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Sample records for probing structure property

  1. Probing electron transport and structural properties of nanostructures on Si with a quadraprobe scanning tunneling microscope

    SciTech Connect

    Kim, Tae Hwan; Wendelken, J F; Li, An-Ping

    2008-01-01

    The electron transport and structural properties of nanostructured materials have been examined with a newly developed low temperature quadraprobe scanning tunneling microscope (STM) system. The quadraprobe STM system, as a "nano" version of a four-probe station provides an integrated research platform with a low temperature four-probe STM, a molecular-beam epitaxy growth chamber, a high resolution scanning electron microscope, and a scanning Auger microscope. The four STM probes can be driven independently with sub-nanometer precision, enabling conventional STM imaging and four-point electrical transport study of surface electronic systems and nanostructured materials at temperatures down to 10 K. Self-assembled nanostructures grown on Si by doping with metal atoms (Au, Gd, Ag) have been fabricated and characterized in situ.

  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. 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.

  4. 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.

  5. 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.

  6. Properties of Broezel static probe

    NASA Astrophysics Data System (ADS)

    Gašparovič, Peter; Semrád, Karol; Cúttová, Miroslava

    2016-03-01

    The properties of flat static probe designed by Broezel and used in sailplanes are investigated for its planned use in low speed tunnel. Both the numerical CFD model and experiment in low speed wind tunnel confirm yaw insensitivity of the static pressure measured by the probe. The results indicate that the probe is sufficiently accurate for its planned use in wind tunnel measurements.

  7. Probing the Glass Transition from Structural and Vibrational Properties of Zero-Temperature Glasses

    NASA Astrophysics Data System (ADS)

    Wang, Lijin; Xu, Ning

    2014-02-01

    We find that the density dependence of the glass transition temperature of Lennard-Jones (LJ) and Weeks-Chandler-Andersen (WCA) systems can be predicted from properties of the zero-temperature (T=0) glasses. Below a crossover density ρs, LJ and WCA glasses show different structures, leading to different vibrational properties and consequently making LJ glasses more stable with higher glass transition temperatures than WCA ones. Above ρs, structural and vibrational quantities of the T =0 glasses show scaling collapse. From scaling relations and dimensional analysis, we predict a density scaling of the glass transition temperature, in excellent agreement with simulation results. We also propose an empirical expression of the glass transition temperature using structural and vibrational properties of the T=0 glasses, which works well over a wide range of densities.

  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. 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.

  10. Probing depth dependent structure and magnetic properties of thin films using polarized neutron reflectivity

    SciTech Connect

    Singh, Surendra; Basu, Saibal

    2015-06-24

    Novel properties of materials produced using nanoscale manufacturing processes often arise from interactions across interfaces between dissimilar materials. In order to understand the physical and magnetic properties of such nanostructures, a thorough and detailed structural and magnetic characterization with interface specificity is required. X-ray reflectivity and polarized neutron reflectivity (PNR) are two nondestructive techniques that provide quantitative measures of the chemical and magnetic depth profiles of the films with less than nanometer resolution averaged over the lateral dimensions of the entire sample (typically 100 mm{sup 2}). PNR specifically gives simultaneous structure and magnetic information of the interfaces. Unquestionably, neutron reflectivity has played a decisive role in the development and study of new emergent phenomena at interfaces.

  11. A novel approach to study the structure-property relationships and applications in living systems of modular Cu(2+) fluorescent probes.

    PubMed

    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 Cu(2+) 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 Cu(2+) 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. 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

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

    PubMed

    Felicia, Leona J; Philip, John

    2013-01-01

    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. PMID:23210900

  14. Structural properties of GaNAs nanowires probed by micro-Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Filippov, S.; Ishikawa, F.; Chen, W. M.; Buyanova, I. A.

    2016-02-01

    GaNAs-based nanowires (NWs) form a novel material system of potential importance for applications in advanced optoelectronic and photonic devices, thanks to the advantages provided by band-structure engineering, one-dimensional architecture and the possibility to combine them with mainstream silicon technology. In this work we utilize the micro-Raman scattering technique to systematically study the structural properties of such GaAs/GaNAs core/shell NW structures grown by molecular beam epitaxy on a Si substrate. It is shown that the employed one-dimensional architecture allows the fabrication of a GaNAs shell with a low degree of alloy disorder and weak residual strain, at least within the studied range of nitrogen (N) compositions [N] < 0.6%. Raman scattering by the GaAs-like and GaN-like phonons is found to be enhanced when the excitation energy approaches the E+ transition energy. Since this effect is found to be more pronounced for the GaN-like phonons, the involved intermediate states are concluded to be localized in proximity to N impurities, i.e. they likely represent N-related cluster states located in proximity to E+.

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

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

    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 4) 2, calcium dodecahydro- closo-dodecaborate was isolated and characterized by diffraction and spectroscopic techniques. The crystal structure of CaB 12H 12 was determined from powder XRD data and confirmed by DFT and neutron vibrational spectroscopy studies. Attempts to dehydrogenate/hydrogenate mixtures of CaB 12H 12 and CaH 2 were made under conditions known to favor partial reversibility in calcium borohydride. However, up to 670 K no notable formation of Ca(BH 4) 2 (during hydrogenation) or CaB 6 (during dehydrogenation) occurred. It was demonstrated that the stability of CaB 12H 12 can be significantly altered using CaH 2 as a destabilizing agent to favor the hydrogen release.

  16. CONDENSED MATTER: STRUCTURE, MECHANICAL AND THERMAL PROPERTIES: Capillary Interactions between a Probe Tip and a Nanoparticle

    NASA Astrophysics Data System (ADS)

    Sun, Li-Ning; Wang, Le-Feng; Rong, Wei-Bin

    2008-05-01

    To understand capillary interactions between probe tips and nanoparticles under ambient conditions, a theoretical model of capillary forces between them is developed based on the geometric relations. It is found that the contribution of surface tension force to the total capillary force attains to similar order of magnitude as the capillary pressure force in many cases. It is also shown that the tip shape and the radial distance of the meniscus have great influence on the capillary force. The capillary force decreases with the increasing separation distances, and the variance of the contact angles may change the magnitudes of capillary forces several times at large radial distances. The applicability of the symmetric meniscus approximation is discussed.

  17. 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.

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

    PubMed

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

    2011-05-01

    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. PMID:21437303

  19. Fluorescent probes for G-quadruplex structures.

    PubMed

    Vummidi, Balayeshwanth R; Alzeer, Jawad; Luedtke, Nathan W

    2013-03-18

    Mounting evidence supports the presence of biologically relevant G-quadruplexes in single-cell organisms, but the existence of endogenous G-quadruplex structures in mammalian cells remains highly controversial. This is due, in part, to the common misconception that DNA and RNA molecules are passive information carriers with relatively little structural or functional complexity. For those working in the field, however, the lack of available tools for characterizing DNA structures in vivo remains a major limitation to addressing fundamental questions about structure-function relationships of nucleic acids. In this review, we present progress towards the direct detection of G-quadruplex structures by using small molecules and modified oligonucleotides as fluorescent probes. While most development has focused on cell-permeable probes that selectively bind to G-quadruplex structures with high affinity, these same probes can induce G-quadruplex folding, thereby making the native conformation of the DNA or RNA molecule (i.e., in the absence of probe) uncertain. For this reason, modified oligonucleotides and fluorescent base analogues that serve as "internal" fluorescent probes are presented as an orthogonal means for detecting conformational changes, without necessarily perturbing the equilibria between G-quadruplex, single-stranded, and duplex DNA. The major challenges and motivation for the development of fluorescent probes for G-quadruplex structures are presented, along with a summary of the key photophysical, biophysical, and biological properties of reported examples. PMID:23440895

  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 Carrier Transport and Structure-Property Relationship of Highly Ordered Organic Semiconductors at the Two-Dimensional Limit

    NASA Astrophysics Data System (ADS)

    Zhang, Yuhan; Qiao, Jingsi; Gao, Si; Hu, Fengrui; He, Daowei; Wu, Bing; Yang, Ziyi; Xu, Bingchen; Li, Yun; Shi, Yi; Ji, Wei; Wang, Peng; Wang, Xiaoyong; Xiao, Min; Xu, Hangxun; Xu, Jian-Bin; Wang, Xinran

    2016-01-01

    One of the basic assumptions in organic field-effect transistors, the most fundamental device unit in organic electronics, is that charge transport occurs two dimensionally in the first few molecular layers near the dielectric interface. Although the mobility of bulk organic semiconductors has increased dramatically, direct probing of intrinsic charge transport in the two-dimensional limit has not been possible due to excessive disorders and traps in ultrathin organic thin films. Here, highly ordered single-crystalline mono- to tetralayer pentacene crystals are realized by van der Waals (vdW) epitaxy on hexagonal BN. We find that the charge transport is dominated by hopping in the first conductive layer, but transforms to bandlike in subsequent layers. Such an abrupt phase transition is attributed to strong modulation of the molecular packing by interfacial vdW interactions, as corroborated by quantitative structural characterization and density functional theory calculations. The structural modulation becomes negligible beyond the second conductive layer, leading to a mobility saturation thickness of only ˜3 nm . Highly ordered organic ultrathin films provide a platform for new physics and device structures (such as heterostructures and quantum wells) that are not possible in conventional bulk crystals.

  3. Probing Carrier Transport and Structure-Property Relationship of Highly Ordered Organic Semiconductors at the Two-Dimensional Limit.

    PubMed

    Zhang, Yuhan; Qiao, Jingsi; Gao, Si; Hu, Fengrui; He, Daowei; Wu, Bing; Yang, Ziyi; Xu, Bingchen; Li, Yun; Shi, Yi; Ji, Wei; Wang, Peng; Wang, Xiaoyong; Xiao, Min; Xu, Hangxun; Xu, Jian-Bin; Wang, Xinran

    2016-01-01

    One of the basic assumptions in organic field-effect transistors, the most fundamental device unit in organic electronics, is that charge transport occurs two dimensionally in the first few molecular layers near the dielectric interface. Although the mobility of bulk organic semiconductors has increased dramatically, direct probing of intrinsic charge transport in the two-dimensional limit has not been possible due to excessive disorders and traps in ultrathin organic thin films. Here, highly ordered single-crystalline mono- to tetralayer pentacene crystals are realized by van der Waals (vdW) epitaxy on hexagonal BN. We find that the charge transport is dominated by hopping in the first conductive layer, but transforms to bandlike in subsequent layers. Such an abrupt phase transition is attributed to strong modulation of the molecular packing by interfacial vdW interactions, as corroborated by quantitative structural characterization and density functional theory calculations. The structural modulation becomes negligible beyond the second conductive layer, leading to a mobility saturation thickness of only ∼3  nm. Highly ordered organic ultrathin films provide a platform for new physics and device structures (such as heterostructures and quantum wells) that are not possible in conventional bulk crystals. PMID:26799035

  4. The use of ultrasound to probe structural and material properties of bone: State-of-the art

    NASA Astrophysics Data System (ADS)

    Laugier, Pascal

    2004-10-01

    The knowledge of the elastic properties of bone can be used to investigate the effects of aging, disease, and treatments. Elastic properties are also required as input for both computational and analytic models. An alternative approach to direct bone mechanical testing is to use ultrasonic testing. Furthermore, ultrasound is appropriate for multiscale analysis. In vitro, ultrasound has been widely used to derive nondestructively the stiffness coefficients or the elastic moduli at the whole specimen level at low frequency (structural elasticity) or at the tissue level at higher frequency (material stiffness). Quantitative ultrasound (QUS) techniques have also been developed for in vivo skeletal status assessment based on the assumption that ultrasonic properties reflect skeletal factors of bone fragility. In vivo QUS is then used to predict fracture risk. Several different techniques are currently available or under development involving different type of waves (bulk compressional waves, surface waves, guided modes). Measured ultrasonic properties in transmission or in reflection depend on a variety of material properties and macro- or micro structural characteristics. However, the complexity of the interaction mechanisms between the incident ultrasonic field and bone is still not fully elucidated and requires a better understanding.

  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 structural and dynamical properties of liquid water with models including non-local electron correlation

    NASA Astrophysics Data System (ADS)

    Del Ben, Mauro; Hutter, Jürg; VandeVondele, Joost

    2015-08-01

    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.

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

    PubMed

    Del Ben, Mauro; Hutter, Jürg; VandeVondele, Joost

    2015-08-01

    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. PMID:26254660

  8. FDR probe structure influence on the soil dielectric spectrum measurement

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The soil dielectric spectrum are related to the soil physical properties, and those are affected by the structure of the probe too. In order to determine how the probe structure influence the soil dielectric spectrum measurement, the two kinds of soils were measured at four water content level by 10...

  9. 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.

  10. 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.

  11. 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. PMID:26812447

  12. 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.

  13. Probing small non-coding RNAs structures.

    PubMed

    Philippe, Jean-Vincent; Ayadi, Lilia; Branlant, Christiane; Behm-Ansmant, Isabelle

    2015-01-01

    The diverse roles of RNAs depend on their ability to fold so as to form biologically functional structures. Thus, understanding the function of a given RNA molecule often requires experimental analysis of its secondary structure by in vitro RNA probing, which is more accurate than using prediction programs only. This chapter presents in vitro RNA probing protocols that we routinely use, from RNA transcript production and purification to RNA structure determination using enzymatic (RNases T1, T2, and V1) and chemical (DMS, CMCT, kethoxal, and Pb(2+)) probing performed on both unlabeled and end-labeled RNAs. PMID:25791596

  14. Near edge X-ray absorption fine structure spectroscopy as a tool to probe electronic and structural properties of thin organic films and liquids.

    PubMed

    Hähner, Georg

    2006-12-01

    Synchrotron-based spectroscopic techniques have contributed significantly to a better understanding of the properties of materials on the macroscopic and microscopic scale over the last decades. They can be applied to samples from a diversity of fields, including Biology, Life Sciences, Chemistry and Materials. One of these techniques is Near Edge X-Ray Absorption Fine Structure (NEXAFS) spectroscopy, revealing electronic structure and information on the orientation of adsorbed molecules. The present article describes the basics of the technique and the progress it has made over the last three decades, and summarizes some of its more recent developments and applications. This tutorial review article should be accessible for novices to the field from Physics, Chemistry, Biology, Materials, and the Life Sciences, interested in thin organic films and liquid systems. PMID:17225886

  15. Current perspectives on RNA secondary structure probing.

    PubMed

    Kenyon, Julia; Prestwood, Liam; Lever, Andrew

    2014-08-01

    The range of roles played by structured RNAs in biological systems is vast. At the same time as we are learning more about the importance of RNA structure, recent advances in reagents, methods and technology mean that RNA secondary structural probing has become faster and more accurate. As a result, the capabilities of laboratories that already perform this type of structural analysis have increased greatly, and it has also become more widely accessible. The present review summarizes established and recently developed techniques. The information we can derive from secondary structural analysis is assessed, together with the areas in which we are likely to see exciting developments in the near future. PMID:25110033

  16. Nonlinear optical properties and nonlinear optical probes of organic materials

    NASA Astrophysics Data System (ADS)

    Meredith, Gerald R.

    1992-02-01

    Nonlinear optical processes and electro-optical effects are expected to have increasing importance as the information age matures and photonics augment electronics in various high density and high bandwidth technologies. Whereas for electronics the emphasis is in construction of smaller device structures from a few parent materials, for organic materials the direction of materials research has been reversed. For some time it's been known that some molecular structures engender exceptionally large molecular nonlinear-polarization responses. If such molecules could be assembled in convenient, versatile, and reliable ways, the resulting materials would be very useful or even enabling in various photonics applications. The mature science and art of chemistry allows very good control over molecular composition and structure and, as will be illustrated in this talk, our knowledge of hyperpolarizability structure- property relationships is advancing rapidly. However, the science of fabrication and arrangement in molecular ensembles and polymers is rather primitive. Thus the goal to develop the appropriately structured materials for utilization in nonlinear and electro-optics has fostered the widespread use of nonlinear optical processes to probe the nature of supramolecular order and assembly. Examples of intrinsic and artificially assembled structures of crystals, molecular aggregates, polymeric orientational electrets and molecular mono- and multi-layer thin films will be shown. Nonlinear optical processes, primarily second-harmonic generation, provide unique probes of these structures, their assembly, and evolution.

  17. 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

  18. Single Probes, Double Probes, and the Structure of Memory Traces.

    ERIC Educational Resources Information Center

    Bruce, Darryl

    1980-01-01

    Memory for names was queried by single probes consisting of conceptual information about the persons or by double probes combining two single cues. Results were viewed as consistent with Jones's fragmentation hypothesis and with the general class of associative theories of memory. (Author/RD)

  19. 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.

