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

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.

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

DOE PAGES

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

2014-12-15

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

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

PubMed Central

2016-01-01

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

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

PubMed

Doughty, Christopher E; Wolf, Adam

2016-01-01

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

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.

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

NASA Astrophysics Data System (ADS)

Walrath, Jenna Cherie

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

Continuous-variable quantum probes for structured environments

NASA Astrophysics Data System (ADS)

Bina, Matteo; Grasselli, Federico; Paris, Matteo G. A.

2018-01-01

We address parameter estimation for structured environments and suggest an effective estimation scheme based on continuous-variables quantum probes. In particular, we investigate the use of a single bosonic mode as a probe for Ohmic reservoirs, and obtain the ultimate quantum limits to the precise estimation of their cutoff frequency. We assume the probe prepared in a Gaussian state and determine the optimal working regime, i.e., the conditions for the maximization of the quantum Fisher information in terms of the initial preparation, the reservoir temperature, and the interaction time. Upon investigating the Fisher information of feasible measurements, we arrive at a remarkable simple result: homodyne detection of canonical variables allows one to achieve the ultimate quantum limit to precision under suitable, mild, conditions. Finally, upon exploiting a perturbative approach, we find the invariant sweet spots of the (tunable) characteristic frequency of the probe, able to drive the probe towards the optimal working regime.

High-Resolution Structural and Electronic Properties of Epitaxial Topological Crystalline Insulator Films

NASA Astrophysics Data System (ADS)

Dagdeviren, Omur; Zhou, Chao; Zou, Ke; Simon, Georg; Albright, Stephen; Mandal, Subhasish; Morales-Acosta, Mayra; Zhu, Xiaodong; Ismail-Beigi, Sohrab; Walker, Frederick; Ahn, Charles; Schwarz, Udo; Altman, Eric

Revealing the local electronic properties of surfaces and their link to structural properties is an important problem for topological crystalline insulators (TCI) in which metallic surface states are protected by crystal symmetry. The microstructure and electronic properties of TCI SnTe film surfaces grown by molecular beam epitaxy were characterized using scanning probe microscopy. These results reveal the influence of various defects on the electronic properties: tilt boundaries leading to dislocation arrays that serve as periodic nucleation sites for pit growth; screw dislocations, and point defects. These features have varying length scale and display variations in the electronic structure of the surface, which are mapped with scanning tunneling microscopy images as standing waves superimposed on atomic scale images of the surface topography that consequently shape the wave patterns. Since the growth process results in symmetry breaking defects that patterns the topological states, we propose that the scanning probe tip can pattern the surface and electronic structure and enable the fabrication of topological devices on the SnTe surface. Financial support from the National Science Foundation through the Yale Materials Research Science and Engineering Center (Grant No. MRSEC DMR-1119826) and FAME.

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

NASA Astrophysics Data System (ADS)

Huang, Yuping; Lu, Renfu; Chen, Kunjie

2017-05-01

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

A novel constant-force scanning probe incorporating mechanical-magnetic coupled structures.

PubMed

Wang, Hongxi; Zhao, Jian; Gao, Renjing; Yang, Yintang

2011-07-01

A one-dimensional scanning probe with constant measuring force is designed and fabricated by utilizing the negative stiffness of the magnetic coupled structure, which mainly consists of the magnetic structure, the parallel guidance mechanism, and the pre-stressed spring. Based on the theory of material mechanics and the equivalent surface current model for computing the magnetic force, the analytical model of the scanning probe subjected to multi-forces is established, and the nonlinear relationship between the measuring force and the probe displacement is obtained. The practicability of introducing magnetic coupled structure in the constant-force probe is validated by the consistency of the results in numerical simulation and experiments.

nextPARS: parallel probing of RNA structures in Illumina

PubMed Central

Saus, Ester; Willis, Jesse R.; Pryszcz, Leszek P.; Hafez, Ahmed; Llorens, Carlos; Himmelbauer, Heinz

2018-01-01

RNA molecules play important roles in virtually every cellular process. These functions are often mediated through the adoption of specific structures that enable RNAs to interact with other molecules. Thus, determining the secondary structures of RNAs is central to understanding their function and evolution. In recent years several sequencing-based approaches have been developed that allow probing structural features of thousands of RNA molecules present in a sample. Here, we describe nextPARS, a novel Illumina-based implementation of in vitro parallel probing of RNA structures. Our approach achieves comparable accuracy to previous implementations, while enabling higher throughput and sample multiplexing. PMID:29358234

Electrostatic Structure and Double-Probe Performance in Tenuous Plasmas

NASA Astrophysics Data System (ADS)

Cully, C. M.; Ergun, R. E.

2006-12-01

Many in-situ plasma instruments are affected by the local electrostatic structure surrounding the spacecraft. In order to better understand this structure, we have developed a fully 3-dimensional self-consistent model that uses realistic spacecraft geometry, including thin (<1 mm) wires and long (>100m) booms, with open boundary conditions. One of the more surprising results is that in tenuous plasmas, the charge on the booms can dominate over the charge on the spacecraft body. For instruments such as electric field double probes and boom-mounted low-energy particle detectors, this challenges the existing paradigm: long booms do not allow the probes to escape the spacecraft potential. Instead, the potential structure simply expands as the boom is deployed. We then apply our model to the double-probe Electric Field and Waves (EFW) instruments on Cluster, and predict the magnitudes of the main error sources. The overall error budget is consistent with experiment, and the model yields some additional interesting insights. We show that the charge in the photoelectron cloud is relatively unimportant, and that the spacecraft potential is typically underestimated by about 20% by double-probe experiments.

Resonant Slit-type Probe with Rounded Matching Structure for Terahertz Imaging

NASA Astrophysics Data System (ADS)

Kim, Geun-Ju; Kim, Jung-Il; Kim, Sanghoon; Lee, Jeong-Hun; Jeon, Tae-In

2018-05-01

We propose a resonant slit-type probe with a rounded matching structure in the inner corner of the probe slit, for high-resolution terahertz (THz) imaging. The proposed probe can achieve high coupling efficiency and maintain a stable resonant frequency in spite of the increase in slit thickness. The THz signal measured by the proposed probe was 1.7 times more sensitive than that by a right angle structure probe when a 50 μm diameter metal ball was located 100 um away from the slits. The resonant frequency and return loss |S11| measurements of the prototype resonant probe using a vector network analyzer (VNA) were in good agreement with a simulation results. We achieved a spatial resolution of 100 μm with a slit height of 140 μm. Also, to determine the potential of the proposed probe in the THz applications, we measured THz images according to the thickness of covering flour and the distance between the probe and the flour for the foreign objects in the flour. The proposed probe detected a metal wire with a diameter of 70 μm beneath 1.5 mm of flour at a distance between flour and probe of 1 mm. Consequently, we confirmed that the proposed probe could potentially be applied as a new THz probe.

Two-photon probes for in vivo multicolor microscopy of the structure and signals of brain cells.

PubMed

Ricard, Clément; Arroyo, Erica D; He, Cynthia X; Portera-Cailliau, Carlos; Lepousez, Gabriel; Canepari, Marco; Fiole, Daniel

2018-05-11

Imaging the brain of living laboratory animals at a microscopic scale can be achieved by two-photon microscopy thanks to the high penetrability and low phototoxicity of the excitation wavelengths used. However, knowledge of the two-photon spectral properties of the myriad fluorescent probes is generally scarce and, for many, non-existent. In addition, the use of different measurement units in published reports further hinders the design of a comprehensive imaging experiment. In this review, we compile and homogenize the two-photon spectral properties of 280 fluorescent probes. We provide practical data, including the wavelengths for optimal two-photon excitation, the peak values of two-photon action cross section or molecular brightness, and the emission ranges. Beyond the spectroscopic description of these fluorophores, we discuss their binding to biological targets. This specificity allows in vivo imaging of cells, their processes, and even organelles and other subcellular structures in the brain. In addition to probes that monitor endogenous cell metabolism, studies of healthy and diseased brain benefit from the specific binding of certain probes to pathology-specific features, ranging from amyloid-β plaques to the autofluorescence of certain antibiotics. A special focus is placed on functional in vivo imaging using two-photon probes that sense specific ions or membrane potential, and that may be combined with optogenetic actuators. Being closely linked to their use, we examine the different routes of intravital delivery of these fluorescent probes according to the target. Finally, we discuss different approaches, strategies, and prerequisites for two-photon multicolor experiments in the brains of living laboratory animals.

Coaxial-probe contact-force monitoring for dielectric properties measurements

USDA-ARS?s Scientific Manuscript database

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

Monitoring Coaxial-Probe Contact Force for Dielectric Properties Measurement

USDA-ARS?s Scientific Manuscript database

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

Integrated in-situ probes for structural and dynamic properties of geological materials at ultrahigh pressures and temperatures

NASA Astrophysics Data System (ADS)

Mao, H.; Mao, W. L.

2005-12-01

Multiple x-ray and allied probes have been recently developed and integrated with diamond-anvil cells at synchrotron facilities. They have effectively opened up the vast field area of the Earth's interior to direct, in-situ study. For instance, x-ray emission spectroscopy identifies the high-spin-low-spin transition that governs Fe-Mg partitioning, the most important factor in element differentiation in the mantle. Inelastic x-ray near-edge spectroscopy reveals the bonding nature of light elements that control the phase transitions, structure and partitioning of these elements (e.g., carbon bonding changes as an element, and in oxides, carbonates, and silicates). X-ray diffraction combined with laser-heated diamond anvil cell determines crystal structures and P-V-T equations of state. Shear moduli, single-crystal elasticity, and phonon dynamics can be measured to the core pressures with newly-enabled, complementary techniques, including radial x-ray diffraction, nuclear resonant inelastic x-ray scattering, non-resonant inelastic x-ray scattering, high-temperature Raman spectroscopy, and Brillouin scattering spectroscopy. The nonhydrostatic stress in solid samples which was previously regarded as a nuisance that degraded the experiments, can now be used for extracting important rheological information, including deformation mechanisms, preferred orientation, slip systems, plasticity, failure, and shear strength of major mantle and core minerals at high pressures. With the new arsenal of experimental techniques over the extended P-T-x regimes at we can now address questions that were not conceivable only a decade ago. Knowledge of the high P-T properties is leading to fundamental improvements in interpreting seismological observations and understanding the structure, dynamics, and evolution of the Earth's deep interior.

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

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

USDA-ARS?s Scientific Manuscript database

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

Sensitive Phonon-Based Probe for Structure Identification of 1T' MoTe 2

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

Zhou, Lin; Huang, Shengxi; Tatsumi, Yuki

In this work, by combining transmission electron microscopy and polarized Raman spectroscopy for the 1T' MoTe 2 flakes with different thicknesses, we found that the polarization dependence of Raman intensity is given as a function of excitation laser wavelength, phonon symmetry, and phonon frequency, but has weak dependence on the flake thickness from few-layer to multilayer. Additionally, the frequency of Raman peaks and the relative Raman intensity are sensitive to flake thickness, which manifests Raman spectroscopy as an effective probe for thickness of 1T' MoTe 2. This work demonstrates that polarized Raman spectroscopy is a powerful and nondestructive method tomore » quickly identify the crystal structure and thickness of 1T' MoTe 2 simultaneously, which opens up opportunities for the in situ probe of anisotropic properties and broad applications of this novel material.« less

Sensitive Phonon-Based Probe for Structure Identification of 1T' MoTe 2

DOE PAGES

Zhou, Lin; Huang, Shengxi; Tatsumi, Yuki; ...

2017-05-25

In this work, by combining transmission electron microscopy and polarized Raman spectroscopy for the 1T' MoTe 2 flakes with different thicknesses, we found that the polarization dependence of Raman intensity is given as a function of excitation laser wavelength, phonon symmetry, and phonon frequency, but has weak dependence on the flake thickness from few-layer to multilayer. Additionally, the frequency of Raman peaks and the relative Raman intensity are sensitive to flake thickness, which manifests Raman spectroscopy as an effective probe for thickness of 1T' MoTe 2. This work demonstrates that polarized Raman spectroscopy is a powerful and nondestructive method tomore » quickly identify the crystal structure and thickness of 1T' MoTe 2 simultaneously, which opens up opportunities for the in situ probe of anisotropic properties and broad applications of this novel material.« less

Blending Gelators to Tune Gel Structure and Probe Anion-Induced Disassembly

PubMed Central

Foster, Jonathan A; Edkins, Robert M; Cameron, Gary J; Colgin, Neil; Fucke, Katharina; Ridgeway, Sam; Crawford, Andrew G; Marder, Todd B; Beeby, Andrew; Cobb, Steven L; Steed, Jonathan W

2014-01-01

Blending different low molecular weight gelators (LMWGs) provides a convenient route to tune the properties of a gel and incorporate functionalities such as fluorescence. Blending a series of gelators having a common bis-urea motif, and functionalised with different amino acid-derived end-groups and differing length alkylene spacers is reported. Fluorescent gelators incorporating 1-and 2-pyrenyl moieties provide a probe of the mixed systems alongside structural and morphological data from powder diffraction and electron microscopy. Characterisation of the individual gelators reveals that although the expected α-urea tape motif is preserved, there is considerable variation in the gelation properties, molecular packing, fibre morphology and rheological behaviour. Mixing of the gelators revealed examples in which: 1) the gels formed separate, orthogonal networks maintaining their own packing and morphology, 2) the gels blended together into a single network, either adopting the packing and morphology of one gelator, or 3) a new structure not seen for either of the gelators individually was created. The strong binding of the urea functionalities to anions was exploited as a means of breaking down the gel structure, and the use of fluorescent gel blends provides new insights into anion-mediated gel dissolution. PMID:24302604

Pyrene maleimide as a probe of microenvironmental and dynamics properties of protein binding sites

NASA Astrophysics Data System (ADS)

Benci, S.; Vaccari, S.; Schianchi, G.; Locatelli, Donata; Vaghi, P.; Bottiroli, Giovanni F.

1995-01-01

N-(1-Pyrene)maleimide is highly fluorescent upon covalent binding with sulfhydryl and amino groups of the proteins. Multiexponential fluorescence decays were observed for the dye bound to different proteins even when a single binding site is involved. The lack of information about the fluorescence decay of free dye does not allow to define the variations of fluorescence parameter following the conjugation and their correlation with the binding properties of the fluorophore. In this work, a study of the fluorescence of the probe, free in solution, bound to different antibodies and to the antigen-antibody complex both in solution and in cell, has been performed. The experimental results showed that chemico-physical properties of the medium influence the fluorescence decay of the probe in both the free and bound forms, although to a different extent. The variations of fluorescence decay and anisotropy of the bound probe are related to the electronic characteristics of microenvironment and show an increased stabilization of the probe binding site with the increasing complexity of the substrate. The sensitivity of the fluorescence properties of the probe to the binding site environment opens interesting perspectives concerning the application of Py- maleimide fluorochromization to assess the degree of specificity of immunocytochemical labelling.

Flexible deep brain neural probes based on a parylene tube structure

NASA Astrophysics Data System (ADS)

Zhao, Zhiguo; Kim, Eric; Luo, Hao; Zhang, Jinsheng; Xu, Yong

2018-01-01

Most microfabricated neural probes have limited shank length, which prevents them from reaching many deep brain structures. This paper reports deep brain neural probes with ultra-long penetrating shanks based on a simple but novel parylene tube structure. The mechanical strength of the parylene tube shank is temporarily enhanced during implantation by inserting a metal wire. The metal wire can be removed after implantation, making the implanted probe very flexible and thus minimizing the stress caused by micromotions of brain tissues. Optogenetic stimulation and chemical delivery capabilities can be potentially integrated by taking advantage of the tube structure. Single-shank prototypes with a shank length of 18.2 mm have been developed. The microfabrication process comprises of deep reactive ion etching (DRIE) of silicon, parylene conformal coating/refilling, and XeF2 isotropic silicon etching. In addition to bench-top insertion characterization, the functionality of developed probes has been preliminarily demonstrated by implanting into the amygdala of a rat and recording neural signals.

Universal structural parameter to quantitatively predict metallic glass properties

DOE PAGES

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

2016-12-12

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

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

NASA Astrophysics Data System (ADS)

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

2006-05-01

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

Probing Human Telomeric DNA and RNA Topology and Ligand Binding in a Cellular Model by Using Responsive Fluorescent Nucleoside Probes.

PubMed

Manna, Sudeshna; Panse, Cornelia H; Sontakke, Vyankat A; Sangamesh, Sarangamath; Srivatsan, Seergazhi G

2017-08-17

The development of biophysical systems that enable an understanding of the structure and ligand-binding properties of G-quadruplex (GQ)-forming nucleic acid sequences in cells or models that mimic the cellular environment would be highly beneficial in advancing GQ-directed therapeutic strategies. Herein, the establishment of a biophysical platform to investigate the structure and recognition properties of human telomeric (H-Telo) DNA and RNA repeats in a cell-like confined environment by using conformation-sensitive fluorescent nucleoside probes and a widely used cellular model, bis(2-ethylhexyl) sodium sulfosuccinate reverse micelles (RMs), is described. The 2'-deoxy and ribonucleoside probes, composed of a 5-benzofuran uracil base analogue, faithfully report the aqueous micellar core through changes in their fluorescence properties. The nucleoside probes incorporated into different loops of H-Telo DNA and RNA oligonucleotide repeats are minimally perturbing and photophysically signal the formation of respective GQ structures in both aqueous buffer and RMs. Furthermore, these sensors enable a direct comparison of the binding affinity of a ligand to H-Telo DNA and RNA GQ structures in the bulk and confined environment of RMs. These results demonstrate that this combination of a GQ nucleoside probe and easy-to-handle RMs could provide new opportunities to study and devise screening-compatible assays in a cell-like environment to discover GQ binders of clinical potential. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effects of skeleton structure on necrosis targeting and clearance properties of radioiodinated dianthrones.

PubMed

Zhang, Dongjian; Jiang, Cuihua; Yang, Shengwei; Gao, Meng; Huang, Dejian; Wang, Xiaoning; Shao, Haibo; Feng, Yuanbo; Sun, Ziping; Ni, Yicheng; Zhang, Jian; Yin, Zhiqi

2016-01-01

Necrosis avid agents (NAAs) can be used for diagnose of necrosis-related diseases, evaluation of therapeutic responses and targeted therapeutics of tumor. In order to probe into the effects of molecular skeleton structure on necrosis targeting and clearance properties of radioiodinated dianthrones, four dianthrone compounds with the same substituents but different skeletal structures, namely Hypericin (Hyp), protohypericin (ProHyp), emodin dianthrone mesomer (ED-1) and emodin dianthrone raceme (ED-2) were synthesized and radioiodinated. Then radioiodinated dianthrones were evaluated in vitro for their necrosis avidity in A549 lung cancer cells untreated and treated with H2O2. Their biodistribution and pharmacokinetic properties were determined in rat models of induced necrosis. In vitro cell assay revealed that destruction of rigid skeleton structure dramatically reduced their necrosis targeting ability. Animal studies demonstrated that destruction of rigid skeleton structure dramatically reduced the necrotic tissue uptake and speed up the clearance from the most normal tissues for the studied compounds. Among these (131)I-dianthrones, (131)I-Hyp exhibited the highest uptake and persistent retention in necrotic tissues. Hepatic infarction could be clearly visualized by SPECT/CT using (131)I-Hyp as an imaging probe. The results suggest that the skeleton structure of Hyp is the lead structure for further structure optimization of this class of NAAs.

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

PubMed Central

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

2015-01-01

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

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

PubMed Central

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

2011-01-01

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

In-cell RNA structure probing with SHAPE-MaP.

PubMed

Smola, Matthew J; Weeks, Kevin M

2018-06-01

This protocol is an extension to: Nat. Protoc. 10, 1643-1669 (2015); doi:10.1038/nprot.2015.103; published online 01 October 2015RNAs play key roles in many cellular processes. The underlying structure of RNA is an important determinant of how transcripts function, are processed, and interact with RNA-binding proteins and ligands. RNA structure analysis by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) takes advantage of the reactivity of small electrophilic chemical probes that react with the 2'-hydroxyl group to assess RNA structure at nucleotide resolution. When coupled with mutational profiling (MaP), in which modified nucleotides are detected as internal miscodings during reverse transcription and then read out by massively parallel sequencing, SHAPE yields quantitative per-nucleotide measurements of RNA structure. Here, we provide an extension to our previous in vitro SHAPE-MaP protocol with detailed guidance for undertaking and analyzing SHAPE-MaP probing experiments in live cells. The MaP strategy works for both abundant-transcriptome experiments and for cellular RNAs of low to moderate abundance, which are not well examined by whole-transcriptome methods. In-cell SHAPE-MaP, performed in roughly 3 d, can be applied in cell types ranging from bacteria to cultured mammalian cells and is compatible with a variety of structure-probing reagents. We detail several strategies by which in-cell SHAPE-MaP can inform new biological hypotheses and emphasize downstream analyses that reveal sequence or structure motifs important for RNA interactions in cells.

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

PubMed

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

2016-11-01

High-throughput sequencing has been used to study posttranscriptional regulations, where the identification of protein-RNA binding is a major and fast-developing sub-area, which is in turn benefited by the sequencing methods for whole-transcriptome probing of RNA secondary structures. In the study of RNA secondary structures using high-throughput sequencing, bases are modified or cleaved according to their structural features, which alter the resulting composition of sequencing reads. In the study of protein-RNA binding, methods have been proposed to immuno-precipitate (IP) protein-bound RNA transcripts in vitro or in vivo By sequencing these transcripts, the protein-RNA interactions and the binding locations can be identified. For both types of data, read counts are affected by a combination of confounding factors, including expression levels of transcripts, sequence biases, mapping errors and the probing or IP efficiency of the experimental protocols. Careful processing of the sequencing data and proper extraction of important features are fundamentally important to a successful analysis. Here we review and compare different experimental methods for probing RNA secondary structures and binding sites of RNA-binding proteins (RBPs), and the computational methods proposed for analyzing the corresponding sequencing data. We suggest how these two types of data should be integrated to study the structural properties of RBP binding sites as a systematic way to better understand posttranscriptional regulations. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Investigating the topological structure of quenched lattice QCD with overlap fermions using a multi-probing approximation

NASA Astrophysics Data System (ADS)

Zou, You-Hao; Zhang, Jian-Bo; Xiong, Guang-Yi; Chen, Ying; Liu, Chuan; Liu, Yu-Bin; Ma, Jian-Ping

2017-10-01

The topological charge density and topological susceptibility are determined by a multi-probing approximation using overlap fermions in quenched SU(3) gauge theory. Then we investigate the topological structure of the quenched QCD vacuum, and compare it with results from the all-scale topological density. The results are consistent. Random permuted topological charge density is used to check whether these structures represent underlying ordered properties. The pseudoscalar glueball mass is extracted from the two-point correlation function of the topological charge density. We study 3 ensembles of different lattice spacing a with the same lattice volume 163×32. The results are compatible with the results of all-scale topological charge density, and the topological structures revealed by multi-probing are much closer to all-scale topological charge density than those from eigenmode expansion. Supported by National Natural Science Foundation of China (NSFC) (11335001, 11275169, 11075167), It is also supported in part by the DFG and the NSFC (11261130311) through funds provided to the Sino-German CRC 110 "Symmetries and the Emergence of Structure in QCD". This work was also funded in part by National Basic Research Program of China (973 Program) (2015CB856700)

The effect of crystal structure on the electromechanical properties of piezoelectric Nylon-11 nanowires.

PubMed

Choi, Yeon Sik; Kim, Sung Kyun; Williams, Findlay; Calahorra, Yonatan; Elliott, James A; Kar-Narayan, Sohini

2018-06-19

Crystal structure is crucial in determining the properties of piezoelectric polymers, particularly at the nanoscale where precise control of the crystalline phase is possible. Here, we investigate the electromechanical properties of three distinct crystalline phases of Nylon-11 nanowires using advanced scanning probe microscopy techniques. Stiff α-phase nanowires exhibited a low piezoelectric response, while relatively soft δ'-phase nanowires displayed an enhanced piezoelectric response.

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

NASA Astrophysics Data System (ADS)

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

2007-04-01

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

Design and Investigation of Optical Properties of N-(Rhodamine-B)-Lactam-Ethylenediamine (RhB-EDA) Fluorescent Probe.

PubMed

Soršak, Eva; Volmajer Valh, Julija; Korent Urek, Špela; Lobnik, Aleksandra

2018-04-14

This study presents chemical modification of a Rhodamine B (RhB) sensor probe by ethylenediamine (EDA), and investigation of its spectral as well as sensor properties to the various metals. The synthesised N -(Rhodamine-B)-lactam-ethylenediamine (RhB-EDA) fluorescent probe shows interesting optical sensor properties, and high sensitivity and selectivity to Ag⁺ ions among all the tested metal ions (K⁺, Mg 2+ , Cu 2+ , Ni 2+ , Fe 2+ , Pb 2+ , Na⁺, Mn 2+ , Li⁺, Al 3+ , Co 2+ , Hg 2+ , Sr 2+ , Ca 2+ , Ag⁺, Cd 2+ and Zn 2+ ), while the well-known Rhodamine B (RhB) fluorescent probe shows much less sensitivity to Ag⁺ ions, but high sensitivity to Fe 2+ ions. The novel fluorescent sensor probe RhB-EDA has the capabilities to sense Ag⁺ ions up to µM ranges by using the fluorescence quenching approach. The probe displayed a dynamic response to Ag⁺ in the range of 0.43 × 10 -3 -10 -6 M with a detection limit of 0.1 μM. The sensing system of an RhB-EDA novel fluorescent probe was optimised according to the spectral properties, effect of pH and buffer, photostability, incubation time, sensitivity, and selectivity. Since all the spectral and sensing properties were tested in green aqueous media, although many other similar sensor systems rely on organic solvent solutions, the RhB-EDA sensing probe may be a good candidate for measuring Ag⁺ ions in real-life applications.

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.

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

USDA-ARS?s Scientific Manuscript database

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

Tissue-like Neural Probes for Understanding and Modulating the Brain.

PubMed

Hong, Guosong; Viveros, Robert D; Zwang, Theodore J; Yang, Xiao; Lieber, Charles M

2018-03-19

Electrophysiology tools have contributed substantially to understanding brain function, yet the capabilities of conventional electrophysiology probes have remained limited in key ways because of large structural and mechanical mismatches with respect to neural tissue. In this Perspective, we discuss how the general goal of probe design in biochemistry, that the probe or label have a minimal impact on the properties and function of the system being studied, can be realized by minimizing structural, mechanical, and topological differences between neural probes and brain tissue, thus leading to a new paradigm of tissue-like mesh electronics. The unique properties and capabilities of the tissue-like mesh electronics as well as future opportunities are summarized. First, we discuss the design of an ultraflexible and open mesh structure of electronics that is tissue-like and can be delivered in the brain via minimally invasive syringe injection like molecular and macromolecular pharmaceuticals. Second, we describe the unprecedented tissue healing without chronic immune response that leads to seamless three-dimensional integration with a natural distribution of neurons and other key cells through these tissue-like probes. These unique characteristics lead to unmatched stable long-term, multiplexed mapping and modulation of neural circuits at the single-neuron level on a year time scale. Last, we offer insights on several exciting future directions for the tissue-like electronics paradigm that capitalize on their unique properties to explore biochemical interactions and signaling in a "natural" brain environment.

A theoretical investigation of two typical two-photon pH fluorescent probes.

PubMed

Xu, Zhong; Ren, Ai-Min; Guo, Jing-Fu; Liu, Xiao-Ting; Huang, Shuang; Feng, Ji-Kang

2013-01-01

Intracellular pH plays an important role in many cellular events, such as cell growth, endocytosis, cell adhesion and so on. Some pH fluorescent probes have been reported, but most of them are one-photon fluorescent probes, studies about two-photon fluorescent probes are very rare. In this work, the geometrical structure, electronic structure and one-photon properties of a series of two-photon pH fluorescent probes have been theoretically studied by using density functional theory (DFT) method. Their two-photon absorption (TPA) properties are calculated using the method of ZINDO/sum-over-states method. Two types of two-photon pH fluorescent probes have been investigated by theoretical methods. The mechanisms of the Photoinduced Charge Transfer (PCT) probes and the Photoinduced Electron Transfer (PET) probes are verified specifically. Some designed strategies of good two-photon pH fluorescent probes are suggested on the basis of the investigated results of two mechanisms. For the PCT probes, substituting a stronger electron-donating group for the terminal methoxyl group is an advisable choice to increase the TPA cross section. For the PET probes, the TPA cross sections increase upon protonation. © 2012 Wiley Periodicals, Inc. Photochemistry and Photobiology © 2012 The American Society of Photobiology.

Probing Protein Structure and Folding in the Gas Phase by Electron Capture Dissociation

NASA Astrophysics Data System (ADS)

Schennach, Moritz; Breuker, Kathrin

2015-07-01

The established methods for the study of atom-detailed protein structure in the condensed phases, X-ray crystallography and nuclear magnetic resonance spectroscopy, have recently been complemented by new techniques by which nearly or fully desolvated protein structures are probed in gas-phase experiments. Electron capture dissociation (ECD) is unique among these as it provides residue-specific, although indirect, structural information. In this Critical Insight article, we discuss the development of ECD for the structural probing of gaseous protein ions, its potential, and limitations.

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.

Functional Scanning Probe Imaging of Nanostructured Solar Energy Materials.

PubMed

Giridharagopal, Rajiv; Cox, Phillip A; Ginger, David S

2016-09-20

From hybrid perovskites to semiconducting polymer/fullerene blends for organic photovoltaics, many new materials being explored for energy harvesting and storage exhibit performance characteristics that depend sensitively on their nanoscale morphology. At the same time, rapid advances in the capability and accessibility of scanning probe microscopy methods over the past decade have made it possible to study processing/structure/function relationships ranging from photocurrent collection to photocarrier lifetimes with resolutions on the scale of tens of nanometers or better. Importantly, such scanning probe methods offer the potential to combine measurements of local structure with local function, and they can be implemented to study materials in situ or devices in operando to better understand how materials evolve in time in response to an external stimulus or environmental perturbation. This Account highlights recent advances in the development and application of scanning probe microscopy methods that can help address such questions while filling key gaps between the capabilities of conventional electron microscopy and newer super-resolution optical methods. Focusing on semiconductor materials for solar energy applications, we highlight a range of electrical and optoelectronic scanning probe microscopy methods that exploit the local dynamics of an atomic force microscope tip to probe key properties of the solar cell material or device structure. We discuss how it is possible to extract relevant device properties using noncontact scanning probe methods as well as how these properties guide materials development. Specifically, we discuss intensity-modulated scanning Kelvin probe microscopy (IM-SKPM), time-resolved electrostatic force microscopy (trEFM), frequency-modulated electrostatic force microscopy (FM-EFM), and cantilever ringdown imaging. We explain these developments in the context of classic atomic force microscopy (AFM) methods that exploit the physics of

Functional Scanning Probe Imaging of Nanostructured Solar Energy Materials

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

Giridharagopal, Rajiv; Cox, Phillip A.; Ginger, David S.

From hybrid perovskites to semiconducting polymer/fullerene blends for organic photovoltaics, many new materials being explored for energy harvesting and storage exhibit performance characteristics that depend sensitively on their nanoscale morphology. At the same time, rapid advances in the capability and accessibility of scanning probe microscopy methods over the past decade have made it possible to study processing/structure/function relationships ranging from photocurrent collection to photocarrier lifetimes with resolutions on the scale of tens of nanometers or better. Importantly, such scanning probe methods offer the potential to combine measurements of local structure with local function, and they can be implemented to studymore » materials in situ or devices in operando to better understand how materials evolve in time in response to an external stimulus or environmental perturbation. This Account highlights recent advances in the development and application of scanning probe microscopy methods that can help address such questions while filling key gaps between the capabilities of conventional electron microscopy and newer super-resolution optical methods. Focusing on semiconductor materials for solar energy applications, we highlight a range of electrical and optoelectronic scanning probe microscopy methods that exploit the local dynamics of an atomic force microscope tip to probe key properties of the solar cell material or device structure. We discuss how it is possible to extract relevant device properties using noncontact scanning probe methods as well as how these properties guide materials development. Specifically, we discuss intensity-modulated scanning Kelvin probe microscopy (IM-SKPM), time-resolved electrostatic force microscopy (trEFM), frequency-modulated electrostatic force microscopy (FM-EFM), and cantilever ringdown imaging. We explain these developments in the context of classic atomic force microscopy (AFM) methods that exploit the

Functional Scanning Probe Imaging of Nanostructured Solar Energy Materials

DOE PAGES

Giridharagopal, Rajiv; Cox, Phillip A.; Ginger, David S.

2016-08-30

From hybrid perovskites to semiconducting polymer/fullerene blends for organic photovoltaics, many new materials being explored for energy harvesting and storage exhibit performance characteristics that depend sensitively on their nanoscale morphology. At the same time, rapid advances in the capability and accessibility of scanning probe microscopy methods over the past decade have made it possible to study processing/structure/function relationships ranging from photocurrent collection to photocarrier lifetimes with resolutions on the scale of tens of nanometers or better. Importantly, such scanning probe methods offer the potential to combine measurements of local structure with local function, and they can be implemented to studymore » materials in situ or devices in operando to better understand how materials evolve in time in response to an external stimulus or environmental perturbation. This Account highlights recent advances in the development and application of scanning probe microscopy methods that can help address such questions while filling key gaps between the capabilities of conventional electron microscopy and newer super-resolution optical methods. Focusing on semiconductor materials for solar energy applications, we highlight a range of electrical and optoelectronic scanning probe microscopy methods that exploit the local dynamics of an atomic force microscope tip to probe key properties of the solar cell material or device structure. We discuss how it is possible to extract relevant device properties using noncontact scanning probe methods as well as how these properties guide materials development. Specifically, we discuss intensity-modulated scanning Kelvin probe microscopy (IM-SKPM), time-resolved electrostatic force microscopy (trEFM), frequency-modulated electrostatic force microscopy (FM-EFM), and cantilever ringdown imaging. We explain these developments in the context of classic atomic force microscopy (AFM) methods that exploit the

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

PubMed

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

2015-10-14

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

Structure-activity relationships and colorimetric properties of specific probes for the putative cancer biomarker human arylamine N-acetyltransferase 1.

PubMed

Egleton, James E; Thinnes, Cyrille C; Seden, Peter T; Laurieri, Nicola; Lee, Siu Po; Hadavizadeh, Kate S; Measures, Angelina R; Jones, Alan M; Thompson, Sam; Varney, Amy; Wynne, Graham M; Ryan, Ali; Sim, Edith; Russell, Angela J

2014-06-01

A naphthoquinone inhibitor of human arylamine N-acetyltransferase 1 (hNAT1), a potential cancer biomarker and therapeutic target, has been reported which undergoes a distinctive concomitant color change from red to blue upon binding to the enzyme. Here we describe the use of in silico modeling alongside structure-activity relationship studies to advance the hit compound towards a potential probe to quantify hNAT1 levels in tissues. Derivatives with both a fifty-fold higher potency against hNAT1 and a two-fold greater absorption coefficient compared to the initial hit have been synthesized; these compounds retain specificity for hNAT1 and its murine homologue mNat2 over the isoenzyme hNAT2. A relationship between pKa, inhibitor potency and colorimetric properties has also been uncovered. The high potency of representative examples against hNAT1 in ZR-75-1 cell extracts also paves the way for the development of inhibitors with improved intrinsic sensitivity which could enable detection of hNAT1 in tissue samples and potentially act as tools for elucidating the unknown role hNAT1 plays in ER+ breast cancer; this could in turn lead to a therapeutic use for such inhibitors. Copyright © 2014. Published by Elsevier Ltd.

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.

Spectroscopic study of fluorescent probes based on G-quadruplex oligonucleotides labeled with ethynylpyrenyldeoxyuridine.

PubMed

Switalska, Angelika; Kierzek, Ryszard; Dembska, Anna; Juskowiak, Bernard

2017-12-01

The design, synthesis, and spectral properties of four pyrene labeled oligonucleotide probes with G-quadruplex structure (Tel22-Tpy, Tel22-Upy, Tel22-6Upy, Tel22-18Upy) based on the 22-mer human telomeric sequence (Tel22) have been reported. Pyrene labels in the form of ethynylpyrenyldeoxyuridine have been inserted efficiently into oligodeoxynucleotides probes using phosphoramidite chemistry. The probes exhibited abilities to fold into G-quadruplex structures and to bind metal cations (Na + and K + ). Folding properties of probes and their spectral behavior were examined by recording the UV-vis, fluorescence, and CD spectra as well as by analyzing melting profiles. Fluorescence characteristics and G-quadruplex folding of probes were also studied at the interface of cationic dioctadecyldimethylammonium bromide (DODAB) monolayer. Investigations included film balance measurements (π-A isotherms) and fluorescence spectra recording using a fiber optic accessory interfaced with a spectrofluorimeter. Copyright © 2017 Elsevier B.V. All rights reserved.

Structural and transport properties of Yb substituted YBaCo4O7

NASA Astrophysics Data System (ADS)

Singh, Bharat; Kumar, Naresh; Gaur, N. K.; Rayaprol, S.

2012-06-01

We investigate a series of compounds of the type, Y1-xYbxBaCo4O7, to study the effect of chemical pressure on the structural and electrical transport properties of a geometrically frustrated cobaltite, YBaCo4O7. Rietveld analysis of XRD data were carried out for all the samples studied. The four probe resistivity measurements were carried out to understand the transport mechanism in these compounds at temperatures below room temperatures. These results are presented and discussed in the context of ongoing efforts in studying geometrically frustrated magnetic compounds with novel physical properties.

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

Peptide Probe for Crystalline Hydroxyapatite: In Situ Detection of Biomineralization

NASA Astrophysics Data System (ADS)

Cicerone, Marcus; Becker, Matthew; Simon, Carl; Chatterjee, Kaushik

2009-03-01

While cells template mineralization in vitro and in vivo, specific detection strategies that impart chemical and structural information on this process have proven elusive. Recently we have developed an in situ based peptide probe via phage display methods that is specific to crystalline hydroxyapatite (HA). We are using this in fluorescence based assays to characterize mineralization. One application being explored is the screening of tissue engineering scaffolds for their ability to support osteogenesis. Specifically, osteoblasts are being cultured in hydrogel scaffolds possessing property gradients to provide a test bed for the HA peptide probe. Hydrogel properties that support osteogenesis and HA deposition will be identified using the probe to demonstrate its utility in optimizing design of tissue scaffolds.

Improving the psychometric properties of dot-probe attention measures using response-based computation.

PubMed

Evans, Travis C; Britton, Jennifer C

2018-09-01

Abnormal threat-related attention in anxiety disorders is most commonly assessed and modified using the dot-probe paradigm; however, poor psychometric properties of reaction-time measures may contribute to inconsistencies across studies. Typically, standard attention measures are derived using average reaction-times obtained in experimentally-defined conditions. However, current approaches based on experimentally-defined conditions are limited. In this study, the psychometric properties of a novel response-based computation approach to analyze dot-probe data are compared to standard measures of attention. 148 adults (19.19 ± 1.42 years, 84 women) completed a standardized dot-probe task including threatening and neutral faces. We generated both standard and response-based measures of attention bias, attentional orientation, and attentional disengagement. We compared overall internal consistency, number of trials necessary to reach internal consistency, test-retest reliability (n = 72), and criterion validity obtained using each approach. Compared to standard attention measures, response-based measures demonstrated uniformly high levels of internal consistency with relatively few trials and varying improvements in test-retest reliability. Additionally, response-based measures demonstrated specific evidence of anxiety-related associations above and beyond both standard attention measures and other confounds. Future studies are necessary to validate this approach in clinical samples. Response-based attention measures demonstrate superior psychometric properties compared to standard attention measures, which may improve the detection of anxiety-related associations and treatment-related changes in clinical samples. Copyright © 2018 Elsevier Ltd. All rights reserved.

Precise dielectric property measurements and E-field probe calibration for specific absorption rate measurements using a rectangular waveguide

PubMed Central

Hakim, B M; Beard, B B; Davis, C C

2018-01-01

Specific absorption rate (SAR) measurements require accurate calculations of the dielectric properties of tissue-equivalent liquids and associated calibration of E-field probes. We developed a precise tissue-equivalent dielectric measurement and E-field probe calibration system. The system consists of a rectangular waveguide, electric field probe, and data control and acquisition system. Dielectric properties are calculated using the field attenuation factor inside the tissue-equivalent liquid and power reflectance inside the waveguide at the air/dielectric-slab interface. Calibration factors were calculated using isotropicity measurements of the E-field probe. The frequencies used are 900 MHz and 1800 MHz. The uncertainties of the measured values are within ±3%, at the 95% confidence level. Using the same waveguide for dielectric measurements as well as calibrating E-field probes used in SAR assessments eliminates a source of uncertainty. Moreover, we clearly identified the system parameters that affect the overall uncertainty of the measurement system. PMID:29520129

Instant live-cell super-resolution imaging of cellular structures by nanoinjection of fluorescent probes.

PubMed

Hennig, Simon; van de Linde, Sebastian; Lummer, Martina; Simonis, Matthias; Huser, Thomas; Sauer, Markus

2015-02-11

Labeling internal structures within living cells with standard fluorescent probes is a challenging problem. Here, we introduce a novel intracellular staining method that enables us to carefully control the labeling process and provides instant access to the inner structures of living cells. Using a hollow glass capillary with a diameter of <100 nm, we deliver functionalized fluorescent probes directly into the cells by (di)electrophoretic forces. The label density can be adjusted and traced directly during the staining process by fluorescence microscopy. We demonstrate the potential of this technique by delivering and imaging a range of commercially available cell-permeable and nonpermeable fluorescent probes to cells.

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

Fast probe of local electronic states in nanostructures utilizing a single-lead quantum dot

PubMed Central

Otsuka, Tomohiro; Amaha, Shinichi; Nakajima, Takashi; Delbecq, Matthieu R.; Yoneda, Jun; Takeda, Kenta; Sugawara, Retsu; Allison, Giles; Ludwig, Arne; Wieck, Andreas D.; Tarucha, Seigo

2015-01-01

Transport measurements are powerful tools to probe electronic properties of solid-state materials. To access properties of local electronic states in nanostructures, such as local density of states, electronic distribution and so on, micro-probes utilizing artificial nanostructures have been invented to perform measurements in addition to those with conventional macroscopic electronic reservoirs. Here we demonstrate a new kind of micro-probe: a fast single-lead quantum dot probe, which utilizes a quantum dot coupled only to the target structure through a tunneling barrier and fast charge readout by RF reflectometry. The probe can directly access the local electronic states with wide bandwidth. The probe can also access more electronic states, not just those around the Fermi level, and the operations are robust against bias voltages and temperatures. PMID:26416582

Pneumatic Proboscis Heat-Flow Probe

NASA Technical Reports Server (NTRS)

Zacny, Kris; Hedlund, Magnus; Mumm, Eric; Shasho, Jeffrey; Chu, Philip; Kumar, Nishant

2013-01-01

Heat flow is a fundamental property of a planet, and provides significant constraints on the abundance of radiogenic isotopes, the thermal evolution and differentiation history, and the mechanical properties of the lithosphere. Heat-flow measurements are also essential in achieving at least four of the goals set out by the National Research Council for future lunar exploration. The heat-flow probe therefore directly addresses the goal of the Lunar Geophysical Network, which is to understand the interior structure and composition of the Moon. A key challenge for heat flow measurement is to install thermal sensors to the depths approximately equal to 3 m that are not influenced by the diurnal, annual, and longer-term fluctuations of the surface thermal environment. In addition, once deployed, the heat flow probe should cause little disturbance to the thermal regime of the surrounding regolith. A heat-flow probe system was developed that has two novel features: (1) it utilizes a pneumatic (gas) approach, excavates a hole by lofting the lunar soil out of the hole, and (2) deploys the heat flow probe, which utilizes a coiled up tape as a thermal probe to reach greater than 3-meter depth. The system is a game-changer for small lunar landers as it exhibits extremely low mass, volume, and simple deployment. The pneumatic system takes advantage of the helium gas used for pressurizing liquid propellant of the lander. Normally, helium is vented once the lander is on the surface, but it can be utilized for powering pneumatic systems. Should sufficient helium not be available, a simple gas delivery system may be taken specifically for the heat flow probe. Either way, the pneumatic heat flow probe system would be much lighter than other systems that entirely rely on the electrical power of the lander.

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

2016-01-08

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.

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.

Ion Spectral Structures Observed by the Van Allen Probes and Cluster

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

Cantilevered probe detector with piezoelectric element

DOEpatents

Adams, Jesse D; Sulchek, Todd A; Feigin, Stuart C

2014-04-29

A disclosed chemical detection system for detecting a target material, such as an explosive material, can include a cantilevered probe, a probe heater coupled to the cantilevered probe, and a piezoelectric element disposed on the cantilevered probe. The piezoelectric element can be configured as a detector and/or an actuator. Detection can include, for example, detecting a movement of the cantilevered probe or a property of the cantilevered probe. The movement or a change in the property of the cantilevered probe can occur, for example, by adsorption of the target material, desorption of the target material, reaction of the target material and/or phase change of the target material. Examples of detectable movements and properties include temperature shifts, impedance shifts, and resonant frequency shifts of the cantilevered probe. The overall chemical detection system can be incorporated, for example, into a handheld explosive material detection system.

Cantilevered probe detector with piezoelectric element

DOEpatents

Adams, Jesse D; Sulchek, Todd A; Feigin, Stuart C

2013-04-30

A disclosed chemical detection system for detecting a target material, such as an explosive material, can include a cantilevered probe, a probe heater coupled to the cantilevered probe, and a piezoelectric element disposed on the cantilevered probe. The piezoelectric element can be configured as a detector and/or an actuator. Detection can include, for example, detecting a movement of the cantilevered probe or a property of the cantilevered probe. The movement or a change in the property of the cantilevered probe can occur, for example, by adsorption of the target material, desorption of the target material, reaction of the target material and/or phase change of the target material. Examples of detectable movements and properties include temperature shifts, impedance shifts, and resonant frequency shifts of the cantilevered probe. The overall chemical detection system can be incorporated, for example, into a handheld explosive material detection system.

Cantilevered probe detector with piezoelectric element

DOEpatents

Adams, Jesse D [Reno, NV; Sulchek, Todd A [Oakland, CA; Feigin, Stuart C [Reno, NV

2012-07-10

A disclosed chemical detection system for detecting a target material, such as an explosive material, can include a cantilevered probe, a probe heater coupled to the cantilevered probe, and a piezoelectric element disposed on the cantilevered probe. The piezoelectric element can be configured as a detector and/or an actuator. Detection can include, for example, detecting a movement of the cantilevered probe or a property of the cantilevered probe. The movement or a change in the property of the cantilevered probe can occur, for example, by adsorption of the target material, desorption of the target material, reaction of the target material and/or phase change of the target material. Examples of detectable movements and properties include temperature shifts, impedance shifts, and resonant frequency shifts of the cantilevered probe. The overall chemical detection system can be incorporated, for example, into a handheld explosive material detection system.

Cantilevered probe detector with piezoelectric element

DOEpatents

Adams, Jesse D.; Sulchek, Todd A.; Feigin, Stuart C.

2010-04-06

A disclosed chemical detection system for detecting a target material, such as an explosive material, can include a cantilevered probe, a probe heater coupled to the cantilevered probe, and a piezoelectric element disposed on the cantilevered probe. The piezoelectric element can be configured as a detector and/or an actuator. Detection can include, for example, detecting a movement of the cantilevered probe or a property of the cantilevered probe. The movement or a change in the property of the cantilevered probe can occur, for example, by adsorption of the target material, desorption of the target material, reaction of the target material and/or phase change of the target material. Examples of detectable movements and properties include temperature shifts, impedance shifts, and resonant frequency shifts of the cantilevered probe. The overall chemical detection system can be incorporated, for example, into a handheld explosive material detection system.

