribution in stabilizing structures and revealed the strong relativistic effects of the gold atoms.

  9. Monitoring biophysical properties of lipid membranes by environment-sensitive fluorescent probes.

    PubMed

    Demchenko, Alexander P; Mély, Yves; Duportail, Guy; Klymchenko, Andrey S

    2009-05-06

    We review the main trends in the development of fluorescence probes to obtain information about the structure, dynamics, and interactions in biomembranes. These probes are efficient for studying the microscopic analogs of viscosity, polarity, and hydration, as well as the molecular order, environment relaxation, and electrostatic potentials at the sites of their location. Progress is being made in increasing the information content and spatial resolution of the probe responses. Multichannel environment-sensitive probes that can distinguish between different membrane physicochemical properties through multiple spectroscopic parameters show considerable promise.

  10. Monitoring Biophysical Properties of Lipid Membranes by Environment-Sensitive Fluorescent Probes

    PubMed Central

    Demchenko, Alexander P.; Mély, Yves; Duportail, Guy; Klymchenko, Andrey S.

    2009-01-01

    We review the main trends in the development of fluorescence probes to obtain information about the structure, dynamics, and interactions in biomembranes. These probes are efficient for studying the microscopic analogs of viscosity, polarity, and hydration, as well as the molecular order, environment relaxation, and electrostatic potentials at the sites of their location. Progress is being made in increasing the information content and spatial resolution of the probe responses. Multichannel environment-sensitive probes that can distinguish between different membrane physicochemical properties through multiple spectroscopic parameters show considerable promise. PMID:19413953

  11. Probing the structural and electronic properties of bimetallic chromium-gold clusters CrmAun(m+n≤6): comparison with pure chromium and gold clusters.

    PubMed

    Lu, Peng; Liu, Guang-Hua; Kuang, Xiao-Yu

    2014-08-01

    Bimetallic chromium-gold CrmAun(m+n≤6) clusters are systematically investigated using the density functional theory at PW91P86 level with LanL2TZ basis set to understand the evolution of various structural, electronic, magnetic, and energetic properties as a function of size (m+n) and composition (m/n) of the system. Theoretical results show a logical evolution of the properties depending on the size and the composition of the system. Cr m clusters clearly prefer 3D structures while Au n clusters favor planar configurations. The geometry of the bimetallic Cr m Au n clusters mainly depends on their composition, i.e., clusters enriched in Cr atoms prefer 3D structures while increasing Au contents promotes planar configurations. The stability is maximized when the composition of binary Cr m Au n clusters is nearly balanced. Meanwhile, the number of hetero Cr-Au bonds and charge transfer from Cr to Au are maximized for clusters with m≈n. The most probable dissociation channels of the Cr m Au n clusters are calculated and analyzed. Natural population analysis reveals that Au atoms tend to be negatively charged while Cr atoms tend to be positively charged. Combined with the trend that Au atoms favor the surface/edges/vertices and Cr atoms tend to be inside, the outer part of the cluster tends to be negatively charged, and the inner part tends to be positively charged.

  12. Auroral Spatial Structures Probe sounding rocket mission

    NASA Astrophysics Data System (ADS)

    Stromberg, E. M.; Swenson, C.; Fish, C. S.

    2011-12-01

    The Auroral Spatial Structures Probe (ASSP) is a NASA sounding rocket mission that, will be used to study both the spatial and temporal small scale variation of the E-fields during breakup aurora and geomagnetically active conditions. This will be accomplished through the use of a constellation of small payloads that separate relative to each other throughout a sounding rocket flight. The multiple baseline observations of the electric and magnetic fields will be used to observe variability of both the E-field and the Poynting flux. These observations will be placed in the context of available data, including winds, large scale E-fields, and proxy conductivity (airglow images) observations. In this way we will address the main scientific objective of this mission which is: What are the contributions of small spatial scale and rapid temporal scale fluctuations of electric fields relative to the larger-scale electrodynamic processes? The high altitude rocket will be launched along the magnetic field line and carry six sub-payloads to be ejected from the main payload at high velocity. The sub-payloads will be deployed both along the flight path and perpendicular to the flight path so that both spatial features and temporal-spatial ambiguities can be explored. The low-mass sub-payloads that, for a fixed ejection impulse will achieve at least a 50 km separation by the end of the flight are key to the observational success. Each sub-payload will carry a crossed pair of double-probe sensors to measure in-situ electric fields, a three axis magnetometer, a Langmuir probe and a GPS receiver. In this poster we review the ASSP science and mission concepts.

  13. Mechanical properties of plant cell walls probed by relaxation spectra.

    PubMed

    Hansen, Steen Laugesen; Ray, Peter Martin; Karlsson, Anders Ola; Jørgensen, Bodil; Borkhardt, Bernhard; Petersen, Bent Larsen; Ulvskov, Peter

    2011-01-01

    Transformants and mutants with altered cell wall composition are expected to display a biomechanical phenotype due to the structural role of the cell wall. It is often quite difficult, however, to distinguish the mechanical behavior of a mutant's or transformant's cell walls from that of the wild type. This may be due to the plant's ability to compensate for the wall modification or because the biophysical method that is often employed, determination of simple elastic modulus and breakstrength, lacks the resolving power necessary for detecting subtle mechanical phenotypes. Here, we apply a method, determination of relaxation spectra, which probes, and can separate, the viscoelastic properties of different cell wall components (i.e. those properties that depend on the elastic behavior of load-bearing wall polymers combined with viscous interactions between them). A computer program, BayesRelax, that deduces relaxation spectra from appropriate rheological measurements is presented and made accessible through a Web interface. BayesRelax models the cell wall as a continuum of relaxing elements, and the ability of the method to resolve small differences in cell wall mechanical properties is demonstrated using tuber tissue from wild-type and transgenic potatoes (Solanum tuberosum) that differ in rhamnogalacturonan I side chain structure.

  14. Probing the hammerhead ribozyme structure with ribonucleases.

    PubMed Central

    Hodgson, R A; Shirley, N J; Symons, R H

    1994-01-01

    Susceptibility to RNase digestion has been used to probe the conformation of the hammerhead ribozyme structure prepared from chemically synthesised RNAs. Less than about 1.5% of the total sample was digested to obtain a profile of RNase digestion sites. The observed digestion profiles confirmed the predicted base-paired secondary structure for the hammerhead. Digestion profiles of both cis and trans hammerhead structures were nearly identical which indicated that the structural interactions leading to self-cleavage were similar for both systems. Furthermore, the presence or absence of Mg2+ did not affect the RNase digestion profiles, thus indicating that Mg2+ did not modify the hammerhead structure significantly to induce self-cleavage. The base-paired stems I and II in the hammerhead structure were stable whereas stem III, which was susceptible to digestion, appeared to be an unstable region. The single strand domains separating the stems were susceptible to digestion with the exception of sites adjacent to guanosines; GL2.1 in the stem II loop and G12 in the conserved GAAAC sequence, which separates stems II and III. The absence of digestion at GL2.1 in the stem II hairpin loop of the hammerhead complex was maintained in uncomplexed ribozyme and in short oligonucleotides containing only the stem II hairpin region. In contrast, the G12 site became susceptible when the ribozyme was not complexed with its substrate. Overall the results are consistent with the role of Mg2+ in the hammerhead self-cleavage reaction being catalytic and not structural. Images PMID:8202361

  15. Properties of contact pressure induced by manually operated fiber-optic probes

    NASA Astrophysics Data System (ADS)

    Bregar, Maksimilijan; Cugmas, Blaž; Naglič, Peter; Hartmann, Daniela; Pernuš, Franjo; Likar, Boštjan; Bürmen, Miran

    2015-12-01

    We assess the properties of contact pressure applied by manually operated fiber-optic probes as a function of the operator, probe contact area, and sample stiffness. First, the mechanical properties of human skin sites with different skin structures, thicknesses, and underlying tissues were studied by in vivo indentation tests. According to the obtained results, three different homogeneous silicone skin phantoms were created to encompass the observed range of mechanical properties. The silicon phantoms were subsequently used to characterize the properties of the contact pressure by 10 experienced probe operators employing fiber-optic probes with different contact areas. A custom measurement system was used to collect the time-lapse of diffuse reflectance and applied contact pressure. The measurements were characterized by a set of features describing the transient and steady-state properties of the contact pressure and diffuse reflectance in terms of rise time, optical coupling, average value, and variability. The average applied contact pressure and contact pressure variability were found to significantly depend on the probe operator, probe contact area, and surprisingly also on the sample stiffness. Based on the presented results, we propose a set of practical guidelines for operators of manual probes.

  16. Design of two chimaeric human-rat class alpha glutathione transferases for probing the contribution of C-terminal segments of protein structure to the catalytic properties.

    PubMed Central

    Björnestedt, R; Widersten, M; Board, P G; Mannervik, B

    1992-01-01

    Two chimaeric human-rat class Alpha glutathione transferases were constructed by fusion of DNA segments derived from the plasmids pTGT2-AT and pGTB38 and expression of the corresponding proteins in Escherichia coli. The recombinant proteins H1R1/1 and H1R1/2 encoded by plasmids pH1R1/1 and pH1R1/2 are composed of a segment of the human class Alpha subunit 1 from the N-terminus to His-143 and Pro-207 respectively, followed by the complementary C-terminal portion of the rat class Alpha subunit 1 sequence. Compared with the parental human enzyme, H1R1/1 is altered in 20 positions due to the introduction of 79 residues from the rat enzyme, while H1R1/2 is altered in five positions out of 15 in the C-terminal region. The design of mutant H1R1/1 is equivalent to introduction of exons 6 and 7 of the rat subunit 1 gene in place of the homologous human nucleotide sequence. The two chimaeric proteins are enzymatically active with several substrates, even though the activity in most cases is somewhat decreased in comparison with the wild-type human enzyme. Inhibition studies show that the kinetic properties mimic those of the human enzyme, indicating that the N-terminal two-thirds of the primary structure plays the major role in governing the catalytic properties. The results of this study demonstrate that recombination of segments of primary structure between homologous enzymes may serve as a useful cassette technique for design of novel catalytically active proteins. PMID:1546966

  17. Measuring Mechanical Properties by Staring: Using Stress Assessment from Local Structural Anisotropy (SALSA) to Probe Viscosity and Visualize Stress Networks in Colloidal Suspensions

    NASA Astrophysics Data System (ADS)

    Cohen, Itai; Bierbaum, Matthew; Sethna, James; Lin, Neil

    2014-11-01

    Measurement of stress induced thermal fluctuations in materials can be used to determine macroscopic mechanical properties including viscosity in fluids, as well as bulk and shear moduli in solids. When extended to the single particle scale, such measurements also reveal underlying spatially inhomogeneous response mechanisms in systems such as glasses, gels, and polycrystals. Unfortunately, it is not possible to experimentally measure these temporal and spatial stress fluctuations in a colloidal suspension using conventional rheometers. Here however, we show that using fast confocal microscopy it is possible conduct a Stress Assessment from Local Structural Anisotropy (SALSA) to measure such spatio-temporal stress fluctuations. We directly image the microstructure of a nearly hard-sphere suspension using a high-speed confocal microscope and determine particle positions. We compute the structure anisotropy of the suspension and building on the Brady formalism, calculate particle-level stresses. In conjunction with the fluctuation-dissipation theorem, we then determine the bulk viscosity of a colloidal liquid. Furthermore, we show our local measurements allow direct visualization of the complex stress networks in a 3D supercooled liquid under compression. Our method provides an experimental approach that applies to a broad range of processes arising in sheared glasses, compressed gels, and even indented crystals.

  18. Complex quantum networks as structured environments: engineering and probing

    NASA Astrophysics Data System (ADS)

    Nokkala, Johannes; Galve, Fernando; Zambrini, Roberta; Maniscalco, Sabrina; Piilo, Jyrki

    2016-05-01

    We consider structured environments modeled by bosonic quantum networks and investigate the probing of their spectral density, structure, and topology. We demonstrate how to engineer a desired spectral density by changing the network structure. Our results show that the spectral density can be very accurately detected via a locally immersed quantum probe for virtually any network configuration. Moreover, we show how the entire network structure can be reconstructed by using a single quantum probe. We illustrate our findings presenting examples of spectral densities and topology probing for networks of genuine complexity.

  19. Complex quantum networks as structured environments: engineering and probing

    PubMed Central

    Nokkala, Johannes; Galve, Fernando; Zambrini, Roberta; Maniscalco, Sabrina; Piilo, Jyrki

    2016-01-01

    We consider structured environments modeled by bosonic quantum networks and investigate the probing of their spectral density, structure, and topology. We demonstrate how to engineer a desired spectral density by changing the network structure. Our results show that the spectral density can be very accurately detected via a locally immersed quantum probe for virtually any network configuration. Moreover, we show how the entire network structure can be reconstructed by using a single quantum probe. We illustrate our findings presenting examples of spectral densities and topology probing for networks of genuine complexity. PMID:27230125

  20. Spatially resolved imaging of inhomogeneous charge transfer behavior in polymorphous molybdenum oxide. I. Correlation of localized structural, electronic, and chemical properties using conductive probe atomic force microscopy and Raman microprobe spectroscopy.

    PubMed

    McEvoy, Todd M; Stevenson, Keith J

    2005-04-12

    A detailed study of electrochemically deposited molybdenum oxide thin films has been carried out after they were sintered at 250 degrees C. Conductive probe atomic force microscopy (CP-AFM), Raman microscopy, and X-ray photoelectron spectroscopy (XPS) techniques were employed to assess the complex structural, electronic, and compositional properties of these films. Spatially resolved Raman microprobe spectroscopy studies reveal that sintered molybdenum oxide is polymorphous and phase segregated with three types of domains observed comprising orthorhombic alpha-MoO3, monoclinic beta-MoO3, and intermixed alpha-/beta-MoO3. CP-AFM studies conducted in concert with Raman microprobe spectroscopy allowed for correlation between specific compositional regions and localized electronic properties. Single point tunneling spectroscopy studies of chemically distinct regions show semiconducting current-voltage (I-V) behavior with the beta-MoO3 polymorph exhibiting higher electronic conductivity than intermixed alpha-/beta-MoO3 or microcrystalline alpha-MoO3 domains. XPS valence level spectra of beta-MoO3 films display a small structured band near the Fermi level, indicative of an increased concentration of oxygen vacancies. This accounts for the greatly enhanced electronic conductivity of beta-MoO3 as these positively charged cationic defects (anion vacancies) act to trap excess electrons. Connections between structural features, electronic properties, and chemical composition are established and discussed. Importantly, this work highlights the value of using spatially resolved techniques for correlating structural and compositional features with electrochemical behaviors of disordered, mixed-phase lithium insertion oxides.

  1. Seismic probes of solar interior magnetic structure.

    PubMed

    Hanasoge, Shravan; Birch, Aaron; Gizon, Laurent; Tromp, Jeroen

    2012-09-07

    Sun spots are prominent manifestations of solar magnetoconvection, and imaging their subsurface structure is an outstanding problem of wide physical importance. Travel times of seismic waves that propagate through these structures are typically used as inputs to inversions. Despite the presence of strongly anisotropic magnetic waveguides, these measurements have always been interpreted in terms of changes to isotropic wave speeds and flow-advection-related Doppler shifts. Here, we employ partial-differential-equation-constrained optimization to determine the appropriate parametrization of the structural properties of the magnetic interior. Seven different wave speeds fully characterize helioseismic wave propagation: the isotropic sound speed, a Doppler-shifting flow-advection velocity, and an anisotropic magnetic velocity. The structure of magnetic media is sensed by magnetoacoustic slow and fast modes and Alfvén waves, each of which propagates at a different wave speed. We show that even in the case of weak magnetic fields, significant errors may be incurred if these anisotropies are not accounted for in inversions. Translation invariance is demonstrably lost. These developments render plausible the accurate seismic imaging of magnetoconvection in the Sun.

  2. Probing myosin head structure with monoclonal antibodies.

    PubMed

    Winkelmann, D A; Lowey, S

    1986-04-20

    Monoclonal antibodies that react with defined regions of the heavy and light chains of chicken skeletal muscle myosin have been used to provide a correlation between the primary and the tertiary structures of the head. Electron microscopy of rotary shadowed antibody-myosin complexes shows that the sites for three epitopes in the 25,000 Mr tryptic fragment (25k) of subfragment-1, including one within 4000 Mr of the amino terminus of the myosin heavy chain, are clustered 145(+/- 20) A from the head-rod junction. An epitope in the 50,000 Mr fragment maps even further out on the head. These antibodies bind to the head in several orientations, suggesting that each of the heads can rotate can rotate 180 degrees about the head-rod junction. The epitopes are accessible on subfragment-1 bound to actin when they were probed with Fab fragments; therefore, none of these heavy chain sites is is on the contact surface between the head and actin. Two of the anti-25k antibodies affect the K+-EDTA-and Ca2+-ATPase activities of myosin in a manner that mimics the effect on activity of the modification of the reactive thiol, SH-1. These two antibodies also inhibit the actin-activated ATPase non-competitively with respect to actin. None of the other eight antibodies tested had any marked effect on activity. A monoclonal antibody that reacts with an epitope in the amino-terminal third of myosin light chain 2 maps close to the head-rod junction. A polyclonal antibody specific for the amino terminus of light chain 3 binds further up in the "neck region" of the head, indicating that these portions of the two classes of light chains are located at different sites.

  3. Monitoring Coaxial-Probe Contact Force for Dielectric Properties Measurement

    USDA-ARS?s Scientific Manuscript database

    A means is described for measuring and monitoring the contact force applied to a material sample with an open-ended coaxial-line probe for purposes of measuring the dielectric properties of semisolid material samples such as fruit, vegetable and animal tissues. The equipment consists of a stainless...

  4. Probing the properties of extragalactic SNRs

    NASA Astrophysics Data System (ADS)

    Leonidaki, Ioanna

    2016-06-01

    The investigation of extragalactic SNRs gives us the advantage of surmounting the challenges we are usually confronted with when observing Galactic SNRs, most notably Galactic extinction and distance uncertainties. At the same time, by obtaining larger samples of SNRs, we are allowed to cover a wider range of environments and ISM parameters than our Galaxy, providing us a more complete and representative picture of SNR populations. I will outline the recent progress on extragalactic surveys of SNR populations focusing on the optical, radio, and X-ray bands. Multi-wavelength surveys can provide several key aspects of the physical processes taking place during the evolution of SNRs while at the same time can overcome possible selection effects that are inherent from monochromatic surveys. I will discuss the properties derived in each band (e.g. line ratios, luminosities, densities, temperatures) and their connection in order to yield information on various aspects of their behaviour and evolution. For example their interplay with the surrounding medium, their correlation with star formation activity, their luminosity distributions and their dependence on galaxy types.

  5. Oxygen transport as a structure probe for heterogeneous polymeric systems

    NASA Astrophysics Data System (ADS)

    Hu, Yushan

    Although permeability of small molecules is often measured as an important performance property, deeper analysis of the transport characteristics provides insight into polymer structure, especially if used in combination with other characterization techniques. Transport of small gas molecules senses the permeable amorphous structure and probes the nature of free volume. This work focuses on oxygen transport, supplemented with other methods of physical analysis, as a probe for: (1) the nature of free volume and crystalline morphology in the crystallized glassy state, (2) the nature of free volume and hierarchical structure in liquid crystalline polymers, and (3) the role of dispersed polyamide phase geometry on oxygen barrier properties of poly(ethylene terephthalate) (PET)/polyamide blends. In the first part, the improvement in oxygen-barrier properties of glassy polyesters by crystallization was examined. Examples included poly(ethylene naphthalate) (PEN), and a copolymer based on PET in which 55 mol% terephthalate was replaced with 4,4'-bibenzoate. Explanation of the unexpectedly high solubility of crystallized PEN required a two-phase transport model consisting of an impermeable crystalline phase of constant density and a permeable amorphous phase of variable density. The resulting relationship between oxygen solubility and amorphous phase density was consistent with free volume concepts of gas sorption. In the second part, oxygen barrier properties of liquid crystalline (LC) polyesters based on poly(diethylene glycol 4,4'-bibenzoate) (PDEGBB) were studied. This study extended the 2-phase transport model for oxygen transport of non-LC crystalline polymers to a smectic LCP. It was possible to systematically vary the solid state structure of (PDEGBB) from LC glass to crystallized LC glass. The results were consistent with a liquid crystalline state intermediate between the permeable amorphous glass and the impermeable 3-dimensional crystal. In this interpretation

  6. Electropolymerizable 2,2'-Carboranyldithiophenes. Structure-Property Investigations of the Corresponding Conducting Polymer Films by Electrochemistry, UV-Visible Spectroscopy and Conducting Probe Atomic Force Microscopy.

    PubMed

    Barrière, Frédéric; Fabre, Bruno; Hao, Erhong; Lejeune, Zorabel M; Hwang, Euiyong; Garno, Jayne C; Nesterov, Evgueni E; Vicente, M Graça H

    2009-04-28

    Carborane-functionalized conducting polymer films have been electrogenerated in dichloromethane from the anodic oxidation of ortho- (1), meta- (3) and para-carborane (4) isomers linked to two 2-thienyl units. The corresponding electrochemical response was characterized by a broad reversible redox system corresponding to the p-doping/undoping of the polythiophene backbone, the formal potential of which increased in the order poly(1) < poly(3) < poly(4), from ca. 0.50 to 1.15 V vs Ag/Ag(+) 10(-2) M. From further UV-visible spectroscopy analysis, the optical band gap was estimated at 1.8, 2.0 and 2.2 eV for poly(1), poly(3) and poly(4), respectively. The more conjugated and electroconductive character of poly(1) is ascribed to a more planar conformation of the conjugated backbone resulting from an intramolecular β-β' cyclization reaction in the monomer, consequently yielding a fused conjugated polymer. Molecular modeling calculations using the DFT method support this hypothesis. The surface topography and maps of the conductive domains of the electropolymerized films were evaluated by conducting probe AFM. The three polymers exhibit fairly similar morphological characteristics and a surface roughness of ~2 nm. Current-voltage (I-V) characteristics of conducting AFM tip-carborane polymer-ITO junctions showed that poly(1) had the highest conductivity.

  7. Using magnons to probe spintronic materials properties

    NASA Astrophysics Data System (ADS)

    McMichael, Robert

    2012-02-01

    For many spin-based electronic devices, from the read sensors in modern hard disk drives to future spintronic logic concepts, the device physics originates in spin polarized currents in ferromagnetic metals. In this talk, I will describe a novel ``Spin Wave Doppler'' method that uses the interaction of spin waves with spin-polarized currents to determine the spin drift velocity and the spin current polarization [1]. Owing to differences between the band structures of majority-spin and minority-spin electrons, the electrical current also carries an angular momentum current and magnetic moment current. Passing these coupled currents though a magnetic wire changes the linear excitations of the magnetization, i.e spin waves. Interestingly, the excitations can be described as drifting ``downstream'' with the electron flow. We measure this drift velocity by monitoring the spin-wave-mediated transmission between pairs of periodically patterned antennas on magnetic wires as a function of current density in the wire. The transmission frequency resonance shifts by 2πδf = vk where the drift velocity v is proportional to both the current density and the current polarization P. I will discuss measurements of the spin polarization of the current in Ni80Fe20 [2], and novel alloys (CoFe)1-xGax [3] and (Ni80Fe20)1-xGdx [4]. [4pt] [1] V. Vlaminck and M. Bailleul, Science, 322, 410 (2008) [0pt] [2] M. Zhu, C. L. Dennis, and R. D. McMichael, Phys. Rev. B, 81, 140407 (2010). [0pt] [3] M. Zhu, B. D. Soe, R. D. McMichael, M. J. Carey, S. Maat, and J. R. Childress, Appl. Phys. Lett., 98, 072510 (2011). [0pt] [4] R. L. Thomas, M. Zhu, C. L. Dennis, V. Misra and R. D. McMichael, J. Appl. Phys., 110, 033902 (2011).

  8. Structural probing of a pathogenic tRNA dimer

    PubMed Central

    ROY, MARC D.; WITTENHAGEN, LISA M.; KELLEY, SHANA O.

    2005-01-01

    The A3243G mutation within the human mitochondrial (hs mt) tRNALeu(UUR) gene is associated with maternally inherited deafness and diabetes (MIDD) and other mitochondrial encephalopathies. One of the most pronounced structural effects of this mutation is the disruption of the native structure through stabilization of a high-affinity dimeric complex. We conducted a series of studies that address the structural properties of this tRNA dimer, and we assessed its formation under physiological conditions. Enzymatic probing was used to directly define the dimeric interface for the complex, and a discrete region of the D-stem and loop of hs mt tRNALeu(UUR) was identified. The dependence of dimerization on magnesium ions and temperature was also tested. The formation of the tRNA dimer is influenced by temperature, with dimerization becoming more efficient at physiological temperature. Complexation of the mutant tRNA is also affected by the amount of magnesium present, and occurs at concentrations present intracellularly. Terbium probing experiments revealed a specific metal ion-binding site localized at the site of the A3243G mutation that is unique to the dimer structure. This metal ion-binding site presents a striking parallel to dimeric complexes of viral RNAs, which use the same hexanucleotide sequence for complexation and feature a similarly positioned metal ion-binding site within the dimeric structure. Taken together, these results indicate that the unique dimeric complex formed by the hs mt tRNALeu(UUR) A3243G mutant exhibits interesting similarities to biological RNA dimers, and may play a role in the loss of function caused by this mutation in vivo. PMID:15701731

  9. Structure of the ionospheric disturbances about planetary entry probes

    NASA Technical Reports Server (NTRS)

    Weil, H.; Jew, H.; Samir, U.

    1973-01-01

    Local ionospheric disturbances which would be created by a planetary entry probe are investigated. Competing theories of spacecraft-ambient plasma interactions are used to estimate computationally the perturbations of the plasma, particularly the structure of the near wake behind planetary entry vehicles. The results have bearing on the location and operation of plasma diagnostic instrumentation aboard planetary entry vehicles. Recent estimates of Mars ionospheric properties plus vehicle dimensions and speeds similar to those of the Viking Mars Lander are used to define the parameters essential to the theory. Smaller entry bodies are also considered. Comparisons are made of the results based on the different theories for a given assumed planetary atmosphere, and also with the perturbations a similar vehicle would generate in the earth's ionosphere.

  10. Probing the Properties of Two Galaxies with Planetary Nebulae

    NASA Astrophysics Data System (ADS)

    Fogel, J. K. J.; Jacoby, G. H.; Shaw, R. A.; Stanghellini, L.; Van de Steene, G. C.; Dopita, M.

    2002-12-01

    By measuring the abundances in nebulae, and distinguishing the enrichment of processed elements (primarily He, C, N, and O) from non-processed elements, (chiefly Ar, Ne, S) we are able to probe both the chemical enrichment around the planetary nebula and the population type of the progenitor star. Where we can also determine the evolutionary state, and therefore the mass, of the central star, we can also determine the time since the progenitor was formed. Because of these useful properties, studies of 18 PNs in the Large Magellanic Cloud (LMC) and six PNs in the Galactic bulge were undertaken to investigate the stellar population and PN properties in these contrasting environments. We also have spectra for eight more PN of sufficient quality to perform this analysis on them for a total of 14 planetaries out of the 95 new PN identified by Jacoby & Van de Steene. Neither of these sets of planetaries had been studied before because of the observational difficulties in obtaining high quality data. For the PNs in the Galactic center, the high extinction made it difficult to obtain the traditional optical diagnostic lines; while the study of LMC PNs required the high spatial resolution of HST to resolve the nebular structure. Moderate-dispersion spectra from MSSSO and spectral images from HST/STIS were used to examine in more detail the results of Stanghellini et al. (2000), where chemical enrichments were found in asymmetric PNs, relative to round or elliptical PNs. For the LMC planetaries, where we observed many diagnostic lines, it was straightforward to create models that matched the observed quantities very well, which then yielded a direct determination of the chemical abundances. Moderate dispersion spectra of the Galactic center PNs yielded far fewer measurable emission lines, and required extensive modeling using Gary Ferland's CLOUDY code to determine the chemical abundances. Jeffrey Fogel's research was supported by the NOAO/KPNO Research Experiences for

  11. Probing of structural relaxation times in the glassy state of sucrose and trehalose based on dynamical properties of two secondary relaxation processes

    SciTech Connect

    Kaminski, K.; Adrjanowicz, K.; Paluch, M.; Kaminska, E.

    2011-06-15

    Time-dependent isothermal dielectric measurements were carried out deeply in the glassy state on two very important saccharides: sucrose and trehalose. In both compounds two prominent secondary relaxation processes were identified. The faster one is an inherent feature of the whole family of carbohydrates. The slower one can also be detected in oligo- and polysaccharides. It was shown earlier that the {beta} process is the Johari-Goldstein (JG) relaxation coupled to motions of the glycosidic linkage, while the {gamma} relaxation originates from motions of the exocyclic hydroxymethyl unit. Recently, it was shown that the JG relaxation process can be used to determine structural relaxation times in the glassy state [R. Casalini and C. M. Roland, Phys. Rev. Lett. 102, 035701 (2009)]. In this paper we present the results of an analysis of the data obtained during aging using two independent approaches. The first was proposed by Casalini and Roland, and the second one is based on the variation of the dielectric strength of the secondary relaxation process during aging [J. K. Vij and G. Power, J. Non-Cryst. Solids 357, 783 (2011)]. Surprisingly, we found that the estimated structural relaxation times in the glassy state of both saccharides are almost the same, independent of the type of secondary mode. This finding calls into question the common view that secondary modes of intramolecular origin do not provide information about the dynamics of the glassy state.

  12. Nanoparticle Probes for Structural and Functional Photoacoustic Molecular Tomography

    PubMed Central

    Chen, Haobin; Yuan, Zhen; Wu, Changfeng

    2015-01-01

    Nowadays, nanoparticle probes have received extensive attention largely due to its potential biomedical applications in structural, functional, and molecular imaging. In addition, photoacoustic tomography (PAT), a method based on the photoacoustic effect, is widely recognized as a robust modality to evaluate the structure and function of biological tissues with high optical contrast and high acoustic resolution. The combination of PAT with nanoparticle probes holds promises for detecting and imaging diseased tissues or monitoring their treatments with high sensitivity. This review will introduce the recent advances in the emerging field of nanoparticle probes and their preclinical applications in PAT, as well as relevant perspectives on future development. PMID:26609534

  13. Probing the electronic structure and property of neutral and charged arsenic clusters (As(n)(+1,0,-1), n≤8) using Gaussian-3 theory.

    PubMed

    Liang, Gang; Wu, Qiang; Yang, Jucai

    2011-07-28

    The structures and energies of As(n) (n = 2-8) neutrals, anions, and cations have been systematically investigated by means of the G3 schemes. The electron affinities, ionization potentials, binding energies, and several dissociation energies have been calculated and compared with limited experimental values. The results revealed that the potential surfaces of neutral As(n) clusters are very shallow, and two types of structural patterns compete with each other for the ground-state structure of As(n) with n ≥ 6. One type is derived from the benzvalene form of As(6), and another is derived from the trigonal prism of As(6). The previous photoelectron spectrum (taken from J. Chem. Phys. 1998 , 109 , 10727 ) for As(3) has been reassigned in light of the G3 results. The experimental electron affinities of As(3) were measured to be 1.81 eV, not 1.45 eV. We inferred from the conclusion of G3 and density functional theory that the experimental electron affinities of 1.7 and 3.51 eV for As(5) are unreliable. The reliable electron affinities were predicted to be 0.83 eV for As(2), 1.80 eV for As(3), 0.54 eV for As(4), 3.01 eV for As(5), 2.08 eV for As(6), 2.93 eV for As(7), and 2.02 eV for As(8). The G3 ionization potentials were calculated to be 9.87 eV for As(2), 7.33 eV for As(3), 8.65 eV for As(4), 6.68 eV for As(5), 7.97 eV for As(6), 6.58 eV for As(7), and 7.65 eV for As(8). The binding energies per atom were evaluated to be 1.99 eV for As(2), 2.01 eV for As(3), 2.61 eV for As(4), 2.39 eV for As(5), 2.51 eV for As(6), 2.55 eV for As(7), and 2.67 eV for As(8). These theoretical values of As(2), As(3), and As(4) are in excellent agreement with those of experimental results. Several dissociation energies were carried out to examine relative stabilities. This characterized the even-numbered clusters as more stable than the odd-numbered species.

  14. Probing of structural relaxation times in the glassy state of sucrose and trehalose based on dynamical properties of two secondary relaxation processes

    NASA Astrophysics Data System (ADS)

    Kaminski, K.; Adrjanowicz, K.; Kaminska, E.; Paluch, M.

    2011-06-01

    Time-dependent isothermal dielectric measurements were carried out deeply in the glassy state on two very important saccharides: sucrose and trehalose. In both compounds two prominent secondary relaxation processes were identified. The faster one is an inherent feature of the whole family of carbohydrates. The slower one can also be detected in oligo- and polysaccharides. It was shown earlier that the β process is the Johari-Goldstein (JG) relaxation coupled to motions of the glycosidic linkage, while the γ relaxation originates from motions of the exocyclic hydroxymethyl unit. Recently, it was shown that the JG relaxation process can be used to determine structural relaxation times in the glassy state [R. Casalini and C. M. Roland, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.102.035701 102, 035701 (2009)]. In this paper we present the results of an analysis of the data obtained during aging using two independent approaches. The first was proposed by Casalini and Roland, and the second one is based on the variation of the dielectric strength of the secondary relaxation process during aging [J. K. Vij and G. Power, J. Non-Cryst. SolidsJNCSBJ0022-309310.1016/j.jnoncrysol.2010.07.067 357, 783 (2011)]. Surprisingly, we found that the estimated structural relaxation times in the glassy state of both saccharides are almost the same, independent of the type of secondary mode. This finding calls into question the common view that secondary modes of intramolecular origin do not provide information about the dynamics of the glassy state.

  15. Probing the complex ionic structure of warm dense carbon

    NASA Astrophysics Data System (ADS)

    Kraus, Dominik

    2014-10-01

    The carbon phase diagram at extreme pressure conditions has received broad interest for modeling planetary interiors and high energy density laboratory experiments. Numerous theoretical models and simulations have recently been performed but critical experimental data at the phase boundaries and of the microscopic physical properties remain very scarce. In this work, we present novel experimental observations of the complex ion structure in warm dense carbon at pressures from 20 to 220 GPa and temperatures of several thousand Kelvins. Our experiments employ powerful x-ray sources at kilo-joule class laser facilities and at the Linac Coherent Light Source to perform spectrally and angularly resolved x-ray scattering from shock-compressed graphite samples; the absolute static ion structure factor is directly measured by resolving the ratio of elastically and inelastically scattered radiation. Using different types of graphite and varying drive laser intensity, we were able to probe conditions below and above the melting line, resolving the shock-induced graphite-to-diamond and graphite-to-liquid transitions on nanosecond time scale. Our results confirm a complex ionic structure predicted by QMD simulations and demonstrate the importance of chemical bonds at extreme conditions similar to those found in the interiors of giant planets. The evidence presented here thus provides a firmer ground for modeling the evolution and current structure of carbon-bearing icy giants like Neptune, Uranus, and a number of extra-solar planets.

  16. Probing-directed identification of novel structured RNAs

    PubMed Central

    Vinogradova, Svetlana V.; Sutormin, Roman A.; Mironov, Andrey A.; Soldatov, Ruslan A.

    2016-01-01

    ABSTRACT Transcripts often harbor RNA elements, which regulate cell processes co- or post-transcriptionally. The functions of many regulatory RNA elements depend on their structure, thus it is important to determine the structure as well as to scan genomes for structured elements. State of the art ab initio approaches to predict structured RNAs rely on DNA sequence analysis. They use 2 major types of information inferred from a sequence: thermodynamic stability of an RNA structure and evolutionary footprints of base-pair interactions. In recent years, chemical probing of RNA has arisen as an alternative source of structural information. RNA probing experiments detect positions accessible to specific types of chemicals or enzymes indicating their propensity to be in a paired or unpaired state. There exist several strategies to integrate probing data into RNA secondary structure prediction algorithms that substantially improve the prediction quality. However, whether and how probing data could contribute to detection of structured RNAs remains an open question. We previously developed the energy-based approach RNASurface to detect locally optimal structured RNA elements. Here, we integrate probing data into the RNASurface energy model using a general framework. We show that the use of experimental data allows for better discrimination of ncRNAs from other transcripts. Application of RNASurface to genome-wide analysis of the human transcriptome with PARS data identifies previously undetectable segments, with evidence of functionality for some of them. PMID:26732206

  17. Probing Zeolite Crystal Architecture and Structural Imperfections using Differently Sized Fluorescent Organic Probe Molecules

    PubMed Central

    Hendriks, Frank C.; Schmidt, Joel E.; Rombouts, Jeroen A.; Lammertsma, Koop; Bruijnincx, Pieter C. A.

    2017-01-01

    Abstract A micro‐spectroscopic method has been developed to probe the accessibility of zeolite crystals using a series of fluorescent 4‐(4‐diethylaminostyryl)‐1‐methylpyridinium iodide (DAMPI) probes of increasing molecular size. Staining large zeolite crystals with MFI (ZSM‐5) topology and subsequent mapping of the resulting fluorescence using confocal fluorescence microscopy reveal differences in structural integrity: the 90° intergrowth sections of MFI crystals are prone to develop structural imperfections, which act as entrance routes for the probes into the zeolite crystal. Polarization‐dependent measurements provide evidence for the probe molecule's alignment within the MFI zeolite pore system. The developed method was extended to BEA (Beta) crystals, showing that the previously observed hourglass pattern is a general feature of BEA crystals with this morphology. Furthermore, the probes can accurately identify at which crystal faces of BEA straight or sinusoidal pores open to the surface. The results show this method can spatially resolve the architecture‐dependent internal pore structure of microporous materials, which is difficult to assess using other characterization techniques such as X‐ray diffraction. PMID:28217845

  18. Growth of cosmic structure: Probing dark energy beyond expansion

    NASA Astrophysics Data System (ADS)

    Huterer, Dragan; Kirkby, David; Bean, Rachel; Connolly, Andrew; Dawson, Kyle; Dodelson, Scott; Evrard, August; Jain, Bhuvnesh; Jarvis, Michael; Linder, Eric; Mandelbaum, Rachel; May, Morgan; Raccanelli, Alvise; Reid, Beth; Rozo, Eduardo; Schmidt, Fabian; Sehgal, Neelima; Slosar, Anže; van Engelen, Alex; Wu, Hao-Yi; Zhao, Gongbo

    2015-03-01

    The quantity and quality of cosmic structure observations have greatly accelerated in recent years, and further leaps forward will be facilitated by imminent projects. These will enable us to map the evolution of dark and baryonic matter density fluctuations over cosmic history. The way that these fluctuations vary over space and time is sensitive to several pieces of fundamental physics: the primordial perturbations generated by GUT-scale physics; neutrino masses and interactions; the nature of dark matter and dark energy. We focus on the last of these here: the ways that combining probes of growth with those of the cosmic expansion such as distance-redshift relations will pin down the mechanism driving the acceleration of the Universe. One way to explain the acceleration of the Universe is invoke dark energy parameterized by an equation of state w. Distance measurements provide one set of constraints on w, but dark energy also affects how rapidly structure grows; the greater the acceleration, the more suppressed the growth of structure. Upcoming surveys are therefore designed to probe w with direct observations of the distance scale and the growth of structure, each complementing the other on systematic errors and constraints on dark energy. A consistent set of results will greatly increase the reliability of the final answer. Another possibility is that there is no dark energy, but that General Relativity does not describe the laws of physics accurately on large scales. While the properties of gravity have been measured with exquisite precision at stellar system scales and densities, within our solar system and by binary pulsar systems, its properties in different environments are poorly constrained. To fully understand if General Relativity is the complete theory of gravity we must test gravity across a spectrum of scales and densities. Rapid developments in gravitational wave astronomy and numerical relativity are directed at testing gravity in the high

  19. Nuclear structure studies with intermediate energy probes

    SciTech Connect

    Lee, T.S.H.

    1993-10-01

    Nuclear structure studies with pions are reviewed. Results from a recent study of 1 p-shell nuclei using (e,e{prime}), ({pi}, {pi}{prime}), and ({gamma},{pi}) reactions are reported. Future nuclear structure studies with GeV electrons at CEBAF are also briefly discussed.

  20. A quadruple-scanning-probe force microscope for electrical property measurements of microscopic materials.

    PubMed

    Higuchi, Seiji; Kubo, Osamu; Kuramochi, Hiromi; Aono, Masakazu; Nakayama, Tomonobu

    2011-07-15

    Four-terminal electrical measurement is realized on a microscopic structure in air, without a lithographic process, using a home-built quadruple-scanning-probe force microscope (QSPFM). The QSPFM has four probes whose positions are individually controlled by obtaining images of a sample in the manner of atomic force microscopy (AFM), and uses the probes as contacting electrodes for electrical measurements. A specially arranged tuning fork probe (TFP) is used as a self-detection force sensor to operate each probe in a frequency modulation AFM mode, resulting in simultaneous imaging of the same microscopic feature on an insulator using the four TFPs. Four-terminal electrical measurement is then demonstrated in air by placing each probe electrode in contact with a graphene flake exfoliated on a silicon dioxide film, and the sheet resistance of the flake is measured by the van der Pauw method. The present work shows that the QSPFM has the potential to measure the intrinsic electrical properties of a wide range of microscopic materials in situ without electrode fabrication.

  1. A quadruple-scanning-probe force microscope for electrical property measurements of microscopic materials

    NASA Astrophysics Data System (ADS)

    Higuchi, Seiji; Kubo, Osamu; Kuramochi, Hiromi; Aono, Masakazu; Nakayama, Tomonobu

    2011-07-01

    Four-terminal electrical measurement is realized on a microscopic structure in air, without a lithographic process, using a home-built quadruple-scanning-probe force microscope (QSPFM). The QSPFM has four probes whose positions are individually controlled by obtaining images of a sample in the manner of atomic force microscopy (AFM), and uses the probes as contacting electrodes for electrical measurements. A specially arranged tuning fork probe (TFP) is used as a self-detection force sensor to operate each probe in a frequency modulation AFM mode, resulting in simultaneous imaging of the same microscopic feature on an insulator using the four TFPs. Four-terminal electrical measurement is then demonstrated in air by placing each probe electrode in contact with a graphene flake exfoliated on a silicon dioxide film, and the sheet resistance of the flake is measured by the van der Pauw method. The present work shows that the QSPFM has the potential to measure the intrinsic electrical properties of a wide range of microscopic materials in situ without electrode fabrication.

  2. Auroral Spatial Structures Probe Sub-Orbital Mission Preliminary Results

    NASA Astrophysics Data System (ADS)

    Pratt, J.; Swenson, C.; Martineau, R. J.; Fish, C. S.; Conde, M.; Hampton, D.; Crowley, G.

    2015-12-01

    The NASA Auroral Spatial Structures Probe, 49.002, was launched January 28, 2015 from the Poker Flat Research Range into active aurora over the northern coast of Alaska. The primary objective of this mission was to determine the contribution of small spatial and temporal scale fluctuations of the electric fields to the larger-scale energy deposition processes associated with the aurora. The Auroral Spatial Structures Probe Sub-Orbital Mission consisted of a formation of 7 spacecraft (a main payload with 6 deployable sub-payloads) designed for multiple temporally spaced co-located measurements of electric and magnetic fields in the earth's ionosphere. The mission was able to make observations at a short time scale and small spatial scale convergence that is unobservable by either satellite or ground-based observations. The payloads included magnetometers, electric field double probes, and Langmuir probes as well as a sweeping impedance probe on the main payload. We present here preliminary results from the measurements taken that hint at the underlying spatial structure of the currents and energy deposition in the aurora. The Poynting flux derived from the observations is shown and implications are discussed in terms of the contribution of small spatial scale, rapid temporal scale fluctuations in the currents that deposit energy in the auroral region. Funding provided by NASA Grants NNX11AE23G and NNX13AN20A.

  3. The Large-scale Structure of the Universe: Probes of Cosmology and Structure Formation

    NASA Astrophysics Data System (ADS)

    Noh, Yookyung

    The usefulness of large-scale structure as a probe of cosmology and structure formation is increasing as large deep surveys in multi-wavelength bands are becoming possible. The observational analysis of large-scale structure guided by large volume numerical simulations are beginning to offer us complementary information and crosschecks of cosmological parameters estimated from the anisotropies in Cosmic Microwave Background (CMB) radiation. Understanding structure formation and evolution and even galaxy formation history is also being aided by observations of different redshift snapshots of the Universe, using various tracers of large-scale structure. This dissertation work covers aspects of large-scale structure from the baryon acoustic oscillation scale, to that of large scale filaments and galaxy clusters. First, I discuss a large- scale structure use for high precision cosmology. I investigate the reconstruction of Baryon Acoustic Oscillation (BAO) peak within the context of Lagrangian perturbation theory, testing its validity in a large suite of cosmological volume N-body simulations. Then I consider galaxy clusters and the large scale filaments surrounding them in a high resolution N-body simulation. I investigate the geometrical properties of galaxy cluster neighborhoods, focusing on the filaments connected to clusters. Using mock observations of galaxy clusters, I explore the correlations of scatter in galaxy cluster mass estimates from multi-wavelength observations and different measurement techniques. I also examine the sources of the correlated scatter by considering the intrinsic and environmental properties of clusters.

  4. Substrate texture properties induce triatomine probing on bitten warm surfaces

    PubMed Central

    2011-01-01

    Background In this work we initially evaluated whether the biting process of Rhodnius prolixus relies on the detection of mechanical properties of the substrate. A linear thermal source was used to simulate the presence of a blood vessel under the skin of a host. This apparatus consisted of an aluminium plate and a nickel-chrome wire, both thermostatized and presented at 33 and 36°C, respectively. To evaluate whether mechanical properties of the substrate affect the biting behaviour of bugs, this apparatus was covered by a latex membrane. Additionally, we evaluated whether the expression of probing depends on the integration of bilateral thermal inputs from the antennae. Results The presence of a latex cover on a thermal source induced a change in the biting pattern shown by bugs. In fact, with latex covered sources it was possible to observe long bites that were never performed in response to warm metal surfaces. The total number of bites was higher in intact versus unilaterally antennectomized insects. These bites were significantly longer in intact than in unilaterally antennectomized insects. Conclusions Our results suggest that substrate recognition by simultaneous input through thermal and mechanical modalities is required for triggering maxillary probing activity. PMID:21682881

  5. Probing the structure of cometary ice

    NASA Technical Reports Server (NTRS)

    Wilson, Michael A.; Pohorille, Andrew; Jenniskens, Peter; Blake, David F.

    1995-01-01

    Computer simulations of bulk and vapor deposited amorphous ices are presented. The structure of the bulk low density amorphous ice is in good agreement with experiments on pressure disordered amorphous ice. Both the low density bulk ice and the vapor deposited ices exhibit strong ordering. Vapor deposition of hot (300 K) water molecules onto a cold (77 K) substrate yields less porous ices than deposition of cold (77 K) water molecules onto a cold substrate. Both vapor deposited ices are more porous than the bulk amorphous ice. The structure of bulk high density amorphous ice is only in fair agreement with experimental results. Attempts to simulate high density amorphous ice via vapor deposition were not successful. Electron diffraction results on vapor deposited amorphous ice indicate that the temperature of the nucleation of the cubic phase depends upon the amount of time between the deposition and the onset of crystallization, suggesting that freshly deposited ice layers reconstruct on time of the order of hours. The temperature dependence of the microporosity of the vapor deposited amorphous ices might affect laboratory experiments that are aimed at simulating astrophysical ices in the context of the origin of prebiotic organic material and its transport to the Earth.

  6. Probing the Physical Structures of Dense Filaments

    NASA Astrophysics Data System (ADS)

    Li, Di

    2015-08-01

    Filament is a common feature in cosmological structures of various scales, ranging from dark matter cosmic web, galaxy clusters, inter-galactic gas flows, to Galactic ISM clouds. Even within cold dense molecular cores, filaments have been detected. Theories and simulations with (or without) different combination of physical principles, including gravity, thermal balance, turbulence, and magnetic field, can reproduce intriguing images of filaments. The ubiquity of filaments and the similarity in simulated ones make physical parameters, beyond dust column density, a necessity for understanding filament evolution. I report three projects attempting to measure physical parameters of filaments. We derive the volume density of a dense Taurus filament based on several cyanoacetylene transitions observed by GBT and ART. We measure the gas temperature of the OMC 2-3 filament based on combined GBT+VLA ammonia images. We also measured the sub-millimeter polarization vectors along OMC3. These filaments were found to be likely a cylinder-type structure, without dynamic heating, and likely accreting mass along the magnetic field lines.

  7. Oxygen as a site specific structural probe in neutron diffraction

    SciTech Connect

    Neuefeind, Joerg C; Simonson, J Michael {Mike}; Salmon, Phil; Zeidler, Anita; Fischer, Henry E; Rauch, Helmut; Markland, Thomas; Lemmel, Hartmut

    2011-01-01

    Oxygen is a ubiquitous element, playing an essential role in most scientific and technological disciplines, and is often incorporated within a structurally disordered material where examples include molten silicates in planetary science, glasses used for lasers and optical communication, and water in biological processes. Establishing the structure of a liquid or glassy oxide and thereby its relation to the functional properties of a material is not, however, a trivial task owing to the complexity associated with atomic disorder. Here we approach this challenge by measuring the bound coherent neutron scattering lengths of the oxygen isotopes with the sensitive technique of neutron interferometry. We find that there is a small but finite contrast of 0.204(6) fm between the scattering lengths of the isotope 18O and oxygen of natural isotopic abundance natO, contrary to tables of recommended values. This has enabled us to investigate the structure of both light and heavy water by exploiting, for the first time, the method of oxygen isotope substitution in neutron diffraction, thus circumventing many of the significant problems associated with more traditional methods in which hydrogen is substituted by deuterium. We find a difference of ~0.5% between the O-H and O-D intra-molecular bond distances which is much smaller than recent estimates based on diffraction data and is found to be in excellent agreement with path integral molecular dynamics simulations made with a flexible polarisable water model. Our results demonstrate the potential for using oxygen isotope substitution as a powerful and effective site specific probe in a plethora of materials, of pertinence as instrumentation at next generation neutron sources comes online

  8. Computational analysis of RNA structures with chemical probing data

    PubMed Central

    Ge, Ping; Zhang, Shaojie

    2015-01-01

    RNAs play various roles, not only as the genetic codes to synthesize proteins, but also as the direct participants of biological functions determined by their underlying high-order structures. Although many computational methods have been proposed for analyzing RNA structures, their accuracy and efficiency are limited, especially when applied to the large RNAs and the genome-wide data sets. Recently, advances in parallel sequencing and high-throughput chemical probing technologies have prompted the development of numerous new algorithms, which can incorporate the auxiliary structural information obtained from those experiments. Their potential has been revealed by the secondary structure prediction of ribosomal RNAs and the genome-wide ncRNA function annotation. In this review, the existing probing-directed computational methods for RNA secondary and tertiary structure analysis are discussed. PMID:25687190

  9. Probing physical properties at the nanoscale using atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Ditzler, Lindsay Rachel

    Techniques that measure physical properties at the nanoscale with high sensitivity are significantly limited considering the number of new nanomaterials being developed. The development of atomic force microscopy (AFM) has lead to significant advancements in the ability to characterize physical properties of materials in all areas of science: chemistry, physics, engineering, and biology have made great scientific strides do to the versatility of the AFM. AFM is used for quantification of many physical properties such as morphology, electrical, mechanical, magnetic, electrochemical, binding interactions, and protein folding. This work examines the electrical and mechanical properties of materials applicable to the field of nano-electronics. As electronic devices are miniaturized the demand for materials with unique electrical properties, which can be developed and exploited, has increased. For example, discussed in this work, a derivative of tetrathiafulvalene, which exhibits a unique loss of conductivity upon compression of the self-assembled monolayer could be developed into a molecular switch. This work also compares tunable organic (tetraphenylethylene tetracarboxylic acid and bis(pyridine)s assemblies) and metal-organic (Silver-stilbizole coordination compounds) crystals which show high electrical conductivity. The electrical properties of these materials vary depending on their composition allowing for the development of compositionally tunable functional materials. Additional work was done to investigate the effects of molecular environment on redox active 11-ferroceneyl-1 undecanethiol (Fc) molecules. The redox process of mixed monolayers of Fc and decanethiol was measured using conductive probe atomic force microscopy and force spectroscopy. As the concentration of Fc increased large, variations in the force were observed. Using these variations the number of oxidized molecules in the monolayer was determined. AFM is additionally capable of investigating

  10. Statistical Properties of Plasmaspheric Hiss from Van Allen Probes Observations

    NASA Astrophysics Data System (ADS)

    Hartley, D.; Kletzing, C.; Santolik, O.; Bounds, S. R.; Kurth, W. S.; Hospodarsky, G. B.

    2016-12-01

    Plasmaspheric hiss wave properties are investigated using Van Allen Probes observations of both electric and magnetic wave field power spectra. The analysis reveals that at L-shells greater than 3.5, the wave normal vector is predominantly field aligned. However, at L-shells less than 3.5 the wave normal angle may be significantly more oblique, particularly at frequencies greater than 1 kHz. Analysis of this region (L < 3.5) reveals two populations of the plasmaspheric hiss wave mode; i) a population with wave normal angles less than approximately 50° containing power in both the electric and magnetic field (electromagnetic) and, ii) a population at very oblique wave normal angles (θk > 70°) with a weak magnetic component and strong electric component (more electrostatic). The distribution of these two populations are presented both as a function of magnetic local time and geomagnetic activity, with their distinguishing features identified and discussed.

  11. Quantum probes for the spectral properties of a classical environment

    NASA Astrophysics Data System (ADS)

    Benedetti, Claudia; Buscemi, Fabrizio; Bordone, Paolo; Paris, Matteo G. A.

    2014-03-01

    We address the use of simple quantum probes for the spectral characterization of classical noisy environments. In our scheme a qubit interacts with a classical stochastic field describing environmental noise and is then measured after a given interaction time in order to estimate the characteristic parameters of the noise. In particular, we address estimation of the spectral parameters of two relevant kinds of non-Gaussian noise: random telegraph noise with a Lorentzian spectrum and colored noise with a 1/fα spectrum. We analyze in detail the estimation precision achievable by quantum probes and prove that population measurement on the qubit is optimal for noise estimation in both cases. We also evaluate the optimal interaction times for the quantum probe, i.e., the values maximizing the quantum Fisher information (QFI) and the quantum signal-to-noise ratio. For random telegraph noise the QFI is inversely proportional to the square of the switching rate, meaning that the quantum signal-to-noise ratio is constant and thus the switching rate may be uniformly estimated with the same precision in its whole range of variation. For colored noise, the precision achievable in the estimation of "color," i.e., of the exponent α, strongly depends on the structure of the environment, i.e., on the number of fluctuators describing the classical environment. For an environment modeled by a single random fluctuator estimation is more precise for pink noise, i.e., for α =1, whereas by increasing the number of fluctuators, the quantum signal-to-noise ratio has two local maxima, with the largest one drifting towards α =2, i.e., brown noise.

  12. Effect of probe geometry and optical properties on the sampling depth for diffuse reflectance spectroscopy.

    PubMed

    Hennessy, Ricky; Goth, Will; Sharma, Manu; Markey, Mia K; Tunnell, James W

    2014-01-01

    The sampling depth of light for diffuse reflectance spectroscopy is analyzed both experimentally and computationally. A Monte Carlo (MC) model was used to investigate the effect of optical properties and probe geometry on sampling depth. MC model estimates of sampling depth show an excellent agreement with experimental measurements over a wide range of optical properties and probe geometries. The MC data are used to define a mathematical expression for sampling depth that is expressed in terms of optical properties and probe geometry parameters.

  13. ProbFold: a probabilistic method for integration of probing data in RNA secondary structure prediction.

    PubMed

    Sahoo, Sudhakar; Świtnicki, Michał P; Pedersen, Jakob Skou

    2016-09-01

    Recently, new RNA secondary structure probing techniques have been developed, including Next Generation Sequencing based methods capable of probing transcriptome-wide. These techniques hold great promise for improving structure prediction accuracy. However, each new data type comes with its own signal properties and biases, which may even be experiment specific. There is therefore a growing need for RNA structure prediction methods that can be automatically trained on new data types and readily extended to integrate and fully exploit multiple types of data. Here, we develop and explore a modular probabilistic approach for integrating probing data in RNA structure prediction. It can be automatically trained given a set of known structures with probing data. The approach is demonstrated on SHAPE datasets, where we evaluate and selectively model specific correlations. The approach often makes superior use of the probing data signal compared to other methods. We illustrate the use of ProbFold on multiple data types using both simulations and a small set of structures with both SHAPE, DMS and CMCT data. Technically, the approach combines stochastic context-free grammars (SCFGs) with probabilistic graphical models. This approach allows rapid adaptation and integration of new probing data types. ProbFold is implemented in C ++. Models are specified using simple textual formats. Data reformatting is done using separate C ++ programs. Source code, statically compiled binaries for x86 Linux machines, C ++ programs, example datasets and a tutorial is available from http://moma.ki.au.dk/prj/probfold/ : jakob.skou@clin.au.dk Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  14. Ion spectral structures observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Ferradas, C.; Zhang, J.; Spence, H. E.; Kistler, L. M.; Larsen, B.; Reeves, G. D.; Skoug, R. M.; Funsten, H. O.

    2015-12-01

    During the last decades several missions have recorded the presence of dynamic spectral features of energetic ions in the inner magnetosphere. Previous studies have reported single "nose-like" structures occurring alone and simultaneous nose-like structures (up to three). These ion structures are named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. They constitute the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. The HOPE mass spectrometer onboard the Van Allen Probes measures energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet, where these ion structures are observed. We present a statistical study of nose-like structures, using 2-years measurements from the HOPE instrument. The results provide important details about the spatial distribution (dependence on geocentric distance), spectral features of the structures (differences among species), and geomagnetic conditions under which these structures occur.

  15. Three-Dimensional RNA Structure Refinement by Hydroxyl Radical Probing

    PubMed Central

    Ding, Feng; Lavender, Christopher A.; Weeks, Kevin M.; Dokholyan, Nikolay V.

    2012-01-01

    Molecular modeling guided by experimentally-derived structural information is an attractive approach for three-dimensional structure determination of complex RNAs that are not amenable to study by high-resolution methods. Hydroxyl radical probing (HRP), performed routinely in many laboratories, provides a measure of solvent accessibility at individual nucleotides. HRP measurements have, to date, only been used to evaluate RNA models qualitatively. Here, we report development of a quantitative structure refinement approach using HRP measurements to drive discrete molecular dynamics simulations for RNAs ranging in size from 80 to 230 nucleotides. HRP reactivities were first used to identify RNAs that form extensive helical packing interactions. For these RNAs, we achieved highly significant structure predictions, given inputs of RNA sequence and base pairing. This HRP-directed tertiary structure refinement approach generates robust structural hypotheses useful for guiding explorations of structure-function interrelationships in RNA. PMID:22504587

  16. Probing the structure of nucleic acids with Ni(II) complexes

    SciTech Connect

    Chen, Xiaoying.

    1992-01-01

    The structure of nucleic acids determines their biological function. Interest in the development of novel probes from structures of nucleic acid has led to the discovery of conformation-specific oxidation of guanine sites in DNA and RNA using Ni(II) complexes. The reaction is highly dependent upon the nature of Ni(II) complexes with the most important feature of a strong in-plane ligand field. The unique properties of Ni(II) complexes combining redox and coordination features provide sensitive probes for nucleic acid conformation. One of these nickel complexes, NiCR, has been shown to selectively promote cleavage of DNA at guanine sites held accessible through the formation of unusual secondary structures such as ends, mismatches, bulges and loops. An unique mechanism for the base and conformation-specific oxidation of DNA promoted by Ni(II) complexes is proposed, involving direct ligation of nickel to N-7 of guanine delivering a non-diffusible oxidizing species. NiCR has been proved to be a sensitive and predictable probe for the tertiary structure of RNAs. The specific sites of oxidation of tRNS[sup phe] promoted by NiCR correspond to the most accessible guanine residues determined by theoretic calculations. NiCR has also been successfully applied to probe the tertiary structure of self-splicing Tetrahymena pre-rRNA intron, and has provided important information about the folding of this intron, especially in the region of the catalytic core.

  17. Chemical probes for higher-order structure in RNA.

    PubMed Central

    Peattie, D A; Gilbert, W

    1980-01-01

    Three chemical reactions can probe the secondary and tertiary interactions of RNA molecules in solution. Dimethyl sulfate monitors the N-7 of guanosines and senses tertiary interactions there, diethyl pyrocarbonate detects stacking of adenosines, and an alternate dimethyl sulfate reaction examines the N-3 of cytidines and thus probes base pairing. The reactions work between 0 degrees C and 90 degrees C and at pH 4.5--8.5 in a variety of buffers. As an example we follow the progressive denaturation of yeast tRNAPhe terminally labeled with 32P as the tertiary and secondary structures sequentially melt out. A single autoradiograph of a terminally labeled molecule locates regions of higher-order structure and identifies the bases involved. Images PMID:6159633

  18. Structural dynamics inside a functionalized metal–organic framework probed by ultrafast 2D IR spectroscopy

    DOE PAGES

    Nishida, Jun; Tamimi, Amr; Fei, Honghan; ...

    2014-12-15

    One key property of metal-organic frameworks (MOFs) are their structural elasticity. IHere we show that 2D IR spectroscopy with pulse-shaping techniques can probe the ultrafast structural fluctuations of MOFs. 2D IR data, obtained from a vibrational probe attached to the linkers of UiO-66 MOF in low concentration, revealed that the structural fluctuations have time constants of 7 and 670 ps with no solvent. Filling the MOF pores with dimethylformamide (DMF) slows the structural fluctuations by reducing the ability of the MOF to undergo deformations, and the dynamics of the DMF molecules are also greatly restricted. Finally, methodology advances were requiredmore » to remove the severe light scattering caused by the macroscopic-sized MOF particles, eliminate interfering oscillatory components from the 2D IR data, and address Förster vibrational excitation transfer.« less

  19. Probe-rotating atomic force microscopy for determining material properties

    SciTech Connect

    Lee, Sang Heon

    2014-03-15

    In this paper, we propose a probe-rotating atomic force microscope that enables scan in an arbitrary direction in the contact imaging mode, which is difficult to achieve using a conventional atomic force microscope owing to the orientation-dependent probe and the inability to rotate the probe head. To enable rotation of the probe about its vertical axis, we employed a compact and light probe head, the sensor of which is made of an optical disk drive pickup unit. Our proposed mechanical configuration, operating principle, and control system enables axial and lateral scan in various directions.

  20. The Structures & Properties of Carbon

    ERIC Educational Resources Information Center

    Castellini, Olivia M.; Lisensky, George C.; Ehrlich, Jennifer; Zenner, Greta M.; Crone, Wendy C.

    2006-01-01

    The four main forms of carbon--diamond, graphite, buckyballs, and carbon nanotubes (CNTs)--are an excellent vehicle for teaching fundamental principles of chemical bonding, material structure, and properties. Carbon atoms form a variety of structures that are intrinsically connected to the properties they exhibit. Educators can take advantage of…

  1. The Structures & Properties of Carbon

    ERIC Educational Resources Information Center

    Castellini, Olivia M.; Lisensky, George C.; Ehrlich, Jennifer; Zenner, Greta M.; Crone, Wendy C.

    2006-01-01

    The four main forms of carbon--diamond, graphite, buckyballs, and carbon nanotubes (CNTs)--are an excellent vehicle for teaching fundamental principles of chemical bonding, material structure, and properties. Carbon atoms form a variety of structures that are intrinsically connected to the properties they exhibit. Educators can take advantage of…

  2. Synthesis, spectroscopic properties, and biological applications of eight novel chlorinated fluorescent proteins-labeling probes.

