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Sample records for probing intra-molecular mechanics

  1. Intra-molecular G-quadruplex structure generated by DNA-templated click chemistry: "turn-on" fluorescent probe for copper ions.

    PubMed

    Shen, Qinpeng; Zhou, Lifen; Yuan, Yijia; Huang, Yan; Xiang, Binbin; Chen, Chunyan; Nie, Zhou; Yao, Shouzhuo

    2014-05-15

    A novel homogenous fluorescent sensor for signal-on detection of Cu(2+) has been developed based on intra-molecular G-quadruplex formed by DNA-templated click reaction and crystal violet (CV) as label-free signal reporter. The clickable DNA probe consists of two G-rich strands (A and B) bearing azide and alkyne group, respectively, and a template strand (C) locating two proximate reactants by pairing with A and B. The sequences of A and B are derived from asymmetric split of the G-quadruplex sequence (TTAGGG)4. In the presence of Cu(2+), the whole G-quadruplex sequence A-B is generated by chemical ligation of A and B via copper ion-catalyzed alkyne-azide cycloaddition, then released from template by toehold strand displacement, and consequently forming a stable intra-molecular G-quadruplex, which binds with CV to generate a strong fluorescent signal. Oppositely, weak fluorescence was obtained without Cu(2+) because of unstable intermolecular G-quadruplex formed by A and B and lack of lateral loop connection. Therefore, the Cu(2+) can be sensitively and specifically detected by the fluorescence of the CV-stained G-quadruplex with a low detection limit of 65nM and a linear range of 0.1-3µM. This method rationally integrated the DNA-templated synthesis and G-quadruplex structure-switch, presenting a simple and promising approach for biosensor development.

  2. Rotary probe traversing mechanism

    NASA Astrophysics Data System (ADS)

    Hokenson, Gustave J.

    1985-04-01

    A simple mechanical device is presented which allows a probe to scan a plane in space without translating the probe support. The mechanism relies on the rotation of two shafts, one of which rotates the probe through space and the other controls the probe offset from the axis of rotation. The characteristic width of the area swept out is four times the characteristic width of the device. A simple ratcheting gear allows adjacent planes to be scanned for the purpose of obtaining gradients. Computerized control of the shafts rotations also allows noncircular domains to be scanned.

  3. Nano Mechanical Machining Using AFM Probe

    NASA Astrophysics Data System (ADS)

    Mostofa, Md. Golam

    Complex miniaturized components with high form accuracy will play key roles in the future development of many products, as they provide portability, disposability, lower material consumption in production, low power consumption during operation, lower sample requirements for testing, and higher heat transfer due to their very high surface-to-volume ratio. Given the high market demand for such micro and nano featured components, different manufacturing methods have been developed for their fabrication. Some of the common technologies in micro/nano fabrication are photolithography, electron beam lithography, X-ray lithography and other semiconductor processing techniques. Although these methods are capable of fabricating micro/nano structures with a resolution of less than a few nanometers, some of the shortcomings associated with these methods, such as high production costs for customized products, limited material choices, necessitate the development of other fabricating techniques. Micro/nano mechanical machining, such an atomic force microscope (AFM) probe based nano fabrication, has, therefore, been used to overcome some the major restrictions of the traditional processes. This technique removes material from the workpiece by engaging micro/nano size cutting tool (i.e. AFM probe) and is applicable on a wider range of materials compared to the photolithographic process. In spite of the unique benefits of nano mechanical machining, there are also some challenges with this technique, since the scale is reduced, such as size effects, burr formations, chip adhesions, fragility of tools and tool wear. Moreover, AFM based machining does not have any rotational movement, which makes fabrication of 3D features more difficult. Thus, vibration-assisted machining is introduced into AFM probe based nano mechanical machining to overcome the limitations associated with the conventional AFM probe based scratching method. Vibration-assisted machining reduced the cutting forces

  4. Intra-molecular Triplet Energy Transfer is a General Approach to Improve Organic Fluorophore Photostability

    PubMed Central

    Zheng, Qinsi; Jockusch, Steffen; Rodríguez-Calero, Gabriel G.; Zhou, Zhou; Zhao, Hong; Altman, Roger B.; Abruña, Héctor D.; Blanchard, Scott C.

    2015-01-01

    Bright, long-lasting and non-phototoxic organic fluorophores are essential to the continued advancement of biological imaging. Traditional approaches towards achieving photostability, such as the removal of molecular oxygen and the use of small-molecule additives in solution, suffer from potentially toxic side effects, particularly in the context of living cells. The direct conjugation of small-molecule triplet state quenchers, such as cyclooctatetraene (COT), to organic fluorophores has the potential to bypass these issues by restoring reactive fluorophore triplet states to the ground state through intra-molecular triplet energy transfer. Such methods have enabled marked improvement in cyanine fluorophore photostability spanning the visible spectrum. However, the generality of this strategy to chemically and structurally diverse fluorophore species has yet to be examined. Here, we show that the proximal linkage of COT increases the photon yield of a diverse range of organic fluorophores widely used in biological imaging applications, demonstrating that the intra-molecular triplet energy transfer mechanism is a potentially general approach for improving organic fluorophore performance and photostability. PMID:26700693

  5. Intra-molecular triplet energy transfer is a general approach to improve organic fluorophore photostability.

    PubMed

    Zheng, Qinsi; Jockusch, Steffen; Rodríguez-Calero, Gabriel G; Zhou, Zhou; Zhao, Hong; Altman, Roger B; Abruña, Héctor D; Blanchard, Scott C

    2016-02-01

    Bright, long-lasting and non-phototoxic organic fluorophores are essential to the continued advancement of biological imaging. Traditional approaches towards achieving photostability, such as the removal of molecular oxygen and the use of small-molecule additives in solution, suffer from potentially toxic side effects, particularly in the context of living cells. The direct conjugation of small-molecule triplet state quenchers, such as cyclooctatetraene (COT), to organic fluorophores has the potential to bypass these issues by restoring reactive fluorophore triplet states to the ground state through intra-molecular triplet energy transfer. Such methods have enabled marked improvement in cyanine fluorophore photostability spanning the visible spectrum. However, the generality of this strategy to chemically and structurally diverse fluorophore species has yet to be examined. Here, we show that the proximal linkage of COT increases the photon yield of a diverse range of organic fluorophores widely used in biological imaging applications, demonstrating that the intra-molecular triplet energy transfer mechanism is a potentially general approach for improving organic fluorophore performance and photostability.

  6. Probing cell mechanical properties with microfluidic devices

    NASA Astrophysics Data System (ADS)

    Rowat, Amy

    2012-02-01

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

  7. Optimized measurements of separations and angles between intra-molecular fluorescent markers

    PubMed Central

    Mortensen, Kim I.; Sung, Jongmin; Flyvbjerg, Henrik; Spudich, James A.

    2015-01-01

    We demonstrate a novel, yet simple tool for the study of structure and function of biomolecules by extending two-colour co-localization microscopy to fluorescent molecules with fixed orientations and in intra-molecular proximity. From each colour-separated microscope image in a time-lapse movie and using only simple means, we simultaneously determine both the relative (x,y)-separation of the fluorophores and their individual orientations in space with accuracy and precision. The positions and orientations of two domains of the same molecule are thus time-resolved. Using short double-stranded DNA molecules internally labelled with two fixed fluorophores, we demonstrate the accuracy and precision of our method using the known structure of double-stranded DNA as a benchmark, resolve 10-base-pair differences in fluorophore separations, and determine the unique 3D orientation of each DNA molecule, thereby establishing short, double-labelled DNA molecules as probes of 3D orientation of anything to which one can attach them firmly. PMID:26509412

  8. Accounting for intra-molecular vibrational modes in open quantum system description of molecular systems.

    PubMed

    Roden, Jan; Strunz, Walter T; Whaley, K Birgitta; Eisfeld, Alexander

    2012-11-28

    Electronic-vibrational dynamics in molecular systems that interact with an environment involve a large number of degrees of freedom and are therefore often described by means of open quantum system approaches. A popular approach is to include only the electronic degrees of freedom into the system part and to couple these to a non-Markovian bath of harmonic vibrational modes that is characterized by a spectral density. Since this bath represents both intra-molecular and external vibrations, it is important to understand how to construct a spectral density that accounts for intra-molecular vibrational modes that couple further to other modes. Here, we address this problem by explicitly incorporating an intra-molecular vibrational mode together with the electronic degrees of freedom into the system part and using the Fano theory for a resonance coupled to a continuum to derive an "effective" bath spectral density, which describes the contribution of intra-molecular modes. We compare this effective model for the intra-molecular mode with the method of pseudomodes, a widely used approach in simulation of non-Markovian dynamics. We clarify the difference between these two approaches and demonstrate that the respective resulting dynamics and optical spectra can be very different.

  9. Mean-Field Theory of Intra-Molecular Charge Ordering in (TTM--TTP)I3

    NASA Astrophysics Data System (ADS)

    Omori, Yukiko; Tsuchiizu, Masahisa; Suzumura, Yoshikazu

    2011-02-01

    We examine an intra-molecular charge-ordered (ICO) state in the multi-orbital molecular compound (TTM--TTP)I3 on the basis of an effective two-orbital model derived from ab initio calculations. Representing the model in terms of the fragment molecular-orbital (MO) picture, the ICO state is described as the charge disproportionation on the left and right fragment MOs. By applying the mean-field theory, the phase diagram of the ground state is obtained as a function of the inter-molecular Coulomb repulsion and the intra-molecular transfer integral. The ICO state is stabilized by large inter-fragment Coulomb interactions, and the small intra-molecular transfer energy between two fragment MOs. Furthermore, we examine the finite-temperature phase diagram. The relevance to the experimental observations in the molecular compound of (TTM--TTP)I3 is also discussed.

  10. Environmental genotoxicity: Probing the underlying mechanisms

    SciTech Connect

    Shugart, L.; Theodorakis, C.

    1993-12-31

    Environmental pollution is a complex issue because of the diversity of anthropogenic agents, both chemical and physical, that have been detected and catalogued. The consequences to biota from exposure to genotoxic agents present an additional problem because of the potential for these agents to produce adverse change at the cellular and organismal levels. Past studies in genetic toxicology at the Oak Ridge National Laboratory have focused on structural damage to the DNA of environmental species that may occur after exposure to genotoxic agents and the use of this information to document exposure and to monitor remediation. In an effort to predict effects at the population, community and ecosystem levels, current studies in genetic ecotoxicology are attempting to characterize the biological mechanisms at the gene level that regulate and limit the response of an individual organism to genotoxic factors in their environment.

  11. Probing quarkonium production mechanisms with jet substructure

    NASA Astrophysics Data System (ADS)

    Baumgart, Matthew; Leibovich, Adam K.; Mehen, Thomas; Rothstein, Ira Z.

    2014-11-01

    We use fragmenting jet functions (FJFs) in the context of quarkonia to study the production channels predicted by NRQCD (3 S {1/(1)}, 3 S {1/(8)}, 1 S {0/(8)}, 3 P {/J (8)}). We choose a set of FJFs that give the probability to find a quarkonium with a given momentum fraction inside a cone-algorithm jet with fixed cone size and energy. This observable gives several lever arms that allow one to distinguish different production channels. In particular, we show that at fixed momentum fraction the individual production mechanisms have distinct behaviors as a function of the the jet energy. As a consequence of this fact, we arrive at the robust prediction that if the depolarizing 1 S {0/(8)} matrix element dominates, then the gluon FJF will diminish with increasing energy for fixed momentum fraction, z, and z >0.5.

  12. Environmental genotoxicity: probing the underlying mechanisms.

    PubMed Central

    Shugart, L; Theodorakis, C

    1994-01-01

    Environmental pollution is a complex issue because of the diversity of anthropogenic agents, both chemical and physical, that have been detected and catalogued. The consequences to biota from exposure to genotoxic agents present an additional problem because of the potential for these agents to produce adverse change at the cellular and organismal levels. Past studies in genetic toxicology at the Oak Ridge National Laboratory have focused on structural damage to the DNA of environmental species that may occur after exposure to genotoxic agents and the use of this information to document exposure and to monitor remediation. In an effort to predict effects at the population, community, and ecosystem levels, current studies in genetic ecotoxicology are attempting to characterize the biologic mechanisms at the gene level that regulate and limit the response of an individual organism to genotoxic factors in their environment. PMID:7713026

  13. Studies of enzyme mechanism using isotopic probes

    SciTech Connect

    Chen, C.

    1987-01-01

    The isotope partitioning studies of the Ascaris suum NAD-malic enzyme reaction were examined with five transitory complexes including E:NAD, E:NAD:Mg, E:malate, E:Mg:malate, and E:NAD:malate. Three productive complexes, E:NAD, E:NAD:Mg, and E:Mg:malate, were obtained, suggesting a steady-state random mechanism. Data for trapping with E:/sup 14/C-NAD indicate a rapid equilibrium addition of Mg/sup 2 +/ prior to the addition of malate. Trapping with /sup 14/C-malate could only be obtained from the E:Mg/sup 2 +/:/sup 14/C-malate complex, while no trapping from E:/sup 14/C-malate was obtained under feasible experimental conditions. The equations for the isotope partitioning studies varying two substrates in the chase solution in an ordered terreactant reaction were derived, allowing a determination of the relative rates of substrate dissociation to the catalytic reaction for each of the productive transitory complexes. NAD and malate are released from the central complex at an identical rate, equal to the catalytic rate. The release of NAD from E:NAD and E:NAD:Mg complexes is 2- to 4-fold and 5- to 9-fold V/sub max//E/sub t/, respectively. The release of malate from the E:Mg:malate complex is 0.1- to 0.3-fold of V/sub max//E/sub t/. The individual rate constants for association and dissociation of the substrates, NAD and malate have been estimated.

  14. Strategies to enhance the excitation energy-transfer efficiency in a light-harvesting system using the intra-molecular charge transfer character of carotenoids.

    PubMed

    Yukihira, Nao; Sugai, Yuko; Fujiwara, Masazumi; Kosumi, Daisuke; Iha, Masahiko; Sakaguchi, Kazuhiko; Katsumura, Shigeo; Gardiner, Alastair T; Cogdell, Richard J; Hashimoto, Hideki

    2017-03-15

    Fucoxanthin is a carotenoid that is mainly found in light-harvesting complexes from brown algae and diatoms. Due to the presence of a carbonyl group attached to polyene chains in polar environments, excitation produces an excited intra-molecular charge transfer. This intra-molecular charge transfer state plays a key role in the highly efficient (∼95%) energy-transfer from fucoxanthin to chlorophyll a in the light-harvesting complexes from brown algae. In purple bacterial light-harvesting systems the efficiency of excitation energy-transfer from carotenoids to bacteriochlorophylls depends on the extent of conjugation of the carotenoids. In this study we were successful, for the first time, in incorporating fucoxanthin into a light-harvesting complex 1 from the purple photosynthetic bacterium, Rhodospirillum rubrum G9+ (a carotenoidless strain). Femtosecond pump-probe spectroscopy was applied to this reconstituted light-harvesting complex in order to determine the efficiency of excitation energy-transfer from fucoxanthin to bacteriochlorophyll a when they are bound to the light-harvesting 1 apo-proteins.

  15. Probe into the Internal Mechanism of Interlanguage Fossilization

    ERIC Educational Resources Information Center

    Huang, Qian

    2009-01-01

    Interlanguage fossilization is normal for second language acquisition. It is also a hotspot for studies on theory of foreign language acquisition. Many reasons cause the interlanguage fossilization. This paper probes into the internal mechanism of interlanguage fossilization from five aspects, namely the physiological aspect, the psychological…

  16. Probing single-cell mechanics with picosecond ultrasonics.

    PubMed

    Dehoux, Thomas; Abi Ghanem, Maroun; Zouani, Omar F; Ducousso, Mathieu; Chigarev, Nikolay; Rossignol, Clément; Tsapis, Nicolas; Durrieu, Marie-Christine; Audoin, Bertrand

    2015-02-01

    The mechanical properties of cells play a key role in several fundamental biological processes, such as migration, proliferation, differentiation and tissue morphogenesis. The complexity of the inner cell composition and the intricate meshwork formed by transmembrane cell-substrate interactions demands a non-invasive technique to probe cell mechanics and cell adhesion at a subcell scale. In this paper we review the use of laser-generated GHz acoustic waves--a technique called picosecond ultrasonics (PU)--to probe the mechanical properties of single cells. We first describe applications to vegetal cells and biomimetic systems. We show how these systems can be used as simple models to understand more complex animal cells. We then present an opto-acoustic bio-transducer designed for in vivo measurements in physiological conditions. We illustrate the use of this transducer through the simultaneous probing of the density and compressibility of Allium cepa cells. Finally, we demonstrate that this technique can quantify animal-cell adhesion on metallic surfaces by analyzing the acoustic pulses reflected off the cell-metal interface. This innovative approach allows investigating quantitatively cell mechanics without fluorescent labels or mechanical contact to the cell.

  17. 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

  18. Mechanics from Calorimetry: Probing the Elasticity of Responsive Hydrogels

    NASA Astrophysics Data System (ADS)

    Aangenendt, Frank J.; Mattsson, Johan; Ellenbroek, Wouter G.; Wyss, Hans M.

    2017-07-01

    Temperature-sensitive hydrogels based on polymers such as poly(N -isopropylacrylamide) (PNIPAM) undergo a volume phase transition in response to changes in temperature. During this transition, distinct changes in both thermal and mechanical properties are observed. Here, we illustrate and exploit the inherent thermodynamic link between thermal and mechanical properties by showing that the compressive elastic modulus of PNIPAM hydrogels can be probed using differential scanning calorimetry. We validate our approach by using conventional osmotic compression tests. Our method could be particularly valuable for determining the mechanical response of thermosensitive submicron-sized and/or oddly shaped particles, to which standard methods are not readily applicable.

  19. Identifying mechanism-of-action targets for drugs and probes

    PubMed Central

    Gregori-Puigjané, Elisabet; Setola, Vincent; Hert, Jérôme; Crews, Brenda A.; Irwin, John J.; Lounkine, Eugen; Marnett, Lawrence; Roth, Bryan L.; Shoichet, Brian K.

    2012-01-01

    Notwithstanding their key roles in therapy and as biological probes, 7% of approved drugs are purported to have no known primary target, and up to 18% lack a well-defined mechanism of action. Using a chemoinformatics approach, we sought to “de-orphanize” drugs that lack primary targets. Surprisingly, targets could be easily predicted for many: Whereas these targets were not known to us nor to the common databases, most could be confirmed by literature search, leaving only 13 Food and Drug Administration—approved drugs with unknown targets; the number of drugs without molecular targets likely is far fewer than reported. The number of worldwide drugs without reasonable molecular targets similarly dropped, from 352 (25%) to 44 (4%). Nevertheless, there remained at least seven drugs for which reasonable mechanism-of-action targets were unknown but could be predicted, including the antitussives clemastine, cloperastine, and nepinalone; the antiemetic benzquinamide; the muscle relaxant cyclobenzaprine; the analgesic nefopam; and the immunomodulator lobenzarit. For each, predicted targets were confirmed experimentally, with affinities within their physiological concentration ranges. Turning this question on its head, we next asked which drugs were specific enough to act as chemical probes. Over 100 drugs met the standard criteria for probes, and 40 did so by more stringent criteria. A chemical information approach to drug-target association can guide therapeutic development and reveal applications to probe biology, a focus of much current interest. PMID:22711801

  20. [Probe into monitoring mechanism of Chinese materia medica resources].

    PubMed

    Zhang, Xiao-Bo; Li, Da-Ning; Guo, Lan-Ping; Lu, Jian-Wei; Sun, Li-Ying; Huang, Lu-Qi

    2013-10-01

    Focusing on the problems of Chinese materia medica resources,and combining with the national Chinese materia medica resources survey, the paper probes into monitoring mechanism of Chinese materia medica resources. The establishment of the monitoring mechanism needs one organization and management agencies to supervise and guide monitoring work, one network system to gather data information, a group of people to perform monitoring work, a system of technical methods to assure monitoring work scientific and practical, a series of achievements and products to figure out the methods for solving problems, a group of monitoring index system to accumulate basic data, and a plenty of funds to keep normal operation of monitoring work.

  1. Atomic force microscopy probing in the measurement of cell mechanics

    PubMed Central

    Kirmizis, Dimitrios; Logothetidis, Stergios

    2010-01-01

    Atomic force microscope (AFM) has been used incrementally over the last decade in cell biology. Beyond its usefulness in high resolution imaging, AFM also has unique capabilities for probing the viscoelastic properties of living cells in culture and, even more, mapping the spatial distribution of cell mechanical properties, providing thus an indirect indicator of the structure and function of the underlying cytoskeleton and cell organelles. AFM measurements have boosted our understanding of cell mechanics in normal and diseased states and provide future potential in the study of disease pathophysiology and in the establishment of novel diagnostic and treatment options. PMID:20463929

  2. Mechanism of cis-prenyltransferase reaction probed by substrate analogues.

    PubMed

    Lu, Yen-Pin; Liu, Hon-Ge; Teng, Kuo-Hsun; Liang, Po-Huang

    2010-10-01

    Undecaprenyl pyrophosphate synthase (UPPS) is a cis-type prenyltransferases which catalyzes condensation reactions of farnesyl diphosphate (FPP) with eight isopentenyl pyrophosphate (IPP) units to generate C(55) product. In this study, we used two analogues of FPP, 2-fluoro-FPP and [1,1-(2)H(2)]FPP, to probe the reaction mechanism of Escherichia coli UPPS. The reaction rate of 2-fluoro-FPP with IPP under single-turnover condition is similar to that of FPP, consistent with the mechanism without forming a farnesyl carbocation intermediate. Moreover, the deuterium secondary KIE of 0.985±0.022 measured for UPPS reaction using [1,1-(2)H(2)]FPP supports the associative transition state. Unlike the sequential mechanism used by trans-prenyltransferases, our data demonstrate E. coli UPPS utilizes the concerted mechanism. Copyright © 2010 Elsevier Inc. All rights reserved.

  3. Astrophysical probes of the Vainshtein mechanism: Stars and galaxies

    NASA Astrophysics Data System (ADS)

    Koyama, Kazuya; Sakstein, Jeremy

    2015-06-01

    Ghost-free theories beyond the Horndeski class exhibit a partial breaking of the Vainshtein mechanism inside nonrelativistic sources of finite extent. We exploit this breaking to identify new and novel astrophysical probes of these theories. Nonrelativistic objects feel a gravitational force that is weaker than that predicted by general relativity. The new equation of hydrostatic equilibrium is derived and solved to predict the modified behavior of stars. It is found that main-sequence stars are dimmer and cooler than their general relativity counterparts but the red giant phase is largely indistinguishable. The rotation curves and lensing potential of Milky Way-like galaxies are calculated. The circular velocities are smaller than predicted by general relativity at fixed radius and the lensing mass is smaller than the dynamical mass. We discuss potential astrophysical probes of these theories and identify strong lensing as a particularly promising candidate.

  4. Probing multiscale mechanics of collagen with optical tweezers

    NASA Astrophysics Data System (ADS)

    Shayegan, Marjan; Rezaei, Naghmeh; Lam, Norman H.; Altindal, Tuba; Wieczorek, Andrew; Forde, Nancy R.

    2013-09-01

    How the molecular structure of the structural, extracellular matrix protein collagen correlates with its mechanical properties at different hierarchical structural levels is not known. We demonstrate the utility of optical tweezers to probe collagen's mechanical response throughout its assembly hierarchy, from single molecule force-extension measurements through microrheology measurements on solutions of collagen molecules, collagen fibrillar gels and gelatin. These experiments enable the determination of collagen's flexibility, mechanics, and timescales and strengths of interaction at different levels of hierarchy, information critical to developing models of how collagen's physiological function and stability are influenced by its chemical composition. By investigating how the viscoelastic properties of collagen are affected by the presence of telopeptides, protein domains that strongly influence fibril formation, we demonstrate that these play a role in conferring transient elasticity to collagen solutions.

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

    NASA Astrophysics Data System (ADS)

    Meng, Zhaokai; Yakovlev, Vladislav V.

    2015-02-01

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

  6. Determination of distance of intra-molecular hydrogen bonding in (Ala-Gly)15 with silk I form after removal of the effect of MAS frequency in REDOR experiment.

    PubMed

    Kameda, Tsunenori; Zhao, Chenhua; Ashida, Jun; Asakura, Tetsuo

    2003-02-01

    It is important to know the structure of silk I (Bombyx mori silk structure before spinning in the solid state) in order to understand the mechanism of fiber formation at the atomic level. In this study, 15N-dephased, 13C-observe REDOR has been carried out to determine the atomic distance of intra-molecular hydrogen bond between the 13C=O carbon of the 14th Gly residue and the 15N nitrogen of the 17th Ala residue of (AG)(6)A[1-13C]GAG[15N]AG(AG)(6) with silk I form after removal of the effect of MAS frequency on the re-coupling. The distance was determined to be 4.3A, which confirmed the intra-molecular hydrogen bonding formation between these two atomic sites.

  7. Determination of distance of intra-molecular hydrogen bonding in (Ala-Gly) 15 with silk I form after removal of the effect of MAS frequency in REDOR experiment

    NASA Astrophysics Data System (ADS)

    Kameda, Tsunenori; Zhao, Chenhua; Ashida, Jun; Asakura, Tetsuo

    2003-02-01

    It is important to know the structure of silk I ( Bombyx mori silk structure before spinning in the solid state) in order to understand the mechanism of fiber formation at the atomic level. In this study, 15N-dephased, 13C-observe REDOR has been carried out to determine the atomic distance of intra-molecular hydrogen bond between the 13C O carbon of the 14th Gly residue and the 15N nitrogen of the 17th Ala residue of ( AG) 6A[1 -13C] GAG[ 15N] AG( AG) 6 with silk I form after removal of the effect of MAS frequency on the re-coupling. The distance was determined to be 4.3 Å, which confirmed the intra-molecular hydrogen bonding formation between these two atomic sites.

  8. Mechanism of cis-prenyltransferase reaction probed by substrate analogues

    SciTech Connect

    Lu, Yen-Pin; Liu, Hon-Ge; Teng, Kuo-Hsun; Liang, Po-Huang

    2010-10-01

    Research highlights: {yields} The extremely slow trans-OPPS reaction using 2-Fluoro-FPP supports the sequential mechanism with the carbocation intermediate. {yields} The similar UPPS reaction rate under single turnover supports the concerted mechanism, without the carbocation intermediate. {yields} The secondary kinetic isotope effect also supports associate transition state for UPPS reaction, without the carbocation intermediate. -- Abstract: Undecaprenyl pyrophosphate synthase (UPPS) is a cis-type prenyltransferases which catalyzes condensation reactions of farnesyl diphosphate (FPP) with eight isopentenyl pyrophosphate (IPP) units to generate C{sub 55} product. In this study, we used two analogues of FPP, 2-fluoro-FPP and [1,1-{sup 2}H{sub 2}]FPP, to probe the reaction mechanism of Escherichia coli UPPS. The reaction rate of 2-fluoro-FPP with IPP under single-turnover condition is similar to that of FPP, consistent with the mechanism without forming a farnesyl carbocation intermediate. Moreover, the deuterium secondary KIE of 0.985 {+-} 0.022 measured for UPPS reaction using [1,1-{sup 2}H{sub 2}]FPP supports the associative transition state. Unlike the sequential mechanism used by trans-prenyltransferases, our data demonstrate E. coli UPPS utilizes the concerted mechanism.

  9. Probing neutrino flavor transition mechanism with ultrahigh energy astrophysical neutrinos

    NASA Astrophysics Data System (ADS)

    Lai, Kwang-Chang; Lin, Guey-Lin; Liu, Tsung-Che

    2014-02-01

    Observation of ultrahigh energy astrophysical neutrinos and identification of their flavors have been proposed for future neutrino telescopes. The flavor ratio of astrophysical neutrinos observed on the Earth depends on both the initial flavor ratio at the source and flavor transitions taking place during propagations of these neutrinos. The flavor transition mechanisms are well classified with our model-independent parametrization. We find that a new parameter R ≡ϕe/(ϕμ+ϕτ) can probe directly the flavor transition in the framework of our model-independent parametrization, without the assumption of the νμ-ντ symmetry. A few flavor-transition models are employed to test our parametrization with this new observable. The observational constraints on flavor transition mechanisms by the new observable are discussed through our model-independent parametrization.

  10. Extreme Mechanics of Probing the Ultimate Strength of Nanotwinned Diamond

    NASA Astrophysics Data System (ADS)

    Li, Bing; Sun, Hong; Chen, Changfeng

    2016-09-01

    Recently synthesized nanotwinned diamond (NTD) exhibits unprecedented Vickers hardness exceeding 200 GPa [Q. Huang et al., Nature (London) 510, 250 (2014)]. This extraordinary finding challenges the prevailing understanding of material deformation and stress response under extreme loading conditions. Here we unveil by first-principles calculations a novel indenter-deformation generated stress confinement mechanism that suppresses the graphitization or bond collapse failure modes commonly known in strong covalent solids, leading to greatly enhanced peak stress and strain range in the indented diamond lattice. Moreover, the twin boundaries in NTD promote a strong stress concentration that drives preferential bond realignments, producing a giant indentation strain stiffening. These results explain the exceptional indentation strength of NTD and offer insights into the extreme mechanics of the intricate interplay of the indenter and indented crystal in probing ultrahard materials.

  11. Extreme Mechanics of Probing the Ultimate Strength of Nanotwinned Diamond.

    PubMed

    Li, Bing; Sun, Hong; Chen, Changfeng

    2016-09-09

    Recently synthesized nanotwinned diamond (NTD) exhibits unprecedented Vickers hardness exceeding 200 GPa [Q. Huang et al., Nature (London) 510, 250 (2014)]. This extraordinary finding challenges the prevailing understanding of material deformation and stress response under extreme loading conditions. Here we unveil by first-principles calculations a novel indenter-deformation generated stress confinement mechanism that suppresses the graphitization or bond collapse failure modes commonly known in strong covalent solids, leading to greatly enhanced peak stress and strain range in the indented diamond lattice. Moreover, the twin boundaries in NTD promote a strong stress concentration that drives preferential bond realignments, producing a giant indentation strain stiffening. These results explain the exceptional indentation strength of NTD and offer insights into the extreme mechanics of the intricate interplay of the indenter and indented crystal in probing ultrahard materials.

  12. Probing the core-collapse supernova mechanism with gravitational waves

    NASA Astrophysics Data System (ADS)

    Ott, Christian D.

    2009-10-01

    The mechanism of core-collapse supernova explosions must draw on the energy provided by gravitational collapse and transfer the necessary fraction to the kinetic and internal energy of the ejecta. Despite many decades of concerted theoretical effort, the detailed mechanism of core-collapse supernova explosions is still unknown, but indications are strong that multi-D processes lie at its heart. This opens up the possibility of probing the supernova mechanism with gravitational waves, carrying direct dynamical information from the supernova engine deep inside a dying massive star. I present a concise overview of the physics and primary multi-D dynamics in neutrino-driven, magnetorotational, and acoustically driven core-collapse supernova explosion scenarios. Discussing and contrasting estimates for the gravitational-wave emission characteristics of these mechanisms, I argue that their gravitational-wave signatures are clearly distinct and that the observation (or non-observation) of gravitational waves from a nearby core-collapse event could put strong constraints on the supernova mechanism.

  13. Intra-molecular cross-linking of acidic residues for protein structure studies.

    SciTech Connect

    Kruppa, Gary Hermann; Young, Malin M.; Novak, Petr; Schoeniger, Joseph S.

    2005-03-01

    Intra-molecular cross-linking has been suggested as a method of obtaining distance constraints that would be useful in developing structural models of proteins. Recent work published on intra-molecular cross-linking for protein structural studies has employed commercially available primary amine selective reagents that can cross-link lysine residues to other lysine residues or the amino terminus. Previous work using these cross-linkers has shown that for several proteins of known structure, the number of cross-links that can be obtained experimentally may be small compared to what would be expected from the known structure, due to the relative reactivity, distribution, and solvent accessibility of the lysines in the protein sequence. To overcome these limitations we have investigated the use of cross-linking reagents that can react with other reactive sidechains in proteins. We used 1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) to activate the carboxylic acid containing residues, aspartic acid (D), glutamic acid (E), and the carboxy terminus (O), for cross-linking reactions. Once activated, the DEO sidechains can react to form 'zero-length' cross-links with nearby primary amine containing resides, lysines (K) and the amino terminus (X), via the formation of a new amide bond. We also show that the EDC-activated DEO sidechains can be cross-linked to each other using dihydrazides, two hydrazide moieties connected by an alkyl cross-linker ann of variable length. Using these reagents, we have found three new 'zero-length' cross-links in ubiquitin consistent with its known structure (M1-E16, M1-E18, and K63-E64). Using the dihydrazide cross-linkers, we have identified 2 new cross-links (D21-D32 and E24-D32) unambiguously. Using a library of dihydrazide cross-linkers with varying arm length, we have shown that there is a minimum arm length required for the DEO-DEO cross-links of 5.8 angstroms. These results show that additional structural information

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

    NASA Astrophysics Data System (ADS)

    Virwani, Kumar

    2011-03-01

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

  15. The interplay between inter- and intra-molecular dynamics in a series of alkylcitrates

    SciTech Connect

    Kipnusu, Wycliffe Kiprop; Kossack, Wilhelm; Iacob, Ciprian; Zeigermann, Philipp; Jasiurkowska, Malgorzata; Sangoro, Joshua R; Valiullin, Rustem; Kremer, Friedrich

    2013-01-01

    The inter- and intra-molecular dynamics in a series of glass-forming alkylcitrates is studied by a combination of Broadband Dielectric Spectroscopy (BDS), Pulsed Field Gradient Nuclear Magnetic Resonance (PFG NMR), Fourier-Transform Infrared (FTIR) spectroscopy and Differential Scanning Calorimetry (DSC). Analyzing the temperature dependencies of specific IR absorption bands in terms of their spectral position and the corresponding oscillator strengths enables one to unravel the intramolecular dynamics of specific molecular moieties and to compare them with the (primarily dielectrically) determined intermolecular dynamics. With decreasing temperature, the IR band positions of carbonyls (part of the core units) and H-bonded moieties of citrates show a red shift with a kink at the calorimetric glass transition temperature (Tg) while other moieties, whose dynamics are decoupled from those of the core units, exhibit a blue shift with nominal changes at Tg. The oscillator strength of all units in citrates depicts stronger temperature dependencies above Tg and in some, the ester linkage and H-bonded units show a change of slope at a temperature where structural and faster secondary relaxations merge. By that, a wealth of novel information is obtained proving the fundamental importance of intramolecular mobility in the process of glass formation, beyond coarse-grained descriptions.

  16. The topology and dynamics of protein complexes: insights from intra- molecular network theory.

    PubMed

    Hu, Guang; Zhou, Jianhong; Yan, Wenying; Chen, Jiajia; Shen, Bairong

    2013-03-01

    Intra-molecular interactions within complex systems play a pivotal role in the biological function. They form a major challenge to computational structural proteomics. The network paradigm treats any system as a set of nodes linked by edges corresponding to the relations existing between the nodes. It offers a computationally efficient tool to meet this challenge. Here, we review the recent advances in the use of network theory to study the topology and dynamics of protein- ligand and protein-nucleic acid complexes. The study of protein complexes networks not only involves the topological classification in term of network parameters, but also reveals the consistent picture of intrinsic functional dynamics. Current dynamical analysis focuses on a plethora of functional phenomena: the process of allosteric communication, the binding induced conformational changes, prediction and identification of binding sites of protein complexes, which will give insights into intra-protein complexes interactions. Furthermore, such computational results may elucidate a variety of known biological processes and experimental data, and thereby demonstrate a huge potential for applications such as drug design and functional genomics. Finally we describe some web-based resources for protein complexes, as well as protein network servers and related bioinformatics tools.

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

    PubMed

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

    2011-01-01

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

  18. A new pair for inter- and intra-molecular FRET measurement

    SciTech Connect

    Yang Xiaofei; Xu Pingyong; Xu Tao . E-mail: xutao@sun5.ibp.ac.cn

    2005-05-13

    Fluorescence resonance energy transfer between mutant green fluorescent proteins provides powerful means to monitor in vivo protein-protein proximity and intracellular signaling. However, the current widely applied FRET pair of this class (CFP/YFP) requires excitation by expensive UV lasers, thereby hindering FRET imaging on many confocal microscopes. Further challenges arise from the large spectral overlap of CFP/YFP emission. Another FRET pair GFP/DsRed could obviate such limitations. However, the use of DsRed as a FRET acceptor is hampered by several critical problems, including a slow and incomplete maturation and obligate tetramerization. A tandem dimer mutant of DsRed (TDimer2) has similar spectral properties as those of DsRed. The rapid maturation and non-oligomerization make TDimer2 a promising substitute for DsRed in FRET experiments. Here, we have explored the possibility of using TDimer2 as a FRET acceptor for the donor EGFP. FRET was demonstrated between the EGFP-TDimer2 chimeric fusion protein. By substituting CFP/YFP in the Ca{sup 2+}-sensor cameleon with EGFP/TDimer2, dynamic changes in cytosolic free Ca{sup 2+} concentrations were observed with 488 nm excitation under conventional wide-field microscopy. The EGFP/TDimer2 pair was further successfully employed to monitor inter-molecular interaction between Syntaxin and SNAP25. These results reveal EGFP/TDimer2 as a promising FRET pair in monitoring intra-molecular conformation change as well as inter-molecular interaction.

  19. Alkaline niobate nanowires as opto-mechanical probes

    NASA Astrophysics Data System (ADS)

    Dutto, Fabrizia; Radenovic, Aleksandra

    2012-10-01

    Perovskite alkaline niobate (XNbO3) nanowires are attracting lots of attention having a variety of interesting properties such as significant nonlinear optical response, pronounced birefringence, considerable piezoelectric, pyroelectric, photorefractive, and photocatalytic response, as well as superior mechanical and chemical stability. Their ability to efficiently generate second harmonic signals (SHG) and their birefringence allow the use of these nanostructures as local mechano-optical probes for single molecule detection. To assess which type of nanowires is suitable for specific application, we performed a comparative study on the nonlinear optical response of the different types of chemically synthesized alkaline niobate nanowires: sodium niobate (NaNbO3), potassium niobate (KNbO3) and lithium niobate (LiNbO3) nanowires. An optical trap setup has been used to demonstrate the possibility to steadily trap the nanowires, their ability to generate high second harmonic signals, to waveguide this signal and to be rotated under a highly focused laser beam with changing polarization. Different applications are suggested for the three materials, such as LiNbO3 nanowires as imaging markers, while KNbO3 and NaNbO3 nanowires for trapping and torque experiments and NaNbO3 nanowires to waveguide SHG light. Functionalization of the XNbO3 nanowires has been studied and successfully implemented. This is a first crucial step toward their use in biomedical imaging and single molecule applications.

  20. Stability Mechanisms of a Thermophilic Laccase Probed by Molecular Dynamics

    PubMed Central

    Christensen, Niels J.; Kepp, Kasper P.

    2013-01-01

    Laccases are highly stable, industrially important enzymes capable of oxidizing a large range of substrates. Causes for their stability are, as for other proteins, poorly understood. In this work, multiple-seed molecular dynamics (MD) was applied to a Trametes versicolor laccase in response to variable ionic strengths, temperatures, and glycosylation status. Near-physiological conditions provided excellent agreement with the crystal structure (average RMSD ∼0.92 Å) and residual agreement with experimental B-factors. The persistence of backbone hydrogen bonds was identified as a key descriptor of structural response to environment, whereas solvent-accessibility, radius of gyration, and fluctuations were only locally relevant. Backbone hydrogen bonds decreased systematically with temperature in all simulations (∼9 per 50 K), probing structural changes associated with enthalpy-entropy compensation. Approaching Topt (∼350 K) from 300 K, this change correlated with a beginning “unzipping” of critical β-sheets. 0 M ionic strength triggered partial denucleation of the C-terminal (known experimentally to be sensitive) at 400 K, suggesting a general salt stabilization effect. In contrast, F− (but not Cl−) specifically impaired secondary structure by formation of strong hydrogen bonds with backbone NH, providing a mechanism for experimentally observed small anion destabilization, potentially remedied by site-directed mutagenesis at critical intrusion sites. N-glycosylation was found to support structural integrity by increasing persistent backbone hydrogen bonds by ∼4 across simulations, mainly via prevention of F− intrusion. Hydrogen-bond loss in distinct loop regions and ends of critical β-sheets suggest potential strategies for laboratory optimization of these industrially important enzymes. PMID:23658618

  1. Design Approaches for Stealthy Probing Mechanisms in Battlefield Networks

    DTIC Science & Technology

    2008-09-01

    pings are an effective tool for detecting network nodes that have been compromised by an attacker who tries to delay or drop traffic passing through...the captured node. However, an intelligent attacker may evade detection by giving preferential treatment to probe traffic. This is usually possible...stealthy manner so as to avoid identification of probes by an attacker and to ensure the collection of accurate system health statistics. In this

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

    PubMed

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

    2009-09-30

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

  3. A mechanically tunable and efficient ceramic probe for MR-microscopy at 17 Tesla

    NASA Astrophysics Data System (ADS)

    Kurdjumov, Sergei; Glybovski, Stanislav; Hurshkainen, Anna; Webb, Andrew; Abdeddaim, Redha; Ciobanu, Luisa; Melchakova, Irina; Belov, Pavel

    2017-09-01

    In this contribution we propose and study numerically a new probe (radiofrequency coil) for magnetic resonance mi-croscopy in the field of 17T. The probe is based on two coupled donut resonators made of a high-permittivity and low-loss ceramics excited by a non-resonant inductively coupled loop attached to a coaxial cable. By full-wave numerical simulation it was shown that the probe can be precisely tuned to the Larmor frequency of protons (723 MHz) by adjusting a gap between the two resonators. Moreover, the impedance of the probe can be matched by varying the distance from one of the resonators to the loop. As a result, a compact and mechanically tunable resonant probe was demonstrated for 17 Tesla applications using no lumped capacitors for tuning and matching. The new probe was numerically compared to a conventional solenoidal probe showing better efficiency.

  4. Constructing thioether-tethered cyclic peptides via on-resin intra-molecular thiol-ene reaction.

    PubMed

    Zhao, Bingchuan; Zhang, Qingzhou; Li, Zigang

    2016-08-01

    Thiol-ene reactions have been used in a variety of applications that mostly involve an inter-molecular pathway. Herein, we report a facile method to construct thioether-tethered cyclic peptides via an intra-molecular thiol-ene reaction. This reaction is efficient, selective, and has good residue compatibility. Short peptides with thioether tethers were constructed and were used to construct longer cyclic peptides. This synthetic method may be useful for constructing bioactive peptides. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

  5. Probing Mechanical Properties of Rock with InSAR

    NASA Astrophysics Data System (ADS)

    Jónsson, S.

    2012-04-01

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

  6. Monolithically Integrated, Mechanically Resilient Carbon-Based Probes for Scanning Probe Microscopy

    NASA Technical Reports Server (NTRS)

    Kaul, Anupama B.; Megerian, Krikor G.; Jennings, Andrew T.; Greer, Julia R.

    2010-01-01

    Scanning probe microscopy (SPM) is an important tool for performing measurements at the nanoscale in imaging bacteria or proteins in biology, as well as in the electronics industry. An essential element of SPM is a sharp, stable tip that possesses a small radius of curvature to enhance spatial resolution. Existing techniques for forming such tips are not ideal. High-aspect-ratio, monolithically integrated, as-grown carbon nanofibers (CNFs) have been formed that show promise for SPM applications by overcoming the limitations present in wet chemical and separate substrate etching processes.

  7. Mechanical design and force calibration of dual-axis micromechanical probe for friction force microscopy

    SciTech Connect

    Fukuzawa, Kenji; Terada, Satoshi; Shikida, Mitsuhiro; Amakawa, Hiroaki; Zhang, Hedong; Mitsuya, Yasunaga

    2007-02-01

    A dual-axis micromechanical probe that combines a double cantilever and torsion beams is presented. This probe can reduce the mechanical cross-talk between the lateral and vertical force detections. In addition, dual-axis forces can be detected by measuring the dual-axis displacement of the probe end using the optical lever-based method used in conventional friction force microscopes (FFMs). In this paper, the mechanical design of the probe, the details of the fabrication method, FFM performance, and calibration of the friction force are discussed. The mechanical design and the microfabrication method for probes that can provide a force resolution of the order of 1 nN without mechanical cross-talk are presented. Calibration of the lateral force signal is possible by using the relationship between the lateral force and the piezodisplacement at the onset of the probe scanning. The micromechanical probe enables simultaneous and independent detection of atomic and friction forces. This leads to accurate investigation of nanotribological phenomena and visualization of the distribution of the friction properties, which helps the identification of the material properties.

  8. Fluorescence probes for studying the mechanisms of transcription activation

    NASA Astrophysics Data System (ADS)

    Heyduk, Tomasz; Callaci, Sandhya

    1994-08-01

    Regulation of transcription involves a complex interplay between protein-ligand, protein-DNA, and protein-protein interactions. Fluorescence probes seem to be very well suited to study such complex systems since the selectivity and sensitivity of fluorescence makes possible to select only a part of the system for observation leaving the rest of it transparent to the technique. We have used fluorescence spectroscopy to study the activation of E.coli RNA polymerase by cAMP receptor protein (CRP). The cAMP interactions with CRP, domain flexibility in CRP molecule, the structure of CRP-DNA complex, and interaction of CRP with RNA-polymerase have been studied. Here we report the preparation and properties of 5-OH-Trp derivative of the sigma subunit of E.coli RNA polymerase. This subunit is responsible for specific promoter recognition. The obtained results show that the biological activities of the derivative are identical as observed for the native protein. Comparison of fluorescence properties of the 5-OH-Trp sigma derivative free and bound to the core RNA polymerase suggests a conformational change in the sigma protein induced by this interaction. These data show that replacement of Trp residues with 5-OH-Trp can be a very useful approach to prepare specific fluorescence derivatives of multimeric proteins.

  9. Axial scanning laser Doppler velocimeter using wavelength change without moving mechanism in sensor probe.

    PubMed

    Maru, Koichi

    2011-03-28

    A scanning laser Doppler velocimeter (LDV) without any moving mechanism in its sensor probe is proposed. In the proposed scanning LDV, the measurement position is axially scanned by change in the wavelength of the light input to the sensor probe, instead of using a moving mechanism in the sensor probe. For this purpose, a tunable laser and diffraction gratings are used, and the sensor probe including the gratings is separated from the main body including the tunable laser. To demonstrate the scanning function based on the proposed concept, an experiment was conducted using optical fibers, a commercial tunable laser and a setup of the sensor probe consisting of bulk optical components. As the experimental result, it is found that the measurement positions estimated from the measured beat frequencies are in good agreement with the theoretical values. The scan ranges over a wavelength range of 30 nm are estimated to be 29.3 mm when the beam angle to the measurement position at the wavelength of 1540 nm is 10° and 20.8 mm when the beam angle is 15°. The result indicates that the scanning function by means of changing the wavelength input to the sensor probe is successfully demonstrated for the first time. The proposed method has the potential for realizing a scanning LDV with a simple, compact and reliable sensor probe.

  10. Probing the mechanical architecture of the vertebrate meiotic spindle.

    PubMed

    Itabashi, Takeshi; Takagi, Jun; Shimamoto, Yuta; Onoe, Hiroaki; Kuwana, Kenta; Shimoyama, Isao; Gaetz, Jedidiah; Kapoor, Tarun M; Ishiwata, Shin'ichi

    2009-02-01

    Accurate chromosome segregation during meiosis depends on the assembly of a microtubule-based spindle of proper shape and size. Current models for spindle-size control focus on reaction diffusion-based chemical regulation and balance in activities of motor proteins. Although several molecular perturbations have been used to test these models, controlled mechanical perturbations have not been possible. Here we report a piezoresistive dual cantilever-based system to test models for spindle-size control and examine the mechanical features, such as deformability and stiffness, of the vertebrate meiotic spindle. We found that meiotic spindles prepared in Xenopus laevis egg extracts were viscoelastic and recovered their original shape in response to small compression. Larger compression resulted in plastic deformation, but the spindle adapted to this change, establishing a stable mechanical architecture at different sizes. The technique we describe here may also be useful for examining the micromechanics of other cellular organelles.

  11. Probing transmembrane mechanical coupling and cytomechanics using magnetic twisting cytometry

    NASA Technical Reports Server (NTRS)

    Wang, N.; Ingber, D. E.

    1995-01-01

    We recently developed a magnetic twisting cytometry technique that allows us to apply controlled mechanical stresses to specific cell surface receptors using ligand-coated ferromagnetic microbeads and to simultaneously measure the mechanical response in living cells. Using this technique, we have previously shown the following: (i) beta 1 integrin receptors mediate mechanical force transfer across the cell surface and to the cytoskeleton, whereas other transmembrane receptors (e.g., scavenger receptors) do not; (ii) cytoskeletal stiffness increases in direct proportion to the level of stress applied to integrins; and (iii) the slope of this linear stiffening response differs depending on the shape of the cell. We now show that different integrins (beta 1, alpha V beta 3, alpha V, alpha 5, alpha 2) and other transmembrane receptors (scavenger receptor, platelet endothelial cell adhesion molecule) differ in their ability to mediate force transfer across the cell surface. In addition, the linear stiffening behavior previously observed in endothelial cells was found to be shared by other cell types. Finally, we demonstrate that dynamic changes in cell shape that occur during both cell spreading and retraction are accompanied by coordinate changes in cytoskeletal stiffness. Taken together, these results suggest that the magnetic twisting cytometry technique may be a powerful and versatile tool for studies analyzing the molecular basis of transmembrane mechanical coupling to the cytoskeleton as well as dynamic relations between changes in cytoskeletal structure and alterations in cell form and function.

  12. Probing transmembrane mechanical coupling and cytomechanics using magnetic twisting cytometry

    NASA Technical Reports Server (NTRS)

    Wang, N.; Ingber, D. E.

    1995-01-01

    We recently developed a magnetic twisting cytometry technique that allows us to apply controlled mechanical stresses to specific cell surface receptors using ligand-coated ferromagnetic microbeads and to simultaneously measure the mechanical response in living cells. Using this technique, we have previously shown the following: (i) beta 1 integrin receptors mediate mechanical force transfer across the cell surface and to the cytoskeleton, whereas other transmembrane receptors (e.g., scavenger receptors) do not; (ii) cytoskeletal stiffness increases in direct proportion to the level of stress applied to integrins; and (iii) the slope of this linear stiffening response differs depending on the shape of the cell. We now show that different integrins (beta 1, alpha V beta 3, alpha V, alpha 5, alpha 2) and other transmembrane receptors (scavenger receptor, platelet endothelial cell adhesion molecule) differ in their ability to mediate force transfer across the cell surface. In addition, the linear stiffening behavior previously observed in endothelial cells was found to be shared by other cell types. Finally, we demonstrate that dynamic changes in cell shape that occur during both cell spreading and retraction are accompanied by coordinate changes in cytoskeletal stiffness. Taken together, these results suggest that the magnetic twisting cytometry technique may be a powerful and versatile tool for studies analyzing the molecular basis of transmembrane mechanical coupling to the cytoskeleton as well as dynamic relations between changes in cytoskeletal structure and alterations in cell form and function.

  13. Using experimental evolution to probe molecular mechanisms of protein function.

    PubMed

    Fischer, Marlies; Kang, Mandeep; Brindle, Nicholas Pj

    2016-02-01

    Directed evolution is a powerful tool for engineering protein function. The process of directed evolution involves iterative rounds of sequence diversification followed by assaying activity of variants and selection. The range of sequence variants and linked activities generated in the course of an evolution are a rich information source for investigating relationships between sequence and function. Key residue positions determining protein function, combinatorial contributors to activity and even potential functional mechanisms have been revealed in directed evolutions. The recent application of high throughput sequencing substantially increases the information that can be retrieved from directed evolution experiments. Combined with computational analysis this additional sequence information has allowed high-resolution analysis of individual residue contributions to activity. These developments promise to significantly enhance the depth of insight that experimental evolution provides into mechanisms of protein function.

  14. Probing the mechanisms of silicon-mediated pathogen resistance

    PubMed Central

    Gao, Dan; Chen, Jining; Luo, Shiming

    2009-01-01

    Silicon is the second most abundant mineral element in soil, it has important role in alleviating various environmental stresses and enhancing plant resistance against pathogen, but the exact mechanism by which Si mediates pathogen resistance remains unclear. One of the resistance mechanisms is related to silicon deposition in leaf that acts as a physical barrier to hinder pathogen penetration. But more evidence show that silicon can induce defense responses that are functionally similar to systemic acquired resistance, Si-treated plants can significantly increase antioxidant enzyme activities and the production of antifungal compounds such as phenolic metabolism product, phytoalexins and pathogenesis-related proteins etc. Molecular and biochemical detections show that Si can activate the expression of defense-related genes and may play important role in the transduction of plant stress signal such as salicylic acid, jasmonic acid and ethylene. PMID:19568332

  15. Probing Mechanics of Crumpled Two-Dimensional Membranes and Cantilevers

    NASA Astrophysics Data System (ADS)

    Nicholl, Ryan; Conley, Hiram; Lavrik, Nickolay; Vlassiouk, Ivan; Puzyrev, Yevgeniy; Sreenivas, Vijayashree Parsi; Pantelides, Sokrates; Bolotin, Kirill

    Two-dimensional materials (2DMs) are inevitably crumpled in the out-of-plane direction due to both static wrinkling associated with uneven stresses and dynamic wrinkling resulting from flexural phonons. Here, we investigate the effect of this crumpling on mechanical properties of 2DMs - in-plane stiffness and bending rigidity. To carry out these measurements, we developed techniques to fabricate graphene membranes and singly clamped graphene cantilevers that are stable in vacuum and air. The measurements are performed by actuating these devices electrostatically and monitoring their displacement via sensitive interferometric profilometry both at room and low temperatures. We find that crumpling lowers the in-plane stiffness and strongly increases the bending rigidity of 2DMs. Furthermore, we unravel the relative contribution of static and dynamic wrinkling to observed renormalization of the effective mechanical constants.

  16. Probing Mechanisms That Underlie Human Neurodegenerative Diseases in Drosophila

    PubMed Central

    Jaiswal, M.; Sandoval, H.; Zhang, K.; Bayat, V.; Bellen, H.J.

    2013-01-01

    The fruit fly, Drosophila melanogaster, is an excellent organism for the study of the genetic and molecular basis of metazoan development. Drosophila provides numerous tools and reagents to unravel the molecular and cellular functions of genes that cause human disease, and the past decade has witnessed a significant expansion of the study of neurodegenerative disease mechanisms in flies. Here we review the interplay between oxidative stress and neuronal toxicity. We cover some of the studies that show how proteasome degradation of protein aggregates, autophagy, mitophagy, and lysosomal function affect the quality control mechanisms required for neuronal survival. We discuss how forward genetic screens in flies have led to the isolation of a few loci that cause neurodegeneration, paving the way for large-scale systematic screens to identify such loci in flies as well as promoting gene discovery in humans. PMID:22974305

  17. Probing the mechanisms of silicon-mediated pathogen resistance.

    PubMed

    Cai, Kunzheng; Gao, Dan; Chen, Jining; Luo, Shiming

    2009-01-01

    Silicon is the second most abundant mineral element in soil, it has important role in alleviating various environmental stresses and enhancing plant resistance against pathogen, but the exact mechanism by which Si mediates pathogen resistance remains unclear. One of the resistance mechanisms is related to silicon deposition in leaf that acts as a physical barrier to hinder pathogen penetration. But more evidence show that silicon can induce defense responses that are functionally similar to systemic acquired resistance, Si-treated plants can significantly increase antioxidant enzyme activities and the production of antifungal compounds such as phenolic metabolism product, phytoalexins and pathogenesis-related proteins etc. Molecular and biochemical detections show that Si can activate the expression of defense-related genes and may play important role in the transduction of plant stress signal such as salicylic acid, jasmonic acid and ethylene.

  18. Probing embryonic tissue mechanics with laser hole drilling.

    PubMed

    Ma, Xiaoyan; Lynch, Holley E; Scully, Peter C; Hutson, M Shane

    2009-05-01

    We use laser hole drilling to assess the mechanics of an embryonic epithelium during development-in vivo and with subcellular resolution. We ablate a subcellular cylindrical hole clean through the epithelium and track the subsequent recoil of adjacent cells (on ms time scales). We investigate dorsal closure in the fruit fly with emphasis on apical constriction of amnioserosa cells. The mechanical behavior of this epithelium falls between that of a continuous sheet and a 2D cellular foam (a network of tensile interfaces). Tensile stress is carried both by cell-cell interfaces and by the cells' apical actin networks. Our results show that stress is slightly concentrated along interfaces (1.6-fold), but only in early closure. Furthermore, closure is marked by a decrease in the recoil power-law exponent, implying a transition to a more solid-like tissue. We use the site and stage dependence of the recoil kinetics to constrain how the cellular mechanics change during closure. We apply these results to test extant computational models.