Fluorogenic PNA probes

PubMed Central

2018-01-01

Fluorogenic oligonucleotide probes that can produce a change in fluorescence signal upon binding to specific biomolecular targets, including nucleic acids as well as non-nucleic acid targets, such as proteins and small molecules, have applications in various important areas. These include diagnostics, drug development and as tools for studying biomolecular interactions in situ and in real time. The probes usually consist of a labeled oligonucleotide strand as a recognition element together with a mechanism for signal transduction that can translate the binding event into a measurable signal. While a number of strategies have been developed for the signal transduction, relatively little attention has been paid to the recognition element. Peptide nucleic acids (PNA) are DNA mimics with several favorable properties making them a potential alternative to natural nucleic acids for the development of fluorogenic probes, including their very strong and specific recognition and excellent chemical and biological stabilities in addition to their ability to bind to structured nucleic acid targets. In addition, the uncharged backbone of PNA allows for other unique designs that cannot be performed with oligonucleotides or analogues with negatively-charged backbones. This review aims to introduce the principle, showcase state-of-the-art technologies and update recent developments in the areas of fluorogenic PNA probes during the past 20 years. PMID:29507634

Lanthanide complexes with aromatic o-phosphorylated ligands: synthesis, structure elucidation and photophysical properties.

PubMed

Shuvaev, Sergey; Utochnikova, Valentina; Marciniak, Łukasz; Freidzon, Alexandra; Sinev, Ilya; Van Deun, Rik; Freire, Ricardo O; Zubavichus, Yan; Grünert, Wolfgang; Kuzmina, Natalia

2014-02-28

Lanthanide complexes LnL3 (Ln = Sm, Eu, Tb, Dy, Tm, Yb, Lu) with aromatic o-phosphorylated ligands (HL(1) and HL(2)) have been synthesized and identified. Their molecular structure was proposed on the basis of a new complex approach, including DFT calculations, Sparkle/PM3 modelling, EXAFS spectroscopy and luminescent probing. The photophysical properties of all of the complexes were investigated in detail to obtain a deeper insight into the energy transfer processes.

Structure-property relationships in semicrystalline copolymers and ionomers

NASA Astrophysics Data System (ADS)

Wakabayashi, Katsuyuki

Many outstanding physical properties of ethylene/(meth)acrylic acid (E/(M)AA) copolymers and ionomers are associated with their nanometer-scale morphology, which consists of ethylene crystallites, amorphous segments, and acid/ionic functional groups. The goal of this dissertation is a fundamental understanding of the interplay between these structural motifs and the consequent effects on the material properties. We identify small-strain modulus as a key mechanical property and investigate its dependence upon material structure through X-ray scattering, calorimetry, and mechanical property measurements. We first treat E/(M)AA copolymers as composites of polyethylene crystallites and amorphous regions, and establish a quantitative combining rule to describe the copolymer modulus. At temperatures above the Tg of the copolymers, a monotonic increase in modulus with crystallinity is quantitatively described by the Davies equation for two-phase composites, which serves as the basis for separating the effects of amorphous and crystalline phases throughout this dissertation. The room-temperature modulus of E/(M)AA copolymers is concurrently affected by ethylene crystallinity and proximity to the amorphous phase Tg, which rises through room temperature with increasing comonomer content. In E/(M)AA ionomers, phase separation and aggregation of ionic groups provide additional stiffness and toughness. Ionomers are modeled as composites of crystallites and ionically crosslinked rubber, whose amorphous phase modulus far above the ionomer Tg is satisfactorily described by simple rubber elasticity theory. Thermomechanical analyses probe the multi-step relaxation behavior of E/(M)AA ionomers and lead to the development of a new semicrystalline ionomer morphological model, wherein secondary crystallites and ionic aggregates together form rigid percolated pathways throughout the amorphous phase. Metal soaps are oligomeric analogs of E/(M)AA ionomers, which can be blended into

Mesh electronics: a new paradigm for tissue-like brain probes.

PubMed

Hong, Guosong; Yang, Xiao; Zhou, Tao; Lieber, Charles M

2018-06-01

Existing implantable neurotechnologies for understanding the brain and treating neurological diseases have intrinsic properties that have limited their capability to achieve chronically-stable brain interfaces with single-neuron spatiotemporal resolution. These limitations reflect what has been dichotomy between the structure and mechanical properties of living brain tissue and non-living neural probes. To bridge the gap between neural and electronic networks, we have introduced the new concept of mesh electronics probes designed with structural and mechanical properties such that the implant begins to 'look and behave' like neural tissue. Syringe-implanted mesh electronics have led to the realization of probes that are neuro-attractive and free of the chronic immune response, as well as capable of stable long-term mapping and modulation of brain activity at the single-neuron level. This review provides a historical overview of a 10-year development of mesh electronics by highlighting the tissue-like design, syringe-assisted delivery, seamless neural tissue integration, and single-neuron level chronic recording stability of mesh electronics. We also offer insights on unique near-term opportunities and future directions for neuroscience and neurology that now are available or expected for mesh electronics neurotechnologies. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

The electronic properties of high (Tc) superconductors probed by positron annihilation

NASA Astrophysics Data System (ADS)

Sundar, C. S.; Bharathi, A.; Jean, Y. C.; Hinks, D. G.; Dabrowski, B.; Zheng, Y.; Mitchell, A. W.; Ho, J. C.; Howell, K. H.; Wachs, A. L.

1989-06-01

The discovery of superconductivity at 30 K in Ba(.6)K(.4) BiO3 has generated considerable excitement in view of the contrasting properties of the Ba-K-Bi-O system when compared to the well known Cu-O based high temperature superconductors. Positron annihilation spectroscopy, which is a sensitive local probe of the electronic and defect properties of a solid, was extensively applied in the study of Cu-O based superconductors. The results of positron lifetime as a function of temperature in Ba-K-Bi-O are presented and compared with the known results in the cuprate superconductors. Plausible reasons for the observed temperature dependence of positron lifetime are presented.

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. © 2015 American Society of Plant Biologists. All Rights Reserved.

Evaluating Protein Structure and Dynamics Using Co-Solvents, Photochemical Triggers, and Site-Specific Spectroscopic Probes

NASA Astrophysics Data System (ADS)

Abaskharon, Rachel M.

As ubiquitous and diverse biopolymers, proteins are dynamic molecules that are constantly engaging in inter- and intramolecular interactions responsible for their structure, fold, and function. Because of this, gaining a comprehensive understanding of the factors that control protein conformation and dynamics remains elusive as current experimental techniques often lack the ability to initiate and probe a specific interaction or conformational transition. For this reason, this thesis aims to develop methods to control and monitor protein conformations, conformational transitions, and dynamics in a site-specific manner, as well as to understand how specific and non-specific interactions affect the protein folding energy landscape. First, by using the co-solvent, trifluoroethanol (TFE), we show that the rate at which a peptide folds can be greatly impacted and thus controlled by the excluded volume effect. Secondly, we demonstrate the utility of several light-responsive molecules and reactions as methods to manipulate and investigate protein-folding processes. Using an azobenzene linker as a photo-initiator, we are able to increase the folding rate of a protein system by an order of magnitude by channeling a sub-population through a parallel, faster folding pathway. Additionally, we utilize a tryptophan-mediated electron transfer process to a nearby disulfide bond to strategically unfold a protein molecule with ultraviolet light. We also demonstrate the potential of two ruthenium polypyridyl complexes as ultrafast phototriggers of protein reactions. Finally, we develop several site-specific spectroscopic probes of protein structure and environment. Specifically, we demonstrate that a 13C-labeled aspartic acid residue constitutes a useful site-specific infrared probe for investigating salt-bridges and hydration dynamics of proteins, particularly in proteins containing several acidic amino acids. We also show that a proline-derivative, 4-oxoproline, possesses novel

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

DOE PAGES

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

2016-07-11

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

Probing the Unique Role of Gallium in Amorphous Oxide Semiconductors through Structure-Property Relationships

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

Moffitt, Stephanie L.; Zhu, Qimin; Ma, Qing

This study explores the unique role of Ga in amorphous (a-) In[BOND]Ga[BOND]O oxide semiconductors through combined theory and experiment. It reveals substitutional effects that have not previously been attributed to Ga, and that are investigated by examining how Ga influences structure–property relationships in a series of pulsed laser deposited a-In[BOND]Ga[BOND]O thin films. Element-specific structural studies (X-ray absorption and anomalous scattering) show good agreement with the results of ab initio molecular dynamics simulations. This structural knowledge is used to understand the results of air-annealing and Hall effect electrical measurements. The crystallization temperature of a-IO is shown to increase by as muchmore » as 325 °C on substituting Ga for In. This increased thermal stability is understood on the basis of the large changes in local structure that Ga undergoes, as compared to In, during crystallization. Hall measurements reveal an initial sharp drop in both carrier concentration and mobility with increasing Ga incorporation, which moderates at >20 at% Ga content. This decline in both the carrier concentration and mobility with increasing Ga is attributed to dilution of the charge-carrying In[BOND]O matrix and to increased structural disorder. The latter effect saturates at high at% Ga.« less

A Guide to Design Functional Molecular Liquids with Tailorable Properties using Pyrene-Fluorescence as a Probe.

PubMed

Lu, Fengniu; Takaya, Tomohisa; Iwata, Koichi; Kawamura, Izuru; Saeki, Akinori; Ishii, Masashi; Nagura, Kazuhiko; Nakanishi, Takashi

2017-06-13

Solvent-free, nonvolatile, room-temperature alkylated-π functional molecular liquids (FMLs) are rapidly emerging as a new generation of fluid matter. However, precision design to tune their physicochemical properties remains a serious challenge because the properties are governed by subtle π-π interactions among functional π-units, which are very hard to control and characterize. Herein, we address the issue by probing π-π interactions with highly sensitive pyrene-fluorescence. A series of alkylated pyrene FMLs were synthesized. The photophysical properties were artfully engineered with rational modulation of the number, length, and substituent motif of alkyl chains attached to the pyrene unit. The different emission from the excimer to uncommon intermediate to the monomer scaled the pyrene-pyrene interactions in a clear trend, from stronger to weaker to negligible. Synchronously, the physical nature of these FMLs was regulated from inhomogeneous to isotropic. The inhomogeneity, unexplored before, was thoroughly investigated by ultrafast time-resolved spectroscopy techniques. The result provides a clearer image of liquid matter. Our methodology demonstrates a potential to unambiguously determine local molecular organizations of amorphous materials, which cannot be achieved by conventional structural analysis. Therefore this study provides a guide to design alkylated-π FMLs with tailorable physicochemical properties.

Atomic structure and electronic properties of MgO grain boundaries in tunnelling magnetoresistive devices

PubMed Central

Bean, Jonathan J.; Saito, Mitsuhiro; Fukami, Shunsuke; Sato, Hideo; Ikeda, Shoji; Ohno, Hideo; Ikuhara, Yuichi; McKenna, Keith P.

2017-01-01

Polycrystalline metal oxides find diverse applications in areas such as nanoelectronics, photovoltaics and catalysis. Although grain boundary defects are ubiquitous their structure and electronic properties are very poorly understood since it is extremely challenging to probe the structure of buried interfaces directly. In this paper we combine novel plan-view high-resolution transmission electron microscopy and first principles calculations to provide atomic level understanding of the structure and properties of grain boundaries in the barrier layer of a magnetic tunnel junction. We show that the highly [001] textured MgO films contain numerous tilt grain boundaries. First principles calculations reveal how these grain boundaries are associated with locally reduced band gaps (by up to 3 eV). Using a simple model we show how shunting a proportion of the tunnelling current through grain boundaries imposes limits on the maximum magnetoresistance that can be achieved in devices. PMID:28374755

Molecular Modeling of a Probe in 2D IR Spectroscopy

NASA Astrophysics Data System (ADS)

Cooper, Anthony; Larini, Luca

Proteins must adopt a precise three dimensional structure in the folding process in order to perform its designated function. Although much has been learned about folding, there are still many details in structural dynamics that are difficult to characterize by existing experimental techniques. In order to overcome these challenges, novel infrared and fluorescent spectroscopic techniques have recently been employed to probe the molecular structure at the atomistic scale. These techniques rely on the spectroscopic properties of the nitrile group attached to a phenylalanine. In this study, we model this probe and we compute its properties in different solvents. This is done by performing Molecular Dynamics simulations with a PheCN solvated in water, urea and TMAO. We measure the decay rate of the vibrational stretching of the CN group in order to characterize the effects of different solvents on the local structure of the molecule. This data can be used to identify non-trivial conformational changes of the protein in the folding process. Preliminary results show agreement with current experimental data on 2D IR spectroscopy.

Studying the Structure and Dynamics of Biomolecules by Using Soluble Paramagnetic Probes

PubMed Central

Hocking, Henry G; Zangger, Klaus; Madl, Tobias

2013-01-01

Characterisation of the structure and dynamics of large biomolecules and biomolecular complexes by NMR spectroscopy is hampered by increasing overlap and severe broadening of NMR signals. As a consequence, the number of available NMR spectroscopy data is often sparse and new approaches to provide complementary NMR spectroscopy data are needed. Paramagnetic relaxation enhancements (PREs) obtained from inert and soluble paramagnetic probes (solvent PREs) provide detailed quantitative information about the solvent accessibility of NMR-active nuclei. Solvent PREs can be easily measured without modification of the biomolecule; are sensitive to molecular structure and dynamics; and are therefore becoming increasingly powerful for the study of biomolecules, such as proteins, nucleic acids, ligands and their complexes in solution. In this Minireview, we give an overview of the available solvent PRE probes and discuss their applications for structural and dynamic characterisation of biomolecules and biomolecular complexes. PMID:23836693

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.

Dynamic characterization of small fibers based on the flexural vibrations of a piezoelectric cantilever probe

NASA Astrophysics Data System (ADS)

Zhang, Xiaofei; Ye, Xuan; Li, Xide

2016-08-01

In this paper, we present a cantilever-probe system excited by a piezoelectric actuator, and use it to measure the dynamic mechanical properties of a micro- and nanoscale fiber. Coupling the fiber to the free end of the cantilever probe, we found the dynamic stiffness and damping coefficient of the fiber from the resonance frequency and the quality factor of the fiber-cantilever-probe system. The properties of Bacillus subtilis fibers measured using our proposed system agreed with tensile measurements, validating our method. Our measurements show that the piezoelectric actuator coupled to cantilever probe can be made equivalent to a clamped cantilever with an effective length, and calculated results show that the errors of measured natural frequency of the system can be ignored if the coupled fiber has an inclination angle of alignment of less than 10°. A sensitivity analysis indicates that the first or second resonant mode is the sensitive mode to test the sample’s dynamic stiffness, while the damping property has different sensitivities for the first four modes. Our theoretical analysis demonstrates that the double-cantilever probe is also an effective sensitive structure that can be used to perform dynamic loading and characterize dynamic response. Our method has the advantage of using amplitude-frequency curves to obtain the dynamic mechanical properties without directly measuring displacements and forces as in tensile tests, and it also avoids the effects of the complex surface structure and deformation presenting in contact resonance method. Our method is effective for measuring the dynamic mechanical properties of fiber-like one-dimensional (1D) materials.

Probing Protein Structure in Vivo with FRET

PubMed Central

Davis, Trisha; Muller, Eric

2012-01-01

Fluorescence resonance energy transfer (FRET) is widely used to construct probes for cellular activities and to complement two-hybrid results that predict protein-protein interactions. The Yeast Resource Center promotes an underutilized potential of FRET as an in vivo tool to position proteins within low resolution structures derived from electron microscopy. The success of this approach using widefield microscopy depends upon the choice of filter sets, standardized image acquisition, a robust metric and controls matched to the structure under investigation. A comparison of various CFP and YFP filter combinations from Chroma and Semrock demonstrated the strength of the Chroma filters when coupled with our FRET metric, termed FretR. Coupling CFP and YFP to a selection of proteins of known structure allowed us to create a standard curve of FretR versus distance. How well other FRET metrics conform was also evaluated. Finally FretR was linked to an approximation of the efficiency of energy transfer. Together this feature set has allowed us to contribute to our understanding of the organization of the yeast spindle pole body, cohesin complex and gamma-tubulin complex.

FRET study of G-quadruplex forming fluorescent oligonucleotide probes at the lipid monolayer interface.

PubMed

Swiatkowska, Angelika; Kosman, Joanna; Juskowiak, Bernard

2016-01-05

Spectral properties and G-quadruplex folding ability of fluorescent oligonucleotide probes at the cationic dioctadecyldimethylammonium bromide (DODAB) monolayer interface are reported. Two oligonucleotides, a 19-mer bearing thrombin binding aptamer sequence and a 21-mer with human telomeric sequence, were end-labeled with fluorescent groups (FAM and TAMRA) to give FRET probes F19T and F21T, respectively. The probes exhibited abilities to fold into a quadruplex structure and to bind metal cations (Na(+) and K(+)). Fluorescence spectra of G-quadruplex FRET probes at the monolayer interface are reported for the first time. Investigations included film balance measurements (π-A isotherms) and fluorescence spectra recording using a fiber optic accessory interfaced with a spectrofluorimeter. The effect of the presence of DODAB monolayer, metal cations and the surface pressure of monolayer on spectral behavior of FRET probes were examined. Adsorption of probe at the cationic monolayer interface resulted in the FRET signal enhancement even in the absence of metal cations. Variation in the monolayer surface pressure exerted rather modest effect on the spectral properties of probes. The fluorescence energy transfer efficiency of monolayer adsorbed probes increased significantly in the presence of sodium or potassium ion in subphase, which indicated that the probes retained their cation binding properties when adsorbed at the monolayer interface. Copyright © 2015 Elsevier B.V. All rights reserved.

Optical Probing of Low-Pressure Solution Grown GaN Crystal Properties

DTIC Science & Technology

2010-04-01

observed in Mg and Si doped epitaxial films deposited by MBE and MOCVD on freestanding GaN HVPE substrates [23–25]. Considering the purity of the precursors...bands with similar energy positions here reported, a dominant deeper acceptor impurity has been assigned to Zn , a well known deep acceptor in GaN . Room...00-00-2010 to 00-00-2010 4. TITLE AND SUBTITLE Optical probing of low-pressure solution grown GaN crystal properties 5a. CONTRACT NUMBER 5b

Probing the Structural, Electronic, and Magnetic Properties of Ag n V (n = 1-12) Clusters.

PubMed

Xiong, Ran; Die, Dong; Xiao, Lu; Xu, Yong-Gen; Shen, Xu-Ying

2017-12-16

The structural, electronic, and magnetic properties of Ag n V (n = 1-12) clusters have been studied using density functional theory and CALYPSO structure searching method. Geometry optimizations manifest that a vanadium atom in low-energy Ag n V clusters favors the most highly coordinated location. The substitution of one V atom for an Ag atom in Ag n + 1 (n ≥ 5) cluster modifies the lowest energy structure of the host cluster. The infrared spectra, Raman spectra, and photoelectron spectra of Ag n V (n = 1-12) clusters are simulated and can be used to determine the most stable structure in the future. The relative stability, dissociation channel, and chemical activity of the ground states are analyzed through atomic averaged binding energy, dissociation energy, and energy gap. It is found that V atom can improve the stability of the host cluster, Ag 2 excepted. The most possible dissociation channels are Ag n V = Ag + Ag n - 1 V for n = 1 and 4-12 and Ag n V = Ag 2  + Ag n - 2 V for n = 2 and 3. The energy gap of Ag n V cluster with odd n is much smaller than that of Ag n + 1 cluster. Analyses of magnetic property indicate that the total magnetic moment of Ag n V cluster mostly comes from V atom and varies from 1 to 5 μ B . The charge transfer between V and Ag atoms should be responsible for the change of magnetic moment.

Chemical sensing flow probe

DOEpatents

Laguna, George R.; Peter, Frank J.; Butler, Michael A.

1999-01-01

A new chemical probe determines the properties of an analyte using the light absorption of the products of a reagent/analyte reaction. The probe places a small reaction volume in contact with a large analyte volume. Analyte diffuses into the reaction volume. Reagent is selectively supplied to the reaction volume. The light absorption of the reaction in the reaction volume indicates properties of the original analyte. The probe is suitable for repeated use in remote or hostile environments. It does not require physical sampling of the analyte or result in significant regent contamination of the analyte reservoir.

Chemical sensing flow probe

DOEpatents

Laguna, G.R.; Peter, F.J.; Butler, M.A.

1999-02-16

A new chemical probe determines the properties of an analyte using the light absorption of the products of a reagent/analyte reaction. The probe places a small reaction volume in contact with a large analyte volume. Analyte diffuses into the reaction volume. Reagent is selectively supplied to the reaction volume. The light absorption of the reaction in the reaction volume indicates properties of the original analyte. The probe is suitable for repeated use in remote or hostile environments. It does not require physical sampling of the analyte or result in significant regent contamination of the analyte reservoir. 7 figs.

Thermoelectric Properties of the Chemically Doped Ca3Co4O9 System: A Structural Perspective

NASA Astrophysics Data System (ADS)

Wu, Tao; Tyson, Trevor; Wang, Hsin; Li, Qiang

2010-03-01

Cu doped and Y doped [Ca2CoO3][CoO2]1.61 (referred to as Ca3Co4O9) were prepared by solid state reaction. Temperature dependent thermoelectric properties, resistivity (ρ), Seeback coefficient (S) and thermal conductivity (κ), were measured. As seen before, it is found that doping by Cu and Y significantly enhances the thermoelectric properties. In order to understand the origin of these changes in properties in terms of the atomic structure, synchrotron x-ray diffraction and x-ray absorption spectroscopy were applied to probe the change in the average structure and the location of the dopants. The details of the location and coordination of Co and Y in the host lattice and the effect on the figure of merit are discussed. This work is supported by DOE Grant DE-FG02-07ER46402.

Design Mechanism and Property of the Novel Fluorescent Probes for the Identification of Microthrix parvicella In Situ

PubMed Central

Jiao, Xiumei; Fei, Xuening; Li, Songya; Lin, Dayong; Ma, Huaji; Zhang, Baolian

2017-01-01

In this study, two novel fluorescent probes, probe A and probe B were designed, synthesized and characterized, based on Microthrix parvicella (M. parvicella) preferring to utilize long-chain fatty acid (LCFA), for the labeling of M. parvicella in activated sludge. The molecular structure of probe A and probe B include long-chain alkane and LCFA, respectively. The results indicated that probe A and probe B had a large stokes shift of 118 nm and 120 nm and high quantum yield of 0.1043 and 0.1058, respectively, which were significantly helpful for the fluorescent labeling. As probe A was more stable than probe B in activated sludge, and the fluorescence intensity keep stable during 24 h, probe A was more suitable for labeling M. parvicella in situ. In addition, through the Image Pro Plus 6 (IPP 6) analysis, a quantitative relationship was established between sludge volume index (SVI) and integral optical density (IOD) of the labeled M. parvicella in activated sludge samples. The relationship between IOD and SVI conforms to Logistic curve (R2 = 0.94). PMID:28773166

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

NASA Astrophysics Data System (ADS)

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

2017-03-01

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

EDITORIAL: Probing the nanoworld Probing the nanoworld

NASA Astrophysics Data System (ADS)

Miles, Mervyn

2009-10-01

In nanotechnology, it is the unique properties arising from nanometre-scale structures that lead not only to their technological importance but also to a better understanding of the underlying science. Over the last twenty years, material properties at the nanoscale have been dominated by the properties of carbon in the form of the C60 molecule, single- and multi-wall carbon nanotubes, nanodiamonds, and recently graphene. During this period, research published in the journal Nanotechnology has revealed the amazing mechanical properties of such materials as well as their remarkable electronic properties with the promise of new devices. Furthermore, nanoparticles, nanotubes, nanorods, and nanowires from metals and dielectrics have been characterized for their electronic, mechanical, optical, chemical and catalytic properties. Scanning probe microscopy (SPM) has become the main characterization technique and atomic force microscopy (AFM) the most frequently used SPM. Over the past twenty years, SPM techniques that were previously experimental in nature have become routine. At the same time, investigations using AFM continue to yield impressive results that demonstrate the great potential of this powerful imaging tool, particularly in close to physiological conditions. In this special issue a collaboration of researchers in Europe report the use of AFM to provide high-resolution topographical images of individual carbon nanotubes immobilized on various biological membranes, including a nuclear membrane for the first time (Lamprecht C et al 2009 Nanotechnology 20 434001). Other SPM developments such as high-speed AFM appear to be making a transition from specialist laboratories to the mainstream, and perhaps the same may be said for non-contact AFM. Looking to the future, characterisation techniques involving SPM and spectroscopy, such as tip-enhanced Raman spectroscopy, could emerge as everyday methods. In all these advanced techniques, routinely available probes will

Multidetector Scattering as a Probe of Local Structure in Disordered Phases

NASA Astrophysics Data System (ADS)

Clark, Noel A.; Ackerson, Bruce J.; Hurd, Alan J.

1983-05-01

The local translational structure of a two-dimensional colloidal liquid is observed by use of cross correlation of the intensity fluctuations of light scattered by the liquid through two different wave vectors. The utility of multidetector scattering in probing multipoint correlations in disordered phases is thereby demonstrated unambiguously.

Fluorescent water-Soluble Probes Based on Ammonium Cation Peg Substituted Perylenepisimides: Synthesis, Photophysical Properties, and Live Cell Images

NASA Astrophysics Data System (ADS)

Yang, Wei; Cai, Jiaxuan; Zhang, Shuchen; Yi, Xuegang; Gao, Baoxiang

2018-01-01

To synthesize perylenbisimides (PBI) fluorescent probes that will improve the water-soluble ability and the cytocompatibility, the synthesis and properties of fluorescent water-soluble probes based on dendritic ammonium cation polyethylene glycol (PEG) substituted perylenebisimides(GPDIs) are presented. As we expected, with increased ammonium cation PEG, the aggregation of the PBI in an aqueous solution is completely suppressed by the hydrophilic ammonium cation PEG groups. And the fluorescence quantum yield increases from 25% for GPDI-1 to 62% for GPDI-2. When incubated with Hela cells for 48 h, the viabilities are 71% (for GPDI-1) and 76% (for GPDI-2). Live cell imaging shows that these probes are efficiently internalized by HeLa cells. The study of the photophysical properties indicated increasing the ammonium cation PEG generation can increase the fluorescence quantum yield. Live cell imaging shows that with the ammonium cation PEG chains of perylenebisimides has high biocompatibility. The exceptionally low cytotoxicity is ascribed to the ammonium cation PEG chains, which protect the dyes from nonspecifically interacting with the extracellular proteins. Live cell imaging shows that ammonium cations PEG chains can promote the internalization of these probes.

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

Inspecting Friction Stir Welding using Electromagnetic Probes

NASA Technical Reports Server (NTRS)

Kinchen, David G.

2004-01-01

A report describes the use of advanced electromagnetic probes to measure the dimensions, the spatial distribution of electrical conductivity, and related other properties of friction stir welds (FSWs) between parts made of the same or different aluminum alloy(s). The probes are of the type described in in another Tech Brief. To recapitulate: A probe of this type is essentially an eddy-current probe that includes a primary (driver) winding that meanders and multiple secondary (sensing) windings that meander along the primary winding. Electrical conductivity is commonly used as a measure of heat treatment and tempering of aluminum alloys, but prior to the development of these probes, the inadequate sensitivity and limited accuracy of electrical-conductivity probes precluded such use on FSWs between different aluminum alloys, and the resolution of those probes was inadequate for measurement of FSW dimensions with positions and metallurgical properties. In contrast, the present probes afford adequate accuracy and spatial resolution for the purposes of measuring the dimensions of FSW welds and correlating spatially varying electrical conductivities with metallurgical properties, including surface defects.

Structural, electrical and mechanical properties of selenium doped thallium based high-temperature superconductors

NASA Astrophysics Data System (ADS)

Cavdar, S.; Kol, N.; Koralay, H.; Ozturk, O.; Asikuzun, E.; Tasci, A. T.

2016-01-01

In this study, highly-refined chemical powders were synthesized by having them ready in appropriate stoichiometric proportions with conventional solid state reaction method so that they would produce the superconductor TlPb0.3Sr2Ca1-xSexCu2Oy (x = 0; 0.4; 0.6; 1.0). This study aims to understand effect of the selenium doping on the superconducting, structural and mechanical properties of the aforementioned superconducting material. The effect of the doping rates on the structural and electrical properties of the sample has been identified. Electrical characteristics of the TlPb0.3Sr2Ca1-xSexCu2Oy material were measured using standard four point probe method. Structural characteristics were examined with the powder X-ray diffractometer (XRD) and scanning electron microscope (SEM). Mechanical properties were analyzed with Vickers microhardness measurements on the sample surface. According to the results, it was observed that the reflection comes from the (00l) and parallel planes increased with Se doping. Particle size increases with increasing doping ratio. According to results of the mechanical measurements, all samples exhibit indentation size effect (ISE) behavior. Comparing the obtained results with theoretical studies, it was understood that Hays Kendall approach is the best method in determination of mechanical properties and analyzing microhardness of the materials.

Structure design and characteristic analysis of micro-nano probe based on six dimensional micro-force measuring principle

NASA Astrophysics Data System (ADS)

Yang, Hong-tao; Cai, Chun-mei; Fang, Chuan-zhi; Wu, Tian-feng

2013-10-01

In order to develop micro-nano probe having error self-correcting function and good rigidity structure, a new micro-nano probe system was developed based on six-dimensional micro-force measuring principle. The structure and working principle of the probe was introduced in detail. The static nonlinear decoupling method was established with BP neural network to do the static decoupling for the dimension coupling existing in each direction force measurements. The optimal parameters of BP neural network were selected and the decoupling simulation experiments were done. The maximum probe coupling rate after decoupling is 0.039% in X direction, 0.025% in Y direction and 0.027% in Z direction. The static measurement sensitivity of the probe can reach 10.76μɛ / mN in Z direction and 14.55μɛ / mN in X and Y direction. The modal analysis and harmonic response analysis under three dimensional harmonic load of the probe were done by using finite element method. The natural frequencies under different vibration modes were obtained and the working frequency of the probe was determined, which is higher than 10000 Hz . The transient response analysis of the probe was done, which indicates that the response time of the probe can reach 0.4 ms. From the above results, it is shown that the developed micro-nano probe meets triggering requirements of micro-nano probe. Three dimension measuring force can be measured precisely by the developed probe, which can be used to predict and correct the force deformation error and the touch error of the measuring ball and the measuring rod.

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

Probing the hammerhead ribozyme structure with ribonucleases.

PubMed Central

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

1994-01-01

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

Structural properties of oligonucleotide monolayers on gold surfaces probed by fluorescence investigations.

PubMed

Rant, Ulrich; Arinaga, Kenji; Fujita, Shozo; Yokoyama, Naoki; Abstreiter, Gerhard; Tornow, Marc

2004-11-09

We present optical investigations on the conformation of oligonucleotide layers on Au surfaces. Our studies concentrate on the effect of varying surface coverage densities on the structural properties of layers of 12- and 24mer single-stranded DNA, tethered to the Au surface at one end while being labeled with a fluorescent marker at the opposing end. The distance-dependent energy transfer from the marker dye to the metal surface, which causes quenching of the observed fluorescence, is used to provide information on the orientation of the DNA strands relative to the surface. Variations in the oligonucleotide coverage density, as determined from electrochemical quantification, over 2 orders of magnitude are achieved by employing different preparation conditions. The observed enhancement in fluorescence intensity with increasing DNA coverage can be related to a model involving mutual steric interactions of oligonucleotides on the surface, as well as fluorescence quenching theory. Finally, the applicability of the presented concepts for investigations of heterogeneous monolayers is demonstrated by means of studying the coadsorption of mercaptohexanol onto DNA-modified Au surfaces.

Structurally-driven Enhancement of Thermoelectric Properties within Poly(3,4-ethylenedioxythiophene) thin Films

PubMed Central

Petsagkourakis, Ioannis; Pavlopoulou, Eleni; Portale, Giuseppe; Kuropatwa, Bryan A.; Dilhaire, Stefan; Fleury, Guillaume; Hadziioannou, Georges

2016-01-01

Due to the rising need for clean energy, thermoelectricity has raised as a potential alternative to reduce dependence on fossil fuels. Specifically, thermoelectric devices based on polymers could offer an efficient path for near-room temperature energy harvesters. Thus, control over thermoelectric properties of conducting polymers is crucial and, herein, the structural, electrical and thermoelectric properties of poly(3,4-ethylenedioxythiophene) (PEDOT) thin films doped with p-toluenesulfonate (Tos) molecules were investigated with regards to thin film processing. PEDOT:Tos thin films were prepared by in-situ polymerization of (3,4-ethylenedioxythiophene) monomers in presence of iron(III) p-toluenesulfonate with different co-solvents in order to tune the film structure. While the Seebeck coefficient remained constant, a large improvement in the electrical conductivity was observed for thin films processed with high boiling point additives. The increase of electrical conductivity was found to be solely in-plane mobility-driven. Probing the thin film structure by Grazing Incidence Wide Angle X-ray Scattering has shown that this behavior is dictated by the structural properties of the PEDOT:Tos films; specifically by the thin film crystallinity combined to the preferential edge-on orientation of the PEDOT crystallites. Consequentially enhancement of the power factor from 25 to 78.5 μW/mK2 has been readily obtained for PEDOT:Tos thin films following this methodology. PMID:27470637

Structurally-driven Enhancement of Thermoelectric Properties within Poly(3,4-ethylenedioxythiophene) thin Films.

PubMed

Petsagkourakis, Ioannis; Pavlopoulou, Eleni; Portale, Giuseppe; Kuropatwa, Bryan A; Dilhaire, Stefan; Fleury, Guillaume; Hadziioannou, Georges

2016-07-29

Due to the rising need for clean energy, thermoelectricity has raised as a potential alternative to reduce dependence on fossil fuels. Specifically, thermoelectric devices based on polymers could offer an efficient path for near-room temperature energy harvesters. Thus, control over thermoelectric properties of conducting polymers is crucial and, herein, the structural, electrical and thermoelectric properties of poly(3,4-ethylenedioxythiophene) (PEDOT) thin films doped with p-toluenesulfonate (Tos) molecules were investigated with regards to thin film processing. Tos thin films were prepared by in-situ polymerization of (3,4-ethylenedioxythiophene) monomers in presence of iron(III) p-toluenesulfonate with different co-solvents in order to tune the film structure. While the Seebeck coefficient remained constant, a large improvement in the electrical conductivity was observed for thin films processed with high boiling point additives. The increase of electrical conductivity was found to be solely in-plane mobility-driven. Probing the thin film structure by Grazing Incidence Wide Angle X-ray Scattering has shown that this behavior is dictated by the structural properties of the Tos films; specifically by the thin film crystallinity combined to the preferential edge-on orientation of the PEDOT crystallites. Consequentially enhancement of the power factor from 25 to 78.5 μW/mK(2) has been readily obtained for Tos thin films following this methodology.

The solar probe and coronal dynamics

NASA Technical Reports Server (NTRS)

Belcher, J.; Heinemann, M.; Goodrich, C.

1978-01-01

The discovery of coronal holes led to basic changes in ideas about the structure of the low corona and its expansion into the solar wind. The nature of the energy flux is not understood. Current ideas include enhanced thermal conductivities, extended MHD wave heating, and wave momentum transfer, all in rapidly diverging geometries. There is little feel for the relative importance of these processes. The Solar Probe, with its penetration deep into the solar corona, could lead to observational constraints on their relative importance, and thus to an understanding of the origin of the solar wind. Observations from the Solar Probe will also bear on such questions as to whether small scale "intrastream" structure is common close to the Sun in open field-line regions, whether the properties of the wind are pronouncedly different over closed and open field-line regions at five solar radii, and many others. The resolution of these questions requires measurements of the magnetic field and of the proton and electron distribution functions.

Design and preparation of quantum dots fluorescent probes for in situ identification of Microthrix parvicella in bulking sludge.

PubMed

Fei, Xuening; Sun, Wenke; Cao, Lingyun; Jiao, Xiumei; Lin, Dayong; Jia, Guozhi

2016-01-01

A series of quantum dots (QDs) fluorescent probes for the in situ identification of Microthrix parvicella (M. parvicella) in bulking sludge were designed and prepared. In the preparation of CdTe/CdS QDs, the 11-mercaptoundecanoic acid (11-acid) and 16-mercaptohexadecanoic acid (16-acid) were used as the stabilizer. The prepared QDs probes were characterized by Fourier transform infrared (FT-IR), X-ray diffraction (XRD), and transmission electron microscopy (TEM), and the results showed that the CdTe/CdS QDs formed a core-shell structure and the long carbon chain was successfully grafted onto its surface. And the three QDs probes had different crystallinity and particle size, which was due to the inhibition effect of long carbon chain. The optical properties test results showed that although the formed core-shell structure and long carbon chain affected the fluorescent intensity, adsorption, and emission spectra of the QDs probes, the probes B and C had a large stokes-shift of 82 and 101 nm, which was a benefit for their fluorescent labeling property. In the fluorescent identification of M. parvicella, the probes B and C effectively adsorbed onto the surface of M. parvicella through a hydrophobic bond, and then identified M. parvicella by their unique fluorescence. In addition, it was found that a better hydrophobic property resulted in better identification efficiency.

Outer planet atmospheric entry probes - An overview of technology readiness

NASA Technical Reports Server (NTRS)

Vojvodich, N. S.; Reynolds, R. T.; Grant, T. L.; Nachtsheim, P. R.

1975-01-01

Entry probe systems for characterizing, by in situ measurements, the atmospheric properties, chemical composition, and cloud structure of the planets Saturn, Uranus, and Jupiter are examined from the standpoint of unique mission requirements, associated subsystem performance, and degree of commonality of design. Past earth entry vehicles (PAET) and current planetary spacecraft (Pioneer Venus probes and Viking lander) are assessed to identify the extent of potential subsystem inheritance, as well as to establish the significant differences, in both form and function, relative to outer planet requirements. Recent research results are presented and reviewed for the most critical probe technology areas, including: science accommodation, telecommunication, and entry heating and thermal protection. Finally presented is a brief discussion of the use of decision analysis techniques for quantifying various probe heat-shield test alternatives and performance risk.

Rarefaction effects on Galileo probe aerodynamics

NASA Technical Reports Server (NTRS)

Moss, James N.; LeBeau, Gerald J.; Blanchard, Robert C.; Price, Joseph M.

1996-01-01

Solutions of aerodynamic characteristics are presented for the Galileo Probe entering Jupiter's hydrogen-helium atmosphere at a nominal relative velocity of 47.4 km/s. Focus is on predicting the aerodynamic drag coefficient during the transitional flow regime using the direct simulation Monte Carlo (DSMC) method. Accuracy of the probe's drag coefficient directly impacts the inferred atmospheric properties that are being extracted from the deceleration measurements made by onboard accelerometers as part of the Atmospheric Structure Experiment. The range of rarefaction considered in the present study extends from the free molecular limit to continuum conditions. Comparisons made with previous calculations and experimental measurements show the present results for drag to merge well with Navier-Stokes and experimental results for the least rarefied conditions considered.

Characterization of structural and electrostatic complexity in pentacene thin films by scanning probe microscopy

NASA Astrophysics Data System (ADS)

Puntambekar, Kanan Prakash

The advancement of organic electronics for applications in solar energy conversion, printed circuitry, displays, and solid-state lighting depends upon optimization of structure and properties for a variety of organic semiconductor interfaces. Organic semiconductor/insulator (O/I) and organic-metal (O/M) interfaces, in particular, are critical to the operation of organic thin film transistors (OTFTs) currently being developed for printed flexible electronics. Scanning probe microscopy (SPM) is a powerful tool to isolate and characterize the bottlenecks to charge transport at these interfaces. This thesis establishes a direct correlation between the structural disorder and electrical complexity at these interfaces, using various SPM based methods and discusses the implications of such complexity on device performance. To examine the O/M interfaces, surface potentials of operating pentacene TFTs with two different contact geometries (bottom or top) were mapped by Kelvin probe force microscopy (KFM). The surface potential distribution was used to isolate the potential drops at the source and drain contacts. Simultaneously obtained topography and surface potential maps elucidated the correlation between the morphology and contact resistance at the O/M interface; the bottom contact TFTs were observed to be contact limited at large gate voltages, while the top contact TFTs were not contact limited. A direct correlation between structural defects and electric potential variations at the pentacene and silicon dioxide, a common insulator, is demonstrated. Lateral force microscopy (LFM) generates striking images of the polycrystalline microstructure of a monolayer thick pentacene film, allowing clear visualization of the grain boundary network. Further more, surface potential wells localized at the grain boundaries were observed by KFM, suggesting that the grain boundaries may serve as charge carrier (hole) traps. Line dislocations were also revealed in the second monolayer

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.

Estimating the similarity of alternative Affymetrix probe sets using transcriptional networks

PubMed Central

2013-01-01

Background The usefulness of the data from Affymetrix microarray analysis depends largely on the reliability of the files describing the correspondence between probe sets, genes and transcripts. Particularly, when a gene is targeted by several probe sets, these files should give information about the similarity of each alternative probe set pair. Transcriptional networks integrate the multiple correlations that exist between all probe sets and supply much more information than a simple correlation coefficient calculated for two series of signals. In this study, we used the PSAWN (Probe Set Assignment With Networks) programme we developed to investigate whether similarity of alternative probe sets resulted in some specific properties. Findings PSAWNpy delivered a full textual description of each probe set and information on the number and properties of secondary targets. PSAWNml calculated the similarity of each alternative probe set pair and allowed finding relationships between similarity and localisation of probes in common transcripts or exons. Similar alternative probe sets had very low negative correlation, high positive correlation and similar neighbourhood overlap. Using these properties, we devised a test that allowed grouping similar probe sets in a given network. By considering several networks, additional information concerning the similarity reproducibility was obtained, which allowed defining the actual similarity of alternative probe set pairs. In particular, we calculated the common localisation of probes in exons and in known transcripts and we showed that similarity was correctly correlated with them. The information collected on all pairs of alternative probe sets in the most popular 3’ IVT Affymetrix chips is available in tabular form at http://bns.crbm.cnrs.fr/download.html. Conclusions These processed data can be used to obtain a finer interpretation when comparing microarray data between biological conditions. They are particularly well

Synthesis and photonic property study of ZnO nanowires for a real time photodynamic therapy monitoring probe

NASA Astrophysics Data System (ADS)

Sridhar, D.; Xie, Jining; Abraham, Jose K.; Varadan, Vijay K.

2007-04-01

In this paper, we present how the photonic properties of zinc oxide (ZnO) nanowires can be used to potentially advance the effectiveness of Photodynamic therapy (PDT), one of the most recent and promising approaches among cancer therapies. Presently, PDT employs laser light to activate intravenously or topically administered photosensitizers to give rise to highly reactive singlet oxygen which has a very short lifetime and is capable of biochemical damage to cell membranes of the tumor. A probe that can monitor in real time the penetration depth of the laser in the tumor and also the evolution of the singlet oxygen, which is critical for tumor eradication, is capable of improving the efficacy of PDT quite significantly. Such a probe, by providing real time feedback, can help us determine whether to increase or decrease the light exposure dose and also if further local administration of photosensitizers is required or not. ZnO nanowires are known to be photoconductive and recent research also demonstrated the temperature dependence of the photocurrent in the nanowires. They are also sensitive to blue and other near UV spectra which is same range of activation wavelengths of most photosensitizers, and hence making them a good candidate for a potential PDT monitoring probe. ZnO nanowires were fabricated on silicon substrates by vapor phase deposition using e-beam evaporated gold as a catalyst. Control of the dimensions of the nanowires could be achieved by varying the dimensions of the catalyst by means of e-beam evaporation process. Photoluminescence properties of ZnO nanowires were investigated at UV and near UV wavelengths. Further, ZnO is also known for its antimicrobial properties, thereby ruling out any possibility of bacterial infection because of the implanted probe. This study was done to compliment the existing expertise of our research group in the design and fabrication of several nanowire based probes and microsensors specifically for neuroelectronic and

Robot friendly probe and socket assembly

NASA Technical Reports Server (NTRS)

Nyberg, Karen L. (Inventor)

1994-01-01

A probe and socket assembly for serving as a mechanical interface between structures is presented. The assembly comprises a socket having a housing adapted for connection to a first supporting structure and a probe which is readily connectable to a second structure and is designed to be easily grappled and manipulated by a robotic device for insertion and coupling with the socket. Cooperable automatic locking means are provided on the probe shaft and socket housing for automatically locking the probe in the socket when the probe is inserted a predetermined distance. A second cooperable locking means on the probe shaft and housing are adapted for actuation after the probe has been inserted the predetermined distance. Actuation means mounted on the probe and responsive to the grip of the probe handle by a gripping device, such as a robot for conditioning the probe for insertion and are also responsive to release of the grip of the probe handle to actuate the second locking means to provide a hard lock of the probe in the socket.

Diffusion of uncharged probe reveals structural changes in polyacids initiated by their neutralization: poly(acrylic acids).

PubMed

Hyk, Wojciech; Masiak, Michal; Stojek, Zbigniew; Ciszkowska, Malgorzata

2005-03-17

The diffusion studies of the uncharged probe (1,1'-ferrocenedimethanol) have been successfully applied for the evaluation of the changes in the three-dimensional structure of poly(acrylic acids) of various molecular weights (ranging from 2000 to 4,000,000 g/mol) during their neutralization with a strong base. The qualitative picture of the macromolecule arrangement during the titration of the polyacids has been obtained from the conductometric measurements. The characteristic changes in the poly(acrylic acid) conductivity are practically the same for all polyacids examined and are in a very good agreement with the predictions of our theoretical model of the polyelectrolyte conductance. The transformation of the polyelectrolyte solution into the gel-like or gel phase has been investigated more quantitatively by tracing the changes in the diffusion coefficient of the uncharged probe redox system. The probe diffusivities, D, were determined using steady-state voltammetry at microelectrodes for a wide range of neutralization degree, alpha, of the polyacids tested. The dependencies of D versus alpha are of similar shape for all poly(acrylic acids). The first parts of the dependencies reflect a rapid increase in D (up to neutralization degree of either 45% for the lowest molecular-weight poly(acrylic acid) or 75-80% for other polyacids). They are followed by the parts of a slight drop in the diffusion coefficient. The changes in the probe diffusivity become stronger as the molecular weight of poly(acrylic acid) increases. The maximum probe diffusion coefficients are greater than the initial values in the pure polyacid solutions by 14, 24, 19, 30, and 28% for poly(acrylic acid) of molecular weights of 2000, 450,000, 1,250,000, 3,000,000, and 4,000,000 g/mol, respectively. The variation in the probe diffusion coefficient qualitatively follows the line of the changes in the macroscopic viscosity of the polyelectrolyte system. This is in contrast to the predictions of the

Transmission X-ray scattering as a probe for complex liquid-surface structures

DOE PAGES

Fukuto, Masafumi; Yang, Lin; Nykypanchuk, Dmytro; ...

2016-01-28

The need for functional materials calls for increasing complexity in self-assembly systems. As a result, the ability to probe both local structure and heterogeneities, such as phase-coexistence and domain morphologies, has become increasingly important to controlling self-assembly processes, including those at liquid surfaces. The traditional X-ray scattering methods for liquid surfaces, such as specular reflectivity and grazing-incidence diffraction, are not well suited to spatially resolving lateral heterogeneities due to large illuminated footprint. A possible alternative approach is to use scanning transmission X-ray scattering to simultaneously probe local intermolecular structures and heterogeneous domain morphologies on liquid surfaces. To test the feasibilitymore » of this approach, transmission small- and wide-angle X-ray scattering (TSAXS/TWAXS) studies of Langmuir films formed on water meniscus against a vertically immersed hydrophilic Si substrate were recently carried out. First-order diffraction rings were observed in TSAXS patterns from a monolayer of hexagonally packed gold nanoparticles and in TWAXS patterns from a monolayer of fluorinated fatty acids, both as a Langmuir monolayer on water meniscus and as a Langmuir–Blodgett monolayer on the substrate. The patterns taken at multiple spots have been analyzed to extract the shape of the meniscus surface and the ordered-monolayer coverage as a function of spot position. These results, together with continual improvement in the brightness and spot size of X-ray beams available at synchrotron facilities, support the possibility of using scanning-probe TSAXS/TWAXS to characterize heterogeneous structures at liquid surfaces.« less

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.

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.