    PubMed

    Wu, Xianglong; Tian, Min; Fan, Wutu; Pan, Yalei; Zhai, Yuankun; Niu, Yinbo; Li, Chenrui; Lu, Tingli; Mei, Qibing

    2014-05-01

    Eight novel chlorinated fluorescent proteins-labeling probes with a linker and reactive group were prepared in 7 steps by the reaction of chlorinated resorcinols with 3, 6-dichloro-4-carboxyphthalic anhydride in the presence of methanesulfonic acid. Structures of target compounds and intermediates were determined via IR, MS, (1)H NMR and element analysis. The spectral properties of the chlorinated fluoresceins were studied. These fluorescent probes showed absorbance peaks at 508-536 nm and fluorescence peaks at 524-550 nm. It was found that they have absorption and emission maxima at long wavelengths and high fluorescence quantum yields. Emission spectra of chlorinated fluoresceins shifted towards long wavelength with increase in chlorine. The probes were used for fluorescence imaging of cells in order to investigate whether they can conjugate to cells. The fluorescence imaging of living cells showed that they were localized in cell nucleus. However, they were localized in cytosol of chemically fixed cells. These probes will be useful reagents for the preparation of stable fluorescent conjugates.

  3. Measuring dielectric properties of concrete by a wide coaxial probe with an open end

    NASA Astrophysics Data System (ADS)

    Filali, B.; Rhazi, J. E.; Ballivy, G.

    2006-05-01

    We present nondestructive measurements of dielectric properties of concrete and mortar. The measures are made using a coaxial probe with a 32.5 mm open end, engineered specially for this work. The frequency domain goes from 100 to 900 MHz and includes frequently found frequencies in radars used for the auscultation of concrete structures. The probe was calibrated, and the measures were validated successfully on two solutions of different salinity, as well as on limestone and granite samples. Measures were also carried out on two mortars and six concretes of different recipes. We studied the effect of porosity and water content on the measures. The statistical analysis of the results indicates thatthe dispersion of measurements on these heterogeneous materials (granulometry from 5 to 20 nm) is comparable to that observed in limestone and granite. Our results confirm those from other authors who used more complicated techniques.

  4. Detecting 3D Vegetation Structure with the Galileo Space Probe: Can a Distant Probe Detect Vegetation Structure on Earth?

    PubMed Central

    2016-01-01

    Sagan et al. (1993) used the Galileo space probe data and first principles to find evidence of life on Earth. Here we ask whether Sagan et al. (1993) could also have detected whether life on Earth had three-dimensional structure, based on the Galileo space probe data. We reanalyse the data from this probe to see if structured vegetation could have been detected in regions with abundant photosynthetic pigments through the anisotropy of reflected shortwave radiation. We compare changing brightness of the Amazon forest (a region where Sagan et al. (1993) noted a red edge in the reflectance spectrum, indicative of photosynthesis) as the planet rotates to a common model of reflectance anisotropy and found measured increase of surface reflectance of 0.019 ± 0.003 versus a 0.007 predicted from only anisotropic effects. We hypothesize the difference was due to minor cloud contamination. However, the Galileo dataset had only a small change in phase angle (sun-satellite position) which reduced the observed anisotropy signal and we demonstrate that theoretically if the probe had a variable phase angle between 0–20°, there would have been a much larger predicted change in surface reflectance of 0.1 and under such a scenario three-dimensional vegetation structure on Earth could possibly have been detected. These results suggest that anisotropic effects may be useful to help determine whether exoplanets have three-dimensional vegetation structure in the future, but that further comparisons between empirical and theoretical results are first necessary. PMID:27973530

  5. Detecting 3D Vegetation Structure with the Galileo Space Probe: Can a Distant Probe Detect Vegetation Structure on Earth?

    PubMed

    Doughty, Christopher E; Wolf, Adam

    2016-01-01

    Sagan et al. (1993) used the Galileo space probe data and first principles to find evidence of life on Earth. Here we ask whether Sagan et al. (1993) could also have detected whether life on Earth had three-dimensional structure, based on the Galileo space probe data. We reanalyse the data from this probe to see if structured vegetation could have been detected in regions with abundant photosynthetic pigments through the anisotropy of reflected shortwave radiation. We compare changing brightness of the Amazon forest (a region where Sagan et al. (1993) noted a red edge in the reflectance spectrum, indicative of photosynthesis) as the planet rotates to a common model of reflectance anisotropy and found measured increase of surface reflectance of 0.019 ± 0.003 versus a 0.007 predicted from only anisotropic effects. We hypothesize the difference was due to minor cloud contamination. However, the Galileo dataset had only a small change in phase angle (sun-satellite position) which reduced the observed anisotropy signal and we demonstrate that theoretically if the probe had a variable phase angle between 0-20°, there would have been a much larger predicted change in surface reflectance of 0.1 and under such a scenario three-dimensional vegetation structure on Earth could possibly have been detected. These results suggest that anisotropic effects may be useful to help determine whether exoplanets have three-dimensional vegetation structure in the future, but that further comparisons between empirical and theoretical results are first necessary.

  6. Probing the electronic and catalytic properties of a bimetallic surface with 3 nm resolution

    NASA Astrophysics Data System (ADS)

    Zhong, Jin-Hui; Jin, Xi; Meng, Lingyan; Wang, Xiang; Su, Hai-Sheng; Yang, Zhi-Lin; Williams, Christopher T.; Ren, Bin

    2016-11-01

    An atomic- and molecular-level understanding of heterogeneous catalysis is required to characterize the nature of active sites and improve the rational design of catalysts. Achieving this level of characterization requires techniques that can correlate catalytic performances to specific surface structures, so as to avoid averaging effects. Tip-enhanced Raman spectroscopy combines scanning probe microscopy with plasmon-enhanced Raman scattering and provides simultaneous topographical and chemical information at the nano/atomic scale from ambient to ultrahigh-vacuum and electrochemical environments. Therefore, it has been used to monitor catalytic reactions and is proposed to correlate the local structure and function of heterogeneous catalysts. Bimetallic catalysts, such as Pd-Au, show superior performance in various catalytic reactions, but it has remained challenging to correlate structure and reactivity because of their structural complexity. Here, we show that TERS can chemically and spatially probe the site-specific chemical (electronic and catalytic) and physical (plasmonic) properties of an atomically well-defined Pd(sub-monolayer)/Au(111) bimetallic model catalyst at 3 nm resolution in real space using phenyl isocyanide as a probe molecule (Fig. 1a). We observe a weakened N≡C bond and enhanced reactivity of phenyl isocyanide adsorbed at the Pd step edge compared with that at the Pd terrace. Density functional theory corroborates these observations by revealing a higher d-band electronic profile for the low-coordinated Pd step edge atoms. The 3 nm spatial resolution we demonstrate here is the result of an enhanced electric field and distinct electronic properties at the step edges.

  7. Probing the electronic and catalytic properties of a bimetallic surface with 3 nm resolution

    NASA Astrophysics Data System (ADS)

    Zhong, Jin-Hui; Jin, Xi; Meng, Lingyan; Wang, Xiang; Su, Hai-Sheng; Yang, Zhi-Lin; Williams, Christopher T.; Ren, Bin

    2017-02-01

    An atomic- and molecular-level understanding of heterogeneous catalysis is required to characterize the nature of active sites and improve the rational design of catalysts. Achieving this level of characterization requires techniques that can correlate catalytic performances to specific surface structures, so as to avoid averaging effects. Tip-enhanced Raman spectroscopy combines scanning probe microscopy with plasmon-enhanced Raman scattering and provides simultaneous topographical and chemical information at the nano/atomic scale from ambient to ultrahigh-vacuum and electrochemical environments. Therefore, it has been used to monitor catalytic reactions and is proposed to correlate the local structure and function of heterogeneous catalysts. Bimetallic catalysts, such as Pd-Au, show superior performance in various catalytic reactions, but it has remained challenging to correlate structure and reactivity because of their structural complexity. Here, we show that TERS can chemically and spatially probe the site-specific chemical (electronic and catalytic) and physical (plasmonic) properties of an atomically well-defined Pd(sub-monolayer)/Au(111) bimetallic model catalyst at 3 nm resolution in real space using phenyl isocyanide as a probe molecule (Fig. 1a). We observe a weakened N≡C bond and enhanced reactivity of phenyl isocyanide adsorbed at the Pd step edge compared with that at the Pd terrace. Density functional theory corroborates these observations by revealing a higher d-band electronic profile for the low-coordinated Pd step edge atoms. The 3 nm spatial resolution we demonstrate here is the result of an enhanced electric field and distinct electronic properties at the step edges.

  8. Structural Stability of Giant Polyoxomolybdate Molecules as Probed by EXAFS

    SciTech Connect

    Frenkel,A.; Frenkel, S.; Liu, T.

    2005-01-01

    Recent progress in synthesis of 'giant' polyoxomolybdate (POM) molecules that have a structure of hollow spheres or wheels and size of several nanometers in diameter has emphasized the need in their accurate structural investigation. Our temperature-dependent EXAFS studies demonstrated that the first generation POM molecules containing 132 Mo atoms, undergo irreversible structural transformations at ca. 500 K, while the recently synthesized second generation POM at ca. 400 K. The number of different structural units in these molecules can be accurately obtained from EXAFS analysis and compared with model structure calculations. In our method of analysis, we use theoretical calculations of pair radial distribution functions from the model structures as initial approximations to analyze the structures of these molecules. Our analysis allowed us to identify the new POM structure as a giant sphere, similar to the {l_brace}Mo{sub 132}{r_brace} structure but containing 522 Mo atoms. Our results also demonstrate that the structural rigidity of different building blocks of these molecules can be quantitatively probed by EXAFS.

  9. Osmium tetroxide as a probe of RNA structure.

    PubMed

    Zhang, Jing; Li, Danbin; Zhang, Jun; Chen, Dongrong; Murchie, Alastair I H

    2017-04-01

    Structured RNAs have a central role in cellular function. The capability of structured RNAs to adopt fixed architectural structures or undergo dynamic conformational changes contributes to their diverse role in the regulation of gene expression. Although numerous biophysical and biochemical tools have been developed to study structured RNAs, there is a continuing need for the development of new methods for the investigation of RNA structures, especially methods that allow RNA structure to be studied in solution close to its native cellular conditions. Here we use osmium tetroxide (OsO4) as a chemical probe of RNA structure. In this method, we have used fluorescence-based sequencing technologies to detect OsO4 modified RNA. We characterized the requirements for OsO4 modification of RNA by investigating three known structured RNAs: the M-box, glycine riboswitch RNAs, and tRNA(asp) Our results show that OsO4 predominantly modifies RNA at uracils that are conformationally exposed on the surface of the RNA. We also show that changes in OsO4 reactivity at flexible positions in the RNA correlate with ligand-driven conformational changes in the RNA structure. Osmium tetroxide modification of RNA will provide insights into the structural features of RNAs that are relevant to their underlying biological functions. © 2017 Zhang et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  10. Probing electronic structure of stoichiometric and defective Sn O2

    NASA Astrophysics Data System (ADS)

    Moreno, M. S.; Kas, J. J.; Ma, C.; Wang, F.; Rehr, J. J.; Malac, M.

    2017-06-01

    The electronic structure of stoichiometric tin dioxide (Sn O2 ) is studied by probing its unoccupied states using the fine structure in the electron energy-loss spectra (EELS) at the oxygen-K (O-K ) edge. The spectral measurements were performed both at room and at high temperatures (773 K) and compared to ab initio calculations carried out using the real-space multiple-scattering and linearized augmented-plane-wave methods. Important many-body effects are included via quasiparticle corrections calculated within the many-pole G W self-energy approximation. An additional energy-dependent damping is calculated to account for vibrational effects. Results from this paper demonstrated that quantitative agreement between theoretical and experimental spectra can be obtained when nonspherical potentials and quasiparticle self-energy effects are considered and vibrational broadening is included. Modifications of the electronic structure by single oxygen vacancies, both in the bulk and at the (110) surface, also are predicted. Our predictions support the use of O-K EELS as a probe of the defect structures in Sn O2 surfaces and nanoparticles.

  11. Probing and controlling terahertz-driven structural dynamics with surface sensitivity

    DOE PAGES

    Bowlan, Pamela Renee; Bowlan, J.; Trugman, S. A.; ...

    2017-03-17

    Intense, single-cycle terahertz (THz) pulses are powerful tools to understand and control material properties through low-energy resonances, such as phonons. Combining this with optical second harmonic generation (SHG) makes it possible to observe the resulting ultrafast structural changes with surface sensitivity. This makes SHG an ideal method to probe phonon dynamics in topological insulators (TI), materials with unique surface transport properties. Here, we resonantly excite a phonon mode in the TI Bi2Se3with THz pulses and use SHG to separate the resulting symmetry changes at the surface from the bulk. Furthermore, we coherently control the lattice vibrations with a pair ofmore » THz pulses. Lastly, our work demonstrates a versatile, table-top tool to probe and control phonon dynamics in a range of systems, particularly at surfaces and interfaces.« less

  12. Toward structurally defined carbon dots as ultracompact fluorescent probes.

    PubMed

    LeCroy, Gregory Ethan; Sonkar, Sumit Kumar; Yang, Fan; Veca, L Monica; Wang, Ping; Tackett, Kenneth N; Yu, Jing-Jiang; Vasile, Eugeniu; Qian, Haijun; Liu, Yamin; Luo, Pengju George; Sun, Ya-Ping

    2014-05-27

    There has been much discussion on the need to develop fluorescent quantum dots (QDs) as ultracompact probes, with overall size profiles comparable to those of the genetically encoded fluorescent tags. In the use of conventional semiconductor QDs for such a purpose, the beautifully displayed dependence of fluorescence color on the particle diameter becomes a limitation. More recently, carbon dots have emerged as a new platform of QD-like fluorescent nanomaterials. The optical absorption and fluorescence emissions in carbon dots are not bandgap in origin, different from those in conventional semiconductor QDs. The absence of any theoretically defined fluorescence color-dot size relationships in carbon dots may actually be exploited as a unique advantage in the size reduction toward having carbon dots serve as ultracompact QD-like fluorescence probes. Here we report on carbon dots of less than 5 nm in the overall dot diameter with the use of 2,2'-(ethylenedioxy)bis(ethylamine) (EDA) molecules for the carbon particle surface passivation. The EDA-carbon dots were found to be brightly fluorescent, especially over the spectral range of green fluorescent protein. These aqueous soluble smaller carbon dots also enabled more quantitative characterizations, including the use of solution-phase NMR techniques, and the results suggested that the dot structures were relatively simple and better-defined. The potential for these smaller carbon dots to serve as fluorescence probes of overall sizes comparable to those of fluorescent proteins is discussed.

  13. Emerging approaches to probing ion channel structure and function.

    PubMed

    Li, Wei-Guang; Xu, Tian-Le

    2012-08-01

    Ion channels, as membrane proteins, are the sensors of the cell. They act as the first line of communication with the world beyond the plasma membrane and transduce changes in the external and internal environments into unique electrical signals to shape the responses of excitable cells. Because of their importance in cellular communication, ion channels have been intensively studied at the structural and functional levels. Here, we summarize the diverse approaches, including molecular and cellular, chemical, optical, biophysical, and computational, used to probe the structural and functional rearrangements that occur during channel activation (or sensitization), inactivation (or desensitization), and various forms of modulation. The emerging insights into the structure and function of ion channels by multidisciplinary approaches allow the development of new pharmacotherapies as well as new tools useful in controlling cellular activity.

  14. The use of multiple probe molecules for the study of the acid-base properties of aluminium hydroxyfluoride having the hexagonal tungsten bronze structure: FTIR and [36Cl] radiotracer studies.

    PubMed

    Dambournet, Damien; Leclerc, Hervé; Vimont, Alexandre; Lavalley, Jean-Claude; Nickkho-Amiry, Mahmood; Daturi, Marco; Winfield, John M

    2009-03-07

    The combination of several probe molecules has enabled the construction of a detailed picture of the surface of aluminium hydroxyl fluoride, AlF(2.6)(OH)(0.4), which has the hexagonal tungsten bronze (HTB) structure. Using pyridine as a probe leads to features at 1628 cm(-1), ascribed to very strong Lewis acid sites, and at 1620-1623 cm(-1), which is the result of several different types of Lewis sites. This heterogeneity is indicated also from CO adsorption at 100 K; the presence of five different types of Lewis site is deduced and is suggested to arise from the hydroxylated environment. Brønsted acid sites of medium strength are indicated by adsorption of lutidine and CO. Adsorption of lutidine occurs at OH groups, which are exposed at the surface and CO reveals that these OH groups have a single environment that can be correlated with their specific location inside the bulk, assuming that the surface OH group may reflect the bulk OH periodicity. A correlation between the data obtained from CO and pyridine molecules has been established using co-adsorption experiments, which also highlight the inductive effect produced by pyridine. Adsorption of the strong Brønsted acid, anhydrous hydrogen chloride, detected by monitoring the beta(-) emission of [(36)Cl]-HCl at the surface, indicates that surface hydroxyl groups can behave also as a Brønsted base and that H(2)O-HCl interactions, either within the hexagonal channels or at the surface are possible. Finally, the formation of strongly bound H(36)Cl as a result of the room temperature dehydrochlorination of [(36)Cl]-labelled tert-butyl chloride provides additional evidence that HTB-AlF(2.6)(OH)(0.4) can behave as a Lewis acid.

  15. Deep Interior: Probing the Structure of Primitive Bodies

    NASA Astrophysics Data System (ADS)

    Asphaug, Erik; Scheeres, Daniel; Safaeinili, Ali

    Deep Interior is a mature Discovery-class mission concept focused on probing the geophysical behavior of primitive bodies, from the mechanics of their exterior materials to the structures of their interiors. Its theme is to discover how small bodies work - to learn the natural origin and evolution of asteroids, comets and other primitive bodies through radar reflection tomography and through detailed observations of the local and global effects of cratering. Learning the structure and mechanical response of asteroids and comets is also a precursor to resource utilization and hazardous asteroid mitigation. Overall the mission is aligned with NASA strategic sub-goal 3C, to advance scientific knowledge of the origin and history of the solar system ... and the hazards and resources present as humans explore space. Deep Interior deploys no complex landers or sub-spacecraft; the scientific instruments are a radar and a camera. A blast cratering experiments triggered by grenades leads to a low cost seismological investigation which complements the radar investigation. A desired addition is an imaging spectrometer. The science instruments are high heritage, as are the navigation techniques for orbiting and station-keeping. The mission conducts the following investigations at one or more asteroids: Radar Reflection Tomography (RRT). The first science phase is to operate a penetrating radar during each several-month rendezvous, deployed in reflection mode in the manner of ongoing radar investigations underway by Mars Express, Mars Reconnaissance Orbiter, and Kaguya. The RRT technique (Safaeinili et al., MAPS 2002) is analogous to performing a "CAT scan" from orbit: closely sampled radar echoes are processed to yield volumetric maps of mechanical and compositional boundaries, and to measure interior dielectric properties. Deep Interior utilizes a polar orbit (or station keeping) while the asteroid spins underneath; the result is to "peel the apple" with thousands of unique

  16. Reconstruction of the trajectory of the Huygens probe using the Huygens Atmospheric Structure Instrument (HASI)

    NASA Astrophysics Data System (ADS)

    Colombatti, G.; Withers, P.; Ferri, F.; Aboudan, A.; Ball, A. J.; Bettanini, C.; Gaborit, V.; Harri, A. M.; Hathi, B.; Leese, M. R.; Makinen, T.; Stoppato, P. L.; Towner, M. C.; Zarnecki, J. C.; Angrilli, F.; Fulchignoni, M.

    2008-04-01

    The Huygens probe returned scientific measurements from the atmosphere and surface of Titan on 14 January 2005. Knowledge of the trajectory of Huygens is necessary for scientific analysis of those measurements. We use measurements from the Huygens Atmospheric Structure Instrument (HASI) to reconstruct the trajectory of Huygens during its mission. The HASI Accelerometer subsystem measured the axial acceleration of the probe with errors of 3E-6 m s -2, the most accurate measurements ever made by an atmospheric structure instrument on another planetary body. The atmosphere was detected at an altitude of 1498 km. Measurements of the normal acceleration of the probe, which are important for determining the probe's attitude during hypersonic entry, were significantly less accurate and limited by transverse sensitivity of the piezo sensors. Peak acceleration of 121.2 m s -2 occurred at 234.9 km altitude. The parachute deployment sequence started at 157.1 km and a speed of 342.1 m s -1. Direct measurements of pressure and temperature began shortly afterwards. The measured accelerations and equations of motion have been used to reconstruct the trajectory prior to parachute deployment. Measured pressures and temperatures, together with the equation of hydrostatic equilibrium and the equation of state, have been used to reconstruct the trajectory after parachute deployment. Uncertainties in the entry state of Huygens at the top of the atmosphere are significant, but can be reduced by requiring that the trajectory and atmospheric properties be continuous at parachute deployment.

  17. Investigation of material property influenced stoichiometric deviations as evidenced during UV laser-assisted atom probe tomography in fluorite oxides

    NASA Astrophysics Data System (ADS)

    Valderrama, Billy; Henderson, Hunter B.; Yablinsky, Clarissa A.; Gan, Jian; Allen, Todd R.; Manuel, Michele V.

    2015-09-01

    Oxide materials are used in numerous applications such as thermal barrier coatings, nuclear fuels, and electrical conductors and sensors, all applications where nanometer-scale stoichiometric changes can affect functional properties. Atom probe tomography can be used to characterize the precise chemical distribution of individual species and spatially quantify the oxygen to metal ratio at the nanometer scale. However, atom probe analysis of oxides can be accompanied by measurement artifacts caused by laser-material interactions. In this investigation, two technologically relevant oxide materials with the same crystal structure and an anion to cation ratio of 2.00, pure cerium oxide (CeO2) and uranium oxide (UO2) are studied. It was determined that electronic structure, optical properties, heat transfer properties, and oxide stability strongly affect their evaporation behavior, thus altering their measured stoichiometry, with thermal conductance and thermodynamic stability being strong factors.

  18. Four-probe measurements of the in-plane thermoelectric properties of nanofilms

    SciTech Connect

    Mavrokefalos, Anastassios; Pettes, Michael T.; Zhou Feng; Shi Li

    2007-03-15

    Measuring in-plane thermoelectric properties of submicron thin films has remained a challenging task. Here we report a method based on a suspended microdevice for four-probe measurements of the Seebeck coefficient, thermal conductivity, electrical conductivity, and thermoelectric figure of merit of patterned indium arsenide (InAs) nanofilms assembled on the microdevice. The contact thermal resistance and intrinsic thermal resistance of the 40 nm thick InAs nanofilm sample were measured by using the nanofilm itself as a differential thermocouple to determine the temperature drops at the contacts. The microdevice was also used to measure a 190 nm thick silicon dioxide (SiO{sub 2}) film and the results were compared with those reported in the literature. A through-substrate hole under the suspended microdevice allows for transmission electron microscopy characterization of the nanofilm sample assembled on the device. This capability enables one to correlate the measured thermoelectric properties with the crystal structures of the nanofilm.

  19. Four-probe measurements of the in-plane thermoelectric properties of nanofilms.

    PubMed

    Mavrokefalos, Anastassios; Pettes, Michael T; Zhou, Feng; Shi, Li

    2007-03-01

    Measuring in-plane thermoelectric properties of submicron thin films has remained a challenging task. Here we report a method based on a suspended microdevice for four-probe measurements of the Seebeck coefficient, thermal conductivity, electrical conductivity, and thermoelectric figure of merit of patterned indium arsenide (InAs) nanofilms assembled on the microdevice. The contact thermal resistance and intrinsic thermal resistance of the 40 nm thick InAs nanofilm sample were measured by using the nanofilm itself as a differential thermocouple to determine the temperature drops at the contacts. The microdevice was also used to measure a 190 nm thick silicon dioxide (SiO(2)) film and the results were compared with those reported in the literature. A through-substrate hole under the suspended microdevice allows for transmission electron microscopy characterization of the nanofilm sample assembled on the device. This capability enables one to correlate the measured thermoelectric properties with the crystal structures of the nanofilm.

  20. Four-probe measurements of the in-plane thermoelectric properties of nanofilms

    NASA Astrophysics Data System (ADS)

    Mavrokefalos, Anastassios; Pettes, Michael T.; Zhou, Feng; Shi, Li

    2007-03-01

    Measuring in-plane thermoelectric properties of submicron thin films has remained a challenging task. Here we report a method based on a suspended microdevice for four-probe measurements of the Seebeck coefficient, thermal conductivity, electrical conductivity, and thermoelectric figure of merit of patterned indium arsenide (InAs) nanofilms assembled on the microdevice. The contact thermal resistance and intrinsic thermal resistance of the 40nm thick InAs nanofilm sample were measured by using the nanofilm itself as a differential thermocouple to determine the temperature drops at the contacts. The microdevice was also used to measure a 190nm thick silicon dioxide (SiO2) film and the results were compared with those reported in the literature. A through-substrate hole under the suspended microdevice allows for transmission electron microscopy characterization of the nanofilm sample assembled on the device. This capability enables one to correlate the measured thermoelectric properties with the crystal structures of the nanofilm.

  1. Effect of probe geometry and optical properties on the sampling depth for diffuse reflectance spectroscopy

    PubMed Central

    Hennessy, Ricky; Goth, Will; Sharma, Manu; Markey, Mia K.; Tunnell, James W.

    2014-01-01

    Abstract. The sampling depth of light for diffuse reflectance spectroscopy is analyzed both experimentally and computationally. A Monte Carlo (MC) model was used to investigate the effect of optical properties and probe geometry on sampling depth. MC model estimates of sampling depth show an excellent agreement with experimental measurements over a wide range of optical properties and probe geometries. The MC data are used to define a mathematical expression for sampling depth that is expressed in terms of optical properties and probe geometry parameters. PMID:25349033

  2. Probing the nucleon structure with SIDIS at Jefferson Lab

    SciTech Connect

    Pereira, Sergio Anafalos

    2013-01-01

    In recent years, measurements of azimuthal moments of polarized hadronic cross sections in hard processes have emerged as a powerful tool to probe nucleon structure. Many experiments worldwide are currently trying to pin down various effects related to nucleon structure through Semi-Inclusive Deep-Inelastic Scattering (SIDIS). Azimuthal distributions of final-state particles in semi-inclusive deep inelastic scattering, in particular, are sensitive to the orbital motion of quarks and play an important role in the study of Transverse Momentum Dependent parton distribution functions (TMDs) of quarks in the nucleon. The CLAS spectrometer, installed in Hall-B at Jefferson Lab, has collected semi-inclusive data using the CEBAF 6 GeV polarized electron beam on polarized solid NH{sub 3} and ND{sub 3} targets. An overview of these measurements is presented.

  3. Analyzing piezoresponse force microscopy for reconstruction of probed ferroelectric structures

    NASA Astrophysics Data System (ADS)

    Pan, K.; Liu, Y. Y.; Liu, Y. M.; Li, J. Y.

    2012-09-01

    Piezoresponse force microscopy (PFM) has emerged as the tool of choice for characterizing piezoelectric and ferroelectric materials at nanoscale, yet the interpretation of PFM remains to be difficult and sometimes ambiguous. Built on earlier works, we developed a numerical integration scheme to analyze the expected PFM response in ferroelectrics with arbitrary domain configurations, with the ultimate goal to accurately reconstruct the underlying ferroelectric structure from PFM measurements. Using such technique, we demonstrated that the relationship between the effective and intrinsic piezoelectric coefficients is sensitive to a variety of factors that are intrinsic to the probed materials, and showed that the PFM mapping is not only influenced by polarization distribution on the sample surface but also three-dimensional polarization distribution inside the material. While relatively simple domain structures were used for demonstration, the approach is general, and can be applied to ferroelectrics with arbitrary polarization distributions.

  4. Surface properties of graphite and LaB6 materials used for laser heated emissive probe diagnostic

    NASA Astrophysics Data System (ADS)

    Mehta, P.; Sarma, A.; Sivagami, A. D.; HariPrakash, N.; Gopi, S.; Sarma, B.; Ghosh, J.

    2017-02-01

    Laser heated emissive probe (LHEP) has been used as an alternative diagnostics to measure direct plasma potential. In this case, surface properties of LHEP materials have been studied before and after exposing it to high power laser. A high density small diameter (0.5 mm) laser light of variable power density is used to heat the probe tip. Two types of probe tip material are used in this experiment, viz, Graphite (Coarse grain and HOPG) and LaB6. Purity of material is dependent on the constituents of the same. Surface properties of these materials before and after laser exposure and plasma conditions have been characterized by scanning electron microscopy (SEM) and the energy dispersive X-ray spectroscopy. In order to achieve higher sensitivity on carbon surface and other layers the low-energy probing ( 1.0 keV), the energy dispersive spectroscopy is used. Data of the energy dispersive X-ray spectroscopy allows us to obtain the structure of the materials as well as different elements present in these materials. To understand the surface morphology more critically, open source software named Gwyddion ( version 2.35) has been used for processing of the SEM images. The 3-D visualization of the probe tip at different experimental conditions has been made using the Interactive 3-D surface plot plug-in of Gwyddion. Optical properties are also analyzed using diffusion reflectance spectroscopy and from which band gap energy of the same has been estimated.

  5. RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data.

    PubMed

    Wu, Yang; Qu, Rihao; Huang, Yiming; Shi, Binbin; Liu, Mengrong; Li, Yang; Lu, Zhi John

    2016-07-08

    Several high-throughput technologies have been developed to probe RNA base pairs and loops at the transcriptome level in multiple species. However, to obtain the final RNA secondary structure, extensive effort and considerable expertise is required to statistically process the probing data and combine them with free energy models. Therefore, we developed an RNA secondary structure prediction server that is enhanced by experimental data (RNAex). RNAex is a web interface that enables non-specialists to easily access cutting-edge structure-probing data and predict RNA secondary structures enhanced by in vivo and in vitro data. RNAex annotates the RNA editing, RNA modification and SNP sites on the predicted structures. It provides four structure-folding methods, restrained MaxExpect, SeqFold, RNAstructure (Fold) and RNAfold that can be selected by the user. The performance of these four folding methods has been verified by previous publications on known structures. We re-mapped the raw sequencing data of the probing experiments to the whole genome for each species. RNAex thus enables users to predict secondary structures for both known and novel RNA transcripts in human, mouse, yeast and Arabidopsis The RNAex web server is available at http://RNAex.ncrnalab.org/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data

    PubMed Central

    Wu, Yang; Qu, Rihao; Huang, Yiming; Shi, Binbin; Liu, Mengrong; Li, Yang; Lu, Zhi John

    2016-01-01

    Several high-throughput technologies have been developed to probe RNA base pairs and loops at the transcriptome level in multiple species. However, to obtain the final RNA secondary structure, extensive effort and considerable expertise is required to statistically process the probing data and combine them with free energy models. Therefore, we developed an RNA secondary structure prediction server that is enhanced by experimental data (RNAex). RNAex is a web interface that enables non-specialists to easily access cutting-edge structure-probing data and predict RNA secondary structures enhanced by in vivo and in vitro data. RNAex annotates the RNA editing, RNA modification and SNP sites on the predicted structures. It provides four structure-folding methods, restrained MaxExpect, SeqFold, RNAstructure (Fold) and RNAfold that can be selected by the user. The performance of these four folding methods has been verified by previous publications on known structures. We re-mapped the raw sequencing data of the probing experiments to the whole genome for each species. RNAex thus enables users to predict secondary structures for both known and novel RNA transcripts in human, mouse, yeast and Arabidopsis. The RNAex web server is available at http://RNAex.ncrnalab.org/. PMID:27137891

  7. Probing the Evolution of the Shell Structures in Exotic Nuclei

    SciTech Connect

    De Angelis, Giacomo

    2008-11-11

    Magic numbers are a key feature in finite Fermion systems since they are strongly related to the underlying mean field. The size of the shell gaps and their evolution far from stability can be linked to the shape and symmetry of the nuclear mean field. Moreover the study of nuclei with large neutron/proton ratio allow to probe the density dependence of the effective interaction. Changes of the nuclear density and size in nuclei with increasing N/Z ratios are expected to lead to different nuclear symmetries and excitations. In this contribution I will discuss some selected examples which show the big potential of stable beams and of binary reactions for the study of the properties of the neutron-rich nuclear many body systems.

  8. Multispectral phloem-mobile probes: properties and applications.

    PubMed

    Knoblauch, Michael; Vendrell, Marc; de Leau, Erica; Paterlini, Andrea; Knox, Kirsten; Ross-Elliot, Tim; Reinders, Anke; Brockman, Stephen A; Ward, John; Oparka, Karl

    2015-04-01

    Using Arabidopsis (Arabidopsis thaliana) seedlings, we identified a range of small fluorescent probes that entered the translocation stream and were unloaded at the root tip. These probes had absorbance/emission maxima ranging from 367/454 to 546/576 nm and represent a versatile toolbox for studying phloem transport. Of the probes that we tested, naturally occurring fluorescent coumarin glucosides (esculin and fraxin) were phloem loaded and transported in oocytes by the sucrose transporter, AtSUC2. Arabidopsis plants in which AtSUC2 was replaced with barley (Hordeum vulgare) sucrose transporter (HvSUT1), which does not transport esculin in oocytes, failed to load esculin into the phloem. In wild-type plants, the fluorescence of esculin decayed to background levels about 2 h after phloem unloading, making it a suitable tracer for pulse-labeling studies of phloem transport. We identified additional probes, such as carboxytetraethylrhodamine, a red fluorescent probe that, unlike esculin, was stable for several hours after phloem unloading and could be used to study phloem transport in Arabidopsis lines expressing green fluorescent protein.

  9. Development of a multichannel hyperspectral imaging probe for food property and quality assessment

    USDA-ARS?s Scientific Manuscript database

    This paper reports on the development, calibration and evaluation of a new multipurpose, multichannel hyperspectral imaging probe for property and quality assessment of food products. The new multichannel probe consists of a 910-miscrometer fiber as a point light source and 30 light receiving fibers...

  10. Development of a multichannel hyperspectral imaging probe for property and quality assessment of horticultural products

    USDA-ARS?s Scientific Manuscript database

    This paper reports on the development, calibration and evaluation of a new multipurpose, multichannel hyperspectral imaging probe for property and quality assessment of food products. The new multichannel probe consists of a 910-miscrometer fiber as a point light source and 30 light receiving fibers...

  11. 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.

  12. Probing Micromechanical Properties of the Extracellular Matrix of Soft Tissues by Atomic Force Microscopy.

    PubMed

    Jorba, Ignasi; Uriarte, Juan J; Campillo, Noelia; Farré, Ramon; Navajas, Daniel

    2017-01-01

    The extracellular matrix (ECM) determines 3D tissue architecture and provides structural support and chemical and mechanical cues to the cells. Atomic force microscopy (AFM) has unique capabilities to measure ECM mechanics at the scale at which cells probe the mechanical features of their microenvironment. Moreover, AFM measurements can be readily combined with bright field and fluorescence microscopy. Performing reliable mechanical measurements with AFM requires accurate calibration of the device and correct computation of the mechanical parameters. A suitable approach to isolate ECM mechanics from cell contribution is removing the cells by means of an effective decellularization process that preserves the composition, structure and mechanical properties of the ECM. AFM measurement of ECM micromechanics provides important insights into organ biofabrication, cell-matrix mechanical crosstalk and disease-induced tissue stiffness alterations. J. Cell. Physiol. 232: 19-26, 2017. © 2016 Wiley Periodicals, Inc.

  13. Probing Mechanical Properties of Rock with InSAR

    NASA Astrophysics Data System (ADS)

    Jónsson, S.

    2012-04-01

    Interferometric Synthetic Aperture Radar (InSAR) observations from satellites have revolutionized our crustal deformation measurement capabilities with its high spatial resolution, global coverage, and low cost. The high spatial resolution (typically 5-20 m) allows us to map many small-scale surface deformation phenomena in great detail. These include surface faulting, fissuring, fault creep, and other strain localization phenomena. Another advantage of the small-scale deformation mapping is that it can provide information about mechanical properties of near-surface rocks. Several studies have already been published on using InSAR to probe material properties of rock. Strain localizations at fault zones have been observed in co-seismic deformation fields near to large earthquakes and interpreted as expressions of weak fault zone materials that are a factor of two more compliant than the surrounding unbroken rock [Fialko et al., 2002]. Peltzer et al. [1999] argued that asymmetries in coseismic deformation patterns observed by InSAR showed evidence for non-linear elasticity, i.e. that the elastic moduli of shallow crustal material are different for compression and extension, due to small-scale cracks in the medium. This interpretation was later disputed by Funning et al. [2007], who provided an alternative explanation for observed deformation pattern based on along-strike variations in fault geometry and slip. In addition, observations and modeling of poro-elastic rebound after earthquakes have provided information about the difference in undrained and drained Poisson's ratio values of the near-surface rocks [Peltzer et al., 1996; Jónsson et al., 2003]. More recently we have used InSAR observations to put bounds on the tensional bulk strength of surface rocks. A dyke intrusion that took place in western Saudi Arabia in 2009 caused many moderate-sized earthquakes and extensive surface faulting. InSAR data of the area show that large-scale (40 km x 40 km) east

  14. Ion nose spectral structures observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Ferradas, C. P.; Zhang, J.-C.; Spence, H. E.; Kistler, L. M.; Larsen, B. A.; Reeves, G.; Skoug, R.; Funsten, H.

    2016-12-01

    We present a statistical study of nose-like structures observed in energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet. Nose structures are spectral features named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. Using 22 months of observations from the Helium Oxygen Proton Electron instrument onboard Van Allen Probe A, we determine the number of noses observed, and the minimum L shell reached and energy of each nose on each pass through the inner magnetosphere. We find that multiple noses occur more frequently in heavy ions than in H+ and are most often observed during quiet times. The heavy-ion noses penetrate to lower L shells than H+ noses, and there is an energy-magnetic local time (MLT) dependence in the nose locations and energies that is similar for all species. The observations are interpreted by using a steady state model of ion drift in the inner magnetosphere. The model is able to explain the energy and MLT dependence of the different types of nose structures. Different ion charge-exchange lifetimes are the main cause for the deeper penetration of heavy-ion noses. The species dependence and preferred geomagnetic conditions of multiple-nose events indicate that they must be on long drift paths, leading to strong charge-exchange effects. The results provide important insight into the spatial distribution, species dependence, and geomagnetic conditions under which nose structures occur.

  15. Probing topological protection using a designer surface plasmon structure

    DOE PAGES

    Gao, Fei; Gao, Zhen; Shi, Xihang; ...

    2016-05-20

    Topological photonic states, inspired by robust chiral edge states in topological insulators, have recently been demonstrated in a few photonic systems, including an array of coupled on-chip ring resonators at communication wavelengths. However, the intrinsic difference between electrons and photons determines that the 'topological protection' in time-reversal-invariant photonic systems does not share the same robustness as its counterpart in electronic topological insulators. Here in a designer surface plasmon platform consisting of tunable metallic sub-wavelength structures, we construct photonic topological edge states and probe their robustness against a variety of defect classes, including some common time-reversal-invariant photonic defects that can breakmore » the topological protection, but do not exist in electronic topological insulators. Furthermore, this is also an experimental realization of anomalous Floquet topological edge states, whose topological phase cannot be predicted by the usual Chern number topological invariants.« less

  16. Probing topological protection using a designer surface plasmon structure

    SciTech Connect

    Gao, Fei; Gao, Zhen; Shi, Xihang; Yang, Zhaoju; Lin, Xiao; Xu, Hongyi; Joannopoulos, John D.; Soljacic, Marin; Chen, Hongsheng; Lu, Ling; Chong, Yidong; Zhang, Baile

    2016-05-20

    Topological photonic states, inspired by robust chiral edge states in topological insulators, have recently been demonstrated in a few photonic systems, including an array of coupled on-chip ring resonators at communication wavelengths. However, the intrinsic difference between electrons and photons determines that the 'topological protection' in time-reversal-invariant photonic systems does not share the same robustness as its counterpart in electronic topological insulators. Here in a designer surface plasmon platform consisting of tunable metallic sub-wavelength structures, we construct photonic topological edge states and probe their robustness against a variety of defect classes, including some common time-reversal-invariant photonic defects that can break the topological protection, but do not exist in electronic topological insulators. Furthermore, this is also an experimental realization of anomalous Floquet topological edge states, whose topological phase cannot be predicted by the usual Chern number topological invariants.

  17. Growth of Cosmic Structure: Probing Dark Energy Beyond Expansion

    DOE PAGES

    Huterer, Dragan; Kirkby, David; Bean, Rachel; ...

    2014-03-15

    The quantity and quality of cosmic structure observations have greatly accelerated in recent years, and further leaps forward will be facilitated by imminent projects. These will enable us to map the evolution of dark and baryonic matter density fluctuations over cosmic history. The way that these fluctuations vary over space and time is sensitive to several pieces of fundamental physics: the primordial perturbations generated by GUT-scale physics; neutrino masses and interactions; the nature of dark matter and dark energy. We focus on the last of these here: the ways that combining probes of growth with those of the cosmic expansionmore » such as distance-redshift relations will pin down the mechanism driving the acceleration of the Universe.« less

  18. Growth of Cosmic Structure: Probing Dark Energy Beyond Expansion

    SciTech Connect

    Huterer, Dragan; Kirkby, David; Bean, Rachel; Connolly, Andrew; Dawson, Kyle; Dodelson, Scott; Evrard, August; Jain, Bhuvnesh; Jarvis, Michael; Linder, Eric; Mandelbaum, Rachel; May, Morgan; Raccanelli, Alvise; Reid, Beth; Rozo, Eduardo; Schmidt, Fabian; Sehgal, Neelima; Slosar, Anze; Van Engelen, Alex; Wu, Hao-Yi; Zhao, Gongbo

    2014-03-15

    The quantity and quality of cosmic structure observations have greatly accelerated in recent years, and further leaps forward will be facilitated by imminent projects. These will enable us to map the evolution of dark and baryonic matter density fluctuations over cosmic history. The way that these fluctuations vary over space and time is sensitive to several pieces of fundamental physics: the primordial perturbations generated by GUT-scale physics; neutrino masses and interactions; the nature of dark matter and dark energy. We focus on the last of these here: the ways that combining probes of growth with those of the cosmic expansion such as distance-redshift relations will pin down the mechanism driving the acceleration of the Universe.

  19. Nuclear structure studies with medium energy probes. [Northwestern Univ

    SciTech Connect

    Seth, Kamal K.

    1980-01-01

    Progress in the continuing program of experimental research in nuclear structure with medium-energy probes during the year 1979-1980 is reviewed, and the research activities planned for the year 1980-1981 are discussed. In the study of pion-induced reactions emphasis is placed on investigation of isovector characteristics of nuclear excitations and on double charge exchange reactions. Pion production studies form the major part of the program of experiments with proton beams of 400 to 800 MeV at LAMPF. Current emphasis is on the bearing of these investigations on di-baryon existence. The study of high-spin states and magnetic scattering constitute the main goals of the electron scattering program at Bates. Representative results are presented; completed work is reported in the usual publications. (RWR)

  20. Growth of cosmic structure: Probing dark energy beyond expansion

    SciTech Connect

    Huterer, Dragan; Kirkby, David; Bean, Rachel; Connolly, Andrew; Dawson, Kyle; Dodelson, Scott; Evrard, August; Jain, Bhuvnesh; Jarvis, Michael; Linder, Eric; Mandelbaum, Rachel; May, Morgan; Raccanelli, Alvise; Reid, Beth; Rozo, Eduardo; Schmidt, Fabian; Sehgal, Neelima; Slosar, Anže; van Engelen, Alex; Wu, Hao-Yi; Zhao, Gongbo

    2015-03-01

    The quantity and quality of cosmic structure observations have greatly accelerated in recent years, and further leaps forward will be facilitated by imminent projects. These will enable us to map the evolution of dark and baryonic matter density fluctuations over cosmic history. The way that these fluctuations vary over space and time is sensitive to several pieces of fundamental physics: the primordial perturbations generated by GUT-scale physics; neutrino masses and interactions; the nature of dark matter and dark energy. We focus on the last of these here: the ways that combining probes of growth with those of the cosmic expansion such as distance-redshift relations will pin down the mechanism driving the acceleration of the Universe.

  1. Probing topological protection using a designer surface plasmon structure

    PubMed Central

    Gao, Fei; Gao, Zhen; Shi, Xihang; Yang, Zhaoju; Lin, Xiao; Xu, Hongyi; Joannopoulos, John D.; Soljačić, Marin; Chen, Hongsheng; Lu, Ling; Chong, Yidong; Zhang, Baile

    2016-01-01

    Topological photonic states, inspired by robust chiral edge states in topological insulators, have recently been demonstrated in a few photonic systems, including an array of coupled on-chip ring resonators at communication wavelengths. However, the intrinsic difference between electrons and photons determines that the ‘topological protection' in time-reversal-invariant photonic systems does not share the same robustness as its counterpart in electronic topological insulators. Here in a designer surface plasmon platform consisting of tunable metallic sub-wavelength structures, we construct photonic topological edge states and probe their robustness against a variety of defect classes, including some common time-reversal-invariant photonic defects that can break the topological protection, but do not exist in electronic topological insulators. This is also an experimental realization of anomalous Floquet topological edge states, whose topological phase cannot be predicted by the usual Chern number topological invariants. PMID:27197877

  2. SPECS: The Submillimeter Probe of the Evolution of Cosmic Structures

    NASA Technical Reports Server (NTRS)

    Rinehart, Stephen

    2006-01-01

    The idea for the Submillimeter Probe of the Evolution of Cosmic Structure (SPECS) was investigated through NASA Vision Missions Program. In the course of this study, a compelling need for high spatial-resolution far-infrared/submillimeter observations with high angular resolution (50 milliarcseconds) was identified. In order to achieve these scientific goals, a kilometer-baseline FIR/SMM Michelson stellar interferometer is required, operating in the 40-640 micron range with fully cryogenically cooled optics and photon-limited detectors. There are significant technological challenges to developing this mission, including controllable tethered flight, detector equipment, and large cryogenic mechanisms. We present here a concept for SPECS and discuss some of the relevant technical aspects of the mission.

  3. The Biophysical Probes 2-fluorohistidine and 4-fluorohistidine: Spectroscopic Signatures and Molecular Properties

    NASA Astrophysics Data System (ADS)

    Kasireddy, Chandana; Ellis, Jonathan M.; Bann, James G.; Mitchell-Koch, Katie R.

    2017-02-01

    Fluorinated amino acids serve as valuable biological probes, by reporting on local protein structure and dynamics through 19F NMR chemical shifts. 2-fluorohistidine and 4-fluorohistidine, studied here with DFT methods, have even more capabilities for biophysical studies, as their altered pKa values, relative to histidine, allow for studies of the role of proton transfer and tautomeric state in enzymatic mechanisms. Considering the two tautomeric forms of histidine, it was found that 2-fluorohistidine primarily forms the common (for histidine) τ-tautomer at neutral pH, while 4-fluorohistidine exclusively forms the less common π-tautomer. This suggests the two isomers of fluorohistidine can also serve as probes of tautomeric form within biomolecules, both by monitoring NMR chemical shifts and by potential perturbation of the tautomeric equilibrium within biomolecules. Fluorine also enables assignment of tautomeric states in crystal structures. The differences in experimental pKa values between the isomers was found to arise from solvation effects, providing insight into the polarization and molecular properties of each isomer. Results also encompass 13C and 19F NMR chemical shifts, from both tautomers of 2-fluorohistidine and 4-fluorohistidine in a number of different environments. This work can serve as a guide for interpretation of spectroscopic results in biophysical studies employing 2-fluorohistidine and 4-fluorohistidine.

  4. The Biophysical Probes 2-fluorohistidine and 4-fluorohistidine: Spectroscopic Signatures and Molecular Properties

    PubMed Central

    Kasireddy, Chandana; Ellis, Jonathan M.; Bann, James G.; Mitchell-Koch, Katie R.

    2017-01-01

    Fluorinated amino acids serve as valuable biological probes, by reporting on local protein structure and dynamics through 19F NMR chemical shifts. 2-fluorohistidine and 4-fluorohistidine, studied here with DFT methods, have even more capabilities for biophysical studies, as their altered pKa values, relative to histidine, allow for studies of the role of proton transfer and tautomeric state in enzymatic mechanisms. Considering the two tautomeric forms of histidine, it was found that 2-fluorohistidine primarily forms the common (for histidine) τ-tautomer at neutral pH, while 4-fluorohistidine exclusively forms the less common π-tautomer. This suggests the two isomers of fluorohistidine can also serve as probes of tautomeric form within biomolecules, both by monitoring NMR chemical shifts and by potential perturbation of the tautomeric equilibrium within biomolecules. Fluorine also enables assignment of tautomeric states in crystal structures. The differences in experimental pKa values between the isomers was found to arise from solvation effects, providing insight into the polarization and molecular properties of each isomer. Results also encompass 13C and 19F NMR chemical shifts, from both tautomers of 2-fluorohistidine and 4-fluorohistidine in a number of different environments. This work can serve as a guide for interpretation of spectroscopic results in biophysical studies employing 2-fluorohistidine and 4-fluorohistidine. PMID:28198426

  5. Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the RNA Affinity, Nuclease Resistance, and Crystal Structure of Ten 2'-O-Ribonucleic Acid Modifications

    SciTech Connect

    Egli, Martin; Minasov, George; Tereshko, Valentina; Pallan, Pradeep S.; Teplova, Marianna; Inamati, Gopal B.; Lesnik, Elena A.; Owens, Steve R.; Ross, Bruce S.; Prakash, Thazha P.; Manoharan, Muthiah

    2010-03-05

    The syntheses of 10 new RNA 2'-O-modifications, their incorporation into oligonucleotides, and an evaluation of their properties such as RNA affinity and nuclease resistance relevant to antisense activity are presented. All modifications combined with the natural phosphate backbone lead to significant gains in terms of the stability of hybridization to RNA relative to the first-generation DNA phosphorothioates (PS-DNA). The nuclease resistance afforded in particular by the 2'-O-modifications carrying a positive charge surpasses that of PS-DNA. However, small electronegative 2'-O-substituents, while enhancing the RNA affinity, do not sufficiently protect against degradation by nucleases. Similarly, oligonucleotides containing 3'-terminal residues modified with the relatively large 2'-O-[2-(benzyloxy)ethyl] substituent are rapidly degraded by exonucleases, proving wrong the assumption that steric bulk will generally improve protection against nuclease digestion. To analyze the factors that contribute to the enhanced RNA affinity and nuclease resistance we determined crystal structures of self-complementary A-form DNA decamer duplexes containing single 2'-O-modified thymidines per strand. Conformational preorganization of substituents, favorable electrostatic interactions between substituent and sugar-phosphate backbone, and a stable water structure in the vicinity of the 2'-O-modification all appear to contribute to the improved RNA affinity. Close association of positively charged substituents and phosphate groups was observed in the structures with modifications that protect most effectively against nucleases. The promising properties exhibited by some of the analyzed 2'-O-modifications may warrant a more detailed evaluation of their potential for in vivo antisense applications. Chemical modification of RNA can also be expected to significantly improve the efficacy of small interfering RNAs (siRNA). Therefore, the 2'-O-modifications introduced here may benefit the

  6. Nanoscale resolved infrared probing of crystal structure and of plasmon-phonon coupling.

    PubMed

    Huber, A; Ocelic, N; Taubner, T; Hillenbrand, R

    2006-04-01

    We show that slight variations of a crystal lattice cause significant spectral modifications of phonon-polariton resonant near-field interaction between polar semiconductor crystals and a scanning metal tip. Exploiting the effect for near-field imaging a SiC polytype boundary, we establish infrared mapping of crystal structure and crystal defects at 20 nm spatial resolution (lambda/500). By spectroscopic probing of doped SiC polytypes, we find that phonon-polariton resonant near-field interaction is also sensitive to electronic properties due to plasmon-phonon coupling in the crystals.

  7. Semiconductor alloys - Structural property engineering

    NASA Technical Reports Server (NTRS)

    Sher, A.; Van Schilfgaarde, M.; Berding, M.; Chen, A.-B.

    1987-01-01

    Semiconductor alloys have been used for years to tune band gaps and average bond lengths to specific applications. Other selection criteria for alloy composition, and a growth technique designed to modify their structural properties, are presently considered. The alloys Zn(1-y)Cd(y)Te and CdSe(y)Te(1-y) are treated as examples.

  8. Semiconductor alloys - Structural property engineering

    NASA Technical Reports Server (NTRS)

    Sher, A.; Van Schilfgaarde, M.; Berding, M.; Chen, A.-B.

    1987-01-01

    Semiconductor alloys have been used for years to tune band gaps and average bond lengths to specific applications. Other selection criteria for alloy composition, and a growth technique designed to modify their structural properties, are presently considered. The alloys Zn(1-y)Cd(y)Te and CdSe(y)Te(1-y) are treated as examples.

  9. Mechanical Properties of Plant Cell Walls Probed by Relaxation Spectra1[W][OA

    PubMed Central

    Hansen, Steen Laugesen; Ray, Peter Martin; Karlsson, Anders Ola; Jørgensen, Bodil; Borkhardt, Bernhard; Petersen, Bent Larsen; Ulvskov, Peter

    2011-01-01

    Transformants and mutants with altered cell wall composition are expected to display a biomechanical phenotype due to the structural role of the cell wall. It is often quite difficult, however, to distinguish the mechanical behavior of a mutant's or transformant's cell walls from that of the wild type. This may be due to the plant’s ability to compensate for the wall modification or because the biophysical method that is often employed, determination of simple elastic modulus and breakstrength, lacks the resolving power necessary for detecting subtle mechanical phenotypes. Here, we apply a method, determination of relaxation spectra, which probes, and can separate, the viscoelastic properties of different cell wall components (i.e. those properties that depend on the elastic behavior of load-bearing wall polymers combined with viscous interactions between them). A computer program, BayesRelax, that deduces relaxation spectra from appropriate rheological measurements is presented and made accessible through a Web interface. BayesRelax models the cell wall as a continuum of relaxing elements, and the ability of the method to resolve small differences in cell wall mechanical properties is demonstrated using tuber tissue from wild-type and transgenic potatoes (Solanum tuberosum) that differ in rhamnogalacturonan I side chain structure. PMID:21075961

  10. Mechanical properties of interphase nuclei probed by cellular strain application.

    PubMed

    Lammerding, Jan; Lee, Richard T

    2009-01-01

    The mechanical properties of the interphase nucleus have important implications for cellular function and can reflect changes in nuclear envelope structure and/or chromatin organization. Mutations in the nuclear envelope proteins lamin A and C cause several human diseases, such as Emery-Dreifuss muscular dystrophy, and dramatic changes in nuclear stiffness have been reported in cells from lamin A/C-deficient mice. We have developed a cellular strain technique to measure nuclear stiffness in intact, adherent cells and have applied this experimental method to fibroblasts from mouse models of Emery-Dreifuss muscular dystrophy and to skin fibroblasts from laminopathy patients and healthy control subjects. The experimental protocol is based on measuring induced nuclear deformations in cells plated on a flexible silicone substrate; the nuclear stiffness can subsequently be inferred from the ratio of induced nuclear strain to the applied membrane strain. These experiments reveal that lamins A and C are important determinants of nuclear stiffness and that lamin mutations associated with muscular dystrophies and other laminopathies often result in disturbed nuclear stiffness that could contribute to the tissue-specific disease phenotypes.

  11. Donor-Acceptor Conjugated Linear Polyenes: A Study of Excited State Intramolecular Charge Transfer, Photoisomerization and Fluorescence Probe Properties.

    PubMed

    Hota, Prasanta Kumar; Singh, Anil Kumar

    2014-07-27

    Numerous studies of donor-acceptor conjugated linear polyenes have been carried out with the goal to understand the exact nature of the excited state electronic structure and dynamics. In this article we discuss our endeavours with regard to the excited state intramolecular charge transfer, photoisomerization and fluorescence probe properties of various donor-acceptor substituted compounds of diphenylpolyene [Ar(CH = CH) n Ar] series and ethenylindoles.

  12. Probing Structural and Electronic Dynamics with Ultrafast Electron Microscopy

    SciTech Connect

    Plemmons, DA; Suri, PK; Flannigan, DJ

    2015-05-12

    In this Perspective, we provide an overview,of the field of ultrafast electron microscopy (UEM). We begin by briefly discussing the emergence of methods for probing ultrafast structural dynamics and the information that can be obtained. Distinctions are drawn between the two main types a probes for femtosecond (fs) dynamics fast electrons and X-ray photons and emphasis is placed on hour the nature of charged particles is exploited in ultrafast electron-based' experiments:. Following this, we describe the versatility enabled by the ease with which electron trajectories and velocities can be manipulated with transmission electron microscopy (TEM): hardware configurations, and we emphasize how this is translated to the ability to measure scattering intensities in real, reciprocal, and energy space from presurveyed and selected rianoscale volumes. Owing to decades of ongoing research and development into TEM instrumentation combined with advances in specimen holder technology, comprehensive experiments can be conducted on a wide range of materials in various phases via in situ methods. Next, we describe the basic operating concepts, of UEM, and we emphasize that its development has led to extension of several of the formidable capabilities of TEM into the fs domain, dins increasing the accessible temporal parameter spade by several orders of magnitude. We then divide UEM studies into those conducted in real (imaging), reciprocal (diffraction), and energy (spectroscopy) spate. We begin each of these sections by providing a brief description of the basic operating principles and the types of information that can be gathered followed by descriptions of how these approaches are applied in UM, the type of specimen parameter space that can be probed, and an example of the types of dynamics that can be resolved. We conclude with an Outlook section, wherein we share our perspective on some future directions of the field pertaining to continued instrument development and

  13. Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

    PubMed Central

    Rutenberg-Schoenberg, Michael; Simon, Matthew D.

    2015-01-01

    The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5’-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function. PMID:26646615

  14. Probing Xist RNA Structure in Cells Using Targeted Structure-Seq.

    PubMed

    Fang, Rui; Moss, Walter N; Rutenberg-Schoenberg, Michael; Simon, Matthew D

    2015-12-01

    The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5'-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function.

  15. Measuring the electric properties of planetary environments with Mutual Impedance (MI) Probes

    NASA Astrophysics Data System (ADS)

    Trautner, R.; Grard, R.

    2002-10-01

    Mutual Impedance Probes measure the complex permittivity of material by means of a quadrupolar array of electrodes and associated electronics for generating, recording and processing waveforms. MI instruments have been developed for a number of ongoing space missions. The HASI/PWA MI probe will determine the electric properties of the atmosphere of Titan, Saturn's largest moon, during the descent of the Huygens probe. After landing, the instrument will provide data on the properties of Titan's surface materials. The permittivity probe PP, as part of the SESAME instrument package for the Rosetta Lander, will determine the electrical properties of comet Wirtanen's surface. The main features of MI probes are first recapitulated. Instrument architectures for atmospheric, surface and subsurface investigations are described. Results from recent field test campaigns in harsh environments are presented. A new MI probe prototype employing a linear electrode array for application on mobile platforms or on penetrator devices is described. New application areas for future MI probes and relevant technology requirements are discussed.

  16. Ion nose spectral structures observed by the Van Allen Probes

    DOE PAGES

    Ferradas, C. P.; Zhang, J. -C.; Spence, H. E.; ...

    2016-11-22

    Here, we present a statistical study of nose-like structures observed in energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet. Nose structures are spectral features named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. Using 22 months of observations from the Helium Oxygen Proton Electron (HOPE) instrument onboard Van Allen Probe A, we determine the number of noses observed, and the minimum L-shell reached and energy of each nose on each pass through the inner magnetosphere. We find that multiple noses occur more frequentlymore » in heavy ions than in H+, and are most often observed during quiet times. The heavy-ion noses penetrate to lower L shells than H+ noses and there is an energy-magnetic local time (MLT) dependence in the nose locations and energies that is similar for all species. The observations are interpreted using a steady-state model of ion drift in the inner magnetosphere. The model is able to explain the energy and MLT dependence of the different types of nose structures. Different ion charge exchange lifetimes are the main cause for the deeper penetration of heavy-ion noses. The species dependence and preferred geomagnetic conditions of multiple-nose events indicate that they must be on long drift paths, leading to strong charge-exchange effects. The results provide important insight into the spatial distribution, species dependence, and geomagnetic conditions under which nose structures occur.« less

  17. Ion nose spectral structures observed by the Van Allen Probes

    SciTech Connect

    Ferradas, C. P.; Zhang, J. -C.; Spence, H. E.; Kistler, L. M.; Larsen, Brian Arthur; Reeves, Geoffrey D.; Skoug, Ruth M.; Funsten, Herbert O.

    2016-11-22

    Here, we present a statistical study of nose-like structures observed in energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet. Nose structures are spectral features named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. Using 22 months of observations from the Helium Oxygen Proton Electron (HOPE) instrument onboard Van Allen Probe A, we determine the number of noses observed, and the minimum L-shell reached and energy of each nose on each pass through the inner magnetosphere. We find that multiple noses occur more frequently in heavy ions than in H+, and are most often observed during quiet times. The heavy-ion noses penetrate to lower L shells than H+ noses and there is an energy-magnetic local time (MLT) dependence in the nose locations and energies that is similar for all species. The observations are interpreted using a steady-state model of ion drift in the inner magnetosphere. The model is able to explain the energy and MLT dependence of the different types of nose structures. Different ion charge exchange lifetimes are the main cause for the deeper penetration of heavy-ion noses. The species dependence and preferred geomagnetic conditions of multiple-nose events indicate that they must be on long drift paths, leading to strong charge-exchange effects. The results provide important insight into the spatial distribution, species dependence, and geomagnetic conditions under which nose structures occur.

  18. Transparent Window Vibrational Probes for the Characterization of Proteins With High Structural and Temporal Resolution.

    PubMed

    Adhikary, Ramkrishna; Zimmermann, Jörg; Romesberg, Floyd E

    2017-02-08

    Vibrational spectroscopy provides a direct route to the physicochemical characterization of molecules. While both IR and Raman spectroscopy have been used for decades to provide detailed characterizations of small molecules, similar studies with proteins are largely precluded due to spectral congestion. However, the vibrational spectra of proteins do include a "transparent window", between ∼1800 and ∼2500 cm(-1), and progress is now being made to develop site-specifically incorporated carbon-deuterium (C-D), cyano (CN), thiocyanate (SCN), and azide (N3) "transparent window vibrational probes" that absorb within this window and report on their environment to facilitate the characterization of proteins with small molecule-like detail. This Review opens with a brief discussion of the advantages and limitations of conventional vibrational spectroscopy and then discusses the strengths and weaknesses of the different transparent window vibrational probes, methods by which they may be site-specifically incorporated into peptides and proteins, and the physicochemical properties they may be used to study, including electrostatics, stability and folding, hydrogen bonding, protonation, solvation, dynamics, and interactions with inhibitors. The use of the probes to vibrationally image proteins and other biomolecules within cells is also discussed. We then present four case studies, focused on ketosteroid isomerase, the SH3 domain, dihydrofolate reductase, and cytochrome c, where the transparent window vibrational probes have already been used to elucidate important aspects of protein structure and function. The Review concludes by highlighting the current challenges and future potential of using transparent window vibrational probes to understand the evolution and function of proteins and other biomolecules.