  19. Structure and dynamical intra-molecular heterogeneity of star polymer melts above glass transition temperature.

    PubMed

    Chremos, Alexandros; Glynos, Emmanouil; Green, Peter F

    2015-01-28

    Structural and dynamical properties of star melts have been investigated with molecular dynamics simulations of a bead-spring model. Star polymers are known to be heterogeneous, but a systematic simulation study of their properties in melt conditions near the glass transition temperature was lacking. To probe their properties, we have expanded from linear to star polymers the applicability of Dobkowski's chain-length dependence correlation function [Z. Dobkowski, Eur. Polym. J. 18, 563 (1982)]. The density and the isokinetic temperature, based on the canonical definition of the laboratory glass-transition, can be described well by the correlation function and a subtle behavior manifests as the architecture becomes more complex. For linear polymer chains and low functionality star polymers, we find that an increase of the arm length would result in an increase of the density and the isokinetic temperature, but high functionality star polymers have the opposite behavior. The effect between low and high functionalities is more pronounced for short arm lengths. Complementary results such as the specific volume and number of neighbors in contact provide further insights on the subtle relation between structure and dynamics. The findings would be valuable to polymer, colloidal, and nanocomposites fields for the design of materials in absence of solution with the desired properties.

  20. Structure and dynamical intra-molecular heterogeneity of star polymer melts above glass transition temperature

    NASA Astrophysics Data System (ADS)

    Chremos, Alexandros; Glynos, Emmanouil; Green, Peter F.

    2015-01-01

    Structural and dynamical properties of star melts have been investigated with molecular dynamics simulations of a bead-spring model. Star polymers are known to be heterogeneous, but a systematic simulation study of their properties in melt conditions near the glass transition temperature was lacking. To probe their properties, we have expanded from linear to star polymers the applicability of Dobkowski's chain-length dependence correlation function [Z. Dobkowski, Eur. Polym. J. 18, 563 (1982)]. The density and the isokinetic temperature, based on the canonical definition of the laboratory glass-transition, can be described well by the correlation function and a subtle behavior manifests as the architecture becomes more complex. For linear polymer chains and low functionality star polymers, we find that an increase of the arm length would result in an increase of the density and the isokinetic temperature, but high functionality star polymers have the opposite behavior. The effect between low and high functionalities is more pronounced for short arm lengths. Complementary results such as the specific volume and number of neighbors in contact provide further insights on the subtle relation between structure and dynamics. The findings would be valuable to polymer, colloidal, and nanocomposites fields for the design of materials in absence of solution with the desired properties.

  1. Subnanometre enzyme mechanics probed by single-molecule force spectroscopy

    NASA Astrophysics Data System (ADS)

    Pelz, Benjamin; Žoldák, Gabriel; Zeller, Fabian; Zacharias, Martin; Rief, Matthias

    2016-02-01

    Enzymes are molecular machines that bind substrates specifically, provide an adequate chemical environment for catalysis and exchange products rapidly, to ensure fast turnover rates. Direct information about the energetics that drive conformational changes is difficult to obtain. We used subnanometre single-molecule force spectroscopy to study the energetic drive of substrate-dependent lid closing in the enzyme adenylate kinase. Here we show that in the presence of the bisubstrate inhibitor diadenosine pentaphosphate (AP5A), closing and opening of both lids is cooperative and tightly coupled to inhibitor binding. Surprisingly, binding of the substrates ADP and ATP exhibits a much smaller energetic drive towards the fully closed state. Instead, we observe a new dominant energetic minimum with both lids half closed. Our results, combining experiment and molecular dynamics simulations, give detailed mechanical insights into how an enzyme can cope with the seemingly contradictory requirements of rapid substrate exchange and tight closing, to ensure efficient catalysis.

  2. Probing protein mechanical stability with controlled shear flows

    NASA Astrophysics Data System (ADS)

    Dusting, Jonathan; Ashton, Lorna; Leontini, Justin; Blanch, Ewan; Balabani, Stavroula

    2009-11-01

    Understanding and controlling protein aggregation or misfolding is of both fundamental and medical interest. The structural changes experienced by proteins in response to forces such as those generated within flows have not been well characterised, despite the importance of mechanics in many biological processes. By monitoring the structural conformation of proteins in different concentric cylinder flows using Raman Spectroscopy we have quantified the relative stability of β-sheet dominated proteins compared with those containing a greater proportion of α-helix. To ensure that the fluid stresses are quantified accurately, a combined DNS and PIV approach has been undertaken for flow cell characterisation across the full range of operating Re. This is important for practical concentric cylinder geometries where the shear components are non-zero and spatially dependent, with the peak stresses located near the endwalls. Furthermore, recirculation regions appear well below the crtical Reynolds number for Taylor vortex formation.

  3. Subnanometre enzyme mechanics probed by single-molecule force spectroscopy

    PubMed Central

    Pelz, Benjamin; Žoldák, Gabriel; Zeller, Fabian; Zacharias, Martin; Rief, Matthias

    2016-01-01

    Enzymes are molecular machines that bind substrates specifically, provide an adequate chemical environment for catalysis and exchange products rapidly, to ensure fast turnover rates. Direct information about the energetics that drive conformational changes is difficult to obtain. We used subnanometre single-molecule force spectroscopy to study the energetic drive of substrate-dependent lid closing in the enzyme adenylate kinase. Here we show that in the presence of the bisubstrate inhibitor diadenosine pentaphosphate (AP5A), closing and opening of both lids is cooperative and tightly coupled to inhibitor binding. Surprisingly, binding of the substrates ADP and ATP exhibits a much smaller energetic drive towards the fully closed state. Instead, we observe a new dominant energetic minimum with both lids half closed. Our results, combining experiment and molecular dynamics simulations, give detailed mechanical insights into how an enzyme can cope with the seemingly contradictory requirements of rapid substrate exchange and tight closing, to ensure efficient catalysis. PMID:26906294

  4. Probing the mechanical properties of dental porcelain through nanoindentation

    NASA Astrophysics Data System (ADS)

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

    2012-11-01

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

  5. Mechanical design control and implementation of a new movable diagnostic probe for the TRIUMF cyclotron

    SciTech Connect

    Ries, T.C.

    1994-10-10

    A new movable probe has been installed into the TRIUMF H{sup {minus}} cyclotron. It is intended to measure the distribution of betatron amplitudes, in the vertical plane, of the circulating beam and to scrape halo. The probe, however, may also be scanned in the radial direction. The head may be positioned vertically and horizontally to an accuracy of 0.002{double_prime}. The device is mechanically modular to facilitate fast and easy handling for maintenance in a radioactive area. The beam sensor on the probe head is a 1.25{double_prime}{times}3{double_prime}{times}0.003{double_prime} tantalum foil and its overall coverage is 3.00{double_prime}{times}7.25{double_prime} in a vertical plane orthogonal to, and crossing through the beam orbit plane. Presently its radial center line location corresponds to a proton beam energy of about 430 MeV at radius 296{double_prime}, however, the probe device may be easily relocated to operate from any 4{double_prime} port, and, with an adaptor port flange, may be installed into any port in the cyclotron vacuum tank. A stationary catcher below the probe path collects those electrons stripped from the H{sup {minus}} beam and scattered out from the probe head. The probe axis is vertical and the tank aperture is narrow so a worm gear arrangement combined with a modified ``Evans``-parallel linkage mechanism is used to transform vertical rotary motion into horizontal linear motion. The actuators are dc servo motors with tachometers driven by pulse width modulated servo amplifiers. Position sensing is done by variable reluctance type absolute rotary encoders and the higher level positioning is performed by TRIMAC based control software. The precision of movement and jitter was measured in the laboratory. Examples will be given of the probe use with beam.

  6. Mechanical design control and implementation of a new movable diagnostic probe for the TRIUMF cyclotron

    NASA Astrophysics Data System (ADS)

    Ries, Thomas C.

    1994-10-01

    A new movable probe has been installed into the TRIUMF H- cyclotron. It is intended to measure the distribution of betatron amplitudes, in the vertical plane, of the circulating beam and to scrape halo. The probe, however, may also be scanned in the radial direction. The head may be positioned vertically and horizontally to an accuracy of 0.002`. The device is mechanically modular to facilitate fast and easy handling for maintenance in a radioactive area. The beam sensor on the probe head is a 1.25`×3`×0.003` tantalum foil and its overall coverage is 3.00`×7.25` in a vertical plane orthogonal to, and crossing through the beam orbit plane. Presently its radial center line location corresponds to a proton beam energy of about 430 MeV at radius 296`, however, the probe device may be easily relocated to operate from any 4` port, and, with an adaptor port flange, may be installed into any port in the cyclotron vacuum tank. A stationary catcher below the probe path collects those electrons stripped from the H- beam and scattered out from the probe head. The probe axis is vertical and the tank aperture is narrow so a worm gear arrangement combined with a modified ``Evans''-parallel linkage mechanism is used to transform vertical rotary motion into horizontal linear motion. The actuators are dc servo motors with tachometers driven by pulse width modulated servo amplifiers. Position sensing is done by variable reluctance type absolute rotary encoders and the higher level positioning is performed by TRIMAC based control software. The precision of movement and jitter was measured in the laboratory. Examples will be given of the probe use with beam.

  7. Probing mechanical principles of cell-nanomaterial interactions

    NASA Astrophysics Data System (ADS)

    Gao, Huajian

    2014-01-01

    With the rapid development of nanotechnology, various types of nanoparticles, nanowires, nanofibers, nanotubes, and atomically thin plates and sheets have emerged as candidates for an ever increasing list of potential applications for next generation electronics, microchips, composites, barrier coatings, biosensors, drug delivery, and energy harvesting and conversion systems. There is now an urgent societal need to understand both beneficial and hazardous effects of nanotechnology which is projected to produce and release thousands of tons of nanomaterials into the environment in the coming decades. This paper aims to present an overview of some recent studies conducted at Brown University on the mechanics of cell-nanomaterial interactions, including the modeling of nanoparticles entering cells by receptor-mediated endocytosis and coarse-grained molecular dynamics simulations of nanoparticles interacting with cell membranes. The discussions will be organized around the following questions: Why and how does cellular uptake of nanoparticles depend on particle size, shape, elasticity and surface structure? In particular, we will discuss the effect of nanoparticle size on receptor-mediated endocytosis, the effect of elastic stiffness on cell-particle interactions, how high aspect ratio nanomaterials such as carbon nanotubes and graphenes enter cells and how different geometrical patterns of ligands on a nanoparticle can be designed to control the rate of particle uptake.

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

    PubMed

    Lammerding, Jan; Lee, Richard T

    2009-01-01

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

  9. Telomere elongation involves intra-molecular DNA replication in cells utilizing alternative lengthening of telomeres

    PubMed Central

    Muntoni, Alessandra; Neumann, Axel A.; Hills, Mark; Reddel, Roger R.

    2009-01-01

    Alternative lengthening of telomeres (ALT) is a telomere length maintenance mechanism based on recombination, where telomeres use other telomeric DNA as a template for DNA synthesis. About 10% of all human tumors depend on ALT for their continued growth, and understanding its molecular details is critically important for the development of cancer treatments that target this mechanism. We have previously shown that telomeres of ALT-positive human cells can become lengthened via inter-telomeric copying, i.e. by copying the telomere of another chromosome. The possibility that such telomeres could elongate by using other sources of telomeric DNA as copy templates has not been investigated previously. In this study, we have determined whether a telomere can become lengthened by copying its own sequences, without the need for using another telomere as a copy template. To test this, we transduced an ALT cell line with a telomere-targeting construct and obtained clones with a single tagged telomere. We showed that the telomere tag can be amplified without the involvement of other telomeres, indicating that telomere elongation can also occur by intra-telomeric DNA copying. This is the first direct evidence that the ALT mechanism involves more than one method of telomere elongation. PMID:19095716

  10. Cyclopalladation of dimesityl selenide: synthesis, reactivity, structural characterization, isolation of an intermediate complex with C-H···Pd intra-molecular interaction and computational studies.

    PubMed

    Kolay, Siddhartha; Wadawale, Amey; Das, Dasarathi; Kisan, Hemanta K; Sunoj, Raghavan B; Jain, Vimal K

    2013-08-14

    The reaction of dimesityl selenide (Mes2Se) with either PdCl2(PhCN)2 in toluene or PdCl2 in toluene-acetonitrile yields a chloro-bridged binuclear palladium complex, [Pd2Cl2(μ-Cl)2(Mes2Se)2] (1), whereas with Na2PdCl4 in refluxing ethanol, a cyclometallated palladium complex, [Pd2(μ-Cl)2{MesSeC6H2(Me2)CH2}2] (2) is afforded. 2 can also be obtained when 1 is refluxed in ethanol. On treatment with Pb(Epy)2 in dichloromethane, 2 afforded the Epy-bridged binuclear complexes, [Pd2(μ-Epy)2{MesSeC6H2(Me2)CH2}2] (3; E = S (3a) or Se (3b)). Treatment of 2 with PPh3 yields a bridge-cleaved monomeric complex, [PdCl{MesSeC6H2(Me2)CH2}(PPh3)]. The molecular structures of 1-3 were established by X-ray diffraction analyses. All the complexes are dimeric, with the palladium atoms acquiring a distorted square planar configuration. There are intra-molecular C-H···Pd interactions (d(M-H): 2.75 Å and mechanism of formation of the dimeric species 2 is examined using DFT (B3LYP) computations.

  11. Low Energy Electrons as Probing Tool for Astrochemical Reaction Mechanisms

    NASA Astrophysics Data System (ADS)

    Hendrik Bredehöft, Jan; Swiderek, Petra; Hamann, Thorben

    The complexity of molecules found in space varies widely. On one end of the scale of molecular complexity is the hydrogen molecule H2 . Its formation from H atoms is if not understood than at least thoroughly investigated[1]. On the other side of said spectrum the precursors to biopolymers can be found, such as amino acids[2,3], sugars[4], lipids, cofactors[5], etc, and the kerogen-like organic polymer material in carbonaceous meteorites called "black stuff" [6]. These have also received broad attention in the last decades. Sitting in the middle between these two extremes are simple molecules that are observed by radio astronomy throughout the Universe. These are molecules like methane (CH4 ), methanol (CH3 OH), formaldehyde (CH2 O), hydrogen cyanide (HCN), and many many others. So far more than 40 such species have been identified.[7] They are often used in laboratory experiments to create larger complex molecules on the surface of simulated interstellar dust grains.[2,8] The mechanisms of formation of these observed starting materials for prebiotic chemistry is however not always clear. Also the exact mechanisms of formation of larger molecules in photochemical experiments are largely unclear. This is mostly due to the very complex chemistry going on which involves many different radicals and ions. The creation of radicals and ions can be studied in detail in laboratory simulations. They can be created in a setup mimicking interstellar grain chemistry using slow electrons. There is no free electron radiation in space. What can be found though is a lot of radiation of different sorts. There is electromagnetic radiation (UV light, X-Rays, rays, etc.) and there is particulate radiation as well in the form of high energy ions. This radiation can provide energy that drives chemical reactions in the ice mantles of interstellar dust grains. And while the multitude of different kinds of radiation might be a little confusing, they all have one thing in common: Upon

  12. Sharipov holds the probe-and-cone docking mechanism in the SM during Expedition 10

    NASA Image and Video Library

    2005-03-03

    ISS010-E-19105 (3 March 2005) --- Cosmonaut Salizhan S. Sharipov, Expedition 10 flight engineer representing Russia's Federal Space Agency, holds the Progress supply vehicle probe-and-cone docking mechanism in the Zvezda Service Module of the International Space Station (ISS).

  13. PERSPECTIVE: Intra-molecular chaperone: the role of the N-terminal in conformational selection and kinetic control

    NASA Astrophysics Data System (ADS)

    Tsai, Chung-Jung; Ma, Buyong; Nussinov, Ruth

    2009-03-01

    The vast majority of the proteins in nature are under thermodynamic control, consistent with the universally accepted notion that proteins exist in their thermodynamically most stable state. Yet, recently a number of examples of proteins whose fold is under kinetic control have come to light. Their functions and environments vary. The first among these are some proteases, discovered in the early 1990s. There, an N-terminal proregion is self-cleaved after the protein folded, leaving the remainder of the chain in a kinetically trapped state. A related scenario was observed for microcin J25, an antibacterial peptide. This peptide presents a trapped covalently knotted conformation. The third and the most recently discovered case is the multidrug-resistant transporter protein, P-glycoprotein. There, a synonymous 'silent' mutation leads to ribosome stalling with a consequent altered kinetically trapped state. Here we argue that in all three examples, the N-terminal plays the role of an intra-molecular chaperone, that is, the N-terminal conformation selects among all competing local conformations of a downstream segment. By providing a pattern, the N-terminal chaperone segment assists the protein folding process. If the N-terminal is subsequently cleaved, the protein can be under kinetic control, since it is trapped in a thermodynamically less-stable state.

  14. PTM-driven differential peptide display: survey of peptides containing inter/intra-molecular disulfide bridges in frog venoms.

    PubMed

    Evaristo, Geisa P C; Verhaert, Peter D E M; Pinkse, Martijn W H

    2012-12-21

    Amphibian defensive skin secretions are complex species-specific mixtures of biologically active molecules, including many uncharacterized peptides. Many of these peptides are post-translationally modified and amongst the modifications discovered so far on amphibian defense peptides, disulfide bonds are quite frequently encountered. The presence of this PTM often complicates the MS-based sequencing. Here we demonstrate a method to target peptides containing inter/intra-molecular S-S bonds applying a PTM-driven differential display. Upon reduction of the disulfide bond both molecular mass and retention time of a peptide are altered. Assembling the LC-MS data by plotting the m/z data against retention time generates a peptide display and overlaying peptide displays of untreated and DTT-reduced material yields a differential display. From such an overlay, peptides originally carrying a disulfide bond are recognized due to the shift in both retention time and m/z values, whereas non cystine containing peptides remain unaltered in the differential display. The success of this approach is demonstrated by the visualization of the cystines-containing peptides in the skin secretion of Odorrana schmackeri, Phyllomedusa burmeisteri, Phyllomedusa rohdei, Kassina senegalensis, and Bombina variegata. The venoms from these different species yield complicated differential displays, showing interesting peptides, allowing one to target them for more detailed structural characterization. Copyright © 2012 Elsevier B.V. All rights reserved.

  15. Intra-molecular cohesion of coils mediated by phenylalanine-glycine motifs in the natively unfolded domain of a nucleoporin

    SciTech Connect

    Krishnan, V V; Lau, E Y; Yamada, J; Denning, D P; Patel, S S; Colvin, M E; Rexach, M F

    2007-04-19

    The nuclear pore complex (NPC) provides the sole aqueous conduit for macromolecular exchange between the nucleus and cytoplasm of cells. Its conduit contains a size-selective gate and is populated by a family of NPC proteins that feature long natively-unfolded domains with phenylalanine-glycine repeats. These FG nucleoporins play key roles in establishing the NPC permeability barrier, but little is known about their dynamic structure. Here we used molecular modeling and biophysical techniques to characterize the dynamic ensemble of structures of a representative FG domain from the yeast nucleoporin Nup116. The results show that its FG motifs function as intra-molecular cohesion elements that impart order to the FG domain. The cohesion of coils mediated by FG motifs in the natively unfolded domain of Nup116 supports a type of tertiary structure, a native pre-molten globule, that could become quaternary at the NPC through recruitment of neighboring FG nucleoporins, forming one cohesive meshwork of intertwined filaments capable of gating protein diffusion across the NPC by size exclusion.

  16. Inter- and intra-molecular interactions of Arabidopsis thaliana DELLA protein RGL1

    PubMed Central

    Sheerin, David J.; Buchanan, Jeremy; Kirk, Chris; Harvey, Dawn; Sun, Xiaolin; Spagnuolo, Julian; Li, Sheng; Liu, Tong; Woods, Virgil A.; Foster, Toshi; Jones, William T.; Rakonjac, Jasna

    2011-01-01

    The phytohormone gibberellin and the DELLA proteins act together to control key aspects of plant development. Gibberellin induces degradation of DELLA proteins by recruitment of an F-box protein using a molecular switch: a gibberellin-bound nuclear receptor interacts with the N-terminal domain of DELLA proteins, and this event primes the DELLA C-terminal domain for interaction with the F-box protein. However, the mechanism of signalling between the N- and C-terminal domains of DELLA proteins is unresolved. In the present study, we used in vivo and in vitro approaches to characterize di- and tri-partite interactions of the DELLA protein RGL1 (REPRESSOR OF GA1-3-LIKE 1) of Arabidopsis thaliana with the gibberellin receptor GID1A (GIBBERELLIC ACID-INSENSITIVE DWARF-1A) and the F-box protein SLY1 (SLEEPY1). Deuterium-exchange MS unequivocally showed that the entire N-terminal domain of RGL1 is disordered prior to interaction with the GID1A; furthermore, association/dissociation kinetics, determined by surface plasmon resonance, predicts a two-state conformational change of the RGL1 N-terminal domain upon interaction with GID1A. Additionally, competition assays with monoclonal antibodies revealed that contacts mediated by the short helix Asp-Glu-Leu-Leu of the hallmark DELLA motif are not essential for the GID1A–RGL1 N-terminal domain interaction. Finally, yeast two- and three-hybrid experiments determined that unabated communication between N- and C-terminal domains of RGL1 is required for recruitment of the F-box protein SLY1. PMID:21323638

  17. Self-curable solid-state elastic dye lasers capable of mechanical stress probing.

    PubMed

    Yang, Yu; Liao, Zhifu; Zhou, Yuan; Cui, Yuanjing; Qian, Guodong

    2013-05-15

    Herein, a highly sensitive stress probe is reported based on pyrromethene 597 (PM597) doped elastic polydimethylsiloxane films. By sandwiching the dye doped elastic film with two plano dichromatic mirrors, a solid-sate microcavity laser with low laser threshold (~0.2 μJ) is presented as a straightforward probing method for mechanical stress, which is monitored by the laser output spectra, demonstrating a resolution limit higher than 0.01 MPa. The photostability of PM597 doped into the microcavity laser is higher than 7222 GJ/mol, which is among the highest record ever reported to our knowledge and a fast self-recovery on the laser output in less than 1 h, attributed to diffusion of dye molecules is observed, indicating a practical durability for such stress probes.

  18. Lighting Up the Force: Investigating Mechanisms of Mechanotransduction Using Fluorescent Tension Probes

    PubMed Central

    Jurchenko, Carol

    2015-01-01

    The ability of cells to sense the physical nature of their surroundings is critical to the survival of multicellular organisms. Cellular response to physical cues from adjacent cells and the extracellular matrix leads to a dynamic cycle in which cells respond by remodeling their local microenvironment, fine-tuning cell stiffness, polarity, and shape. Mechanical regulation is important in cellular development, normal morphogenesis, and wound healing. The mechanisms by which these finely balanced mechanotransduction events occur, however, are not well understood. In large part, this is due to the limited availability of tools to study molecular mechanotransduction events in live cells. Several classes of molecular tension probes have been recently developed which are rapidly transforming the study of mechanotransduction. Molecular tension probes are primarily based on fluorescence resonance energy transfer (FRET) and report on piconewton scale tension events in live cells. In this minireview, we describe the two main classes of tension probes, genetically encoded tension sensors and immobilized tension sensors, and discuss the advantages and limitations of each type. We discuss future opportunities to address major biological questions and outline the challenges facing the next generation of molecular tension probes. PMID:26031334

  19. Braided multi-electrode probes: mechanical compliance characteristics and recordings from spinal cords

    PubMed Central

    Kim, Taegyo; Branner, Almut; Gulati, Tanuj

    2013-01-01

    Objective To test a novel braided multi-electrode probe design with compliance exceeding that of a 50-micron microwire, thus reducing micromotion and macromotion induced tissue stress. Approach We use up to 24 ultra-fine wires interwoven into a tubular braid to obtain a highly flexible multi-electrode probe. The tether-portion wires are simply non-braided extensions of the braid structure, allowing the microprobe to follow gross neural tissue movements. Mechanical calculation and direct measurements evaluated bending stiffness and axial compression forces in the probe and tether system. These were compared to 50μm Nichrome microwire standards. Recording tests were performed in decerebrate animals. Main results Mechanical bending tests on braids comprising 9.6μm or 12.7μm Nichrome wires showed that implants (braided portions) had 4 to 21 times better mechanical compliance than a single 50μm wire and non-braided tethers were 6 to 96 times better. Braided microprobes yielded robust neural recordings from animals’ spinal cords throughout cord motions. Significance Microwire electrode arrays that can record and withstand tissue micro- and macromotion of spinal cord tissues are demonstrated. This technology may provide a stable chronic neural interface into spinal cords of freely moving animals, is extensible to various applications, and may reduce mechanical tissue stress. PMID:23723128

  20. Braided multi-electrode probes: mechanical compliance characteristics and recordings from spinal cords

    NASA Astrophysics Data System (ADS)

    Kim, Taegyo; Branner, Almut; Gulati, Tanuj; Giszter, Simon F.

    2013-08-01

    Objective. To test a novel braided multi-electrode probe design with compliance exceeding that of a 50 µm microwire, thus reducing micromotion- and macromotion-induced tissue stress. Approach. We use up to 24 ultra-fine wires interwoven into a tubular braid to obtain a highly flexible multi-electrode probe. The tether-portion wires are simply non-braided extensions of the braid structure, allowing the microprobe to follow gross neural tissue movements. Mechanical calculation and direct measurements evaluated bending stiffness and axial compression forces in the probe and tether system. These were compared to 50 µm nichrome microwire standards. Recording tests were performed in decerebrate animals. Main results. Mechanical bending tests on braids comprising 9.6 or 12.7 µm nichrome wires showed that implants (braided portions) had 4 to 21 times better mechanical compliance than a single 50 µm wire and non-braided tethers were 6 to 96 times better. Braided microprobes yielded robust neural recordings from animals' spinal cords throughout cord motions. Significance. Microwire electrode arrays that can record and withstand tissue micro- and macromotion of spinal cord tissues are demonstrated. This technology may provide a stable chronic neural interface into spinal cords of freely moving animals, is extensible to various applications, and may reduce mechanical tissue stress.

  1. Probing the mechanics of the complete DNA transcription cycle in real-time using optical tweezers.

    PubMed

    Baumann, Christoph G; Cross, Stephen J

    2011-01-01

    RNA polymerase (RNAP) is a DNA-dependent motor protein that links ribonucleotide polymerization to force generation and DNA translocation through its active site, i.e., mechanical work. Single-molecule studies using optical tweezers have allowed researchers to probe the load-dependent ribonucleotide incorporation rate and processivity of both single-subunit viral and multisubunit prokaryotic and eukaryotic RNAPs engaged in transcription elongation. A single-molecule method is described here, which allows the complete transcription cycle (i.e., promoter binding, initiation, elongation and termination) to be followed in real-time using dual-trap optical tweezers and a unique "three-bead" geometry. This single-molecule transcription assay can be used to probe the mechanics of both stationary and moving RNAP-DNA complexes engaged in different stages of transcription.

  2. Phillips with probe-and-cone docking mechanism (StM) in the Zvezda module

    NASA Image and Video Library

    2005-06-19

    ISS011-E-09205 (19 June 2005) --- Astronaut John L. Phillips, Expedition 11 NASA ISS science officer and flight engineer, works on the dismantled probe-and-cone docking mechanism from the Progress 18 spacecraft in the Zvezda Service Module of the International Space Station (ISS). The Progress docked to the aft port of the Service Module at 7:42 p.m. (CDT) as the two spacecraft flew approximately 225 statute miles, above a point near Beijing, China.

  3. Krikalev with probe-and-cone docking mechanism (StM) in the Zvezda module

    NASA Image and Video Library

    2005-06-19

    ISS011-E-09210 (19 June 2005) --- Cosmonaut Sergei K. Krikalev, Expedition 11 commander representing Russia's Federal Space Agency, holds the dismantled probe-and-cone docking mechanism from the Progress 18 spacecraft in the Zvezda Service Module of the International Space Station (ISS). The Progress docked to the aft port of the Service Module at 7:42 p.m. (CDT) as the two spacecraft flew approximately 225 statute miles, above a point near Beijing, China.

  4. Probing wave function collapse models with a classically driven mechanical oscillator

    NASA Astrophysics Data System (ADS)

    Ho, Melvyn; Lafont, Ambroise; Sangouard, Nicolas; Sekatski, Pavel

    2016-03-01

    We show that the interaction of a pulsed laser light with a mechanical oscillator through the radiation pressure results in an opto-mechanical entangled state in which the photon number is correlated with the oscillator position. Interestingly, the mechanical oscillator can be delocalized over a large range of positions when driven by an intense laser light. This provides a simple yet sensitive method to probe hypothetical post-quantum theories including an explicit wave function collapse model, like the Diosi & Penrose model. We propose an entanglement witness to reveal the quantum nature of this opto-mechanical state as well as an optical technique to record the decoherence of the mechanical oscillator. We also report on a detailed feasibility study giving the experimental challenges that need to be overcome in order to confirm or rule out predictions from explicit wave function collapse models.

  5. Probe Scanning Support System by a Parallel Mechanism for Robotic Echography

    NASA Astrophysics Data System (ADS)

    Aoki, Yusuke; Kaneko, Kenta; Oyamada, Masami; Takachi, Yuuki; Masuda, Kohji

    We propose a probe scanning support system based on force/visual servoing control for robotic echography. First, we have designed and formulated its inverse kinematics the construction of mechanism. Next, we have developed a scanning method of the ultrasound probe on body surface to construct visual servo system based on acquired echogram by the standalone medical robot to move the ultrasound probe on patient abdomen in three-dimension. The visual servo system detects local change of brightness in time series echogram, which is stabilized the position of the probe by conventional force servo system in the robot, to compensate not only periodical respiration motion but also body motion. Then we integrated control method of the visual servo with the force servo as a hybrid control in both of position and force. To confirm the ability to apply for actual abdomen, we experimented the total system to follow the gallbladder as a moving target to keep its position in the echogram by minimizing variation of reaction force on abdomen. As the result, the system has a potential to be applied to automatic detection of human internal organ.

  6. A servomechanism for a micro-electro-mechanical-system-based scanning-probe data storage device

    NASA Astrophysics Data System (ADS)

    Pantazi, A.; Lantz, M. A.; Cherubini, G.; Pozidis, H.; Eleftheriou, E.

    2004-10-01

    Micro-electro-mechanical-system (MEMS)-based scanning-probe data storage devices are emerging as potential ultra-high-density, low-access-time, and low-power alternatives to conventional data storage. One implementation of probe-based storage uses thermomechanical means to store and retrieve information in thin polymer films. One of the challenges in building such devices is the extreme accuracy and the short latency required in the navigation of the probes over the polymer medium. This paper focuses on the design and characterization of a servomechanism to achieve such accurate positioning in a probe-based storage prototype. In our device, the polymer medium is positioned on a MEMS scanner with x/y-motion capabilities of about 100 µm. The device also includes thermal position sensors that provide x/y-position information to the servo controller. Based on a discrete state-space model of the scanner dynamics, a controller is designed using the linear quadratic Gaussian approach with state estimation. The random seek performance of this approach is evaluated and compared with that of the conventional proportional, integrator, and derivative (PID) approach. The results demonstrate the superiority of the state-space approach, which achieves seek times of about 4 ms in a ± 50 µm range. Finally, the experimental results show that closed-loop track following using the thermal position-sensor signals is feasible and yields a position-error standard deviation of approximately 2 nm.

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

    PubMed

    Sander, Mathias; Flesch, Julia; Ott, Albrecht

    2015-01-01

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

  8. Using optical forces to probe mechanical response from single molecules to biomaterials

    NASA Astrophysics Data System (ADS)

    Forde, Nancy

    2010-10-01

    In the past decade, the ability to manipulate and measure forces exerted by single biological molecules has transformed our understanding of their mechanical response, stability, and the mechanisms by which they operate. One of the essential tools in this revolution has been optical tweezers, which use a focused laser beam to ``trap'' (hold stably in three dimensions) micrometer-sized refractive particles. In this talk, I will briefly describe how optical tweezers work and how they can be used to manipulate and probe the mechanical response of single DNA and protein molecules. I will then describe the technique of holographic optical tweezers, which modify the phase of a laser beam in order to generate multiple optical traps at specified locations in three dimensions within a sample. I will discuss our work towards applying this technique to mechanical studies of protein-based biomaterials on the microscale.

  9. Second-order decoherence mechanisms of a transmon qubit probed with thermal microwave states

    NASA Astrophysics Data System (ADS)

    Goetz, J.; Deppe, F.; Eder, P.; Fischer, M.; Müting, M.; Puertas Martínez, J.; Pogorzalek, S.; Wulschner, F.; Xie, E.; Fedorov, K. G.; Marx, A.; Gross, R.

    2017-06-01

    Thermal microwave states are omnipresent noise sources in superconducting quantum circuits covering all relevant frequency regimes. We use them as a probe to identify three second-order decoherence mechanisms of a superconducting transmon qubit. First, we quantify the efficiency of a resonator filter in the dispersive Jaynes-Cummings regime and find evidence for parasitic loss channels. Second, we probe second-order noise in the low-frequency regime and demonstrate the expected T 3 temperature dependence of the qubit dephasing rate. Finally, we show that qubit parameter fluctuations due to two-level states are enhanced under the influence of thermal microwave states. In particular, we experimentally confirm the T 2-dependence of the fluctuation spectrum expected for noninteracting two-level states.

  10. Unravelling the quenching mechanisms of a luminescent Ru(II) probe for Cu(II).

    PubMed

    Santos, André Ribeiro; Escudero, Daniel; González, Leticia; Orellana, Guillermo

    2015-03-01

    We have investigated the photophysical and photochemical features of a luminescent heteroleptic Ru(II)-polypyridyl probe and of its corresponding Ru(II)-Cu(II) dinuclear complex formed upon the analyte binding through extensive density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations. The molecular probe contains the tailored imidazo[4,5-f]-1,10-phenanthroline (IIP) ligand for simultaneously binding the Ru(II) core and the target metal ion in aqueous solution. We have rationalized the static photoluminescence quenching observed upon the Cu(II) coordination, on the grounds of distinct excited state deactivation mechanisms which are absent in the free Ru(II) complex probe. Additionally, the emission quenching found upon increasing the solution pH has also been investigated. When coordinated IIP deprotonates, the nature of the lowest excited state of its complex changes from (3)MLCT to (3)LLCT/(3)IL. The strong base-induced emission quenching can be understood in terms of both the energy-gap law, since the (3)LLCT/(3)IL states lie at a significantly lower energy than the (3)MLCT state increasing the contribution of non-radiative mechanisms, and the expected slower radiative rates from such (3)LLCT/(3)IL states. After Cu(II) binding, the lowest triplet excited state is similar to the analyte-free probe in both energy and electronic nature. However, Cu-centered non-radiative excited states, populated after photoinduced electron transfer and intersystem crossing processes, are responsible for the population drainage of the emissive state.

  11. 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.

  12. The Mechanisms and Biomedical Applications of an NIR BODIPY-Based Switchable Fluorescent Probe.

    PubMed

    Cheng, Bingbing; Bandi, Venugopal; Yu, Shuai; D'Souza, Francis; Nguyen, Kytai T; Hong, Yi; Tang, Liping; Yuan, Baohong

    2017-02-11

    Highly environment-sensitive fluorophores have been desired for many biomedical applications. Because of the noninvasive operation, high sensitivity, and high specificity to the microenvironment change, they can be used as excellent probes for fluorescence sensing/imaging, cell tracking/imaging, molecular imaging for cancer, and so on (i.e., polarity, viscosity, temperature, or pH measurement). In this work, investigations of the switching mechanism of a recently reported near-infrared environment-sensitive fluorophore, ADP(CA)₂, were conducted. Besides, multiple potential biomedical applications of this switchable fluorescent probe have been demonstrated, including wash-free live-cell fluorescence imaging, in vivo tissue fluorescence imaging, temperature sensing, and ultrasound-switchable fluorescence (USF) imaging. The fluorescence of the ADP(CA)₂ is extremely sensitive to the microenvironment, especially polarity and viscosity. Our investigations showed that the fluorescence of ADP(CA)₂ can be switched on by low polarity, high viscosity, or the presence of protein and surfactants. In wash-free live-cell imaging, the fluorescence of ADP(CA)₂ inside cells was found much brighter than the dye-containing medium and was retained for at least two days. In all of the fluorescence imaging applications conducted in this study, high target-to-noise (>5-fold) was achieved. In addition, a high temperature sensitivity (73-fold per Celsius degree) of ADP(CA)₂-based temperature probes was found in temperature sensing.

  13. The Mechanisms and Biomedical Applications of an NIR BODIPY-Based Switchable Fluorescent Probe

    PubMed Central

    Cheng, Bingbing; Bandi, Venugopal; Yu, Shuai; D’Souza, Francis; Nguyen, Kytai T.; Hong, Yi; Tang, Liping; Yuan, Baohong

    2017-01-01

    Highly environment-sensitive fluorophores have been desired for many biomedical applications. Because of the noninvasive operation, high sensitivity, and high specificity to the microenvironment change, they can be used as excellent probes for fluorescence sensing/imaging, cell tracking/imaging, molecular imaging for cancer, and so on (i.e., polarity, viscosity, temperature, or pH measurement). In this work, investigations of the switching mechanism of a recently reported near-infrared environment-sensitive fluorophore, ADP(CA)2, were conducted. Besides, multiple potential biomedical applications of this switchable fluorescent probe have been demonstrated, including wash-free live-cell fluorescence imaging, in vivo tissue fluorescence imaging, temperature sensing, and ultrasound-switchable fluorescence (USF) imaging. The fluorescence of the ADP(CA)2 is extremely sensitive to the microenvironment, especially polarity and viscosity. Our investigations showed that the fluorescence of ADP(CA)2 can be switched on by low polarity, high viscosity, or the presence of protein and surfactants. In wash-free live-cell imaging, the fluorescence of ADP(CA)2 inside cells was found much brighter than the dye-containing medium and was retained for at least two days. In all of the fluorescence imaging applications conducted in this study, high target-to-noise (>5-fold) was achieved. In addition, a high temperature sensitivity (73-fold per Celsius degree) of ADP(CA)2-based temperature probes was found in temperature sensing. PMID:28208666

  14. Mechanisms of small molecule–DNA interactions probed by single-molecule force spectroscopy

    PubMed Central

    Almaqwashi, Ali A.; Paramanathan, Thayaparan; Rouzina, Ioulia; Williams, Mark C.

    2016-01-01

    There is a wide range of applications for non-covalent DNA binding ligands, and optimization of such interactions requires detailed understanding of the binding mechanisms. One important class of these ligands is that of intercalators, which bind DNA by inserting aromatic moieties between adjacent DNA base pairs. Characterizing the dynamic and equilibrium aspects of DNA-intercalator complex assembly may allow optimization of DNA binding for specific functions. Single-molecule force spectroscopy studies have recently revealed new details about the molecular mechanisms governing DNA intercalation. These studies can provide the binding kinetics and affinity as well as determining the magnitude of the double helix structural deformations during the dynamic assembly of DNA–ligand complexes. These results may in turn guide the rational design of intercalators synthesized for DNA-targeted drugs, optical probes, or integrated biological self-assembly processes. Herein, we survey the progress in experimental methods as well as the corresponding analysis framework for understanding single molecule DNA binding mechanisms. We discuss briefly minor and major groove binding ligands, and then focus on intercalators, which have been probed extensively with these methods. Conventional mono-intercalators and bis-intercalators are discussed, followed by unconventional DNA intercalation. We then consider the prospects for using these methods in optimizing conventional and unconventional DNA-intercalating small molecules. PMID:27085806

  15. Probing cell mechanics with subcellular laser dissection of actomyosin networks in the early developing Drosophila embryo.

    PubMed

    Rauzi, M; Lenne, P-F

    2015-01-01

    Laser dissection is a useful tool in developmental biology to probe mechanical forces from the subcellular to the tissue/embryo scale. During tissue morphogenesis, cells are equipped with networks of actomyosin that generate forces. Here we present a technique based on near-infrared (NIR) femtosecond (fs) pulsed laser dissection that allows subcellular ablation of actomyosin networks. This technique allows to selectively ablate actomyosin networks while preserving cell plasma membrane. The resulting relaxation of the remaining network after laser dissection is imaged and analyzed to deduce local forces responsible for tissue morphogenesis in the developing Drosophila embryo.

  16. A new method of probing mechanical losses of coatings at cryogenic temperatures

    NASA Astrophysics Data System (ADS)

    Galliou, Serge; Deléglise, Samuel; Goryachev, Maxim; Neuhaus, Leonhard; Cagnoli, Gianpietro; Zerkani, Salim; Dolique, Vincent; Bon, Jérémy; Vacheret, Xavier; Abbé, Philippe; Pinard, Laurent; Michel, Christophe; Karassouloff, Thibaut; Briant, Tristan; Cohadon, Pierre-François; Heidmann, Antoine; Tobar, Michael E.; Bourquin, Roger

    2016-12-01

    A new method of probing mechanical losses and comparing the corresponding deposition processes of metallic and dielectric coatings in 1-100 MHz frequency range and cryogenic temperatures is presented. The method is based on the use of high-quality quartz acoustic cavities whose internal losses are orders of magnitude lower than any available coating nowadays. The approach is demonstrated for chromium, chromium/gold, and multilayer tantala/silica coatings. The Ta2O5/SiO2 coating has been found to exhibit a loss angle lower than 1.6 × 10-5 near 30 MHz at 4 K. The results are compared to the previous measurements.

  17. Probing cell structure responses through a shear and stretching mechanical stimulation technique.

    PubMed

    Steward, Robert L; Cheng, Chao-Min; Wang, Danny L; LeDuc, Philip R

    2010-04-01

    Cells are complex, dynamic systems that respond to various in vivo stimuli including chemical, mechanical, and scaffolding alterations. The influence of mechanics on cells is especially important in physiological areas that dictate what modes of mechanics exist. Complex, multivariate physiological responses can result from multi-factorial, multi-mode mechanics, including tension, compression, or shear stresses. In this study, we present a novel device based on elastomeric materials that allowed us to stimulate NIH 3T3 fibroblasts through uniaxial strip stretching or shear fluid flow. Cell shape and structural response was observed using conventional approaches such as fluorescent microscopy. Cell orientation and actin cytoskeleton alignment along the direction of applied force were observed to occur after an initial 3 h time period for shear fluid flow and static uniaxial strip stretching experiments although these two directions of alignment were oriented orthogonal relative to each other. This response was then followed by an increasingly pronounced cell and actin cytoskeleton alignment parallel to the direction of force after 6, 12, and 24 h, with 85% of the cells aligned along the direction of force after 24 h. These results indicate that our novel device could be implemented to study the effects of multiple modes of mechanical stimulation on living cells while probing their structural response especially with respect to competing directions of alignment and orientation under these different modes of mechanical stimulation. We believe that this will be important in a diversity of fields including cell mechanotransduction, cell-material interactions, biophysics, and tissue engineering.

  18. Crowding by a single bar: probing pattern recognition mechanisms in the visual periphery.

    PubMed

    Põder, Endel

    2014-11-06

    Whereas visual crowding does not greatly affect the detection of the presence of simple visual features, it heavily inhibits combining them into recognizable objects. Still, crowding effects have rarely been directly related to general pattern recognition mechanisms. In this study, pattern recognition mechanisms in visual periphery were probed using a single crowding feature. Observers had to identify the orientation of a rotated T presented briefly in a peripheral location. Adjacent to the target, a single bar was presented. The bar was either horizontal or vertical and located in a random direction from the target. It appears that such a crowding bar has very strong and regular effects on the identification of the target orientation. The observer's responses are determined by approximate relative positions of basic visual features; exact image-based similarity to the target is not important. A version of the "standard model" of object recognition with second-order features explains the main regularities of the data. © 2014 ARVO.

  19. Mechanical Response to Isotropic Shrinkage of Fibroblasts Measured by Scanning Probe Microscopy

    NASA Astrophysics Data System (ADS)

    Kawamoto, Taisuke; Haga, Hisashi; Tamura, Kazushi; Mizutani, Takeomi; Kawabata, Kazushige

    2008-07-01

    Mechanical stimuli such as cyclic stretch and fluid stress affect various cellular physiologies, including proliferation, morphology, and differentiation. We investigated cellular response to shrinking stimuli by developing an isotropic deformation device and observing cellular elasticity with mechanical scanning probe microscopy (M-SPM). The isotropic deformation device consists of a steel ring and a deformable elastic culture dish made of transparent silicone rubber. The M-SPM can visualize topography and spatial distribution of local elasticity of biomaterials in solution. Fibroblasts became softer in response to 6% shrinkage. Cell elasticity did not increase for 1 h after the shrinking stimulus. Inhibitory studies using lysophosphatidic acid and calyculin-A revealed that myosin light chain phosphatase leading to dephospholylation of myosin II regulatory light chain is involved in cell softening.

  20. Probing the Mechanism of 1,4-Conjugate Elimination Reactions Catalyzed by Terpene Synthases

    PubMed Central

    Faraldos, Juan A.; Gonzalez, Veronica; Li, Amang; Yu, Fanglei; Köksal, Mustafa; Christianson, David W.; Allemann, Rudolf K.

    2012-01-01

    The reaction mechanisms of (E)-β-farnesene synthase (EBFS) and isoprene synthase (ISPS), enzymes that catalyze a formal regioespecific 1,4-conjugate elimination of hydrogen-diphosphate from (E, E)-farnesyl and dimethylallyl diphosphate (FDP and DMADP) to generate the semiochemicals (E)-β-farnesene and isoprene, respectively, were probed with substrate analogs and kinetic measurements. The results support stepwise reaction mechanisms through analogous enzyme-bound allylic cationic intermediates. For EBFS, we demonstrate that the elimination reaction can proceed via the enzyme-bound intermediate trans-nerolidyl diphosphate, while for ISPS the intermediacy of 2-methylbut-3-enyl 2-diphosphate can be inferred from the product outcome when deuterated DMADPs are used as substrates. Possible implications derived from the mechanistic details of the EBFS catalyzed reaction for the evolution of sesquiterpene synthases are discussed. PMID:23214943

  1. Mechanical and Electrical Behavior of Organic Solar Cells Probed Through Detailed Morphological Control

    NASA Astrophysics Data System (ADS)

    Awartani, Omar Marwan

    One of the main advantages of organic solar cells is their potential to be used in flexible or even stretchable applications. Most research in the field of organic solar cells is focused on materials synthesis, device physics, and the relationship between morphology and the optoelectronic performance. In order for this technology to be commercially competitive, especially for flexible applications, a more complete picture that explores the mechanical properties of organic materials and how they relate to their optoelectronic properties is necessary. This thesis consists of two main research tracks: The first track focuses mainly on the effect of morphology on the mechanical, electrical and optical performance of organic solar cells controlled through varying processing conditions. Two mechanical properties are investigated including the elastic modulus and crack onset strain of P3HT, PCBM and blend (BHJ) films. The second track utilizes the high achievable ductility of organic semiconducting films that is investigated in the first track of the thesis, to create novel solar cell device architectures and to gain insight into the performance and recombination losses of organic solar cells. Processing ductile BHJ films is used to create organic solar cells with controlled level of polarization with both opaque and semi-transparent architectures. Moreover, using the strain-alignment method the efficiency of low and high order P3HT aggregates is probed within the same film to show similar internal quantum efficiency for the two different morphological P3HT domains. This selective probing technique provides significant insight into performance loss mechanisms in organic solar cells.

  2. Single-Nanowire Electrochemical Probe Detection for Internally Optimized Mechanism of Porous Graphene in Electrochemical Devices.

    PubMed

    Hu, Ping; Yan, Mengyu; Wang, Xuanpeng; Han, Chunhua; He, Liang; Wei, Xiujuan; Niu, Chaojiang; Zhao, Kangning; Tian, Xiaocong; Wei, Qiulong; Li, Zijia; Mai, Liqiang

    2016-03-09

    Graphene has been widely used to enhance the performance of energy storage devices due to its high conductivity, large surface area, and excellent mechanical flexibility. However, it is still unclear how graphene influences the electrochemical performance and reaction mechanisms of electrode materials. The single-nanowire electrochemical probe is an effective tool to explore the intrinsic mechanisms of the electrochemical reactions in situ. Here, pure MnO2 nanowires, reduced graphene oxide/MnO2 wire-in-scroll nanowires, and porous graphene oxide/MnO2 wire-in-scroll nanowires are employed to investigate the capacitance, ion diffusion coefficient, and charge storage mechanisms in single-nanowire electrochemical devices. The porous graphene oxide/MnO2 wire-in-scroll nanowire delivers an areal capacitance of 104 nF/μm(2), which is 4.0 and 2.8 times as high as those of reduced graphene oxide/MnO2 wire-in-scroll nanowire and MnO2 nanowire, respectively, at a scan rate of 20 mV/s. It is demonstrated that the reduced graphene oxide wrapping around the MnO2 nanowire greatly increases the electronic conductivity of the active materials, but decreases the ion diffusion coefficient because of the shielding effect of graphene. By creating pores in the graphene, the ion diffusion coefficient is recovered without degradation of the electron transport rate, which significantly improves the capacitance. Such single-nanowire electrochemical probes, which can detect electrochemical processes and behavior in situ, can also be fabricated with other active materials for energy storage and other applications in related fields.

  3. Understanding the mechanisms of radiation belt dropouts observed by Van Allen Probes

    DOE PAGES

    Xiang, Zheng; Tu, Weichao; Li, Xinlin; ...

    2017-08-30

    To achieve a better understanding of the dominant loss mechanisms for the rapid dropouts of radiation belt electrons, three distinct radiation belt dropout events observed by Van Allen Probes are comprehensively investigated. For each event, observations of the pitch angle distribution of electron fluxes and electromagnetic ion cyclotron (EMIC) waves are analyzed to determine the effects of atmospheric precipitation loss due to pitch angle scattering induced by EMIC waves. Last closed drift shells (LCDS) and magnetopause standoff position are obtained to evaluate the effects of magnetopause shadowing loss. Evolution of electron phase space density (PSD) versus L* profiles and themore » μ and K (first and second adiabatic invariants) dependence of the electron PSD drops are calculated to further analyze the dominant loss mechanisms at different L*. Here, our findings suggest that these radiation belt dropouts can be classified into distinct classes in terms of dominant loss mechanisms: magnetopause shadowing dominant, EMIC wave scattering dominant, and combination of both mechanisms. Different from previous understanding, our results show that magnetopause shadowing can deplete electrons at L* < 4, while EMIC waves can efficiently scatter electrons at L* > 4. Compared to the magnetopause standoff position, it is more reliable to use LCDS to evaluate the impact of magnetopause shadowing. Finally, the evolution of electron PSD versus L* profile and the μ, K dependence of electron PSD drops can provide critical and credible clues regarding the mechanisms responsible for electron losses at different L* over the outer radiation belt.« less

  4. Three-dimensional microfiber devices that mimic physiological environments to probe cell mechanics and signaling.

    PubMed

    Ruder, Warren C; Pratt, Erica D; Bakhru, Sasha; Sitti, Metin; Zappe, Stefan; Cheng, Chao-Min; Antaki, James F; LeDuc, Philip R

    2012-04-24

    Many physiological systems are regulated by cells that alter their behavior in response to changes in their biochemical and mechanical environment. These cells experience this dynamic environment through an endogenous biomaterial matrix that transmits mechanical force and permits chemical exchange with the surrounding tissue. As a result, in vitro systems that mimic three-dimensional, in vivo cellular environments can enable experiments that reveal the nuanced interplay between biomechanics and physiology. Here we report the development of a minimal-profile, three-dimensional (MP3D) experimental microdevice that confines cells to a single focal plane, while allowing the precise application of mechanical displacement to cells and concomitant access to the cell membrane for perfusion with biochemical agonists. The MP3D device--an ordered microfiber scaffold erected on glass--provides a cellular environment that induces physiological cell morphologies. Small manipulations of the scaffold's microfibers allow attached cells to be mechanically probed. Due to the scaffold's minimal height profile, MP3D devices confine cells to a single focal plane, facilitating observation with conventional epifluorescent microscopy. When examining fibroblasts within MP3D devices, we observed robust cellular calcium responses to both a chemical stimulus as well as mechanical displacement of the cell membrane. The observed response differed significantly from previously reported, mechanically-induced calcium responses in the same cell type. Our findings demonstrate a key link between environment, cell morphology, mechanics, and intracellular signal transduction. We anticipate that this device will broadly impact research in fields including biomaterials, tissue engineering, and biophysics.

  5. A beginner's guide to atomic force microscopy probing for cell mechanics

    PubMed Central

    2016-01-01

    Abstract Atomic Force microscopy (AFM) is becoming a prevalent tool in cell biology and biomedical studies, especially those focusing on the mechanical properties of cells and tissues. The newest generation of bio‐AFMs combine ease of use and seamless integration with live‐cell epifluorescence or more advanced optical microscopies. As a unique feature with respect to other bionanotools, AFM provides nanometer‐resolution maps for cell topography, stiffness, viscoelasticity, and adhesion, often overlaid with matching optical images of the probed cells. This review is intended for those about to embark in the use of bio‐AFMs, and aims to assist them in designing an experiment to measure the mechanical properties of adherent cells. In addition to describing the main steps in a typical cell mechanics protocol and explaining how data is analysed, this review will also discuss some of the relevant contact mechanics models available and how they have been used to characterize specific features of cellular and biological samples. Microsc. Res. Tech. 80:75–84, 2017. © 2016 Wiley Periodicals, Inc. PMID:27676584

  6. Non-contact acoustic radiation force impulse microscopy via photoacoustic detection for probing breast cancer cell mechanics

    PubMed Central

    Hwang, Jae Youn; Kang, Bong Jin; Lee, Changyang; Kim, Hyung Ham; Park, Jinhyoung; Zhou, Qifa; Shung, K. Kirk

    2014-01-01

    We demonstrate a novel non-contact method: acoustic radiation force impulse microscopy via photoacoustic detection (PA-ARFI), capable of probing cell mechanics. A 30 MHz lithium niobate ultrasound transducer is utilized for both detection of phatoacoustic signals and generation of acoustic radiation force. To track cell membrane displacements by acoustic radiation force, functionalized single-walled carbon nanotubes are attached to cell membrane. Using the developed microscopy evaluated with agar phantoms, the mechanics of highly- and weakly-metastatic breast cancer cells are quantified. These results clearly show that the PA-ARFI microscopy may serve as a novel tool to probe mechanics of single breast cancer cells. PMID:25657870

  7. Mechanism-based protein cross-linking probes to investigate carrier protein-mediated biosynthesis.

    PubMed

    Worthington, Andrew S; Rivera, Heriberto; Torpey, Justin W; Alexander, Matthew D; Burkart, Michael D

    2006-12-20

    Fatty acid, polyketide, and nonribosomal peptide biosynthetic enzymes perform structural modifications upon small molecules that remain tethered to a carrier protein. This manuscript details the design and analysis of cross-linking substrates that are selective for acyl carrier proteins and their cognate condensing enzymes. These inactivators are engineered through a covalent linkage to fatty acid acyl carrier protein via post-translational modification to contain a reactive probe that traps the active site cysteine residue of ketosynthase domains. These proteomic tools are applied to Escherichia coli fatty acid synthase enzymes, where KASI and KASII selectively cross-link ACP-bound epoxide and chloroacrylate moieties. These mechanism-based, protein-protein fusion reagents also demonstrated cross-linking of KASI to type II polyketide ACPs, while nonribosomal peptide carrier proteins showed no reactivity. Similar investigations into protein-protein interactions, proximity effects, and substrate specificities will be required to complete the mechanistic understanding of these pathways.

  8. 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

  9. Quantitatively probing propensity for structural transitions in engineered virus nanoparticles by single-molecule mechanical analysis

    NASA Astrophysics Data System (ADS)

    Castellanos, Milagros; Carrillo, Pablo J. P.; Mateu, Mauricio G.