Mechanisms of Probe Tack Adhesion of Model Acrylic Elastomers

NASA Astrophysics Data System (ADS)

Lakrout, Hamed; Creton, Costantino; Ahn, Dongchan; Shull, Kenneth R.

1997-03-01

The adhesion mechanisms of model acrylate homopolymers and copolymers are studied with an instrumented probe tack test. A video camera positioned under the transparent glass substrate records the bonding and debonding process while the force displacement curve is acquired. This setup allows to couple the observation of the cavitation and fibrillation mechanisms, occurring during the debonding of the film from the stainless steel probe, with the mechanical measurement of stress and strain. The transitions between different debonding mechanisms are critically dicussed in terms of the bulk and surface properties of the adhesive and its molecular structure.

Iron phosphate glasses: Bulk properties and atomic scale structure

NASA Astrophysics Data System (ADS)

Joseph, Kitheri; Stennett, Martin C.; Hyatt, Neil C.; Asuvathraman, R.; Dube, Charu L.; Gandy, Amy S.; Govindan Kutty, K. V.; Jolley, Kenny; Vasudeva Rao, P. R.; Smith, Roger

2017-10-01

Bulk properties such as glass transition temperature, density and thermal expansion of iron phosphate glass compositions, with replacement of Cs by Ba, are investigated as a surrogate for the transmutation of 137Cs to 137Ba, relevant to the immobilisation of Cs in glass. These studies are required to establish the appropriate incorporation rate of 137Cs in iron phosphate glass. Density and glass transition temperature increases with the addition of BaO indicating the shrinkage and reticulation of the iron phosphate glass network. The average thermal expansion coefficient reduces from 19.8 × 10-6 K-1 to 13.4 × 10-6 K-1, when 25 wt. % of Cs2O was replaced by 25 wt. % of BaO in caesium loaded iron phosphate glass. In addition to the above bulk properties, the role of Ba as a network modifier in the structure of iron phosphate glass is examined using various spectroscopic techniques. The FeII content and average coordination number of iron in the glass network was estimated using Mössbauer spectroscopy. The FeII content in the un-doped iron phosphate glass and barium doped iron phosphate glasses was 20, 21 and 22 ± 1% respectively and the average Fe coordination varied from 5.3 ± 0.2 to 5.7 ± 0.2 with increasing Ba content. The atomic scale structure was further probed by Fe K-edge X-ray absorption spectroscopy. The average coordination number provided by extended X-ray absorption fine structure spectroscopy and X-ray absorption near edge structure was in good agreement with that given by the Mössbauer data.

Self-force as probe of internal structure

NASA Astrophysics Data System (ADS)

Isoyama, Soichiro; Poisson, Eric

2012-08-01

The self-force acting on a (scalar or electric) charge held in place outside a massive body contains information about the body’s composition, and can therefore be used as a probe of internal structure. We explore this theme by computing the (scalar or electromagnetic) self-force when the body is a spherical ball of perfect fluid in hydrostatic equilibrium, under the assumption that its rest-mass density and pressure are related by a polytropic equation of state. The body is strongly self-gravitating, and all computations are performed in exact general relativity. The dependence on internal structure is best revealed by expanding the self-force in powers of r-10, with r0 denoting the radial position of the charge outside the body. To the leading order, the self-force scales as r-30 and depends only on the square of the charge and the body’s mass; the leading self-force is universal. The dependence on internal structure is seen at the next order, r-50, through a structure factor that depends on the equation of state. We compute this structure factor for relativistic polytropes, and show that for a fixed mass, it increases linearly with the body’s radius in the case of the scalar self-force, and quadratically with the body’s radius in the case of the electromagnetic self-force. In both cases we find that for a fixed mass and radius, the self-force is smaller if the body is more centrally dense, and larger if the mass density is more uniformly distributed.

Probing Chemical Properties of Interstitial Micro-fluids in Ice

NASA Astrophysics Data System (ADS)

Cheng, J.; Colussi, A. J.; Hoffmann, M. R.

2007-12-01

Liquid is present as microscopic channels in polycrystalline ice at sub-freezing and even sub-eutectic temperatures. Not only do chemicals tend to concentrate substantially in this microscopic liquid phase, but local physicochemical properties may also differ widely from the bulk counterparts, therefore critically affecting the thermodynamics and kinetics of chemical processes occurring in frozen media such as snow, frost, and frost- flowers. This phenomenon has important implications in atmospheric chemistry such as affecting the composition of the atmospheric boundary layer in snow-covered regions. A method using con-focal laser scanning microscope equipped with a cryostat has been developed to measure physicochemical properties of the microscopic liquid phase in ice that are not readily extrapolated from the bulk data. The experimental setup allows for monitoring the freezing process of an aqueous solution with a sub- second time resolution and a submicron 3D spatial resolution. The physicochemical properties (e.g. viscosity, polarity, and acidity) can, in theory, be deduced from features of the fluorescence spectra of particular fluorescent indicators. For example, the acidity change during the freezing and melting process of electrolyte solutions has been monitored in real time by a pH-dependent dual emission fluorescent probe C-SNARF-1. The effects of temperature, freezing rate, and added electrolytes such as ammonium sulfate, sodium chloride and zwitterions are also examined. The findings complement the theory and previous experimental evidence of freezing hydrolysis.

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

Understanding of Jupiter's Atmosphere after the Galileo Probe Entry

NASA Technical Reports Server (NTRS)

Fonda, Mark (Technical Monitor); Young, Richard E.

2003-01-01

Instruments on the Galileo probe measured composition, cloud properties, thermal structure, winds, radiative energy balance, and electrical properties of the Jovian atmosphere. As expected the probe results confirm some expectations about Jupiter's atmosphere, refute others, and raise new questions which still remain unanswered. This talk will concentrate on those aspects of the probe observations which either raised new questions or remain unresolved. The Galileo probe observations of composition and clouds provided some of the biggest surprises of the mission. Helium abundance measured by the probe differed significantly from the remote sensing derivations from Voyager. Discrepancy between the Voyager helium abundance determinations for Jupiter and the Galileo probe value have now led to a considerably increased helium determination for Saturn. Global abundance of N in the form of ammonia was observed to be super-solar by approximately the same factor as carbon, in contrast to expectations that C/N would be significantly larger than solar. This has implications for the formation and evolution of Jupiter. The cloud structure was not what was generally anticipated, even though most previous remote sensing results below the uppermost cloud referred to 5 micron hot spots, local regions with reduced cloud opacity. The Galileo probe descended in one of these hot spots. Only a tenuous, presumed ammomium hydrosulfide, cloud was detected, and no significant water cloud or super-solar water abundance was measured. The mixing ratios as a function of depth for the condensibles ammonia, hydrogen sulfide, and water, exhibited no apparent correlation with either condensation levels or with each other, an observation that is still a puzzle, although there are now dynamical models of hot spots which show promise in being able to explain such behavior. Probe tracked zonal winds show that wind magnitude increases with depth to pressures of about 4 bars, with the winds extending to

Understanding of Jupiter's Atmosphere After the Galileo Probe Entry

NASA Technical Reports Server (NTRS)

Young, Richard E.; DeVincenzi, Donald (Technical Monitor)

2001-01-01

Instruments on the Galileo probe measured composition, cloud properties, thermal structure. winds, radiative energy balance, and electrical properties of the Jovian atmosphere. As expected the probe results confirm some expectations about Jupiter's atmosphere, refute others, and raise new questions which still remain unanswered. This talk will concentrate on those aspects of the probe observations which either raised new questions or remain unresolved. The Galileo probe observations of composition and clouds provided some of the biggest surprises of the mission. Helium abundance measured by the probe differed significantly from the remote sensing derivations from Voyager. discrepancy between the Voyager helium abundance determinations for Jupiter and the Galileo probe value have now led to a considerably increased helium determination for Saturn. Global abundance of N in the form of ammonia was observed to be supersolar by approximately the same factor as carbon, in contrast to expectations that C/N would be significantly larger than solar. This has implications for the formation and evolution of Jupiter. The cloud structure was not what was generally anticipated, even though most previous remote sensing results below the uppermost cloud referred to 5 micron hot spots, local regions with reduced cloud opacity. The Galileo probe descended in one of these hot spots. Only a tenuous, presumed ammonium hydrosulfide, cloud was detected, and no significant water cloud or super-solar water abundance was measured. The mixing ratios as a function of depth for the condensibles ammonia, hydrogen sulfide, and water, exhibited no apparent correlation with either condensation levels or with each other, an observation that is still a puzzle, although there are now dynamical models of hot spots which show promise in being able to explain such behavior. Probe tracked zonal winds show that wind magnitude increases with depth to pressures of about 4 bars, with the winds extending to

H II regions as probes of galaxy evolution and the properties of massive stars

NASA Technical Reports Server (NTRS)

Garnett, Donald R.

1993-01-01

The use of H II regions as probes to study the chemical evolution of galaxies and the spectral properties of hot, massive stars is reviewed. The observable parameters for this task are the physical conditions, elemental abundances, and ionization balance in the ionized gas. Some outstanding uncertainties in the determination of these parameters and some approaches to remedy or circumvent the problems are discussed.

Study of Some Planetary Atmospheres Features by Probe Entry and Descent Simulations

NASA Technical Reports Server (NTRS)

Gil, P. J. S.; Rosa, P. M. B.

2005-01-01

Characterization of planetary atmospheres is analyzed by its effects in the entry and descent trajectories of probes. Emphasis is on the most important variables that characterize atmospheres e.g. density profile with altitude. Probe trajectories are numerically determined with ENTRAP, a developing multi-purpose computational tool for entry and descent trajectory simulations capable of taking into account many features and perturbations. Real data from Mars Pathfinder mission is used. The goal is to be able to determine more accurately the atmosphere structure by observing real trajectories and what changes are to expect in probe descent trajectories if atmospheres have different properties than the ones assumed initially.

Use of terbium as a probe of tRNA tertiary structure and folding.

PubMed Central

Hargittai, M R; Musier-Forsyth, K

2000-01-01

Lanthanide metals such as terbium have previously been shown to be useful for mapping metal-binding sites in RNA. Terbium binds to the same sites on RNA as magnesium, however, with a much higher affinity. Thus, low concentrations of terbium ions can easily displace magnesium and promote phosphodiester backbone scission. At higher concentrations, terbium cleaves RNA in a sequence-independent manner, with a preference for single-stranded, non-Watson-Crick base-paired regions. Here, we show that terbium is a sensitive probe of human tRNALys,3 tertiary structure and folding. When 1 microM tRNA is used, the optimal terbium ion concentration for detecting Mg2+-induced tertiary structural changes is 50-60 microM. Using these concentrations of RNA and terbium, a magnesium-dependent folding transition with a midpoint (KMg) of 2.6 mM is observed for unmodified human tRNALys,3. At lower Tb3+ concentrations, cleavage is restricted to nucleotides that constitute specific metal-binding pockets. This small chemical probe should also be useful for detecting protein induced structural changes in RNA. PMID:11105765

Site-Specific Infrared Probes of Proteins

PubMed Central

Ma, Jianqiang; Pazos, Ileana M.; Zhang, Wenkai; Culik, Robert M.; Gai, Feng

2015-01-01

Infrared spectroscopy has played an instrumental role in studying a wide variety of biological questions. However, in many cases it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and/or environmental information in a site-specific manner. To overcome this limitation, many recent efforts have been dedicated to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural and/or environmental properties. In this Review, we highlight some recent advancements of this rapidly growing research area. PMID:25580624

Silver ions-mediated conformational switch: facile design of structure-controllable nucleic acid probes.

PubMed

Wang, Yongxiang; Li, Jishan; Wang, Hao; Jin, Jianyu; Liu, Jinhua; Wang, Kemin; Tan, Weihong; Yang, Ronghua

2010-08-01

Conformationally constraint nucleic acid probes were usually designed by forming an intramolecular duplex based on Watson-Crick hydrogen bonds. The disadvantages of these approaches are the inflexibility and instability in complex environment of the Watson-Crick-based duplex. We report that this hydrogen bonding pattern can be replaced by metal-ligation between specific metal ions and the natural bases. To demonstrate the feasibility of this principle, two linear oligonucleotides and silver ions were examined as models for DNA hybridization assay and adenosine triphosphate detection. The both nucleic acids contain target binding sequences in the middle and cytosine (C)-rich sequences at the lateral portions. The strong interaction between Ag(+) ions and cytosines forms stable C-Ag(+)-C structures, which promises the oligonucleotides to form conformationally constraint formations. In the presence of its target, interaction between the loop sequences and the target unfolds the C-Ag(+)-C structures, and the corresponding probes unfolding can be detected by a change in their fluorescence emission. We discuss the thermodynamic and kinetic opportunities that are provided by using Ag(+) ion complexes instead of traditional Watson-Crick-based duplex. In particular, the intrinsic feature of the metal-ligation motif facilitates the design of functional nucleic acids probes by independently varying the concentration of Ag(+) ions in the medium.

Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package

PubMed Central

Kumar, Yadhu; Westram, Ralf; Kipfer, Peter; Meier, Harald; Ludwig, Wolfgang

2006-01-01

Background Availability of high-resolution RNA crystal structures for the 30S and 50S ribosomal subunits and the subsequent validation of comparative secondary structure models have prompted the biologists to use three-dimensional structure of ribosomal RNA (rRNA) for evaluating sequence alignments of rRNA genes. Furthermore, the secondary and tertiary structural features of rRNA are highly useful and successfully employed in designing rRNA targeted oligonucleotide probes intended for in situ hybridization experiments. RNA3D, a program to combine sequence alignment information with three-dimensional structure of rRNA was developed. Integration into ARB software package, which is used extensively by the scientific community for phylogenetic analysis and molecular probe designing, has substantially extended the functionality of ARB software suite with 3D environment. Results Three-dimensional structure of rRNA is visualized in OpenGL 3D environment with the abilities to change the display and overlay information onto the molecule, dynamically. Phylogenetic information derived from the multiple sequence alignments can be overlaid onto the molecule structure in a real time. Superimposition of both statistical and non-statistical sequence associated information onto the rRNA 3D structure can be done using customizable color scheme, which is also applied to a textual sequence alignment for reference. Oligonucleotide probes designed by ARB probe design tools can be mapped onto the 3D structure along with the probe accessibility models for evaluation with respect to secondary and tertiary structural conformations of rRNA. Conclusion Visualization of three-dimensional structure of rRNA in an intuitive display provides the biologists with the greater possibilities to carry out structure based phylogenetic analysis. Coupled with secondary structure models of rRNA, RNA3D program aids in validating the sequence alignments of rRNA genes and evaluating probe target sites

Comparative testing of pulse oximeter probes.

PubMed

van Oostrom, Johannes H; Melker, Richard J

2004-05-01

The testing of pulse oximeter probes is generally limited to the integrity of the electrical circuit and does not include the optical properties of the probes. Few pulse oximeter testers evaluate the accuracy of both the monitor and the probe. We designed a study to compare the accuracy of nonproprietary probes (OSS Medical) designed for use with Nellcor, Datex-Ohmeda, and Criticare pulse oximeter monitors with that of their corresponding proprietary probes by using a commercial off-the-shelf pulse oximeter tester (Index). The Index pulse oximeter tester does include testing of the optical properties of the pulse oximeter probes. The pulse oximeter tester was given a controlled input that simulated acute apnea. Desaturation curves were automatically recorded from the pulse oximeter monitors with a data-collection computer. Comparisons between equivalent proprietary and nonproprietary probes were performed. Data were analyzed by using univariate and multivariate general linear model analysis. Five OSS Medical probe models were statistically better than the equivalent proprietary probes. The remainder of the probes were statistically similar. Comparative and simulation studies can have significant advantages over human studies because they are cost-effective, evaluate equipment in a clinically relevant scenario, and pose no risk to patients, but they are limited by the realism of the simulation. We studied the performance of pulse oximeter probes in a simulated environment. Our results show significant differences between some probes that affect the accuracy of measurement.

Imaging deep skeletal muscle structure using a high-sensitivity ultrathin side-viewing optical coherence tomography needle probe

PubMed Central

Yang, Xiaojie; Lorenser, Dirk; McLaughlin, Robert A.; Kirk, Rodney W.; Edmond, Matthew; Simpson, M. Cather; Grounds, Miranda D.; Sampson, David D.

2013-01-01

We have developed an extremely miniaturized optical coherence tomography (OCT) needle probe (outer diameter 310 µm) with high sensitivity (108 dB) to enable minimally invasive imaging of cellular structure deep within skeletal muscle. Three-dimensional volumetric images were acquired from ex vivo mouse tissue, examining both healthy and pathological dystrophic muscle. Individual myofibers were visualized as striations in the images. Degradation of cellular structure in necrotic regions was seen as a loss of these striations. Tendon and connective tissue were also visualized. The observed structures were validated against co-registered hematoxylin and eosin (H&E) histology sections. These images of internal cellular structure of skeletal muscle acquired with an OCT needle probe demonstrate the potential of this technique to visualize structure at the microscopic level deep in biological tissue in situ. PMID:24466482

Probing C60

NASA Astrophysics Data System (ADS)

Curl, Robert F.; Smalley, Richard E.

1988-11-01

Experiments involving the laser vaporization of graphite have indicated that one particular cluster of carbon, C60, is preeminently stable; this special stability may be evidence that C60 can readily take the form of a hollow truncated icosahedron (a sort of molecular soccerball). If true, this structure for C60 would be the first example of a spherical aromatic molecule. In fact, because of symmetry properties unique to the number 60, it may be the most perfectly spherical, edgeless molecule possible. Its rapid formation in condensing carbon vapors and its extreme chemical and photophysical stability may have far-reaching implications in a number of areas, particularly combustion science and astrophysics. For these reasons C60 and other clusters of carbon have continued to be the subject of intense research. This article provides a short review of the many new experimental probes of the properties of C60 and related carbon clusters.

Elucidating the Structure-Reactivity Correlations of Phenothiazine-Based Fluorescent Probes toward ClO.

PubMed

Wang, Shichao; Zhang, Boyu; Wang, Wenjing; Feng, Gang; Yuan, Daqiang; Zhang, Xuanjun

2018-06-07

In this work, with the aim of developing effective molecular probes and investigating the structure-reactivity correlation, a short series of phenothiazine-based fluorescent probes are designed for the detection of ClO - with differing electron push-pull groups. Sensing experiment results and single-crystal X-ray analysis with the aid of time-dependent DFT (TD-DFT) calculations reveal that substituting groups with increasing electron-withdrawing ability can increase the dihedral angle of the phenothiazine moiety and reduce the gap energy of the probes, leading to enhanced reactivity toward ClO - . Both PT1 and PT2 show two-color switching upon detection of ClO - . PT1, with the strong electron-donating group thiophene, shows a fluorescence color switch from salmon to blue. PT2, with a medium electron-donating/accepting group benzothiazole, shows a fluorescence color switch from red to green. However, both PT1 and PT2 show almost no response to ONOO - . Through the introduction of strong electron-withdrawing ketone combined with a cyano group, PT3 shows a cyan emission upon detection of ClO - and weak red emission upon detection of ONOO - . HRMS and 1 H NMR results confirm that PT1 and PT2 have the same sensing mode, in which the divalent sulfur of phenothiazine can be oxidized to sulfoxide by ClO - . Upon reaction with ClO - , PT3 experiences two-step reactions. It is first oxidized into the sulfone structure by ClO - , and then transformed into sulfoxide phenothiazine aldehyde. Upon encountering ONOO - , PT3 changes into an aldehyde structure and some nonfluorescent byproducts. Owing to their special selectivity and high sensitivity, PT1 and PT2 are applied to image the endogenous ClO - in macrophage cells and zebrafish larvae. This study is expected to provide useful guidelines for probe design for various applications. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

NASA Astrophysics Data System (ADS)

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

2016-10-01

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

Method And Apparatus For Two Dimensional Surface Property Analysis Based On Boundary Measurement

DOEpatents

Richardson, John G.

2005-11-15

An apparatus and method for determining properties of a conductive film is disclosed. A plurality of probe locations selected around a periphery of the conductive film define a plurality of measurement lines between each probe location and all other probe locations. Electrical resistance may be measured along each of the measurement lines. A lumped parameter model may be developed based on the measured values of electrical resistance. The lumped parameter model may be used to estimate resistivity at one or more selected locations encompassed by the plurality of probe locations. The resistivity may be extrapolated to other physical properties if the conductive film includes a correlation between resistivity and the other physical properties. A profile of the conductive film may be developed by determining resistivity at a plurality of locations. The conductive film may be applied to a structure such that resistivity may be estimated and profiled for the structure's surface.

Probe pressure effects on human skin diffuse reflectance and fluorescence spectroscopy measurements

PubMed Central

Lim, Liang; Nichols, Brandon; Rajaram, Narasimhan; Tunnell, James W.

2011-01-01

Diffuse reflectance and fluorescence spectroscopy are popular research techniques for noninvasive disease diagnostics. Most systems include an optical fiber probe that transmits and collects optical spectra in contact with the suspected lesion. The purpose of this study is to investigate probe pressure effects on human skin spectroscopic measurements. We conduct an in-vivo experiment on human skin tissue to study the short-term (<2 s) and long-term (>30 s) effects of probe pressure on diffuse reflectance and fluorescence measurements. Short-term light probe pressure (P0 < 9 mN∕mm2) effects are within 0 ± 10% on all physiological properties extracted from diffuse reflectance and fluorescence measurements, and less than 0 ± 5% for diagnostically significant physiological properties. Absorption decreases with site-specific variations due to blood being compressed out of the sampled volume. Reduced scattering coefficient variation is site specific. Intrinsic fluorescence shows a large standard error, although no specific pressure-related trend is observed. Differences in tissue structure and morphology contribute to site-specific probe pressure effects. Therefore, the effects of pressure can be minimized when the pressure is small and applied for a short amount of time; however, long-term and large pressures induce significant distortions in measured spectra. PMID:21280899

Near-infrared fluorescent probes in cancer imaging and therapy: an emerging field

PubMed Central

Yi, Xiaomin; Wang, Fuli; Qin, Weijun; Yang, Xiaojian; Yuan, Jianlin

2014-01-01

Near-infrared fluorescence (NIRF) imaging is an attractive modality for early cancer detection with high sensitivity and multi-detection capability. Due to convenient modification by conjugating with moieties of interests, NIRF probes are ideal candidates for cancer targeted imaging. Additionally, the combinatory application of NIRF imaging and other imaging modalities that can delineate anatomical structures extends fluorometric determination of biomedical information. Moreover, nanoparticles loaded with NIRF dyes and anticancer agents contribute to the synergistic management of cancer, which integrates the advantage of imaging and therapeutic functions to achieve the ultimate goal of simultaneous diagnosis and treatment. Appropriate probe design with targeting moieties can retain the original properties of NIRF and pharmacokinetics. In recent years, great efforts have been made to develop new NIRF probes with better photostability and strong fluorescence emission, leading to the discovery of numerous novel NIRF probes with fine photophysical properties. Some of these probes exhibit tumoricidal activities upon light radiation, which holds great promise in photothermal therapy, photodynamic therapy, and photoimmunotherapy. This review aims to provide a timely and concise update on emerging NIRF dyes and multifunctional agents. Their potential uses as agents for cancer specific imaging, lymph node mapping, and therapeutics are included. Recent advances of NIRF dyes in clinical use are also summarized. PMID:24648733

Near-infrared fluorescent probes in cancer imaging and therapy: an emerging field.

PubMed

Yi, Xiaomin; Wang, Fuli; Qin, Weijun; Yang, Xiaojian; Yuan, Jianlin

2014-01-01

Near-infrared fluorescence (NIRF) imaging is an attractive modality for early cancer detection with high sensitivity and multi-detection capability. Due to convenient modification by conjugating with moieties of interests, NIRF probes are ideal candidates for cancer targeted imaging. Additionally, the combinatory application of NIRF imaging and other imaging modalities that can delineate anatomical structures extends fluorometric determination of biomedical information. Moreover, nanoparticles loaded with NIRF dyes and anticancer agents contribute to the synergistic management of cancer, which integrates the advantage of imaging and therapeutic functions to achieve the ultimate goal of simultaneous diagnosis and treatment. Appropriate probe design with targeting moieties can retain the original properties of NIRF and pharmacokinetics. In recent years, great efforts have been made to develop new NIRF probes with better photostability and strong fluorescence emission, leading to the discovery of numerous novel NIRF probes with fine photophysical properties. Some of these probes exhibit tumoricidal activities upon light radiation, which holds great promise in photothermal therapy, photodynamic therapy, and photoimmunotherapy. This review aims to provide a timely and concise update on emerging NIRF dyes and multifunctional agents. Their potential uses as agents for cancer specific imaging, lymph node mapping, and therapeutics are included. Recent advances of NIRF dyes in clinical use are also summarized.

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.

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…

Neptune Polar Orbiter with Probes

NASA Technical Reports Server (NTRS)

Bienstock, Bernard; Atkinson, David; Baines, Kevin; Mahaffy, Paul; Steffes, Paul; Atreya, Sushil; Stern, Alan; Wright, Michael; Willenberg, Harvey; Smith, David;

Functionalized nanoparticle probes for protein detection

NASA Astrophysics Data System (ADS)

Park, Do Hyun; Lee, Jae-Seung

2015-05-01

In this Review, we discuss representative studies of recent advances in the development of nanoparticle-based protein detection methods, with a focus on the properties and functionalization of nanoparticle probes, as well as their use in detection schemes. We have focused on functionalized nanoparticle probes because they offer a number of advantages over conventional assays and because their use for detecting protein targets for diagnostic purposed has been demonstrated. In this report, we discuss nanoparticle probes classified by material type (gold, silver, silica, semiconductor, carbon, and virus) and surface functionality (antibody, aptamer, and DNA), which play a critical role in enhancing the sensitivity, selectivity, and efficiency of the detection systems. In particular, the synergistic function of each component of the nanoparticle probe is emphasized in terms of specific chemical and physical properties. This research area is in its early stages with many milestones to reach before nanoparticle probes are successfully applied in the field; however, the substantial ongoing efforts of researchers underline the great promise offered by nanoparticlebased probes for future applications. [Figure not available: see fulltext.

Structural and dynamical properties of the porins OmpF and OmpC: insights from molecular simulations

NASA Astrophysics Data System (ADS)

Kumar, Amit; Hajjar, Eric; Ruggerone, Paolo; Ceccarelli, Matteo

2010-11-01

In this paper we investigate the structural and dynamical properties of the two major porins (OmpF and OmpC) in Escherichia coli, using molecular dynamics (MD) simulations. In particular we characterized the atomic fluctuations, correlated motions, temperature dependence, solvent-accessible cross-sectional area and water dynamics in the key regions of the two channels. Our in-depth analysis allows us to highlight the importance of both the key conserved and substituted residues between OmpF and OmpC. The latter is characterized by a narrower and longer constriction region with respect to OmpF. OmpC also showed a higher stability upon increasing temperature. We then present the results of transport properties by using accelerated MD simulations to probe the diffusion of norfloxacin (a fluoroquinolone antibiotic) through the two porins OmpF/OmpC. Our study constitutes a step forward towards understanding the structure-function relationship of the two porins' channels. This will benefit the research of antibacterials with improved permeation properties and nanopores that aim to use these porins as sensing systems.

An uracil-linked hydroxyflavone probe for the recognition of ATP

PubMed Central

Bojtár, Márton; Janzsó-Berend, Péter Zoltán; Mester, Dávid; Hessz, Dóra; Kállay, Mihály; Kubinyi, Miklós

2018-01-01

Background: Nucleotides are essential molecules in living systems due to their paramount importance in various physiological processes. In the past years, numerous attempts were made to selectively recognize and detect these analytes, especially ATP using small-molecule fluorescent chemosensors. Despite the various solutions, the selective detection of ATP is still challenging due to the structural similarity of various nucleotides. In this paper, we report the conjugation of a uracil nucleobase to the known 4’-dimethylamino-hydroxyflavone fluorophore. Results: The complexation of this scaffold with ATP is already known. The complex is held together by stacking and electrostatic interactions. To achieve multi-point recognition, we designed the uracil-appended version of this probe to include complementary base-pairing interactions. The theoretical calculations revealed the availability of multiple complex structures. The synthesis was performed using click chemistry and the nucleotide recognition properties of the probe were evaluated using fluorescence spectroscopy. Conclusions: The first, uracil-containing fluorescent ATP probe based on a hydroxyflavone fluorophore was synthesized and evaluated. A selective complexation with ATP was observed and a ratiometric response in the excitation spectrum. PMID:29719572

Doped and undoped graphene platforms: the influence of structural properties on the detection of polyphenols

PubMed Central

Chng, Chu’Er; Sofer, Zdenek; Pumera, Martin; Bonanni, Alessandra

2016-01-01

There is a huge interest in doped graphene and how doping can tune the material properties for the specific application. It was recently demonstrated that the effect of doping can have different influence on the electrochemical detection of electroactive probes, depending on the analysed probe, on the structural characteristics of the graphene materials and on the type and amount of heteroatom used for the doping. In this work we wanted to investigate the effect of doping on graphene materials used as platform for the detection of catechin, a standard probe which is commonly used for the measurement of polyphenols in food and beverages. To this aim we compared undoped graphene with boron-doped graphene and nitrogen doped graphene platforms for the electrochemical detection of standard catechin oxidation. Finally, the material providing the best electrochemical performance was employed for the analysis of real samples. We found that the undoped graphene, possessing lower amount of oxygen functionalities, higher density of defects and larger electroactive surface area provided the best electroanalytical performance for the determination of catechin in commercial beer samples. Our findings are important for the development of novel graphene platforms for the electrochemical assessment of food quality. PMID:26861507

Doped and undoped graphene platforms: the influence of structural properties on the detection of polyphenols

NASA Astrophysics Data System (ADS)

Chng, Chu'Er; Sofer, Zdenek; Pumera, Martin; Bonanni, Alessandra

2016-02-01

There is a huge interest in doped graphene and how doping can tune the material properties for the specific application. It was recently demonstrated that the effect of doping can have different influence on the electrochemical detection of electroactive probes, depending on the analysed probe, on the structural characteristics of the graphene materials and on the type and amount of heteroatom used for the doping. In this work we wanted to investigate the effect of doping on graphene materials used as platform for the detection of catechin, a standard probe which is commonly used for the measurement of polyphenols in food and beverages. To this aim we compared undoped graphene with boron-doped graphene and nitrogen doped graphene platforms for the electrochemical detection of standard catechin oxidation. Finally, the material providing the best electrochemical performance was employed for the analysis of real samples. We found that the undoped graphene, possessing lower amount of oxygen functionalities, higher density of defects and larger electroactive surface area provided the best electroanalytical performance for the determination of catechin in commercial beer samples. Our findings are important for the development of novel graphene platforms for the electrochemical assessment of food quality.

Surface topography acquisition method for double-sided near-right-angle structured surfaces based on dual-probe wavelength scanning interferometry.

PubMed

Zhang, Tao; Gao, Feng; Jiang, Xiangqian

2017-10-02

This paper proposes an approach to measure double-sided near-right-angle structured surfaces based on dual-probe wavelength scanning interferometry (DPWSI). The principle and mathematical model is discussed and the measurement system is calibrated with a combination of standard step-height samples for both probes vertical calibrations and a specially designed calibration artefact for building up the space coordinate relationship of the dual-probe measurement system. The topography of the specially designed artefact is acquired by combining the measurement results with white light scanning interferometer (WLSI) and scanning electron microscope (SEM) for reference. The relative location of the two probes is then determined with 3D registration algorithm. Experimental validation of the approach is provided and the results show that the method is able to measure double-sided near-right-angle structured surfaces with nanometer vertical resolution and micrometer lateral resolution.

XRD- and infrared-probed anisotropic thermal expansion properties of an organic semiconducting single crystal.

PubMed

Mohanraj, J; Capria, E; Benevoli, L; Perucchi, A; Demitri, N; Fraleoni-Morgera, A

2018-01-17

The anisotropic thermal expansion properties of an organic semiconducting single crystal constituted by 4-hydroxycyanobenzene (4HCB) have been probed by XRD in the range 120-300 K. The anisotropic thermal expansion coefficients for the three crystallographic axes and for the crystal volume have been determined. A careful analysis of the crystal structure revealed that the two different H-bonds stemming from the two independent, differently oriented 4HCB molecules composing the unit cell have different rearrangement patterns upon temperature variations, in terms of both bond length and bond angle. Linearly Polarized Mid InfraRed (LP-MIR) measurements carried out in the same temperature range, focused on the O-H bond spectral region, confirm this finding. The same LP-MIR measurements, on the basis of a semi-empirical relation and of geometrical considerations and assumptions, allowed calculation of the -CNH-O- hydrogen bond length along the a and b axes of the crystal. In turn, the so-calculated -CNH-O- bond lengths were used to derive the thermal expansion coefficients along the corresponding crystal axes, as well as the volumetric one, using just the LP-MIR data. Reasonable to good agreement with the same values obtained from XRD measurements was obtained. This proof-of-principle opens interesting perspectives about the possible development of a rapid, low cost and industry-friendly assessment of the thermal expansion properties of organic semiconducting single crystals (OSSCs) involving hydrogen bonds.

Combining Structural Probes in the Gas Phase - Ion Mobility- Resolved Action-FRET

NASA Astrophysics Data System (ADS)

Daly, Steven; MacAleese, Luke; Dugourd, Philippe; Chirot, Fabien

2018-01-01

In the context of native mass spectrometry, the development of gas-phase structural probes sensitive to the different levels of structuration of biomolecular assemblies is necessary to push forward conformational studies. In this paper, we provide the first example of the combination of ion mobility (IM) and Förster resonance energy transfer (FRET) measurements within the same experimental setup. The possibility to obtain mass- and mobility-resolved FRET measurements is demonstrated on a model peptide and applied to monitor the collision-induced unfolding of ubiquitin. [Figure not available: see fulltext.

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).

Electrical resistivity probes

DOEpatents

Lee, Ki Ha; Becker, Alex; Faybishenko, Boris A.; Solbau, Ray D.

2003-10-21

A miniaturized electrical resistivity (ER) probe based on a known current-voltage (I-V) electrode structure, the Wenner array, is designed for local (point) measurement. A pair of voltage measuring electrodes are positioned between a pair of current carrying electrodes. The electrodes are typically about 1 cm long, separated by 1 cm, so the probe is only about 1 inch long. The electrodes are mounted to a rigid tube with electrical wires in the tube and a sand bag may be placed around the electrodes to protect the electrodes. The probes can be positioned in a borehole or on the surface. The electrodes make contact with the surrounding medium. In a dual mode system, individual probes of a plurality of spaced probes can be used to measure local resistance, i.e. point measurements, but the system can select different probes to make interval measurements between probes and between boreholes.

Method for analyzing nucleic acids by means of a substrate having a microchannel structure containing immobilized nucleic acid probes

DOEpatents

Ramsey, J. Michael; Foote, Robert S.

2003-12-09

A method and apparatus for analyzing nucleic acids includes immobilizing nucleic probes at specific sites within a microchannel structure and moving target nucleic acids into proximity to the probes in order to allow hybridization and fluorescence detection of specific target sequences.

Method for analyzing nucleic acids by means of a substrate having a microchannel structure containing immobilized nucleic acid probes

DOEpatents

Ramsey, J. Michael; Foote, Robert S.

2002-01-01

A method and apparatus for analyzing nucleic acids includes immobilizing nucleic probes at specific sites within a microchannel structure and moving target nucleic acids into proximity to the probes in order to allow hybridization and fluorescence detection of specific target sequences.

Using a biased qubit to probe complex systems

NASA Astrophysics Data System (ADS)

Pollock, Felix A.; Checińska, Agata; Pascazio, Saverio; Modi, Kavan

2016-09-01

Complex mesoscopic systems play increasingly important roles in modern science, from understanding biological functions at the molecular level to designing solid-state information processing devices. The operation of these systems typically depends on their energetic structure, yet probing their energy landscape can be extremely challenging; they have many degrees of freedom, which may be hard to isolate and measure independently. Here, we show that a qubit (a two-level quantum system) with a biased energy splitting can directly probe the spectral properties of a complex system, without knowledge of how they couple. Our work is based on the completely positive and trace-preserving map formalism, which treats any unknown dynamics as a "black-box" process. This black box contains information about the system with which the probe interacts, which we access by measuring the survival probability of the initial state of the probe as function of the energy splitting and the process time. Fourier transforming the results yields the energy spectrum of the complex system. Without making assumptions about the strength or form of its coupling, our probe could determine aspects of a complex molecule's energy landscape as well as, in many cases, test for coherent superposition of its energy eigenstates.

Effect of structure on sensing performance of a target induced signaling probe shifting DNA-based (TISPS-DNA) sensor.

PubMed

Yu, Xiang; Yu, Zhigang; Li, Fengqin; Xu, Yanmei; He, Xunjun; Xu, Lan; Shi, Wenbing; Zhang, Guiling; Yan, Hong

2017-05-15

A type of "signal on" displacement-based sensors named target induced signaling probe shifting DNA-based (TISPS-DNA) sensor were developed for a designated DNA detection. The signaling mechanism of the signaling probe (SP) shifting different from the classical conformation/flexibility change mode endows the sensor with high sensitivity. Through using thiolated or no thiolated capturing probe (CP), two 3-probe sensing structures, sensor-1 and sensor-2, were designed and constructed. The systematical comparing research results show that both sensors exhibit some similarities or big differences in sensing performance. On the one hand, the similarity in structures determines the similarity in some aspects of signaling mechanism, background signal, signal changing form, anti-fouling ability and versatility; on the other hand, the slight difference in structures also results in two opposite hybridization modes of gradual increasing resistance and gradual decreasing resistance which can affect the hybridization efficiency between the assistant probe (AP) and the SP, further producing some big differences in sensing performance, for example, apparently different signal enhancement (SE) change, point mutation discrimination ability and response speed. Under the optimized fabrication and detection conditions, both sensors feature high sensitivity for target DNAs with the detection limits of ∼10 fM for sensor-1 and ∼7 fM for sensor-2, respectively. Among many acquired sensing virtues, the sensor-1 shows a peculiar specificity adjustability which is also a highlight in this work. Copyright © 2017 Elsevier B.V. All rights reserved.

Foldable polymers as probes

DOEpatents

Li, Alexander D. Q. [Pullman, WA; Wang, Wei [Pullman, WA

2007-07-03

Disclosed herein are novel probes, which can be used to detect and identify target molecules of interest in a sample. The disclosed probes can be used to monitor conformational changes induced by molecular recognition events in addition to providing signaling the presence and/or identity of a target molecule. Methods, including solid phase synthesis techniques, for making probe molecules that exhibit changes in their optical properties upon target molecule binding are described in the disclosure. Also disclosed herein are novel chromophore moieties, which have tailored fluorescent emission spectra.

Foldable polymers as probes

DOEpatents

Li, Alexander D. Q. [Pullman, WA; Wang, Wei [Pullman, WA

2009-07-07

Disclosed herein are novel probes, which can be used to detect and identify target molecules of interest in a sample. The disclosed probes can be used to monitor conformational changes induced by molecular recognition events in addition to providing signaling the presence and/or identity of a target molecule. Methods, including solid phase synthesis techniques, for making probe molecules that exhibit changes in their optical properties upon target molecule binding are described in the disclosure. Also disclosed herein are novel chromophore moieties, which have tailored fluorescent emission spectra.

Size-dependent characterization of embedded Ge nanocrystals: Structural and thermal properties

NASA Astrophysics Data System (ADS)

Araujo, L. L.; Giulian, R.; Sprouster, D. J.; Schnohr, C. S.; Llewellyn, D. J.; Kluth, P.; Cookson, D. J.; Foran, G. J.; Ridgway, M. C.

2008-09-01

A combination of conventional and synchrotron-based techniques has been used to characterize the size-dependent structural and thermal properties of Ge nanocrystals (NCs) embedded in a silica (a-SiO2) matrix. Ge NC size distributions with four different diameters ranging from 4.0 to 9.0 nm were produced by ion implantation and thermal annealing as characterized with small-angle x-ray scattering and transmission electron microscopy. The NCs were well represented by the superposition of bulklike crystalline and amorphous environments, suggesting the formation of an amorphous layer separating the crystalline NC core and the a-SiO2 matrix. The amorphous fraction was quantified with x-ray-absorption near-edge spectroscopy and increased as the NC diameter decreased, consistent with the increase in surface-to-volume ratio. The structural parameters of the first three nearest-neighbor shells were determined with extended x-ray-absorption fine-structure (EXAFS) spectroscopy and evolved linearly with inverse NC diameter. Specifically, increases in total disorder, interatomic distance, and the asymmetry in the distribution of distances were observed as the NC size decreased, demonstrating that finite-size effects govern the structural properties of embedded Ge NCs. Temperature-dependent EXAFS measurements in the range of 15-300 K were employed to probe the mean vibrational frequency and the variation of the interatomic distance distribution (mean value, variance, and asymmetry) with temperature for all NC distributions. A clear trend of increased stiffness (higher vibrational frequency) and decreased thermal expansion with decreasing NC size was evident, confirming the close relationship between the variation of structural and thermal/vibrational properties with size for embedded Ge NCs. The increase in surface-to-volume ratio and the presence of an amorphous Ge layer separating the matrix and crystalline NC core are identified as the main factors responsible for the observed

Theoretical Design of a Two-Photon Fluorescent Probe for Nitric Oxide with Enhanced Emission Induced by Photoninduced Electron Transfer.

PubMed

Zhang, Yujin; Leng, Jiancai; Hu, Wei

2018-04-25

In the present work, we systematically investigate the sensing abilities of two recently literature-reported two-photon fluorescent NO probes, i.e., the o-phenylenediamine derivative of Nile Red and the p-phenylenediamine derivative of coumarin. The recognition mechanisms of these probes are studied by using the molecular orbital classifying method, which demonstrates the photoinduced electron transfer process. In addition, we have designed two new probes by swapping receptor units present on fluorophores, i.e., the p-phenylenediamine derivative of Nile Red and the o-phenylenediamine derivative of coumarin. However, it illustrates that only the latter has ability to function as off-on typed fluorescent probe for NO. More importantly, calculations on the two-photon absorption properties of the probes demonstrate that both receptor derivatives of coumarin possess larger TPA cross-sections than Nile Red derivatives, which makes a better two photon fluorescent probe. Our theoretical investigations reveal that the underlying mechanism satisfactorily explain the experimental results, providing a theoretical basis on the structure-property relationships which is beneficial to developing new two-photon fluorescent probes for NO.

Structure-Dependent Optical Properties of Self-Organized Bi2Se3 Nanostructures: From Nanocrystals to Nanoflakes.

PubMed

Yang, Shang-Dong; Yang, Liao; Zheng, Yu-Xiang; Zhou, Wen-Jie; Gao, Meng-Yu; Wang, Song-You; Zhang, Rong-Jun; Chen, Liang-Yao

2017-08-30

Bismuth selenide (Bi 2 Se 3 ), with a wide bulk band gap and single massless Dirac cone at the surface, is a promising three-dimensional topological insulator. Bi 2 Se 3 possesses gapless surface states and an insulator-like bulk band gap as a new type of quantum matter. Different Bi 2 Se 3 nanostructures were prepared using electron beam evaporation with high production efficiency. Structural investigations by energy-dispersive X-ray analysis, scanning electron microscopy, and X-ray diffraction revealed the sample stoichiometries and the structural transition mechanism from nanocrystals to nanoflakes. The optical properties systematically probed and analyzed by spectroscopic ellipsometry showed strong dependence on the nanostructures and were also predicted to have structure-modifiable technological prospects. The optical parameters, plasma frequencies, scattering rates of the free electrons, and optical band gaps were related to the topological properties of the Bi 2 Se 3 nanostructures via light-matter interactions, offering new opportunities and approaches for studies on topological insulators and spintronics. The high-quality Bi 2 Se 3 nanostructures provide advantages in exploring novel physics and exploiting prospective applications.

Structure, processing, and properties of potatoes

NASA Astrophysics Data System (ADS)

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

1992-06-01

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.

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.

Rapid laboratory investigation of the thermal properties of planetary analogues by using the EXTASE thermal probe.

NASA Astrophysics Data System (ADS)

Nadalini, R.; Extase Team

The thermal properties of the constituent materials of the upper meters of planets and planetary bodies are of extreme interest. During the design and the verification of various planetary missions, the need to model and test appropriate simulants in laboratory is often raised. To verify the thermal properties of deployed laboratory simulants, the EXTASE thermal probe is a fast, precise, and easy-to-use tool. EXTASE is a thermal profile probe, able to measure the temperature and inject heat into the selected material at 16 different locations along its 45cm long slender cylindrical body. It has been developed following the experience of MUPUS, with the purpose of observing such properties on Earth, in situ and in a short time. We have used EXTASE, under laboratory cold and standard conditions, on several sand mixtures, soils, granular and compact ices, under vacuum and at normal pressure levels, to collect a great number of time- and depth-dependent temperature curves that represent the thermal dynamical response of the material. At the same time, two independent models have been developed to verify the experimental results by reaching the same results with a simulation of the same process. The models, analytical and numerical, which account for all material parameters (conductivity, density, capacity), have been developed and fine tuned until their results are superposed to the experimental curves, thus allowing the determination of the distinct thermal properties. In addition, a test campaign is under planning to use EXTASE to determine, rapidly and efficiently, the thermal properties of various regolith simulants to be used in the simulation of planetary subsurface processes.

In Situ Live-Cell Nucleus Fluorescence Labeling with Bioinspired Fluorescent Probes.

PubMed

Ding, Pan; Wang, Houyu; Song, Bin; Ji, Xiaoyuan; Su, Yuanyuan; He, Yao

2017-08-01

Fluorescent imaging techniques for visualization of nuclear structure and function in live cells are fundamentally important for exploring major cellular events. The ideal cellular labeling method is capable of realizing label-free, in situ, real-time, and long-term nucleus labeling in live cells, which can fully obtain the nucleus-relative information and effectively alleviate negative effects of alien probes on cellular metabolism. However, current established fluorescent probes-based strategies (e.g., fluorescent proteins-, organic dyes-, fluorescent organic/inorganic nanoparticles-based imaging techniques) are unable to simultaneously realize label-free, in situ, long-term, and real-time nucleus labeling, resulting in inevitable difficulties in fully visualizing nuclear structure and function in live cells. To this end, we present a type of bioinspired fluorescent probes, which are highly efficacious for in situ and label-free tracking of nucleus in long-term and real-time manners. Typically, the bioinspired polydopamine (PDA) nanoparticles, served as fluorescent probes, can be readily synthesized in situ within live cell nucleus without any further modifications under physiological conditions (37 °C, pH ∼7.4). Compared with other conventional nuclear dyes (e.g., propidium iodide (PI), Hoechst), superior spectroscopic properties (e.g., quantum yield of ∼35.8% and high photostability) and low cytotoxicity of PDA-based probes enable long-term (e.g., 3 h) fluorescence tracking of nucleus. We also demonstrate the generality of this type of bioinspired fluorescent probes in different cell lines and complex biological samples.

Fluoromodule-based reporter/probes designed for in vivo fluorescence imaging

PubMed Central

Zhang, Ming; Chakraborty, Subhasish K.; Sampath, Padma; Rojas, Juan J.; Hou, Weizhou; Saurabh, Saumya; Thorne, Steve H.; Bruchez, Marcel P.; Waggoner, Alan S.

2015-01-01

Optical imaging of whole, living animals has proven to be a powerful tool in multiple areas of preclinical research and has allowed noninvasive monitoring of immune responses, tumor and pathogen growth, and treatment responses in longitudinal studies. However, fluorescence-based studies in animals are challenging because tissue absorbs and autofluoresces strongly in the visible light spectrum. These optical properties drive development and use of fluorescent labels that absorb and emit at longer wavelengths. Here, we present a far-red absorbing fluoromodule–based reporter/probe system and show that this system can be used for imaging in living mice. The probe we developed is a fluorogenic dye called SC1 that is dark in solution but highly fluorescent when bound to its cognate reporter, Mars1. The reporter/probe complex, or fluoromodule, produced peak emission near 730 nm. Mars1 was able to bind a variety of structurally similar probes that differ in color and membrane permeability. We demonstrated that a tool kit of multiple probes can be used to label extracellular and intracellular reporter–tagged receptor pools with 2 colors. Imaging studies may benefit from this far-red excited reporter/probe system, which features tight coupling between probe fluorescence and reporter binding and offers the option of using an expandable family of fluorogenic probes with a single reporter gene. PMID:26348895

Pre-Assembly of Near-Infrared Fluorescent Multivalent Molecular Probes for Biological Imaging.