  19. Development of a multichannel hyperspectral imaging probe for food property and quality assessment

    NASA Astrophysics Data System (ADS)

    Huang, Yuping; Lu, Renfu; Chen, Kunjie

    2017-05-01

    This paper reports on the development, calibration and evaluation of a new multipurpose, multichannel hyperspectral imaging probe for property and quality assessment of food products. The new multichannel probe consists of a 910 μm fiber as a point light source and 30 light receiving fibers of three sizes (i.e., 50 μm, 105 μm and 200 μm) arranged in a special pattern to enhance signal acquisitions over the spatial distances of up to 36 mm. The multichannel probe allows simultaneous acquisition of 30 spatially-resolved reflectance spectra of food samples with either flat or curved surface over the spectral region of 550-1,650 nm. The measured reflectance spectra can be used for estimating the optical scattering and absorption properties of food samples, as well as for assessing the tissues of the samples at different depths. Several calibration procedures that are unique to this probe were carried out; they included linearity calibrations for each channel of the hyperspectral imaging system to ensure consistent linear responses of individual channels, and spectral response calibrations of individual channels for each fiber size group and between the three groups of different size fibers. Finally, applications of this new multichannel probe were demonstrated through the optical property measurement of liquid model samples and tomatoes of different maturity levels. The multichannel probe offers new capabilities for optical property measurement and quality detection of food and agricultural products.

  20. Functional Properties of Chondrocytes and Articular Cartilage using Optical Imaging to Scanning Probe Microscopy.

    PubMed

    Xia, Yang; Darling, Eric M; Herzog, Walter

    2017-10-03

    Mature chondrocytes in adult articular cartilage vary in number, size, and shape, depending on their depth in the tissue, location in the joint, and source species. Chondrocytes are the primary structural, functional, and metabolic unit in articular cartilage, the loss of which will induce fatigue to the extracellular matrix (ECM), eventually leading to failure of the cartilage and impairment of the joint as a whole. This brief review focuses on the functional and biomechanical studies of chondrocytes and articular cartilage, using microscopic imaging from optical microscopies to scanning probe microscopy. Three topics are covered in this review, including the functional studies of chondrons by optical imaging (unpolarized and polarized light and infrared light, two-photon excitation microscopy), the probing of chondrocytes and cartilage directly using microscale measurement techniques, and different imaging approaches that can measure chondrocyte mechanics and chondrocyte biological signaling under in situ and in vivo environments. Technical advancement in chondrocyte research during recent years has enabled new ways to study the biomechanical and functional properties of these cells and cartilage. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  1. Probing the DNA Structural Requirements for Facilitated Diffusion

    PubMed Central

    2015-01-01

    DNA glycosylases perform a genome-wide search to locate damaged nucleotides among a great excess of undamaged nucleotides. Many glycosylases are capable of facilitated diffusion, whereby multiple sites along the DNA are sampled during a single binding encounter. Electrostatic interactions between positively charged amino acids and the negatively charged phosphate backbone are crucial for facilitated diffusion, but the extent to which diffusing proteins rely on the double-helical structure DNA is not known. Kinetic assays were used to probe the DNA searching mechanism of human alkyladenine DNA glycosylase (AAG) and to test the extent to which diffusion requires B-form duplex DNA. Although AAG excises εA lesions from single-stranded DNA, it is not processive on single-stranded DNA because dissociation is faster than N-glycosidic bond cleavage. However, the AAG complex with single-stranded DNA is sufficiently stable to allow for DNA annealing when a complementary strand is added. This observation provides evidence of nonspecific association of AAG with single-stranded DNA. Single-strand gaps, bubbles, and bent structures do not impede the search by AAG. Instead, these flexible or bent structures lead to the capture of a nearby site of damage that is more efficient than that of a continuous B-form duplex. The ability of AAG to negotiate these helix discontinuities is inconsistent with a sliding mode of diffusion but can be readily explained by a hopping mode that involves microscopic dissociation and reassociation. These experiments provide evidence of relatively long-range hops that allow a searching protein to navigate around DNA binding proteins that would serve as obstacles to a sliding protein. PMID:25495964

  2. Probing the DNA structural requirements for facilitated diffusion.

    PubMed

    Hedglin, Mark; Zhang, Yaru; O'Brien, Patrick J

    2015-01-20

    DNA glycosylases perform a genome-wide search to locate damaged nucleotides among a great excess of undamaged nucleotides. Many glycosylases are capable of facilitated diffusion, whereby multiple sites along the DNA are sampled during a single binding encounter. Electrostatic interactions between positively charged amino acids and the negatively charged phosphate backbone are crucial for facilitated diffusion, but the extent to which diffusing proteins rely on the double-helical structure DNA is not known. Kinetic assays were used to probe the DNA searching mechanism of human alkyladenine DNA glycosylase (AAG) and to test the extent to which diffusion requires B-form duplex DNA. Although AAG excises εA lesions from single-stranded DNA, it is not processive on single-stranded DNA because dissociation is faster than N-glycosidic bond cleavage. However, the AAG complex with single-stranded DNA is sufficiently stable to allow for DNA annealing when a complementary strand is added. This observation provides evidence of nonspecific association of AAG with single-stranded DNA. Single-strand gaps, bubbles, and bent structures do not impede the search by AAG. Instead, these flexible or bent structures lead to the capture of a nearby site of damage that is more efficient than that of a continuous B-form duplex. The ability of AAG to negotiate these helix discontinuities is inconsistent with a sliding mode of diffusion but can be readily explained by a hopping mode that involves microscopic dissociation and reassociation. These experiments provide evidence of relatively long-range hops that allow a searching protein to navigate around DNA binding proteins that would serve as obstacles to a sliding protein.

  3. Probing of the Assembly Structure and Dynamics within Nanoparticles during Interaction with Blood Proteins

    PubMed Central

    Li, Yuanpei; Budamagunta, Madhu S.; Luo, Juntao; Xiao, Wenwu; Voss, John C.; Lam, Kit S.

    2012-01-01

    Fully understanding the influence of blood proteins on the assembly structure and dynamics within nanoparticles is difficult because of the complexity of the system and the difficulty in probing the diverse elements and milieus involved. Here we show the use of site-specific labeling with spin probes and fluorophores combined with electron paramagnetic resonance (EPR) spectroscopy and fluorescence resonance energy transfer (FRET) measurements to provide insights into the molecular architecture and dynamics within nanoparticles. These tools are especially useful for determining nanoparticle stability in the context of blood proteins and lipoproteins, and have allowed us to quantitatively analyze the dynamic changes in assembly structure, local stability and cargo diffusion of a class of novel telodendrimer-based micellar nanoparticles. When combined with human plasma and individual plasma components, we find that non-crosslinked nanoparticles immediately lose their original assembly structure and release their payload upon interaction with lipoproteins. In contrast, serum albumins and immunoglobulin gamma have moderate affects on the integrity of the nanoparticles. Disulfide crosslinked nanoparticles show minimal interaction with lipoproteins, and can better retain their assembly structure and payload in vitro and in vivo. We further demonstrate how the enhanced stability and release property of disulfide crosslinked nanoparticles can be reversed in reductive conditions. These findings identify factors are crucial to the performance of nanomedicines and provide design modes to control their interplay with blood factors. PMID:23106540

  4. Probing of the assembly structure and dynamics within nanoparticles during interaction with blood proteins.

    PubMed

    Li, Yuanpei; Budamagunta, Madhu S; Luo, Juntao; Xiao, Wenwu; Voss, John C; Lam, Kit S

    2012-11-27

    Fully understanding the influence of blood proteins on the assembly structure and dynamics within nanoparticles is difficult because of the complexity of the system and the difficulty in probing the diverse elements and milieus involved. Here we show the use of site-specific labeling with spin probes and fluorophores combined with electron paramagnetic resonance (EPR) spectroscopy and fluorescence resonance energy transfer (FRET) measurements to provide insights into the molecular architecture and dynamics within nanoparticles. These tools are especially useful for determining nanoparticle stability in the context of blood proteins and lipoproteins and have allowed us to quantitatively analyze the dynamic changes in assembly structure, local stability, and cargo diffusion of a class of novel telodendrimer-based micellar nanoparticles. When combined with human plasma and individual plasma components, we find that non-cross-linked nanoparticles immediately lose their original assembly structure and release their payload upon interaction with lipoproteins. In contrast, serum albumins and immunoglobulin gamma have moderate affects on the integrity of the nanoparticles. Disulfide cross-linked nanoparticles show minimal interaction with lipoproteins and can better retain their assembly structure and payload in vitro and in vivo. We further demonstrate how the enhanced stability and release property of disulfide cross-linked nanoparticles can be reversed in reductive conditions. These findings identify factors that are crucial to the performance of nanomedicines and provide design modes to control their interplay with blood factors.

  5. Laurdan and Di-4-ANEPPDHQ probe different properties of the membrane

    NASA Astrophysics Data System (ADS)

    Amaro, Mariana; Reina, Francesco; Hof, Martin; Eggeling, Christian; Sezgin, Erdinc

    2017-04-01

    Lipid packing is a crucial feature of cellular membranes. Quantitative analysis of membrane lipid packing can be achieved using polarity sensitive probes whose emission spectrum depends on the lipid packing. However, detailed insights into the exact mechanisms that cause the changes in the spectra are necessary to interpret experimental fluorescence emission data correctly. Here, we analysed frequently used polarity sensitive probes, Laurdan and di-4-ANEPPDHQ, to test whether the underlying physical mechanisms of their spectral changes are the same and, thus, whether they report on the same physico-chemical properties of the cell membrane. Steady-state spectra as well as time-resolved emission spectra of the probes in solvents and model membranes revealed that they probe different properties of the lipid membrane. Our findings are important for the application of these dyes in cell biology.

  6. Probing local structural fluctuations in myoglobin by size-dependent thiol-disulfide exchange

    PubMed Central

    Stratton, Margaret M; Cutler, Thomas A; Ha, Jeung-Hoi; Loh, Stewart N

    2010-01-01

    All proteins undergo local structural fluctuations (LSFs) or breathing motions. These motions are likely to be important for function but are poorly understood. LSFs were initially defined by amide hydrogen exchange (HX) experiments as opening events, which expose a small number of backbone amides to 1H/2H exchange, but whose exchange rates are independent of denaturant concentration. Here, we use size-dependent thiol-disulfide exchange (SX) to characterize LSFs in single cysteine-containing variants of myoglobin (Mb). SX complements HX by providing information on motions that disrupt side chain packing interactions. Most importantly, probe reagents of different sizes and chemical properties can be used to characterize the size of structural opening events and the properties of the open state. We use thiosulfonate reagents (126–274 Da) to survey access to Cys residues, which are buried at specific helical packing interfaces in Mb. In each case, the free energy of opening increases linearly with the radius of gyration of the probe reagent. The slope and the intercept are interpreted to yield information on the size of the opening events that expose the buried thiol groups. The slope parameter varies by over 10-fold among Cys positions tested, suggesting that the sizes of breathing motions vary substantially throughout the protein. Our results provide insight to the longstanding question: how rigid or flexible are proteins in their native states? PMID:20572017

  7. The viscoelastic properties of the vitreous humor measured using an optically trapped local probe

    NASA Astrophysics Data System (ADS)

    Watts, Fiona; Tan, Lay Ean; Tassieri, Manlio; McAlinden, Niall; Wilson, Clive G.; Girkin, John M.; Wright, Amanda J.

    2011-10-01

    We present results demonstrating for the first time that an optically trapped bead can be used as a local probe to measure the variation in the viscoelastic properties of the vitreous humor of a rabbit eye. The Brownian motion of the optically trapped bead was monitored on a fast CCD camera on the millisecond timescale. Analysis of the bead trajectory provides local information about the viscoelastic properties of the medium surrounding the particle. Previous, bulk, methods for measuring the viscoelastic properties of the vitreous destroy the sample and allow only a single averaged measurement to be taken per eye. Whereas, with our approach, we were able to observe local behaviour typical of non-Newtonian and gel-like materials, along with the homogenous and in-homogeneous nature of different regions of the dissected vitreous humor. The motivation behind these measurements is to gain a better understanding of the structure of the vitreous humor in order to design effective drug delivery techniques. In particular, we are interested in methods for delivering drug to the retina of the eye in order to treat sight threatening diseases such as age related macular degeneration.

  8. Heat Transport as a Probe of Superconducting Gap Structure

    SciTech Connect

    Petrovic, C.; Shakeripour, H.; Taillefer, L.

    2009-05-29

    The structure of the superconducting gap provides important clues on the symmetry of the order parameter and the pairing mechanism. The presence of nodes in the gap function imposed by symmetry implies an unconventional order parameter, other than s-wave. Here we show how measurements of the thermal conductivity at very low temperature can be used to determine whether such nodes are present in a particular superconductor, and shed light on their nature and location. We focus on the residual linear term at T {yields} 0. A finite value in zero magnetic field is strong evidence for symmetry-imposed nodes, and the dependence on impurity scattering can distinguish between a line of nodes or point nodes. Application of a magnetic field probes the low-energy quasiparticle excitations, whether associated with nodes or with a small value of the gap on some part of the Fermi surface, as in a multi-band superconductor. We frame our discussion around archetypal materials: Nb for s-wave, Tl{sub 2}Ba{sub 2}CuO{sub 6+{delta}} for d-wave, Sr{sub 2}RuO{sub 4} for p-wave, and NbSe{sub 2} for multi-band superconductivity. In that framework, we discuss three heavy-fermion superconductors: CeIrIn{sub 5}, CeCoIn{sub 5} and UPt{sub 3}.

  9. Multi-Array Probing of Lower Mantle Structure

    NASA Astrophysics Data System (ADS)

    Stipcevic, J.; Tkalcic, H.; Kennett, B. L. N.

    2014-12-01

    Array processing of seismic waveforms from many sensors allows the enhancement of coherent signals and the suppression of incoherent "noise". Time correction of a waveform enhances weak seismic phases and provides constraints on the azimuth and inclination of the incoming energy. Furthermore, signal amplification allows the use of higher frequencies, which effectively increases the imaging resolution. Although array stacking is effective in amplifying weak seismic signals, its inherent weakness lies in the assumption of the instantaneous plane wave arriving at the array. This assumption limits the size of the array (short aperture) to insure the signal coherence, which in turn limits the size of the area within the Earth's interior that we can probe. Small array size also means that we cannot use energy scattered off a great circle path. In this study we address the above-mentioned issues by installing new and combing the existing several short-aperture arrays in Australia. By exploiting these multiple short aperture arrays we can pinpoint the source of scattered energy to map detailed patterns of heterogeneity in the lower mantle. The concept of multiple arrays allows us to illuminate specific point in the Earth from many different directions. The method is based on a similar approach to that the back-projection technique uses, where the point in time (i.e. part of the seismic wavetrain) is mapped onto the specific point in space through ray tracing. This allows us to achieve multiple illumination of the same structure and thereby minimize source effects. Using scattered energy enables us to cover and probe a larger area of the Earth's interior. We test the feasibility of our approach deploying the precursors to PcP and PKP seismic phases. We also test our method on synthetically created traces (both monochromatic and multi-frequency waves) varying the depths of the scatterers. We detect significant improvements, both in the signal quality and resolution, with an

  10. Real-space imaging of molecular structure and chemical bonding by single-molecule inelastic tunneling probe.

    PubMed

    Chiang, Chi-lun; Xu, Chen; Han, Zhumin; Ho, W

    2014-05-23

    The arrangement of atoms and bonds in a molecule influences its physical and chemical properties. The scanning tunneling microscope can provide electronic and vibrational signatures of single molecules. However, these signatures do not relate simply to the molecular structure and bonding. We constructed an inelastic tunneling probe based on the scanning tunneling microscope to sense the local potential energy landscape of an adsorbed molecule with a carbon monoxide (CO)-terminated tip. The skeletal structure and bonding of the molecule are revealed from imaging the spatial variations of a CO vibration as the CO-terminated tip probes the core of the interactions between adjacent atoms. An application of the inelastic tunneling probe reveals the sharing of hydrogen atoms among multiple centers in intramolecular and extramolecular bonding.

  11. Probing the Structure-Function Relationships of Microbial Systems

    SciTech Connect

    Plomp, M; Leighton, T J; Holman, H; Malkin, A J

    2005-11-03

    The elucidation of microbial surface architecture and function is critical to determining mechanisms of pathogenesis, immune response, physicochemical properties, environmental resistance and development of countermeasures against bioterrorist agents. We have utilized high-resolution in vitro AFM for studies of structure, assembly, function and environmental dynamics of several microbial systems including bacteria and bacterial spores. Lateral resolutions of {approx}2.0 nm were achieved on pathogens, in vitro. We have demonstrated, using various species of Bacillus and Clostridium bacterial spores, that in vitro AFM can address spatially explicit spore coat protein interactions, structural dynamics in response to environmental changes, and the life cycle of pathogens at near-molecular resolution under physiological conditions. We found that strikingly different species-dependent crystalline structures of the spore coat appear to be a consequence of nucleation and crystallization mechanisms that regulate the assembly of the outer spore coat, and we proposed a unifying mechanism for outer spore coat self-assembly. Furthermore, we revealed molecular-scale transformations of the spore coat during the germination process, which include profound, previously unrecognized changes of the spore coat. We will present data on the direct visualization of stress-induced environmental response of metal-resistant Arthrobacter oxydans bacteria to Cr (VI) exposure, resulting in the formation of a supramolecular crystalline hexagonal structure on the cell surface. At higher Cr (VI) concentrations the formation of microbial extracellular polymers, which cover microbial colony was observed. High-resolution visualization of stress-induced structures on bacterial surfaces builds a foundation for real time in vitro molecular scale studies of structural dynamics of metal-resistant bacteria in response to environmental stimuli. In the case of the bacterium Chlamedia trachomatis, we were

  12. Ultrafast laser-probing spectroscopy for studying molecular structure of protein aggregates.

    PubMed

    Jung, Huihun; Szwejkowski, Chester J; Pena-Francesch, Abdon; Tomko, John A; Allen, Benjamin; Özdemir, Şahin Kaya; Hopkins, Patrick; Demirel, Melik C

    2017-03-09

    We report the development of a new technique to screen protein aggregation based on laser-probing spectroscopy with sub-picosecond resolution. Protein aggregation is an important topic for materials science, fundamental biology as well as clinical studies in neurodegenerative diseases and translation studies in biomaterials engineering. However, techniques to study protein aggregation and assembly are limited to infrared spectroscopy, fluorescent assays, immunostaining, or functional assays among others. Here, we report a new technique to characterize protein structure-property relationship based on ultrafast laser-probing spectroscopy. First, we show theoretically that the temperature dependence of the refractive index of a protein is correlated to its crystallinity. Then, we performed time-domain thermo-transmission experiments on purified semi-crystalline proteins, both native and recombinant (i.e., silk and squid ring teeth), and also on intact E. coli cells bearing overexpressed recombinant protein. Our results demonstrate, for the first time, relative quantification of crystallinity in real time for protein aggregates. Our approach can potentially be used for screening an ultra-large number of proteins in vivo. Using this technique, we could answer many fundamental questions in structural protein research, such as the underlying sequence-structure relationship for protein assembly and aggregation.

  13. Probing large-scale structure with radio observations

    NASA Astrophysics Data System (ADS)

    Brown, Shea D.

    This thesis focuses on detecting magnetized relativistic plasma in the intergalactic medium (IGM) of filamentary large-scale structure (LSS) by observing synchrotron emission emitted by structure formation shocks. Little is known about the IGM beyond the largest clusters of galaxies, and synchrotron emission holds enormous promise as a means of probing magnetic fields and relativistic particle populations in these low density regions. I'll first report on observations taken at the Very Large Array and the Westerbork Synthesis Radio Telescope of the diffuse radio source 0809+39. I use these observations to demonstrate that 0809+39 is likely the first "radio relic" discovered that is not associated with a rich |"X-ray emitting cluster of galaxies. I then demonstrate that an unconventional reprocessing of the NVSS polarization survey can reveal structures on scales from 15' to hundreds of degrees, far larger than the nominal shortest-baseline scale. This yields hundreds of new diffuse sources as well as the identification of a new nearby galactic loop . These observations also highlight the major obstacle that diffuse galactic foreground emission poses for any search for large-scale, low surface- brightness extragalactic emission. I therefore explore the cross-correlation of diffuse radio emission with optical tracers of LSS as a means of statistically detecting the presence of magnetic fields in the low-density regions of the cosmic web. This initial study with the Bonn 1.4 GHz radio survey yields an upper limit of 0.2 mG for large-scale filament magnetic fields. Finally, I report on new Green Bank Telescope and Westerbork Synthesis Radio Telescope observations of the famous Coma cluster of galaxies. Major findings include an extension to the Coma cluster radio relic source 1253+275 which makes its total extent ~2 Mpc, as well as a sharp edge, or "front", on the Western side of the radio halo which shows a strong correlation with merger activity associated with an

  14. Probing of the pseudogap via thermoelectric properties in the Au-Al-Gd quasicrystal approximant

    NASA Astrophysics Data System (ADS)

    Ishikawa, Asuka; Takagiwa, Yoshiki; Kimura, Kaoru; Tamura, Ryuji

    2017-03-01

    The pseudogap of the recently discovered Au-Al-Gd quasicrystal approximant crystal (AC) is investigated over a wide electron-per-atom (e /a ) ratio of ˜0.5 using thermoelectric properties as an experimental probe. This Au-Al-Gd AC provides an ideal platform for fine probing of the pseudogap among a number of known ACs because the Au-Al-Gd AC possesses an extraordinarily wide single-phase region with respect to the variation in the electron concentration [A. Ishikawa, T. Hiroto, K. Tokiwa, T. Fujii, and R. Tamura, Phys. Rev. B 93, 024416 (2016), 10.1103/PhysRevB.93.024416], in striking contrast to, for instance, binary stoichiometric C d6R ACs. As a result, a salient peak structure is observed in the Seebeck coefficient, S , with the composition as well as that of the power factor S2σ , in addition to a gradual variation in the conductivity, σ , and S . These two features are directly associated with rapid and slow variations, respectively, of spectral conductivity σ (E ) , and hence the fine structure inside the pseudogap, in the vicinity of the Fermi level EF. Based on the observed continuous variation of the Fermi wave vector reported in the previous experimental work, fine tuning of EF toward an optimal position was attempted, which led to the successful observation of a sharp peak in S2σ with a value of ˜270 μ W /m .K2 at 873 K. This is the highest value ever reported among both Tsai-type and Bergman-type compounds. The dimensionless figure of merit was determined as 0.026 at 873 K, which is also the highest reported among both Tsai-type and Bergman-type compounds.

  15. Probing the Microscopic with the Macroscopic: from Properties of Star Cluster Systems to Properties of Cluster-Forming Regions

    NASA Astrophysics Data System (ADS)

    Parmentier, G.

    To understand how systems of star clusters have reached their presently observed properties constitutes a powerful probe into the physics of cluster formation, without needing to resort to high spatial resolution observations of individual cluster-forming regions (CFRg) in distant galaxies. In this contribution I focus on the mass-radius relation of CFRgs, how it can be uncovered by studying the gas expulsion phase of forming star clusters, and what the implications are. I demonstrate that, through the tidal field impact upon exposed star clusters, the CFRg mass-radius relation rules cluster infant weight-loss in dependence of cluster mass. The observational constraint of a time-invariant slope for the power-law young cluster mass function is robustly satisfied by CFRgs with a constant mean volume density. In contrast, a constant mean surface density would be conducive to the preferential destruction of high-mass clusters. A purely dynamical line-of-reasoning leads therefore to a conclusion consistent with star formation a process driven by a volume density threshold. Developing this concept further, properties of molecular clumps and CFRgs naturally get dissociated. This allows to understand: (i) why the star cluster mass function is steeper than the molecular cloud/clump mass function; (ii) the presence of a massive star formation limit in the mass-size space of molecular structures.

  16. [Structure and properties of pectin].

    PubMed

    Wikiera, Agnieszka; Mika, Magdalena

    2013-01-01

    Pectin represents a very complex, heterogeneous family of plant cell wall polysaccharides that play a significant role in plant growth, morphology, development, and plant defense and also serves as a gelling and stabilizing polymer in diverse food and specialty products and has positive effects on human health. In this review functional and structural characteristic of pectin molecule elements and their interconnections are described. Attention is also given to process of commercial production of pectin with special emphasis on composition and physical properties of commercial pectin as a result of the acid extraction.

  17. Measuring The Electric Properties of Planetary Surface Materials With Mutual Impedance (mi) Probes

    NASA Astrophysics Data System (ADS)

    Trautner, R.; Grard, R.

    Mutual Impedance Probes have been developed for a number of ongoing space mis- sions. The HASI/PWA MI probe will determine the electric properties of the atmo- sphere and surface of Saturn's largest moon, Titan, in 2004. The Permittivity Probe of the SESAME instrument package on the Rosetta Lander will attempt to measure the conductivity and permittivity of the cometary surface material. While both instruments have similar objectives, their architecture (design and integration into the spacecraft, electrode geometry) and properties (measurement range and precision) differ signif- icantly. The main features of the Huygens PWA and Rosetta Lander SESAME MI probes are first recapitulated and their expected performances are assessed. A new MI probe prototype employing a linear electrode array for application on mobile platforms or penetrator devices is then described. Results from a recent field test campaign in the Australian desert are presented and the prototype performance is evaluated. New application areas for future MI probes and relevant technology requirements are dis- cussed.

  18. Probing biomechanical properties with a centrifugal force quartz crystal microbalance.

    PubMed

    Webster, Aaron; Vollmer, Frank; Sato, Yuki

    2014-10-21

    Application of force on biomolecules has been instrumental in understanding biofunctional behaviour from single molecules to complex collections of cells. Current approaches, for example, those based on atomic force microscopy or magnetic or optical tweezers, are powerful but limited in their applicability as integrated biosensors. Here we describe a new force-based biosensing technique based on the quartz crystal microbalance. By applying centrifugal forces to a sample, we show it is possible to repeatedly and non-destructively interrogate its mechanical properties in situ and in real time. We employ this platform for the studies of micron-sized particles, viscoelastic monolayers of DNA and particles tethered to the quartz crystal microbalance surface by DNA. Our results indicate that, for certain types of samples on quartz crystal balances, application of centrifugal force both enhances sensitivity and reveals additional mechanical and viscoelastic properties.

  19. Probing model tumor interfacial properties using piezoelectric cantilevers

    NASA Astrophysics Data System (ADS)

    Yegingil, Hakki; Shih, Wan Y.; Shih, Wei-Heng

    2010-09-01

    Invasive malignant breast cancers are typically branchy and benign breast tumors are typically smooth. It is of interest to characterize tumor branchiness (roughness) to differentiate invasive malignant breast cancer from noninvasive ones. In this study, we examined the shear modulus (G) to elastic modulus (E) ratio, G /E, as a quantity to describe model tumor interfacial roughness using a piezoelectric cantilever capable of measuring both tissue elastic modulus and tissue shear modulus. The piezoelectric cantilever used had two lead zirconate titanate layers to facilitate all-electrical elastic (shear) modulus measurements using one single device. We constructed model tissues with tumors by embedding one-dimensional (1D) corrugated inclusions and three-dimensional (3D) spiky-ball inclusions made of modeling clay in gelatin. We showed that for smooth inclusions, G /E was 0.3 regardless of the shear direction. In contrast, for a 1D corrugated rough inclusion G /E was 0.3 only when the shear was parallel to corrugation and G /E increased with an increasing angle between the shear direction and the corrugation. When the shear was perpendicular to corrugation, G /E became >0.7. For 3D isotropic spiky-ball inclusions we showed that the G /E depended on the degree of the roughness. Using the ratio s /r of the spike length (s) to the overall inclusion radius (r) as a roughness parameter, we showed that for inclusions with s /r larger than or equal to 0.28, the G /E ratio over the inclusions was larger than 0.7 whereas for inclusions with s /r less than 0.28, the G /E decreased with decreasing s /r to around 0.3 at s /r=0. In addition, we showed that the depth limit of the G /E measurement is twice the width of the probe area of the piezoelectric cantilever.

  20. Improved thermometry of low-temperature quantum systems by a ring-structure probe

    NASA Astrophysics Data System (ADS)

    Guo, Li-Sha; Xu, Bao-Ming; Zou, Jian; Shao, Bin

    2015-11-01

    The thermometry precision of a sample is a question of both fundamental and technological importance. In this paper, we consider a ring-structure system as our probe to estimate the temperature of a bath. Based on the Markovian master equation of the probe, we calculate the quantum Fisher information (QFI) of the probe at any time. We find that for the thermal equilibrium thermometry, the ferromagnetic structure can measure a lower temperature of the bath with a higher precision compared with the nonstructure probe, while for the dynamical thermometry, the antiferromagnetic structure can make the QFI of the probe in the dynamical process much larger than that in equilibrium with the bath, which is somewhat counterintuitive. Moreover, the best accuracy for the thermometry achieved in the antiferromagnetic structure case can be much higher than that in the nonstructure case. The physical mechanisms of the above phenomena are given in this paper.

  1. Probing qubit by qubit: Properties of the POVM and the information/disturbance tradeoff

    NASA Astrophysics Data System (ADS)

    Sparaciari, Carlo; Paris, Matteo G. A.

    2014-04-01

    We address the class of positive operator-valued measures (POVMs) for qubit systems that are obtained by coupling the signal qubit with a probe qubit and then performing a projective measurement on the sole probe system. These POVMs, which represent the simplest class of qubit POVMs, depends on 3 + 3 + 2 = 8 free parameters describing the initial preparation of the probe qubit, the Cartan representative of the unitary coupling, and the projective measurement at the output, respectively. We analyze in some detail the properties of the POVM matrix elements, and investigate their values for given ranges of the free parameters. We also analyze in detail the tradeoff between information and disturbance for different ranges of the free parameters, showing, among other things, that (i) typical values of the tradeoff are close to optimality and (ii) even using a maximally mixed probe one may achieve optimal tradeoff.

  2. Conferring Phosphorogenic Properties on Iridium(III)-Based Bioorthogonal Probes through Modification with a Nitrone Unit.

    PubMed

    Lee, Lawrence Cho-Cheung; Lau, Jonathan Chun-Wai; Liu, Hua-Wei; Lo, Kenneth Kam-Wing

    2016-01-18

    The use of bioorthogonal probes that display fluorogenic or phosphorogenic properties is advantageous to the labeling and imaging of biomolecules in live cells and organisms. Herein we present the design of three iridium(III) complexes containing a nitrone moiety as novel phosphorogenic bioorthogonal probes. These probes were non-emissive owing to isomerization of the C=N group but showed significant emission enhancement upon cycloaddition reaction with strained cyclooctynes. Interestingly, the connection of the nitrone ligand to the cationic iridium(III) center led to accelerated reaction kinetics. These nitrone complexes were also identified as phosphorogenic bioorthogonal labels and imaging reagents for cyclooctyne-modified proteins. These findings contribute to the development of phosphorogenic bioorthogonal probes and imaging reagents. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Fiber-optic probe design and optical property recovery algorithm for optical biopsy of brain tissue.

    PubMed

    Cappon, Derek J; Farrell, Thomas J; Fang, Qiyin; Hayward, Joseph E

    2013-10-01

    Optical biopsy techniques offer a minimally invasive, real-time alternative to traditional biopsy and pathology during tumor resection surgery. Diffuse reflectance spectroscopy (DRS) is a commonly used technique in optical biopsy. Optical property recovery from spatially resolved DRS data allows quantification of the scattering and absorption properties of tissue. Monte Carlo simulation methods were used to evaluate a unique fiber-optic probe design for a DRS instrument to be used specifically for optical biopsy of the brain. The probe diameter was kept to a minimum to allow usage in small surgical cavities at least 1 cm in diameter. Simulations showed that the close proximity of fibers to the edge of the probe resulted in boundary effects due to reflection of photons from the surrounding air-tissue interface. A new algorithm for rapid optical property recovery was developed that accounts for this reflection and therefore overcomes these effects. The parameters of the algorithm were adjusted for use over the wide range of optical properties encountered in brain tissue, and its precision was evaluated by subjecting it to random noise. This algorithm can be adapted to work with any probe geometry to allow optical property recovery in small surgical cavities.

  4. Development of a noncontact diffuse optical spectroscopy probe for measuring tissue optical properties

    PubMed Central

    Bish, Sheldon F.; Rajaram, Narasimhan; Nichols, Brandon; Tunnell, James W.

    2011-01-01

    Optical reflectance probes are often used as tools to obtain optical spectra from superficial tissues and subsequently determine optical and physiological properties associated with early stage cancer. These probes, when placed directly on the tissue, are known to cause significant pressure-dependent changes in local optical properties. To address this, we fit the probe with an optical device that images the illumination and collection fibers onto the tissue surface, eliminating the influence of contact probe pressure on the sampling area. The noncontact probe addition addresses new optical conditions that may affect its performance such as tissue surface contour, and specular reflections by implementing an autofocusing mechanism and cross polarization. Extracted optical properties of tissue simulating phantoms yield errors of 3.46% in reduced scattering and 8.62% in absorbance. Autofocusing has extended the depth of field from 4 mm to throughout the 12 mm range of autofocus travel, while cross polarization has removed the incidence angle dependent specular reflection component from the collected signal. PMID:22191909

  5. Time-resolved spectroscopy of the probe fluorescence in the study of human blood protein dynamic structure on SR beam

    NASA Astrophysics Data System (ADS)

    Dobretsov, G. E.; Kurek, N. K.; Syrejshchikova, T. I.; Yakimenko, M. N.; Clarke, D. T.; Jones, G. R.; Munro, I. H.

    2000-06-01

    Time-resolved spectroscopy on the SRS of the Daresbury Laboratory was used for the study of the human serum lipoproteins and human blood albumins with fluorescent probes K-37 and K-35, developed in Russia. The probe K-37 was found sensitive to the difference in dynamic properties of the lipid objects. Two sets of the parameters were used for the description of lipid dynamic structure: (1) time-resolved fluorescence spectra and (2) time-resolved fluorescence depolarization as a function of rotational mobility of lipid molecules. Each measured dynamic parameter reflected the monotonous changes of dynamic properties in the range: lipid spheres-very low density lipoproteins-low density lipoproteins-high density lipoproteins-phospholipid liposomes. The range is characterized by the increase of the ratio polar/ nonpolar lipids. Thus, time-resolved fluorescence could be used to detect some structural modifications in lipoproteins related to atherosclerosis and subsequent cardiovascular diseases development.

  6. Probing physical properties of confined fluids within individual nanobubbles.

    PubMed

    Taverna, D; Kociak, M; Stéphan, O; Fabre, A; Finot, E; Décamps, B; Colliex, C

    2008-01-25

    Spatially resolved electron energy-loss spectroscopy (EELS) in a scanning transmission electron microscope (STEM) has been used to investigate a He fluidic phase in nanobubbles embedded in a metallic Pd(90)Pt(10) matrix. Using the 1s-->2p excitation of the He atoms, maps of the He density and pressure in bubbles of different diameters have been realized, to provide an indication of the bubble formation mechanism. Detailed local variations of the He K-line characteristics have been measured and interpreted as modifications of the electromagnetic properties of the He atom close to a metallic interface, which affects a correct estimation of the densities within the smallest bubbles.

  7. Probing surface properties of Jupiter Trojans by polarimetric observations

    NASA Astrophysics Data System (ADS)

    Belskaya, I.; Bagnulo, S.; Stinson, A.; Christou, A.; Muinonen, K.

    2014-07-01

    We present the first polarimetric observations of six Jupiter Trojans, namely (588) Achilles, (1583) Antilochus, (3548) Eurybates, (4543) Phoinix, (6545) 1986 TR_6, and (21601) 1998 XO_{89}. All these objects belong to the L4 population of Jupiter Trojans and have diameters in the range of 50-160 km (Grav et al. 2011). The observations were carried out in 2013 at ESO VLT. Each object was observed at 3-4 different phase angles in the phase-angle range from 7 deg up to 11-12 deg, the largest possible phase angles in the ground-based observations of Trojans. Observations were made in the R band with a typical accuracy of 0.05 %. We have measured negative polarization branch for each object with polarization minima varying from -1 % to -1.3 %. The polarization-phase-angle behavior of the observed Trojans is found to be very similar to that of some low-albedo main-belt asteroids, in particular, the P-type asteroids. We compare photometric and polarimetric phase dependencies of Trojans to the phase curves of inner and outer Solar System bodies. Possible relationships of phase-curve parameters with albedos and spectral properties are investigated. Constraints on the surface properties of Jupiter Trojans from the polarimetric observations are discussed.

  8. Probing the hydrogen bonding structure in the Rieske protein.

    PubMed

    El Khoury, Youssef; Trivella, Aurélien; Gross, Julien; Hellwig, Petra

    2010-10-25

    The use of the far-infrared spectral range presents a novel approach for analysis of the hydrogen bonding in proteins. Here it is presented for the analysis of Fe--S vibrations (500-200 cm(-1)) and of the intra- and intermolecular hydrogen bonding signature (300-50 cm(-1)) in the Rieske protein from Thermus thermophilus as a function of temperature and pH. Three pH values were adequately chosen in order to study all the possible protonation states of the coordinating histidines. The Fe--S vibrations showed pH-dependent shifts in the FIR spectra in line with the change of protonation state of the histidines coordinating the [2Fe--2S] cluster. Measurements of the low-frequency signals between 300 and 30 K demonstrated the presence of a distinct overall hydrogen bonding network and a more rigid structure for a pH higher than 10. To further support the analysis, the redox-dependent shifts of the secondary structure were investigated by means of an electrochemically induced FTIR difference spectroscopic approach in the mid infrared. The results confirmed a clear pH dependency and an influence of the immediate environment of the cluster on the secondary structure. The results support the hypothesis that structure-mediated changes in the environment of iron--sulfur centers play a critical role in regulating enzymatic catalysis. The data point towards the role of the overall internal hydrogen bonding organization for the geometry and the electronic properties of the cluster.

  9. Electronic Structure of Germanium Nanocrystal Films Probed with Synchrotron Radiation

    SciTech Connect

    Bostedt, C

    2002-05-01

    The fundamental structure--property relationship of semiconductor quantum dots has been investigated. For deposited germanium nanocrystals strong quantum confinement effects have been determined with synchrotron radiation based x-ray absorption and photoemission techniques. The nanocrystals are condensed out of the gas phase with a narrow size distribution and subsequently deposited in situ onto various substrates. The particles are crystalline in the cubic phase with a structurally disordered surface shell and the resulting film morphology depends strongly on the substrate material and condition. The disordered surface region has an impact on the overall electronic structure of the particles. In a size-dependent study, the conduction and valence band edge of germanium nanocrystals have been measured for the first time and compared to the bulk crystal. The band edges move to higher energies as the particle size is decreased, consistent with quantum confinement theory. To obtain a more accurate analysis of confinement effects in the empty states, a novel analysis method utilizing an effective particle size for the x-ray absorption experiment, which allows a deconvolution of absorption edge broadening effects, has been introduced. Comparison of the present study to earlier studies on silicon reveals that germanium exhibits stronger quantum confinement effects than silicon. Below a critical particle size of 2.3 {+-} 0.7 nm, the band gap of germanium becomes larger than that of silicon--even if it is the opposite for bulk materials. This result agrees phenomenologically with effective mass and tight binding theories but contradicts the findings of recent pseudopotential calculations. The discrepancy between theory and experiments is attributed to the differences in the theoretical models and experimental systems. The experimentally observed structural disorder of the particle surface has to be included in the theoretical models.

  10. Probing structure-antifouling activity relationships of polyacrylamides and polyacrylates.

    PubMed

    Zhao, Chao; Zhao, Jun; Li, Xiaosi; Wu, Jiang; Chen, Shenfu; Chen, Qiang; Wang, Qiuming; Gong, Xiong; Li, Lingyan; Zheng, Jie

    2013-07-01

    We have synthesized two different polyacrylamide polymers with amide groups (polySBAA and polyHEAA) and two corresponding polyacrylate polymers without amide groups (polySBMA and polyHEA), with particular attention to the evaluation of the effect of amide group on the hydration and antifouling ability of these systems using both computational and experimental approaches. The influence of polymer architectures of brushes, hydrogels, and nanogels, prepared by different polymerization methods, on antifouling performance is also studied. SPR and ELISA data reveal that all polymers exhibit excellent antifouling ability to repel proteins from undiluted human blood serum/plasma, and such antifouling ability can be further enhanced by presenting amide groups in polySBAA and polyHEAA as compared to polySBMA and polyHEA. The antifouling performance is positively correlated with the hydration properties. Simulations confirm that four polymers indeed have different hydration characteristics, while all presenting a strong hydration overall. Integration of amide group with pendant hydroxyl or sulfobetaine group in polymer backbones is found to increase their surface hydration of polymer chains and thus to improve their antifouling ability. Importantly, we present a proof-of-concept experiment to synthesize polySBAA nanogels, which show a switchable property between antifouling and pH-responsive functions driven by acid-base conditions, while still maintaining high stability in undiluted fetal bovine serum and minimal toxicity to cultured cells. This work provides important structural insights into how very subtle structural changes in polymers can yield great improvement in biological activity, specifically the inclusion of amide group in polymer backbone/sidechain enables to obtain antifouling materials with better performance for biomedical applications.

  11. Probing Induced Structural Changes in Biomimetic Bacterial Cell Membrane Interactions with Divalent Cations

    SciTech Connect

    Holt, Allison M; Standaert, Robert F; Jubb, Aaron M; Katsaras, John; Johs, Alexander

    2017-01-01

    Biological membranes, formed primarily by the self-assembly of complex mixtures of phospholipids, provide a structured scaffold for compartmentalization and structural processes in living cells. The specific physical properties of phospholipid species present in a given membrane play a key role in mediating these processes. Phosphatidylethanolamine (PE), a zwitterionic lipid present in bacterial, yeast, and mammalian cell membranes, is exceptional. In addition to undergoing the standard lipid polymorphic transition between the gel and liquid-crystalline phase, it can also assume an unusual polymorphic state, the inverse hexagonal phase (HII). Divalent cations are among the factors that drive the formation of the HII phase, wherein the lipid molecules form stacked tubular structures by burying the hydrophilic head groups and exposing the hydrophobic tails to the bulk solvent. Most biological membranes contain a lipid species capable of forming the HII state suggesting that such lipid polymorphic structural states play an important role in structural biological processes such as membrane fusion. In this study, the interactions between Mg2+ and biomimetic bacterial cell membranes composed of PE and phosphatidylglycerol (PG) were probed using differential scanning calorimetry (DSC), small-angle x-ray scattering (SAXS), and fluorescence spectroscopy. The lipid phase transitions were examined at varying ratios of PE to PG and upon exposure to physiologically relevant concentrations of Mg2+. An understanding of these basic interactions enhances our understanding of membrane dynamics and how membrane-mediated structural changes may occur in vivo.

  12. Probing the molecular structure of interfacial films and crystals

    NASA Astrophysics Data System (ADS)

    Wang, Anfeng

    The properties of outside surfaces were found to play an important role in the nucleation and crystallization processes. Thus controlling the surface properties would provide an effective means for crystal engineering. Hydrophobic surface is prepared by self-assembled monolayer (SAM) formation of octadecyltrichlorosilane (OTS) on silicon surface, with the hydrophobicity adjusted by the monolayer coverage. Silicon wafer treated by RCA method is hydrophilic, so are SAMs formed by two amine-terminated organosilanes on silicon. However these three hydrophilic surfaces are unstable, due to contamination of the amine-terminated SAMs and hydrolysis of RCA treated silicon. Polymethine dyes, BDH+Cl- and BDH +ClO4-, are synthesized and characterized by UV spectra and crystal morphology. They have identical UV spectrum in dilute solutions due to the same chromophore, and J-aggregation happens at much higher concentrations. IR spectra are analyzed to monitor the crystallization process of BDH+Cl- OTS SAM surface and the crystallization process of BDH+Cl- on substrates with varying hydrophobicity was monitored by optical microscopy and compared. Due to the extreme flexibility of polysiloxane, silicone surfactants can arrange themselves at the interfaces quickly to adopt configurations with minimum free energy. Polysiloxane is hydrophobic but not oleophilic, which makes them effective emulsifiers and stabilizers in aqueous and nonaqueous media. The interaction between an AFM Si3N4 tip and a hydrophobic surface in silicone polyether (SPE) solution in the presence of ethanol was investigated by Atomic Force Microscopy (AFM) force measurement. ABA triblock type and comb-type SPE surfactants, adsorbed at the liquid-solid interface, provide steric barriers, even with significant addition of ethanol. On the contrary, conventional low-molecular weight and polymeric alkyl surfactants display no steric barrier even in the presence of moderate amount of ethanol. This unique property makes

  13. Probing Surface Structures of Shewanella spp. by Microelectrophoresis

    PubMed Central

    Dague, Etienne; Duval, Jérôme; Jorand, Frédéric; Thomas, Fabien; Gaboriaud, Fabien

    2006-01-01

    Long-range electrostatic forces substantially influence bacterial interactions and bacterial adhesion during the preliminary steps of biofilm formation. The strength of these forces depends strongly on the structure of the bacterium surfaces investigated. The latter may be addressed from appropriate analysis of electrophoretic mobility measurements. Due to the permeable character of the bacterium wall and/or surrounding polymer layer, bacteria may be regarded as paradigms of soft bioparticles. The electrophoretic motion of such particles in a direct-current electric field differs considerably from that of their rigid counterparts in the sense that electroosmotic flow takes place around and within the soft surface layer. Recent developments of electrokinetic theories for soft particles now render possible the evaluation of the softness degree (or equivalently the hydrodynamic permeability) from the raw electrokinetic data. In this article, the electrophoretic mobilities of three Shewanella strains (MR-4, CN32, and BrY) presenting various and well-characterized phenotypes of polymer fringe are reported over a wide range of pH and ionic strength conditions. The data are quantitatively analyzed on the basis of a rigorous numerical evaluation of the governing electrostatic and hydrodynamic equations for soft particles. It is clearly shown how the peculiar surface structures of the bacteria investigated are reflected in their electrohydrodynamic properties. PMID:16415062

  14. Coaxial-probe contact-force monitoring for dielectric properties measurements

    USDA-ARS?s Scientific Manuscript database

    A means is described for measuring and monitoring the contact force applied to a material sample with an open-ended coaxial-line probe for purposes of measuring the dielectric properties of semisolid material samples such as fruit, vegetable and animal tissues. The equipment consists of a stainless...

  15. Ratiometric fluorescent probe with AIE property for monitoring endogenous hydrogen peroxide in macrophages and cancer cells.

    PubMed

    Liu, Yong; Nie, Jing; Niu, Jie; Meng, Fangfang; Lin, Weiying

    2017-08-04

    Hydrogen peroxide (H2O2) plays a key role in the progression of human illnesses, such as autoimmune and auto-inflammatory diseases, infectious diseases, diabetes, and cancer, etc. In this work, we have discribed a novel probe, TPE-TLE, which remarkably displayed AIE property and ratiometric fluorescence emission profiles in the presence of H2O2. This ratiometric fluorescent probe with AIE property exhibits outstanding features such as the well-resolved emission peaks, high sensitivity, high selectivity, low cytotoxicity, and good cell-membrane permeability. These excellent attributes enable us to demonstrate the ratiometric imaging of endogenously produced H2O2 in macrophages and cancer cells based on the novel ratiometric probe with AIE property for the first time. By comparing two kinds of cells, it is firstly found that cancer cells should contain much more endogenous H2O2 than macrophages. We expect that TPE-TLE will be useful fluorescent platform for the development of a variety of ratiometric fluorescent probes with AIE property to achieve unique biological applications.

  16. Probing the Galactic Centre: Black hole properties, magnetars and pulsars

    NASA Astrophysics Data System (ADS)

    Kramer, Michael

    2015-08-01

    We report on new observations and ongoing efforts to precisely measure the properties of the central black hole (BH). This is possible by combining imaging efforts of SGR A* using mm-VLBI and potential timing observations of pulsars orbiting SGR A*. We show that pulsar-enabled measurements of the BH spin (to 0.1% precision, including its 3D orientation) and the quadrupole moment (to 1%), can be uniquely combined with Event Horizon Telescope imaging. On the way towards finding suitable pulsars, we discovered the radio-loud magnetar SGR J1745-2900 in only 0.1 pc distance with the Effelsberg telescope. We report here also on continued studies, using simultaneous observations of the magnetar at frequencies from 2.57 to 225GHz. We detect SGR J1745-2900 up to 225GHz, the highest radio frequency detection of pulsed emission from a neutron star to date. We also detect strong single pulses from 4.85 up to 154GHz and report on efforts at even higher frequencies. While these results show that strongly magnetized neutron stars can be effective radio emitters at frequencies notably higher to what was previously known, providing very interesting clues on the physics of these objects, we also review the implications for the precision measurements of the central BH.

  17. Real-time probe based quantitative determination of material properties at the nanoscale.

    PubMed

    Saraswat, G; Agarwal, P; Haugstad, G; Salapaka, M V

    2013-07-05

    Tailoring the properties of a material at the nanoscale holds the promise of achieving hitherto unparalleled specificity of the desired behavior of the material. Key to realizing this potential of tailoring materials at the nanoscale are methods for rapidly estimating physical properties of the material at the nanoscale. In this paper, we report a method for simultaneously determining the topography, stiffness and dissipative properties of materials at the nanoscale in a probe based dynamic mode operation. The method is particularly suited for investigating soft-matter such as polymers and bio-matter. We use perturbation analysis tools for mapping dissipative and stiffness properties of material into parameters of an equivalent linear time-invariant model. Parameters of the equivalent model are adaptively estimated, where, for robust estimation, a multi-frequency excitation of the probe is introduced. We demonstrate that the reported method of simultaneously determining multiple material properties can be implemented in real-time on existing probe based instruments. We further demonstrate the effectiveness of the method by investigating properties of a polymer blend in real-time.

  18. Switchable bi-stable multilayer magnetic probes for imaging of soft magnetic structures.

    PubMed

    Wren, Tom; Puttock, Robb; Gribkov, Boris; Vdovichev, Sergey; Kazakova, Olga

    2017-03-28

    We present the use of custom-made multilayer (ML) magnetic probes in magnetic force microscopy (MFM) for imaging soft magnetic structures, i.e. nickel submicron disks of different dimensions. One of the main advantages of a custom-made ML probe is that it can be controllably switched between standard (parallel) and low moment (antiparallel) states. We demonstrate that the predicted vortex and stripe domain states in the disks are observed when using the ML probes both in the antiparallel and parallel states. However, while the phase contrast is significantly larger in the parallel state, the images are dominated by strong sample - probe interactions that obscure the image. By comparison of the stripe domain width observed by MFM with the ML probe and those expected from the Kittel model, we show that the resolution of the probe in the AP and P states is ∼30-40nm, i.e. of the order of the probe geometrical apex and thus approaching the limit of spatial resolution. The ML probes are further compared to the commercial standard and low moment ones, showing that the quality of images obtained with the ML probe is superior to both commercial probes.

  19. A low-profile three-dimensional neural probe array using a silicon lead transfer structure

    NASA Astrophysics Data System (ADS)

    Cheng, Ming-Yuan; Je, Minkyu; Tan, Kwan Ling; Lim Tan, Ee; Lim, Ruiqi; Yao, Lei; Li, Peng; Park, Woo-Tae; Phua, Eric Jian Rong; Lip Gan, Chee; Yu, Aibin

    2013-09-01

    This paper presents a microassembly method for low-profile three-dimensional probe arrays for neural prosthesis and neuroscience applications. A silicon (Si) lead transfer structure, Si interposer, is employed to form electrical connections between two orthogonal planes—the two dimensional probes and the dummy application-specific integrated circuit (ASIC) chip. In order to hold the probe array and facilitate the alignment of probes during assembly, a Si platform is designed to have through-substrate slots for the insertion of probes and cavities for holding the Si interposers. The electrical interconnections between the probes and the dummy ASIC chip are formed by solder reflow, resulting in greatly improved throughput in the proposed assembly method. Moreover, since the backbone of the probe can be embedded inside the cavity of the Si platform, the profile of the probe array above the cortical surface can be controlled within 750 µm. This low-profile allows the probe array not to touch the skull after it is implanted on the brain. The impedance of the assembled probe is also measured and discussed.

  20. Probing the mechanical properties of dental porcelain through nanoindentation

    NASA Astrophysics Data System (ADS)

    Manda, Marianthi; Moschakis, Nikolaos; Konstantinidis, Avraam; Christophilos, Demetrios; Papadopoulou, Lambrini; Koidis, Petros; Aifantis, Elias

    2012-11-01

    The purpose of this short communication is to report on some micro/nanoscale aspects of the mechanical behavior of dental porcelain. Specimens were characterized by micro-Raman spectroscopy and scanning electron microscopy (SEM) coupled with energy dispersive spectroscopy (EDS). Massive nanoindentation experiments on the surface of the specimens were performed, and typical load-displacement or load-depth (P-h) curves were obtained, which in turn were used to determine the Young modulus (E) and nanoindentation hardness (n-H), based on the Oliver-Pharr method [1]. Statistical analyses were carried out to determine the Spearman’s rank correlation coefficient (Spearman’s ρ), along with non-parametric linear regression analysis by employing Kolmogorov-Smirnov and Two-Step Cluster tests. Densification due to grain boundary diffusion and open-pore elimination was revealed by SEM. EDS analysis indicated a leucite-dispersed silicate glass matrix, as well as its contamination by traces of other minerals. Raman spectroscopy supported the EDS assignments. The P-h curves suggested that inelastic deformation and material flow increases at larger depths. Spearman’s ρ value showed strong dependence of E and n-H on h, indicating the occurrence of a size effect. The logarithmic data of E and n-H as functions of h were fitted by using linear regression analysis. The data did not obey a normal distribution (as the Kolmogorov-Smirnov test showed) due to the chemical heterogeneity involved. The Two-Step Cluster analysis indicated clustering in four groups associated with the chemical heterogeneity of the surface. Similar works using nanoindentation to determine the mechanical properties of dental materials can be found, for example, in [2, 3]. Corresponding methods for extracting the values of E and n-H from P-h experimental curves can be found, for example, in [4-6].

  1. Probing Neutrino Properties with Long-Baseline Neutrino Beams

    SciTech Connect

    Marino, Alysia

    2015-06-29

    This final report on an Early Career Award grant began in April 15, 2010 and concluded on April 14, 2015. Alysia Marino's research is focussed on making precise measurements of neutrino properties using intense accelerator-generated neutrino beams. As a part of this grant, she is collaborating on the Tokai-to-Kamioka (T2K) long-baseline neutrino experiment, currently taking data in Japan, and on the Deep Underground Neutrino Experiment (DUNE) design effort for a future Long-Baseline Neutrino Facility (LBNF) in the US. She is also a member of the NA61/SHINE particle production experiment at CERN, but as that effort is supported by other funds, it will not be discussed further here. T2K was designed to search for the disappearance of muon neutrinos (νμ) and the appearance of electron neutrinos (νe), using a beam of muon neutrino beam that travels 295 km across Japan towards the Super-Kamiokande detector. In 2011 T2K first reported indications of νe appearance, a previously unobserved mode of neutrino oscillations. In the past year, T2K has published a combined analysis of νμ disappearance and νe appearance, and began collecting taking data with a beam of anti-neutrinos, instead of neutrinos, to search for hints of violation of the CP symmetry of the universe. The proposed DUNE experiment has similar physics goals to T2K, but will be much more sensitive due to its more massive detectors and new higher-intensity neutrino beam. This effort will be very high-priority particle physics project in the US over the next decade.

  2. Using Dwarf Spheroidal Satellites as Probes of Galaxy Properties

    NASA Astrophysics Data System (ADS)

    Choudhury, Abrar; Guhathakurta, P.; Gilbert, K. M.; Beaton, R. L.; Tollerud, E. J.; SPLASH Collaboration

    2012-01-01

    We present a Keck/DEIMOS spectroscopic study of fifteen dwarf spheroidal (dSph) satellites of the Andromeda galaxy. Our aim is to understand the properties of both the dSphs and Andromeda. Previously, detailed spectroscopic studies were carried out on six of these dSphs using smaller data sets, and limited spectroscopic studies were carried out on the remaining nine. The data sets analyzed in this research include more stars and higher quality data than those of previous studies. In order to accurately study the dSphs, we have developed a method that uses the stars’ velocities, metallicities, and projected distances from the center of each dSph to separate members from non-members of the dSphs. The resulting samples are expected to have a low fraction of contamination by non-members, which makes this method critical for all future studies of Andromeda dSphs. We calculate the mean radial velocities and velocity dispersions of the dSphs, and the new dSph velocity measurements are used to estimate Andromeda's dynamical mass. This mass estimate is more accurate than previous ones because it uses more dynamical tracers. The dSph-based mass estimate is corroborated by a different mass estimate based on the kinematics of Andromeda's field halo stars. This is the first time the mass of Andromeda has been calculated using its halo stars. Future steps will include calculating the dark matter content of the dSphs and comparing their chemical abundances to those of Andromeda's halo, which is made up of former dSphs. This research was supported by the Science Internship Program (SIP) at UCSC and the National Science Foundation.

  3. Probing the surface magnetic field structure in RX J1856.5-3754

    NASA Astrophysics Data System (ADS)

    Popov, S. B.; Taverna, R.; Turolla, R.

    2017-02-01

    The evolution of magnetic field in isolated neutron stars is one of the most important ingredients in the attempt to build a unified description of these objects. A prediction of field evolution models is the existence of an equilibrium configuration, in which the Hall cascade vanishes. Recent calculations have explored the field structure in this stage, called the Hall attractor. We use X-ray data of near-by, cooling neutron stars to probe this prediction, as these sources are surmised to be close to or at Hall attractor phase. We show that the source RX J1856.5-3754 might be closer to the attractor than other sources of its class. Our modelling indicates that the properties of surface thermal emission, assuming that the star is in the Hall attractor, are in contradiction to the spectral data of RX J1856.5-3754.

  4. Probing the surface structure of divalent transition metals using surface specific solid-state NMR spectroscopy.

    PubMed

    Mason, Harris E; Harley, Stephen J; Maxwell, Robert S; Carroll, Susan A

    2012-03-06

    Environmental and geochemical systems containing paramagnetic species could benefit by using nuclear magnetic resonance (NMR) spectroscopy due to the sensitivity of the spectral response to small amounts paramagnetic interactions. In this study, we apply commonly used solid-state NMR spectroscopic methods combined with chemometrics analysis to probe sorption behavior of the paramagnetic cations Cu(2+) and Ni(2+)at the amorphous silica surface. We exploit the unique properties of paramagnets to derive meaningful structural information in these systems at low, environmentally relevant cation surface loadings by comparing the NMR response of sorption samples to paramagnetic free samples. These data suggest that a simple sorption model where the cation sorbs as inner sphere complexes at negatively charged, deprotonated silanol sites is appropriate. These results help constrain sorption models that are used to describe metal fate and transport.

  5. Spectral properties of molecular charge-transfer probe QMOM

    NASA Astrophysics Data System (ADS)

    Tomin, V. I.; Jaworski, R.; Yushchenko, D. A.

    2010-09-01

    The spectral characteristics of solutions of a dye with dual fluorescence, 1-methyl-2-(4-methoxy)phenyl-3-hydroxy-4(1H)-quinolone, in acetonitrile are studied upon selective excitation. This dye is a structural analogue of 3-hydroxyflavone and also exhibits excited-state proton transfer, which, as well as in the case of 3-hydroxyflavone, has a kinetic nature. The fluorescence spectra are studied upon excitation by photons of various energies, and the excitation spectra are recorded at wavelengths of different fluorescence bands. It is found that the intensity ratio of the emission of the normal and tautomeric forms (at wavelength of 415 and 518 nm, respectively) is almost the same (0.23-0.25) for excitation in the regions of the main and the second absorption bands. At the same time, in the case of excitation between these bands, this ratio decreases to 0.19. The second interesting feature is the existence of a third latent emission band peaked at about 480 nm, which is reliably detected upon excitation at wavelengths in the region of 400-450 nm. This study shows that this emission belongs to the anionic form of the dye. This form is also responsible for a decrease in the intensity ratio of the emission of the two main forms in the case of excitation between the first and second absorption bands.

  6. PROPERTIES OF DUST GRAINS PROBED WITH EXTINCTION CURVES

    SciTech Connect

    Nozawa, Takaya; Fukugita, Masataka

    2013-06-10

    Modern data of the extinction curve from the ultraviolet to the near-infrared are revisited to study properties of dust grains in the Milky Way (MW) and the Small Magellanic Cloud (SMC). We confirm that the graphite-silicate mixture of grains yields the observed extinction curve with the simple power-law distribution of the grain size but with a cutoff at some maximal size: the parameters are tightly constrained to be q = 3.5 {+-} 0.2 for the size distribution a {sup -q} and the maximum radius a{sub max} = 0.24 {+-} 0.05 {mu}m, for both MW and SMC. The abundance of grains, and hence the elemental abundance, is constrained from the reddening versus hydrogen column density, E(B - V)/N{sub H}. If we take the solar elemental abundance as the standard for the MW, >56% of carbon should be in graphite dust, while it is <40% in the SMC using its available abundance estimate. This disparity and the relative abundance of C to Si explain the difference of the two curves. We find that 50%-60% of carbon may not necessarily be in graphite but in the amorphous or glassy phase. Iron may also be in the metallic phase or up to {approx}80% in magnetite rather than in silicates, so that the Mg/Fe ratio in astronomical olivine is arbitrary. With these substitutions, the parameters of the grain size remain unchanged. The mass density of dust grains relative to hydrogen is {rho}{sub dust}/{rho}{sub H}= 1 / (120{sup +10}{sub -16}) for the MW and 1 / (760{sup +70}{sub -90}) for the SMC under the elemental abundance constraints. We underline the importance of the wavelength dependence of the extinction curve in the near-infrared in constructing the dust model: if A{sub {lambda}}{proportional_to}{lambda}{sup -{gamma}} with {gamma} {approx_equal} 1.6, the power-law grain-size model fails, whereas it works if {gamma} {approx_equal} 1.8-2.0.

  7. Probing the electronic structures and properties of neutral and charged arsenic sulfides [Asn S₂ (⁻¹,⁰,⁺¹), n = 1-6] with Gaussian-3 theory.

    PubMed

    Hou, Liyuan; Yang, Jucai; Ning, Hongmei

    2014-10-01

    The structures and energies of neutral and charged arsenic sulfides As n S2 ((-1,0,+1)) (n = 1-6) were investigated systematically by means of the Gaussian-3 (G3) scheme. The ground-state structures of these species are presented. The ground-state structures of As n S2 can be viewed as the lowest-energy structure of neutral As n+1S by replacing an As atom with a S atom. To be more precise, the ground-state structures of As n S2 can be viewed as the lowest-energy structure of neutral As n+2 by replacing two As atoms with two S atoms, in which the feature of sulfur bonding is edge-bridging. No rule could be found for the ground state structure of As n S2 (-) and As n S2 (+). In As n S2 (-), the feature of sulfur bonding is either edge-bridging or a terminal atom, and in AsnS2 (+) the feature of sulfur bonding is edge-bridging analogous to As n S2. The potential energy surfaces of As4S2 and its charged species are very flat. So co-existence for many isomers of As4S2 and its charged species are possible. The reliable adiabatic electron affinities (AEAs) and adiabatic ionization potentials (AIPs) of As n S2 were estimated. There are odd-even alternations in both AEAs and AIPs as a function of size of As n S2. The dissociation energies (DEs) of S [and/or its ion S((-/+))] from As n S2 clusters and their ions were calculated and used to reveal relative stability.

  8. Electrostatic properties of aqueous interfaces probed by small solutes

    NASA Astrophysics Data System (ADS)

    Pohorille, Andrew; Wilson, Michael A.; Schweighofer, Karl

    1999-11-01

    The excess chemical potentials of methane and its four fluorinated derivatives across the water-hexane, water-octanol, water-glycerol 1-monooleate and water-1-palmitoyl 2-oleoyl sn-glycero 3-phosphatidylcholine (POPC) interfaces are calculated using the particle insertion method. In all cases, the polar species exhibit interfacial minima indicating that these molecules tend to accumulate in the interfacial region, while the non-polar molecules exhibit no such minimum. The excess chemical potentials are further partitioned into electrostatic and non-electrostatic terms. For polar molecules, the electrostatic term changes nearly linearly over the distance of approximately 10 Å in the interfacial region and appears to depend only weakly on the nature of the interface. Solute molecules are not oriented isotropically at the interface, but tend to align themselves with the excess electric field created by the anisotropic interfacial environment. Using dipoles in a cavity as models, it is further shown that, in the water-POPC system, the electrostatic term changes with the size of the dipole according to the predictions of linear response theory. This approximation does not work as well for the other interfacial systems investigated. This may be an artifact due to the neglect of long-range effects in those simulations. The non-electrostatic term, dominated by the reversible work of cavity formation, shows interfacially induced structure. In particular, it is responsible for a maximum of the excess chemical potential on the dense, water side of the water-POPC interface. The results of this study provide guidance to developing simple but accurate implicit models of interfacial systems.