    2015-03-01

    Viruses are increasingly being studied from the perspective of fundamental physics at the nanoscale as biologically evolved nanodevices with many technological applications. In viral particles of the minute virus of mice (MVM), folded segments of the single-stranded DNA genome are bound to the capsid inner wall and act as molecular buttresses that increase locally the mechanical stiffness of the particle. We have explored whether a quantitative linkage exists in MVM particles between their DNA-mediated stiffening and impairment of a heat-induced, virus-inactivating structural change. A series of structurally modified virus particles with disrupted capsid-DNA interactions and/or distorted capsid cavities close to the DNA-binding sites were engineered and characterized, both in classic kinetics assays and by single-molecule mechanical analysis using atomic force microscopy. The rate constant of the virus inactivation reaction was found to decrease exponentially with the increase in elastic constant (stiffness) of the regions closer to DNA-binding sites. The application of transition state theory suggests that the height of the free energy barrier of the virus-inactivating structural transition increases linearly with local mechanical stiffness. From a virological perspective, the results indicate that infectious MVM particles may have acquired the biological advantage of increased survival under thermal stress by evolving architectural elements that rigidify the particle and impair non-productive structural changes. From a nanotechnological perspective, this study provides proof of principle that determination of mechanical stiffness and its manipulation by protein engineering may be applied for quantitatively probing and tuning the conformational dynamics of virus-based and other protein-based nanoassemblies.Viruses are increasingly being studied from the perspective of fundamental physics at the nanoscale as biologically evolved nanodevices with many technological

  10. Quantitatively probing propensity for structural transitions in engineered virus nanoparticles by single-molecule mechanical analysis.

    PubMed

    Castellanos, Milagros; Carrillo, Pablo J P; Mateu, Mauricio G

    2015-03-19

    Viruses are increasingly being studied from the perspective of fundamental physics at the nanoscale as biologically evolved nanodevices with many technological applications. In viral particles of the minute virus of mice (MVM), folded segments of the single-stranded DNA genome are bound to the capsid inner wall and act as molecular buttresses that increase locally the mechanical stiffness of the particle. We have explored whether a quantitative linkage exists in MVM particles between their DNA-mediated stiffening and impairment of a heat-induced, virus-inactivating structural change. A series of structurally modified virus particles with disrupted capsid-DNA interactions and/or distorted capsid cavities close to the DNA-binding sites were engineered and characterized, both in classic kinetics assays and by single-molecule mechanical analysis using atomic force microscopy. The rate constant of the virus inactivation reaction was found to decrease exponentially with the increase in elastic constant (stiffness) of the regions closer to DNA-binding sites. The application of transition state theory suggests that the height of the free energy barrier of the virus-inactivating structural transition increases linearly with local mechanical stiffness. From a virological perspective, the results indicate that infectious MVM particles may have acquired the biological advantage of increased survival under thermal stress by evolving architectural elements that rigidify the particle and impair non-productive structural changes. From a nanotechnological perspective, this study provides proof of principle that determination of mechanical stiffness and its manipulation by protein engineering may be applied for quantitatively probing and tuning the conformational dynamics of virus-based and other protein-based nanoassemblies.

  11. Probing the mechanism of water adsorption in carbon micropores with multitemperature isotherms and water preadsorption experiments.

    PubMed

    Rutherford, S W

    2006-11-21

    The phenomenon of water adsorption in carbon micropores is examined through the study of water adsorption equilibrium in molecular sieving carbon. Adsorption and desorption isotherms are obtained over a wide range of concentrations from less than 0.1% to beyond 80% of the vapor pressure. Evidence is provided in support of a proposed bimodal water adsorption mechanism that involves the interaction of water molecules with functional groups at low relative pressures and the adsorption of water molecules between graphene layers at higher pressures. Decomposition of the equilibrium isotherm data through application of the extended cooperative multimolecular sorption theory, together with favorable quantitative comparison, provides support for the proposed adsorption mechanism. Additional support is obtained from a multitemperature study of water equilibrium. Temperatures of 20, 50, and 60 degrees C were probed in this investigation in order to provide isosteric heat of adsorption data for water interaction with the carbon molecular sieve. At low loading, the derived isosteric heat of adsorption is estimated to be 69 kJ/mol. This value is indicative of the adsorption of water to functional groups. At higher loading, the isosteric heat of adsorption decreases with increasing loading and approaches the heat of condensation, indicative of adsorption between graphene layers. Further support for the proposed adsorption mechanism is derived from carbon dioxide adsorption experiments on carbon molecular sieve that is preadsorbed with various amounts of water. Significant exclusion of carbon dioxide occurs, and a quantitative analysis that is based on the proposed bimodal water adsorption mechanism is employed in this investigation.

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

    PubMed

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

    2015-10-01

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

  13. Probing matrix and tumor mechanics with in situ calibrated optical trap based active microrheology

    NASA Astrophysics Data System (ADS)

    Staunton, Jack Rory; Vieira, Wilfred; Tanner, Kandice; Tissue Morphodynamics Unit Team

    Aberrant extracellular matrix deposition and vascularization, concomitant with proliferation and phenotypic changes undergone by cancer cells, alter mechanical properties in the tumor microenvironment during cancer progression. Tumor mechanics conversely influence progression, and the identification of physical biomarkers promise improved diagnostic and prognostic power. Optical trap based active microrheology enables measurement of forces up to 0.5 mm within a sample, allowing interrogation of in vitro biomaterials, ex vivo tissue sections, and small organisms in vivo. We fabricated collagen I hydrogels exhibiting distinct structural properties by tuning polymerization temperature Tp, and measured their shear storage and loss moduli at frequencies 1-15k Hz at multiple amplitudes. Lower Tp gels, with larger pore size but thicker, longer fibers, were stiffer than higher Tp gels; decreasing strain increased loss moduli and decreased storage moduli at low frequencies. We subcutanously injected probes with metastatic murine melanoma cells into mice. The excised tumors displayed storage and loss moduli 40 Pa and 10 Pa at 1 Hz, increasing to 500 Pa and 1 kPa at 15 kHz, respectively.

  14. Nanoscale thermal-mechanical probe determination of 'softening transitions' in thin polymer films.

    PubMed

    Zhou, Jing; Berry, Brian; Douglas, Jack F; Karim, Alamgir; Snyder, Chad R; Soles, Christopher

    2008-12-10

    We report a quantitative study of the softening behavior of glassy polystyrene (PS) films at length scales on the order of 100 nm using nano-thermomechanometry (nano-TM), an emerging scanning probe technique in which a highly doped silicon atomic force microscopy (AFM) tip is resistively heated on the surface of a polymer film. The apparent 'softening temperature' T(s) of the film is found to depend on the logarithm of the square root of the thermal ramping rate R. This relation allows us to estimate a quasi-equilibrium (or zero rate) softening transition temperature T(s0) by extrapolation. We observe marked shifts of T(s0) with decreasing film thickness, but the nature of these shifts, and even their sign, depend strongly on both the thermal and mechanical properties of the supporting substrate. Finite element simulations suggest that thin PS films on rigid substrates with large thermal conductivities lead to increasing T(s0) with decreasing film thickness, whereas softer, less thermally conductive substrates promote reductions in T(s0). Experimental observations on a range of substrates confirm this behavior and indicate a complicated interplay between the thermal and mechanical properties of the thin PS film and the substrate. This study directly points to relevant factors for quantitative measurements of thermophysical properties of materials at the nanoscale using this nano-TM based method.

  15. The strained sesquiterpene β-caryophyllene as a probe for the solvent-assisted epoxidation mechanism.

    PubMed

    Steenackers, Bart; Neirinckx, Alexander; De Cooman, Luc; Hermans, Ive; De Vos, Dirk

    2014-04-04

    In our attempt to synthesize β-caryophyllene oxide in food-compatible conditions, we observed the uncatalyzed and highly selective epoxidation of β-caryophyllene, a strained bicyclic sesquiterpene, in ethanol with aqueous H2 O2 under radical-suppressing conditions without the addition of a catalyst. The unusual reactivity of β-caryophyllene allowed us to use it as a probe for the mechanism of the solvent-assisted epoxidation in a wide range of organic solvents. A kinetic study was performed to investigate the epoxidation mechanism; an excellent correlation was found between the observed epoxidation rates in different solvents and the Abraham's hydrogen bond formation parameters of these solvents. By means of computational analysis, it was found that the main role of the solvent consists of the stabilization of the elongated OO bond of H2 O2 in the transition state through hydrogen-bond donation to the leaving OH moiety of H2 O2 . α-Humulene was found to possess similar reactivity as β-caryophyllene whereas isocaryophyllene-the unstrained isomer of β-caryophyllene-was unreactive.

  16. Interfacial tension in oil-water-surfactant systems: on the role of intra-molecular forces on interfacial tension values using DPD simulations.

    PubMed

    Deguillard, E; Pannacci, N; Creton, B; Rousseau, B

    2013-04-14

    We have computed interfacial tension in oil-water-surfactant model systems using dissipative particle dynamics (DPD) simulations. Oil and water molecules are modelled as single DPD beads, whereas surfactant molecules are composed of head and tail beads linked together by a harmonic potential to form a chain molecule. We have investigated the influence of the harmonic potential parameters, namely, the force constant K and the equilibrium distance r0, on the interfacial tension values. For both parameters, the range investigated has been chosen in agreement with typical values in the literature. Surprisingly, we observe a large effect on interfacial tension values, especially at large surfactant concentration. We demonstrate that, due to a subtle balance between intra-molecular and inter-molecular interactions, the local structure of surfactants at the oil-water interface is modified, the interfacial tension is changed and the interface stability is affected.

  17. Combining colloidal probe atomic force and reflection interference contrast microscopy to study the compressive mechanics of hyaluronan brushes.

    PubMed

    Attili, Seetharamaiah; Richter, Ralf P

    2012-02-14

    We describe a method that combines colloidal probe atomic force microscopy (AFM) and reflection interference contrast microscopy (RICM) to characterize the mechanical properties of thin and solvated polymer films. When analyzing polymer films, a fundamental problem in colloidal probe AFM experiments is to determine the distance at closest approach between the probe and the substrate on which the film is deposited. By combining AFM and RICM in situ, forces and absolute distances can be measured simultaneously. Using the combined setup, we quantify the compressive mechanics of films of the polysaccharide hyaluronan that is end-grafted to a supported lipid bilayer. The experimental data, and comparison with polymer theory, show that hyaluronan films are well-described as elastic, very soft and highly solvated polymer brushes. The data on these well-defined films should be a useful reference for the investigation of the more complex hyaluronan-rich coats that surround many living cells.

  18. Tungstate (VI) sorption on hematite: An in situ ATR-FTIR probe on the mechanism.

    PubMed

    Rakshit, Sudipta; Sallman, Bryan; Davantés, Athénais; Lefèvre, Grégory

    2017-02-01

    Owing to the suspected toxicity and carcinogenicity of tungstate (VI) oxyanions [i.e. mono tungstate and several polytungstate, generally represented by W (VI)], the environmental fate of W (VI) has been widely studied. Sorption is regarded as a major mechanism by which W (VI) species are retained in the solid/water interface. Iron (hydr)oxides have been considered important environmental sinks for W (VI) species. Here we report sorption mechanisms of W (VI) on a common iron oxide mineral-hematite under environmentally relevant solution properties using in situ attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopic probes. Initial W (VI) loadings varied from 10 to 200 μM at fixed pH values ranged from 4.6 to 8.1. For pH envelop (pHs = 4.6, 5.0, 5.5, 6.0, 6.5, 7.5, and 8.1) experiments, fixed W (VI) concentrations (i.e. 10 & 200 μM) were used to understand the effects of pH. The results indicated that at acidic pH values (pH < 6.0) the sorbed polytungstate surface species are prominent at 200 μM initial W (VI) conc. The pH envelop experiments revealed that sorbed polytungstates can be present even at lower initial W (VI) conc. (i.e. 10 μM) at pH values <5.5. Overall, our in situ ATR-FTIR experiments indicated that W (VI) forms inner-sphere type bonds on hematite surface and the strength of the interaction increases with decreasing pH. In addition, initial W (VI) concentration affected the sorption mechanisms of W (VI) on hematite. Our study will aid the molecular level understanding of W (VI) retention on iron oxide surfaces. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Probing interfacial dynamics and mechanics using submerged particle microrheology. I. Theory

    NASA Astrophysics Data System (ADS)

    Shlomovitz, Roie; Evans, Arthur A.; Boatwright, Thomas; Dennin, Michael; Levine, Alex J.

    2014-07-01

    Microrheology relies on tracking the thermal or driven motion of microscopic particles in a soft material. It is well suited to the study of materials that have no three-dimensional realization, which makes them difficult to study using a macroscopic rheometer. For this reason, microrheology is becoming an important rheological probe of Langmuir monolayers and membranes. Interfacial microrheology, however, has been difficult to reconcile quantitatively with more traditional macroscopic approaches. We suggest that uncertainties in accounting for the mechanical coupling of the tracer particle to the interface or membrane are responsible for these discrepancies. To resolve them, we propose a new non-contact approach to interfacial microrheology that uses particles submerged in the subphase a known distance below the interface. In this first of two papers, we present calculations of the response function (and thus the equilibrium fluctuation spectrum) of a spherical particle submerged below a viscoelastic surface that has a finite surface tension and/or bending modulus. In the second paper, we compare these results to submerged particle microrheology in a few example systems, showing quantitative agreement.

  20. Chloromethane to olefins over H-SAPO-34: Probing the hydrocarbon pool mechanism

    SciTech Connect

    Fickel, Dustin W.; Sabnis, Kaiwalya D.; Li, Luanyi; Kulkarni, Neeta; Winter, Lea R.; Yan, Binhang; Chen, Jingguang G.

    2016-09-09

    In this paper, by means of in situ FTIR and ex situ13C NMR studies, the initial periods of the chloromethane-to-olefins (CTO) reaction over SAPO-34 were probed in order to investigate the activation period of the reaction and to elucidate the formation of the catalyst active site. A methylated benzene species has been observed to form during the initial activation period of the reaction, and a direct positive correlation was constructed between the formation of this species and the catalytic activity. The data thus indicate that these methylated benzene species contribute to the formation of active sites within SAPO-34 for the CTO reaction. This is the first known report identifying a direct semi-quantitative correlation between the catalyst activity and growth of a methylated benzene active species, during the activation period of the chloromethane to olefins reaction. Finally, the findings here in correspond well to those reported for the methanol to olefins reaction, suggesting that a similar ‘hydrocarbon pool’ mechanism may be responsible for the formation of light olefins in CTO chemistry as well.

  1. Chloromethane to olefins over H-SAPO-34: Probing the hydrocarbon pool mechanism

    SciTech Connect

    Fickel, Dustin W.; Sabnis, Kaiwalya D.; Li, Luanyi; Kulkarni, Neeta; Winter, Lea R.; Yan, Binhang; Chen, Jingguang G.

    2016-09-09

    In this paper, by means of in situ FTIR and ex situ13C NMR studies, the initial periods of the chloromethane-to-olefins (CTO) reaction over SAPO-34 were probed in order to investigate the activation period of the reaction and to elucidate the formation of the catalyst active site. A methylated benzene species has been observed to form during the initial activation period of the reaction, and a direct positive correlation was constructed between the formation of this species and the catalytic activity. The data thus indicate that these methylated benzene species contribute to the formation of active sites within SAPO-34 for the CTO reaction. This is the first known report identifying a direct semi-quantitative correlation between the catalyst activity and growth of a methylated benzene active species, during the activation period of the chloromethane to olefins reaction. Finally, the findings here in correspond well to those reported for the methanol to olefins reaction, suggesting that a similar ‘hydrocarbon pool’ mechanism may be responsible for the formation of light olefins in CTO chemistry as well.

  2. Chloromethane to olefins over H-SAPO-34: Probing the hydrocarbon pool mechanism

    DOE PAGES

    Fickel, Dustin W.; Sabnis, Kaiwalya D.; Li, Luanyi; ...

    2016-09-09

    In this paper, by means of in situ FTIR and ex situ13C NMR studies, the initial periods of the chloromethane-to-olefins (CTO) reaction over SAPO-34 were probed in order to investigate the activation period of the reaction and to elucidate the formation of the catalyst active site. A methylated benzene species has been observed to form during the initial activation period of the reaction, and a direct positive correlation was constructed between the formation of this species and the catalytic activity. The data thus indicate that these methylated benzene species contribute to the formation of active sites within SAPO-34 for themore » CTO reaction. This is the first known report identifying a direct semi-quantitative correlation between the catalyst activity and growth of a methylated benzene active species, during the activation period of the chloromethane to olefins reaction. Finally, the findings here in correspond well to those reported for the methanol to olefins reaction, suggesting that a similar ‘hydrocarbon pool’ mechanism may be responsible for the formation of light olefins in CTO chemistry as well.« less

  3. Mechanisms of catalytic dehydrogenation of alkanes by rhodium clusters Rhn+ probed by isotope labelling

    NASA Astrophysics Data System (ADS)

    Adlhart, Christian; Uggerud, Einar

    2006-03-01

    The regioselectivity for the dehydrogenation of alkanes by rhodium clusters was investigated by reacting Rhn+, n = 1-20, with the isotopically labelled alkanes ethane-1,1,1-d3 and propane-1,1,1,3,3,3-d6. For Rh+ reacting with propane a clear preference for a 1,2- over a 1,1- and 1,3-mechanism was observed. For larger clusters, hydrogen scrambling is faster than hydrogen elimination, which essentially leads to statistical formation of the neutrals H2, HD, and D2. Isotope scrambling with D2 was also used as a structural probe for the reaction products of rhodium clusters with ethane. The intactness of the CH bonds was demonstrated for (n > 6). The studies are completed with a detailed kinetic analysis for the reaction of Rh7+ with ethane and ethane/hydrogen and ethane/helium mixtures. An over-all picture with efficient CH bond activation and fast and reversible hydrogen rearrangements emerges on the basis of these experiments. Some of the dehydrogenation reactions appear to be reversible.

  4. A laser-induced ultrasonic probe of the mechanical properties of aligned lipid multibilayers.

    PubMed

    Eyring, G; Fayer, M D

    1985-01-01

    The recently developed laser-induced phonon spectroscopy (LIPS) technique is applied to the determination of dynamic mechanical properties of aligned dilauroylphosphatidylcholine (DLPC) multibilayer arrays containing 2 and 20% water by weight. Sample excitation by two crossed 100-ps laser pulses generates a longitudinal ultrasonic wave whose wavelength depends on the crossing angle. In these experiments, the acoustic wave propagates parallel to the bilayer planes. The ultrasonic velocity and attenuation are monitored through the diffraction of a variably delayed probe pulse by the acoustic grating. The velocity measures the lateral area compressibility of the bilayers, while the attenuation is related to the viscosity. Velocities obtained in the gel and liquid crystal phases are compared with those found previously using Brillouin scattering. The acoustic attenuation is shown to be an order of magnitude more sensitive to the gel-liquid crystal phase transition than the velocity. The lipid area compressibility and viscosity of DLPC-20% water multilayers with and without 100 mM CaCl2 are found to be identical within our experimental error.

  5. Hydrophobic Interactions Contribute to Conformational Stabilization of Endoglycoceramidase II by Mechanism-Based Probes.

    PubMed

    Ben Bdira, Fredj; Jiang, Jianbing; Kallemeijn, Wouter; de Haan, Annett; Florea, Bogdan I; Bleijlevens, Boris; Boot, Rolf; Overkleeft, Herman S; Aerts, Johannes M; Ubbink, Marcellus

    2016-08-30

    Small compound active site interactors receive considerable attention for their ability to positively influence the fold of glycosidases. Endoglycoceramidase II (EGCII) from Rhodococcus sp. is an endo-β-glucosidase releasing the complete glycan from ceramide in glycosphingolipids. Cleavage of the β-glycosidic linkage between glucose and ceramide is also catalyzed by glucocerebrosidase (GBA), the exo-β-glucosidase deficient in Gaucher disease. We demonstrate that established β-glucoside-configured cyclophellitol-type activity-based probes (ABPs) for GBA also are effective, mechanism-based, and irreversible inhibitors of EGCII. The stability of EGCII is markedly enhanced by formation of covalent complexes with cyclophellitol ABPs substituted with hydrophobic moieties, as evidenced by an increased melting temperature, resistance against tryptic digestion, changes in (15)N-(1)H transverse relaxation optimized spectroscopy spectra of the [(15)N]Leu-labeled enzyme, and relative hydrophobicity as determined by 8-anilino-1-naphthalenesulfonic acid fluorescence. The stabilization of EGCII conformation correlates with the shape and hydrophobicity of the substituents of the ABPs. We conclude that the amphipathic active site binders with aliphatic moieties act as a "hydrophobic zipper" on the flexible EGCII protein structure.

  6. Nanosecond Time-Resolved Polarization Spectroscopies: Tools for Probing Protein Reaction Mechanisms

    PubMed Central

    Chen, Eefei; Goldbeck, Robert A.; Kliger, David S.

    2010-01-01

    Polarization methods, introduced in the 1800’s, offered one of the earliest ways to examine protein structure. Since then, many other structure-sensitive probes have been developed, but circular dichroism (CD) remains a powerful technique because of its versatility and the specificity of protein structural information that can be explored. With improvements in time-resolution, from millisecond to picosecond CD measurements, it has proven to be an important tool for studying the mechanism of folding and function in many biomolecules. For example, nanosecond time-resolved CD (TRCD) studies of the sub-microsecond events of reduced cytochrome c folding have provided direct experimental evidence of kinetic heterogeneity, which is an inherent property of the diffusional nature of early folding dynamics on the energy landscape. In addition, TRCD has been applied to the study of many biochemical processes, such as ligand rebinding in hemoglobin and myoglobin and signaling state formation in photoactive yellow protein and prototropin 1 LOV2. The basic approach to TRCD has also been extended to include a repertoire of nanosecond polarization spectroscopies: optical rotatory dispersion (ORD), magnetic CD and ORD, and linear dichroism. This article will discuss the details of the polarization methods used in this laboratory, as well as the coupling of timeresolved ORD with the temperature-jump trigger so that protein folding can be studied in a larger number of proteins. PMID:20438842

  7. Probing the Failure Mechanism of SnO2 Nanowires for Sodium-ion Batteries

    SciTech Connect

    Gu, Meng; Kushima, Akihiro; Shao, Yuyan; Zhang, Jiguang; Liu, Jun; Browning, Nigel D.; Li, Ju; Wang, Chong M.

    2013-09-30

    Non-lithium metals such as sodium have attracted wide attention as a potential charge carrying ion for rechargeable batteries, performing the same role as lithium in lithium- ion batteries. As sodium and lithium have the same +1 charge, it is assumed that what has been learnt about the operation of lithium ion batteries can be transferred directly to sodium batteries. Using in-situ TEM, in combination with DFT calculations, we probed the structural and chemical evolution of SnO2 nanowire anodes in Na-ion batteries and compared them quantitatively with results from Li-ion batteries [Science 330 (2010) 1515]. Upon Na insertion into SnO2, a displacement reaction occurs, leading to the formation of amorphous NaxSn nanoparticles covered by crystalline Na2O shell. With further Na insertion, the NaxSn core crystallized into Na15Sn4 (x=3.75). Upon extraction of Na (desodiation), the NaxSn core transforms to Sn nanoparticles. Associated with a volume shrinkage, nanopores appear and metallic Sn particles are confined in hollow shells of Na2O, mimicking a peapod structure. These pores greatly increase electrical impedance, therefore naturally accounting for the poor cyclability of SnO2. DFT calculations indicate that Na+ diffuses 30 times slower than Li+ in SnO2, in agreement with in-situ TEM measurement. Insertion of Na can chemo-mechanically soften the reaction product to greater extent than in lithiation. Therefore, in contrast to the lithiation of SnO2, no dislocation plasticity was seen ahead of the sodiation front. This direct comparison of the results from Na and Li highlights the critical role of ionic size and electronic structure of different ionic species on the charge/discharge rate and failure mechanisms in these batteries.

  8. THERMAL PROBING OF E. COLI RNA POLYMERASE OFF-PATHWAY MECHANISMS

    PubMed Central

    Mejia, Yara X.; Mao, Hanbin; Forde, Nancy R.; Bustamante, Carlos

    2008-01-01

    RNA polymerase is an essential enzyme for cellular gene expression. In an effort to further understand the enzyme’s importance in the cell’s response to temperature, we have probed the kinetic mechanism of E. coli RNA polymerase (RNAP) by studying the force-velocity behavior of individual RNAP complexes at temperatures between 7°C and 45°C using optical tweezers. Within this temperature range and at saturating nucleotide concentrations, the pause-free transcription velocity of RNAP was independent of force and increased monotonically with temperature with an elongation activation energy of 9.7 ± 0.7 kcal/mole. Interestingly, the pause density at cold temperatures (7 °C to 21 °C) was five times higher than that measured above room temperature. A simple kinetic model revealed a value of 1.29 ± 0.05 kcal/mol for the activation energy of pause entry, suggesting that pause entry is indeed a thermally accessible process. The dwell time distribution of all observable pauses was independent of temperature, directly confirming a prediction of the model recently proposed for Pol II in which pauses are diffusive backtracks along the DNA. Additionally, we find that the force at which the polymerase arrests (the arrest force) presents a maximum at 21 °C, an unexpected result as this is not the optimum temperature for bacterial growth. This observation suggests that arrest could play a regulatory role in vivo, possibly through interactions with specific elongation factors. PMID:18647607

  9. UbFluor: A Mechanism-Based Probe for HECT E3 Ligases

    PubMed Central

    Krist, David T.; Park, Sungjin; Boneh, Galyah H.; Rice, Sarah E.; Statsyuk, Alexander V.

    2016-01-01

    Homologous to E6AP Carboxyl Terminus E3 ubiquitin ligases (HECT, ~28 known) are genetically implicated in cancer, neurological, hypertensive, and autoimmune disorders, and are potential drug targets to treat these diseases. The major bottleneck in the field of HECT E3s is a lack of simple assays to quantify the enzymatic activity of these enzymes in the presence of small molecules. Typical assays require E1, E2, HECT E3, ubiquitin (Ub), ATP and additional reagents to detect the resulting free poly-ubiquitin chains. To address this need, we developed UbFluor, a fluorescent thioester conjugate between the C-terminus of Ub and fluorescein-thiol (Fluor-SH). UbFluor is a mechanism-based probe that undergoes a direct transthiolation reaction with the catalytic cysteine of the model HECT E3 ligase Rsp5, producing the catalytically active Rsp5~Ub (~ indicates thioester) accompanied by release of Fluor-SH. The kinetics of this two-component reaction can be easily monitored with real-time fluorescence polarization (FP) assays. Importantly, UbFluor eliminates the need to use SDS-PAGE, ATP, E1, E2 enzymes, and extra poly-ubiquitin chain detection reagents. Although the developed system lacks ATP, E1 and E2 enzymes, we show that UbFluor can recapitulate the native ubiquitination reaction by detecting and quantifying defects in transthiolation and isopeptide ligation of Rsp5 HECT E3 alanine mutants. Based on our findings, we show that UbFluor can be utilized to conduct high-throughput screens (HTS) of small molecules against HECT ligases. PMID:27482366

  10. Probing the failure mechanism of SnO2 nanowires for sodium-ion batteries.

    PubMed

    Gu, Meng; Kushima, Akihiro; Shao, Yuyan; Zhang, Ji-Guang; Liu, Jun; Browning, Nigel D; Li, Ju; Wang, Chongmin

    2013-11-13

    Nonlithium metals such as sodium have attracted wide attention as a potential charge carrying ion for rechargeable batteries. Using in situ transmission electron microscopy in combination with density functional theory calculations, we probed the structural and chemical evolution of SnO2 nanowire anodes in Na-ion batteries and compared them quantitatively with results from Li-ion batteries (Huang, J. Y.; et al. Science 2010, 330, 1515 - 1520). Upon Na insertion into SnO2, a displacement reaction occurs, leading to the formation of amorphous NaxSn nanoparticles dispersed in Na2O matrix. With further Na insertion, the NaxSn crystallized into Na15Sn4 (x = 3.75). Upon extraction of Na (desodiation), the NaxSn transforms to Sn nanoparticles. Associated with the dealloying, pores are found to form, leading to a structure of Sn particles confined in a hollow matrix of Na2O. These pores greatly increase electrical impedance, therefore accounting for the poor cyclability of SnO2. DFT calculations indicate that Na(+) diffuses 30 times slower than Li(+) in SnO2, in agreement with in situ TEM measurement. Insertion of Na can chemomechanically soften the reaction product to a greater extent than in lithiation. Therefore, in contrast to the lithiation of SnO2 significantly less dislocation plasticity was seen ahead of the sodiation front. This direct comparison of the results from Na and Li highlights the critical role of ionic size and electronic structure of different ionic species on the charge/discharge rate and failure mechanisms in these batteries.

  11. Interaction Mechanism of Oil-in-Water Emulsions with Asphaltenes Determined Using Droplet Probe AFM.

    PubMed

    Shi, Chen; Zhang, Ling; Xie, Lei; Lu, Xi; Liu, Qingxia; Mantilla, Cesar A; van den Berg, Frans G A; Zeng, Hongbo

    2016-03-15

    Emulsions with interface-active components at the oil/water interface have long been of fundamental and practical interest in many fields. In this work, the interaction forces between two oil droplets in water in the absence/presence of asphaltenes were directly measured using droplet probe atomic force microscopy (AFM) and analyzed using a theoretical model based on Reynolds lubrication theory and the augmented Young-Laplace equation by including the effects of disjoining pressure. It was revealed that the interaction forces measured between two pristine oil droplets (i.e., toluene) could be well described by the classical Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, while an additional steric interaction should be included in the presence of asphaltenes in the oil. The surface interaction and the stability of oil droplets in aqueous solution were demonstrated to be significantly influenced by the asphaltenes concentration in oil, salt concentration, pH, and presence of divalent ions (Ca(2+)) in water. Adsorbed asphaltenes at the oil/water interface led to more negative surface potential of the oil/water interface and also induced steric repulsion between oil droplets, inhibiting the drop coalescence and stabilizing the oil-in-water emulsion. Lower pH of aqueous solution could lead to less negative surface potential and weaken the repulsion between oil droplets. Addition of divalent ions (Ca(2+)) was found to disrupt the protecting effects of adsorbed asphaltenes at oil/water interface and induce coalescence of oil droplets. Our results provide a useful methodology for quantifying the interaction forces and investigating the properties of asphaltenes at the oil/water interfaces and provide insights into the stabilization mechanism of oil-in-water emulsions due to asphaltenes in oil production and water treatment.

  12. Probing Mechanisms for Enzymatic Activity Enhancement of Organophosphorus Hydrolase in Functionalized Mesoporous Silica

    SciTech Connect

    Chen, Baowei; Lei, Chenghong; Shin, Yongsoon; Liu, Jun

    2009-12-25

    We have previously reported that organophosphorus hydrolase (OPH) can be spontaneously entrapped in functionalized mesoporous silica (FMS) with HOOC - as the functional groups and the entrapped OPH in HOOC-FMS showed enhanced enzyme specific activity. This work is to study the mechanisms that why OPH entrapped in FMS displayed the enhanced activity in views of OPH-FMS interactions using spectroscopic methods. The circular dichroism (CD) spectra show that, comparing to the secondary structure of OPH free in solution, OPH in HOOC-FMS displayed increased a-helix/b-strand transition of OPH with increased OPH loading density. The fluorescence emission spectra of Trp residues were used to assess the tertiary structural changes of the enzyme. There was a 42% increase in fluorescence. This is in agreement with the fact that the fluorescence intensity of OPH was increased accompanying with the increased OPH activity when decreasing urea concentrations in solution. The steady-state anisotropy was increased after OPH entrapping in HOOC-FMS comparing to the free OPH in solution, indicating that protein mobility was reduced upon entrapment. The solvent accessibility of Trp residues of OPH was probed by using acrylamide as a collisional quencher. Trp residues of OPH-FMS had less solvent exposure comparing with free OPH in solution due to its electrostatical binding to HOOC-FMS thereby displaying the increased fluorescence intensity. These results suggest the interactions of OPH with HOOC-FMS resulted in the protein immobilization and a favorable conformational change for OPH in the crowded confinement space and accordingly the enhanced activity.

  13. HNO/NO Conversion Mechanisms of Cu-Based HNO Probes with Implications for Cu,Zn-SOD

    PubMed Central

    2015-01-01

    HNO has broad biological effects and pharmacological activities. Direct HNO probes for in vivo applications were recently reported, which are CuII-based complexes having fluorescence reporters with reaction to HNO resulting in CuI systems and the release of NO. Their coordination environments are similar to that in Cu,Zn-superoxide dismutase (SOD), which plays a significant role in cellular HNO/NO conversion. However, none of these conversion mechanisms are known. A quantum chemical investigation was performed here to provide structural, energetic, and electronic profiles of HNO/NO conversion pathways via the first CuII-based direct HNO probe. Results not only are consistent with experimental observations but also provide numerous structural and mechanistic details unknown before. Results also suggest the first HNO/NO conversion mechanism for Cu,Zn-SOD, as well as useful guidelines for future design of metal-based HNO probes. These results shall facilitate development of direct HNO probes and studies of HNO/NO conversions via metal complexes and metalloproteins. PMID:24803995

  14. Effect of insertion speed on tissue response and insertion mechanics of a chronically implanted silicon-based neural probe.

    PubMed

    Welkenhuysen, M; Andrei, A; Ameye, L; Eberle, W; Nuttin, B

    2011-11-01

    In this study, the effect of insertion speed on long-term tissue response and insertion mechanics was investigated. A dummy silicon parylene-coated probe was used in this context and implanted in the rat brain at 10 μm/s (n = 6) or 100 μm/s (n = 6) to a depth of 9 mm. The insertion mechanics were assessed by the dimpling distance, and the force at the point of penetration, at the end of the insertion phase, and after a 3-min rest period in the brain. After 6 weeks, the tissue response was evaluated by estimating the amount of gliosis, inflammation, and neuronal cell loss with immunohistochemistry. No difference in dimpling, penetration force, or the force after a 3-min rest period in the brain was observed. However, the force at the end of the insertion phase was significantly higher when inserting the probes at 100 μm/s compared to 10 μm/s. Furthermore, an expected tissue response was seen with an increase of glial and microglial reactivity around the probe. This reaction was similar along the entire length of the probe. However, evidence for a neuronal kill zone was observed only in the most superficial part of the implant. In this region, the lesion size was also greatest. Comparison of the tissue response between insertion speeds showed no differences.

  15. Probing the micro-mechanical behavior of bone via high-energy x-rays.

    SciTech Connect

    Almer, J.; Stock, S. R.; X-Ray Science Division; Northwestern Univ.

    2006-01-01

    Bone is a highly-adaptive, particulate-reinforced composite which, through a complex hierarchical structure, achieves excellent mechanical performance. The composite preserves, to a large degree, the desirable properties of the individual components: high toughness of the bone matrix, collagen fibrils stabilized by water, and high stiffness of the reinforcing phase, nano-sized crystallites of carbonated apatite. Understanding bone fragility (osteoporosis) requires quantifying mechanical input to bone and identifying 'weak-link' microstructures. This mechanical input has been quantified in vivo with strain gages attached to cortical bone, but attached strain gages do not probe subsurface mechanical response. We addressed this shortcoming recently by appling wide- and small-angle x-ray scattering to canine fibula sections, to study the micro-mechanical response of bone on different length scales. These data provide a unique view of load partition between the constituent phases of bone, and here we extend these measurements to an entire rat tibia, where strain gradients due to bending are anticipated. Tibiae of 14 week old Sprague-Dawley rats were studied. A 3D microCT rendering of the sample and definitions of the loading (y) and transverse (x) directions appear in Fig.1, with the y-axis approximately parallel to the bone's longitudinal axis. Due to the curved shape of the tibia, significant sample bending in the x-direction was anticipated even under uniaxial compression, similar to that expected in vivo (there was little curvature in the y-z plane). The sample cross-section at y=0 was determined by microCT to be approximately 4 mm{sup 2}. The sample was potted in epoxy and compressed in a load frame designed for in situ x-ray scattering studies. Loading was in displacement control, at a rate of 0.06 {micro}m/sec. The aggregate macroscopic response was followed using a load cell combined with strain gages located on both the 'convex' (-x) and 'concave' (+x) sides of

  16. Inter and Intra Molecular Phase Separation Environment Effects on PI-PEO Block Copolymers for Batteries and Fuel Cells

    NASA Technical Reports Server (NTRS)

    Xue, Chen-Chen; Meador, Mary Ann B.; Eby, R. K.; Cheng, Stephen Z. D.; Ge, Jason J.; Cubon, Valerie A.

    2002-01-01

    Rod-coil molecules have been introduced as a novel type of block copolymers with unique microstructure due to their ability to self-assemble to various ordered morphologies on a nanometer length scale. These molecules, comprised two homo polymers joined together at one end, microphase separate into ordered, periodic arrays of spheres, cylinders in the bulk state and or solution. To get ordered structure in a reasonable scale, additional force field are applied, such as mechanical shearing, electric field and magnetic field. Recently, progress has made it a possible to develop a new class of polyimides (PI)-Polyethylene oxide (PEO) that are soluble in polar organic solvents. The solvent-soluble PI-PEO has a wide variety of applications in microelectronics, since these PI-PEO films exhibit a high degree of thermal and chemical stability. In this paper, we report the self-assembled ordered structure of PI-PEO molecules formed from concentrate solution.

  17. Influence of intra-molecular flexibility on the elastic property of double-stranded DNA film on a substrate

    NASA Astrophysics Data System (ADS)

    Wu, Jun-Zheng; Meng, Wei-Lie; Tang, Heng-Song; Zhang, Neng-Hui

    2017-05-01

    DNA film self-assembled or nanografted on a substrate, as a kind of soft matter, consists of fixed DNA chains endowed with negative charges and an aqueous solution full of cations, anions and water molecules. Their thermal/electrical/mechanical properties are closely related to the complex biodetection signals in nano-/micro-scale biosensors and other new genome technologies. This makes it important to properly characterize these properties. In this paper, the effect of flexible micro-scale configurations on the elastic moduli of DNA films is investigated. First, illuminated by Qiu’s sphere model, an alternative bead-chain model in terms of the Yukawa potential is presented for flexible intra-DNA configurations to describe interactions between DNA fragments. The effective charges of coarse-grained DNA beads could be derived, in which the empirical parameters are identified by curve fitting with Qiu’s experimental data. Second, the updated mesoscopic bead-chain model and the thought experiment of a continuum compression bar are used to compare the elastic moduli of double-stranded DNA (dsDNA) films prepared by self-assembling and nanografting techniques. Configurational sampling is achieved via Monte Carlo simulation. Our predictions quantitatively or qualitatively agree well with the relevant experiments on the effective charge of dsDNA from low to moderate monovalent counterion concentration, immobilization deflection of single-stranded DNA (ssDNA) or dsDNA microcantilever with the variation of salt concentration, and elastic modulus of ssDNA film in the air. The results reveal that different solution environment stimulates the diverse mechanical properties of dsDNA film on a substrate, and the end effect (i.e. terminal group effect) makes self-assembling dsDNA film stiffer in the sense of the same average packing density.

  18. Krikalev dismantles probe-and-cone docking mechanism (StM) in the Progress M-53 (18P)

    NASA Image and Video Library

    2005-06-19

    ISS011-E-09204 (19 June 2005) --- Cosmonaut Sergei K. Krikalev, Expedition 11 commander representing Russia's Federal Space Agency, dismantles the probe-and-cone docking mechanism in the Progress 18 spacecraft. The Progress docked to the aft port of the Zvezda Service Module of the International Space Station (ISS) at 7:42 p.m. (CDT) as the Station flew approximately 225 statute miles, above a point near Beijing, China.

  19. Uptake and localization mechanisms of fluorescent and colored lipid probes. Part 2. QSAR models that predict localization of fluorescent probes used to identify ("specifically stain") various biomembranes and membranous organelles.

    PubMed

    Horobin, R W; Stockert, J C; Rashid-Doubell, F

    2015-05-01

    We discuss a variety of biological targets including generic biomembranes and the membranes of the endoplasmic reticulum, endosomes/lysosomes, Golgi body, mitochondria (outer and inner membranes) and the plasma membrane of usual fluidity. For each target, we discuss the access of probes to the target membrane, probe uptake into the membrane and the mechanism of selectivity of the probe uptake. A statement of the QSAR decision rule that describes the required physicochemical features of probes that enable selective staining also is provided, followed by comments on exceptions and limits. Examples of probes typically used to demonstrate each target structure are noted and decision rule tabulations are provided for probes that localize in particular targets; these tabulations show distribution of probes in the conceptual space defined by the relevant structure parameters ("parameter space"). Some general implications and limitations of the QSAR models for probe targeting are discussed including the roles of certain cell and protocol factors that play significant roles in lipid staining. A case example illustrates the predictive ability of QSAR models. Key limiting values of the head group hydrophilicity parameter associated with membrane-probe interactions are discussed in an appendix.

  20. 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.

  1. Miniature probe for mechanical properties of vascular lesions using acoustic radiation force optical coherence elastography (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Qu, Yueqiao; Ma, Teng; He, Youmin; Yu, Mingyue; Li, Rui; Zhu, Jiang; Dai, Cuixia; Piao, Zhonglie; Shung, K. Kirk; Zhou, Qifa; Chen, Zhongping

    2016-03-01

    Changes in tissue biomechanical properties often signify the onset and progression of diseases, such as in determining the vulnerability of atherosclerotic plaques. Acoustic radiation force optical coherence elastography (ARF-OCE) has been used in the detection of tissue elasticity to obtain high-resolution elasticity maps. We have developed a probe-based ARF-OCE technology that utilizes a miniature 10 MHz ring ultrasonic transducer for excitation and Doppler optical coherence tomography (OCT) for detection. The transducer has a small hole in the center for the OCT light to propagate through. This allows for a confocal stress field and light detection within a small region for high sensitivity and localized excitation. This device is a front-facing probe that is only 3.5 mm in diameter and it is the smallest ARF-OCE catheter to the best of our knowledge. We have tested the feasibility of the probe by measuring the point displacement of an agarose tissue-mimicking phantom using different ARF excitation voltages. Small displacement values ranging from 30 nm to 90 nm have been detected and are shown to be directly proportional to the excitation voltage as expected. We are currently working on obtaining 2D images using a scanning mechanism. We will be testing to capture 2D elastograms of phantoms to further verify feasibility, and eventually characterize the mechanical properties of cardiovascular tissue. With its high portability and sensitivity, this novel technology can be applied to the diagnosis and characterization of vulnerable atherosclerotic plaques.

  2. Probing Nucleobase Interactions and Predicting Mechanisms of Synthetic Interest Using Computational Chemistry, and Furthering the Development of BVI Education in Chemistry

    ERIC Educational Resources Information Center

    Harrison, Jason Gordon

    2013-01-01

    Quantum mechanical (QM) and molecular docking methods are used to probe systems of biological and synthetic interest. Probing interactions of nucleobases within proteins, and properly modeling said interactions toward novel nucleobase development, is extremely difficult, and of great utility in RNA interference (RNAi) therapeutics. The issues in…

  3. Probing Nucleobase Interactions and Predicting Mechanisms of Synthetic Interest Using Computational Chemistry, and Furthering the Development of BVI Education in Chemistry

    ERIC Educational Resources Information Center

    Harrison, Jason Gordon

    2013-01-01

    Quantum mechanical (QM) and molecular docking methods are used to probe systems of biological and synthetic interest. Probing interactions of nucleobases within proteins, and properly modeling said interactions toward novel nucleobase development, is extremely difficult, and of great utility in RNA interference (RNAi) therapeutics. The issues in…

  4. Mechanism of Carbamate Inactivation of FAAH: Implications for the Design of Covalent Inhibitors and In Vivo Functional Probes for Enzymes

    PubMed Central

    Alexander, Jessica P.; Cravatt, Benjamin F.

    2006-01-01

    Summary Fatty acid amide hydrolase (FAAH) regulates a large class of signaling lipids, including the endocannabinoid anandamide. Carbamate inhibitors of FAAH display analgesic and anxiolytic properties in rodents. However, the mechanism by which carbamates inhibit FAAH remains obscure. Here, we provide biochemical evidence that carbamates covalently modify the active site of FAAH by adopting an orientation opposite of that originally predicted from modeling. Based on these results, a series of carbamates was designed that display enhanced potency. One agent was converted into a “click chemistry” probe to comprehensively evaluate the proteome reactivity of FAAH-directed carbamates in vivo. These inhibitors were selective for FAAH in the nervous system, but they reacted with several enzymes in peripheral tissues. The experimental strategy described herein can be used to create in vivo probes for any enzyme susceptible to covalent inhibition. PMID:16298297

  5. An improvement of mechanical pain sensitivity measurement method: the smaller sized probes may detect heterogeneous sensory threshold in healthy male subjects.

    PubMed

    Duan, Guangyou; Xiang, Guifang; Zhang, Xianwei; Guo, Shanna; Zhang, Yuhao

    2014-02-01

    On the basis of our experience in the application of the mechanical algometer and a number of pilot experiments, we speculated that 0.1- and 0.01-cm(2) probes might improve the measurement of mechanical pain sensitivity relative to the conventional 1-cm(2) probe. Here, we examined the accuracy, feasibility, and applicability of these probes in detecting the mechanical pain sensitivity. Mechanical pain threshold and tolerance tests were performed on subjects using the three probes of 1, 0.1, and 0.01 cm(2) in random order. We compared the application of these probes. The study was set at the Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. Fifty healthy male Han Chinese subjects were recruited. We compared the qualities of stimulus-evoked pain, test stability, the measuring time, the subjects' acceptance level of the procedure, the validity of pain measurement, and the arduousness of the task for the investigator among the three different size probes. Compared with the conventional 1-cm(2) probe, the 0.01- and 0.1-cm(2) probes resulted in the subjects responding to stimulus-evoked pain more quickly, accurately, and consistently, and also made the measurement more comfortable for investigators. Up to 80% of the subjects reported the pain quality as a pricking sensation when the 0.01-cm(2) probe was used. The use of the 0.1-cm(2) probe might be more suitable as an optimized method for the detection of pressure pain sensitivity in clinical studies. In addition, the 0.01-cm(2) probe could potentially serve as an alternative to the weighted needle pinprick, providing continuous quantizing detection for pricking pain sensitivity. Wiley Periodicals, Inc.

  6. Structure of the Receptor-Binding Carboxy-Terminal Domain of the Bacteriophage T5 L-Shaped Tail Fibre with and without Its Intra-Molecular Chaperone

    PubMed Central

    Garcia-Doval, Carmela; Castón, José R.; Luque, Daniel; Granell, Meritxell; Otero, José M.; Llamas-Saiz, Antonio L.; Renouard, Madalena; Boulanger, Pascale; van Raaij, Mark J.

    2015-01-01

    Bacteriophage T5, a Siphovirus belonging to the order Caudovirales, has a flexible, three-fold symmetric tail, to which three L-shaped fibres are attached. These fibres recognize oligo-mannose units on the bacterial cell surface prior to infection and are composed of homotrimers of the pb1 protein. Pb1 has 1396 amino acids, of which the carboxy-terminal 133 residues form a trimeric intra-molecular chaperone that is auto-proteolyzed after correct folding. The structure of a trimer of residues 970–1263 was determined by single anomalous dispersion phasing using incorporated selenomethionine residues and refined at 2.3 Å resolution using crystals grown from native, methionine-containing, protein. The protein inhibits phage infection by competition. The phage-distal receptor-binding domain resembles a bullet, with the walls formed by partially intertwined beta-sheets, conferring stability to the structure. The fold of the domain is novel and the topology unique to the pb1 structure. A site-directed mutant (Ser1264 to Ala), in which auto-proteolysis is impeded, was also produced, crystallized and its 2.5 Å structure solved by molecular replacement. The additional chaperone domain (residues 1263–1396) consists of a central trimeric alpha-helical coiled-coil flanked by a mixed alpha-beta domain. Three long beta-hairpin tentacles, one from each chaperone monomer, extend into long curved grooves of the bullet-shaped domain. The chaperone-containing mutant did not inhibit infection by competition. PMID:26670244

  7. Structure of the Receptor-Binding Carboxy-Terminal Domain of the Bacteriophage T5 L-Shaped Tail Fibre with and without Its Intra-Molecular Chaperone.

    PubMed

    Garcia-Doval, Carmela; Castón, José R; Luque, Daniel; Granell, Meritxell; Otero, José M; Llamas-Saiz, Antonio L; Renouard, Madalena; Boulanger, Pascale; van Raaij, Mark J

    2015-12-08

    Bacteriophage T5, a Siphovirus belonging to the order Caudovirales, has a flexible, three-fold symmetric tail, to which three L-shaped fibres are attached. These fibres recognize oligo-mannose units on the bacterial cell surface prior to infection and are composed of homotrimers of the pb1 protein. Pb1 has 1396 amino acids, of which the carboxy-terminal 133 residues form a trimeric intra-molecular chaperone that is auto-proteolyzed after correct folding. The structure of a trimer of residues 970-1263 was determined by single anomalous dispersion phasing using incorporated selenomethionine residues and refined at 2.3 Å resolution using crystals grown from native, methionine-containing, protein. The protein inhibits phage infection by competition. The phage-distal receptor-binding domain resembles a bullet, with the walls formed by partially intertwined beta-sheets, conferring stability to the structure. The fold of the domain is novel and the topology unique to the pb1 structure. A site-directed mutant (Ser1264 to Ala), in which auto-proteolysis is impeded, was also produced, crystallized and its 2.5 Å structure solved by molecular replacement. The additional chaperone domain (residues 1263-1396) consists of a central trimeric alpha-helical coiled-coil flanked by a mixed alpha-beta domain. Three long beta-hairpin tentacles, one from each chaperone monomer, extend into long curved grooves of the bullet-shaped domain. The chaperone-containing mutant did not inhibit infection by competition.

  8. Mechanical Properties of Silicone Rubber Acoustic Lens Material Doped with Fine Zinc Oxide Powders for Ultrasonic Medical Probe

    NASA Astrophysics Data System (ADS)

    Yamamoto, Noriko; Yohachi; Yamashita; Itsumi, Kazuhiro

    2009-07-01

    The mechanical properties of high-temperature-vulcanization silicone (Q) rubber doped with zinc oxide (ZnO) fine powders have been investigated to develop an acoustic lens material with high reliability. The ZnO-doped Q rubber with an acoustic impedance (Z) of 1.46×106 kg·m-2·s-1 showed a tear strength of 43 N/mm and an elongation of 560%. These mechanical property values were about 3 times higher than those of conventional acoustic Q lens materials. The ZnO-doped Q rubbers also showed a lower abrasion loss. These superior characteristics are attributable to the microstructure with fewer origins of breaks; few pores and spherical fine ZnO powder. The high mechanical properties of ZnO-doped Q rubber acoustic lenses enable higher performance during long-life and safe operation during diagnosis using medical array probe applications.

  9. A new method of optical biopsy: demonstration of mechanical contrast in deep tissue using an optical coherence elastography needle probe

    NASA Astrophysics Data System (ADS)

    Kennedy, Kelsey M.; Kennedy, Brendan F.; McLaughlin, Robert A.; Sampson, David D.

    2012-02-01

    We incorporate for the first time optical coherence elastography (OCE) into a needle probe and demonstrate its ability to provide depth-resolved information about the mechanical properties of soft tissues. This allows analysis of tissues located much deeper than has previously been possible with other forms of OCE. OCE exploits the microscopic resolution of optical coherence tomography (OCT) to produce high-resolution maps of tissue mechanical properties. While OCE has potential to delineate diseased and healthy tissues (e.g., stiff tumor in soft tissue), standard techniques are limited by the penetration depth of OCT in tissue (2-3 mm). Our OCE needle probe overcomes this limitation, as it may be inserted deep within the body to perform measurements. We tested needle-based OCE in tissue-mimicking phantoms and ex vivo porcine airway tissue comprising layers of varying stiffness. Results demonstrate mechanical differentiation of tissues and identification of tissue interfaces. The proof-of-principle results presented here pave the way for future measurements in human breast tissue that will aim to establish needle-based OCE as a viable technique for intraoperative guidance of breast cancer surgery.

  10. Oxygen isotope effects as probes of electron transfer mechanisms and structures of activated O2.

    PubMed

    Roth, Justine P

    2009-03-17

    Competitively determined oxygen ((18)O) isotope effects can be powerful probes of chemical and biological transformations involving molecular oxygen as well as superoxide and hydrogen peroxide. They play a complementary role to crystallography and spectroscopy in the study of activated oxygen intermediates by forging a link between electronic/vibrational structure and the bonding that occurs within ground and transition states along the reaction coordinate. Such analyses can be used to assess the plausibility of intermediates and their catalytic relevance in oxidative processes. This Account describes efforts to advance oxygen kinetic isotope effects ((18)O KIEs) and equilibrium isotope effects ((18)O EIEs) as mechanistic probes of reactive, oxygen-derived species. We focus primarily on transition metal mediated oxidations, outlining both advances over the past five years and current limitations of this approach. Computational methods are now being developed to probe transition states and the accompanying kinetic isotope effects. In particular, we describe the importance of using a full-frequency model to accurately predict the magnitudes as well as the temperature dependence of the isotope effects. Earlier studies have used a "cut-off model," which employs only a few isotopic vibrational modes, and such models tend to overestimate (18)O EIEs. Researchers in mechanistic biological inorganic chemistry would like to differentiate "inner-sphere" from "outer-sphere" reactivity of O(2), a designation that describes the extent of the bonding interaction between metal and oxygen in the transition state. Though this problem remains unsolved, we expect that this isotopic approach will help differentiate these processes. For example, comparisons of (18)O KIEs to (18)O EIEs provide benchmarks that allow us to calibrate computationally derived reaction coordinates. Once the physical origins of heavy atom isotope effects are better understood, researchers will be able to apply

  11. Emergence of Form from Function - Mechanical Engineering Approaches to Probe the Role of Stem Cell Mechanoadaptation in Sealing Cell Fate.

    PubMed

    Knothe Tate, Melissa L; Gunning, Peter W; Sansalone, Vittorio

    2016-10-14

    Stem cell "mechanomics" refers to the effect of mechanical cues on stem cell and matrix biology, where cell shape and fate are intrinsic manifestations of form and function. Before specialization, the stem cell itself serves as a sensor and actuator; its structure emerges from its local mechanical milieu as the cell adapts over time. Coupling of novel spatiotemporal imaging and computational methods allows for linking of the energy of adaptation to the structure, biology and mechanical function of the cell. Cutting edge imaging methods enable probing of mechanisms by which stem cells' emergent anisotropic architecture and fate commitment occurs. A novel cell-scale model provides a mechanistic framework to describe stem cell growth and remodeling through mechanical feedback; making use of a generalized virtual power principle, the model accounts for the rate of doing work or the rate of using energy to effect the work. This coupled approach provides a basis to elucidate mechanisms underlying the stem cell's innate capacity to adapt to mechanical stimuli as well as the role of mechanoadaptation in lineage commitment. An understanding of stem cell mechanoadaptation is key to deciphering lineage commitment, during prenatal development, postnatal wound healing, and engineering of tissues.

  12. Probe tip heating assembly

    SciTech Connect

    Schmitz, Roger William; Oh, Yunje

    2016-10-25

    A heating assembly configured for use in mechanical testing at a scale of microns or less. The heating assembly includes a probe tip assembly configured for coupling with a transducer of the mechanical testing system. The probe tip assembly includes a probe tip heater system having a heating element, a probe tip coupled with the probe tip heater system, and a heater socket assembly. The heater socket assembly, in one example, includes a yoke and a heater interface that form a socket within the heater socket assembly. The probe tip heater system, coupled with the probe tip, is slidably received and clamped within the socket.

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

    PubMed Central

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

    2006-01-01

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

  14. 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.

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

    PubMed

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

    2006-03-28

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

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

    DOE PAGES

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

    2015-01-22

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

  17. Mechanism-based triarylphosphine-ester probes for capture of endogenous RSNOs.

    PubMed

    Seneviratne, Uthpala; Godoy, Luiz C; Wishnok, John S; Wogan, Gerald N; Tannenbaum, Steven R

    2013-05-22

    Nitrosothiols (RSNOs) have been proposed as important intermediates in nitric oxide (NO(•)) metabolism, storage, and transport as well as mediators in numerous NO-signaling pathways. RSNO levels are finely regulated, and dysregulation is associated with the etiology of several pathologies. Current methods for RSNO quantification depend on indirect assays that limit their overall specificity and reliability. Recent developments of phosphine-based chemical probes constitute a promising approach for the direct detection of RSNOs. We report here results from a detailed mechanistic and kinetic study for trapping RSNOs by three distinct phosphine probes, including structural identification of novel intermediates and stability studies under physiological conditions. We further show that a triarylphosphine-thiophenyl ester can be used in the absolute quantification of endogenous GSNO in several cancer cell lines, while retaining the elements of the SNO functional group, using an LC-MS-based assay. Finally, we demonstrate that a common product ion (m/z = 309.0), derived from phosphine-RSNO adducts, can be used for the detection of other low-molecular weight nitrosothiols (LMW-RSNOs) in biological samples. Collectively, these findings establish a platform for the phosphine ligation-based, specific and direct detection of RSNOs in biological samples, a powerful tool for expanding the knowledge of the biology and chemistry of NO(•)-mediated phenomena.