PubMed

Peck, Evan M; Battles, Paul M; Rice, Douglas R; Roland, Felicia M; Norquest, Kathryn A; Smith, Bradley D

2016-05-18

A programmable pre-assembly method is described and shown to produce near-infrared fluorescent molecular probes with tunable multivalent binding properties. The modular assembly process threads one or two copies of a tetralactam macrocycle onto a fluorescent PEGylated squaraine scaffold containing a complementary number of docking stations. Appended to the macrocycle periphery are multiple copies of a ligand that is known to target a biomarker. The structure and high purity of each threaded complex was determined by independent spectrometric methods and also by gel electrophoresis. Especially helpful were diagnostic red-shift and energy transfer features in the absorption and fluorescence spectra. The threaded complexes were found to be effective multivalent molecular probes for fluorescence microscopy and in vivo fluorescence imaging of living subjects. Two multivalent probes were prepared and tested for targeting of bone in mice. A pre-assembled probe with 12 bone-targeting iminodiacetate ligands produced more bone accumulation than an analogous pre-assembled probe with six iminodiacetate ligands. Notably, there was no loss in probe fluorescence at the bone target site after 24 h in the living animal, indicating that the pre-assembled fluorescent probe maintained very high mechanical and chemical stability on the skeletal surface. The study shows how this versatile pre-assembly method can be used in a parallel combinatorial manner to produce libraries of near-infrared fluorescent multivalent molecular probes for different types of imaging and diagnostic applications, with incremental structural changes in the number of targeting groups, linker lengths, linker flexibility, and degree of PEGylation.

Structure-property relationships: asymmetric alkylphenyl-substituted anthracene molecules for use in small-molecule solar cells.

PubMed

Kim, Yu Jin; Ahn, Eun Soo; Jang, Sang Hun; An, Tae Kyu; Kwon, Soon-Ki; Chung, Dae Sung; Kim, Yun-Hi; Park, Chan Eon

2015-05-11

Two asymmetric anthracene-based organic molecules, NDHPEA and TNDHPEA, were prepared without or with a thiophene spacer between the anthracene and naphthalene units. These asymmetric oligomers displayed different degrees of coplanarity, as evidenced by differences in the dihedral angles calculated by using DFT. Differential scanning calorimetry and XRD studies were used to probe the crystallization characteristics and molecular packing structures in the active layers. The coplanarity of the molecules in the asymmetric structure significantly affected the crystallization behavior and the formation of crystalline domains in the solid state. The small-molecule crystalline properties were correlated with the device physics by determining the J-V characteristics and hole mobilities of the devices. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Gamma-Ray Pulsar Light Curves as Probes of Magnetospheric Structure

NASA Technical Reports Server (NTRS)

Harding, A. K.

2016-01-01

The large number of gamma-ray pulsars discovered by the Fermi Gamma-Ray Space Telescope since its launch in 2008 dwarfs the handful that were previously known. The variety of observed light curves makes possible a tomography of both the ensemble-averaged field structure and the high-energy emission regions of a pulsar magnetosphere. Fitting the gamma-ray pulsar light curves with model magnetospheres and emission models has revealed that most of the high-energy emission, and the particles acceleration, takes place near or beyond the light cylinder, near the current sheet. As pulsar magnetosphere models become more sophisticated, it is possible to probe magnetic field structure and emission that are self-consistently determined. Light curve modeling will continue to be a powerful tool for constraining the pulsar magnetosphere physics.

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

DOE PAGES

Li, Y.; Zakharov, D.; Zhao, S.; ...

2015-06-29

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

Selectivity on-target of bromodomain chemical probes by structure-guided medicinal chemistry and chemical biology

PubMed Central

Galdeano, Carles; Ciulli, Alessio

2017-01-01

Targeting epigenetic proteins is a rapidly growing area for medicinal chemistry and drug discovery. Recent years have seen an explosion of interest in developing small molecules binding to bromodomains, the readers of acetyl-lysine modifications. A plethora of co-crystal structures has motivated focused fragment-based design and optimization programs within both industry and academia. These efforts have yielded several compounds entering the clinic, and many more are increasingly being used as chemical probes to interrogate bromodomain biology. High selectivity of chemical probes is necessary to ensure biological activity is due to an on-target effect. Here, we review the state-of-the-art of bromodomain-targeting compounds, focusing on the structural basis for their on-target selectivity or lack thereof. We also highlight chemical biology approaches to enhance on-target selectivity. PMID:27193077

Fluorescence studies with DNA probes: dynamic aspects of DNA structure and DNA-protein interactions

NASA Astrophysics Data System (ADS)

Millar, David P.; Carver, Theodore E.

1994-08-01

Time-resolved fluorescence measurements of optical probes incorporated at specific sites in DNA provides a new approach to studies of DNA structure and DNA:protein interactions. This approach can be used to study complex multi-state behavior, such as the folding of DNA into alternative higher order structures or the transfer of DNA between multiple binding sites on a protein. In this study, fluorescence anisotropy decay of an internal dansyl probe attached to 17/27-mer oligonucleotides was used to monitor the distribution of DNA 3' termini bound at either the polymerase of 3' to 5' exonuclease sites of the Klenow fragment of DNA polymerase I. Partitioning of the primer terminus between the two active sites of the enzyme resulted in a heterogeneous probe environment, reflected in the associative behavior of the fluorescence anisotropy decay. Analysis of the anisotropy decay with a two state model of solvent-exposed and protein-associated dansyl probes was used to determine the fraction of DNA bound at each site. We examined complexes of Klenow fragment with DNAs containing various base mismatches. Single mismatches at the primer terminus caused a 3-fold increase in the equilibrium partitioning of DNA into the exonuclease site, while two or more consecutive G:G mismatches caused the DNA to bind exclusively at the exonuclease site, with a partitioning constant at least 250- fold greater than that of the corresponding matched DNA sequence. Internal single mismatches located up to four bases from the primer terminus produced larger effects than the same mismatch at the primer terminus. These results provide insight into the recognition mechanisms that enable DNA polymerases to proofread misincorporated bases during DNA replication.

Novel benzanthrone probes for membrane and protein studies

NASA Astrophysics Data System (ADS)

Ryzhova, Olga; Vus, Kateryna; Trusova, Valeriya; Kirilova, Elena; Kirilov, Georgiy; Gorbenko, Galyna; Kinnunen, Paavo

2016-09-01

The applicability of a series of novel benzanthrone dyes to monitoring the changes in physicochemical properties of lipid bilayer and to differentiating between the native and aggregated protein states has been evaluated. Based on the quantitative parameters of the dye-membrane and dye-protein binding derived from the fluorimetric titration data, the most prospective membrane probes and amyloid tracers have been selected from the group of examined compounds. Analysis of the red edge excitation shifts of the membrane- and amyloid-bound dyes provided information on the properties of benzanthrone binding sites within the lipid and protein matrixes. To understand how amyloid specificity of benzanthrones correlates with their structure, quantitative structure activity relationship (QSAR) analysis was performed involving a range of quantum chemical molecular descriptors. A statistically significant model was obtained for predicting the sensitivity of novel benzanthrone dyes to amyloid fibrils.

In situ electronic probing of semiconducting nanowires in an electron microscope.

PubMed

Fauske, V T; Erlbeck, M B; Huh, J; Kim, D C; Munshi, A M; Dheeraj, D L; Weman, H; Fimland, B O; Van Helvoort, A T J

2016-05-01

For the development of electronic nanoscale structures, feedback on its electronic properties is crucial, but challenging. Here, we present a comparison of various in situ methods for electronically probing single, p-doped GaAs nanowires inside a scanning electron microscope. The methods used include (i) directly probing individual as-grown nanowires with a sharp nano-manipulator, (ii) contacting dispersed nanowires with two metal contacts and (iii) contacting dispersed nanowires with four metal contacts. For the last two cases, we compare the results obtained using conventional ex situ litho-graphy contacting techniques and by in situ, direct-write electron beam induced deposition of a metal (Pt). The comparison shows that 2-probe measurements gives consistent results also with contacts made by electron beam induced deposition, but that for 4-probe, stray deposition can be a problem for shorter nanowires. This comparative study demonstrates that the preferred in situ method depends on the required throughput and reliability. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

Femtosecond Pump-Push-Probe and Pump-Dump-Probe Spectroscopy of Conjugated Polymers: New Insight and Opportunities.

PubMed

Kee, Tak W

2014-09-18

Conjugated polymers are an important class of soft materials that exhibit a wide range of applications. The excited states of conjugated polymers, often referred to as excitons, can either deactivate to yield the ground state or dissociate in the presence of an electron acceptor to form charge carriers. These interesting properties give rise to their luminescence and the photovoltaic effect. Femtosecond spectroscopy is a crucial tool for studying conjugated polymers. Recently, more elaborate experimental configurations utilizing three optical pulses, namely, pump-push-probe and pump-dump-probe, have been employed to investigate the properties of excitons and charge-transfer states of conjugated polymers. These studies have revealed new insight into femtosecond torsional relaxation and detrapping of bound charge pairs of conjugated polymers. This Perspective highlights (1) the recent achievements by several research groups in using pump-push-probe and pump-dump-probe spectroscopy to study conjugated polymers and (2) future opportunities and potential challenges of these techniques.

Aircraft Structural Mass Property Prediction Using Conceptual-Level Structural Analysis

NASA Technical Reports Server (NTRS)

Sexstone, Matthew G.

1998-01-01

This paper describes a methodology that extends the use of the Equivalent LAminated Plate Solution (ELAPS) structural analysis code from conceptual-level aircraft structural analysis to conceptual-level aircraft mass property analysis. Mass property analysis in aircraft structures has historically depended upon parametric weight equations at the conceptual design level and Finite Element Analysis (FEA) at the detailed design level. ELAPS allows for the modeling of detailed geometry, metallic and composite materials, and non-structural mass coupled with analytical structural sizing to produce high-fidelity mass property analyses representing fully configured vehicles early in the design process. This capability is especially valuable for unusual configuration and advanced concept development where existing parametric weight equations are inapplicable and FEA is too time consuming for conceptual design. This paper contrasts the use of ELAPS relative to empirical weight equations and FEA. ELAPS modeling techniques are described and the ELAPS-based mass property analysis process is detailed. Examples of mass property stochastic calculations produced during a recent systems study are provided. This study involved the analysis of three remotely piloted aircraft required to carry scientific payloads to very high altitudes at subsonic speeds. Due to the extreme nature of this high-altitude flight regime, few existing vehicle designs are available for use in performance and weight prediction. ELAPS was employed within a concurrent engineering analysis process that simultaneously produces aerodynamic, structural, and static aeroelastic results for input to aircraft performance analyses. The ELAPS models produced for each concept were also used to provide stochastic analyses of wing structural mass properties. The results of this effort indicate that ELAPS is an efficient means to conduct multidisciplinary trade studies at the conceptual design level.

Aircraft Structural Mass Property Prediction Using Conceptual-Level Structural Analysis

NASA Technical Reports Server (NTRS)

Sexstone, Matthew G.

1998-01-01

This paper describes a methodology that extends the use of the Equivalent LAminated Plate Solution (ELAPS) structural analysis code from conceptual-level aircraft structural analysis to conceptual-level aircraft mass property analysis. Mass property analysis in aircraft structures has historically depended upon parametric weight equations at the conceptual design level and Finite Element Analysis (FEA) at the detailed design level ELAPS allows for the modeling of detailed geometry, metallic and composite materials, and non-structural mass coupled with analytical structural sizing to produce high-fidelity mass property analyses representing fully configured vehicles early in the design process. This capability is especially valuable for unusual configuration and advanced concept development where existing parametric weight equations are inapplicable and FEA is too time consuming for conceptual design. This paper contrasts the use of ELAPS relative to empirical weight equations and FEA. ELAPS modeling techniques are described and the ELAPS-based mass property analysis process is detailed Examples of mass property stochastic calculations produced during a recent systems study are provided This study involved the analysis of three remotely piloted aircraft required to carry scientific payloads to very high altitudes at subsonic speeds. Due to the extreme nature of this high-altitude flight regime,few existing vehicle designs are available for use in performance and weight prediction. ELAPS was employed within a concurrent engineering analysis process that simultaneously produces aerodynamic, structural, and static aeroelastic results for input to aircraft performance analyses. The ELAPS models produced for each concept were also used to provide stochastic analyses of wing structural mass properties. The results of this effort indicate that ELAPS is an efficient means to conduct multidisciplinary trade studies at the conceptual design level.

Pump and probe spectroscopy with continuous wave quantum cascade lasers.

PubMed

Kirkbride, James M R; Causier, Sarah K; Dalton, Andrew R; Weidmann, Damien; Ritchie, Grant A D

2014-02-07

This paper details infra-red pump and probe studies on nitric oxide conducted with two continuous wave quantum cascade lasers both operating around 5 μm. The pump laser prepares a velocity selected population in a chosen rotational quantum state of the v = 1 level which is subsequently probed using a second laser tuned to a rotational transition within the v = 2 ← v = 1 hot band. The rapid frequency scan of the probe (with respect to the molecular collision rate) in combination with the velocity selective pumping allows observation of marked rapid passage signatures in the transient absorption profiles from the polarized vibrationally excited sample. These coherent transient signals are influenced by the underlying hyperfine structure of the pump and probe transitions, the sample pressure, and the coherent properties of the lasers. Pulsed pump and probe studies show that the transient absorption signals decay within 1 μs at 50 mTorr total pressure, reflecting both the polarization and population dephasing times of the vibrationally excited sample. The experimental observations are supported by simulation based upon solving the optical Bloch equations for a two level system.

Probing the electronic structure of platinum(II) chromophores: crystal structures, NMR structures, and photophysical properties of six new bis- and di- phenolate/thiolate Pt(II)diimine chromophores.

PubMed

Weinstein, Julia A; Tierney, Mark T; Davies, E Stephen; Base, Karel; Robeiro, Anthony A; Grinstaff, Mark W

2006-05-29

A general route for synthesis of six structurally similar Pt(II) diimine thiolate/phenolates chromophores possessing bulky phenolate or thiolate ligands is reported. The Pt chromophores were characterized using an array of techniques including 1H, 13C, and 195Pt NMR, absorption, emission, (spectro)electrochemistry, and EPR spectroscopy. Systematic variation of the electronic structure of the Pt(II) chromophores studied was achieved by (i) changing solvent polarity; (ii) substituting oxygen for sulfur in the donor ligand; (iii) alternating donor ligands from bis- to di-coordination; and (iv) changing the electron donating/withdrawing properties of the ligand(s). The lowest excited state in these new chromophores was assigned to a [charge-transfer-to-diimine] transition from the HOMO of mixed Pt/S (or Pt/O) character on the basis of absorption and emission spectroscopy, UV/vis (spectro)electrochemistry, and EPR spectroscopy. One of the chromophores, Pt(dpphen)(3,5-di-tert-butyl-catecholate) represents an example of a Pt(II) diimine phenolate chromophore that possesses a reversible oxidation centered predominantly on the donor ligand. Results from EPR spectroscopy indicate participation of the Pt(II) orbitals in the HOMO. There is a dramatic difference in the photophysical properties of carborane complexes compared to other mixed-ligand Pt(II) compounds, which includes room-temperature emission and photostability. The charge-transfer character of the lowest excited state in this series of chromophores is maintained throughout. Moreover, the absorption and emission energies and the redox properties of the excited state can be significantly tuned.

Theoretical Studies on Two-Photon Fluorescent Hg2+ Probes Based on the Coumarin-Rhodamine System.

PubMed

Zhang, Yujin; Leng, Jiancai

2017-07-20

The development of fluorescent sensors for Hg 2+ has attracted much attention due to the well-known adverse effects of mercury on biological health. In the present work, the optical properties of two newly-synthesized Hg 2+ chemosensors based on the coumarin-rhodamine system (named Pro1 and Pro2) were systematically investigated using time-dependent density functional theory. It is shown that Pro1 and Pro2 are effective ratiometric fluorescent Hg 2+ probes, which recognize Hg 2+ by Förster resonance energy transfer and through bond energy transfer mechanisms, respectively. To further understand the mechanisms of the two probes, we have developed an approach to predict the energy transfer rate between the donor and acceptor. Using this approach, it can be inferred that Pro1 has a six times higher energy transfer rate than Pro2. Thus the influence of spacer group between the donor and acceptor on the sensing performance of the probe is demonstrated. Specifically, two-photon absorption properties of these two probes are calculated. We have found that both probes show significant two-photon responses in the near-infrared light region. However, only the maximum two-photon absorption cross section of Pro1 is greatly enhanced with the presence of Hg 2+ , indicating that Pro1 can act as a potential two-photon excited fluorescent probe for Hg 2+ . The theoretical investigations would be helpful to build a relationship between the structure and the optical properties of the probes, providing information on the design of efficient two-photon fluorescent sensors that can be used for biological imaging of Hg 2+ in vivo.

Probing long-range structural order in SnPc/Ag(111) by umklapp process assisted low-energy angle-resolved photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Jauernik, Stephan; Hein, Petra; Gurgel, Max; Falke, Julian; Bauer, Michael

2018-03-01

Laser-based angle-resolved photoelectron spectroscopy is performed on tin-phthalocyanine (SnPc) adsorbed on silver Ag(111). Upon adsorption of SnPc, strongly dispersing bands are observed which are identified as secondary Mahan cones formed by surface umklapp processes acting on photoelectrons from the silver substrate as they transit through the ordered adsorbate layer. We show that the photoemission data carry quantitative structural information on the adsorbate layer similar to what can be obtained from a conventional low-energy electron diffraction (LEED) study. More specifically, we compare photoemission data and LEED data probing an incommensurate-to-commensurate structural phase transition of the adsorbate layer. Based on our results we propose that Mahan-cone spectroscopy operated in a pump-probe configuration can be used in the future to probe structural dynamics at surfaces with a temporal resolution in the sub-100-fs regime.

An integrated fiber-optic probe combined with support vector regression for fast estimation of optical properties of turbid media.

PubMed

Zhou, Yang; Fu, Xiaping; Ying, Yibin; Fang, Zhenhuan

2015-06-23

A fiber-optic probe system was developed to estimate the optical properties of turbid media based on spatially resolved diffuse reflectance. Because of the limitations in numerical calculation of radiative transfer equation (RTE), diffusion approximation (DA) and Monte Carlo simulations (MC), support vector regression (SVR) was introduced to model the relationship between diffuse reflectance values and optical properties. The SVR models of four collection fibers were trained by phantoms in calibration set with a wide range of optical properties which represented products of different applications, then the optical properties of phantoms in prediction set were predicted after an optimal searching on SVR models. The results indicated that the SVR model was capable of describing the relationship with little deviation in forward validation. The correlation coefficient (R) of reduced scattering coefficient μ'(s) and absorption coefficient μ(a) in the prediction set were 0.9907 and 0.9980, respectively. The root mean square errors of prediction (RMSEP) of μ'(s) and μ(a) in inverse validation were 0.411 cm(-1) and 0.338 cm(-1), respectively. The results indicated that the integrated fiber-optic probe system combined with SVR model were suitable for fast and accurate estimation of optical properties of turbid media based on spatially resolved diffuse reflectance. Copyright © 2015 Elsevier B.V. All rights reserved.

Fluorescence energy transfer as a probe for nucleic acid structures and sequences.

PubMed Central

Mergny, J L; Boutorine, A S; Garestier, T; Belloc, F; Rougée, M; Bulychev, N V; Koshkin, A A; Bourson, J; Lebedev, A V; Valeur, B

1994-01-01

The primary or secondary structure of single-stranded nucleic acids has been investigated with fluorescent oligonucleotides, i.e., oligonucleotides covalently linked to a fluorescent dye. Five different chromophores were used: 2-methoxy-6-chloro-9-amino-acridine, coumarin 500, fluorescein, rhodamine and ethidium. The chemical synthesis of derivatized oligonucleotides is described. Hybridization of two fluorescent oligonucleotides to adjacent nucleic acid sequences led to fluorescence excitation energy transfer between the donor and the acceptor dyes. This phenomenon was used to probe primary and secondary structures of DNA fragments and the orientation of oligodeoxynucleotides synthesized with the alpha-anomers of nucleoside units. Fluorescence energy transfer can be used to reveal the formation of hairpin structures and the translocation of genes between two chromosomes. PMID:8152922

A functional probe with bowtie aperture and bull's eye structure for nanolithograph

NASA Astrophysics Data System (ADS)

Wang, Shuo; Li, Xu-Feng; Wang, Qiao; Guo, Ying-Yan; Pan, Shi

2012-10-01

The bowtie aperture surrounded by concentric gratings (the bull's eye structure) integrated on the near-field scanning optical microscopy (NSOM) probe (aluminum coated fiber tip) for nanolithography has been investigated using the finite-difference time domain (FDTD) method. By modifying the parameters of the bowtie aperture and the concentric gratings, a maximal field enhancement factor of 391.69 has been achieved, which is 18 times larger than that obtained from the single bowtie aperture. Additionally, the light spot depends on the gap size of the bowtie aperture and can be confined to sub-wavelength. The superiority of the combination of the bowtie aperture and the bull's eye structure is confirmed, and the mechanism for the electric field enhancement in this derived structure is analyzed.

Acoustic dynamics of supercooled indomethacin probed by Brillouin light scattering.

PubMed

De Panfilis, S; Pogna, E A A; Virga, A; Scopigno, T

2014-07-21

Acoustics dynamics of the molecular glass-former indomethacin (IMC) have been investigated by Brillouin light scattering (BLS) at GHz frequencies. Elastic response of the system has been tracked from the melting temperature down to the glass transition through the supercooled liquid. Both the structural arrest and the vibrational dynamics are described by modeling the experimentally determined dynamic structure factor within the framework of the Langevin equation, through a simplified choice of memory function which allows one to determine sound velocity and the acoustic attenuation coefficient as a function of temperature. The density fluctuation spectra in the glassy phase, as probed by BLS, are compared with time-domain results from photoacoustics experiments. The arising scenario is discussed in the context of current literature reporting inelastic X-ray scattering and BLS in platelet geometry. The link between the probed elastic properties and the non-ergodicity factor of the glass phase is finally scrutinized.

Database architecture and query structures for probe data processing.

DOT National Transportation Integrated Search

2012-03-01

This report summarizes findings and implementations of probe vehicle data collection based on Bluetooth MAC address matching technology. Probe vehicle travel time data are studied in the following field deployment case studies: analysis of traffic ch...

Mechanical Deformation Mechanisms and Properties of Prion Fibrils Probed by Atomistic Simulations

NASA Astrophysics Data System (ADS)

Choi, Bumjoon; Kim, Taehee; Ahn, Eue Soo; Lee, Sang Woo; Eom, Kilho

2017-03-01

Prion fibrils, which are a hallmark for neurodegenerative diseases, have recently been found to exhibit the structural diversity that governs disease pathology. Despite our recent finding concerning the role of the disease-specific structure of prion fibrils in determining their elastic properties, the mechanical deformation mechanisms and fracture properties of prion fibrils depending on their structures have not been fully characterized. In this work, we have studied the tensile deformation mechanisms of prion and non-prion amyloid fibrils by using steered molecular dynamics simulations. Our simulation results show that the elastic modulus of prion fibril, which is formed based on left-handed β-helical structure, is larger than that of non-prion fibril constructed based on right-handed β-helix. However, the mechanical toughness of prion fibril is found to be less than that of non-prion fibril, which indicates that infectious prion fibril is more fragile than non-infectious (non-prion) fibril. Our study sheds light on the role of the helical structure of amyloid fibrils, which is related to prion infectivity, in determining their mechanical deformation mechanisms and properties.

Engineering Metallic Nanoparticles for Enhancing and Probing Catalytic Reactions.

PubMed

Collins, Gillian; Holmes, Justin D

2016-07-01

Recent developments in tailoring the structural and chemical properties of colloidal metal nanoparticles (NPs) have led to significant enhancements in catalyst performance. Controllable colloidal synthesis has also allowed tailor-made NPs to serve as mechanistic probes for catalytic processes. The innovative use of colloidal NPs to gain fundamental insights into catalytic function will be highlighted across a variety of catalytic and electrocatalytic applications. The engineering of future heterogenous catalysts is also moving beyond size, shape and composition considerations. Advancements in understanding structure-property relationships have enabled incorporation of complex features such as tuning surface strain to influence the behavior of catalytic NPs. Exploiting plasmonic properties and altering colloidal surface chemistry through functionalization are also emerging as important areas for rational design of catalytic NPs. This news article will highlight the key developments and challenges to the future design of catalytic NPs. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

[Development of fluorescent probes for bone imaging in vivo ~Fluorescent probes for intravital imaging of osteoclast activity~.

PubMed

Minoshima, Masafumi; Kikuchi, Kazuya

Fluorescent molecules are widely used as a tool to directly visualize target biomolecules in vivo. Fluorescent probes have the advantage that desired function can be rendered based on rational design. For bone-imaging fluorescent probes in vivo, they should be delivered to bone tissue upon administration. Recently, a fluorescent probe for detecting osteoclast activity was developed. The fluorescent probe has acid-sensitive fluorescence property, specific delivery to bone tissue, and durability against laser irradiation, which enabled real-time intravital imaging of bone-resorbing osteoclasts for a long period of time.

Probing porous media with gas diffusion NMR

NASA Technical Reports Server (NTRS)

Mair, R. W.; Wong, G. P.; Hoffmann, D.; Hurlimann, M. D.; Patz, S.; Schwartz, L. M.; Walsworth, R. L.

1999-01-01

We show that gas diffusion nuclear magnetic resonance (GD-NMR) provides a powerful technique for probing the structure of porous media. In random packs of glass beads, using both laser-polarized and thermally polarized xenon gas, we find that GD-NMR can accurately measure the pore space surface-area-to-volume ratio, S/V rho, and the tortuosity, alpha (the latter quantity being directly related to the system's transport properties). We also show that GD-NMR provides a good measure of the tortuosity of sandstone and complex carbonate rocks.

Cellulose nanomaterials review: structure, properties and nanocomposites

Treesearch

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

2011-01-01

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

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

PubMed

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)PLEEE81539-375510.1103/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 d_{T}, in addition to those length scales already relevant: monomer bead size d, probe size R, polymer radius of gyration R_{g}, 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 M_{w}^{3}. 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 L_{S} of the shell around the particle that contains the added mass, L_{S}>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.

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.

The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure.

PubMed

Leontis, N B; Westhof, E

1998-09-01

A significant fraction of the bases in a folded, structured RNA molecule participate in noncanonical base pairing interactions, often in the context of internal loops or multi-helix junction loops. The appearance of each new high-resolution RNA structure provides welcome data to guide efforts to understand and predict RNA 3D structure, especially when the RNA in question is a functionally conserved molecule. The recent publication of the crystal structure of the "Loop E" region of bacterial 5S ribosomal RNA is such an event [Correll CC, Freeborn B, Moore PB, Steitz TA, 1997, Cell 91:705-712]. In addition to providing more examples of already established noncanonical base pairs, such as purine-purine sheared pairings, trans-Hoogsteen UA, and GU wobble pairs, the structure provides the first high-resolution views of two new purine-purine pairings and a new GU pairing. The goal of the present analysis is to expand the capabilities of both chemical probing and phylogenetic analysis to predict with greater accuracy the structures of RNA molecules. First, in light of existing chemical probing data, we investigate what lessons could be learned regarding the interpretation of this widely used method of RNA structure probing. Then we analyze the 3D structure with reference to molecular phylogeny data (assuming conservation of function) to discover what alternative base pairings are geometrically compatible with the structure. The comparisons between previous modeling efforts and crystal structures show that the intricate involvements of ions and water molecules in the maintenance of non-Watson-Crick pairs render the process of correctly identifying the interacting sites in such pairs treacherous, except in cases of trans-Hoogsteen A/U or sheared A/G pairs for the adenine N1 site. The phylogenetic analysis identifies A/A, A/C, A/U and C/A, C/C, and C/U pairings isosteric with sheared A/G, as well as A/A and A/C pairings isosteric with both G/U and G/G bifurcated pairings

Probe measurements of the three-dimensional magnetic field structure in a rotating magnetic field sustained field-reversed configuration

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

Velas, K. M.; Milroy, R. D.

A translatable three-axis probe was constructed and installed on the translation, confinement, and sustainment upgrade (TCSU) experiment. With ninety windings, the probe can simultaneously measure B{sub r}, B{sub θ}, and B{sub z} at 30 radial positions, and can be placed at any desired axial position within the field reversed configuration (FRC) confinement chamber. Positioning the probe at multiple axial positions and taking multiple repeatable shots allows for a full r-z map of the magnetic field. Measurements were made for odd-parity rotating magnetic field (RMF) antennas and even-parity RMF. The steady state data from applying a 10 kHz low pass filter usedmore » in conjunction with data at the RMF frequency yields a map of the full 3D rotating field structure. Comparisons will be made to the 3D magnetic structure predicted by NIMROD simulations, with parameters adjusted to match that of the TCSU experiments. The probe provides sufficient data to utilize a Maxwell stress tensor approach to directly measure the torque applied to the FRC's electrons, which combined with a resistive torque model, yields an estimate of the average FRC resistivity.« less

Hydroxyl group as IR probe to detect the structure of ionic liquid-acetonitrile mixtures

NASA Astrophysics Data System (ADS)

Xu, Jing; Deng, Geng; Zhou, Yu; Ashraf, Hamad; Yu, Zhi-Wu

2018-06-01

Task-specific ionic liquids (ILs) are those with functional groups introduced in the cations or anions of ILs to bring about specific properties for various tasks. In this work, the hydrogen bonding interactions between a hydroxyl functionalized IL 1-(2-hydroxylethyl)-3-methylimidazolium tetrafluoroborate ([C2OHMIM][BF4]) and acetonitrile were investigated in detail by infrared spectroscopy, excess spectroscopy, two-dimensional correlation spectroscopy, combined with hydrogen nuclear magnetic resonance and density functional theory calculations (DFT). The hydroxyl group rather than C2sbnd H is found to be the main interaction site in the cation. And the ν(Osbnd H) is more sensitive than v(C-Hs) to the environment, which has been taken as an intrinsic probe to reflect the structural change of IL. Examining the region of ν(Osbnd H), by combining excess spectroscopy and DFT calculation, a number of species were identified in the mixtures. Other than the hydrogen bond between a cation and an anion, the hydroxyl group allows the formation of a hydrogen bond between two like-charged cations. The Osbnd H⋯O hydrogen bonding interactions in the hydroxyl-mediated cation-cation complexes are cooperative, while Osbnd H⋯F and C2sbnd H⋯F hydrogen bonding interactions in cation-anion complexes are anti-cooperative. These in-depth studies on the properties of the ionic liquid-acetonitrile mixtures may shed light on exploring their applications as mixed solvents and understanding the nature of doubly ionic hydrogen bonds.

Influence of Donor on the Sensing Performance of a Series of Through-Bond Energy Transfer-Based Two-photon Fluorescent Cu(2+) Probes.

PubMed

Zhang, Yu-Jin; Wang, Xin; Zhou, Yong; Wang, Chuan-Kui

2016-07-01

Optical properties of a series of molecular two-photon fluorescent Cu(2+) probes containing the same acceptor (rhodamine group) are analyzed using time-dependent density functional theory in combination with analytical response theory. Special emphasis is placed on evolution of the probes' optical properties in the presence of Cu(2+) . In this study, the compound with naphthalene as the donor is shown to be excellent ratiometric fluorescent chemosensor, whereas the compound with quinoline derivative as the donor shows off/on-typed colorimetric fluorescent response. For the compound with naphthalimide derivative as the donor, changing the connection between the donor and acceptor can efficiently prevent the fluorescent quenching of the probe both in the absence and presence of Cu(2+) . The donor moiety and the connection between donor and acceptor are thus found to play dominant roles on sensing performance of these probes. Moreover, distributions of molecular orbitals involved in the excitation and emission of the probes are analyzed to explore responsive mechanism of the probes. The through-bond energy transfer process is theoretically demonstrated. Our results are used to elucidate the available experimental measurements. This work is helpful to understand the relationships of structure with optical properties for the studied probes. © 2016 The American Society of Photobiology.

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

Highlighting cancer cells with macromolecular probes

NASA Astrophysics Data System (ADS)

Tang, Sicheng; Zhang, Yang; Thapaliya, Ek Raj; Brown, Adrienne S.; Wilson, James N.; Raymo, Françisco M.

2017-02-01

Conventional fluorophore-ligand constructs for the detection of cancer cells generally produce relatively weak signals with modest contrast. The inherently low brightness accessible per biding event with the pairing of a single organic fluorophore to a single ligand as well as the contribution of unbound probes to background fluorescence are mainly responsible for these limitations. Our laboratories identified a viable structural design to improve both brightness and contrast. It is based on the integration of activatable fluorophores and targeting ligands within the same macromolecular construct. The chromophoric components are engineered to emit bright fluorescence exclusively in acidic environments. The targeting agents are designed to bind complementary receptors overexpressed on the surface of cancer cells and allow internalization of the macromolecules into acidic organelles. As a result of these properties, our macromolecular probes switch their intense emission on exclusively in the intracellular space of target cells with minimal background fluorescence from the extracellular matrix. In fact, these operating principles translate into a 170-fold enhancement in brightness, relative to equivalent but isolated chromophoric components, and a 3-fold increase in contrast, relative to model but non-activatable fluorophores. Thus, our macromolecular probes might ultimately evolve into valuable analytical tools to highlight cancer cells with optimal signal-to-noise ratios in a diversity of biomedical applications.

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

PubMed

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

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

PubMed Central

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

2014-01-01

We used photoactive substrates consisting of about 1 nm coating of a metal oxide on glass substrates to investigate the impact of the structures of colloidal quantum dots on their photophysical and photochemical properties. We showed during irradiation these substrates can interact uniquely with such quantum dots, inducing distinct forms of photo-induced processes when they have different cores, shells, or ligands. In particular, our results showed that for certain types of core-shell quantum dot structures an ultrathin layer of a metal oxide can reduce suppression of quantum efficiency of the quantum dots happening when they undergo extensive photo-oxidation. This suggests the possibility of shrinking the sizes of quantum dots without significant enhancement of their non-radiative decay rates. We show that such quantum dots are not influenced significantly by Coulomb blockade or photoionization, while those without a shell can undergo a large amount of photo-induced fluorescence enhancement via such blockade when they are in touch with the metal oxide. PMID:25316953

PEGylated Red-Emitting Calcium Probe with Improved Sensing Properties for Neuroscience.

PubMed

Ponsot, Flavien; Shen, Weida; Ashokkumar, Pichandi; Audinat, Etienne; Klymchenko, Andrey S; Collot, Mayeul

2017-11-22

Monitoring calcium concentration in the cytosol is of main importance as this ion drives many biological cascades within the cell. To this end, molecular calcium probes are widely used. Most of them, especially the red emitting probes, suffer from nonspecific interactions with inner membranes due to the hydrophobic nature of their fluorophore. To circumvent this issue, calcium probes conjugated to dextran can be used to enhance the hydrophilicity and reduce the nonspecific interaction and compartmentalization. However, dextran conjugates also feature important drawbacks including lower affinity, lower dynamic range, and slow diffusion. Herein, we combined the advantage of molecular probes and dextran conjugate without their drawbacks by designing a new red emitting turn-on calcium probe based on PET quenching, Rhod-PEG, in which the rhodamine fluorophore bears four PEG 4 units. This modification led to a high affinity calcium probe (K d = 748 nM) with reduced nonspecific interactions, enhanced photostability, two-photon absorbance, and brightness compared to the commercially available Rhod-2. After spectral characterizations, we showed that Rhod-PEG quickly and efficiently diffused through the dendrites of pyramidal neurons with an enhanced sensitivity (ΔF/F 0 ) at shorter time after patching compared to Rhod-2.

Growth of Cosmic Structure: Probing Dark Energy Beyond Expansion

DOE PAGES

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

2014-03-15

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

Growth of Cosmic Structure: Probing Dark Energy Beyond Expansion

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

Huterer, Dragan; Kirkby, David; Bean, Rachel

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

Outer planet entry probe system study. Volume 4: Common Saturn/Uranus probe studies

NASA Technical Reports Server (NTRS)

1973-01-01

Results are summarized of a common scientific probe study to explore the atmospheres of Saturn and Uranus. This was a three-month follow-on effort to the Outer Planet Entry Probe System study. The report presents: (1) a summary, conclusions and recommendations of this study, (2) parametric analysis conducted to support the two system definitions, (3) common Saturn/Uranus probe system definition using the Science Advisory Group's exploratory payload and, (4) common Saturn/Uranus probe system definition using an expanded science complement. Each of the probe system definitions consists of detailed discussions of the mission, science, system and subsystems including telecommunications, data handling, power, pyrotechnics, attitude control, structures, propulsion, thermal control and probe-to-spacecraft integration. References are made to the contents of the first three volumes where it is feasible to do so.

The Measurement of Unsteady Surface Pressure Using a Remote Microphone Probe.

PubMed

Guan, Yaoyi; Berntsen, Carl R; Bilka, Michael J; Morris, Scott C

2016-12-03

Microphones are widely applied to measure pressure fluctuations at the walls of solid bodies immersed in turbulent flows. Turbulent motions with various characteristic length scales can result in pressure fluctuations over a wide frequency range. This property of turbulence requires sensing devices to have sufficient sensitivity over a wide range of frequencies. Furthermore, the small characteristic length scales of turbulent structures require small sensing areas and the ability to place the sensors in very close proximity to each other. The complex geometries of the solid bodies, often including large surface curvatures or discontinuities, require the probe to have the ability to be set up in very limited spaces. The development of a remote microphone probe, which is inexpensive, consistent, and repeatable, is described in the present communication. It allows for the measurement of pressure fluctuations with high spatial resolution and dynamic response over a wide range of frequencies. The probe is small enough to be placed within the interior of typical wind tunnel models. The remote microphone probe includes a small, rigid, and hollow tube that penetrates the model surface to form the sensing area. This tube is connected to a standard microphone, at some distance away from the surface, using a "T" junction. An experimental method is introduced to determine the dynamic response of the remote microphone probe. In addition, an analytical method for determining the dynamic response is described. The analytical method can be applied in the design stage to determine the dimensions and properties of the RMP components.

Mechanism for starch granule ghost formation deduced from structural and enzyme digestion properties.

PubMed

Zhang, Bin; Dhital, Sushil; Flanagan, Bernadine M; Gidley, Michael J

2014-01-22

After heating in excess water under little or no shear, starch granules do not dissolve completely but persist as highly swollen fragile forms, commonly termed granule "ghosts". The macromolecular architecture of these ghosts has not been defined, despite their importance in determining characteristic properties of starches. In this study, amylase digestion of isolated granule ghosts from maize and potato starches is used as a probe to study the mechanism of ghost formation, through microstructural, mesoscopic, and molecular scale analyses of structure before and after digestion. Digestion profiles showed that neither integral nor surface proteins/lipids were crucial for control of either ghost digestion or integrity. On the basis of the molecular composition and conformation of enzyme-resistant fractions, it was concluded that the condensed polymeric surface structure of ghost particles is mainly composed of nonordered but entangled amylopectin (and some amylose) molecules, with limited reinforcement through partially ordered enzyme-resistant structures based on amylose (for maize starch; V-type order) or amylopectin (for potato starch; B-type order). The high level of branching and large molecular size of amylopectin is proposed to be the origin for the unusual stability of a solid structure based primarily on temporary entanglements.

Structure and composition of insulin fibril surfaces probed by TERS

PubMed Central

Kurouski, Dmitry; Deckert-Gaudig, Tanja; Deckert, Volker; Lednev, Igor K.

2012-01-01

Amyloid fibrils associated with many neurodegenerative diseases are the most intriguing targets of modern structural biology. Significant knowledge has been accumulated about the morphology and fibril-core structure recently. However, no conventional methods could probe the fibril surface despite its significant role in the biological activity. Tip-enhanced Raman spectroscopy (TERS) offers a unique opportunity to characterize the surface structure of an individual fibril due to a high depth and lateral spatial resolution of the method in the nanometer range. Here, TERS is utilized for characterizing the secondary structure and amino acid residue composition of the surface of insulin fibrils. It was found that the surface is strongly heterogeneous and consists of clusters with various protein conformations. More than 30% of the fibril surface is dominated by β-sheet secondary structure, further developing Dobson’s model of amyloid fibrils (Jimenez et al. Proc. Natl. Acad. Sci. USA 2002). The propensity of various amino acids on the fibril surface and specific surface secondary structure elements were evaluated. β-sheet areas are rich in cysteine and aromatic amino acids, such as phenylalanine and tyrosine, whereas proline was found only in α-helical and unordered protein clusters. In addition, we showed that carboxyl, amino and imino groups are nearly equally distributed over β-sheet and α-helix/unordered regions. Overall, this study provides valuable new information about the structure and composition of the insulin fibril surface and demonstrates the power of TERS for fibril characterization. PMID:22813355

The Antartic Ice Borehole Probe

NASA Technical Reports Server (NTRS)

Behar, A.; Carsey, F.; Lane, A.; Engelhardt, H.

2000-01-01

The Antartic Ice Borehole Probe mission is a glaciological investigation, scheduled for November 2000-2001, that will place a probe in a hot-water drilled hole in the West Antartic ice sheet. The objectives of the probe are to observe ice-bed interactions with a downward looking camera, and ice inclusions and structure, including hypothesized ice accretion, with a side-looking camera.

Engineering and Probing Topological Properties of Dirac Semimetal Films by Asymmetric Charge Transfer.

PubMed

Villanova, John W; Barnes, Edwin; Park, Kyungwha

2017-02-08

Dirac semimetals (DSMs) have topologically robust three-dimensional Dirac (doubled Weyl) nodes with Fermi-arc states. In heterostructures involving DSMs, charge transfer occurs at the interfaces, which can be used to probe and control their bulk and surface topological properties through surface-bulk connectivity. Here we demonstrate that despite a band gap in DSM films, asymmetric charge transfer at the surface enables one to accurately identify locations of the Dirac-node projections from gapless band crossings and to examine and engineer properties of the topological Fermi-arc surface states connecting the projections, by simulating adatom-adsorbed DSM films using a first-principles method with an effective model. The positions of the Dirac-node projections are insensitive to charge transfer amount or slab thickness except for extremely thin films. By varying the amount of charge transfer, unique spin textures near the projections and a separation between the Fermi-arc states change, which can be observed by gating without adatoms.

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

Physical probing of cells

NASA Astrophysics Data System (ADS)

Rehfeldt, Florian; Schmidt, Christoph F.

2017-11-01

In the last two decades, it has become evident that the mechanical properties of the microenvironment of biological cells are as important as traditional biochemical cues for the control of cellular behavior and fate. The field of cell and matrix mechanics is quickly growing and so is the development of the experimental approaches used to study active and passive mechanical properties of cells and their surroundings. Within this topical review we will provide a brief overview, on the one hand, over how cellular mechanics can be probed physically, how different geometries allow access to different cellular properties, and, on the other hand, how forces are generated in cells and transmitted to the extracellular environment. We will describe the following experimental techniques: atomic force microscopy, traction force microscopy, magnetic tweezers, optical stretcher and optical tweezers pointing out both their advantages and limitations. Finally, we give an outlook on the future of the physical probing of cells.

Modeling adsorption properties of structurally deformed metal–organic frameworks using structure–property map

PubMed Central

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

2017-01-01

Structural deformation and collapse in metal-organic frameworks (MOFs) can lead to loss of long-range order, making it a challenge to model these amorphous materials using conventional computational methods. In this work, we show that a structure–property map consisting of simulated data for crystalline MOFs can be used to indirectly obtain adsorption properties of structurally deformed MOFs. The structure–property map (with dimensions such as Henry coefficient, heat of adsorption, and pore volume) was constructed using a large data set of over 12000 crystalline MOFs from molecular simulations. By mapping the experimental data points of deformed SNU-200, MOF-5, and Ni-MOF-74 onto this structure–property map, we show that the experimentally deformed MOFs share similar adsorption properties with their nearest neighbor crystalline structures. Once the nearest neighbor crystalline MOFs for a deformed MOF are selected from a structure–property map at a specific condition, then the adsorption properties of these MOFs can be successfully transformed onto the degraded MOFs, leading to a new way to obtain properties of materials whose structural information is lost. PMID:28696307

Could Nano-Structured Materials Enable the Improved Pressure Vessels for Deep Atmospheric Probes?

NASA Technical Reports Server (NTRS)

Srivastava, D.; Fuentes, A.; Bienstock, B.; Arnold, J. O.

2005-01-01

A viewgraph presentation on the use of Nano-Structured Materials to enable pressure vessel structures for deep atmospheric probes is shown. The topics include: 1) High Temperature/Pressure in Key X-Environments; 2) The Case for Use of Nano-Structured Materials Pressure Vessel Design; 3) Carbon based Nanomaterials; 4) Nanotube production & purification; 5) Nanomechanics of Carbon Nanotubes; 6) CNT-composites: Example (Polymer); 7) Effect of Loading sequence on Composite with 8% by volume; 8) Models for Particulate Reinforced Composites; 9) Fullerene/Ti Composite for High Strength-Insulating Layer; 10) Fullerene/Epoxy Composite for High Strength-Insulating Layer; 11) Models for Continuous Fiber Reinforced Composites; 12) Tensile Strength for Discontinuous Fiber Composite; 13) Ti + SWNT Composites: Thermal/Mechanical; 14) Ti + SWNT Composites: Tensile Strength; and 15) Nano-structured Shell for Pressure Vessels.

Carbon phenolic heat shields for Jupiter/Saturn/Uranus entry probes

NASA Technical Reports Server (NTRS)

Mezines, S.

1974-01-01

Carbon phenolic heat shield technology is reviewed. Heat shield results from the outer planetary probe mission studies are summarized along with results of plasma jet testing of carbon phenolic conducted in a ten megawatt facility. Missile flight data is applied to planetary entry conditions. A carbon phenolic heat shield material is utilized and tailored to accommodate each of the probe missions. An integral heat shield approach is selected over in order to eliminate a high temperature interface problem and permit direct bonding of the carbon phenolic to the structural honeycomb sandwich. The sandwich is filled with a very fine powder to minimize degradation of its insulation properties by the high conductive hydrogen/helium gases during the long atmospheric descent phase.

A Study on the Plasmonic Properties of Silver Core Gold Shell Nanoparticles: Optical Assessment of the Particle Structure

NASA Astrophysics Data System (ADS)

Mott, Derrick; Lee, JaeDong; Thi Bich Thuy, Nguyen; Aoki, Yoshiya; Singh, Prerna; Maenosono, Shinya

2011-06-01

This paper reports a qualitative comparison between the optical properties of a set of silver core, gold shell nanoparticles with varying composition and structure to those calculated using the Mie solution. To achieve this, silver nanoparticles were synthesized in aqueous phase from a silver hydroxide precursor with sodium acrylate as dual reducing-capping agent. The particles were then coated with a layer of gold with controllable thickness through a reduction-deposition process. The resulting nanoparticles reveal well defined optical properties that make them suitable for comparison to ideal calculated results using the Mie solution. The discussion focuses on the correlation between the synthesized core shell nanoparticles with varying Au shell thickness and the Mie solution results in terms of the optical properties. The results give insight in how to design and synthesize silver core, gold shell nanoparticles with controllable optical properties (e.g., SPR band in terms of intensity and position), and has implications in creating nanoparticle materials to be used as biological probes and sensing elements.