  9. Probing viral genomic structure: alternative viewpoints and alternative structures for satellite tobacco mosaic virus RNA.

    PubMed

    Schroeder, Susan J

    2014-11-04

    Viral RNA structure prediction is a valuable tool for development of drugs against viral disease. This work discusses different approaches to predicting encapsidated viral RNA and highlights satellite tobacco mosaic virus (STMV) RNA as a model system with excellent crystallography data. Fundamentally important issues for debate include thermodynamic versus kinetic control of virus assembly and the possible consequences of quasi-species in the primary structure on RNA secondary structure prediction of a single structure or an ensemble of structures. Multiple computational tools and chemical reagents are now available for improved viral RNA structure prediction. Two different predicted structures for encapsidated STMV RNA result from differences in three main areas: a different approach and philosophy to studying encapsidated viral RNA, an emphasis on different RNA motifs, and technical differences in computational methods and chemical reagents. The experiments with traditional chemical probing and SHAPE reagents are compared in terms of chemistry, results, and interpretation for STMV RNA as well as other RNA protein assemblies, such as the 5'UTR of HIV and the ribosome. This discussion of the challenges of viral RNA structure prediction will lead to new experiments and improved future predictions for viral RNA.

  10. Measurement of thermal properties of white radish (R. raphanistrum) using easily constructed probes

    PubMed Central

    Obot, Mfrekemfon Samuel; Li, Changcheng; Fang, Ting; Chen, Jinquan

    2017-01-01

    Thermal properties are necessary for the design and control of processes and storage facilities of food materials. This study proposes the measurement of thermal properties using easily constructed probes with specific heat capacity calculated, as opposed to the use of Differential Scanning Calorimeter (DSC) or other. These probes were constructed and used to measure thermal properties of white radish in the temperature range of 80–20°C and moisture content of 91–6.1% wb. Results showed thermal properties were within the range of 0.71–0.111 Wm-1 C-1 for thermal conductivity, 1.869×10−7–0.72×10−8 m2s-1 for thermal diffusivity and 4.316–1.977 kJ kg-1C-1for specific heat capacity. These results agree with reports for similar products studied using DSC and commercially available line heat source probes. Empirical models were developed for each property through linear multiple regressions. The data generated would be useful in modeling and control of its processing and equipment design. PMID:28288175

  11. Cellulose nanomaterials review: structure, properties and nanocomposites

    Treesearch

    Robert J. Moon; Ashlie Martini; John Nairn; John Simonsen; Jeff Youngblood

    2011-01-01

    This critical review provides a processing-structure-property perspective on recent advances in cellulose nanoparticles and composites produced from them. It summarizes cellulose nanoparticles in terms of particle morphology, crystal structure, and properties. Also described are the self-assembly and rheological properties of cellulose nanoparticle suspensions. The...

  12. Probing Nucleon Structure with Meson Electro-production in Hall C

    SciTech Connect

    Wood, Stephen

    2011-02-01

    Meson electro-production is used in Hall C at Jefferson Lab to probe nucleon, baryon and nuclear structure. The experimental program in Hall C includes studies of semi-inclusive pion production, p, d(e, e'π±)X, where low energy factorization has been observed, suggesting that these reactions can be used to probe nucleon structure, including transverse momentum distributions of quarks, at energies available at JLab after the upcoming 12 GeV upgrade.

  13. Synthesis, Physiochemical Properties, Photochemical Probe, and Antimicrobial Effects of Novel Norfloxacin Analogues

    PubMed Central

    Bakhotmah, Dina A.; Abdul-Rahman, Reda M.; Makki, Mohammad S.; El-Zahabi, Mohamed A.; Suliman, Mansor

    2011-01-01

    The emerging resistance to antimicrobial drugs demands the synthesis of new remedies for microbial infections. Attempts have been made to prepare new compounds by modifications in the quinolone structure. An important method for the synthesis of new quinolone is using Vilsmeier approach but has its own limitations. The present work aimed to synthesize novel norfloxacin analogues using modified Vilsmeier approach and conduct preliminary investigations for the evaluation of their physicochemical properties, photochemical probe, and antimicrobial effects. In an effort to synthesize norfloxacin analogues, only 7-bromo-6-N-benzyl piperazinyl-4-oxoquinoline-3-carboxylic acid was isolated using Vilsmeier approach at high temperature, where N, N′-bis-(4-fluoro-3-nitrophenyl)-oxalamide and N, N′-bis-(3-chloro-4-fluorophenyl)-malonamide were obtained at low temperature. Correlation results showed that lipophilicity, molecular mass, and electronic factors might influence the activity. The synthesized compounds were evaluated for their antimicrobial effects against important pathogens, for their potential use in the inhibition of vitiligo. PMID:24052816

  14. SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data.

    PubMed

    Poulsen, Line Dahl; Kielpinski, Lukasz Jan; Salama, Sofie R; Krogh, Anders; Vinther, Jeppe

    2015-05-01

    Selective 2' Hydroxyl Acylation analyzed by Primer Extension (SHAPE) is an accurate method for probing of RNA secondary structure. In existing SHAPE methods, the SHAPE probing signal is normalized to a no-reagent control to correct for the background caused by premature termination of the reverse transcriptase. Here, we introduce a SHAPE Selection (SHAPES) reagent, N-propanone isatoic anhydride (NPIA), which retains the ability of SHAPE reagents to accurately probe RNA structure, but also allows covalent coupling between the SHAPES reagent and a biotin molecule. We demonstrate that SHAPES-based selection of cDNA-RNA hybrids on streptavidin beads effectively removes the large majority of background signal present in SHAPE probing data and that sequencing-based SHAPES data contain the same amount of RNA structure data as regular sequencing-based SHAPE data obtained through normalization to a no-reagent control. Moreover, the selection efficiently enriches for probed RNAs, suggesting that the SHAPES strategy will be useful for applications with high-background and low-probing signal such as in vivo RNA structure probing. © 2015 Poulsen et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  15. SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data

    PubMed Central

    Poulsen, Line Dahl; Kielpinski, Lukasz Jan; Salama, Sofie R.; Krogh, Anders; Vinther, Jeppe

    2015-01-01

    Selective 2′ Hydroxyl Acylation analyzed by Primer Extension (SHAPE) is an accurate method for probing of RNA secondary structure. In existing SHAPE methods, the SHAPE probing signal is normalized to a no-reagent control to correct for the background caused by premature termination of the reverse transcriptase. Here, we introduce a SHAPE Selection (SHAPES) reagent, N-propanone isatoic anhydride (NPIA), which retains the ability of SHAPE reagents to accurately probe RNA structure, but also allows covalent coupling between the SHAPES reagent and a biotin molecule. We demonstrate that SHAPES-based selection of cDNA–RNA hybrids on streptavidin beads effectively removes the large majority of background signal present in SHAPE probing data and that sequencing-based SHAPES data contain the same amount of RNA structure data as regular sequencing-based SHAPE data obtained through normalization to a no-reagent control. Moreover, the selection efficiently enriches for probed RNAs, suggesting that the SHAPES strategy will be useful for applications with high-background and low-probing signal such as in vivo RNA structure probing. PMID:25805860

  16. Using cell monolayer rheology to probe average single cell mechanical properties.

    PubMed

    Sander, Mathias; Flesch, Julia; Ott, Albrecht

    2015-01-01

    The cell monolayer rheology technique consists of a commercial rotational rheometer that probes the mechanical properties of a monolayer of isolated cells. So far we have described properties of an entire monolayer. In this short communication, we show that we can deduce average single cell properties. Results are in very good agreement with earlier work on single cell mechanics. Our approach provides a mean of 105-106 adherent cells within a single experiment. This makes the results very reproducible. We extend our work on cell adhesion strength and deduce cell adhesion forces of fibroblast cells on fibronectin coated glass substrates.

  17. Probing the electronic structures and properties of neutral and charged monomethylated arsenic species (CH3As(n)((-1,0,+1)), n = 1-7) using Gaussian-3 theory.

    PubMed

    Bai, Xue; Zhang, Qiancheng; Yang, Jucai; Ning, Hongmei

    2012-09-20

    The structures and energies of neutral and charged monomethylated arsenic species CH(3)As(n)((-1,0,+1)) (n = 1-7) have been systematically investigated with the Gaussian-3 (G3) method. The ground-state structures of monomethylated arsenic species including the neutrals and the ions are vertex-methylated type. The lowest-energy structures of neutral methylated arsenic species and their ions can be viewed as being derived from corresponding to neutral and ionic arsenic clusters, respectively. The reliable electron affinities and ionization potentials of CH(3)As(n) have been evaluated. And there are odd-even alternations in both electron affinities and ionization potentials as a function of size of CH(3)As(n). The dissociation energies of CH(3) from neutral CH(3)As(n) and their ions have been calculated to examine relative stabilities. The results characterized the odd-numbered neutral CH(3)As(n) as more stable than the even-numbered systems, and the even-numbered cationic CH(3)As(n)(+) as more stable than the odd-numbered species with the exception of n = 1. The dissociation energy of CH(3)As(+) is the maximum among all of these values. There are no odd-even alternations for anionic CH(3)As(n)(-) with n ≤ 7.

  18. Remote Magnetic Actuation of Micrometric Probes for in situ 3D Mapping of Bacterial Biofilm Physical Properties

    PubMed Central

    Galy, Olivier; Zrelli, Kais; Latour-Lambert, Patricia; Kirwan, Lyndsey; Henry, Nelly

    2014-01-01

    Bacterial adhesion and growth on interfaces lead to the formation of three-dimensional heterogeneous structures so-called biofilms. The cells dwelling in these structures are held together by physical interactions mediated by a network of extracellular polymeric substances. Bacterial biofilms impact many human activities and the understanding of their properties is crucial for a better control of their development — maintenance or eradication — depending on their adverse or beneficial outcome. This paper describes a novel methodology aiming to measure in situ the local physical properties of the biofilm that had been, until now, examined only from a macroscopic and homogeneous material perspective. The experiment described here involves introducing magnetic particles into a growing biofilm to seed local probes that can be remotely actuated without disturbing the structural properties of the biofilm. Dedicated magnetic tweezers were developed to exert a defined force on each particle embedded in the biofilm. The setup is mounted on the stage of a microscope to enable the recording of time-lapse images of the particle-pulling period. The particle trajectories are then extracted from the pulling sequence and the local viscoelastic parameters are derived from each particle displacement curve, thereby providing the 3D-spatial distribution of the parameters. Gaining insights into the biofilm mechanical profile is essential from an engineer's point of view for biofilm control purposes but also from a fundamental perspective to clarify the relationship between the architectural properties and the specific biology of these structures. PMID:24837001

  19. Remote magnetic actuation of micrometric probes for in situ 3D mapping of bacterial biofilm physical properties.

    PubMed

    Galy, Olivier; Zrelli, Kais; Latour-Lambert, Patricia; Kirwan, Lyndsey; Henry, Nelly

    2014-05-02

    Bacterial adhesion and growth on interfaces lead to the formation of three-dimensional heterogeneous structures so-called biofilms. The cells dwelling in these structures are held together by physical interactions mediated by a network of extracellular polymeric substances. Bacterial biofilms impact many human activities and the understanding of their properties is crucial for a better control of their development - maintenance or eradication - depending on their adverse or beneficial outcome. This paper describes a novel methodology aiming to measure in situ the local physical properties of the biofilm that had been, until now, examined only from a macroscopic and homogeneous material perspective. The experiment described here involves introducing magnetic particles into a growing biofilm to seed local probes that can be remotely actuated without disturbing the structural properties of the biofilm. Dedicated magnetic tweezers were developed to exert a defined force on each particle embedded in the biofilm. The setup is mounted on the stage of a microscope to enable the recording of time-lapse images of the particle-pulling period. The particle trajectories are then extracted from the pulling sequence and the local viscoelastic parameters are derived from each particle displacement curve, thereby providing the 3D-spatial distribution of the parameters. Gaining insights into the biofilm mechanical profile is essential from an engineer's point of view for biofilm control purposes but also from a fundamental perspective to clarify the relationship between the architectural properties and the specific biology of these structures.

  20. Probing atmospheric structure with infrasonic ambient noise interferometry (Invited)

    NASA Astrophysics Data System (ADS)

    Haney, M. M.; Evers, L. G.; Fricke, J.

    2010-12-01

    Ambient noise interferometry attempts to reconstruct the impulse response of a linear system undergoing excitations by a random forcing. The method has proven to be quite general, finding applications in diverse fields such as ultrasonics, helioseismology, regional and global seismology, ocean acoustics, and exploration seismology. Due to the pervasive random forcing of microbaroms, the study of atmospheric infrasound can benefit from approaches developed in the field of interferometry as well. Moreover, continuous noise sources, such as microbaroms, provide a means to quantify the strong time-dependent changes inherent in the structure of the atmosphere. For pairs of infrasonic sensors separated by distances between 1 and 15 km, direct arrivals have been observed in long-time correlations of ambient noise from stations within 3 different networks: the network operated by the Alaska Volcano Observatory, the I53US array, and the Utah 07 experiment. As in seismic ambient noise studies, these interferometric arrivals show dispersive properties characteristic of guided wave propagation. As a result, infrasonic ambient noise interferometry can provide information on the gross structure of the atmospheric boundary layer. At Fourpeaked Volcano, Alaska, a surface-based temperature inversion produced a strong waveguide between two infrasound sensors. The propagation time of the interferometric arrivals shifted over the course of several days in close correspondence with regional temperature trends at nearby meteorological stations. Independent ECMWF data confirms the existence of a temperature inversion during this time period. Analysis of 4 infrasound sensors near Park City, Utah, further demonstrates the ability of infrasonic ambient noise interferometry to retrieve guided waves between stations separated by 5 to 10 km. Among the 4 stations, we observe strong interferometric arrivals on different station pairs at different times, attesting to variable atmospheric

  1. RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data.

    PubMed

    Incarnato, Danny; Neri, Francesco; Anselmi, Francesca; Oliviero, Salvatore

    2016-02-01

    The rapidly increasing number of discovered non-coding RNAs makes the understanding of their structure a key feature toward a deeper comprehension of gene expression regulation. Various enzymatic- and chemically- based approaches have been recently developed to allow whole-genome studies of RNA secondary structures. Several methods have been recently presented that allow high-throughput RNA structure probing (CIRS-seq, Structure-seq, SHAPE-seq, PARS, etc.) and unbiased structural inference of residues within RNAs in their native conformation. We here present an analysis toolkit, named RNA Structure Framework (RSF), which allows fast and fully-automated analysis of high-throughput structure probing data, from data pre-processing to whole-transcriptome RNA structure inference. RSF is written in Perl and is freely available under the GPLv3 license from http://rsf.hugef-research.org. salvatore.oliviero@hugef-torino.org Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  2. Analysis of sequencing data for probing RNA secondary structures and protein-RNA binding in studying posttranscriptional regulations.

    PubMed

    Hu, Xihao; Wu, Yang; Lu, Zhi John; Yip, Kevin Y

    2016-11-01

    High-throughput sequencing has been used to study posttranscriptional regulations, where the identification of protein-RNA binding is a major and fast-developing sub-area, which is in turn benefited by the sequencing methods for whole-transcriptome probing of RNA secondary structures. In the study of RNA secondary structures using high-throughput sequencing, bases are modified or cleaved according to their structural features, which alter the resulting composition of sequencing reads. In the study of protein-RNA binding, methods have been proposed to immuno-precipitate (IP) protein-bound RNA transcripts in vitro or in vivo By sequencing these transcripts, the protein-RNA interactions and the binding locations can be identified. For both types of data, read counts are affected by a combination of confounding factors, including expression levels of transcripts, sequence biases, mapping errors and the probing or IP efficiency of the experimental protocols. Careful processing of the sequencing data and proper extraction of important features are fundamentally important to a successful analysis. Here we review and compare different experimental methods for probing RNA secondary structures and binding sites of RNA-binding proteins (RBPs), and the computational methods proposed for analyzing the corresponding sequencing data. We suggest how these two types of data should be integrated to study the structural properties of RBP binding sites as a systematic way to better understand posttranscriptional regulations.

  3. Universal structural parameter to quantitatively predict metallic glass properties

    SciTech Connect

    Ding, Jun; Cheng, Yong-Qiang; Sheng, Howard; Asta, Mark; Ritchie, Robert O.; Ma, Evan

    2016-12-12

    Quantitatively correlating the amorphous structure in metallic glasses (MGs) with their physical properties has been a long-sought goal. Here we introduce flexibility volume' as a universal indicator, to bridge the structural state the MG is in with its properties, on both atomic and macroscopic levels. The flexibility volume combines static atomic volume with dynamics information via atomic vibrations that probe local configurational space and interaction between neighbouring atoms. We demonstrate that flexibility volume is a physically appropriate parameter that can quantitatively predict the shear modulus, which is at the heart of many key properties of MGs. Moreover, the new parameter correlates strongly with atomic packing topology, and also with the activation energy for thermally activated relaxation and the propensity for stress-driven shear transformations. These correlations are expected to be robust across a very wide range of MG compositions, processing conditions and length scales.

  4. Universal structural parameter to quantitatively predict metallic glass properties

    PubMed Central

    Ding, Jun; Cheng, Yong-Qiang; Sheng, Howard; Asta, Mark; Ritchie, Robert O.; Ma, Evan

    2016-01-01

    Quantitatively correlating the amorphous structure in metallic glasses (MGs) with their physical properties has been a long-sought goal. Here we introduce ‘flexibility volume' as a universal indicator, to bridge the structural state the MG is in with its properties, on both atomic and macroscopic levels. The flexibility volume combines static atomic volume with dynamics information via atomic vibrations that probe local configurational space and interaction between neighbouring atoms. We demonstrate that flexibility volume is a physically appropriate parameter that can quantitatively predict the shear modulus, which is at the heart of many key properties of MGs. Moreover, the new parameter correlates strongly with atomic packing topology, and also with the activation energy for thermally activated relaxation and the propensity for stress-driven shear transformations. These correlations are expected to be robust across a very wide range of MG compositions, processing conditions and length scales. PMID:27941922

  5. Universal structural parameter to quantitatively predict metallic glass properties

    DOE PAGES

    Ding, Jun; Cheng, Yong-Qiang; Sheng, Howard; ...

    2016-12-12

    Quantitatively correlating the amorphous structure in metallic glasses (MGs) with their physical properties has been a long-sought goal. Here we introduce flexibility volume' as a universal indicator, to bridge the structural state the MG is in with its properties, on both atomic and macroscopic levels. The flexibility volume combines static atomic volume with dynamics information via atomic vibrations that probe local configurational space and interaction between neighbouring atoms. We demonstrate that flexibility volume is a physically appropriate parameter that can quantitatively predict the shear modulus, which is at the heart of many key properties of MGs. Moreover, the new parametermore » correlates strongly with atomic packing topology, and also with the activation energy for thermally activated relaxation and the propensity for stress-driven shear transformations. These correlations are expected to be robust across a very wide range of MG compositions, processing conditions and length scales.« less

  6. Universal structural parameter to quantitatively predict metallic glass properties.

    PubMed

    Ding, Jun; Cheng, Yong-Qiang; Sheng, Howard; Asta, Mark; Ritchie, Robert O; Ma, Evan

    2016-12-12

    Quantitatively correlating the amorphous structure in metallic glasses (MGs) with their physical properties has been a long-sought goal. Here we introduce 'flexibility volume' as a universal indicator, to bridge the structural state the MG is in with its properties, on both atomic and macroscopic levels. The flexibility volume combines static atomic volume with dynamics information via atomic vibrations that probe local configurational space and interaction between neighbouring atoms. We demonstrate that flexibility volume is a physically appropriate parameter that can quantitatively predict the shear modulus, which is at the heart of many key properties of MGs. Moreover, the new parameter correlates strongly with atomic packing topology, and also with the activation energy for thermally activated relaxation and the propensity for stress-driven shear transformations. These correlations are expected to be robust across a very wide range of MG compositions, processing conditions and length scales.

  7. Universal structural parameter to quantitatively predict metallic glass properties

    NASA Astrophysics Data System (ADS)

    Ding, Jun; Cheng, Yong-Qiang; Sheng, Howard; Asta, Mark; Ritchie, Robert O.; Ma, Evan

    2016-12-01

    Quantitatively correlating the amorphous structure in metallic glasses (MGs) with their physical properties has been a long-sought goal. Here we introduce `flexibility volume' as a universal indicator, to bridge the structural state the MG is in with its properties, on both atomic and macroscopic levels. The flexibility volume combines static atomic volume with dynamics information via atomic vibrations that probe local configurational space and interaction between neighbouring atoms. We demonstrate that flexibility volume is a physically appropriate parameter that can quantitatively predict the shear modulus, which is at the heart of many key properties of MGs. Moreover, the new parameter correlates strongly with atomic packing topology, and also with the activation energy for thermally activated relaxation and the propensity for stress-driven shear transformations. These correlations are expected to be robust across a very wide range of MG compositions, processing conditions and length scales.

  8. Structure of the Ribosomal RNA Decoding Site Containing a Selenium-Modified Responsive Fluorescent Ribonucleoside Probe.

    PubMed

    Nuthanakanti, Ashok; Boerneke, Mark A; Hermann, Thomas; Srivatsan, Seergazhi G

    2017-03-01

    Comprehensive understanding of the structure-function relationship of RNA both in real time and at atomic level will have a profound impact in advancing our understanding of RNA functions in biology. Here, we describe the first example of a multifunctional nucleoside probe, containing a conformation-sensitive fluorophore and an anomalous X-ray diffraction label (5-selenophene uracil), which enables the correlation of RNA conformation and recognition under equilibrium and in 3D. The probe incorporated into the bacterial ribosomal RNA decoding site, fluorescently reports antibiotic binding and provides diffraction information in determining the structure without distorting native RNA fold. Further, by comparing solution binding data and crystal structure, we gained insight on how the probe senses ligand-induced conformational change in RNA. Taken together, our nucleoside probe represents a new class of biophysical tool that would complement available tools for functional RNA investigations.

  9. Simulation of Probe Position-Dependent Electron Energy-Loss Fine Structure

    SciTech Connect

    Oxley, M. P.; Kapetanakis, M. D.; Prange, Micah P.; Varela, M.; Pennycook, Stephen J.; Pantelides, Sokrates T.

    2014-03-31

    We present a theoretical framework for calculating probe-position-dependent electron energy-loss near-edge structure for the scanning transmission electron microscope by combining density functional theory with dynamical scattering theory. We show how simpler approaches to calculating near-edge structure fail to include the fundamental physics needed to understand the evolution of near-edge structure as a function of probe position and investigate the dependence of near-edge structure on probe size. It is within this framework that density functional theory should be presented, in order to ensure that variations of near-edge structure are truly due to local electronic structure and how much from the diffraction and focusing of the electron beam.

  10. Reproducible Analysis of Sequencing-Based RNA Structure Probing Data with User-Friendly Tools.

    PubMed

    Kielpinski, Lukasz Jan; Sidiropoulos, Nikolaos; Vinther, Jeppe

    2015-01-01

    RNA structure-probing data can improve the prediction of RNA secondary and tertiary structure and allow structural changes to be identified and investigated. In recent years, massive parallel sequencing has dramatically improved the throughput of RNA structure probing experiments, but at the same time also made analysis of the data challenging for scientists without formal training in computational biology. Here, we discuss different strategies for data analysis of massive parallel sequencing-based structure-probing data. To facilitate reproducible and standardized analysis of this type of data, we have made a collection of tools, which allow raw sequencing reads to be converted to normalized probing values using different published strategies. In addition, we also provide tools for visualization of the probing data in the UCSC Genome Browser and for converting RNA coordinates to genomic coordinates and vice versa. The collection is implemented as functions in the R statistical environment and as tools in the Galaxy platform, making them easily accessible for the scientific community. We demonstrate the usefulness of the collection by applying it to the analysis of sequencing-based hydroxyl radical probing data and comparing different normalization strategies. © 2015 Elsevier Inc. All rights reserved.

  11. Interface Properties of Wide Bandgap Semiconductor Structures

    DTIC Science & Technology

    1992-12-01

    Metal Contacts XIII. Chemical and Electrical Mechanisms in Titanium , Platinum, and 108 Hafnium Contacts to Alpha (6H) Silicon Carbide Atomic Layer...and (2) the negative electron affinity and formation of metal-diamond interfaces. The surface and interface properties are probed with STM, Raman ...show distinct I-V ch-act.risti,-, of the nuclei and the substrate. The presence of optical defects and the diamond quality are studied with micro- Raman

  12. Probing Y-shaped DNA structure with time-resolved FRET

    NASA Astrophysics Data System (ADS)

    Chatterjee, Subhasish; Lee, Jong Bum; Valappil, Nikesh V.; Luo, Dan; Menon, Vinod M.

    2012-02-01

    Self-assembly based on nucleic acid systems has become highly attractive for bottom-up fabrication of programmable matter due to the highly selective molecular recognition property of biomolecules. In this context, Y-shaped DNA (Y-DNA) provides an effective building block for forming unique self-assembled large-scale architectures. The dimension and growth of the nano- and microstructures depend significantly on the configurational stability of Y-DNA as a building block. Here we present structural studies of Y-DNA systems using a time-resolved FRET (Förster resonance energy transfer) technique. A fluorophore (Alexa 488) and an acceptor (DABCYL) were placed at two different ends of Y-DNA, and the lifetime of the fluorophore was measured to probe the relative distance between the donor and acceptor. Our results confirmed different distances between the arms of the Y-DNA and highlighted the overall structural integrity of the Y-DNA system as a leading building block for molecular self-assembly. Temperature dependent lifetime measurements indicated configurational changes in the overall Y-DNA nanoarchitecture above 40 °C.Self-assembly based on nucleic acid systems has become highly attractive for bottom-up fabrication of programmable matter due to the highly selective molecular recognition property of biomolecules. In this context, Y-shaped DNA (Y-DNA) provides an effective building block for forming unique self-assembled large-scale architectures. The dimension and growth of the nano- and microstructures depend significantly on the configurational stability of Y-DNA as a building block. Here we present structural studies of Y-DNA systems using a time-resolved FRET (Förster resonance energy transfer) technique. A fluorophore (Alexa 488) and an acceptor (DABCYL) were placed at two different ends of Y-DNA, and the lifetime of the fluorophore was measured to probe the relative distance between the donor and acceptor. Our results confirmed different distances between

  13. Transverse mechanical properties of cell walls of single living plant cells probed by laser-generated acoustic waves.

    PubMed

    Gadalla, Atef; Dehoux, Thomas; Audoin, Bertrand

    2014-05-01

    Probing the mechanical properties of plant cell wall is crucial to understand tissue dynamics. However, the exact symmetry of the mechanical properties of this anisotropic fiber-reinforced composite remains uncertain. For this reason, biologically relevant measurements of the stiffness coefficients on individual living cells are a challenge. For this purpose, we have developed the single-cell optoacoustic nanoprobe (SCOPE) technique, which uses laser-generated acoustic waves to probe the stiffness, thickness and viscosity of live single-cell subcompartments. This all-optical technique offers a sub-micrometer lateral resolution, nanometer in-depth resolution, and allows the non-contact measurement of the mechanical properties of live turgid tissues without any assumption of mechanical symmetry. SCOPE experiments reveal that single-cell wall transverse stiffness in the direction perpendicular to the epidermis layer of onion cells is close to that of cellulose. This observation demonstrates that cellulose microfibrils are the main load-bearing structure in this direction, and suggests strong bonding of microfibrils by hemicelluloses. Altogether our measurement of the viscosity at high frequencies suggests that the rheology of the wall is dominated by glass-like dynamics. From a comparison with literature, we attribute this behavior to the influence of the pectin matrix. SCOPE's ability to unravel cell rheology and cell anisotropy defines a new class of experiments to enlighten cell nano-mechanics.

  14. Probing Actinide Electronic Structure through Pu Cluster Calculations

    SciTech Connect

    Ryzhkov, Mickhail V.; Mirmelstein, Alexei; Yu, Sung-Woo; Chung, Brandon W.; Tobin, James G.

    2013-02-26

    The calculations for the electronic structure of clusters of plutonium have been performed, within the framework of the relativistic discrete-variational method. Moreover, these theoretical results and those calculated earlier for related systems have been compared to spectroscopic data produced in the experimental investigations of bulk systems, including photoelectron spectroscopy. Observation of the changes in the Pu electronic structure as a function of size provides powerful insight for aspects of bulk Pu electronic structure.

  15. Probing Actinide Electronic Structure through Pu Cluster Calculations

    DOE PAGES

    Ryzhkov, Mickhail V.; Mirmelstein, Alexei; Yu, Sung-Woo; ...

    2013-02-26

    The calculations for the electronic structure of clusters of plutonium have been performed, within the framework of the relativistic discrete-variational method. Moreover, these theoretical results and those calculated earlier for related systems have been compared to spectroscopic data produced in the experimental investigations of bulk systems, including photoelectron spectroscopy. Observation of the changes in the Pu electronic structure as a function of size provides powerful insight for aspects of bulk Pu electronic structure.

  16. Structural organization of mammalian prions as probed by limited proteolysis

    USDA-ARS?s Scientific Manuscript database

    The GPI- transgenic mouse model was used to study the structure of GPI- prions. We obtained valuable information about the structure of prions by performing limited proteolysis of the GPI- prions and analyzing the results by mass spectrometry and Western blot. This information coupled with previous ...

  17. Structure-Property Relationships of Solids in Pharmaceutical Processing

    NASA Astrophysics Data System (ADS)

    Chattoraj, Sayantan

    Pharmaceutical development and manufacturing of solid dosage forms is witnessing a seismic shift in the recent years. In contrast to the earlier days when drug development was empirical, now there is a significant emphasis on a more scientific and structured development process, primarily driven by the Quality-by-Design (QbD) initiatives of US Food and Drug Administration (US-FDA). Central to such an approach is the enhanced understanding of solid materials using the concept of Materials Science Tetrahedron (MST) that probes the interplay between four elements, viz., the structure, properties, processing, and performance of materials. In this thesis work, we have investigated the relationships between the structure and those properties of pharmaceutical solids that influence their processing behavior. In all cases, we have used material-sparing approaches to facilitate property assessment using very small sample size of materials, which is a pre-requisite in the early stages of drug development when the availability of materials, drugs in particular, is limited. The influence of solid structure, either at the molecular or bulk powder levels, on crystal plasticity and powder compaction, powder flow, and solid-state amorphization during milling, has been investigated in this study. Through such a systematic evaluation, we have captured the involvement of structure-property correlations within a wide spectrum of relevant processing behaviors of pharmaceutical solids. Such a holistic analysis will be beneficial for addressing both regulatory and scientific issues in drug development.

  18. Boron as a Probe of Stellar Structure and Mass Loss

    NASA Astrophysics Data System (ADS)

    Duncan, Douglas

    1991-07-01

    Observations of Boron, an easily destroyed element, will be used to probe processes which circulate or remove and destroy material in cool stars. These include mass loss, diffusion, meridional circulation, convective overshoot, and turbulence and rotationially-driven mixing. 1. The destruction of light elements in the sun is not understood but is a key to understanding internal mixing in cool stars. Alpha Centauri A and B will be measured to study mixing in stars respectively slightly more and less massive than the sun. Beta Hyi will be studied as an example of a 1.0 solar mass, partially evolved star. 2. The rates of mixing processes, especialy those which are expected to operate only on long timescales, will be studied by observing two stars in the intermediate age cluster NGC 752. One star will be from inside the "Lithium Gap" region in the F stars, and one star from outside the gap. 3. Two red giants and subgiants will be observed to help measure the amount of mass lost on the giant branch. . . . . . . . . . . . . . . . . . . . . . . NOTE: THIS PROPOSAL ONLY USES SIDE 2 OF THE GHRS. We are aware of the GHRS condition (as the P.I. is GHRS Instrument Scientist.)

  19. Structure, processing, and properties of potatoes

    NASA Technical Reports Server (NTRS)

    Lloyd, Isabel K.; Kolos, Kimberly R.; Menegaux, Edmond C.; Luo, Huy; Mccuen, Richard H.; Regan, Thomas M.

    1992-01-01

    The objective of this experiment and lesson intended for high school students in an engineering or materials science course or college freshmen is to demonstrate the relation between processing, structure, and thermodynamic and physical properties. The specific objectives are to show the effect of structure and structural changes on thermodynamic properties (specific heat) and physical properties (compressive strength); to illustrate the first law of thermodynamics; to compare boiling a potato in water with cooking it in a microwave in terms of the rate of structural change and the energy consumed to 'process' the potato; and to demonstrate compression testing.

  20. Photoexcited State Molecular Structures in Solution Studied by Pump-Probe XAFS

    NASA Astrophysics Data System (ADS)

    Chen, Lin

    2002-03-01

    The photoexcitation causes displacement of electron densities within or among molecules, which consequently leads to nuclear movements. Such nuclear displacements often occur in transient states with short lifetimes. Knowing transient molecular structures during photochemical reactions is important for understanding fundamental aspects of solar energy conversion and storage. Fast x-ray techniques provide direct probes for these transient structures. Using x-ray pulses from the Advanced Photon Source at Argonne, a laser pulse pump, x-ray pulse probe XAFS technique has been developed to capture transient molecular structures in disordered media with nanosecond time resolution. We have carried out several pump-probe XAFS measurements on 1)identifying a transient molecular structure of the photodissociation product of nickel-tetraphenylporphyrin with piperidine axial ligands (NiTPP-L2); 2)determination of the MLCT state structure of Bis(2,9-dimethyl-1,10-phenanthroline) Copper(I) [Cu(I)(dmp)2]+, and 3) triplet state molecular structures of metalloporphyrins. These studies not only prove the feasibility of the technique, but also gain structural information that otherwise will not be available. Future studies include probing transient structures in electron donor-acceptor complexes and optical polarization selected XAFS (OPS-XAFS) using the same technique with a 100-ps time resolution. This work is supported by the Division of Chemical Sciences, Office of Basic Energy Sciences, U. S. Department of Energy, under contract W-31-109-Eng-38.

  1. Probing Properties of Glassy Water and Other Liquids with Site Selective Spectroscopies

    SciTech Connect

    Dang, Nhan Chuong

    2005-01-01

    The standard non-photochemical hole burning (NPHB) mechanism, which involves phonon-assisted tunneling in the electronically excited state, was originally proposed to explain the light-induced frequency change of chemically stable molecules in glassy solids at liquid helium temperatures by this research group more than two decades ago. The NPHB mechanism was then further elucidated and the concept of intrinsic to glass configurational relaxation processes as pre-mediating step to the hole burning process was introduced. The latter provided the theoretical basis for NPHB to evolve into a powerful tool probing the dynamics and nature of amorphous media, which aside from ''simple'' inorganic glasses may include also ''complex'' biological systems such as living cells and cancerous/normal tissues. Presented in this dissertation are the experimental and theoretical results of hole burning properties of aluminum phthalocyanine tetrasulphonate (APT) in several different matrices: (1) hyperquenched glassy water (HGW); (2) cubic ice (Ic); and (3) water confined into poly(2-hydroxyethylmethacrylate) (poly-HEMA). In addition, results of photochemical hole burning (PHB) studies obtained for phthalocyanine tetrasulphonate (PcT) in HGW and free base phthalocyanine (Pc) in ortho-dichlorobenzene (DCB) glass are reported. The goal of this dissertation was to provide further evidence supporting the NPHB mechanism and to provide more insight that leads to a better understanding of the kinetic events (dynamics) in glasses, and various dynamical processes of different fluorescent chromorphores in various amorphous solids and the liquid that exist above the glass transition temperature (Tg). The following issues are addressed in detail: (1) time evolution of hole being burned under different conditions and in different hole burning systems; (2) temperature dependent hole profile; and (3) the structure/dynamics of water in confined space, which

  2. Nanoscale Structure and Spectroscopic Probing of Aβ1-40 Fibril Bundle Formation

    PubMed Central

    Psonka-Antonczyk, Katarzyna M.; Hammarström, Per; Johansson, Leif B. G.; Lindgren, Mikael; Stokke, Bjørn T.; Nilsson, K. Peter R.; Nyström, Sofie

    2016-01-01

    Amyloid plaques composed of fibrillar Amyloid-β (Aβ) are hallmarks of Alzheimer's disease. However, Aβ fibrils are morphologically heterogeneous. Conformation sensitive luminescent conjugated oligothiophenes (LCOs) are versatile tools for monitoring such fibril polymorphism in vivo and in vitro. Biophysical methods applied on in vitro generated Aβ fibrils, stained with LCOs with different binding and fluorescence properties, can be used to characterize the Aβ fibrillation in depth, far beyond that possible for in vivo generated amyloid plaques. In this study, in vitro fibrillation of the Aβ1-40 peptide was monitored by time-lapse transmission electron microscopy, LCO fluorescence, and atomic force microscopy. Differences in the LCO binding in combination with nanoscale imaging revealed that spectral variation correlated with fibrils transforming from solitary filaments (Ø~2.5 nm) into higher order bundled structures (Ø~5 nm). These detailed in vitro experiments can be used to derive data that reflects the heterogeneity of in vivo generated Aβ plaques observed by LCO fluorescence. Our work provides new structural basis for targeted drug design and molecular probe development for amyloid imaging. PMID:27921029

  3. Nanoscale structure and spectroscopic probing of Aβ1-40 fibril bundle formation

    NASA Astrophysics Data System (ADS)

    Psonka-Antonczyk, Katarzyna; Hammarström, Per; Johansson, Leif; Lindgren, Mikael; Stokke, Bjørn Torger; Nilsson, Peter; Nyström, Sofie

    2016-11-01

    Amyloid plaques composed of fibrillar Amyloid-β (Aβ) is a hallmark of Alzheimer’s disease. However, Aβ fibrils are morphologically heterogeneous. Conformation sensitive luminescent conjugated oligothiophenes (LCOs) are versatile tools for monitoring such fibril polymorphism in vivo and in vitro. Biophysical methods applied on in vitro generated Aβ fibrils, stained with LCOs with different binding and fluorescence properties, can be used to characterize the Aβ fibrillation in depth, far beyond that possible for in vivo generated amyloid plaques. In this study, in vitro fibrillation of the Aβ1-40 peptide was monitored by time-lapse transmission electron microscopy, LCO fluorescence and atomic force microscopy. Differences in the LCO binding in combination with nanoscale imaging revealed that spectral variation correlated with fibrils transforming from solitary filaments (Ø 2.5 nm) into higher order bundled structures (Ø 5 nm). These detailed in vitro experiments can be used to derive data that reflects the heterogeneity of in vivo generated Aβ plaques observed by LCO fluorescence. Our work provides new structural basis for targeted drug design and molecular probe development for amyloid imaging.

  4. A Study of the Structure of the Source Region of the Solar Wind in Support of a Solar Probe Mission

    NASA Technical Reports Server (NTRS)

    Habbal , Shadia R.

    1998-01-01

    Despite the richness of the information about the physical properties and the structure of the solar wind provided by the Ulysses and SOHO observations, fundamental questions regarding the nature of the coronal heating mechanisms, their source, and the manifestations of the fast and slow solar wind, still remain unanswered. The last unexplored frontier to establish the connection between the structure and dynamics of the solar atmosphere, its extension into interplanetary space, and the mechanisms responsible for the evolution of the solar wind, is the corona between 1 and 30 R(sub s). A Solar Probe mission offers an unprecedented opportunity to explore this frontier. The uniqueness of this mission stems from its trajectory in a plane perpendicular to the ecliptic which reaches within 9 R(sub s), of the solar surface over the poles and 3 - 9 R(sub s), at the equator. With a complement of simultaneous in situ and remote sensing observations, this mission is destined to have a significant impact on our understanding of the fundamental processes that heat the corona and drive the solar wind. The Solar Probe should be able to detect remnants and signatures of the processes which heat the corona and accelerate the solar wind. The primary objective of this proposal was to explore the structure of the different source regions of the solar wind through complementary observational and theoretical studies in support of a Solar Probe mission.

  5. Fluorescent probe environment and the structural and charge changes in energy coupling of mitochondrial membranes.

    PubMed

    Chance, B

    1970-10-01

    The use of fluorescent probes to give continuous readouts of the structural states of mitochondrial membranes during energy coupling seems a logical extension of their use in the study of protein structural changes. A clear correlation of the probes' fluorescence characteristics with the acquisition of energy coupling can be demonstrated in fragmented and natural membrane using 1-anilinonaphthalene-8-sulfonate (ANS) and ethidium bromide respectively. The present contribution attempts to bring together contemporary viewpoints of this and other laboratories and the recent experimental data and give some detailed information on probe environment and on the structural or charge changes occurring upon energization. The energy-dependent region of the membrane is located at an aqueous interface between an outer layer of proteins (presumably cytochromes) and the membrane permeability barrier; the aromatic portion of ANS appears to be located in the lipid phase and the sulfonic acid group in the aqueous phase. The aqueous phase is probably a structured water region near paramagnetic membrane components such as cytochrome. Membrane energization arising from altered redox potential changes of cytochromes (b(T)) is communicated to the water structure through altered structural states of the hemoproteins, causing a decreased volume of the structured water region and increased interaction with the paramagnetic components in the energized state. Attendant alterations of protonic equilibria of membrane components induce both local and transmembrane changes in charge distribution, with consequent movements of ions, including the probe molecules themselves.

  6. Structure and physical properties of silkworm cocoons

    PubMed Central

    Chen, Fujia; Porter, David; Vollrath, Fritz

    2012-01-01

    Silkworm cocoons have evolved a wide range of different structures and combinations of physical and chemical properties in order to cope with different threats and environmental conditions. We present our observations and measurements on 25 diverse types of cocoons in a first attempt to correlate physical properties with the structure and morphology of the cocoons. These two architectural parameters appear to be far more important than the material properties of the silk fibres themselves. We consider tensile and compressive mechanical properties and gas permeation of the cocoon walls, and in each case identify mechanisms or models that relate these properties to cocoon structure, usually based upon non-woven fibre composites. These properties are of relevance also for synthetic non-woven composite materials and our studies will help formulate bio-inspired design principles for new materials. PMID:22552916

  7. New hairpin-structured DNA probes: alternatives to classical molecular beacons

    NASA Astrophysics Data System (ADS)

    Friedrich, Achim; Habl, Gregor; Sauer, Markus; Wolfrum, Jürgen; Hoheisel, Jörg; Marmé, Nicole; Knemeyer, Jens-Peter

    2007-02-01

    In this article we report on two different classes of self-quenching hairpin-structured DNA probes that can be used as alternatives to Molecular Beacons. Compared to other hairpin-structured DNA probes, the so-called smart probes are labeled with only one extrinsic dye. The fluorescence of this dye is efficiently quenched by intrinsic guanine bases via a photo-induced electron transfer reaction in the closed hairpin. After hybridization to a target DNA, the distance between dye and the guanines is enlarged and the fluorescence is restored. The working mechanism of the second class of hairpin DNA probes is similar, but the probe oligonucleotide is labeled at both ends with an identical chromophore and thus the fluorescence of the closed hairpin is reduced due to formation of non-fluorescent dye dimers. Both types of probes are appropriate for the identification of single nucleotide polymorphisms and in combination with confocal single-molecule spectroscopy sensitivities in the picomolar range can be achieved.

  8. Bayesian hierarchical structured variable selection methods with application to molecular inversion probe studies in breast cancer

    PubMed Central

    Zhang, Lin; Baladandayuthapani, Veerabhadran; Mallick, Bani K.; Manyam, Ganiraju C.; Thompson, Patricia A.; Bondy, Melissa L.; Do, Kim-Anh

    2015-01-01

    Summary The analysis of alterations that may occur in nature when segments of chromosomes are copied (known as copy number alterations) has been a focus of research to identify genetic markers of cancer. One high-throughput technique recently adopted is the use of molecular inversion probes (MIPs) to measure probe copy number changes. The resulting data consist of high-dimensional copy number profiles that can be used to ascertain probe-specific copy number alterations in correlative studies with patient outcomes to guide risk stratification and future treatment. We propose a novel Bayesian variable selection method, the hierarchical structured variable selection (HSVS) method, which accounts for the natural gene and probe-within-gene architecture to identify important genes and probes associated with clinically relevant outcomes. We propose the HSVS model for grouped variable selection, where simultaneous selection of both groups and within-group variables is of interest. The HSVS model utilizes a discrete mixture prior distribution for group selection and group-specific Bayesian lasso hierarchies for variable selection within groups. We provide methods for accounting for serial correlations within groups that incorporate Bayesian fused lasso methods for within-group selection. Through simulations we establish that our method results in lower model errors than other methods when a natural grouping structure exists. We apply our method to an MIP study of breast cancer and show that it identifies genes and probes that are significantly associated with clinically relevant subtypes of breast cancer. PMID:25705056

  9. Infrared Pump-Probe Study of Nanoconfined Water Structure in Reverse Micelle.

    PubMed

    Lee, Jooyong; Maj, Michał; Kwak, Kyungwon; Cho, Minhaeng

    2014-10-02

    The influence of nanoconfinement on water structure is studied with time- and frequency-resolved vibrational spectroscopy of hydrazoic acid (HN3) encapsulated in reverse micelle. The azido stretch mode of HN3 is found to be a promising infrared probe for studying the structure and local hydrogen-bond environment of confined and interfacial water in reverse micelle due to its narrow spectral bandwidth and large transition dipole moment. The results show a clear separation between the core and shell spectral components, making it advantageous over the previously studied infrared probes. The measured vibrational lifetimes appear to be substantially different for the interfacial and bulk-like environments but show no remarkable size dependency, which indicates that water structures around this IR probe are distinctively different in the core and shell regions. The influence of local hydrogen bond network in the first and higher solvation shells on the vibrational dynamics of HN3 is further discussed.

  10. Probing Microarcsecond Structure in AGN using Continuous Flux Density Monitoring

    NASA Astrophysics Data System (ADS)

    Senkbeil, C.; Lovell, J.; Ellingsen, S.; Jauncey, D.; Cimò, G.

    2009-08-01

    Active Galactic Nuclei (AGN) exhibit radio flux density variability on a wide range of time scales from hours to years. The rapid cm-wavelength variability on timescales from hours to days has been shown to be caused by interstellar scintillation. Interstellar scintillation implies the presence of microarcsecond scale structure in the scintillating source. We have quasi-continuously monitored the 6.7 GHz flux density of six interstellar scintillating sources since 2003 using the University of Tasmania Ceduna Radio Telescope. The launch of the VSOP 2 ASTRO-G mission will allow us to compare the microarcsecond AGN structure at 22 and 43 GHz with microarcsecond structure implied by scintillation at 5 GHz using the Hobart Interferometer, which will supersede the Ceduna flux density monitoring program in 2009.

  11. Structure and electronic properties of lead-selenide nanocrystal solids

    NASA Astrophysics Data System (ADS)

    Whitham, Kevin

    Recent advances in the controlled formation of nanocrystal superlattices have potential for creating materials with properties by design. The ability to tune nanocrystal size, shape and composition as well as symmetry of the superlattice opens routes to new materials. Calculations of such materials predict interesting electronic phenomena including topological states and Dirac cones, however experimental support is lacking. We have investigated electron localization in nanocrystal superlattices using a combination of advanced structural characterization techniques and charge transport measurements. Recent experimental efforts to improve the electronic properties of nanocrystal solids have focused on increasing inter-dot coupling. However, this approach only leads to electronic bands if the coupling energy can overcome energetic and translational disorder. We have investigated oriented-attachment as a method to create nanocrystal superlattices with increased coupling and translational order. We show that epitaxially connected superlattices form by a coherent phase transformation that is sensitive to structural defects and ligand length. In order to measure intrinsic electronic properties we demonstrate control over electronic defects by tailoring surface chemistry and device architecture. To probe charge transport in these structures we performed variable temperature field-effect measurements. By integrating structure analysis, surface chemistry, and transport measurements we find that carriers are localized to a few superlattice constants due to disorder. Importantly, our analysis shows that greater delocalization is possible by optimizing dot-to-dot bonding, thus providing a path forward to create quantum dot solids in which theoretically predicted properties can be realized.

  12. Structural dynamics of N-propionyl-D-glucosamine probed by infrared spectroscopies and ab initio computations.

    PubMed

    Han, Chen; Zhao, Juan; Yang, Fan; Wang, Jianping

    2013-07-25

    N-Acylglucosamine is an important component in many oligosaccharides in eukaryotes, where it plays a very important biological role. Located between a glucose ring and an alkyl group of such species is an amide unit (-CONH-), which exhibits an infrared absorption band, mainly due to the C═O stretching, in the region of 1600-1700 cm(-1), similar to the amide-I band found in polypeptides. In this work, vibrational properties of such an "amide-I mode" in N-propionyl-d-glucosamine (GlcNPr) are examined in three typical solvents (water, methanol, and dimethylsulfoxide) by using steady-state infrared and femtosecond infrared dispersed pump-probe spectroscopies. As a result of solute-solvent interactions, multiple structured GlcNPr-solvent clusters are formed in water and methanol but are unlikely in dimethylsulfoxide. The vibrational relaxation rate of the amide-I mode is slightly frequency-dependent, supporting the presence of multiple solvated structures. Further, the amide-I lifetime is significantly shorter in GlcNPr than that in a well-known monopeptide, N-methylacetamide, which can be attributed to the presence of additional downstream vibrational modes caused by the sugar unit. Ab initio molecular dynamics simulations are used to reveal microscopic details of the first solvation shell of GlcNPr. Our results demonstrate that the amide-I mode in glucosamine exhibits both structural and solvent sensitivities that can be used to characterize the three-dimensional arrangement of sugar residues and their structural dynamics in glycopeptides.

  13. Probing RNA tertiary structure: interhelical crosslinking of the hammerhead ribozyme.

    PubMed Central

    Sigurdsson, S T; Tuschl, T; Eckstein, F

    1995-01-01

    Distinct structural models for the hammerhead ribozyme derived from single-crystal X-ray diffraction and fluorescence resonance energy transfer (FRET) measurements have been compared. Both models predict the same overall geometry, a wishbone shape with helices II and III nearly colinear and helix I positioned close to helix II. However, the relative orientations of helices I and II are different. To establish whether one of the models represents a kinetically active structure, a new crosslinking procedure was developed in which helices I and II of hammerhead ribozymes were disulfide-crosslinked via the 2' positions of specific sugar residues. Crosslinking residues on helices I and II that are close according to the X-ray structure did not appreciably reduce the catalytic efficiency. In contrast, crosslinking residues closely situated according to the FRET model dramatically reduced the cleavage rate by at least three orders of magnitude. These correlations between catalytic efficiencies and spatial proximities are consistent with the X-ray structure. PMID:7489517

  14. Probing local structure in glass by the application of shear

    NASA Astrophysics Data System (ADS)

    Weingartner, Nicholas B.; Nussinov, Zohar

    2016-09-01

    The glass transition remains one of the great unsolved mysteries of contemporary condensed matter physics. When crystallization is bypassed by rapid cooling, a supercooled liquid, retaining amorphous particle arrangement, results. The physical phenomenology of supercooled liquids is as vast as it is interesting. Most significant, the viscosity of the supercooled liquid displays an incredible increase over a narrow temperature range. Eventually, the supercooled liquid ceases to flow, becomes a glass, and gains rigidity and solid-like behaviors. Understanding what underpins the monumental growth of viscosity, and how rigidity results without long range order is a long-sought goal. Furthermore, discerning what role local structure plays in the kinetics of supercooled liquids remains an open question. Many theories of the glassy slowdown require the growth of static lengthscale related to structure with lowering of the temperature and provide a link between slowdown and propagation of ‘amorphous order’. In light of this, we examine the recently proposed shear penetration depth in the context of other length scales and its relation to local structure. We provide numerical data, based on the simulations of NiZr2, illustrating that this length scale exhibits dramatic growth upon approach to the glass transition and further discuss this in relation to percolating structural connectivity in similar glassforming systems.

  15. Cellulose nanomaterials review: structure, properties and nanocomposites.

    PubMed

    Moon, Robert J; Martini, Ashlie; Nairn, John; Simonsen, John; Youngblood, Jeff

    2011-07-01

    This critical review provides a processing-structure-property perspective on recent advances in cellulose nanoparticles and composites produced from them. It summarizes cellulose nanoparticles in terms of particle morphology, crystal structure, and properties. Also described are the self-assembly and rheological properties of cellulose nanoparticle suspensions. The methodology of composite processing and resulting properties are fully covered, with an emphasis on neat and high fraction cellulose composites. Additionally, advances in predictive modeling from molecular dynamic simulations of crystalline cellulose to the continuum modeling of composites made with such particles are reviewed (392 references).

  16. Variation of local atomic structure due to devitrification of Ni-Zr alloy thin films probed by EXAFS measurements

    SciTech Connect

    Bhattacharya, Debarati Basu, S.; Tiwari, Nidhi; Bhattacharyya, Dibyendu; Jha, S. N.

    2016-05-23

    Thin film metallic glasses (TFMGs) exhibit properties superior to their bulk counterparts allowing them to be potentially useful in many practical applications. Apart from their technological interest, when converted to crystallized state (devitrification) TFMGs can also act as precursors for partially crystallized or fully crystallized forms. Such devitrified forms are attractive due to their novel structural and magnetic properties. The amorphous-to-crystalline transformation of co-sputtered Ni-Zr alloy thin films through annealing was studied using EXAFS (Extended X-ray Absorption Fine Structure) measurements. Investigation through an atomic probe gives a better insight into the local environment of the atomic species, rendering a deeper understanding of thermal evolution of such materials.

  17. Black Hole Mergers as Probes of Structure Formation

    NASA Technical Reports Server (NTRS)

    Alicea-Munoz, Emily

    2008-01-01

    Observations of gravitational waves from massive black hole (MBH) mergers can provide us with important clues about the era of structure formation in the early universe. Previous research in this field has been limited to calculating merger rates of MBHs using different models where many assumptions are made about the specific values of physical parameters of the mergers, resulting in merger rate estimates that span 5 to 6 orders of magnitude. We develop a semi-analytical, phenomenological model that includes plausible combinations of several physical parameters involved in the mergers. which we then turn around to determine how well LISA observations will be able to enhance our understanding of the universe during the critical z approximately equal to 5-30 structure formation era. We do this by generating synthetic LISA observable data (masses, redshifts, merger rates), which are then analyzed using a Markov Chain Monte Carlo (MCMC) method. This allows us to constrain the physical parameters of the mergers.

  18. Black Hole Mergers as Probes of Structure Formation

    NASA Technical Reports Server (NTRS)

    Alicea-Munoz, Emily

    2008-01-01

    Observations of gravitational waves from massive black hole (MBH) mergers can provide us with important clues about the era of structure formation in the early universe. Previous research in this field has been limited to calculating merger rates of MBHs using different models where many assumptions are made about the specific values of physical parameters of the mergers, resulting in merger rate estimates that span 5 to 6 orders of magnitude. We develop a semi-analytical, phenomenological model that includes plausible combinations of several physical parameters involved in the mergers. which we then turn around to determine how well LISA observations will be able to enhance our understanding of the universe during the critical z approximately equal to 5-30 structure formation era. We do this by generating synthetic LISA observable data (masses, redshifts, merger rates), which are then analyzed using a Markov Chain Monte Carlo (MCMC) method. This allows us to constrain the physical parameters of the mergers.

  19. Deeper Probing of the Fine-structure Constant

    NASA Astrophysics Data System (ADS)

    Goradia, Shantilal

    2008-10-01

    In our earlier attempt in [1] to derive fine-structure constant, one subtle reason why the natural logarithm of the age of the universe in Planck times comes out to be slightly greater than the reciprocal of the fine structure constant is that the variable W in Boltzmann's expression should be the age of the universe in Planck times divided by the bit depth for our specific application. Since we cannot decode the nature's bit depth, we cannot come up with the expected value of ALPHA. For an assumed bit depth of 10, the reciprocal of ALPHA goes down by ln10 (2.3) without having a significant impact on the order of magnitude of the baud rate (baud rate = bits per second/bit depth = 10^43 (Planck time/second)/10 = 10^42). Use of terms and equations from informatics in both of author's interrelated abstracts this meeting is meant to engage a wider audience simply. [1] Goradia, Shantilal ``What is Fine-structure Constant?'' http://www.arXiv.org/pdf/physics/0210040v3.

  20. Nuclear magnetic resonance probes of membrane biophysics: Structure and dynamics

    NASA Astrophysics Data System (ADS)

    Leftin, Avigdor

    The phospholipid membrane is a self-assembled, dynamic molecular system that may exist alone in association with only water, or in complex systems comprised of multiple lipid types and proteins. In this dissertation the intra- and inter-molecular forces responsible for the atomistic, molecular and collective equilibrium structure and dynamics are studied by nuclear magnetic resonance spectroscopy (NMR). The multinuclear NMR measurements and various experimental techniques are able to provide data that enable the characterization of the hierarchical spatio-temporal organization of the phospholipid membrane. The experimental and theoretical studies conducted target membrane interactions ranging from model systems composed of only water and lipids, to multiple component domain forming membranes that are in association with peripheral and trans-membrane proteins. These measurements consisit of frequency spectrum lineshapes and nuclear-spin relaxation rates obtained using 2H NMR, 13C NMR, 31P NMR and 1H NMR. The changes of these experimental observables are interpreted within a statistical thermodynamic framework that allows the membrane structure, activation energies, and correlation times of motion to be determined. The cases presented demonstrate how fundamental principles of NMR spectroscopy may be applied to a host of membranes, leading to the biophysical characterization of membrane structure and dynamics.

  1. Cd in SnO: Probing structural effects on the electronic structure of doped oxide semiconductors through the electric field gradient at the Cd nucleus

    NASA Astrophysics Data System (ADS)

    Errico, Leonardo A.; Rentería, Mario; Petrilli, Helena M.

    2007-04-01

    We perform an ab initio study of the electric field gradient (EFG) at the nucleus of Cd impurities at substitutional Sn sites in crystalline SnO. The full-potential linearized-augmented plane wave and the projector augmented wave methods used here allow us to treat the electronic structure of the doped system and the atomic relaxations introduced by the impurities in the host in a fully self-consistent way using a supercell approach in a state-of-the-art way. Effects of the impurity charge state on the electronic and structural properties are also discussed. Since the EFG is a very subtle quantity, its determination is very useful to probe ground-state properties such as the charge density. We show that the EFG is very sensitive to structural relaxations induced by the impurity. Our theoretical predictions are compared with available experimental results.

  2. Multi-Probe Investigation of Proteomic Structure of Pathogens

    SciTech Connect

    Malkin, A J; Plomp, M; Leighton, T J; Vogelstein, B; Wheeler, K E

    2008-01-24

    Complete genome sequences are available for understanding biotransformation, environmental resistance and pathogenesis of microbial, cellular and pathogen systems. The present technological and scientific challenges are to unravel the relationships between the organization and function of protein complexes at cell, microbial and pathogens surfaces, to understand how these complexes evolve during the bacterial, cellular and pathogen life cycles, and how they respond to environmental changes, chemical stimulants and therapeutics. In particular, elucidating the molecular structure and architecture of human pathogen surfaces is essential to understanding mechanisms of pathogenesis, immune response, physicochemical interactions, environmental resistance and development of countermeasures against bioterrorist agents. The objective of this project was to investigate the architecture, proteomic structure, and function of bacterial spores through a combination of high-resolution in vitro atomic force microscopy (AFM) and AFM-based immunolabeling with threat-specific antibodies. Particular attention in this project was focused on spore forming Bacillus species including the Sterne vaccine strain of Bacillus anthracis and the spore forming near-neighbor of Clostridium botulinum, C. novyi-NT. Bacillus species, including B. anthracis, the causative agent of inhalation anthrax are laboratory models for elucidating spore structure/function. Even though the complete genome sequence is available for B. subtilis, cereus, anthracis and other species, the determination and composition of spore structure/function is not understood. Prof. B. Vogelstein and colleagues at the John Hopkins University have recently developed a breakthrough bacteriolytic therapy for cancer treatment (1). They discovered that intravenously injected Clostridium novyi-NT spores germinate exclusively within the avascular regions of tumors in mice and destroy advanced cancerous lesions. The bacteria were also

  3. Probing Temporal Structures in the Nonstationarity of Physiological Signals

    NASA Astrophysics Data System (ADS)

    Ivanov, Plamen Ch.; Bernaola-Galvan, Pedro; Amaral, Luis A. N.; Goldberger, Ary L.; Stanley, H. Eugene

    2000-03-01

    We ask if there is an element of complexity to the nonstationarity in physiological signals. We hypothesise that appearence of segments with different mean values in the signal is related to different physiologic responses to external stimuli. We focus on the statistical properties and temporal organization of segments in the signal with well defined mean, significantly different from the mean of the adjacent segments. For that we subdivide heartbeat time series in such a way as to maximize the difference in the mean values between adjacent segments. To identify different segments we develop a new technique based on the Student's statistics. We observe that the distribution of the lenghts of segments follows a power law for the data during wake activity from both healthy subjects and patients with congestive heart failure. Data from both groups during sleep showes a breakdown in this power-law behavior with a crossover at lenght at ≈ 300 beats.

  4. Microbial Nanowire Electronic Structure Probed by Scanning Tunneling Microscopy

    NASA Astrophysics Data System (ADS)

    Veazey, Joshua P.; Lampa-Pastirk, Sanela; Reguera, Gemma; Tessmer, Stuart H.

    2010-03-01

    Complex molecules produced by living organisms provide laboratories for interesting physical properties. The study of such interesting physics, likewise, gives new insight into intriguing biological processes. We have studied the pilus nanowires expressed by the bacterium, Geobacter sulfurreducens, using high resolution scanning tunneling microscopy (STM). G. sulfurreducens is a metal reducing bacterium that has evolved electrically conductive pili to efficiently transfer electrons across large distances.footnotetextG. Reguera, K.D. McCarthy, T. Mehta, J.S. Nicoll, M.T. Tuominen, and D.R. Lovley, Nature 435, 1098 (2005) Here we employ the electronic sensitivity of STM to resolve the molecular substructure and the local electronic density of states (LDOS) along the nanowire, in an effort to elucidate the mechanism of conduction. We observe LDOS dependent upon the location of the tip above the nanowire.

  5. Black Hole Mergers as Probes of Structure Formation

    NASA Technical Reports Server (NTRS)

    Alicea-Munoz, E.; Miller, M. Coleman

    2008-01-01

    Intense structure formation and reionization occur at high redshift, yet there is currently little observational information about this very important epoch. Observations of gravitational waves from massive black hole (MBH) mergers can provide us with important clues about the formation of structures in the early universe. Past efforts have been limited to calculating merger rates using different models in which many assumptions are made about the specific values of physical parameters of the mergers, resulting in merger rate estimates that span a very wide range (0.1 - 104 mergers/year). Here we develop a semi-analytical, phenomenological model of MBH mergers that includes plausible combinations of several physical parameters, which we then turn around to determine how well observations with the Laser Interferometer Space Antenna (LISA) will be able to enhance our understanding of the universe during the critical z 5 - 30 structure formation era. We do this by generating synthetic LISA observable data (total BH mass, BH mass ratio, redshift, merger rates), which are then analyzed using a Markov Chain Monte Carlo method. This allows us to constrain the physical parameters of the mergers. We find that our methodology works well at estimating merger parameters, consistently giving results within 1- of the input parameter values. We also discover that the number of merger events is a key discriminant among models. This helps our method be robust against observational uncertainties. Our approach, which at this stage constitutes a proof of principle, can be readily extended to physical models and to more general problems in cosmology and gravitational wave astrophysics.