  20. Single molecule probes of membrane structure: orientation of BODIPY probes in DPPC as a function of probe structure.

    PubMed

    Armendariz, Kevin P; Huckabay, Heath A; Livanec, Philip W; Dunn, Robert C

    2012-03-21

    Single molecule fluorescence measurements have recently been used to probe the orientation of fluorescent lipid analogs doped into lipid films at trace levels. Using defocused polarized total internal reflection fluorescence microscopy (PTIRF-M), these studies have shown that fluorophore orientation responds to changes in membrane surface pressure and composition, providing a molecular level marker of membrane structure. Here we extend those studies by characterizing the single molecule orientations of six related BODIPY probes doped into monolayers of DPPC. Langmuir-Blodgett monolayers transferred at various surface pressures are used to compare the response from fluorescent lipid analogs in which the location of the BODIPY probe is varied along the length of the acyl chain. For each BODIPY probe location along the chain, comparisons are made between analogs containing phosphocholine and smaller fatty acid headgroups. Together these studies show a general propensity of the BODIPY analogs to insert into membranes with the BODIPY probe aligned along the acyl chains or looped back to interact with the headgroups. For all BODIPY probes studied, a bimodal orientation distribution is observed which is sensitive to surface pressure, with the population of BODIPY probes aligned along the acyl chains increasing with elevated surface pressure. Trends in the single molecule orientations for the six analogs reveal a configuration where optimal placement of the BODIPY probe within the acyl chain maximizes its sensitivity to the surrounding membrane structure. These results are discussed in terms of balancing the effects of headgroup association with acyl chain length in designing the optimal placement of the BODIPY probe. PMID:22322157

  1. The theory of Langmuir probes in strong electrostatic potential structures

    NASA Technical Reports Server (NTRS)

    Borovsky, J. E.

    1986-01-01

    The operation of collecting and emitting Langmuir probes and double probes within time-stationary strong electrostatic potential structures is analyzed. The cross sections of spherical and cylindrical probes to charged particles within the structures are presented and used to obtain the current-voltage characteristics of idealized probes. The acquisition of plasma parameters from these characteristics is outlined, and the operation of idealized floating double-probe systems is analyzed. Probe surface effects are added to the idealized theory, and some surface effects pertinent to spacecraft probes are quantified. Magnetic field effects on idealized probes are examined, and the time required for floating probes to change their potentials by collecting charge and by emitting photoelectrons is discussed. Calculations on the space-charge effects of probe-perturbed beams and on the space-charge limiting of electron emission are given in an appendix.

  2. 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.

  3. 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.

  4. Advances in Structural Studies of Materials using Scattering Probes

    SciTech Connect

    Huq, Ashfia; Bozin, Emil; Welberry, Dr. Richard

    2010-01-01

    Study of contemporary materials and their remarkable properties is a challenging problem. To understand these complex properties and develop better materials it is essential to understand their structures, as the two are intimately linked. Great advances in materials scattering have been achieved due to the advent of synchrotron and neutron sources along with the availability of high-speed computational algorithms. Materials scientists can now collect data with high resolution, high throughput from very small amount of sample (both single crystal and powder), and analyze vast amount of data to unravel detailed structural description that was not possible before. This article presents some of these great advances in using scattering probes for materials characterization.

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

    PubMed

    Bregar, Maksimilijan; Cugmas, Blaž; Naglic, 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. PMID:26720880

  6. 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.

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

    PubMed

    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

  8. 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

  9. Probing Water Structures in Nanopores Using Tunneling Currents

    NASA Astrophysics Data System (ADS)

    Boynton, P.; Di Ventra, M.

    2013-11-01

    We study the effect of volumetric constraints on the structure and electronic transport properties of distilled water in a nanopore with embedded electrodes. Combining classical molecular dynamics simulations with quantum scattering theory, we show that the structural motifs water exhibits inside the pore can be probed directly by tunneling. In particular, we show that the current does not follow a simple exponential curve at a critical pore diameter of about 8 Å, rather it is larger than the one expected from simple tunneling through a barrier. This is due to a structural transition from bulklike to “nanodroplet” water domains. Our results can be tested with present experimental capabilities to develop our understanding of water as a complex medium at nanometer length scales.

  10. Oxygen transport as a structure probe for amorphous polymeric systems

    NASA Astrophysics Data System (ADS)

    Liu, Richard Yufeng

    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 in the oriented glassy state, (2) the role of amorphous phase orientation and strain-induced crystallization on oxygen barrier properties of polyester blends, and (3) the nature of interphase between immiscible amorphous polymers in forced-assemblies. In the first part, the mechanism of oxygen transport in oriented glassy polyesters is examined. PET, PETBB55, and PEN were oriented by cold-drawing. Densification of the glassy state correlates with conformational transformation of glycol linkages from gauche to trans. Orientation is seen as a process of decreasing the amount of excess-hole free volume and bringing the nonequilibrium polymer glass closer to the equilibrium condition. Further insights into the free volume structure are obtained by exploring the relationships between free volume structure and oxygen transport property using a simple lattice-hole model. In the second part, oxygen transport through polyester blends is investigated. It is found that cold-drawing the blocky PET/PETBB55 produces highly oriented PETBB55 frustrated LCP microfibrils, which prevent relaxation of the continuous PET phase. On the other hand, careful examination of oxygen barrier for the PET/PEI blends leads to a two-phase model from which the amount of crystallinity and the amorphous phase density are determined. In the third part, oxygen permeability is utilized as a powerful probe for interphase thickness between immiscible polymers, which is as thin as a few nanometers. We

  11. Probing semiconductor band structures and heterojunction interface properties with ballistic carrier emission: GaAs/AlxGa1-xAs as a model system

    NASA Astrophysics Data System (ADS)

    Yi, Wei; Narayanamurti, Venkatesh; Lu, Hong; Scarpulla, Michael A.; Gossard, Arthur C.

    2010-06-01

    Utilizing three-terminal tunnel emission of ballistic electrons and holes in a planar tunnel transistor with a Mott-barrier collector, we have developed a method to self-consistently determine the energy gap of a semiconductor and band discontinuities at a semiconductor heterojunction without using a priori material parameters. Measurements are performed on lattice-matched GaAs/AlxGa1-xAs (100) single-barrier double heterostructures with AlxGa1-xAs as the model ternary III-V compounds. Electronic band gaps of the AlGaAs alloys and band offsets at the GaAs/AlGaAs (100) interfaces are measured with a resolution of several meV at 4.2 K. The direct-gap Γ band offset ratio for the GaAs/AlGaAs (100) interface is found to be 59:41 (±3%) . Reexamination of our previous experiment [W. Yi , Appl. Phys. Lett. 95, 112102 (2009)10.1063/1.3224914] revealed that, in the indirect-gap regime, ballistic electrons from direct tunnel emissions probe the X valley in the conduction band, while those from Auger-like scattering processes in the metal base film probe the higher-lying L valley. Such selective electron collection may be explained by their different momentum distributions and parallel momentum conservation at the quasiepitaxial Al/GaAs (100) interface. We argue that the present method is in principle applicable to arbitrary type-I semiconductor heterostructures.

  12. Seismic probes of solar interior magnetic structure.

    PubMed

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

    2012-09-01

    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. PMID:23005276

  13. Atom-probe and field emission electron spectroscopy studies of ordered structures and electronic properties of Ge overlayers on Ir-tips

    NASA Astrophysics Data System (ADS)

    Ashino, Makoto; Tomitori, Masahiko; Nishikawa, Osamu

    1994-03-01

    The combined instrument of an atom probe (AP) and a field emission electron spectroscope (FEES) was employed to investigate the crystallinity and the surface electronic state of Ge overlayers deposited on Ir tips. The crystallinity of Ge overlayers deposited at 300 and 420 K, and those annealed after the deposition, is better than that of the overlayers deposited at 50 K. The surface electronic state of the well-crystallized Ge overlayer is semiconductive at the thickness of ≈4 ML. When the degree of crystallinity is rather low or Ir atoms exist in the Ge overlayer, even a thick overlayer exhibits metallic surface electronic states. When an Ir atom exists on the overlayer surface, a small peak appears at ≈ 0.3 eV below the Fermi level in the field emission electron distribution (FEED), indicating a local state of the Ir atom.

  14. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  16. 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).

  17. 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

  18. 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.

  19. Association dynamics and linear and nonlinear optical properties of an N-acetylaladanamide probe in a POPC membrane.

    PubMed

    Murugan, N Arul; Apostolov, Rossen; Rinkevicius, Zilvinas; Kongsted, Jacob; Lindahl, Erik; Ågren, Hans

    2013-09-11

    Along with the growing evidence that relates membrane abnormalities to various diseases, biological membranes have been acknowledged as targets for therapy. Any such abnormality in the membrane structure alters the membrane potential which in principle can be captured by measuring properties of specific optical probes. There exists by now many molecular probes with absorption and fluorescence properties that are sensitive to local membrane structure and to the membrane potential. To suggest new high-performance optical probes for membrane-potential imaging it is important to understand in detail the membrane-induced structural changes in the probe, the membrane association dynamics of the probe, and its membrane-specific optical properties. To contribute to this effort, we here study an optical probe, N-acetylaladanamide (NAAA), in the presence of a POPC lipid bilayer using a multiscale integrated approach to assess the probe structure, dynamics, and optical properties in its membrane-bound status and in water solvent. We find that the probe eventually assimilates into the membrane with a specific orientation where the hydrophobic part of the probe is buried inside the lipid bilayer, while the hydrophilic part is exposed to the water solvent. The computed absorption maximum is red-shifted when compared to the gas phase. The computations of the two-photon absorption and second harmonic generation cross sections of the NAAA probe in its membrane-bound state which is of its first kind in the literature suggest that this probe can be used for imaging the membrane potential using nonlinear optical microscopy. PMID:23951997

  20. 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

  1. 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.

  2. Probing Nuclear Structure with Fast Neutrons

    SciTech Connect

    Yates, Steven W.

    2009-01-28

    The advantages of using inelastic neutron scattering with detection of the emitted {gamma} rays, i.e., the (n,n'{gamma}) reaction, for exploring the structure of stable nuclei are reviewed. Examples of the information available with these techniques are provided and progress in understanding multiphonon excitations is described. The unique nuclear structure of {sup 94}Zr is discussed.

  3. 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.

  4. 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.

  5. 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

  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. 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

  8. Gravitational Microlensing as a probe of Quasar Structure

    NASA Astrophysics Data System (ADS)

    Floyd, David

    2011-01-01

    Gravitational microlensing provides information at the micro-to-nano arcsecond scale necessary to probe the structure of the central engine of quasars. We can now determine the radius of the broad line emitting regions, and measure the temperature profile of the continuum emitting region using single-epoch observations. I will present X-shooter spectroscopy that provides new insight into the accretion mechanism, and the structure of the broad line region.

  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. Predicting RNA secondary structures from sequence and probing data.

    PubMed

    Lorenz, Ronny; Wolfinger, Michael T; Tanzer, Andrea; Hofacker, Ivo L

    2016-07-01

    RNA secondary structures have proven essential for understanding the regulatory functions performed by RNA such as microRNAs, bacterial small RNAs, or riboswitches. This success is in part due to the availability of efficient computational methods for predicting RNA secondary structures. Recent advances focus on dealing with the inherent uncertainty of prediction by considering the ensemble of possible structures rather than the single most stable one. Moreover, the advent of high-throughput structural probing has spurred the development of computational methods that incorporate such experimental data as auxiliary information. PMID:27064083

  11. Probing mechanical properties of liposomes using acoustic sensors.

    PubMed

    Melzak, Kathryn A; Bender, Florian; Tsortos, Achilleas; Gizeli, Electra

    2008-08-19

    Acoustic devices were employed to characterize variations in the mechanical properties (density and viscoelasticity) of liposomes composed of 1-oleoyl-2-palmitoyl- sn-glycero-3-phosphocholine (POPC) and cholesterol. Liposome properties were modified in three ways. In some experiments, the POPC/cholesterol ratio was varied prior to deposition on the device surface. Alternatively, the ratio was changed in situ via either insertion of cholesterol or removal of cholesterol with beta-cyclodextrin. This was done for liposomes adsorbed directly on the device surface and for liposomes attached via a biotin-terminated poly(ethylene glycol) linker. The acoustic measurements make use of two simultaneous time-resolved signals: one signal is related to the velocity of the acoustic wave, while the second is related to dissipation of acoustic energy. Together, they provide information not only about the mass (or density) of the probed medium but also about its viscoelastic properties. The cholesterol-induced increase in the surface density of the lipid bilayer was indeed observed in the acoustic data, but the resulting change in signal was larger than expected from the change in surface density. In addition, increasing the bilayer resistance to stretching was found to lead to a greater dissipation of the acoustic energy. The acoustic response is assessed in terms of the possible distortions of the liposomes and the known effects of cholesterol on the mechanical properties of the lipid bilayer that encloses the aqueous core of the liposome. To aid the interpretation of the acoustic response, it is discussed how the above changes in the lipid bilayer will affect the effective viscoelastic properties of the entire liposome/solvent film on the scale of the acoustic wavelength. It was found that the acoustic device is very sensitive to the mechanical properties of lipid vesicles; the response of the acoustic device is explained, and the basic underlying mechanisms of interaction are

  12. 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.

  13. Cysteine Modification: Probing Channel Structure, Function and Conformational Change.

    PubMed

    Akabas, Myles H

    2015-01-01

    Cysteine substitution has been a powerful tool to investigate the structure and function of proteins. It has been particularly useful for studies of membrane proteins in their native environment, embedded in phospholipid membranes. Among the 20 amino acids, cysteine is uniquely reactive. This reactivity has motivated the synthesis of a wide array of sulfhydryl reactive chemicals. The commercially available array of sulfhydryl reactive reagents has allowed investigators to probe the local steric and electrostatic environment around engineered cysteines and to position fluorescent, paramagnetic and mass probes at specific sites within proteins and for distance measurements between pairs of sites. Probing the reactivity and accessibility of engineered cysteines has been extensively used in Substituted Cysteine Accessibility Method (SCAM) investigations of ion channels, membrane transporters and receptors. These studies have successfully identified the residues lining ion channels, agonist/antagonist and allosteric modulator binding sites, and regions whose conformation changes as proteins transition between different functional states. The thousands of cysteine-substitution mutants reported in the literature demonstrate that, in general, mutation to cysteine is well tolerated. This has allowed systematic studies of residues in transmembrane segments and in other parts of membrane proteins. Finally, by inserting pairs of cysteines and assaying their ability to form disulfide bonds, changes in proximity and mobility relationships between specific positions within a protein can be inferred. Thus, cysteine mutagenesis has provided a wealth of data on the structure of membrane proteins in their functional environment. This data can complement the structural insights obtained from the burgeoning number of crystal structures of detergent solubilized membrane proteins whose functional state is often uncertain. This article will review the use of cysteine mutagenesis to probe

  14. Hydration effects on membrane structure probed by single molecule orientations.

    PubMed

    Huckabay, Heath A; Dunn, Robert C

    2011-03-15

    Single molecule fluorescence measurements are used to probe the structural changes in glass-supported DPPC bilayers as a function of relative humidity (RH). Defocused polarized total internal reflection fluorescence microscopy is employed to determine the three-dimensional orientation of the fluorescent lipid analogue BODIPY-PC, doped into DPPC membranes in trace amounts. Supported DPPC bilayers formed using vesicle fusion and Langmuir-Blodgett/Langmuir-Schäfer (LB/LS) transfer are compared and show similar trends as a function of relative humidity. Population histograms of the emission dipole tilt angle reveal bimodal distributions as observed previously for BODIPY-PC in DPPC. These distributions are dominated by large populations of BODIPY-PC molecules with emission dipoles oriented parallel (≥81°) and normal (≤10°) to the membrane plane, with less than 25% oriented at intermediate tilts. As the relative humidity is increased from 13% to 95%, the population of molecules oriented normal to the surface decreases with a concomitant increase in those oriented parallel to the surface. The close agreement in trends observed for bilayers formed from vesicle fusion and LB/LS transfer supports the assignment of an equivalent surface pressure of 23 mN/m for bilayers formed from vesicle fusion. At each RH condition, a small population of BODIPY-PC dye molecules are laterally mobile in both bilayer preparations. This population exponentially increases with RH but never exceeds 6% of the total population. Interestingly, even under conditions where there is little lateral diffusion, fluctuations in the single molecule orientations can be observed which suggests there is appreciable freedom in the acyl chain region. Dynamic measurements of single molecule orientation changes, therefore, provide a new view into membrane properties at the single molecule level. PMID:21319764

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

    PubMed Central

    Nishida, Jun; Tamimi, Amr; Fei, Honghan; Pullen, Sonja; Ott, Sascha; Cohen, Seth M.; Fayer, Michael D.