Probing the onset of structural instabilities as a tool for detection of staling of dairy milk: A permittivity and conductivity study

NASA Astrophysics Data System (ADS)

Madhurima, V.; Harindran, Aswini

2018-05-01

Dairy milk is a worldwide drink and a versatile raw material for food industries too. The major issue regarding dairy milk is their contamination by micro-organisms and subsequent spoiling. Pasteurization and sealed packing are used to minimize this contamination. The presence of pathogenic micro-organisms like psychrotrophs, reduces the pH of fresh milk by fermenting the lactose into lactic acid leading to the spoiling of milk. While there are various tests to check the spoilage of milk, there is no unique test to detect the onset of the complex dynamics of spoilage. There have been some studies on the dielectric properties of dairy milk but the primary method of identification of freshness of milk is through the measurement of pH. In this study, broadband dielectric spectroscopy is used as a tool to probe the spoiling of milk and that provides the information about the structural changes of milk during spoilage. The gamma dispersion explains the influence of free water content which is found to be a sensitive tool to probe the onset of milk spoilage process. The observations here are further backed by studies on the particle size and zeta potential.

Redox properties of structural Fe in clay minerals: 3. Relationships between smectite redox and structural properties.

PubMed

Gorski, Christopher A; Klüpfel, Laura E; Voegelin, Andreas; Sander, Michael; Hofstetter, Thomas B

2013-01-01

Structural Fe in clay minerals is an important redox-active species in many pristine and contaminated environments as well as in engineered systems. Understanding the extent and kinetics of redox reactions involving Fe-bearing clay minerals has been challenging due to the inability to relate structural Fe(2+)/Fe(total) fractions to fundamental redox properties, such as reduction potentials (EH). Here, we overcame this challenge by using mediated electrochemical reduction (MER) and oxidation (MEO) to characterize the fraction of redox-active structural Fe (Fe(2+)/Fe(total)) in smectites over a wide range of applied EH-values (-0.6 V to +0.6 V). We examined Fe(2+)/Fe(total )- EH relationships of four natural Fe-bearing smectites (SWy-2, SWa-1, NAu-1, NAu-2) in their native, reduced, and reoxidized states and compared our measurements with spectroscopic observations and a suite of mineralogical properties. All smectites exhibited unique Fe(2+)/Fe(total) - EH relationships, were redox active over wide EH ranges, and underwent irreversible electron transfer induced structural changes that were observable with X-ray absorption spectroscopy. Variations among the smectite Fe(2+)/Fe(total) - EH relationships correlated well with both bulk and molecular-scale properties, including Fe(total) content, layer charge, and quadrupole splitting values, suggesting that multiple structural parameters determined the redox properties of smectites. The Fe(2+)/Fe(total) - EH relationships developed for these four commonly studied clay minerals may be applied to future studies interested in relating the extent of structural Fe reduction or oxidation to EH-values.

Structure-property study of keto-ether polyimides

NASA Technical Reports Server (NTRS)

Dezern, James F.; Croall, Catharine I.

1991-01-01

As part of an on-going effort to develop an understanding of how changes in the chemical structure affect polymer properties, an empirical study was performed on polyimides containing only ether and/or carbonyl connecting groups in the polymer backbone. During the past two decades the structure-property relationships in linear aromatic polyimides have been extensively investigated. More recently, work has been performed to study the effect of isomeric attachment of keto-ether polyimides on properties such as glass transition temperature and solubility. However, little work has been reported on the relation of polyimide structure to mechanical properties. The purpose of this study was to determine the effect of structural changes in the backbone of keto-ether polyimides on their mechanical properties, specifically, unoriented thin film tensile properties. This study was conducted in two stages. The purpose of the initial stage was to examine the physical and mechanical properties of a representative group (four) of polyimide systems to determine the optimum solvent and cure cycle requirements. These optimum conditions were then utilized in the second stage to prepare films of keto-ether polyimides which were evaluated for mechanical and physical properties. All of the polyimides were prepared using isomers of oxydianiline (ODA) and diaminobenzophenone (DABP) in combination with 3,3',4,4'-benzophenonetetracarboxylic dianhydride (BTDA) and 4,4'-oxydiphthalic anhydride (ODPA).

Impedance-controlled ultrasound probe

NASA Astrophysics Data System (ADS)

Gilbertson, Matthew W.; Anthony, Brian W.

2011-03-01

An actuated hand-held impedance-controlled ultrasound probe has been developed. The controller maintains a prescribed contact state (force and velocity) between the probe and a patient's body. The device will enhance the diagnostic capability of free-hand elastography and swept-force compound imaging, and also make it easier for a technician to acquire repeatable (i.e. directly comparable) images over time. The mechanical system consists of an ultrasound probe, ball-screw-driven linear actuator, and a force/torque sensor. The feedback controller commands the motor to rotate the ball-screw to translate the ultrasound probe in order to maintain a desired contact force. It was found that users of the device, with the control system engaged, maintain a constant contact force with 15 times less variation than without the controller engaged. The system was used to determine the elastic properties of soft tissue.

RaptorX-Property: a web server for protein structure property prediction.

PubMed

Wang, Sheng; Li, Wei; Liu, Shiwang; Xu, Jinbo

2016-07-08

RaptorX Property (http://raptorx2.uchicago.edu/StructurePropertyPred/predict/) is a web server predicting structure property of a protein sequence without using any templates. It outperforms other servers, especially for proteins without close homologs in PDB or with very sparse sequence profile (i.e. carries little evolutionary information). This server employs a powerful in-house deep learning model DeepCNF (Deep Convolutional Neural Fields) to predict secondary structure (SS), solvent accessibility (ACC) and disorder regions (DISO). DeepCNF not only models complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent property labels. Our experimental results show that, tested on CASP10, CASP11 and the other benchmarks, this server can obtain ∼84% Q3 accuracy for 3-state SS, ∼72% Q8 accuracy for 8-state SS, ∼66% Q3 accuracy for 3-state solvent accessibility, and ∼0.89 area under the ROC curve (AUC) for disorder prediction. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Structural Properties of Barium Stannate.

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

Phelan, D.; Han, F.; Lopez-Bezanilla, A.

2018-06-01

BaSnO3 has attracted attention as a transparent conducting oxide with high room temperature carrier mobility. We report a series of measurements that were carried out to assess the structure of BaSnO3 over a variety of length scales. Measurements included single crystal neutron and x-ray diffraction, Rietveld and pair distribution analysis of neutron powder diffraction, Raman scattering, and high-pressure x-ray diffraction. Results from the various diffraction probes indicate that both the long-range and local structures are consistent with the cubic symmetry. The diffraction data under pressure was consistent with a robustly cubic phase up to 48.9 GPa, which is supported bymore » density functional calculations. Additionally, transverse phonon velocities were determined from measured dispersion of the transverse acoustic phonon branches, the results of which are in good agreement with previous theoretical estimates and ultrasound measurements.« less

Structural properties of barium stannate

NASA Astrophysics Data System (ADS)

Phelan, D.; Han, F.; Lopez-Bezanilla, A.; Krogstad, M. J.; Gim, Y.; Rong, Y.; Zhang, Junjie; Parshall, D.; Zheng, H.; Cooper, S. L.; Feygenson, M.; Yang, Wenge; Chen, Yu-Sheng

2018-06-01

BaSnO3 has attracted attention as a transparent conducting oxide with high room temperature carrier mobility. We report a series of measurements that were carried out to assess the structure of BaSnO3 over a variety of length scales. Measurements included single crystal neutron and x-ray diffraction, Rietveld and pair distribution analysis of neutron powder diffraction, Raman scattering, and high-pressure x-ray diffraction. Results from the various diffraction probes indicate that both the long-range and local structures are consistent with the cubic symmetry. The diffraction data under pressure was consistent with a robustly cubic phase up to 48.9 GPa, which is supported by density functional calculations. Additionally, transverse phonon velocities were determined from measured dispersion of the transverse acoustic phonon branches, the results of which are in good agreement with previous theoretical estimates and ultrasound measurements.

Low-Temperature Scanning Capacitance Probe for Imaging Electron Motion

NASA Astrophysics Data System (ADS)

Bhandari, S.; Westervelt, R. M.

2014-12-01

Novel techniques to probe electronic properties at the nanoscale can shed light on the physics of nanoscale devices. In particular, studying the scattering of electrons from edges and apertures at the nanoscale and imaging the electron profile in a quantum dot, have been of interest [1]. In this paper, we present the design and implementation of a cooled scanning capacitance probe that operates at liquid He temperatures to image electron waves in nanodevices. The conducting tip of a scanned probe microscope is held above the nanoscale structure, and an applied sample-to-tip voltage creates an image charge that is measured by a cooled charge amplifier [2] adjacent to the tip. The circuit is based on a low-capacitance, high- electron-mobility transistor (Fujitsu FHX35X). The input is a capacitance bridge formed by a low capacitance pinched-off HEMT transistor and tip-sample capacitance. We have achieved low noise level (0.13 e/VHz) and high spatial resolution (100 nm) for this technique, which promises to be a useful tool to study electronic behavior in nanoscale devices.

Probing the structural and electronic properties of cationic rubidium-gold clusters: [AunRb]+ (n = 1-10)

NASA Astrophysics Data System (ADS)

Zhao, Ya-Ru; Zhang, Hai-Rong; Qian, Yu; Duan, Xu-Chao; Hu, Yan-Fei

2016-03-01

Density functional theory has been applied to study the geometric structures, relative stabilities, and electronic properties of cationic [AunRb]+ and Aun + 1+ (n = 1-10) clusters. For the lowest energy structures of [AunRb]+ clusters, the planar to three-dimensional transformation is found to occur at cluster size n = 4 and the Rb atoms prefer being located at the most highly coordinated position. The trends of the averaged atomic binding energies, fragmentation energies, second-order difference of energies, and energy gaps show pronounced even-odd alternations. It indicated that the clusters containing odd number of atoms maintain greater stability than the clusters in the vicinity. In particular, the [Au6Rb]+ clusters are the most stable isomer for [AunRb]+ clusters in the region of n = 1-10. The charges in [AunRb]+ clusters transfer from the Rb atoms to Aun host. Density of states revealed that the Au-5d, Au-5p, and Rb-4p orbitals hardly participated in bonding. In addition, it is found that the most favourable channel of the [AunRb]+ clusters is Rb+ cation ejection. The electronic localisation function (ELF) analysis of the [AunRb]+ clusters shown that strong interactions are not revealed in this study.

How does a probe inserted into the discharge influence the plasma structure?

NASA Astrophysics Data System (ADS)

Yordanov, D.; Lishev, St.; Shivarova, A.

2016-05-01

Shielding the bias applied to the probe by the sheath formed around it and determination of parameters of unperturbed plasmas are in the basis of the probe diagnostics. The results from a two-dimensional model of a discharge with a probe inserted in it show that the probe influences the spatial distribution of the plasma parameters in the entire discharge. The increase (although slight) in the electron temperature, due to the increased losses of charged particles on the additional wall in the discharge (mainly the probe holder), leads to redistribution of the plasma density and plasma potential, as shown by the results obtained at the floating potential of the probe. The deviations due to the bias applied to the probe tip are stronger in the ion saturation region of the probe characteristics. The pattern of the spatial redistribution of the plasma parameters advances together with the movement of the probe deeper in the discharge. Although probe sheaths and probe characteristics resulting from the model are shown, the study does not aim at discussions on the theories for determination of the plasma density from the ion saturation current. Regardless of the modifications in the plasma behavior in the entire discharge, the deviations of the plasma parameters at the position of the probe tip and, respectively, the uncertainty which should be added as an error when the accuracy of the probe diagnostics is estimated do not exceed 10%. Consequently, the electron density and temperature obtained, respectively, at the position of the plasma potential on the probe characteristics and from its transition region are in reasonable agreement with the results from the model of the discharge without a probe. Being in the scope of research on a source of negative hydrogen ions with the design of a matrix of small radius inductive discharges, the model is specified for a low-pressure hydrogen discharge sustained in a small-radius tube.

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

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

Patty, Kira; Campbell, Quinn; Hamilton, Nathan

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 suggestsmore » 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.« less

Investigating the Synthesis, Structure, and Catalytic Properties of Versatile Gold-Based Nanocatalvsts

NASA Astrophysics Data System (ADS)

Pretzer, Lori A.

Transition metal nanomaterials are used to catalyze many chemical reactions, including those key to environmental, medicinal, and petrochemical fields. Improving their catalytic properties and lifetime would have significant economic and environmental rewards. Potentially expedient options to make such advancements are to alter the shape, size, or composition of transition metal nanocatalysts. This work investigates the relationships between structure and catalytic properties of synthesized Au, Pd-on-Au, and Au-enzyme model transition metal nanocatalysts. Au and Pd-on-Au nanomaterials were studied due to their wide-spread application and structure-dependent electronic and geometric properties. The goal of this thesis is to contribute design procedures and synthesis methods that enable the preparation of more efficient transition metal nanocatalysts. The influence of the size and composition of Pd-on-Au nanoparticles (NPs) was systematically investigated and each was found to affect the catalyst's surface structure and catalytic properties. The catalytic hydrodechlorination of trichloroethene and reduction of 4-nitrophenol by Pd-on-Au nanoparticles were investigated as these reactions are useful for environmental and pharmaceutical synthesis applications, respectively. Structural characterization revealed that the dispersion and oxidation state of surface Pd atoms are controlled by the Au particle size and concentration of Pd. These structural changes are correlated with observed Pd-on-Au NP activities for both probe reactions, providing new insight into the structure-activity relationships of bimetallic nanocatalysts. Using the structure-dependent electronic properties of Au NPs, a new type of light-triggered biocatalyst was prepared and used to remotely control a model biochemical reaction. This biocatalyst consists of a model thermophilic glucokinase enzyme covalently attached to the surface of Au nanorods. The rod-like shape of the Au nanoparticles made the

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

NASA Astrophysics Data System (ADS)

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

2006-03-01

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

Accuracy of probing attachment levels using a new computerized cemento-enamel junction probe.

PubMed

Deepa, R; Prakash, Shobha

2012-01-01

The assessment of clinical attachment level (CAL) represents the gold standard for diagnosing and monitoring periodontal disease. The aim of the present study was to evaluate the performance of the newly introduced cemento-enamel junction (CEJ) probe in detecting CAL, using CEJ as a fixed reference point, and to compare the CEJ probe with the Florida stent probe (FSP) as well as with a standard manual probe, University of North Carolina-15 (UNC-15). Three examiners recorded the probing attachment level in 384 sites in case group (chronic periodontitis), and in 176 sites, in control group (healthy periodontal status), using the three probes. Subjects included both the sexes and ranged from 35 to 45 years. The experimental design was structured to balance the intra- and inter-examiner consistency at the same site during the two visits. CEJ probe showed higher intra-and inter-examiner consistency over both FSP and UNC-15 in both the case and control groups. Frequency distribution of differences of various magnitudes of repeated measurements ≤1 mm was in the higher range of 86.8% to 87.5% for CEJ probe. The FSP was more reproducible than UNC-15 in detecting relative attachment level (RAL). CEJ automated probe was found to have greatest potential for accuracy and consistency in detecting CAL than FSP and UNC-15. The automated probes appeared to be more reproducible than manual probes.

Structure and vibrational properties of the dominant O-H center in β-Ga2O3

NASA Astrophysics Data System (ADS)

Weiser, Philip; Stavola, Michael; Fowler, W. Beall; Qin, Ying; Pearton, Stephen

2018-06-01

Hydrogen has a strong influence on the electrical properties of transparent conducting oxides where it can give rise to shallow donors and can passivate deep compensating defects. We have carried out infrared absorption experiments on H- and D-doped β-Ga2O3 that involve temperature- and polarization-dependent effects as well as relative H- and D-concentrations to probe the defect structures that hydrogen can form. The results of analysis of these data, coupled with detailed theoretical calculations, show that the dominant O-H vibrational line observed at 3437 cm-1 for hydrogenated Ga2O3 is due to a relaxed VGa-2H center.

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

Effect of structure variation of the aptamer-DNA duplex probe on the performance of displacement-based electrochemical aptamer sensors.

PubMed

Pang, Jie; Zhang, Ziping; Jin, Haizhu

2016-03-15

Electrochemical aptamer-based (E-AB) sensors employing electrode-immobilized, redox-tagged aptamer probes have emerged as a promising platform for the sensitive and quick detection of target analytes ranging from small molecules to proteins. Signal generation in this class of sensor is linked to change in electron transfer efficiency upon binding-induced change in flexibility/conformation of the aptamer probe. Because of this signaling mechanism, signal gains of these sensors can be improved by employing a displacement-based recognition system, which links target binding with a large-scale flexibility/conformation shift from the aptamer-DNA duplex to the single-stranded DNA or the native aptamer. Despite the relatively large number of displacement-based E-AB sensor samples, little attention has been paid to the structure variation of the aptamer-DNA duplex probe. Here we detail the effects of complementary length and position of the aptamer-DNA duplex probe on the performance of a model displacement-based E-AB sensor for ATP. We find that, greater background suppression and signal gain are observed with longer complementary length of the aptamer-DNA duplex probe. However, sensor equilibration time slows monotonically with increasing complementary length; and with too many target binding sites in aptamer sequence being occupied by the complementary DNA, the aptamer-target binding does not occur and no signal gain observed. We also demonstrate that signal gain of the displacement-based E-AB sensor is strongly dependent on the complementary position of the aptamer-DNA duplex probe, with complementary position located at the electrode-attached or redox-tagged end of the duplex probe, larger background suppression and signal increase than that of the middle position are observed. These results highlight the importance of rational structure design of the aptamer-DNA duplex probe and provide new insights into the optimization of displacement-based E-AB sensors. Copyright

Trans-acting RNAs as molecular probes for monitoring time-dependent structural change of an RNA complex adapting two structures.

PubMed

Maeda, Yuri; Furuta, Hiroyuki; Ikawa, Yoshiya

2011-03-01

As dynamic structural changes are pivotal for the functions of some classes of RNA molecule, it is important to develop methods to monitor structural changes in RNA in a time-dependent manner without chemical modification. Based on previous reports that trans-acting RNAs can be used as probes for analysis and control of 3D structures of target RNAs, we applied this method to monitor time-dependent structural changes in RNA. We designed and performed a proof-of-principle study using a simple model RNA complex that adopts two different structures as a target. The time-dependent structural changes in the target RNA were successfully monitored using two trans-acting RNAs, which stably form a ternary complex with the bimolecular target RNA and act as a catalyst to join two RNA fragments of the target complex, respectively. Copyright © 2010 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Kinetic Control of Aqueous Hydrolysis: Modulating Structure/Property Relationships in Inorganic Crystals

NASA Astrophysics Data System (ADS)

Neilson, James R.

2011-12-01

or structure, yet subtle and systematic changes in the mean-field spin interaction strength and spin entropy loss. Meanwhile, neutron powder diffraction reveals a fully compensated Ńeel state; a detailed analysis of the local structure defines the aperiodic clusters of polyhedra responsible for magnetic order. The rate of hydrolysis of metal precursors modulates the disposition of these polyhedral clusters. The strategy of kinetically controlling aqueous hydrolysis also extends to the formation of stoichiometrically ordered bimetallic crystals [MSn(OH)6], where the hydrolysis behavior for dissimilar metal cations must be controlled via counteranions or precursor selection. In the formation of these ordered double perovskite hydroxides, the rate of hydrolysis is held constant in the limit of kinetic control. Instead, the propensities of different cations to undergo controlled hydrolysis are probed by their ability to form ordered crystals. Collectively, these studies demonstrate how systematic variation in the kinetic conditions of materials preparation and the character of each solute control the structure and properties of materials, with a precision not attainable through traditional or near-equilibrium approaches.

Smart near-infrared fluorescence probes with donor-acceptor structure for in vivo detection of β-amyloid deposits.

PubMed

Cui, Mengchao; Ono, Masahiro; Watanabe, Hiroyuki; Kimura, Hiroyuki; Liu, Boli; Saji, Hideo

2014-03-05

The deposition of β-amyloid (Aβ) plaques in the parenchymal and cortical brain is accepted as the main pathological hallmark of Alzheimer's disease (AD); however, early detection of AD still presents a challenge. With the assistance of molecular imaging techniques, imaging agents specifically targeting Aβ plaques in the brain may lead to the early diagnosis of AD. Herein, we report the design, synthesis, and evaluation of a series of smart near-infrared fluorescence (NIRF) imaging probes with donor-acceptor architecture bridged by a conjugated π-electron chain for Aβ plaques. The chemical structure of these NIRF probes is completely different from Congo Red and Thioflavin-T. Probes with a longer conjugated π system (carbon-carbon double bond) displayed maximum emission in PBS (>650 nm), which falls in the best range for NIRF probes. These probes were proved to have affinity to Aβ plaques in fluorescent staining of brain sections from an AD patient and double transgenic mice, as well as in an in vitro binding assay using Aβ(1-42) aggregates. One probe with high affinity (K(i) = 37 nM, K(d) = 27 nM) was selected for in vivo imaging. It can penetrate the blood-brain barrier of nude mice efficiently and is quickly washed out of the normal brain. Moreover, after intravenous injection of this probe, 22-month-old APPswe/PSEN1 mice exhibited a higher relative signal than control mice over the same period of time, and ex vivo fluorescent observations confirmed the existence of Aβ plaques. In summary, this probe meets most of the requirements for a NIRF contrast agent for the detection of Aβ plaques both in vitro and in vivo.

Investigations on structural, vibrational and dielectric properties of nanosized Cu doped Mg-Zn ferrites

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

Yadav, Anand; Department of Physics, MEDICAPS Institute of Science and Technology, Pithampur 453331; Rajpoot, Rambabu

2016-05-23

Transition metal Cu{sup 2+} doped Mg-Zn ferrite [Mg{sub 0.5}Zn{sub 0.5-x}Cu{sub x}Fe{sub 2}O{sub 4} (0.0 ≤ x ≤ 0.5)] were prepared by sol gel auto combustion (SGAC) method to probe the structural, vibrational and electrical properties. X-ray diffraction (XRD) pattern reveals a single-phase cubic spinel structure without the presence of any secondary phase corresponding to other structure. The average particle size of the parent Mg{sub 0.5}Zn{sub 0.5}Fe{sub 2}O{sub 4} is found to be ~29.8 nm and is found to increase with Cu{sup 2+} doping. Progressive reduction in lattice parameter of Mg{sub 0.5}Zn{sub 0.5}Fe{sub 2}O{sub 4} has been observed due to difference inmore » ionic radii of cations with improved Cu doping. Spinel cubic structure is further confirmed by Raman spectroscopy. Small shift in Raman modes towards higher wave number has been observed in doped Mg-Zn ferrites. The permittivity and dielectric loss decreases at lower doping and increases at higher order doping of Cu{sup 2+}.« less

Rotating concave eddy current probe

DOEpatents

Roach, Dennis P [Albuquerque, NM; Walkington, Phil [Albuquerque, NM; Rackow, Kirk A [Albuquerque, NM; Hohman, Ed [Albuquerque, NM

2008-04-01

A rotating concave eddy current probe for detecting fatigue cracks hidden from view underneath the head of a raised head fastener, such as a buttonhead-type rivet, used to join together structural skins, such as aluminum aircraft skins. The probe has a recessed concave dimple in its bottom surface that closely conforms to the shape of the raised head. The concave dimple holds the probe in good alignment on top of the rivet while the probe is rotated around the rivet's centerline. One or more magnetic coils are rigidly embedded within the probe's cylindrical body, which is made of a non-conducting material. This design overcomes the inspection impediment associated with widely varying conductivity in fastened joints.

Structure and Soot Properties of Nonbuoyant Ethylene/Air Laminar Jet Diffusion Flames. Appendix I

NASA Technical Reports Server (NTRS)

Urban, D. L.; Yuan, Z.-G.; Sunderland, P. B.; Linteris, G. T.; Voss, J. E.; Lin, K.-C.; Dai, Z.; Sun, K.; Faeth, G. M.; Ross, Howard D. (Technical Monitor)

2000-01-01

The structure and soot properties of round, soot-emitting, nonbuoyant, laminar jet diffusion flames are described, based on long-duration (175-230/s) experiments at microgravity carried out on orbit In the Space Shuttle Columbia. Experiments] conditions included ethylene-fueled flames burning in still air at nominal pressures of 50 and 100 kPa and an ambient temperature of 300 K with luminous Annie lengths of 49-64 mm. Measurements included luminous flame shapes using color video imaging, soot concentration (volume fraction) distributions using deconvoluted laser extinction imaging, soot temperature distributions using deconvoluted multiline emission imaging, gas temperature distributions at fuel-lean (plume) conditions using thermocouple probes, not structure distributions using thermophoretic sampling and analysis by transmission electron microscopy, and flame radiation using a radiometer. The present flames were larger, and emitted soot men readily, than comparable observed during ground-based microgravity experiments due to closer approach to steady conditions resulting from the longer test times and the reduced gravitational disturbances of the space-based experiments.

Optoelectronic Properties of X-Doped (X = O, S, Te) Photovoltaic CSe with Puckered Structure.

PubMed

Zhang, Qiang; Xin, Tianyuan; Lu, Xiaoke; Wang, Yuexia

2018-03-16

We exploited novel two-dimensional (2D) carbon selenide (CSe) with a structure analogous to phosphorene, and probed its electronics and optoelectronics. Calculating phonon spectra using the density functional perturbation theory (DFPT) method indicated that 2D CSe possesses dynamic stability, which made it possible to tune and equip CSe with outstanding properties by way of X-doping (X = O, S, Te), i.e., X substituting Se atoms. Then systematic investigation on the structural, electronic, and optical properties of pristine and X-doped monolayer CSe was carried out using the density functional theory (DFT) method. It was found that the bonding feature of C-X is intimately associated with the electronegativity and radius of the doping atoms, which leads to diverse electronic and optical properties for doping different group VI elements. All the systems possess direct gaps, except for O-doping. Substituting O for Se atoms in monolayer CSe brings about a transition from a direct Γ-Γ band gap to an indirect Γ-Y band gap. Moreover, the value of the band gap decreases with increased doping concentration and radius of doping atoms. A red shift in absorption spectra occurs toward the visible range of radiation after doping, and the red-shift phenomenon becomes more obvious with increased radius and concentration of doping atoms. The results can be useful for filtering doping atoms according to their radius or electronegativity in order to tailor optical spectra efficiently.

Optoelectronic Properties of X-Doped (X = O, S, Te) Photovoltaic CSe with Puckered Structure

PubMed Central

Zhang, Qiang; Xin, Tianyuan; Lu, Xiaoke; Wang, Yuexia

2018-01-01

We exploited novel two-dimensional (2D) carbon selenide (CSe) with a structure analogous to phosphorene, and probed its electronics and optoelectronics. Calculating phonon spectra using the density functional perturbation theory (DFPT) method indicated that 2D CSe possesses dynamic stability, which made it possible to tune and equip CSe with outstanding properties by way of X-doping (X = O, S, Te), i.e., X substituting Se atoms. Then systematic investigation on the structural, electronic, and optical properties of pristine and X-doped monolayer CSe was carried out using the density functional theory (DFT) method. It was found that the bonding feature of C-X is intimately associated with the electronegativity and radius of the doping atoms, which leads to diverse electronic and optical properties for doping different group VI elements. All the systems possess direct gaps, except for O-doping. Substituting O for Se atoms in monolayer CSe brings about a transition from a direct Γ-Γ band gap to an indirect Γ-Y band gap. Moreover, the value of the band gap decreases with increased doping concentration and radius of doping atoms. A red shift in absorption spectra occurs toward the visible range of radiation after doping, and the red-shift phenomenon becomes more obvious with increased radius and concentration of doping atoms. The results can be useful for filtering doping atoms according to their radius or electronegativity in order to tailor optical spectra efficiently. PMID:29547504

Effects of methotrexate on the viscoelastic properties of single cells probed by atomic force microscopy.

PubMed

Li, Mi; Liu, Lianqing; Xiao, Xiubin; Xi, Ning; Wang, Yuechao

2016-10-01

Methotrexate is a commonly used anti-cancer chemotherapy drug. Cellular mechanical properties are fundamental parameters that reflect the physiological state of a cell. However, so far the role of cellular mechanical properties in the actions of methotrexate is still unclear. In recent years, probing the behaviors of single cells with the use of atomic force microscopy (AFM) has contributed much to the field of cell biomechanics. In this work, with the use of AFM, the effects of methotrexate on the viscoelastic properties of four types of cells were quantitatively investigated. The inhibitory and cytotoxic effects of methotrexate on the proliferation of cells were observed by optical and fluorescence microscopy. AFM indenting was used to measure the changes of cellular viscoelastic properties (Young's modulus and relaxation time) by using both conical tip and spherical tip, quantitatively showing that the stimulation of methotrexate resulted in a significant decrease of both cellular Young's modulus and relaxation times. The morphological changes of cells induced by methotrexate were visualized by AFM imaging. The study improves our understanding of methotrexate action and offers a novel way to quantify drug actions at the single-cell level by measuring cellular viscoelastic properties, which may have potential impacts on developing label-free methods for drug evaluation.

Connecting Structural and Transport Properties of Ionic Liquids with Cationic Oligoether Chains

DOE PAGES

Lall-Ramnarine, Sharon I.; Zhao, Man; Rodriguez, Chanele; ...

2017-06-01

We used X-ray diffraction and molecular dynamics simulations to probe the structures of two families of ionic liquids containing oligoether tails on the cations. Imidazolium and pyrrolidinium bis(trifluoromethylsulfonyl)amide ILs with side chains ranging from 4 to 10 atoms in length, including both linear alkyl and oligo-ethylene oxide tails, were prepared. Furthermore, their physical properties, such as viscosity, conductivity and thermal profile, were measured and compared for systematic trends. Consistent with earlier literature, a single ether substituent substantially decreases the viscosity of pyrrolidinium and imidazolium ILs compared to their alkyl congeners. Remarkably, as the number of ether units in the pyrrolidiniummore » ILs increases there is hardly any increase in the viscosity, in contrast to alkylpyrrolidinium ILs where the viscosity increases steadily with chain length. Viscosities of imidazolium ether ILs increase with chain length but always remain well below their alkyl congeners. To complement the experimentally determined properties, molecular dynamics simulations were run on the two ILs with the longest ether chains. Our results point to specific aspects that could be useful for researchers designing ILs for specific applications.« less

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.

Surface-enhanced Raman scattering (SERS) dosimeter and probe

DOEpatents

Vo-Dinh, Tuan

1995-01-01

A dosimeter and probe for measuring exposure to chemical and biological compounds is disclosed. The dosimeter or probe includes a collector which may be analyzed by surface-enhanced Raman spectroscopy. The collector comprises a surface-enhanced Raman scattering-active material having a coating applied thereto to improve the adsorption properties of the collector. The collector may also be used in automated sequential devises, in probe array devices.

Harnessing cell-to-cell variations to probe bacterial structure and biophysics

NASA Astrophysics Data System (ADS)

Cass, Julie A.

Advances in microscopy and biotechnology have given us novel insights into cellular biology and physics. While bacteria were long considered to be relatively unstructured, the development of fluorescence microscopy techniques, and spatially and temporally resolved high-throughput quantitative studies, have uncovered that the bacterial cell is highly organized, and its structure rigorously maintained. In this thesis I will describe our gateTool software, designed to harness cell-to-cell variations to probe bacterial structure, and discuss two exciting aspects of structure that we have employed gateTool to investigate: (i) chromosome organization and the cellular mechanisms for controlling DNA dynamics, and (ii) the study of cell wall synthesis, and how the genes in the synthesis pathway impact cellular shape. In the first project, we develop a spatial and temporal mapping of cell-cycle-dependent chromosomal organization, and use this quantitative map to discover that chromosomal loci segregate from midcell with universal dynamics. In the second project, I describe preliminary time- lapse and snapshot imaging analysis suggesting phentoypical coherence across peptidoglycan synthesis pathways.

Graphene oxide based contacts as probes of biomedical signals

NASA Astrophysics Data System (ADS)

Hallfors, N. G.; Devarajan, A.; Farhat, I. A. H.; Abdurahman, A.; Liao, K.; Gater, D. L.; Elnaggar, M. I.; Isakovic, A. F.

We have developed a series of graphene oxide (GOx) on polymer contacts and have demonstrated these to be useful for collection of standard biomedically relevant signals, such as electrocardiogram (ECG). The process is wet solution-based and allows for control and tuning of the basic physical parameters of GOx, such as electrical and optical properties, simply by choosing the number of GOx layers. Our GOx characterization measurements show spectral (FTIR, XPS, IR absorbance) features most relevant to such performance, and point towards the likely explanations about the mechanisms for controlling the physical properties relevant for the contact performance. Structural (X-ray topography) and surface characterization (AFM, SEM) indicates to what degree these contacts can be considered homogeneous and therefore provide information on yield and repeatability. We compare the ECG signals recorded by standard commercial probes (Ag/AgCl) and GOx probes, displaying minor differences the solution to which may lead to a whole new way we perform ECG data collection, including wearable electronics and IoT friendly ECG monitoring. We acknowledge support from Mubadala-SRC AC4ES and from SRC 2011-KJ-2190. We thank J. B. Warren and G. L. Carr (BNL) for assistance.

Effect of annealing on structure, morphology and optoelectronic properties of nanocrystalline CuO thin films

NASA Astrophysics Data System (ADS)

Jundale, D. M.; Pawar, S. G.; Patil, S. L.; Chougule, M. A.; Godse, P. R.; Patil, V. B.

2011-10-01

The nanocrystalline CuO thin films were prepared on glass substrates by the sol-gel method. The structural, morphological, electrical and optical properties of CuO thin films, submitted to an annealing treatment in the 400-700 °C ranges are studied by X-ray diffraction (XRD), Scanning Electron Microscopy (SEM), Four Probe Technique and UV-visible spectroscopic. XRD measurements show that all the films are crystallized in the monoclinic phase and present a random orientation. Four prominent peaks, corresponding to the (110) phase (2θ≈32.70°), (002) phase (2θ≈35.70°), (111) phase (2θ≈38.76°) and (202) phase (2θ≈49.06°) appear on the diffractograms. The crystallite size increases with increasing annealing temperature. These modifications influence the microstructure, electrical and optical properties. The optical band gap energy decreases with increasing annealing temperature. These mean that the optical quality of CuO films is improved by annealing.

Evolution of Structural and Electrical Properties of Oxygen-Deficient VO2 under Low Temperature Heating Process.

PubMed

Zhang, Jiasong; Zhao, Zhengjing; Li, Jingbo; Jin, Haibo; Rehman, Fida; Chen, Pengwan; Jiang, Yijie; Chen, Chunxu; Cao, Maosheng; Zhao, Yongjie

2017-08-16

Structural stability and functional performances of vanadium dioxide (VO 2 ) are strongly influenced by oxygen vacancies. However, the mechanism of metal-insulator transition (MIT) influenced by defects is still under debate. Here, we study the evolution of structure and electrical property of oxygen-deficient VO 2 by a low temperature annealing process (LTP) based on a truss-structured VO 2 nanonet. The oxygenation process of the oxygen-deficient VO 2 is greatly prolonged, which enables us to probe the gradual change of properties of the oxygen-deficient VO 2 . A continuous lattice reduction is observed during LTP. No recrystallization and structural collapse of the VO 2 nanonet can be found after LTP. The valence-band X-ray photoelectron spectroscopy (XPS) measurements indicate that the oxygen deficiency strongly affects the energy level of the valence band edge. Correspondingly, the resistance changes of the VO 2 films from 1 to 4.5 orders of magnitude are achieved by LTP. The effect of oxygen vacancy on the electric field driven MIT is investigated. The threshold value of voltage triggering the MIT decreases with increasing the oxygen vacancy concentration. This work demonstrates a novel and effective way to control the content of oxygen vacancies in VO 2 and the obvious impact of oxygen vacancy on MIT, facilitating further research on the role of oxygen vacancy in structure and MIT of VO 2 , which is important for the deep understanding of MIT and exploiting innovative functional application of VO 2 .

Radical probing of spliceosome assembly.

PubMed

Grewal, Charnpal S; Kent, Oliver A; MacMillan, Andrew M

2017-08-01

Here we describe the synthesis and use of a directed hydroxyl radical probe, tethered to a pre-mRNA substrate, to map the structure of this substrate during the spliceosome assembly process. These studies indicate an early organization and proximation of conserved pre-mRNA sequences during spliceosome assembly. This methodology may be adapted to the synthesis of a wide variety of modified RNAs for use as probes of RNA structure and RNA-protein interaction. Copyright © 2017 Elsevier Inc. All rights reserved.

Synthesis of novel taspine diphenyl derivatives as fluorescence probes and inhibitors of breast cancer cell proliferation.

PubMed

He, Huaizhen; Zhan, Yingzhuan; Zhang, Yanmin; Zhang, Jie; He, Langchong

2012-01-01

Two novel taspine diphenyl derivatives (Ta-dD) were designed and synthesized by introducing different coumarin fluorescent groups into the basic structure of Ta-dD. The main advantage of these two compounds is that they can be used as fluorescence probes and inhibitors simultaneously. In the present study, the fluorescent properties of the probes were measured and their inhibition of four breast cancer cell lines was tested. Different concentrations of the fluorescence probe were added to MCF-7 breast cancer cells for fluorescence imaging analysis under normal conditions. The results suggested that both of the new compounds have not only fluorescence but also the ability to inhibit effects on different breast cancer cell lines, which indicates their possible further use as dual functional fluorescence probes in tracer analysis. Copyright © 2011 John Wiley & Sons, Ltd.

Correlative STED and Atomic Force Microscopy on Live Astrocytes Reveals Plasticity of Cytoskeletal Structure and Membrane Physical Properties during Polarized Migration

PubMed Central

Curry, Nathan; Ghézali, Grégory; Kaminski Schierle, Gabriele S.; Rouach, Nathalie; Kaminski, Clemens F.

2017-01-01

The plasticity of the cytoskeleton architecture and membrane properties is important for the establishment of cell polarity, adhesion and migration. Here, we present a method which combines stimulated emission depletion (STED) super-resolution imaging and atomic force microscopy (AFM) to correlate cytoskeletal structural information with membrane physical properties in live astrocytes. Using STED compatible dyes for live cell imaging of the cytoskeleton, and simultaneously mapping the cell surface topology with AFM, we obtain unprecedented detail of highly organized networks of actin and microtubules in astrocytes. Combining mechanical data from AFM with optical imaging of actin and tubulin further reveals links between cytoskeleton organization and membrane properties. Using this methodology we illustrate that scratch-induced migration induces cytoskeleton remodeling. The latter is caused by a polarization of actin and microtubule elements within astroglial cell processes, which correlates strongly with changes in cell stiffness. The method opens new avenues for the dynamic probing of the membrane structural and functional plasticity of living brain cells. It is a powerful tool for providing new insights into mechanisms of cell structural remodeling during physiological or pathological processes, such as brain development or tumorigenesis. PMID:28469559

Short-distance probes for protein backbone structure based on energy transfer between bimane and transition metal ions

PubMed Central

Taraska, Justin W.; Puljung, Michael C.; Zagotta, William N.

2009-01-01

The structure and dynamics of proteins underlies the workings of virtually every biological process. Existing biophysical methods are inadequate to measure protein structure at atomic resolution, on a rapid time scale, with limited amounts of protein, and in the context of a cell or membrane. FRET can measure distances between two probes, but depends on the orientation of the probes and typically works only over long distances comparable with the size of many proteins. Also, common probes used for FRET can be large and have long, flexible attachment linkers that position dyes far from the protein backbone. Here, we improve and extend a fluorescence method called transition metal ion FRET that uses energy transfer to transition metal ions as a reporter of short-range distances in proteins with little orientation dependence. This method uses a very small cysteine-reactive dye monobromobimane, with virtually no linker, and various transition metal ions bound close to the peptide backbone as the acceptor. We show that, unlike larger fluorophores and longer linkers, this donor–acceptor pair accurately reports short-range distances and changes in backbone distances. We further extend the method by using cysteine-reactive metal chelators, which allow the technique to be used in protein regions of unknown secondary structure or when native metal ion binding sites are present. This improved method overcomes several of the key limitations of classical FRET for intramolecular distance measurements. PMID:19805285

Intercomparison of Microphysical Properties Derived from In-Situ Cloud and Remote Sensing Probes over the South East Atlantic Ocean

NASA Astrophysics Data System (ADS)

Miller, R.; McFarquhar, G. M.; Gupta, S.; Poellot, M.; O'Brien, J.; Delene, D. J.

2017-12-01

During the Observations of Aerosols Above Clouds and their Interactions (ORACLES) field campaigns, the NASA P3-Orion was equipped with in-situ probes measuring aerosol and cloud microphysical properties, while the NASA ER-2 was equipped with remote sensors retrieving cloud and aerosol quantities. During ORACLES 2017, the P-3 aircraft was equipped with two Clouds Droplet Probes (CDPs) sizing droplets with diameters (D) between 2 and 50µm. The two CDPs were mounted on pylons with different designs, the CDP on the newly designed left wing pylon positioned further below and ahead of the wing, whereas that on the right wing pylon directly below the wing. The P-3 was also equipped with a Cloud and Aerosol Spectrometer (CAS) sizing droplets with 0.51 µm < D < 50 µm, and three optical array probes: a 2D-stero probe (2DS) for 10 µm < D < 1280 µm; a High Volume Precipitation Sampler (HVPS-3), for 150 µm < D < 1.92 cm; and a Cloud Imaging Probe (CIP) for 25 µm < D < 1600 µm. In addition, a Phase Doppler Interferometer (PDI) for 0.5 µm < D < 2500 µm was included. In this presentation, the number distribution functions n(D) derived from different probes in their overlap ranges and bulk quantities, such as liquid water content (LWC), effective radius (re), total number concentration, extinction, skewness, dispersion and kurtosis derived by different probes over equivalent size ranges are compared. Additional comparison with bulk parameters (e.g., LWC measured by King and hot wire probes) and remotely sensed values are also made. The effect of the software package used to process the data is also examined by using two different packages, the National Center for Atmospheric Research Software for OAP Data Analysis (SODA2), and the University of Oklahoma/Illinois' Processing Software (UIOOPS) to process the optical array probe data. These intercomparisons, as a function of aircraft parameters and environmental conditions, help quantify uncertainties in measurements

Magnetic Barkhausen Noise Measurements Using Tetrapole Probe Designs

NASA Astrophysics Data System (ADS)

McNairnay, Paul

A magnetic Barkhausen noise (MBN) testing system was developed for Defence Research and Development Canada (DRDC) to perform MBN measurements on the Royal Canadian Navy's Victoria class submarine hulls that can be correlated with material properties, including residual stress. The DRDC system was based on the design of a MBN system developed by Steven White at Queen's University, which was capable of performing rapid angular dependent measurements through the implementation of a flux controlled tetrapole probe. In tetrapole probe designs, the magnetic excitation field is rotated in the surface plane of the sample under the assumption of linear superposition of two orthogonal magnetic fields. During the course of this work, however, the validity of flux superposition in ferromagnetic materials, for the purpose of measuring MBN, was brought into question. Consequently, a study of MBN anisotropy using tetrapole probes was performed. Results indicate that MBN anisotropy measured under flux superposition does not simulate MBN anisotropy data obtained through manual rotation of a single dipole excitation field. It is inferred that MBN anisotropy data obtained with tetrapole probes is the result of the magnetic domain structure's response to an orthogonal magnetization condition and not necessarily to any bulk superposition magnetization in the sample. A qualitative model for the domain configuration under two orthogonal magnetic fields is proposed to describe the results. An empirically derived fitting equation, that describes tetrapole MBN anisotropy data, is presented. The equation describes results in terms of two largely independent orthogonal fields, and includes interaction terms arising due to competing orthogonally magnetized domain structures and interactions with the sample's magnetic easy axis. The equation is used to fit results obtained from a number of samples and tetrapole orientations and in each case correctly identifies the samples' magnetic easy axis.

Confocal Rheology Probes the Structure and Mechanics of Collagen through the Sol-Gel Transition.

PubMed

Tran-Ba, Khanh-Hoa; Lee, Daniel J; Zhu, Jieling; Paeng, Keewook; Kaufman, Laura J

2017-10-17

Fibrillar type I collagen-based hydrogels are commonly used in tissue engineering and as matrices for biophysical studies. Mechanical and structural properties of these gels are known to be governed by the conditions under which fibrillogenesis occurs, exhibiting variation as a function of protein concentration, temperature, pH, and ionic strength. Deeper understanding of how macroscopic structure affects viscoelastic properties of collagen gels over the course of fibrillogenesis provides fundamental insight into biopolymer gel properties and promises enhanced control over the properties of such gels. Here, we investigate type I collagen fibrillogenesis using confocal rheology-simultaneous confocal reflectance microscopy, confocal fluorescence microscopy, and rheology. The multimodal approach allows direct comparison of how viscoelastic properties track the structural evolution of the gel on fiber and network length scales. Quantitative assessment and comparison of each imaging modality and the simultaneously collected rheological measurements show that the presence of a system-spanning structure occurs at a time similar to rheological determinants of gelation. Although this and some rheological measures are consistent with critical gelation through percolation, additional rheological and structural properties of the gel are found to be inconsistent with this theory. This study clarifies how structure sets viscoelasticity during collagen fibrillogenesis and more broadly highlights the utility of multimodal measurements as critical test-beds for theoretical descriptions of complex systems. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Probing disk wind and other properties of 4U 1630-47

NASA Astrophysics Data System (ADS)

Bhattacharyya, Sudip

2015-09-01

The accreting Galactic black hole transient 4U 1630-47, which is currently in outburst, is an ideal source to probe two types of accreted matter ejection: (1) via disk wind and (2) via jet, both using the observed narrow spectral lines (Diaz Trigo et al., 2013, Nature, 504, 206; Neilsen et al. 2014; Diaz Trigo et al. 2014). Chandra gratings are ideal to study such lines. The source also showed indications of high-frequency (HF) quasi-periodic oscillations (QPOs) in a rather high (150-450 Hz) frequency range, which can be extremely useful to probe the strong gravity regime. The AstroSat satellite, because of its large area and high timing resolution in a broad energy band, can potentially detect and measure HF QPOs and probe the source broadband spectrum and state. Hence, our proposed 30 ks Chandra exposure, nearly contemporaneous with complementary AstroSat observations, will provide an excellent way to probe the accretion and ejection mechanism in the strong gravity regime.

Systems design study of the Pioneer Venus spacecraft. Appendices to volume 1, sections 3-6 (part 1 of 3). [design of Venus probe windows

NASA Technical Reports Server (NTRS)

1973-01-01

The design is described of the Venus probe windows, which are required to measure solar flux, infrared flux, aureole, and cloud particles. Window heating and structural materials for the probe window assemblies are discussed along with the magnetometer. The command lists for science, power and communication requirements, telemetry sign characteristics, mission profile summary, mass properties of payloads, and failure modes are presented.

Surface-enhanced Raman scattering (SERS) dosimeter and probe

DOEpatents

Vo-Dinh, T.

1995-03-21

A dosimeter and probe for measuring exposure to chemical and biological compounds is disclosed. The dosimeter or probe includes a collector which may be analyzed by surface-enhanced Raman spectroscopy. The collector comprises a surface-enhanced Raman scattering-active material having a coating applied thereto to improve the adsorption properties of the collector. The collector may also be used in automated sequential devices, in probe array devices. 10 figures.

A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography

PubMed Central

van Thor, Jasper J.; Madsen, Anders

2015-01-01

In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL) operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/σI) must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or “probe-pump-probe”) which will allow experimental determination of the photo-induced structure factor amplitude differences, ΔF, in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse. PMID:26798786

A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography

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

van Thor, Jasper J.; Madsen, Anders

In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL) operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/σI) must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or “probe-pump-probe”) which will allow experimental determination of the photo-induced structure factor amplitude differences, ΔF,more » in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse.« less

A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography

DOE PAGES

van Thor, Jasper J.; Madsen, Anders

2015-01-01

In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL) operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/σI) must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or “probe-pump-probe”) which will allow experimental determination of the photo-induced structure factor amplitude differences, ΔF,more » in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse.« less

Scanning Probe Microscopy for Identifying the Component Materials of a Nanostripe Structure

NASA Astrophysics Data System (ADS)

Mizuno, Akira; Ando, Yasuhisa

2010-08-01

The authors prepared a nanostripe structure in which two types of metal are arranged alternately, and successfully identified the component materials using scanning probe microscopy (SPM) to measure the lateral force distribution image. The nanostripe structure was prepared using a new method developed by the authors and joint development members. The lateral force distribution image was measured in both friction force microscopy (FFM) and lateral modulation friction force microscopy (LM-FFM) modes. In FFM mode, the effect of slope angle appeared in the lateral force distribution image; therefore, no difference in the type of material was observed. On the other hand, in LM-FFM mode, the effect of surface curvature was observed in the lateral force distribution image. A higher friction force on chromium than on gold was identified, enabling material identification.