  6. Probing Asymmetric Structures in the Outskirts of Galaxies

    NASA Astrophysics Data System (ADS)

    Wen, Zhang Zheng; Zheng, Xian Zhong; An, Fang Xia

    2014-06-01

    Upcoming large imaging surveys will allow detailed studies of the structure and morphology of galaxies aimed at addressing how galaxies form and evolve. Computational approaches are needed to characterize their morphologies over large samples. We introduce an automatic method to quantify the outer structure of galaxies. The key to our approach is the division of a galaxy image into two sections delineated by the isophote, which encloses half the total brightness of the galaxy. We call the central section the inner half-flux region (IHR) and the outer section the outer half-flux region (OHR). From this division, we derive two parameters: A o, which measures the asymmetry of the OHR, and D o, which measures the deviation of the intensity weighted centroid of the OHR from that of the IHR relative to the effective radius. We derive the two parameters from HST/ACS z 850-band images for a sample of 764 galaxies with z 850 < 22 mag and 0.35 < z < 0.9 selected from the GEMS and GOODS-South surveys. We show that the sample galaxies having strong asymmetric structures, particularly tidal tails, are well-separated from those with regular morphologies in the A o-D o space. Meanwhile, the widely used CAS and Gini-M 20 methods turn out to be insensitive to such morphological features. We stress that the A o-D o method is an efficient way to select galaxies with significant asymmetric features like tidal tails and study galaxy mergers in the dynamical phase traced by these delicate features.

  7. Probing ionospheric structures using the LOFAR radio telescope

    NASA Astrophysics Data System (ADS)

    Mevius, M.; van der Tol, S.; Pandey, V. N.; Vedantham, H. K.; Brentjens, M. A.; de Bruyn, A. G.; Abdalla, F. B.; Asad, K. M. B.; Bregman, J. D.; Brouw, W. N.; Bus, S.; Chapman, E.; Ciardi, B.; Fernandez, E. R.; Ghosh, A.; Harker, G.; Iliev, I. T.; Jelić, V.; Kazemi, S.; Koopmans, L. V. E.; Noordam, J. E.; Offringa, A. R.; Patil, A. H.; van Weeren, R. J.; Wijnholds, S.; Yatawatta, S.; Zaroubi, S.

    2016-07-01

    LOFAR is the LOw-Frequency Radio interferometer ARray located at midlatitude (52°53'N). Here we present results on ionospheric structures derived from 29 LOFAR nighttime observations during the winters of 2012/2013 and 2013/2014. We show that LOFAR is able to determine differential ionospheric total electron content values with an accuracy better than 0.001 total electron content unit = 1016m-2 over distances ranging between 1 and 100 km. For all observations the power law behavior of the phase structure function is confirmed over a long range of baseline lengths, between 1 and 80 km, with a slope that is, in general, larger than the 5/3 expected for pure Kolmogorov turbulence. The measured average slope is 1.89 with a one standard deviation spread of 0.1. The diffractive scale, i.e., the length scale where the phase variance is 1rad2, is shown to be an easily obtained single number that represents the ionospheric quality of a radio interferometric observation. A small diffractive scale is equivalent to high phase variability over the field of view as well as a short time coherence of the signal, which limits calibration and imaging quality. For the studied observations the diffractive scales at 150 MHz vary between 3.5 and 30 km. A diffractive scale above 5 km, pertinent to about 90% of the observations, is considered sufficient for the high dynamic range imaging needed for the LOFAR epoch of reionization project. For most nights the ionospheric irregularities were anisotropic, with the structures being aligned with the Earth magnetic field in about 60% of the observations.

  8. Predicting EMIC wave properties from ring current conditions observed by Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Jordanova, V.; Fu, X.; Cowee, M.; Gary, S. P.; Winske, D.; Reeves, G. D.

    2016-12-01

    Recently, we have developed a model to predict amplitude and spectrum of the electromagnetic ion cyclotron (EMIC) wave from the anisotropic ring current ion distributions. The model is derived from linear theory and nonlinear hybrid simulations in a large parameter space for homogeneous plasmas consisting of electrons, protons, and helium ions. In this study we apply our model to selected EMIC events observed by Van Allen Probes satellites. Using the plasma conditions measured by the HOPE instrument, we predict EMIC properties and compare them to wave measurements by the EMFISIS instrument. Detailed analysis of these events will be shown.

  9. Wetting properties of AFM probes by means of contact angle measurement

    NASA Astrophysics Data System (ADS)

    Tao, Zhenhua; Bhushan, Bharat

    2006-09-01

    An atomic force microscopy (AFM) based technique was developed to measure the wetting properties of probe tips. By advancing and receding the AFM tip across the water surface, the meniscus force between the tip and the liquid was measured at the tip-water separation. The water contact angle was determined from the meniscus force. The obtained contact angle results were compared with that by the sessile drop method. It was found that the AFM based technique provided higher contact angle values than the sessile drop method. The mechanisms responsible for the difference are discussed.

  10. Spectral and photophysical properties of intramolecular charge transfer fluorescence probe: 4'-Dimethylamino-2,5-dihydroxychalcone

    NASA Astrophysics Data System (ADS)

    Xu, Zhicheng; Bai, Guan; Dong, Chuan

    2005-12-01

    The spectral and photophysical properties of a new intramolecular charge transfer (ICT) probe, namely 4'-dimethylamino-2,5-dihydroxychalcone (DMADHC) were studied in different solvents by using steady-state absorption and emission spectroscopy. Whereas the absorption spectrum undergoes minor change with increasing polarity of the solvents, the fluorescence spectrum experiences a distinct bathochromic shift in the band position and the fluorescence quantum yield increases reaching a maximum before decrease with increasing the solvent polarity. The magnitude of change in the dipole moment was calculated based on the Lippert-Mataga equation. These results give the evidence about the intramolecular charge transfer character in the emitting singlet state of this compound.

  11. Probing and extracting the structure of vibrating SF6 molecules with inner-shell photoelectrons

    NASA Astrophysics Data System (ADS)

    Nguyen, Ngoc-Ty; Lucchese, R. R.; Lin, C. D.; Le, Anh-Thu

    2016-06-01

    We propose a scheme for probing the structure of vibrating molecules with photoelectrons generated from ultrashort soft-x-ray pulses. As an example we analyze below-100-eV photoelectrons liberated from the S (2 p ) orbital of vibrating SF6 molecules to image very small structural changes of molecular vibration. In particular, photoionization cross sections and photoelectron angular distributions (PAD) at nonequilibrium geometries can be retrieved accurately with photoelectrons near the shape resonance at 13 eV. This is achieved with a pump-probe scheme, in which the symmetric stretch mode is first Raman excited predominantly by a relatively short laser pulse and then later probed at different time delays by a few-femtosecond soft-x-ray pulse with photon energy near 200 eV.

  12. Genome-Wide Probing of RNA Structures In Vitro Using Nucleases and Deep Sequencing.

    PubMed

    Wan, Yue; Qu, Kun; Ouyang, Zhengqing; Chang, Howard Y

    2016-01-01

    RNA structure probing is an important technique that studies the secondary and tertiary conformations of an RNA. While it was traditionally performed on one RNA at a time, recent advances in deep sequencing has enabled the secondary structure mapping of thousands of RNAs simultaneously. Here, we describe the method Parallel Analysis for RNA Structures (PARS), which couples double and single strand specific nuclease probing to high throughput sequencing. Upon cloning of the cleavage sites into a cDNA library, deep sequencing and mapping of reads to the transcriptome, the position of paired and unpaired bases along cellular RNAs can be identified. PARS can be performed under diverse solution conditions and on different organismal RNAs to provide genome-wide RNA structural information. This information can also be further used to constrain computational predictions to provide better RNA structure models under different conditions.

  13. Progress and challenges for chemical probing of RNA structure inside living cells

    PubMed Central

    Kubota, Miles; Tran, Catherine; Spitale, Robert C

    2016-01-01

    Proper gene expression is essential for the survival of every cell. Once thought to be a passive transporter of genetic information, RNA has recently emerged as a key player in nearly every pathway in the cell. A full description of its structure is critical to understanding RNA function. Decades of research have focused on utilizing chemical tools to interrogate the structures of RNAs, with recent focus shifting to performing experiments inside living cells. This Review will detail the design and utility of chemical reagents used in RNA structure probing. We also outline how these reagents have been used to gain a deeper understanding of RNA structure in vivo. We review the recent merger of chemical probing with deep sequencing. Finally, we outline some of the hurdles that remain in fully characterizing the structure of RNA inside living cells, and how chemical biology can uniquely tackle such challenges. PMID:26575240

  14. Determinants of Long Bone Structural Properties

    NASA Technical Reports Server (NTRS)

    Cleek, T. M.; Katz, B.; Whalen, R. T.; Wade, Charles E. (Technical Monitor)

    1994-01-01

    The objective of our research is to determine whether a non-invasive determination of long bone cross-sectional areal properties using only the mineral component of bone accurately predicts the true structural properties. In this study section properties of a whole long bone were compared using two methods: (1) special analysis of bone densitometry data, and (2) experimental determination of flexural rigidities from bone surface strain measurements during controlled loading.

  15. Design, synthesis, and characterization of novel nanowire structures for photovoltaics and intracellular probes*

    PubMed Central

    Lieber, Charles M.

    2012-01-01

    Semiconductor nanowires (NWs) represent a unique system for exploring phenomena at the nanoscale and are expected to play a critical role in future electronic, optoelectronic, and miniaturized biomedical devices. Modulation of the composition and geometry of nanostructures during growth could encode information or function, and realize novel applications beyond the conventional lithographical limits. This review focuses on the fundamental science aspects of the bottom-up paradigm, which are synthesis and physical property characterization of semiconductor NWs and NW heterostructures, as well as proof-of-concept device concept demonstrations, including solar energy conversion and intracellular probes. A new NW materials synthesis is discussed and, in particular, a new “nanotectonic” approach is introduced that provides iterative control over the NW nucleation and growth for constructing 2D kinked NW superstructures. The use of radial and axial p-type/intrinsic/n-type (p-i-n) silicon NW (Si-NW) building blocks for solar cells and nanoscale power source applications is then discussed. The critical benefits of such structures and recent results are described and critically analyzed, together with some of the diverse challenges and opportunities in the near future. Finally, results are presented on several new directions, which have recently been exploited in interfacing biological systems with NW devices. PMID:22707797

  16. Excited state X-ray absorption spectroscopy: Probing both electronic and structural dynamics.

    PubMed

    Neville, Simon P; Averbukh, Vitali; Ruberti, Marco; Yun, Renjie; Patchkovskii, Serguei; Chergui, Majed; Stolow, Albert; Schuurman, Michael S

    2016-10-14

    We investigate the sensitivity of X-ray absorption spectra, simulated using a general method, to properties of molecular excited states. Recently, Averbukh and co-workers [M. Ruberti et al., J. Chem. Phys. 140, 184107 (2014)] introduced an efficient and accurate L(2) method for the calculation of excited state valence photoionization cross-sections based on the application of Stieltjes imaging to the Lanczos pseudo-spectrum of the algebraic diagrammatic construction (ADC) representation of the electronic Hamiltonian. In this paper, we report an extension of this method to the calculation of excited state core photoionization cross-sections. We demonstrate that, at the ADC(2)x level of theory, ground state X-ray absorption spectra may be accurately reproduced, validating the method. Significantly, the calculated X-ray absorption spectra of the excited states are found to be sensitive to both geometric distortions (structural dynamics) and the electronic character (electronic dynamics) of the initial state, suggesting that core excitation spectroscopies will be useful probes of excited state non-adiabatic dynamics. We anticipate that the method presented here can be combined with ab initio molecular dynamics calculations to simulate the time-resolved X-ray spectroscopy of excited state molecular wavepacket dynamics.

  17. Design, synthesis, and characterization of novel nanowire structures for photovoltaics and intracellular probes.

    PubMed

    Tian, Bozhi; Lieber, Charles M

    2011-01-01

    Semiconductor nanowires (NWs) represent a unique system for exploring phenomena at the nanoscale and are expected to play a critical role in future electronic, optoelectronic, and miniaturized biomedical devices. Modulation of the composition and geometry of nanostructures during growth could encode information or function, and realize novel applications beyond the conventional lithographical limits. This review focuses on the fundamental science aspects of the bottom-up paradigm, which are synthesis and physical property characterization of semiconductor NWs and NW heterostructures, as well as proof-of-concept device concept demonstrations, including solar energy conversion and intracellular probes. A new NW materials synthesis is discussed and, in particular, a new "nanotectonic" approach is introduced that provides iterative control over the NW nucleation and growth for constructing 2D kinked NW superstructures. The use of radial and axial p-type/intrinsic/n-type (p-i-n) silicon NW (Si-NW) building blocks for solar cells and nanoscale power source applications is then discussed. The critical benefits of such structures and recent results are described and critically analyzed, together with some of the diverse challenges and opportunities in the near future. Finally, results are presented on several new directions, which have recently been exploited in interfacing biological systems with NW devices.

  18. Excited state X-ray absorption spectroscopy: Probing both electronic and structural dynamics

    NASA Astrophysics Data System (ADS)

    Neville, Simon P.; Averbukh, Vitali; Ruberti, Marco; Yun, Renjie; Patchkovskii, Serguei; Chergui, Majed; Stolow, Albert; Schuurman, Michael S.

    2016-10-01

    We investigate the sensitivity of X-ray absorption spectra, simulated using a general method, to properties of molecular excited states. Recently, Averbukh and co-workers [M. Ruberti et al., J. Chem. Phys. 140, 184107 (2014)] introduced an efficient and accurate L 2 method for the calculation of excited state valence photoionization cross-sections based on the application of Stieltjes imaging to the Lanczos pseudo-spectrum of the algebraic diagrammatic construction (ADC) representation of the electronic Hamiltonian. In this paper, we report an extension of this method to the calculation of excited state core photoionization cross-sections. We demonstrate that, at the ADC(2)x level of theory, ground state X-ray absorption spectra may be accurately reproduced, validating the method. Significantly, the calculated X-ray absorption spectra of the excited states are found to be sensitive to both geometric distortions (structural dynamics) and the electronic character (electronic dynamics) of the initial state, suggesting that core excitation spectroscopies will be useful probes of excited state non-adiabatic dynamics. We anticipate that the method presented here can be combined with ab initio molecular dynamics calculations to simulate the time-resolved X-ray spectroscopy of excited state molecular wavepacket dynamics.

  19. Probing the temperature dependence of the mechanical properties of polymers at the nanoscale with band excitation thermal scanning probe microscopy.

    PubMed

    Nikiforov, M P; Jesse, S; Morozovska, A N; Eliseev, E A; Germinario, L T; Kalinin, S V

    2009-09-30

    Understanding local mechanisms for temperature-induced phase transitions in polymers requires quantitative measurements of the thermomechanical behavior, including glass transition and melting temperatures as well as temperature dependent elastic and loss modulus and thermal expansion coefficients in nanoscale volumes. Here, we demonstrate an approach for probing local thermal phase transitions based on the combination of thermal field confinement by a heated SPM probe and multi-frequency thermomechanical detection. The local measurement of the glass transition temperature is demonstrated and the detection limits are established.

  20. Probing Atomic Dynamics and Structures Using Optical Patterns

    NASA Astrophysics Data System (ADS)

    Schmittberger, Bonnie L.; Gauthier, Daniel J.

    2015-05-01

    Pattern formation is a widely studied phenomenon that can provide fundamental insights into nonlinear systems. Emergent patterns in cold atoms are of particular interest in condensed matter physics and quantum information science because one can relate optical patterns to spatial structures in the atoms. In our experimental system, we study multimode optical patterns generated from a sample of cold, thermal atoms. We observe this nonlinear optical phenomenon at record low input powers due to the highly nonlinear nature of the spatial bunching of atoms in an optical lattice. We present a detailed study of the dynamics of these bunched atoms during optical pattern formation. We show how small changes in the atomic density distribution affect the symmetry of the generated patterns as well as the nature of the nonlinearity that describes the light-atom interaction. We gratefully acknowledge the financial support of the National Science Foundation through Grant #PHY-1206040.

  1. Probing the Density Structure of 48 Librae's Circumstellar Disk

    NASA Astrophysics Data System (ADS)

    Silaj, J.; Jones, C. E.; Carciofi, A. C.; Escolano, C.; Tycner, C.

    2016-11-01

    48 Librae is a well-known Be shell star that exhibits spectacular cyclic V/R asymmetries in its Balmer emission lines. In this work, we use the HDUST code to investigate the disk density structure required to produce this signature. By modelling one representative Hα profile, we obtain the two initial densities required to match each peak, and from this we infer the average initial disk density. Furthermore, we investigate the parameters of the central star by modelling the SED, and we constrain the inclination angle of the system with polarization measurements. We find 48 Lib is best represented by a B3V central star surrounded by a very dense disk with an average initial density of 1.1×10-10 g cm-3, and that the system is oriented at 85°.

  2. Macromolecular properties and polymeric structure of canine tracheal mucins.

    PubMed Central

    Shankar, V; Virmani, A K; Naziruddin, B; Sachdev, G P

    1991-01-01

    Two high-Mr mucus glycoproteins (mucins), CTM-A and CTM-B, were highly purified from canine tracheal pouch secretions, and their macromolecular properties as well as polymeric structure were investigated. On SDS/composite-gel electrophoresis, a diffuse band was observed for each mucin. Polyacrylamide-gel electrophoresis using 6% gels also showed the absence of low-Mr contaminants in the mucins. Comparison of chemical and amino acid compositions revealed significant differences between the two mucins. Using a static-laser-light-scattering technique, CTM-A and CTM-B were found to have weight-average Mr values of about 11.0 x 10(6) and 1.4 x 10(6) respectively. Both mucins showed concentration-dependent aggregation in buffer containing 6 M-guanidine hydrochloride. Under similar experimental conditions, reduced-alkylated CTM-A had an Mr of 5.48 x 10(6) and showed no concentration-dependent aggregation. Hydrophobic properties of the mucins, investigated by the fluorescent probe technique using mansylphenylalanine as the probe, showed the presence of a large number of low-affinity (KD approx. 10(5) M) binding sites. These sites appeared to be located on the non-glycosylated regions of the protein core, since Pronase digestion of the mucins almost completely eliminated probe binding. Reduction of disulphide bonds of CTM-A and CTM-B did not significantly alter the probe-binding properties. Also, addition of increasing NaCl concentrations (0.03-1.0 M) to the buffer caused only a small change in the hydrophobic properties of native and reduced-alkylated mucins. CTM-A was deglycosylated, without notable in the hydrophobic properties of native and reduced-alkylated mucins. CTM-A was deglycosylated, without notable degradation, using a combination of chemical and enzymic methods. On SDS/PAGE the protein core was estimated to have an Mr of approx. 60,000. On the basis of the protein and carbohydrate contents of the major mucin CTM-A, the mucin monomer was calculated to have an

  3. Probing nuclear bubble structure via neutron star asteroseismology

    NASA Astrophysics Data System (ADS)

    Sotani, Hajime; Iida, Kei; Oyamatsu, Kazuhiro

    2017-01-01

    We consider torsional oscillations that are trapped in a layer of spherical-hole (bubble) nuclear structure, which is expected to occur in the deepest region of the inner crust of a neutron star. Because this layer intervenes between the phase of slab nuclei and the outer core of uniform nuclear matter, torsional oscillations in the bubble phase can be excited separately from usual crustal torsional oscillations. We find from eigenmode analyses for various models of the equation of state of uniform nuclear matter that the fundamental frequencies of such oscillations are almost independent of the incompressibility of symmetric nuclear matter, but strongly depend on the slope parameter of the nuclear symmetry energy L. Although the frequencies are also sensitive to the entrainment effect, i.e. what portion of nucleons outside bubbles contribute to the oscillations, by having such a portion fixed, we can successfully fit the calculated fundamental frequencies of torsional oscillations in the bubble phase inside a star of specific mass and radius as a function of L. By comparing the resultant fitting formula to the frequencies of quasi-periodic oscillations (QPOs) observed from the soft-gamma repeaters, we find that each of the observed low-frequency QPOs can be identified either as a torsional oscillation in the bubble phase or as a usual crustal oscillation, given generally accepted values of L for all the stellar models are considered here.

  4. Probing structural heterogeneities and conformational fluctuations of biopolymers

    SciTech Connect

    Laurence, T; Kong, X; Jaeger, M; Weiss, S

    2004-12-15

    We study protein and nucleic acid structure and dynamics using single-molecule fluorescence resonance energy transfer measurements with alternating-laser excitation. Freely diffusing molecules are sorted into subpopulations based on stoichiometry, detecting donor and acceptor coincidence for periods over 100 {micro}s-1 ms. Faster (< 100 {micro}s) fluctuating distance distributions are studied within these subpopulations using time-resolved single photon counting measurements. We find that short double-stranded DNA (dsDNA) is more flexible than expected from persistence lengths measured on long dsDNA. We find that the electrostatic portion of the persistence length of single-stranded poly-dT varies as the ionic strength (I) to the -1/2 power (I{sup -1/2}). Lastly, we find that the unfolded protein Chymotrypsin Inhibitor 2 (CI2) is unstructured at high denaturant. However, in the presence of folded CI2 (at lower denaturant), unfolded CI2 is more compact and displays larger distance fluctuations, possibly due to unsuccessful attempts to cross the folding barrier.

  5. CO ROVIBRATIONAL EMISSION AS A PROBE OF INNER DISK STRUCTURE

    SciTech Connect

    Salyk, C.; Blake, G. A.; Boogert, A. C. A.; Brown, J. M.

    2011-12-20

    We present an analysis of CO emission lines from a sample of T Tauri, Herbig Ae/Be, and transitional disks with known inclinations in order to study the structure of inner disk molecular gas. We calculate CO inner radii by fitting line profiles with a simple parameterized model. We find that, for optically thick disks, CO inner radii are strongly correlated with the total system luminosity (stellar plus accretion) and consistent with the dust sublimation radius. Transitional disk inner radii show the same trend with luminosity, but are systematically larger. Using rotation diagram fits, we derive, for classical T Tauri disks, emitting areas consistent with a ring of width {approx}0.15 AU located at the CO inner radius; emitting areas for transitional disks are systematically smaller. We also measure lower rotational temperatures for transitional disks, and disks around Herbig Ae/Be stars, than for those around T Tauri stars. Finally, we find that rotational temperatures are similar to, or slightly lower than, the expected temperature of blackbody grains located at the CO inner radius, in contrast to expectations of thermal decoupling between gas and dust.

  6. High-precision measurements of planetary spin states as probes of interior structure and processes (Invited)

    NASA Astrophysics Data System (ADS)

    Margot, J.

    2009-12-01

    Profound developments in our understanding of the Earth and Moon have arisen as a direct outcome of rotation studies (e.g., Munk and MacDonald 1960, Lambeck 1980, Wahr 1988, Dickey et al 1994). Measurements of planetary rotation provide powerful probes of planetary interior structure and processes. I will discuss ongoing observations at Mercury, Venus, and Titan, as well as future prospects for other bodies. Observations of radar speckle patterns tied to the rotation of Mercury establish that the planet occupies a Cassini state with obliquity 2.11 +/- 0.1 arcminutes. The measurements show that the planet exhibits librations in longitude that are forced at the 88-day orbital period, as predicted by theory. The amplitude of the oscillations together with spacecraft determinations of the gravitational harmonic coefficient C22 indicates that the mantle of Mercury is decoupled from a core that is at least partially molten. Departures from the exact Cassini state and long-term libration signatures can inform us about core-mantle interactions. New Cassini radar measurements of the spin state of Titan (Stiles et al 2008) can be most readily interpreted as evidence that Titan closely follows a Cassini state. Peale (1969) has shown that, in that state, a clear relationship exists between obliquity and moment of inertia differences. Application of this relationship to Titan in conjunction with measurements of the gravitational harmonic C22 yields a polar moment of inertia that exceeds the 2/5 value for a uniform density sphere, perhaps indicative of a decoupling between core and outer layer, as in Mercury. Libration measurements at Titan require new instrumentation but can provide superb probes of interior structure and dynamical interactions between layers. This also applies to Galilean satellites (Comstock and Bills 2003, Van Hoolst et al 2008). Ongoing measurements of length-of-day variations at Venus are most easily attributed to angular momentum exchange between

  7. Structural properties of compact groups

    NASA Technical Reports Server (NTRS)

    De Carvalho, R. R.; Ribeiro, A. L. B.; Zepf, Stephen E.

    1994-01-01

    We report the results of a systematic study of galaxies in the regions of Hickson compact groups. Our sample is composed of the 22 Hickson groups which are located in the southern hemisphere and have cz less than 9000 km/s. Making use of digitized images of IIIa-J plates that cover an area of 0.5 x 0.5 deg around each group, we were able to detect and classify images down to a magnitude limit of 19.5 in the B band. This limit is typically three magnitudes fainter than previous studies. Most groups show a statistically significant excess of fainter galaxies compared to the background. These fainter galaxies typically have a somewhat more extended spatial distribution than the brighter galaxies originally classified by Hickson. Our data suggest that Hickson groups have a wide range in density and radius, ranging from very compact structures with overdensities of the order of 10(exp 2) and crossing times of roughly 0.01 H(sub 0 sup -1), to much more diffuse structures, similar to loose groups, with overdensities of about 3 and crossing times of roughly 0.5 H(sub 0 sup -1).

  8. Probing the structure of the S105 hole.

    PubMed

    To, Kam H; Young, Ry

    2014-11-01

    For most phages, holins control the timing of host lysis. During the morphogenesis period of the infection cycle, canonical holins accumulate harmlessly in the cytoplasmic membrane until they suddenly trigger to form lethal lesions called holes. The holes can be visualized by cryo-electron microscopy and tomography as micrometer-scale interruptions in the membrane. To explore the fine structure of the holes formed by the lambda holin, S105, a cysteine-scanning accessibility study was performed. A collection of S105 alleles encoding holins with a single Cys residue in different positions was developed and characterized for lytic function. Based on the ability of 4-acetamido-4'-((iodoacetyl) amino) stilbene-2,2'-disulfonic acid, disodium salt (IASD), to modify these Cys residues, one face of transmembrane domain 1 (TMD1) and TMD3 was judged to face the lumen of the S105 hole. In both cases, the lumen-accessible face was found to correspond to the more hydrophilic face of the two TMDs. Judging by the efficiency of IASD modification, it was concluded that the bulk of the S105 protein molecules were involved in facing the lumen. These results are consistent with a model in which the perimeters of the S105 holes are lined by the holin molecules present at the time of lysis. Moreover, the findings that TMD1 and TMD3 face the lumen, coupled with previous results showing TMD2-TMD2 contacts in the S105 dimer, support a model in which membrane depolarization drives the transition of S105 from homotypic to heterotypic oligomeric interactions. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  9. Probing the Structure of the S105 Hole

    PubMed Central

    To, Kam H.

    2014-01-01

    For most phages, holins control the timing of host lysis. During the morphogenesis period of the infection cycle, canonical holins accumulate harmlessly in the cytoplasmic membrane until they suddenly trigger to form lethal lesions called holes. The holes can be visualized by cryo-electron microscopy and tomography as micrometer-scale interruptions in the membrane. To explore the fine structure of the holes formed by the lambda holin, S105, a cysteine-scanning accessibility study was performed. A collection of S105 alleles encoding holins with a single Cys residue in different positions was developed and characterized for lytic function. Based on the ability of 4-acetamido-4′-((iodoacetyl) amino) stilbene-2,2′-disulfonic acid, disodium salt (IASD), to modify these Cys residues, one face of transmembrane domain 1 (TMD1) and TMD3 was judged to face the lumen of the S105 hole. In both cases, the lumen-accessible face was found to correspond to the more hydrophilic face of the two TMDs. Judging by the efficiency of IASD modification, it was concluded that the bulk of the S105 protein molecules were involved in facing the lumen. These results are consistent with a model in which the perimeters of the S105 holes are lined by the holin molecules present at the time of lysis. Moreover, the findings that TMD1 and TMD3 face the lumen, coupled with previous results showing TMD2-TMD2 contacts in the S105 dimer, support a model in which membrane depolarization drives the transition of S105 from homotypic to heterotypic oligomeric interactions. PMID:25092029

  10. Van Allen Probe Measurements of the Scale Sizes and Detailed Properties of EMIC Waves

    NASA Astrophysics Data System (ADS)

    Blum, L. W.; Bonnell, J. W.; Agapitov, O. V.; Mozer, F.

    2016-12-01

    Electromagnetic ion cyclotron (EMIC) waves are able to resonate with MeV electrons and cause precipitation loss of radiation belt electrons. EMIC waves can provide a strong source of electron pitch angle diffusion, but the waves are often quite localized - thus the spatial extents of these waves can have a large effect on their overall scattering efficiency. Using measurements from the dual Van Allen Probes, we characterize the spatial and temporal extents of EMIC wave active regions and how these depend on local time, radial distance, and wave properties (e.g. amplitude, frequency). Analysis of the detailed wave properties is also performed; we estimate the active region and coherence scales of EMIC waves and examine nonlinear features and parallel electric fields present in some events. These investigations help determine the nature of EMIC wave-particle interactions and support more accurate quantification of their effects on the outer radiation belt.

  11. Probing electronic properties of molecular engineered zinc oxide nanowires with photoelectron spectroscopy.

    PubMed

    Aguilar, Carlos A; Haight, Richard; Mavrokefalos, Anastassios; Korgel, Brian A; Chen, Shaochen

    2009-10-27

    ZnO nanowires (NWs) are emerging as key elements for new lasing, photovoltaic and sensing applications but elucidation of their fundamental electronic properties has been hampered by a dearth of characterization tools capable of probing single nanowires. Herein, ZnO NWs were synthesized in solution and integrated into a low energy photoelectron spectroscopy system, where quantitative optical measurements of the NW work function and Fermi level location within the band gap were collected. Next, the NWs were decorated with several dipolar self-assembled monolayers (SAMs) and control over the electronic properties is demonstrated, yielding a completely tunable hybrid electronic material. Using this new metrology approach, a host of other extraordinary interfacial phenomena could be explored on nanowires such as spatial dopant profiling or heterostructures.

  12. Structure and properties of solid surfaces

    NASA Technical Reports Server (NTRS)

    Gatos, H. C.

    1974-01-01

    Difficulties in experimental studies of crystalline surfaces are related to the fact that surface atoms have an intrinsic tendency to react with their environment. A second problem is connected with the effective thickness of surfaces, which ranges from one to several atom layers. The phenomenology of surface interactions with gases are considered, taking into account physical adsorption, chemisorption, and the oxidation of surfaces. Studies of the surface structure are discussed, giving attention to field emission microscopy, field-ion microscopy, electron diffraction techniques, Auger spectroscopy, scanning electron microscopy, electron probe microanalysis, ion microprobe methods, and low-energy backscattering spectroscopy. Investigations of semiconductor surfaces are also described.

  13. Structure and properties of solid surfaces

    NASA Technical Reports Server (NTRS)

    Gatos, H. C.

    1974-01-01

    Difficulties in experimental studies of crystalline surfaces are related to the fact that surface atoms have an intrinsic tendency to react with their environment. A second problem is connected with the effective thickness of surfaces, which ranges from one to several atom layers. The phenomenology of surface interactions with gases are considered, taking into account physical adsorption, chemisorption, and the oxidation of surfaces. Studies of the surface structure are discussed, giving attention to field emission microscopy, field-ion microscopy, electron diffraction techniques, Auger spectroscopy, scanning electron microscopy, electron probe microanalysis, ion microprobe methods, and low-energy backscattering spectroscopy. Investigations of semiconductor surfaces are also described.

  14. Scanning probe acceleration microscopy (SPAM) in fluids: Mapping mechanical properties of surfaces at the nanoscale

    PubMed Central

    Legleiter, Justin; Park, Matthew; Cusick, Brian; Kowalewski, Tomasz

    2006-01-01

    One of the major thrusts in proximal probe techniques is combination of imaging capabilities with simultaneous measurements of physical properties. In tapping mode atomic force microscopy (TMAFM), the most straightforward way to accomplish this goal is to reconstruct the time-resolved force interaction between the tip and surface. These tip–sample forces can be used to detect interactions (e.g., binding sites) and map material properties with nanoscale spatial resolution. Here, we describe a previously unreported approach, which we refer to as scanning probe acceleration microscopy (SPAM), in which the TMAFM cantilever acts as an accelerometer to extract tip–sample forces during imaging. This method utilizes the second derivative of the deflection signal to recover the tip acceleration trajectory. The challenge in such an approach is that with real, noisy data, the second derivative of the signal is strongly dominated by the noise. This problem is solved by taking advantage of the fact that most of the information about the deflection trajectory is contained in the higher harmonics, making it possible to filter the signal by “comb” filtering, i.e., by taking its Fourier transform and inverting it while selectively retaining only the intensities at integer harmonic frequencies. Such a comb filtering method works particularly well in fluid TMAFM because of the highly distorted character of the deflection signal. Numerical simulations and in situ TMAFM experiments on supported lipid bilayer patches on mica are reported to demonstrate the validity of this approach. PMID:16551751

  15. Probing the topological properties of complex networks modeling short written texts.

    PubMed

    Amancio, Diego R

    2015-01-01

    In recent years, graph theory has been widely employed to probe several language properties. More specifically, the so-called word adjacency model has been proven useful for tackling several practical problems, especially those relying on textual stylistic analysis. The most common approach to treat texts as networks has simply considered either large pieces of texts or entire books. This approach has certainly worked well-many informative discoveries have been made this way-but it raises an uncomfortable question: could there be important topological patterns in small pieces of texts? To address this problem, the topological properties of subtexts sampled from entire books was probed. Statistical analyses performed on a dataset comprising 50 novels revealed that most of the traditional topological measurements are stable for short subtexts. When the performance of the authorship recognition task was analyzed, it was found that a proper sampling yields a discriminability similar to the one found with full texts. Surprisingly, the support vector machine classification based on the characterization of short texts outperformed the one performed with entire books. These findings suggest that a local topological analysis of large documents might improve its global characterization. Most importantly, it was verified, as a proof of principle, that short texts can be analyzed with the methods and concepts of complex networks. As a consequence, the techniques described here can be extended in a straightforward fashion to analyze texts as time-varying complex networks.

  16. Scanning probe acceleration microscopy (SPAM) in fluids: Mapping mechanical properties of surfaces at the nanoscale

    NASA Astrophysics Data System (ADS)

    Legleiter, Justin; Park, Matthew; Cusick, Brian; Kowalewski, Tomasz

    2006-03-01

    One of the major thrusts in proximal probe techniques is combination of imaging capabilities with simultaneous measurements of physical properties. In tapping mode atomic force microscopy (TMAFM), the most straightforward way to accomplish this goal is to reconstruct the time-resolved force interaction between the tip and surface. These tip-sample forces can be used to detect interactions (e.g., binding sites) and map material properties with nanoscale spatial resolution. Here, we describe a previously unreported approach, which we refer to as scanning probe acceleration microscopy (SPAM), in which the TMAFM cantilever acts as an accelerometer to extract tip-sample forces during imaging. This method utilizes the second derivative of the deflection signal to recover the tip acceleration trajectory. The challenge in such an approach is that with real, noisy data, the second derivative of the signal is strongly dominated by the noise. This problem is solved by taking advantage of the fact that most of the information about the deflection trajectory is contained in the higher harmonics, making it possible to filter the signal by “comb” filtering, i.e., by taking its Fourier transform and inverting it while selectively retaining only the intensities at integer harmonic frequencies. Such a comb filtering method works particularly well in fluid TMAFM because of the highly distorted character of the deflection signal. Numerical simulations and in situ TMAFM experiments on supported lipid bilayer patches on mica are reported to demonstrate the validity of this approach.

  17. Scanning probe acceleration microscopy (SPAM) in fluids: mapping mechanical properties of surfaces at the nanoscale.

    PubMed

    Legleiter, Justin; Park, Matthew; Cusick, Brian; Kowalewski, Tomasz

    2006-03-28

    One of the major thrusts in proximal probe techniques is combination of imaging capabilities with simultaneous measurements of physical properties. In tapping mode atomic force microscopy (TMAFM), the most straightforward way to accomplish this goal is to reconstruct the time-resolved force interaction between the tip and surface. These tip-sample forces can be used to detect interactions (e.g., binding sites) and map material properties with nanoscale spatial resolution. Here, we describe a previously unreported approach, which we refer to as scanning probe acceleration microscopy (SPAM), in which the TMAFM cantilever acts as an accelerometer to extract tip-sample forces during imaging. This method utilizes the second derivative of the deflection signal to recover the tip acceleration trajectory. The challenge in such an approach is that with real, noisy data, the second derivative of the signal is strongly dominated by the noise. This problem is solved by taking advantage of the fact that most of the information about the deflection trajectory is contained in the higher harmonics, making it possible to filter the signal by "comb" filtering, i.e., by taking its Fourier transform and inverting it while selectively retaining only the intensities at integer harmonic frequencies. Such a comb filtering method works particularly well in fluid TMAFM because of the highly distorted character of the deflection signal. Numerical simulations and in situ TMAFM experiments on supported lipid bilayer patches on mica are reported to demonstrate the validity of this approach.

  18. Probing the Topological Properties of Complex Networks Modeling Short Written Texts

    PubMed Central

    Amancio, Diego R.

    2015-01-01

    In recent years, graph theory has been widely employed to probe several language properties. More specifically, the so-called word adjacency model has been proven useful for tackling several practical problems, especially those relying on textual stylistic analysis. The most common approach to treat texts as networks has simply considered either large pieces of texts or entire books. This approach has certainly worked well—many informative discoveries have been made this way—but it raises an uncomfortable question: could there be important topological patterns in small pieces of texts? To address this problem, the topological properties of subtexts sampled from entire books was probed. Statistical analyses performed on a dataset comprising 50 novels revealed that most of the traditional topological measurements are stable for short subtexts. When the performance of the authorship recognition task was analyzed, it was found that a proper sampling yields a discriminability similar to the one found with full texts. Surprisingly, the support vector machine classification based on the characterization of short texts outperformed the one performed with entire books. These findings suggest that a local topological analysis of large documents might improve its global characterization. Most importantly, it was verified, as a proof of principle, that short texts can be analyzed with the methods and concepts of complex networks. As a consequence, the techniques described here can be extended in a straightforward fashion to analyze texts as time-varying complex networks. PMID:25719799

  19. Retrieval of spectral and dynamic properties from two-dimensional infrared pump-probe experiments.

    PubMed

    Chelli, Riccardo; Volkov, Victor V; Righini, Roberto

    2008-07-15

    We have developed a fitting algorithm able to extract spectral and dynamic properties of a three level oscillator from a two-dimensional infrared spectrum (2D-IR) detected in time resolved nonlinear experiments. Such properties go from the frequencies of the ground-to-first and first-to-second vibrational transitions (and hence anharmonicity) to the frequency-fluctuation correlation function. This last is represented through a general expression that allows one to approach the various strategies of modeling proposed in the literature. The model is based on the Kubo picture of stochastic fluctuations of the transition frequency as a result of perturbations by a fluctuating surrounding. To account for the line-shape broadening due to pump pulse spectral width in double-resonance measurements, we supply the fitting algorithm with the option to perform the convolution of the spectral signal with a Lorentzian function in the pump-frequency dimension. The algorithm is tested here on 2D-IR pump-probe spectra of a Gly-Ala dipeptide recorded at various pump-probe delay times. Speedup benchmarks have been performed on a small Beowulf cluster. The program is written in FORTRAN language for both serial and parallel architectures and is available free of charge to the interested reader.

  20. Interstellar Silicate Dust Grain Properties in Distant Galaxies Probed by Quasar Absorption Systems

    NASA Astrophysics Data System (ADS)

    Aller, Monique C.; Kulkarni, Varsha P.; York, Donald G.; Welty, Daniel E.; Vladilo, Giovanni; Som, Debopam

    2015-01-01

    Dust grains are a fundamental component of the interstellar medium, and significantly impact many of the physical processes driving galaxy evolution, including star formation, and the heating, cooling and ionization of interstellar material. Using the absorption features produced by dust in the spectra of luminous background quasars, it is possible to study the properties of extragalactic interstellar dust grains. We will present results from an ongoing program utilizing existing Spitzer Space Telescope infrared quasar spectra to probe silicate dust grain properties in z<1.4 quasar absorption systems. In combination with complementary ground-based data on associated gas-phase metal absorption lines, we explore connections between the interstellar dust and gas in the quasar absorption systems. Our project yields clear detections of the 10 micron silicate dust absorption feature in the studied systems, as well as detections of the 18 micron silicate dust absorption feature in sources with adequate spectral coverage. Based on measured variations in the breath, peak wavelength, and substructure of the 10 micron absorption features, there appear to be differences in the silicate dust grain properties from system-to-system. We also show indications of trends between the gas-phase metal properties, such as metallicity and gas velocity spread, with the silicate dust grain absorption properties. Support for this work is provided by NASA through an award issued by JPL/Caltech and through NASA grant NNX14AG74G, and from National Science Foundation grants AST-0908890 and AST-1108830 to the University of South Carolina.

  1. Structural properties of scandium inorganic salts

    SciTech Connect

    Sears, Jeremiah M.; Boyle, Timothy J.

    2016-12-16

    Here, the structural properties of reported inorganic scandium (Sc) salts were reviewed, including the halide (Cl, Br, and I), nitrate, sulfate, and phosphate salts. Additional analytical techniques used for characterization of these complexes (metrical data, FTIR and 45Sc NMR spectroscopy) were tabulated. A structural comparison of Sc to select lanthanide (La, Gd, Lu) salt complexes was briefly evaluated.

  2. Structural properties of scandium inorganic salts

    DOE PAGES

    Sears, Jeremiah M.; Boyle, Timothy J.

    2016-12-16

    Here, the structural properties of reported inorganic scandium (Sc) salts were reviewed, including the halide (Cl, Br, and I), nitrate, sulfate, and phosphate salts. Additional analytical techniques used for characterization of these complexes (metrical data, FTIR and 45Sc NMR spectroscopy) were tabulated. A structural comparison of Sc to select lanthanide (La, Gd, Lu) salt complexes was briefly evaluated.

  3. Finite Element Estimation of Meteorite Structural Properties

    NASA Technical Reports Server (NTRS)

    Hart, Kenneth Arthur

    2015-01-01

    The goal of the project titled Asteroid Threat Assessment at NASA Ames Research Center is to develop risk assessment tools. The expertise in atmospheric entry in the Entry Systems and Technology Division is being used to describe the complex physics of meteor breakup in the atmosphere. The breakup of a meteor is dependent on its structural properties, including homogeneity of the material. The present work describes an 11-week effort in which a literature survey was carried for structural properties of meteoritic material. In addition, the effect of scale on homogeneity isotropy was studied using a Monte Carlo approach in Nastran. The properties were then in a static structural response simulation of an irregularly-shape meteor (138-scale version of Asteroid Itokawa). Finally, an early plan was developed for doctoral research work at Georgia Tech. in the structural failure fragmentation of meteors.

  4. Probing magnetic turbulence by synchrotron polarimetry: statistics and structure of magnetic fields from Stokes correlators

    NASA Astrophysics Data System (ADS)

    Waelkens, A. H.; Schekochihin, A. A.; Enßlin, T. A.

    2009-10-01

    We describe a novel technique for probing the statistical properties of cosmic magnetic fields based on radio polarimetry data. Second-order magnetic field statistics like the power spectrum cannot always distinguish between magnetic fields with essentially different spatial structure. Synchrotron polarimetry naturally allows certain fourth-order magnetic field statistics to be inferred from observational data, which lifts this degeneracy and can thereby help us gain a better picture of the structure of the cosmic fields and test theoretical scenarios describing magnetic turbulence. In this work we show that a fourth-order correlator of specific physical interest, the tension force spectrum, can be recovered from the polarized synchrotron emission data. We develop an estimator for this quantity based on polarized emission observations in the Faraday rotation free frequency regime. We consider two cases: a statistically isotropic field distribution, and a statistically isotropic field superimposed on a weak mean field. In both cases the tension force power spectrum is measurable; in the latter case, the magnetic power spectrum may also be obtainable. The method is exact in the idealized case of a homogeneous relativistic electron distribution that has a power-law energy spectrum with a spectral index of p = 3, and assumes statistical isotropy of the turbulent field. We carry out numerical tests of our method using synthetic polarized emission data generated from numerically simulated magnetic fields. We show that the method is valid, that it is not prohibitively sensitive to the value of the electron spectral index p, and that the observed tension force spectrum allows one to distinguish between e.g. a randomly tangled magnetic field (a default assumption in many studies) and a field organized in folded flux sheets or filaments.

  5. Tribological properties of structural ceramics

    NASA Technical Reports Server (NTRS)

    Buckley, D. H.; Miyoshi, K.

    1985-01-01

    The tribological and lubricated behavior of both oxide and nonoxide ceramics are reviewed in this chapter. Ceramics are examined in contact with themselves, other harder materials and metals. Elastic, plastic and fracture behavior of ceramics in solid state contact is discussed. The contact load necessary to initiate fracture in ceramics is shown to be appreciably reduced with tangential motion. Both friction and wear of ceramics are anisotropic and relate to crystal structure as has been observed with metals. Grit size effects in two and three body abrasive wear are observed for ceramics. Both free energy of oxide formation and the d valence bond character of metals are related to the friction and wear characteristics for metals in contact with ceramics. Surface contaminants affect friction and adhesive wear. For example, carbon on silicon carbide and chlorine on aluminum oxide reduce friction while oxygen on metal surfaces in contact with ceramics increases friction. Lubrication increases the critical load necessary to initiate fracture of ceramics both in indentation and with sliding or rubbing. Ceramics compositions both as coatings and in composites are described for the high temperature lubrication of both alloys and ceramics.

  6. Tribological properties of structural ceramics

    NASA Technical Reports Server (NTRS)

    Buckley, Donald H.; Miyoshi, Kazuhisa

    1989-01-01

    The tribological and lubricated behavior of both oxide and nonoxide ceramics are reviewed in this chapter. Ceramics are examined in contact with themselves, other harder materials and metals. Elastic, plastic and fracture behavior of ceramics in solid state contact is discussed. The contact load necessary to initiate fracture in ceramics is shown to be appreciably reduced with tangential motion. Both friction and wear of ceramics are anisotropic and relate to crystal structure as has been observed with metals. Grit size effects in two and three body abrasive wear are observed for ceramics. Both free energy of oxide formation and the d valence bond character of metals are related to the friction and wear characteristics for metals in contact with ceramics. Surface contaminants affect friction and adhesive wear. For example, carbon on silicon carbide and chlorine on aluminum oxide reduce friction while oxygen on metal surfaces in contact with ceramics increases friction. Lubrication increases the critical load necessary to initiate fracture of ceramics both in indentation and with sliding or rubbing. Ceramics compositions both as coatings and in composites are described for the high temperature lubrication of both alloys and ceramics.

  7. Capturing relativistic wakefield structures in plasmas using ultrashort high-energy electrons as a probe.

    PubMed

    Zhang, C J; Hua, J F; Xu, X L; Li, F; Pai, C-H; Wan, Y; Wu, Y P; Gu, Y Q; Mori, W B; Joshi, C; Lu, W

    2016-07-11

    A new method capable of capturing coherent electric field structures propagating at nearly the speed of light in plasma with a time resolution as small as a few femtoseconds is proposed. This method uses a few femtoseconds long relativistic electron bunch to probe the wake produced in a plasma by an intense laser pulse or an ultra-short relativistic charged particle beam. As the probe bunch traverses the wake, its momentum is modulated by the electric field of the wake, leading to a density variation of the probe after free-space propagation. This variation of probe density produces a snapshot of the wake that can directly give many useful information of the wake structure and its evolution. Furthermore, this snapshot allows detailed mapping of the longitudinal and transverse components of the wakefield. We develop a theoretical model for field reconstruction and verify it using 3-dimensional particle-in-cell (PIC) simulations. This model can accurately reconstruct the wakefield structure in the linear regime, and it can also qualitatively map the major features of nonlinear wakes. The capturing of the injection in a nonlinear wake is demonstrated through 3D PIC simulations as an example of the application of this new method.

  8. Capturing relativistic wakefield structures in plasmas using ultrashort high-energy electrons as a probe

    SciTech Connect

    Zhang, C. J.; Hua, J. F.; Xu, X. L.; Li, F.; Pai, C. -H.; Wan, Y.; Wu, Y. P.; Gu, Y. Q.; Mori, W. B.; Joshi, C.; Lu, W.

    2016-07-11

    A new method capable of capturing coherent electric field structures propagating at nearly the speed of light in plasma with a time resolution as small as a few femtoseconds is proposed. This method uses a few femtoseconds long relativistic electron bunch to probe the wake produced in a plasma by an intense laser pulse or an ultra-short relativistic charged particle beam. As the probe bunch traverses the wake, its momentum is modulated by the electric field of the wake, leading to a density variation of the probe after free-space propagation. This variation of probe density produces a snapshot of the wake that can directly give many useful information of the wake structure and its evolution. Furthermore, this snapshot allows detailed mapping of the longitudinal and transverse components of the wakefield. We develop a theoretical model for field reconstruction and verify it using 3-dimensional particle-in-cell (PIC) simulations. This model can accurately reconstruct the wakefield structure in the linear regime, and it can also qualitatively map the major features of nonlinear wakes. As a result, the capturing of the injection in a nonlinear wake is demonstrated through 3D PIC simulations as an example of the application of this new method.

  9. Capturing relativistic wakefield structures in plasmas using ultrashort high-energy electrons as a probe

    DOE PAGES

    Zhang, C. J.; Hua, J. F.; Xu, X. L.; ...

    2016-07-11

    A new method capable of capturing coherent electric field structures propagating at nearly the speed of light in plasma with a time resolution as small as a few femtoseconds is proposed. This method uses a few femtoseconds long relativistic electron bunch to probe the wake produced in a plasma by an intense laser pulse or an ultra-short relativistic charged particle beam. As the probe bunch traverses the wake, its momentum is modulated by the electric field of the wake, leading to a density variation of the probe after free-space propagation. This variation of probe density produces a snapshot of themore » wake that can directly give many useful information of the wake structure and its evolution. Furthermore, this snapshot allows detailed mapping of the longitudinal and transverse components of the wakefield. We develop a theoretical model for field reconstruction and verify it using 3-dimensional particle-in-cell (PIC) simulations. This model can accurately reconstruct the wakefield structure in the linear regime, and it can also qualitatively map the major features of nonlinear wakes. As a result, the capturing of the injection in a nonlinear wake is demonstrated through 3D PIC simulations as an example of the application of this new method.« less

  10. Capturing relativistic wakefield structures in plasmas using ultrashort high-energy electrons as a probe

    PubMed Central

    Zhang, C. J.; Hua, J. F.; Xu, X. L.; Li, F.; Pai, C.-H.; Wan, Y.; Wu, Y. P.; Gu, Y. Q.; Mori, W. B.; Joshi, C.; Lu, W.

    2016-01-01

    A new method capable of capturing coherent electric field structures propagating at nearly the speed of light in plasma with a time resolution as small as a few femtoseconds is proposed. This method uses a few femtoseconds long relativistic electron bunch to probe the wake produced in a plasma by an intense laser pulse or an ultra-short relativistic charged particle beam. As the probe bunch traverses the wake, its momentum is modulated by the electric field of the wake, leading to a density variation of the probe after free-space propagation. This variation of probe density produces a snapshot of the wake that can directly give many useful information of the wake structure and its evolution. Furthermore, this snapshot allows detailed mapping of the longitudinal and transverse components of the wakefield. We develop a theoretical model for field reconstruction and verify it using 3-dimensional particle-in-cell (PIC) simulations. This model can accurately reconstruct the wakefield structure in the linear regime, and it can also qualitatively map the major features of nonlinear wakes. The capturing of the injection in a nonlinear wake is demonstrated through 3D PIC simulations as an example of the application of this new method. PMID:27403561

  11. Molecular Structure and Dynamics Probed by Photoionization Out of Rydberg States

    NASA Astrophysics Data System (ADS)

    Rudakov, Fedor

    2017-06-01

    Probing the structure of a molecule as a chemical reaction unfolds has been a long standing goal in chemical physics. Most spectroscopic and diffraction techniques work well when the molecules are cold and thus vibrational motion is minimized. Yet, the very ability of a molecule to undergo structural changes implies that a significant amount of energy resides within the molecule. In order to probe structures of even medium sized molecules on an ultrafast time scale a technique that is sensitive to the molecular structure, yet insensitive to the vibrational motion is required. In our research we demonstrated that Rydberg electrons are remarkably sensitive to the molecular structure. Photoionization of a molecule out of Rydberg states reveals a purely electronic spectrum which is largely insensitive to vibrational motion. The talk illustrates how Rydberg electrons can serve as a probe for ultrafast structural dynamics in polyatomic molecules. The talk also demonstrates that photoionization through Rydberg states can be utilized for non-intrusive detection of polyatomic combustion intermediates in flames.

  12. Multi-scale Imaging of Cellular and Sub-cellular Structures using Scanning Probe Recognition Microscopy.

    NASA Astrophysics Data System (ADS)

    Chen, Q.; Rice, A. F.

    2005-03-01

    Scanning Probe Recognition Microscopy is a new scanning probe capability under development within our group to reliably return to and directly interact with a specific nanobiological feature of interest. In previous work, we have successfully recognized and classified tubular versus globular biological objects from experimental atomic force microscope images using a method based on normalized central moments [ref. 1]. In this paper we extend this work to include recognition schemes appropriate for cellular and sub-cellular structures. Globular cells containing tubular actin filaments are under investigation. Thus there are differences in external/internal shapes and scales. Continuous Wavelet Transform with a differential Gaussian mother wavelet is employed for multi- scale analysis. [ref. 1] Q. Chen, V. Ayres and L. Udpa, ``Biological Investigation Using Scanning Probe Recognition Microscopy,'' Proceedings 3rd IEEE Conference on Nanotechnology, vol. 2, p 863-865 (2003).

  13. Structure-Based Development of an Affinity Probe for Sirtuin 2.

    PubMed

    Schiedel, Matthias; Rumpf, Tobias; Karaman, Berin; Lehotzky, Attila; Gerhardt, Stefan; Ovádi, Judit; Sippl, Wolfgang; Einsle, Oliver; Jung, Manfred

    2016-02-05

    Sirtuins are NAD(+)-dependent protein deacylases that cleave off acetyl groups, as well as other acyl groups, from the ɛ-amino group of lysines in histones and other substrate proteins. Dysregulation of human Sirt2 activity has been associated with the pathogenesis of cancer, inflammation, and neurodegeneration, thus making Sirt2 a promising target for pharmaceutical intervention. Here, based on a crystal structure of Sirt2 in complex with an optimized sirtuin rearranging ligand (SirReal) that shows improved potency, water solubility, and cellular efficacy, we present the development of the first Sirt2-selective affinity probe. A slow dissociation of the probe/enzyme complex offers new applications for SirReals, such as biophysical characterization, fragment-based screening, and affinity pull-down assays. This possibility makes the SirReal probe an important tool for studying sirtuin biology.

  14. Young's type interference for probing the mode symmetry in photonic structures.

    PubMed

    Intonti, F; Riboli, F; Caselli, N; Abbarchi, M; Vignolini, S; Wiersma, D S; Vinattieri, A; Gerace, D; Balet, L; Li, L H; Francardi, M; Gerardino, A; Fiore, A; Gurioli, M

    2011-04-08

    A revisited realization of the Young's double slit experiment is introduced to directly probe the photonic mode symmetry by photoluminescence experiments. We experimentally measure the far field angular emission pattern of quantum dots embedded in photonic molecules. The experimental data well agree with predictions from Young's interference and numerical simulations. Moreover, the vectorial nature of photonic eigenmodes results in a rather complicated parity property for different polarizations, a feature which has no counterpart in quantum mechanics.

  15. Young's Type Interference for Probing the Mode Symmetry in Photonic Structures

    NASA Astrophysics Data System (ADS)

    Intonti, F.; Riboli, F.; Caselli, N.; Abbarchi, M.; Vignolini, S.; Wiersma, D. S.; Vinattieri, A.; Gerace, D.; Balet, L.; Li, L. H.; Francardi, M.; Gerardino, A.; Fiore, A.; Gurioli, M.

    2011-04-01

    A revisited realization of the Young’s double slit experiment is introduced to directly probe the photonic mode symmetry by photoluminescence experiments. We experimentally measure the far field angular emission pattern of quantum dots embedded in photonic molecules. The experimental data well agree with predictions from Young’s interference and numerical simulations. Moreover, the vectorial nature of photonic eigenmodes results in a rather complicated parity property for different polarizations, a feature which has no counterpart in quantum mechanics.

  16. Asymmetric actuating structure generates negligible influence on the supporting base for high performance scanning probe microscopies

    NASA Astrophysics Data System (ADS)

    Yi Yan, Gang; Bin Liu, Yong; Hua Feng, Zhi

    2014-02-01

    An asymmetric actuating structure generating negligible influence on the supporting base for high performance scanning probe microscopies is proposed in this paper. The actuator structure consists of two piezostacks, one is used for actuating while the other is for counterbalancing. In contrast with balanced structure, the two piezostacks are installed at the same side of the supporting base. The effectiveness of the structure is proved by some experiments with the actuators fixed to the free end of a cantilever. Experimental results show that almost all of the vibration modes of the cantilever are suppressed effectively at a wide frequency range of 90 Hz-10 kHz.

  17. Sensitive force technique to probe molecular adhesion and structural linkages at biological interfaces.

    PubMed

    Evans, E; Ritchie, K; Merkel, R

    1995-06-01

    Adhesion and cytoskeletal structure are intimately related in biological cell function. Even with the vast amount of biological and biochemical data that exist, little is known at the molecular level about physical mechanisms involved in attachments between cells or about consequences of adhesion on the material structure. To expose physical actions at soft biological interfaces, we have combined an ultrasensitive transducer and reflection interference microscopy to image submicroscopic displacements of probe contact with a test surface under minuscule forces. The transducer is a cell-size membrane capsule pressurized by micropipette suction where displacement normal to the membrane under tension is proportional to the applied force. Pressure control of the tension tunes the sensitivity in operation over four orders of magnitude through a range of force from 0.01 pN up to the strength of covalent bonds (approximately 1000 pN)! As the surface probe, a microscopic bead is biochemically glued to the transducer with a densely-bound ligand that is indifferent to the test surface. Movements of the probe under applied force are resolved down to an accuracy of approximately 5 nm from the interference fringe pattern created by light reflected from the bead. With this arrangement, we show that local mechanical compliance of a cell surface can be measured at a displacement resolution set by structural fluctuations. When desired, a second ligand is bound sparsely to the probe for focal adhesion to specific receptors in the test surface. We demonstrate that monitoring fluctuations in probe position at low transducer stiffness enhances detection of molecular adhesion and activation of cytoskeletal structure. Subsequent loading of an attachment tests mechanical response of the receptor-substrate linkage throughout the force-driven process of detachment.

  18. Probing nano-scale structures of SmC* variant phases by resonant x-ray diffraction and optical probes

    NASA Astrophysics Data System (ADS)

    Huang, C. C.

    2005-03-01

    Since the identification of antiferroelectric response in one liquid crystal compound having large polarization by Chandani et al., considerable experimental and theoretical effort has been aimed to gain a much better understanding of the molecular orientation order within each phases and associated molecular interactions. Employing polarization-analyzed resonant x-ray diffraction and specially-designed state-of-the-art ellipsometry systems, we have identified the molecular arrangements in three new SmC* variant phases, namely, SmC(alpha1)*, SmC(FI2)*, and SmC(FI1)*. Moreover, guided by our proposed phenomenological model to explain the stability of these phases, we have developed a novel experimental method to identify a new mesophase, namely, SmC(alpha2)* by employing an optical probe (wavelength = 633nm) to obtain an incommensurate nano-scale helical pitch structure with pitch length < 11nm. Collaborators of this project: P. Mach, P. Johnson, D. Olson, A. Cady, X. F. Han, L. S. Hirst, A. M. Levelut, P. Barois, H. T. Nguyen, J. W. Goodby, M. Hird, H. F. Gleeson, L. Furenlid, W. Caliebe, and R. Pindak.

  19. Ion Spectral Structures Observed by the Van Allen Probes and Cluster

    NASA Astrophysics Data System (ADS)

    Ferradas, C.; Zhang, J.; Luo, H.; Kistler, L. M.; Spence, H. E.; Larsen, B.; Skoug, R. M.; Funsten, H. O.; Reeves, G. D.

    2014-12-01

    During the last decades several missions have recorded the presence of dynamic spectral features of energetic ions in the inner magnetosphere. Previous studies have revealed single "nose-like" structures occurring alone and simultaneous nose-like structures (up to three). In this study we also include signatures of new types of ion structure, namely "trunk-like" and "tusk-like" structures. All the ion structures are named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. They constitute the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. Multi-spacecraft analysis of these structures is important to understand their spatial distribution and temporal evolution. Mass spectrometers onboard Cluster (in a polar orbit) and the Van Allen Probes (in an equatorial orbit) measure energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet, where these ion structures are observed. We present a statistical study of the ion structures, using >1-year measurements from the two missions during the Van Allen Probes era. The results provide important details about the spatial distribution (dependence on geocentric distance and magnetic local time), spectral features of the structures (e.g., characteristic energy and differences among species), and geomagnetic and solar wind conditions under which these structures occur.

  20. Noninvasive method for measuring the electrical properties of deep tissues using an open-ended coaxial probe.

    PubMed

    Aimoto, A; Matsumoto, T

    1996-12-01

    A new noninvasive method of measuring the structure and the electrical properties of bilayered biological tissues was evaluated as a potentially useful diagnostic means for detecting changes in subcutaneous tissues. First, the input impedance of an open-ended coaxial probe radiating into a bilayered model was calculated using a full-wave method, the results showed that the evanescent higher order modes do not have a significant influence on the reflection coefficient of muscle layer surface. Then, it was clearly proven that the phase shift and the modulus of the reflection coefficient of muscle layer surface depending on the frequency are useful to estimate the thickness of fat layer and the electrical properties of muscle respectively. The experimental results showed an excellent agreement with the theoretical relationship between the phase shift and the thickness. The sensitivity of estimation of the electrical properties of muscle was shown to be not enough for differentiating between normal and diseased deep tissue because of noises from the experimental systems.

  1. Individual carbon nanotube probes and field emitters fabrication and their properties

    NASA Astrophysics Data System (ADS)

    Chai, Guangyu

    Since the discovery of carbon nanotubes (CNT) in 1999, they have attracted much attention due to their unique mechanical and electrical properties and potential applications. Yet their nanosize makes the study of individual CNTs easier said than done. In our laboratory, carbon fibers with nanotube cores have been synthesized with conventional chemical vapor deposition (CVD) method. The single multiwall carbon nanotube (MWNT) sticks out as a tip of the carbon fiber. In order to pick up the individual CNT tips, focused ion beam (FIB) technique is applied to cut and adhere the samples. The carbon fiber with nanotube tip was first adhered on a micro-manipulator with the FIB welding function. Afterwards, by applying the FIB milling function, the fiber was cut from the base. This enables us to handle the individual CNT tips conveniently. By the same method, we can attach the nanotube tip on any geometry of solid samples such as conventional atomic force microscopy (AFM) silicon tips. The procedures developed for the FIB assisted individual CNT tip fabrication will be described in detail. Because of their excellent electrical and stable chemical properties, individual CNTs are potential candidates as electron guns for electron based microscopes to produce highly coherent electron beams. Due to the flexibility of the FIB fabrication, the individual CNT tips can be easily fabricated on a sharpened clean tungsten wire for field emission (FE) experimentation. Another promising application for individual CNT tips is as AFM probes. The high aspect ratio and mechanical resilience make individual CNTs ideal for scanning probe microscopy (SPM) tips. Atomic force microscopy with nanotube tips allows us to image relatively deep features of the sample surface at near nanometer resolution. Characterization of AFM with individual CNT tips and field emission properties of single CNT emitters will be studied and presented.