    2014-01-01

    The structural elasticity of metal–organic frameworks (MOFs) is a key property for their functionality. Here, 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. Methodology advances were required 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. PMID:25512539

  16. 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…

  17. Genome-Wide Approaches for RNA Structure Probing.

    PubMed

    Silverman, Ian M; Berkowitz, Nathan D; Gosai, Sager J; Gregory, Brian D

    2016-01-01

    RNA molecules of all types fold into complex secondary and tertiary structures that are important for their function and regulation. Structural and catalytic RNAs such as ribosomal RNA (rRNA) and transfer RNA (tRNA) are central players in protein synthesis, and only function through their proper folding into intricate three-dimensional structures. Studies of messenger RNA (mRNA) regulation have also revealed that structural elements embedded within these RNA species are important for the proper regulation of their total level in the transcriptome. More recently, the discovery of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) has shed light on the importance of RNA structure to genome, transcriptome, and proteome regulation. Due to the relatively small number, high conservation, and importance of structural and catalytic RNAs to all life, much early work in RNA structure analysis mapped out a detailed view of these molecules. Computational and physical methods were used in concert with enzymatic and chemical structure probing to create high-resolution models of these fundamental biological molecules. However, the recent expansion in our knowledge of the importance of RNA structure to coding and regulatory RNAs has left the field in need of faster and scalable methods for high-throughput structural analysis. To address this, nuclease and chemical RNA structure probing methodologies have been adapted for genome-wide analysis. These methods have been deployed to globally characterize thousands of RNA structures in a single experiment. Here, we review these experimental methodologies for high-throughput RNA structure determination and discuss the insights gained from each approach. PMID:27256381

  18. [Effect of radiation on erythrocyte membrane structure using fluorescent probes].

    PubMed

    Gorbenko, G P; Krupin, V D; Tovstiak, V V

    1994-01-01

    The effect of electrons with the energy of 5 MeV on the erythrocyte membrane structure was investigated using a fluorescent probe (4-dimethylaminostiryl)-1-methylpyridinium (DSM). Analysis of a competitive binding of DSM and ribonuclease with the erythrocyte ghosts has shown that irradiation causes an increase in the constant of protein association with membranes. It is suggested that a negative surface change increase with irradiation. PMID:7754561

  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. Investigation of ferromagnetic properties of LSMO nanolayers by laser modulated reflectance probe

    NASA Astrophysics Data System (ADS)

    Pencheva, V.; Alipieva, E.; Penchev, S.; Nedkov, I.; Kutzarova, T.

    2010-10-01

    Modulated optical reflectance (MOR) technique is employed for defectoscopy and structural analysis of La2/3Sr1/3MnO3(LSMO) ferromagnetic nanolayers. The optical reflectance is affected by the change of free charge carrier density due to periodic photothermal modulation described by Drude effect. A dual wavelength setup of a pulsed heating laser and a probe CW laser, whereas the laser focal spots are precisely aligned on the scanned sample surface, provides electrical signal proportional to the variation of optical reflectance at each measurement point. The probe beam is modulated selectively by reflection without interference by the substrate properties or external fields. It is shown theoretically and experimentally that MOR signal is proportional to the thermal derivative of magnetoresistance. The described contactless measurement may find important application in investigation of a range of new magnetoelectric devices.

  1. Mission and instrumentation concept for the baryonic structure probe

    NASA Astrophysics Data System (ADS)

    Ebbets, Dennis; DeCino, James; Turner-Valle, Jennifer; Sembach, Kenneth

    2006-06-01

    There is a growing consensus that a substantial fraction of the matter in the universe, especially what we think of as normal baryonic matter, exists in a tenuous, hot filamentary intergalactic medium often referred to as the Cosmic Web. Improving our understanding of the web has been a high priority scientific goal in NASA's planning and roadmapping activities. NASA recently supported an Origins Probe study that explored the observable phenomenology of the web in detail and developed concepts for the instrumentation and mission. The Baryonic Structure Probe operates in the ultraviolet spectral region, using primarily O VI (λλ 1032, 1038 angstrom) and HI Ly α (λ 1216 angstrom) as tracers of the web. A productive investigation requires both moderate resolution (R = λ/Δλ ~ 30000) absorption line spectroscopy using faint background quasars as continuum sources, and imaging of the diffuse filaments in emission lines of the same ions. Spectroscopic sensitivity to quasars as faint as V ~ 19 will probe a large number of sight lines to derive physical diagnostics over the redshift range 0 < z < 1. Spectral imaging with a wide field of view and sensitivity to a redshift range 0 < z < 0.3 will map the filaments in a large volume of the universe after the web had evolved to near its modern structure. This paper summarizes the scientific goals, identifies the measurement requirements derived from them, and describes the instrument concepts and overall mission architecture developed by the BSP study team.

  2. Probing Electronic and Thermoelectric Properties of Single Molecule Junctions

    NASA Astrophysics Data System (ADS)

    Widawsky, Jonathan R.

    In an effort to further understand electronic and thermoelectric phenomenon at the nanometer scale, we have studied the transport properties of single molecule junctions. To carry out these transport measurements, we use the scanning tunneling microscope-break junction (STM-BJ) technique, which involves the repeated formation and breakage of a metal point contact in an environment of the target molecule. Using this technique, we are able to create gaps that can trap the molecules, allowing us to sequentially and reproducibly create a large number of junctions. By applying a small bias across the junction, we can measure its conductance and learn about the transport mechanisms at the nanoscale. The experimental work presented here directly probes the transmission properties of single molecules through the systematic measurement of junction conductance (at low and high bias) and thermopower. We present measurements on a variety of molecular families and study how conductance depends on the character of the linkage (metal-molecule bond) and the nature of the molecular backbone. We start by describing a novel way to construct single molecule junctions by covalently connecting the molecular backbone to the electrodes. This eliminates the use of linking substituents, and as a result, the junction conductance increases substantially. Then, we compare transport across silicon chains (silanes) and saturated carbon chains (alkanes) while keeping the linkers the same and find a stark difference in their electronic transport properties. We extend our studies of molecular junctions by looking at two additional aspects of quantum transport -- molecular thermopower and molecular current-voltage characteristics. Each of these additional parameters gives us further insight into transport properties at the nanoscale. Evaluating the junction thermopower allows us to determine the nature of charge carriers in the system and we demonstrate this by contrasting the measurement of amine

  3. Using Directional Emissivity as a Probe of Particle Microphysical Properties

    NASA Astrophysics Data System (ADS)

    Pitman, K. M.; Wolff, M. J.; Bandfield, J. L.; Clayton, G. C.

    2002-09-01

    Real surfaces are not expected to be diffuse emitters, thus observed emissivity values are a function of viewing geometry. This fact has strong implications for analyses of the MGS/TES emission phase function (EPF) sequences and the upcoming Mars Exploration Rover mini-TES dataset. As reviewed previously [1], in the absence of strong thermal gradients, directional emissivity may be obtained via a combination of reciprocity and Kirchhoff's Law. Here we focus on the potential utility of directional emissivity as a direct probe of surface particle microphysical properties. We explore the effects of particle size and composition on observed radiances in the TES spectral regime using a combination of multiple scattering radiative transfer and Mie scattering algorithms. Comparisons of these simulated spectra to TES EPF observations of typical surface units (e.g., high and low albedo regions) will also be made. This work is supported through NASA grant NAGS-9820 (MJW) and LSU Board of Regents (KMP). [1] Pitman, K.M., et al. (2001), AAS-DPS meeting # 33, # 36.01.

  4. Perspective: Probing 2-D magnetic structures in a 3-D world

    NASA Astrophysics Data System (ADS)

    Grutter, A. J.

    2016-03-01

    Magnetic interfaces have been identified as promising systems upon which to base next-generation spintronic devices. In these nearly two-dimensional systems, deviations from bulk electronic structure and competition between nearly degenerate magnetic ground states allow the stabilization of widely tunable emergent properties. However, ever smaller length scales pose new challenges which must be overcome in order to understand and control magnetic properties at the atomic level. Using recent examples in oxide heterostructures and topological insulators, we discuss how combining techniques such as neutron scattering, X-ray scattering, X-ray spectroscopy, and transmission electron microscopy enables the probing of magnetism on the Angstrom scale.

  5. The electronic structure of diodes probed under bias

    NASA Astrophysics Data System (ADS)

    Glans, Per-Anders; Guo, Jinghua; Park, Jeong; Gabor, Somorjai

    2009-03-01

    Chemists have known for decades that when metal nano-particles are affixed to a catalytically inactive oxide surface, the catalytic turnover rate of the array is more than 10 times that of a metal surface alone. However, the mechanism behind the effect is not clear. To understand the catalytic activity of the interface between the metal nano-structures and the oxide substrate, we have investigated the electronic structure of Pt and Pd doped diodes on a TiO2 substrate. The devices were put under bias during the measurements in an attempt to reproduce the potential differences found over the diode when used as a catalyst. This is challenging for electron based measuring techniques, but using photon-in, photon-out techniques we have successfully probed the electronic structure of Pt and Pd doped diodes under bias. The results from soft x-ray absorption and emission will be presented.

  6. 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

    2009-03-01

    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. PMID:19224038

  7. Probing the structure of the cold dark matter halo using ancient mica

    SciTech Connect

    Baltz, E.A.; Westphal, A.J.; Snowden-Ifft, D.P.

    1999-01-01

    Mica can store (for {gt}1thinspGyr) etchable tracks caused by atoms recoiling from WIMPs. Ancient mica is a directional detector despite the complex motions it makes with respect to the WIMP {open_quotes}wind.{close_quotes} We can exploit the properties of directionality and long integration time to probe for structure in the dark matter halo of our galaxy. We compute a sample of possible signals in mica for a plausible model of halo structure. {copyright} {ital 1998} {ital The American Physical Society}

  8. 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

  9. 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.

  10. 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

    2016-07-01

    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

  11. 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

  12. An advanced AFM sensor: its profile accuracy and low probe wear property for high aspect ratio patterns

    NASA Astrophysics Data System (ADS)

    Watanabe, Masahiro; Baba, Shuichi; Nakata, Toshihiko; Kurenuma, Toru; Kunitomo, Yuichi; Edamura, Manabu

    2007-03-01

    Design rule shrinkage and wider adoption of new device structures such as STI, copper damascene interconnects, and deep trench structures have made the need for in-line process monitoring of step heights and profiles of device structures more urgent. To monitor active device patterns, as opposed to test patterns as in OCD, AFM is the only non-destructive 3D monitoring tool. The barriers to using AFM in-line monitoring are its slow throughput and the accuracy degradation associated with probe tip wear and spike noise caused by unwanted oscillation on the steep slopes of high-aspect-ratio patterns. Our proprietary AFM scanning method, StepIn TM mode, is the method best suited to measuring high-aspect-ratio pattern profiles. Because the probe is not dragged on the sample surface as in conventional AFM, the profile trace fidelity across steep slopes is excellent. Because the probe does not oscillate and hit the sample at a high frequency, as in AC scanning mode, this mode is free from unwanted spurious noises on steep sample slopes and incurs extremely little probe tip wear. To take full advantage of the above properties, we have developed an AFM sensor that is optimized for in-line use and produces accurate profile data at high speeds and incurs little probe tip wear. The control scheme we have developed for the AFM sensor, which we call "Advanced StepIn TM", elaborately analyses the contact force signal, enabling efficient probe tip scanning and a low and stable contact force. With a developed AFM sensor that realizes this concept, we conducted an intensive evaluation on the effect of low and stable contact force scan. Probes with HDC (high density carbon) tips were used for the evaluation. The experiment proves that low contact force enhances the measured profile fidelity by preventing probe tip slip on steep slopes. Dynamics simulation of these phenomena was also conducted, and its results agreed well with the experimental results. The low contact force scan also

  13. 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.

  14. 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.

  15. 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. PMID:25653316

  16. Multispectral Phloem-Mobile Probes: Properties and Applications1

    PubMed Central

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

    2015-01-01

    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. PMID:25653316

  17. 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

  18. 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

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

    DOE PAGESBeta

    Huterer, Dragan; Kirkby, David; Bean, Rachel; Connolly, Andrew; Dawson, Kyle; Dodelson, Scott; Evrard, August; Jain, Bhuvnesh; Jarvis, Michael; Linder, Eric; et al

    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

  20. 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)

  1. Probing topological protection using a designer surface plasmon structure.

    PubMed

    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. 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.

  3. Probing topological protection using a designer surface plasmon structure

    NASA Astrophysics Data System (ADS)

    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

    2016-05-01

    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.

  4. Probing topological protection using a designer surface plasmon structure

    DOE PAGESBeta

    Gao, Fei; Gao, Zhen; Shi, Xihang; Yang, Zhaoju; Lin, Xiao; Xu, Hongyi; Joannopoulos, John D.; Soljacic, Marin; Chen, Hongsheng; Lu, Ling; et al

    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

  5. 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.

  6. Lead-catalyzed cleavage of ribonuclease P RNA as a probe for integrity of tertiary structure.

    PubMed Central

    Zito, K; Hüttenhofer, A; Pace, N R

    1993-01-01

    Pb(2+)-catalyzed cleavage of RNA has been shown previously to be a useful probe for tertiary structure. In the present study, Pb2+ cleavage patterns were identified for ribonuclease P RNAs from three phylogenetically disparate organisms, Escherichia coli, Chromatium vinosum, Bacillus subtilis, and for E. coli RNase P RNAs that had been altered by deletions. Each of the native RNAs undergoes cleavage at several sites in the core structure that is common to all bacterial RNase P RNAs. All the cleavages occur in non-paired regions of the secondary structure models of the RNAs, in regions likely to be involved in tertiary interactions. Two cleavage sites occur at homologous positions in all the native RNAs, regardless of sequence variation, suggesting common tertiary structural features. The Pb2+ cleavage sites in four deletion mutants of E. coli RNase P RNA differed from the native pattern, indicating alterations in the tertiary structures of the mutant RNAs. This conclusion is consistent with previously characterized properties of the mutant RNAs. The Pb2+ cleavage assay is thus a useful probe to reveal alteration of tertiary structure in RNase P RNA. Images PMID:7507234

  7. 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. PMID:16608282

  8. 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

  9. Monitoring membrane properties and apoptosis using membrane probes of the 3-hydroxyflavone family.

    PubMed

    Darwich, Zeinab; Klymchenko, Andrey S; Mély, Yves

    2014-01-01

    Environment-sensitive fluorescent membrane probes are attractive tools for investigating the membrane properties and their changes under perturbing conditions. Membrane probes of the 3-hydroxyflavone family are of particular interest due to their excited-state intramolecular proton transfer (ESIPT) reaction, which confers a dual emission highly sensitive to the polarity and hydration of the environment. In the present work, we will describe the protocols used with these probes in order to monitor the physicochemical properties of lipid membrane models and cell plasma membranes and to detect apoptosis. PMID:24108636

  10. 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

  11. 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

  12. Screening properties of graphene layers studied by Kelvin Probe Force Microscopy and Landau Level Spectroscopy

    NASA Astrophysics Data System (ADS)

    Vetick, John; Lu, Chih-Pin; Altvater, Michael; Duan, Junxi; Li, Guohong; Andrei, Eva Y.

    2015-03-01

    Graphene is one of the best conductors known, but due to its two dimensional structure and the need to support it on insulating substrates, its electronic properties are often masked by substrate-induced random potential fluctuations. In order to realize graphene's full potential for electronic application it is therefore important to understand its screening properties and to find ways to minimize substrate invasiveness. We employed Kelvin Probe Force microscopy (KPFM) to investigate the screening properties of CVD grown graphene crystals as a function of layer number and substrate material using a gated device geometry. The KPFM study was complemented by low temperature scanning tunneling microscopy and Landau level spectroscopy in similar samples and device configurations. Measurements were carried out on single layer, bilayer, trilayer and twisted bilayer samples deposited on SiO2 and hBN substrates. Our findings show that twisted graphene layers provide superior screening of charged impurities and random potentials while at the same time preserving the unique electronic band structure of single layer graphene. Work Supported by DOE-FG02-99ER45742 and NSF DMR 1207108.

  13. Properties of a hairpin probe in a strongly magnetized plasma

    NASA Astrophysics Data System (ADS)

    Karkari, S. K.; Gogna, G. S.; Boilson, D.