Probing the structural evolution and bonding properties of PtnC2-/0 (n = 1-7) clusters by density functional calculations

NASA Astrophysics Data System (ADS)

Lu, Sheng-Jie

2018-05-01

We present a theoretical investigation on the structural evolution and bonding properties of PtnC2-/0 (n = 1-7) clusters using density functional theoretical calculations. The results showed that both anionic and neutral PtnC2 (n = 1-7) clusters primarily adopt 2D planar chain-shaped or ring-based structures. The two C atoms directly interact with each other to form a Csbnd C bond for n = 1-3, while the two C atoms are separated by the Pt atoms for n = 4-7, except for neutral Pt5C2. Pt4C2- anion and Pt4C2 neutral both show σ plus π double delocalized bonding patterns.

Weak lensing probe of cubic Galileon model

NASA Astrophysics Data System (ADS)

Dinda, Bikash R.

2018-06-01

The cubic Galileon model containing the lowest non-trivial order action of the full Galileon action can produce the stable late-time cosmic acceleration. This model can have a significant role in the growth of structures. The signatures of the cubic Galileon model in the structure formation can be probed by the weak lensing statistics. Weak lensing convergence statistics is one of the strongest probes to the structure formation and hence it can probe the dark energy or modified theories of gravity models. In this work, we investigate the detectability of the cubic Galileon model from the ΛCDM model or from the canonical quintessence model through the convergence power spectrum and bi-spectrum.

Electrical, thermal, catalytic and magnetic properties of nano-structured materials and their applications

NASA Astrophysics Data System (ADS)

Liu, Zuwei

Nanotechnology is a subject that studies the fabrication, properties, and applications of materials on the nanometer-scale. Top-down and bottom-up approaches are commonly used in nano-structure fabrication. The top-down approach is used to fabricate nano-structures from bulk materials by lithography, etching, and polishing etc. It is commonly used in mechanical, electronic, and photonic devices. Bottom-up approaches fabricate nano-structures from atoms or molecules by chemical synthesis, self-assembly, and deposition, such as sol-gel processing, molecular beam epitaxy (MBE), focused ion beam (FIB) milling/deposition, chemical vapor deposition (CVD), and electro-deposition etc. Nano-structures can have several different dimensionalities, including zero-dimensional nano-structures, such as fullerenes, nano-particles, quantum dots, nano-sized clusters; one-dimensional nano-structures, such as carbon nanotubes, metallic and semiconducting nanowires; two-dimensional nano-structures, such as graphene, super lattice, thin films; and three-dimensional nano-structures, such as photonic structures, anodic aluminum oxide, and molecular sieves. These nano-structured materials exhibit unique electrical, thermal, optical, mechanical, chemical, and magnetic properties in the quantum mechanical regime. Various techniques can be used to study these properties, such as scanning probe microscopy (SPM), scanning/transmission electron microscopy (SEM/TEM), micro Raman spectroscopy, etc. These unique properties have important applications in modern technologies, such as random access memories, display, solar energy conversion, chemical sensing, and bio-medical devices. This thesis includes four main topics in the broad area of nanoscience: magnetic properties of ferro-magnetic cobalt nanowires, plasmonic properties of metallic nano-particles, photocatalytic properties of titanium dioxide nanotubes, and electro-thermal-optical properties of carbon nanotubes. These materials and their

Amyloid-β Deposits Target Efficient Near-Infrared Fluorescent Probes: Synthesis, in Vitro Evaluation, and in Vivo Imaging.

PubMed

Fu, Hualong; Tu, Peiyu; Zhao, Liu; Dai, Jiapei; Liu, Boli; Cui, Mengchao

2016-02-02

The formation of extracellular amyloid-β (Aβ) plaques is a common molecular change that underlies several debilitating human conditions, including Alzheimer's disease (AD); however, the existing near-infrared (NIR) fluorescent probes for the in vivo detection of Aβ plaques are limited by undesirable fluorescent properties and poor brain kinetics. In this work, we designed, synthesized, and evaluated a new family of efficient NIR probes that target Aβ plaques by incorporating hydroxyethyl groups into the ligand structure. Among these probes, DANIR 8c showed excellent fluorescent properties with an emission maximum above 670 nm upon binding to Aβ aggregates and also displayed a high sensitivity (a 629-fold increase in fluorescence intensity) and affinity (Kd = 14.5 nM). Because of the improved hydrophilicity that was induced by hydroxyls, 8c displayed increased initial brain uptake and a fast washout from the brain, as well as an acceptable biostability in the brain. In vivo NIR fluorescent imaging revealed that 8c could efficiently distinguish between AD transgenic model mice and normal controls. Overall, 8c is an efficient and veritable NIR fluorescent probe for the in vivo detection of Aβ plaques in the brain.

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).

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.

Probing topological protection using a designer surface plasmon structure

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

Gao, Fei; Gao, Zhen; Shi, Xihang

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

Probing topological protection using a designer surface plasmon structure

DOE PAGES

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

2016-05-20

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

Impact of nucleation of carbonaceous clusters on structural, electrical and optical properties of Cr+-implanted PMMA

NASA Astrophysics Data System (ADS)

Arif, Shafaq; Rafique, M. Shahid; Saleemi, Farhat; Naab, Fabian; Toader, Ovidiu; Mahmood, Arshad; Aziz, Uzma

2016-09-01

Specimens of polymethylmethacrylate (PMMA) have been implanted with 400 keV Cr+ ions at different ion fluences ranging from 5 × 1013 to 5 × 1015 ions/cm2. The possible chemical reactions involved in the nucleation of conjugated carbonaceous clusters in implanted PMMA are discussed. Furthermore, impact of formation of carbonaceous clusters on structural, optical, electrical and morphological properties of implanted PMMA has been examined. The structural modifications in implanted PMMA are observed by Raman spectroscopy. The variation in optical band gap and Urbach energy is measured using UV-visible spectroscopic analysis. The effects of Cr+ ion implantation on electrical and morphological properties are investigated by four-probe apparatus and atomic force microscopy, respectively. The Raman spectroscopic analysis confirmed the formation of carbonaceous clusters with the transformation of implanted layer of PMMA into amorphous carbon. Simultaneously, the optical band gap of implanted PMMA has reduced from 3.13 to 0.85 eV. The increase in Urbach energy favors the decline in band gap together with the structural modification in implanted PMMA. As a result of Cr+ ion implantation, the electrical conductivity of PMMA has improved from 2.14 ± 0.06 × 10-10 S/cm (pristine) to 7.20 ± 0.36 × 10-6 S/cm. The AFM images revealed a decrease in surface roughness with an increment in ion fluence up to 5 × 1014 ions/cm2. The modification in the electrical, optical and structural properties makes the PMMA a promising candidate for its future utilization, as a semiconducting and optically active material, in various fields like plastic electronics and optoelectronic devices.

Void structure of O+ ions in the inner magnetosphere observed by the Van Allen Probes

NASA Astrophysics Data System (ADS)

Nakayama, Y.; Ebihara, Y.; Ohtani, S.; Gkioulidou, M.; Takahashi, K.; Kistler, L. M.; Tanaka, T.

2016-12-01

The Van Allen Probes Helium Oxygen Proton Electron instrument observed a new type of enhancement of O+ ions in the inner magnetosphere during substorms. As the satellite moved outward in the premidnight sector, the flux of the O+ ions with energy 10 keV appeared first in the energy-time spectrograms. Then, the enhancement of the flux spread toward high and low energies. The enhanced flux of the O+ ions with the highest energy remained, whereas the flux of the ions with lower energy vanished near apogee, forming what we call the void structure. The structure cannot be found in the H+ spectrogram. We studied the generation mechanism of this structure by using numerical simulation. We traced the trajectories of O+ ions in the electric and magnetic fields from the global magnetohydrodynamics simulation and calculated the flux of O+ ions in the inner magnetosphere in accordance with the Liouville theorem. The simulated spectrograms are well consistent with the ones observed by Van Allen Probes. We suggest the following processes. (1) When magnetic reconnection starts, an intensive equatorward and tailward plasma flow appears in the plasma lobe. (2) The flow transports plasma from the lobe to the plasma sheet where the radius of curvature of the magnetic field line is small. (3) The intensive dawn-dusk electric field transports the O+ ions earthward and accelerates them nonadiabatically to an energy threshold; (4) the void structure appears at energies below the threshold.

Nanoscale structural and functional mapping of nacre by scanning probe microscopy techniques

NASA Astrophysics Data System (ADS)

Zhou, Xilong; Miao, Hongchen; Li, Faxin

2013-11-01

Nacre has received great attention due to its nanoscale hierarchical structure and extraordinary mechanical properties. Meanwhile, the nanoscale piezoelectric properties of nacre have also been investigated but the structure-function relationship has never been addressed. In this work, firstly we realized quantitative nanomechanical mapping of nacre of a green abalone using atomic force acoustic microscopy (AFAM). The modulus of the mineral tablets is determined to be ~80 GPa and that of the organic biopolymer no more than 23 GPa, and the organic-inorganic interface width is determined to be about 34 +/- 9 nm. Then, we conducted both AFAM and piezoresponse force microscopy (PFM) mapping in the same scanning area to explore the correlations between the nanomechanical and piezoelectric properties. The PFM testing shows that the organic biopolymer exhibits a significantly stronger piezoresponse than the mineral tablets, and they permeate each other, which is very difficult to reproduce in artificial materials. Finally, the phase hysteresis loops and amplitude butterfly loops were also observed using switching spectroscopy PFM, implying that nacre may also be a bio-ferroelectric material. The obtained nanoscale structural and functional properties of nacre could be very helpful in understanding its deformation mechanism and designing biomimetic materials of extraordinary properties.

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

PubMed

Lv, Yi; Cui, Jian; Jiang, Zuimin M; Yang, Xinju

2012-11-29

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.

Estimation and imaging of breast lesions using a two-layer tissue structure by ultrasound-guided optical tomography

PubMed Central

Xu, Yan; Zhu, Quing

2015-01-01

Abstract. A new two-step estimation and imaging method is developed for a two-layer breast tissue structure consisting of a breast tissue layer and a chest wall underneath. First, a smaller probe with shorter distance source-detector pairs was used to collect the reflected light mainly from the breast tissue layer. Then, a larger probe with 9×14 source-detector pairs and a centrally located ultrasound transducer was used to collect reflected light from the two-layer tissue structure. The data collected from the smaller probe were used to estimate breast tissue optical properties. With more accurate estimation of the average breast tissue properties, the second layer properties can be assessed from data obtained from the larger probe. Using this approach, the unknown variables have been reduced from four to two and the estimated bulk tissue optical properties are more accurate and robust. In addition, a two-step reconstruction using a genetic algorithm and conjugate gradient method is implemented to simultaneously reconstruct the absorption and reduced scattering maps of targets inside a two-layer tissue structure. Simulations and phantom experiments have been performed to validate the new reconstruction method, and a clinical example is given to demonstrate the feasibility of this approach. PMID:26046722

On the Development, Characterization, and Use of Protein Fluorescence and Infrared Spectroscopic Probes

NASA Astrophysics Data System (ADS)

Hilaire, Mary Rose

Proteins possess unique physical and chemical properties that allow them to carry out a wide variety of biological activities and functions. While it is generally understood that a protein's function is dictated by its structure and dynamics, arriving at a molecule-level understanding of the underlying structure-dynamics-function relationship still poses a challenging task in many cases. This is due, at least in part, to the fact that we lack the ability to take snapshots along the reaction coordinate of proteins with sufficient temporal and structural resolution. Therefore, to improve one's ability to acquire site-specific structural and/or environmental information of proteins via either infrared (IR) or fluorescence spectroscopy, the main focus of this thesis is to develop and characterize amino acid-based spectroscopic probes as well as to use such probes to study important biological questions. Specifically, we show that (1) p-cyanophenylalanine and selenomethionine constitute an efficient fluorophore-quencher pair, useful for characterizing protein conformational changes that occur on a short distance; (2) 4-cyanotryptophan is a novel blue fluorescent amino acid, applicable for biological imaging due to its unique photophysical properties; (3) the dielectric constant inside the hydrophobic interior of staphylococcal nuclease is about 10-15, significantly larger than previously assumed; and (4) a single mutation in a short segment of the protein transthyretin (i.e., 110-115) induces formation of amyloid fibrils consisting of both beta- and alpha-sheets, where the latter is a proposed structure in proteins, but has never been observed previously.

Bunker probe: A plasma potential probe almost insensitive to its orientation with the magnetic field

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

Costea, S., E-mail: stefan.costea@uibk.ac.at; Schneider, B. S.; Schrittwieser, R.

Due to their ability to suppress a large part of the electron current and thus measuring directly the plasma potential, ion sensitive probes have begun to be widely tested and used in fusion devices. For these probes to work, almost perfect alignment with the total magnetic field is necessary. This condition cannot always be fulfilled due to the curvature of magnetic fields, complex magnetic structure, or magnetic field reconnection. In this perspective, we have developed a plasma potential probe (named Bunker probe) based on the principle of the ion sensitive probe but almost insensitive to its orientation with the totalmore » magnetic field. Therefore it can be used to measure the plasma potential inside fusion devices, especially in regions with complex magnetic field topology. Experimental results are presented and compared with Ball-Pen probe measurements taken under identical conditions. We have observed that the floating potential of the Bunker probe is indeed little affected by its orientation with the magnetic field for angles ranging from 90° to 30°, in contrast to the Ball-Pen probe whose floating potential decreases towards that of a Langmuir probe if not properly aligned with the magnetic field.« less

Modeling the Insertion Mechanics of Flexible Neural Probes Coated with Sacrificial Polymers for Optimizing Probe Design

PubMed Central

Singh, Sagar; Lo, Meng-Chen; Damodaran, Vinod B.; Kaplan, Hilton M.; Kohn, Joachim; Zahn, Jeffrey D.; Shreiber, David I.

2016-01-01

Single-unit recording neural probes have significant advantages towards improving signal-to-noise ratio and specificity for signal acquisition in brain-to-computer interface devices. Long-term effectiveness is unfortunately limited by the chronic injury response, which has been linked to the mechanical mismatch between rigid probes and compliant brain tissue. Small, flexible microelectrodes may overcome this limitation, but insertion of these probes without buckling requires supporting elements such as a stiff coating with a biodegradable polymer. For these coated probes, there is a design trade-off between the potential for successful insertion into brain tissue and the degree of trauma generated by the insertion. The objective of this study was to develop and validate a finite element model (FEM) to simulate insertion of coated neural probes of varying dimensions and material properties into brain tissue. Simulations were performed to predict the buckling and insertion forces during insertion of coated probes into a tissue phantom with material properties of brain. The simulations were validated with parallel experimental studies where probes were inserted into agarose tissue phantom, ex vivo chick embryonic brain tissue, and ex vivo rat brain tissue. Experiments were performed with uncoated copper wire and both uncoated and coated SU-8 photoresist and Parylene C probes. Model predictions were found to strongly agree with experimental results (<10% error). The ratio of the predicted buckling force-to-predicted insertion force, where a value greater than one would ideally be expected to result in successful insertion, was plotted against the actual success rate from experiments. A sigmoidal relationship was observed, with a ratio of 1.35 corresponding to equal probability of insertion and failure, and a ratio of 3.5 corresponding to a 100% success rate. This ratio was dubbed the “safety factor”, as it indicated the degree to which the coating should be over

Direct imaging of thermally-activated grain-boundary diffusion in Cu/Co/IrMn/Pt exchange-bias structures using atom-probe tomography

NASA Astrophysics Data System (ADS)

Letellier, F.; Lechevallier, L.; Lardé, R.; Le Breton, J.-M.; Akmaldinov, K.; Auffret, S.; Dieny, B.; Baltz, V.

2014-11-01

Magnetic devices are often subject to thermal processing steps, such as field cooling to set exchange bias and annealing to crystallize amorphous magnetic electrodes. These processing steps may result in interdiffusion and the subsequent deterioration of magnetic properties. In this study, we investigated thermally-activated diffusion in Cu/Co/IrMn/Pt exchange biased polycrystalline thin-film structures using atom probe tomography. Images taken after annealing at 400 °C for 60 min revealed Mn diffusion into Co grains at the Co/IrMn interface and along Pt grain boundaries for the IrMn/Pt stack, i.e., a Harrison type C regime. Annealing at 500 °C showed further Mn diffusion into Co grains. At the IrMn/Pt interface, annealing at 500 °C led to a type B behavior since Mn diffusion was detected both along Pt grain boundaries and also into Pt grains. The deterioration of the films' exchange bias properties upon annealing was correlated to the observed diffusion. In particular, the topmost Pt capping layer thickness turned out to be crucial since a faster deterioration of the exchange bias properties for thicker caps was observed. This is consistent with the idea that Pt acts as a getter for Mn, drawing Mn out of the IrMn layer.

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

NASA Astrophysics Data System (ADS)

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

2014-02-01

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

Ion nose spectral structures observed by the Van Allen Probes

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Microarcsecond Astrometry As A Probe Of Circumstellar Structure

NASA Astrophysics Data System (ADS)

Velusamy, T.; Turyshev, S. G.

1999-12-01

The Space Interferometry Mission (SIM) is a space-based long-baseline optical interferometer for precision astrometry. This mission will open up many areas of astrophysics, via astrometry with unprecedented accuracy. Wide-angle measurements, which include annual parallax, will reach a design accuracy of 4 μ as. Over a narrow field of view the relative accuracy is better, and SIM is expected to achieve an accuracy of 1 μ as. In this mode, SIM will search for planetary companions to nearby stars, by detecting the astrometric `wobble' relative to a nearby (<= 1o) reference star. The expected proper motion accuracy is 2 μ as yr-1, corresponding to a transverse velocity of 10 m s-1 at a distance of 1 kpc. Such an accuracy of the future SIM instrument provides a very useful astrometric tool for probing the circumstellar structure. The motion of the photo center as detected by SIM is not necessarily that of the center of mass. It is expected that unmodelled dynamics of the stellar systems may be a potential source for systematic astrometric errors. In this paper we discuss the possibility of using SIM's precision astrometry not only to detect Keplerian signatures due to the planetary motion around nearby stars, but also to characterize the structure of the planetary and proto-planetary orbits, accretions disks, debris disks, circumstellar material, jets and other types of the mass transfer mechanisms. We evaluate possible astrometric signatures due to different types of dynamical processes (both gravitational, non-gravitational) and characterize the magnitude of the corresponding astrometric signal. We attempt to address the most natural scenario of non-Keplerian motion, caused by an extended structure and complex dynamics of the stellar systems that may produce a detectable wobble in the motion of the optical center of a target star. We examine the use of μ as astrometry, as complementary to high resolution imaging, to detect some of the structures present around

Bis-pyridinium quadrupolar derivatives. High Stokes shift selective probes for bio-imaging

NASA Astrophysics Data System (ADS)

Salice, Patrizio; Versari, Silvia; Bradamante, Silvia; Meinardi, Francesco; Macchi, Giorgio; Pagani, Giorgio A.; Beverina, Luca

2013-11-01

We describe the design, synthesis and characterization of five high Stokes shift quadrupolar heteroaryl compounds suitable as fluorescent probes in bio-imaging. In particular, we characterize the photophysical properties and the intracellular localization in Human Umbilical Vein Endothelial Cells (HUVEC) and Human Mesenchymal Stem Cells (HMSCs) for each dye. We show that, amongst all of the investigated derivatives, the 2,5-bis[1-(4-N-methylpyridinium)ethen-2-yl)]- N-methylpyrrole salt is the best candidates as selective mitochondrial tracker. Finally, we recorded the full emission spectrum of the most performing - exclusively mitochondrial selective - fluorescent probe directly from HUVEC stained cells. The emission spectrum collected from the stained mitochondria shows a remarkably more pronounced vibronic structure with respect to the emission of the free fluorophore in solution.

Predicting structural properties of fluids by thermodynamic extrapolation

NASA Astrophysics Data System (ADS)

Mahynski, Nathan A.; Jiao, Sally; Hatch, Harold W.; Blanco, Marco A.; Shen, Vincent K.

2018-05-01

We describe a methodology for extrapolating the structural properties of multicomponent fluids from one thermodynamic state to another. These properties generally include features of a system that may be computed from an individual configuration such as radial distribution functions, cluster size distributions, or a polymer's radius of gyration. This approach is based on the principle of using fluctuations in a system's extensive thermodynamic variables, such as energy, to construct an appropriate Taylor series expansion for these structural properties in terms of intensive conjugate variables, such as temperature. Thus, one may extrapolate these properties from one state to another when the series is truncated to some finite order. We demonstrate this extrapolation for simple and coarse-grained fluids in both the canonical and grand canonical ensembles, in terms of both temperatures and the chemical potentials of different components. The results show that this method is able to reasonably approximate structural properties of such fluids over a broad range of conditions. Consequently, this methodology may be employed to increase the computational efficiency of molecular simulations used to measure the structural properties of certain fluid systems, especially those used in high-throughput or data-driven investigations.

Development of Mackintosh Probe Extractor

NASA Astrophysics Data System (ADS)

Rahman, Noor Khazanah A.; Kaamin, Masiri; Suwandi, Amir Khan; Sahat, Suhaila; Jahaya Kesot, Mohd

2016-11-01

Dynamic probing is a continuous soil investigation technique, which is one of the simplest soil penetration test. It basically consist of repeatedly driving a metal tipped probe into the ground using a drop weight of fixed mass and travel. Testing was carried out continuously from ground level to the final penetration depth. Once the soil investigation work done, it is difficult to pull out the probe rod from the ground, due to strong soil structure grip against probe cone and prevent the probe rod out from the ground. Thus, in this case, a tool named Extracting Probe was created to assist in the process of retracting the probe rod from the ground. In addition, Extracting Probe also can reduce the time to extract the probe rod from the ground compare with the conventional method. At the same time, it also can reduce manpower cost because only one worker involve to handle this tool compare with conventional method used two or more workers. From experiment that have been done we found that the time difference between conventional tools and extracting probe is significant, average time difference is 155 minutes. In addition the extracting probe can reduce manpower usage, and also labour cost for operating the tool. With all these advantages makes this tool has the potential to be marketed.

Non-toxic fluorescent phosphonium probes to detect mitochondrial potential.

PubMed

Šarić, Ana; Crnolatac, Ivo; Bouillaud, Frédéric; Sobočanec, Sandra; Mikecin, Ana-Matea; Mačak Šafranko, Željka; Delgeorgiev, Todor; Piantanida, Ivo; Balog, Tihomir; Petit, Patrice X

2017-03-22

We evaluated our phosphonium-based fluorescent probes for selective staining of mitochondria. Currently used probes for monitoring mitochondrial membrane potential show varying degrees of interference with cell metabolism, photo-induced damage and probe binding. Here presented probes are characterised by highly efficient cellular uptake and specific accumulation in mitochondria. Fluorescent detection of the probes was accomplished using flow cytometry and confocal microscopy imaging of yeast and mammalian cells. Toxicity analysis (impedimetry-xCELLigence for the cellular proliferation and Seahorse technology for respiratory properties) confirms that these dyes exhibit no-toxicity on mitochondrial or cellular functioning even for long time incubation. The excellent chemical and photophysical stability of the dyes makes them promising leads toward improved fluorescent probes. Therefore, the probes described here offer to circumvent the problems associated with existing-probe's limitations.

Probing Structural and Electronic Dynamics with Ultrafast Electron Microscopy

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

Plemmons, DA; Suri, PK; Flannigan, DJ

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 emphasizemore » 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

Characterizing molecular probes for diffusion measurements in the brain

PubMed Central

Kaur, Gurjinder; Hrabetova, Sabina; Guilfoyle, David N.; Nicholson, Charles; Hrabe, Jan

2008-01-01

Brain diffusion properties are at present most commonly evaluated by magnetic resonance (MR) diffusion imaging. MR cannot easily distinguish between the extracellular and intracellular signal components, but the older technique of Real-Time Iontophoresis (RTI) detects exclusively extracellular diffusion. Interpretation of the MR results would therefore benefit from auxiliary RTI measurements. This requires a molecular probe detectable by both techniques. Our aim was to specify a minimum set of requirements that such a diffusion probe should fulfill and apply it to two candidate probes: the cation tetramethylammonium (TMA+), used routinely in the RTI experiments, and the anion hexafluoroantimonate (SbF6−). Desirable characteristics of a molecular diffusion probe include predictable diffusion properties, stability, minimum interaction with cellular physiology, very slow penetration into the cells, and sufficiently strong and selective MR and RTI signals. These properties were evaluated using preparations of rat neocortical slices under normal and ischemic conditions, as well as solutions and agarose gel. While both molecules can be detected by MR and RTI, neither proved an ideal candidate. TMA+ was very stable but it penetrated into the cells and accumulated there within tens of minutes. SbF6− did not enter the cells as readily but it was not stable, particularly in ischemic tissue and at higher temperatures. Its presence also resulted in a decreased extracellular volume. These probe properties help to interpret previously published MR data on TMA+ diffusion and might play a role in other diffusion experiments obtained with them. PMID:18466980

Synthesis and characterization of the fluorescent probes for the labeling of Microthrix parvicella.

PubMed

Li, Songya; Fei, Xuening; Jiao, Xiumei; Lin, Dayong; Zhang, Baolian; Cao, Lingyun

2016-03-01

Although the fluorescent in situ hybridization (FISH) has been widely used to identify the Microthrix parvicella (M. parvicella), there are a few disadvantages and difficulties, such as complicated process, time consuming, etc. In this work, a series of fluorescent probes, which were modified by long-chain alkane with hydrophobic property and based on the property of M. parvicella utilizing long-chain fatty acids (LCFA), for the labeling of M. parvicella in bulking sludge were designed, synthesized, and characterized. The probes were characterized by ultraviolet-visible (UV-Vis) absorption spectra, fluorescence spectra, (1)H NMR spectra, and mass spectra, and the photostability and hydrophobic property of probes were investigated. All the results showed that the probes were quite stable and suitable for the fluorescent labeling. The probes had a large stoke shift of 98-137 nm, which was benefit for the fluorescent labeling. In the fluorescent labeling of M. parvicella by the synthesized probes, the probes had excellent labeling effects. By comparison of the images and the Image Pro Plus 6.0 analysis, the optimal concentration of the probes in the activated sludge sample for labeling was 0.010 mmol/L and the probe 3d had the best labeling. In addition, the effect of the duration time of probes was also investigated, and the results showed that the fluorescent intensity of probes hardly changed in a long period of time and it was suitable for labeling.

Probing Phonon Dynamics in Individual Single-Walled Carbon Nanotubes.

PubMed

Jiang, Tao; Hong, Hao; Liu, Can; Liu, Wei-Tao; Liu, Kaihui; Wu, Shiwei

2018-04-11

Interactions between elementary excitations, such as carriers, phonons, and plasmons, are critical for understanding the optical and electronic properties of materials. The significance of these interactions is more prominent in low-dimensional materials and can dominate their physical properties due to the enhanced interactions between these excitations. One-dimensional single-walled carbon nanotubes provide an ideal system for studying such interactions due to their perfect physical structures and rich electronic properties. Here we investigated G-mode phonon dynamics in individual suspended chirality-resolved single-walled carbon nanotubes by time-resolved anti-Stokes Raman spectroscopy. The improved technique allowed us to probe the intrinsic phonon information on a single-tube level and exclude the influences of tube-tube and tube-substrate interactions. We found that the G-mode phonon lifetime ranges from 0.75-2.25 ps and critically depends on whether the tube is metallic or semiconducting. In comparison with the phonon lifetimes in graphene and graphite, we revealed structure-dependent carrier-phonon and phonon-phonon interactions in nanotubes. Our results provide new information for optimizing the design of nanotube electronic/optoelectronic devices by better understanding and utilizing their phonon decay channels.

Noninvasive encapsulated fiber optic probes for interferometric measurement

NASA Astrophysics Data System (ADS)

Zboril, O.; Cubik, J.; Kepak, S.; Nedoma, J.; Fajkus, M.; Zavodny, P.; Vasinek, V.

2017-10-01

This article focuses on the sensitivity of encapsulated interferometric probes. These probes are used mainly for BioMed and security applications. Fiber-optic sensors are interesting for these applications, as they are resistant to electromagnetic interference (EMI) and that also do not affect the surrounding medical and security equipment. Using a loop of the optical fiber with is not a suitable for these measurements. The optical fiber should be fixed to one position, and should not significantly bend. For these reasons, the optical fiber is encapsulated. Furthermore, it is necessary that the encapsulated measuring probes were flexible, inert, water resistant and not toxic. Fiber-optic sensors shouldn't be magnetically active, so they can be used for example, in magnetic resonance environments (MR). Probes meeting these requirements can be widely used in health care and security applications. Encapsulation of interferometric measuring arm brings changes in susceptibility of measurements in comparison with the optical fiber without encapsulation. To evaluate the properties of the encapsulated probes, series of probes made from different materials for encapsulation was generated, using two types of optical fibers with various degrees of protection. Comparison of the sensitivity of different encapsulated probes was performed using a series of measurements at various frequencies. The measurement results are statistically compared in the article and commented. Given the desired properties polydimethylsiloxane (PDMS) polymer has been proven the most interesting encapsulating material for further research.

Indirect consequences of exciplex states on the phosphorescence lifetime of phenazine-based 1,2,3-triazole luminescent probes.

PubMed

Costa, Bárbara B A; Jardim, Guilherme A M; Santos, Paloma L; Calado, Hállen D R; Monkman, Andrew P; Dias, Fernando B; da Silva Júnior, Eufrânio N; Cury, Luiz A

2017-02-01

The optical properties of phenazine derivative probe solutions involving intersystem crossing from singlet to triplet states were investigated by time resolved spectroscopy. The room temperature phosphorescence emission presented different time responses when Cd 2+ ions were bound to the probe chemical structure. The complex exciplex formation observed to occur in this case was not directly responsible for the change in the phosphorescence lifetime. This was more influenced by the new molecular conformation and modified spin-orbit coupling imposed by the binding of the Cd 2+ ions to the phenazine molecules.

Work on Planetary Atmospheres and Planetary Atmosphere Probes

NASA Technical Reports Server (NTRS)

Lester, Peter

1999-01-01

A summary final report of work accomplished is presented. Work was performed in the following areas: (1) Galileo Probe science analysis, (2) Galileo probe Atmosphere Structure Instrument, (3) Mars Pathfinder Atmosphere Structure/Meteorology instrument, (4) Mars Pathfinder data analysis, (5) Science Definition for future Mars missions, (6) Viking Lander data analysis, (7) winds in Mars atmosphere Venus atmospheric dynamics, (8) Pioneer Venus Probe data analysis, (9) Pioneer Venus anomaly analysis, (10) Discovery Venus Probe Titan probe instrument design, and (11) laboratory studies of Titan probe impact phenomena. The work has resulted in more than 10 articles published in archive journals, 2 encyclopedia articles, and many working papers. This final report is organized around the four planets on which there was activity, Jupiter, Mars, Venus, and Titan, with a closing section on Miscellaneous Activities. A major objective was to complete the fabrication, test, and evaluation of the atmosphere structure experiment on the Galileo probe, and to receive, analyze and interpret data received from the spacecraft. The instrument was launched on April 14, 1989. Calibration data were taken for all experiment sensors. The data were analyzed, fitted with algorithms, and summarized in a calibration report for use in analyzing and interpreting data returned from Jupiter's atmosphere. The sensors included were the primary science pressure, temperature and acceleration sensors, and the supporting engineering temperature sensors. Computer programs were written to decode the Experiment Data Record and convert the digital numbers to physical quantities, i.e., temperatures, pressures, and accelerations. The project office agreed to obtain telemetry of checkout data from the probe. Work to extend programs written for use on the Pioneer Venus project included: (1) massive heat shield ablation leading to important mass loss during entry; and (2) rapid planet rotation, which introduced

Effects of strain relaxation in Pr 0.67Sr 0.33MnO 3 films probed by polarization dependent X-ray absorption near edge structure

DOE PAGES

zhang, Bangmin; Chen, Jingsheng; Venkatesan, T.; ...

2016-01-28

In this study, the Mn K edge X-ray absorption near edge structure (XANES) of Pr 0.67Sr 0.33MnO 3 films with different thicknesses on (001) LaAlO 3 substrate were measured, and the effects of strain relaxation on film properties were investigated. The films experienced in-plane compressive strain and out-of-plane tensile strain. Strain relaxation evolved with the film thickness. In the polarization dependent XANES measurements, the in-plane (parallel) and out-of-plane (perpendicular) XANES spectrocopies were anisotropic with different absorption energy E r. The resonance energy Er along two directions shifted towards each other with increasing film thickness. Based on the X-ray diffraction results,more » it was suggested that the strain relaxation weakened the difference of the local environment and probability of electronic charge transfer (between Mn 3d and O 2p orbitals) along the in-plane and out-of-plane directions, which was responsible for the change of E r. XANES is a useful tool to probe the electronic structures, of which the effects on magnetic properties with the strain relaxation was also been studied.« less

Development of novel imaging probe for optical/acoustic radiation imaging (OARI).

PubMed

Ejofodomi, O'tega A; Zderic, Vesna; Zara, Jason M

2013-11-01

Optical/acoustic radiation imaging (OARI) is a novel imaging modality being developed to interrogate the optical and mechanical properties of soft tissues. OARI uses acoustic radiation force to generate displacement in soft tissue. Optical images before and after the application of the force are used to generate displacement maps that provide information about the mechanical properties of the tissue under interrogation. Since the images are optical images, they also represent the optical properties of the tissue as well. In this paper, the authors present the first imaging probe that uses acoustic radiation force in conjunction with optical coherence tomography (OCT) to provide information about the optical and mechanical properties of tissues to assist in the diagnosis and staging of epithelial cancers, and in particular bladder cancer. The OARI prototype probe consisted of an OCT probe encased in a plastic sheath, a miniaturized transducer glued to a plastic holder, both of which were encased in a 10 cm stainless steel tube with an inner diameter of 10 mm. The transducer delivered an acoustic intensity of 18 W/cm(2) and the OCT probe had a spatial resolution of approximately 10-20 μm. The tube was filled with deionized water for acoustic coupling and covered by a low density polyethylene cap. The OARI probe was characterized and tested on bladder wall phantoms. The phantoms possessed Young's moduli ranging from 10.2 to 12 kPa, mass density of 1.05 g/cm(3), acoustic attenuation coefficient of 0.66 dB/cm MHz, speed of sound of 1591 m/s, and optical scattering coefficient of 1.80 mm(-1). Finite element model (FEM) theoretical simulations were performed to assess the performance of the OARI probe. The authors obtained displacements of 9.4, 8.7, and 3.4 μm for the 3%, 4%, and 5% bladder wall phantoms, respectively. This shows that the probe is capable of generating optical images, and also has the ability to generate and track displacements in tissue. This will

2'-Bispyrene-modified 2'-O-methyl RNA probes as useful tools for the detection of RNA: synthesis, fluorescent properties, and duplex stability.

PubMed

Krasheninina, Olga A; Novopashina, Darya S; Lomzov, Alexander A; Venyaminova, Alya G

2014-09-05

The synthesis and properties two series of new 2'-O-methyl RNA probes, each containing a single insertion of a 2'-bispyrenylmethylphosphorodiamidate derivative of a nucleotide (U, C, A, and G), are described. As demonstrated by UV melting studies, the probes form stable complexes with model RNAs and DNAs. Significant increases (up to 21-fold) in pyrene excimer fluorescence intensity were observed upon binding of most of the probes with complementary RNAs, but not with DNAs. The fluorescence spectra are independent of the nature of the modified nucleotides. The nucleotides on the 5'-side of the modified nucleotide have no effect on the fluorescence spectra, whereas the natures of the two nucleotides on the 3'-side are important: CC, CG, and UC dinucleotide units on the 3'-side of the modified nucleotide provide the maximum increases in excimer fluorescence intensity. This study suggests that these 2'-bispyrene-labeled 2'-O-methyl RNA probes might be useful tools for detection of RNAs. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Modular Rake of Pitot Probes

NASA Technical Reports Server (NTRS)

Dunlap, Timothy A.; Henry, Michael W.; Homyk, Raymond P.

2004-01-01

The figure presents selected views of a modular rake of 17 pitot probes for measuring both transient and steady-state pressures in a supersonic wind tunnel. In addition to pitot tubes visible in the figure, the probe modules contain (1) high-frequency dynamic-pressure transducers connected through wires to remote monitoring circuitry and (2) flow passages that lead to tubes that, in turn, lead to remote steady-state pressure transducers. Prior pitot-probe rakes were fabricated as unitary structures, into which the individual pitot probes were brazed. Repair or replacement of individual probes was difficult, costly, and time-consuming because (1) it was necessary to remove entire rakes in order to unbraze individual malfunctioning probes and (2) the heat of unbrazing a failed probe and of brazing a new probe in place could damage adjacent probes. In contrast, the modules in the present probe are designed to be relatively quickly and easily replaceable with no heating and, in many cases, without need for removal of the entire rake from the wind tunnel. To remove a malfunctioning probe, one first removes a screw-mounted V-cross-section cover that holds the probe and adjacent probes in place. Then one removes a screw-mounted cover plate to gain access to the steady-state pressure tubes and dynamicpressure wires. Next, one disconnects the tube and wires of the affected probe. Finally, one installs a new probe in the reverse of the aforementioned sequence. The wire connections can be made by soldering, but to facilitate removal and installation, they can be made via miniature plugs and sockets. The connections between the probe flow passages and the tubes leading to the remote pressure sensors can be made by use of any of a variety of readily available flexible tubes that can be easily pulled off and slid back on for removal and installation, respectively.

Structural formation of huntingtin-like aggregates probed by small-angle neutron scattering

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

Stanley, Christopher B; Perevozchikova, Tatiana; Berthelier-Jung, Valerie M

2011-01-01

In several neurodegenerative disorders, including Huntington s disease (HD), aspects concerning the earliest of protein structures that form along the aggregation pathway have increasingly gained attention since these particular species are likely to be neurotoxic. We used time-resolved small-angle neutron scattering (SANS) to probe in solution these transient structures formed by peptides having the N-terminal sequence context of mutant huntingtin (Htt) exon 1. We obtained snapshots of the formed aggregates as the kinetic reaction ensued to yield quantitative information on their size and mass. At the early stage, small precursor species with an initial radius of gyration (Rg) of 16.1more » 5.9 and average mass of a dimer to trimer were monitored. Structural growth was treated as two modes with a transition from three-dimensional early aggregate formation to two-dimensional fibril growth and association. Our SANS results on the internal structure of the mature fibrils demonstrate loose packing with about 1 peptide per 4.75 -sheet repeat distance, which is shown to be quantitatively consistent with a -helix model. This research provides new insights into the structures forming along the pathway of Htt exon 1 aggregation and should assist in determining the role that precursors play in neuronal toxicity.« less

Simultaneous determination of micellar structure and drag reduction in a surfactant solution flow using the fluorescence probe method

NASA Astrophysics Data System (ADS)

Wakimoto, Tatsuro; Araga, Koichi; Katoh, Kenji

2018-03-01

As widely known, the addition of a specific type of surfactant to water reduces drag in a pipe flow. This effect is considered to be a result of the suppression of turbulent transition caused by the ordered structure of rod-like micelles that is referred to as a shear-induced structure (SIS). However, it is typically difficult to determine the SIS since it is necessary to noninvasively detect the SIS with several hundred nanometers in the actual moving flow. In this study, we used the fluorescence probe method to locally determine the SIS in a pipe flow. When hydrophobic fluorescence molecules are added to the surfactant solution, the fluorescence molecules are trapped in micelles. Thus, fluorescence intensity varies based on the change in the micellar structure. We verified the applicability of the fluorescence probe method to the SIS detection and determined the relationship between the micellar structure and the drag reduction in the pipe flow by simultaneously measuring the fluorescence intensity and pipe friction factor. The experimental result demonstrates that the SIS formation in the near-wall region is closely correlated with the drag reduction and suggests that the near-wall SIS suppresses the turbulent transition.

The Saturn Probe Interior and aTmosphere Explorer (SPRITE) Mission

NASA Astrophysics Data System (ADS)

Simon, Amy; Banfield, Donald; Atkinson, David; SPRITE Science Team

2018-01-01

A key question in planetary science is how the planets formed in our Solar System, and, by extension, in exoplanet systems. The abundances of the noble gases (He, Ne, Ar, Kr, Xe), heavy elements (C, N, O, S), and their isotopes provide important forensic clues as to location and time of formation in the early Solar System. Jupiter and Saturn contain most of the planetary mass in our solar system, and their chemical fingerprints will distinguish between competing models of the formation of all the planets. After the end of the Cassini mission, some of these elements have only ambiguous values above the cloud tops, while others (particularly the noble gases) have not been measured at all. Resolving this requires direct in situ measurements. The proposed NASA New Frontiers Saturn PRobe Interior and aTmosphere Explorer (SPRITE) mission delivers an instrumented entry probe from a carrier relay spacecraft that also provides context imaging. The powerful probe instrument suite is comprised of a Quadrupole Mass Spectrometer, a Tunable Laser Spectrometer, and an Atmospheric Structure Instrument including a Doppler Wind Experiment and a simple backscatter nephelometer. These instruments measure the elemental and isotopic abundances of helium, the heavier noble gases, and the major elements, as well as constraining cloud properties, 3-D atmospheric dynamics, and disequilibrium chemistry to at least 10 bars in Saturn's troposphere. In situ measurements of Saturn's atmosphere by SPRITE will provide a significantly improved context for interpreting the results from the Galileo probe, Juno, and Cassini missions. SPRITE will revolutionize our understanding of the formation and evolution of the gas giant planets, and ultimately the present-day structure of the Solar System.

The GalileoJupiter Probe Doppler Wind Experiment

NASA Astrophysics Data System (ADS)

Atkinson, D. H.

2001-09-01

The GalileoJupiter atmospheric entry probe was launched along with the Galileoorbiter spacecraft from Cape Canaveral in Florida, USA, on October 18, 1989. Following a cruise of greater than six years, the probe arrived at Jupiter on December 7, 1995. During its 57-minute descent, instruments on the probe studied the atmospheric composition and structure, the clouds, lightning, and energy structure of the upper Jovian atmosphere. One of the two radio channels over which the experiment data was transmitted to the orbiter was driven by an ultrastable oscillator. All motions of the probe and orbiter, including the speed of probe descent, Jupiter's rotation, and the atmospheric winds, contributed to a Doppler shift of the probe radio frequency. By accurately measuring the frequency of the probe radio signal, an accurate time history of the probe-orbiter relative motions could be reconstructed. Knowledge of the nominal probe and orbiter trajectories allowed the nominal Doppler shift to be removed from the probe radio frequency leaving a measurable frequency residual arising primarily from the zonal winds in Jupiter's atmosphere, and micromotions of the probe arising from probe spin, swing under the parachute, atmospheric turbulence, and aerodynamic effects. Assuming that the zonal horizontal winds dominate the residual probe motion, a profile of frequency residuals was generated. Inversion of the frequency residuals resulted in the first in situ measurements of the vertical profile of Jupiter's deep zonal winds. It is found that beneath 700 mb, the winds are strong and prograde, rising rapidly to 170 m/s between 1 and 4 bars. Beneath 4 bars to 21 bars, the depth at which the link with the probe was lost, the winds remain constant and strong. When corrections for the high temperatures encountered by the probe are considered, there is no evidence of diminishing or strengthening of the zonal winds in the deepest regions explored by the Galileoprobe. Following the wind

Probing the nature of Dark Matter with the SKA

NASA Astrophysics Data System (ADS)

Colafrancesco, S.; Regis, M.; Marchegiani, P.; Beck, G.; Beck, R.; Zechlin, H.; Lobanov, A.; Horns, D.

2015-04-01

Dark Matter (DM) is a fundamental ingredient of our Universe and of structure formation, and yet its nature is elusive to astrophysical probes. Information on the nature and physical properties of the WIMP (neutralino) DM (the leading candidate for a cosmologically relevant DM) can be obtained by studying the astrophysical signals of their annihilation/decay. Among the various e.m. signals, secondary electrons produced by neutralino annihilation generate synchrotron emission in the magnetized atmosphere of galaxy clusters and galaxies which could be observed as a diffuse radio emission (halo or haze) centered on the DM halo. A deep search for DM radio emission with SKA in local dwarf galaxies, galaxy regions with low star formation and galaxy clusters (with offset DM-baryonic distribution, like e.g. the Bullet cluster) can be very effective in constraining the neutralino mass, composition and annihilation cross-section. For the case of a dwarf galaxy, like e.g. Draco, the constraints on the DM annihilation cross-section obtainable with SKA1-MID will be at least a factor $\\sim 10^3$ more stringent than the limits obtained by Fermi-LAT in the $\\gamma$-rays. These limits scale with the value of the B field, and the SKA will have the capability to determine simultaneously both the magnetic field in the DM-dominated structures and the DM particle properties. The optimal frequency band for detecting the DM-induced radio emission is around $\\sim 1$ GHz, with the SKA1-MID Band 1 and 4 important to probe the synchrotron spectral curvature at low-$\

Application of spatially modulated near-infrared structured light to study changes in optical properties of mouse brain tissue during heatstress.

PubMed

Shaul, Oren; Fanrazi-Kahana, Michal; Meitav, Omri; Pinhasi, Gad A; Abookasis, David

2017-11-10

Heat stress (HS) is a medical emergency defined by abnormally elevated body temperature that causes biochemical, physiological, and hematological changes. The goal of the present research was to detect variations in optical properties (absorption, reduced scattering, and refractive index coefficients) of mouse brain tissue during HS by using near-infrared (NIR) spatial light modulation. NIR spatial patterns with different spatial phases were used to differentiate the effects of tissue scattering from those of absorption. Decoupling optical scattering from absorption enabled the quantification of a tissue's chemical constituents (related to light absorption) and structural properties (related to light scattering). Technically, structured light patterns at low and high spatial frequencies of six wavelengths ranging between 690 and 970 nm were projected onto the mouse scalp surface while diffuse reflected light was recorded by a CCD camera positioned perpendicular to the mouse scalp. Concurrently to pattern projection, brain temperature was measured with a thermal camera positioned slightly off angle from the mouse head while core body temperature was monitored by thermocouple probe. Data analysis demonstrated variations from baseline measurements in a battery of intrinsic brain properties following HS.

Morphology and mechanical properties of multi-stranded amyloid fibrils probed by atomistic and coarse-grained simulations

NASA Astrophysics Data System (ADS)

Yoon, Gwonchan; Lee, Myeongsang; Kim, Kyungwoo; In Kim, Jae; Chang, Hyun Joon; Baek, Inchul; Eom, Kilho; Na, Sungsoo

2015-12-01

Amyloid fibrils are responsible for pathogenesis of various diseases and exhibit the structural feature of an ordered, hierarchical structure such as multi-stranded helical structure. As the multi-strandedness of amyloid fibrils has recently been found to be highly correlated with their toxicity and infectivity, it is necessary to study how the hierarchical (i.e. multi-stranded) structure of amyloid fibril is formed. Moreover, although it has recently been reported that the nanomechanics of amyloid proteins plays a key role on the amyloid-induced pathogenesis, a critical role that the multi-stranded helical structure of the fibrils plays in their nanomechanical properties has not fully characterized. In this work, we characterize the morphology and mechanical properties of multi-stranded amyloid fibrils by using equilibrium molecular dynamics simulation and elastic network model. It is shown that the helical pitch of multi-stranded amyloid fibril is linearly proportional to the number of filaments comprising the amyloid fibril, and that multi-strandedness gives rise to improving the bending rigidity of the fibril. Moreover, we have also studied the morphology and mechanical properties of a single protofilament (filament) in order to understand the effect of cross-β structure and mutation on the structures and mechanical properties of amyloid fibrils. Our study sheds light on the underlying design principles showing how the multi-stranded amyloid fibril is formed and how the structure of amyloid fibrils governs their nanomechanical properties.