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

    SciTech Connect

    Lechtenberg, Bernhard C.; Robinson, Howard R.; Kasperkiewicz, Paulina; Drag, Marcin; Riedl, Stefan J.

    2015-01-22

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

  19. Probing neural mechanisms underlying auditory stream segregation in humans by transcranial direct current stimulation (tDCS).

    PubMed

    Deike, Susann; Deliano, Matthias; Brechmann, André

    2016-10-01

    One hypothesis concerning the neural underpinnings of auditory streaming states that frequency tuning of tonotopically organized neurons in primary auditory fields in combination with physiological forward suppression is necessary for the separation of representations of high-frequency A and low-frequency B tones. The extent of spatial overlap between the tonotopic activations of A and B tones is thought to underlie the perceptual organization of streaming sequences into one coherent or two separate streams. The present study attempts to interfere with these mechanisms by transcranial direct current stimulation (tDCS) and to probe behavioral outcomes reflecting the perception of ABAB streaming sequences. We hypothesized that tDCS by modulating cortical excitability causes a change in the separateness of the representations of A and B tones, which leads to a change in the proportions of one-stream and two-stream percepts. To test this, 22 subjects were presented with ambiguous ABAB sequences of three different frequency separations (∆F) and had to decide on their current percept after receiving sham, anodal, or cathodal tDCS over the left auditory cortex. We could confirm our hypothesis at the most ambiguous ∆F condition of 6 semitones. For anodal compared with sham and cathodal stimulation, we found a significant decrease in the proportion of two-stream perception and an increase in the proportion of one-stream perception. The results demonstrate the feasibility of using tDCS to probe mechanisms underlying auditory streaming through the use of various behavioral measures. Moreover, this approach allows one to probe the functions of auditory regions and their interactions with other processing stages. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  20. Sensing surface mechanical deformation using active probes driven by motor proteins

    PubMed Central

    Inoue, Daisuke; Nitta, Takahiro; Kabir, Arif Md. Rashedul; Sada, Kazuki; Gong, Jian Ping; Konagaya, Akihiko; Kakugo, Akira

    2016-01-01

    Studying mechanical deformation at the surface of soft materials has been challenging due to the difficulty in separating surface deformation from the bulk elasticity of the materials. Here, we introduce a new approach for studying the surface mechanical deformation of a soft material by utilizing a large number of self-propelled microprobes driven by motor proteins on the surface of the material. Information about the surface mechanical deformation of the soft material is obtained through changes in mobility of the microprobes wandering across the surface of the soft material. The active microprobes respond to mechanical deformation of the surface and readily change their velocity and direction depending on the extent and mode of surface deformation. This highly parallel and reliable method of sensing mechanical deformation at the surface of soft materials is expected to find applications that explore surface mechanics of soft materials and consequently would greatly benefit the surface science. PMID:27694937

  1. Mechanical gate control for atom-by-atom cluster assembly with scanning probe microscopy.

    PubMed

    Sugimoto, Yoshiaki; Yurtsever, Ayhan; Hirayama, Naoki; Abe, Masayuki; Morita, Seizo

    2014-07-11

    Nanoclusters supported on substrates are of great importance in physics and chemistry as well as in technical applications, such as single-electron transistors and nanocatalysts. The properties of nanoclusters differ significantly from those of either the constituent atoms or the bulk solid, and are highly sensitive to size and chemical composition. Here we propose a novel atom gating technique to assemble various atom clusters composed of a defined number of atoms at room temperature. The present gating operation is based on the transfer of single diffusing atoms among nanospaces governed by gates, which can be opened in response to the chemical interaction force with a scanning probe microscope tip. This method provides an alternative way to create pre-designed atom clusters with different chemical compositions and to evaluate their chemical stabilities, thus enabling investigation into the influence that a single dopant atom incorporated into the host clusters has on a given cluster stability.

  2. Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase

    NASA Astrophysics Data System (ADS)

    Forde, Nancy R.; Izhaky, David; Woodcock, Glenna R.; Wuite, Gijs J. L.; Bustamante, Carlos

    2002-09-01

    Escherichia coli RNA polymerase translocates along the DNA discontinuously during the elongation phase of transcription, spending proportionally more time at some template positions, known as pause and arrest sites, than at others. Current models of elongation suggest that the enzyme backtracks at these locations, but the dynamics are unresolved. Here, we study the role of lateral displacement in pausing and arrest by applying force to individually transcribing molecules. We find that an assisting mechanical force does not alter the translocation rate of the enzyme, but does reduce the efficiency of both pausing and arrest. Moreover, arrested molecules cannot be rescued by force, suggesting that arrest occurs by a bipartite mechanism: the enzyme backtracks along the DNA followed by a conformational change of the ternary complex (RNA polymerase, DNA and transcript), which cannot be reversed mechanically.

  3. Reinforcement Mechanism Of Polyurethane-Urea/Clay Nanocomposites Probed By Positron Annihilation Lifetime Spectroscopy And Dynamic Mechanical Analysis

    SciTech Connect

    Rath, S. K.; Patri, M.; Sudarshan, K.; Pujari, P. K.; Khakhar, D. V.

    2010-12-01

    A basis for quantitative analysis of the reinforcement mechanism of polyurethane-urea/clay nanocomposites using two characterization methods, positron annihilation life time spectroscopy (PALS) and dynamic mechanical analysis (DMA) is provided. DMA was used to measure the constrained volume fraction of amorphous soft segments induced by nanoclay and the storage modulus of the nanocomposites. The interfacial interactions in the nanocomposites were investigated by PALS. The modulus enhancement of the organoclay nanocomposites was found to have a good correlation with the volume fraction of the constrained region and the interfacial interactions.

  4. Vertical nanopillars for in situ probing of nuclear mechanics in adherent cells

    NASA Astrophysics Data System (ADS)

    Hanson, Lindsey; Zhao, Wenting; Lou, Hsin-Ya; Lin, Ziliang Carter; Lee, Seok Woo; Chowdary, Praveen; Cui, Yi; Cui, Bianxiao

    2015-06-01

    The mechanical stability and deformability of the cell nucleus are crucial to many biological processes, including migration, proliferation and polarization. In vivo, the cell nucleus is frequently subjected to deformation on a variety of length and time scales, but current techniques for studying nuclear mechanics do not provide access to subnuclear deformation in live functioning cells. Here we introduce arrays of vertical nanopillars as a new method for the in situ study of nuclear deformability and the mechanical coupling between the cell membrane and the nucleus in live cells. Our measurements show that nanopillar-induced nuclear deformation is determined by nuclear stiffness, as well as opposing effects from actin and intermediate filaments. Furthermore, the depth, width and curvature of nuclear deformation can be controlled by varying the geometry of the nanopillar array. Overall, vertical nanopillar arrays constitute a novel approach for non-invasive, subcellular perturbation of nuclear mechanics and mechanotransduction in live cells.

  5. Complex fluids: probing mechanical properties of biological systems with optical tweezers.

    PubMed

    Ou-Yang, H Daniel; Wei, Ming-Tzo

    2010-01-01

    The mechanical properties of cells are crucial for cell sensing and reaction to mechanical environments. This review describes the basic principles of optical tweezers and their use as force sensors for studying the mechanical properties of biological systems. It covers experiments of four groups of biological systems arranged by increasing complexity: (a) packaging DNA into viral capsids by bacteriophage portal motors and the dynamical stiffness of DNA upon protein binding, (b) actin-coated giant vesicles and the myosin-II embedded actin polymer network, (c) suspension cells, and (d) adhesion cells. These examples demonstrate how optical tweezers have been used to improve the understanding of the mechanical properties of biological systems at subcellular and molecular levels.

  6. Vertical nanopillars for in situ probing of nuclear mechanics in adherent cells

    PubMed Central

    Hanson, Lindsey; Zhao, Wenting; Lou, Hsin-Ya; Lin, Ziliang Carter; Lee, Seok Woo; Chowdary, Praveen; Cui, Yi; Cui, Bianxiao

    2016-01-01

    The mechanical stability and deformability of the cell nucleus are crucial to many biological processes, including migration, proliferation and polarization. In vivo, the cell nucleus is frequently subjected to deformation on a variety of length and time scales, but current techniques for studying nuclear mechanics do not provide access to subnuclear deformation in live functioning cells. Here we introduce arrays of vertical nanopillars as a new method for the in situ study of nuclear deformability and the mechanical coupling between the cell membrane and the nucleus in live cells. Our measurements show that nanopillar-induced nuclear deformation is determined by nuclear stiffness, as well as opposing effects from actin and intermediate filaments. Furthermore, the depth, width and curvature of nuclear deformation can be controlled by varying the geometry of the nanopillar array. Overall, vertical nanopillar arrays constitute a novel approach for non-invasive, subcellular perturbation of nuclear mechanics and mechanotransduction in live cells. PMID:25984833

  7. Vertical nanopillars for in situ probing of nuclear mechanics in adherent cells.

    PubMed

    Hanson, Lindsey; Zhao, Wenting; Lou, Hsin-Ya; Lin, Ziliang Carter; Lee, Seok Woo; Chowdary, Praveen; Cui, Yi; Cui, Bianxiao

    2015-06-01

    The mechanical stability and deformability of the cell nucleus are crucial to many biological processes, including migration, proliferation and polarization. In vivo, the cell nucleus is frequently subjected to deformation on a variety of length and time scales, but current techniques for studying nuclear mechanics do not provide access to subnuclear deformation in live functioning cells. Here we introduce arrays of vertical nanopillars as a new method for the in situ study of nuclear deformability and the mechanical coupling between the cell membrane and the nucleus in live cells. Our measurements show that nanopillar-induced nuclear deformation is determined by nuclear stiffness, as well as opposing effects from actin and intermediate filaments. Furthermore, the depth, width and curvature of nuclear deformation can be controlled by varying the geometry of the nanopillar array. Overall, vertical nanopillar arrays constitute a novel approach for non-invasive, subcellular perturbation of nuclear mechanics and mechanotransduction in live cells.

  8. Shape of clusters of galaxies as a probe of screening mechanisms in modified gravity.

    PubMed

    Llinares, Claudio; Mota, David F

    2013-04-12

    Scalar fields are crucial components in high energy physics and extensions of general relativity. The fact that they are not observed in the Solar System may be due to a mechanism which screens their presence in high dense regions. We show how observations of the ellipticity of galaxy clusters can discriminate between models with and without scalar fields and even between different screening mechanisms. Using current x-ray observations we put novel constraints on the different models.

  9. Mechanical failure modes of chronically implanted planar silicon-based neural probes for laminar recording.

    PubMed

    Kozai, Takashi D Y; Catt, Kasey; Li, Xia; Gugel, Zhannetta V; Olafsson, Valur T; Vazquez, Alberto L; Cui, X Tracy

    2015-01-01

    Penetrating intracortical electrode arrays that record brain activity longitudinally are powerful tools for basic neuroscience research and emerging clinical applications. However, regardless of the technology used, signals recorded by these electrodes degrade over time. The failure mechanisms of these electrodes are understood to be a complex combination of the biological reactive tissue response and material failure of the device over time. While mechanical mismatch between the brain tissue and implanted neural electrodes have been studied as a source of chronic inflammation and performance degradation, the electrode failure caused by mechanical mismatch between different material properties and different structural components within a device have remained poorly characterized. Using Finite Element Model (FEM) we simulate the mechanical strain on a planar silicon electrode. The results presented here demonstrate that mechanical mismatch between iridium and silicon leads to concentrated strain along the border of the two materials. This strain is further focused on small protrusions such as the electrical traces in planar silicon electrodes. These findings are confirmed with chronic in vivo data (133-189 days) in mice by correlating a combination of single-unit electrophysiology, evoked multi-unit recordings, electrochemical impedance spectroscopy, and scanning electron microscopy from traces and electrode sites with our modeling data. Several modes of mechanical failure of chronically implanted planar silicon electrodes are found that result in degradation and/or loss of recording. These findings highlight the importance of strains and material properties of various subcomponents within an electrode array. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Mechanical failure modes of chronically implanted planar silicon-based neural probes for laminar recording

    PubMed Central

    Kozai, Takashi D. Y.; Catt, Kasey; Li, Xia; Gugel, Zhannetta V.; Olafsson, Valur T.; Vazquez, Alberto L.; Cui, X. Tracy

    2014-01-01

    Penetrating intracortical electrode arrays that record brain activity longitudinally are powerful tools for basic neuroscience research and emerging clinical applications. However, regardless of the technology used, signals recorded by these electrodes degrade over time. The failure mechanisms of these electrodes are understood to be a complex combination of the biological reactive tissue response and material failure of the device over time. While mechanical mismatch between the brain tissue and implanted neural electrodes have been studied as a source of chronic inflammation and performance degradation, the electrode failure caused by mechanical mismatch between different material properties and different structural components within a device have remained poorly characterized. Using Finite Element Model (FEM) we simulate the mechanical strain on a planar silicon electrode. The results presented here demonstrate that mechanical mismatch between iridium and silicon leads to concentrated strain along the border of the two materials. This strain is further focused on small protrusions such as the electrical traces in planar silicon electrodes. These findings are confirmed with chronic in vivo data (133–189 days) in mice by correlating a combination of single-unit electrophysiology, evoked multi-unit recordings, electrochemical impedance spectroscopy, and scanning electron microscopy from traces and electrode sites with our modeling data. Several modes of mechanical failure of chronically implanted planar silicon electrodes are found that result in degradation and/or loss of recording. These findings highlight the importance of strains and material properties of various subcomponents within an electrode array. PMID:25453935

  11. Mechanisms for transcellular diapedesis: probing and pathfinding by 'invadosome-like protrusions'.

    PubMed

    Carman, Christopher V

    2009-09-01

    Immune-system functions require that blood leukocytes continuously traffic throughout the body and repeatedly cross endothelial barriers (i.e. diapedese) as they enter (intravasate) and exit (extravasate) the circulation. The very earliest studies to characterize diapedesis directly in vivo suggested the coexistence of two distinct migratory pathways of leukocytes: between (paracellular pathway) and directly through (transcellular pathway) individual endothelial cells. In vivo studies over the past 50 years have demonstrated significant use of the transcellular diapedesis pathway in bone marrow, thymus, secondary lymphoid organs, various lymphatic structures and peripheral tissues during inflammation and across the blood-brain barrier and blood-retinal barrier during inflammatory pathology. Recently, the first in vitro reports of transcellular diapedesis have emerged. Together, these in vitro and in vivo observations suggest a model of migratory pathfinding in which dynamic 'invadosome-like protrusions' formed by leukocytes have a central role in both identifying and exploiting endothelial locations that are permissive for transcellular diapedesis. Such 'probing' activity might have additional roles in this and other settings.

  12. Probing molecular adsorption and mechanics at the atomic scale: The Nanocar family of molecules

    NASA Astrophysics Data System (ADS)

    Osgood, Andrew J.

    Molecular machines, typically thought to be only the fanciful imaginings of speculative fiction, have taken great strides in recent years towards real-world viability and usefulness. Under variable temperature scanning tunneling microscopy, (STM) one family of these nascent devices is characterized with atomic resolution, and probed and manipulated with sub-angstrom precision, adding to the growing body of knowledge of how molecular devices behave and react at nanometer scales. Evidence of temperature-dependent rolling of wheel-like fullerene constituents on the Nanocar is discussed in light of newly developed image analysis techniques. Additionally, charge-transfer mediated behavior at step edges, both static and dynamic, is investigated on a Au(111) surface for a more complete understanding of translation and surface diffusion. Molecular flexibility is thought to aid in this three-dimensional atomic-step-crossing diffusion, and is explored and discussed across many species in the Nanocar family of molecules. In all, many similar molecules have been characterized and explored via STM with an eye towards their dynamic capabilities and surface behaviors, in the hopes that future, more complex versions can build on the nascent knowledge base beginning to be established here.

  13. Mechanical-plowing-based high-speed patterning on hard material via advanced-control and ultrasonic probe vibration

    SciTech Connect

    Wang, Zhihua; Zou, Qingze; Tan, Jun; Jiang, Wei

    2013-11-15

    In this paper, we present a high-speed direct pattern fabrication on hard materials (e.g., a tungsten-coated quartz substrate) via mechanical plowing. Compared to other probe-based nanolithography techniques based on chemical- and/or physical-reactions (e.g., the Dip-pen technique), mechanical plowing is meritorious for its low cost, ease of process control, and capability of working with a wide variety of materials beyond conductive and/or soft materials. However, direct patterning on hard material faces two daunting challenges. First, the patterning throughput is ultimately hindered by the “writing” (plowing) speed, which, in turn, is limited by the adverse effects that can be excited/induced during high-speed, and/or large-range plowing, including the vibrational dynamics of the actuation system (the piezoelectric actuator, the cantilever, and the mechanical fixture connecting the cantilever to the actuator), the dynamic cross-axis coupling between different axes of motion, and the hysteresis and the drift effects related to the piezoelectric actuators. Secondly, it is very challenging to directly pattern on ultra-hard materials via plowing. Even with a diamond probe, the line depth of the pattern via continuous plowing on ultra-hard materials such as tungsten, is still rather small (<0.5 nm), particularly when the “writing” speed becomes high. To overcome these two challenges, we propose to utilize a novel iterative learning control technique to achieve precision tracking of the desired pattern during high-speed, large-range plowing, and introduce ultrasonic vibration of the probe in the normal (vertical) direction during the plowing process to enable direct patterning on ultra hard materials. The proposed approach was implemented to directly fabricate patterns on a mask with tungsten coating and quartz substrate. The experimental results demonstrated that a large-size pattern of four grooves (20 μm in length with 300 nm spacing between lines) can be

  14. Hydrodynamic ultrasonic probe

    DOEpatents

    Day, Robert A.; Conti, Armond E.

    1980-01-01

    An improved probe for in-service ultrasonic inspection of long lengths of a workpiece, such as small diameter tubing from the interior. The improved probe utilizes a conventional transducer or transducers configured to inspect the tubing for flaws and/or wall thickness variations. The probe utilizes a hydraulic technique, in place of the conventional mechanical guides or bushings, which allows the probe to move rectilinearly or rotationally while preventing cocking thereof in the tube and provides damping vibration of the probe. The probe thus has lower friction and higher inspection speed than presently known probes.

  15. Tryptophan as a probe to study the anticancer mechanism of action and specificity of α-helical anticancer peptides.

    PubMed

    Li, Guirong; Huang, Yibing; Feng, Qi; Chen, Yuxin

    2014-08-13

    In the present study, a single tryptophan, as a fluorescence probe, was shifted from the N-terminus to the middle and to the C-terminus of a 26-residue α-helical anticancer peptide sequence to study the mechanism of action and specificity. The hydrophobicity of peptides, as well as peptide helicity and self-associating ability, were slightly influenced by the position change of tryptophan in the peptide sequence, while the hemolytic activity and anticancer activity of the peptide analogs remained the same. The tryptophan fluorescence experiment demonstrated that peptide analogs were more selective against LUVs mimicking cancer cell membranes than LUVs mimicking normal cell membranes. During the interaction with target membranes, the N-terminus of an anticancer peptide may be inserted vertically or tilted into the hydrophobic components of the phospholipid bilayer first. The thermodynamic parameters of the peptides PNW and PCW, when interacting with zwitterionic DMPC or negatively charged DMPS, were determined by ITC. DSC experiments showed that peptide analogs significantly altered the phase transition profiles of DMPC, but did not dramatically modify the phase transition of DMPS. It is demonstrated that hydrophobic interactions are the main driving force for peptides interacting with normal cell membranes, whilst, electrostatic interactions dominate the interactions between peptides and cancer cell membranes. Utilizing tryptophan as a fluorescence probe molecule appears to be a practicable approach to determine the interaction of peptides with phospholipid bilayers.

  16. Common and differential electrophysiological mechanisms underlying semantic object memory retrieval probed by features presented in different stimulus types.

    PubMed

    Chiang, Hsueh-Sheng; Eroh, Justin; Spence, Jeffrey S; Motes, Michael A; Maguire, Mandy J; Krawczyk, Daniel C; Brier, Matthew R; Hart, John; Kraut, Michael A

    2016-08-01

    How the brain combines the neural representations of features that comprise an object in order to activate a coherent object memory is poorly understood, especially when the features are presented in different modalities (visual vs. auditory) and domains (verbal vs. nonverbal). We examined this question using three versions of a modified Semantic Object Retrieval Test, where object memory was probed by a feature presented as a written word, a spoken word, or a picture, followed by a second feature always presented as a visual word. Participants indicated whether each feature pair elicited retrieval of the memory of a particular object. Sixteen subjects completed one of the three versions (N=48 in total) while their EEG were recorded simultaneously. We analyzed EEG data in four separate frequency bands (delta: 1-4Hz, theta: 4-7Hz; alpha: 8-12Hz; beta: 13-19Hz) using a multivariate data-driven approach. We found that alpha power time-locked to response was modulated by both cross-modality (visual vs. auditory) and cross-domain (verbal vs. nonverbal) probing of semantic object memory. In addition, retrieval trials showed greater changes in all frequency bands compared to non-retrieval trials across all stimulus types in both response-locked and stimulus-locked analyses, suggesting dissociable neural subcomponents involved in binding object features to retrieve a memory. We conclude that these findings support both modality/domain-dependent and modality/domain-independent mechanisms during semantic object memory retrieval.

  17. Tritiated chiral alkanes as substrates for soluble methane monooxygenase from Methylococcus capsulatus (Bath): Probes for the mechanism of hydroxylation

    SciTech Connect

    Valentine, A.M.; Liu, K.E.; Komar-Panicucci, S.; Lippard, S.J.; Wilkinson, B.; Priestley, N.D.; Floss, H.G.; Williams, P.G.; Morimoto, Hiromi

    1997-02-26

    The tritiated chiral alkanes (S)-[1-{sup 2}H{sub 1}, 1-{sup 3}H]ethane, (R)-[1-{sup 2}H{sub 1},1-{sup 3}H]ethane, (S)-[1-{sup 2}H{sub 1},1-{sup 3}H]butane, (R)-[1-{sup 2}H{sub 1}, 1-{sup 3}H]butane, (S)-[2-{sup 3}H]butane, (R)-[2-{sup 3}H]butane, and racemic [2-{sup 3}H]butane were oxidized by soluble methane monooxygenase (sMMO) from Methylococcus capsulatus (Bath), and the absolute stereochemistry of the resulting product alcohols was determined in order to probe the mechanism of substrate hydroxylation. When the hydroxylations were performed with purified hydroxylase but only a partially purified cellular extract for the coupling and reductase proteins, different product distributions were observed. These apparently anomalous results could be explained by invoking exchange of hydrogen atoms at the {alpha} carbon of the product alcohols. The characteristics of this exchange reaction are discussed. Together with the mechanistic information available from a range of substrate probes, the results are best accounted for by a nonsynchronous concerted process involving attack on the C-H bond by one or more of several pathways discussed in the text. 65 refs., 5 figs., 3 tabs.

  18. MUPUS - a thermal and mechanical properties probe for the Rosetta Lander Philae

    NASA Astrophysics Data System (ADS)

    Knollenberg, Jörg; Spohn, Tilman; Seiferlin, Karsten; Hagermann, Axel; Ball, Andrew; Banaszkiewicz, Marek; Grygorczuk, Jerzy; Grott, Matthias; Kargl, Günter; Kuehrt, Ekkehard; Koemle, Norbert; Marczewski, Wojciech

    2014-05-01

    MUPUS, the multi purpose sensor package onboard the Rosetta lander PHILAE, will measure the energy balance and the thermophysical and mechnical parameters in the near-surface layers - up to about 30 cm depth- of the nucleus of Rosetta's target comet Churyumov-Gerasimenko. Moreover it will monitor changes in these parameters over time as the comet approaches the Sun. The data should increase our knowledge of how comets work, and how the coma gases form. The data may also be used to constrain the microstructure of the nucleus material. Changes with time of physical properties will reveal timescales and possibly the nature of processes that modify the material close to the surface. Thereby, the data will indicate how pristine cometary matter sampled and analysed by other experiments on PHILAE really is. The MUPUS package consists of three major parts, the penetrator MUPUS PEN with ist sub-systems, the radiometer MUPUS TM, and the anchor sensors MUPUS ANC. the PEN is equipped with 16 RTD-type sensors along the penetrator tube aimed at measuring the temperature profile. Furthermore, they can also be actively heated in order to be used as a thermal conductivity probe. TM uses 4 thermopile sensors and different filters covering the wavelength range from 6-25 µm to measure the emitted flux from the comets surface. Both anchors are equipped with an accelerometer (ANC-M) and a Pt-100 temperature sensor to determine the hardness profile at the landing site and the thermal diffusivity at the final depth. An update of the status of the instrument after about 10 years in space with emphasis on the results of the latest tests performed during the post-hibernation commissioning will be given. Furthermore, an overview of related modelling efforts as well as supporting laboratory work in preparation of the data analysis will be provided.

  19. Carotenoid radical cations as a probe for the molecular mechanism of nonphotochemical quenching in oxygenic photosynthesis.

    PubMed

    Amarie, Sergiu; Standfuss, Jörg; Barros, Tiago; Kühlbrandt, Werner; Dreuw, Andreas; Wachtveitl, Josef

    2007-04-05

    Nonphotochemical quenching (NPQ) is a fundamental mechanism in photosynthesis which protects plants against excess excitation energy and is of crucial importance for their survival and fitness. Recently, carotenoid radical cation (Car*+) formation has been discovered to be a key step for the feedback deexcitation quenching mechanism (qE), a component of NPQ, of which the molecular mechanism and location is still unknown. We have generated and characterized carotenoid radical cations by means of resonant two color, two photon ionization (R2C2PI) spectroscopy. The Car*+ bands have maxima located at 830 nm (violaxanthin), 880 nm (lutein), 900 nm (zeaxanthin), and 920 nm (beta-carotene). The positions of these maxima depend strongly on solution conditions, the number of conjugated C=C bonds, and molecular structure. Furthermore, R2C2PI measurements on the light-harvesting complex of photosystem II (LHC II) samples with or without zeaxanthin (Zea) reveal the violaxanthin (Vio) radical cation (Vio*+) band at 909 nm and the Zea*+ band at 983 nm. The replacement of Vio by Zea in the light-harvesting complex II (LHC II) has no influence on the Chl excitation lifetime, and by exciting the Chls lowest excited state, no additional rise and decay corresponding to the Car*+ signal observed previously during qE was detected in the spectral range investigated (800-1050 nm). On the basis of our findings, the mechanism of qE involving the simple replacement of Vio with Zea in LHC II needs to be reconsidered.

  20. The ROSETTA PHILAE Lander damping mechanism as probe for the Comet soil strength.

    NASA Astrophysics Data System (ADS)

    Roll, R.

    2015-10-01

    The ROSETTA Lander is equipped with an one axis damping mechanism to dissipate kinetic energy during the touch down. This damping is necessary to avoid damages to the Lander by a hard landing shock and more important to avoid re-bouncing from ground with high velocity. The damping mechanism works best for perpendicular impact, which means the velocity vector is parallel to the damper axis and all three feet touch the ground at the same time. That is usually not the case. Part of the impact energy can be transferred into rotational energy at ground contact if the impact is not perpendicular. This energy will lift up the Lander from the ground if the harpoons and the hold down thruster fail, as happen in mission. The damping mechanism itself is an electrical generator, driven by a spindle inside a telescopic tube. This tube was extended in mission for landing by 200mm. A maximum damping length of 140mm would be usually required to compensate a landing velocity of 1m/s, if the impact happens perpendicular on hard ground. After landing the potentiometer of the telescopic tube reading shows a total damping length of only 42,5mm. The damping mechanism and the overall mechanical behavior of the Lander at touch down are well tested and characterized and transferred to a multi-body computer model. The incoming and outgoing flightpath of PHILAE allow via computer-simulation the reconstruction of the touch down. It turns out, that the outgoing flight direction is dominated by the local ground slope and that the damping length is strongly dependent on the soil strength. Damping of soft comet ground must be included to fit the damping length measured. Scenario variations of the various feet contact with different local surface features (stone or regolith) and of different soil models finally lead to a restricted range for the soil strength at the touch down area.

  1. Probing mechanical principles of focal contacts in cell–matrix adhesion with a coupled stochastic–elastic modelling framework

    PubMed Central

    Gao, Huajian; Qian, Jin; Chen, Bin

    2011-01-01

    Cell–matrix adhesion depends on the collective behaviours of clusters of receptor–ligand bonds called focal contacts between cell and extracellular matrix. While the behaviour of a single molecular bond is governed by statistical mechanics at the molecular scale, continuum mechanics should be valid at a larger scale. This paper presents an overview of a series of recent theoretical studies aimed at probing the basic mechanical principles of focal contacts in cell–matrix adhesion via stochastic–elastic models in which stochastic descriptions of molecular bonds and elastic descriptions of interfacial traction–separation are unified in a single modelling framework. The intention here is to illustrate these principles using simple analytical and numerical models. The aim of the discussions is to provide possible clues to the following questions: why does the size of focal adhesions (FAs) fall into a narrow range around the micrometre scale? How can cells sense and respond to substrates of varied stiffness via FAs? How do the magnitude and orientation of mechanical forces affect the binding dynamics of FAs? The effects of cluster size, cell–matrix elastic modulus, loading direction and cytoskeletal pretension on the lifetime of FA clusters have been investigated by theoretical arguments as well as Monte Carlo numerical simulations, with results showing that intermediate adhesion size, stiff substrate, cytoskeleton stiffening, low-angle pulling and moderate cytoskeletal pretension are factors that contribute to stable FAs. From a mechanistic point of view, these results provide possible explanations for a wide range of experimental observations and suggest multiple mechanisms by which cells can actively control adhesion and de-adhesion via cytoskeletal contractile machinery in response to mechanical properties of their surroundings. PMID:21632610

  2. Theoretical investigation on ratiometric two-photon fluorescent probe for Zn2+ detection based on ICT mechanism

    NASA Astrophysics Data System (ADS)

    Huang, Shuang; Yang, Bao-Zhu; Ren, Ai-Min

    2016-06-01

    OPA (one-photon absorption), TPA (two-photon absorption) and fluorescence properties of a free ligand L upon coordination with Zn2+, and the regeneration with CN- were investigated in theory. According to our research, OPA spectra of ligand L show red-shift binding with Zn2+ while blue-shift with CN-. The fluorescence spectra and TPA wavelength are shifted in the same situation as those of OPA spectra. The value of TPA cross-section decreased at first, and then increased to 1813 GM for [L-Zn(CN)4]2-. Intramolecular charge transfer (ICT) mechanism was investigated by natural bond orbital (NBO) analysis. It demonstrates that L is hopeful to be a good ratiometric fluorescent probe for zinc ion detection in solution, and it can regenerate after CN- was introduced.

  3. Electrical transport and mechanical properties of alkylsilane self-assembled monolayers on silicon surfaces probed by atomic force microscopy

    SciTech Connect

    Park, Jeong Young; Qi, Yabing; Ashby, Paul D.; Hendriksen, Bas L.M.; Salmeron, Miquel

    2009-02-06

    The correlation between molecular conductivity and mechanical properties (molecular deformation and frictional responses) of hexadecylsilane self-assembled monolayers was studied with conductive probe atomic force microscopy/friction force microscopy in ultrahigh vacuum. Current and friction were measured as a function of applied pressure, simultaneously, while imaging the topography of self-assembled monolayer molecule islands and silicon surfaces covered with a thin oxide layer. Friction images reveal lower friction over the molecules forming islands than over the bare silicon surface, indicating the lubricating functionality of alkylsilane molecules. By measuring the tunneling current change due to changing of the height of the molecular islands by tilting the molecules under pressure from the tip, we obtained an effective conductance decay constant ({beta}) of 0.52/{angstrom}.

  4. Mechanical spectra measurement to probe the magnetolattice coupling in cupric oxide

    NASA Astrophysics Data System (ADS)

    Ying, X. N.; Wang, Y. N.

    2005-12-01

    Mechanical spectra (complex Young's modulus Y*=Y‧+i Y″ versus frequency and temperature) of polycrystalline cupric oxide CuO were measured by vibrating reed method from liquid nitrogen temperature to room temperature at the kilohertz frequency. The abnormal behavior of internal friction and the change of slope of the real part of the complex Young's modulus versus temperature are observed around 213 and 230 K, where two successive magnetic transitions were established. At low temperatures, below 130 K, a higher internal friction platform with the decrease of temperature was clearly observed which might show a phase transition. Our study indicates that mechanical spectrum is an effective tool to detect subtle phase transitions and there is a strong magnetolattice coupling in CuO.

  5. Accessing thermo-mechanical properties of semiconductors using a pump-probe surface displacement method

    NASA Astrophysics Data System (ADS)

    González-Borrero, P. P.; Lukasievicz, G. V. B.; Zanuto, V. S.; Astrath, N. G. C.; Malacarne, L. C.

    2017-05-01

    Description of the physical mechanism leading to laser induced thermal and electronic effects in semiconductors is crucial in both basic research and technological applications. In this paper, we present a thermal mirror technique to study the thermo-mechanical properties of semiconductors. A detailed theoretical investigation is presented, and the dominant effects are described in terms of the physical properties of the material. The effect of heat coupling between the sample and the surrounding fluid was taken into account and considerations on the time and spatial approximations to the photogenerated carriers profile were used to simplify the theoretical model. These approximations were then compared to numerical models and the results hold for high recombination rate semiconductors. Experiments were performed to validate the theoretical model, and the thermal diffusivity and photogenerated heat in the sample were determined. The values obtained for these properties were found to be in good agreement with literature.

  6. Probing the mechanism of cardiovascular drugs using a covalent levosimendan analog.

    PubMed

    Pineda-Sanabria, Sandra E; Robertson, Ian M; Sun, Yin-Biao; Irving, Malcolm; Sykes, Brian D

    2016-03-01

    One approach to improve contraction in the failing heart is the administration of calcium (Ca(2+)) sensitizers. Although it is known that levosimendan and other sensitizers bind to troponin C (cTnC), their in vivo mechanism is not fully understood. Based on levosimendan, we designed a covalent Ca(2+) sensitizer (i9) that targets C84 of cTnC and exchanged this complex into cardiac muscle. The NMR structure of the covalent complex showed that i9 binds deep in the hydrophobic pocket of cTnC. Despite slightly reducing troponin I affinity, i9 enhanced the Ca(2+) sensitivity of cardiac muscle. We conclude that i9 enhances Ca(2+) sensitivity by stabilizing the open conformation of cTnC. These findings provide new insights into the in vivo mechanism of Ca(2+) sensitization and demonstrate that directly targeting cTnC has significant potential in cardiovascular therapy.

  7. A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems

    NASA Astrophysics Data System (ADS)

    Kruse, Holger; Grimme, Stefan

    2012-04-01

    A semi-empirical counterpoise-type correction for basis set superposition error (BSSE) in molecular systems is presented. An atom pair-wise potential corrects for the inter- and intra-molecular BSSE in supermolecular Hartree-Fock (HF) or density functional theory (DFT) calculations. This geometrical counterpoise (gCP) denoted scheme depends only on the molecular geometry, i.e., no input from the electronic wave-function is required and hence is applicable to molecules with ten thousands of atoms. The four necessary parameters have been determined by a fit to standard Boys and Bernadi counterpoise corrections for Hobza's S66×8 set of non-covalently bound complexes (528 data points). The method's target are small basis sets (e.g., minimal, split-valence, 6-31G*), but reliable results are also obtained for larger triple-ζ sets. The intermolecular BSSE is calculated by gCP within a typical error of 10%-30% that proves sufficient in many practical applications. The approach is suggested as a quantitative correction in production work and can also be routinely applied to estimate the magnitude of the BSSE beforehand. The applicability for biomolecules as the primary target is tested for the crambin protein, where gCP removes intramolecular BSSE effectively and yields conformational energies comparable to def2-TZVP basis results. Good mutual agreement is also found with Jensen's ACP(4) scheme, estimating the intramolecular BSSE in the phenylalanine-glycine-phenylalanine tripeptide, for which also a relaxed rotational energy profile is presented. A variety of minimal and double-ζ basis sets combined with gCP and the dispersion corrections DFT-D3 and DFT-NL are successfully benchmarked on the S22 and S66 sets of non-covalent interactions. Outstanding performance with a mean absolute deviation (MAD) of 0.51 kcal/mol (0.38 kcal/mol after D3-refit) is obtained at the gCP-corrected HF-D3/(minimal basis) level for the S66 benchmark. The gCP-corrected B3LYP-D3/6-31G* model

  8. Mechanical Probing of the Intermediate Filament-Rich Caenorhabditis Elegans Intestine.

    PubMed

    Jahnel, Oliver; Hoffmann, Bernd; Merkel, Rudolf; Bossinger, Olaf; Leube, Rudolf E

    2016-01-01

    It is commonly accepted that intermediate filaments have an important mechanical function. This function relies not only on intrinsic material properties but is also determined by dynamic interactions with other cytoskeletal filament systems, distinct cell adhesion sites, and cellular organelles which are fine-tuned by multiple signaling pathways. While aspects of these properties and processes can be studied in vitro, their full complexity can only be understood in a viable tissue context. Yet, suitable and easily accessible model systems for monitoring tissue mechanics at high precision are rare. We show that the dissected intestine of the genetic model organism Caenorhabditis elegans fulfills this requirement. The 20 intestinal cells, which are arranged in an invariant fashion, are characterized by a dense subapical mesh of intermediate filaments that are attached to the C. elegans apical junction. We present procedures to visualize details of the characteristic intermediate filament-junctional complex arrangement in living animals. We then report on methods to prepare intestines with a fully intact intermediate filament cytoskeleton and detail procedures to assess their viability. A dual micropipette assay is described to measure mechanical properties of the dissected intestine while monitoring the spatial arrangement of the intermediate filament system. Advantages of this approach are (i) the high reproducibility of measurements because of the uniform architecture of the intestine and (ii) the high degree of accessibility allowing not only mechanical manipulation of an intact tissue but also control of culture medium composition and addition of drugs as well as visualization of cell structures. With this method, examination of worms carrying mutations in the intermediate filament system, its interacting partners and its regulators will become feasible. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Probing the two-metal ion mechanism in the restriction endonuclease BamHI.

    PubMed

    Mones, Letif; Kulhánek, Petr; Florián, Jan; Simon, István; Fuxreiter, Monika

    2007-12-18

    The choreography of restriction endonuclease catalysis is a long-standing paradigm in molecular biology. Bivalent metal ions are required almost for all PD..D/ExK type enzymes, but the number of cofactors essential for the DNA backbone scission remained ambiguous. On the basis of crystal structures and biochemical data for various restriction enzymes, three models have been developed that assign critical roles for one, two, or three metal ions during the phosphodiester hydrolysis. To resolve this apparent controversy, we investigated the mechanism of BamHI catalysis using quantum mechanical/molecular mechanical simulation techniques and determined the activation barriers of three possible pathways that involve a Glu-113 or a neighboring water molecule as a general base or an external nucleophile that penetrated from bulk solution. The extrinsic mechanism was found to be the most favorable with an activation free energy of 23.4 kcal/mol, in reasonable agreement with the experimental data. On the basis of the effect of the individual metal ions on the activation barrier, metal ion A was concluded to be pivotal for the reaction, while the enzyme lacking metal ion B still has moderate efficiency. Thus, we propose that the catalytic scheme of BamHI does not involve a general base for nucleophile generation and requires one obligatory metal ion for catalysis that stabilizes the attacking nucleophile and coordinates it throughout the nucleophilic attack. Such a model may also explain the variation in the number of metal ions in the crystal structures and thus could serve as a framework for a unified catalytic scheme of type II restriction endonucleases.

  10. Fluorescence probing investigation of the mechanism of formation of MSU-type mesoporous silica prepared in fluoride medium.

    PubMed

    Lesaint, Cédric; Lebeau, Bénédicte; Marichal, Claire; Patarin, Joël; Zana, Raoul

    2005-09-13

    The mechanism of formation of a MSU-type siliceous material from tetraethyl orthosilicate (TEOS) in the presence of the nonionic surfactant tergitol T-15-S-12, sulfuric acid, and sodium fluoride has been investigated using mainly fluorescence probing techniques and, to a lesser extent, dynamic light scattering (DLS) and 29Si NMR spectroscopy. The tergitol micelles present in the systems obtained by progressively generating the reaction mixture giving rise to the mesostructured material by adding to an appropriate tergitol solution sulfuric acid, TEOS, and NaF were characterized by fluorescence probing (micelle aggregation number, micropolarity, and microviscosity) and also by dynamic light scattering (apparent micelle diameter). 29Si NMR experiments were also performed on selected systems after hydrolysis of the TEOS. The fluorescence probing techniques were also used to follow the changes of micelle characteristics with time during the evolution of the full reaction mixture from a limpid solution to a system containing a minor amount of condensed siliceous material. The synthesized solid material was characterized by X-ray diffraction and nitrogen adsorption-desorption analyses. The micelle aggregation number N was found to change only little, and the micropolarity remained constant when going from the tergitol solution to the full reaction mixture. The results of DLS measurements agree with this finding. Besides, while the condensation of silica took place after addition of NaF, the N value increased only very little with time up to the point where a small amount of mesostructured material precipitated out. These results indicate that the interaction between tergitol micelles and the siliceous species formed in the system by the hydrolysis of TEOS and also between micelles and the growing siliceous species must be very weak. As in our previous studies of the mechanism of formation of MCM41-type material from sodium silicate in the presence of

  11. Probing Mechanical Properties of Jurkat Cells under the Effect of ART Using Oscillating Optical Tweezers

    PubMed Central

    2015-01-01

    Acute lymphoid leukemia is a common type of blood cancer and chemotherapy is the initial treatment of choice. Quantifying the effect of a chemotherapeutic drug at the cellular level plays an important role in the process of the treatment. In this study, an oscillating optical tweezer was employed to characterize the frequency-dependent mechanical properties of Jurkat cells exposed to the chemotherapeutic agent, artesunate (ART). A motion equation for a bead bound to a cell was applied to describe the mechanical characteristics of the cell cytoskeleton. By comparing between the modeling results and experimental results from the optical tweezer, the stiffness and viscosity of the Jurkat cells before and after the ART treatment were obtained. The results demonstrate a weak power-law dependency of cell stiffness with frequency. Furthermore, the stiffness and viscosity were increased after the treatment. Therefore, the cytoskeleton cell stiffness as the well as power-law coefficient can provide a useful insight into the chemo-mechanical relationship of drug treated cancer cells and may serve as another tool for evaluating therapeutic performance quantitatively. PMID:25928073

  12. DNA mechanics as a tool to probe helicase and translocase activity.

    PubMed

    Lionnet, Timothée; Dawid, Alexandre; Bigot, Sarah; Barre, François-Xavier; Saleh, Omar A; Heslot, François; Allemand, Jean-François; Bensimon, David; Croquette, Vincent

    2006-01-01

    Helicases and translocases are proteins that use the energy derived from ATP hydrolysis to move along or pump nucleic acid substrates. Single molecule manipulation has proved to be a powerful tool to investigate the mechanochemistry of these motors. Here we first describe the basic mechanical properties of DNA unraveled by single molecule manipulation techniques. Then we demonstrate how the knowledge of these properties has been used to design single molecule assays to address the enzymatic mechanisms of different translocases. We report on four single molecule manipulation systems addressing the mechanism of different helicases using specifically designed DNA substrates: UvrD enzyme activity detection on a stretched nicked DNA molecule, HCV NS3 helicase unwinding of a RNA hairpin under tension, the observation of RecBCD helicase/nuclease forward and backward motion, and T7 gp4 helicase mediated opening of a synthetic DNA replication fork. We then discuss experiments on two dsDNA translocases: the RuvAB motor studied on its natural substrate, the Holliday junction, and the chromosome-segregation motor FtsK, showing its unusual coupling to DNA supercoiling.

  13. Probing the mechanism of recognition of ssDNA by the Cdc13-DBD.

    PubMed

    Eldridge, Aimee M; Wuttke, Deborah S

    2008-03-01

    The Saccharomyces cerevisiae protein Cdc13 tightly and specifically binds the conserved G-rich single-stranded overhang at telomeres and plays an essential role in telomere end-protection and length regulation. The 200 residue DNA-binding domain of Cdc13 (Cdc13-DBD) binds an 11mer single-stranded representative of the yeast telomeric sequence [Tel11, d(GTGTGGGTGTG)] with a 3 pM affinity and specificity for three bases (underlined) at the 5' end. The structure of the Cdc13-DBD bound to Tel11 revealed a large, predominantly aromatic protein interface with several unusual features. The DNA adopts an irregular, extended structure, and the binding interface includes a long ( approximately 30 amino acids) structured loop between strands beta2-beta3 (L(2-3)) of an OB-fold. To investigate the mechanism of ssDNA binding, we studied the free and bound states of Cdc13-DBD using NMR spectroscopy. Chemical shift changes indicate that the basic topology of the domain, including L(2-3), is essentially intact in the free state. Changes in slow and intermediate time scale dynamics, however, occur in L(2-3), while conformational changes distant from the DNA interface suggest an induced fit mechanism for binding in the 'hot spot' for binding affinity and specificity. These data point to an overall binding mechanism well adapted to the heterogeneous nature of yeast telomeres.

  14. Probing the mechanism of rubredoxin thermal unfolding in the absence of salt bridges by temperature jump experiments.

    PubMed

    Henriques, Bárbara J; Saraiva, Lígia M; Gomes, Cláudio M

    2005-08-05

    Rubredoxins are the simplest type of iron-sulphur proteins and in recent years they have been used as model systems in protein folding and stability studies, especially the proteins from thermophilic sources. Here, we report our studies on the rubredoxin from the hyperthermophile Methanococcus jannaschii (T opt = 85 degrees C), which was investigated in respect to its thermal unfolding kinetics by temperature jump experiments. Different spectroscopic probes were used to monitor distinct structural protein features during the thermal transition: the integrity of the iron-sulphur centre was monitored by visible absorption spectroscopy, whereas tertiary structure was followed by intrinsic tryptophan fluorescence and exposure of protein hydrophobic patches was sensed by 1-anilinonaphthalene-8-sulphonate fluorescence. The studies were performed at acidic pH conditions in which any stabilising contributions from salt bridges are annulled due to protonation of protein side chain groups. In these conditions, M. jannaschii rubredoxin assumes a native-like, albeit more flexible and open conformation, as indicated by a red shift in the tryptophan emission maximum and 1-anilinonaphthalene-8-sulphonate binding. Temperature jumps were monitored by the three distinct techniques and showed that the protein undergoes thermal denaturation via a simple two step mechanism, as loss of tertiary structure, hydrophobic collapse, and disintegration of the iron-sulphur centre are concomitant processes. The proposed mechanism is framed with the multiphasic one proposed for Pyrococcus furiosus rubredoxin, showing that a common thermal unfolding mechanism is not observed between these two closely related thermophilic rubredoxins.

  15. Probing the effect of elevated cholesterol on the mechanical properties of membrane-cytoskeleton by optical tweezers

    NASA Astrophysics Data System (ADS)

    Rajkumar, Arun S.; Muley, Ajit; Chatterjee, Suvro; Jaffar Ali, B. M.

    2010-08-01

    The composition of the cell membrane and the surrounding physiological factors determine the nature and dynamics of membrane-cytoskeleton coupling. Mechanical strength of a cell is mainly derived from such coupling. In this article, we investigate the effect of extra cellular cholesterol on the membrane-cytoskelaton connectivity of single cell endothelium and consequent remodeling of its mechanical properties. Using optical tweezers as a force probe, we have measured membrane stiffness (km), membrane microviscosity (ηeff ) and the two-dimensional shear modulus (G'(f)) as a function of extracellular cholesterol in the range of 0.1mM to 6mM. We find that membrane stiffness and shear modulus are dependent on cholesterol-induced membrane-cytoskeletal organization. Further, by disrupting the membranecytoskeletal connectivity with Cytochalasin D, an actin delpolymerizing molecule, we recover pure membrane behaviour devoid of any cytoskeleton attachment. However, behaviour of ηeff was found to be unaffected by disruption of membrane-cytoskeleton organization. We infer that cholesterol is playing a distinct role in modulating membrane organization and membrane-cytoskeleton connectivity independently. We further discuss implications of our approach in characterizing cellular mechanics.

  16. Probing opto-mechanical stresses within azobenzene-containing photosensitive polymer films by a thin metal film placed above.

    PubMed

    Yadavalli, Nataraja Sekhar; Korolkov, Denis; Moulin, Jean-François; Krutyeva, Margarita; Santer, Svetlana

    2014-07-23

    Azo-modified photosensitive polymers offer the interesting possibility to reshape bulk polymers and thin films by UV-irradiation while being in the solid glassy state. The polymer undergoes considerable mass transport under irradiation with a light interference pattern resulting in the formation of surface relief grating (SRG). The forces inscribing this SRG pattern into a thin film are hard to assess experimentally directly. In the current study, we are proposing a method to probe opto-mechanical stresses within polymer films by characterizing the mechanical response of thin metal films (10 nm) deposited on the photosensitive polymer. During irradiation, the metal film not only deforms along with the SRG formation but ruptures in a regular and complex manner. The morphology of the cracks differs strongly depending on the electrical field distribution in the interference pattern, even when the magnitude and the kinetics of the strain are kept constant. This implies a complex local distribution of the opto-mechanical stress along the topography grating. In addition, the neutron reflectivity measurements of the metal/polymer interface indicate the penetration of a metal layer within the polymer, resulting in a formation of a bonding layer that confirms the transduction of light-induced stresses in the polymer layer to a metal film.

  17. Probing the mechanism of rubredoxin thermal unfolding in the absence of salt bridges by temperature jump experiments

    SciTech Connect

    Henriques, Barbara J.; Saraiva, Ligia M.; Gomes, Claudio M. . E-mail: gomes@itqb.unl.pt

    2005-08-05

    Rubredoxins are the simplest type of iron-sulphur proteins and in recent years they have been used as model systems in protein folding and stability studies, especially the proteins from thermophilic sources. Here, we report our studies on the rubredoxin from the hyperthermophile Methanococcus jannaschii (T {sub opt} = 85 deg C), which was investigated in respect to its thermal unfolding kinetics by temperature jump experiments. Different spectroscopic probes were used to monitor distinct structural protein features during the thermal transition: the integrity of the iron-sulphur centre was monitored by visible absorption spectroscopy, whereas tertiary structure was followed by intrinsic tryptophan fluorescence and exposure of protein hydrophobic patches was sensed by 1-anilinonaphthalene-8-sulphonate fluorescence. The studies were performed at acidic pH conditions in which any stabilising contributions from salt bridges are annulled due to protonation of protein side chain groups. In these conditions, M. jannaschii rubredoxin assumes a native-like, albeit more flexible and open conformation, as indicated by a red shift in the tryptophan emission maximum and 1-anilinonaphthalene-8-sulphonate binding. Temperature jumps were monitored by the three distinct techniques and showed that the protein undergoes thermal denaturation via a simple two step mechanism, as loss of tertiary structure, hydrophobic collapse, and disintegration of the iron-sulphur centre are concomitant processes. The proposed mechanism is framed with the multiphasic one proposed for Pyrococcus furiosus rubredoxin, showing that a common thermal unfolding mechanism is not observed between these two closely related thermophilic rubredoxins.

  18. Probing the Role of HDACs and Mechanisms of Chromatin-Mediated Neuroplasticity

    PubMed Central

    Haggarty, Stephen J.; Tsai, Li-Huei

    2011-01-01

    Advancing our understanding of neuroplasticity and the development of novel therapeutics based upon this knowledge is critical in order to improve the treatment and prevention of a myriad of nervous system disorders. Epigenetic mechanisms of neuroplasticity involve the post-translational modification of chromatin and the recruitment or loss of macromolecular complexes that control neuronal activity-dependent gene expression. While over a century after Ramón y Cajal first described nuclear subcompartments and foci that we now know correspond to sites of active transcription with acetylated histones that are under epigenetic control, the rate and extent to which epigenetic processes act in a dynamic and combinatorial fashion to shape experience-dependent phenotypic and behavioral plasticity in response to various types of neuronal stimuli over a range of time scales is only now coming into focus. With growing recognition that a subset of human diseases involving cognitive dysfunction can be classified as ‘chromatinopathies’, in which aberrant chromatin-mediated neuroplasticity plays a causal role in the underlying disease pathophysiology, understanding the molecular nature of epigenetic mechanisms in the nervous system may provide important new avenues for the development of novel therapeutics. In this review, we discuss the chemistry and neurobiology of the histone deacetylase (HDAC) family of chromatin-modifying enzymes, outline the role of HDACs in the epigenetic control of neuronal function, and discuss the potential relevance of these epigenetic mechanisms to the development of therapeutics aiming to enhance memory and neuroplasticity. Finally, open questions, challenges, and critical needs for the field of ‘neuroepigenetics’ in the years to come will be summarized. PMID:21545841

  19. Mechanism-based inactivators as probes of cytochrome P450 structure and function.

    PubMed

    Kent, U M; Juschyshyn, M I; Hollenberg, P F

    2001-09-01

    The cytochromes P450 superfamily of enzymes is a group of hemeproteins that catalyze the metabolism of an extensive series of compounds including drugs, chemical carcinogens, fatty acids, and steroids. They oxidize substrates ranging in size from ethylene to cyclosporin. Although significant efforts have been made to obtain structural information on the active sites of the microbial P450s, relatively little is currently known regarding the identities of the critical amino acid residues in the P450 active sites that are involved in substrate binding and catalysis. Since information on the crystal structures of the eukaryotic P450s has been relatively limited, investigators have used a variety of other techniques in attempts to elucide the structural features that play a role in the catalytic properties and substrate specificity at the enzyme active site. These include site-directed mutagenesis, natural mutations, homology modeling, mapping with aryl-iron complexes, affinity and photoaffinity labeling, and mechanism-based inactivators. A variety of different mechanism-based inactivators have proven to be useful in identifiying active site amino acid residues involved in substrate binding and catalysis. In this review we present a sampling of the types of studies that can be conducted using mechanism-based inactivators and highlight studies with several classes of compounds including acetylenes, isothiocyanates, xanthates, aminobenzotriazoles, phencyclidine, and furanocoumarins. Labeled peptides isolated from the inactivated proteins have been analyzed by N-terminal amino acid sequencing in conjunction with mass spectrometry to determine the sites of covalent modification. Mechanistic studies aimed at identifying the basis for the inactivation following adduct formation are also presented.

  20. Use of molecular modelling to probe the mechanism of the nucleoside transporter NupG.

    PubMed

    Vaziri, Hamidreza; Baldwin, Stephen A; Baldwin, Jocelyn M; Adams, David G; Young, James D; Postis, Vincent L G

    2013-03-01

    Nucleosides play key roles in biology as precursors for salvage pathways of nucleotide synthesis. Prokaryotes import nucleosides across the cytoplasmic membrane by proton- or sodium-driven transporters belonging to the Concentrative Nucleoside Transporter (CNT) family or the Nucleoside:H(+) Symporter (NHS) family of the Major Facilitator Superfamily. The high resolution structure of a CNT from Vibrio cholerae has recently been determined, but no similar structural information is available for the NHS family. To gain a better understanding of the molecular mechanism of nucleoside transport, in the present study the structures of two conformations of the archetypical NHS transporter NupG from Escherichia coli were modelled on the inward- and outward-facing conformations of the lactose transporter LacY from E. coli, a member of the Oligosaccharide:H(+) Symporter (OHS) family. Sequence alignment of these distantly related proteins (∼ 10% sequence identity), was facilitated by comparison of the patterns of residue conservation within the NHS and OHS families. Despite the low sequence similarity, the accessibilities of endogenous and introduced cysteine residues to thiol reagents were found to be consistent with the predictions of the models, supporting their validity. For example C358, located within the predicted nucleoside binding site, was shown to be responsible for the sensitivity of NupG to inhibition by p-chloromercuribenzene sulphonate. Functional analysis of mutants in residues predicted by the models to be involved in the translocation mechanism, including Q261, E264 and N228, supported the hypothesis that they play important roles, and suggested that the transport mechanisms of NupG and LacY, while different, share common features.

  1. Simultaneous optical and mechanical probes to investigate complex cellular responses to physical cues

    NASA Astrophysics Data System (ADS)

    Haase, Kristina; Al-Rekabi, Zeinab; Guolla, Louise; Hickey, Ryan; Tremblay, Dominique; Pelling, Andrew E.