    2009-10-01

    Understanding of the physics in the filter field region of a neutral beam injection source for ITER under development is very important, as this region is where the negative ions are generated and extracted. For accurately determining electron densities in this complex plasma, a floating hairpin probe is applied on the KAMABOKO III ion source, at the MANTIS test bed at CEA Cadarache. The technique is based on measuring the probes resonance frequency (few GHz) shift in plasma with respect to that obtained in vacuum. The resonance frequency is proportional to the permittivity of the medium filling the space between the wires of the hairpin resonator. Using this technique we obtained the electron density variation as function of discharge power and on the external grid bias in front of the plasma grid.

  14. High harmonics from solids probe Angstrom scale structure

    NASA Astrophysics Data System (ADS)

    You, Yong Sing; Reis, David; Ghimire, Shambhu

    2016-05-01

    The basic microscopic mechanism for the high harmonics generation (HHG) in isolated atoms and molecules has been understood in the 90's. Since then the gas harmonics have been utilized widely in ultrafast x-ray science, from attosecond pulse generation to imaging molecular orbitals of the target molecule. In contrast, the solid-state harmonic generation mechanism is currently being investigated following the recent experimental discovery in zinc oxide crystal. In particular, because of the fundamental differences, attributed to the high density and periodicity of the crystal, it was not clear if the solid-state harmonics could be used to reveal bonding structures in crystals. Here we report our experimental results on generation of XUV harmonics in single crystal MgO subjected to the field strengths on the order of 1V/Å without damage. High harmonics in MgO show strong crystal orientation dependence as well as a strong laser ellipticity dependence. By exploiting these unique characteristics, we demonstrate that XUV harmonics from bulk crystals can probe Angstrom scale electronic structure of the crystal.

  15. 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

  16. 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.

  17. Visualizing chemical structure-subcellular localization relationships using fluorescent small molecules as probes of cellular transport

    PubMed Central

    2013-01-01

    Background To study the chemical determinants of small molecule transport inside cells, it is crucial to visualize relationships between the chemical structure of small molecules and their associated subcellular distribution patterns. For this purpose, we experimented with cells incubated with a synthetic combinatorial library of fluorescent, membrane-permeant small molecule chemical agents. With an automated high content screening instrument, the intracellular distribution patterns of these chemical agents were microscopically captured in image data sets, and analyzed off-line with machine vision and cheminformatics algorithms. Nevertheless, it remained challenging to interpret correlations linking the structure and properties of chemical agents to their subcellular localization patterns in large numbers of cells, captured across large number of images. Results To address this challenge, we constructed a Multidimensional Online Virtual Image Display (MOVID) visualization platform using off-the-shelf hardware and software components. For analysis, the image data set acquired from cells incubated with a combinatorial library of fluorescent molecular probes was sorted based on quantitative relationships between the chemical structures, physicochemical properties or predicted subcellular distribution patterns. MOVID enabled visual inspection of the sorted, multidimensional image arrays: Using a multipanel desktop liquid crystal display (LCD) and an avatar as a graphical user interface, the resolution of the images was automatically adjusted to the avatar’s distance, allowing the viewer to rapidly navigate through high resolution image arrays, zooming in and out of the images to inspect and annotate individual cells exhibiting interesting staining patterns. In this manner, MOVID facilitated visualization and interpretation of quantitative structure-localization relationship studies. MOVID also facilitated direct, intuitive exploration of the relationship between the

  18. 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

  19. Acoustic Properties of Lens Materials for Ultrasonic Probes

    NASA Astrophysics Data System (ADS)

    Fujii, Hideji; Nakaya, Chitose; Takeuchi, Hiroshi; Kondo, Toshio; Ishikawa, Yasuo

    1995-01-01

    The acoustic velocities and densities of 20 types of commercial rubber have been measured at a frequency of 2 MHz at room temperature, and they are evaluated in terms of their application to an acoustic lens or an acoustic window of probes of an ultrasonic diagnostic instrument. Fluorosilicone rubber and phoshazene rubber have lower acoustic velocities than the human body, and they have excellent impedance matching with the human body. Both the acoustic velocities and densities of butadiene rubber, polybutadiene rubber, acrylic rubber and polyurethane match those of the human body. It is also described that rubber having good impedance matching with the human body can be fabricated by adjusting the volume fraction of the added filler.

  20. Perichromism: a powerful tool for probing the properties of cellulose and its derivatives.

    PubMed

    Fidale, Ludmila C; Heinze, Thomas; El Seoud, Omar A

    2013-03-01

    This overview is concerned with the use of certain dyes (perichromic indicators, hereafter designated as "probes") in order to determine the properties of cellulose, its solutions and solid derivatives. It is arranged as follows: (i) the properties of cellulose and its derivatives that are relevant to their applications are listed; (ii) a general discussion is presented on how perichromism can be employed in order to gain information on the medium where the probe is present; (iii) the results of perichromism, as applied to cellulose, cellulose solutions, and derivative films are discussed. PMID:23465911

  1. Point group sensitive probes of the pseudogap electronic structure in Bi2212

    NASA Astrophysics Data System (ADS)

    Hinton, J. P.; Koralek, J. D.; Orenstein, J.; Firmo, I.; Hamidian, M.; Fujita, K.; Davis, J. C.

    2011-03-01

    We combine optical transient grating spectroscopy (TGS) and spectroscopic imaging scanning tunneling microscopy (SI-STM) to study the pseudogap electronic structure in the underdoped cuprate superconductor Bi 2 Sr 2 CaCu 2 O8 + δ . In TGS a pair of 50 fs pump pulses at 800 nm coincident on the sample surface generate a sinusoidal variation in the index of refraction. This index grating is phase sensitively probed, allowing us to clearly resolve two components in the optical response below Tc. We attribute one of the components to a coherent nonlinear optical process, whose properties are sensitive to the point group symmetry of the pseudogap electronic structure. We compare the results of these optical experiments with recent analysis of SI-STM data (M. J. Lawler et al Nature 466 , 347 (2010)) which measures the amplitude of peaks at various reciprocal lattice vectors in the Fourier transform of atomically resolved images of the pseudogap electronic structure. The symmetry properties of the SI-STM Bragg amplitudes provide additional evidence relevant to the point group of the pseudogap electronic structure.

  2. Probing the role of Ga in amorphous conducting oxides through local structure studies

    NASA Astrophysics Data System (ADS)

    Moffitt, Stephanie; Zhu, Qimin; Ma, Qing; Buchholz, Donald; Chang, Robert; Mason, Thomas; Marks, Tobin; Bedzyk, Michael

    2015-03-01

    The study of amorphous (a-) conducting oxides is an emerging field. The lack of grain boundaries, smooth surfaces, and low temperature deposition position these materials as ideal candidates for large area applications and flexible electronics. Most impressively, these materials maintain high electron mobility in the amorphous state. These benefits have led the recent commercialization of a-IGZO (Ga and Zn doped indium oxide) as a replacement for a-Si as the channel layer of thin film transistors in display technology. Despite this success, fundamental understanding of structure-property relationships is still lacking and must be improved to guide further development of amorphous conducting oxides. X-ray absorption spectroscopy (XAS) is one of the few tools that can be used to probe the structure of amorphous materials. Amorphous indium oxide doped with Ga (a-IGO) is a model system to help develop the role of dopants in amorphous oxides. An in depth XAS study was carried out to determine inter-atomic distances, coordination numbers, and structural disorder parameters as a function of Ga doping level. The correlation between XAS-derived structural features and the dopant-dependent evolution of both electrical properties and thermal stability of a-IGO will be discussed. This work is supported by the NSF MRSEC Program No. DMR1121262.

  3. Probing model tumor interfacial properties using piezoelectric cantilevers.

    PubMed

    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. PMID:20887005

  4. 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.

  5. The environmental properties of galaxies probed by marked statistics

    NASA Astrophysics Data System (ADS)

    Mateus, A.

    2014-10-01

    Galaxies are generally treated as point particles in clustering analysis. However, these objects have physical and stellar population properties that must be taken into account if one wants to study the environmental effects on galaxy evolution. In this work, we applied a statistical method to investigate the role of environment in driving galaxy properties based on the marked correlation function. This methodology was applied to a galaxy sample drawn from the Sloan Digital Sky Survey Data Release 7, where the clustering of galaxies was weighted by particular galaxy properties, like luminosity and stellar mass, thus more directly quantifying the correlations between these attributes and large-scale environment. We show that marked statistics are powerful to reproduce environmental trends for variables like luminosities and stellar masses, as well as to quantify the relative importance of them with respect to the environment. For low density regions in the local universe, mark correlations relative to the mean are stronger compared to dense regions. This implies that the clustering of stellar mass, for instance, is more sensitive to environments associated to individual halos in close galaxy pairs than to massive halos found in clusters, where the correlations don't show any difference relative to the mean. We conclude that in nearby galaxy clusters, dominated by massive objects, galaxies are equally clustered (marked correlation = average clustering). On the other hand, galaxies in low density regions span a wide range in stellar mass (halo sizes) where the correlations appear more dramatically.

  6. Determination of Relationship between Dielectric Properties, Compressive Strength, and Age of Concrete with Rice Husk Ash Using Planar Coaxial Probe

    NASA Astrophysics Data System (ADS)

    Piladaeng, Nawarat; Angkawisittpan, Niwat; Homwuttiwong, Sahalaph

    2016-02-01

    This paper deals with an investigation of the dielectric properties of concretes that includes rice husk ash using a planar coaxial probe. The planar coaxial probe has a planar structure with a microstrip and coaxial features. The measurement was performed over the frequency range of 0.5-3.5 GHz, and concrete specimens with different percentages of rice husk ash were tested. The results indicated that the dielectric constant of the concretes was inversely proportional to the frequency, while the conductivity was proportional to the frequency. The dielectric constant decreased with the increasing age of the concrete at the frequency of 1 GHz. The conductivity of the concrete decreased with the increasing age of the concrete at the frequency of 3.2 GHz. In addition, the dielectric constant and the conductivity decreased when the compressive strength increased. It was also shown that the obtained dielectric properties of the concrete could be used to investigate the relationship between the compressive strength and age of the concrete. Moreover, there is an opportunity to apply the proposed probe to determine the dielectric properties of other materials.

  7. 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.

  8. 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. PMID:23562049

  9. Structural evaluation of thermocouple probes for 241-AZ-101 waste tank

    SciTech Connect

    Kanjilal, S.K.

    1994-12-06

    This document reports on the structural analysis of the thermocouple probe to be installed in 241-AZ-101 waste tank. The thermocouple probe is analyzed for normal pump mixing operation and potential earthquake induced loads required by the Hanford Site Design Criteria SDC-4.1.

  10. Probing surface structures of Shewanella spp. by microelectrophoresis.

    PubMed

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

    2006-04-01

    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

  11. 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.

  12. Probing mechanical properties of living cells by magnetopneumography.

    PubMed

    Möller, W; Takenaka, S; Rust, M; Stahlhofen, W; Heyder, J

    1997-01-01

    Magnetopneumography (MPG) has been used to study long-term particle clearance from human lungs as well as cellular motility of pulmonary macrophages (PMs). This study describes an extension of the method enabling the measurement of mechanical properties of PM cells in vivo. Ferromagnetic microparticles are inhaled and then retained in the alveolar region of the lungs, where they are phagocytized within hours by PMs. The magnetic particles can be rotated in weak magnetic fields, and the response to this twisting shear (force) is detected as a macroscopic magnetic field producing a measure of cytoskeletal mechanics. Cytoplasmic viscosity is very high compared with that of water and is strongly non-Newtonian. Under rotational stresses from 0.4 to 6.4 Pa, it acts like a pseudoplastic fluid showing a characteristic shear rate dependence. The viscosity as well as the stiffness of the cytoskeleton increases with increasing shear stress as seems typical for living tissue and evidence for an intact cytoskeletal matrix. The particle recoil as measured by the amount of recoverable strain following a short twisting force describes a cytoplasmic elasticity that depends on both level and duration of stress. These investigations on the mechanical properties of living human cells are promising and should lead to better understanding of cellular dysfunction in disease as well as pathways for drug administration. PMID:10174196

  13. The investigation of time dependent flame structure by ionization probes

    NASA Technical Reports Server (NTRS)

    Ventura, J. M. P.; Suzuki, T.; Yule, A. J.; Ralph, S.; Chigier, N. A.

    1980-01-01

    Ionization probes were used to measure mean ionization current and frequency spectra, auto-correlations and cross-correlations in jet flames with variation in the initial Reynolds numbers and equivalence ratios. Special attention was paid to the transitional region between the burner exit plane and the plane of onset of turbulence.

  14. Elastic properties of epithelial cells probed by atomic force microscopy.

    PubMed

    Brückner, Bastian R; Janshoff, Andreas

    2015-11-01

    Cellular mechanics plays a crucial role in many biological processes such as cell migration, cell growth, embryogenesis, and oncogenesis. Epithelia respond to environmental cues comprising biochemical and physical stimuli through defined changes in cell elasticity. For instance, cells can differentiate between certain properties such as viscoelasticity or topography of substrates by adapting their own elasticity and shape. A living cell is a complex viscoelastic body that not only exhibits a shell architecture composed of a membrane attached to a cytoskeleton cortex but also generates contractile forces through its actomyosin network. Here we review cellular mechanics of single cells in the context of epithelial cell layers responding to chemical and physical stimuli. This article is part of a Special Issue entitled: Mechanobiology. PMID:26193077

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  16. Probing mechanical properties of fully hydrated gels and biological tissues.

    PubMed

    Constantinides, Georgios; Kalcioglu, Z Ilke; McFarland, Meredith; Smith, James F; Van Vliet, Krystyn J

    2008-11-14

    A longstanding challenge in accurate mechanical characterization of engineered and biological tissues is maintenance of both stable sample hydration and high instrument signal resolution. Here, we describe the modification of an instrumented indenter to accommodate nanomechanical characterization of biological and synthetic tissues in liquid media, and demonstrate accurate acquisition of force-displacement data that can be used to extract viscoelastoplastic properties of hydrated gels and tissues. We demonstrate the validity of this approach via elastoplastic analysis of relatively stiff, water-insensitive materials of elastic moduli E>1000 kPa (borosilicate glass and polypropylene), and then consider the viscoelastic response and representative mechanical properties of compliant, synthetic polymer hydrogels (polyacrylamide-based hydrogels of varying mol%-bis crosslinker) and biological tissues (porcine skin and liver) of E<500 kPa. Indentation responses obtained via loading/unloading hystereses and contact creep loading were highly repeatable, and the inferred E were in good agreement with available macroscopic data for all samples. As expected, increased chemical crosslinking of polyacrylamide increased stiffness (E40 kPa) and decreased creep compliance. E of porcine liver (760 kPa) and skin (222 kPa) were also within the range of macroscopic measurements reported for a limited subset of species and disease states. These data show that instrumented indentation of fully immersed samples can be reliably applied for materials spanning several orders of magnitude in stiffness (E=kPa-GPa). These capabilities are particularly important to materials design and characterization of macromolecules, cells, explanted tissues, and synthetic extracellular matrices as a function of spatial position, degree of hydration, or hydrolytic/enzymatic/corrosion reaction times. PMID:18922534

  17. RR Lyrae stars as probes of the Milky Way structure and formation

    NASA Astrophysics Data System (ADS)

    Pietrukowicz, Pawel

    2016-08-01

    RR Lyrae stars being distance indicators and tracers of old population serve as excellent probes of the structure, formation, and evolution of our Galaxy. Thousands of them are being discovered in ongoing wide-field surveys. The OGLE project conducts the Galaxy Variability Survey with the aim to detect and analyze variable stars, in particular of RRab type, toward the Galactic bulge and disk, covering a total area of 3000 deg2. Observations in these directions also allow detecting background halo variables and unique studies of their properties and distribution at distances from the Galactic Center to even 40 kpc. In this contribution, we present the first results on the spatial distribution of the observed RRab stars, their metallicity distribution, the presence of multiple populations, and relations with the old bulge. We also show the most recent results from the analysis of RR Lyrae stars of the Sgr dwarf spheroidal galaxy, including its center, the globular cluster M54.

  18. Cataclysmic variables as probes of x-ray properties of interstellar grains

    SciTech Connect

    Bode, M.F.; Evans, A.; Norwell, G.A.

    1983-01-01

    Interstellar-grain properties have previously been probed at wavelengths ranging from the infrared to the ultraviolet. Recent work by other authors has shown that we may also observe the effects of scattering by such grains at x-ray wavelengths. In this paper we suggest that investigations of the x-ray properties of interstellar grains may profitably be conducted in sight lines to variable sources. Particular emphasis is given in this context to cataclysmic variables and related objects.