A multi-signal fluorescent probe for simultaneously distinguishing and sequentially sensing cysteine/homocysteine, glutathione, and hydrogen sulfide in living cells† †Electronic supplementary information (ESI) available: Experimental details for chemical synthesis of all compounds, chemical structure characterization, supplementary spectra of probe, and fluorescence imaging methods and data. See DOI: 10.1039/c7sc00423k Click here for additional data file.

PubMed Central

He, Longwei; Yang, Xueling; Xu, Kaixin; Kong, Xiuqi

2017-01-01

Biothiols, which have a close network of generation and metabolic pathways among them, are essential reactive sulfur species (RSS) in the cells and play vital roles in human physiology. However, biothiols possess highly similar chemical structures and properties, resulting in it being an enormous challenge to simultaneously discriminate them from each other. Herein, we develop a unique fluorescent probe (HMN) for not only simultaneously distinguishing Cys/Hcy, GSH, and H2S from each other, but also sequentially sensing Cys/Hcy/GSH and H2S using a multi-channel fluorescence mode for the first time. When responding to the respective biothiols, the robust probe exhibits multiple sets of fluorescence signals at three distinct emission bands (blue-green-red). The new probe can also sense H2S at different concentration levels with changes of fluorescence at the blue and red emission bands. In addition, the novel probe HMN is able to discriminate and sequentially sense biothiols in biological environments via three-color fluorescence imaging. We expect that the development of the robust probe HMN will provide a powerful strategy to design fluorescent probes for the discrimination and sequential detection of biothiols, and offer a promising tool for exploring the interrelated roles of biothiols in various physiological and pathological conditions. PMID:28989659

PALS: A unique probe for the molecular organisation of biopolymer matrices

NASA Astrophysics Data System (ADS)

Roussenova, M.; Alam, M. A.

2013-06-01

This short review aims to illustrate the versatility of Positron Annihilation Lifetime Spectroscopy (PALS) when utilized for the characterization of biopolymers (e.g.: starch, fractionated maltooligomers, gelatin and cellulose derivatives) commonly used for the formulation of pharmaceutical encapsulants. By showing examples from a number of recent PALS studies, we illustrate that this technique can be used to probe the changes in thermodynamic state and molecular packing for a wide range of biopolymer matrices as a function of temperature, matrix composition and water content. This provides a basis for establishing composition-structure-property relationships for these materials, which would eventually enable the rational control of their macroscopic properties and the design of optimal encapsulating matrices and intelligent drug delivery systems.

Planetary Wind Determination by Doppler Tracking of a Small Entry Probe Network

NASA Astrophysics Data System (ADS)

Atkinson, D. H.; Asmar, S.; Lazio, J.; Preston, R. A.

2017-12-01

along a single vertical atmospheric slice cannot adequately represent the overall dynamical properties of the atmosphere. To more completely characterize the dynamical structure of a planetary atmosphere, it is proposed that future in situ planetary missions include a network of small probes dedicated to wind measurements.

Redox-Responsive Fluorescent Probes with Different Design Strategies.

PubMed

Lou, Zhangrong; Li, Peng; Han, Keli

2015-05-19

In an aerobic organism, reactive oxygen species (ROS) are an inevitable metabolic byproduct. Endogenously produced ROS have a significant role in physiological processes, but excess ROS can cause oxidative stress and can damage tissue. Cells possess elaborate mechanisms to regulate their internal redox status. The intracellular redox homeostasis plays an essential role in maintaining cellular function. However, moderate alterations in redox balance can accompany major transitions in a cell's life cycle. Because of the role of ROS in physiology and in pathology, researchers need new tools to study redox chemistry in biological systems.In recent years, researchers have made remarkable progress in developing new, highly sensitive and selective fluorescent probes that respond to redox changes, and in this Account we highlight related research, primarily from our own group. We present an overview of the design, photophysical properties, and fluorescence transduction mechanisms of reported molecules that probe redox changes. We have designed and synthesized a series of fluorescent probes for redox cycles in biological systems relying on the active center of glutathione peroxidase (GPx). We have also constructed probes based on the oxidation and reduction of hydroquinone and of 2,2,6,6-tetramethylpiperidinooxy (TEMPO). Most of these probes exhibit high sensitivity and good selectivity, absorb in the near-infrared, and respond rapidly. Such probes are useful for confocal fluorescence microscopy, a dynamic imaging technique that could allow researchers to observe biologically important ROS and antioxidants in real time. This technique and these probes provide potentially useful tools for exploring the generation, transport, physiological function, and pathogenic mechanisms of ROS and antioxidants.We also describe features that could improve the properties of redox-responsive fluorescent probes: greater photostability; rapid, dynamic, cyclic and ratiometric responses; and

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

NASA Astrophysics Data System (ADS)

Xu, Zhicheng; Bai, Guan; Dong, Chuan

2005-12-01

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

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

PubMed

Xu, Zhicheng; Bai, Guan; Dong, Chuan

2005-12-01

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

Supramolecular Amino Acid Based Hydrogels: Probing the Contribution of Additive Molecules using NMR Spectroscopy

PubMed Central

Ramalhete, Susana M.; Nartowski, Karol P.; Sarathchandra, Nichola; Foster, Jamie S.; Round, Andrew N.; Angulo, Jesús

2017-01-01

Abstract Supramolecular hydrogels are composed of self‐assembled solid networks that restrict the flow of water. l‐Phenylalanine is the smallest molecule reported to date to form gel networks in water, and it is of particular interest due to its crystalline gel state. Single and multi‐component hydrogels of l‐phenylalanine are used herein as model materials to develop an NMR‐based analytical approach to gain insight into the mechanisms of supramolecular gelation. Structure and composition of the gel fibres were probed using PXRD, solid‐state NMR experiments and microscopic techniques. Solution‐state NMR studies probed the properties of free gelator molecules in an equilibrium with bound molecules. The dynamics of exchange at the gel/solution interfaces was investigated further using high‐resolution magic angle spinning (HR‐MAS) and saturation transfer difference (STD) NMR experiments. This approach allowed the identification of which additive molecules contributed in modifying the material properties. PMID:28401991

Non-toxic fluorescent phosphonium probes to detect mitochondrial potential

NASA Astrophysics Data System (ADS)

Šarić, Ana; Crnolatac, Ivo; Bouillaud, Frédéric; Sobočanec, Sandra; Mikecin, Ana-Matea; Mačak Šafranko, Željka; Delgeorgiev, Todor; Piantanida, Ivo; Balog, Tihomir; Petit, Patrice X.

2017-03-01

We evaluated our phosphonium-based fluorescent probes for selective staining of mitochondria. Currently used probes for monitoring mitochondrial membrane potential show varying degrees of interference with cell metabolism, photo-induced damage and probe binding. Here presented probes are characterised by highly efficient cellular uptake and specific accumulation in mitochondria. Fluorescent detection of the probes was accomplished using flow cytometry and confocal microscopy imaging of yeast and mammalian cells. Toxicity analysis (impedimetry—xCELLigence for the cellular proliferation and Seahorse technology for respiratory properties) confirms that these dyes exhibit no-toxicity on mitochondrial or cellular functioning even for long time incubation. The excellent chemical and photophysical stability of the dyes makes them promising leads toward improved fluorescent probes. Therefore, the probes described here offer to circumvent the problems associated with existing-probe’s limitations.

An ESIPT fluorescent probe sensitive to protein α-helix structures.

PubMed

Jiang, Nan; Yang, Chanli; Dong, Xiongwei; Sun, Xianglang; Zhang, Dan; Liu, Changlin

2014-07-28

A large majority of membrane proteins have one or more transmembrane regions consisting of α-helices. Membrane protein levels differ from one type of cell to another, and the expression of membrane proteins also changes from normal to diseased cells. For example, prostate cancer cells have been reported to have downregulated expression of membrane proteins, including zinc transporters, compared with normal prostate cells. These reports inspired us to design a fluorescence probe sensitive to protein α-helical structures to discriminate individual prostate cancer cells from normal ones. A benzazole derivative ( in this study) was observed to emit strong fluorescence resulting from an excited-state intramolecular proton transfer (ESIPT) in protein α-helical environments. The intensity of ESIPT fluorescence of was observed to be positively correlated with the α-helix content of proteins. The molecular docking simulation suggested that it had low energy for the binding of to proteins when the binding sites were localized within the α-helical regions of protein via H-bonds. Furthermore, was found to be localized in cell membranes through binding to transmembrane α-helical regions of membrane proteins, and was capable of probing differences in the α-helix contents of membrane proteins between normal and cancerous prostate cells through changes in the ESIPT emission intensity. These results indicated that could distinguish individual prostate cancer cells from normal ones, as the changes in the ESIPT fluorescence intensity of could reflect the regulation in expression of the membrane proteins including zinc transporters. This recognition strategy of individual prostate cancer cells might contribute to early diagnosis techniques for prostate cancer.

Contact resonances of U-shaped atomic force microscope probes

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

Rezaei, E.; Turner, J. A., E-mail: jaturner@unl.edu

Recent approaches used to characterize the elastic or viscoelastic properties of materials with nanoscale resolution have focused on the contact resonances of atomic force microscope (CR-AFM) probes. The experiments for these CR-AFM methods involve measurement of several contact resonances from which the resonant frequency and peak width are found. The contact resonance values are then compared with the noncontact values in order for the sample properties to be evaluated. The data analysis requires vibration models associated with the probe during contact in order for the beam response to be deconvolved from the measured spectra. To date, the majority of CR-AFMmore » research has used rectangular probes that have a relatively simple vibration response. Recently, U-shaped AFM probes have created much interest because they allow local sample heating. However, the vibration response of these probes is much more complex such that CR-AFM is still in its infancy. In this article, a simplified analytical model of U-shaped probes is evaluated for contact resonance applications relative to a more complex finite element (FE) computational model. The tip-sample contact is modeled using three orthogonal Kelvin-Voigt elements such that the resonant frequency and peak width of each mode are functions of the contact conditions. For the purely elastic case, the frequency results of the simple model are within 8% of the FE model for the lowest six modes over a wide range of contact stiffness values. Results for the viscoelastic contact problem for which the quality factor of the lowest six modes is compared show agreement to within 13%. These results suggest that this simple model can be used effectively to evaluate CR-AFM experimental results during AFM scanning such that quantitative mapping of viscoelastic properties may be possible using U-shaped probes.« less

Ion nose spectral structures observed by the Van Allen Probes

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

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

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

Ion nose spectral structures observed by the Van Allen Probes

DOE PAGES

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

2016-11-22

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

Nanobits, Nembranes and Micro Four-Point Probes: Customizable Tools for insitu Manipulation and Characterisation of Nanostructures

NASA Astrophysics Data System (ADS)

Boggild, Peter; Hjorth Petersen, Dirch; Sardan Sukas, Ozlem; Dam, Henrik Friis; Lei, Anders; Booth, Timothy; Molhave, Kristian; Eicchorn, Volkmar

2010-03-01

We present a range of highly adaptable microtools for direct interaction with nanoscale structures; (i) semiautomatic pick-and-place assembly of multiwalled carbon nanotubes onto cantilevers for high-aspect ratio scanning probe microscopy, using electrothermal microgrippers inside a SEM. Topology optimisation was used to calculate the optimal gripper shape defined by the boundary conditions, resulting in 10-100 times better performance. By instead pre-defining detachable tips using electron beam lithography, free-form scanning probe tips (Nanobits) can be mounted in virtually any position on a cantilever; (ii) scanning micro four point probes allow fast, non- destructive mapping of local electrical properties (sheet resistance and Hall mobility) and hysteresis effects of graphene sheets; (iii) sub 100 nm freestanding devices with wires, heaters, actuators, sensors, resonators and probes were defined in a 100 nm thin membrane with focused ion beam milling. By patterning generic membrane templates (Nembranes) the fabrication time of a TEM compatible NEMS device is effectively reduced to less around 20 minutes.

Implications of contamination and surface area ratios for Langmuir probe diagnostics on CubeSats

NASA Astrophysics Data System (ADS)

Suresh, P.; Swenson, C.

2009-12-01

Theories describing the current collected by a biased probe under various conditions are necessary for such observation to be used to accurately determine plasma properties. Langmuir probes are routinely used on spacecraft to measure plasma parameters such as density, temperature, and vehicle charging. The collected current is a function of the potential between the surrounding plasma and probe surface. There have been both observations of and concepts for unaccounted variations of this potential which limit the application of Langmuir probe theory for determining plasma properties. These variations occur due to spatial variations of the work function across the probe surface due to non-uniformity of the crystalline surface properties and surface contamination of the probe. Currently we do not have theoretical expressions which consider these factors as first principles in their derivation. In the event of these surface potential variations, the analysis of the plasma using the currently available theories of the Langmuir probe yield erroneous results. We present a theory which models the current as a function of the surface potential variations. Another consideration for Langmuir probes on CubeSats is the ratio of the probe area to the return current collection area. If the area ratio is unfavorable this can also lead to erroneous results in the interpretation of observations. A mathematical formulation of the current collected by the probe for contaminated surfaces is presented and compared with data from a Langmuir probe flown on a sounding rocket mission. The implications of using Langmuir probes on CubeSats given the engineering limitations of probe cleanliness and area ratios are reviewed.

Probing Structural Transitions in the Intrinsically Disordered C-Terminal Domain of the Measles Virus Nucleoprotein by Vibrational Spectroscopy of Cyanylated Cysteines

PubMed Central

Bischak, Connor G.; Longhi, Sonia; Snead, David M.; Costanzo, Stéphanie; Terrer, Elodie; Londergan, Casey H.

2010-01-01

Four single-cysteine variants of the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (NTAIL) were cyanylated at cysteine and their infrared spectra in the C≡N stretching region were recorded both in the absence and in the presence of one of the physiological partners of NTAIL, namely the C-terminal X domain (XD) of the viral phosphoprotein. Consistent with previous studies showing that XD triggers a disorder-to-order transition within NTAIL, the C≡N stretching bands of the infrared probe were found to be significantly affected by XD, with this effect being position-dependent. When the cyanylated cysteine side chain is solvent-exposed throughout the structural transition, its changing linewidth reflects a local gain of structure. When the probe becomes partially buried due to binding, its frequency reports on the mean hydrophobicity of the microenvironment surrounding the labeled side chain of the bound form. The probe moiety is small compared to other common covalently attached spectroscopic probes, thereby minimizing possible steric hindrance/perturbation at the binding interface. These results show for the first time to our knowledge the suitability of site-specific cysteine mutagenesis followed by cyanylation and infrared spectroscopy to document structural transitions occurring within intrinsically disordered regions, with regions involved in binding and folding being identifiable at the residue level. PMID:20816082

On the vibration properties of composite materials and structures

NASA Astrophysics Data System (ADS)

Lu, Y. P.; Neilson, H. C.; Roscoe, A. J.

1993-01-01

In recent years, there has been a widespread assumption that composite materials and structures offer enhanced vibration and acoustic properties. This assumption has to be evaluated or validated. The objective of this article is to address the subject of vibration characteristics and the related force transmissibility properties of composite structures. For a given composite beam made of Hercules AS4/3501-6 graphite/epoxy with a layered structure sequence of (0,0,30,-30)(sub 6S), resonance frequencies, structural damping, responses, impedances, and force transmissibility properties are determined, discussed, and compared with those of a steel beam. This article proposes a procedure to evaluate the vibration properties of individual composites. The criterion defined for performance comparison between composite materials and conventional materials is also discussed.

Effect of processing on Polymer/Composite structure and properties

NASA Technical Reports Server (NTRS)

1982-01-01

Advances in the vitality and economic health of the field of polymer forecasting are discussed. A consistent and rational point of view which considers processing as a participant in the underlying triad of relationships which comprise materials science and engineering is outlined. This triad includes processing as it influences material structure, and ultimately properties. Methods in processing structure properties, polymer science and engineering, polymer chemistry and synthesis, structure and modification and optimization through processing, and methods of melt flow modeling in processing structure property relations of polymer were developed. Mechanical properties of composites are considered, and biomedical materials research to include polymer processing effects are studied. An analysis of the design technology of advances graphite/epoxy composites is also reported.

Electrical Study of Trapped Charges in Copper-Doped Zinc Oxide Films by Scanning Probe Microscopy for Nonvolatile Memory Applications

PubMed Central

Su, Ting; Zhang, Haifeng

2017-01-01

Charge trapping properties of electrons and holes in copper-doped zinc oxide (ZnO:Cu) films have been studied by scanning probe microscopy. We investigated the surface potential dependence on the voltage and duration applied to the copper-doped ZnO films by Kelvin probe force microscopy. It is found that the Fermi Level of the 8 at.% Cu-doped ZnO films shifted by 0.53 eV comparing to undoped ZnO films. This shift indicates significant change in the electronic structure and energy balance in Cu-doped ZnO films. The Fermi Level (work function) of zinc oxide films can be tuned by Cu doping, which are important for developing this functional material. In addition, Kelvin probe force microscopy measurements demonstrate that the nature of contact at Pt-coated tip/ZnO:Cu interface is changed from Schottky contact to Ohmic contact by increasing sufficient amount of Cu ions. The charge trapping property of the ZnO films enhance greatly by Cu doping (~10 at.%). The improved stable bipolar charge trapping properties indicate that copper-doped ZnO films are promising for nonvolatile memory applications. PMID:28135335

Open-Ended Coaxial Dielectric Probe Effective Penetration Depth Determination.

PubMed

Meaney, Paul M; Gregory, Andrew P; Seppälä, Jan; Lahtinen, Tapani

2016-03-01

We have performed a series of experiments which demonstrate the effect of open-ended coaxial diameter on the depth of penetration. We used a two layer configuration of a liquid and movable cylindrical piece of either Teflon or acrylic. The technique accurately demonstrates the depth in a sample for which a given probe diameter provides a reasonable measure of the bulk dielectric properties for a heterogeneous volume. In addition we have developed a technique for determining the effective depth for a given probe diameter size. Using a set of simulations mimicking four 50 Ω coaxial cable diameters, we demonstrate that the penetration depth in both water and saline has a clear dependence on probe diameter but is remarkably uniform over frequency and with respect to the intervening liquid permittivity. Two different 50 Ω commercial probes were similarly tested and confirm these observations. This result has significant implications to a range of dielectric measurements, most notably in the area of tissue property studies.

Open-Ended Coaxial Dielectric Probe Effective Penetration Depth Determination

PubMed Central

Meaney, Paul M.; Gregory, Andrew P.; Seppälä, Jan; Lahtinen, Tapani

2016-01-01

We have performed a series of experiments which demonstrate the effect of open-ended coaxial diameter on the depth of penetration. We used a two layer configuration of a liquid and movable cylindrical piece of either Teflon or acrylic. The technique accurately demonstrates the depth in a sample for which a given probe diameter provides a reasonable measure of the bulk dielectric properties for a heterogeneous volume. In addition we have developed a technique for determining the effective depth for a given probe diameter size. Using a set of simulations mimicking four 50 Ω coaxial cable diameters, we demonstrate that the penetration depth in both water and saline has a clear dependence on probe diameter but is remarkably uniform over frequency and with respect to the intervening liquid permittivity. Two different 50 Ω commercial probes were similarly tested and confirm these observations. This result has significant implications to a range of dielectric measurements, most notably in the area of tissue property studies. PMID:27346890

Probing Quark-Gluon-Plasma properties with a Bayesian model-to-data comparison

NASA Astrophysics Data System (ADS)

Cai, Tianji; Bernhard, Jonah; Ke, Weiyao; Bass, Steffen; Duke QCD Group Team

2016-09-01

Experiments at RHIC and LHC study a special state of matter called the Quark Gluon Plasma (QGP), where quarks and gluons roam freely, by colliding relativistic heavy-ions. Given the transitory nature of the QGP, its properties can only be explored by comparing computational models of its formation and evolution to experimental data. The models fall, roughly speaking, under two categories-those solely using relativistic viscous hydrodynamics (pure hydro model) and those that in addition couple to a microscopic Boltzmann transport for the later evolution of the hadronic decay products (hybrid model). Each of these models has multiple parameters that encode the physical properties we want to probe and that need to be calibrated to experimental data, a task which is computationally expensive, but necessary for the knowledge extraction and determination of the models' quality. Our group has developed an analysis technique based on Bayesian Statistics to perform the model calibration and to extract probability distributions for each model parameter. Following the previous work that applies the technique to the hybrid model, we now perform a similar analysis on a pure-hydro model and display the posterior distributions for the same set of model parameters. We also develop a set of criteria to assess the quality of the two models with respect to their ability to describe current experimental data. Funded by Duke University Goldman Sachs Research Fellowship.

21-cm radiation: a new probe of variation in the fine-structure constant.

PubMed

Khatri, Rishi; Wandelt, Benjamin D

2007-03-16

We investigate the effect of variation in the value of the fine-structure constant (alpha) at high redshifts (recombination > z > 30) on the absorption of the cosmic microwave background (CMB) at 21 cm hyperfine transition of the neutral atomic hydrogen. We find that the 21 cm signal is very sensitive to the variations in alpha and it is so far the only probe of the fine-structure constant in this redshift range. A change in the value of alpha by 1% changes the mean brightness temperature decrement of the CMB due to 21 cm absorption by >5% over the redshift range z < 50. There is an effect of similar magnitude on the amplitude of the fluctuations in the brightness temperature. The redshift of maximum absorption also changes by approximately 5%.

Hierarchical structure and mechanical properties of remineralized dentin.

PubMed

Chen, Yi; Wang, Jianming; Sun, Jian; Mao, Caiyun; Wang, Wei; Pan, Haihua; Tang, Ruikang; Gu, Xinhua

2014-12-01

It is widely accepted that the mechanical properties of dentin are significantly determined by its hierarchical structure. The current correlation between the mechanical properties and the hierarchical structure was mainly established by studying altered forms of dentin, which limits the potential outcome of the research. In this study, dentins with three different hierarchical structures were obtained via two different remineralization procedures and at different remineralization stages: (1) a dentin structure with amorphous minerals incorporated into the collagen fibrils, (2) a dentin with crystallized nanominerals incorporated into the collagen fibrils, and (3) a dentin with an out-of-order mineral layer filling the collagen fibrils matrix. Nanoindentation tests were performed to investigate the mechanical behavior of the remineralized dentin slides. The results showed that the incorporation of the crystallized nanominerals into the acid-etched demineralized organic fibrils resulted in a remarkable improvement of the mechanical properties of the dentin. In contrast, for the other two structures, i.e. the amorphous minerals inside the collagen fibrils and the out-of-order mineral layer within the collagen fibrils matrix, the excellent mechanical properties of dentin could not be restored. Copyright © 2014 Elsevier Ltd. All rights reserved.

Amylopectin molecular structure in relation to physicochemical properties of quinoa starch.

PubMed

Li, Guantian; Zhu, Fan

2017-05-15

Structure-function relationships of starch components remain a subject of research interest. Quinoa starch has very small granules (∼2μm) with unique properties. In this study, nine quinoa starches varied greatly in composition, structure, and physicochemical properties were selected for the analysis of structure-function relationships. Pearson correlation analysis revealed that the properties related to gelatinization such as swelling power, water solubility index, crystallinity, pasting, and thermal properties are much affected by the amylopectin chain profile and amylose content. The parameters of gel texture and amylose leaching are much related to amylopectin internal structure. Other properties such as enzyme susceptibility and particle size distribution are also strongly correlated with starch composition and amylopectin structure. Interesting findings indicate the importance of amylopectin internal structure and individual unit chain profile in determining the physicochemical properties of starch. This work highlights some relationships among composition, amylopectin structure and physicochemical properties of quinoa starch. Copyright © 2017 Elsevier Ltd. All rights reserved.

The melting of native domain structure in effector activation of IgG studied by using congo red as a specific probe.

PubMed

Piekarska, B; Roterman, I; Rybarska, J; Koniczny, L; Kaszuba, J

1994-03-01

The nature of structural changes in IgG molecules associated with the binding to antigen and/or heat aggregation was studied using bis azo dye (Congo Red) as the specific probe. It was found, that protein conformation responsible for binding the dye represents an unfolding intermediate with properties corresponding to a molten globule state. The properties of the dye-protein complex reveal the signs of an unfolding of the peptide chain with simultaneously preserved relatively compact packing. Immunoglobulins which were induced by heating, or binding to antigen in order to form the complex with dye ligands, become more susceptible for digestion. The main peptide of molecular weight 30,000 D which appears in products was suggested to originate from a heavy chain after its splitting in the region of CH1 domain. The energetic evaluation of stability of IgG domains also indicates that CH1 is the least stable fragment of the heavy chain and its conformation may be destabilized first. It was concluded that destabilized tertiary packing of antibodies bound to antigen may favour the association of closely situated immunoglobulin molecules increasing the stability of the immune complex and influencing in the result its effector activity.

Hall-Effect Measurements Probing the Degree of Charge-Carrier Delocalization in Solution-Processed Crystalline Molecular Semiconductors

NASA Astrophysics Data System (ADS)

Chang, Jui-Fen; Sakanoue, Tomo; Olivier, Yoann; Uemura, Takafumi; Dufourg-Madec, Marie-Beatrice; Yeates, Stephen G.; Cornil, Jérôme; Takeya, Jun; Troisi, Alessandro; Sirringhaus, Henning

2011-08-01

Intramolecular structure and intermolecular packing in crystalline molecular semiconductors should have profound effects on the charge-carrier wave function, but simple drift mobility measurements are not very sensitive to this. Here we show that differences in the Hall resistance of two soluble pentacene derivatives can be explained with different degrees of carrier delocalization being limited by thermal lattice fluctuations. A combination of Hall measurements, optical spectroscopy, and theoretical simulations provides a powerful probe of structure-property relationships at a molecular level.

An optical fiber taper fluorescent probe for detection of nitro-explosives based on tetraphenylethylene with aggregation-induced emission

NASA Astrophysics Data System (ADS)

Liu, Fukun; Cui, Minxin; Ma, Jiajun; Zou, Gang; Zhang, Qijin

2017-07-01

In this work, we report a novel optical fiber taper fluorescent probe for detection of nitro-explosives. The probe was fabricated by an in-situ photo-plating through evanescent wave and transmitted light initiated thiol-ene ;click; reaction, from which a cross-linked fluorescence porous polymer film was covalently bonded on the surface of the fiber taper. The film exhibits well-organized porous structure due to the presence of polyhedral oligomeric vinylsilsesquioxane moieties, and simultaneously displays strong fluorescence from tetraphenylethylene with aggregation-induced emission property. These two characters make the probe show a remarkable sensitivity, anti-photo-bleaching and a repeatability in detection of TNT and DNT vapors by fluorescence quenching. In addition, the detection is not interfered in the presence of other volatile organic gases.

Intrauterine photoacoustic and ultrasound imaging probe

NASA Astrophysics Data System (ADS)

Miranda, Christopher; Barkley, Joel; Smith, Barbara S.

2018-04-01

Intrauterine photoacoustic and ultrasound imaging are probe-based imaging modalities with translational potential for use in detecting endometrial diseases. This deep-tissue imaging probe design allows for the retrofitting of commercially available endometrial sampling curettes. The imaging probe presented here has a 2.92-mm diameter and approximate length of 26 cm, which allows for entry into the human endometrial cavity, making it possible to use photoacoustic imaging and high-resolution ultrasound to characterize the uterus. We demonstrate the imaging probes' ability to provide structural information of an excised pig uterus using ultrasound imaging and detect photoacoustic signals at a radial depth of 1 cm.

Homogeneous versus heterogeneous probes for microbial ecological microarrays.

PubMed

Bae, Jin-Woo; Park, Yong-Ha

2006-07-01

Microbial ecological microarrays have been developed for investigating the composition and functions of microorganism communities in environmental niches. These arrays include microbial identification microarrays, which use oligonucleotides, gene fragments or microbial genomes as probes. In this article, the advantages and disadvantages of each type of probe are reviewed. Oligonucleotide probes are currently useful for probing uncultivated bacteria that are not amenable to gene fragment probing, whereas the functional gene fragments amplified randomly from microbial genomes require phylogenetic and hierarchical categorization before use as microbial identification probes, despite their high resolution for both specificity and sensitivity. Until more bacteria are sequenced and gene fragment probes are thoroughly validated, heterogeneous bacterial genome probes will provide a simple, sensitive and quantitative tool for exploring the ecosystem structure.

Manipulating transmission and reflection properties of a photonic crystal doped with quantum dot nanostructures

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

Solookinejad, G.; Panahi, M.; Sangachin, E. A.

The transmission and reflection properties of incident light in a defect dielectric structure is studied theoretically. The defect structure consists of donor and acceptor quantum dot nanostructures embedded in a photonic crystal. It is shown that the transmission and reflection properties of incident light can be controlled by adjusting the corresponding parameters of the system. The role of dipole–dipole interaction is considered as a new parameter in our calculations. It is noted that the features of transmission and reflection curves can be adjusted in the presence of dipole–dipole interaction. It is found that the absorption of weak probe light canmore » be converted to the probe amplification in the presence of dipole–dipole interaction. Moreover, the group velocity of transmitted and reflected probe light is discussed in detail in the absence and presence of dipole–dipole interaction. Our proposed model can be used as a new all-optical devices based on photonic materials doped with nanoparticles.« less

Long-wavelength analyte-sensitive luminescent probes and optical (bio)sensors

PubMed Central

Staudinger, Christoph; Borisov, Sergey M

2016-01-01

Long-wavelength luminescent probes and sensors become increasingly popular. They offer the advantage of lower levels of autofluorescence in most biological probes. Due to high penetration depth and low scattering of red and NIR light such probes potentially enable in vivo measurements in tissues and some of them have already reached a high level of reliability required for such applications. This review focuses on the recent progress in development and application of long-wavelength analyte-sensitive probes which can operate both reversibly and irreversibly. Photophysical properties, sensing mechanisms, advantages and limitations of individual probes are discussed. PMID:27134748

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.

Probing low-energy hyperbolic polaritons in van der Waals crystals with an electron microscope.

PubMed

Govyadinov, Alexander A; Konečná, Andrea; Chuvilin, Andrey; Vélez, Saül; Dolado, Irene; Nikitin, Alexey Y; Lopatin, Sergei; Casanova, Fèlix; Hueso, Luis E; Aizpurua, Javier; Hillenbrand, Rainer

2017-07-21

Van der Waals materials exhibit intriguing structural, electronic, and photonic properties. Electron energy loss spectroscopy within scanning transmission electron microscopy allows for nanoscale mapping of such properties. However, its detection is typically limited to energy losses in the eV range-too large for probing low-energy excitations such as phonons or mid-infrared plasmons. Here, we adapt a conventional instrument to probe energy loss down to 100 meV, and map phononic states in hexagonal boron nitride, a representative van der Waals material. The boron nitride spectra depend on the flake thickness and on the distance of the electron beam to the flake edges. To explain these observations, we developed a classical response theory that describes the interaction of fast electrons with (anisotropic) van der Waals slabs, revealing that the electron energy loss is dominated by excitation of hyperbolic phonon polaritons, and not of bulk phonons as often reported. Thus, our work is of fundamental importance for interpreting future low-energy loss spectra of van der Waals materials.Here the authors adapt a STEM-EELS system to probe energy loss down to 100 meV, and apply it to map phononic states in hexagonal boron nitride, revealing that the electron loss is dominated by hyperbolic phonon polaritons.

Probing Anisotropic Surface Properties of Molybdenite by Direct Force Measurements.

PubMed

Lu, Zhenzhen; Liu, Qingxia; Xu, Zhenghe; Zeng, Hongbo

2015-10-27

Probing anisotropic surface properties of layer-type mineral is fundamentally important in understanding its surface charge and wettability for a variety of applications. In this study, the surface properties of the face and the edge surfaces of natural molybdenite (MoS2) were investigated by direct surface force measurements using atomic force microscope (AFM). The interaction forces between the AFM tip (Si3N4) and face or edge surface of molybdenite were measured in 10 mM NaCl solutions at various pHs. The force profiles were well-fitted with classical DLVO (Derjaguin-Landau-Verwey-Overbeek) theory to determine the surface potentials of the face and the edge surfaces of molybdenite. The surface potentials of both the face and edge surfaces become more negative with increasing pH. At neutral and alkaline conditions, the edge surface exhibits more negative surface potential than the face surface, which is possibly due to molybdate and hydromolybdate ions on the edge surface. The point of zero charge (PZC) of the edge surface was determined around pH 3 while PZC of the face surface was not observed in the range of pH 3-11. The interaction forces between octadecyltrichlorosilane-treated AFM tip (OTS-tip) and face or edge surface of molybdenite were also measured at various pHs to study the wettability of molybdenite surfaces. An attractive force between the OTS-tip and the face surface was detected. The force profiles were well-fitted by considering DLVO forces and additional hydrophobic force. Our results suggest the hydrophobic feature of the face surface of molybdenite. In contrast, no attractive force between the OTS-tip and the edge surface was detected. This is the first study in directly measuring surface charge and wettability of the pristine face and edge surfaces of molybdenite through surface force measurements.

Determining the Mechanical Properties of Lattice Block Structures

NASA Technical Reports Server (NTRS)

Wilmoth, Nathan

2013-01-01

Lattice block structures and shape memory alloys possess several traits ideal for solving intriguing new engineering problems in industries such as aerospace, military, and transportation. Recent testing at the NASA Glenn Research Center has investigated the material properties of lattice block structures cast from a conventional aerospace titanium alloy as well as lattice block structures cast from nickel-titanium shape memory alloy. The lattice block structures for both materials were sectioned into smaller subelements for tension and compression testing. The results from the cast conventional titanium material showed that the expected mechanical properties were maintained. The shape memory alloy material was found to be extremely brittle from the casting process and only compression testing was completed. Future shape memory alloy lattice block structures will utilize an adjusted material composition that will provide a better quality casting. The testing effort resulted in baseline mechanical property data from the conventional titanium material for comparison to shape memory alloy materials once suitable castings are available.

Research on the Sensing Performance of the Tuning Fork-Probe as a Micro Interaction Sensor

PubMed Central

Gao, Fengli; Li, Xide

2015-01-01

The shear force position system has been widely used in scanning near-field optical microscopy (SNOM) and recently extended into the force sensing area. The dynamic properties of a tuning fork (TF), the core component of this system, directly determine the sensing performance of the shear positioning system. Here, we combine experimental results and finite element method (FEM) analysis to investigate the dynamic behavior of the TF probe assembled structure (TF-probe). Results from experiments under varying atmospheric pressures illustrate that the oscillation amplitude of the TF-probe is linearly related to the quality factor, suggesting that decreasing the pressure will dramatically increase the quality factor. The results from FEM analysis reveal the influences of various parameters on the resonant performance of the TF-probe. We compared numerical results of the frequency spectrum with the experimental data collected by our recently developed laser Doppler vibrometer system. Then, we investigated the parameters affecting spatial resolution of the SNOM and the dynamic response of the TF-probe under longitudinal and transverse interactions. It is found that the interactions in transverse direction is much more sensitive than that in the longitudinal direction. Finally, the TF-probe was used to measure the friction coefficient of a silica–silica interface. PMID:26404310

A novel polymer probe for Zn(II) detection with ratiometric fluorescence signal

NASA Astrophysics Data System (ADS)

Diao, Haipeng; Guo, Lixia; Liu, Wen; Feng, Liheng

2018-05-01

A conjugated polymer probe comprised of fluorene, quinolone and benzothiazole units was designed and synthesized by the Suzuki coupling reaction. Through the studies of photophysical and thermal properties, the polymer displays blue-emitting feature and good thermal stability. A ratiometric fluorescence signal of the probe for Zn(II) was observed in ethanol with a new emission peak at 555 nm. The probe possesses a high selectivity and sensitivity for Zn(II) during familiar metal ions in ethanol. The detection limit of the probe for Zn (II) is up to 10-8 mol/L. The electron distributions of the polymer before and after bonding with Zn (II) were investigated by the Gaussian 09 software, which agreed with the experimental results. Noticeably, based on the color property of the probe with Zn(II), a series of color test paper were developed for visual detecting Zn(II) ions. This work helps to provide a platform or pattern for the development of polymer fluorescence probe in the chemosensor field.

Creating 3D Physical Models to Probe Student Understanding of Macromolecular Structure

ERIC Educational Resources Information Center

Cooper, A. Kat; Oliver-Hoyo, M. T.

2017-01-01

The high degree of complexity of macromolecular structure is extremely difficult for students to process. Students struggle to translate the simplified two-dimensional representations commonly used in biochemistry instruction to three-dimensional aspects crucial in understanding structure-property relationships. We designed four different physical…

Endocavity Ultrasound Probe Manipulators

PubMed Central

Stoianovici, Dan; Kim, Chunwoo; Schäfer, Felix; Huang, Chien-Ming; Zuo, Yihe; Petrisor, Doru; Han, Misop

2014-01-01

We developed two similar structure manipulators for medical endocavity ultrasound probes with 3 and 4 degrees of freedom (DoF). These robots allow scanning with ultrasound for 3-D imaging and enable robot-assisted image-guided procedures. Both robots use remote center of motion kinematics, characteristic of medical robots. The 4-DoF robot provides unrestricted manipulation of the endocavity probe. With the 3-DoF robot the insertion motion of the probe must be adjusted manually, but the device is simpler and may also be used to manipulate external-body probes. The robots enabled a novel surgical approach of using intraoperative image-based navigation during robot-assisted laparoscopic prostatectomy (RALP), performed with concurrent use of two robotic systems (Tandem, T-RALP). Thus far, a clinical trial for evaluation of safety and feasibility has been performed successfully on 46 patients. This paper describes the architecture and design of the robots, the two prototypes, control features related to safety, preclinical experiments, and the T-RALP procedure. PMID:24795525

Scaling of structure and electrical properties in ultrathin epitaxial ferroelectric heterostructures

NASA Astrophysics Data System (ADS)

Nagarajan, V.; Junquera, J.; He, J. Q.; Jia, C. L.; Waser, R.; Lee, K.; Kim, Y. K.; Baik, S.; Zhao, T.; Ramesh, R.; Ghosez, Ph.; Rabe, K. M.

2006-09-01

Scaling of the structural order parameter, polarization, and electrical properties was investigated in model ultrathin epitaxial SrRuO3/PbZr0.2Ti0.8O3/SrRuO3/SrTiO3 heterostructures. High-resolution transmission electron microscopy images revealed the interfaces to be sharp and fully coherent. Synchrotron x-ray studies show that a high tetragonality (c /a˜1.058) is maintained down to 50Å thick films, suggesting indirectly that ferroelectricity is fully preserved at such small thicknesses. However, measurement of the switchable polarization (ΔP) using a pulsed probe setup and the out-of-plane piezoelectric response (d33) revealed a systematic drop from ˜140μC/cm2 and 60pm/V for a 150Å thick film to 11μC/cm2 and 7pm/V for a 50Å thick film. This apparent contradiction between the structural measurements and the measured switchable polarization is explained by an increasing presence of a strong depolarization field, which creates a pinned 180° polydomain state for the thinnest films. Existence of a polydomain state is demonstrated by piezoresponse force microscopy images of the ultrathin films. These results suggest that the limit for a ferroelectric memory device may be much larger than the fundamental limit for ferroelectricity.

Probing receptor structure/function with chimeric G-protein-coupled receptors.

PubMed

Yin, Dezhong; Gavi, Shai; Wang, Hsien-yu; Malbon, Craig C

2004-06-01

Owing its name to an image borrowed from Greek mythology, a chimera is seen to represent a new entity created as a composite from existing creatures or, in this case, molecules. Making use of various combinations of three basic domains of the receptors (i.e., exofacial, transmembrane, and cytoplasmic segments) that couple agonist binding into activation of effectors through heterotrimeric G-proteins, molecular pharmacology has probed the basic organization, structure/function relationships of this superfamily of heptahelical receptors. Chimeric G-protein-coupled receptors obviate the need for a particular agonist ligand when the ligand is resistant to purification or, in the case of orphan receptors, is not known. Chimeric receptors created from distant members of the heptahelical receptors enable new strategies in understanding how these receptors transduce agonist binding into receptor activation and may be able to offer insights into the evolution of G-protein-coupled receptors from yeast to humans.

Designing Probes for Immunodiagnostics: Structural Insights into an Epitope Targeting Burkholderia Infections.

PubMed

Capelli, Riccardo; Matterazzo, Elena; Amabili, Marco; Peri, Claudio; Gori, Alessandro; Gagni, Paola; Chiari, Marcella; Lertmemongkolchai, Ganjana; Cretich, Marina; Bolognesi, Martino; Colombo, Giorgio; Gourlay, Louise J

2017-10-13

Structure-based epitope prediction drives the design of diagnostic peptidic probes to reveal specific antibodies elicited in response to infections. We previously identified a highly immunoreactive epitope from the peptidoglycan-associated lipoprotein (Pal) antigen from Burkholderia pseudomallei, which could also diagnose Burkholderia cepacia infections. Here, considering the high phylogenetic conservation within Burkholderia species, we ask whether cross-reactivity can be reciprocally displayed by the synthetic epitope from B. cenocepacia. We perform comparative analyses of the conformational preferences and diagnostic performances of the corresponding epitopes from the two Burkholderia species when presented in the context of the full-length proteins or as isolated peptides. The effects of conformation on the diagnostic potential and cross-reactivity of Pal peptide epitopes are rationalized on the basis of the 1.8 Å crystal structure of B. cenocepacia Pal and through computational analyses. Our results are discussed in the context of designing new diagnostic molecules for the early detection of infectious diseases.

[Fluorescence property of a chemical probe for naked-eye and detection of Fe3+].

PubMed

Song, Yu-Min; Ma, Xin-Xian; Yang, Wu

2012-12-01

A higher selective and sensitive probe for the detection of Fe(III) in aqueous media was made using 2,4-Diisocyanatotoluene (TDI) as a bridge to couple Fe3 O4 nanoparticles(NPs) and Rhodamine-6G hydrazide. The characterization of composite materials with Infrared spectra(IR), Thermal Gravimetric analysis(TGA) and Transmission Emission Microscopy(TEM) points to the graft of Rhodamine-6G hydrazide onto the surface of the Fe3O4. The obvious color change of the probe solution from light grey to pink upon the addition of Fe3+ demonstrated the probe could be used for "naked-eye" detection of Fe3+ in water at pH 7. The presence of 1 equivalent (10 micromol x L(-1) microm) of each of these metal ions, including Mn2+, Ni2+, Y2+, Eu3+, Ce3+, La3+, Pr3+, Cd2+, Cr3+, Sm3+, Fe2+, Cu2+ and Zn2+ ions, did not demonstrate any obvious fluorescence change of the probe water solution, which confirmed the probe was a probe with remarkable selectivity for Fe3+. And the fluorescence images of HeLa cells in physiological solutions after incubation with Fe3+ and then further incubated with the probe leading to a strong intracellular fluorescence, which suggested the probe could penetrate the HeLa cell membrane and could respond to Fe3+ in intracellular within living cells.

Dendrimer probes for enhanced photostability and localization in fluorescence imaging.

PubMed

Kim, Younghoon; Kim, Sung Hoon; Tanyeri, Melikhan; Katzenellenbogen, John A; Schroeder, Charles M

2013-04-02

Recent advances in fluorescence microscopy have enabled high-resolution imaging and tracking of single proteins and biomolecules in cells. To achieve high spatial resolutions in the nanometer range, bright and photostable fluorescent probes are critically required. From this view, there is a strong need for development of advanced fluorescent probes with molecular-scale dimensions for fluorescence imaging. Polymer-based dendrimer nanoconjugates hold strong potential to serve as versatile fluorescent probes due to an intrinsic capacity for tailored spectral properties such as brightness and emission wavelength. In this work, we report a new, to our knowledge, class of molecular probes based on dye-conjugated dendrimers for fluorescence imaging and single-molecule fluorescence microscopy. We engineered fluorescent dendritic nanoprobes (FDNs) to contain multiple organic dyes and reactive groups for target-specific biomolecule labeling. The photophysical properties of dye-conjugated FDNs (Cy5-FDNs and Cy3-FDNs) were characterized using single-molecule fluorescence microscopy, which revealed greatly enhanced photostability, increased probe brightness, and improved localization precision in high-resolution fluorescence imaging compared to single organic dyes. As proof-of-principle demonstration, Cy5-FDNs were used to assay single-molecule nucleic acid hybridization and for immunofluorescence imaging of microtubules in cytoskeletal networks. In addition, Cy5-FDNs were used as reporter probes in a single-molecule protein pull-down assay to characterize antibody binding and target protein capture. In all cases, the photophysical properties of FDNs resulted in enhanced fluorescence imaging via improved brightness and/or photostability. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Design and Realization of 3D Printed AFM Probes.

PubMed

Alsharif, Nourin; Burkatovsky, Anna; Lissandrello, Charles; Jones, Keith M; White, Alice E; Brown, Keith A

2018-05-01

Atomic force microscope (AFM) probes and AFM imaging by extension are the product of exceptionally refined silicon micromachining, but are also restricted by the limitations of these fabrication techniques. Here, the nanoscale additive manufacturing technique direct laser writing is explored as a method to print monolithic cantilevered probes for AFM. Not only are 3D printed probes found to function effectively for AFM, but they also confer several advantages, most notably the ability to image in intermittent contact mode with a bandwidth approximately ten times larger than analogous silicon probes. In addition, the arbitrary structural control afforded by 3D printing is found to enable programming the modal structure of the probe, a capability that can be useful in the context of resonantly amplifying nonlinear tip-sample interactions. Collectively, these results show that 3D printed probes complement those produced using conventional silicon micromachining and open the door to new imaging techniques. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Computational and experimental studies of microvascular void features for passive-adaptation of structural panel dynamic properties

NASA Astrophysics Data System (ADS)

Sears, Nicholas C.; Harne, Ryan L.

2018-01-01

The performance, integrity, and safety of built-up structural systems are critical to their effective employment in diverse engineering applications. In conflict with these goals, harmonic or random excitations of structural panels may promote large amplitude oscillations that are particularly harmful when excitation energies are concentrated around natural frequencies. This contributes to fatigue concerns, performance degradation, and failure. While studies have considered active or passive damping treatments that adapt material characteristics and configurations for structural control, it remains to be understood how vibration properties of structural panels may be tailored via internal material transitions. Motivated to fill this knowledge gap, this research explores an idea of adapting the static and dynamic material distribution of panels through embedded microvascular channels and strategically placed voids that permit the internal movement of fluids within the panels for structural dynamic control. Finite element model and experimental investigations probe how redistributing material in the form of microscale voids influences the global vibration modes and natural frequencies of structural panels. Through parameter studies, the relationships among void shape, number, size, and location are quantified towards their contribution to the changing structural dynamics. For the panel composition and boundary conditions considered in this report, the findings reveal that transferring material between strategically placed voids may result in eigenfrequency changes as great as 10.0, 5.0, and 7.4% for the first, second, and third modes, respectively.

Probing the electronic and defect structure of perovskite superconductors

NASA Astrophysics Data System (ADS)

Fluss, M. J.; Wachs, A. L.; Turchi, P. E. A.; Howell, R. H.; Jean, Y. C.; Kyle, J.; Nakanishi, H.; Chu, C. W.; Meng, R. L.; Hor, H. P.

1988-02-01

Positrons, either localized or delocalized, in the perovskite superconductors are sensitive to changes in electron density accompanying the normal-to-superconducting transition. We have been using this probe in our laboratory to study the nature of this new phenomena. Our work to date, which is briefly reviewed here, has consisted of a series of lifetime studies on La(sub 1.85)Sr(sub 0.15)CuO4 and YBa2Cu3O(sub 7-d) superconducting samples, the determination of the positron wave function in the perfect crystal, and a direct measurement of the electron momentum density in single crystal La2CuO4. Several important observations have resulted from this early work: the similar response of the positron annihilation lifetime to superconductivity in both La(sub 1.85)Sr(sub 0.15)CuO4 and YBa2Cu3O7, and a quantitative description of the electronic structure for La(sub 1.85)Sr(sub 0.15)CuO4 in terms of a linear combination of atomic orbital-molecular orbital (LCAO-MO) model.