    2015-03-01

    Living cells possess an exquisite ability to sense and respond to physical information in their microenvironment. This ability plays a key role in many fundamentally important physiological and pathological processes. We will describe our work utilizing a variety of biophysical tools to investigate the dynamic responses of cells to mechanical stimuli and how physical cues can be employed to re-purpose and manipulate biological processes. These responses to physical cues are not simply a side-product of biology but are key components of biological and physical feedback loops that govern the life of a cell.

  2. Probing photocurrent generation mechanisms in hybrid IR-senstive quantum dot/conjugated polymer solar cells

    NASA Astrophysics Data System (ADS)

    Strein, Elisabeth

    The work in this dissertation aims to improve the ability of hybrid polymer/quantum dot solar cells to harvest and utilize sunlight by contributing mechanistic insights into photocurrent generation. The mechanisms of charge transfer and energy transfer are explored spectroscopically in chapter three and both are found to contribute to photocurrent. Chapter four looks at excitation energy in excess of the bandgap and finds a rise in polaron yield which correlates with excess photon energy. Chapter two discusses details of the experimental techniques used to access the data discussed in the chapters that follow.

  3. Type II Isopentenyl Diphosphate Isomerase: Probing the Mechanism with Alkyne/Allene Diphosphate Substrate Analogues†

    PubMed Central

    Sharma, Nagendra K.; Pan, Jian-Jung; Poulter, C. Dale

    2010-01-01

    Isopentenyl diphosphate isomerase (IDI) catalyzes the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), the basic five-carbon building blocks of isoprenoid molecules. Two structurally unrelated classes of IDI are known. Type I IPP isomerase (IDI-1) utilizes a divalent metal in a protonation-deprotonation reaction. In contrast, the type II enzyme (IDI-2) requires reduced flavin, raising the possibility that the reaction catalyzed by IDI-2 involves the net addition/abstraction of a hydrogen atom. As part of our studies of the mechanism of isomerization for IDI-2, we synthesized allene and alkyne substrate analogues for the enzyme. These molecules are predicted to be substantially less reactive toward proton addition than IPP and DMAPP, but have similar reactivities toward hydrogen atom addition. This prediction was verified by calculations of gas phase heats of reaction for addition of a proton and of a hydrogen atom to 1-butyne (3) and 1,2-butadiene (4) to form the 1-buten-2-yl carbocation and radical, respectively, and related affinities for 2-methyl-1-butene (5) and 2-methyl-2-butene (6) using G3MP2B3 and CBS-QB3 protocols. Alkyne 1-OPP and allene 2-OPP were not substrates for Thermus thermophilus IDI-2 or Escherichia coli IDI-1, but instead were competitive inhibitors. The experimental and computational results are consistent with a protonation-deprotonation mechanism for the enzyme-catalyzed isomerization of IPP and DMAPP. PMID:20560533

  4. Mechanics of Pickering Drops Probed by Electric Field–Induced Stress

    PubMed Central

    Mikkelsen, Alexander; Dommersnes, Paul; Rozynek, Zbigniew; Gholamipour-Shirazi, Azarmidokht; da Silveira Carvalho, Marcio; Fossum, Jon Otto

    2017-01-01

    Fluid drops coated with particles, so-called Pickering drops, play an important role in emulsion and capsule applications. In this context, knowledge of mechanical properties and stability of Pickering drops are essential. Here we prepare Pickering drops via electric field-driven self-assembly. We use direct current (DC) electric fields to induce mechanical stress on these drops, as a possible alternative to the use of, for example, fluid flow fields. Drop deformation is monitored as a function of the applied electric field strength. The deformation of pure silicone oil drops is enhanced when covered by insulating polyethylene (PE) particles, whereas drops covered by conductive clay particles can also change shape from oblate to prolate. We attribute these results to changes in the electric conductivity of the drop interface after adding particles, and have developed a fluid shell description to estimate the conductivity of Pickering particle layers that are assumed to be non-jammed and fluid-like. Retraction experiments in the absence of electric fields are also performed. Particle-covered drops retract slower than particle-free drops, caused by increased viscous dissipation due to the presence of the Pickering particle layer. PMID:28772796

  5. Probing the mechanical properties of TNF-α stimulated endothelial cell with atomic force microscopy

    PubMed Central

    Lee, Sei-Young; Zaske, Ana-Maria; Novellino, Tommaso; Danila, Delia; Ferrari, Mauro; Conyers, Jodie; Decuzzi, Paolo

    2011-01-01

    TNF-α (tumor necrosis factor-α) is a potent pro-inflammatory cytokine that regulates the permeability of blood and lymphatic vessels. The plasma concentration of TNF-α is elevated (> 1 pg/mL) in several pathologies, including rheumatoid arthritis, atherosclerosis, cancer, pre-eclampsia; in obese individuals; and in trauma patients. To test whether circulating TNF-α could induce similar alterations in different districts along the vascular system, three endothelial cell lines, namely HUVEC, HPMEC, and HCAEC, were characterized in terms of 1) mechanical properties, employing atomic force microscopy; 2) cytoskeletal organization, through fluorescence microscopy; and 3) membrane overexpression of adhesion molecules, employing ELISA and immunostaining. Upon stimulation with TNF-α (10 ng/mL for 20 h), for all three endothelial cells, the mechanical stiffness increased by about 50% with a mean apparent elastic modulus of E ~5 ± 0.5 kPa (~3.3 ± 0.35 kPa for the control cells); the density of F-actin filaments increased in the apical and median planes; and the ICAM-1 receptors were overexpressed compared with controls. Collectively, these results demonstrate that sufficiently high levels of circulating TNF-α have similar effects on different endothelial districts, and provide additional information for unraveling the possible correlations between circulating pro-inflammatory cytokines and systemic vascular dysfunction. PMID:21499414

  6. Responsive mechanism of a newly synthesized fluorescent probe for sensing H2O2, NO and H2O2/NO

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

    Optical properties of a newly synthesized fluorescent probe for H2O2, NO and H2O2/NO are investigated by employing time-dependent density functional theory. Three different sets of fluorescence signals are obtained when the probe reacts with H2O2, NO and H2O2/NO. Analysis of molecular orbitals is presented to explore responsive mechanism of the probe for the detected objects, where the fluorescent resonance energy transfer process is for H2O2 (H2O2/NO) and the intramolecular charge transfer process is for NO. Our results provide theoretical explanation of the experimental results, and importantly, suggest possibility of the probe as a two-photon fluorescent sensor.

  7. Vibrational coherence probes the mechanism of ultrafast electron transfer in polymer-fullerene blends

    NASA Astrophysics Data System (ADS)

    Song, Yin; Clafton, Scott N.; Pensack, Ryan D.; Kee, Tak W.; Scholes, Gregory D.

    2014-09-01

    The conversion of photoexcitations into charge carriers in organic solar cells is facilitated by the dissociation of excitons at the donor/acceptor interface. The ultrafast timescale of charge separation demands sophisticated theoretical models and raises questions about the role of coherence in the charge-transfer mechanism. Here, we apply two-dimensional electronic spectroscopy to study the electron transfer process in poly(3-hexylthiophene)/PCBM (P3HT/PCBM) blends. We report dynamics maps showing the pathways of charge transfer that clearly expose the significance of hot electron transfer. During this ultrafast electron transfer, vibrational coherence is directly transferred from the P3HT exciton to the P3HT hole polaron in the crystalline domain. This result reveals that the exciton converts to a hole with a similar spatial extent on a timescale far exceeding other photophysical dynamics including vibrational relaxation.

  8. Molecular mechanisms of ionic liquid cytotoxicity probed by an integrated experimental and computational approach

    SciTech Connect

    Yoo, Brian; Jing, Benxin; Jones, Stuart E.; Lamberti, Gary A.; Zhu, Yingxi; Shah, Jindal K.; Maginn, Edward J.

    2016-02-02

    Ionic liquids (ILs) are salts that remain liquid down to low temperatures, and sometimes well below room temperature. ILs have been called “green solvents” because of their extraordinarily low vapor pressure and excellent solvation power, but ecotoxicology studies have shown that some ILs exhibit greater toxicity than traditional solvents. A fundamental understanding of the molecular mechanisms responsible for IL toxicity remains elusive. Here we show that one mode of IL toxicity on unicellular organisms is driven by swelling of the cell membrane. Cytotoxicity assays, confocal laser scanning microscopy, and molecular simulations reveal that IL cations nucleate morphological defects in the microbial cell membrane at concentrations near the half maximal effective concentration (EC50) of several microorganisms. Lastly, cytotoxicity increases with increasing alkyl chain length of the cation due to the ability of the longer alkyl chain to more easily embed in, and ultimately disrupt, the cell membrane.

  9. Molecular mechanisms of ionic liquid cytotoxicity probed by an integrated experimental and computational approach

    NASA Astrophysics Data System (ADS)

    Yoo, Brian; Jing, Benxin; Jones, Stuart E.; Lamberti, Gary A.; Zhu, Yingxi; Shah, Jindal K.; Maginn, Edward J.

    2016-02-01

    Ionic liquids (ILs) are salts that remain liquid down to low temperatures, and sometimes well below room temperature. ILs have been called “green solvents” because of their extraordinarily low vapor pressure and excellent solvation power, but ecotoxicology studies have shown that some ILs exhibit greater toxicity than traditional solvents. A fundamental understanding of the molecular mechanisms responsible for IL toxicity remains elusive. Here we show that one mode of IL toxicity on unicellular organisms is driven by swelling of the cell membrane. Cytotoxicity assays, confocal laser scanning microscopy, and molecular simulations reveal that IL cations nucleate morphological defects in the microbial cell membrane at concentrations near the half maximal effective concentration (EC50) of several microorganisms. Cytotoxicity increases with increasing alkyl chain length of the cation due to the ability of the longer alkyl chain to more easily embed in, and ultimately disrupt, the cell membrane.

  10. Probing X-Ray Jet Emission Mechanisms in a Complete Blazar Sample

    NASA Astrophysics Data System (ADS)

    Kharb, Preeti

    2008-09-01

    We propose deep (70 ksec) followup Chandra X-ray observations and new HST WFPC2/F450W observations of two quasars belonging to the complete flux-limited MOJAVE Chandra blazar sample. These two quasars have HST WFPC2/F702W data available in the archive. Combining the existing optical and radio data with the new Chandra and HST data at an additional optical band we aim to construct asignificantly more accurate multi-waveband (four frequency) spectral energy distributions for distinct knots in the jets. This will serve as a first step towards resolving longstanding ambiguities surrounding the primary X-ray emission mechanisms in a well-defined sample of powerful FR-II class jets.

  11. Probing X-Ray Jet Emission Mechanisms in a Complete Blazar Sample

    NASA Astrophysics Data System (ADS)

    Kharb, Preeti

    2009-07-01

    We propose deep {70 ksec} followup Chandra X-ray observations and new HST ACS/WFC/F475W observations of two quasars, viz., 0106+013 and 1641+399, belonging to the complete flux-limited MOJAVE Chandra blazar sample. These two quasars have HST WFPC2/F702W data available in the archive. Combining the existing optical and radio data with the new Chandra and HST data at an additional optical band we aim to construct a significantly more accurate multi-waveband {four frequency} spectral energy distributions for distinct knots in the jets. This will serve as a first step towards resolving longstanding ambiguities surrounding the primary X-ray emission mechanisms in a well-defined sample of powerful FR-II class jets.

  12. Molecular mechanisms of ionic liquid cytotoxicity probed by an integrated experimental and computational approach

    PubMed Central

    Yoo, Brian; Jing, Benxin; Jones, Stuart E.; Lamberti, Gary A.; Zhu, Yingxi; Shah, Jindal K.; Maginn, Edward J.

    2016-01-01

    Ionic liquids (ILs) are salts that remain liquid down to low temperatures, and sometimes well below room temperature. ILs have been called “green solvents” because of their extraordinarily low vapor pressure and excellent solvation power, but ecotoxicology studies have shown that some ILs exhibit greater toxicity than traditional solvents. A fundamental understanding of the molecular mechanisms responsible for IL toxicity remains elusive. Here we show that one mode of IL toxicity on unicellular organisms is driven by swelling of the cell membrane. Cytotoxicity assays, confocal laser scanning microscopy, and molecular simulations reveal that IL cations nucleate morphological defects in the microbial cell membrane at concentrations near the half maximal effective concentration (EC50) of several microorganisms. Cytotoxicity increases with increasing alkyl chain length of the cation due to the ability of the longer alkyl chain to more easily embed in, and ultimately disrupt, the cell membrane. PMID:26831599

  13. Excess white noise to probe transport mechanisms in a membrane channel

    NASA Astrophysics Data System (ADS)

    Queralt-Martín, María; López, M. Lidón; Alcaraz, Antonio

    2015-06-01

    Current fluctuation analysis has been successfully used over the years to investigate the physical properties of different systems. Here, we perform single-channel time-resolved current experiments in a protein channel to evaluate the different transport mechanisms governing the channel function. Using different salts of monovalent and divalent cations in a wide range of concentrations and applied potentials, we analyze current fluctuations focusing on the voltage dependence of the additional white noise that appears in the low-frequency range of the spectra. We demonstrate that the channel displays two characteristic transport regimes: at low salt concentrations (10 mM to 1 M) ion permeation is controlled by the protein fixed charges that induce accumulation or exclusion of ions to preserve local electroneutrality. At high salt concentrations (>1 M ) adsorption processes associated to the binding of cations to the channel charges regulate the transport properties.

  14. Molecular mechanisms of ionic liquid cytotoxicity probed by an integrated experimental and computational approach

    DOE PAGES

    Yoo, Brian; Jing, Benxin; Jones, Stuart E.; ...

    2016-02-02

    Ionic liquids (ILs) are salts that remain liquid down to low temperatures, and sometimes well below room temperature. ILs have been called “green solvents” because of their extraordinarily low vapor pressure and excellent solvation power, but ecotoxicology studies have shown that some ILs exhibit greater toxicity than traditional solvents. A fundamental understanding of the molecular mechanisms responsible for IL toxicity remains elusive. Here we show that one mode of IL toxicity on unicellular organisms is driven by swelling of the cell membrane. Cytotoxicity assays, confocal laser scanning microscopy, and molecular simulations reveal that IL cations nucleate morphological defects in themore » microbial cell membrane at concentrations near the half maximal effective concentration (EC50) of several microorganisms. Lastly, cytotoxicity increases with increasing alkyl chain length of the cation due to the ability of the longer alkyl chain to more easily embed in, and ultimately disrupt, the cell membrane.« less

  15. Lithium insertion mechanism in iron-based oxyfluorides with anionic vacancies probed by PDF analysis

    DOE PAGES

    Dambournet, Damien; Chapman, Karena W.; Duttine, Mathieu; ...

    2015-06-25

    The mechanism of lithium insertion that occurs in an iron oxyfluoride sample with a hexagonal–tungsten–bronze (HTB)-type structure was investigated by the pair distribution function. This study reveals that upon lithiation, the HTB framework collapses to yield disordered rutile and rock salt phases followed by a conversion reaction of the fluoride phase toward lithium fluoride and nanometer-sized metallic iron. The occurrence of anionic vacancies in the pristine framework was shown to strongly impact the electrochemical activity, that is, the reversible capacity scales with the content of anionic vacancies. Similar to FeOF-type electrodes, upon de-lithiation, a disordered rutile phase forms, showing thatmore » the anionic chemistry dictates the atomic arrangement of the re-oxidized phase. Finally, it was shown that the nanoscaling and structural rearrangement induced by the conversion reaction allow the in situ formation of new electrode materials with enhanced electrochemical properties.« less

  16. Lithium Insertion Mechanism in Iron-Based Oxyfluorides with Anionic Vacancies Probed by PDF Analysis.

    PubMed

    Dambournet, Damien; Chapman, Karena W; Duttine, Mathieu; Borkiewicz, Olaf; Chupas, Peter J; Groult, Henri

    2015-08-01

    The mechanism of lithium insertion that occurs in an iron oxyfluoride sample with a hexagonal-tungsten-bronze (HTB)-type structure was investigated by the pair distribution function. This study reveals that upon lithiation, the HTB framework collapses to yield disordered rutile and rock salt phases followed by a conversion reaction of the fluoride phase toward lithium fluoride and nanometer-sized metallic iron. The occurrence of anionic vacancies in the pristine framework was shown to strongly impact the electrochemical activity, that is, the reversible capacity scales with the content of anionic vacancies. Similar to FeOF-type electrodes, upon de-lithiation, a disordered rutile phase forms, showing that the anionic chemistry dictates the atomic arrangement of the re-oxidized phase. Finally, it was shown that the nanoscaling and structural rearrangement induced by the conversion reaction allow the in situ formation of new electrode materials with enhanced electrochemical properties.

  17. Lithium Insertion Mechanism in Iron-Based Oxyfluorides with Anionic Vacancies Probed by PDF Analysis

    PubMed Central

    Dambournet, Damien; Chapman, Karena W; Duttine, Mathieu; Borkiewicz, Olaf; Chupas, Peter J; Groult, Henri

    2015-01-01

    The mechanism of lithium insertion that occurs in an iron oxyfluoride sample with a hexagonal–tungsten–bronze (HTB)-type structure was investigated by the pair distribution function. This study reveals that upon lithiation, the HTB framework collapses to yield disordered rutile and rock salt phases followed by a conversion reaction of the fluoride phase toward lithium fluoride and nanometer-sized metallic iron. The occurrence of anionic vacancies in the pristine framework was shown to strongly impact the electrochemical activity, that is, the reversible capacity scales with the content of anionic vacancies. Similar to FeOF-type electrodes, upon de-lithiation, a disordered rutile phase forms, showing that the anionic chemistry dictates the atomic arrangement of the re-oxidized phase. Finally, it was shown that the nanoscaling and structural rearrangement induced by the conversion reaction allow the in situ formation of new electrode materials with enhanced electrochemical properties. PMID:26478837

  18. Probing Mechanical Properties of Chemical Vapor Deposition Graphene Membranes Using Indentation Methods

    NASA Astrophysics Data System (ADS)

    Lee, Gwan-Hyoung; Cooper, Ryan; An, Sungjoo; van der Zande, Arend; Petrone, Nicholas; Lee, Sunwoo; Hammerberg, Alex; Lee, Changgu; Crawford, Bryan; Kysar, Jeffrey; Hone, James

    2012-02-01

    Recent experimental studies have shown that two-dimensional pristine graphene is the strongest material ever measured. We used Atomic Force Microscopy (AFM) and Agilent G200 nanoindenter to measure the mechanical properties of graphene films obtained by Chemical Vapor Deposition (CVD). CVD graphene with different grain size and number of layers were produced in controlled synthetic conditions and transferred onto silicon dioxide substrate with holes of various diameters. Nano-indentation measurement revealed that stiffness and fracture strength of CVD graphene membranes are similar to those of pristine graphene membranes under the condition that suspended graphene membrane is within a single grain boundary without defects. Furthermore, elastic modulus and fracture strength of multi-layer graphene membranes increase with respect to the number of layers.

  19. Simulated Microgravity as a Probe for Understanding the Mechanisms of Early Pattern Specification

    NASA Technical Reports Server (NTRS)

    Neff, A. W.; Malacinski, G. M.

    1985-01-01

    Early pattern specification (e.g., axial structure morphogenesis, doreal ventral polarity, etc.) is monitored in amphibian eggs which were subjected to microgravity simulation by constant rotation on a horizontal clinostat. In contrast to previous clinostat experiments, rotation is initiated either prior to fertilization or immediately thereafter. Large proportions of clinostated eggs developed normal axial structures. A model which employs a multiple set of signals for specifying early pattern is discussed. Effects of microgravity simulation on the earliest post fertilization pattern specification event dorsal/ventral polarization is analyzed in detail. Other models are developed and they are discussed. As a general mechanism for explaining the manner in which regional developmental patterns emerge from the initial, radially symmetrial egg, the density compartment model is described. The identification of the various zones or compartments of egg cytoplasm using inverted eggs is explained.

  20. Probing the failure mechanism of nanoscale LiFePO₄ for Li-ion batteries

    SciTech Connect

    Gu, Meng; Shi, Wei; Zheng, Jianming; Yan, Pengfei; Zhang, Ji-guang; Wang, Chongmin

    2015-05-18

    LiFePO4 is a high power rate cathode material for lithium ion battery and shows remarkable capacity retention, featuring a 91% capacity retention after 3300 cycles. In this work, we use high-resolution transmission electron microscopy (HRTEM), energy dispersive x-ray spectroscopy (EDS), and electron energy loss spectroscopy (EELS) to study the gradual capacity fading mechanism of LiFePO4 materials. We found that upon prolonged electrochemical cycling of the battery, the LiFePO4 cathode shows surface amorphization and loss of oxygen species, which directly contribute to the gradual capacity fading of the battery. The finding is of great importance for the design and improvement of new LiFePO4 cathode for high-energy and high-power rechargeable battery for electric transportation.

  1. Probing the Crystal Structure and Formation Mechanism of Lanthanide-Doped Upconverting Nanocrystals

    SciTech Connect

    Hudry, Damien; Abeykoon, A. M. M.; Dooryhee, E.; Nykypanchuk, D.; Dickerson, J. H.

    2016-11-23

    Lanthanide (Ln)-doped upconverting nanocrystals (UCNCs), such as NaLnF4 (with Ln = lanthanide), constitute an important class of nanoscale materials due to their capacity to convert near-infrared photons into near-ultraviolet or visible light. Although under intense investigation for more than a decade, UCNCs have been relatively underexplored especially regarding their crystal structure and mechanisms of formation in organic media. The former is needed to explain the relationship between atomic scale structure and upconversion (UC) properties of UCNCs (i.e., local symmetry for 4f–4f transition probability, Ln3+ distances for energy migration), while the latter is essential to finely tune the size, morphology, chemical composition, and architecture of well-defined upconverting nanostructures, which constitute the experimental levers to modify the optical properties. In this contribution, we use synchrotron-based diffraction experiments coupled to Rietveld and pair distribution function (PDF) analyses to understand the formation of NaGdF4:Yb:Er UCNCs in organic media and to investigate their crystal structure. Our results reveal a complex mechanism of the formation of NaGdF4:Yb:Er UCNCs based on chemical reactions involving molecular clusters and in situ-generated, crystalline sodium fluoride at high temperature. Additionally, a detailed crystallographic investigation of NaGdF4:Yb:Er UCNCs is presented. Our Rietveld and PDF analyses show that the space group P$\\bar{6}$ is the one that best describes the crystal structure of NaGdF4:Yb:Er UCNCs contrary to what has been recently proposed. Further, our Rietveld and PDF data reveal the formation of bulk-like crystal structure down to 10 nm with limited distortions. Finally, the results presented in this paper constitute an important step toward the comprehensive understanding of the underlying picture that governs UC properties of lanthanide

  2. Probing Molecular Mechanisms of the Hsp90 Chaperone: Biophysical Modeling Identifies Key Regulators of Functional Dynamics

    PubMed Central

    Dixit, Anshuman; Verkhivker, Gennady M.

    2012-01-01

    Deciphering functional mechanisms of the Hsp90 chaperone machinery is an important objective in cancer biology aiming to facilitate discovery of targeted anti-cancer therapies. Despite significant advances in understanding structure and function of molecular chaperones, organizing molecular principles that control the relationship between conformational diversity and functional mechanisms of the Hsp90 activity lack a sufficient quantitative characterization. We combined molecular dynamics simulations, principal component analysis, the energy landscape model and structure-functional analysis of Hsp90 regulatory interactions to systematically investigate functional dynamics of the molecular chaperone. This approach has identified a network of conserved regions common to the Hsp90 chaperones that could play a universal role in coordinating functional dynamics, principal collective motions and allosteric signaling of Hsp90. We have found that these functional motifs may be utilized by the molecular chaperone machinery to act collectively as central regulators of Hsp90 dynamics and activity, including the inter-domain communications, control of ATP hydrolysis, and protein client binding. These findings have provided support to a long-standing assertion that allosteric regulation and catalysis may have emerged via common evolutionary routes. The interaction networks regulating functional motions of Hsp90 may be determined by the inherent structural architecture of the molecular chaperone. At the same time, the thermodynamics-based “conformational selection” of functional states is likely to be activated based on the nature of the binding partner. This mechanistic model of Hsp90 dynamics and function is consistent with the notion that allosteric networks orchestrating cooperative protein motions can be formed by evolutionary conserved and sparsely connected residue clusters. Hence, allosteric signaling through a small network of distantly connected residue clusters

  3. Probing the Crystal Structure and Formation Mechanism of Lanthanide-Doped Upconverting Nanocrystals

    DOE PAGES

    Hudry, Damien; Abeykoon, A. M. M.; Dooryhee, E.; ...

    2016-11-23

    Lanthanide (Ln)-doped upconverting nanocrystals (UCNCs), such as NaLnF4 (with Ln = lanthanide), constitute an important class of nanoscale materials due to their capacity to convert near-infrared photons into near-ultraviolet or visible light. Although under intense investigation for more than a decade, UCNCs have been relatively underexplored especially regarding their crystal structure and mechanisms of formation in organic media. The former is needed to explain the relationship between atomic scale structure and upconversion (UC) properties of UCNCs (i.e., local symmetry for 4f–4f transition probability, Ln3+ distances for energy migration), while the latter is essential to finely tune the size, morphology, chemical composition, and architecture of well-defined upconverting nanostructures, which constitute the experimental levers to modify the optical properties. In this contribution, we use synchrotron-based diffraction experiments coupled to Rietveld and pair distribution function (PDF) analyses to understand the formation of NaGdF4:Yb:Er UCNCs in organic media and to investigate their crystal structure. Our results reveal a complex mechanism of the formation of NaGdF4:Yb:Er UCNCs based on chemical reactions involving molecular clusters and in situ-generated, crystalline sodium fluoride at high temperature. Additionally, a detailed crystallographic investigation of NaGdF4:Yb:Er UCNCs is presented. Our Rietveld and PDF analyses show that the space group Pmore » $$\\bar{6}$$ is the one that best describes the crystal structure of NaGdF4:Yb:Er UCNCs contrary to what has been recently proposed. Further, our Rietveld and PDF data reveal the formation of bulk-like crystal structure down to 10 nm with limited distortions. Finally, the results presented in this paper constitute an important step toward the comprehensive understanding of the underlying picture that governs UC properties of lanthanide-doped nanostructures.« less

  4. Modeling single molecule junction mechanics as a probe of interface bonding

    DOE PAGES

    Hybertsen, Mark S.

    2017-03-07

    Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of an ensemble of nanoscale junction structures. This paper focuses on the relationship between the measured force extension characteristics including bond rupture and the properties of the interface bonds in the junction. We analyzed a set of exemplary model junction structures using density functional theory based calculations to simulate the adiabatic potential surface that governs the junction elongation. The junction structures include representative molecules that bond tomore » the electrodes through amine, methylsulfide, and pyridine links. The force extension characteristics are shown to be most effectively analyzed in a scaled form with maximum sustainable force and the distance between the force zero and force maximum as scale factors. Widely used, two parameter models for chemical bond potential energy versus bond length are found to be nearly identical in scaled form. Furthermore, they fit well to the present calculations of N–Au and S–Au donor-acceptor bonds, provided no other degrees of freedom are allowed to relax. Examination of the reduced problem of a single interface, but including relaxation of atoms proximal to the interface bond, shows that a single-bond potential form renormalized by an effective harmonic potential in series fits well to the calculated results. This, then, allows relatively accurate extraction of the interface bond energy. Analysis of full junction models shows cooperative effects that go beyond the mechanical series inclusion of the second bond in the junction, the spectator bond that does not rupture. Calculations for a series of diaminoalkanes as a function of molecule length indicate that the most important cooperative effect is due to the interactions between the dipoles induced by

  5. Probing the Mechanical Strength of an Armored Bubble and Its Implication to Particle-Stabilized Foams

    NASA Astrophysics Data System (ADS)

    Taccoen, Nicolas; Lequeux, François; Gunes, Deniz Z.; Baroud, Charles N.

    2016-01-01

    Bubbles are dynamic objects that grow and rise or shrink and disappear, often on the scale of seconds. This conflicts with their uses in foams where they serve to modify the properties of the material in which they are embedded. Coating the bubble surface with solid particles has been demonstrated to strongly enhance the foam stability, although the mechanisms for such stabilization remain mysterious. In this paper, we reduce the problem of foam stability to the study of the behavior of a single spherical bubble coated with a monolayer of solid particles. The behavior of this armored bubble is monitored while the ambient pressure around it is varied, in order to simulate the dissolution stress resulting from the surrounding foam. We find that above a critical stress, localized dislocations appear on the armor and lead to a global loss of the mechanical stability. Once these dislocations appear, the armor is unable to prevent the dissolution of the gas into the surrounding liquid, which translates into a continued reduction of the bubble volume, even for a fixed overpressure. The observed route to the armor failure therefore begins from localized dislocations that lead to large-scale deformations of the shell until the bubble completely dissolves. The critical value of the ambient pressure that leads to the failure depends on the bubble radius, with a scaling of Δ Pcollapse∝R-1 , but does not depend on the particle diameter. These results disagree with the generally used elastic models to describe particle-covered interfaces. Instead, the experimental measurements are accounted for by an original theoretical description that equilibrates the energy gained from the gas dissolution with the capillary energy cost of displacing the individual particles. The model recovers the short-wavelength instability, the scaling of the collapse pressure with bubble radius, and the insensitivity to particle diameter. Finally, we use this new microscopic understanding to predict

  6. Modeling single molecule junction mechanics as a probe of interface bonding

    NASA Astrophysics Data System (ADS)

    Hybertsen, Mark S.

    2017-03-01

    Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of an ensemble of nanoscale junction structures. This paper focuses on the relationship between the measured force extension characteristics including bond rupture and the properties of the interface bonds in the junction. A set of exemplary model junction structures has been analyzed using density functional theory based calculations to simulate the adiabatic potential surface that governs the junction elongation. The junction structures include representative molecules that bond to the electrodes through amine, methylsulfide, and pyridine links. The force extension characteristics are shown to be most effectively analyzed in a scaled form with maximum sustainable force and the distance between the force zero and force maximum as scale factors. Widely used, two parameter models for chemical bond potential energy versus bond length are found to be nearly identical in scaled form. Furthermore, they fit well to the present calculations of N-Au and S-Au donor-acceptor bonds, provided no other degrees of freedom are allowed to relax. Examination of the reduced problem of a single interface, but including relaxation of atoms proximal to the interface bond, shows that a single-bond potential form renormalized by an effective harmonic potential in series fits well to the calculated results. This allows relatively accurate extraction of the interface bond energy. Analysis of full junction models shows cooperative effects that go beyond the mechanical series inclusion of the second bond in the junction, the spectator bond that does not rupture. Calculations for a series of diaminoalkanes as a function of molecule length indicate that the most important cooperative effect is due to the interactions between the dipoles induced by the donor

  7. A laser probe based on a Sagnac interferometer with fast mechanical scan for RF surface and bulk acoustic wave devices.

    PubMed

    Hashimoto, Ken-ya; Kashiwa, Keiskue; Wu, Nan; Omori, Tatsuya; Yamaguchi, Masatsune; Takano, Osamu; Meguro, Sakae; Akahane, Koichi

    2011-01-01

    This paper describes the development of a phasesensitive laser probe with fast mechanical scan for RF surface and bulk acoustic wave (SAW/BAW) devices. The Sagnac interferometer composed of micro-optic elements was introduced for the selective detection of RF vertical motion associated with RF SAW/BAW propagation and vibration. A high-pass characteristic of the interferometer makes the measurement very insensitive to low-frequency vibration. This feature allows us to apply the fast mechanical scan to the interferometric measurement without badly sacrificing its SNR and spatial resolution. The system was applied to the visualization of a field pattern on the vibrating surface of an RF BAW resonator operating in the 2 GHz range. The field pattern was obtained in 17 min as a 2-D image (500 × 750 pixel with 0.4 μm resolution and SNR of 40 dB). The system was also applied to the characterization of an RF SAW resonator operating in the 1 GHz range, and the applicability of the system was demonstrated.

  8. Elliptic flow as a probe for the ψ (2 S ) production mechanism in relativistic heavy ion collisions

    NASA Astrophysics Data System (ADS)

    Chen, Baoyi

    2017-03-01

    I discuss the elliptic flows of ψ (2 S ) with different production mechanisms in √{sN N}=2.76 TeV Pb-Pb collisions. If the final ψ (2 S )s are mainly from the recombination of uncorrelated charm and anticharm quarks at T ≈Tc , charm and anticharm quarks will carry large collective flows of the bulk medium, which will be inherited by the regenerated ψ (2 S )s . This indicates a larger elliptic flow of ψ (2 S ) than that of J /ψ which can be regenerated at T ≥Tc , v2ψ (2 S )>v2J /ψ . However, if the final ψ (2 S )s are mainly from the transitions of J /ψ →ψ (2 S ) caused by the color screening of quark-gluon plasma its elliptic flow should be close to the elliptic flow of J /ψ , v2ψ (2 S )˜v2J /ψ . Therefore, ψ (2 S ) elliptic flow is a sensitive probe for its production mechanisms in relativistic heavy ion collisions.

  9. The accumulation mechanism of the hypoxia imaging probe "FMISO" by imaging mass spectrometry: possible involvement of low-molecular metabolites.

    PubMed

    Masaki, Yukiko; Shimizu, Yoichi; Yoshioka, Takeshi; Tanaka, Yukari; Nishijima, Ken-Ichi; Zhao, Songji; Higashino, Kenichi; Sakamoto, Shingo; Numata, Yoshito; Yamaguchi, Yoshitaka; Tamaki, Nagara; Kuge, Yuji

    2015-11-19

    (18)F-fluoromisonidazole (FMISO) has been widely used as a hypoxia imaging probe for diagnostic positron emission tomography (PET). FMISO is believed to accumulate in hypoxic cells via covalent binding with macromolecules after reduction of its nitro group. However, its detailed accumulation mechanism remains unknown. Therefore, we investigated the chemical forms of FMISO and their distributions in tumours using imaging mass spectrometry (IMS), which visualises spatial distribution of chemical compositions based on molecular masses in tissue sections. Our radiochemical analysis revealed that most of the radioactivity in tumours existed as low-molecular-weight compounds with unknown chemical formulas, unlike observations made with conventional views, suggesting that the radioactivity distribution primarily reflected that of these unknown substances. The IMS analysis indicated that FMISO and its reductive metabolites were nonspecifically distributed in the tumour in patterns not corresponding to the radioactivity distribution. Our IMS search found an unknown low-molecular-weight metabolite whose distribution pattern corresponded to that of both the radioactivity and the hypoxia marker pimonidazole. This metabolite was identified as the glutathione conjugate of amino-FMISO. We showed that the glutathione conjugate of amino-FMISO is involved in FMISO accumulation in hypoxic tumour tissues, in addition to the conventional mechanism of FMISO covalent binding to macromolecules.

  10. Atom Probe Tomography Unveils Formation Mechanisms of Wear-Protective Tribofilms by ZDDP, Ionic Liquid, and Their Combination

    DOE PAGES

    Guo, Wei; Zhou, Yan; Sang, Xiahan; ...

    2017-06-20

    The development of advanced lubricant additives has been a critical component in paving the way for increasing energy efficiency and durability for numerous industry applications. However, the formation mechanisms of additive-induced protective tribofilms are not yet fully understood because of the complex chemomechanical interactions at the contact interface and the limited spatial resolution of many characterizing techniques currently used. In this paper, the tribofilms on a gray cast iron surface formed by three antiwear additives are systematically studied; a phosphonium-phosphate ionic liquid (IL), a zinc dialkyldithiophosphate (ZDDP), and an IL+ZDDP combination. All three additives provide excellent wear protection, with themore » IL+ZDDP combination exhibiting a synergetic effect, resulting in further reduced friction and wear. Atom probe tomography (APT) and scanning transmission electron microscopy (STEM) imaging and electron energy loss spectroscopy (EELS) were used to interrogate the subnm chemistry and bonding states for each of the tribofilms of interest. The IL tribofilm appeared amorphous and was Fe, P, and O rich. Wear debris particles having an Fe-rich core and an oxide shell were present in this tribofilm and a transitional oxide (Fe2O3)-containing layer was identified at the interface between the tribofilm and the cast iron substrate. The ZDDP+IL tribofilm shared some of the characteristics found in the IL and ZDDP tribofilms. Finally, tribofilm formation mechanisms are proposed on the basis of the observations made at the atomic level.« less

  11. Atom Probe Tomography Unveils Formation Mechanisms of Wear-Protective Tribofilms by ZDDP, Ionic Liquid, and Their Combination.

    PubMed

    Guo, Wei; Zhou, Yan; Sang, Xiahan; Leonard, Donovan N; Qu, Jun; Poplawsky, Jonathan D

    2017-07-12

    The development of advanced lubricant additives has been a critical component in paving the way for increasing energy efficiency and durability for numerous industry applications. However, the formation mechanisms of additive-induced protective tribofilms are not yet fully understood because of the complex chemomechanical interactions at the contact interface and the limited spatial resolution of many characterizing techniques currently used. Here, the tribofilms on a gray cast iron surface formed by three antiwear additives are systematically studied; a phosphonium-phosphate ionic liquid (IL), a zinc dialkyldithiophosphate (ZDDP), and an IL+ZDDP combination. All three additives provide excellent wear protection, with the IL+ZDDP combination exhibiting a synergetic effect, resulting in further reduced friction and wear. Atom probe tomography (APT) and scanning transmission electron microscopy (STEM) imaging and electron energy loss spectroscopy (EELS) were used to interrogate the subnm chemistry and bonding states for each of the tribofilms of interest. The IL tribofilm appeared amorphous and was Fe, P, and O rich. Wear debris particles having an Fe-rich core and an oxide shell were present in this tribofilm and a transitional oxide (Fe2O3)-containing layer was identified at the interface between the tribofilm and the cast iron substrate. The ZDDP+IL tribofilm shared some of the characteristics found in the IL and ZDDP tribofilms. Tribofilm formation mechanisms are proposed on the basis of the observations made at the atomic level.

  12. Surface transport mechanisms in molecular glasses probed by the exposure of nano-particles

    NASA Astrophysics Data System (ADS)

    Ruan, Shigang; Musumeci, Daniele; Zhang, Wei; Gujral, Ankit; Ediger, M. D.; Yu, Lian

    2017-05-01

    For a glass-forming liquid, the mechanism by which its surface contour evolves can change from bulk viscous flow at high temperatures to surface diffusion at low temperatures. We show that this mechanistic change can be conveniently detected by the exposure of nano-particles native in the material. Despite its high chemical purity, the often-studied molecular glass indomethacin contains low-concentration particles approximately 100 nm in size and 0.3% in volume fraction. Similar particles are present in polystyrene, another often-used model. In the surface-diffusion regime, particles are gradually exposed in regions vacated by host molecules, for example, the peak of a surface grating and the depletion zone near a surface crystal. In the viscous-flow regime, particle exposure is not observed. The surface contour around an exposed particle widens over time in a self-similar manner as 3 (Bt)1/4, where B is a surface mobility constant and the same constant obtained by surface grating decay. This work suggests that in a binary system composed of slow- and fast-diffusing molecules, slow-diffusing molecules can be stranded in surface regions vacated by fast-diffusing molecules, effectively leading to phase separation.

  13. Non-Natural Nucleotides as Probes for the Mechanism and Fidelity of DNA Polymerases

    PubMed Central

    Lee, Irene; Berdis, Anthony J.

    2009-01-01

    DNA is a remarkable macromolecule that functions primarily as the carrier of the genetic information of organisms ranging from viruses to bacteria to eukaryotes. The ability of DNA polymerases to efficiently and accurately replicate genetic material represents one of the most fundamental yet complex biological processes found in nature. The central dogma of DNA polymerization is that the efficiency and fidelity of this biological process is dependent upon proper hydrogen-bonding interactions between an incoming nucleotide and its templating partner. However, the foundation of this dogma has been recently challenged by the demonstration that DNA polymerases can effectively and, in some cases, selectively incorporate non-natural nucleotides lacking classic hydrogen-bonding capabilities into DNA. In this review, we describe the results of several laboratories that have employed a variety of non-natural nucleotide analogs to decipher the molecular mechanism of DNA polymerization. The use of various non-natural nucleotides has lead to the development of several different models that can explain how efficient DNA synthesis can occur in the absence of hydrogen-bonding interactions. These models include the influence of steric fit and shape complementarity, hydrophobicity and solvation energies, base-stacking capabilities, and negative selection as alternatives to rules invoking simple recognition of hydrogen bonding patterns. Discussions are also provided regarding how the kinetics of primer extension and exonuclease proofreading activities associated with high-fidelity DNA polymerases are influenced by the absence of hydrogen-bonding functional groups exhibited by non-natural nucleotides. PMID:19733263

  14. Probing Photocurrent Generation, Charge Transport, and Recombination Mechanisms in Mesostructured Hybrid Perovskite through Photoconductivity Measurements.

    PubMed

    Sveinbjörnsson, Kári; Aitola, Kerttu; Zhang, Xiaoliang; Pazoki, Meysam; Hagfeldt, Anders; Boschloo, Gerrit; Johansson, Erik M J

    2015-11-05

    Conductivity of methylammonium lead triiodide (MAPbI3) perovskite was measured on different mesoporous metal oxide scaffolds: TiO2, Al2O3, and ZrO2, as a function of incident light irradiation and temperature. It was found that MAPbI3 exhibits intrinsic charge separation, and its conductivity stems from a majority of free charge carriers. The crystal morphology of the MAPbI3 was found to significantly affect the photoconductivity, whereas in the dark the conductivity is governed by the perovskite in the pores of the mesoporous scaffold. The temperature-dependent conductivity measurements also indicate the presence of states within the band gap of the perovskite. Despite a relatively large amount of crystal defects in the measured material, the main recombination mechanism of the photogenerated charges is bimolecular (band-to-band), which suggests that the defect states are rather inactive in the recombination. This may explain the remarkable efficiencies obtained for perovskite solar cells prepared with wet-chemical methods.

  15. Probing irradiation induced DNA damage mechanisms using excited state Car-Parrinello molecular dynamics

    NASA Astrophysics Data System (ADS)

    Markwick, Phineus R. L.; Doltsinis, Nikos L.; Schlitter, Jürgen

    2007-01-01

    Photoinduced proton transfer in the Watson-Crick guanine (G)-cytosine (C) base pair has been studied using Car-Parrinello molecular dynamics (CP-MD). A flexible mechanical constraint acting on all three hydrogen bonds in an unbiased fashion has been devised to explore the free energy profile along the proton transfer coordinate. The lowest barrier has been found for proton transfer from G to C along the central hydrogen bond. The resulting charge transfer excited state lies energetically close to the electronic ground state suggesting the possibility of efficient radiationless decay. It is found that dynamic, finite temperature fluctuations significantly reduce the energy gap between the ground and excited states for this charge transfer product, promoting the internal conversion process. A detailed analysis of the internal degrees of freedom reveals that the energy gap is considerably reduced by out-of-plane molecular vibrations, in particular. Consequently, it appears that considering only the minimum energy path provides an upper-bound estimate of the associated energy gap compared to the full-dimension dynamical reaction coordinate. Furthermore, the first CP-MD simulations of the G-C base pair in liquid water are presented, and the effects of solvation on its electronic structure are analyzed.

  16. A Novel Ratiometric Fluorescent Mercury Probe Based on Deprotonation-ICT Mechanism.

    PubMed

    Xie, Puhui; Guo, Fengqi; Yang, Sen; Yao, Denghui; Yang, Guoyu; Xie, Lixia

    2014-03-01

    A new NBD-rhodamine dye (1) was developed as a colorimetric and ratiometric fluorescent chemosensor for Hg(2+) with good selectivity in aqueous ethanol solutions under neutral to basic conditions. Sensor 1 showed absorption at 468 nm and a weak emission at 529 nm (ϕ F  = 0.063) in ethanol/aqueous tris buffer (9:1, v/v) of pH 9.17 solution. Bathochromic shifts in both absorption (492 nm) and fluorescence spectra (569 nm, ϕ F  = 0.129), respectively upon addition of 2 equiv. of Hg(2+) were observed. The ring-opening reaction of the spirolactam form to the corresponding xanthene form was not found. The interaction of Hg(2+) with chemosensor 1 resulted in the deprotonation of the secondary amine conjugated to the NBD component so that the electron-donating ability of the N atom was enhanced. Deprotonation-ICT mechanism of secondary amines was suggested for the ratiometric fluorescent chemosensing for Hg(2+).

  17. Probing Microplasticity in Small-Scale FCC Crystals via Dynamic Mechanical Analysis

    NASA Astrophysics Data System (ADS)

    Ni, Xiaoyue; Papanikolaou, Stefanos; Vajente, Gabriele; Adhikari, Rana X.; Greer, Julia R.

    2017-04-01

    In small-scale metallic systems, collective dislocation activity has been correlated with size effects in strength and with a steplike plastic response under uniaxial compression and tension. Yielding and plastic flow in these samples is often accompanied by the emergence of multiple dislocation avalanches. Dislocations might be active preyield, but their activity typically cannot be discerned because of the inherent instrumental noise in detecting equipment. We apply alternate current load perturbations via dynamic mechanical analysis during quasistatic uniaxial compression experiments on single crystalline Cu nanopillars with diameters of 500 nm and compute dynamic moduli at frequencies 0.1, 0.3, 1, and 10 Hz under progressively higher static loads until yielding. By tracking the collective aspects of the oscillatory stress-strain-time series in multiple samples, we observe an evolving dissipative component of the dislocation network response that signifies the transition from elastic behavior to dislocation avalanches in the globally preyield regime. We postulate that microplasticity, which is associated with the combination of dislocation avalanches and slow viscoplastic relaxations, is the cause of the dependency of dynamic modulus on the driving rate and the quasistatic stress. We construct a continuum mesoscopic dislocation dynamics model to compute the frequency response of stress over strain and obtain a consistent agreement with experimental observations. The results of our experiments and simulations present a pathway to discern and quantify correlated dislocation activity in the preyield regime of deforming crystals.

  18. Probing the Catalytic Mechanism of Copper Amine Oxidase from Arthrobacter globiformis with Halide Ions*

    PubMed Central

    Murakawa, Takeshi; Hamaguchi, Akio; Nakanishi, Shota; Kataoka, Misumi; Nakai, Tadashi; Kawano, Yoshiaki; Yamaguchi, Hiroshi; Hayashi, Hideyuki; Tanizawa, Katsuyuki; Okajima, Toshihide

    2015-01-01

    The catalytic reaction of copper amine oxidase proceeds through a ping-pong mechanism comprising two half-reactions. In the initial half-reaction, the substrate amine reduces the Tyr-derived cofactor, topa quinone (TPQ), to an aminoresorcinol form (TPQamr) that is in equilibrium with a semiquinone radical (TPQsq) via an intramolecular electron transfer to the active-site copper. We have analyzed this reductive half-reaction in crystals of the copper amine oxidase from Arthrobacter globiformis. Anerobic soaking of the crystals with an amine substrate shifted the equilibrium toward TPQsq in an “on-copper” conformation, in which the 4-OH group ligated axially to the copper center, which was probably reduced to Cu(I). When the crystals were soaked with substrate in the presence of halide ions, which act as uncompetitive and noncompetitive inhibitors with respect to the amine substrate and dioxygen, respectively, the equilibrium in the crystals shifted toward the “off-copper” conformation of TPQamr. The halide ion was bound to the axial position of the copper center, thereby preventing TPQamr from adopting the on-copper conformation. Furthermore, transient kinetic analyses in the presence of viscogen (glycerol) revealed that only the rate constant in the step of TPQamr/TPQsq interconversion is markedly affected by the viscogen, which probably perturbs the conformational change. These findings unequivocally demonstrate that TPQ undergoes large conformational changes during the reductive half-reaction. PMID:26269595

  19. Probing irradiation induced DNA damage mechanisms using excited state Car-Parrinello molecular dynamics.

    PubMed

    Markwick, Phineus R L; Doltsinis, Nikos L; Schlitter, Jürgen

    2007-01-28

    Photoinduced proton transfer in the Watson-Crick guanine (G)-cytosine (C) base pair has been studied using Car-Parrinello molecular dynamics (CP-MD). A flexible mechanical constraint acting on all three hydrogen bonds in an unbiased fashion has been devised to explore the free energy profile along the proton transfer coordinate. The lowest barrier has been found for proton transfer from G to C along the central hydrogen bond. The resulting charge transfer excited state lies energetically close to the electronic ground state suggesting the possibility of efficient radiationless decay. It is found that dynamic, finite temperature fluctuations significantly reduce the energy gap between the ground and excited states for this charge transfer product, promoting the internal conversion process. A detailed analysis of the internal degrees of freedom reveals that the energy gap is considerably reduced by out-of-plane molecular vibrations, in particular. Consequently, it appears that considering only the minimum energy path provides an upper-bound estimate of the associated energy gap compared to the full-dimension dynamical reaction coordinate. Furthermore, the first CP-MD simulations of the G-C base pair in liquid water are presented, and the effects of solvation on its electronic structure are analyzed.

  20. Intra-molecular interactions dominating the dehydration of a poly(2-isopropyl-2-oxazoline)-based densely grafted polymer comb in aqueous solution and hysteretic liquid-liquid phase separation.

    PubMed

    Zhou, Yuanyuan; Tang, Hui; Wu, Peiyi

    2017-03-01

    Temperature-induced phase transition together with the liquid-liquid phase separation (LLPS) phenomenon of poly(oligo(2-isopropyl-2-oxazoline)methacrylate) with the comb-shaped architecture (comb-PiPOx) in aqueous solution has been discussed at the molecular level. Differing from linear poly(2-isopropyl-2-oxazoline) (linear-PiPOx), polymer-rich liquid droplets appear at higher temperature compared with the phase transition determined by differential scanning calorimetry (DSC) in comb-PiPOx solution. As investigated using variable-temperature Fourier transform infrared (FTIR) spectra analysis, the densely grafted architecture gives rise to an intra-molecular interaction (hydrophobic interaction of alkyl groups and H-bond of carbonyl groups) dominating the dehydration process of comb-PiPOx. With temperature increment, most of the water within hydrated polymers is expelled to the outer water phase through intra-molecular association, corresponding to the transition temperature. Afterwards, the dehydration of methyl groups on side chain ends reflects the massive aggregation of polymer chains through inter-molecular association, accompanied by hysteretic LLPS.

  1. Hydrogels as potential probes for investigating the mechanism of lenticular presbyopia.

    PubMed

    Murthy, S K; Ravi, N

    2001-05-01

    To synthesize and characterize hydrogels with viscoelastic properties comparable to those of the natural lens. Hydrogels were synthesized in water by free-radical polymerization of the monomer poly(ethyleneglycol)-monomethacrylate. Three different molecular weights of poly(ethyleneglycol)-dimethacrylates were used as crosslinkers. For each crosslinker used, five different monomer-to-crosslinker weight ratios were utilized while the total mass of the reactants was kept constant. In another series, the concentration of the reactants was varied while the weight ratio of monomer to crosslinker was kept constant at 95 : 5. The percent optical transmission, equilibrium water content, moduli (elastic, shear, storage, and loss), and retardation time constant of the hydrogels were determined. In addition, endocapsular polymerization was performed in the capsular bag of porcine eyes. The hydrogels examined exhibited the following ranges for viscoelastic properties: elastic modulus, 1.33-2.37 x 10(4) Pa; shear modulus, 3.35-6.72 x 10(3) Pa; storage modulus, 1.65-6.24 x 10(4) Pa. For any given hydrogel, raising its crosslinker's weight ratio increased its moduli and decreased its equilibrium water content and optical transmission. For any given monomer-to-crosslinker weight ratio, increasing the molecular weight of the crosslinker reversed these trends. Reactant concentrations increased the elastic modulus and decreased the equilibrium water content. The hydrogels formed ex vivo (in the evacuated capsular bag of porcine eyes) allowed for the clear and undistorted viewing of objects. Hydrogels that exhibit physical and mechanical properties comparable to those of the natural lens were successfully identified, synthesized, and characterized, and the feasibility of endocapsular polymerization was demonstrated.

  2. Probing the Catalytic Mechanism of Vibrio harveyi GH20 β-N-Acetylglucosaminidase by Chemical Rescue

    PubMed Central

    Meekrathok, Piyanat; Suginta, Wipa

    2016-01-01

    Background Vibrio harveyi GH20 β-N-acetylglucosaminidase (VhGlcNAcase) is a chitinolytic enzyme responsible for the successive degradation of chitin fragments to GlcNAc monomers, activating the onset of the chitin catabolic cascade in marine Vibrios. Methods Two invariant acidic pairs (Asp303-Asp304 and Asp437-Glu438) of VhGlcNAcase were mutated using a site-directed mutagenesis strategy. The effects of these mutations were examined and the catalytic roles of these active-site residues were elucidated using a chemical rescue approach. Enhancement of the enzymic activity of the VhGlcNAcase mutants was evaluated by a colorimetric assay using pNP-GlcNAc as substrate. Results Substitution of Asp303, Asp304, Asp437 or Glu438 with Ala/Asn/Gln produced a dramatic loss of the GlcNAcase activity. However, the activity of the inactive D437A mutant was recovered in the presence of sodium formate. Our kinetic data suggest that formate ion plays a nucleophilic role by mimicking the β-COO-side chain of Asp437, thereby stabilizing the reaction intermediate during both the glycosylation and the deglycosylation steps. Conclusions Chemical rescue of the inactive D437A mutant of VhGlcNAcase by an added nucleophile helped to identify Asp437 as the catalytic nucleophile/base, and hence its acidic partner Glu438 as the catalytic proton donor/acceptor. General Significance Identification of the catalytic nucleophile of VhGlcNAcases supports the proposal of a substrate-assisted mechanism of GH20 GlcNAcases, requiring the catalytic pair Asp437-Glu438 for catalysis. The results suggest the mechanistic basis of the participation of β-N-acetylglucosaminidase in the chitin catabolic pathway of marine Vibrios. PMID:26870945

  3. Utilizing Supernova Remnants as Probes of Explosion Mechanisms and Progenitor Systems

    NASA Astrophysics Data System (ADS)

    Milisavljevic, Dan

    2015-08-01

    Theory and observation strongly favor the notion that asymmetric explosions drive core-collapse supernovae. Where and how this asymmetry is introduced is uncertain, in part because of limited constraints on the various processes that may be taking place deep inside massive stars. Observations of extragalactic supernovae have shed some light on the issue. However, distant supernovae, by nature, appear as unresolved point sources, which severely restricts our ability to extract key properties of the explosion dynamics via detailed knowledge of the three-dimensional kinematics of the expanding ejecta. Progress requires an alternative approach, and to this end there have been successful efforts towards understanding core-collapse supernova explosions through studies of their remnants in our own Milky Way galaxy. Such investigations provide information about the explosion-driven mixing of the progenitor star's chemically distinct layers, the star's mass loss history before explosion, and the fate of its remnant core - all at extremely fine scales. Particularly of note are observations of the young supernova remnant Cassiopeia A, which is the descendant of a massive star that was mostly stripped of its hydrogen envelope. Cassiopeia A's debris field has a bubble-like morphology that may have originated from turbulent mixing processes that encouraged the development of outwardly expanding plumes of radioactive 56Ni-rich ejecta. Important aspects of these observations conflict with sophisticated explosion models and we presently do not have a good understanding of how the 56Ni was mixed. Considering Cassiopeia A's kinematic properties are not unique and likely reflect a common phenomenon of core-collapse supernovae, this conflict represents a big problem that cannot be ignored. Unraveling whether the mixing that we see originates from an asymmetric explosion mechanism or is more tightly associated with a turbulent interior structure will be a challenge, but there is hope.

  4. Concanavalin A as a probe for studying the mechanism of metabolic stimulation of leukocytes.

    PubMed

    Romeo, D; Zabucchi, G; Jug, M; Miani, N; Soranzo, M R

    1975-01-01

    The disruption of the molecular organization of the plasma membrane of leukocytes by phagocytosable particles, or by agents such as surfactants, antibodies, phospholipase C, fatty acids and chemotactic factors, leads to a stimulation of the phagocyte oxidative metabolism. Concanavalin A (Con A) has been used as a tool to study the mechanism of this metabolic regulation. The binding of Con A to the surface of polymorphonuclear leukocytes (PMNL) or macrophages produces a rapid enhancement of oxygen uptake and glucose oxidation through the hexose monophosphate pathway (HMP). This is explained by an activation of the granular NADPH oxidase, the key enzyme in the metabolic stimulation. The effect of Con A is not due to endocytosed lectin, since Con A covalently coupled to large sepharose beads still acts as stimulant. The metabolic changes caused by Con A are reversible. If, after the onset of stimulation, sugars with high affinity for Con A are added to the leukocyte suspension, the activity of granular NADPH oxidase and the rate of respiration and glucose oxidation return to their resting values. The metabolic burst, while partially supressed by treatment of PMNL with iodoacetate, sodium flouride and cytochalasin B, is slightly increased by colchicine. Con A induces a selective release of granular enzymes (beta-glucuronidase, peroxidase, alkaline phosphatase) from PMNL, whereas no leakage of cytoplasmic enzymes is observed. The enzyme release is inhibited by iodoacetate and by drugs known to increase cell levels of cyclic AMP. Based on a current view of the mode of interaction between Con A and cell surfaces, a model of the metabolic disruption of leukocytes is presented.