  19. Develop Infrared Structural Biology for Probing Structural Dynamics of Protein Functions

    NASA Astrophysics Data System (ADS)

    Xie, Aihua; Kang, Zhouyang; Causey, Oliver; Liu, Charle

    2015-03-01

    Protein functions are carried out through a series of structural transitions. Lack of knowledge on functionally important structural motions of proteins impedes our understanding of protein functions. Infrared structural biology is an emerging technology with powerful applications for protein structural dynamics. One key element of infrared structural biology is the development of vibrational structural marker (VSM) database library that translates infrared spectroscopic signals into specific structural information. We report the development of VSM for probing the type, geometry and strength of hydrogen bonding interactions of buried COO- side chains of Asp and Glu in proteins. Quantum theory based first principle computational studies combined with bioinformatic hydrogen bond analysis are employed in this study. We will discuss the applications of VSM in mechanistic studies of protein functions. Infrared structural biology is expected to emerge as a powerful technique for elucidating the functional mechanism of a broad range of proteins, including water soluble and membrane proteins. This work is supported by OCAST HR10-078 and NSF DBI1338097.

  20. Structure-Dependent Viscoelastic Properties of C(9)-Alkanethiol Monolayers

    SciTech Connect

    Mayer, Thomas M.; Michalske, Terry A.; Shinn, Neal D.

    1999-08-10

    Quartz crystal microbalance techniques and in situ spectroscopic ellipsometry are used to probe the structure-dependent intrinsic viscoelastic properties of self-assembled CH{sub 3}(CH{sub 2}){sub 8}SH alkanethiol monolayer adsorbed from the gas phase onto Au(111)-textured substrates. Physisorbed molecules, mixed chemisorbed-fluid/solid phases and solid-phase domain boundaries make sequentially dominant contributions to the measured energy dissipation in the growing monolayer. Deviations from Langmuir adsorption kinetics reveal a precursor-mediated adsorption channel. These studies reveal the impact of structural heterogeneity in tribological studies of monolayer lubricants.

  1. 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].

  2. Probing the Surface Properties of Gold at Low Electrolyte Concentration.

    PubMed

    Tivony, Ran; Klein, Jacob

    2016-07-26

    Using the surface force balance (SFB), we studied the surface properties of gold in aqueous solution with low electrolyte concentration (∼10(-5) M and pH = 5.8), i.e., water with no added salt, by directly measuring the interaction between an ultrasmooth gold surface (ca. 0.2 nm rms roughness) and a mica surface. Under these conditions, specific adsorption of ions is minimized and its influence on the surface charge and surface potential of gold is markedly reduced. At open circuit potential, the electrostatic interaction between gold and mica was purely attractive and gold was found to be positively charged. This was further confirmed by force measurements against a positively charged surface, poly-l-lysine coated mica. Successive force measurements unambiguously showed that once gold and mica reach contact all counterions are expelled from the gap, confirming that at contact the surface charge of gold is equal and opposite in charge to that of mica. Further analysis of adhesion energy between the surfaces indicated that adhesion is mostly governed by vdW dispersion force and to a lesser extent by electrostatic interaction. Force measurements under external applied potentials showed that the gold-mica interaction can be regulated as a function of applied potential even at low electrolyte concentration. The gold-mica interaction was described very precisely by the nonlinearized Poisson-Boltzmann (PB) equation, where one of the surfaces is at constant charge, i.e., mica, and the other, i.e., gold, is at constant potential. Consequently, the gold surface potential could be determined accurately both at open circuit potential (OCP) and under different applied potentials. Using the obtained surface potentials, we were able to derive fundamental characteristics of the gold surface, e.g., its surface charge density and potential of zero charge (PZC), at very low electrolyte concentration. PMID:27357375

  3. 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.

  4. 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.

  5. 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.

  6. FDTD simulations and analysis of thin sample dielectric properties measurements using coaxial probes

    SciTech Connect

    Bringhurst, S.; Iskander, M.F.; White, M.J.

    1996-12-31

    A metallized ceramic probe has been designed for high temperature broadband dielectric properties measurements. The probe was fabricated out of an alumina tube and rod as the outer and inner conductors respectively. The alumina was metallized with a 3 mil layer of moly-manganese and then covered with a 0.5 mil protective layer of nickel plating. The probe has been used to make complex dielectric properties measurements over the complete frequency band from 500 MHz to 3 GHz, and for temperatures as high as 1,000 C. A 3D Finite-Difference Time-Domain (FDTD) code was used to help investigate the feasibility of this probe to measure the complex permittivity of thin samples. It is shown that by backing the material under test with a standard material of known dielectric constant, the complex permittivity of thin samples can be measured accurately using the developed FDTD algorithm. This FDTD procedure for making thin sample dielectric properties measurements will be described.

  7. Strain-Rate Frequency Superposition (SRFS) - A rheological probe of structural relaxation in soft materials

    NASA Astrophysics Data System (ADS)

    Wyss, Hans M.

    2007-03-01

    The rheological properties of soft materials such as concentrated suspensions, emulsions, or foams often exhibit surprisingly universal linear and nonlinear features. Here we show that their linear and nonlinear viscoelastic responses can be unified in a single picture by considering the effect of the strain-rate amplitude on the structural relaxation of the material. We present a new approach to oscillatory rheology, which keeps the strain rate amplitude fixed as the oscillation frequency is varied. This allows for a detailed study of the effects of strain rate on the structural relaxation of soft materials. Our data exhibits a characteristic scaling, which isolates the response due to structural relaxation, even when it occurs at frequencies too low to be accessible with standard techniques. Our approach is reminiscent of a technique called time-temperature superposition (TTS), where rheological curves measured at different temperatures are shifted onto a single master curve that reflects the viscoelastic behavior in a dramatically extended range of frequencies. By analogy, we call our approach strain-rate frequency superposition (SRFS). Our experimental results show that nonlinear viscoelastic measurements contain useful information on the slow relaxation dynamics of soft materials. The data indicates that the yielding behavior of soft materials directly probes the structural relaxation process itself, shifted towards higher frequencies by an applied strain rate. This suggests that SRFS will provide new insight into the physical mechanisms that govern the viscoelastic response of a wide range of soft materials.

  8. Nanomechanical properties of lithiated Si nanowires probed with atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Lee, Hyunsoo; Shin, Weonho; Choi, Jang Wook; Park, Jeong Young

    2012-07-01

    The nanomechanical properties of fully lithiated and pristine Si nanowires (NWs) deposited on a Si substrate were studied with atomic force microscopy (AFM). Si NWs were synthesized using the vapour-liquid-solid process on stainless-steel substrates using an Au catalyst. Fully lithiated Si NWs were obtained using the electrochemical method, followed by drop-casting on a Si substrate. The roughness of the Si NWs, which was derived from AFM images, is greater for the lithiated Si NWs than for the pristine Si NWs. Force spectroscopy was used to study the influence of lithiation on the tip-surface adhesion force. The lithiated Si NWs revealed a smaller tip-surface adhesion force than the Si substrate by a factor of two, while the adhesion force of the Si NWs is similar to that of the Si substrate. Young's modulus, obtained from the force-distance curve, also shows that the pristine Si NWs have a relatively higher value than the lithiated Si NWs due to the elastically soft and amorphous structures of the lithiated region. These results suggest that force spectroscopy can be used to probe the degree of lithiation at nanometer scale during the charging and discharging processes.

  9. 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

  10. 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.

  11. Optical properties of microfabricated fully-metal-coated near-field probes in collection mode.

    PubMed

    Descrovi, Emiliano; Vaccaro, Luciana; Aeschimann, Laure; Nakagawa, Wataru; Staufer, Urs; Herzig, Hans-Peter

    2005-07-01

    A study of the optical properties of microfabricated, fully-metal-coated quartz probes collecting longitudinal and transverse optical fields is presented. The measurements are performed by raster scanning the focal plane of an objective, focusing azimuthally and radially polarized beams by use of two metal-coated quartz probes with different metal coatings. A quantitative estimation of the collection efficiencies and spatial resolutions in imaging both longitudinal and transverse fields is made. Longitudinally polarized fields are collected with a resolution approximately 1.5 times higher as compared with transversely polarized fields, and this behavior is almost independent of the roughness of the probe's metal coating. Moreover, the coating roughness is a critical parameter in the relative collection efficiency of the two field orientations. PMID:16053165

  12. Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces

    PubMed Central

    Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme

    2016-01-01

    Systematic structure probing experiments (e.g. SHAPE) of RNA mutants such as the mutate-and-map (MaM) protocol give us a direct access into the genetic robustness of ncRNA structures. Comparative studies of homologous sequences provide a distinct, yet complementary, approach to analyze structural and functional properties of non-coding RNAs. In this paper, we introduce a formal framework to combine the biochemical signal collected from MaM experiments, with the evolutionary information available in multiple sequence alignments. We apply neutral theory principles to detect complex long-range dependencies between nucleotides of a single stranded RNA, and implement these ideas into a software called aRNhAck. We illustrate the biological significance of this signal and show that the nucleotides networks calculated with aRNhAck are correlated with nucleotides located in RNA–RNA, RNA–protein, RNA–DNA and RNA–ligand interfaces. aRNhAck is freely available at http://csb.cs.mcgill.ca/arnhack. PMID:27095200

  13. Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces.

    PubMed

    Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme

    2016-06-20

    Systematic structure probing experiments (e.g. SHAPE) of RNA mutants such as the mutate-and-map (MaM) protocol give us a direct access into the genetic robustness of ncRNA structures. Comparative studies of homologous sequences provide a distinct, yet complementary, approach to analyze structural and functional properties of non-coding RNAs. In this paper, we introduce a formal framework to combine the biochemical signal collected from MaM experiments, with the evolutionary information available in multiple sequence alignments. We apply neutral theory principles to detect complex long-range dependencies between nucleotides of a single stranded RNA, and implement these ideas into a software called aRNhAck We illustrate the biological significance of this signal and show that the nucleotides networks calculated with aRNhAck are correlated with nucleotides located in RNA-RNA, RNA-protein, RNA-DNA and RNA-ligand interfaces. aRNhAck is freely available at http://csb.cs.mcgill.ca/arnhack. PMID:27095200

  14. Ultrafast X-ray probing of water structure below the homogeneous ice nucleation temperature.

    PubMed

    Sellberg, J A; Huang, C; McQueen, T A; Loh, N D; Laksmono, H; Schlesinger, D; Sierra, R G; Nordlund, D; Hampton, C Y; Starodub, D; DePonte, D P; Beye, M; Chen, C; Martin, A V; Barty, A; Wikfeldt, K T; Weiss, T M; Caronna, C; Feldkamp, J; Skinner, L B; Seibert, M M; Messerschmidt, M; Williams, G J; Boutet, S; Pettersson, L G M; Bogan, M J; Nilsson, A

    2014-06-19

    Water has a number of anomalous physical properties, and some of these become drastically enhanced on supercooling below the freezing point. Particular interest has focused on thermodynamic response functions that can be described using a normal component and an anomalous component that seems to diverge at about 228 kelvin (refs 1-3). This has prompted debate about conflicting theories that aim to explain many of the anomalous thermodynamic properties of water. One popular theory attributes the divergence to a phase transition between two forms of liquid water occurring in the 'no man's land' that lies below the homogeneous ice nucleation temperature (TH) at approximately 232 kelvin and above about 160 kelvin, and where rapid ice crystallization has prevented any measurements of the bulk liquid phase. In fact, the reliable determination of the structure of liquid water typically requires temperatures above about 250 kelvin. Water crystallization has been inhibited by using nanoconfinement, nanodroplets and association with biomolecules to give liquid samples at temperatures below TH, but such measurements rely on nanoscopic volumes of water where the interaction with the confining surfaces makes the relevance to bulk water unclear. Here we demonstrate that femtosecond X-ray laser pulses can be used to probe the structure of liquid water in micrometre-sized droplets that have been evaporatively cooled below TH. We find experimental evidence for the existence of metastable bulk liquid water down to temperatures of 227(-1)(+2) kelvin in the previously largely unexplored no man's land. We observe a continuous and accelerating increase in structural ordering on supercooling to approximately 229 kelvin, where the number of droplets containing ice crystals increases rapidly. But a few droplets remain liquid for about a millisecond even at this temperature. The hope now is that these observations and our detailed structural data will help identify those theories that best

  15. Probing Warm Dense Matter electronic structure using X-ray absorption Near Edge Spectroscopy (XANES)

    NASA Astrophysics Data System (ADS)

    Benuzzi Mounaix, Alessandra

    2011-06-01

    The behavior and physical properties of warm dense matter, fundamental for various branches of physics including planetology and Inertial Confinement Fusion, are non trivial to simulate either theoretically, numerically or experimentally. Despite important progress obtained in the last decade on macroscopic characterization (e.g. equations of state), microscopic studies are today necessary to investigate finely the WDM structure changes, the phase transitions and to test physical hypothesis and approximations commonly used in calculations. In this work, highly compressed aluminum has been investigated with the aim of bringing information on the evolution of its electronic structure by using K-edge shift and XANES. The experiment was performed at LULI laboratory where we used one long pulse (500 ps, IL ~ 8 1013 W/cm2) to create a uniform shock and a second ps beam (IL ~ 1017 W/cm2) to generate an ultra-short broadband X-ray source near the Al K-edge. The spectra were registered by using two conical KAP Bragg crystals. The main target was designed to probe the Aluminum in reshocked conditions allowing us to probe and to test theories in an extreme regime up to now unexplored (ρ ~ 3 ρ0 and T ~ 8 eV). The hydrodynamical Al conditions were measured by using VISARs interferometers and self-emission diagnostics. By increasing the delay between the two beams, we have been able to observe the modification of absorption spectra for unloading Al conditions (ρ >= 0.5 g/cc), and to put in evidence the relocalization of the 3p valence electrons occurring in the metal-non metal transition. All data have been compared to ab initio and dense plasma calculations.

  16. 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. PMID:24615232

  17. Correctness properties for iterated hardware structures

    NASA Technical Reports Server (NTRS)

    Windley, Phillip J.

    1993-01-01

    Iterated structures occur frequently in hardware. This paper describes properties required of mathematical relations that can be implemented iteratively and demonstrates the use of these properties on a generalized class of adders. This work provides a theoretical basis for the correct synthesis of iterated arithmetic structures.

  18. 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.

  19. Probing Actinide Electronic Structure through Pu Cluster Calculations

    DOE PAGESBeta

    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.

  20. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  2. Probing Flexural Properties of Cellulose Nanocrystal-Graphene Nanomembranes with Force Spectroscopy and Bulging Test.

    PubMed

    Kim, Sunghan; Xiong, Rui; Tsukruk, Vladimir V

    2016-05-31

    The flexural properties of ultrathin freely standing composite nanomembranes from reduced graphene oxide (rGO) and cellulose nanocrystals (CNC) have been probed by combining force spectroscopy for local nanomechanical properties and bulging test for global mechanical properties. We observed that the flexural properties of these rGO-CNC nanomembranes are controlled by rGO content and deformational regimes. The nanomembranes showed the enhanced mechanical properties due to the strong interfacial interactions between interwoven rGO and CNC components. The presence of weak interfacial interactions resulted in time-dependent behavior with the relaxation time gradually decreased with increasing the deformational rate owing to the reducing viscous damping at faster probing regimes close to 10 Hz. We observed that the microscopic elastic bending modulus of 141 GPa from local force spectroscopy is close to the elastic tensile modulus evaluated from macroscopic bulging test, indicating the consistency of both approaches for analyzing the ultrathin nanomembranes at different spatial scales of deformation. We showed that the flexible rGO-CNC nanomembranes are very resilient in terms of their capacity to recover back into original shape. PMID:27149011

  3. 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.

  4. High-K States as a Probe of Nuclear Structure

    NASA Astrophysics Data System (ADS)

    Dracoulis, G. D.

    High-K states played a key part in the discovery and understanding of deformed nuclei. An example is given of the recent use of high-K states as a signature of axially-symmetric prolate deformation in a nucleus which is predicted to show co-existence between spherical, oblate and prolate shapes. When associated bands can be identified, high-K states can also be used as a probe of pairing, and its modifiication of rotational motion. New results in 178W imply that the underlying rigid moment-of-inertia revealed when orbits are blocked to form multi-quasiparticle high-K states is substantially less than the “classical” rigid-body value. The corollary is that static pairing is quenched when only a few orbits are blocked. Recent measurements of g-factors in related high-K states in 179W allow the extraction of gR values whose behaviour as a function of seniority agrees with this suggestion.

  5. 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

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

    SciTech Connect

    Nhan Chuong Dang

    2005-08-12

    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 (I{sub c}); 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 (T{sub g}). 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 has been studied, in part

  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. Properties of polyethylene glycol/cyclodextrin hydrogels revealed by spin probes and spin labelling methods.