  2. Using DLS Spectroscopy and Optical Probe Diffusion to examine structure of Brij Micelles

    NASA Astrophysics Data System (ADS)

    Wilson, Karen; Lekan, Mike; Streletzky, Kiril

    2008-03-01

    We studied properties of Brij-35 surfactant micelles in solution using Dynamic Light Scattering (DLS) Spectroscopy and Optical Probe Diffusion method. Aqueous solutions of Brij-35 with concentrations ranging from 2 to 100g/L were prepared, both with and without polystyrene latex probes of diameters 24, 50, 186, 282 and 792nm. Solutions were studied at four temperatures of 10, 25, 40 and 70^oC with DLS to obtain micelle and probe diffusion coefficients (Dm, Dp). Using both diffusion coefficients we deduced micelle radius (am), micelle water content (δ), and number of surfactant molecules per micelle (N) using two different models. First, hard sphere model of micelles/probe interaction was used to analyze the data by two methods, after am was obtained from intercept of Dm(c). The first method uses the slope of Dm(c) and size of probes to determine N and δ. The second method uses the linear least-squares fit of Dp(c) for different probe sizes to determine N and δ. Both methods reveal that with increase in solution temperature am increases by 10%, N increases and δ decreases by a factor of 2. The second model treats micelles as core-shell particles with corona radius (ac). This model used two different approaches based on linear least-squares fits of Dm(c) and Dp(c). We found am to be 4-4.5nm and ac-am to be 1nm without relying on Stokes-Einstein equation. Results for N and δg were also consistent.

  3. Novel flexible Parylene neural probe with 3D sheath structure for enhancing tissue integration.

    PubMed

    Kuo, Jonathan T W; Kim, Brian J; Hara, Seth A; Lee, Curtis D; Gutierrez, Christian A; Hoang, Tuan Q; Meng, Ellis

    2013-02-21

    A Parylene C neural probe with a three dimensional sheath structure was designed, fabricated, and characterized. Multiple platinum (Pt) electrodes for recording neural signals were fabricated on both inner and outer surfaces of the sheath structure. Thermoforming of Parylene was used to create the three dimensional sheath structures from flat surface micromachined microchannels using solid microwires as molds. Benchtop electrochemical characterization was performed on the thin film Pt electrodes using cyclic voltammetry and electrochemical impedance spectroscopy and showed that electrodes possessed low impedances suitable for neuronal recordings. A procedure for implantation of the neural probe was developed and successfully demonstrated in vitro into an agarose brain tissue model. The electrode-lined sheath will be decorated with eluting neurotrophic factors to promote in vivo neural tissue ingrowth post-implantation. These features will enhance tissue integration and improve recording quality towards realizing reliable chronic neural interfaces.

  4. Structure Property Relationships of Carboxylic Acid Isosteres.

    PubMed

    Lassalas, Pierrik; Gay, Bryant; Lasfargeas, Caroline; James, Michael J; Tran, Van; Vijayendran, Krishna G; Brunden, Kurt R; Kozlowski, Marisa C; Thomas, Craig J; Smith, Amos B; Huryn, Donna M; Ballatore, Carlo

    2016-04-14

    The replacement of a carboxylic acid with a surrogate structure, or (bio)-isostere, is a classical strategy in medicinal chemistry. The general underlying principle is that by maintaining the features of the carboxylic acid critical for biological activity, but appropriately modifying the physicochemical properties, improved analogs may result. In this context, a systematic assessment of the physicochemical properties of carboxylic acid isosteres would be desirable to enable more informed decisions of potential replacements to be used for analog design. Herein we report the structure-property relationships (SPR) of 35 phenylpropionic acid derivatives, in which the carboxylic acid moiety is replaced with a series of known isosteres. The data set generated provides an assessment of the relative impact on the physicochemical properties that these replacements may have compared to the carboxylic acid analog. As such, this study presents a framework for how to rationally apply isosteric replacements of the carboxylic acid functional group.

  5. Probing structure of blood plasma proteins with solvatochromic fluorescent probes based on Nile red and its derivatives

    NASA Astrophysics Data System (ADS)

    Kaler, Gregory V.; Ivanov, Andrei I.; Konev, Sergei V.

    1997-05-01

    Uncharged long-wave fluorescent probes, Nile red and its derivatives varying in lipophilicity, were used for probing hydrophobic binding sites of human serum albumin (HSA) and lipoproteins (LP) in norm and pathology. The synchro-scan fluorescence spectra (synchronous scanning of both excitation and emission wavelengths at constant (Delta) (lambda) ) of the probes were studied in HSA solutions and in whole blood plasma. The parameters of the spectra were sensitive to pH-induced conformational NyieldsB transition in HSA. In blood plasma, each of the probes displayed a two-component synchro-scan spectrum revealing two pools of the dye bound to HSA (longer wavelength) and LP (shorter wavelength). The probe distribution between LP and HSA was also sensitive to NyieldsB transition. The LP/HSA probe distribution ratio was shown to increase significantly in certain pathologies, due to either hypoalbuminemia or lowered ligand-binding capacity of HSA. Also, spectral shifts were observed in the band of albumin-bound probe. The determination of the distribution parameter may be proposed as an informative and feasible diagnostic test.

  6. Structure Defect Property Relationships in Binary Intermetallics

    NASA Astrophysics Data System (ADS)

    Medasani, Bharat; Ding, Hong; Chen, Wei; Persson, Kristin; Canning, Andrew; Haranczyk, Maciej; Asta, Mark

    2015-03-01

    Ordered intermetallics are light weight materials with technologically useful high temperature properties such as creep resistance. Knowledge of constitutional and thermal defects is required to understand these properties. Vacancies and antisites are the dominant defects in the intermetallics and their concentrations and formation enthalpies could be computed by using first principles density functional theory and thermodynamic formalisms such as dilute solution method. Previously many properties of the intermetallics such as melting temperatures and formation enthalpies were statistically analyzed for large number of intermetallics using structure maps and data mining approaches. We undertook a similar exercise to establish the dependence of the defect properties in binary intermetallics on the underlying structural and chemical composition. For more than 200 binary intermetallics comprising of AB, AB2 and AB3 structures, we computed the concentrations and formation enthalpies of vacancies and antisites in a small range of stoichiometries deviating from ideal stoichiometry. The calculated defect properties were datamined to gain predictive capabilities of defect properties as well as to classify the intermetallics for their suitability in high-T applications. Supported by the US DOE under Contract No. DEAC02-05CH11231 under the Materials Project Center grant (Award No. EDCBEE).

  7. Simultaneous folding of alternative RNA structures with mutual constraints: an application to next-generation sequencing-based RNA structure probing.

    PubMed

    Zhong, Cuncong; Zhang, Shaojie

    2014-08-01

    Recent advances in next-generation sequencing technology have significantly promoted high-throughput experimental probing of RNA secondary structures. The resulting enzymatic or chemical probing information is then incorporated into a minimum free energy folding algorithm to predict more accurate RNA secondary structures. A drawback of this approach is that it does not consider the presence of alternative RNA structures. In addition, the alternative RNA structures may contaminate experimental probing information of each other and direct the minimum free-energy folding to a wrong direction. In this article, we present a combinatorial solution for this problem, where two alternative structures can be folded simultaneously given the experimental probing information regarding the mixture of these two alternative structures. We have tested our algorithm with artificially generated mixture probing data on adenine riboswitch and thiamine pyrophosphate (TPP) riboswitch. The experimental results show that our algorithm can successfully recover the ON and OFF structures of these riboswitches.

  8. Structure--properties relationships for manganese perovskites

    SciTech Connect

    Dabrowski, B.; Xiong, X.; Chmaissem, O.; Bukowski, Z.; Jorgensen, J. D.

    1999-10-14

    By combining the results of dc magnetization, ac susceptibility, magnetoresistivity, magnetostriction, and x-ray and neutron powder diffraction data for stoichiometric La{sub 1{minus}x}Sr{sub x}MnO{sub 3} the authors have constructed a phase diagram that describes the magnetic, transport, and structural properties and the relationships among them as a function of composition and temperature. Correlations among physical and structural properties have been observed that are consistent with a competition between ferromagnetism and JT distortion. A metallic state occurs below the Curie temperature when both coherent and incoherent JT distortions are suppressed.

  9. Annealing and structural properties of composite films

    NASA Astrophysics Data System (ADS)

    Kotov, L. N.; Ustyugov, V. A.; Vlasov, V. S.; Turkov, V. K.; Dianov, M. Yu; Antonets, I. V.; Kalinin, Yu E.; Sitnikov, A. V.; Golubev, E. A.

    2017-02-01

    The composite films were investigated by AFM methods before and after annealing. Topographic and phase-contrast AFM images of the composite films at different annealing temperature were obtained. The separate metal granules and larger-scale labyrinth-like formations were described. These formations appear by the process of the film growth, also by film annealing. Strong changes of the structural properties of the films are observed after the percolation transition. The significant changes of the structural properties are connected with nanostructural transformations in the metal granules topology and presence of metal crystal phase.

  10. Modeling adsorption properties of structurally deformed metal-organic frameworks using structure-property map.

    PubMed

    Jeong, WooSeok; Lim, Dae-Woon; Kim, Sungjune; Harale, Aadesh; Yoon, Minyoung; Suh, Myunghyun Paik; Kim, Jihan

    2017-07-25

    Structural deformation and collapse in metal-organic frameworks (MOFs) can lead to loss of long-range order, making it a challenge to model these amorphous materials using conventional computational methods. In this work, we show that a structure-property map consisting of simulated data for crystalline MOFs can be used to indirectly obtain adsorption properties of structurally deformed MOFs. The structure-property map (with dimensions such as Henry coefficient, heat of adsorption, and pore volume) was constructed using a large data set of over 12000 crystalline MOFs from molecular simulations. By mapping the experimental data points of deformed SNU-200, MOF-5, and Ni-MOF-74 onto this structure-property map, we show that the experimentally deformed MOFs share similar adsorption properties with their nearest neighbor crystalline structures. Once the nearest neighbor crystalline MOFs for a deformed MOF are selected from a structure-property map at a specific condition, then the adsorption properties of these MOFs can be successfully transformed onto the degraded MOFs, leading to a new way to obtain properties of materials whose structural information is lost.

  11. Elucidating the higher-order structure of biopolymers by structural probing and mass spectrometry: MS3D

    PubMed Central

    Fabris, Daniele; Yu, Eizadora T.

    2010-01-01

    Chemical probing represents a very versatile alternative for studying the structure and dynamics of substrates that are intractable by established high-resolution techniques. The implementation of MS-based strategies for the characterization of probing products has not only extended the range of applicability to virtually all types of biopolymers, but has also paved the way for the introduction of new reagents that would not have been viable with traditional analytical platforms. As the availability of probing data is steadily increasing on the wings of the development of dedicated interpretation aids, powerful computational approaches have been explored to enable the effective utilization of such information to generate valid molecular models. This combination of factors has contributed to making the possibility of obtaining actual 3D structures by MS-based technologies (MS3D) a reality. Although approaches for achieving structure determination of unknown substrates or assessing the dynamics of known structures may share similar reagents and development trajectories, they clearly involve distinctive experimental strategies, analytical concerns, and interpretation paradigms. This Perspective offers a commentary on methods aimed at obtaining distance constraints for the modeling of full-fledged structures, while highlighting common elements, salient distinctions, and complementary capabilities exhibited by methods employed in dynamics studies. We discuss critical factors to be addressed for completing effective structural determinations and expose possible pitfalls of chemical methods. We survey programs developed for facilitating the interpretation of experimental data and discuss possible computational strategies for translating sparse spatial constraints into all-atom models. Examples are provided to illustrate how the concerted application of very diverse probing techniques can lead to the solution of actual biological substrates. PMID:20648672

  12. Use of genetic algorithms to optimize fiber optic probe design for the extraction of tissue optical properties.

    PubMed

    Palmer, Gregory M; Ramanujam, Nirmala

    2007-08-01

    This paper outlines a framework by which the optimal illumination/collection geometry can be identified for a particular biomedical application. In this paper, this framework was used to identify the optimal probe geometry for the accurate determination of tissue optical properties representative of that in the ultraviolet-visible (UV-VIS) spectral range. An optimal probe geometry was identified which consisted of a single illumination and two collection fibers, one of which is insensitive to changes in scattering properties, and the other is insensitive to changes in the attenuation coefficient. Using this probe geometry in conjunction with a neural network algorithm, the optical properties could be extracted with root-mean-square errors of 0.30 cm(-1) for the reduced scattering coefficient (tested range of 3-40 cm(-1)), and 0.41 cm(-1) for the absorption coefficient (tested range of 0-80 cm(-1)).

  13. Modulating molecular level space proximity: a simple and efficient strategy to design structured DNA probes.

    PubMed

    Zheng, Jing; Li, Jishan; Gao, Xiaoxia; Jin, Jianyu; Wang, Kemin; Tan, Weihong; Yang, Ronghua

    2010-05-01

    To construct efficient oligonucleotide probes, specific nucleic acid is designed as a conformationally constrained form based on the formation of a Watson-Crick-based duplex. However, instability of Watson-Crick hydrogen bonds in a complex biological environment usually leads to high background signal from the probe itself and false positive signal caused by nonspecific binding. To solve this problem, we propose a way to restrict the labeled-dyes in a hydrophobic cavity of cyclodextrin. This bounding, which acts like extra base pairs to form the Watson-Crick duplex, achieves variation of level of space proximity of the two labels and thus the degree of conformational constraint. To demonstrate the feasibility of the design, a stem-containing oligonucleotide probe (P1) for DNA hybridization assay and a stemless one (P2) for protein detection were examined as models. Both oligonucleotides were doubly labeled with pyrene at the 5'- and 3'- ends, respectively. It is the cyclodextrin/pyrene inclusion interaction that allows modulating the degree of conformational constraints of P1 and P2 and thus their background signals and selectivity. Under the optimal conditions, the ratio of signal-to-background of P1/gamma-CD induced by 1.0 equiv target DNA is near 174, which is 4-fold higher than that in the absence of gamma-CD. In addition, the usage of gamma-CD shifts the melting temperature of P1 from 57 to 68 degrees C, which is reasonable for improving target-binding selectivity. This approach is simple in design, avoiding any variation of the stem's length and sequences. Furthermore, the strategy is generalizable which is suited for not only the stem-containing probe but also the linear probe with comparable sensitivity and selectivity to conventional structured DNA probes.

  14. FoldAtlas: a repository for genome-wide RNA structure probing data.

    PubMed

    Norris, Matthew; Kwok, Chun Kit; Cheema, Jitender; Hartley, Matthew; Morris, Richard J; Aviran, Sharon; Ding, Yiliang

    2017-01-15

    Most RNA molecules form internal base pairs, leading to a folded secondary structure. Some of these structures have been demonstrated to be functionally significant. High-throughput RNA structure chemical probing methods generate millions of sequencing reads to provide structural constraints for RNA secondary structure prediction. At present, processed data from these experiments are difficult to access without computational expertise. Here we present FoldAtlas, a web interface for accessing raw and processed structural data across thousands of transcripts. FoldAtlas allows a researcher to easily locate, view, and retrieve probing data for a given RNA molecule. We also provide in silico and in vivo secondary structure predictions for comparison, visualized in the browser as circle plots and topology diagrams. Data currently integrated into FoldAtlas are from a new high-depth Structure-seq data analysis in Arabidopsis thaliana, released with this work. The FoldAtlas website can be accessed at www.foldatlas.com Source code is freely available at github.com/mnori/foldatlas under the MIT license. Raw reads data are available under the NCBI SRA accession SRP066985. yiliang.ding@jic.ac.uk or matthew.norris@jic.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  15. Dynamical probe of thermodynamical properties in three-dimensional hairy AdS black holes

    NASA Astrophysics Data System (ADS)

    Zou, De-Cheng; Liu, Yunqi; Zhang, Cheng-Yong; Wang, Bin

    2016-11-01

    We study separatively the quasinormal modes (QNM) of electromagnetic perturbations around three-dimensional anti-de Sitter (AdS) black holes in Jordan and Einstein frames, which are related by the conformal transformations and a redefinition of a scalar field. We find that, in the Jordan frame, the imaginary parts of QNM frequencies can reflect the thermodynamical stabilities of hairy black holes, including the possible phase transition between the hairy black hole and BTZ black hole, disclosed by examining the corresponding free energies. Similar results are also uncovered in the Einstein frame. The obtained results further support that the QNM can be a dynamic probe of the thermodynamic properties in black holes.

  16. Probing the photoluminescence properties of gold nanoclusters by fluorescence lifetime correlation spectroscopy

    SciTech Connect

    Yuan, C. T. Lin, T. N.; Shen, J. L.; Lin, C. A.; Chang, W. H.; Cheng, H. W.; Tang, J.

    2013-12-21

    Gold nanoclusters (Au NCs) have attracted much attention for promising applications in biological imaging owing to their tiny sizes and biocompatibility. So far, most efforts have been focused on the strategies for fabricating high-quality Au NCs and then characterized by conventional ensemble measurement. Here, a fusion single-molecule technique combining fluorescence correlation spectroscopy and time-correlated single-photon counting can be successfully applied to probe the photoluminescence (PL) properties for sparse Au NCs. In this case, the triplet-state dynamics and diffusion process can be observed simultaneously and the relevant time constants can be derived. This work provides a complementary insight into the PL mechanism at the molecular levels for Au NCs in solution.

  17. Fluorescent eosin probe in investigations of structural changes in glycated proteins

    NASA Astrophysics Data System (ADS)

    Pravdin, A. B.; Kochubey, V. I.; Mel'Nikov, A. G.

    2010-08-01

    The possibility of using the luminescent-kinetic probe method to investigate structural changes in bovine serum albumin (BSA) upon nonenzymatic thermal glycation is studied. An increase in the glycation time lead to a decrease in the intensity of the probe (eosin) fluorescence and to a long-wavelength shift of its maximum, as well as to an increase in the eosin phosphorescence intensity, which indicates that eosin binds to hydrophobic regions of protein at any times of incubation of BSA with glucose. From a decrease in the rate constant of the triplet-triplet energy transfer between the donor (eosin) and acceptor (anthracene) bound to proteins, it is found that the changes observed in the spectral characteristics of eosin are caused by structural changes in albumin globules as a result of glycosylation.

  18. Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes

    SciTech Connect

    Li, Y.; Zakharov, D.; Zhao, S.; Tappero, R.; Jung, U.; Elsen, A.; Baumann, Ph.; Nuzzo, R. G.; Stach, E. A.; Frenkel, A. I.

    2015-06-29

    Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction—ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. Lastly, this method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes.

  19. Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes

    DOE PAGES

    Li, Y.; Zakharov, D.; Zhao, S.; ...

    2015-06-29

    Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction—ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. Lastly,more » this method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes.« less

  20. Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes

    PubMed Central

    Li, Y.; Zakharov, D.; Zhao, S.; Tappero, R.; Jung, U.; Elsen, A.; Baumann, Ph.; Nuzzo, R.G.; Stach, E.A.; Frenkel, A.I.

    2015-01-01

    Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction—ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. This method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes. PMID:26119246

  1. Probing the structural dynamics of proteins and nucleic acids with optical tweezers.

    PubMed

    Ritchie, Dustin B; Woodside, Michael T

    2015-10-01

    Conformational changes are an essential feature of most molecular processes in biology. Optical tweezers have emerged as a powerful tool for probing conformational dynamics at the single-molecule level because of their high resolution and sensitivity, opening new windows on phenomena ranging from folding and ligand binding to enzyme function, molecular machines, and protein aggregation. By measuring conformational changes induced in a molecule by forces applied by optical tweezers, new insight has been gained into the relationship between dynamics and function. We discuss recent advances from studies of how structure forms in proteins and RNA, including non-native structures, fluctuations in disordered proteins, and interactions with chaperones assisting native folding. We also review the development of assays probing the dynamics of complex protein-nucleic acid and protein-protein assemblies that reveal the dynamic interactions between biomolecular machines and their substrates. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes

    NASA Astrophysics Data System (ADS)

    Li, Y.; Zakharov, D.; Zhao, S.; Tappero, R.; Jung, U.; Elsen, A.; Baumann, Ph.; Nuzzo, R. G.; Stach, E. A.; Frenkel, A. I.

    2015-06-01

    Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction--ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. This method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes.

  3. Selective selenol fluorescent probes: design, synthesis, structural determinants, and biological applications.

    PubMed

    Zhang, Baoxin; Ge, Chunpo; Yao, Juan; Liu, Yaping; Xie, Huichen; Fang, Jianguo

    2015-01-21

    Selenium (Se) is an essential micronutrient element, and the biological significance of Se is predominantly dependent on its incorporation as selenocysteine (Sec), the genetically encoded 21st amino acid in protein synthesis, into the active site of selenoproteins, which have broad functions, ranging from redox regulation and anti-inflammation to the production of active thyroid hormones. Compared to its counterpart Cys, there are only limited probes for selective recognition of Sec, and such selectivity is strictly restricted at low pH conditions. We reported herein the design, synthesis, and biological evaluations of a series of potential Sec probes based on the mechanism of nucleophilic aromatic substitution. After the initial screening, the structural determinants for selective recognition of Sec were recapitulated. The follow-up studies identified that probe 19 (Sel-green) responds to Sec and other selenols with more than 100-fold increase of emission in neutral aqueous solution (pH 7.4), while there is no significant interference from the biological thiols, amines, or alcohols. Sel-green was successfully applied to quantify the Sec content in the selenoenzyme thioredoxin reductase and image endogenous Sec in live HepG2 cells. With the aid of Sel-green, we further demonstrated that the cytotoxicity of different selenocompounds is correlated to their ability metabolizing to selenols in cells. To the best of our knowledge, Sel-green is the first selenol probe that works under physiological conditions. The elucidation of the structure-activity relationship for selective recognition of selenols paves the way for further design of novel probes to better understand the pivotal role of Sec as well as selenoproteins in vivo.

  4. Probing the micro-rheological properties of aerosol particles using optical tweezers.

    PubMed

    Power, Rory M; Reid, Jonathan P

    2014-07-01

    The use of optical trapping techniques to manipulate probe particles for performing micro-rheological measurements on a surrounding fluid is well-established. Here, we review recent advances made in the use of optical trapping to probe the rheological properties of trapped particles themselves. In particular, we review observations of the continuous transition from liquid to solid-like viscosity of sub-picolitre supersaturated solution aerosol droplets using optical trapping techniques. Direct measurements of the viscosity of the particle bulk are derived from the damped oscillations in shape following coalescence of two particles, a consequence of the interplay between viscous and surface forces and the capillary driven relaxation of the approximately spheroidal composite particle. Holographic optical tweezers provide a facile method for the manipulation of arrays of particles allowing coalescence to be controllably induced between two micron-sized aerosol particles. The optical forces, while sufficiently strong to confine the composite particle, are several orders of magnitude weaker than the capillary forces driving relaxation. Light, elastically back-scattered by the particle, is recorded with sub-100 ns resolution allowing measurements of fast relaxation (low viscosity) dynamics, while the brightfield image can be used to monitor the shape relaxation extending to times in excess of 1000 s. For the slowest relaxation dynamics studied (particles with the highest viscosity) the presence and line shape of whispering gallery modes in the cavity enhanced Raman spectrum can be used to infer the relaxation time while serving the dual purpose of allowing the droplet size and refractive index to be measured with accuracies of ±0.025% and ±0.1%, respectively. The time constant for the damped relaxation can be used to infer the bulk viscosity, spanning from the dilute solution limit to a value approaching that of a glass, typically considered to be >10(12)

  5. Spectrophotometric probe

    DOEpatents

    Prather, William S.; O'Rourke, Patrick E.

    1994-01-01

    A support structure bearing at least one probe for making spectrophotometric measurements of a fluid using a source of light and a spectrophotometer. The probe includes a housing with two optical fibers and a planoconvex lens. A sleeve bearing a mirror surrounds the housing. The lens is separated from the mirror by a fixed distance, defining an interior space for receiving a volume of the fluid sample. A plurality of throughholes extending through the sleeve communicate between the sample volume and the exterior of the probe, all but one hole bearing a screen. A protective jacket surrounds the probe. A hollow conduit bearing a tube is formed in the wall of the probe for venting any air in the interior space when fluid enters. The probe is held at an acute angle so the optic fibers carrying the light to and from the probe are not bent severely on emergence from the probe.

  6. Spectrophotometric probe

    DOEpatents

    Prather, W.S.; O'Rourke, P.E.

    1994-08-02

    A support structure is described bearing at least one probe for making spectrophotometric measurements of a fluid using a source of light and a spectrophotometer. The probe includes a housing with two optical fibers and a planoconvex lens. A sleeve bearing a mirror surrounds the housing. The lens is separated from the mirror by a fixed distance, defining an interior space for receiving a volume of the fluid sample. A plurality of throughholes extending through the sleeve communicate between the sample volume and the exterior of the probe, all but one hole bearing a screen. A protective jacket surrounds the probe. A hollow conduit bearing a tube is formed in the wall of the probe for venting any air in the interior space when fluid enters. The probe is held at an acute angle so the optic fibers carrying the light to and from the probe are not bent severely on emergence from the probe. 3 figs.

  7. Structure-function relationships in the hammerhead ribozyme probed by base rescue.

    PubMed Central

    Peracchi, A; Matulic-Adamic, J; Wang, S; Beigelman, L; Herschlag, D

    1998-01-01

    We previously showed that the deleterious effects from introducing abasic nucleotides in the hammerhead ribozyme core can, in some instances, be relieved by exogenous addition of the ablated base and that the relative ability of different bases to rescue catalysis can be used to probe functional aspects of the ribozyme structure [Peracchi et al., Proc NatAcad Sci USA 93:11522]. Here we examine rescue at four additional positions, 3, 9, 12 and 13, to probe transition state interactions and to demonstrate the strengths and weaknesses of base rescue as a tool for structure-function studies. The results confirm functional roles for groups previously probed by mutagenesis, provide evidence that specific interactions observed in the ground-state X-ray structure are maintained in the transition state, and suggest formation in the transition state of other interactions that are absent in the ground state. In addition, the results suggest transition state roles for some groups that did not emerge as important in previous mutagenesis studies, presumably because base rescue has the ability to reveal interactions that are obscured by local structural redundancy in traditional mutagenesis. The base rescue results are complemented by comparing the effects of the abasic and phenyl nucleotide substitutions. The results together suggest that stacking of the bases at positions 9, 13 and 14 observed in the ground state is important for orienting other groups in the transition state. These findings add to our understanding of structure-function relationships in the hammerhead ribozyme and help delineate positions that may undergo rearrangements in the active hammerhead structure relative to the ground-state structure. Finally, the particularly efficient rescue by 2-methyladenine at position 13 relative to adenine and other bases suggests that natural base modifications may, in some instance, provide additional stability by taking advantage of hydrophobic interactions in folded RNAs

  8. Wireless Displacement Sensing Enabled by Metamaterial Probes for Remote Structural Health Monitoring

    PubMed Central

    Ozbey, Burak; Unal, Emre; Ertugrul, Hatice; Kurc, Ozgur; Puttlitz, Christian M.; Erturk, Vakur B.; Altintas, Ayhan; Demir, Hilmi Volkan

    2014-01-01

    We propose and demonstrate a wireless, passive, metamaterial-based sensor that allows for remotely monitoring submicron displacements over millimeter ranges. The sensor comprises a probe made of multiple nested split ring resonators (NSRRs) in a double-comb architecture coupled to an external antenna in its near-field. In operation, the sensor detects displacement of a structure onto which the NSRR probe is attached by telemetrically tracking the shift in its local frequency peaks. Owing to the NSRR's near-field excitation response, which is highly sensitive to the displaced comb-teeth over a wide separation, the wireless sensing system exhibits a relatively high resolution (<1 μm) and a large dynamic range (over 7 mm), along with high levels of linearity (R2 > 0.99 over 5 mm) and sensitivity (>12.7 MHz/mm in the 1–3 mm range). The sensor is also shown to be working in the linear region in a scenario where it is attached to a standard structural reinforcing bar. Because of its wireless and passive nature, together with its low cost, the proposed system enabled by the metamaterial probes holds a great promise for applications in remote structural health monitoring. PMID:24445416

  9. Structure, chemistry, and properties of mineral nanoparticles

    SciTech Connect

    Waychunas, G.A.; Zhang, H.; Gilbert, B.

    2008-12-02

    Nanoparticle properties can depart markedly from their bulk analog materials, including large differences in chemical reactivity, molecular and electronic structure, and mechanical behavior. The greatest changes are expected at the smallest sizes, e.g. 10 nm and below, where surface effects are expected to dominate bonding, shape and energy considerations. The precise chemistry at nanoparticle interfaces can have a profound effect on structure, phase transformations, strain, and reactivity. Certain phases may exist only as nanoparticles, requiring transformations in chemistry, stoichiometry and structure with evolution to larger sizes. In general, mineralogical nanoparticles have been little studied.

  10. Structure-property relationships in fluorinated polyimides

    SciTech Connect

    Auman, B.C.

    1995-12-01

    Over the past several years we have been exploring new fluorinated polyimides for electronics applications. In this paper we explore the effects of fluorine incorporation into polyimides by various methods. These include backbone modification via fluorinated linking groups and/or aromatic ring substitution, and incorporation of pendant fluoroalkyl side chains. Factors such as structural and positional isomerism of certain fluorinated groups on the properties of polyimide films are also considered. The properties investigated include dielectric constant, moisture absorption, thermal expansion coefficient, thermal stability, glass transition temperature, mechanical properties and solubility. The goal of this work has been to define the most fortuitous method of fluorine incorporation that will allow the optimum combination of properties for electronics.

  11. Structure Property Relationships of Carboxylic Acid Isosteres

    PubMed Central

    2016-01-01

    The replacement of a carboxylic acid with a surrogate structure, or (bio)-isostere, is a classical strategy in medicinal chemistry. The general underlying principle is that by maintaining the features of the carboxylic acid critical for biological activity, but appropriately modifying the physicochemical properties, improved analogs may result. In this context, a systematic assessment of the physicochemical properties of carboxylic acid isosteres would be desirable to enable more informed decisions of potential replacements to be used for analog design. Herein we report the structure–property relationships (SPR) of 35 phenylpropionic acid derivatives, in which the carboxylic acid moiety is replaced with a series of known isosteres. The data set generated provides an assessment of the relative impact on the physicochemical properties that these replacements may have compared to the carboxylic acid analog. As such, this study presents a framework for how to rationally apply isosteric replacements of the carboxylic acid functional group. PMID:26967507

  12. MASPROP- MASS PROPERTIES OF A RIGID STRUCTURE

    NASA Technical Reports Server (NTRS)

    Hull, R. A.

    1994-01-01

    The computer program MASPROP was developed to rapidly calculate the mass properties of complex rigid structural systems. This program's basic premise is that complex systems can be adequately described by a combination of basic elementary structural shapes. Thirteen widely used basic structural shapes are available in this program. They are as follows: Discrete Mass, Cylinder, Truncated Cone, Torus, Beam (arbitrary cross section), Circular Rod (arbitrary cross section), Spherical Segment, Sphere, Hemisphere, Parallelepiped, Swept Trapezoidal Panel, Symmetric Trapezoidal Panels, and a Curved Rectangular Panel. MASPROP provides a designer with a simple technique that requires minimal input to calculate the mass properties of a complex rigid structure and should be useful in any situation where one needs to calculate the center of gravity and moments of inertia of a complex structure. Rigid body analysis is used to calculate mass properties. Mass properties are calculated about component axes that have been rotated to be parallel to the system coordinate axes. Then the system center of gravity is calculated and the mass properties are transferred to axes through the system center of gravity by using the parallel axis theorem. System weight, moments of inertia about the system origin, and the products of inertia about the system center of mass are calculated and printed. From the information about the system center of mass the principal axes of the system and the moments of inertia about them are calculated and printed. The only input required is simple geometric data describing the size and location of each element and the respective material density or weight of each element. This program is written in FORTRAN for execution on a CDC 6000 series computer with a central memory requirement of approximately 62K (octal) of 60 bit words. The development of this program was completed in 1978.

  13. Synthesis and properties of fluorescence probe for detection of peroxides in mitochondria.

    PubMed

    Shioji, Kosei; Oyama, Yu; Okuma, Kentaro; Nakagawa, Hiroyuki

    2010-07-01

    In this study, a new type of fluorescence probe, diphenylpyrenylphosphine-conjugated alkyltriphenylphosphonium iodide which was accumulated in mitochondria, has been synthesized. This probe was detected peroxide in living cell. Comparison of the reactivity toward several peroxide indicated that the probe was existed in mitochondrial membrane. Using this probe, generation of peroxide in mitochondria of living cell was successfully visualized. 2010 Elsevier Ltd. All rights reserved.

  14. Method for analyzing nucleic acids by means of a substrate having a microchannel structure containing immobilized nucleic acid probes

    DOEpatents

    Ramsey, J. Michael; Foote, Robert S.

    2003-12-09

    A method and apparatus for analyzing nucleic acids includes immobilizing nucleic probes at specific sites within a microchannel structure and moving target nucleic acids into proximity to the probes in order to allow hybridization and fluorescence detection of specific target sequences.

  15. Method for analyzing nucleic acids by means of a substrate having a microchannel structure containing immobilized nucleic acid probes

    DOEpatents

    Ramsey, J. Michael; Foote, Robert S.

    2002-01-01

    A method and apparatus for analyzing nucleic acids includes immobilizing nucleic probes at specific sites within a microchannel structure and moving target nucleic acids into proximity to the probes in order to allow hybridization and fluorescence detection of specific target sequences.

  16. Probing nanoscale chemical segregation and surface properties of antifouling hybrid xerogel films.

    PubMed

    Destino, Joel F; Gatley, Caitlyn M; Craft, Andrew K; Detty, Michael R; Bright, Frank V

    2015-03-24

    Over the past decade there has been significant development in hybrid polymer coatings exhibiting tunable surface morphology, surface charge, and chemical segregation-all believed to be key properties in antifouling (AF) coating performance. While a large body of research exists on these materials, there have yet to be studies on all the aforementioned properties in a colocalized manner with nanoscale spatial resolution. Here, we report colocalized atomic force microscopy, scanning Kelvin probe microscopy, and confocal Raman microscopy on a model AF xerogel film composed of 1:9:9 (mol:mol:mol) 3-aminopropyltriethoxysilane (APTES), n-octyltriethoxysilane (C8), and tetraethoxysilane (TEOS) formed on Al2O3. This AF film is found to consist of three regions that are chemically and physically unique in 2D and 3D across multiple length scales: (i) a 1.5 μm thick base layer derived from all three precursors; (ii) 2-4 μm diameter mesa-like features that are enriched in free amine (from APTES), depleted in the other species and that extend 150-400 nm above the base layer; and (iii) 1-2 μm diameter subsurface inclusions within the base layer that are enriched in hydrogen-bonded amine (from APTES) and depleted in the other species.

  17. Engineering and Probing Topological Properties of Dirac Semimetal Films by Asymmetric Charge Transfer.

    PubMed

    Villanova, John W; Barnes, Edwin; Park, Kyungwha

    2017-02-08

    Dirac semimetals (DSMs) have topologically robust three-dimensional Dirac (doubled Weyl) nodes with Fermi-arc states. In heterostructures involving DSMs, charge transfer occurs at the interfaces, which can be used to probe and control their bulk and surface topological properties through surface-bulk connectivity. Here we demonstrate that despite a band gap in DSM films, asymmetric charge transfer at the surface enables one to accurately identify locations of the Dirac-node projections from gapless band crossings and to examine and engineer properties of the topological Fermi-arc surface states connecting the projections, by simulating adatom-adsorbed DSM films using a first-principles method with an effective model. The positions of the Dirac-node projections are insensitive to charge transfer amount or slab thickness except for extremely thin films. By varying the amount of charge transfer, unique spin textures near the projections and a separation between the Fermi-arc states change, which can be observed by gating without adatoms.

  18. New chorus wave properties near the equator from Van Allen Probes wave observations

    NASA Astrophysics Data System (ADS)

    Li, W.; Santolik, O.; Bortnik, J.; Thorne, R. M.; Kletzing, C. A.; Kurth, W. S.; Hospodarsky, G. B.

    2016-05-01

    The chorus wave properties are evaluated using Van Allen Probes data in the Earth's equatorial magnetosphere. Two distinct modes of lower band chorus are identified: a quasi-parallel mode and a quasi-electrostatic mode, whose wave normal direction is close to the resonance cone. Statistical results indicate that the quasi-electrostatic (quasi-parallel) mode preferentially occurs during relatively quiet (disturbed) geomagnetic activity at lower (higher) L shells. Although the magnetic intensity of the quasi-electrostatic mode is considerably weaker than the quasi-parallel mode, their electric intensities are comparable. A newly identified feature of the quasi-electrostatic mode is that its frequency peaks at higher values compared to the quasi-parallel mode that exhibits a broad frequency spectrum. Moreover, upper band chorus wave normal directions vary between 0° and the resonance cone and become more parallel as geomagnetic activity increases. Our new findings suggest that chorus-driven energetic electron dynamics needs a careful examination by considering the properties of these two distinct modes.

  19. Probing Quark-Gluon-Plasma properties with a Bayesian model-to-data comparison

    NASA Astrophysics Data System (ADS)

    Cai, Tianji; Bernhard, Jonah; Ke, Weiyao; Bass, Steffen; Duke QCD Group Team

    2016-09-01

    Experiments at RHIC and LHC study a special state of matter called the Quark Gluon Plasma (QGP), where quarks and gluons roam freely, by colliding relativistic heavy-ions. Given the transitory nature of the QGP, its properties can only be explored by comparing computational models of its formation and evolution to experimental data. The models fall, roughly speaking, under two categories-those solely using relativistic viscous hydrodynamics (pure hydro model) and those that in addition couple to a microscopic Boltzmann transport for the later evolution of the hadronic decay products (hybrid model). Each of these models has multiple parameters that encode the physical properties we want to probe and that need to be calibrated to experimental data, a task which is computationally expensive, but necessary for the knowledge extraction and determination of the models' quality. Our group has developed an analysis technique based on Bayesian Statistics to perform the model calibration and to extract probability distributions for each model parameter. Following the previous work that applies the technique to the hybrid model, we now perform a similar analysis on a pure-hydro model and display the posterior distributions for the same set of model parameters. We also develop a set of criteria to assess the quality of the two models with respect to their ability to describe current experimental data. Funded by Duke University Goldman Sachs Research Fellowship.

  20. Structural rearrangements of membrane proteins probed by water-edited solid-state NMR spectroscopy.

    PubMed

    Ader, Christian; Schneider, Robert; Seidel, Karsten; Etzkorn, Manuel; Becker, Stefan; Baldus, Marc

    2009-01-14

    We show that water-edited solid-state NMR spectroscopy allows for probing global protein conformation and residue-specific solvent accessibility in a lipid bilayer environment. The transfer dynamics can be well described by a general time constant, irrespective of protein topology and lipid environment. This approach was used to follow structural changes in response to protein function in the chimeric potassium channel KcsA-Kv1.3. Data obtained as a function of pH link earlier biochemical data to changes in protein structure in a functional bilayer setting.

  1. Mechanical Deformation Mechanisms and Properties of Prion Fibrils Probed by Atomistic Simulations

    NASA Astrophysics Data System (ADS)

    Choi, Bumjoon; Kim, Taehee; Ahn, Eue Soo; Lee, Sang Woo; Eom, Kilho

    2017-03-01

    Prion fibrils, which are a hallmark for neurodegenerative diseases, have recently been found to exhibit the structural diversity that governs disease pathology. Despite our recent finding concerning the role of the disease-specific structure of prion fibrils in determining their elastic properties, the mechanical deformation mechanisms and fracture properties of prion fibrils depending on their structures have not been fully characterized. In this work, we have studied the tensile deformation mechanisms of prion and non-prion amyloid fibrils by using steered molecular dynamics simulations. Our simulation results show that the elastic modulus of prion fibril, which is formed based on left-handed β-helical structure, is larger than that of non-prion fibril constructed based on right-handed β-helix. However, the mechanical toughness of prion fibril is found to be less than that of non-prion fibril, which indicates that infectious prion fibril is more fragile than non-infectious (non-prion) fibril. Our study sheds light on the role of the helical structure of amyloid fibrils, which is related to prion infectivity, in determining their mechanical deformation mechanisms and properties.

  2. Structural properties of small rhodium clusters

    SciTech Connect

    Soon, Yee Yeen; Yoon, Tiem Leong; Lim, Thong Leng

    2015-04-24

    We report a systematic study of the structural properties of rhodium clusters at the atomistic level. A novel global-minimum search algorithm, known as parallel tempering multicanonical basin hopping plus genetic algorithm (PTMBHGA), is used to obtain the geometrical structures with lowest minima at the semi-empirical level where Gupta potential is used to describe the atomic interaction among the rhodium atoms. These structures are then re-optimized at the density functional theory (DFT) level with exchange-correlation energy approximated by Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA). The structures are optimized for different spin multiplicities. The ones with lowest energies will be taken as ground-state structures. In most cases, we observe only minor changes in the geometry and bond length of the clusters as a result of DFT-level re-optimization. Only in some limited cases, the initial geometries obtained from the PTMBHGA are modified by the re-optimization. The variation of structural properties, such as ground-state geometry, symmetry and binding energy, with respect to the cluster size is studied and agreed well with other results available in the literature.

  3. Annexins V and XII alter the properties of planar lipid bilayers seen by conductance probes.

    PubMed

    Sokolov, Y; Mailliard, W S; Tranngo, N; Isas, M; Luecke, H; Haigler, H T; Hall, J E

    2000-05-01

    Annexins are proteins that bind lipids in the presence of calcium. Though multiple functions have been proposed for annexins, there is no general agreement on what annexins do or how they do it. We have used the well-studied conductance probes nonactin, alamethicin, and tetraphenylborate to investigate how annexins alter the functional properties of planar lipid bilayers. We found that annexin XII reduces the nonactin-induced conductance to approximately 30% of its original value. Both negative lipid and approximately 30 microM Ca(2+) are required for the conductance reduction. The mutant annexin XIIs, E105K and E105K/K68A, do not reduce the nonactin conductance even though both bind to the membrane just as wild-type does. Thus, subtle changes in the interaction of annexins with the membrane seem to be important. Annexin V also reduces nonactin conductance in nearly the same manner as annexin XII. Pronase in the absence of annexin had no effect on the nonactin conductance. But when added to the side of the bilayer opposite that to which annexin was added, pronase increased the nonactin-induced conductance toward its pre-annexin value. Annexins also dramatically alter the conductance induced by a radically different probe, alamethicin. When added to the same side of the bilayer as alamethicin, annexin has virtually no effect, but when added trans to the alamethicin, annexin dramatically reduces the asymmetry of the I-V curve and greatly slows the kinetics of one branch of the curve without altering those of the other. Annexin also reduces the rate at which the hydrophobic anion, tetraphenylborate, crosses the bilayer. These results suggest that annexin greatly reduces the ability of small molecules to cross the membrane without altering the surface potential and that at least some fraction of the active annexin is accessible to pronase digestion from the opposite side of the membrane.

  4. Silver ions-mediated conformational switch: facile design of structure-controllable nucleic acid probes.

    PubMed

    Wang, Yongxiang; Li, Jishan; Wang, Hao; Jin, Jianyu; Liu, Jinhua; Wang, Kemin; Tan, Weihong; Yang, Ronghua

    2010-08-01

    Conformationally constraint nucleic acid probes were usually designed by forming an intramolecular duplex based on Watson-Crick hydrogen bonds. The disadvantages of these approaches are the inflexibility and instability in complex environment of the Watson-Crick-based duplex. We report that this hydrogen bonding pattern can be replaced by metal-ligation between specific metal ions and the natural bases. To demonstrate the feasibility of this principle, two linear oligonucleotides and silver ions were examined as models for DNA hybridization assay and adenosine triphosphate detection. The both nucleic acids contain target binding sequences in the middle and cytosine (C)-rich sequences at the lateral portions. The strong interaction between Ag(+) ions and cytosines forms stable C-Ag(+)-C structures, which promises the oligonucleotides to form conformationally constraint formations. In the presence of its target, interaction between the loop sequences and the target unfolds the C-Ag(+)-C structures, and the corresponding probes unfolding can be detected by a change in their fluorescence emission. We discuss the thermodynamic and kinetic opportunities that are provided by using Ag(+) ion complexes instead of traditional Watson-Crick-based duplex. In particular, the intrinsic feature of the metal-ligation motif facilitates the design of functional nucleic acids probes by independently varying the concentration of Ag(+) ions in the medium.

  5. Polar structure of disclination loops in nematic liquid crystals probed by second-harmonic-light scattering.

    PubMed

    Pardaev, Shokir A; Williams, J C; Twieg, R J; Jakli, A; Gleeson, J T; Ellman, B; Sprunt, S

    2015-03-01

    Angle-resolved, second-harmonic-light scattering (SHLS) measurements are reported for three different classes of thermotropic nematic liquid crystals (NLCs): polar and nonpolar rodlike compounds and a bent-core compound. Results revealing well-defined scattering peaks are interpreted in terms of the electric polarization induced by distortions of the nematic orientational field ("flexopolarity") associated with inversion wall defects, nonsingular disclinations, analogous to Neel walls in ferromagnets, that often exhibit a closed loop morphology in NLCs. Analysis of the SHLS patterns based on this model provides a "proof-of-concept" for a potentially useful method to probe the flexopolar properties of NLCs.

  6. Perspective: Structure and dynamics of water at surfaces probed by scanning tunneling microscopy and spectroscopy

    NASA Astrophysics Data System (ADS)

    Guo, Jing; Bian, Ke; Lin, Zeren; Jiang, Ying

    2016-10-01

    The detailed and precise understanding of water-solid interaction largely relies on the development of atomic-scale experimental techniques, among which scanning tunneling microscopy (STM) has proven to be a noteworthy example. In this perspective, we review the recent advances of STM techniques in imaging, spectroscopy, and manipulation of water molecules. We discuss how those newly developed techniques are applied to probe the structure and dynamics of water at solid surfaces with single-molecule and even submolecular resolution, paying particular attention to the ability of accessing the degree of freedom of hydrogen. In the end, we present an outlook on the directions of future STM studies of water-solid interfaces as well as the challenges faced by this field. Some new scanning probe techniques beyond STM are also envisaged.

  7. Perspective: Structure and dynamics of water at surfaces probed by scanning tunneling microscopy and spectroscopy.

    PubMed

    Guo, Jing; Bian, Ke; Lin, Zeren; Jiang, Ying

    2016-10-28

    The detailed and precise understanding of water-solid interaction largely relies on the development of atomic-scale experimental techniques, among which scanning tunneling microscopy (STM) has proven to be a noteworthy example. In this perspective, we review the recent advances of STM techniques in imaging, spectroscopy, and manipulation of water molecules. We discuss how those newly developed techniques are applied to probe the structure and dynamics of water at solid surfaces with single-molecule and even submolecular resolution, paying particular attention to the ability of accessing the degree of freedom of hydrogen. In the end, we present an outlook on the directions of future STM studies of water-solid interfaces as well as the challenges faced by this field. Some new scanning probe techniques beyond STM are also envisaged.

  8. Microsurgery-aided in-situ force probing reveals extensibility and viscoelastic properties of individual stress fibers

    PubMed Central

    Labouesse, Céline; Gabella, Chiara; Meister, Jean-Jacques; Vianay, Benoît; Verkhovsky, Alexander B.

    2016-01-01

    Actin-myosin filament bundles (stress fibers) are critical for tension generation and cell shape, but their mechanical properties are difficult to access. Here we propose a novel approach to probe individual peripheral stress fibers in living cells through a microsurgically generated opening in the cytoplasm. By applying large deformations with a soft cantilever we were able to fully characterize the mechanical response of the fibers and evaluate their tension, extensibility, elastic and viscous properties. PMID:27025817

  9. Fluorescence studies with DNA probes: dynamic aspects of DNA structure and DNA-protein interactions

    NASA Astrophysics Data System (ADS)

    Millar, David P.; Carver, Theodore E.

    1994-08-01

    Time-resolved fluorescence measurements of optical probes incorporated at specific sites in DNA provides a new approach to studies of DNA structure and DNA:protein interactions. This approach can be used to study complex multi-state behavior, such as the folding of DNA into alternative higher order structures or the transfer of DNA between multiple binding sites on a protein. In this study, fluorescence anisotropy decay of an internal dansyl probe attached to 17/27-mer oligonucleotides was used to monitor the distribution of DNA 3' termini bound at either the polymerase of 3' to 5' exonuclease sites of the Klenow fragment of DNA polymerase I. Partitioning of the primer terminus between the two active sites of the enzyme resulted in a heterogeneous probe environment, reflected in the associative behavior of the fluorescence anisotropy decay. Analysis of the anisotropy decay with a two state model of solvent-exposed and protein-associated dansyl probes was used to determine the fraction of DNA bound at each site. We examined complexes of Klenow fragment with DNAs containing various base mismatches. Single mismatches at the primer terminus caused a 3-fold increase in the equilibrium partitioning of DNA into the exonuclease site, while two or more consecutive G:G mismatches caused the DNA to bind exclusively at the exonuclease site, with a partitioning constant at least 250- fold greater than that of the corresponding matched DNA sequence. Internal single mismatches located up to four bases from the primer terminus produced larger effects than the same mismatch at the primer terminus. These results provide insight into the recognition mechanisms that enable DNA polymerases to proofread misincorporated bases during DNA replication.

  10. The Structure and Properties of Parachute Cloths

    NASA Technical Reports Server (NTRS)

    Mcnicholas, H J; Hedrick, F

    1930-01-01

    The requisite properties of a parachute cloth are discussed and the methods for measuring these properties described. In addition to the structural analysis of the cloths, the properties measured were weight, breaking strength, tear resistance, elasticity, and air permeability. Thirty-six silk cloths of domestic manufacture, not previously used in parachute construction are compared with some silk cloths of foreign manufacture. These foreign cloths were ones proven by trial and extended use to be suitable materials for parachute construction. Contrary to the belief that domestic woven cloths were not suitable materials for parachute construction, it is shown that many domestic silk cloths are satisfactory and in some respects superior to the foreign products. Based on a comparative study of all the cloths, specifications are drawn for the manufacture of silk parachute cloth.

  11. Dynamically hot galaxies. I - Structural properties

    NASA Technical Reports Server (NTRS)

    Bender, Ralf; Burstein, David; Faber, S. M.

    1992-01-01

    Results are reported from an analysis of the structural properties of dynamically hot galaxies which combines central velocity dispersion, effective surface brightness, and effective radius into a new 3-space (k), in which the axes are parameters that are physically meaningful. Hot galaxies are found to divide into groups in k-space that closely parallel conventional morphological classifications, namely, luminous ellipticals, compacts, bulges, bright dwarfs, and dwarf spheroidals. A major sequence is defined by luminous ellipticals, bulges, and most compacts, which together constitute a smooth continuum in k-space. Several properties vary smoothly with mass along this continuum, including bulge-to-disk ratio, radio properties, rotation, degree of velocity anisotropy, and 'unrelaxed'. A second major sequence is comprised of dwarf ellipticals and dwarf spheroidals. It is suggested that mass loss is a major factor in hot dwarf galaxies, but the dwarf sequence cannot be simply a mass-loss sequence, as it has the wrong direction in k-space.

  12. Polarization properties of localized structures in VCSELs

    NASA Astrophysics Data System (ADS)

    Averlant, Etienne; Tlidi, Mustapha; Ackemann, Thorsten; Thienpont, Hugo; Panajotov, Krassimir

    2016-04-01

    Broad area Vertical-Cavity Surface-Emitting Lasers (VCSELs) have peculiar polarization properties which are a field of study by itself.1-3 These properties have already been used for localized structure generation, in a simple configuration, where only one polarization component was used.4 Here, we present new experimental and theoretical results on the complex polarization behavior of localized structures generated in an optically-injected broad area VCSEL. A linear stability analysis of the spin-flip VCSEL model is performed for the case of broad area devices, in a restrained and experimentally relevant parameter set. Numerical simulations are performed, in one and two dimensions. They reveal existence of vector localized structures. These structures have a complex polarization state, which is not simply a linear polarization following the one of the optical injection. Experimental results confirm theoretical predictions. Applications of this work can lead to the encoding of small color images in the polarization state of an ensemble of localized structures at the surface of a broad area VCSEL.

  13. Thermal and structural properties of ionic fluids.

    PubMed

    Bartsch, Hendrik; Dannenmann, Oliver; Bier, Markus

    2015-04-01

    The electrostatic interaction in ionic fluids is well known to give rise to a characteristic phase behavior and structure. Sometimes its long range is proposed to single out the electrostatic potential over other interactions with shorter ranges. Here the importance of the range for the phase behavior and the structure of ionic fluids is investigated by means of grandcanonical Monte Carlo simulations of the lattice restricted primitive model (LRPM). The long-ranged electrostatic interaction is compared to various types of short-ranged potentials obtained by sharp and/or smooth cutoff schemes. Sharply cutoff electrostatic potentials are found to lead to a strong dependence of the phase behavior and the structure on the cutoff radius. However, when combined with a suitable additional smooth cutoff, the short-ranged LRPM is found to exhibit quantitatively the same phase behavior and structure as the conventional long-ranged LRPM. Moreover, the Stillinger-Lovett perfect screening property, which is well known to be generated by the long-ranged electrostatic potential, is also fulfilled by short-ranged LRPMs with smooth cutoffs. By showing that the characteristic phase behavior and structure of ionic fluids can also be found in systems with short-ranged potentials, one can conclude that the decisive property of the electrostatic potential in ionic fluids is not the long range but rather the valency dependence.

  14. Acoustical properties of nonwoven fiber network structures

    NASA Astrophysics Data System (ADS)

    Tascan, Mevlut

    Sound insulation is one of the most important issues for the automotive and building industries. Because they are porous fibrous structures, textile materials can be used as sound insulating and sound absorbing materials. Very high-density materials such as steel can insulate sound very effectively but these rigid materials reflect most of the sound back to the environment, causing sound pollution. Additionally, because high-density, rigid materials are also heavy and high cost, they cannot be used for sound insulation for the automotive and building industries. Nonwoven materials are more suitable for these industries, and they can also absorb sound in order to decrease sound pollution in the environment. Therefore, nonwoven materials are one of the most important materials for sound insulation and absorption applications materials. Insulation and absorption properties of nonwoven fabrics depend on fiber geometry and fiber arrangement within the fabric structure. Because of their complex structure, it is very difficult to define the microstructure of nonwovens. The structure of nonwovens only has fibers and voids that are filled by air. Because of the complexity of fiber-void geometry, there is still not a very accurate theory or model that defines the structural arrangement. A considerable amount of modeling has been reported in literature [1--19], but most models are not accurate due to the assumptions made. Voids that are covered by fibers are called pores in nonwoven structures and their geometry is very important, especially for the absorption properties of nonwovens. In order to define the sound absorption properties of nonwoven fabrics, individual pore structure and the number of pores per unit thickness of the fabric should be determined. In this research, instead of trying to define pores, the properties of the fibers are investigated and the number of fibers per volume of fabric is taken as a parameter in the theory. Then the effect of the nonwoven

  15. Could Nano-Structured Materials Enable the Improved Pressure Vessels for Deep Atmospheric Probes?

    NASA Technical Reports Server (NTRS)

    Srivastava, D.; Fuentes, A.; Bienstock, B.; Arnold, J. O.

    2005-01-01

    A viewgraph presentation on the use of Nano-Structured Materials to enable pressure vessel structures for deep atmospheric probes is shown. The topics include: 1) High Temperature/Pressure in Key X-Environments; 2) The Case for Use of Nano-Structured Materials Pressure Vessel Design; 3) Carbon based Nanomaterials; 4) Nanotube production & purification; 5) Nanomechanics of Carbon Nanotubes; 6) CNT-composites: Example (Polymer); 7) Effect of Loading sequence on Composite with 8% by volume; 8) Models for Particulate Reinforced Composites; 9) Fullerene/Ti Composite for High Strength-Insulating Layer; 10) Fullerene/Epoxy Composite for High Strength-Insulating Layer; 11) Models for Continuous Fiber Reinforced Composites; 12) Tensile Strength for Discontinuous Fiber Composite; 13) Ti + SWNT Composites: Thermal/Mechanical; 14) Ti + SWNT Composites: Tensile Strength; and 15) Nano-structured Shell for Pressure Vessels.

  16. Probing Interstellar Silicate Dust Grain Properties in Quasar Absorption Systems at Redshifts z<1.4

    NASA Astrophysics Data System (ADS)

    Aller, M.; Kulkarni, V. P.; York, D. G.; Welty, D. E.; Vladilo, G.; Som, D.

    Absorption lines in the spectra of distant quasars whose sightlines serendipitously pass through foreground galaxies provide a valuable tool to simultaneously probe the dust and gas compositions of the interstellar medium (ISM) in galaxies. In particular, the damped and sub-damped Lyman- α (DLA/sub-DLA) absorbers trace gas-rich galaxies, independent of the intrinsic luminosities or star-formation rates of the associated galaxy stellar populations. The first evidence of silicate dust in a quasar absorption system was provided through our detection of the 10 µ m silicate feature in the z=0.52 DLA absorber toward the quasar AO 0235+164. We present results from 2 follow-up programs using archival Spitzer Space Telescope infrared spectra to study the interstellar silicate dust grain properties in a total of 13 quasar absorption systems at 0.1 < z < 1.4. We find clear detections of the 10 µ m silicate feature in the quasar absorption systems studied. In addition, we also detect the 18 µ m silicate feature in the sources with adequate spectral coverage. We find variations in the breadth, peak wavelength, and substructure of the 10 µ m interstellar silicate absorption features among the absorbers. This suggests that the silicate dust grain properties in these distant galaxies may differ relative to one another, and relative to those in the Milky Way. We also find suggestions in several sources, based on comparisons with laboratory-derived profiles from the literature, that the silicate dust grains may be significantly more crystalline than those in the amorphous Milky Way ISM. This is particularly evident in the z=0.89 absorber toward the quasar PKS 1830-211, where substructure near 10 µ m is consistent with a crystalline olivine composition. If confirmed, these grain property variations may have implications for both dust and galaxy evolution over the past 9 Gyrs, and for the commonly-made assumption that highredshift dust is similar to local dust. We also discuss

  17. Bio-related noble metal nanoparticle structure property relationships

    NASA Astrophysics Data System (ADS)

    Leonard, Donovan Nicholas

    Structure property relationships of noble metal nanoparticles (NPs) can be drastically different than bulk properties of the same metals. This research study used state-of-the-art analytical electron microscopy and scanned probe microscopy to determine material properties on the nanoscale of bio-related Au and Pd NPs. Recently, it has been demonstrated the self-assembly of Au NPs on functionalized silica surfaces creates a conductive surface. Determination of the aggregate morphology responsible for electron conduction was studied by atomic force microscopy (AFM) and scanning electron microscopy (SEM). In addition, changes in the electrical properties of the substrates after low temperature (<350°C) annealing was also studied. It was found that coalescence and densification of the Au NP aggregates disrupted the interconnected network which subsequently created a loss of conductivity. Investigation of bio-related Au/SiO2 core-shell NPs determined why published experimental results showed the sol-gel silica shell improved, by almost an order of magnitude, the detection efficiency of a DNA detection assay. Novel 360° rotation scanning TEM (STEM) imaging allowed study of individual NP surface morphology and internal structure. Electron energy loss spectroscopy (EELS) spectrum imaging determined optoelectronic properties and chemical composition of the silica shell used to encapsulate Au NPs. Results indicated the sol-gel deposited SiO2 had a band gap energy of ˜8.9eV, bulk plasmon-peak energy of ˜25.5eV and chemical composition of stoichiometric SiO2. Lastly, an attempt to elicit structure property relationships of novel RNA mediated Pd hexagon NPs was performed. Selected area electron diffraction (SAD), low voltage scanning transmission electron microscopy (LV-STEM), electron energy loss spectroscopy (EELS) and energy dispersive spectroscopy (EDS) were chosen for characterization of atomic ordering, chemical composition and optoelectronic properties of the novel

  18. Structure-property relationships in semicrystalline copolymers and ionomers

    NASA Astrophysics Data System (ADS)

    Wakabayashi, Katsuyuki

    Many outstanding physical properties of ethylene/(meth)acrylic acid (E/(M)AA) copolymers and ionomers are associated with their nanometer-scale morphology, which consists of ethylene crystallites, amorphous segments, and acid/ionic functional groups. The goal of this dissertation is a fundamental understanding of the interplay between these structural motifs and the consequent effects on the material properties. We identify small-strain modulus as a key mechanical property and investigate its dependence upon material structure through X-ray scattering, calorimetry, and mechanical property measurements. We first treat E/(M)AA copolymers as composites of polyethylene crystallites and amorphous regions, and establish a quantitative combining rule to describe the copolymer modulus. At temperatures above the Tg of the copolymers, a monotonic increase in modulus with crystallinity is quantitatively described by the Davies equation for two-phase composites, which serves as the basis for separating the effects of amorphous and crystalline phases throughout this dissertation. The room-temperature modulus of E/(M)AA copolymers is concurrently affected by ethylene crystallinity and proximity to the amorphous phase Tg, which rises through room temperature with increasing comonomer content. In E/(M)AA ionomers, phase separation and aggregation of ionic groups provide additional stiffness and toughness. Ionomers are modeled as composites of crystallites and ionically crosslinked rubber, whose amorphous phase modulus far above the ionomer Tg is satisfactorily described by simple rubber elasticity theory. Thermomechanical analyses probe the multi-step relaxation behavior of E/(M)AA ionomers and lead to the development of a new semicrystalline ionomer morphological model, wherein secondary crystallites and ionic aggregates together form rigid percolated pathways throughout the amorphous phase. Metal soaps are oligomeric analogs of E/(M)AA ionomers, which can be blended into

  19. Void structure of O+ ions in the inner magnetosphere observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Nakayama, Y.; Ebihara, Y.; Ohtani, S.; Gkioulidou, M.; Takahashi, K.; Kistler, L. M.; Tanaka, T.

    2016-12-01

    The Van Allen Probes Helium Oxygen Proton Electron instrument observed a new type of enhancement of O+ ions in the inner magnetosphere during substorms. As the satellite moved outward in the premidnight sector, the flux of the O+ ions with energy 10 keV appeared first in the energy-time spectrograms. Then, the enhancement of the flux spread toward high and low energies. The enhanced flux of the O+ ions with the highest energy remained, whereas the flux of the ions with lower energy vanished near apogee, forming what we call the void structure. The structure cannot be found in the H+ spectrogram. We studied the generation mechanism of this structure by using numerical simulation. We traced the trajectories of O+ ions in the electric and magnetic fields from the global magnetohydrodynamics simulation and calculated the flux of O+ ions in the inner magnetosphere in accordance with the Liouville theorem. The simulated spectrograms are well consistent with the ones observed by Van Allen Probes. We suggest the following processes. (1) When magnetic reconnection starts, an intensive equatorward and tailward plasma flow appears in the plasma lobe. (2) The flow transports plasma from the lobe to the plasma sheet where the radius of curvature of the magnetic field line is small. (3) The intensive dawn-dusk electric field transports the O+ ions earthward and accelerates them nonadiabatically to an energy threshold; (4) the void structure appears at energies below the threshold.

  20. Probing myosin structural conformation in vivo by second-harmonic generation microscopy

    PubMed Central

    Pavone, F. S.