  5. Interaction of water with a benzimidazole derivative: fluorescence and colorimetric recognition of trace level water involving intra-molecular charge transfer process.

    PubMed

    Nandi, Sandip; Mandal, Sandip; Matalobos, Jesus Sanmartin; Sahana, Animesh; Das, Debasis

    2016-01-01

    Benzimidazole-derived ICT-based probe, DFPBEN is developed for trace level determination of water. In presence of water, the naked eye color of DFPBEN changes from red to yellow, while it turns to green from red under UV light. Upon addition of water, DFPBEN shows a ratiometric absorbance change in methanol. Copyright © 2015 John Wiley & Sons, Ltd.

  6. Human augmenter of liver regeneration: probing the catalytic mechanism of a flavin-dependent sulfhydryl oxidase.

    PubMed

    Schaefer-Ramadan, Stephanie; Gannon, Shawn A; Thorpe, Colin

    2013-11-19

    Augmenter of liver regeneration is a member of the ERV family of small flavin-dependent sulfhydryl oxidases that contain a redox-active CxxC disulfide bond in redox communication with the isoalloxazine ring of bound FAD. These enzymes catalyze the oxidation of thiol substrates with the reduction of molecular oxygen to hydrogen peroxide. This work studies the catalytic mechanism of the short, cytokine form of augmenter of liver regeneration (sfALR) using model thiol substrates of the enzyme. The redox potential of the proximal disulfide in sfALR was found to be approximately 57 mV more reducing than the flavin chromophore, in agreement with titration experiments. Rapid reaction studies show that dithiothreitol (DTT) generates a transient mixed disulfide intermediate with sfALR signaled by a weak charge-transfer interaction between the thiolate of C145 and the oxidized flavin. The subsequent transfer of reducing equivalents to the flavin ring is relatively slow, with a limiting apparent rate constant of 12.4 s(-1). However, reoxidation of the reduced flavin by molecular oxygen is even slower (2.3 s(-1) at air saturation) and thus largely limits turnover at 5 mM DTT. The nature of the charge-transfer complexes observed with DTT was explored using a range of simple monothiols to mimic the initial nucleophilic attack on the proximal disulfide. While β-mercaptoethanol is a very poor substrate of sfALR (∼0.3 min(-1) at 100 mM thiol), it rapidly generates a mixed disulfide intermediate allowing the thiolate of C145 to form a strong charge-transfer complex with the flavin. Unlike the other monothiols tested, glutathione is unable to form charge-transfer complexes and is an undetectable substrate of the oxidase. These data are rationalized on the basis of the stringent steric requirements for thiol-disulfide exchange reactions. The inability of the relatively bulky glutathione to attain the in-line geometry required for efficient disulfide exchange in sfALR may be

  7. Multi-Isotope Analysis as a Natural Reaction Probe of Biodegradation Mechanisms of 1,2- Dichloroethane

    NASA Astrophysics Data System (ADS)

    Hirschorn, S. K.; Dinglasan-Panlilio, M.; Edwards, E. A.; Lacrampe-Couloume, G.; Sherwood Lollar, B.

    2006-12-01

    1,2-Dichloroethane (1,2-DCA), a chlorinated aliphatic hydrocarbon, is an EPA priority pollutant and a widespread groundwater contaminant. Stable isotope fractionation during biodegradation of 1,2-DCA occurs due to differences in the reaction rates of heavy versus light atoms present at a reacting bond in the 1,2-DCA molecule. In general, light isotopic bonds react more quickly, producing a relative enrichment in the heavy isotope in the remaining contaminant pool. Compound specific isotope analysis has the potential to demonstrate the occurrence and extent of biodegradation at chlorinated solvent contaminated groundwater sites. In this study, stable carbon isotope fractionation was used as a novel reaction probe to provide information about the mechanism of 1,2-DCA biodegradation. Isotopic fractionation was measured during 1,2-DCA degradation by a microbial culture capable of degrading 1,2-DCA under O2-reducing and NO3-reducing conditions. The microbial culture produced isotopic enrichment values that are not only large and reproducible, but are the same whether O2 or NO3 was used as an electron acceptor. The mean isotopic enrichment value of -25.8 permil measured for the microbial culture during 1,2-DCA degradation under both O2 and NO3- reducing conditions can be converted into a kinetic isotope effect (KIE) value to relate the observed isotopic fractionation to the mechanism of degradation. This KIE value (1.05) is consistent with degradation via a hydrolysis (SN2) reaction under both electron-accepting conditions. Isotope analysis was able to provide a first line of evidence for the reaction mechanism of 1,2-DCA biodegradation by the microbial culture. Using a multi-isotope approach incorporating both carbon and hydrogen isotopic data, compound specific isotope analysis also has the potential to determine degradation mechanisms for 1,2-DCA under aerobic conditions where 1,2-DCA is known to be degraded by two distinct enzymatic pathways. Biodegradation of 1

  8. Design of modular probes for stratospheric balloon mission: Thermo mechanical aspects and lession learned from SORA mission.

    NASA Astrophysics Data System (ADS)

    Bettanini, Carlo; Friso, Enrico; Colombatti, Giacomo; Aboudan, Alessio; Flamini, Enrico; Pirrotta, Simone; Debei, Stefano

    Stratospheric balloon missions provide a very effective facility for testing instruments in a space-like environment with drastically lower requirements in funding and sensibly shorter timelines than common space mission. Mainly during ascent to operative altitude and parachuted de-scent the flight units face fast changing environmental conditions which may induce issues in the mechanical and thermal behavior of the equipment. A new concept modular gondola was engineered by CISAS "G.Colombo" at University of Padova,to be easily reconfigured to host scientific experiments with different power and thermal requirements thus sensibly reducing development times and costs. The gondola was mechanically designed to withstand dynamic loads related to parachute opening and ground impact and provided a 1 m x 1m x 0.3 m volume for scientific payloads which is pressure regulated with the use of relief valves and thermally controlled by main CDMU.Furthermore the whole system was able to float in case of descent in water thanks to an optmised design of the main aluminium structure and use of hermetic connections. A custom Command and Data Management Unit with hard-real-time control capabilities has been developed to manage sensors acquisition, data storage, and experiments monitoring and control. The gondola was equipped with IMU, GPS, a downward looking cam-era and a set of health check and housekeeping sensors which sample key parameters as attitude, acceleration and temperature in several parts of the structure feeding housekeeping data to the main pc in order to monitor overall system health. The unit was successfully assembled and tested at University of Padova and used in the flight of the SORA mission launched in summer 2009 from Svalbard islands to map with a penetrating radar the stratification of ice and rock above Northern Greenland. Because of unexpected wind directions the mission trajectory was several hundred kilometers southern than predicted terminating with a

  9. Pushing the Limits of a Molecular Mechanics Force Field To Probe Weak CH···π Interactions in Proteins.

    PubMed

    Barman, Arghya; Batiste, Bruce; Hamelberg, Donald

    2015-04-14

    The relationship among biomolecular structure, dynamics, and function is far from being understood, and the role of subtle, weak interactions in stabilizing different conformational states is even less well-known. The cumulative effect of these interactions has broad implications for biomolecular stability and recognition and determines the equilibrium distribution of the ensemble of conformations that are critical for function. Here, we accurately capture the stabilizing effects of weak CH···π interaction using an empirical molecular mechanics force field in excellent agreement with experiments. We show that the side chain of flanking C-terminal aromatic residues preferentially stabilize the cis isomer of the peptidyl-prolyl bond of the protein backbone through this weak interaction. Cis-trans isomerization of peptidyl-prolyl protein bond plays a pivotal role in many cellular processes, including signal transduction, substrate recognition, and many diseases. Although the cis isomer is relatively less stable than the trans isomer, aromatic side chains of neighboring residues can play a significant role in stabilizing the cis relative to the trans isomer. We carry out extensive regular and accelerated molecular dynamics simulations and establish an approach to simulate the pH profile of the cis/trans ratio in order to probe the stabilizing role of the CH···π interaction. The results agree very well with NMR experiments, provide detailed atomistic description of this crucial biomolecular interaction, and underscore the importance of weak stabilizing interactions in protein function.

  10. Mechanisms of deformation-induced trace element migration in zircon resolved by atom probe and correlative microscopy

    NASA Astrophysics Data System (ADS)

    Reddy, Steven M.; van Riessen, Arie; Saxey, David W.; Johnson, Tim E.; Rickard, William D. A.; Fougerouse, Denis; Fischer, Sebastian; Prosa, Ty J.; Rice, Katherine P.; Reinhard, David A.; Chen, Yimeng; Olson, David

    2016-12-01

    The widespread use of zircon in geochemical and geochronological studies of crustal rocks is underpinned by an understanding of the processes that may modify its composition. Deformation during tectonic and impact related strain is known to modify zircon trace element compositions, but the mechanisms by which this occurs remain unresolved. Here we combine electron backscatter diffraction, transmission Kikuchi diffraction and atom probe microscopy to investigate trace element migration associated with a ∼20 nm wide, 2° low-angle subgrain boundary formed in zircon during a single, high-strain rate, deformation associated with a bolide impact. The low-angle boundary shows elevated concentrations of both substitutional (Y) and interstitial (Al, Mg and Be) ions. The observed compositional variations reflect a dynamic process associated with the recovery of shock-induced vacancies and dislocations into lower energy low-angle boundaries. Y segregation is linked to the migration and localisation of oxygen vacancies, whilst the interstitial ions migrate in association with dislocations. These data represent the direct nanoscale observation of geologically-instantaneous, trace element migration associated with crystal plasticity of zircon and provide a framework for further understanding mass transfer processes in zircon.

  11. Location and binding mechanism of an ESIPT probe 3-hydroxy-2-naphthoic acid in unsaturated fatty acid bound serum albumins.

    PubMed

    Ghorai, Shyamal Kr; Tripathy, Debi Ranjan; Dasgupta, Swagata; Ghosh, Sanjib

    2014-02-05

    The binding site and the binding mechanism of 3-hydroxy-2-naphthoic acid (3HNA) in oleic acid (OA) bound serum albumins (bovine serum albumin (BSA) and human serum albumin (HSA)) have been determined using steady state and time resolved emission of tryptophan residues (Trp) in proteins and the ESIPT emission of 3HNA. Time resolved anisotropy of the probe 3HNA and low temperature phosphorescence of Trp residues of BSA in OA bound BSA at 77K reveals a drastic change of the binding site of 3HNA in the ternary system compared to that in the free protein. 3HNA binds near Trp213 in the ternary system whereas 3HNA binds near Trp134 in the free protein. The structure of OA bound BSA generated using docking methodology exhibits U-bend configuration of all bound OA. The docked pose of 3HNA in the free protein and in OA bound albumins (ternary systems) and the concomitant perturbation of the structure of proteins around the binding region of 3HNA corroborate the enhanced ESIPT emission of 3HNA and the energy transfer efficiency from the donor Trp213 of BSA to 3HNA acceptor in 3HNA-OA-BSA system.

  12. Probing the Additional Capacity and Reaction Mechanism of the RuO2 Anode in Lithium Rechargeable Batteries.

    PubMed

    Kim, Yunok; Muhammad, Shoaib; Kim, Hyunchul; Cho, Yong-Hun; Kim, Hansu; Kim, Ji Man; Yoon, Won-Sub

    2015-07-20

    The structural changes and electrochemical behavior of RuO2 are investigated by using in situ XRD, X-ray absorption spectroscopy, and electrochemical techniques to understand the electrochemical reaction mechanism of this metal oxide anode material. Intermediate phase-assisted transformation of RuO2 to LiRuO2 takes place at the start of discharge. Upon further lithiation, LiRuO2 formed by intercalation decomposes to nanosized Ru metal and Li2 O by a conversion reaction. A reversible capacity in addition to its theoretical capacity is observed on discharging below 0.5 V during which no redox activity involving Ru is observed. TEM, X-ray photoelectron spectroscopy, and the galvanostatic intermittent titration technique are used to probe this additional capacity. The results show that the additional capacity is a result of Li storage in the grain boundary between nanosized Ru metal and Li2 O. Findings of this study provide a better understanding of the quantitative share of capacity by a unique combination of intercalation, conversion, and interfacial Li storage in a RuO2 anode. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Probing the mechanism of interaction of metoprolol succinate with human serum albumin by spectroscopic and molecular docking analysis.

    PubMed

    Pawar, Suma K; Jaldappagari, Seetharamappa

    2017-09-01

    In the present work, the mechanism of the interaction between a β1 receptor blocker, metoprolol succinate (MS) and human serum albumin (HSA) under physiological conditions was investigated by spectroscopic techniques, namely fluorescence, Fourier transform infra-red spectroscopy (FT-IR), fluorescence lifetime decay and circular dichroism (CD) as well as molecular docking and cyclic voltammetric methods. The fluorescence and lifetime decay results indicated that MS quenched the intrinsic intensity of HSA through a static quenching mechanism. The Stern-Volmer quenching constants and binding constants for the MS-HSA system at 293, 298 and 303 K were obtained from the Stern-Volmer plot. Thermodynamic parameters for the interaction of MS with HSA were evaluated; negative values of entropy change (ΔG°) indicated the spontaneity of the MS and HSA interaction. Thermodynamic parameters such as negative ΔH° and positive ΔS° values revealed that hydrogen bonding and hydrophobic forces played a major role in MS-HSA interaction and stabilized the complex. The binding site for MS in HSA was identified by competitive site probe experiments and molecular docking studies. These results indicated that MS was bound to HSA at Sudlow's site I. The efficiency of energy transfer and the distance between the donor (HSA) and acceptor (MS) was calculated based on the theory of Fosters' resonance energy transfer (FRET). Three-dimensional fluorescence spectra and CD results revealed that the binding of MS to HSA resulted in an obvious change in the conformation of HSA. Cyclic voltammograms of the MS-HSA system also confirmed the interaction between MS and HSA. Furthermore, the effects of metal ions on the binding of MS to HSA were also studied. Copyright © 2017 John Wiley & Sons, Ltd.

  14. Probing binding sites and mechanisms of action of an I(Ks) activator by computations and experiments.

    PubMed

    Xu, Yu; Wang, Yuhong; Zhang, Mei; Jiang, Min; Rosenhouse-Dantsker, Avia; Wassenaar, Tsjerk; Tseng, Gea-Ny

    2015-01-06

    The slow delayed rectifier (IKs) channel is composed of the KCNQ1 channel and KCNE1 auxiliary subunit, and functions to repolarize action potentials in the human heart. IKs activators may provide therapeutic efficacy for treating long QT syndromes. Here, we show that a new KCNQ1 activator, ML277, can enhance IKs amplitude in adult guinea pig and canine ventricular myocytes. We probe its binding site and mechanism of action by computational analysis based on our recently reported KCNQ1 and KCNQ1/KCNE1 3D models, followed by experimental validation. Results from a pocket analysis and docking exercise suggest that ML277 binds to a side pocket in KCNQ1 and the KCNE1-free side pocket of KCNQ1/KCNE1. Molecular-dynamics (MD) simulations based on the most favorable channel/ML277 docking configurations reveal a well-defined ML277 binding space surrounded by the S2-S3 loop and S4-S5 helix on the intracellular side, and by S4-S6 transmembrane helices on the lateral sides. A detailed analysis of MD trajectories suggests two mechanisms of ML277 action. First, ML277 restricts the conformational dynamics of the KCNQ1 pore, optimizing K(+) ion coordination in the selectivity filter and increasing current amplitudes. Second, ML277 binding induces global motions in the channel, including regions critical for KCNQ1 gating transitions. We conclude that ML277 activates IKs by binding to an intersubunit space and allosterically influencing pore conductance and gating transitions. KCNE1 association protects KCNQ1 from an arrhythmogenic (constitutive current-inducing) effect of ML277, but does not preclude its current-enhancing effect.

  15. Probing structure-function relationships and gating mechanisms in the CorA Mg2+ transport system.

    PubMed

    Payandeh, Jian; Li, Canhui; Ramjeesingh, Mohabir; Poduch, Ewa; Bear, Christine E; Pai, Emil F

    2008-04-25

    Recent crystal structures of the CorA Mg(2+) transport protein from Thermotoga maritima (TmCorA) revealed an unusually long ion pore putatively gated by hydrophobic residues near the intracellular end and by universally conserved asparagine residues at the periplasmic entrance. A conformational change observed in an isolated funnel domain structure also led to a proposal for the structural basis of gating. Because understanding the molecular mechanisms underlying ion channel and transporter gating remains an important challenge, we have undertaken a structure-guided engineering approach to probe structure-function relationships in TmCorA. The intracellular funnel domain is shown to constitute an allosteric regulatory module that can be engineered to promote an activated or closed state. A periplasmic gate centered about a proline-induced kink of the pore-lining helix is described where "helix-straightening" mutations produce a dramatic gain-of-function. Mutation to the narrowest constriction along the pore demonstrates that a hydrophobic gate is operational within this Mg(2+)-selective transport protein and likely forms an energetic barrier to ion flux. We also provide evidence that highly conserved acidic residues found in the short periplasmic loop are not essential for TmCorA function or Mg(2+) selectivity but may be required for proper protein folding and stability. This work extends our gating model for the CorA-Alr1-Mrs2 superfamily and reveals features that are characteristic of an ion channel. Aspects of these results that have broader implications for a range of channel and transporter families are highlighted.

  16. [Probing the mechanism and Ca-DPA concentration of individual Bacillus spores using trapping and Raman spectroscopy].

    PubMed

    Huang, Xi; Huang, Rong-shao; Lai, Jun-zhuo; Xu, Lan-lan; Li, Yong-qing; Li, Zhen-chong; Huang, Shu-shi

    2010-08-01

    Measuring the levels of 2,6-pyridine dicarboxylic acid (DPA) in bacteria spores could provide the information about the DPA function, resistance mechanism and the mechanism of spore germination. The authors have measured levels of Ca-DPA of individual spores of different 19 kinds of Bacillus which from different sources, species, and strains by using laser tweezers Raman spectroscopy (LTRS). Also we have verified the reproducibility of the system simultaneously. To investigate the biochemical components and structure in single spore, a Raman tweezers setup was used to record the Raman spectrum of single spore. A NIR laser beam (30 mW, 785 nm) was introduced into an inverted microscope to form a tweezers for trapping the spore suspended in water, and the Raman scatter was excited by the same beam. Raman spectra of 30 spores of 19 bacillus strains which collected from different area in China were recorded, and 100 spores of B. subtilis ACCC10243 were measured. A spore of the same strain was probed 100 times for verifying the reproducibility of the LTRS system. A Matlab 7.0 edited program and Origin 8.0 were used to process the spectral data. Because Ca-DPA is the chelate of DPA and the calcium ion, and the strongest Raman bands at 1 017 cm(-1) was from Ca-DPA component of the spore, its intensity was linearly with the Ca-DPA concentration. Therefore, the 1017 cm(-1) bands of Ca-DPA could be used as the quantitative standard peak, and then calculated the concentration of Ca-DPA could be calculated according the intensity of 1017 cm(-1) peak. The results showed that Raman spectra of single spore can reflect the characteristics information of it. The diversity of Ca-DPA levels not only happened between different species and strains of bacillus, but also happened between different individual spores in the same strains of bacillus. Conclusion from these measurements is that there is heterogeneity in different individual spores. It is convenient to trapping and collecting

  17. Utilization of a photoactivatable antigen system to examine B-cell probing termination and the B-cell receptor sorting mechanisms during B-cell activation

    PubMed Central

    Wang, Jing; Tang, Shan; Wan, Zhengpeng; Gao, Yiren; Cao, Yiyun; Yi, Junyang; Si, Yanyan; Zhang, Haowen; Liu, Lei; Liu, Wanli

    2016-01-01

    Antigen binding to the B-cell receptor (BCR) induces several responses, resulting in B-cell activation, proliferation, and differentiation. However, it has been difficult to study these responses due to their dynamic, fast, and transient nature. Here, we attempted to solve this problem by developing a controllable trigger point for BCR and antigen recognition through the construction of a photoactivatable antigen, caged 4-hydroxy-3-nitrophenyl acetyl (caged-NP). This photoactivatable antigen system in combination with live cell and single molecule imaging techniques enabled us to illuminate the previously unidentified B-cell probing termination behaviors and the precise BCR sorting mechanisms during B-cell activation. B cells in contact with caged-NP exhibited probing behaviors as defined by the unceasing extension of membrane pseudopods in random directions. Further analyses showed that such probing behaviors are cell intrinsic with strict dependence on F-actin remodeling but not on tonic BCR signaling. B-cell probing behaviors were terminated within 4 s after photoactivation, suggesting that this response was sensitive and specific to BCR engagement. The termination of B-cell probing was concomitant with the accumulation response of the BCRs into the BCR microclusters. We also determined the Brownian diffusion coefficient of BCRs from the same B cells before and after BCR engagement. The analysis of temporally segregated single molecule images of both BCR and major histocompatibility complex class I (MHC-I) demonstrated that antigen binding induced trapping of BCRs into the BCR microclusters is a fundamental mechanism for B cells to acquire antigens. PMID:26764382

  18. Utilization of a photoactivatable antigen system to examine B-cell probing termination and the B-cell receptor sorting mechanisms during B-cell activation.

    PubMed

    Wang, Jing; Tang, Shan; Wan, Zhengpeng; Gao, Yiren; Cao, Yiyun; Yi, Junyang; Si, Yanyan; Zhang, Haowen; Liu, Lei; Liu, Wanli

    2016-02-02

    Antigen binding to the B-cell receptor (BCR) induces several responses, resulting in B-cell activation, proliferation, and differentiation. However, it has been difficult to study these responses due to their dynamic, fast, and transient nature. Here, we attempted to solve this problem by developing a controllable trigger point for BCR and antigen recognition through the construction of a photoactivatable antigen, caged 4-hydroxy-3-nitrophenyl acetyl (caged-NP). This photoactivatable antigen system in combination with live cell and single molecule imaging techniques enabled us to illuminate the previously unidentified B-cell probing termination behaviors and the precise BCR sorting mechanisms during B-cell activation. B cells in contact with caged-NP exhibited probing behaviors as defined by the unceasing extension of membrane pseudopods in random directions. Further analyses showed that such probing behaviors are cell intrinsic with strict dependence on F-actin remodeling but not on tonic BCR signaling. B-cell probing behaviors were terminated within 4 s after photoactivation, suggesting that this response was sensitive and specific to BCR engagement. The termination of B-cell probing was concomitant with the accumulation response of the BCRs into the BCR microclusters. We also determined the Brownian diffusion coefficient of BCRs from the same B cells before and after BCR engagement. The analysis of temporally segregated single molecule images of both BCR and major histocompatibility complex class I (MHC-I) demonstrated that antigen binding induced trapping of BCRs into the BCR microclusters is a fundamental mechanism for B cells to acquire antigens.

  19. Quantitative optical coherence elastography based on fiber-optic probe for in situ measurement of tissue mechanical properties.

    PubMed

    Qiu, Yi; Wang, Yahui; Xu, Yiqing; Chandra, Namas; Haorah, James; Hubbi, Basil; Pfister, Bryan J; Liu, Xuan

    2016-02-01

    We developed a miniature quantitative optical coherence elastography (qOCE) instrument with an integrated Fabry-Perot force sensor, for in situ elasticity measurement of biological tissue. The technique has great potential for biomechanics modeling and clinical diagnosis. We designed the fiber-optic qOCE probe that was used to exert a compressive force to deform tissue at the tip of the probe. Using the space-division multiplexed optical coherence tomography (OCT) signal detected by a spectral domain OCT engine, we were able to quantify the probe deformation that was proportional to the force applied, and to quantify the tissue deformation corresponding to the external stimulus. Simultaneous measurement of force and displacement allowed us to extract Young's modulus of biological tissue. We experimentally calibrated our qOCE instrument, and validated its effectiveness on tissue mimicking phantoms and biological tissues.

  20. Quantitative optical coherence elastography based on fiber-optic probe for in situ measurement of tissue mechanical properties

    PubMed Central

    Qiu, Yi; Wang, Yahui; Xu, Yiqing; Chandra, Namas; Haorah, James; Hubbi, Basil; Pfister, Bryan J.; Liu, Xuan

    2016-01-01

    We developed a miniature quantitative optical coherence elastography (qOCE) instrument with an integrated Fabry-Perot force sensor, for in situ elasticity measurement of biological tissue. The technique has great potential for biomechanics modeling and clinical diagnosis. We designed the fiber-optic qOCE probe that was used to exert a compressive force to deform tissue at the tip of the probe. Using the space-division multiplexed optical coherence tomography (OCT) signal detected by a spectral domain OCT engine, we were able to quantify the probe deformation that was proportional to the force applied, and to quantify the tissue deformation corresponding to the external stimulus. Simultaneous measurement of force and displacement allowed us to extract Young’s modulus of biological tissue. We experimentally calibrated our qOCE instrument, and validated its effectiveness on tissue mimicking phantoms and biological tissues. PMID:26977372

  1. Triphenylamine-based Schiff bases as the High sensitive Al(3+) or Zn(2+) fluorescence turn-on probe: Mechanism and application in vitro and in vivo.

    PubMed

    Li, Wei; Tian, Xiaohe; Huang, Bei; Li, Huijuan; Zhao, Xiaoyu; Gao, Shan; Zheng, Jun; Zhang, Xiuzhen; Zhou, Hongping; Tian, Yupeng; Wu, Jieying

    2016-03-15

    Two novel similar structural triphenylamine-based Schiff base fluorescent probes (L1/L2) were designed, prepared and characterized. Distinctive recognition mechanisms of L1 and L2 toward Al(3+) and Zn(2+) have been established by UV/vis, fluorescence spectra, mass spectra and (1)H NMR studies, respectively. To further explore their utility in biological system, L2 was selected as a probe for live cell endogenous Zn(2+) indicator and showed superb sensitivity on Zn(2+) intracellular distribution. Furthermore, L2 was employed to selectively detect Zn(2+) in live tissues at both extracellular and intracellular level, qualitatively indicated varies zinc concentration as a function of different organs. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Mechanism-based inactivation of lacrimal-gland peroxidase by phenylhydrazine: a suicidal substrate to probe the active site.

    PubMed Central

    Mazumdar, A; Adak, S; Chatterjee, R; Banerjee, R K

    1997-01-01

    Humans are exposed to various hydrazine derivatives for therapeutic control of several diseases, and mammalian peroxidases are implicated in the oxidative metabolism of many drugs. The results presented here indicate that lacrimal-gland peroxidase is irreversibly inactivated in a mechanism-based way by phenylhydrazine, which acts as a suicidal substrate in the presence of H2O2. The pseudo-first-order kinetic constants for inactivation at pH 5.5 are Ki=18 microM, kinact=0.25 min-1 and tau50=2.75 min, with a second-order rate constant of 0.75x10(4) M-1.min-1. Approx. 27 mol of phenylhydrazine and 54 mol of H2O2 are required per mol of enzyme for complete inactivation. The pH-dependent inactivation kinetics indicate the involvement of an ionizable group on the enzyme with a pKa value of 5.4, protonation of which favours inactivation. SCN-, the plausible physiological electron donor of the enzyme, protects it from inactivation. Binding studies by optical difference spectroscopy indicate that phenylhydrazine interacts with the enzyme with a KD value of 60 microM, and its binding is prevented by the presence of SCN-. The enzyme is also protected by 5, 5-dimethyl-1-pyrroline N-oxide, a free-radical trap, suggesting the involvement of a radical species in the inactivation. ESR studies indicate the formation of a spin-trapped phenyl radical (aN=15.9G and abetaH=24.8G) generated on incubation of phenylhydrazine with the enzyme and H2O2. A 75% loss of the Soret spectrum is observed when the enzyme is completely inactivated. However, in the presence of the spin trap, spectral loss is prevented and the enzyme compound II is readily reduced to the native state by phenylhydrazine. The phenylhydrazine-inactivated enzyme reacts with H2O2 or CN- to form compound II or the cyanide complex with a characteristic spectrum, indicating that haem iron is protected from attack by the radical species. The inactivated enzyme binds SCN- with a KD value similar to that of the native enzyme (15

  3. If Cell Mechanics Can Be Described by Elastic Modulus: Study of Different Models and Probes Used in Indentation Experiments

    PubMed Central

    Guz, Nataliia; Dokukin, Maxim; Kalaparthi, Vivekanand; Sokolov, Igor

    2014-01-01

    Here we investigated the question whether cells, being highly heterogeneous objects, could be described with the elastic modulus (effective Young’s modulus) in a self-consistent way. We performed a comparative analysis of the elastic modulus derived from the indentation data obtained with atomic force microscopy (AFM) on human cervical epithelial cells (both normal and cancerous). Both sharp (cone) and dull (2500-nm radius sphere) AFM probes were used. The indentation data were processed through different elastic models. The cell was approximated as a homogeneous elastic medium that had either 1), smooth hemispherical boundary (Hertz/Sneddon models) or 2), the boundary covered with a layer of glycocalyx and membrane protrusions (“brush” models). Consistency of these approximations was investigated. Specifically, we tested the independence of the elastic modulus of the indentation depth, which is assumed in these models. We demonstrated that only one model showed consistency in treating cells as a homogeneous elastic medium, namely, the brush model, when processing the indentation data collected with the dull AFM probe. The elastic modulus demonstrated strong depth dependence in all models: Hertz/Sneddon models (no brush taken into account), and when the brush model was applied to the data collected with sharp conical probes. We conclude that it is possible to describe the elastic properties of the cell body by means of an effective elastic modulus, used in a self-consistent way, when using the brush model to analyze data collected with a dull AFM probe. The nature of these results is discussed. PMID:25099796

  4. Multi-photon absorption effect and intra-molecular charge transfer of donor-π-acceptor chromophore ethyl p-amino benzoate.

    PubMed

    Sajan, D; Vijayan, N; Safakath, K; Philip, Reji; Karabacak, M

    2013-05-01

    Fourier transform (FT)-Raman and infrared (IR) spectra of the nonlinear optical (NLO) material ethyl p-amino benzoate (EPAB) have been recorded and analyzed. The geometry and harmonic vibrational wavenumbers are calculated with the help of B3LYP density functional theory method. The detailed interpretation of the vibrational spectra has been carried out with the aid of normal coordinate analysis following the scaled quantum mechanical force field methodology. Stability of the molecule arising from hyperconjugative interactions leading to its NLO activity and charge delocalization have been analyzed using natural bond orbital (NBO) analysis. Employing the open-aperture z-scan technique, NLO absorption of the sample has been studied in two excitation regimes, using 100 fs and 5 ns laser pulses respectively. It is found that EPAB is a three-photon absorber for 100 fs pulses at the excitation wavelength of 800 nm. For ns pulses at 532 nm it exhibits strong optical limiting, indicating possible photonics applications.

  5. FT-IR spectroscopy, intra-molecular C-H⋯O interactions, HOMO, LUMO, MESP analysis and biological activity of two natural products, triclisine and rufescine: DFT and QTAIM approaches

    NASA Astrophysics Data System (ADS)

    Srivastava, Ambrish Kumar; Pandey, Anoop Kumar; Jain, Sudha; Misra, Neeraj

    2015-02-01

    The present study deals with two natural products, triclisine and rufescine which are extracted from the Amazonian wines but ubiquitous in nature. The quantum chemical density functional method at B3PW91/6-311+G(d,p) level is used to obtain the equilibrium geometries of these molecules. The quantum theory of atoms-in-molecule approach is employed to study various intra-molecular C-H⋯O interactions within these molecules. We have also performed vibrational analyses of triclisine and rufescine at their equilibrium geometries and presented the complete assignments of the significant vibrational modes. The calculated vibrational frequencies are shown to be in perfect agreement with the experimentally observed FTIR spectra of molecules under study. In addition, the electronic properties of these molecules are also discussed with the help of HOMO-LUMO and MESP surfaces and a number of electronic as well as thermodynamic parameters are calculated which are closely related to their chemical reactivity and reaction paths. The biological activities of both molecules have also been predicted which highlight their pharmacological importance.

  6. Mechanics of liquid helium in a partially filled rotating dewar in low gravity with application to Gravity Probe-B

    NASA Technical Reports Server (NTRS)

    Schafer, C. F.; Lowry, S. A.

    1983-01-01

    The Gravity Probe-B spacecraft is composed largely of a liquid helium dewar containing an experiment package. It is shown that an unsymmetric liquid helium distribution in the dewar can cause unacceptably high forces, gravitational and gravity gradient forces, at the experiment location. It is further shown that for the planned spacecraft configuration and operational parameters, it is very likely that the liquid helium distribution in the dewar will be unsymmetric. The required symmetry can be attained by using higher operational spacecraft rotation rates.

  7. 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.

  8. 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.

  9. Batch-fabrication of cantilevered magnets on attonewton-sensitivity mechanical oscillators for scanned-probe nanoscale magnetic resonance imaging

    PubMed Central

    Hickman, Steven A.; Moore, Eric W.; Lee, SangGap; Longenecker, Jonilyn G.; Wright, Sarah J.; Harrell, Lee E.; Marohn, John A.

    2015-01-01

    We have batch-fabricated cantilevers with ~100 nm diameter nickel nanorod tips and force sensitivities of a few attonewtons at 4.2 kelvin. The magnetic nanorods were engineered to overhang the leading edge of the cantilever and, consequently, the cantilevers experience what we believe is the lowest surface noise ever achieved in a scanned probe experiment. Cantilever magnetometry indicated that the tips were well magnetized, with a ≤ 20 nm dead layer; the composition of the dead layer was studied by electron microscopy and electron energy loss spectroscopy. In what we believe is the first demonstration of scanned probe detection of electron-spin resonance from a batch fabricated tip, the cantilevers were used to observe electron-spin resonance from nitroxide spin labels in a film via force-gradient-induced shifts in cantilever resonance frequency. The magnetic field dependence of the magnetic resonance signal suggests a non-uniform tip magnetization at an applied field near 0.6 T. PMID:21082863

  10. Batch-fabrication of cantilevered magnets on attonewton-sensitivity mechanical oscillators for scanned-probe nanoscale magnetic resonance imaging.

    PubMed

    Hickman, Steven A; Moore, Eric W; Lee, SangGap; Longenecker, Jonilyn G; Wright, Sarah J; Harrell, Lee E; Marohn, John A

    2010-12-28

    We have batch-fabricated cantilevers with ∼100 nm diameter nickel nanorod tips and force sensitivities of a few attonewtons at 4.2 K. The magnetic nanorods were engineered to overhang the leading edge of the cantilever, and consequently the cantilevers experience what we believe is the lowest surface noise ever achieved in a scanned probe experiment. Cantilever magnetometry indicated that the tips were well magnetized, with a ≤ 20 nm dead layer; the composition of the dead layer was studied by electron microscopy and electron energy loss spectroscopy. In what we believe is the first demonstration of scanned probe detection of electron-spin resonance from a batch-fabricated tip, the cantilevers were used to observe electron-spin resonance from nitroxide spin labels in a film via force-gradient-induced shifts in cantilever resonance frequency. The magnetic field dependence of the magnetic resonance signal suggests a nonuniform tip magnetization at an applied field near 0.6 T.

  11. Cross-bridge cycling gives rise to spatiotemporal heterogeneity of dynamic subcellular mechanics in cardiac myocytes probed with atomic force microscopy.

    PubMed

    Azeloglu, Evren U; Costa, Kevin D

    2010-03-01

    To study how the dynamic subcellular mechanical properties of the heart relate to the fundamental underlying process of actin-myosin cross-bridge cycling, we developed a novel atomic force microscope elastography technique for mapping spatiotemporal stiffness of isolated, spontaneously beating neonatal rat cardiomyocytes. Cells were indented repeatedly at a rate close but unequal to their contractile frequency. The resultant changes in pointwise apparent elastic modulus cycled at a predictable envelope frequency between a systolic value of 26.2 +/- 5.1 kPa and a diastolic value of 7.8 +/- 4.1 kPa at a representative depth of 400 nm. In cells probed along their major axis, spatiotemporal changes in systolic stiffness displayed a heterogeneous pattern, reflecting the banded sarcomeric structure of underlying myofibrils. Treatment with blebbistatin eliminated contractile activity and resulted in a uniform apparent modulus of 6.5 +/- 4.8 kPa. This study represents the first quantitative dynamic mechanical mapping of beating cardiomyocytes. The technique provides a means of probing the micromechanical effects of disease processes and pharmacological treatments on beating cardiomyocytes, providing new insights and relating subcellular cardiac structure and function.

  12. Electron temperature probe

    NASA Astrophysics Data System (ADS)

    Oyama, K.-I.; Cheng, C. Z.

    2013-11-01

    The electron temperature probe (ETP) was invented in Japan in 1970's. The probe measures the electron temperature accurately and the measurement is not influenced by the electrode contamination. The instrument has low weight, low data transmission bit rate and low power consumption. The probe has been deployed in many sounding rockets, Earth orbiting scientific satellites, and Mars exploration spacecraft in Japan. The probe has also been deployed in sounding rockets in West Germany, India, Canada, USA, and Brazil. The probe has also been deployed in Brazilian satellites, Korean satellites, and recently as a Taiwan satellite payload. The manuscript describes the principle of the ETP instrument, the system configuration, the mechanical interface with respect to the sensor location, the control timing between data processing units; some useful information, the interference with other instruments, and future improvements and tasks. Some useful information for conducting performance check after the instrument fabrication and before the flight deployment is also presented in Appendix A.

  13. Mechanical Anisotropy and Pressure Induced Structural Changes in Piroxicam Crystals Probed by In Situ Indentation and Raman Spectroscopy

    NASA Astrophysics Data System (ADS)

    Manimunda, Praveena; Hintsala, Eric; Asif, Syed; Mishra, Manish Kumar

    2017-01-01

    The ability to correlate mechanical and chemical characterization techniques in real time is both lacking and powerful tool for gaining insights into material behavior. This is demonstrated through use of a novel nanoindentation device equipped with Raman spectroscopy to explore the deformation-induced structural changes in piroxicam crystals. Mechanical anisotropy was observed in two major faces ( 0bar{1}1 ) and (011), which are correlated to changes in the interlayer interaction from in situ Raman spectra recorded during indentation. The results of this study demonstrate the considerable potential of an in situ Raman nanoindentation instrument for studying a variety of topics, including stress-induced phase transformation mechanisms, mechanochemistry, and solid state reactivity under mechanical forces that occur in molecular and pharmaceutical solids.

  14. Probing the Nanodomain Origin and Phase Transition Mechanisms in (Un)Poled PMN-PT Single Crystals and Textured Ceramics

    PubMed Central

    Slodczyk, Aneta; Colomban, Philippe

    2010-01-01

    Outstanding electrical properties of solids are often due to the composition heterogeneity and/or the competition between two or more sublattices. This is true for superionic and superprotonic conductors and supraconductors, as well as for many ferroelectric materials. As in PLZT ferroelectric materials, the exceptional ferro- and piezoelectric properties of the PMN-PT ((1−x)PbMg1/3Nb2/3O3−xPbTiO3) solid solutions arise from the coexistence of different symmetries with long and short scales in the morphotropic phase boundary (MPB) region. This complex physical behavior requires the use of experimental techniques able to probe the local structure at the nanoregion scale. Since both Raman signature and thermal expansion behavior depend on the chemical bond anharmonicity, these techniques are very efficient to detect and then to analyze the subtitle structural modifications with an efficiency comparable to neutron scattering. Using the example of poled (field cooling or room temperature) and unpoled PMN-PT single crystal and textured ceramic, we show how the competition between the different sublattices with competing degrees of freedom, namely the Pb-Pb dominated by the Coulombian interactions and those built of covalent bonded entities (NbO6 and TiO6), determine the short range arrangement and the outstanding ferro- and piezoelectric properties. PMID:28883367

  15. BEAM CONTROL PROBE

    DOEpatents

    Chesterman, A.W.

    1959-03-17

    A probe is described for intercepting a desired portion of a beam of charged particles and for indicating the spatial disposition of the beam. The disclosed probe assembly includes a pair of pivotally mounted vanes moveable into a single plane with adjacent edges joining and a calibrated mechanical arrangement for pivoting the vancs apart. When the probe is disposed in the path of a charged particle beam, the vanes may be adjusted according to the beam current received in each vane to ascertain the dimension of the beam.

  16. Probing cytoskeletal pre-stress and nuclear mechanics in endothelial cells with spatiotemporally controlled (de-)adhesion kinetics on micropatterned substrates

    PubMed Central

    Versaevel, Marie; Riaz, Maryam; Corne, Tobias; Grevesse, Thomas; Lantoine, Joséphine; Mohammed, Danahe; Bruyère, Céline; Alaimo, Laura; De Vos, Winnok H.; Gabriele, Sylvain

    2017-01-01

    ABSTRACT The mechanical properties of living cells reflect their propensity to migrate and respond to external forces. Both cellular and nuclear stiffnesses are strongly influenced by the rigidity of the extracellular matrix (ECM) through reorganization of the cyto- and nucleoskeletal protein connections. Changes in this architectural continuum affect cell mechanics and underlie many pathological conditions. In this context, an accurate and combined quantification of the mechanical properties of both cells and nuclei can contribute to a better understanding of cellular (dys-)function. To address this challenge, we have established a robust method for probing cellular and nuclear deformation during spreading and detachment from micropatterned substrates. We show that (de-)adhesion kinetics of endothelial cells are modulated by substrate stiffness and rely on the actomyosin network. We combined this approach with measurements of cell stiffness by magnetic tweezers to show that relaxation dynamics can be considered as a reliable parameter of cellular pre-stress in adherent cells. During the adhesion stage, large cellular and nuclear deformations occur over a long time span (>60 min). Conversely, nuclear deformation and condensed chromatin are relaxed in a few seconds after detachment. Finally, our results show that accumulation of farnesylated prelamin leads to modifications of the nuclear viscoelastic properties, as reflected by increased nuclear relaxation times. Our method offers an original and non-intrusive way of simultaneously gauging cellular and nuclear mechanics, which can be extended to high-throughput screens of pathological conditions and potential countermeasures. PMID:27111836

  17. Coomassie brilliant blue R-250 as a new surface-enhanced Raman scattering probe for prion protein through a dual-aptamer mechanism.

    PubMed

    Hu, Ping Ping; Liu, Hui; Zhan, Lei; Zheng, Lin Ling; Huang, Cheng Zhi

    2015-07-01

    Surface-enhanced Raman scattering (SERS) spectra, which can provide large information about trace amount of chemical and biological species have been widely performed as a well-established tool in complex biological system. In this work, coomassie brilliant blue (R-250) with high affinity to proteins and high Raman activity was employed as a Raman reporter to probe prion protein (PrP) through a dual-aptamer mechanism, and thus an original strategy for PrP determination was proposed, which showed great potential to turn on the SERS response through specific recognition of anti-prion aptamers towards the target protein. Aptamers (Apt1 and Apt 2) recognizing distinct epitopes of PrP with high affinity were first conjugated to Ag@Si NPs, and Ag@Si-PrP/R-250-Ag@Si conjugates were obtained in the presence of PrP/R-250, inducing dramatically enhanced Raman signal. SERS responses enhanced with increasing amount of PrP and a linear equation of ISERS=6729.7+3091.2 cPrP was obtained in the range of 3.0-12.0×10(-9)M with the determination coefficient of 0.988. The proposed strategy is simple, rapid, and high specificity to probe protein-aptamer recognition in the solution. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Modelling mechanical heating in star-forming galaxies: CO and 13CO Line ratios as sensitive probes

    NASA Astrophysics Data System (ADS)

    Kazandjian, M. V.; Pelupessy, I.; Meijerink, R.; Israel, F. P.; Spaans, M.

    2016-11-01

    We apply photo-dissociation region (PDR) molecular line emission models, that have varying degrees of enhanced mechanical heating rates, to the gaseous component of simulations of star-forming galaxies taken from the literature. Snapshots of these simulations are used to produce line emission maps for the rotational transitions of the CO molecule and its 13CO isotope up to J = 4-3. We use these maps to investigate the occurrence and effect of mechanical feedback on the physical parameters obtained from molecular line intensity ratios. We consider two galaxy models: a small disk galaxy of solar metallicity and a lighter dwarf galaxy with 0.2 Z⊙ metallicity. Elevated excitation temperatures for CO(1-0) correlate positively with mechanical feedback, that is enhanced towards the central region of both model galaxies. The emission maps of these model galaxies are used to compute line ratios of CO and 13CO transitions. These line ratios are used as diagnostics where we attempt to match them These line ratios are used as diagnostics where we attempt to match them to mechanically heated single component (i.e. uniform density, Far-UV flux, visual extinction and velocity gradient) equilibrium PDR models. We find that PDRs ignoring mechanical feedback in the heating budget over-estimate the gas density by a factor of 100 and the far-UV flux by factors of 10-1000. In contrast, PDRs that take mechanical feedback into account are able to fit all the line ratios for the central <2 kpc of the fiducial disk galaxy quite well. The mean mechanical heating rate per H atom that we recover from the line ratio fits of this region varies between 10-27-10-26 erg s-1. Moreover, the mean gas density, mechanical heating rate, and the AV are recovered to less than half dex. On the other hand, our single component PDR model fit is not suitable for determining the actual gas parameters of the dwarf galaxy, although the quality of the fit line ratios are comparable to that of the disk galaxy.

  19. A novel near-infrared fluorescent probe for H2O2 in alkaline environment and the application for H2O2 imaging in vitro and in vivo.

    PubMed

    Liu, Keyin; Shang, Huiming; Kong, Xiuqi; Ren, Mingguang; Wang, Jian-Yong; Liu, Yong; Lin, Weiying

    2016-09-01

    H2O2 as one of the most important ROS (Reactive Oxygen Species) has more attack activity to biomolecules such as DNA, RNA, protein and enzyme in alkaline environment and leads to a series of disease. However, no attention has been paid to the fluorescent detection of H2O2 in alkaline environment in the past. Herein, we reported the first ratiometric near-infrared fluorescent probe based on a boric acid derivative of Changsha near-infrared dye (CSBOH) for H2O2 detection in alkaline condition and the application for H2O2 imaging in vivo. ICT (intra-molecular charge transfer) mechanism was used in CSBOH to modulate the fluorescence change. The photophysical change of CSBOH was investigated by comparison with a phenol derivative of Changsha near-infrared dye (CSOH), a structural analogue bearing phenol group. In the presence of H2O2, CSBOH exhibited remarkably different fluorescence change at 650 nm and 720 nm when excited by 560 nm and 670 nm light respectively in alkaline buffer and showed high selectivity toward H2O2. Cellular experiments demonstrate that CSBOH can image endogenously generated H2O2 in macrophages and A431 cells. In vivo experiment demonstrates that both CSOH and CSBOH can be used for bio-imaging, and CSBOH can image H2O2 in living animal successfully.

  20. Probing the Selectivity and Protein•Protein Interactions of a Non-Reducing Fungal Polyketide Synthase Using Mechanism-Based Crosslinkers

    PubMed Central

    Bruegger, Joel; Haushalter, Bob; Vagstad, Anna; Shakya, Gaurav; Mih, Nathan; Townsend, Craig A.; Burkart, Michael D.; Tsai, Shiou-Chuan

    2013-01-01

    SUMMARY Protein•protein interactions, which often involve interactions between an acyl carrier protein (ACP) and its partner enzymes, are important for coordinating polyketide biosynthesis. However, the nature of such interactions is not well understood, especially in the fungal non-reducing polyketide synthases (NR-PKSs) that biosynthesize toxic and pharmaceutically important polyketides. Here, we employ a mechanism-based crosslinker to successfully probe ACP and ketosynthase (KS) domain interactions in NR-PKSs. We found that crosslinking efficiency is closely correlated with the strength of ACP•KS interactions, and that KS demonstrates strong starter unit selectivity. We further identified positively charged surface residues by KS mutagenesis, which mediate key interactions with the negatively-charged ACP surface. Such complementary/matching contact pairs can serve as “adapter surfaces” for future efforts to generate new polyketides using NR-PKSs. PMID:23993461

  1. Probing the meiotic mechanism of intergenomic exchanges by genomic in situ hybridization on lampbrush chromosomes of unisexual Ambystoma (Amphibia: Caudata).

    PubMed

    Bi, Ke; Bogart, James P

    2010-04-01

    The meiotic mechanism of unisexual salamanders in the genus Ambystoma was previously explained by observing lampbrush chromosomes (LBCs). In polyploid unisexual females, a pre-meiotic endomitotic event doubles the chromosome number so that, after meiotic reduction, the mature eggs have the same ploidy as the female. It was assumed that synapses during meiotic I prophase, which result in observed bivalents, join duplicated sister chromosomes. Previous studies also found LBC quadrivalents in some oocytes that could be explained by occasional synapses between homologs. The discovery of widespread intergenomic exchanges among unisexual populations has prompted new speculations on this meiotic mechanism. Synapses that involve homeologous chromosomes may be frequent during meiosis and could be responsible for intergenomic exchanges and the high embryonic mortality of unisexuals. Furthermore, LBC quadrivalents may be established by associations between homeologous rather than homologous chromosomes. The present study investigated these two important aspects pertaining to the mechanism of intergenomic exchanges: the frequency of homeologous synapses and the relationship between homeologous associations and meiotic quadrivalents. We applied genomic in situ hybridization (GISH) on LBCs from oocytes of 14 triploid and two tetraploid unisexual females. Homeologous bivalents were not observed, and all 13 LBC quadrivalents that we found were the result of homologous synapses and were not associated with any homeologous or exchanged LBCs. Intergenomic exchanges were used as markers to compare the same chromosomes at meiotic diplotene and mitotic metaphase stages. We conclude that contemporary intergenomic exchanges are very rare, and no direct link exists between intergenomic exchanges and high embryonic mortality. The actual mechanisms and evolutionary implications of intergenomic exchanges appear to be complicated and difficult to assess. The application of GISH-type molecular

  2. Probing the chemical mechanism and critical regulatory amino acid residues of Drosophila melanogaster arylalkylamine N-acyltransferase like 2.

    PubMed

    Dempsey, Daniel R; Carpenter, Anne-Marie; Ospina, Santiago Rodriguez; Merkler, David J

    2015-11-01

    Arylalkylamine N-acyltransferase like 2 (AANATL2) catalyzes the formation of N-acylarylalkylamides from the corresponding acyl-CoA and arylalkylamine. The N-acylation of biogenic amines in Drosophila melanogaster is a critical step for the inactivation of neurotransmitters, cuticle sclerotization, and melatonin biosynthesis. In addition, D. melanogaster has been used as a model system to evaluate the biosynthesis of fatty acid amides: a family of potent cell signaling lipids. We have previously showed that AANATL2 catalyzes the formation of N-acylarylakylamides, including long-chain N-acylserotonins and N-acyldopamines. Herein, we define the kinetic mechanism for AANATL2 as an ordered sequential mechanism with acetyl-CoA binding first followed by tyramine to generate the ternary complex prior to catalysis. Bell shaped kcat,app - acetyl-CoA and (kcat/Km)app - acetyl-CoA pH-rate profiles identified two apparent pKa,app values of ∼7.4 and ∼8.9 that are critical to catalysis, suggesting the AANATL2-catalyzed formation of N-acetyltyramine occurs through an acid/base chemical mechanism. Site-directed mutagenesis of a conserved glutamate that corresponds to the catalytic base for other D. melanogaster AANATL enzymes did not produce a substantial depression in the kcat,app value nor did it abolish the pKa,app value attributed to the general base in catalysis (pKa ∼7.4). These data suggest that AANATL2 catalyzes the formation of N-acylarylalkylamides using either different catalytic residues or a different chemical mechanism relative to other D. melanogaster AANATL enzymes. In addition, we constructed other site-directed mutants of AANATL2 to help define the role of targeted amino acids in substrate binding and/or enzyme catalysis.

  3. Simulation of the mechanical unfolding of ubiquitin: Probing different unfolding reaction coordinates by changing the pulling geometry

    NASA Astrophysics Data System (ADS)

    Li, Pai-Chi; Makarov, Dmitrii E.

    2004-09-01

    Motivated by the recent experimental atomic force microscopy (AFM) measurements of the mechanical unfolding of proteins pulled in different directions [D. J. Brockwell et al., Nat. Struct. Biol. 10, 731 (2003); M. Carrion-Vazquez et al., ibid 10, 738 (2003)] we have computed the unfolding free energy profiles for the ubiquitin domain when it is stretched between its (A) N and C termini, (B) Lys48 and C terminus, (C) Lys11 and C terminus, and (D) N terminus and Lys63. Our results for cases (A) and (B) are in good agreement with the experimental unfolding forces measured for the N-C and Lys48-C linked polyubiquitin, in particular, indicating a considerably lower unfolding force in the latter case. Mechanical unfolding in case (A) involves longitudinal shearing of the terminal parallel strands while in case (C) the same strands are "unzipped" by the force. The computed unfolding forces in case (C) are found to be very low, less than 50 pN for pulling rates typical of AFM experiments. The unfolding free energy barrier found in case (C) is ˜13 kcal/mol, which corresponds to a zero-force unfolding rate constant that is comparable to the rate of chemical unfolding extrapolated to zero denaturant concentration. The unfolding barrier calculated in case (A) in the limit of zero force is much higher, suggesting that mechanical unfolding in this case follows a pathway that is different from that of thermal/chemical denaturation.

  4. Probing the mechanism of nitrogen transfer in Escherichia coli asparagine synthetase by using heavy atom isotope effects.

    PubMed

    Stoker, P W; O'Leary, M H; Boehlein, S K; Schuster, S M; Richards, N G

    1996-03-05

    In experiments aimed at determining the mechanism of nitrogen transfer in purF amidotransferase enzymes, 13C and 15N kinetic isotope effects have been measured for both of the glutamine-dependent activities of Escherichia coli asparagine synthetase B (AS-B). For the glutaminase reaction catalyzed by AS-B at pH 8.0, substitution heavy atom labels in the side chain amide of the substrate yields observed values of 1.0245 and 1.0095 for the amide carbon and amide nitrogen isotope effects, respectively. In the glutamine-dependent synthesis of asparagine at pH 8.0, the amide carbon and amide nitrogen isotope effects have values of 1.0231 and 1.0222, respectively. We interpret these results to mean that nitrogen transfer does not proceed by the formation of free ammonia in the active site of the enzyme and probably involves a series of intermediates in which glutamine becomes covalently attached to aspartate. While a number of mechanisms are consistent with the observed isotope effects, a likely reaction pathway involves reaction of an oxyanion with beta-aspartyl-AMP. This yields an intermediate in which C-N bond cleavage gives an acylthioenzyme and a second tetrahedral intermediate. Loss of AMP from the latter gives asparagine. An alternate reaction mechanism in which asparagine is generated from an imide intermediate also appears consistent with the observed kinetic isotope effects.

  5. Probing the Degradation Mechanisms in Electrolyte Solutions for Li-ion Batteries by In-Situ Transmission Electron Microscopy

    SciTech Connect

    Abellan Baeza, Patricia; Mehdi, Beata L.; Parent, Lucas R.; Gu, Meng; Park, Chiwoo; Xu, Wu; Zhang, Yaohui; Arslan, Ilke; Zhang, Jiguang; Wang, Chong M.; Evans, James E.; Browning, Nigel D.

    2014-02-21

    One of the goals in the development of new battery technologies is to find new electrolytes with increased electrochemical stability. In-situ (scanning) transmission electron microscopy ((S)TEM) using an electrochemical fluid cell provides the ability to rapidly and directly characterize electrode/electrolyte interfacial reactions under battery relevant electrochemical conditions. Furthermore, as the electron beam itself causes a localized electrochemical reaction when it interacts with the electrolyte, the breakdown products that occur during the first stages of battery operation can potentially be simulated and characterized using a straightforward in-situ liquid stage (without electrochemical biasing capabilities). In this paper, we have studied the breakdown of a range of inorganic/salt complexes that are used in state-of-the-art Li-ion battery systems. The results of the in-situ (S)TEM experiments matches with previous stability tests performed during battery operation and the breakdown products and mechanisms are also consistent with known mechanisms. This analysis indicates that in-situ liquid stage (S)TEM observations can be used to directly test new electrolyte designs and provide structural insights into the origin of the solid electrolyte interphase (SEI) formation mechanism.