    PubMed

    Ionita, Gabriela; Ariciu, Ana Maria; Turcu, Ioana Maria; Chechik, Victor

    2014-03-21

    The properties of a gel consisting of a covalent network formed by the reaction of isocyanate end-capped polyethylene glycol (PEG) with β-cyclodextrin, were investigated by EPR spectroscopy. Spin-labelled cyclodextrin was incorporated into the cross-link points of the gel and at the chain ends. The dynamics of the gel fibres as reported by the spin label, was found to be sensitive to the H-bonding ability of the solvent, density of cross-links and temperature. Addition of spin probes (e.g., TEMPO and adamantane-TEMPO) to the unlabelled gel made it possible to characterise the solvent pools in the gel. While TEMPO was uniformly distributed throughout the solvent pools, the adamantane derivative was located at the gel fibre-solvent pool interface; these two probes thus reported on the different locations in the solvent pools. At low temperature, the gels were shown to prevent ice crystallisation in the solvent pools resulting in the formation of supercooled water. Both probes showed that the water froze at ca. 250 K, thus suggesting that the properties of the supercooled water are uniform across the solvent pools. PMID:24651650

  9. Probing mechanical properties of living cells by atomic force microscopy with blunted pyramidal cantilever tips.

    PubMed

    Rico, Félix; Roca-Cusachs, Pere; Gavara, Núria; Farré, Ramon; Rotger, Mar; Navajas, Daniel

    2005-08-01

    Atomic force microscopy (AFM) allows the acquisition of high-resolution images and the measurement of mechanical properties of living cells under physiological conditions. AFM cantilevers with blunted pyramidal tips are commonly used to obtain images of living cells. Measurement of mechanical properties with these tips requires a contact model that takes into account their blunted geometry. The aim of this work was to develop a contact model of a blunted pyramidal tip and to assess the suitability of pyramidal tips for probing mechanical properties of soft gels and living cells. We developed a contact model of a blunted pyramidal tip indenting an elastic half-space. We measured Young's modulus (E) and the complex shear modulus (G*= G' +i G" ) of agarose gels and A549 alveolar epithelial cells with pyramidal tips and compared them with those obtained with spherical tips. The gels exhibited an elastic behavior with almost coincident loading and unloading force curves and negligible values of G". E fell sharply with indentation up to approximately 300 nm , showing a linear regime for deeper indentations. A similar indentation dependence of E with twofold lower values at the linear regime was obtained with the spherical tip fitted with Hertz's model. The dependence of E on indentation in cells paralleled that found in gels. Cells exhibited viscoelastic behavior with G"/G' approximately 1/4 . Pyramidal tips commonly used for AFM imaging are suitable for probing mechanical properties of soft gels and living cells. PMID:16196611

  10. Luminescent and redox probes of structure and dynamics in quaternized poly(4-vinylpyridine) films on electrodes

    SciTech Connect

    Oh, Seungmo; Faulkner, L.R. )

    1989-07-19

    The properties of partially quaternized poly(4-vinylpyridine) films have been studied by coordinatively attaching luminescent and redox probes to free pyridine units within the polymer. Samples were examined as thin films spin coated onto glass or electrodes. The luminescent moiety was Re(CO){sub 3}(phen) (phen = 1,10-phenanthroline). It showed properties that depended strongly on the identity of the anion in the supporting electrolyte adjacent to the film. The emission maximum shifted to the red, and the quantum yield decreased in the order dry film > 0.1 M NaClO{sub 4} > 0.1 M potassium p-toluenesulfonate > 0.1 M KNO{sub 3}. The isotope effect caused by changing the solvent from H{sub 2}O to D{sub 2}O fell in the reverse order. The results show that the anion has a large impact on film structure. In nitrate the films are strongly hydrated, but in perchlorate they are dry and compact. The redox moiety was Ru(bpy){sub 2}Cl{sup 2+/1+}. The activation energies for electron diffusion in the network of redox centers were assessed by temperature-resolved chronocoulometry. The activation energies were independent of the concentration of redox centers in the film but were ordered according to electrolyte as given above. They were roughly linearly dependent on the degree of chemical cross-linking. The permeabilities of the films to redox-active ions in solution were larger than the electron diffusion coefficients by an order of magnitude but were strongly dependent on the anion of the supporting electrolyte, inversely in the order given above. The results suggest that electron diffusion is controlled by segmental motions within the polymer and that the anion dependence is a structural effect.

  11. Probing the local structure of high-{Tc} superconductors using XAFS spectroscopy

    SciTech Connect

    Bridges, F.; Booth, C.H.; Li, G.G.; Bauer, E.D.; Boyce, J.; Claeson, T.

    1996-12-31

    X-ray Absorption Fine-Structure (XAFS) is a local structural probe that is complementary to diffraction techniques. The authors discuss the types of information that can be obtained using this probe and then consider several examples, including the distortion about Co in YBa{sub 2}Cu{sub 3}O{sub 7} (YBCO), an unusual negative correlation of atom pair displacements in HgBa{sub 2}CuO{sub 4+{delta}}, and the distortions about the O(4) atom in thin films and single crystals of YBCO.

  12. Using probe secondary structure information to enhance Affymetrix GeneChip background estimates

    PubMed Central

    Gharaibeh, Raad Z.; Fodor, Anthony A.; Gibas, Cynthia J.

    2007-01-01

    High-density short oligonucleotide microarrays are a primary research tool for assessing global gene expression. Background noise on microarrays comprises a significant portion of the measured raw data. A number of statistical techniques have been developed to correct for this background noise. Here, we demonstrate that probe minimum folding energy and structure can be used to enhance a previously existing model for background noise correction. We estimate that probe secondary structure accounts for up to 3% of all variation on Affymetrix microarrays. PMID:17387043

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    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.

  15. 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.

  16. Probes of large-scale structure in the universe

    NASA Technical Reports Server (NTRS)

    Suto, Yasushi; Gorski, Krzysztof; Juszkiewicz, Roman; Silk, Joseph

    1988-01-01

    A general formalism is developed which shows that the gravitational instability theory for the origin of the large-scale structure of the universe is now capable of critically confronting observational results on cosmic background radiation angular anisotropies, large-scale bulk motions, and large-scale clumpiness in the galaxy counts. The results indicate that presently advocated cosmological models will have considerable difficulty in simultaneously explaining the observational results.

  17. 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

  18. Relaxation, Structure, and Properties of Semicoherent Interfaces

    NASA Astrophysics Data System (ADS)

    Shao, S.; Wang, J.

    2016-01-01

    Materials containing a high density of interfaces are promising candidates for future energy technologies because interfaces acting as sources, sinks, and barriers for defects can improve mechanical and irradiation properties of materials. A semicoherent interface widely occurring in various materials is composed of a network of misfit dislocations and coherent regions separated by misfit dislocations. In this article, we review the relaxation mechanisms, structure, and properties of (111) semicoherent interfaces in face-centered cubic structures.

  19. 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.

  20. 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.

  1. Probing asymmetric structures in the outskirts of galaxies

    SciTech Connect

    Wen, Zhang Zheng; Zheng, Xian Zhong; An, Fang Xia E-mail: xzzheng@pmo.ac.cn

    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 {sub o}, which measures the asymmetry of the OHR, and D {sub 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 {sub 850}-band images for a sample of 764 galaxies with z {sub 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 {sub o}-D {sub o} space. Meanwhile, the widely used CAS and Gini-M {sub 20} methods turn out to be insensitive to such morphological features. We stress that the A {sub o}-D {sub 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.

  2. 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.

  3. Dual-cycle dielectrophoretic collection rates for probing the dielectric properties of nanoparticles

    PubMed Central

    Bakewell, David J; Holmes, David

    2013-01-01

    A new DEP spectroscopy method and supporting theoretical model is developed to systematically quantify the dielectric properties of nanoparticles using continuously pulsed DEP collection rates. Initial DEP collection rates, that are dependent on the nanoparticle dielectric properties, are an attractive alternative to the crossover frequency method for determining dielectric properties. The new method introduces dual-cycle amplitude modulated and frequency-switched DEP (dual-cycle DEP) where the first collection rate with a fixed frequency acts as a control, and the second collection rate frequency is switched to a chosen value, such that, it can effectively probe the dielectric properties of the nanoparticles. The application of the control means that measurement variation between DEP collection experiments is reduced so that the frequency-switched probe collection is more effective. A mathematical model of the dual-cycle method is developed that simulates the temporal dynamics of the dual-cycle DEP nanoparticle collection system. A new statistical method is also developed that enables systematic bivariate fitting of the multifrequency DEP collection rates to the Clausius–Mossotti function, and is instrumental for determining dielectric properties. A Monte-Carlo simulation validates that collection rates improve estimation of the dielectric properties, compared with the crossover method, by exploiting a larger number of independent samples. Experiments using 200 nm diameter latex nanospheres suspended in 0.2 mS/m KCl buffer yield a nanoparticle conductivity of 26 mS/m that lies within 8% of the expected value. The results show that the dual-frequency method has considerable promise particularly for automated DEP investigations and associated technologies. PMID:23172363

  4. CP Stars - probing stellar surface structure with BRITE Constellation

    NASA Astrophysics Data System (ADS)

    Lüftinger, T.; Weiss, W. W.

    2008-01-01

    More than 170 chemically peculiar (CP) stars will be observable by BRITE Constellation. These stars host a complex interplay of phenomena like strong magnetic fields, chemical diffusion, pulsation and rotation in the same object. Thus they serve as unique stellar laboratories where we can observe the correlation and interaction of these fundamental physical processes. We present here a summary of the unique potentials BRITE Constellation offers to obtain new insights in the atmospheric structure formation and the complex interplay of abundance variations, pulsation and magnetic fields under conditions that could never be reproduced on Earth.

  5. Probing the Absorption Structures in Seyfert Galaxies with X-ray Spectroscopy

    NASA Astrophysics Data System (ADS)

    Gelbord, J.

    2001-12-01

    The paradigm of the unified model for Seyfert galaxies has had many successes in explaining the range of phenomena observed in active galaxies. However, the structures invoked in this scenario have been difficult to observe due to their limited sizes and due to contaminating flux from other regions. As a result, some of these structures, notably the putative obscuring torus, are poorly constrained. The difficulty in isolating the emission from the central regions can be mitigated (but not eliminated!) by focusing upon high-energy radiation, which is dominated by direct and reprocessed radiation from the nuclear region. We have drawn upon the large number of X-ray spectra available in the ASCA archive in order to study the distribution of properties in a large sample of high-energy observations. Furthermore, by uniformly processing the data ourselves, we minimize systematic effects. One asset of X-rays is that they provide a sensitive probe of absorbers in the line of sight toward the central region, because photoelectric absorption cuts off the continuum at low energies. In the ASCA bandpass column densities of ~1021-23 cm-2 can be measured. This is an interesting range of densities because it allows us to distinguish between absorption in a torus or possibly a warped accretion disk (where column densities are expected to be high) and absorption taking place at larger scales in the host galaxy (where column densities are expected to be closer to Galactic values of 1020-21 cm-2). This data is then compared to data from other wavebands. Published radio studies (e.g.: Nagar & Wilson 1999, Kinney et al. 2000) have put constraints on the orientations of the accretion systems in Seyfert galaxies. We combine these and the X-ray measurements for the ~50 sources in these studies which have ASCA data in order to constrain the various possible absorption structures and test the unification scenario.

  6. 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

  7. 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. PMID:22707797

  8. 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

  9. Probing microscopic structure and braid statistics in rotating Bose gases

    NASA Astrophysics Data System (ADS)

    Zhao, Jianshi; Jacome, Louis; Gemelke, Nathan

    2015-05-01

    It has been predicted that interacting bosonic atoms confined in a rapidly rotating two dimensional harmonic trap exhibit ground states analogous to fractional quantum Hall (FQH) states, and exhibit non-Landau-Ginzburg order and long range entanglement. Some of these states are expected to have excitations which possess fractional statistics, although no convincing measurement has yet been made. We describe an experiment which seeks to realize FQH physics using cold Rb-87 atoms confined to an optical lattice with rotating lattice sites. In these experiments, FQH droplets can be imaged using two high-resolution quantum gas microscopes (N.A. = 0.4, 0.8) which allow for occupancy resolved measurements, imaging in three dimensions, and expand on previous measurements by providing an unambiguous identification of states through microscopic time-of-flight. The latter permits identification of novel properties through counting statistics - using impurity atoms (in a minority spin state), pair correlation measurements can reveal an effectively fractionalized relative angular momentum, indicative of fractionalized braid statistics. Supported by NSF Grant No. PHY-1068570.

  10. 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).

  11. 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.

  12. Synthetic melanin thin films: Structural and electrical properties

    NASA Astrophysics Data System (ADS)

    da Silva, M. I. N.; Dezidério, S. N.; Gonzalez, J. C.; Graeff, C. F. O.; Cotta, M. A.

    2004-11-01

    Scanning probe microscopy was used to investigate the structural and electrical organization at the nanoscopic level of hydrated melanin thin films synthesized by oxidizing L-3-(3,4-dihydroxyphenyl)-alanine (L-dopa) in dimethyl sulfoxide. Atomic force microscopy (AFM) provided the morphologies of the L-dopa melanin films. Electrostatic force microscopy and conductive-AFM were used to spatially resolve the electrical properties of the material. Using a simple parallel plate capacitor model a method to measure the charge distribution on the sample was developed. The correlations between topography, electric charge, and current images of the sample demonstrated that the hydration process produces a restructuring of melanin observed not only through topographic variations, but also through the creation of areas with different electrical properties.

  13. Flux properties in Bi-2212 single crystals studied by spin-probe ESR

    NASA Astrophysics Data System (ADS)

    Nishida, Akihiko; Taka, Chihiro; Yasuda, Takashi; Horai, Kazumi

    2000-07-01

    Flux properties in Bi 2Sr 2CaCu 2O 8+ x (Bi-2212) single crystals are studied by spin-probe method. ESR line widths of a very thin layer of DPPH free radical on the surface of the crystals begin to increase upon the superconducting transitions. At further low temperatures below irreversibility lines, distinct hysteresis is observed between ESR profiles for field increase and decrease. The resonance fields and intensities also indicate characteristic changes. Close correlations between ESR anomalies and vortex behaviors are discussed, comparing results of as-grown and optimally doped crystals.

  14. Nanoscale electrical property studies of individual GeSi quantum rings by conductive scanning probe microscopy

    PubMed Central

    2012-01-01

    The nanoscale electrical properties of individual self-assembled GeSi quantum rings (QRs) were studied by scanning probe microscopy-based techniques. The surface potential distributions of individual GeSi QRs are obtained by scanning Kelvin microscopy (SKM). Ring-shaped work function distributions are observed, presenting that the QRs' rim has a larger work function than the QRs' central hole. By combining the SKM results with those obtained by conductive atomic force microscopy and scanning capacitance microscopy, the correlations between the surface potential, conductance, and carrier density distributions are revealed, and a possible interpretation for the QRs' conductance distributions is suggested. PMID:23194252

  15. 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.

  16. Structural Properties of Mismatched Alloys

    NASA Astrophysics Data System (ADS)

    Mousseau, Normand

    The problem of understanding the local structure of disordered alloys has been around for a long time. In this thesis, I look more specifically at the effect of size-mismatch disorder in binary alloys under many forms: metallic and semiconductor alloys, bulk and surfaces, two and three dimensional systems. I have studied the limitations of a central-force model (CFM) and an embedded-atom potential (EAM) in describing the local structure of binary metallic alloys composed of Ag, Au, Cu, Ni, Pd, or Pt. Although an analytical model developed using the CFM explains qualitatively well the experimental and numerical results, in many cases, it is important to add electronic density effects through a more sophisticated potential like EAM in order to agree quantitatively with experiment. I have also looked at amorphous and crystalline silicon-germanium alloys. It turns out that the effect of size-mismatch is the same on a crystalline and an amorphous lattice. In the latter case, it can be seen as a perturbation of the much larger disorder due to the amorphisation process. However, the analytical predictions differ, for both the crystalline and amorphous alloys, from the experimental results. If one is to believe the data, there is only one possible explanation for this inconsistency: large amounts of hydrogen are present in the samples used for the measurements. Since the data analysis of EXAFS results is not always straightforward, I have proposed some experiments that could shed light on this problem. One of these experiments would be to look at the (111) surface of a Si-Ge alloy with a scanning tunneling microscope. I also present in this thesis the theoretical predictions for the height distribution at the surface as well as some more general structural information about the relaxation in the network as one goes away from the surface. Finally, I have studied the effect of size -mismatch in a purely two dimensional lattice, looking for mismatch-driven phase transitions

  17. Autoclave foam concrete: Structure and properties

    NASA Astrophysics Data System (ADS)

    Mestnikov, Alexei; Semenov, Semen; Strokova, Valeria; Nelubova, Viktoria

    2016-01-01

    This paper describes the technology and properties of autoclaved foam concrete taking into account practical experience and laboratory studies. The results of study of raw materials and analysis of structure and properties of foam-concrete before and after autoclave treatment are basic in this work. Experimental studies of structure and properties of foam concrete are carried out according to up-to-date methods and equipment on the base of the shared knowledge centers. Results of experimental studies give a deep understanding of properties of raw materials, possible changes and new formations in inner layers of porous material providing the improvement of constructional and operational properties of autoclaved foam concrete. Principal directions of technology enhancement as well as developing of production of autoclave foam concretes under cold-weather conditions in Russia climate are justified.