    2010-01-01

    Understanding of complex biological processes requires knowledge of molecular structures and measurement of their dynamics in vivo. The collective chemomechanical action of myosin molecules (the molecular motors) in the muscle sarcomere represents a paradigmatic example in this respect. Here, we describe a label-free imaging method sensitive to protein conformation in vivo. We employed the order-based contrast enhancement by second-harmonic generation (SHG) for the functional imaging of muscle cells. We found that SHG polarization anisotropy (SPA) measurements report on the structural state of the actomyosin motors, with significant sensitivity to the conformation of myosin. In fact, each physiological/biochemical state we probed (relaxed, rigor, isometric contraction) produced a distinct value of polarization anisotropy. Employing a full reconstruction of the contributing elementary SHG emitters in the actomyosin motor array at atomic scale, we provide a molecular interpretation of the SPA measurements in terms of myosin conformations. We applied this method to the discrimination between attached and detached myosin heads in an isometrically contracting intact fiber. Our observations indicate that isometrically contracting muscle sustains its tetanic force by steady-state commitment of 30% of myosin heads. Applying SPA and molecular structure modeling to the imaging of unstained living tissues provides the basis for a generation of imaging and diagnostic tools capable of probing molecular structures and dynamics in vivo. PMID:20385845

  1. Effective structural properties in polycrystalline graphene

    NASA Astrophysics Data System (ADS)

    Hossain, Zubaer

    This talk will discuss effective structural properties in polycrystalline graphene under the presence of atomic scale heterogeneity. Polycrystallinity is ubiquitous in solids, but theories describing their effective behavior remain limited, particularly when heterogeneity is present in the form of nonuniform deformation or composition. Over the decades, exploration of the effective transport and strength properties of heterogeneous systems has been carried out mostly with random distribution of grains or regular periodic structures under various approximations, in translating the underlying physics into a single representative volume element. Although heterogeneity can play a critical role in modulating the basic behavior of low-dimensional materials, it is difficult to capture the local characteristics accurately by these approximations. Taking polycrystalline graphene as an example material, we study the effective structural properties (such as Young's Modulus, Poisson's ratio and Toughness) by using a combination of density functional theory and molecular dynamic simulations. We identify the key mechanisms that govern their effective behavior and exploit the understanding to engineer the behavior by doping with a carefully selected choice of chemical elements.

  2. Probing the clumping structure of giant molecular clouds through the spectrum, polarisation and morphology of X-ray reflection nebulae

    NASA Astrophysics Data System (ADS)

    Molaro, Margherita; Khatri, Rishi; Sunyaev, Rashid A.

    2016-05-01

    We introduce a new method for probing global properties of clump populations in giant molecular clouds (GMCs) in the case where these act as X-ray reflection nebulae (XRNe), based on the study of the clumping's overall effect on the reflected X-ray signal, in particular on the Fe K-α line's shoulder. We consider the particular case of Sgr B2, one of the brightest and most massive XRN in the Galactic center (GC) region. We parametrise the gas distribution inside the cloud using a simple clumping model with theslope of the clump mass function (α), the minimum clump mass (mmin), the fraction of the cloud's mass contained in clumps (fDGMF), and the mass-size relation of individual clumps as free parameters, and investigate how these affect the reflected X-ray spectrum. In the case of very dense clumps, similar to those presently observed in Sgr B2, these occupy a small volume of the cloud and present a small projected area to the incoming X-ray radiation. We find that these contribute negligibly to the scattered X-rays. Clump populations with volume-filling factors of >10-3 do leave observational signatures, that are sensitive to the clump model parameters, in the reflected spectrum and polarisation. Future high angular resolution X-ray observations could therefore complement the traditional optical and radio observations of these GMCs, and prove to be a powerful probe in the study of their internal structure. Clumps in GMCs should further be visible both as bright spots and regions of heavy absorption in high resolution X-ray observations. We therefore also study the time-evolution of the X-ray morphology, under illumination by a transient source, as a probe of the 3D distribution and column density of individual clumps by future X-ray observatories.

  3. Probing the Thermodynamic Properties of Mantle Rocks in Solid and Liquid States

    NASA Astrophysics Data System (ADS)

    Wolf, Aaron S.

    Our understanding of the structure and evolution of the deep Earth is strongly linked to knowledge of the thermodynamic properties of rocky materials at extreme temperatures and pressures. In this thesis, I present work that helps constrain the equation of state properties of iron-bearing Mg-silicate perovskite as well as oxide-silicate melts. I use a mixture of experimental, statistical, and theoretical techniques to obtain knowledge about these phases. These include laser-heated diamond anvil cell experiments, Bayesian statistical analysis of powder diffraction data, and the development of a new simplified model for understanding oxide and silicate melts at mantle conditions. By shedding light on the thermodynamic properties of such ubiquitous Earth-forming materials, I hope to aid our community's progress toward understanding the large-scale processes operating in the Earth's mantle, both in the modern day and early in Earth's history.

  4. Diffraction of Laser Light as a Probe of Ordered Tissue Structure

    NASA Astrophysics Data System (ADS)

    Stewart, Cody; Forrester, Kevin; Frank, C. B.; Irvine-Halliday, David; Muldrew, Ken; Shrive, Nigel; Thompson, Robert

    2002-05-01

    Laser light transmitted through thin slices of ordered tissue, such as tendon and ligament, forms a diffraction pattern elongated in the direction perpendicular to the alignment direction of the tissue fibers. The degree of elongation provides information on the degree of order in the tissue sample and thus provides a probe of the presence of scar tissue since, when damaged, collagen fibers reform more randomly than in healthy tissue. Small Angle Light Scattering (SALS) is an established technique that utilizes the diffraction properties of ordered tissue to determine bulk properties such as angle and degree of fiber orientation. This presentation will present experimental data that appears to dispute certain basic assumptions inherent in the method, as well as a basic theoretical explanation for why these assumptions may be inadequate under some experimental conditions.

  5. Structural and dynamical properties of complex networks

    NASA Astrophysics Data System (ADS)

    Ghoshal, Gourab

    Recent years have witnessed a substantial amount of interest within the physics community in the properties of networks. Techniques from statistical physics coupled with the widespread availability of computing resources have facilitated studies ranging from large scale empirical analysis of the worldwide web, social networks, biological systems, to the development of theoretical models and tools to explore the various properties of these systems. Following these developments, in this dissertation, we present and solve for a diverse set of new problems, investigating the structural and dynamical properties of both model and real world networks. We start by defining a new metric to measure the stability of network structure to disruptions, and then using a combination of theory and simulation study its properties in detail on artificially generated networks; we then compare our results to a selection of networks from the real world and find good agreement in most cases. In the following chapter, we propose a mathematical model that mimics the structure of popular file-sharing websites such as Flickr and CiteULike and demonstrate that many of its properties can solved exactly in the limit of large network size. The remaining part of the dissertation primarily focuses on the dynamical properties of networks. We first formulate a model of a network that evolves under the addition and deletion of vertices and edges, and solve for the equilibrium degree distribution for a variety of cases of interest. We then consider networks whose structure can be manipulated by adjusting the rules by which vertices enter and leave the network. We focus in particular on degree distributions and show that, with some mild constraints, it is possible by a suitable choice of rules to arrange for the network to have any degree distribution we desire. In addition we define a simple local algorithm by which appropriate rules can be implemented in practice. Finally, we conclude our

  6. Structure Property Relationships of Biobased Epoxy Resins

    NASA Astrophysics Data System (ADS)

    Maiorana, Anthony Surraht

    The thesis is about the synthesis, characterization, development, and application of epoxy resins derived from sustainable feedstocks such as lingo-cellulose, plant oils, and other non-food feedstocks. The thesis can be divided into two main topics 1) the synthesis and structure property relationship investigation of new biobased epoxy resin families and 2) mixing epoxy resins with reactive diluents, nanoparticles, toughening agents, and understanding co-curing reactions, filler/matrix interactions, and cured epoxy resin thermomechanical, viscoelastic, and dielectric properties. The thesis seeks to bridge the gap between new epoxy resin development, application for composites and advanced materials, processing and manufacturing, and end of life of thermoset polymers. The structures of uncured epoxy resins are characterized through traditional small molecule techniques such as nuclear magnetic resonance, high resolution mass spectrometry, and infrared spectroscopy. The structure of epoxy resin monomers are further understood through the process of curing the resins and cured resins' properties through rheology, chemorheology, dynamic mechanical analysis, tensile testing, fracture toughness, differential scanning calorimetry, scanning electron microscopy, thermogravimetric analysis, and notched izod impact testing. It was found that diphenolate esters are viable alternatives to bisphenol A and that the structure of the ester side chain can have signifi-cant effects on monomer viscosity. The structure of the cured diphenolate based epoxy resins also influence glass transition temperature and dielectric properties. Incorporation of reactive diluents and flexible resins can lower viscosity, extend gel time, and enable processing of high filler content composites and increase fracture toughness. Incorpora-tion of high elastic modulus nanoparticles such as graphene can provide increases in physical properties such as elastic modulus and fracture toughness. The synthesis

  7. Vibrationally Excited HCN around AFGL 2591: A Probe of Protostellar Structure

    NASA Astrophysics Data System (ADS)

    Veach, Todd J.; Groppi, Christopher E.; Hedden, Abigail

    2013-03-01

    Vibrationally excited molecules with submillimeter rotational transitions are potentially excellent probes of physical conditions near protostars. This study uses observations of the v = 1 and v = 2 ro-vibrational modes of HCN (4-3) to probe this environment. The presence or absence and relative strengths of these ro-vibrational lines probe the gas excitation mechanism and physical conditions in warm, dense material associated with protostellar disks. We present pilot observations from the Heinrich Hertz Submillimeter Telescope and follow-up observations from the Submillimeter Array. All vibrationally excited HCN (4-3) v = 0, v = 1, and v = 2 lines were observed. The existence of the three v = 2 lines at approximately equal intensity imply collisional excitation with a density of greater than (1010 cm-3) and a temperature of >1000 K for the emitting gas. This warm, high-density material should directly trace structures formed in the protostellar envelope and disk environment. Further, the line shapes of the v = 2 emission may suggest a Keplerian disk. This Letter demonstrates the utility of this technique which is of particular interest due to the recent inauguration of the Atacama Large Millimeter Array.

  8. Dual-targeting peptide probe for sequence- and structure-sensitive sensing of serum albumin.

    PubMed

    Yu, Yang; Huang, Yanyan; Jin, Yulong; Zhao, Rui

    2017-08-15

    Peptide-protein interactions mediate numerous biologic processes and provide great opportunity for developing peptide probes and analytical approaches for detecting and interfering with recognition events. Molecular interactions usually take place on the heterogeneous surface of proteins, and the spatial distribution and arrangement of probes are therefore crucial for achieving high specificity and sensitivity in the bioassays. In this study, small linear peptides, homogenous peptide dimers and hetero bivalent peptides were designed for site-specific recognition of human serum albumin (HSA). Three hydrophilic regions located at different subdomains of HSA were chosen as targets for the molecular design. The binding affinity, selectivity and kinetics of the candidates were screened with surface plasmon resonance imaging (SPRi) and fluoroimmuno assays. Benefiting from the synergistic effect from the surface-targeted peptide binders and the flexible spacer, a heterogenetic dimer peptide (heter-7) with fast binding and slow dissociation behavior was identified as the optimized probe. Heter-7 specifically recognizes the target protein HSA, and effectively blocks the binding of antibody to HSA. Its inhibitory activity was estimated as 83nM. It is noteworthy that heter-7 can distinguish serum albumins from different species despite high similarities in sequence and structure of these proteins. This hetero bivalent peptide shows promise for use in serum proteomics, disease detection and drug transport, and provides an effective approach for promoting the affinity and selectivity of ligands to achieve desirable chemical and biological outcomes. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. VIBRATIONALLY EXCITED HCN AROUND AFGL 2591: A PROBE OF PROTOSTELLAR STRUCTURE

    SciTech Connect

    Veach, Todd J.; Groppi, Christopher E.; Hedden, Abigail

    2013-03-10

    Vibrationally excited molecules with submillimeter rotational transitions are potentially excellent probes of physical conditions near protostars. This study uses observations of the v = 1 and v = 2 ro-vibrational modes of HCN (4-3) to probe this environment. The presence or absence and relative strengths of these ro-vibrational lines probe the gas excitation mechanism and physical conditions in warm, dense material associated with protostellar disks. We present pilot observations from the Heinrich Hertz Submillimeter Telescope and follow-up observations from the Submillimeter Array. All vibrationally excited HCN (4-3) v = 0, v = 1, and v = 2 lines were observed. The existence of the three v = 2 lines at approximately equal intensity imply collisional excitation with a density of greater than (10{sup 10} cm{sup -3}) and a temperature of >1000 K for the emitting gas. This warm, high-density material should directly trace structures formed in the protostellar envelope and disk environment. Further, the line shapes of the v = 2 emission may suggest a Keplerian disk. This Letter demonstrates the utility of this technique which is of particular interest due to the recent inauguration of the Atacama Large Millimeter Array.

  10. Effect of contact force on breast tissue optical property measurements using a broadband diffuse optical spectroscopy handheld probe

    PubMed Central

    Cerussi, Albert; Siavoshi, Sarah; Durkin, Amanda; Chen, Cynthia; Tanamai, Wendy; Hsiang, David; Tromberg, Bruce J.

    2010-01-01

    We investigated the effects of operator-applied force on diffuse optical spectroscopy (DOS) by integrating a force transducer into the handheld probe. Over the typical range of contact forces measured in the breasts of eight patients, absorption and reduced scattering coefficients (650 to 1000 nm) variance was 3.1 ± 1.0% and 1.0 ± 0.4%. For trained operators, we observed <5% variation in hemoglobin and <2% variation in water and lipids. Contact force is not a significant source of variation, most likely because of a relatively wide probe surface area and the stability of the DOS method for calculating tissue optical properties. PMID:19623242

  11. Structural Properties of Defects in Glassy Liquids.

    PubMed

    Cubuk, Ekin D; Schoenholz, Samuel S; Kaxiras, Efthimios; Liu, Andrea J

    2016-07-07

    At zero temperature a disordered solid corresponds to a local minimum in the energy landscape. As the temperature is raised or the system is driven with a mechanical load, the system explores different minima via dynamical events in which particles rearrange their relative positions. We have shown recently that the dynamics of particle rearrangements are strongly correlated with a structural quantity associated with each particle, "softness", which we can identify using supervised machine learning. Particles of a given softness have a well-defined energy scale that governs local rearrangements; because of this property, softness greatly simplifies our understanding of glassy dynamics. Here we investigate the correlation of softness with other commonly used structural quantities, such as coordination number and local potential energy. We show that although softness strongly correlates with these properties, its predictive power for rearrangement dynamics is much higher. We introduce a useful metric for quantifying the quality of structural quantities as predictors of dynamics. We hope that, in the future, authors introducing new structural measures of dynamics will compare their proposals quantitatively to softness using this metric. We also show how softness correlations give insight into rearrangements. Finally, we explore the physical meaning of softness using unsupervised dimensionality reduction and reduced curve-fitting models, and show that softness can be recast in a form that is amenable to analytical treatment.

  12. Electronic and structural properties of functional nanostructures

    NASA Astrophysics Data System (ADS)

    Yang, Teng

    In this Thesis, I present a study of electronic and structural properties of functional nanostructures such as MoSxIy nanowires, self-assembled monolayer on top of metallic surfaces and structural changes induced in graphite by photo excitations. MoSxI y nanowires, which can be easily synthesized in one step, show many advantages over conventional carbon nanotubes in molecular electronics and many other applications. But how to self-assemble them into desired pattern for practical electronic network? Self-assembled monolayers of polymers on metallic surfaces may help to guide pattern formation of some nanomaterials such as MoSxIy nanowires. I have investigated the physical properties of these nanoscale wires and microscopic self-assembly mechanisms of patterns by total energy calculations combined with molecular dynamics simulations and structure optimization. First, I studied the stability of novel Molybdenum chaicohalide nanowires, a candidate for molecular electronics applications. Next, I investigated the self-assembly of nanoparticles into ordered arrays with the aid of a template. Such templates, I showed, can be formed by polymer adsorption on surfaces such as highly ordered pyrolytic graphite and Ag(111). Finally, I studied the physical origin of of structural changes induced in graphite by light in form of a femtosecond laser pulse.

  13. Fluorescent probe based on heteroatom containing styrylcyanine: pH-sensitive properties and bioimaging in vivo.

    PubMed

    Yang, Xiaodong; Gao, Ya; Huang, Zhibing; Chen, Xiaohui; Ke, Zhiyong; Zhao, Peiliang; Yan, Yichen; Liu, Ruiyuan; Qu, Jinqing

    2015-01-01

    A novel fluorescent probe based on heteroatom containing styrylcyanine is synthesized. The fluorescence of probe is bright green in basic and neutral media but dark orange in strong acidic environments, which could be reversibly switched. Such behavior enables it to work as a fluorescent pH sensor in the solution state and a chemosensor for detecting acidic and basic volatile organic compounds. Analyses by NMR spectroscopy confirm that the protonation or deprotonation of pyridinyl moiety is responsible for the sensing process. In addition, the fluorescent microscopic images of probe in live cells and zebrafish are achieved successfully, suggesting that the probe has good cell membrane permeability and low cytotoxicity.

  14. A laser-induced ultrasonic probe of the mechanical properties of aligned lipid multibilayers.

    PubMed

    Eyring, G; Fayer, M D

    1985-01-01

    The recently developed laser-induced phonon spectroscopy (LIPS) technique is applied to the determination of dynamic mechanical properties of aligned dilauroylphosphatidylcholine (DLPC) multibilayer arrays containing 2 and 20% water by weight. Sample excitation by two crossed 100-ps laser pulses generates a longitudinal ultrasonic wave whose wavelength depends on the crossing angle. In these experiments, the acoustic wave propagates parallel to the bilayer planes. The ultrasonic velocity and attenuation are monitored through the diffraction of a variably delayed probe pulse by the acoustic grating. The velocity measures the lateral area compressibility of the bilayers, while the attenuation is related to the viscosity. Velocities obtained in the gel and liquid crystal phases are compared with those found previously using Brillouin scattering. The acoustic attenuation is shown to be an order of magnitude more sensitive to the gel-liquid crystal phase transition than the velocity. The lipid area compressibility and viscosity of DLPC-20% water multilayers with and without 100 mM CaCl2 are found to be identical within our experimental error.

  15. Pilot model expansion tunnel test flow properties obtained from velocity, pressure, and probe measurements

    NASA Technical Reports Server (NTRS)

    Friesen, W. J.; Moore, J. A.

    1973-01-01

    Velocity-profile, pitot-pressure, and supplemental probe measurements were made at the nozzle exist of an expansion tunnel (a modification to the Langley pilot model expansion tube) for a nozzle net condition of a nitrogen test sample with a velocity of 4.5 km/sec and a density 0.005 times the density of nitrogen at standard conditions, both with the nozzle initially immersed in a helium atmosphere and with the nozzle initially evacuated. The purpose of the report is to present the results of these measurements and some of the physical properties of the nitrogen test sample which can be inferred from the measured results. The main conclusions reached are that: the velocity profiles differ for two nozzle conditions; regions of the flow field can be found where the velocity is uniform to within 5 percent and constant for several hundred microseconds; the velocity of the nitrogen test sample is reduced due to passage through the nozzle; and the velocity profiles do not significantly reflect the large variations which occur in the inferred density profiles.

  16. PROBING THE LOCAL BUBBLE WITH DIFFUSE INTERSTELLAR BANDS. II. THE DIB PROPERTIES IN THE NORTHERN HEMISPHERE

    SciTech Connect

    Farhang, Amin; Khosroshahi, Habib G.; Javadi, Atefeh; Molaeinezhad, Alireza; Tavasoli, Saeed; Habibi, Farhang; Kourkchi, Ehsan; Rezaei, Sara; Saberi, Maryam; Van Loon, Jacco Th.; Bailey, Mandy; Hardy, Liam

    2015-02-10

    We present a new high signal-to-noise ratio spectroscopic survey of the Northern hemisphere to probe the Local Bubble and its surroundings using the λ5780 Å and λ5797 Å diffuse interstellar bands (DIBs). We observed 432 sightlines to a distance of 200 pc over a duration of three years. In this study, we establish the λ5780 and λ5797 correlations with Na I, Ca II and E {sub B-V}, for both inside and outside the Local Bubble. The correlations show that among all neutral and ionized atoms, the correlation between Ca II and λ5780 is stronger than its correlation with λ5797, suggesting that λ5780 is more associated with regions where Ca{sup +} is more abundant. We study the λ5780 correlation with λ5797, which shows a tight correlation within and outside the Local Bubble. In addition, we investigate the DIB properties in UV irradiated and UV shielded regions. We find that, within and beyond the Local Bubble, λ5797 is located in denser parts of clouds, protected from UV irradiation, while λ5780 is located in the low-density regions of clouds.

  17. Correlations between chorus properties and electron velocity distributions: Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Fu, X.; Cowee, M.; Gary, S. P.; Liu, K.; Min, K.; Winske, D.

    2014-12-01

    Magnetospheric chorus consists of whistler waves driven unstable by anisotropicelectron velocity distributions. A gap in the power spectrum of chorus at a fre-quency close to half the electron cyclotron frequency (Ωe/2) are often observedso that chorus can be categorized into four types accordingly: banded chorus(with two bands in the spectrum separated by Ωe/2), lower band only (withonly one band below Ωe/2), upper band only (with only one band above Ωe/2)and broadband (with only one band including Ωe/2). Here we present a studyto correlate chorus properties with electron velocity distributions based on thehypothesis that each band of chorus is excited by an anisotropic electron com-ponent. On Jan 14 2013, Van Allen Probes satellite A measured strong chorusactivity, and all four types were observed. We analyze HOPE and EMFISIS dataand show that there is a good correlation between the observed wave frequencyand propagation direction and the predictions of kinetic linear dispersion theoryusing electron component densities and temperatures obtained by fitting HOPEdata to a multi-component bi-Maxwellian distribution function. However, thetemperature anisotropies observed by HOPE are usually close to the instabil-ity threshold and therefore it is not possible at this point to predict whether acertain band can be excited based on measured electron velocity distributions.LA-UR-14-26177.

  18. Transmission X-ray scattering as a probe for complex liquid-surface structures

    SciTech Connect

    Fukuto, Masafumi; Yang, Lin; Nykypanchuk, Dmytro; Kuzmenko, Ivan

    2016-01-28

    The need for functional materials calls for increasing complexity in self-assembly systems. As a result, the ability to probe both local structure and heterogeneities, such as phase-coexistence and domain morphologies, has become increasingly important to controlling self-assembly processes, including those at liquid surfaces. The traditional X-ray scattering methods for liquid surfaces, such as specular reflectivity and grazing-incidence diffraction, are not well suited to spatially resolving lateral heterogeneities due to large illuminated footprint. A possible alternative approach is to use scanning transmission X-ray scattering to simultaneously probe local intermolecular structures and heterogeneous domain morphologies on liquid surfaces. To test the feasibility of this approach, transmission small- and wide-angle X-ray scattering (TSAXS/TWAXS) studies of Langmuir films formed on water meniscus against a vertically immersed hydrophilic Si substrate were recently carried out. First-order diffraction rings were observed in TSAXS patterns from a monolayer of hexagonally packed gold nanoparticles and in TWAXS patterns from a monolayer of fluorinated fatty acids, both as a Langmuir monolayer on water meniscus and as a Langmuir–Blodgett monolayer on the substrate. The patterns taken at multiple spots have been analyzed to extract the shape of the meniscus surface and the ordered-monolayer coverage as a function of spot position. These results, together with continual improvement in the brightness and spot size of X-ray beams available at synchrotron facilities, support the possibility of using scanning-probe TSAXS/TWAXS to characterize heterogeneous structures at liquid surfaces.

  19. Transmission X-ray scattering as a probe for complex liquid-surface structures

    DOE PAGES

    Fukuto, Masafumi; Yang, Lin; Nykypanchuk, Dmytro; ...

    2016-01-28

    The need for functional materials calls for increasing complexity in self-assembly systems. As a result, the ability to probe both local structure and heterogeneities, such as phase-coexistence and domain morphologies, has become increasingly important to controlling self-assembly processes, including those at liquid surfaces. The traditional X-ray scattering methods for liquid surfaces, such as specular reflectivity and grazing-incidence diffraction, are not well suited to spatially resolving lateral heterogeneities due to large illuminated footprint. A possible alternative approach is to use scanning transmission X-ray scattering to simultaneously probe local intermolecular structures and heterogeneous domain morphologies on liquid surfaces. To test the feasibilitymore » of this approach, transmission small- and wide-angle X-ray scattering (TSAXS/TWAXS) studies of Langmuir films formed on water meniscus against a vertically immersed hydrophilic Si substrate were recently carried out. First-order diffraction rings were observed in TSAXS patterns from a monolayer of hexagonally packed gold nanoparticles and in TWAXS patterns from a monolayer of fluorinated fatty acids, both as a Langmuir monolayer on water meniscus and as a Langmuir–Blodgett monolayer on the substrate. The patterns taken at multiple spots have been analyzed to extract the shape of the meniscus surface and the ordered-monolayer coverage as a function of spot position. These results, together with continual improvement in the brightness and spot size of X-ray beams available at synchrotron facilities, support the possibility of using scanning-probe TSAXS/TWAXS to characterize heterogeneous structures at liquid surfaces.« less

  20. Transmission X-ray scattering as a probe for complex liquid-surface structures

    SciTech Connect

    Fukuto, Masafumi; Yang, Lin; Nykypanchuk, Dmytro; Kuzmenko, Ivan

    2016-01-28

    The need for functional materials calls for increasing complexity in self-assembly systems. As a result, the ability to probe both local structure and heterogeneities, such as phase-coexistence and domain morphologies, has become increasingly important to controlling self-assembly processes, including those at liquid surfaces. The traditional X-ray scattering methods for liquid surfaces, such as specular reflectivity and grazing-incidence diffraction, are not well suited to spatially resolving lateral heterogeneities due to large illuminated footprint. A possible alternative approach is to use scanning transmission X-ray scattering to simultaneously probe local intermolecular structures and heterogeneous domain morphologies on liquid surfaces. To test the feasibility of this approach, transmission small- and wide-angle X-ray scattering (TSAXS/TWAXS) studies of Langmuir films formed on water meniscus against a vertically immersed hydrophilic Si substrate were recently carried out. First-order diffraction rings were observed in TSAXS patterns from a monolayer of hexagonally packed gold nanoparticles and in TWAXS patterns from a monolayer of fluorinated fatty acids, both as a Langmuir monolayer on water meniscus and as a Langmuir–Blodgett monolayer on the substrate. The patterns taken at multiple spots have been analyzed to extract the shape of the meniscus surface and the ordered-monolayer coverage as a function of spot position. These results, together with continual improvement in the brightness and spot size of X-ray beams available at synchrotron facilities, support the possibility of using scanning-probe TSAXS/TWAXS to characterize heterogeneous structures at liquid surfaces.

  1. Probing electric properties at the boundary of planar 2D heterostructure

    NASA Astrophysics Data System (ADS)

    Park, Jewook

    The quest for novel two-dimensional (2D) materials has led to the discovery of hybridized 2D atomic crystals. Especially, planar 2D heterostructure provides opportunities to explore fascinating electric properties at abrupt one-dimensional (1D) boundaries reminiscent to those seen in the 2D interfaces of complex oxides. By implementing the concept of epitaxy to 2D space, we developed a new growth technique to epitaxially grow hexagonal boron nitride (hBN) from the edges of graphene, forming a coherent planar heterostructure. At the interface of hBN and graphene, a polar-on-nonpolar 1D boundary can be formed which is expected to possess peculiar electronic states associated with the polarity of hBN and edge states of graphene Scanning tunneling microscopy and spectroscopy (STM/S) measurements revealed an abrupt 1D zigzag oriented boundary, with boundary states about 0.6 eV below or above the Fermi level depending on the termination of the hBN at the boundary. The boundary states are extended along the boundary and exponentially decay into the bulk of graphene and hBN. Combined STM/S and first-principles theory study not only disclose spatial and energetic distribution of interfacial state but also reveal the origin of boundary states and the effect of the polarity discontinuity at the interface By probing electric properties at the boundary in the atomic scale, planar 2D heterostructure is demonstrated as a promising platform for discovering emergent phenomena at the 1D interface in 2D materials. This research was conducted at the Center for Nanophase Materials Sciences, which is a DOE Office of Science User Facility.

  2. Probing the Physical Properties of High-Redshift Lyman-Alpha Emitters with Spitzer

    NASA Astrophysics Data System (ADS)

    Finkelstein, Keely; Finkelstein, Steven; Rhoads, James E.; Malhotra, Sangeeta

    2015-08-01

    Abstract: Studies of Lyman Alpha emitting galaxies (LAEs) offer insight into an understanding of early galaxies and the build-up of galaxies at early times. To better understand these objects and constrain their stellar properties, we have observed a sample of 162 z=4.5 and 14 z=5.7 LAEs with deep Spitzer IRAC 3.6 and 4.5 micron imaging from the Spitzer Lyman Alpha Survey. This is by far the largest sample of high-redshift LAEs imaged with Spitzer, which probes rest-frame optical wavelengths at these redshifts, dramatically improving constraints on the stellar masses and star-formation rates. By fitting the spectral energy distributions of individual LAEs using ground-based optical, HST near-IR, and Spitzer mid-IR imaging, we show that our sample of LAEs has a wide range of stellar properties. For individual LAEs detected with IRAC, stellar mass ranges from 5x10^8 - 10^11 solar masses. In addition, we find a correlation between stellar mass and star formation rate (SFR), similar to trends measured at lower redshift (e.g. Noeske et al. 2007; Daddi et al. 2007). However for this sample of higher redshift LAEs, the LAE sequence is elevated compared to continuum-selected galaxies at the same redshift, meaning that for a given stellar mass, the LAEs tend to have higher star formation rates. However, a subset of massive LAEs sits on the continuum-selected galaxy trend, tentatively implying that there may be two mechanisms for Lyman alpha escape.

  3. OPEN CLUSTERS AS PROBES OF THE GALACTIC MAGNETIC FIELD. I. CLUSTER PROPERTIES

    SciTech Connect

    Hoq, Sadia; Clemens, D. P. E-mail: clemens@bu.edu

    2015-10-15

    Stars in open clusters are powerful probes of the intervening Galactic magnetic field via background starlight polarimetry because they provide constraints on the magnetic field distances. We use 2MASS photometric data for a sample of 31 clusters in the outer Galaxy for which near-IR polarimetric data were obtained to determine the cluster distances, ages, and reddenings via fitting theoretical isochrones to cluster color–magnitude diagrams. The fitting approach uses an objective χ{sup 2} minimization technique to derive the cluster properties and their uncertainties. We found the ages, distances, and reddenings for 24 of the clusters, and the distances and reddenings for 6 additional clusters that were either sparse or faint in the near-IR. The derived ranges of log(age), distance, and E(B−V) were 7.25–9.63, ∼670–6160 pc, and 0.02–1.46 mag, respectively. The distance uncertainties ranged from ∼8% to 20%. The derived parameters were compared to previous studies, and most cluster parameters agree within our uncertainties. To test the accuracy of the fitting technique, synthetic clusters with 50, 100, or 200 cluster members and a wide range of ages were fit. These tests recovered the input parameters within their uncertainties for more than 90% of the individual synthetic cluster parameters. These results indicate that the fitting technique likely provides reliable estimates of cluster properties. The distances derived will be used in an upcoming study of the Galactic magnetic field in the outer Galaxy.

  4. Resonant inelastic x-ray scattering as a probe of band structure effects in cuprates

    NASA Astrophysics Data System (ADS)

    Kanász-Nagy, M.; Shi, Y.; Klich, I.; Demler, E. A.

    2016-10-01

    We analyze within quasiparticle theory a recent resonant inelastic x-ray scattering (RIXS) experiment on YBa2Cu3O6+x with the incoming photon energy detuned at several values from the resonance maximum [Minola et al., Phys. Rev. Lett. 114, 217003 (2015), 10.1103/PhysRevLett.114.217003]. Surprisingly, the data show a much weaker dependence on detuning than expected from recent measurements on a different cuprate superconductor, Bi2Sr2CuO6+x [Guarise et al., Nat. Commun. 5, 5760 (2014), 10.1038/ncomms6760]. We demonstrate here that this discrepancy, originally attributed to collective magnetic excitations, can be understood in terms of the differences between the band structures of these materials. We find good agreement between theory and experiment over a large range of dopings, both in the underdoped and overdoped regimes. Moreover, we demonstrate that the RIXS signal depends sensitively on excitations at energies well above the Fermi surface that are inaccessible to traditionally used band structure probes, such as angle-resolved photoemission spectroscopy. This makes RIXS a powerful probe of band structure, not suffering from surface preparation problems and small sample sizes, making it potentially applicable to a number of cuprate materials.

  5. Use of terbium as a probe of tRNA tertiary structure and folding.

    PubMed Central

    Hargittai, M R; Musier-Forsyth, K

    2000-01-01

    Lanthanide metals such as terbium have previously been shown to be useful for mapping metal-binding sites in RNA. Terbium binds to the same sites on RNA as magnesium, however, with a much higher affinity. Thus, low concentrations of terbium ions can easily displace magnesium and promote phosphodiester backbone scission. At higher concentrations, terbium cleaves RNA in a sequence-independent manner, with a preference for single-stranded, non-Watson-Crick base-paired regions. Here, we show that terbium is a sensitive probe of human tRNALys,3 tertiary structure and folding. When 1 microM tRNA is used, the optimal terbium ion concentration for detecting Mg2+-induced tertiary structural changes is 50-60 microM. Using these concentrations of RNA and terbium, a magnesium-dependent folding transition with a midpoint (KMg) of 2.6 mM is observed for unmodified human tRNALys,3. At lower Tb3+ concentrations, cleavage is restricted to nucleotides that constitute specific metal-binding pockets. This small chemical probe should also be useful for detecting protein induced structural changes in RNA. PMID:11105765

  6. Spectrally encoded fiber-based structured lighting probe for intraoperative 3D imaging

    PubMed Central

    Clancy, Neil T.; Stoyanov, Danail; Maier-Hein, Lena; Groch, Anja; Yang, Guang-Zhong; Elson, Daniel S.

    2011-01-01

    Three dimensional quantification of organ shape and structure during minimally invasive surgery (MIS) could enhance precision by allowing the registration of multi-modal or pre-operative image data (US/MRI/CT) with the live optical image. Structured illumination is one technique to obtain 3D information through the projection of a known pattern onto the tissue, although currently these systems tend to be used only for macroscopic imaging or open procedures rather than in endoscopy. To account for occlusions, where a projected feature may be hidden from view and/or confused with a neighboring point, a flexible multispectral structured illumination probe has been developed that labels each projected point with a specific wavelength using a supercontinuum laser. When imaged by a standard endoscope camera they can then be segmented using their RGB values, and their 3D coordinates calculated after camera calibration. The probe itself is sufficiently small (1.7 mm diameter) to allow it to be used in the biopsy channel of commonly used medical endoscopes. Surgical robots could therefore also employ this technology to solve navigation and visualization problems in MIS, and help to develop advanced surgical procedures such as natural orifice translumenal endoscopic surgery. PMID:22076272

  7. Resonant inelastic x-ray scattering as a band structure probe of high-temperature superconductors

    NASA Astrophysics Data System (ADS)

    Kanasz-Nagy, Marton; Shi, Yifei; Klich, Israel; Demler, Eugene

    I will analyze recent resonant inelastic x-ray scattering (RIXS) experimental data on YBa2Cu3O6 + x [Minola et al., Phys. Rev. Lett. 114, 217003 (2015)] within quasi-particle theory. This measurement has been performed with the incoming photon energy detuned at several values from the resonance maximum, and, surprisingly, the data shows much weaker dependence on detuning than expected from recent measurements on a different cuprate superconductor, Bi2Sr2CuO6 + x [Guarise et al., Nat. Commun. 5, 5760 (2014)]. I will demonstrate, that this discrepancy, originally attributed to collective magnetic excitations, can be understood in terms of the differences between the band structures of these materials. We found good agreement between theory and experiment over a large range of dopings [M. Kanasz-Nagy et al., arXiv:1508.06639]. Moreover, I will demonstrate that the RIXS signal depends sensitively on excitations at energies well above the Fermi surface, that are inaccessible to traditionally used band structure probes, such as angle-resolved photoemission spectroscopy. This makes RIXS a powerful probe of band structure, not suffering from surface preparation problems and small sample sizes, making it potentially applicable to a wide range of materials. The work of M. K.-N. was supported by the Harvard-MIT CUA, NSF Grant No. DMR-1308435, AFOSR Quantum Simulation MURI, the ARO-MURI on Atomtronics, and ARO MURI Quism program.

  8. Optical properties of honeycomb photonic structures

    NASA Astrophysics Data System (ADS)

    Sinelnik, Artem D.; Rybin, Mikhail V.; Lukashenko, Stanislav Y.; Limonov, Mikhail F.; Samusev, Kirill B.

    2017-06-01

    We study, theoretically and experimentally, optical properties of different types of honeycomb photonic structures, known also as "photonic graphene." First, we employ the two-photon polymerization method to fabricate the honeycomb structures. In the experiment, we observe a strong diffraction from a finite number of elements, thus providing a unique tool to define the exact number of scattering elements in the structure with the naked eye. Next, we study theoretically the transmission spectra of both honeycomb single layer and two-dimensional (2D) structures of parallel dielectric circular rods. When the dielectric constant of the rod materials ɛ is increasing, we reveal that a 2D photonic graphene structure transforms into a metamaterial when the lowest TE 01 Mie gap opens up below the lowest Bragg band gap. We also observe two Dirac points in the band structure of 2D photonic graphene at the K point of the Brillouin zone and demonstrate a manifestation of Dirac lensing for the TM polarization. The performance of the Dirac lens is that the 2D photonic graphene layer converts a wave from point source into a beam with flat phase surfaces at the Dirac frequency for the TM polarization.

  9. Probing zeolite internal structures using very low temperature {sup 129}Xe NMR

    SciTech Connect

    Labouriau, A.; Crawford, S.N.; Earl, W.L.; Pietrass, T.; Weber, W.A.; Panjabi, G.; Gates, B.C.

    1998-08-01

    In recent years, probing pore structure with {sup 129}Xe NMR has received a bad reputation. This is due to the fact that the method is more complex than was originally suggested so the data is somewhat difficult to interpret. The authors find that the use of a wide temperature range (40--350 K) allows them to interpret {sup 129}Xe chemical shifts in terms of van der Waals attraction between the xenon atom and oxygen in zeolite walls. Using rather simple models from the literature, they can extract useful pore size information as well as the van der Waals potential energy.

  10. Probing photonic and optoelectronic structures by apertureless scanning near-field optical microscopy.

    PubMed

    Bachelot, Renaud; Lerondel, Gilles; Blaize, Sylvain; Aubert, Sebastien; Bruyant, Aurelien; Royer, Pascal

    2004-08-01

    This report presents the Apertureless Scanning Optical Near-Field Microscope as a powerful tool for the characterization of modern optoelectronic and photonic components with sub-wavelength resolution. We present an overview of the results we obtained in our laboratory over the past few years. By significant examples, it is shown that this specific probe microscopy allows for in situ local quantitative study of semiconductor lasers in operation, integrated optical waveguides produced by ion exchange (single channel or Y junction), and photonic structures. 2004 Wiley-Liss, Inc.

  11. Probing of electronic structures of La@C82 superatoms upon clustering realized using glycine nanocavities

    NASA Astrophysics Data System (ADS)

    Taninaka, Atsushi; Ochiai, Takahiro; Kanazawa, Ken; Takeuchi, Osamu; Shigekawa, Hidemi

    2015-12-01

    We have succeeded in the first direct probe of the change in the electronic structures of La@C82 superatoms upon clustering by scanning tunneling microscopy/spectroscopy (STM/STS). An array of ∼1.3-nm-diameter glycine nanocavities self-assembled on a Cu(111) surface was used as a template. Isolated La@C82 superatoms were stably observed on terraces without diffusion to step edges, which enabled us to observe the change in the electronic structures associated with single, dimer, and clustered La@C82. A cluster with four La@C82 superatoms showed electronic structures similar to those obtained for thin films in previous works.

  12. Utilizing the Dyn2 dimerization-zipper as a tool to probe NPC structure and function.

    PubMed

    Flemming, Dirk; Stelter, Philipp; Hurt, Ed

    2014-01-01

    The discovery of dynein light chain 2 (Dyn2) as a member of the nucleoporins in yeast led to a series of applications to study NPC structure and function. Its intriguing ability to act as a hub for the parallel dimerization of two short amino acid sequence motifs (DID) prompted us to utilize it as a tool for probing nucleocytoplasmic transport in vivo. Further, the distinct structure of the Dyn2-DID rod, which is easily visible in the electron microscope, allowed us to develop a precise structural label on proteins or protein complexes. This label was used to identify the position of subunits in NPC subcomplexes or to derive at pseudo-atomic models of single large Nups. The versatility for various applications of the DID-Dyn2 system makes it an attractive molecular tool beyond the nuclear pore and transport field. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. Chemical Probes Allow Structural Insight into the Condensation Reaction of Nonribosomal Peptide Synthetases.

    PubMed

    Bloudoff, Kristjan; Alonzo, Diego A; Schmeing, T Martin

    2016-03-17

    Nonribosomal peptide synthetases (NRPSs) synthesize a vast variety of small molecules, including antibiotics, antitumors, and immunosuppressants. The NRPS condensation (C) domain catalyzes amide bond formation, the central chemical step in nonribosomal peptide synthesis. The catalytic mechanism and substrate determinants of the reaction are under debate. We developed chemical probes to structurally study the NRPS condensation reaction. These substrate analogs become covalently tethered to a cysteine introduced near the active site, to mimic covalent substrate delivery by carrier domains. They are competent substrates in the condensation reaction and behave similarly to native substrates. Co-crystal structures show C domain-substrate interactions, and suggest that the catalytic histidine's principle role is to position the α-amino group for nucleophilic attack. Structural insight provided by these co-complexes also allowed us to alter the substrate specificity profile of the reaction with a single point mutation. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Detecting the local transport properties and the dimensionality of transport of epitaxial graphene by a multi-point probe approach

    NASA Astrophysics Data System (ADS)

    Barreto, Lucas; Perkins, Edward; Johannsen, Jens; Ulstrup, Søren; Fromm, Felix; Raidel, Christian; Seyller, Thomas; Hofmann, Philip

    2013-01-01

    The electronic transport properties of epitaxial monolayer graphene (MLG) and hydrogen-intercalated quasi free-standing bilayer graphene (QFBLG) on SiC(0001) are investigated by micro multi-point probes. Using a probe with 12 contacts, we perform four-point probe measurements with the possibility to effectively vary the contact spacing over more than one order of magnitude, allowing us to establish that the transport is purely two-dimensional. Combined with the carrier density obtained by angle-resolved photoemission spectroscopy, we find the room temperature mobility of MLG to be (870±120) cm2/V s. The transport in QFBLG is also found to be two-dimensional with a mobility of (1600±160) cm2/V s.

  15. [Fluorescence property of a chemical probe for naked-eye and detection of Fe3+].

    PubMed

    Song, Yu-Min; Ma, Xin-Xian; Yang, Wu

    2012-12-01

    A higher selective and sensitive probe for the detection of Fe(III) in aqueous media was made using 2,4-Diisocyanatotoluene (TDI) as a bridge to couple Fe3 O4 nanoparticles(NPs) and Rhodamine-6G hydrazide. The characterization of composite materials with Infrared spectra(IR), Thermal Gravimetric analysis(TGA) and Transmission Emission Microscopy(TEM) points to the graft of Rhodamine-6G hydrazide onto the surface of the Fe3O4. The obvious color change of the probe solution from light grey to pink upon the addition of Fe3+ demonstrated the probe could be used for "naked-eye" detection of Fe3+ in water at pH 7. The presence of 1 equivalent (10 micromol x L(-1) microm) of each of these metal ions, including Mn2+, Ni2+, Y2+, Eu3+, Ce3+, La3+, Pr3+, Cd2+, Cr3+, Sm3+, Fe2+, Cu2+ and Zn2+ ions, did not demonstrate any obvious fluorescence change of the probe water solution, which confirmed the probe was a probe with remarkable selectivity for Fe3+. And the fluorescence images of HeLa cells in physiological solutions after incubation with Fe3+ and then further incubated with the probe leading to a strong intracellular fluorescence, which suggested the probe could penetrate the HeLa cell membrane and could respond to Fe3+ in intracellular within living cells.

  16. Structural and electronic properties for atomic clusters

    NASA Astrophysics Data System (ADS)

    Sun, Yan

    We have studied the structural and electronic properties for different groups of atomic clusters by doing a global search on the potential energy surface using the Taboo Search in Descriptors Space (TSDS) method and calculating the energies with Kohn-Sham Density Functional Theory (KS-DFT). Our goal was to find the structural and electronic principles for predicting the structure and stability of clusters. For Ben (n = 3--20), we have found that the evolution of geometric and electronic properties with size reflects a change in the nature of the bonding from van der Waals to metallic and then bulk-like. The cluster sizes with extra stability agree well with the predictions of the jellium model. In the 4d series of transition metal (TM) clusters, as the d-type bonding becomes more important, the preferred geometric structure changes from icosahedral (Y, Zr), to distorted compact structures (Nb, Mo), and FCC or simple cubic crystal fragments (Tc, Ru, Rh) due to the localized nature of the d-type orbital. Analysis of relative isomer energies and their electronic density of states suggest that these clusters tend to follow a maximum hardness principle (MHP). For A4B12 clusters (A is divalent, B is monovalent), we found unusually large (on average 1.95 eV) HOMO-LUMO gap values. This shows the extra stability at an electronic closed shell (20 electrons) predicted by the jellium model. The importance of symmetry, closed electronic and ionic shells in stability is shown by the relative stability of homotops of Mg4Ag12 which also provides support for the hypothesis that clusters that satisfy more than one stability criterion ("double magic") should be particularly stable.

  17. Native Cellulose: Structure, Characterization and Thermal Properties

    PubMed Central

    Poletto, Matheus; Ornaghi Júnior, Heitor L.; Zattera, Ademir J.

    2014-01-01

    In this work, the relationship between cellulose crystallinity, the influence of extractive content on lignocellulosic fiber degradation, the correlation between chemical composition and the physical properties of ten types of natural fibers were investigated by FTIR spectroscopy, X-ray diffraction and thermogravimetry techniques. The results showed that higher extractive contents associated with lower crystallinity and lower cellulose crystallite size can accelerate the degradation process and reduce the thermal stability of the lignocellulosic fibers studied. On the other hand, the thermal decomposition of natural fibers is shifted to higher temperatures with increasing the cellulose crystallinity and crystallite size. These results indicated that the cellulose crystallite size affects the thermal degradation temperature of natural fibers. This study showed that through the methods used, previous information about the structure and properties of lignocellulosic fibers can be obtained before use in composite formulations. PMID:28788179

  18. Chiral Vibrational Structures of Proteins at Interfaces Probed by Sum Frequency Generation Spectroscopy

    PubMed Central

    Fu, Li; Wang, Zhuguang; Yan, Elsa C.Y.

    2011-01-01

    We review the recent development of chiral sum frequency generation (SFG) spectroscopy and its applications to study chiral vibrational structures at interfaces. This review summarizes observations of chiral SFG signals from various molecular systems and describes the molecular origins of chiral SFG response. It focuses on the chiral vibrational structures of proteins and presents the chiral SFG spectra of proteins at interfaces in the C-H stretch, amide I, and N-H stretch regions. In particular, a combination of chiral amide I and N-H stretches of the peptide backbone provides highly characteristic vibrational signatures, unique to various secondary structures, which demonstrate the capacity of chiral SFG spectroscopy to distinguish protein secondary structures at interfaces. On the basis of these recent developments, we further discuss the advantages of chiral SFG spectroscopy and its potential application in various fields of science and technology. We conclude that chiral SFG spectroscopy can be a new approach to probe chiral vibrational structures of protein at interfaces, providing structural and dynamic information to study in situ and in real time protein structures and dynamics at interfaces. PMID:22272140

  19. Chiral vibrational structures of proteins at interfaces probed by sum frequency generation spectroscopy.

    PubMed

    Fu, Li; Wang, Zhuguang; Yan, Elsa C Y

    2011-01-01

    We review the recent development of chiral sum frequency generation (SFG) spectroscopy and its applications to study chiral vibrational structures at interfaces. This review summarizes observations of chiral SFG signals from various molecular systems and describes the molecular origins of chiral SFG response. It focuses on the chiral vibrational structures of proteins and presents the chiral SFG spectra of proteins at interfaces in the C-H stretch, amide I, and N-H stretch regions. In particular, a combination of chiral amide I and N-H stretches of the peptide backbone provides highly characteristic vibrational signatures, unique to various secondary structures, which demonstrate the capacity of chiral SFG spectroscopy to distinguish protein secondary structures at interfaces. On the basis of these recent developments, we further discuss the advantages of chiral SFG spectroscopy and its potential application in various fields of science and technology. We conclude that chiral SFG spectroscopy can be a new approach to probe chiral vibrational structures of protein at interfaces, providing structural and dynamic information to study in situ and in real time protein structures and dynamics at interfaces.

  20. Characterization of the electronic properties of magnetic and semiconductor devices using scanning probe techniques

    NASA Astrophysics Data System (ADS)

    Schaadt, Daniel Maria

    In the first part of this dissertation, scanning probe techniques are used in the study of localized charge deposition and subsequent transport in Co nanoclusters embedded in a SiO2 matrix are presented, and the application of this material in a hybrid magneto-electronic device for magnetic field sensing is described. Co nanoclusters are charged by applying a bias voltage pulse between a conductive tip and the sample, and electrostatic force microscopy is used to image charged areas. An exponential decay in the peak charge density is observed with decay times dependent on the nominal Co film thickness and on the sign of the deposited charge. The results are interpreted as a consequence of Coulomb-blockade effects. This study leads to the design of a hybrid magneto-electronic device, in which Co nanoclusters embedded in SiO2 are incorporated into the gate of a Si metal-oxide-semiconductor field-effect transistor. Current flow through the Co nanoclusters leads to a buildup of electronic charge within the gate, and consequently to a transistor threshold voltage shift that varies with applied external magnetic field. The shift in threshold voltage results in an exponential change in subthreshold current and a quadratic change in saturation current. A detailed analysis of the device operation is presented. The second part of this dissertation focuses on the characterization of electronic properties of GaN-based heterostructure devices. Scanning capacitance microscopy (SCM) and spectroscopy (SCS) are used to investigate lateral variations in the transistor threshold voltage and the frequency-dependent response of surface charges and of charge in the two-dimensional electron gas (2DEG). The technique is described in detail, electrostatic simulations performed to study the influence of the probe tip geometry on the measured dC/dV spectra are presented, and the limitations of the SCS technique in a variety of applications are evaluated. Features in SCM images and maps of

  1. Probing the graphite band structure with resonant soft-x-ray fluorescence

    SciTech Connect

    Carlisle, J.A.; Shirley, E.L.; Hudson, E.A.

    1997-04-01

    Soft x-ray fluorescence (SXF) spectroscopy using synchrotron radiation offers several advantages over surface sensitive spectroscopies for probing the electronic structure of complex multi-elemental materials. Due to the long mean free path of photons in solids ({approximately}1000 {angstrom}), SXF is a bulk-sensitive probe. Also, since core levels are involved in absorption and emission, SXF is both element- and angular-momentum-selective. SXF measures the local partial density of states (DOS) projected onto each constituent element of the material. The chief limitation of SXF has been the low fluorescence yield for photon emission, particularly for light elements. However, third generation light sources, such as the Advanced Light Source (ALS), offer the high brightness that makes high-resolution SXF experiments practical. In the following the authors utilize this high brightness to demonstrate the capability of SXF to probe the band structure of a polycrystalline sample. In SXF, a valence emission spectrum results from transitions from valence band states to the core hole produced by the incident photons. In the non-resonant energy regime, the excitation energy is far above the core binding energy, and the absorption and emission events are uncoupled. The fluorescence spectrum resembles emission spectra acquired using energetic electrons, and is insensitive to the incident photon`s energy. In the resonant excitation energy regime, core electrons are excited by photons to unoccupied states just above the Fermi level (EF). The absorption and emission events are coupled, and this coupling manifests itself in several ways, depending in part on the localization of the empty electronic states in the material. Here the authors report spectral measurements from highly oriented pyrolytic graphite.

  2. Giant radio galaxies as effective probes of X-ray gas in large-scale structure

    NASA Astrophysics Data System (ADS)

    Saripalli, Lakshmi; Subrahmanyan, Ravi; Malarecki, Jurek; Jones, Heath; Staveley-Smith, Lister

    2015-08-01

    Giant radio galaxies are AGNs with relativistic jets that dynamically evolve into Mpc scale synchrotron lobes around the host elliptical. The thermal gas environment influences the jet advance and lobe formation. Since the host ellipticals are in filamentary low-density galaxy environments, the ambient gas for the Mpc-scale radio structures is likely the warm-hot X-ray gas inhabiting the intergalactic medium. We have, therefore, used large radio galaxies as probes of the distribution of hot and tenuous gas on mega-parsec scales in these relatively low density large-scale structures.For a sample of 19 giant radio galaxies we obtained radio continuum images of the synchrotron structures, and redshifts of a total of nearly 9000 galaxies in their vicinity. The 2-degree field redshift data traces the large-scale galaxy structure around the radio sources. The radio-optical data allows an estimation of the pressure, temperature and distribution of hot thermal gas associated with the large-scale structure in the vicinity of the radio AGN (Malarecki, Staveley-Smith, Saripalli, Subrahmanyan, Jones, Duffy, Rioja 2013, MNRAS 432, 200).Strong correspondence between radio galaxy lobes and galaxy distribution is observed. The data suggests that galaxies trace gas, and that radio jets and lobes of giant radio galaxies are sensitive tracers of gas on mega-parsec scales and may be used as effective probes of the difficult-to-detect IGM (Malarecki, Jones, Saripalli, Stavele-Smith, Subrahmanyan, 2015, MNRAS in press; arXiv150203954).

  3. Structure-Property Relationships of Bismaleimides

    NASA Technical Reports Server (NTRS)

    Tenteris-Noebe, Anita D.

    1997-01-01

    The purpose of this research was to control and systematically vary the network topology of bismaleimides through cure temperature and chemistry (addition of various coreactants) and subsequently attempt to determine structure-mechanical property relationships. Characterization of the bismaleimide structures by dielectric, rheological, and thermal analyses, and density measurements was subsequently correlated with mechanical properties such as modulus, yield strength, fracture energy, and stress relaxation. The model material used in this investigation was 4,4'-BismaleiMidodIphenyl methane (BMI). BMI was coreacted with either 4,4'-Methylene Dianiline (MDA), o,o'-diallyl bisphenol A (DABA) from Ciba Geigy, or Diamino Diphenyl Sulfone (DDS). Three cure paths were employed: a low- temperature cure of 140 C where chain extension should predominate, a high-temperature cure of 220 C where both chain extension and crosslinking should occur simultaneously, and a low-temperature (140 C) cure followed immediately by a high-temperature (220 C) cure where the chain extension reaction or amine addition precedes BMI homopolymerization or crosslinking. Samples of cured and postcured PMR-15 were also tested to determine the effects of postcuring on the mechanical properties. The low-temperature cure condition of BMI/MDA exhibited the highest modulus values for a given mole fraction of BMI with the modulus decreasing with decreasing concentration of BMI. The higher elastic modulus is the result of steric hindrance by unreacted BMI molecules in the glassy state. The moduli values for the high- and low/high-temperature cure conditions of BMI/MDA decreased as the amount of diamine increased. All the moduli values mimic the yield strength and density trends. For the high-temperature cure condition, the room- temperature modulus remained constant with decreasing mole fraction of BMT for the BMI/DABA and BMI/DDS systems. Postcuring PMR-15 increases the modulus over that of the cured

  4. Glycolipid-based TLR4 Modulators and Fluorescent Probes: Rational Design, Synthesis, and Biological Properties.

    PubMed

    Ciaramelli, Carlotta; Calabrese, Valentina; Sestito, Stefania E; Pérez-Regidor, Lucia; Klett, Javier; Oblak, Alja; Jerala, Roman; Piazza, Matteo; Martín-Santamaría, Sonsoles; Peri, Francesco

    2016-08-01

    The cationic glycolipid IAXO-102, a potent TLR4 antagonist targeting both MD-2 and CD14 co-receptors, has been used as scaffold to design new potential TLR4 modulators and fluorescent labels for the TLR4 receptor complex (membrane TLR4.MD-2 dimer and CD14). The primary amino group of IAXO-102, not involved in direct interaction with MD-2 and CD14 receptors, has been exploited to covalently attach a fluorescein (molecules 1 and 2) or to link two molecules of IAXO-102 through diamine and diammonium spacers, obtaining 'dimeric' molecules 3 and 4. The structure-based rational design of compounds 1-4 was guided by the optimization of MD-2 and CD14 binding. Compounds 1 and 2 inhibited TLR4 activation, in a concentration-dependent manner, and signaling in HEK-Blue TLR4 cells. The fluorescent labeling of murine macrophages by molecule 1 was inhibited by LPS and was also abrogated when cell surface proteins were digested by trypsin, thus suggesting an interaction of fluorescent probe 1 with membrane proteins of the TLR4 receptor system.

  5. Structural, electronic and optical properties of carbonnitride

    SciTech Connect

    Cohen, Marvin L.

    1996-01-31

    Carbon nitride was proposed as a superhard material and a structural prototype, Beta-C3N4, was examined using several theoretical models. Some reports claiming experimental verifications have been made recently. The current status of the theory and experiment is reviewed, and a detailed discussion is presented of calculations of the electronic and optical properties of this material. These calculations predict that Beta-C3N4 will have a minimum gap which is indirect at 6.4 plus or minus 0.5 eV. A discussion of the possibility of carbon nitride nanotubes is also presented.

  6. Nanostructured lead sulfide: synthesis, structure and properties

    NASA Astrophysics Data System (ADS)

    Sadovnikov, S. I.; Gusev, A. I.; Rempel, A. A.

    2016-07-01

    The theoretical and experimental results of recent studies dealing with nanostructured lead sulfide are summarized and analyzed. The key methods for the synthesis of nanostructured lead sulfide are described. The crystal structure of PbS in nanopowders and nanofilms is discussed. The influence of the size of nanostructure elements on the optical and thermal properties of lead sulfide is considered. The dependence of the band gap of PbS on the nanoparticle (crystallite) size for powders and films is illustrated. The bibliography includes 222 references.

  7. Structural properties of impact ices accreted on aircraft structures

    NASA Technical Reports Server (NTRS)

    Scavuzzo, R. J.; Chu, M. L.

    1987-01-01

    The structural properties of ice accretions formed on aircraft surfaces are studied. The overall objectives are to measure basic structural properties of impact ices and to develop finite element analytical procedures for use in the design of all deicing systems. The Icing Research Tunnel (IRT) was used to produce simulated natural ice accretion over a wide range of icing conditions. Two different test apparatus were used to measure each of the three basic mechanical properties: tensile, shear, and peeling. Data was obtained on both adhesive shear strength of impact ices and peeling forces for various icing conditions. The influences of various icing parameters such as tunnel air temperature and velocity, icing cloud drop size, material substrate, surface temperature at ice/material interface, and ice thickness were studied. A finite element analysis of the shear test apparatus was developed in order to gain more insight in the evaluation of the test data. A comparison with other investigators was made. The result shows that the adhesive shear strength of impact ice typically varies between 40 and 50 psi, with peak strength reaching 120 psi and is not dependent on the kind of substrate used, the thickness of accreted ice, and tunnel temperature below 4 C.

  8. 'Trunk-like' ion structures observed by the Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Zhang, J.; Kistler, L. M.; Spence, H.; Wolf, R.; Reeves, G. D.; Skoug, R. M.; Funsten, H. O.; Larsen, B.; Niehof, J. T.; MacDonald, E.; Friedel, R. H.

    2013-12-01

    Dynamic ion spectral features in the inner magnetosphere are the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. In this study, we report 'trunk-like' ion structures observed in situ by the Van Allen Probes on 2 November 2012. The trunk structures are present in heavy ions but not in H+. For the particular event, ion energies in the He+ trunks, located at L = 3.7-2.6, MLT = 8.8-10.3, and MLAT = -2.0-0.03°, vary monotonically from 3.5 to 0.04 keV. It is suggested that the trunk phenomenon is due to a combination of 1) deeper ion injections from storm activity, 2) the longer charge exchange lifetimes of heavy ions than H+, 3) the separation of a narrow layer of ions around the Alfvén layer from other convecting ions, and 4) the trajectory of the Van Allen Probes (i.e., an orbital effect). Both observation analysis and numerical modeling are utilized in the study.

  9. Resonant detectors of gravitational wave as a possible probe of the noncommutative structure of space

    NASA Astrophysics Data System (ADS)

    Saha, Anirban; Gangopadhyay, Sunandan

    2016-10-01

    We report the plausibility of using quantum mechanical transitions, induced by the combined effect of gravitational waves (GWs) and noncommutative (NC) structure of space, among the states of a 2-dimensional harmonic oscillator, to probe the spatial NC geometry. The phonon modes excited by the passing GW within the resonant bar-detector or spherical detectors are formally identical to forced harmonic oscillator and they represent a length variation of roughly the same order of magnitude as the characteristic length-scale of spatial noncommutativity estimated from the phenomenological upper bound of the NC parameter. This motivates our present work. We employ various GW wave-forms that are typically expected from possible astronomical sources. We find that the transition probablities are quite sensitive to the nature of polarization of the GW. We also elaborate on the particular type of sources of GW, radiation from which one can induce such transitions. We speculate that this can be used as an effective probe of the spatial noncommutative structure when the quantum limit of sensitivity is achieved/surpassed in resonant bar/spherical detectors of GWs in the near future.

  10. Modifications of the structure of the pericellular matrix measured via optical force probe microscopy

    NASA Astrophysics Data System (ADS)

    McLane, Louis; Kramer, Anthony; Chang, Patrick; Curtis, Jennifer

    2013-03-01

    The pericellular matrix is a large protein and polysaccharide rich polymer layer attached to the surface of many cells, and which often extends several microns out from the cell surface into the surrounding extracellular space. Here we study the intrinsic nature and modifications of the structure of the pericellular coat on rat chondrocytes with the use of optical force probe microscopy. Optical force probe studies allow us to make both dynamic force measurements as well as equilibrium force measurements throughout the coat. These force measurements are used to observe the structural change in the coat with the addition of exogenous aggrecan. Not only does addition of exogenous aggrecan dramatically swell our coat to well over twice in size, our analysis indicates that the addition of exogenous aggrecan decreases the mesh size throughout the coat. We speculate that the added aggrecan binds to available binding sites along the hyaluronan chain, both enlarging the coat's size as well as tightening up the opening within the coat. We further suggest that the available binding sites for the exogenous aggrecan are abundant in the outer edges of the coat, as both the dynamic and equilibrium forces in this region are changed. Here, both force measurements show that forces closest to the cell membrane remain relatively unchanged, while the forces in the outer region of the coat are increased. These results are consistent with those obtained with complementary measurements using quantitative particle exclusion assays.

  11. Charge carrier transport properties in layer structured hexagonal boron nitride

    SciTech Connect

    Doan, T. C.; Li, J.; Lin, J. Y.; Jiang, H. X.