  6. Biophysical assays to probe the mechanical properties of the interphase cell nucleus: substrate strain application and microneedle manipulation.

    PubMed

    Lombardi, Maria L; Zwerger, Monika; Lammerding, Jan

    2011-09-14

    In most eukaryotic cells, the nucleus is the largest organelle and is typically 2 to 10 times stiffer than the surrounding cytoskeleton; consequently, the physical properties of the nucleus contribute significantly to the overall biomechanical behavior of cells under physiological and pathological conditions. For example, in migrating neutrophils and invading cancer cells, nuclear stiffness can pose a major obstacle during extravasation or passage through narrow spaces within tissues.(1) On the other hand, the nucleus of cells in mechanically active tissue such as muscle requires sufficient structural support to withstand repetitive mechanical stress. Importantly, the nucleus is tightly integrated into the cellular architecture; it is physically connected to the surrounding cytoskeleton, which is a critical requirement for the intracellular movement and positioning of the nucleus, for example, in polarized cells, synaptic nuclei at neuromuscular junctions, or in migrating cells.(2) Not surprisingly, mutations in nuclear envelope proteins such as lamins and nesprins, which play a critical role in determining nuclear stiffness and nucleo-cytoskeletal coupling, have been shown recently to result in a number of human diseases, including Emery-Dreifuss muscular dystrophy, limb-girdle muscular dystrophy, and dilated cardiomyopathy.(3) To investigate the biophysical function of diverse nuclear envelope proteins and the effect of specific mutations, we have developed experimental methods to study the physical properties of the nucleus in single, living cells subjected to global or localized mechanical perturbation. Measuring induced nuclear deformations in response to precisely applied substrate strain application yields important information on the deformability of the nucleus and allows quantitative comparison between different mutations or cell lines deficient for specific nuclear envelope proteins. Localized cytoskeletal strain application with a microneedle is used to

  7. Kinetic Isotope Effects as a Probe for the Protonolysis Mechanism of Alkylmetal Complexes: VTST/MT Calculations Based on DFT Potential Energy Surfaces.

    PubMed

    Mai, Binh Khanh; Kim, Yongho

    2016-10-03

    Protonolysis by platinum or palladium complexes has been extensively studied because it is the microscopic reverse of the C-H bond activation reaction. The protonolysis of (COD)Pt(II)Me2, which exhibits abnormally large kinetic isotope effects (KIEs), is proposed to occur via a concerted pathway (SE2 mechanism) with large tunneling. However, further investigation of KIEs for the protonolysis of ZnMe2 and others led to a conclusion that there is no noticeable correlation between the mechanism and magnitude of KIE. In this study, we demonstrated that variational transition state theory including multidimensional tunneling (VTST/MT) could accurately predict KIEs and Arrhenius parameters of the protonolysis of alkylmetal complexes based on the potential energy surfaces generated by density functional theory. The predicted KIEs, Ea(D) - Ea(H) values, and AH/AD ratios for the protonolysis of (COD)Pt(II)Me2 and Zn(II)Me2 by TFA agreed very well with experimental values. The protonolysis of ZnMe2 with the concerted pathway has a very flat potential energy surface, which produces a very small tunneling effect and therefore a small KIE. The predicted KIE for the stepwise protonolysis (SE(ox) mechanism) of (COD)Pt(II)Me2 was much smaller than that of the concerted pathway, but greater than the KIE of the concerted protonolysis of ZnMe2. A large KIE, which entails a significant tunneling effect, could be used as an experimental probe of the concerted pathway. However, a normal or small KIE should not be used as an indicator of the stepwise mechanism, and the interplay between experiments and reliable theory including tunneling would be essential to uncover the mechanism correctly.

  8. Probing the mechanism of saccade-associated head movements through observations of head movement propensity and cognition in the elderly.

    PubMed

    Thumser, Zachary C; Adams, Nancy L; Lerner, Alan J; Stahl, John S

    2010-05-01

    Humans may accomplish gaze shifts by eye-only saccades or combined eye-head saccades. The mechanisms that determine whether the head moves remain poorly understood. Many observations can be explained if phylogenetically ancient circuits generate eye-head saccades by default and frontal cerebral structures interrupt this synergy when eye-only saccades are preferable. Saccade-associated head movements have been reported to increase in the elderly. To test the hypothesis of frontal inhibition of head movements, we investigated whether the increase is associated with a decline in frontal cognitive function. We measured head movement tendencies and cognition in volunteers aged 61-80. Measures of head movement tendency included the customary range of eye eccentricity, customary range of head eccentricity, range of target eccentricities evoking predominantly eye-only saccades, and two measures of head amplitude variation as a function of target eccentricity. Cognitive measures encompassed verbal fluency, verbal memory, non-verbal memory, and executive function. There was no correlation between cognition and any measure of head movement tendency. We combined these elderly data with measurements of head movements in a group aged 21-67 and found mildly reduced, not increased, head movement tendencies with age. However, when confronted with a task that could be accomplished without moving the head, young subjects were more likely to cease all head movements. While inconclusive regarding the hypothesis of inhibition of saccade-associated head movements by cerebral structures, the results indicate the need to distinguish between mechanisms that define head movement tendencies and mechanisms that adapt head motion to the geometry of a specific task.

  9. Probing the catalytic mechanism of bovine CD38/NAD+ glycohydrolase by site directed mutagenesis of key active site residues.

    PubMed

    Kuhn, Isabelle; Kellenberger, Esther; Cakir-Kiefer, Céline; Muller-Steffner, Hélène; Schuber, Francis

    2014-07-01

    Bovine CD38/NAD(+) glycohydrolase catalyzes the hydrolysis of NAD(+) to nicotinamide and ADP-ribose and the formation of cyclic ADP-ribose via a stepwise reaction mechanism. Our recent crystallographic study of its Michaelis complex and covalently-trapped intermediates provided insights into the modalities of substrate binding and the molecular mechanism of bCD38. The aim of the present work was to determine the precise role of key conserved active site residues (Trp118, Glu138, Asp147, Trp181 and Glu218) by focusing mainly on the cleavage of the nicotinamide-ribosyl bond. We analyzed the kinetic parameters of mutants of these residues which reside within the bCD38 subdomain in the vicinity of the scissile bond of bound NAD(+). To address the reaction mechanism we also performed chemical rescue experiments with neutral (methanol) and ionic (azide, formate) nucleophiles. The crucial role of Glu218, which orients the substrate for cleavage by interacting with the N-ribosyl 2'-OH group of NAD(+), was highlighted. This contribution to catalysis accounts for almost half of the reaction energy barrier. Other contributions can be ascribed notably to Glu138 and Asp147 via ground-state destabilization and desolvation in the vicinity of the scissile bond. Key interactions with Trp118 and Trp181 were also proven to stabilize the ribooxocarbenium ion-like transition state. Altogether we propose that, as an alternative to a covalent acylal reaction intermediate with Glu218, catalysis by bCD38 proceeds through the formation of a discrete and transient ribooxocarbenium intermediate which is stabilized within the active site mostly by electrostatic interactions.

  10. Probing the mechanisms of drug release from amorphous solid dispersions in medium-soluble and medium-insoluble carriers.

    PubMed

    Sun, Dajun D; Lee, Ping I

    2015-08-10

    The objective of the current study is to mechanistically differentiate the dissolution and supersaturation behaviors of amorphous drugs from amorphous solid dispersions (ASDs) based on medium-soluble versus medium-insoluble carriers under nonsink dissolution conditions through a direct head-to-head comparison. ASDs of indomethacin (IND) were prepared in several polymers which exhibit different solubility behaviors in acidic (pH1.2) and basic (pH7.4) dissolution media. The selected polymers range from water-soluble (e.g., PVP and Soluplus) and water-insoluble (e.g., ethylcellulose and Eudragit RL PO) to those only soluble in an acidic or basic dissolution medium (e.g., Eudragit E100, Eudragit L100, and HPMCAS). At 20wt.% drug loading, DSC and powder XRD analysis confirmed that the majority of incorporated IND was present in an amorphous state. Our nonsink dissolution results confirm that whether the carrier matrix is medium soluble determines the release mechanism of amorphous drugs from ASD systems which has a direct impact on the rate of supersaturation generation, thus in turn affecting the evolution of supersaturation in amorphous systems. For example, under nonsink dissolution conditions, the release of amorphous IND from medium-soluble carriers is governed by a dissolution-controlled mechanism leading to an initial surge of supersaturation followed by a sharp decline in drug concentration due to rapid nucleation and crystallization. In contrast, the dissolution of IND ASD from medium-insoluble carriers is more gradual as drug release is regulated by a diffusion-controlled mechanism by which drug supersaturation is built up gradually and sustained over an extended period of time without any apparent decline. Since several tested carrier polymers can be switched from soluble to insoluble by simply changing the pH of the dissolution medium, the results obtained here provide unequivocal evidence of the proposed transition of kinetic solubility profiles from the

  11. A study of the feasibility of mechanical pumps for use with the Pioneer-Venus probe mass spectrometer inlet system

    NASA Technical Reports Server (NTRS)

    Thomas, N. C.; Crosmer, W. E.; Nowak, D.

    1973-01-01

    A survey of mechanical vacuum pumps was completed. A small Roots blower for flight mass spectrometer applications was evaluated with respect to system operating parameters in a number of different modes of operation. The survey indicated that a metal bellows pump might be a viable alternative for the systems requirements. The results of the study are given, including current status of possible flight-type pumps, a systems analysis using available pumps, and recommendations for fabrication and tests of a potential flight-type pump.

  12. Susceptibility to distraction in autism spectrum disorder: Probing the integrity of oscillatory alpha-band suppression mechanisms

    PubMed Central

    Murphy, Jeremy W.; Foxe, John J.; Peters, Joanna B.; Molholm, Sophie

    2014-01-01

    Scientific Abstract When attention is directed to one information stream over another, the brain can be configured in advance to selectively process the relevant stream and suppress potentially distracting inputs. One key mechanism of suppression is through the deployment of anticipatory alpha-band (~10Hz) oscillatory activity, with greater alpha-band power observed in cortical regions that will ultimately process the distracting stream. Atypical attention has been implicated in autism spectrum disorder (ASD), including greater interference by distracting task-irrelevant inputs. Here we tested the integrity of these alpha-band mechanisms in ASD using an intersensory attention task. EEG was recorded while participants were cued on a trial-by-trial basis to selectively deploy attention to the visual or auditory modality in anticipation of a target within the cued modality. Whereas typically developing children showed the predicted alpha-band modulation, with increased alpha-band power over parieto-occipital scalp when attention was deployed to the auditory compared to the visual modality, this differential pattern was entirely absent at the group level in the ASD cohort. Further, only the ASD group showed impaired performance due to the presence of task-irrelevant sensory information. These data suggest that impaired modulation of alpha-band activity plays a role in increased distraction from extraneous sensory inputs in ASD. PMID:24678054

  13. Mechanism of the Escherichia coli DNA T:G-mismatch endonuclease (Vsr protein) probed with thiophosphate-containing oligodeoxynucleotides.

    PubMed

    Elliott, Sarah L; Brazier, John; Cosstick, Richard; Connolly, Bernard A

    2005-10-28

    The mechanism of the Escherichia coli DNA T:G mismatch endonuclease (Vsr) has been investigated using oligodeoxynucleotides substituted, at the scissile phosphate, with isomeric phosphorothioates and a 3'-phosphorothiolate. Binding and kinetic data with the phosphorothioates/phosphorothiolate indicate that the two magnesium ions, which constitute essential co-factors, are required to stabilise the extra negative charge developed on the phosphate as the transition state is formed. Additionally one of the magnesium ions serves to activate the leaving group (the non-bridging 3'-oxygen atom of the scissile phosphate) during the hydrolysis reaction. Stereochemical analysis, using the R(p) phosphorothioate isomer, indicates that Vsr carries out a hydrolytic reaction with inversion of stereochemistry at phosphorus, compatible with an in-line attack of water and a pentacovalent transition state with trigonal bipyramidal geometry. In conjunction with structures of Vsr bound to its products, these data allow the reconstruction of the enzyme-substrate complex and a comprehensive description of the hydrolysis mechanism.

  14. Bisubstrate analog probes for the insulin receptor protein tyrosine kinase: molecular yardsticks for analyzing catalytic mechanism and inhibitor design.

    PubMed

    Hines, Aliya C; Parang, Keykavous; Kohanski, Ronald A; Hubbard, Stevan R; Cole, Philip A

    2005-08-01

    Bisubstrate analogs have the potential to provide enhanced specificity for protein kinase inhibition and tools to understand catalytic mechanism. Previous efforts led to the design of a peptide-ATP conjugate bisubstrate analog utilizing aminophenylalanine in place of tyrosine and a thioacetyl linker to the gamma-phosphate of ATP which was a potent inhibitor of the insulin receptor kinase (IRK). In this study, we have examined the contributions of various electrostatic and structural elements in the bisubstrate analog to IRK binding affinity. Three types of changes (seven specific analogs in all) were introduced: a Tyr isostere of the previous aminophenylalanine moiety, modifications of the spacer between the adenine and the peptide, and deletions and substitutions within the peptide moiety. These studies allowed a direct evaluation of the hydrogen bond strength between the anilino nitrogen of the bisubstrate analog and the enzyme catalytic base Asp and showed that it contributes 2.5 kcal/mol of binding energy, in good agreement with previous predictions. Modifications of the linker length resulted in weakened inhibitory affinity, consistent with the geometric requirements of an enzyme-catalyzed dissociative transition state. Alterations in the peptide motif generally led to diminished inhibitory potency, and only some of these effects could be rationalized based on prior kinetic and structural studies. Taken together, these results suggest that a combination of mechanism-based design and empirical synthetic manipulation will be necessary in producing optimized protein kinase bisubstrate analog inhibitors.

  15. Probing the degradation mechanisms in electrolyte solutions for Li-ion batteries by in situ transmission electron microscopy.

    PubMed

    Abellan, Patricia; Mehdi, B Layla; Parent, Lucas R; Gu, Meng; Park, Chiwoo; Xu, Wu; Zhang, Yaohui; Arslan, Ilke; Zhang, Ji-Guang; Wang, Chong-Min; Evans, James E; Browning, Nigel D

    2014-03-12

    Development of novel electrolytes with increased electrochemical stability is critical for the next generation battery technologies. In situ electrochemical fluid cells provide the ability to rapidly and directly characterize electrode/electrolyte interfacial reactions under conditions directly relevant to the operation of practical batteries. In this paper, we have studied the breakdown of a range of inorganic/salt complexes relevant to state-of-the-art Li-ion battery systems by in situ (scanning) transmission electron microscopy ((S)TEM). In these experiments, the electron beam itself caused the localized electrochemical reaction that allowed us to observe electrolyte breakdown in real-time. The results of the in situ (S)TEM experiments matches with previous stability tests performed during battery operation and the breakdown products and mechanisms are also consistent with known mechanisms. This analysis indicates that in situ liquid stage (S)TEM observations could be used to directly test new electrolyte designs and identify a smaller library of candidate solutions deserving of more detailed characterization. A systematic study of electrolyte degradation is also a necessary first step for any future controlled in operando liquid (S)TEM experiments intent on visualizing working batteries at the nanoscale.

  16. Probing the intrinsic failure mechanism of fluorinated amorphous carbon film based on the first-principles calculations

    PubMed Central

    Zhang, Ren-hui; Wang, Li-ping; Lu, Zhi-bin

    2015-01-01

    Fluorinated amorphous carbon films exhibit superlow friction under vacuum, but are prone to catastrophic failure. Thus far, the intrinsic failure mechanism remains unclear. A prevailing view is that the failure of amorphous carbon film results from the plastic deformation of substrates or strong adhesion between two contacted surfaces. In this paper, using first-principles and molecular dynamics methodology, combining with compressive stress-strain relation, we firstly demonstrate that the plastic deformation induces graphitization resulting in strong adhesion between two contacted surfaces under vacuum, which directly corresponds to the cause of the failure of the films. In addition, sliding contact experiments are conducted to study tribological properties of iron and fluorinated amorphous carbon surfaces under vacuum. The results show that the failure of the film is directly attributed to strong adhesion resulting from high degree of graphitization of the film, which are consistent with the calculated results. PMID:25803202

  17. Probing the failure mechanism of nanoscale LiFePO{sub 4} for Li-ion batteries

    SciTech Connect

    Gu, Meng; Yan, Pengfei; Wang, Chongmin; Shi, Wei; Zheng, Jianming; Zhang, Ji-guang

    2015-05-18

    LiFePO{sub 4} is a high power rate cathode material for lithium ion battery and shows remarkable capacity retention, featuring a 91% capacity retention after 3300 cycles. In this work, we use high-resolution transmission electron microscopy and electron energy loss spectroscopy to study the gradual capacity fading mechanism of LiFePO{sub 4} materials. We found that upon prolonged electrochemical cycling of the battery, the LiFePO{sub 4} cathode shows surface amorphization and loss of oxygen species, which directly contribute to the gradual capacity fading of the battery. The finding can guide the design and improvement of LiFePO{sub 4} cathode for high-energy and high-power rechargeable battery for electric transportation.

  18. A Structure-Activity Analysis for Probing the Mechanism of Processive Double-Stranded DNA Digestion by λ Exonuclease Trimers.

    PubMed

    Pan, Xinlei; Smith, Christopher E; Zhang, Jinjin; McCabe, Kimberly A; Fu, Jun; Bell, Charles E

    2015-10-06

    λ exonuclease (λexo) is an ATP-independent 5'-to-3' exonuclease that binds to double-stranded DNA (dsDNA) ends and processively digests the 5'-strand into mononucleotides. The crystal structure of λexo revealed that the enzyme forms a ring-shaped homotrimer with a central funnel-shaped channel for tracking along the DNA. On the basis of this structure, it was proposed that dsDNA enters the open end of the channel, the 5'-strand is digested at one of the three active sites, and the 3'-strand passes through the narrow end of the channel to emerge out the back. This model was largely confirmed by the structure of the λexo-DNA complex, which further revealed that the enzyme unwinds the DNA by 2 bp prior to cleavage, to thread the 5'-end of the DNA into the active site. On the basis of this structure, an "electrostatic ratchet" model was proposed, in which the enzyme uses a hydrophobic wedge to insert into the base pairs to unwind the DNA, a two-metal mechanism for nucleotide hydrolysis, a positively charged pocket to bind to the terminal 5'-phosphate generated after each round of cleavage, and an arginine residue (Arg-45) to bind to the minor groove of the downstream end of the DNA. To test this model, in this study we have determined the effects of 11 structure-based mutations in λexo on DNA binding and exonuclease activities in vitro, and on DNA recombination in vivo. The results are largely consistent with the model for the mechanism that was proposed on the basis of the structure and provide new insights into the roles of particular residues of the protein in promoting the reaction. In particular, a key role for Arg-45 in DNA binding is revealed.

  19. Probing electron transfer mechanisms in Shewanella oneidensis MR-1 using a nanoelectrode platform and single-cell imaging.

    PubMed

    Jiang, Xiaocheng; Hu, Jinsong; Fitzgerald, Lisa A; Biffinger, Justin C; Xie, Ping; Ringeisen, Bradley R; Lieber, Charles M

    2010-09-28

    Microbial fuel cells (MFCs) represent a promising approach for sustainable energy production as they generate electricity directly from metabolism of organic substrates without the need for catalysts. However, the mechanisms of electron transfer between microbes and electrodes, which could ultimately limit power extraction, remain controversial. Here we demonstrate optically transparent nanoelectrodes as a platform to investigate extracellular electron transfer in Shewanella oneidensis MR-1, where an array of nanoholes precludes or single window allows for direct microbe-electrode contacts. Following addition of cells, short-circuit current measurements showed similar amplitude and temporal response for both electrode configurations, while in situ optical imaging demonstrates that the measured currents were uncorrelated with the cell number on the electrodes. High-resolution imaging showed the presence of thin, 4- to 5-nm diameter filaments emanating from cell bodies, although these filaments do not appear correlated with current generation. Both types of electrodes yielded similar currents at longer times in dense cell layers and exhibited a rapid drop in current upon removal of diffusible mediators. Reintroduction of the original cell-free media yielded a rapid increase in current to ∼80% of original level, whereas imaging showed that the positions of > 70% of cells remained unchanged during solution exchange. Together, these measurements show that electron transfer occurs predominantly by mediated mechanism in this model system. Last, simultaneous measurements of current and cell positions showed that cell motility and electron transfer were inversely correlated. The ability to control and image cell/electrode interactions down to the single-cell level provide a powerful approach for advancing our fundamental understanding of MFCs.

  20. Mechanical Properties of Membranes Composed of Gel-Phase or Fluid-Phase Phospholipids Probed on Liposomes by Atomic Force Spectroscopy.

    PubMed

    Et-Thakafy, Oumaima; Delorme, Nicolas; Gaillard, Cédric; Mériadec, Cristelle; Artzner, Franck; Lopez, Christelle; Guyomarc'h, Fanny

    2017-05-30

    In many liposome applications, the nanomechanical properties of the membrane envelope are essential to ensure, e.g., physical stability, protection, or penetration into tissues. Of all factors, the lipid composition and its phase behavior are susceptible to tune the mechanical properties of membranes. To investigate this, small unilamellar vesicles (SUV; diameter < 200 nm), referred to as liposomes, were produced using either unsaturated 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) or saturated 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) in aqueous buffer at pH 6.7. The respective melting temperatures of these phospholipids were -20 and 41 °C. X-ray diffraction analysis confirmed that at 20 °C DOPC was in the fluid phase and DPPC was in the gel phase. After adsorption of the liposomes onto flat silicon substrates, atomic force microscopy (AFM) was used to image and probe the mechanical properties of the liposome membrane. The resulting force-distance curves were treated using an analytical model based on the shell theory to yield the Young's modulus (E) and the bending rigidity (kC) of the curved membranes. The mechanical investigation showed that DPPC membranes were much stiffer (E = 116 ± 45 MPa) than those of DOPC (E = 13 ± 9 MPa) at 20 °C. The study demonstrates that the employed methodology allows discrimination of the respective properties of gel- or fluid-phase membranes when in the shape of liposomes. It opens perspectives to map the mechanical properties of liposomes containing both fluid and gel phases or of biological systems.

  1. The accumulation mechanism of the hypoxia imaging probe “FMISO” by imaging mass spectrometry: possible involvement of low-molecular metabolites

    PubMed Central

    Masaki, Yukiko; Shimizu, Yoichi; Yoshioka, Takeshi; Tanaka, Yukari; Nishijima, Ken-ichi; Zhao, Songji; Higashino, Kenichi; Sakamoto, Shingo; Numata, Yoshito; Yamaguchi, Yoshitaka; Tamaki, Nagara; Kuge, Yuji

    2015-01-01

    18F-fluoromisonidazole (FMISO) has been widely used as a hypoxia imaging probe for diagnostic positron emission tomography (PET). FMISO is believed to accumulate in hypoxic cells via covalent binding with macromolecules after reduction of its nitro group. However, its detailed accumulation mechanism remains unknown. Therefore, we investigated the chemical forms of FMISO and their distributions in tumours using imaging mass spectrometry (IMS), which visualises spatial distribution of chemical compositions based on molecular masses in tissue sections. Our radiochemical analysis revealed that most of the radioactivity in tumours existed as low-molecular-weight compounds with unknown chemical formulas, unlike observations made with conventional views, suggesting that the radioactivity distribution primarily reflected that of these unknown substances. The IMS analysis indicated that FMISO and its reductive metabolites were nonspecifically distributed in the tumour in patterns not corresponding to the radioactivity distribution. Our IMS search found an unknown low-molecular-weight metabolite whose distribution pattern corresponded to that of both the radioactivity and the hypoxia marker pimonidazole. This metabolite was identified as the glutathione conjugate of amino-FMISO. We showed that the glutathione conjugate of amino-FMISO is involved in FMISO accumulation in hypoxic tumour tissues, in addition to the conventional mechanism of FMISO covalent binding to macromolecules. PMID:26582591

  2. Optical probe

    DOEpatents

    Hencken, Kenneth; Flower, William L.

    1999-01-01

    A compact optical probe is disclosed particularly useful for analysis of emissions in industrial environments. The instant invention provides a geometry for optically-based measurements that allows all optical components (source, detector, rely optics, etc.) to be located in proximity to one another. The geometry of the probe disclosed herein provides a means for making optical measurements in environments where it is difficult and/or expensive to gain access to the vicinity of a flow stream to be measured. Significantly, the lens geometry of the optical probe allows the analysis location within a flow stream being monitored to be moved while maintaining optical alignment of all components even when the optical probe is focused on a plurality of different analysis points within the flow stream.

  3. Probing the Catalytic Mechanism of S-Ribosylhomocysteinase (LuxS) with Catalytic Intermediates and Substrate Analogues

    SciTech Connect

    Gopishetty, Bhaskar; Zhu, Jinge; Rajan, Rakhi; Sobczak, Adam J.; Wnuk, Stanislaw F.; Bell, Charles E.; Pei, Dehua

    2009-05-12

    S-Ribosylhomocysteinase (LuxS) cleaves the thioether bond in S-ribosylhomocysteine (SRH) to produce homocysteine (Hcys) and 4,5-dihydroxy-2,3-pentanedione (DPD), the precursor of the type II bacterial quorum sensing molecule (AI-2). The catalytic mechanism of LuxS comprises three distinct reaction steps. The first step involves carbonyl migration from the C1 carbon of ribose to C2 and the formation of a 2-ketone intermediate. The second step shifts the C=O group from the C2 to C3 position to produce a 3-ketone intermediate. In the final step, the 3-ketone intermediate undergoes a {beta}-elimination reaction resulting in the cleavage of the thioether bond. In this work, the 3-ketone intermediate was chemically synthesized and shown to be chemically and kinetically competent in the LuxS catalytic pathway. Substrate analogues halogenated at the C3 position of ribose were synthesized and reacted as time-dependent inhibitors of LuxS. The time dependence was caused by enzyme-catalyzed elimination of halide ions. Examination of the kinetics of halide release and decay of the 3-ketone intermediate catalyzed by wild-type and mutant LuxS enzymes revealed that Cys-84 is the general base responsible for proton abstraction in the three reaction steps, whereas Glu-57 likely facilitates substrate binding and proton transfer during catalysis.

  4. Probing Immobilization Mechanism of alpha-chymotrypsin onto Carbon Nanotube in Organic Media by Molecular Dynamics Simulation

    PubMed Central

    Zhang, Liyun; Xiao, Xiuchan; Yuan, Yuan; Guo, Yanzhi; Li, Menglong; Pu, Xuemei

    2015-01-01

    The enzyme immobilization has been adopted to enhance the activity and stability of enzymes in non-aqueous enzymatic catalysis. However, the activation and stabilization mechanism has been poorly understood on experiments. Thus, we used molecular dynamics simulation to study the adsorption of α-chymotrypsin (α-ChT) on carbon nanotube (CNT) in aqueous solution and heptane media. The results indicate that α-ChT has stronger affinity with CNT in aqueous solution than in heptane media, as confirmed by more adsorption atoms, larger contact area and higher binding free energies. Although the immobilization causes significant structure deviations from the crystal one, no significant changes in secondary structure of the enzyme upon adsorption are observed in the two media. Different from aqueous solution, the stabilization effects on some local regions far from the surface of CNT were observed in heptane media, in particular for S1 pocket, which should contribute to the preservation of specificity reported by experiments. Also, CNT displays to some extent stabilization role in retaining the catalytic H-bond network of the active site in heptane media, which should be associated with the enhanced activity of enzymes. The observations from the work can provide valuable information for improving the catalytic properties of enzymes in non-aqueous media. PMID:25787884

  5. Probing biochemical mechanisms of action of muscarinic M3 receptor antagonists with label-free whole cell assays.

    PubMed

    Deng, Huayun; Wang, Chaoming; Su, Ming; Fang, Ye

    2012-10-02

    Binding kinetics of drugs is increasingly recognized to be important for their in vivo efficacy and safety profiles. However, little is known about the effect of drug binding kinetics on receptor signaling in native cells. Here we used label-free whole cell dynamic mass redistribution (DMR) assays under persistent and duration-controlled stimulation conditions to investigate the influence of the binding kinetics of four antagonists on the signaling of endogenous muscarinic M3 receptor in native HT-29 cells. Results showed that DMR assays under different conditions differentiated the biochemical mechanisms of action of distinct M3 antagonists. When co-stimulated with acetylcholine, tiotropium, a relatively slow binding antagonist, was found to selectively block the late signaling of the receptor, suggesting that acetylcholine attains its binding equilibrium faster than tiotropium does, thereby still being able to initiate its rapid response until the antagonist draws up and fully blocks the signaling. Furthermore, DMR assays under microfluidics allowed estimation of the residence times of these antagonists acting at the receptor in native cells, which were found to be the determining factor for the blockage efficiency of M3 receptor signaling under duration-controlled conditions. This study demonstrates that DMR assays can be used to elucidate the functional consequence of kinetics-driven antagonist occupancy in native cells.

  6. Relaxivity-iron calibration in hepatic iron overload: Probing underlying biophysical mechanisms using a Monte Carlo model

    PubMed Central

    Ghugre, Nilesh R.; Wood, John C.

    2010-01-01

    Iron overload is a serious condition for patients with β-thalassemia, transfusion-dependent sickle cell anemia and inherited disorders of iron metabolism. MRI is becoming increasingly important in non-invasive quantification of tissue iron, overcoming the drawbacks of traditional techniques (liver biopsy). R2*(1/T2*) rises linearly with iron while R2(1/T2) has a curvilinear relationship in human liver. Although recent work has demonstrated clinically-valid estimates of human liver iron, the calibration varies with MRI sequence, field strength, iron chelation therapy and organ imaged, forcing recalibration in patients. To understand and correct these limitations, a thorough understanding of the underlying biophysics is of critical importance. Toward this end, a Monte Carlo based approach, using human liver as a ‘model’ tissue system, was employed to determine the contribution of particle size and distribution on MRI signal relaxation. Relaxivities were determined for hepatic iron concentrations (HIC) ranging from 0.5–40 mg iron/ g dry tissue weight. Model predictions captured the linear and curvilinear relationship of R2* and R2 with HIC respectively and were within in vivo confidence bounds; contact or chemical exchange mechanisms were not necessary. A validated and optimized model will aid understanding and quantification of iron-mediated relaxivity in tissues where biopsy is not feasible (heart, spleen). PMID:21337413

  7. Probe Mössbauer spectroscopy of mechanical alloying in binary Cr‐{sup 57}Fe(1 at%) system

    SciTech Connect

    Elsukov, Evgeny P. Kolodkin, Denis A. Ul'yanov, Alexander L. Porsev, Vitaly E.

    2014-10-27

    Solid state reactions during mechanical alloying (MA) in a binary mixture of powdered Cr and {sup 57}Fe in atomic ratio of 99:1 have been studied using {sup 57}Fe Mössbauer spectroscopy, X-ray diffraction and Auger spectrometry. The proposed model of MA includes formation of Cr(Fe){sub x}O{sub y} oxides at the contact places of Cr and Fe particles, formation of nanostructure with simultaneous dissolution of the oxides, penetration of Fe atoms along grain boundaries in close-to-boundary distorted zones of interfaces in a substitutional position, formation of the substitutional solid solution of Fe in Cr in the body of grains. It was shown that the increase in the BCC lattice parameter on increasing the milling time is due to the dissolution of oxides and formation of interstitial solid solution of O in Cr. There were established substantial differences in consumption of BCC Fe in a Mg → Al → Si → Cr sequence due to the major role of chemical interaction of Mg(Al,Si,Cr) with Fe.

  8. Probing kinetic drug binding mechanism in voltage-gated sodium ion channel: open state versus inactive state blockers.

    PubMed

    Pal, Krishnendu; Gangopadhyay, Gautam

    2015-01-01

    The kinetics and nonequilibrium thermodynamics of open state and inactive state drug binding mechanisms have been studied here using different voltage protocols in sodium ion channel. We have found that for constant voltage protocol, open state block is more efficient in blocking ionic current than inactive state block. Kinetic effect comes through peak current for mexiletine as an open state blocker and in the tail part for lidocaine as an inactive state blocker. Although the inactivation of sodium channel is a free energy driven process, however, the two different kinds of drug affect the inactivation process in a different way as seen from thermodynamic analysis. In presence of open state drug block, the process initially for a long time remains entropy driven and then becomes free energy driven. However in presence of inactive state block, the process remains entirely entropy driven until the equilibrium is attained. For oscillating voltage protocol, the inactive state blocking is more efficient in damping the oscillation of ionic current. From the pulse train analysis it is found that inactive state blocking is less effective in restoring normal repolarisation and blocks peak ionic current. Pulse train protocol also shows that all the inactive states behave differently as one inactive state responds instantly to the test pulse in an opposite manner from the other two states.

  9. Probing the Cognitive Mechanism of Mental Representational Change During Chunk Decomposition: A Parametric fMRI Study.

    PubMed

    Tang, Xiaochen; Pang, Jiaoyan; Nie, Qi-Yang; Conci, Markus; Luo, Junlong; Luo, Jing

    2016-07-01

    Chunk decomposition plays an important role in cognitive flexibility in particular with regards to representational change, which is critical for insight problem solving and creative thinking. In this study, we investigated the cognitive mechanism of decomposing Chinese character chunks through a parametric fMRI design. Our results from this parametric manipulation revealed widely distributed activations in frontal, parietal, and occipital cortex and negative activations in parietal and visual areas in response to chunk tightness during decomposition. To mentally manipulate the element of a given old chunk, superior parietal lobe appears to support element restructuring in a goal-directed way, whereas the negatively activated inferior parietal lobe may support preventing irrelevant objects from being attended. Moreover, determining alternative ways of restructuring requires a constellation of frontal areas in the cognitive control network, such as the right lateral prefrontal cortex in inhibiting the predominant chunk representations, the presupplementary motor area in initiating a transition of mental task set, and the inferior frontal junction in establishing task sets. In conclusion, this suggests that chunk decomposition reflects mental transformation of problem representation from an inappropriate state to a new one alongside with an evaluation of novel and insightful solutions by the caudate in the dorsal striatum. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  10. Molecular mechanism of agonism and inverse agonism in the melanocortin receptors: Zn(2+) as a structural and functional probe.

    PubMed

    Holst, Birgitte; Schwartz, Thue W

    2003-06-01

    Among the rhodopsin-like 7TM receptors, the MC receptors are functionally unique because their high constitutive signaling activity is regulated not only by endogenous peptide agonists-MSH peptides-but also by endogenous inverse agonists, namely, the proteins agouti and AGRP. Moreover, the metal-ion Zn(2+) increases the signaling activity of at least the MC1 and MC4 receptors in three distinct ways: (1). by directly functioning as an agonist; (2). by potentiating the action of the endogenous agonist; and (3). by inhibiting the binding of the endogenous inverse agonist. Structurally the MC receptors are part of a small subset of 7TM receptors in which the main ligand-binding crevice, and especially extracellular loops 2 and 3, appear to be specially designed for easy ligand access and bias towards an active state of the receptor-i.e., constitutive activity. Thus, in the MC receptors extracellular loop 2 is ultrashort because TM-IV basically connects directly into TM-V, whereas extracellular loop 3 appears to be held in a particular, constrained conformation by a putative, internal disulfide bridge. The interaction mode for the small and well-defined zinc-ion between a third, free Cys residue in extracellular loop 3 and conceivably an Asp residue located at the inner face of TM-III gives important information concerning the activation mechanism for the MC receptors.

  11. Probing immobilization mechanism of alpha-chymotrypsin onto carbon nanotube in organic media by molecular dynamics simulation.

    PubMed

    Zhang, Liyun; Xiao, Xiuchan; Yuan, Yuan; Guo, Yanzhi; Li, Menglong; Pu, Xuemei

    2015-03-19

    The enzyme immobilization has been adopted to enhance the activity and stability of enzymes in non-aqueous enzymatic catalysis. However, the activation and stabilization mechanism has been poorly understood on experiments. Thus, we used molecular dynamics simulation to study the adsorption of α-chymotrypsin (α-ChT) on carbon nanotube (CNT) in aqueous solution and heptane media. The results indicate that α-ChT has stronger affinity with CNT in aqueous solution than in heptane media, as confirmed by more adsorption atoms, larger contact area and higher binding free energies. Although the immobilization causes significant structure deviations from the crystal one, no significant changes in secondary structure of the enzyme upon adsorption are observed in the two media. Different from aqueous solution, the stabilization effects on some local regions far from the surface of CNT were observed in heptane media, in particular for S1 pocket, which should contribute to the preservation of specificity reported by experiments. Also, CNT displays to some extent stabilization role in retaining the catalytic H-bond network of the active site in heptane media, which should be associated with the enhanced activity of enzymes. The observations from the work can provide valuable information for improving the catalytic properties of enzymes in non-aqueous media.

  12. Probing the interaction mechanism of small molecule inhibitors with matriptase based on molecular dynamics simulation and free energy calculations.

    PubMed

    Sun, Dong-Ru; Zheng, Qing-Chuan; Zhang, Hong-Xing

    2017-03-01

    Matriptase is a serine protease associated with a wide variety of human tumors and carcinoma progression. Up to now, many promising anti-cancer drugs have been developed. However, the detailed structure-function relationship between inhibitors and matriptase remains elusive. In this work, molecular dynamics simulation and binding free energy studies were performed to investigate the biochemistry behaviors of two class inhibitors binding to matriptase. The binding free energies predicted by MM/GBSA methods are in good agreement with the experimental bioactivities, and the analysis of the individual energy terms suggests that the van der Waals interaction is the major driving force for ligand binding. The key residues responsible for achieving strong binding have been identified by the MM/GBSA free energy decomposition analysis. Especially, Trp215 and Phe99 had an important impact on active site architecture and ligand binding. The results clearly identify the two class inhibitors exist different binding modes. Through summarizing the two different modes, we have mastered some important and favorable interaction patterns between matriptase and inhibitors. Our findings would be helpful for understanding the interaction mechanism between the inhibitor and matriptase and afford important guidance for the rational design of potent matriptase inhibitors.

  13. Eddy current modeling by finite element method for evaluation of mechanical properties of the structure cracked in absolute probe

    NASA Astrophysics Data System (ADS)

    Harzallah, Salaheddine; Chabaat, Mohamed; Belgacem, Fethi Bin Muhammad

    2014-12-01

    In this paper, a nondestructive evaluation by sensor Eddy current is used as a tool to control cracks and micro-cracks in materials. A simulation by a numerical approach based on the finite element method is employed to detect cracks in materials and eventually to study their propagation using a crucial parameter such as a Stress Intensity Factor (SIF). This method has emerged as one of the most efficient techniques for prospecting cracks in materials, evaluating SIFs and analyzing crack's growth in the context of linear elastic fracture mechanics (LEFM). This technique uses extrapolation of displacements from results compared with those obtained by the integral interaction. On the other hand, crack's growth is analyzed as a model by combining the maximum circumferential stress criteria with the critical plane for predicting the direction of crack growth. Moreover, a constant crack growth increment is determined using the modified Paris's model. Furthermore, stress intensity factors needed for these models are calculated using the domain form of the J-integral interactions.

  14. Nitrogenases from Klebsiella pneumoniae and Clostridium pasteurianum. Kinetic investigations of cross-reactions as a probe of the enzyme mechanism.

    PubMed Central

    Smith, B E; Thorneley, R N; Eady, R R; Mortenson, L E

    1976-01-01

    In combination with the Mo-Fe protein of nitrogenase from Klebsiella pneumoniae, the Fe protein of nitrogenase from Clostridium pasteurianum forms an active enzyme with novel properties different from those of either of the homologous nitrogenases. The steady-state rates of reduction of acetylene and H+ are 12% of those of the homologous system from C.pasteurianim. Acetylene reductase activity exhibited an approx. 10min lag at 30 degrees C before the rate of reduction became linear, consistent with a once-only activation step being necessary for acetylene reduction to occur. No such lag was observed for H2 evolution. The activity with N2 as a reducible substrate was very low, implying that acetylene reductase activity is not necessarily an accurate indication of nitrogen-fixing ability. This is of particular relevance to studies on mutant and agronomically important organisms. Stopped-flow spectrophotometric studies showed unimolecular electron transfer from the Fe protein to the Mo-Fe protein to occur at the same rate (k2 = 2.5 X 10(2)s-1) and with the same dependence on ATP concentration (apparent KD = 400 muM) as with the homologous Klebsiella nitrogenase. However, an ATP/2e ratio of 50 was obtained for H2 evolution, indicating that ATP hydrolysis had been uncoupled from electron transfer to substrate. These data indicate that ATP has at least two roles in the mechanism of nitrogenase action. The combination of the Mo-Fe protein of nitrogenase of C.pasteurianim and the Fe protein of K.pneumoniae were inactive in all the above reactions, except for a weak adenosine triphosphatase activity, 0.5% of that of the homologous K.pneumoniae system. Images Fig. 3. PMID:134700

  15. Burst-firing patterns in the prefrontal cortex underlying the neuronal mechanisms of depression probed by antidepressants.

    PubMed

    Guo, Fei; Zhang, Qi; Zhang, Bing; Fu, Zhiwen; Wu, Bin; Huang, Chenggang; Li, Yang

    2014-11-01

    Major depressive disorder (MDD) is one of the leading causes of morbidity worldwide. Several antidepressants have been widely prescribed to treat patients with MDD. However, neuronal changes in brain function remain poorly understood. Based on the standard chronic mild stress (CMS) model of depression in mice, we investigated the neuronal mechanisms of the classic antidepressant, fluoxetine, and a new compound (termed YY-23 in this study) derived from furostanol saponin. The results showed that both fluoxetine and YY-23 normalized CMS-induced depressive-like behaviors. YY-23 caused antidepressant-like behaviors with a faster action than fluoxetine. In terms of in vivo neuronal activities, a CMS-induced decrease in spontaneous firing in burst of medial prefrontal cortex pyramidal neurons rather than ventral tegmental area (VTA) was reversed by the chronic administration of fluoxetine and YY-23. We also found that CMS-induced deficits in the expression of prefrontal brain-derived neurotrophic factor (BDNF) were also restored by chronically administering YY-23 and fluoxetine. In addition, chronic administration of fluoxetine rather than YY-23 resulted in an improvement of antidepressive-like behavior and a change of burst firing of VTA in control-housed animals, indicating that the pharmacological effects of YY-23 were specific to CMS-treated animals. Together, these data suggest that the burst-firing patterns of pyramidal cells may be a neural biomarker of depressive-like mice and antidepressant action. Furthermore, synaptic transmission and BDNF may contribute to the rapid antidepressant-like effects on depression. © 2014 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

  16. (S)-Styryl-α-alanine used to probe the intermolecular mechanism of an intramolecular MIO-aminomutase.

    PubMed

    Wanninayake, Udayanga; Deporre, Yvonne; Ondari, Mark; Walker, Kevin D

    2011-11-22

    A Taxus canadensis phenylalanine aminomutase (TcPAM) catalyzes the isomerization of (S)-α- to (R)-β-phenylalanine, making (E)-cinnamate (~10%) as a byproduct at steady state. A currently accepted mechanism for TcPAM suggests that the amino group is transferred from the substrate to a prosthetic group comprised of an amino acid triad in the active site and then principally rebinds to the carbon skeleton of the cinnamate intermediate to complete the α-β isomerization. In contrast, when (S)-styryl-α-alanine is used as a substrate, TcPAM produces (2E,4E)-styrylacrylate as the major product (>99%) and (R)-styryl-β-alanine (<1%). Comparison of the rates of conversion of the natural substrate (S)-α-phenylalanine and (S)-styryl-α-alanine to their corresponding products (k(cat) values of 0.053 ± 0.001 and 0.082 ± 0.002 s(-1), respectively) catalyzed by TcPAM suggests that the amino group resides in the active site longer than styrylacrylate. To demonstrate this principle, inhibition constants (K(I)) for selected acrylates ranging from 0.6 to 106 μM were obtained, and each had a lower K(I) compared to that of (2E,4E)-styrylacrylate (337 ± 12 μM). Evaluation of the inhibition constants and the rates at which both the α/β-amino acids (between 7 and 80% yield) and styrylacrylate were made from a corresponding arylacrylate and styryl-α-alanine, respectively, by TcPAM catalysis revealed that the reaction progress was largely dependent on the K(I) of the acrylate. Bicyclic amino donor substrates also transferred their amino groups to an arylacrylate, demonstrating for the first time that ring-fused amino acids are productive substrates in the TcPAM-catalyzed reaction. © 2011 American Chemical Society

  17. Probing the mechanisms underlying modulation of quinidine sensitivity to cardiac IKs block by protein kinase A-mediated IKs phosphorylation

    PubMed Central

    Yang, Tao; Kanki, Hideaki; Zhang, Wei; Roden, Dan M

    2009-01-01

    Background and purpose: Cardiac IKs is enhanced by protein kinase A (PKA) stimulation. And PKA-stimulated IKs is about threefold less sensitive to quinidine block than basal current. In this study, we further tested two competing hypotheses: IKs phosphorylation either (i) modulates access of blocking drugs to a binding site; or (ii) destabilizes the drug–channel interaction. Experimental approach: To distinguish between these hypotheses, we studied quinidine block of IKs channels in which three PKA site residues of the α-subunit KCNQ1 were mutated with a bulky negative charged aspartic acid (D). To study alleviation of IKs block by quinidine, we compared activating current at +60 mV, either with or without 5 s hyperpolarizing prepulses to −120 mV. Key results: Without PKA stimulation, quinidine (100 µM) blocked wild-type current to a similar extent with and without the prepulse (93 ± 2% of pre-drug current at +60 mV vs. 95 ± 1%). With PKA-stimulated wild-type channels, however, there was less block with the hyperpolarization to −120 mV: at +60 mV, block was 71 ± 2% (−prepulse) versus 58 ± 3% (+prepulse). Individual D-mutations and the triple-D mutant were resistant to quinidine block similar to that seen with PKA-stimulated wild-type IKs. Conclusions and implications: We conclude that phosphorylation-induced insertion of bulky negative charges alleviates quinidine block and that PKA-induced stimulation, by conferring negative charges to the channels, blunts IKs block as the interaction between the channels and blockers becomes destabilized. These effects would be of clinical significance in providing protective mechanisms against pro-arrhythmias caused by drug-induced inhibition of IKs and IKr. PMID:19522859

  18. Probing the Molecular Mechanism of Human Soluble Guanylate Cyclase Activation by NO in vitro and in vivo

    PubMed Central

    Pan, Jie; Yuan, Hong; Zhang, Xiaoxue; Zhang, Huijuan; Xu, Qiming; Zhou, Yajun; Tan, Li; Nagawa, Shingo; Huang, Zhong-Xian; Tan, Xiangshi

    2017-01-01

    Soluble guanylate cyclase (sGC) is a heme-containing metalloprotein in NO-sGC-cGMP signaling. NO binds to the heme of sGC to catalyze the synthesis of the second messenger cGMP, which plays a critical role in several physiological processes. However, the molecular mechanism for sGC to mediate the NO signaling remains unclear. Here fluorophore FlAsH-EDT2 and fluorescent proteins were employed to study the NO-induced sGC activation. FlAsH-EDT2 labeling study revealed that NO binding to the H-NOX domain of sGC increased the distance between H-NOX and PAS domain and the separation between H-NOX and coiled-coil domain. The heme pocket conformation changed from “closed” to “open” upon NO binding. In addition, the NO-induced conformational change of sGC was firstly investigated in vivo through fluorescence lifetime imaging microscopy. The results both in vitro and in vivo indicated the conformational change of the catalytic domain of sGC from “open” to “closed” upon NO binding. NO binding to the heme of H-NOX domain caused breaking of Fe-N coordination bond, initiated the domain moving and conformational change, induced the allosteric effect of sGC to trigger the NO-signaling from H-NOX via PAS & coiled-coil to the catalytic domain, and ultimately stimulates the cyclase activity of sGC. PMID:28230071

  19. Probing the Molecular Mechanisms Governing the Oncolytic Activity of Paeonia suffruticosa on Triple-negative Breast Cancer Cells In Vitro.

    PubMed

    Kim, Dongyeon; Radin, Daniel; Leonardi, Donna

    2017-09-01

    Extracts of Paeonia suffruticosa are traditionally used in Chinese medicine to increase blood flow. Recently, this extract has been shown to possess anti-tumor and anti-inflammatory properties, though this mechanism remains unknown. In the current work, we prepared extracts of P. suffruticosa and analyzed their effects on MDA-MB-231 triple-negative breast cancer cells. Varying concentrations of an aqueous extract of P. suffruticosa was administered to MDA-MB-231. An MTS assay was used to determine the cell viability. Cytokine production was investigated through enzyme-linked immunosorbent assay (ELISA). Caspase-Glo assays were performed to measure caspase 3/7, 8 and 9 to analyze anti-apoptotic effects. MTS assay for cell viability revealed that the extract increased viability at low concentrations (0.6 mg/ml) and decreased viability observed at concentrations ≥2.5 mg/ml (p<0.01). ELISA for IL-6, IL-2, and TNF-alpha revealed a biphasic dose-response inversely related to viability (p<0.05). IL-24 expression also increased at 2.5 mg/ml and 4.0 mg/ml (p<0.05). Bax levels remained relatively constant while Bcl-2 decreased significantly in all concentrations (p<0.01). Small decreases in Fas ligand levels was observed in parallel with a lack of increase in caspase-8 activity. Most notable was that while 4mg/ml of P. suffruticosa extract reduced MDA-MB-231 viability by >60% (p<0.01), the same concentration reduced the viability of non-transformed HaCat cells by ~8% (p>0.05), suggesting a selective oncolytic effect. P. suffruticosa extract has the ability to modulate the production of several tumor suppressive cytokines, induce intrinsic apoptosis and has the capability of reducing cancer burden while sparing healthy tissue. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  20. On the mechanism of triclinic distortion in Chevrel Phase as probed by in-situ neutron diffraction.

    PubMed

    Levi, E; Mitelman, A; Aurbach, D; Isnard, O

    2007-09-03

    This work presents, for the first time, a general mechanism of a rhombohedral (R)-triclinic (T) phase transition in Chevrel Phases (CPs) with small cations (radius<1 A), which was unclear in spite of intensive studies of these important materials in the past. In contrast to previous interpretation of the R<-->T transition in some CPs as cation ordering, T-distortion is regarded here as a particular case of general adaptation of the framework to cation insertion, which includes the deformations of the coordination polyhedra and their tilting. The research is based on a combination of experimental studies (in-situ neutron diffraction at different temperatures) for one model compound, MgMo6Se8, and structural analysis for a variety of known CPs. This analysis shows that the structure flexibility is fundamentally different for the R and T forms. As a result of the lower flexibility, in the R form, a strict correlation exists between the compression of the framework along the -3 symmetry axis and the cation position in the structure (the so-called 'delocalization'). The decreasing delocalization in the R-CPs, which occurs on cooling, leads to excessive repulsion within the cations pairs (R-Cu1.8Mo6S8 case) or undesirable asymmetry in the cation polyhedra (R-MgMo6Se8 case). The higher flexibility of the T framework allows for relaxation of these structural strains by increasing the cation-cation distances and forming a more symmetric cation environment, sometimes with higher coordination number (CN), like CN=5 in the T-Fe2Mo6S8 type. Thus, this work also proposes possible driving forces for T-distortion in CPs.

  1. Nanofabrication using near-field optical probes

    PubMed Central

    McLeod, Euan; Ozcan, Aydogan

    2012-01-01

    Nanofabrication using near-field optical probes is an established technique for rapid prototyping and automated maskless fabrication of nanostructured devices. In this review, we present the primary types of near-field probes and their physical processing mechanisms. Highlights of recent developments include improved resolution by optimizing the probe shape, incorporation of surface plasmonics in probe design, broader use in biological and magnetic storage applications, and increased throughput using probe arrays as well as high speed writing and patterning. PMID:22713756

  2. How quantum mechanics probes superspace

    NASA Astrophysics Data System (ADS)

    Nicolis, Stam

    2017-03-01

    We study the relation between the partition function of a non-relativistic particle, that describes the equilibrium fluctuations implicitly, and the partition function of the same system, deduced from the Langevin equation, that describes the fluctuations explicitly, of a bath with additive white-noise properties. We show that both can be related to the partition function of an N = 1 supersymmetric theory with one-dimensional bosonic worldvolume and that they can all describe the same physics, since the correlation functions of the observables satisfy the same identities for all systems.The supersymmetric theory provides the consistent closure for describing the fluctuations, even though supersymmetry may be broken, when their backreaction is taken into account. The trajectory of the classical particle becomes a component of a superfield, when fluctuations are taken into account. These statements can be tested by the identities the correlation functions satisfy, by using a lattice regularization of an action that describes commuting fields only.

  3. Pollution Probe.

    ERIC Educational Resources Information Center

    Chant, Donald A.

    This book is written as a statement of concern about pollution by members of Pollution Probe, a citizens' anti-pollution group in Canada. Its purpose is to create public awareness and pressure for the eventual solution to pollution problems. The need for effective government policies to control the population explosion, conserve natural resources,…

  4. Pollution Probe.

    ERIC Educational Resources Information Center

    Chant, Donald A.

    This book is written as a statement of concern about pollution by members of Pollution Probe, a citizens' anti-pollution group in Canada. Its purpose is to create public awareness and pressure for the eventual solution to pollution problems. The need for effective government policies to control the population explosion, conserve natural resources,…

  5. Mechanism of Interaction between the General Anesthetic Halothane and a Model Ion Channel Protein, III: Molecular Dynamics Simulation Incorporating a Cyanophenylalanine Spectroscopic Probe

    PubMed Central

    Zou, Hongling; Liu, Jing; Blasie, J. Kent

    2009-01-01

    A nitrile-derived amino acid, PheCN, has been used as an internal spectroscopic probe to study the binding of an inhalational anesthetic to a model membrane protein. The infrared spectra from experiment showed a blue-shift of the nitrile vibrational frequency in the presence of the anesthetic halothane. To interpret the infrared results and explore the nature of the interaction between halothane and the model protein, all-atom molecular dynamics (MD) simulations have been used to probe the structural and dynamic properties of the protein in the presence and absence of one halothane molecule. The frequency shift analyzed from MD simulations agrees well with the experimental infrared results. Decomposition of the forces acting on the nitrile probes demonstrates an indirect impact on the probes from halothane, namely a change of the protein's electrostatic local environment around the probes induced by halothane. Although the halothane remains localized within the designed hydrophobic binding cavity, it undergoes a significant amount of translational and rotational motion, modulated by the interaction of the trifluorine end of halothane with backbone hydrogens of the residues forming the cavity. This dominant interaction between halothane and backbone hydrogens outweighs the direct interaction between halothane and the nitrile groups, making it a good “spectator” probe of the halothane-protein interaction. These MD simulations provide insight into action of anesthetic molecules on the model membrane protein, and also support the further development of nitrile-labeled amino acids as spectroscopic probes within the designed binding cavity. PMID:19450489

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

    SciTech Connect

    Gracias, David Hugo

    1999-05-01

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

  7. Surgical force detection probe

    NASA Technical Reports Server (NTRS)

    Tcheng, Ping; Roberts, Paul; Scott, Charles; Prass, Richard

    1991-01-01

    The development progress of a precision electro-mechanical instrument which allows the detection and documentation of the forces and moment applied to human tissue during surgery (under actual operation room conditions), is reported. The pen-shaped prototype probe which measures 1/2 inch in diameter and 7 inches in length was fabricated using an aerodynamic balance. The aerodynamic balance, a standard wind tunnel force and moment sensing transducer, measures the forces and the moments transmitted through the surgeon's hand to the human tissue during surgery. The prototype probe which was fabricated as a development tool was tested successfully. The final version of the surgical force detection probe will be designed based on additional laboratory tests in order to establish the full scale loads. It is expected that the final product will require a simplified aerodynamic balance with two or three force components and one moment component with lighter full scale loads. A signal conditioner was fabricated to process and display the outputs from the prototype probe. This unit will be interfaced with a PC-based data system to provide automatic data acquisition, data processing, and graphics display. The expected overall accuracy of the probe is better than one percent full scale.

  8. Convective heat flow probe

    DOEpatents

    Dunn, James C.; Hardee, Harry C.; Striker, Richard P.

    1985-01-01

    A convective heat flow probe device is provided which measures heat flow and fluid flow magnitude in the formation surrounding a borehole. The probe comprises an elongate housing adapted to be lowered down into the borehole; a plurality of heaters extending along the probe for heating the formation surrounding the borehole; a plurality of temperature sensors arranged around the periphery of the probe for measuring the temperature of the surrounding formation after heating thereof by the heater elements. The temperature sensors and heater elements are mounted in a plurality of separate heater pads which are supported by the housing and which are adapted to be radially expanded into firm engagement with the walls of the borehole. The heat supplied by the heater elements and the temperatures measured by the temperature sensors are monitored and used in providing the desired measurements. The outer peripheral surfaces of the heater pads are configured as segments of a cylinder and form a full cylinder when taken together. A plurality of temperature sensors are located on each pad so as to extend along the length and across the width thereof, with a heating element being located in each pad beneath the temperature sensors. An expansion mechanism driven by a clamping motor provides expansion and retraction of the heater pads and expandable packer-type seals are provided along the probe above and below the heater pads.