  18. 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.

  19. Probing RNA Native Conformational Ensembles with Structural Constraints.

    PubMed

    Fonseca, Rasmus; van den Bedem, Henry; Bernauer, Julie

    2016-05-01

    Noncoding ribonucleic acids (RNA) play a critical role in a wide variety of cellular processes, ranging from regulating gene expression to post-translational modification and protein synthesis. Their activity is modulated by highly dynamic exchanges between three-dimensional conformational substates, which are difficult to characterize experimentally and computationally. Here, we present an innovative, entirely kinematic computational procedure to efficiently explore the native ensemble of RNA molecules. Our procedure projects degrees of freedom onto a subspace of conformation space defined by distance constraints in the tertiary structure. The dimensionality reduction enables efficient exploration of conformational space. We show that the conformational distributions obtained with our method broadly sample the conformational landscape observed in NMR experiments. Compared to normal mode analysis-based exploration, our procedure diffuses faster through the experimental ensemble while also accessing conformational substates to greater precision. Our results suggest that conformational sampling with a highly reduced but fully atomistic representation of noncoding RNA expresses key features of their dynamic nature. PMID:27028235

  20. 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.

  1. Scintillation Arcs: Probing Turbulence and Structure in the ISM

    NASA Astrophysics Data System (ADS)

    Stinebring, Daniel R.

    2006-12-01

    Multi-path scattering through inhomogeneities in the interstellar medium causes many related effects. In this review, I concentrate on the phenomenon of scintillation arcs, which are parabolic patterns in the secondary spectrum caused by interference between different angular components of the scatter-broadened image of a pulsar. Scintillation arcs are now fairly well understood. The measured curvature of the arc, together with proper motion and distance information about the pulsar, can be used to determine the location of thin scattering screens along the line of sight to the object. Some recent work of this type is presented. The puzzle of substructure in the power distribution of scintillation arcs is poorly understood, however, and is commented on as an open puzzle. In particular, some inferred physical structures in the ISM are small scale (˜ 1 AU) and over-dense with respect to the background medium. Finally, an application of scintillation arc studies to the correction of high-precision pulsar timing is presented.

  2. 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.

  3. Probing the structure and porosity of the lunar highlands crust

    NASA Astrophysics Data System (ADS)

    Soderblom, Jason M.; Evans, Alexander J.; Johnson, Brandon C.; Melosh, H. Jay; Miljković, Katarina; Phillips, Roger J.; Andrews-Hanna, Jeffrey C.; Milbury, Colleen; Neumann, Gregory A.; Nimmo, Francis; Smith, David E.; Solomon, Sean C.; Sori, Michael M.; Thomason, Carver J.; Wieczorek, Mark A.; Zuber, Maria T.

    2015-04-01

    Impact cratering is held to be the primary mechanism responsible for regulating porosity in primordial planetary lithospheres, increasing porosity via fracturing and dilatant bulking and decreasing porosity via localized heating and compaction. Constraints on these processes, however, are limited to gravity profiles of four lunar craters and gravity and seismic observations of ~50 terrestrial craters, many of which have been substantially modified by erosion and weathering. The Gravity Recovery and Interior Laboratory (GRAIL) mission has afforded unprecedented insight into the structure of the lithosphere of the Moon. We use a Bouguer-corrected GRAIL gravity field to investigate the porosity associated with ~1200 complex lunar highlands craters. We find that the Bouguer anomaly (BA) of these craters is generally negative and scales inversely with crater size, implying that larger impacts result in more extensive fracturing and dilatant bulking. The BA of craters larger than ~93 km is independent of crater diameter, indicating that impact-generated porosity is truncated at depth. Considerable variability in the BA of craters is observed. Some craters, in fact, exhibit positive Bouguer anomalies. We find that positive values of the residual BA, the average BA within the crater rim less the average BA within an outer annulus from the outer flank of the rim to two crater radii from the crater center, correlate with high porosity in the surrounding crust. Our analysis shows that, whereas early impacts generally increased crustal porosity, when crustal porosity becomes too high, impacts reduce porosity, leading to the concept of a steady-state porosity, which we estimate to be ~15±1% for the lunar highlands. Knowledge of the extent and variability of crustal porosity is critical to understanding the thermal and geologic evolution of planetary bodies and to the ancient ecology of Earth.

  4. 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.

  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. Global universe anisotropy probed by the alignment of structures in the cosmic microwave background.

    PubMed

    Wiaux, Y; Vielva, P; Martínez-González, E; Vandergheynst, P

    2006-04-21

    We question the global universe isotropy by probing the alignment of local structures in the cosmic microwave background (CMB) radiation. The original method proposed relies on a steerable wavelet decomposition of the CMB signal on the sphere. The analysis of the first-year Wilkinson Microwave Anisotropy Probe data identifies a mean preferred plane with a normal direction close to the CMB dipole axis, and a mean preferred direction in this plane, very close to the ecliptic poles axis. Previous statistical anisotropy results are thereby synthesized, but further analyses are still required to establish their origin. PMID:16712146

  7. Structural Properties of Barred Galaxies

    NASA Astrophysics Data System (ADS)

    Kim, Taehyun; Gadotti, D. A.; Sheth, K.; Lee, M.; S4G Team

    2014-01-01

    We have performed two-dimensional multicomponent decomposition of 144 local barred spiral galaxies using 3.6 micron images from the Spitzer Survey of Stellar Structure in Galaxies. Our model fit includes up to four components (bulge, disk, bar, and a point source) and, most importantly, takes into account disk breaks. We present that ignoring the disk break and using a single disk scale length in the model fit for Type II (down- bending) disk galaxies can lead to differences of 40% in the disk scale length, 10% in bulge-to-total luminosity ratio (B/T), and 25% in bar-to-total luminosity ratios. We show that for galaxies with B/T > 0.1, the break radius to bar radius, r_br/R_bar, varies between 1 and 3, but as a function of B/T the ratio remains roughly constant. This suggests that in bulge-dominated galaxies the disk break is likely related to the outer Lindblad Resonance (OLR) of the bar, and thus the OLR also moves outwards at the same rate as the bar grows. For galaxies with B/T < 0.1, r_br/R_bar, spans a wide range from 1 to 6. This suggests that the mechanism that produces the break in these galaxies may be different from that in galaxies with more massive bulges. Consistent with previous studies, we conclude that disk breaks in galaxies with small bulges may originate from bar resonances that may be also coupled with the spiral arms, or be related to star formation thresholds. We quantifiy shapes of bar radial surface brightness profiles by measuring their Sersic indices and show that bars in higher B/T galaxies have flatter radial surface brightness profile than bulgeless galaxies do. In particular, bulgeless galaxies mostly have bars with steep profiles. We show that the normalized bar length is correlated with B/T, which is consistent with bars growing longer with time.

  8. Determination of linear viscoelastic properties of an entangled polymer melt by probe rheology simulations

    NASA Astrophysics Data System (ADS)

    Karim, Mir; Indei, Tsutomu; Schieber, Jay D.; Khare, Rajesh

    2016-01-01

    Particle rheology is used to extract the linear viscoelastic properties of an entangled polymer melt from molecular dynamics simulations. The motion of a stiff, approximately spherical particle is tracked in both passive and active modes. We demonstrate that the dynamic modulus of the melt can be extracted under certain limitations using this technique. As shown before for unentangled chains [Karim et al., Phys. Rev. E 86, 051501 (2012), 10.1103/PhysRevE.86.051501], the frequency range of applicability is substantially expanded when both particle and medium inertia are properly accounted for by using our inertial version of the generalized Stokes-Einstein relation (IGSER). The system used here introduces an entanglement length dT, in addition to those length scales already relevant: monomer bead size d , probe size R , polymer radius of gyration Rg, simulation box size L , shear wave penetration length Δ , and wave period Λ . Previously, we demonstrated a number of restrictions necessary to obtain the relevant fluid properties: continuum approximation breaks down when d ≳Λ ; medium inertia is important and IGSER is required when R ≳Λ ; and the probe should not experience hydrodynamic interaction with its periodic images, L ≳Δ . These restrictions are also observed here. A simple scaling argument for entangled polymers shows that the simulation box size must scale with polymer molecular weight as Mw3. Continuum analysis requires the existence of an added mass to the probe particle from the entrained medium but was not observed in the earlier work for unentangled chains. We confirm here that this added mass is necessary only when the thickness LS of the shell around the particle that contains the added mass, LS>d . We also demonstrate that the IGSER can be used to predict particle displacement over a given timescale from knowledge of medium viscoelasticity; such ability will be of interest for designing nanoparticle-based drug delivery.

  9. Resonant ultrasound spectroscopy - a tool to probe magneto-elastic properties of ferromagnetic shape memory alloys

    NASA Astrophysics Data System (ADS)

    Heczko, Oleg; Seiner, Hanuš; Sedlák, Petr; Kopeček, Jaromír; Kopecký, Vít; Landa, Michal

    2013-02-01

    Resonant ultrasound spectroscopy (RUS) was used to investigate the changes of elastic properties induced by magnetic field in magnetic shape memory alloys Ni-Mn-Ga and Co-Ni-Al. In contrast to large magneto-elastic response of Ni2MnGa austenite, there is only very weak response of Co-Ni-Al. This indicates that the austenite phase of Ni-Mn-Ga can have a privileged position and this may be a reason for the existence of magnetic shape memory effect. In contrast to austenite, the magneto-elastic response in Ni-Mn-Ga martensite is very small with large damping due to existence of twin boundaries. The measurement showed that RUS can be a powerful method to probe magneto-elastic properties of shape memory alloys.

  10. Custom-Built Optical Tweezers for Locally Probing the Viscoelastic Properties of Cancer Cells

    NASA Astrophysics Data System (ADS)

    Tavano, Federica; Bonin, Serena; Pinato, Giulietta; Stanta, Giorgio; Cojoc, Dan

    2011-07-01

    We report a home built optical tweezers setup to investigate the mechanism of the membrane tether formation from single cells in vitro. Using an optically trapped microbead as probe, we have determined the force-elongation curve during tether formation and extracted several parameters characterizing the viscoelastic behavior of the cell membrane: tether stiffness, force, and viscosity. Breast cancer MDA-MB-231 cells have been studied in two different conditions, at room and physiological temperatures, showing a strong temperature dependence of the visoelastic properties of the cell membrane. To get detailed inside information about the tether formation mechanism we have extended the analysis of the force-elongation curves fitting them with a Kelvin model. These preliminary results are part of a larger project of whose goal is to compare the viscoelastic properties of several types of cancer cell lines, characterized by different aggressiveness and metastatic potential.

  11. 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

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

    DOE PAGESBeta

    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.; et al

    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

  13. 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

    2016-01-01

    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

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

    NASA Astrophysics Data System (ADS)

    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.

    2016-07-01

    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.

  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. PMID:25719799

  16. 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

  17. Probing liquid surface waves, liquid properties and liquid films with light diffraction

    NASA Astrophysics Data System (ADS)

    Barik, Tarun Kr; Chaudhuri, Partha Roy; Roy, Anushree; Kar, Sayan

    2006-06-01

    Surface waves on liquids act as a dynamical phase grating for incident light. In this paper, we revisit the classical method of probing such waves (wavelengths of the order of mm) as well as inherent properties of liquids and liquid films on liquids, using optical diffraction. A combination of simulation and experiment is proposed to trace out the surface wave profiles in various situations (e.g. for one or more vertical, slightly immersed, electrically driven exciters). Subsequently, the surface tension and the spatial damping coefficient (related to viscosity) of a variety of liquids are measured carefully in order to gauge the efficiency of measuring liquid properties using this optical probe. The final set of results deal with liquid films where dispersion relations, surface and interface modes, interfacial tension and related issues are investigated in some detail, both theoretically and experimentally. On the whole, our observations and analysis seem to support the claim that this simple, low cost apparatus is capable of providing a wealth of information on liquids and liquid surface waves in a non-destructive way.

  18. Amyloid-β probes: Review of structure-activity and brain-kinetics relationships.

    PubMed

    Eckroat, Todd J; Mayhoub, Abdelrahman S; Garneau-Tsodikova, Sylvie

    2013-01-01

    The number of people suffering from Alzheimer's disease (AD) is expected to increase dramatically in the coming years, placing a huge burden on society. Current treatments for AD leave much to be desired, and numerous research efforts around the globe are focused on developing improved therapeutics. In addition, current diagnostic tools for AD rely largely on subjective cognitive assessment rather than on identification of pathophysiological changes associated with disease onset and progression. These facts have led to numerous efforts to develop chemical probes to detect pathophysiological hallmarks of AD, such as amyloid-β plaques, for diagnosis and monitoring of therapeutic efficacy. This review provides a survey of chemical probes developed to date for AD with emphasis on synthetic methodologies and structure-activity relationships with regards to affinity for target and brain kinetics. Several probes discussed herein show particularly promising results and will be of immense value moving forward in the fight against AD. PMID:23766818

  19. 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).

  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. Multi-Scale Mechanical Probing Techniques To Investigate The Stability Of BEOL Layer Stacks With Sub-100 nm Structures

    NASA Astrophysics Data System (ADS)

    Geisler, Holm; Lehr, Matthias U.; Platz, Alexander; Mayer, Ulrich; Hofmann, Petra; Engelmann, Hans-Jürgen

    2011-09-01

    The stress levels induced by chip-package interaction (CPI) impose an increased risk of mechanical failure on advanced backend-of-line (BEOL) layer stacks in microelectronic circuits if they contain fragile ultralow-k (ULK) interlayer dielectric (ILD) films. On the one hand, multilevel finite element modeling is used to assess the potential risk at an early stage of the development of new microelectronic products. On the other hand, the theoretical models need as accurate as possible materials parameters as an input to provide realistic results. Moreover, it is highly desirable to have multi-scale experimental probes available which can provide complementary data to support the modeling calculations. The present paper provides an overview about various mechanical probing techniques which operate on the scale of less than 100 nm up to more than 100 μm. In this way, typical feature sizes are covered which occur from the package level via solder bumps or copper pillars down to small Cu/ULK interconnect structures. The experimental approaches are based on nanoindentation with lateral force detection and in-situ scanning probe microscopy (SPM) imaging capabilities, and they include a novel technique named bump assisted BEOL stability indentation (BABSI) test. Especially, the interrelation between small-scale mechanical properties of ULK dielectric films and stresses acting on larger scales are quantitatively assessed by means of the experimental approaches described here.

  2. Scanning Probe Microscopy Study of Electronic Properties in Alkyl-substituted Oligothiopene-based Field-Effect Transitors

    NASA Astrophysics Data System (ADS)

    Afsharimani, N.; Nysten, B.

    It appeared in the past decades that semi-conducting organic liquid crystals could easily replace the inorganic semi-conductors to manufacture field-effect transistors (FET). They can be easily processed by simple methods such as inkjet printing. These simple and cheap manufacturing methods pave the way to new applications for plastic electronics: electronic tags, biosensors, flexible screens, … The performance of these liquid crystal nanomaterials is due to their specific nanoscale structure. However, one limitation to the improvement of organic electronic devices is an incomplete understanding of their optoelectronic properties at the nanoscale. The organic semiconductor films often contain a combination of many ordered and disordered regions, grain boundaries and localized traps. These features impact charge transport and trapping at the sub-100 nm length scales [1]. Electrical SPM techniques such as STM, KPFM, EFM and CS-AFM have the potential to provide the correlation between the electronic properties directly and local film structure and have already made important contributions to the field of organic electronics. Here we report on the investigation of the structural and electronic properties of p-conductive organic field-effect transistors based on alkyl-substituted oligothiophenes with bottom-contact structure. For this purpose we use atomic force microscopy (AFM) and Kelvin-probe force microscopy (KPFM) in dual frequency mode under ambient conditions. This study helps to determine the local potential in the channel of active OFETs. On the other hand the molecular arrangements of these molecules on the HOPG surface have been studied using scanning tunnelling microscopy (STM) at the liquid-solid interface.