    2014-10-15

    Due to its large in-plane thermal conductivity, high temperature and chemical stability, large energy band gap (~ 6.4 eV), hexagonal boron nitride (hBN) has emerged as an important material for applications in deep ultraviolet photonic devices. Among the members of the III-nitride material system, hBN is the least studied and understood. The study of the electrical transport properties of hBN is of utmost importance with a view to realizing practical device applications. Wafer-scale hBN epilayers have been successfully synthesized by metal organic chemical deposition and their electrical transport properties have been probed by variable temperature Hall effect measurements. The results demonstrate that undoped hBN is a semiconductor exhibiting weak p-type at high temperatures (> 700 °K). The measured acceptor energy level is about 0.68 eV above the valence band. In contrast to the electrical transport properties of traditional III-nitride wide bandgap semiconductors, the temperature dependence of the hole mobility in hBN can be described by the form of μ ∝ (T/T{sub 0}){sup −α} with α = 3.02, satisfying the two-dimensional (2D) carrier transport limit dominated by the polar optical phonon scattering. This behavior is a direct consequence of the fact that hBN is a layer structured material. The optical phonon energy deduced from the temperature dependence of the hole mobility is ħω = 192 meV (or 1546 cm{sup -1}), which is consistent with values previously obtained using other techniques. The present results extend our understanding of the charge carrier transport properties beyond the traditional III-nitride semiconductors.

  12. Structure and Properties of Dense Silica Glass

    PubMed Central

    Wu, Min; Liang, Yunfeng; Jiang, Jian-Zhong; Tse, John S.

    2012-01-01

    The O K-edge x-ray Raman scattering (XRS), Brillouin scattering and diffraction studies on silica glass at high pressure have been elucidated in a unified manner using model structures obtained from First-Principles molecular dynamics calculations. This study provides a comprehensive understanding on how the structure is related to the physical and electronic properties. The origin of the “two peak” pattern in the XRS is found to be the result of increased packing of oxygen near the Si and is not a specific sign for sixfold coordination. The compression mechanism involving the presence of 5- and 6-fold coordinated silicon is confirmed. A slight increase in the silicon-oxygen coordination higher than six was found to accompany the increase in the acoustic wave velocity near 140 GPa. PMID:22570763

  13. Structural and optical properties of nanostructured nickel

    SciTech Connect

    Singh, J. Pandey, J.; Gupta, R.; Tripathi, J.; Kaurav, N.

    2016-05-06

    Metal nanoparticles are attractive because of their special structure and better optical properties. Nickel nanoparticles (Ni-Np) have been synthesized successfully by thermal decomposition method in the presence of trioctyl phosphine (TOP) and oleylamine (OAm). The samples were characterized by X-ray diffraction (XRD), Zetapotential measurement and Fourier transforms infrared (FTIR) spectroscopy. The size of Ni nanoparticles can be readily tuned from 13.86 nm. As-synthesized Ni nanoparticles have hexagonal closed pack (hcp) cubic structure as characterized by power X-ray diffraction (XRD) prepared at 280°C. The possible formation mechanism has also been phenomenological proposed for as synthesized Ni-Np. The value of Zeta potential was found 12.25 mV.

  14. Properties of multilayer nonuniform holographic structures

    SciTech Connect

    Pen, E F; Rodionov, Mikhail Yu

    2010-12-09

    Experimental results and analysis of properties of multilayer nonuniform holographic structures formed in photopolymer materials are presented. The theoretical hypotheses is proved that the characteristics of angular selectivity for the considered structures have a set of local maxima, whose number and width are determined by the thicknesses of intermediate layers and deep holograms and that the envelope of the maxima coincides with the selectivity contour of a single holographic array. It is also experimentally shown that hologram nonuniformities substantially distort shapes of selectivity characteristics: they become asymmetric, the local maxima differ in size and the depths of local minima reduce. The modelling results are made similar to experimental data by appropriately choosing the nonuniformity parameters. (imaging and image processing. holography)

  15. A combined penetrometer-moisture probe (CPMP) for investigating hydrological properties of forested hillslopes

    NASA Astrophysics Data System (ADS)

    Masaoka, N.; Yamakawa, Y.; Kosugi, K.; Mizuyama, T.; Tsutsumi, D.

    2008-12-01

    To predict shallow landslides on steep hillslopes, adequate and precise information on the soil structure and soil water movement are indispensable. A combined penetrometer-moisture probe (CPMP) was developed for measuring vertical profiles of soil water content and penetration resistance simultaneously, and applied to figure out internal structure of the soil mantle. In this study, we measured the profiles of water content and penetration resistance with the CPMP at each of 57 points on a forested valley-side slope in Hirudani research catchment, Hodaka, central Japan. Additionally, we installed tensiometers at each point for continuous measurements of pressure heads at soil-bedrock interface. Thickness of the soil layer was highly variable throughout the slope and the bedrock depression apparently shaped a hollow. Soil water content measured with the CPMP showed high values in the lower section of the slope. The high water content region extended to the upper slope section along the hollow, roughly corresponding with the region with high values of the topographic index. Pressure heads measured with tensiometers were positive throughout the observing period at most of the points where high water contents were detected with the CPMP. At some points in the upper slope section, water contents were especially high in spite of relatively small values of the topographic index. At these points, pressure heads showed delayed peaks in comparison with hyetographs and slow recession limbs, suggesting an existence of groundwater seepage from the bedrock. The other saturated points exhibited almost no responses to hyetographs, and all of the unsaturated points had rapid peaks coinciding with rainfall peaks. In conclusion, the CPMP has a large potential to reveal hydrological processes within hillslopes by providing simultaneous observations of soil water content and penetration resistance.

  16. Probing Cytoskeletal Structures by Coupling Optical Superresolution and AFM Techniques for a Correlative Approach

    PubMed Central

    Chacko, Jenu Varghese; Zanacchi, Francesca Cella; Diaspro, Alberto

    2013-01-01

    In this article, we describe and show the application of some of the most advanced fluorescence superresolution techniques, STED AFM and STORM AFM microscopy towards imaging of cytoskeletal structures, such as microtubule filaments. Mechanical and structural properties can play a relevant role in the investigation of cytoskeletal structures of interest, such as microtubules, that provide support to the cell structure. In fact, the mechanical properties, such as the local stiffness and the elasticity, can be investigated by AFM force spectroscopy with tens of nanometers resolution. Force curves can be analyzed in order to obtain the local elasticity (and the Young's modulus calculation by fitting the force curves from every pixel of interest), and the combination with STED/STORM microscopy integrates the measurement with high specificity and yields superresolution structural information. This hybrid modality of superresolution-AFM working is a clear example of correlative multimodal microscopy. PMID:24027190

  17. Probing Local Structures in ZrO2 Nanocrystals Using EXAFS

    NASA Astrophysics Data System (ADS)

    Soo, Y. L.; Chen, P. J.; Huang, S. H.; Shiu, T. J.; Tsai, T. Y.; Chow, Y. H.; Lin, Y. C.; Weng, S. C.; Chang, S. L.; Lee, J. F.; Cheung, C. L.; Sabirianov, R. F.; Namavar, F.; Mei, W. N.

    2008-03-01

    Extended x-ray absorption fine structure (EXAFS) has been employed to investigate the local structures surrounding Zr in cubic zirconia thin films prepared by an ion beam assisted deposition technique. These materials have demonstrated promising mechanical properties such as improved hardness and lubricant wettability compared to yttria-stabilized zirconia. To verify the cubic structure of zirconia in films prepared under different growth conditions and to fully understand the mechanism leading to their unique physical properties, the structural information is a required prerequisite. Since zirconia is in the form of nanosized crystallets, conventional x-ray diffraction method is not useful for this purpose. Our x-ray results reveal cubic-like structure with O vacancies around Zr in several nanocrystal samples. Powders of cubic zirconia prepared using chemical methods were also measured for comparison.

  18. Extraordinary electronic properties in uncommon structure types

    NASA Astrophysics Data System (ADS)

    Ali, Mazhar Nawaz

    In this thesis I present the results of explorations into several uncommon structure types. In Chapter 1 I go through the underlying idea of how we search for new compounds with exotic properties in solid state chemistry. The ideas of exploring uncommon structure types, building up from the simple to the complex, using chemical intuition and thinking by analogy are discussed. Also, the history and basic concepts of superconductivity, Dirac semimetals, and magnetoresistance are briefly reviewed. In chapter 2, the 1s-InTaS2 structural family is introduced along with the discovery of a new member of the family, Ag0:79VS2; the synthesis, structure, and physical properties of two different polymorphs of the material are detailed. Also in this chapter, we report the observation of superconductivity in another 1s structure, PbTaSe2. This material is especially interesting due to it being very heavy (resulting in very strong spin orbit coulping (SOC)), layered, and noncentrosymmetric. Electronic structure calculations reveal the presence of a bulk 3D Dirac cone (very similar to graphene) that is gapped by SOC originating from the hexagonal Pb layer. In Chapter 3 we show the re-investigation of the crystal structure of the 3D Dirac semimetal, Cd3As2. It is found to be centrosymmetric, rather than noncentrosymmetric, and as such all bands are spin degenerate and there is a 4-fold degenerate bulk Dirac point at the Fermi level, making Cd3As2 a 3D electronic analog to graphene. Also, for the first time, scanning tunneling microscopy experiments identify a 2x2 surface reconstruction in what we identify as the (112) cleavage plane of single crystals; needle crystals grow with a [110] long axis direction. Lastly, in chapter 4 we report the discovery of "titanic" (sadly dubbed ⪉rge, nonsaturating" by Nature editors and given the acronym XMR) magnetoresistance (MR) in the non-magnetic, noncentrosymmetric, layered transition metal dichalcogenide WTe2; over 13 million% at 0.53 K in

  19. Probing structural changes of proteins incorporated into water-in-oil emulsions.

    PubMed

    Jorgensen, Lene; Van de Weert, Marco; Vermehren, Charlotte; Bjerregaard, Simon; Frokjaer, Sven

    2004-07-01

    The applicability of different techniques, that is, Differential Scanning Calorimetry (DSC), Fourier Transform Infrared Spectroscopy (FTIR), and intrinsic tryptophan fluorescence, for probing the structural changes of proteins in the water-in-oil emulsions are investigated using nondefatted bovine (BSA) and human serum albumin (HSA) as model proteins. FTIR shows that the overall secondary structure of the proteins changes to some extent, 12% for BSA and 9% for HSA, when these are incorporated into the emulsion. There was no evidence of changes in the distribution of secondary structural elements apart from the changes in overall secondary structure. A blue shift of 12 to 14 nm in the fluorescence emission maximum was observed for proteins in the emulsion and 3 to 11 nm in the simulated interior of the aqueous phase, thus indicating structural changes around the tryptophan residues. DSC scans indicated that the domains in the proteins change because the shape of the transition peaks changes, when the proteins were incorporated into the emulsions. The total enthalpy decreases for BSA and HSA when these are incorporated into the emulsion, and some changes to the transition temperatures are observed. All the applied techniques supplement each other to give a more complete picture of the structural changes in proteins in intact water-in-oil emulsions. Copyright 2004 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 93:1847-1859, 2004

  20. Evidence of two structurally related solvatochromic probes complexed with β-cyclodextrin by using spectroscopic methods

    NASA Astrophysics Data System (ADS)

    Ghosh, Sujay; Mitra, Amrit Krishna; Pal, Uttam; Basu, Samita; Saha, Chandan

    2017-02-01

    Interaction of two solvatochromic fluorescent 1-keto-1,2,3,4-tetrahydrocabazole (KTHC) derivatives, viz. 6,7-dimethoxy-2,3,4,9-tetrahydrocarbazol-1-one (KTHC-67) and its carboxylic acid derivative 2-[(2-methoxy-8-oxo-5,6,7,9-tetrahydrocarbazol-3-yl)oxy]acetic acid (MOTHCA), with β-cyclodextrin in aqueous solution has been investigated through steady-state absorption, emission and time-resolved emission spectroscopy. Each probe forms inclusion complex with β-cyclodextrin, and thus their absorption spectrum quenches with the formation of an isosbestic point, fluorescence spectrum enhances in intensity with hypsochromically shifted maximum, and a new fluorescence decay component develops and increases in lifetime. The photophysical properties of these two probes are found to follow similar trends, although the carboxylic acid substitution in MOTHCA affects the binding interaction slightly in comparison with KTHC-67. The feasibilities of the formation of inclusion complexes have been computed using molecular docking, and the results satisfactorily explain the experimental findings.

  1. Structure and electrooptical properties of orthoconic antiferroelectric liquid crystalline materials

    NASA Astrophysics Data System (ADS)

    Dąbrowski, R.; Czupryński, K.; Gąsowska, J.; Tykarska, M.; Kula, P.; Dziaduszek, J.; Oton, J.; Castillo, P.; Benis, N.

    2005-09-01

    The optic and electrooptic properties of recently prepared orthoconic antiferroelectrics have been revieved. Relation between their chemical structure and mesogenic properties, smectic layer structure and helical pitch is discussed.

  2. Gamma-Ray Pulsar Light Curves as Probes of Magnetospheric Structure

    NASA Technical Reports Server (NTRS)

    Harding, A. K.

    2016-01-01

    The large number of gamma-ray pulsars discovered by the Fermi Gamma-Ray Space Telescope since its launch in 2008 dwarfs the handful that were previously known. The variety of observed light curves makes possible a tomography of both the ensemble-averaged field structure and the high-energy emission regions of a pulsar magnetosphere. Fitting the gamma-ray pulsar light curves with model magnetospheres and emission models has revealed that most of the high-energy emission, and the particles acceleration, takes place near or beyond the light cylinder, near the current sheet. As pulsar magnetosphere models become more sophisticated, it is possible to probe magnetic field structure and emission that are self-consistently determined. Light curve modeling will continue to be a powerful tool for constraining the pulsar magnetosphere physics.

  3. Five-minute oscillations as a subsurface probe of sunspot structure

    NASA Technical Reports Server (NTRS)

    Thomas, J. H.; Cram, L. E.; Nye, A. H.

    1982-01-01

    Observations of the sun which revealed the presence of oscillations due to the 5-min p-modes in the quiet atmosphere are reported. Umbral oscillations with a 145-190 sec period were detected, along with penumbral waves with a 180-250 sec period. The waves have been linked to resonant magneto-atmospheric wave modes in the sunspot atmosphere. The observations were made with a vacuum tower telescope and echelle spectrograph at Sacramento Peak Observatory. Results are presented of the Fe gamma 6,302.5 line. Irregularities in the umbral structures as to which p-mode initiated the activity are taken as evidence that the oscillations are related to activities in sunspot structure below the solar surface. It is shown that the occurrence of three successive p-mode crossings by the oscillations may be valuable for probing the effective depth of a sunspot.

  4. Establishing the Structural Integrity of Core-Shell Nanoparticles against Elemental Migration using Luminescent Lanthanide Probes.

    PubMed

    Chen, Bing; Peng, Dengfeng; Chen, Xian; Qiao, Xvsheng; Fan, Xianping; Wang, Feng

    2015-10-19

    Core-shell structured nanoparticles are increasingly used to host luminescent lanthanide ions but the structural integrity of these nanoparticles still lacks sufficient understanding. Herein, we present a new approach to detect the diffusion of dopant ions in core-shell nanostructures using luminescent lanthanide probes whose emission profile and luminescence lifetime are sensitive to the chemical environment. We show that dopant ions in solution-synthesized core-shell nanoparticles are firmly confined in the designed locations. However, annealing at certain temperatures (greater than circa 350 °C) promotes diffusion of the dopant ions and leads to degradation of the integrity of the nanoparticles. These insights into core-shell nanostructures should enhance our ability to understand and use lanthanide-doped luminescent nanoparticles.

  5. Directed self-assembly of quantum structures by nanomechanical stamping using probe tips.

    PubMed

    Taylor, Curtis; Marega, Euclydes; Stach, Eric A; Salamo, Gregory; Hussey, Lindsay; Muñoz, Martin; Malshe, Ajay

    2008-01-09

    We demonstrate that nanomechanically stamped substrates can be used as templates to pattern and direct the self-assembly of epitaxial quantum structures such as quantum dots. Diamond probe tips are used to indent or stamp the surface of GaAs(100) to create nanoscale volumes of dislocation-mediated deformation, which alter the growth surface strain. These strained sites act to bias nucleation, hence allowing for selective growth of InAs quantum dots. Patterns of quantum dots are observed to form above the underlying nanostamped template. The strain state of the patterned structures is characterized by micro-Raman spectroscopy. The potential of using nanoprobe tips as a quantum dot nanofabrication technology are discussed.

  6. Probing the structure of 16 S ribosomal RNA from Bacillus brevis.

    PubMed

    Kop, J; Kopylov, A M; Magrum, L; Siegel, R; Gupta, R; Woese, C R; Noller, H F

    1984-12-25

    A majority (approximately 89%) of the nucleotide sequence of Bacillus brevis 16 S rRNA has been determined by a combination of RNA sequencing methods. Several experimental approaches have been used to probe its structure, including (a) partial RNase digestion of 30 S ribosomal subunits, followed by two-dimensional native/denatured gel electrophoresis, in which base-paired fragments were directly identified; (b) identification of positions susceptible to cleavage by RNase A and RNase T1 in 30 S subunits; (c) sites of attack by cobra venom RNase on naked 16 S rRNA; and (d) nucleotides susceptible to attack by bisulfite in 16 S rRNA. These data are discussed with respect to a secondary structure model for B. brevis 16 S rRNA derived by comparative sequence analysis.

  7. Probing the Nodal Structure of Landau Level Wave Functions in Real Space.

    PubMed

    Bindel, J R; Ulrich, J; Liebmann, M; Morgenstern, M

    2017-01-06

    The inversion layer of p-InSb(110) obtained by Cs adsorption of 1.8% of a monolayer is used to probe the Landau level wave functions within smooth potential valleys by scanning tunneling spectroscopy at 14 T. The nodal structure becomes apparent as a double peak structure of each spin polarized first Landau level, while the zeroth Landau level exhibits a single peak per spin level only. The real space data show single rings of the valley-confined drift states for the zeroth Landau level and double rings for the first Landau level. The result is reproduced by a recursive Green function algorithm using the potential landscape obtained experimentally. We show that the result is generic by comparing the local density of states from the Green function algorithm with results from a well-controlled analytic model based on the guiding center approach.

  8. Probing the Nodal Structure of Landau Level Wave Functions in Real Space

    NASA Astrophysics Data System (ADS)

    Bindel, J. R.; Ulrich, J.; Liebmann, M.; Morgenstern, M.

    2017-01-01

    The inversion layer of p -InSb (110 ) obtained by Cs adsorption of 1.8% of a monolayer is used to probe the Landau level wave functions within smooth potential valleys by scanning tunneling spectroscopy at 14 T. The nodal structure becomes apparent as a double peak structure of each spin polarized first Landau level, while the zeroth Landau level exhibits a single peak per spin level only. The real space data show single rings of the valley-confined drift states for the zeroth Landau level and double rings for the first Landau level. The result is reproduced by a recursive Green function algorithm using the potential landscape obtained experimentally. We show that the result is generic by comparing the local density of states from the Green function algorithm with results from a well-controlled analytic model based on the guiding center approach.

  9. Designing Probes for Immunodiagnostics: Structural Insights into an Epitope Targeting Burkholderia Infections.

    PubMed

    Capelli, Riccardo; Matterazzo, Elena; Amabili, Marco; Peri, Claudio; Gori, Alessandro; Gagni, Paola; Chiari, Marcella; Lertmemongkolchai, Ganjana; Cretich, Marina; Bolognesi, Martino; Colombo, Giorgio; Gourlay, Louise J

    2017-07-21

    Structure-based epitope prediction drives the design of diagnostic peptidic probes to reveal specific antibodies elicited in response to infections. We previously identified a highly immunoreactive epitope from the peptidoglycan-associated lipoprotein (Pal) antigen from Burkholderia pseudomallei, which could also diagnose Burkholderia cepacia infections. Here, considering the high phylogenetic conservation within Burkholderia species, we ask whether cross-reactivity can be reciprocally displayed by the synthetic epitope from B. cenocepacia. We perform comparative analyses of the conformational preferences and diagnostic performances of the corresponding epitopes from the two Burkholderia species when presented in the context of the full-length proteins or as isolated peptides. The effects of conformation on the diagnostic potential and cross-reactivity of Pal peptide epitopes are rationalized on the basis of the 1.8 Å crystal structure of B. cenocepacia Pal and through computational analyses. Our results are discussed in the context of designing new diagnostic molecules for the early detection of infectious diseases.

  10. MUPUS - a thermal and mechanical properties probe for the Rosetta Lander Philae

    NASA Astrophysics Data System (ADS)

    Knollenberg, Jörg; Spohn, Tilman; Seiferlin, Karsten; Hagermann, Axel; Ball, Andrew; Banaszkiewicz, Marek; Grygorczuk, Jerzy; Grott, Matthias; Kargl, Günter; Kuehrt, Ekkehard; Koemle, Norbert; Marczewski, Wojciech

    2014-05-01

    MUPUS, the multi purpose sensor package onboard the Rosetta lander PHILAE, will measure the energy balance and the thermophysical and mechnical parameters in the near-surface layers - up to about 30 cm depth- of the nucleus of Rosetta's target comet Churyumov-Gerasimenko. Moreover it will monitor changes in these parameters over time as the comet approaches the Sun. The data should increase our knowledge of how comets work, and how the coma gases form. The data may also be used to constrain the microstructure of the nucleus material. Changes with time of physical properties will reveal timescales and possibly the nature of processes that modify the material close to the surface. Thereby, the data will indicate how pristine cometary matter sampled and analysed by other experiments on PHILAE really is. The MUPUS package consists of three major parts, the penetrator MUPUS PEN with ist sub-systems, the radiometer MUPUS TM, and the anchor sensors MUPUS ANC. the PEN is equipped with 16 RTD-type sensors along the penetrator tube aimed at measuring the temperature profile. Furthermore, they can also be actively heated in order to be used as a thermal conductivity probe. TM uses 4 thermopile sensors and different filters covering the wavelength range from 6-25 µm to measure the emitted flux from the comets surface. Both anchors are equipped with an accelerometer (ANC-M) and a Pt-100 temperature sensor to determine the hardness profile at the landing site and the thermal diffusivity at the final depth. An update of the status of the instrument after about 10 years in space with emphasis on the results of the latest tests performed during the post-hibernation commissioning will be given. Furthermore, an overview of related modelling efforts as well as supporting laboratory work in preparation of the data analysis will be provided.

  11. Maria Goeppert-Mayer Award Talk: Probing the structure and dynamics of biological networks

    NASA Astrophysics Data System (ADS)

    Albert, Reka

    2011-03-01

    The relationship between the structure and dynamics of networks is one of the central topics in network science. In the context of biological regulatory networks at the molecular to cellular level, the dynamics in question is often thought of as information propagation through the network. Quantitative dynamic models help to achieve an understanding of this process, but are difficult to construct and validate because of the scarcity of known mechanistic details and kinetic parameters. Structural and qualitative analysis is emerging as a feasible and useful alternative for interpreting biological signal transduction, and at the same time probing the structure-function relation of these networks. This analysis, however, necessitates the extension of current graph theoretical frameworks to incorporate features such as the positive or negative nature of interactions and synergistic behaviors among multiple components. This talk will present a method for structural analysis in an augmented graph framework that can probe the dynamics of information transfer. The first step is to expand the network to a richer representation that incorporates negative and synergistic regulation by the addition of pseudo-nodes and new edges. Our method simulates both knockout and constitutive activation of components as node disruptions, and takes into account the possible cascading effects of a node's disruption. We introduce the concept of elementary signaling mode (ESM), as the minimal set of nodes that can perform signal transduction independently. As a first application of this method we ranked the importance of signaling components by the effects of their perturbation on the ESMs of the network. Validation on various regulatory networks shows that this method can effectively uncover the essentiality of components mediating a signal transduction process and agrees with dynamic simulation results and experimental observations. Future applications include determining the ESMs that (do

  12. Study of polarization properties of fiber-optics probes with use of a binary phase plate.

    PubMed

    Alferov, S V; Khonina, S N; Karpeev, S V

    2014-04-01

    We conduct a theoretical and experimental study of the distribution of the electric field components in the sharp focal domain when rotating a zone plate with a π-phase jump placed in the focused beam. Comparing the theoretical and experimental results for several kinds of near-field probes, an analysis of the polarization sensitivity of different types of metal-coated aperture probes is conducted. It is demonstrated that with increasing diameter of the non-metal-coated tip part there occurs an essential redistribution of sensitivity in favor of the transverse electric field components and an increase of the probe's energy throughput.

  13. Electron Microscopy and Raman Microspectroscopy as Characterization Tools and Probes of the Chemistry and Properties of Individual Aerosol Particles

    NASA Astrophysics Data System (ADS)

    Grassian, V. H.

    2012-12-01

    Microscopic probes provide useful insights into the physicochemical properties of aerosol particles and their environmental and health effects. The focus of this talk is on the use of microscopic probes in a wide-range of laboratory studies to better understand the physicochemical properties (chemical heterogeneity, morphology, water uptake, infrared extinction and heterogeneous reactivity) of individual atmospheric aerosol particles. Microscopy coupled to energy dispersive X-ray analysis is used in these studies to characterize particles in terms of size and shape as individual particles or as aggregates particles as well as to follow chemical and physical transformations of particles as they undergo reactions under different environmental conditions. Raman microspectroscopy provides additional chemical specific information and the internal mixing of chemical constituents within individual particles. Several examples will be discussed for flyash, mineral dust and sea spray aerosol particles.

  14. Structural properties of autoclaved aerated concrete masonry

    SciTech Connect

    Matthys, J.H.; Nelson, R.L.

    1999-07-01

    Autoclaved aerated concrete masonry units are manufactured from portland cement, quartz sand, water, lime, gypsum and a gas forming agent. The units are steam cured under pressure in an autoclave transforming the material into a hard calcium silicate. The autoclaved aerated concrete masonry units are large-size solid rectangular prisms which are laid using thin-bed mortar layers into masonry assemblages. The system and product are not new--patented in 1924 by Swedish architect Johan Eriksson. Over a period of 60 years this product has been used in all areas of residential and industrial construction and in virtually all climates. However, the principal locations of application have been generally outside the US Little information in the US is available on the structural properties of this product. Due to the interest in use of this product in the construction industry and the construction of production plants in the US, the Construction Research Center at the University of Texas at Arlington and Robert L. Nelson & Associates conducted a series of tests to determine some of the basic structural properties of this product. This paper presents the findings of those investigations.

  15. Experimental Studies of Band-Structure Properties in Bloch Transistors

    NASA Astrophysics Data System (ADS)

    Flees, Daniel J.

    1998-03-01

    One of the most striking features in small SIS tunnel junctions is the energy-band structure produced by Josephson coupling and charging effects. These energy bands are analogous to Bloch bands in crystalline solids. The superconducting single-electron (Bloch) transistor is the simplest system in which the energy bands can be readily studied. It consists of a superconducting island coupled to a source and drain through two small tunnel junctions. The elastic tunneling of Cooper-Pairs onto the island mixes the discrete charge states of the island. The shapes of the resulting energy bands can be modified by changing the electrostatic energies of these charge states with a voltage applied to a capacitively coupled gate. The maximum zero-voltage current (supercurrent) of each band depends upon the shape of the band and so the gate modulates the supercurrent. Each band has a different characteristic supercurrent modulation, with excited bands generally having lower currents. Thus! we can use the reduction in super current associated with a transition to an excited band to begin probing band- structure properties such as the band-gap.(Daniel J. Flees, Siyuan Han, and J.E. Lukens, Phys. Rev. Lett. 78), 4817 (1997).

  16. Dansyl-naphthalimide dyads as molecular probes: effect of spacer group on metal ion binding properties.

    PubMed

    Shankar, Balaraman H; Ramaiah, Danaboyina

    2011-11-17

    Interaction of a few dansyl-naphthalimide conjugates 1a-e linked through polymethylene spacer groups with various metal ions was investigated through absorption, fluorescence, NMR, isothermal calorimetric (ITC), and laser flash photolysis techniques. The characteristic feature of these dyads is that they exhibit competing singlet-singlet energy transfer (SSET) and photoinduced electron transfer (PET) processes, both of which decrease with the increase in spacer length. Depending on the spacer group, these dyads interact selectively with divalent Cu(2+) and Zn(2+) ions, as compared to other mono- and divalent metal ions. Jobs plot analysis showed that these dyads form 2:3 complexes with Cu(2+) ions, while 1:1 complexes were observed with Zn(2+) ions. The association constants for the Zn(2+) and Cu(2+) complexes were determined and are found to be in the order 10(3)-10(5) M(-1). Irrespective of the length of the spacer group, these dyads interestingly act as fluorescence ratiometric molecular probes for Cu(2+) ions by altering the emission intensity of both dansyl and naphthalimide chromophores. In contrast, only the fluorescence intensity of the naphthalimide chromophore of the lower homologues (n = 1-3) was altered by Zn(2+) ions. (1)H NMR and ITC measurements confirmed the involvement of both sulfonamide and dimethylamine groups in the complexation with Cu(2+) ions, while only the latter group was involved with Zn(2+) ions. Laser excitation of the dyads 1a-e showed formation of a transient absorption which can be attributed to the radical cation of the naphthalimide chromophore, whereas only the triplet excited state of the dyads 1a-e was observed in the presence of Cu(2+) ions. Uniquely, the complexation of 1a-e with Cu(2+) ions affects both PET and SSET processes, while only the PET process was partially inhibited by Zn(2+) ions in the lower homologues (n = 1-3) and the higher homologues exhibited negligible changes in their emission properties. Our results

  17. The properties of the cool circumgalactic gas probed with the SDSS, WISE, and GALEX surveys

    SciTech Connect

    Lan, Ting-Wen; Ménard, Brice; Zhu, Guangtun

    2014-11-01

    We explore the distribution of cool (∼10{sup 4} K) gas around galaxies and its dependence on galaxy properties. By cross-correlating about 50,000 Mg II absorbers with millions of sources from the SDSS (optical), WISE (IR), and GALEX (UV) surveys we effectively extract about 2000 galaxy-absorber pairs at z ∼ 0.5 and probe relations between absorption strength and galaxy type, impact parameter and azimuthal angle. We find that cool gas traced by Mg II absorbers exists around both star-forming and passive galaxies with a similar incidence rate on scales greater than 100 kpc but each galaxy type exhibits a different behavior on smaller scales: Mg II equivalent width does not correlate with the presence of passive galaxies whereas stronger Mg II absorbers tend to be found in the vicinity of star-forming galaxies. This effect is preferentially seen along the minor axis of these galaxies, suggesting that some of the gas is associated with outflowing material. In contrast, the distribution of cool gas around passive galaxies is consistent with being isotropic on the same scales. We quantify the average excess Mg II equivalent width 〈δW{sub 0}{sup Mg} {sup II}〉 as a function of galaxy properties and find 〈δW{sub 0}{sup Mg} {sup II}〉∝SFR{sup 1.2}, sSFR{sup 0.5}, and M{sub ∗}{sup 0.4} for star-forming galaxies. This work demonstrates that the dichotomy between star-forming and passive galaxies is reflected in the circumgalactic medium traced by low-ionized gas. We also measure the covering fraction of Mg II absorption and find it to be about 2-10 times higher for star-forming galaxies than passive ones within 50 kpc. We estimate the amount of neutral gas in the halo of (log M {sub *}/M {sub ☉}) ∼ 10.8 galaxies to be a few × 10{sup 9} M {sub ☉} for both types of galaxies. Finally, we find that correlations between absorbers and sources detected in the UV and IR lead to physical trends consistent with those measured in the optical.

  18. Structural properties of Alumnum nitride compound

    NASA Astrophysics Data System (ADS)

    Mohammad, R.; Katırcıoğlu, Ş.

    2014-10-01

    Structural properties of Alumnum nitride in wurtzite, zinc-blende and rock-salt phases have been investigated by Full Potential-Linearized Augmented Plane Waves method based on Density Functional Theory within Local Density Approximation and seven Generalized Gradient schemes. It is found that, Alumnum nitride in wurtzite phase is the stable ground state structure and makes a transition to rock-salt phase at a low transition pressure (11.54 GPa). According to present total energy calculations, zinc-blende phase of Alumnum nitride also makes a transition to rock-salt phase, at a low transition pressure (10.17 GPa). Generalized Gradient functionals of Perdew-Wang-Engel-Vosko and Perdew-Burke-Ernzerhof are found to be more successful than other approximations considered in this work for providing the closest values of the structural features, such as, lattice constants, bulk moduli, first order pressure derivatives of bulk moduli and cohesive energies of Alumnum nitride three phases to available experimental ones. Although Generalized Gradient approaches of Perdew-Wang-Engel-Vosko, Perdew-Burke-Ernzerhof, Becke-Perdew-Wang and Perdew-Burke-Ernzerhof (revised) are found to be accurate schemes for elastic constants of rock-salt AlN, only Perdew-Wang-Engel-Vosko and Perdew-Burke-Ernzerhof functionals are observed to be more successful than the other schemes for supplying accurately both C_{11} and C_{12} of zinc-blende Alumnum nitride structure. Perdew-Wang-Engel-Vosko functional is observed to be superior to Perdew-Burke-Ernzerhof for elastic constants of wurtzite Alumnum nitride structure. Elastic constants of wurtzite Alumnum nitride obtained by self Perdew-Wang-Engel-Vosko approach and Martin's transformation calculations in which elastic constants of zinc-blende Alumnum nitride are calculated with Perdew-Wang-Engel-Vosko scheme, are very close to the experimental ones. Hence, functional of Perdew-Wang-Engel-Vosko is decided to be the most accurate approximation

  19. Probing Milky Way Structure with Near-Infrared Diffuse Interstellar Bands

    NASA Astrophysics Data System (ADS)

    Zasowski, Gail; Ménard, Brice; Bizyaev, Dmitry; Garcia-Hernandez, D.; García Pérez, Ana; Hayden, Michael R.; Hearty, Fred; Holtzman, Jon A.; Johnson, Jennifer; Kinemuchi, Karen; Majewski, Steven R.; Nidever, David L.; Sellgren, Kristen; Shetrone, Matthew D.; Whelan, David G.; Wilson, John C.

    2015-01-01

    Astronomers have studied the set of interstellar absorption features known as the diffuse interstellar bands (DIBs) for nearly a century, characterizing them into families and using them as probes of local interstellar medium (ISM) conditions even while trying to understand their origin. Though most DIB studies have focused on the optical features, recent DIB identifications at infrared (IR) wavelengths -- where extinction by interstellar dust is significantly decreased -- provide us with tracers of ISM along heavily extincted, previously inaccessible sightlines. This talk will briefly summarize results from a project using the strongest of these IR DIBs (detected in more than 60,000 sightlines towards cool, distant giant stars observed as part of the SDSS-III/APOGEE survey) to characterize the large-scale distribution and properties of the Galactic ISM, including in the heavily reddened bulge and inner disk. The DIB absorption's tight correlation with foreground reddening makes it a powerful, independent probe of line-of-sight dust extinction. For the first time, we map the velocity field of a DIB on large scales and find that it displays the signature of the rotating Galactic disk. Three-dimensional modeling of the carrier distribution reveals not only large-scale gradients consistent with other ISM components, but also substructures that coincide with particular Galactic bulge and disk features. Finally, we find that features that are outliers in the distribution of DIB profile shapes may have an origin in circumstellar, rather than interstellar, environments along these particular sightlines, and the properties of these atypical features may contain clues towards identifying the currently-unknown carrier molecule of this DIB.

  20. A flow microslot NMR probe coupled with a capillary isotachophoresis system exhibits improved properties compared to solenoid designs.

    PubMed

    Gogiashvili, Mikheil; Telfah, Ahmad; Lambert, Jörg; Hergenröder, Roland

    2017-03-01

    We report on the hyphenation of capillary isotachophoresis (cITP) separations with online nuclear magnetic resonance (NMR) detection using a planar microslot waveguide probe design. While cITP is commonly coupled with a solenoidal microcoil NMR probe, the structural information provided is limited by broad resonances and poor spectral resolution due to the magnetic field created by the separation current. The microslot probe design described herein allows the separation capillary to be oriented parallel to the static magnetic field, B 0, eliminating the spectral broadening produced by the secondary magnetic field induced by the separation current. This allows high-resolution nuclear magnetic resonance spectra of the charged analytes to be obtained in online mode, whereas conventional solenoidal capillary NMR designs must resort to the stopped flow mode. The potential of the microslot probe for hyphenated electrophoretic separations is demonstrated by performing cITP focusing and online NMR detection of the (1)H NMR spectrum of a system containing spermine and aniline. Graphical Abstract High resolution NMR spectra in flow capillarelectrophoretic separations with microslot NMR probe.

  1. A triphenylamine-based colorimetric and fluorescent probe with donor–bridge–acceptor structure for detection of G-quadruplex DNA.

    PubMed

    Wang, Ming-Qi; Zhu, Wen-Xiang; Song, Zhuan-Zhuan; Li, Shuo; Zhang, Yong-Zhao

    2015-12-15

    In this Letter, three triphenylamine-based dyes (TPA-1, TPA-2a and TPA-2b) with donor–bridge–acceptor (D–p–A) structure were designed and synthesized for the purpose of G-quadruplexes recognition. In aqueous conditions, the interactions of the dyes with G-quadruplexes were studied with the aim to establish the influence of the geometry of the dyes on their binding and probing properties. Results indicate that TPA-2b displays significant selective colorimetric and fluorescent changes upon binding of G-quadruplex DNA. More importantly, its distinct color change enables visual detection and differentiation of G-quadruplexes from single and duplex DNA structures. CD titration date reveals that TPA-2b could induce and stabilize the formation of G-quadruplex structure. All these remarkable properties of TPA-2b suggest that it should have promising application in the field of G-quadruplexes research.

  2. Chemical probing of adenine residues within the secondary structure of rabbit /sup 18/S ribosomal RNA

    SciTech Connect

    Rairkar, A.; Rubino, H.M.; Lockard, R.E.

    1988-01-26

    The location of unpaired adenine residues within the secondary structure of rabbit /sup 18/S ribosomal RNA was determined by chemical probing. Naked /sup 18/S rRNA was first prepared by digestion of purified 40S subunits with matrix-bound proteinase K in sodium dodecyl sulfate, thereby omitting the use of nucleic acid denaturants. Adenines within naked /sup 18/S rRNA were chemically probed by using either diethyl pyrocarbonate or dimethyl sulfate, which specifically react with unpaired nucleotides. Adenine modification sites were identified by polyacrylamide sequencing gel electrophoresis either upon aniline-induced strand scission of /sup 32/P-end-labeled intact and fragmented rRNA or by primer extension using sequence-specific DNA oligomers with reverse transcriptase. The data indicate good agreement between the general pattern of adenine reactivity and the location of unpaired regions in /sup 18/S rRNA determined by comparative sequence analysis. The overall reactivity of adenine residues toward single-strand-specific chemical probes was, also, similar for both rabbit and Escherichia coli small rRNA. The number of strongly reactive adenines appearing within phylogenetically determined helical segments, however, was greater in rabbit /sup 18/S rRNA than for E. coli /sup 16/S rRNA. Some of these adenines were found clustered in specific helices. Such differences suggest a greater irregularity of many of the helical elements within mammalian /sup 18/S rRNA, as compared with prokaryotic /sup 16/S rRNA. These helical irregularities could be important for protein association and also may represent biologically relevant flexible regions of the molecule.

  3. Oxygen isotope effects as probes of electron transfer mechanisms and structures of activated O2.

    PubMed

    Roth, Justine P

    2009-03-17

    Competitively determined oxygen ((18)O) isotope effects can be powerful probes of chemical and biological transformations involving molecular oxygen as well as superoxide and hydrogen peroxide. They play a complementary role to crystallography and spectroscopy in the study of activated oxygen intermediates by forging a link between electronic/vibrational structure and the bonding that occurs within ground and transition states along the reaction coordinate. Such analyses can be used to assess the plausibility of intermediates and their catalytic relevance in oxidative processes. This Account describes efforts to advance oxygen kinetic isotope effects ((18)O KIEs) and equilibrium isotope effects ((18)O EIEs) as mechanistic probes of reactive, oxygen-derived species. We focus primarily on transition metal mediated oxidations, outlining both advances over the past five years and current limitations of this approach. Computational methods are now being developed to probe transition states and the accompanying kinetic isotope effects. In particular, we describe the importance of using a full-frequency model to accurately predict the magnitudes as well as the temperature dependence of the isotope effects. Earlier studies have used a "cut-off model," which employs only a few isotopic vibrational modes, and such models tend to overestimate (18)O EIEs. Researchers in mechanistic biological inorganic chemistry would like to differentiate "inner-sphere" from "outer-sphere" reactivity of O(2), a designation that describes the extent of the bonding interaction between metal and oxygen in the transition state. Though this problem remains unsolved, we expect that this isotopic approach will help differentiate these processes. For example, comparisons of (18)O KIEs to (18)O EIEs provide benchmarks that allow us to calibrate computationally derived reaction coordinates. Once the physical origins of heavy atom isotope effects are better understood, researchers will be able to apply

  4. Exploring High-Latitude Electric Field Variability With the Auroral Spatial Structures Probe Mission

    NASA Astrophysics Data System (ADS)

    Farr, D.; Stromberg, E.; Neilsen, T. L.; Weston, C.; Byers, B.; Frazier, C. A.; Nelson, W.; Perkins, C.; Miller, J.; Swenson, C.; Fish, C. S.

    2012-12-01

    The Auroral Spatial Structures Probe (ASSP) is a NASA sounding rocket mission to be launched in the late January 2014 time frame that, will be used to study both the spatial and temporal small scale variation of the electric and magnetic fields during active aurora and just before the onset of an auroral sub-storm. This will be accomplished through the use of a constellation of small payloads that separate relative to each other throughout a sounding rocket flight. The multiple baseline observations of the electric and magnetic fields will be used to observe variability of both the E-field and the Poynting flux. These observations will be placed in the context of available data, including winds, large scale E-fields, and proxy conductivity (airglow images) observations. In this way we will address the main scientific objective of this mission which is: What are the contributions of small spatial scale and rapid temporal scale fluctuations of electric fields relative to the larger-scale electrodynamic processes? The high altitude rocket will be launched along the magnetic field line and carry six sub-payloads to be ejected from the main payload at high velocity. The sub-payloads will be deployed both along the flight path and perpendicular to the flight path so that both spatial features and temporal-spatial ambiguities can be explored. The low-mass sub-payloads that, for a fixed ejection impulse will achieve at least a 50 km separation by the end of the flight are key to the observational success. Each sub-payload will carry a crossed pair of double-probe sensors to measure in-situ electric fields, a three axis magnetometer, a Langmuir probe and a GPS receiver. In this poster we review the ASSP science and mission, and preliminary design.

  5. The Auroral Spatial Structures Probe: Exploring Small-Scale High-Latitude Electric Field Variability

    NASA Astrophysics Data System (ADS)

    Farr, D.; Weston, C.; Nelson, W.; Stromberg, E. M.; Byers, B.; Frazier, C.; Swenson, A.; Miller, J.; Carrick, B.; Neilsen, T. L.; Hidalgo, J. M.; Cox, W.; Evans, T.; Vangeison, V.; Perkins, C.; Fish, C. S.; Swenson, C.

    2013-12-01

    The Auroral Spatial Structures Probe (ASSP) is a NASA sounding rocket mission to be launched in the late January 2014 time frame that will be used to study both the spatial and temporal small scale variation of the electric and magnetic fields during active aurora and just before the onset of an auroral sub-storm. This will be accomplished through the use of a constellation of small payloads that separate relative to each other throughout a sounding rocket flight. The multiple baseline observations of the electric and magnetic fields will be used to observe variability of both the E-field and the Poynting flux. These observations will be placed in the context of available data, including winds, large scale E-fields, and proxy conductivity (airglow image) observations. In this way we will address the main scientific objective of this mission which is: What are the contributions of small spatial scale and rapid temporal scale fluctuations of electric fields relative to the larger-scale electrodynamic processes? The high altitude rocket will be launched along the magnetic field line and carry six sub-payloads to be ejected from the main payload at high velocity. The sub-payloads will be deployed both along the flight path and perpendicular to the flight path so that both spatial features and temporal-spatial ambiguities can be explored. The low-mass sub-payloads will achieve at least a 35 km separation by the end of the flight and are key to observational success. Each sub-payload will carry a crossed pair of double-probe sensors to measure in-situ electric fields, a three axis magnetometer, a Langmuir probe and a GPS receiver. In this poster we review the ASSP science, mission, and design, and present instrument calibration and testing results.

  6. Electronic structure and spectral properties of RCuSi (R=Nd,Gd) compounds

    NASA Astrophysics Data System (ADS)

    Knyazev, Yu. V.; Lukoyanov, A. V.; Kuz'min, Yu. I.; Gupta, Sachin; Suresh, K. G.

    2016-04-01

    We report a joint experimental and theoretical investigation of optical properties and electronic structure of NdCuSi and GdCuSi compounds. Optical characteristics have been studied employing ellipsometry in a spectral range 0.22-15 μm. Spin-polarized calculations of the electronic structure have been performed using LSDA+U method accounting for electronic correlations in the 4f shell of rare earth elements. Additionally, we probe our electronic structures by calculating the interband optical conductivities and comparing them with spectral measurement. We find that all main features of the experimental curves have been qualitative interpreted using the calculated densities of states.

  7. Hawking Radiation as a Possible Probe for the Interior Structure of Regular Black Holes

    NASA Astrophysics Data System (ADS)

    Deng, Yanbin; Cleaver, Gerald

    2017-03-01

    The notion of black hole singularity and the proof of the singularity theorem were considered great successes in classical general relativity whereas they meanwhile brought with deep puzzles. Conceptual challenges were set up by the intractability of the singularity. The existence of black hole horizons which cover up the black hole interior including the singularity from outside observers, builds an information curtain, further hindering physicists from understanding the nature of the singularity and the interior structure of black holes. The regular black hole is a concept produced out of multiple attempts of establishing a tractable and understandable interior structure for black holes as well as avoiding the singularity behind the black hole horizon. The practicality of the new constructions of black holes would be considered more reliable if there can be found some connection between the interior of regular black holes and some far-reaching signals released from the black hole. After studying the Hawking radiation by fermion tunnelling from one type of regular black hole, structure dependent results were obtained. The result being structure dependent hints the prospects of employing the Hawking radiation as a method to probe into the structure of black holes.

  8. Structural formation of huntingtin-like aggregates probed by small-angle neutron scattering

    SciTech Connect

    Stanley, Christopher B; Perevozchikova, Tatiana; Berthelier-Jung, Valerie M

    2011-01-01

    In several neurodegenerative disorders, including Huntington s disease (HD), aspects concerning the earliest of protein structures that form along the aggregation pathway have increasingly gained attention since these particular species are likely to be neurotoxic. We used time-resolved small-angle neutron scattering (SANS) to probe in solution these transient structures formed by peptides having the N-terminal sequence context of mutant huntingtin (Htt) exon 1. We obtained snapshots of the formed aggregates as the kinetic reaction ensued to yield quantitative information on their size and mass. At the early stage, small precursor species with an initial radius of gyration (Rg) of 16.1 5.9 and average mass of a dimer to trimer were monitored. Structural growth was treated as two modes with a transition from three-dimensional early aggregate formation to two-dimensional fibril growth and association. Our SANS results on the internal structure of the mature fibrils demonstrate loose packing with about 1 peptide per 4.75 -sheet repeat distance, which is shown to be quantitatively consistent with a -helix model. This research provides new insights into the structures forming along the pathway of Htt exon 1 aggregation and should assist in determining the role that precursors play in neuronal toxicity.

  9. Internal Hydration Properties of Single Bacterial Endospores Probed by Electrostatic Force Microscopy.

    PubMed

    Van Der Hofstadt, Marc; Fabregas, Rene; Millan-Solsona, Ruben; Juarez, Antonio; Fumagalli, Laura; Gomila, Gabriel

    2016-12-27

    We show that the internal hydration properties of single Bacillus cereus endospores in air under different relative humidity (RH) conditions can be determined through the measurement of its electric permittivity by means of quantitative electrostatic force microscopy (EFM). We show that an increase in the RH from 0% to 80% induces a large increase in the equivalent homogeneous relative electric permittivity of the bacterial endospores, from ∼4 up to ∼17, accompanied only by a small increase in the endospore height, of just a few nanometers. These results correlate the increase of the moisture content of the endospore with the corresponding increase of environmental RH. Three-dimensional finite element numerical calculations, which include the internal structure of the endospores, indicate that the moisture is mainly accumulated in the external layers of the endospore, hence preserving the core of the endospore at low hydration levels. This mechanism is different from what we observe for vegetative bacterial cells of the same species, in which the cell wall at high humid atmospheric conditions is not able to preserve the cytoplasmic region at low hydration levels. These results show the potential of quantitative EFM under environmental humidity control to study the hygroscopic properties of small-scale biological (and nonbiological) entities and to determine its internal hydration state. A better understanding of nanohygroscopic properties can be of relevance in the study of essential biological processes and in the design of bionanotechnological applications.

  10. An additional S-shaped structure for sensitivity improvement of coaxial probe for permittivity determination of low loss materials

    NASA Astrophysics Data System (ADS)

    Jiao, Xingmin; Jin, Wei; Yang, Xiaoqing

    2015-05-01

    Permittivity measurement of materials is important in microwave chemistry, microwave material processing and microwave heating. The open-ended coaxial line method is one of the most popular and effective means for permittivity measurement. However, the conventional coaxial probe has difficulty in distinguishing small permittivity variations for low loss media. In this paper an additional S-shaped structure is proposed for sensitivity improvement of a coaxial probe for permittivity determination of low loss materials at 2.45 GHz. The small permittivity variation can be distinguished due to field enhancement generated by the additional S-shaped structure. We studied the variation of reflection coefficient amplitude for three kinds of samples with different moisture content, within the probe at different insertion depths. We find that the conventional coaxial probe cannot distinguish small permittivity variations until the moisture content of materials reaches 3%. Meanwhile, the probe with the S-shaped structure can detect such small permittivity variations when the moisture content of samples changes by only 1%. The experimental results demonstrate that the new probe proposed in this paper is reliable and feasible.

  11. The elastase-PK101 structure: Mechanism of an ultrasensitive activity-based probe revealed

    DOE PAGES

    Lechtenberg, Bernhard C.; Robinson, Howard R.; Kasperkiewicz, Paulina; ...

    2015-01-22

    Human neutrophil elastase (HNE) plays a central role in neutrophil host defense, but its broad specificity makes HNE a difficult target for both inhibitor and probe development. Recently, we identified the unnatural amino acid containing activity-based probe PK101, which exhibits astounding sensitivity and selectivity for HNE, yet completely lacks mechanistic explanation for its unique characteristics. Here, we present the crystal structure of the HNE-PK101 complex which not only reveals the basis for PK101 ultrasensitivity but also uncovers so far unrecognized HNE features. Strikingly, the Nle(O-Bzl) function in the P4 position of PK101 reveals and leverages an “exo-pocket” on HNE asmore » a critical factor for selectivity. Furthermore, the PK101 P3 position harbors a methionine dioxide function, which mimics a post-translationally oxidized methionine residue and forms a critical hydrogen bond to the backbone amide of Gly219 of HNE. Gly219 resides in a Gly–Gly motif that is unique to HNE, yet compulsory for this interaction. Consequently, this feature enables HNE to accommodate substrates that have undergone methionine oxidation, which constitutes a hallmark post-translational modification of neutrophil signaling.« less

  12. The elastase-PK101 structure: Mechanism of an ultrasensitive activity-based probe revealed

    SciTech Connect

    Lechtenberg, Bernhard C.; Robinson, Howard R.; Kasperkiewicz, Paulina; Drag, Marcin; Riedl, Stefan J.

    2015-01-22

    Human neutrophil elastase (HNE) plays a central role in neutrophil host defense, but its broad specificity makes HNE a difficult target for both inhibitor and probe development. Recently, we identified the unnatural amino acid containing activity-based probe PK101, which exhibits astounding sensitivity and selectivity for HNE, yet completely lacks mechanistic explanation for its unique characteristics. Here, we present the crystal structure of the HNE-PK101 complex which not only reveals the basis for PK101 ultrasensitivity but also uncovers so far unrecognized HNE features. Strikingly, the Nle(O-Bzl) function in the P4 position of PK101 reveals and leverages an “exo-pocket” on HNE as a critical factor for selectivity. Furthermore, the PK101 P3 position harbors a methionine dioxide function, which mimics a post-translationally oxidized methionine residue and forms a critical hydrogen bond to the backbone amide of Gly219 of HNE. Gly219 resides in a Gly–Gly motif that is unique to HNE, yet compulsory for this interaction. Consequently, this feature enables HNE to accommodate substrates that have undergone methionine oxidation, which constitutes a hallmark post-translational modification of neutrophil signaling.

  13. Study of a vibrating fiber probing system for 3-D micro-structures: performance improvement

    NASA Astrophysics Data System (ADS)

    Murakami, H.; Katsuki, A.; Sajima, T.; Suematsu, T.

    2014-09-01

    This paper presents a system for measuring 3D micro-structures that uses an optical fiber probe equipped with a piezo element that causes the probe to vibrate. The optical fiber probe consists of a stylus shaft with a diameter of 3 µm and a glass ball with a diameter of 5 µm attached to the tip. The stylus is vibrated in a circular motion in a single plane. The vibrator mechanism is introduced to prevent adhesion of the stylus tip to the surface being measured. This adhesion, which adversely affects the accuracy and time of the measurement, is caused by intermolecular, electrostatic, and liquid bridge forces. The measuring principle involves monitoring the vibrational amplitude of the stylus shaft that is required to prevent the adhesion of the stylus tip to the surface being measured, this amplitude being measured optically. In our previous report (Murakami et al 2012 Key Eng. Mater. 523-524 907-12), we found that the stylus shaft actually moves in an elliptical motion when it is set to describe a circular motion in the X-Y plane. Therefore, when a measurement is taken, it is necessary to adjust the motion of the piezoelectric tube to compensate for the difference between the diameter of the perfect circle and the actual elliptical motion of the stylus shaft displacement. In this study, the stylus characteristics were examined and the motion of the stylus shaft was then corrected to attain the desired circular motion. Next, the expansion of the measuring area by using a line laser was investigated. Finally, an experiment involving the measurement of a micro-hole was performed to demonstrate the practicality of the vibrating fiber probe. As a result, it was shown that the displacement between the diameter of the perfect circle and the actual elliptical motion of the stylus tip was about 0.034 µm after compensation. In addition, it was confirmed that the measurement area can be expanded by using an optical slit, but the standard deviation of the

  14. Probing polymer melt structure at the early stages of crystallization by in-situ rheo -SAXS and -WAXD techniques

    NASA Astrophysics Data System (ADS)

    Somani, R. H.; Yang, L.; Hsiao, B. S.; Agarwal, P.; Fruitwala, H.; Tsou, A.

    2002-03-01

    Flow fields strongly affect polymer crystallization, both in terms of phase transition and solid state morphology. Arguments, based on the average properties (such as entropy reduction and related elevation of melting point) of deformed melts does not fully account for high sensitivity of polymer crystallization kinetics to flow and deformation. Local orientation of macromolecular chains and its effect on the primary nucleation step is likely to be the determining phenomenon. In-situ rheo --SAXS (small angle x-ray scattering) and --WAXD (wide angle x-ray diffraction) techniques were used to probe the shear-induced precursor structures (primary nuclei) at the early stages of crystallization in isotactic polypropylene melt near its melting point. Initial SAXS patterns, immediately after shear (rate = 60 s ^--1, ts = 5 s), showed emergence of equatorial streaks due to oriented structures (precursors for microfibrils or shish) parallel to the flow direction and of meridional maxima due to growth of the oriented layer-like structures (precursors for kebabs) perpendicular to the flow; however, no crystal reflections were observed in corresponding WAXD patterns. SAXS and WAXD patterns at later times (t = 120 min after shear) indicated that the induced oriented structures were stable above the nominal melting point of iPP. DSC thermograms of sheared iPP samples confirmed the presence of two populations of crystalline fractions; one at 164 ^oC (corresponding to the normal melting point) and the other at 179 ^oC (corresponding to melting of oriented crystalline structures). \\underline Acknowledgements: We wish to acknowledge the assistance of Drs. Fengji Yeh, Lizhi Liu, Dufei Fang, and Shaofeng Ran of SUNY, Stony Brook for synchrotron SAXS and WAXD experimental setup. The financial support for this work was provided by NSF DMR-9732653 and by ExxonMobil.

  15. Probing structure-nanoaggregation relations of polyaromatic surfactants: a molecular dynamics simulation and dynamic light scattering study.

    PubMed

    Teklebrhan, Robel B; Ge, Lingling; Bhattacharjee, Subir; Xu, Zhenghe; Sjöblom, Johan

    2012-05-24

    Four synthetic perylene bisimide-based polyaromatic (PA) surfactants with a structural or functional group difference in their attached hydrophilic/hydrophobic substituent side chains were used to probe structure-nanoaggregation relations in organic media by molecular dynamics simulations and dynamic light scattering. The results from the simulated radial distribution functions and light scattering experiments indicate that variation in the structure of side chains and polarity of functional groups leads to significant variations in molecular association, dynamics of molecular nanoaggregation and structure of nanoaggregates. The aggregates of PA surfactant molecules grow to much larger sizes in heptane than in toluene. The aromatic solvent is shown to hinder molecular association by weakening π-π stacking, demonstrating the control of molecular aggregation by tuning solvent properties. In aliphatic solvent, the aggregates formed from PA surfactants of aliphatic alkyl groups and phenylalanine derivatives as a side chain usually have a higher solvent accessible surface area to accessible volume ratio (SASA:AV) than that of tryptophan derivatives in their side chains. PA surfactants with an aliphatic functional group in both side chains does not form polyaromatic π-π stacking (T-stacking) due to its strong steric hindrance in both solvents. Depending on the nature of the side chains attached, various stacking distributions, aggregation sizes, and SASA:AV ratios were obtained. In PA surfactant nanoaggregates, all of the solvent molecules were found to be excluded from the interstices of the stacked polyaromatic cores, regardless of whether the solvent molecules are aliphatic or aromatic. Although the change in the structure of side chain substituent in polyaromatic surfactants has a negligible impact on their self-diffusivity, it can strongly influence their intermolecular interactions, leading to different aggregate diffusion coefficients.

  16. An integrated fiber-optic probe combined with support vector regression for fast estimation of optical properties of turbid media.

    PubMed

    Zhou, Yang; Fu, Xiaping; Ying, Yibin; Fang, Zhenhuan

    2015-06-23

    A fiber-optic probe system was developed to estimate the optical properties of turbid media based on spatially resolved diffuse reflectance. Because of the limitations in numerical calculation of radiative transfer equation (RTE), diffusion approximation (DA) and Monte Carlo simulations (MC), support vector regression (SVR) was introduced to model the relationship between diffuse reflectance values and optical properties. The SVR models of four collection fibers were trained by phantoms in calibration set with a wide range of optical properties which represented products of different applications, then the optical properties of phantoms in prediction set were predicted after an optimal searching on SVR models. The results indicated that the SVR model was capable of describing the relationship with little deviation in forward validation. The correlation coefficient (R) of reduced scattering coefficient μ'(s) and absorption coefficient μ(a) in the prediction set were 0.9907 and 0.9980, respectively. The root mean square errors of prediction (RMSEP) of μ'(s) and μ(a) in inverse validation were 0.411 cm(-1) and 0.338 cm(-1), respectively. The results indicated that the integrated fiber-optic probe system combined with SVR model were suitable for fast and accurate estimation of optical properties of turbid media based on spatially resolved diffuse reflectance.

  17. Creating 3D physical models to probe student understanding of macromolecular structure.

    PubMed

    Cooper, A Kat; Oliver-Hoyo, M T

    2017-07-06

    The high degree of complexity of macromolecular structure is extremely difficult for students to process. Students struggle to translate the simplified two-dimensional representations commonly used in biochemistry instruction to three-dimensional aspects crucial in understanding structure-property relationships. We designed four different physical models to address student understanding of electrostatics and noncovalent interactions and their relationship to macromolecular structure. In this study, we have tested these models in classroom settings to determine if these models are effective in engaging students at an appropriate level of difficulty and focusing student attention on the principles of electrostatic attractions. This article describes how to create these unique models for four targeted areas related to macromolecular structure: protein secondary structure, protein tertiary structure, membrane protein solubility, and DNA structure. We also provide evidence that merits their use in classroom settings based on the analysis of assembled models and a behavioral assessment of students enrolled in an introductory biochemistry course. By providing students with three-dimensional models that can be physically manipulated, barriers to understanding representations of these complex structures can be lowered and the focus shifted to addressing the foundational concepts behind these properties. © 2017 by The International Union of Biochemistry and Molecular Biology, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

  18. Nanoscale structural and functional mapping of nacre by scanning probe microscopy techniques

    NASA Astrophysics Data System (ADS)

    Zhou, Xilong; Miao, Hongchen; Li, Faxin

    2013-11-01

    Nacre has received great attention due to its nanoscale hierarchical structure and extraordinary mechanical properties. Meanwhile, the nanoscale piezoelectric properties of nacre have also been investigated but the structure-function relationship has never been addressed. In this work, firstly we realized quantitative nanomechanical mapping of nacre of a green abalone using atomic force acoustic microscopy (AFAM). The modulus of the mineral tablets is determined to be ~80 GPa and that of the organic biopolymer no more than 23 GPa, and the organic-inorganic interface width is determined to be about 34 +/- 9 nm. Then, we conducted both AFAM and piezoresponse force microscopy (PFM) mapping in the same scanning area to explore the correlations between the nanomechanical and piezoelectric properties. The PFM testing shows that the organic biopolymer exhibits a significantly stronger piezoresponse than the mineral tablets, and they permeate each other, which is very difficult to reproduce in artificial materials. Finally, the phase hysteresis loops and amplitude butterfly loops were also observed using switching spectroscopy PFM, implying that nacre may also be a bio-ferroelectric material. The obtained nanoscale structural and functional properties of nacre could be very helpful in understanding its deformation mechanism and designing biomimetic materials of extraordinary properties.

  19. Magnetic domain structure study of a ferromagnetic semiconductor using a home-made low temperature scanning Hall probe microscope

    NASA Astrophysics Data System (ADS)

    Kweon, Seongsoo; de Lozanne, Alex; Samarth, Nitin

    2008-03-01

    GaMnAs is a ferromagnetic semiconductor actively studied for basic research and for the possibility of application to spintronic devices. To study the local magnetic properties of this material the magnetic force microscope (MFM) is too invasive (by affecting the domains in the sample) or not sensitive enough (due to the weak magnetization of the GaMnAs). We have therefore built a scanning Hall probe microscope (SHPM) to complement our MFM studies. We use a lock-in amplifier to supply a bias current of 1-10μA and to measure the Hall voltage. We calibrated this home-made SHPM with a computer hard disk sample. Comparing images of this sample obtained with MFM and SHPM we show that our home-made SHPM is operating well. We observed the domain structure of 30-nm thick Ga0.94Mn0.06As epilayer grown on a 700nm-thick In0.13Ga0.87As buffer covering a GaAs substrate. We will study the magnetic domain structure as a function of temperature with varying external magnetic fields.

  20. Probing Structural Changes in Poly(3-hexylthiophene) (P3HT) During Electrochemical Oxidation with In Situ X-ray Scattering

    NASA Astrophysics Data System (ADS)

    Thelen, Jacob L.; Patel, Shrayesh N.; Javier, Anna E.; Balsara, Nitash P.

    2014-03-01

    Mixtures of poly(3-hexylthiophene)-b-poly(ethylene oxide) (P3HT-b-PEO) block copolymer and lithium bis(trifluromethanesulfonyl) imide (LiTFSI) salt can microphase separate into electron (P3HT) and ion (PEO/LiTFSI) conducting domains. P3HT is a semicrystalline polymer with intrinsically semiconducting electronic properties. Electrochemical oxidation (doping) of the P3HT block provides the P3HT-b-PEO/LiTFSI mixtures with electronic conductivity suitable for lithium battery operation. Due to the presence of the solid-state electrolyte (PEO/LiTFSI) in intimate contact with the microphase separated P3HT domains, electrochemical oxidation of P3HT can be performed entirely in the solid state; therefore, P3HT-b-PEO/LiTFSI provides a unique opportunity to study the structural changes in P3HT induced by oxidation. We use in situ x-ray scattering techniques to