Probing Shells Against Buckling: A Nondestructive Technique for Laboratory Testing

NASA Astrophysics Data System (ADS)

Thompson, J. Michael T.; Hutchinson, John W.; Sieber, Jan

2017-12-01

This paper addresses testing of compressed structures, such as shells, that exhibit catastrophic buckling and notorious imperfection sensitivity. The central concept is the probing of a loaded structural specimen by a controlled lateral displacement to gain quantitative insight into its buckling behavior and to measure the energy barrier against buckling. This can provide design information about a structure’s stiffness and robustness against buckling in terms of energy and force landscapes. Developments in this area are relatively new but have proceeded rapidly with encouraging progress. Recent experimental tests on uniformly compressed spherical shells, and axially loaded cylinders, show excellent agreement with theoretical solutions. The probing technique could be a valuable experimental procedure for testing prototype structures, but before it can be used a range of potential problems must be examined and solved. The probing response is highly nonlinear and a variety of complications can occur. Here, we make a careful assessment of unexpected limit points and bifurcations, that could accompany probing, causing complications and possibly even collapse of a test specimen. First, a limit point in the probe displacement (associated with a cusp instability and fold) can result in dynamic buckling as probing progresses, as demonstrated in the buckling of a spherical shell under volume control. Second, various types of bifurcations which can occur on the probing path which result in the probing response becoming unstable are also discussed. To overcome these problems, we outline the extra controls over the entire structure that may be needed to stabilize the response.

The elastase-PK101 structure: Mechanism of an ultrasensitive activity-based probe revealed

DOE PAGES

Lechtenberg, Bernhard C.; Robinson, Howard R.; Kasperkiewicz, Paulina; ...

2015-01-22

Human neutrophil elastase (HNE) plays a central role in neutrophil host defense, but its broad specificity makes HNE a difficult target for both inhibitor and probe development. Recently, we identified the unnatural amino acid containing activity-based probe PK101, which exhibits astounding sensitivity and selectivity for HNE, yet completely lacks mechanistic explanation for its unique characteristics. Here, we present the crystal structure of the HNE-PK101 complex which not only reveals the basis for PK101 ultrasensitivity but also uncovers so far unrecognized HNE features. Strikingly, the Nle( O-Bzl) function in the P4 position of PK101 reveals and leverages an “exo-pocket” on HNEmore » as a critical factor for selectivity. Furthermore, the PK101 P3 position harbors a methionine dioxide function, which mimics a post-translationally oxidized methionine residue and forms a critical hydrogen bond to the backbone amide of Gly219 of HNE. Gly219 resides in a Gly–Gly motif that is unique to HNE, yet compulsory for this interaction. Consequently, this feature enables HNE to accommodate substrates that have undergone methionine oxidation, which constitutes a hallmark post-translational modification of neutrophil signaling.« less

Self-sensing cantilevers with integrated conductive coaxial tips for high-resolution electrical scanning probe metrology

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

Haemmerli, Alexandre J.; Pruitt, Beth L., E-mail: pruitt@stanford.edu; Harjee, Nahid

The lateral resolution of many electrical scanning probe techniques is limited by the spatial extent of the electrostatic potential profiles produced by their probes. Conventional unshielded conductive atomic force microscopy probes produce broad potential profiles. Shielded probes could offer higher resolution and easier data interpretation in the study of nanostructures. Electrical scanning probe techniques require a method of locating structures of interest, often by mapping surface topography. As the samples studied with these techniques are often photosensitive, the typical laser measurement of cantilever deflection can excite the sample, causing undesirable changes electrical properties. In this work, we present the design,more » fabrication, and characterization of probes that integrate coaxial tips for spatially sharp potential profiles with piezoresistors for self-contained, electrical displacement sensing. With the apex 100 nm above the sample surface, the electrostatic potential profile produced by our coaxial tips is more than 2 times narrower than that of unshielded tips with no long tails. In a scan bandwidth of 1 Hz–10 kHz, our probes have a displacement resolution of 2.9 Å at 293 K and 79 Å at 2 K, where the low-temperature performance is limited by amplifier noise. We show scanning gate microscopy images of a quantum point contact obtained with our probes, highlighting the improvement to lateral resolution resulting from the coaxial tip.« less

Probe-And-Socket Fasteners For Robotic Assembly

NASA Technical Reports Server (NTRS)

Nyberg, Karen

1995-01-01

Self-alignment and simplicity of actuation make mechanism amenable to robotic assembly. Includes socket, mounted on structure at worksite, and probe, mounted on piece of equipment to be attached to structure at socket. Probe-and-socket mechanism used in conjunction with fixed target aiding in placement of end effector of robot during grasping, and with handle or handles on structure. Intended to enable robot to set up workstation in hostile environment. Workstation then used by astronaut, aquanaut, or other human, spending minimum time in environment. Human concentrates on performing quality work rather than on setting up equipment, with consequent reduction of risk.

Fast capacitive probe for electromagnetic pulse diagnostic.

PubMed

Lorusso, A; Nassisi, V; Siciliano, M V

2008-06-01

In this work, we report the study and the development of a capacitive probe which is suitable for getting fast and high voltage/current measurements. Due to the fact that fast pulses propagate generally in coaxial structures, the probe realized in this work was a capacitive divider with the divider electrode properly designed to assure the same characteristic impedance of the coaxial structure and the recombination time of the split signals during the propagation. It was a folded cylindrical ring of 1.4 cm long and 0.8 cm thick, which introduce a theoretical delay time of about 100 ps. Analyzing the behavior of the probe closed on 520 Omega, the voltage amplification resulted to be of (3.6+/-0.1) x 10(-4) and, as a consequence, the current attenuation factor of 56+/-1 AV. The response rise time was less than 320 ps, which was limited by oscilloscope bandwave. The capacitor probe can operate voltage measurements of the order of 100 kV.

Fibrin Formation, Structure and Properties

PubMed Central

Weisel, John W.; Litvinov, Rustem I.

2017-01-01

Fibrinogen and fibrin are essential for hemostasis and are major factors in thrombosis, wound healing, and several other biological functions and pathological conditions. The X-ray crystallographic structure of major parts of fibrin(ogen), together with computational reconstructions of missing portions and numerous biochemical and biophysical studies, have provided a wealth of data to interpret molecular mechanisms of fibrin formation, its organization, and properties. On cleavage of fibrinopeptides by thrombin, fibrinogen is converted to fibrin monomers, which interact via knobs exposed by fibrinopeptide removal in the central region, with holes always exposed at the ends of the molecules. The resulting half-staggered, double-stranded oligomers lengthen into protofibrils, which aggregate laterally to make fibers, which then branch to yield a three-dimensional network. Much is now known about the structural origins of clot mechanical properties, including changes in fiber orientation, stretching and buckling, and forced unfolding of molecular domains. Studies of congenital fibrinogen variants and post-translational modifications have increased our understanding of the structure and functions of fibrin(ogen). The fibrinolytic system, with the zymogen plasminogen binding to fibrin together with tissue-type plasminogen activator to promote activation to the active proteolytic enzyme, plasmin, results in digestion of fibrin at specific lysine residues. In spite of a great increase in our knowledge of all these interconnected processes, much about the molecular mechanisms of the biological functions of fibrin(ogen) remains unknown, including some basic aspects of clotting, fibrinolysis, and molecular origins of fibrin mechanical properties. Even less is known concerning more complex (patho)physiological implications of fibrinogen and fibrin. PMID:28101869

Diamond nanowires: fabrication, structure, properties, and applications.

PubMed

Yu, Yuan; Wu, Liangzhuan; Zhi, Jinfang

2014-12-22

C(sp(3) )C-bonded diamond nanowires are wide band gap semiconductors that exhibit a combination of superior properties such as negative electron affinity, chemical inertness, high Young's modulus, the highest hardness, and room-temperature thermal conductivity. The creation of 1D diamond nanowires with their giant surface-to-volume ratio enhancements makes it possible to control and enhance the fundamental properties of diamond. Although theoretical comparisons with carbon nanotubes have shown that diamond nanowires are energetically and mechanically viable structures, reproducibly synthesizing the crystalline diamond nanowires has remained challenging. We present a comprehensive, up-to-date review of diamond nanowires, including a discussion of their synthesis along with their structures, properties, and applications. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Exploring Orthogonal Hydrogen Bonding towards Designing Organic-Salt-Based Supramolecular Gelators: Synthesis, Structures, and Anticancer Properties.

PubMed

Chakraborty, Poulami; Dastidar, Parthasarathi

2018-05-18

A series of primary ammonium monocarboxylate (PAM) salts derived from β-alanine derivatives of pyrene and naphthalene acetic acid, along with the parent acids, were explored to probe the plausible role of orthogonal hydrogen bonding resulting from amide⋅⋅⋅amide and PAM synthons on gelation. Single-crystal X-ray diffraction (SXRD) studies were performed on two parent acids and five PAM salts in the series. The data revealed that orthogonal hydrogen bonding played an important role in gelation. Structure-property correlation based on SXRD and powder X-ray diffraction data also supported the working hypothesis upon which these gelators were designed. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and cell migration assay on a highly aggressive human breast cancer cell line, MDA-MB-231, revealed that one of the PAM salts in the series, namely, PAA.B2, displayed anticancer properties, and internalization of the gelator salt in the same cell line was confirmed by cell imaging. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Current-Voltage and Floating-Potential characteristics of cylindrical emissive probes from a full-kinetic model based on the orbital motion theory

NASA Astrophysics Data System (ADS)

Chen, Xin; Sánchez-Arriaga, Gonzalo

2018-02-01

To model the sheath structure around an emissive probe with cylindrical geometry, the Orbital-Motion theory takes advantage of three conserved quantities (distribution function, transverse energy, and angular momentum) to transform the stationary Vlasov-Poisson system into a single integro-differential equation. For a stationary collisionless unmagnetized plasma, this equation describes self-consistently the probe characteristics. By solving such an equation numerically, parametric analyses for the current-voltage (IV) and floating-potential (FP) characteristics can be performed, which show that: (a) for strong emission, the space-charge effects increase with probe radius; (b) the probe can float at a positive potential relative to the plasma; (c) a smaller probe radius is preferred for the FP method to determine the plasma potential; (d) the work function of the emitting material and the plasma-ion properties do not influence the reliability of the floating-potential method. Analytical analysis demonstrates that the inflection point of an IV curve for non-emitting probes occurs at the plasma potential. The flat potential is not a self-consistent solution for emissive probes.

Interfacial structure of soft matter probed by SFG spectroscopy.

PubMed

Ye, Shen; Tong, Yujin; Ge, Aimin; Qiao, Lin; Davies, Paul B

2014-10-01

Sum frequency generation (SFG) vibrational spectroscopy, an interface-specific technique in contrast to, for example, attenuated total reflectance spectroscopy, which is only interface sensitive, has been employed to investigate the surface and interface structure of soft matter on a molecular scale. The experimental arrangement required to carry out SFG spectroscopy, with particular reference to soft matter, and the analytical methods developed to interpret the spectra are described. The elucidation of the interfacial structure of soft matter systems is an essential prerequisite in order to understand and eventually control the surface properties of these important functional materials. Copyright © 2014 The Chemical Society of Japan and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural properties of scandium inorganic salts

DOE PAGES

Sears, Jeremiah M.; Boyle, Timothy J.

2016-12-16

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

Recent advances in high-performance fluorescent and bioluminescent RNA imaging probes.

PubMed

Xia, Yuqiong; Zhang, Ruili; Wang, Zhongliang; Tian, Jie; Chen, Xiaoyuan

2017-05-22

RNA plays an important role in life processes. Imaging of messenger RNAs (mRNAs) and micro-RNAs (miRNAs) not only allows us to learn the formation and transcription of mRNAs and the biogenesis of miRNAs involved in various life processes, but also helps in detecting cancer. High-performance RNA imaging probes greatly expand our view of life processes and enhance the cancer detection accuracy. In this review, we summarize the state-of-the-art high-performance RNA imaging probes, including exogenous probes that can image RNA sequences with special modification and endogeneous probes that can directly image endogenous RNAs without special treatment. For each probe, we review its structure and imaging principle in detail. Finally, we summarize the application of mRNA and miRNA imaging probes in studying life processes as well as in detecting cancer. By correlating the structures and principles of various probes with their practical uses, we compare different RNA imaging probes and offer guidance for better utilization of the current imaging probes and the future design of higher-performance RNA imaging probes.

Probing the Structures of Viral RNA Regulatory Elements with SHAPE and Related Methodologies

PubMed Central

Rausch, Jason W.; Sztuba-Solinska, Joanna; Le Grice, Stuart F. J.

2018-01-01

Viral RNAs were selected by evolution to possess maximum functionality in a minimal sequence. Depending on the classification of the virus and the type of RNA in question, viral RNAs must alternately be replicated, spliced, transcribed, transported from the nucleus into the cytoplasm, translated and/or packaged into nascent virions, and in most cases, provide the sequence and structural determinants to facilitate these processes. One consequence of this compact multifunctionality is that viral RNA structures can be exquisitely complex, often involving intermolecular interactions with RNA or protein, intramolecular interactions between sequence segments separated by several thousands of nucleotides, or specialized motifs such as pseudoknots or kissing loops. The fluidity of viral RNA structure can also present a challenge when attempting to characterize it, as genomic RNAs especially are likely to sample numerous conformations at various stages of the virus life cycle. Here we review advances in chemoenzymatic structure probing that have made it possible to address such challenges with respect to cis-acting elements, full-length viral genomes and long non-coding RNAs that play a major role in regulating viral gene expression. PMID:29375504

A rhodamine 6G derived Schiff base as a fluorescent and colorimetric probe for pH detection and its crystal structure

NASA Astrophysics Data System (ADS)

Guo, Ping; Liu, Lijuan; Shi, Qian; Yin, Chunyan; Shi, Xuefang

2017-02-01

A fluorescent and colorimetric pH probe based on a rhodamine 6G derivative, RP1, was designed and synthesized. The probe was based on the pH induced change in the structure between the spirocyclic (non-fluorescent, colorless) and quinoid (fluorescent, pink) forms of rhodamine 6G. The effect of the acid concentration on the fluorescence "off-on" behaviors of RP1 was investigated. RP1 was fluorescent in the pH range of 1.1-3.1 and has a pKa value of 2.08 (±0.07). Thus RP1 should be useful for studies in strongly acidic environments. Possible interferences from fourteen common metal ions were tested and excluded showing the excellent selectivity of the probe. Finally, the probe exhibits an intense color change at pH values lower than 3.1 which makes it useful for naked-eye pH detection.

Where do pulse oximeter probes break?

PubMed

Crede, S; Van der Merwe, G; Hutchinson, J; Woods, D; Karlen, W; Lawn, J

2014-06-01

Pulse oximetry, a non-invasive method for accurate assessment of blood oxygen saturation (SPO2), is an important monitoring tool in health care facilities. However, it is often not available in many low-resource settings, due to expense, overly sophisticated design, a lack of organised procurement systems and inadequate medical device management and maintenance structures. Furthermore medical devices are often fragile and not designed to withstand the conditions of low-resource settings. In order to design a probe, better suited to the needs of health care facilities in low-resource settings this study aimed to document the site and nature of pulse oximeter probe breakages in a range of different probe designs in a low to middle income country. A retrospective review of job cards relating to the assessment and repair of damaged or faulty pulse oximeter probes was conducted at a medical device repair company based in Cape Town, South Africa, specializing in pulse oximeter probe repairs. 1,840 job cards relating to the assessment and repair of pulse oximeter probes were reviewed. 60.2 % of probes sent for assessment were finger-clip probes. For all probes, excluding the neonatal wrap probes, the most common point of failure was the probe wiring (>50 %). The neonatal wrap most commonly failed at the strap (51.5 %). The total cost for quoting on the broken pulse oximeter probes and for the subsequent repair of devices, excluding replacement components, amounted to an estimated ZAR 738,810 (USD $98,508). Improving the probe wiring would increase the life span of pulse oximeter probes. Increasing the life span of probes will make pulse oximetry more affordable and accessible. This is of high priority in low-resource settings where frequent repair or replacement of probes is unaffordable or impossible.

Using Gas-Phase Guest-Host Chemistry to Probe the Structures of b Ions of Peptides

NASA Astrophysics Data System (ADS)

Somogyi, Árpád; Harrison, Alex G.; Paizs, Béla

2012-12-01

Middle-sized b n ( n ≥ 5) fragments of protonated peptides undergo selective complex formation with ammonia under experimental conditions typically used to probe hydrogen-deuterium exchange in Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Other usual peptide fragments like y, a, a*, etc., and small b n ( n ≤ 4) fragments do not form stable ammonia adducts. We propose that complex formation of b n ions with ammonia is characteristic to macrocyclic isomers of these fragments. Experiments on a protonated cyclic peptide and N-terminal acetylated peptides fully support this hypothesis; the protonated cyclic peptide does form ammonia adducts while linear b n ions of acetylated peptides do not undergo complexation. Density functional theory (DFT) calculations on the proton-bound dimers of all-Ala b 4 , b 5 , and b 7 ions and ammonia indicate that the ionizing proton initially located on the peptide fragment transfers to ammonia upon adduct formation. The ammonium ion is then solvated by N+-H…O H-bonds; this stabilization is much stronger for macrocyclic b n isomers due to the stable cage-like structure formed and entropy effects. The present study demonstrates that gas-phase guest-host chemistry can be used to selectively probe structural features (i.e., macrocyclic or linear) of fragments of protonated peptides. Stable ammonia adducts of b 9 , b 9 -A, and b 9 -2A of A8YA, and b 13 of A20YVFL are observed indicating that even these large b-type ions form macrocyclic structures.

Ice-Borehole Probe

NASA Technical Reports Server (NTRS)

Behar, Alberto; Carsey, Frank; Lane, Arthur; Engelhardt, Herman

2006-01-01

An instrumentation system has been developed for studying interactions between a glacier or ice sheet and the underlying rock and/or soil. Prior borehole imaging systems have been used in well-drilling and mineral-exploration applications and for studying relatively thin valley glaciers, but have not been used for studying thick ice sheets like those of Antarctica. The system includes a cylindrical imaging probe that is lowered into a hole that has been bored through the ice to the ice/bedrock interface by use of an established hot-water-jet technique. The images acquired by the cameras yield information on the movement of the ice relative to the bedrock and on visible features of the lower structure of the ice sheet, including ice layers formed at different times, bubbles, and mineralogical inclusions. At the time of reporting the information for this article, the system was just deployed in two boreholes on the Amery ice shelf in East Antarctica and after successful 2000 2001 deployments in 4 boreholes at Ice Stream C, West Antarctica, and in 2002 at Black Rapids Glacier, Alaska. The probe is designed to operate at temperatures from 40 to +40 C and to withstand the cold, wet, high-pressure [130-atm (13.20-MPa)] environment at the bottom of a water-filled borehole in ice as deep as 1.6 km. A current version is being outfitted to service 2.4-km-deep boreholes at the Rutford Ice Stream in West Antarctica. The probe (see figure) contains a sidelooking charge-coupled-device (CCD) camera that generates both a real-time analog video signal and a sequence of still-image data, and contains a digital videotape recorder. The probe also contains a downward-looking CCD analog video camera, plus halogen lamps to illuminate the fields of view of both cameras. The analog video outputs of the cameras are converted to optical signals that are transmitted to a surface station via optical fibers in a cable. Electric power is supplied to the probe through wires in the cable at a

Electrically induced microflows probed by fluorescence correlation spectroscopy.

PubMed

Ybert, C; Nadal, F; Salomé, R; Argoul, F; Bourdieu, L

2005-03-01

We report on the experimental characterisation of electrically induced flows at the micrometer scale through Fluorescence Correlation Spectroscopy (FCS) measurements. We stress the potential of FCS as a useful characterisation technique in microfluidics devices for transport properties cartography. The experimental results obtained in a model situation are in agreement with previous calculations (F. Nadal, F. Argoul, P. Kestener, B. Pouligny, C. Ybert, A. Ajdari, Eur. Phys. J. E 9, 387 (2002)) predicting the structure and electric-field dependency of the induced flow. Additionally, the present study evidences a complex behaviour of the probe nanobeads under electric field whose precise understanding might prove relevant for situations where nano-objects interact with an external electric field.

The Effects of Heteroatoms Si and S on Tuning the Optical Properties of Rhodamine- and Fluorescein-Based Fluorescence Probes: A Theoretical Analysis.

PubMed

Zhou, Panwang; Ning, Cai; Alsaedi, Ahmed; Han, Keli

2016-10-05

The effects of the incorporated heteroatoms Si and S on tuning the optical properties of rhodamine- and fluorescein-based fluorescence probes is investigated using DFT and time-dependent DFT with four different functionals. As previously proposed, the large redshift (90 nm) produced by a Si atom in both the absorption and emission spectra can be attributed to the σ*-π* conjugation between the σ* orbital of the Si atom and the π* orbital of the adjacent carbon atoms. However, the presence of a Si atom does not alter the fluorescence quenching mechanism of the nonfluorescent forms of the investigated compounds. For the first time, these theoretical results indicate that the n orbital of the S atom plays an important role in determining the optical properties of the nonfluorescent form of rhodamine-based fluorescence probes. It alters the fluorescence quenching mechanism by lowering the energy of the dark nπ* state, which is due to breakage of the C10-S52 bond upon photoexcitation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure-Function-Property-Design Interplay in Biopolymers: Spider Silk

PubMed Central

Tokareva, Olena; Jacobsen, Matthew; Buehler, Markus; Wong, Joyce; Kaplan, David L.

2013-01-01

Spider silks have been a focus of research for almost two decades due to their outstanding mechanical and biophysical properties. Recent advances in genetic engineering have led to the synthesis of recombinant spider silks, thus helping to unravel a fundamental understanding of structure-function-property relationships. The relationships between molecular composition, secondary structures, and mechanical properties found in different types of spider silks are described, along with a discussion of artificial spinning of these proteins and their bioapplications, including the role of silks in biomineralization and fabrication of biomaterials with controlled properties. PMID:23962644

Atomic scale structure and chemistry of interfaces by Z-contrast imaging and electron energy loss spectroscopy in the STEM

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

McGibbon, M.M.; Browning, N.D.; Chisholm, M.F.

The macroscopic properties of many materials are controlled by the structure and chemistry at the grain boundaries. A basic understanding of the structure-property relationship requires a technique which probes both composition and chemical bonding on an atomic scale. The high-resolution Z-contrast imaging technique in the scanning transmission electron microscope (STEM) forms an incoherent image in which changes in atomic structure and composition can be interpreted intuitively. This direct image allows the electron probe to be positioned over individual atomic columns for parallel detection electron energy loss spectroscopy (PEELS) at a spatial resolution approaching 0.22nm. The bonding information which can bemore » obtained from the fine structure within the PEELS edges can then be used in conjunction with the Z-contrast images to determine the structure at the grain boundary. In this paper we present 3 examples of correlations between the structural, chemical and electronic properties at materials interfaces in metal-semiconductor systems, superconducting and ferroelectric materials.« less

Structure Property Relationships of Carboxylic Acid Isosteres.

PubMed

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

2016-04-14

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

Nine New Fluorescent Probes

NASA Astrophysics Data System (ADS)

Lin, Tsung-I.; Jovanovic, Misa V.; Dowben, Robert M.

1989-06-01

Absorption and fluorescence spectroscopic studies are reported here for nine new fluorescent probes recently synthesized in our laboratories: four pyrene derivatives with substituents of (i) 1,3-diacetoxy-6,8-dichlorosulfonyl, (ii) 1,3-dihydroxy-6,8-disodiumsulfonate, (iii) 1,3-disodiumsulfonate, and (iv) l-ethoxy-3,6,8-trisodiumsulfonate groups, and five [7-julolidino] coumarin derivatives with substituents of (v) 3-carboxylate-4-methyl, (vi) 3- methylcarboxylate, (vii) 3-acetate-4-methyl, (viii) 3-propionate-4-methyl, and (ix) 3-sulfonate-4-methyl groups. Pyrene compounds i and ii and coumarin compounds v and vi exhibit interesting absorbance and fluorescence properties: their absorption maxima are red shifted compared to the parent compound to the blue-green region, and the band width broadens considerably. All four blue-absorbing dyes fluoresce intensely in the green region, and the two pyrene compounds emit at such long wavelengths without formation of excimers. The fluorescence properties of these compounds are quite environment-sensitive: considerable spectral shifts and fluorescence intensity changes have been observed in the pH range from 3 to 10 and in a wide variety of polar and hydrophobic solvents with vastly different dielectric constants. The high extinction and fluorescence quantum yield of these probes make them ideal fluorescent labeling reagents for proteins, antibodies, nucleic acids, and cellular organelles. The pH and hydrophobicity-dependent fluorescence changes can be utilized as optical pH and/or hydrophobicity indicators for mapping environmental difference in various cellular components in a single cell. Since all nine probes absorb in the UV, but emit at different wavelengths in the visible, these two groups of compounds offer an advantage of utilizing a single monochromatic light source (e.g., a nitrogen laser) to achieve multi-wavelength detection for flow cytometry application. As a first step to explore potential application in

Behavior of Triple Langmuir Probes in Non-Equilibrium Plasmas

NASA Technical Reports Server (NTRS)

Polzin, Kurt A.; Ratcliffe, Alicia C.

2018-01-01

The triple Langmuir probe is an electrostatic probe in which three probe tips collect current when inserted into a plasma. The triple probe differs from a simple single Langmuir probe in the nature of the voltage applied to the probe tips. In the single probe, a swept voltage is applied to the probe tip to acquire a waveform showing the collected current as a function of applied voltage (I-V curve). In a triple probe three probe tips are electrically coupled to each other with constant voltages applied between each of the tips. The voltages are selected such that they would represent three points on the single Langmuir probe I-V curve. Elimination of the voltage sweep makes it possible to measure time-varying plasma properties in transient plasmas. Under the assumption of a Maxwellian plasma, one can determine the time-varying plasma temperature T(sub e)(t) and number density n(sub e)(t) from the applied voltage levels and the time-histories of the collected currents. In the present paper we examine the theory of triple probe operation, specifically focusing on the assumption of a Maxwellian plasma. Triple probe measurements have been widely employed for a number of pulsed and timevarying plasmas, including pulsed plasma thrusters (PPTs), dense plasma focus devices, plasma flows, and fusion experiments. While the equilibrium assumption may be justified for some applications, it is unlikely that it is fully justifiable for all pulsed and time-varying plasmas or for all times during the pulse of a plasma device. To examine a simple non-equilibrium plasma case, we return to basic governing equations of probe current collection and compute the current to the probes for a distribution function consisting of two Maxwellian distributions with different temperatures (the two-temperature Maxwellian). A variation of this method is also employed, where one of the Maxwellians is offset from zero (in velocity space) to add a suprathermal beam of electrons to the tail of the

Fluorescent molecular probes based on excited state prototropism in lipid bilayer membrane

NASA Astrophysics Data System (ADS)

Mohapatra, Monalisa; Mishra, Ashok K.

2012-03-01

Excited state prototropism (ESPT) is observed in molecules having one or more ionizable protons, whose proton transfer efficiency is different in ground and excited states. The interaction of various ESPT molecules like naphthols and intramolecular ESPT (ESIPT) molecules like hydroxyflavones etc. with different microheterogeneous media have been studied in detail and excited state prototropism as a probe concept has been gaining ground. The fluorescence of different prototropic forms of such molecules, on partitioning to an organized medium like lipid bilayer membrane, often show sensitive response to the local environment with respect to the local structure, physical properties and dynamics. Our recent work using 1-naphthol as an ESPT fluorescent molecular probe has shown that the incorporation of monomeric bile salt molecules into lipid bilayer membranes composed from dipalmitoylphosphatidylcholine (DPPC, a lung surfactant) and dimyristoylphosphatidylcholine (DMPC), in solid gel and liquid crystalline phases, induce appreciable wetting of the bilayer up to the hydrocarbon core region, even at very low (<= 1 mM) concentrations of the bile salts. The incorporation and location of fisetin, an ESIPT molecule having antioxidant properties, in lipid bilayer membrane has been sensitively monitored from its intrinsic fluorescence behaviour.

A novel polymer probe for Zn(II) detection with ratiometric fluorescence signal.

PubMed

Diao, Haipeng; Guo, Lixia; Liu, Wen; Feng, Liheng

2018-05-05

A conjugated polymer probe comprised of fluorene, quinolone and benzothiazole units was designed and synthesized by the Suzuki coupling reaction. Through the studies of photophysical and thermal properties, the polymer displays blue-emitting feature and good thermal stability. A ratiometric fluorescence signal of the probe for Zn(II) was observed in ethanol with a new emission peak at 555 nm. The probe possesses a high selectivity and sensitivity for Zn(II) during familiar metal ions in ethanol. The detection limit of the probe for Zn (II) is up to 10 -8  mol/L. The electron distributions of the polymer before and after bonding with Zn (II) were investigated by the Gaussian 09 software, which agreed with the experimental results. Noticeably, based on the color property of the probe with Zn(II), a series of color test paper were developed for visual detecting Zn(II) ions. This work helps to provide a platform or pattern for the development of polymer fluorescence probe in the chemosensor field. Copyright © 2018 Elsevier B.V. All rights reserved.

Hairpin DNA probe with 5'-TCC/CCC-3' overhangs for the creation of silver nanoclusters and miRNA assay.

PubMed

Xia, Xiaodong; Hao, Yuanqiang; Hu, Shengqiang; Wang, Jianxiu

2014-01-15

A facile strategy for the assay of target miRNA using fluorescent silver nanoclusters (AgNCs) has been described. Due to the preferable interaction between cytosine residues and Ag(+), a short cytosine-rich oligonucleotide (ODN) with only six bases 5'-TCCCCC-3' served as an efficient scaffold for the creation of the AgNCs. The AgNCs displayed a bright red emission when excited at 545nm. Such ODN base-stabilized AgNCs have been exploited for miRNA sensing. Overhangs of TCC at the 5' end (5'-TCC) and CCC at the 3' end (CCC-3') (denoted as 5'-TCC/CCC-3') appended to the hairpin ODN probe which also contains recognition sequences for target miRNA were included. Interestingly, the AgNCs/hairpin ODN probe showed similar spectral properties as that templated by 5'-TCCCCC-3'. The formation of the hairpin ODN probe/miRNA duplex separated the 5'-TCC/CCC-3' overhangs, thus disturbing the optical property or structure of the AgNCs. As a result, fluorescence quenching of the AgNCs/hairpin ODN probe was obtained, which allows for facile determination of target miRNA. The proposed method is simple and cost-effective, holding great promise for clinical applications. Copyright © 2013 Elsevier B.V. All rights reserved.

Fibrin mechanical properties and their structural origins.

PubMed

Litvinov, Rustem I; Weisel, John W

2017-07-01

Fibrin is a protein polymer that is essential for hemostasis and thrombosis, wound healing, and several other biological functions and pathological conditions that involve extracellular matrix. In addition to molecular and cellular interactions, fibrin mechanics has been recently shown to underlie clot behavior in the highly dynamic intra- and extravascular environments. Fibrin has both elastic and viscous properties. Perhaps the most remarkable rheological feature of the fibrin network is an extremely high elasticity and stability despite very low protein content. Another important mechanical property that is common to many filamentous protein polymers but not other polymers is stiffening occurring in response to shear, tension, or compression. New data has begun to provide a structural basis for the unique mechanical behavior of fibrin that originates from its complex multi-scale hierarchical structure. The mechanical behavior of the whole fibrin gel is governed largely by the properties of single fibers and their ensembles, including changes in fiber orientation, stretching, bending, and buckling. The properties of individual fibrin fibers are determined by the number and packing arrangements of double-stranded half-staggered protofibrils, which still remain poorly understood. It has also been proposed that forced unfolding of sub-molecular structures, including elongation of flexible and relatively unstructured portions of fibrin molecules, can contribute to fibrin deformations. In spite of a great increase in our knowledge of the structural mechanics of fibrin, much about the mechanisms of fibrin's biological functions remains unknown. Fibrin deformability is not only an essential part of the biomechanics of hemostasis and thrombosis, but also a rapidly developing field of bioengineering that uses fibrin as a versatile biomaterial with exceptional and tunable biochemical and mechanical properties. Copyright © 2016 Elsevier B.V. All rights reserved.

Hierarchical Structure Controls Nanomechanical Properties of Vimentin Intermediate Filaments

PubMed Central

Qin, Zhao; Kreplak, Laurent; Buehler, Markus J.

2009-01-01

Intermediate filaments (IFs), in addition to microtubules and microfilaments, are one of the three major components of the cytoskeleton in eukaryotic cells, playing a vital role in mechanotransduction and in providing mechanical stability to cells. Despite the importance of IF mechanics for cell biology and cell mechanics, the structural basis for their mechanical properties remains unknown. Specifically, our understanding of fundamental filament properties, such as the basis for their great extensibility, stiffening properties, and their exceptional mechanical resilience remains limited. This has prevented us from answering fundamental structure-function relationship questions related to the biomechanical role of intermediate filaments, which is crucial to link structure and function in the protein material's biological context. Here we utilize an atomistic-level model of the human vimentin dimer and tetramer to study their response to mechanical tensile stress, and describe a detailed analysis of the mechanical properties and associated deformation mechanisms. We observe a transition from alpha-helices to beta-sheets with subsequent interdimer sliding under mechanical deformation, which has been inferred previously from experimental results. By upscaling our results we report, for the first time, a quantitative comparison to experimental results of IF nanomechanics, showing good agreement. Through the identification of links between structures and deformation mechanisms at distinct hierarchical levels, we show that the multi-scale structure of IFs is crucial for their characteristic mechanical properties, in particular their ability to undergo severe deformation of ≈300% strain without breaking, facilitated by a cascaded activation of a distinct deformation mechanisms operating at different levels. This process enables IFs to combine disparate properties such as mechanosensitivity, strength and deformability. Our results enable a new paradigm in studying

Hierarchical structure controls nanomechanical properties of vimentin intermediate filaments.

PubMed

Qin, Zhao; Kreplak, Laurent; Buehler, Markus J

2009-10-06

Intermediate filaments (IFs), in addition to microtubules and microfilaments, are one of the three major components of the cytoskeleton in eukaryotic cells, playing a vital role in mechanotransduction and in providing mechanical stability to cells. Despite the importance of IF mechanics for cell biology and cell mechanics, the structural basis for their mechanical properties remains unknown. Specifically, our understanding of fundamental filament properties, such as the basis for their great extensibility, stiffening properties, and their exceptional mechanical resilience remains limited. This has prevented us from answering fundamental structure-function relationship questions related to the biomechanical role of intermediate filaments, which is crucial to link structure and function in the protein material's biological context. Here we utilize an atomistic-level model of the human vimentin dimer and tetramer to study their response to mechanical tensile stress, and describe a detailed analysis of the mechanical properties and associated deformation mechanisms. We observe a transition from alpha-helices to beta-sheets with subsequent interdimer sliding under mechanical deformation, which has been inferred previously from experimental results. By upscaling our results we report, for the first time, a quantitative comparison to experimental results of IF nanomechanics, showing good agreement. Through the identification of links between structures and deformation mechanisms at distinct hierarchical levels, we show that the multi-scale structure of IFs is crucial for their characteristic mechanical properties, in particular their ability to undergo severe deformation of approximately 300% strain without breaking, facilitated by a cascaded activation of a distinct deformation mechanisms operating at different levels. This process enables IFs to combine disparate properties such as mechanosensitivity, strength and deformability. Our results enable a new paradigm in

Lewis acid properties of alumina based catalysts: study by paramagnetic complexes of probe molecules

NASA Astrophysics Data System (ADS)

Fionov, Alexander V.

2002-06-01

Lewis acid properties of LiAl 5O 8/Al 2O 3 (2 wt.% Li) and MgAl 2O 4/Al 2O 3 (3 wt.% Mg) catalysts were studied by EPR of adsorbed probe molecules--anthraquinone and 2,2,6,6-tetramethylpiperidine- N-oxyl (TEMPO). The lesser (in comparison with γ-Al 2O 3) concentration and the strength of Lewis acid sites (LAS) formed on the surface of aluminate layer has been shown. The stability of this layer plays important role in the change of Lewis acid properties during the calcination of modified alumina. The lithium aluminate layer was stable at used calcination temperature, 773 K, meanwhile magnesium aluminate layer observed only at calcination temperature below 723 K. The increase of the calcination temperature to 773 K caused the segregation of MgAl 2O 4 on the surface resulted in the release of alumina surface and recovery of the Lewis acid properties. The differences in the LAS manifestations towards TEMPO and anthraquinone was discussed. The mechanism of the formation of anthraquinone paramagnetic complexes with LAS--three-coordinated aluminum ions--was proposed. This mechanism includes the formation of anthrasemiquinone, and then--anthrasemiquinone ion pair or triple ion. Fragments like -O-Al +-O- play the role of cations in these ion pairs and triple ions. Proposed mechanism can also be applied for the consideration of similar anthraquinone paramagnetic complexes on the surface of gallium oxide containing systems.

Amorphous Iron Borides: Preparation, Structure and Magnetic Properties.

DTIC Science & Technology

1982-09-28

temperature. External magnetic field experiments were performed in a superconducting solenoid with both source and absor- ber at 4.2 K. The observed...D-Ai20 919 AMORPHOUS IRON BORIDES: PREPARATION STRUCTURE AND i/i MAGNETIC PROPERTIES(U) JOHNS HOPKINS UNIV LAUREL NO APPLIED PHYSICS LRB K MOORJRNI...NATIONAL BUREAU OF STANOANOS-93-A 10 AMORPHOUS IRON BORIDES: PREPARATION, STRUCTURE ~AND MAGNETIC PROPERTIES FINAL REPORT Kishin Moorjani September 1982 U

Meso-decorated self-healing gels: network structure and properties

NASA Astrophysics Data System (ADS)

Gong, Jin; Sawamura, Kensuke; Igarashi, Susumu; Furukawa, Hidemitsu

2013-04-01

Gels are a new material having three-dimensional network structures of macromolecules. They possess excellent properties as swellability, high permeability and biocompatibility, and have been applied in various fields of daily life, food, medicine, architecture, and chemistry. In this study, we tried to prepare new multi-functional and high-strength gels by using Meso-Decoration (Meso-Deco), one new method of structure design at intermediate mesoscale. High-performance rigid-rod aromatic polymorphic crystals, and the functional groups of thermoreversible Diels-Alder reaction were introduced into soft gels as crosslinkable pendent chains. The functionalization and strengthening of gels can be realized by meso-decorating the gels' structure using high-performance polymorphic crystals and thermoreversible pendent chains. New gels with good mechanical properties, novel optical properties and thermal properties are expected to be developed.

Refined gravity determination at small bodies through landing probes

NASA Astrophysics Data System (ADS)

Bellerose, J.

2012-02-01

Very small objects of the near-Earth population have not been visited to date, and may be among the next targets for human exploration. As density is a strong indication of the body origin and intrinsic properties, determining the mass is one of the most important goals. The past missions to Eros and Itokawa resulted in mass and density estimates to less than five percent error, allowing precise mission planning while giving new insights on the body structure. Current mass determination techniques have limitations in the low gravity regime, and spacecraft tracking at very small asteroids is challenging. We investigate the constraints on measuring the mass at very small near-Earth objects, and their consequences on proximity operation planning. An alternative option to spacecraft radio tracking is to use surface probes. The near-surface and landing dynamics can be observed and tracked by the host spacecraft, providing higher resolution measurements of the NEA gravity pull. We show analytical methods to estimate the performance of given proximity operations, and simulations of spacecraft and probe dynamics at NEAs less than 100 m in diameter.

Dark energy two decades after: observables, probes, consistency tests.

PubMed

Huterer, Dragan; Shafer, Daniel L

2018-01-01

The discovery of the accelerating universe in the late 1990s was a watershed moment in modern cosmology, as it indicated the presence of a fundamentally new, dominant contribution to the energy budget of the universe. Evidence for dark energy, the new component that causes the acceleration, has since become extremely strong, owing to an impressive variety of increasingly precise measurements of the expansion history and the growth of structure in the universe. Still, one of the central challenges of modern cosmology is to shed light on the physical mechanism behind the accelerating universe. In this review, we briefly summarize the developments that led to the discovery of dark energy. Next, we discuss the parametric descriptions of dark energy and the cosmological tests that allow us to better understand its nature. We then review the cosmological probes of dark energy. For each probe, we briefly discuss the physics behind it and its prospects for measuring dark energy properties. We end with a summary of the current status of dark energy research.

Molecular Dynamic Simulations of Interaction of an AFM Probe with the Surface of an SCN Sample

NASA Technical Reports Server (NTRS)

Bune, Adris; Kaukler, William; Rose, M. Franklin (Technical Monitor)

2001-01-01

Molecular dynamic (MD) simulations is conducted in order to estimate forces of probe-substrate interaction in the Atomic Force Microscope (AFM). First a review of available molecular dynamic techniques is given. Implementation of MD simulation is based on an object-oriented code developed at the University of Delft. Modeling of the sample material - succinonitrile (SCN) - is based on the Lennard-Jones potentials. For the polystyrene probe an atomic interaction potential is used. Due to object-oriented structure of the code modification of an atomic interaction potential is straight forward. Calculation of melting temperature is used for validation of the code and of the interaction potentials. Various fitting parameters of the probe-substrate interaction potentials are considered, as potentials fitted to certain properties and temperature ranges may not be reliable for the others. This research provides theoretical foundation for an interpretation of actual measurements of an interaction forces using AFM.

Fluorescent hybridization probes for nucleic acid detection.

PubMed

Guo, Jia; Ju, Jingyue; Turro, Nicholas J

2012-04-01

Due to their high sensitivity and selectivity, minimum interference with living biological systems, and ease of design and synthesis, fluorescent hybridization probes have been widely used to detect nucleic acids both in vivo and in vitro. Molecular beacons (MBs) and binary probes (BPs) are two very important hybridization probes that are designed based on well-established photophysical principles. These probes have shown particular applicability in a variety of studies, such as mRNA tracking, single nucleotide polymorphism (SNP) detection, polymerase chain reaction (PCR) monitoring, and microorganism identification. Molecular beacons are hairpin oligonucleotide probes that present distinctive fluorescent signatures in the presence and absence of their target. Binary probes consist of two fluorescently labeled oligonucleotide strands that can hybridize to adjacent regions of their target and generate distinctive fluorescence signals. These probes have been extensively studied and modified for different applications by modulating their structures or using various combinations of fluorophores, excimer-forming molecules, and metal complexes. This review describes the applicability and advantages of various hybridization probes that utilize novel and creative design to enhance their target detection sensitivity and specificity.

Donated chemical probes for open science

PubMed Central

Ackloo, Suzanne; Arrowsmith, Cheryl H; Bauser, Marcus; Baryza, Jeremy L; Blagg, Julian; Böttcher, Jark; Bountra, Chas; Brown, Peter J; Bunnage, Mark E; Carter, Adrian J; Damerell, David; Dötsch, Volker; Drewry, David H; Edwards, Aled M; Edwards, James; Elkins, Jon M; Fischer, Christian; Frye, Stephen V; Gollner, Andreas; Grimshaw, Charles E; IJzerman, Adriaan; Hanke, Thomas; Hartung, Ingo V; Hitchcock, Steve; Howe, Trevor; Hughes, Terry V; Laufer, Stefan; Li, Volkhart MJ; Liras, Spiros; Marsden, Brian D; Matsui, Hisanori; Mathias, John; O'Hagan, Ronan C; Owen, Dafydd R; Pande, Vineet; Rauh, Daniel; Rosenberg, Saul H; Roth, Bryan L; Schneider, Natalie S; Scholten, Cora; Singh Saikatendu, Kumar; Simeonov, Anton; Takizawa, Masayuki; Tse, Chris; Thompson, Paul R; Treiber, Daniel K; Viana, Amélia YI; Wells, Carrow I; Willson, Timothy M; Zuercher, William J; Knapp, Stefan

2018-01-01

Potent, selective and broadly characterized small molecule modulators of protein function (chemical probes) are powerful research reagents. The pharmaceutical industry has generated many high-quality chemical probes and several of these have been made available to academia. However, probe-associated data and control compounds, such as inactive structurally related molecules and their associated data, are generally not accessible. The lack of data and guidance makes it difficult for researchers to decide which chemical tools to choose. Several pharmaceutical companies (AbbVie, Bayer, Boehringer Ingelheim, Janssen, MSD, Pfizer, and Takeda) have therefore entered into a pre-competitive collaboration to make available a large number of innovative high-quality probes, including all probe-associated data, control compounds and recommendations on use (https://openscienceprobes.sgc-frankfurt.de/). Here we describe the chemical tools and target-related knowledge that have been made available, and encourage others to join the project. PMID:29676732

Nanoscale thermal cross-talk effect on phase-change probe memory.

PubMed

Wang, Lei; Wen, Jing; Xiong, Bangshu

2018-05-14

Phase-change probe memory is considered as one of the most promising means for next-generation mass storage devices. However, the achievable storage density of phase-change probe memory is drastically affected by the resulting thermal cross-talk effect while previously lacking of detailed study. Therefore, a three dimensional model that couples electrical, thermal, and phase-change processes of the Ge2Sb2Te5 media is developed, and subsequently deployed to assess the thermal cross-talk effect based on Si/TiN/ Ge2Sb2Te5/diamond-like carbon structure by appropriately tailoring the electro-thermal and geometrical properties of the storage media stack for a variety of external excitations. The modeling results show that the diamond-like carbon capping with a thin thickness, a high electrical conductivity, and a low thermal conductivity is desired to minimize the thermal cross-talk, while the TiN underlayer has a slight impact on the thermal cross-talk. Combining the modeling findings with the previous film deposition experience, an optimized phase-change probe memory architecture is presented, and its capability of providing ultra-high recording density simultaneously with a sufficiently low thermal cross-talk is demonstrated. . © 2018 IOP Publishing Ltd.

Properties of the anion-binding site of pharaonis Halorhodopsin studied by ultrafast pump-probe spectroscopy and low-temperature FTIR spectroscopy.

PubMed

Nakashima, Keisuke; Nakamura, Takumi; Takeuchi, Satoshi; Shibata, Mikihiro; Demura, Makoto; Tahara, Tahei; Kandori, Hideki

2009-06-18

Halorhodopsin (HR) is a light-driven chloride pump. Cl(-) is bound in the Schiff base region of the retinal chromophore, and unidirectional Cl(-) transport is probably enforced by the specific hydrogen-bonding interaction with the protonated Schiff base and internal water molecules. It is known that HR from Natronobacterium pharaonis (pHR) also pumps NO(3)(-) with similar efficiency, suggesting that NO(3)(-) binds to the Cl(-)-binding site. In the present study, we investigated the properties of the anion-binding site by means of ultrafast pump-probe spectroscopy and low-temperature FTIR spectroscopy. The obtained data were surprisingly similar between pHR-NO(3)(-) and pHR-Cl(-), even though the shapes and sizes of the two anions are quite different. Femtosecond pump-probe spectroscopy showed very similar excited-state dynamics between pHR-NO(3)(-) and pHR-Cl(-). Low-temperature FTIR spectroscopy of unlabeled and [zeta-(15)N]Lys-labeled pHR revealed almost identical hydrogen-bonding strengths of the protonated retinal Schiff base between pHR-NO(3)(-) and pHR-Cl(-), which is similarly strengthened after retinal isomerization. There were spectral variations for water stretching vibrations between pHR-NO(3)(-) and pHR-Cl(-), suggesting that the water molecules hydrate each anion. Nevertheless, the overall spectral features were similar for the two species. These observations strongly suggest that the anion-binding site has a flexible structure and that the interaction between retinal and the anions is weak, despite the presence of an electrostatic interaction. Such a flexible hydrogen-bonding network in the Schiff base region in HR appears to be in remarkable contrast to that in light-driven proton-pumping proteins.

Surface structure, optoelectronic properties and charge transport in ZnO nanocrystal/MDMO-PPV multilayer films.

PubMed

Lian, Qing; Chen, Mu; Mokhtar, Muhamad Z; Wu, Shanglin; Zhu, Mingning; Whittaker, Eric; O'Brien, Paul; Saunders, Brian R

2018-05-07