  3. Probing the structure-activity relationship of endogenous histone deacetylase complexes with immobilized peptide-inhibitors.

    PubMed

    Sindlinger, Julia; Bierlmeier, Jan; Geiger, Lydia-Christina; Kramer, Katharina; Finkemeier, Iris; Schwarzer, Dirk

    2016-05-01

    Histone deacetylases (HDACs) are key regulators of numerous cellular proteins by removing acetylation marks from modified lysine residues. Peptide-based HDAC probes containing α-aminosuberic acid ω-hydroxamate have been established as useful tools for investigating substrate selectivity and composition of endogenous HDAC complexes in cellular lysates. Here we report a structure-activity study of potential HDAC-probes containing derivatives of the hydroxamate moieties. While most of these probes did not recruit significant amounts of endogenous HDACs from cellular lysates, peptides containing Nε-acetyl-Nε-hydroxy-L-lysine served as HDAC probe. The recruitment efficiency varied between HDACs and was generally lower than that of α-aminosuberic acid ω-hydroxamate probes, but showed a similar global interaction profile. These findings indicate that Nε-acetyl-Nε-hydroxy-L-lysine might be a useful tool for investigations on HDAC complexes and the development of HDAC inhibitors. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd. PMID:27071932

  4. Probing the inner structure of blast furnaces by cosmic-ray muon radiography

    NASA Astrophysics Data System (ADS)

    Nagamine, K.; Tanaka, H. K. M.; Nakamura, S. N.; Ishida, K.; Hashimoto, M.; Shinotake, A.; Naito, M.; Hatanaka, A.

    By using the detection system of the near-horizontal cosmic-ray radiography originally developed for probing inner structure of volcanic mountains, a measurement was conducted to probe the inner structure and its time-dependent change of the blast furnace for iron-making. Precise determination (+/-5 cm) of the thickness of brick used for both base-plate and side-wall was made in 45 days; a crucial information to predict a life-time of the furnace. Also, the local density of iron-rich part was determined in +/-0.2 g/cm2 in 45 days; static structure as well as time-dependent behavior can be monitored for the iron-rich part of the furnace during operation.

  5. 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).

  6. Site-Specific DNA Structural and Dynamic Features Revealed by Nucleotide-Independent Nitroxide Probes

    SciTech Connect

    Popova, Anna; Kalai, Tamas; Hideg, Kalman; Qin, Peter Z.

    2009-09-15

    In site-directed spin labeling, a covalently attached nitroxide probe containing a chemically inert unpaired electron is utilized to obtain information on the local environment of the parent macromolecule. Studies presented here examine the feasibility of probing local DNA structural and dynamic features using a class of nitroxide probes that are linked to chemically substituted phosphorothioate positions at the DNA backbone. Two members of this family, designated as R5 and R5a, were attached to eight different sites of a dodecameric DNA duplex without severely perturbing the native B-form conformation. Measured X-band electron paramagnetic resonance (EPR) spectra, which report on nitroxide rotational motions, were found to vary depending on the location of the label (e.g., duplex center vs termini) and the surrounding DNA sequence. This indicates that R5 and R5a can provide information on the DNA local environment at the level of an individual nucleotide. As these probes can be attached to arbitrary nucleotides within a nucleic acid sequence, they may provide a means to “scan” a given DNA molecule in order to interrogate its local structural and dynamic features.

  7. 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

  8. Visualization of NRAS RNA G-Quadruplex Structures in Cells with an Engineered Fluorogenic Hybridization Probe.

    PubMed

    Chen, Shuo-Bin; Hu, Ming-Hao; Liu, Guo-Cai; Wang, Jin; Ou, Tian-Miao; Gu, Lian-Quan; Huang, Zhi-Shu; Tan, Jia-Heng

    2016-08-24

    The RNA G-quadruplex is an important secondary structure formed by guanine-rich RNA sequences. However, its folding studies have mainly been studied in vitro. Accurate identification of RNA G-quadruplex formation within a sequence of interest remains difficult in cells. Herein, and based on the guanine-rich sequence in the 5'-UTR of NRAS mRNA, we designed and synthesized the first G-quadruplex-triggered fluorogenic hybridization (GTFH) probe, ISCH-nras1, for the unique visualization of the G-quadruplexes that form in this region. ISCH-nras1 is made up of two parts: The first is a fluorescent light-up moiety specific to G-quadruplex structures, and the second is a DNA molecule that can hybridize with a sequence that is adjacent to the guanine-rich sequence in the NRAS mRNA 5'-UTR. Further evaluation studies indicated that ISCH-nras1 could directly and precisely detect the targeted NRAS RNA G-quadruplex structures, both in vitro and in cells. Thus, this GTFH probe was a useful tool for directly investigating the folding of G-quadruplex structures within an RNA of interest and represents a new direction for the design of smart RNA G-quadruplex probes. PMID:27508892

  9. Dopant distributions in n-MOSFET structure observed by atom probe tomography.

    PubMed

    Inoue, K; Yano, F; Nishida, A; Takamizawa, H; Tsunomura, T; Nagai, Y; Hasegawa, M

    2009-11-01

    The dopant distributions in an n-type metal-oxide-semiconductor field effect transistor (MOSFET) structure were analyzed by atom probe tomography. The dopant distributions of As, P, and B atoms in a MOSFET structure (gate, gate oxide, channel, source/drain extension, and halo) were obtained. P atoms were segregated at the interface between the poly-Si gate and the gate oxide, and on the grain boundaries of the poly-Si gate, which had an elongated grain structure along the gate height direction. The concentration of B atoms was enriched near the edge of the source/drain extension where the As atoms were implanted. PMID:19775815

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

    PubMed

    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

  11. 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.

  12. Probing the structure of ribosome assembly intermediates in vivo using DMS and hydroxyl radical footprinting.

    PubMed

    Hulscher, Ryan M; Bohon, Jen; Rappé, Mollie C; Gupta, Sayan; D'Mello, Rhijuta; Sullivan, Michael; Ralston, Corie Y; Chance, Mark R; Woodson, Sarah A

    2016-07-01

    The assembly of the Escherichia coli ribosome has been widely studied and characterized in vitro. Despite this, ribosome biogenesis in living cells is only partly understood because assembly is coupled with transcription, modification and processing of the pre-ribosomal RNA. We present a method for footprinting and isolating pre-rRNA as it is synthesized in E. coli cells. Pre-rRNA synthesis is synchronized by starvation, followed by nutrient upshift. RNA synthesized during outgrowth is metabolically labeled to facilitate isolation of recent transcripts. Combining this technique with two in vivo RNA probing methods, hydroxyl radical and DMS footprinting, allows the structure of nascent RNA to be probed over time. Together, these can be used to determine changes in the structures of ribosome assembly intermediates as they fold in vivo. PMID:27016143

  13. 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.

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

    DOE PAGESBeta

    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,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

  15. 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

  16. 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.

  17. HOT X-RAY CORONAE AROUND MASSIVE SPIRAL GALAXIES: A UNIQUE PROBE OF STRUCTURE FORMATION MODELS

    SciTech Connect

    Bogdan, Akos; Forman, William R.; Vogelsberger, Mark; Sijacki, Debora; Mazzotta, Pasquale; Kraft, Ralph P.; Jones, Christine; David, Laurence P.; Bourdin, Herve; Gilfanov, Marat; Churazov, Eugene

    2013-08-01

    Luminous X-ray gas coronae in the dark matter halos of massive spiral galaxies are a fundamental prediction of structure formation models, yet only a few such coronae have been detected so far. In this paper, we study the hot X-ray coronae beyond the optical disks of two 'normal' massive spirals, NGC 1961 and NGC 6753. Based on XMM-Newton X-ray observations, hot gaseous emission is detected to {approx}60 kpc-well beyond their optical radii. The hot gas has a best-fit temperature of kT {approx} 0.6 keV and an abundance of {approx}0.1 Solar, and exhibits a fairly uniform distribution, suggesting that the quasi-static gas resides in hydrostatic equilibrium in the potential well of the galaxies. The bolometric luminosity of the gas in the (0.05-0.15)r{sub 200} region (r{sub 200} is the virial radius) is {approx}6 Multiplication-Sign 10{sup 40} erg s{sup -1} for both galaxies. The baryon mass fractions of NGC 1961 and NGC 6753 are f{sub b,NGC1961} {approx} 0.11 and f{sub b,NGC6753} {approx} 0.09, which values fall short of the cosmic baryon fraction. The hot coronae around NGC 1961 and NGC 6753 offer an excellent basis to probe structure formation simulations. To this end, the observations are confronted with the moving mesh code AREPO and the smoothed particle hydrodynamics code GADGET. Although neither model gives a perfect description, the observed luminosities, gas masses, and abundances favor the AREPO code. Moreover, the shape and the normalization of the observed density profiles are better reproduced by AREPO within {approx}0.5r{sub 200}. However, neither model incorporates efficient feedback from supermassive black holes or supernovae, which could alter the simulated properties of the X-ray coronae. With the further advance of numerical models, the present observations will be essential in constraining the feedback effects in structure formation simulations.

  18. 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.

  19. 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

  20. 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.

  1. The optical properties of a weak probe field in a graphene ensemble under Raman excitation

    NASA Astrophysics Data System (ADS)

    Raheli, Ali; Hamedi, H. R.; Sahrai, M.

    2016-06-01

    We investigate the coherent manipulation of certain optical properties in graphene under Raman excitation by using a density-matrix approach. It is shown that the absorption and dispersion, the group velocity, and the transmission coefficient of the probe field can be efficiently controlled through proper adjustment of the intensity and frequency detuning of the control field. In addition, the optical bistability (OB) behavior is explored for the proposed system. It is found that the bistable threshold intensity and related hysteresis loop of OB can be controlled by the parameters of the system. The results obtained may be used in real experiments for the development of new types of nanoelectronic devices used for the realization of all-optical switching processes.

  2. Structure-function relationships in the hammerhead ribozyme probed by base rescue.

    PubMed

    Peracchi, A; Matulic-Adamic, J; Wang, S; Beigelman, L; Herschlag, D

    1998-11-01

    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

  3. 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

  4. Use of acoustic sensors to probe the mechanical properties of liposomes.

    PubMed

    Melzak, Kathryn; Tsortos, Achilleas; Gizeli, Electra

    2009-01-01

    Acoustic sensors probe the response of a thin layer to the mechanical displacement associated with an acoustic wave. Acoustic measurements provide two simultaneous time-resolved signals; one signal is related to the velocity or frequency of the acoustic wave and is mainly a function of adsorbed mass, while the second signal, related to the oscillation amplitude, is associated with energy dissipation and is a function of the viscoelastic properties of the adsorbed layer. The methods described in this chapter explore the relationship between the acoustic measurements of adsorbed liposomes and the mechanical properties of the lipid bilayer. This is carried out using a well-characterized model system consisting of liposomes prepared from an unsaturated phospholipid and a range of mole fractions of cholesterol. Real-time acoustic measurements are shown to be sensitive to changes in the liposome cholesterol content, regardless of the mode of attachment of the liposome to the device surface. This sensitivity is not due to changes in the density of the bilayer, or to changes in the extent of liposome-surface interactions, thus leaving the mechanical properties of the bilayer as the feature that is probably being measured. Some mechanisms by which the acoustic response could be generated are suggested in this chapter. PMID:19913160

  5. Synthesis, structure, and properties of glasses under extreme conditions

    NASA Astrophysics Data System (ADS)

    Guerette, Michael J.

    Anomalous mechanical properties of silica glass include stiffening upon heating, initially softening under pressure, and non-linear elastic response to strains. Through understanding structural changes in silica glass under a broad range of temperature, pressure, and strain conditions and how they influence the mechanical properties, insight was gained for how to change the silica glass network to better suit specific uses in extreme conditions. In this dissertation, pressure-quenching routes were used to effectively change the glass atomic packing and to make densified glass. Applied in the non-rigid state near the glass transition temperature, quench pressures up to 8 GPa have been used to achieve density increase of 25% in silica glass. The resulting structure and properties of as-quenched samples have been investigated using XRD, Raman and Brillouin spectroscopy. In-situ Raman and Brillouin light scattering techniques were developed to study the structure, elastic and dynamic properties of silica glass under high temperature, high pressure and high strain conditions. High temperature measurements were carried out in an optical furnace up to 1500°C, a diamond anvil cell was used to carry out high pressure experiments up to 25 GPa, and a two-point bender was used for measuring glasses in excess of 6% strain in both tensile and compressive regions. Pressure-quenching from the non-rigid state near the glass transition temperature imparts structural signatures to densified silica glass that cannot be accomplished through cold compression at room temperature. The unique structures of pressure-quenched silica glass are reflected in decreased anomalous response of silica glass to external stimuli of high temperature or high pressure, and therefore greater thermo-mechanical stability. The nonlinear elastic behavior of silica glass has been directly probed from the compressive to the tensile side of silica fibers in bend by using in-situ Brillouin light scattering. This

  6. Probing the micro-rheological properties of aerosol particles using optical tweezers

    NASA Astrophysics Data System (ADS)

    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 >1012 Pa s, whilst

  7. 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.

  8. 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.

  9. Source and structure of bursty hot electron enhancements in the tail magnetosheath: Simultaneous two-probe observation by ARTEMIS

    NASA Astrophysics Data System (ADS)

    Wang, Chih-Ping; Xing, Xiaoyan; Nakamura, T. K. M.; Lyons, Larry R.; Angelopoulos, Vassilis

    2014-12-01

    Bursty enhancements of hot electrons (≳0.5 keV) with duration of minutes sometimes occur in the tail magnetosheath. In this study we used the unique simultaneous measurements from the two Acceleration Reconnection Turbulence and Electrodynamics of Moon's Interaction with the Sun probes to investigate the likely sources, spatial structures, and responsible processes for these hot electron enhancements. The enhancements can be seen at any distance across the magnetosheath, but those closer to the magnetopause are more often accompanied by magnetosheath density and flow magnitudes changing to more magnetosphere-like values. From simultaneous measurements with the two probes being on either side of magnetopause or both in the magnetosheath, it is evident that these hot electrons come from the magnetosphere near the current sheet without further energization and that the enhancements are a result of bursty lateral magnetosphere intrusion into the magnetosheath, the enhancements and changes in the magnetosheath properties becoming smaller with increasing outward distance from the intrusion. From limited events having specific separation distances and alignments between the probes, we estimated that a single isolated enhancement can have a thin and elongated structure as narrow as 2 RE wide in the X direction, as long as over 7 RE in the Y direction, and as thin as 1 RE in the Z direction. We propose that Kelvin-Helmholtz perturbations at the magnetopause and subsequent magnetosphere-magnetosheath particle mixing due to reconnection or diffusion can plausibly play an important role in generating the bursty magnetosphere intrusion into the magnetosheath and the hot electron enhancements.

  10. Source and Structure of Bursty Hot Electron Enhancements in the Tail Magnetosheath: Simultaneous Two-Probe Observation By Artemis

    NASA Astrophysics Data System (ADS)

    Wang, C. P.; Xing, X.; Lyons, L. R.; Angelopoulos, V.

    2014-12-01

    Bursty enhancements of hot electrons (~0.5 to 5 keV) with duration of minutes often occur in the tail magnetosheath. Determining the sources and energization of these hot electrons is important to understanding the coupling of the mangetosheath with the bowshock or magnetosphere. In this study we used the unique simultaneous measurements from the two ARTEMIS probes to investigate the likely source locations, spatial structures, and responsible processes for these hot electron enhancements. The enhancements can be seen at any distances across the magnetosheath, but those closer to the magnetopause more often have magnetosheath density and flow magnitudes decreased to more magnetosphere-like values. From simultaneous measurements of these enhancements with the two probes being on either side of magnetopause or both in the magnetosheath, it is evident that these hot electrons come from the magnetosphere near the current sheet without further energization, and that the enhancements are a result of bursty lateral magnetosphere intrusion into the magnetosheath, with weaker enhancements and smaller changes in the magnetosheath properties further outward from the intrusion. Using simultaneous observations having different separation distances and alignments between the probes, we estimated that a single isolated enhancement can have a thin and elongated structure as narrow as 2 RE wide in the X direction, as long as more than 7 RE in the Y direction, and as thin as 1 RE in the Z direction. From observed correlations between the enhancements seen on the magnetosheath side and magnetosheath intrusion seen on the magnetosphere side, we propose that Kelvin-Helmholtz perturbations at the magnetopause and subsequent magnetosphere-magnetosheath particle mixing due to reconnection or diffusion can plausibly explain the bursty magnetosphere intrusion deep into the magnetosheath and the different decreases of magnetosheath density and flow associated with the hot electron