  9. Convective heat flow probe

    DOEpatents

    Dunn, J.C.; Hardee, H.C.; Striker, R.P.

    1984-01-09

    A convective heat flow probe device is provided which measures heat flow and fluid flow magnitude in the formation surrounding a borehole. The probe comprises an elongate housing adapted to be lowered down into the borehole; a plurality of heaters extending along the probe for heating the formation surrounding the borehole; a plurality of temperature sensors arranged around the periphery of the probe for measuring the temperature of the surrounding formation after heating thereof by the heater elements. The temperature sensors and heater elements are mounted in a plurality of separate heater pads which are supported by the housing and which are adapted to be radially expanded into firm engagement with the walls of the borehole. The heat supplied by the heater elements and the temperatures measured by the temperature sensors are monitored and used in providing the desired measurements. The outer peripheral surfaces of the heater pads are configured as segments of a cylinder and form a full cylinder when taken together. A plurality of temperature sensors are located on each pad so as to extend along the length and across the width thereof, with a heating element being located in each pad beneath the temperature sensors. An expansion mechanism driven by a clamping motor provides expansion and retraction of the heater pads and expandable packet-type seals are provided along the probe above and below the heater pads.

  10. Quantum-mechanical parameters for the risk assessment of multi-walled carbon-nanotubes: A study using adsorption of probe compounds and its application to biomolecules.

    PubMed

    Chayawan; Vikas

    2016-11-01

    This work forwards new insights into the risk-assessment of multi-walled carbon-nanotubes (MWCNTs) while analysing the role of quantum-mechanical interactions between the electrons in the adsorption of probe compounds and biomolecules by MWCNTs. For this, the quantitative models are developed using quantum-chemical descriptors and their electron-correlation contribution. The major quantum-chemical factors contributing to the adsorption are found to be mean polarizability, electron-correlation energy, and electron-correlation contribution to the absolute electronegativity and LUMO energy. The proposed models, based on only three quantum-chemical factors, are found to be even more robust and predictive than the previously known five or four factors based linear free-energy and solvation-energy relationships. The proposed models are employed to predict the adsorption of biomolecules including steroid hormones and DNA bases. The steroid hormones are predicted to be strongly adsorbed by the MWCNTs, with the order: hydrocortisone > aldosterone > progesterone > ethinyl-oestradiol > testosterone > oestradiol, whereas the DNA bases are found to be relatively less adsorbed but follow the order as: guanine > adenine > thymine > cytosine > uracil. Besides these, the developed electron-correlation based models predict several insecticides, pesticides, herbicides, fungicides, plasticizers and antimicrobial agents in cosmetics, to be strongly adsorbed by the carbon-nanotubes. The present study proposes that the instantaneous inter-electronic interactions may be quite significant in various physico-chemical processes involving MWCNTs, and can be used as a reliable predictor for their risk assessment. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Ultrastrong Carbon Thin Films from Diamond to Graphene under Extreme Conditions: Probing Atomic Scale Interfacial Mechanisms to Achieve Ultralow Friction and Wear

    DTIC Science & Technology

    2016-12-08

    AFRL-AFOSR-JP-TR-2016-0101 Ultrastrong Carbon Thin Films from Diamond to Graphene under Extreme Conditions: Probing Atomic -Scale Interfacial...to 21 Sep 2016 4. TITLE AND SUBTITLE Ultrastrong Carbon Thin Films from Diamond to Graphene under Extreme Conditions: Probing Atomic -Scale...nanotribometry that enables nanoscale visualization and quantification of atomic -level processes of sliding contacts inside the transmission electron

  12. Mechanism of the reaction, CH4+O(1D2)→CH3+OH, studied by ultrafast and state-resolved photolysis/probe spectroscopy of the CH4ṡO3 van der Waals complex

    NASA Astrophysics Data System (ADS)

    Miller, C. Cameron; van Zee, Roger D.; Stephenson, John C.

    2001-01-01

    The mechanism of the reaction CH4+O(1D2)→CH3+OH was investigated by ultrafast, time-resolved and state-resolved experiments. In the ultrafast experiments, short ultraviolet pulses photolyzed ozone in the CH4ṡO3 van der Waals complex to produce O(1D2). The ensuing reaction with CH4 was monitored by measuring the appearance rate of OH(v=0,1;J,Ω,Λ) by laser-induced fluorescence, through the OH A←X transition, using short probe pulses. These spectrally broad pulses, centered between 307 and 316 nm, probe many different OH rovibrational states simultaneously. At each probe wavelength, both a fast and a slow rise time were evident in the fluorescence signal, and the ratio of the fast-to-slow signal varied with probe wavelength. The distribution of OH(v,J,Ω,Λ) states, Pobs(v,J,Ω,Λ), was determined by laser-induced fluorescence using a high-resolution, tunable dye laser. The Pobs(v,J,Ω,Λ) data and the time-resolved data were analyzed under the assumption that different formation times represent different reaction mechanisms and that each mechanism produces a characteristic rovibrational distribution. The state-resolved and the time-resolved data can be fit independently using a two-mechanism model: Pobs(v,J,Ω,Λ) can be decomposed into two components, and the appearance of OH can be fit by two exponential rise times. However, these independent analyses are not mutually consistent. The time-resolved and state-resolved data can be consistently fit using a three-mechanism model. The OH appearance signals, at all probe wavelengths, were fit with times τfast≈0.2 ps, τinter≈0.5 ps and τslow≈5.4 ps. The slowest of these three is the rate for dissociation of a vibrationally excited methanol intermediate (CH3OH*) predicted by statistical theory after complete intramolecular energy redistribution following insertion of O(1D2) into CH4. The Pobs(v,J,Ω,Λ) was decomposed into three components, each with a linear surprisal, under the assumption that the

  13. Water cooled static pressure probe

    NASA Technical Reports Server (NTRS)

    Lagen, Nicholas T. (Inventor); Eves, John W. (Inventor); Reece, Garland D. (Inventor); Geissinger, Steve L. (Inventor)

    1991-01-01

    An improved static pressure probe containing a water cooling mechanism is disclosed. This probe has a hollow interior containing a central coolant tube and multiple individual pressure measurement tubes connected to holes placed on the exterior. Coolant from the central tube symmetrically immerses the interior of the probe, allowing it to sustain high temperature (in the region of 2500 F) supersonic jet flow indefinitely, while still recording accurate pressure data. The coolant exits the probe body by way of a reservoir attached to the aft of the probe. The pressure measurement tubes are joined to a single, larger manifold in the reservoir. This manifold is attached to a pressure transducer that records the average static pressure.

  14. A study of the properties of beryllium doped silicon with particular emphasis on diffusion mechanisms: Profiles of depth dependent conductivity as determined by electrical surface probes

    NASA Technical Reports Server (NTRS)

    Franks, R. K.; Robertson, J. B.

    1972-01-01

    Very large diffusion coefficients were encountered and required the determination of impurity profiles for samples approximately 1 cm thick. Since conductivity values are readily converted into concentrations of electrically active impurities, the major problem became that of accurately determining the conductivity profiles of beryllium diffused silicon samples. Four-point probe measurements on samples having depth conductivities are interpreted in terms of conductivity profiles, based on an exact solution of the problem of exponentially depth dependent conductivity. Applications include surface conductivity determination where the form of the conductivity profile is known, and conductivity profile determination from probe measurements taken as the sample surface is progressively lapped away. The application is limited to samples having conductivity monotonically decreasing with depth from the probed surface.

  15. Contribution of atom-probe tomography to a better understanding of glass alteration mechanisms: Application to a nuclear glass specimen altered 25 years in a granitic environment

    SciTech Connect

    Gin, Stephane; Ryan, Joseph V.; Schreiber, Daniel K.; Neeway, James J.; Cabie, M.

    2013-04-08

    Here, we report and discuss results of atom probe tomography (APT) and energy-filtered transmission electron microscopy (EFTEM) applied to a borosilicate glass sample of nuclear interest altered for nearly 26 years at 90°C in a confined granitic medium in order to better understand the rate-limiting mechanisms under conditions representative of a deep geological repository for vitrified radioactive waste. The APT technique allows the 3D reconstruction of the elemental distribution at the reactive interphase with sub-nanometer precision. Profiles of the B distribution at pristine glass/hydrated glass interface obtained by different techniques are compared to show the challenge of accurate measurements of diffusion profiles at this buried interface on the nanometer length scale. Our results show that 1) Alkali from the glass and hydrogen from the solution exhibit anti-correlated 15 ± 3 nm wide gradients located between the pristine glass and the hydrated glass layer, 2) boron exhibits an unexpectedly sharp profile located just at the outside of the alkali/H interdiffusion layer; this sharp profile is more consistent with a dissolution front than a diffusion-controlled release of boron. The resulting apparent diffusion coefficients derived from the Li and H profiles are DLi = 1.5 × 10-22 m2.s-1 and DH = 6.8 × 10-23 m2.s-1. These values are around two orders of magnitude lower than those observed at the very beginning of the alteration process, which suggests that interdiffusion is slowed at high reaction progress by local conditions that could be related to the porous structure of the interphase. As a result, the accessibility of water to the pristine glass could be the rate-limiting step in these conditions. More generally, these findings strongly support the importance of interdiffusion coupled with hydrolysis reactions of the silicate network on the long-term dissolution

  16. Contribution of atom-probe tomography to a better understanding of glass alteration mechanisms: Application to a nuclear glass specimen altered 25 years in a granitic environment

    DOE PAGES

    Gin, Stephane; Ryan, Joseph V.; Schreiber, Daniel K.; ...

    2013-04-08

    Here, we report and discuss results of atom probe tomography (APT) and energy-filtered transmission electron microscopy (EFTEM) applied to a borosilicate glass sample of nuclear interest altered for nearly 26 years at 90°C in a confined granitic medium in order to better understand the rate-limiting mechanisms under conditions representative of a deep geological repository for vitrified radioactive waste. The APT technique allows the 3D reconstruction of the elemental distribution at the reactive interphase with sub-nanometer precision. Profiles of the B distribution at pristine glass/hydrated glass interface obtained by different techniques are compared to show the challenge of accurate measurements ofmore » diffusion profiles at this buried interface on the nanometer length scale. Our results show that 1) Alkali from the glass and hydrogen from the solution exhibit anti-correlated 15 ± 3 nm wide gradients located between the pristine glass and the hydrated glass layer, 2) boron exhibits an unexpectedly sharp profile located just at the outside of the alkali/H interdiffusion layer; this sharp profile is more consistent with a dissolution front than a diffusion-controlled release of boron. The resulting apparent diffusion coefficients derived from the Li and H profiles are DLi = 1.5 × 10-22 m2.s-1 and DH = 6.8 × 10-23 m2.s-1. These values are around two orders of magnitude lower than those observed at the very beginning of the alteration process, which suggests that interdiffusion is slowed at high reaction progress by local conditions that could be related to the porous structure of the interphase. As a result, the accessibility of water to the pristine glass could be the rate-limiting step in these conditions. More generally, these findings strongly support the importance of interdiffusion coupled with hydrolysis reactions of the silicate network on the long-term dissolution rate, contrary to what has been suggested by recent interfacial dissolution

  17. Multiple-measurement beam probe

    SciTech Connect

    Gilpatrick, J.D.; Grant, D.L.

    1986-01-01

    Particle accelerators are becoming smaller and are producing more intense beams; therefore, it is critical that beam-diagnostic instrumentation provide accelerator operators and automated control systems with a complete set of beam information. Traditionally, these beam data were collected and processed using limited-bandwidth interceptive techniques. For the new-generation accelerators, we are developing a multiple-measurement microstrip probe to obtain broadband beam data from inside a drift tube without perturbing the beam. The cylindrical probe's dimensions are 6-cm OD by 1.0 m long, and the probe is mounted inside a drift tube. The probe (and its associated electronics) monitors bunched-beam current, energy, and transverse position by sensing the beam's electromagnetic fields through the annular opening in the drift tube. The electrical impedance is tightly controlled through the full length of the probe and transmission lines to maintain beam-induced signal fidelity. The probe's small, cylindrical structure is matched to beam-bunch characteristics at specific beamline locations so that signal-to-noise ratios are optimized. Surrounding the probe, a mechanical structure attaches to the drift-tube interior and the quadrupole magnets; thus, the entire assembly's mechanical and electrical centers can be aligned and calibrated with respect to the rest of the linac.

  18. The navigation of space probes

    NASA Technical Reports Server (NTRS)

    Fliegel, H. F.; Ohandley, D. A.; Zielenbach, J. W.

    1974-01-01

    A new navigational method combining electronic measurement procedures and celestial mechanics makes it possible to conduct a space probe very close to a desired point in the neighborhood of a remote planet. Approaches for the determination of the position of the space probe in space are discussed, giving attention to the effects of errors in the employed data. The application of the navigational methods in a number of space missions is also considered.

  19. Overview of Probe-based Storage Technologies

    NASA Astrophysics Data System (ADS)

    Wang, Lei; Yang, Ci Hui; Wen, Jing; Gong, Si Di; Peng, Yuan Xiu

    2016-07-01

    The current world is in the age of big data where the total amount of global digital data is growing up at an incredible rate. This indeed necessitates a drastic enhancement on the capacity of conventional data storage devices that are, however, suffering from their respective physical drawbacks. Under this circumstance, it is essential to aggressively explore and develop alternative promising mass storage devices, leading to the presence of probe-based storage devices. In this paper, the physical principles and the current status of several different probe storage devices, including thermo-mechanical probe memory, magnetic probe memory, ferroelectric probe memory, and phase-change probe memory, are reviewed in details, as well as their respective merits and weakness. This paper provides an overview of the emerging probe memories potentially for next generation storage device so as to motivate the exploration of more innovative technologies to push forward the development of the probe storage devices.

  20. Overview of Probe-based Storage Technologies.

    PubMed

    Wang, Lei; Yang, Ci Hui; Wen, Jing; Gong, Si Di; Peng, Yuan Xiu

    2016-12-01

    The current world is in the age of big data where the total amount of global digital data is growing up at an incredible rate. This indeed necessitates a drastic enhancement on the capacity of conventional data storage devices that are, however, suffering from their respective physical drawbacks. Under this circumstance, it is essential to aggressively explore and develop alternative promising mass storage devices, leading to the presence of probe-based storage devices. In this paper, the physical principles and the current status of several different probe storage devices, including thermo-mechanical probe memory, magnetic probe memory, ferroelectric probe memory, and phase-change probe memory, are reviewed in details, as well as their respective merits and weakness. This paper provides an overview of the emerging probe memories potentially for next generation storage device so as to motivate the exploration of more innovative technologies to push forward the development of the probe storage devices.

  1. Gravity Probe B

    NASA Image and Video Library

    2003-07-13

    In the spacecraft processing facility on North Vandenberg Air Force Base, workers prepare to remove the soft shipping cover from the Gravity Probe B experiment. Immediate processing includes setting up mechanical and electrical ground support equipment, making necessary connections and conditioning the spacecraft battery. The Gravity Probe B will launch a payload of four gyroscopes into low-Earth polar orbit to test two extraordinary predictions of Albert Einstein’s general theory of relativity: the geodetic effect (how space and time are warped by the presence of the Earth) and frame dragging (how Earth’s rotation drags space and time around with it). Once in orbit, for 18 months each gyroscope’s spin axis will be monitored as it travels through local spacetime, observing and measuring these effects. The experiment was developed by Stanford University, Lockheed Martin and NASA’s Marshall Space Flight Center.

  2. Gravity Probe B

    NASA Image and Video Library

    2003-07-11

    Workers in the spacecraft processing facility on North Vandenberg Air Force Base get ready to begin processing the Gravity Probe B experiment, including setting up mechanical and electrical ground support equipment, making necessary connections and conditioning the spacecraft battery. The Gravity Probe B will launch a payload of four gyroscopes into low-Earth polar orbit to test two extraordinary predictions of Albert Einstein’s general theory of relativity: the geodetic effect (how space and time are warped by the presence of the Earth) and frame dragging (how Earth’s rotation drags space and time around with it). Once in orbit, for 18 months each gyroscope’s spin axis will be monitored as it travels through local spacetime, observing and measuring these effects. The experiment was developed by Stanford University, Lockheed Martin and NASA’s Marshall Space Flight Center.

  3. Gravity Probe B

    NASA Image and Video Library

    2003-07-11

    Workers in the spacecraft processing facility on North Vandenberg Air Force Base get ready to begin processing the Gravity Probe B experiment. Mechanical and electrical ground support equipment will be set up and necessary connections made with the spacecraft. Spacecraft battery conditioning will also begin. The Gravity Probe B will launch a payload of four gyroscopes into low-Earth polar orbit to test two extraordinary predictions of Albert Einstein’s general theory of relativity: the geodetic effect (how space and time are warped by the presence of the Earth) and frame dragging (how Earth’s rotation drags space and time around with it). Once in orbit, for 18 months each gyroscope’s spin axis will be monitored as it travels through local spacetime, observing and measuring these effects. The experiment was developed by Stanford University, Lockheed Martin and NASA’s Marshall Space Flight Center.

  4. Mechanism of Interaction between the General Anesthetic Halothane and a Model Ion Channel Protein, II: Fluorescence and Vibrational Spectroscopy Using a Cyanophenylalanine Probe

    SciTech Connect

    Liu, J.; Strzalka, J; Tronin, A; Johansson, J; Blasie, J

    2009-01-01

    We demonstrate that cyano-phenylalanine (PheCN) can be utilized to probe the binding of the inhalational anesthetic halothane to an anesthetic-binding, model ion channel protein hbAP-PheCN. The Trp to PheCN mutation alters neither the a-helical conformation nor the 4-helix bundle structure. The halothane binding properties of this PheCN mutant hbAP-PheCN, based on fluorescence quenching, are consistent with those of the prototype, hbAP1. The dependence of fluorescence lifetime as a function of halothane concentration implies that the diffusion of halothane in the nonpolar core of the protein bundle is one-dimensional. As a consequence, at low halothane concentrations, the quenching of the fluorescence is dynamic, whereas at high concentrations the quenching becomes static. The 4-helix bundle structure present in aqueous detergent solution and at the air-water interface, is preserved in multilayer films of hbAP-PheCN, enabling vibrational spectroscopy of both the protein and its nitrile label (-CN). The nitrile groups' stretching vibration band shifts to higher frequency in the presence of halothane, and this blue-shift is largely reversible. Due to the complexity of this amphiphilic 4-helix bundle model membrane protein, where four PheCN probes are present adjacent to the designed cavity forming the binding site within each bundle, all contributing to the infrared absorption, molecular dynamics (MD) simulation is required to interpret the infrared results. The MD simulations indicate that the blue-shift of -CN stretching vibration induced by halothane arises from an indirect effect, namely an induced change in the electrostatic protein environment averaged over the four probe oscillators, rather than a direct interaction with the oscillators. hbAP-PheCN therefore provides a successful template for extending these investigations of the interactions of halothane with the model membrane protein via vibrational spectroscopy, using cyano-alanine residues to form the

  5. Probing the mechanism of cellulosome attachment to the Clostridium thermocellum cell surface: computer simulation of the Type II Cohesin-Dockerin complex and its variants

    SciTech Connect

    Xu, Jiancong; Smith, Jeremy C

    2010-10-01

    The recalcitrance of lignocellulosic biomass to hydrolysis is the bottleneck in cellulosic ethanol production. Efficient degradation of biomass by the anaerobic bacterium Clostridium thermocellum is carried out by the multicomponent cellulosome complex. The bacterial cell-surface attachment of the cellulosome is mediated by high-affinity protein-protein interactions between the Type II cohesin domain borne by the cell envelope protein and the Type II dockerin domain, together with neighboring X-module present at the C-terminus of the scaffolding protein (Type II coh-Xdoc). Here, the Type II coh-Xdoc interaction is probed using molecular dynamics simulations, free-energy calculations and essential dynamics analyses on both the wild type and various mutants of the C. thermocellum Type II coh-Xdoc in aqueous solution. The simulations identify the hot spots, i.e. the amino acid residues that may lead to a dramatic decrease in binding affinity upon mutation and also probe the effects of mutations on the mode of binding. The results suggest that bulky and hydrophobic residues at the protein interface, which make specific contacts with their counterparts, may play essential roles in retaining a rigid cohesin-dockerin interface. Moreover, dynamical cross-correlation analysis indicates that the X-module has a dramatic effect on the cohesin-dockerin interaction and is required for the dynamical integrity of the interface.

  6. Theoretical investigation of dynamic properties of magnetic molecule systems as probed by NMR and pulsed fields experiments

    NASA Astrophysics Data System (ADS)

    Rousochatzakis, Ioannis

    In this dissertation we theoretically investigate static and especially dynamic properties of magnetic molecules (MM's), as probed by the nuclear spin lattice relaxation rate 1/T1 (first part) and pulsed fields measurements of the magnetization M( t) (second part). In the first part, we provide a general first-principles account for 1/T1, which incorporates the decay of spin fluctuations and the corresponding "broadening" of the discrete magnetic energy levels of MM's. This is achieved by including the interaction of the electronic moments with the local deformation of the host lattice (phonons), in the Markovian regime and employing the quantum regression theorem. Within this framework, we provide a rigorous interpretation of a number of 1/ T1 experimental findings in MM's. We also provide an extensive account of the model spin-1/2 tetramer {V12} by analyzing magnetic susceptibility and 1/T1 data. The second part focuses on phenomena manifested in pulsed fields measurements of M(t), such as hysteresis loops and Landau-Zener-Stuckelberg (LZS) steps. First, we give a theoretical analysis of the low-T hysteresis loops and LZS steps at B ≈ 0 observed in the magnetic molecule {V6}. The loops are successfully reproduced by employing a generalization of the standard Bloch equation which in turn reveals the one-phonon acoustic processes as the dominant source of relaxation in this system. The origin of the US steps is attributed to the presence in {V 6} of a weak intra-molecular anisotropic exchange. The small deviation from the quantum-mechanical prediction of exact magnetization reversals at B ≈ 0 is attributed to the role of the phonon heat bath (dissipative US problem). Second, we provide a general, first-principles account of all dynamic phenomena manifested in pulsed fields experiments, by extending the standard spin-lattice relaxation theory to include time-dependent (pulsed) fields. This theory accounts for: (i) hysteresis effects (including the generalized

  7. On the Stability of Reversely Formed Austenite and Related Mechanism of Transformation in an Fe-Ni-Mn Martensitic Steel Aided by Electron Backscattering Diffraction and Atom Probe Tomography

    NASA Astrophysics Data System (ADS)

    Koohdar, Hamidreza; Nili-Ahmadabadi, Mahmoud; Habibi-Parsa, Mohammad; Jafarian, Hamid Reza; Bhattacharjee, Tilak; Tsuji, Nobuhiro

    2017-08-01

    The stability of reversely formed austenite and related mechanism of transformation were investigated against temperature and time in an Fe-9.6Ni-7.1Mn (at. pct) martensitic steel during intercritical annealing at a dual-phase (α + γ) region. Dilatometry, electron backscattering diffraction (EBSD), atom probe tomography (APT), and X-ray diffraction (XRD) were used to characterize the mechanism of reverse transformation. It was found that under intercritical annealing at 853 K (580 °C), when the heating rate is 20 K/s (20 °C/s), reverse transformation takes place through a mixed diffusion control mechanism, i.e., controlled by bulk diffusion and diffusion along the interface, where Ni controls the diffusion as its diffusivity is lower than that of Mn in the martensite and austenite. Increasing the intercritical annealing to 873 K (600 °C) at an identical heating rate of 20 K/s (20 °C/s) showed that reverse transformation occurs through a sequential combination of both martensitic and diffusional mechanisms. The transition temperature from diffusional to martensitic transformation was obtained close to 858 K (585 °C). Experimental results revealed that the austenite formed by the diffusional mechanism at 853 K (580 °C) mainly remains untransformed after cooling to ambient temperature due to the enrichment with Ni and Mn. It was also found that the stability of the reversely formed austenite by martensitic mechanism at 873 K (600 °C) is related to grain refinement.

  8. Evidence for the Preservation of Native Inter- and Intra-Molecular Hydrogen Bonds in the Desolvated FK-Binding Protein·FK506 Complex Produced by Electrospray Ionization

    NASA Astrophysics Data System (ADS)

    Hopper, Jonathan T. S.; Rawlings, Andrew; Afonso, José P.; Channing, Deborah; Layfield, Robert; Oldham, Neil J.

    2012-10-01

    It is now well established that electrospray ionization (ESI) is capable of introducing noncovalent protein assemblies into a desolvated environment, thereby allowing their analysis by mass spectrometry. The degree to which native interactions from the solution phase are preserved in this environment is less clear. Site-directed mutagenesis of FK506-binding protein (FKBP) has been employed to probe specific intra- and inter-molecular interactions within the complex between FKBP and its ligand FK506. Collisional activation of wild-type and mutant-FKBP•FK506 ions, generated by ESI, demonstrated that removal of native protein-ligand interactions formed between residues Asp37, Tyr82, and FK506 significantly destabilized the complex. Mutation of Arg42 to Ala42, or Tyr26 to Phe26 also resulted in lower energy dissociation of the FKBP·FK506 complex. Although these residues do not form direct H-bonds to FK506, they interact with Asp37, ensuring its correct orientation to associate with the ligand. Comparison with solution-based affinity measurements of these mutants has been discussed, including the stabilization afforded by ordered water molecules. Ion mobility spectrometry (IMS) has been employed to provide gas-phase structural information on the unfolding of the complexes. The [M + 6H]6+ complexes of the wild-type and mutants have been shown to resist unfolding and retain compact conformations. However, removal of the basic Arg42 residue was found to induce significant structural weakening of the [M + 7H]7+ complex when raised to dissociation-level energies. Overall, destabilization of the FKBP·FK506 complex, resulting from targeted removal of specific H-bonds, provides evidence for the preservation of these interactions in the desolvated wild-type complex.

  9. Characterization of Akiyama probe applied to dual-probes atomic force microscope

    NASA Astrophysics Data System (ADS)

    Wang, Hequn; Gao, Sitian; Li, Wei; Shi, Yushu; Li, Qi; Li, Shi; Zhu, Zhendong

    2016-10-01

    The measurement of nano-scale line-width has always been important and difficult in the field of nanometer measurements, while the rapid development of integrated circuit greatly raises the demand again. As one kind of scanning probe microscope (SPM), atomic force microscope (AFM) can realize quasi three-dimensional measurement, which is widely used in nanometer scale line-width measurement. Our team researched a dual-probes atomic force microscope, which can eliminate the prevalent effect of probe width on measurement results. In dual-probes AFM system, a novel head are newly designed. A kind of self-sensing and self-exciting probes which is Nanosensors cooperation's patented probe—Akiyama probe, is used in this novel head. The Akiyama probe applied to dual-probe atomic force microscope is one of the most important issues. The characterization of Akiyama probe would affect performance and accuracy of the whole system. The fundamental features of the Akiyama probe are electrically and optically characterized in "approach-withdraw" experiments. Further investigations include the frequency response of an Akiyama probe to small mechanical vibrations externally applied to the tip and the effective loading force yielding between the tip and the sample during the periodic contact. We hope that the characterization of the Akiyama probe described in this paper will guide application for dual-probe atomic force microscope.

  10. Structural modifications in a Mn54Al43C3 melt-spun alloy induced by mechanical milling and subsequent annealing investigated by atom probe tomography

    SciTech Connect

    Le Breton, JM; Bran, J; Folcke, E; Lucis, M; Larde, R; Jean, M; Shield, JE

    2013-12-25

    The structural changes upon milling and subsequent annealing of a Mn54Al43C3 alloy containing the intermetallic tetragonal L1(0) MnAl phase (tau phase) as the major phase were investigated by X-ray diffraction and atom probe tomography. The analyses show that milling the starting powder for 10 h leads to the nanostructuration of the sample. The milled sample is partly oxidised and contains both non oxidised Mn60 +/- 5Al40 +/- 5 regions and oxidised regions. Annealing the powder for 1 h at 500 degrees C leads to enrichment in Al of the oxidised regions, and to the phase transformation of the non-oxidised regions into a nano-structured beta-Mn-like phase with a composition close to Mn3Al2. (C) 2013 Elsevier B. V. All rights reserved.

  11. 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

  12. A new example of intra-molecular C-H⋯Ni anagostic inter-actions: synthesis, crystal structure and Hirshfeld analysis of cis-bis-[4-methyl-2-(1,2,3,4-tetra-hydro-naphthalen-1-yl-idene)hydrazinecarbo-thio-amidato-κ(2)N(1),S]nickel(II) di-methyl-formamide monosolvate.

    PubMed

    de Oliveira, Adriano Bof; Beck, Johannes; Mellone, Sônia Elizabeth Brown S; Daniels, Jörg

    2017-06-01

    The reaction of Ni(II) acetate tetra-hydrate with 4-methyl-2-(1,2,3,4-tetra-hydro-naphthalen-1-yl-idene)hydrazinecarbo-thio-amide in a 2:1 molar ratio and recrystallization from di-methyl-formamide yielded the title compound, [Ni(C12H14N3S)2]·C3H7NO. The ligands act as monoanionic κ(2)N(1),S-donors, forming five-membered metallarings. The Ni(II) ion is fourfold coordinated in a distorted square-planar cis-configuration, which is rather uncommon for mono-thio-semicarbazone complexes. Intra-molecular H⋯Ni trans-inter-actions are observed [H⋯Ni distances are 2.50 and 2.57 Å] and thus anagostic inter-actions can be suggested. The Hirshfeld surface analysis indicates that the major contributions for the crystal packing are H⋯H (66.6%), H⋯S (12.3%) and H⋯C (10.9%) inter-actions. In the crystal, the complex mol-ecules are linked by di-methyl-formamide solvent mol-ecules through N-H⋯O inter-actions into one-dimensional hydrogen-bonded polymers along [010].

  13. Resistive Switching Mechanisms on TaOx and SrRuO3 Thin-Film Surfaces Probed by Scanning Tunneling Microscopy.

    PubMed

    Moors, Marco; Adepalli, Kiran Kumar; Lu, Qiyang; Wedig, Anja; Bäumer, Christoph; Skaja, Katharina; Arndt, Benedikt; Tuller, Harry Louis; Dittmann, Regina; Waser, Rainer; Yildiz, Bilge; Valov, Ilia

    2016-01-26

    The local electronic properties of tantalum oxide (TaOx, 2 ≤ x ≤ 2.5) and strontium ruthenate (SrRuO3) thin-film surfaces were studied under the influence of electric fields induced by a scanning tunneling microscope (STM) tip. The switching between different redox states in both oxides is achieved without the need for physical electrical contact by controlling the magnitude and polarity of the applied voltage between the STM tip and the sample surface. We demonstrate for TaOx films that two switching mechanisms operate. Reduced tantalum oxide shows resistive switching due to the formation of metallic Ta, but partial oxidation of the samples changes the switching mechanism to one mediated mainly by oxygen vacancies. For SrRuO3, we found that the switching mechanism depends on the polarity of the applied voltage and involves formation, annihilation, and migration of oxygen vacancies. Although TaOx and SrRuO3 differ significantly in their electronic and structural properties, the resistive switching mechanisms could be elaborated based on STM measurements, proving the general capability of this method for studying resistive switching phenomena in different classes of transition metal oxides.

  14. Probing the mechanism of the interaction between l-cysteine-capped-CdTe quantum dots and Hg(2+) using capillary electrophoresis with ensemble techniques.

    PubMed

    Xu, Laifang; Hao, Junjie; Yi, Tao; Xu, Yinyin; Niu, Xiaoying; Ren, Cuiling; Chen, Hongli; Chen, Xingguo

    2015-03-01

    A good understanding of the mechanism of interaction between quantum dots (QDs) and heavy metal ions is essential for the design of more effective sensor systems. In this work, CE was introduced to explore how l-cysteine-capped-CdTe QDs (l-cys-CdTe QDs) interacts with Hg(2+) . The change in electrophoretic mobility can synchronously reflect the change in the composition and property of QDs. The effects of the free and capping ligands on the system are discussed in detail. ESI-MS, dynamic light scattering (DLS), zeta potential, and fluorescence (FL) were also applied as cooperative tools to study the interaction mechanism. Furthermore, the interaction mechanism, which principally depended on the concentration of Hg(2+) , was proposed reasonably. At the low concentration of Hg(2+) , the formation of a static complex between Hg(2+) and the carboxyl and amino groups of l-cys-CdTe QDs surface was responsible for the FL quenching. With the increase of Hg(2+) concentration, the capping l-cys was stripped from the surface of l-cys-CdTe QDs due to the high affinity of Hg(2+) to the thiol group of l-cys. Our study demonstrates that CE can reveal the mechanism of the interaction between QDs and heavy metal ions, such as FL quenching.

  15. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    NASA Astrophysics Data System (ADS)

    Zheng, Wenjun; Glenn, Paul

    2015-01-01

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  16. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    SciTech Connect

    Zheng, Wenjun Glenn, Paul

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  17. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation.

    PubMed

    Zheng, Wenjun; Glenn, Paul

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant--while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  18. Facile sonochemical synthesis and morphology control of CePO₄ nanostructures via an oriented attachment mechanism: application as luminescent probe for selective sensing of Pb²⁺ ion in aqueous solution.

    PubMed

    Shiralizadeh Dezfuli, Amin; Ganjali, Mohammad Reza; Norouzi, Parviz

    2014-09-01

    CePO4 nanostructures with hexagonal phase were controllably synthesized using Ce(NO3)3 reaction with NH4H2PO4 through a sonochemical method by simply varying the reaction conditions. By adding ethanol and polyethylene glycol (PEG), coral-reef nanostructures (CRNs) were synthesized and controlling over pH caused to nanorods/nanowires. Oriented attachment (OA) is proposed as dominant mechanism on the growth of nanostructures which is in competition with Ostwald ripening (OR). The crystal structure and morphology of the nanostructures were characterized by X-ray diffraction (XRD) and field-emission scanning electron microscopy (FE-SEM), respectively. The luminescent properties of CePO4 with different morphologies have been studied. Among the nanostructures, nanoparticles with the highest intensity of fluorescent have been used as luminescent probe for selective sensing of Pb(2+) ion in aqueous solution.

  19. Hot-wire probe

    NASA Technical Reports Server (NTRS)

    Mikulla, V.

    1976-01-01

    High-temperature platinum probe measures turbulence and Reynolds shear stresses in high-temperature compressible flows. Probe does not vibrate at high velocities and does not react like strain gage on warmup.

  20. Probing the Mechanism of the Double C—H (De)Activation Route of a Ru-Based Olefin Metathesis Catalyst

    NASA Astrophysics Data System (ADS)

    Poater, Albert; Cavallo, Luigi

    A theoretical study of a double C—H activation mechanism that deactivates a family of second generation Ru-based catalysts is presented. DFT calculations are used to rationalize the complex mechanistic pathway from the starting precatalyst to the experimentally characterized decomposition products. In particular, we show that all the intermediates proposed by Grubbs and coworkers are indeed possible intermediates in the deactivation pathway, although the sequence of steps is somewhat different

  1. Probing the protective mechanism of poly-ß-hydroxybutyrate against vibriosis by using gnotobiotic Artemia franciscana and Vibrio campbellii as host-pathogen model.

    PubMed

    Baruah, Kartik; Huy, Tran T; Norouzitallab, Parisa; Niu, Yufeng; Gupta, Sanjay K; De Schryver, Peter; Bossier, Peter

    2015-03-30

    The compound poly-ß-hydroxybutyrate (PHB), a polymer of the short chain fatty acid ß-hydroxybutyrate, was shown to protect experimental animals against a variety of bacterial diseases, (including vibriosis in farmed aquatic animals), albeit through undefined mechanisms. Here we aimed at unraveling the underlying mechanism behind the protective effect of PHB against bacterial disease using gnotobiotically-cultured brine shrimp Artemia franciscana and pathogenic Vibrio campbellii as host-pathogen model. The gnotobiotic model system is crucial for such studies because it eliminates any possible microbial interference (naturally present in any type of aquatic environment) in these mechanistic studies and furthermore facilitates the interpretation of the results in terms of a cause effect relationship. We showed clear evidences indicating that PHB conferred protection to Artemia host against V. campbellii by a mechanism of inducing heat shock protein (Hsp) 70. Additionally, our results also showed that this salutary effect of PHB was associated with the generation of protective innate immune responses, especially the prophenoloxidase and transglutaminase immune systems - phenomena possibly mediated by PHB-induced Hsp70. From overall results, we conclude that PHB induces Hsp70 and this induced Hsp70 might contribute in part to the protection of Artemia against pathogenic V. campbellii.

  2. Probing the protective mechanism of poly-ß-hydroxybutyrate against vibriosis by using gnotobiotic Artemia franciscana and Vibrio campbellii as host-pathogen model

    PubMed Central

    Baruah, Kartik; Huy, Tran T.; Norouzitallab, Parisa; Niu, Yufeng; Gupta, Sanjay K.; De Schryver, Peter; Bossier, Peter

    2015-01-01

    The compound poly-ß-hydroxybutyrate (PHB), a polymer of the short chain fatty acid ß-hydroxybutyrate, was shown to protect experimental animals against a variety of bacterial diseases, (including vibriosis in farmed aquatic animals), albeit through undefined mechanisms. Here we aimed at unraveling the underlying mechanism behind the protective effect of PHB against bacterial disease using gnotobiotically-cultured brine shrimp Artemia franciscana and pathogenic Vibrio campbellii as host-pathogen model. The gnotobiotic model system is crucial for such studies because it eliminates any possible microbial interference (naturally present in any type of aquatic environment) in these mechanistic studies and furthermore facilitates the interpretation of the results in terms of a cause effect relationship. We showed clear evidences indicating that PHB conferred protection to Artemia host against V. campbellii by a mechanism of inducing heat shock protein (Hsp) 70. Additionally, our results also showed that this salutary effect of PHB was associated with the generation of protective innate immune responses, especially the prophenoloxidase and transglutaminase immune systems – phenomena possibly mediated by PHB-induced Hsp70. From overall results, we conclude that PHB induces Hsp70 and this induced Hsp70 might contribute in part to the protection of Artemia against pathogenic V. campbellii. PMID:25822312

  3. Probing the Ser-Ser-Lys catalytic triad mechanism of peptide amidase: computational studies of the ground state, transition state, and intermediate.

    PubMed

    Valiña, Anna Liza B; Mazumder-Shivakumar, Devleena; Bruice, Thomas C

    2004-12-21

    Peptide amidase (Pam), a hydrolytic enzyme that belongs to the amidase signature (AS) family, selectively catalyzes the hydrolysis of the C-terminal amide bond (CO-NH(2)) of peptides. The recent availability of the X-ray structures of Pam, fatty acid amide hydrolase, and malonamidase E2 has led to the proposal of a novel Ser-Ser-Lys catalytic triad mechanism for the amide hydrolysis by the AS enzymes. The molecular dynamics (MD) simulations using the CHARMM force field were performed to explore the catalytic mechanism of Pam. The 1.8 A X-ray crystal structure of Pam in complex with the amide analogue of chymostatin was chosen for the initial coordinates for the MD simulations. The five systems that were investigated are as follows: (i) enzyme.substrate with Lys123-NH(2), (ii) enzyme.substrate with Lys123-NH(3)(+), (iii) enzyme.substrate with Lys123-NH(3)(+) and Ser226-O(-), (iv) enzyme.transition state, and (v) enzyme.tetrahedral intermediate. Our data support the presence of the hydrogen bonding network among the catalytic triad residues, Ser226, Ser202, and Lys123, where Ser226 acts as the nucleophile and Ser202 bridges Ser226 and Lys123. The MD simulation supports the catalytic role of the crystallographic waters, Wat1 and Wat2. In all the systems that have been studied, the backbone amide nitrogens of Asp224 and Thr223 create an oxyanion hole by hydrogen bonding to the terminal amide oxygen of the substrate, and stabilize the oxyanion tetrahedral intermediate. The results from both our computational investigation and previously published experimental pH profile support two mechanisms. In a mechanism that is relevant at lower pH, the Lys123-NH(3)(+)-Ser202 dyad provides structural support to the catalytic residue Ser226, which in turn carries out a nucleophilic attack at the substrate amide carbonyl in concert with Wat1-mediated deprotonation and stabilization of the tetrahedral transition state by the oxyanion hole. In the mechanism operating at higher pH, the

  4. A Magnetoresistance Measuring Probe.

    DTIC Science & Technology

    The in line four point probe, commonly used for measuring the sheet resistance in a conductor, cannot measure the anisotropic ferromagnetic magnetoresistance. However, the addition of two contact points that are not collinear with the current contacts give the probe the ability to non-destructively measure the anistropic magnetoresistance. Keywords: Magnetoresistance; Anisotropic; Thin-Film; Permalloy; Four Point Probe; Anisotropic Resistance.

  5. Galileo Probe Battery System

    NASA Technical Reports Server (NTRS)

    Dagarin, B. P.; Taenaka, R. K.; Stofel, E. J.

    1997-01-01

    The conclusions of the Galileo probe battery system are: the battery performance met mission requirements with margin; extensive ground-based and flight tests of batteries prior to probe separation from orbiter provided good prediction of actual entry performance at Jupiter; and the Li-SO2 battery was an important choice for the probe's main power.

  6. MIT validation probe acceptance test procedure

    SciTech Connect

    Escamilla, S.A.

    1994-08-23

    As part of the Multi-Functional Instrument Trees (MITs) a Validation Probe is being fabricated by Los Alamos National Laboratories (LANL). The Validation Probe assembly is equipped with a Winch, depth counter, and a Resistance Temperature Detector (RTD) which will render a means for verifying the temperature readings of which will render a means for verifying the temperature readings of the MIT thermocouples. The purpose of this Acceptance Test Procedure (ATP) is to provide verification that the Validation Probe functions properly and accordingly to LANL design and specification. This ATP will be used for all Validation Probes procured from LANL. The ATP consists of a receiving inspection, RTD ambient temperature; RTD electrical failure, RTD insulation resistance, and accurate depth counter operation inspections. The Validation Probe is composed of an intank probe, a cable and winching system, and a riser extension (probe guide) which bolts onto the MIT. The validation`s thermal sensor is an RTD that is housed in a 0.062 inch diameter, magnesium oxide fill, 316 stainless steel tube. The sheath configuration provides a means for spring loading the sensor firmly against the validation tube`s inner wall. A 45 pound cylindrical body is connected above the sheath and is used as a force to lower the probe into the tank. This cylindrical body also provides the means to interconnect both electrically and mechanically to the winch system which lowers the probe to a specified location within the validation tube located in the tank.

  7. Glass Probe Stimulation of Hair Cell Stereocilia.

    PubMed

    Peng, Anthony W; Ricci, Anthony J

    2016-01-01

    Hair cells are designed to sense mechanical stimuli of sound using their apical stereocilia hair bundles. Mechanical deflection of this hair bundle is converted into an electrical signal through gating of mechano-electric transduction channels. Stiff probe stimulation of hair bundles is an invaluable tool for studying the transduction channel and its associated processes because of the speed and ability to precisely control hair bundle position. Proper construction of these devices is critical to their ultimate performance as is appropriate placement of the probe onto the hair bundle. Here we describe the construction and use of a glass probe coupled to a piezo-electric actuator for stimulating hair bundles, including the basic technique for positioning of the stimulating probe onto the hair bundle. These piezo-electric stimulators can be adapted to other mechanically sensitive systems.

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

    PubMed

    Yang, Ya-li; Kaufman, Laura J

    2009-02-18

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

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

    PubMed Central

    Yang, Ya-li; Kaufman, Laura J.

    2009-01-01

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

  10. Mechanical properties of the tumor stromal microenvironment probed in vitro and ex vivo by in situ-calibrated optical trap-based active microrheology

    PubMed Central

    Staunton, Jack R; Vieira, Wilfred; Fung, King Leung; Lake, Ross; Devine, Alexus; Tanner, Kandice

    2016-01-01

    One of the hallmarks of the malignant transformation of epithelial tissue is the modulation of stromal components of the microenvironment. In particular, aberrant extracellular matrix (ECM) remodeling and stiffening enhances tumor growth and survival and promotes metastasis. Type I collagen is one of the major ECM components. It serves as a scaffold protein in the stroma contributing to the tissue’s mechanical properties, imparting tensile strength and rigidity to tissues such as those of the skin, tendons, and lungs. Here we investigate the effects of intrinsic spatial heterogeneities due to fibrillar architecture, pore size and ligand density on the microscale and bulk mechanical properties of the ECM. Type I collagen hydrogels with topologies tuned by polymerization temperature and concentration to mimic physico-chemical properties of a normal tissue and tumor microenvironment were measured by in situ-calibrated Active Microrheology by Optical Trapping revealing significantly different microscale complex shear moduli at Hz-kHz frequencies and two orders of magnitude of strain amplitude that we compared to data from bulk rheology measurements. Access to higher frequencies enabled observation of transitions from elastic to viscous behavior that occur at ~200Hz to 2750Hz, which largely was dependent on tissue architecture well outside the dynamic range of instrument acquisition possible with SAOS bulk rheology. We determined that mouse melanoma tumors and human breast tumors displayed complex moduli ~5–1000 Pa, increasing with frequency and displaying a nonlinear stress-strain response. Thus, we show the feasibility of a mechanical biopsy in efforts to provide a diagnostic tool to aid in the design of therapeutics complementary to those based on standard histopathology. PMID:27752289

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

  12. Probing the binding mechanisms of α-tocopherol to trypsin and pepsin using isothermal titration calorimetry, spectroscopic, and molecular modeling methods.

    PubMed

    Li, Xiangrong; Ni, Tianjun

    2016-06-01

    α-Tocopherol is a required nutrient for a variety of biological functions. In this study, the binding of α-tocopherol to trypsin and pepsin was investigated using isothermal titration calorimetry (ITC), steady-state and time-resolved fluorescence measurements, circular dichroism (CD) spectroscopy, and molecular modeling methods. Thermodynamic investigations reveal that α-tocopherol binds to trypsin/pepsin is synergistically driven by enthalpy and entropy. The fluorescence experimental results indicate that α-tocopherol can quench the fluorescence of trypsin/pepsin through a static quenching mechanism. The binding ability of α-tocopherol with trypsin/pepsin is in the intermediate range, and one molecule of α-tocopherol combines with one molecule of trypsin/pepsin. As shown by circular dichroism (CD) spectroscopy, α-tocopherol may induce conformational changes of trypsin/pepsin. Molecular modeling displays the specific binding site and gives information about binding forces and α-tocopherol-tryptophan (Trp)/tyrosine (Tyr) distances. In addition, the inhibition rate of α-tocopherol on trypsin and pepsin was studied. The study provides a basic data set for clarifying the binding mechanisms of α-tocopherol with trypsin and pepsin and is helpful for understanding its biological activity in vivo.

  13. Aggregation kinetics of single-walled carbon nanotubes investigated using mechanically wrapped multinuclear complexes: probing the tube-tube repulsive barrier.

    PubMed

    Ameen, Anjail A; Giordano, Andrea N; Alston, Jeffrey R; Forney, Michael W; Herring, Natalie P; Kobayashi, Shiho; Ridlen, Shawn G; Subaran, Sarah S; Younts, Thomas J; Poler, J C

    2014-03-28

    The rational design of supraparticle assemblies requires a detailed understanding of directed assembly processes. The stability of dispersions of nanoscale materials, like single-walled carbon nanotubes (SWCNTs), is still not fully understood, nor are the mechanisms of aggregation and assembly. A detailed balance of attractive van der Waals type interactions with various repulsive barrier mechanisms is needed to control the assembly of industrially viable and functional hybrid-nanoscale supraparticles. We report a detailed study of SWCNT dispersion stability and aggregation kinetics as a function of the nature of the coagulant used in various solvent systems. We explore three classes of coagulants that vary in charge, size, shape, solvation energy, and the ability to bind to the SWCNTs. We use these kinetic data to assess the tube-solvent-coagulant-tube interactions. We compare the relative contributions from two types of repulsive barriers. We find that tube-mediated structured solvent around the SWCNTs does not sufficiently describe our measured kinetic data. A DLVO type, electrical double layer repulsion is used to rationalize our observations. The data presented in this paper require a more detailed theoretical understanding of the physico-chemical environment near nanoparticle surfaces such as aggregating SWCNTs.

  14. Fusinite: A coal-derived EPR probe for O[sub 2]. Mechanism and application in vivo and in vitro. [EPR (electron paramagnetic resonance)

    SciTech Connect

    Vahidi, N.

    1993-01-01

    Fusinite, an inertinite coal maceral, exhibits a symmetric and exchange-narrowed electron paramagnetic resonance (EPR) line (g = 2.00276), with a first derivative peak-to-peak linewidth ([Delta]B) which is reversibly broaded by molecular O[sub 2]. To explain the mechanism of this type of broadening, pulse and multifrequency EPR measurements (0.25-250 GHz) were carried out in conjunction with O[sub 2] adsorption isotherm studies. The data suggest that, at ambient temperatures, homogeneous broadening of the EPR line of fusinite probably occurs by the exchange modulation of a group of delocalized unpaired electrons at the surface of fusinite by physical adsorbed O[sub 2]. At temperatures below 260[degrees] K, dipole-dipole mechanism begin to contribute more to the broadening of this component. The possibility of two different classes of sites for interaction with O[sub 2] is discussed. The extent of broadening per unit concentration of molecular oxygen is unusually large. This paramagnetic property of fusinite, combined with its very table physiochemical properties and low toxicity, is of utility for the measurement of the concentration of oxygen or [O[sub 2

  15. Probing the mechanical properties and microstructure of WSi2/SixGe1-x multiphase thermoelectric material by nanoindentation, electron and focused ion beam microscopy methods

    NASA Astrophysics Data System (ADS)

    Sola, Francisco; Dynys, Frederick

    2015-03-01

    Silicon germanium (SiGe) thermoelectric (TE) alloys have been traditionally used in radioisotope thermoelectric generators (RTG) NASA applications. While RTG applications is the main driver of our current research, we are exploring other applications in the energy harvesting arena. There is still a need to improve the TE figure of merit (ZT) of SiGe based TE alloys and we have been working on ways to improve it by incorporating tungsten di-silicide (WSi2) phases in to the matrix by directional solidification process. Considerable efforts have been focused until now in microstructural engineering methods that can lead to ZT improvement by microstructure optimization. Although critical for the previous mentioned applications, work pertinent to the mechanical integrity of WSi2/SiGe based TE materials is lacking. In this presentation, we report local mechanical properties (hardness, modulus and fracture toughness) and microstructure of WSi2/SiGe multiphase thermoelectric material by nanoindentation, scanning electron microscopy, focused ion beam and transmission electron microscopy methods.

  16. Isotope Probing of the UDP‐Apiose/UDP‐Xylose Synthase Reaction: Evidence of a Mechanism via a Coupled Oxidation and Aldol Cleavage

    PubMed Central

    Eixelsberger, Thomas; Horvat, Doroteja; Gutmann, Alexander; Weber, Hansjörg

    2017-01-01

    Abstract The C‐branched sugar d‐apiose (Api) is essential for plant cell‐wall development. An enzyme‐catalyzed decarboxylation/pyranoside ring‐contraction reaction leads from UDP‐α‐d‐glucuronic acid (UDP‐GlcA) to the Api precursor UDP‐α‐d‐apiose (UDP‐Api). We examined the mechanism of UDP‐Api/UDP‐α‐d‐xylose synthase (UAXS) with site‐selectively 2H‐labeled and deoxygenated substrates. The analogue UDP‐2‐deoxy‐GlcA, which prevents C‐2/C‐3 aldol cleavage as the plausible initiating step of pyranoside‐to‐furanoside conversion, did not give the corresponding Api product. Kinetic isotope effects (KIEs) support an UAXS mechanism in which substrate oxidation by enzyme‐NAD+ and retro‐aldol sugar ring‐opening occur coupled in a single rate‐limiting step leading to decarboxylation. Rearrangement and ring‐contracting aldol addition in an open‐chain intermediate then give the UDP‐Api aldehyde, which is intercepted via reduction by enzyme‐NADH. PMID:28102965

  17. Probing the Effects and Mechanisms of Electroacupuncture at Ipsilateral or Contralateral ST36-ST37 Acupoints on CFA-induced Inflammatory Pain.

    PubMed

    Lu, Kung-Wen; Hsu, Chao-Kuei; Hsieh, Ching-Liang; Yang, Jun; Lin, Yi-Wen

    2016-02-24

    Transient receptor potential vanilloid 1 (TRPV1) and associated signaling pathways have been reported to be increased in inflammatory pain signaling. There are accumulating evidences surrounding the therapeutic effect of electroacupuncture (EA). EA can reliably attenuate the increase of TRPV1 in mouse inflammatory pain models with unclear signaling mechanisms. Moreover, the difference in the clinical therapeutic effects between using the contralateral and ipsilateral acupoints has been rarely studied. We found that inflammatory pain, which was induced by injecting the complete Freund's adjuvant (CFA), (2.14 ± 0.1, p < 0.05, n = 8) can be alleviated after EA treatment at either ipsilateral (3.91 ± 0.21, p < 0.05, n = 8) or contralateral acupoints (3.79 ± 0.25, p < 0.05, n = 8). EA may also reduce nociceptive Nav sodium currents in dorsal root ganglion (DRG) neurons. The expression of TRPV1 and associated signaling pathways notably increased after the CFA injection; this expression can be further attenuated significantly in EA treatment. TRPV1 and associated signaling pathways can be prevented in TRPV1 knockout mice, suggesting that TRPV1 knockout mice are resistant to inflammatory pain. Through this study, we have increased the understanding of the mechanism that both ipsilateral and contralateral EA might alter TRPV1 and associated signaling pathways to reduce inflammatory pain.

  18. Probing the Effects and Mechanisms of Electroacupuncture at Ipsilateral or Contralateral ST36–ST37 Acupoints on CFA-induced Inflammatory Pain

    PubMed Central

    Lu, Kung-Wen; Hsu, Chao-Kuei; Hsieh, Ching-Liang; Yang, Jun; Lin, Yi-Wen

    2016-01-01

    Transient receptor potential vanilloid 1 (TRPV1) and associated signaling pathways have been reported to be increased in inflammatory pain signaling. There are accumulating evidences surrounding the therapeutic effect of electroacupuncture (EA). EA can reliably attenuate the increase of TRPV1 in mouse inflammatory pain models with unclear signaling mechanisms. Moreover, the difference in the clinical therapeutic effects between using the contralateral and ipsilateral acupoints has been rarely studied. We found that inflammatory pain, which was induced by injecting the complete Freund’s adjuvant (CFA), (2.14 ± 0.1, p < 0.05, n = 8) can be alleviated after EA treatment at either ipsilateral (3.91 ± 0.21, p < 0.05, n = 8) or contralateral acupoints (3.79 ± 0.25, p < 0.05, n = 8). EA may also reduce nociceptive Nav sodium currents in dorsal root ganglion (DRG) neurons. The expression of TRPV1 and associated signaling pathways notably increased after the CFA injection; this expression can be further attenuated significantly in EA treatment. TRPV1 and associated signaling pathways can be prevented in TRPV1 knockout mice, suggesting that TRPV1 knockout mice are resistant to inflammatory pain. Through this study, we have increased the understanding of the mechanism that both ipsilateral and contralateral EA might alter TRPV1 and associated signaling pathways to reduce inflammatory pain. PMID:26906464

  19. Probing Cellular and Molecular Mechanisms of Cigarette Smoke-Induced Immune Response in the Progression of Chronic Obstructive Pulmonary Disease Using Multiscale Network Modeling

    PubMed Central

    Pan, Zhichao; Yu, Haishan; Liao, Jie-Lou

    2016-01-01

    Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory disorder characterized by progressive destruction of lung tissues and airway obstruction. COPD is currently the third leading cause of death worldwide and there is no curative treatment available so far. Cigarette smoke (CS) is the major risk factor for COPD. Yet, only a relatively small percentage of smokers develop the disease, showing that disease susceptibility varies significantly among smokers. As smoking cessation can prevent the disease in some smokers, quitting smoking cannot halt the progression of COPD in others. Despite extensive research efforts, cellular and molecular mechanisms of COPD remain elusive. In particular, the disease susceptibility and smoking cessation effects are poorly understood. To address these issues in this work, we develop a multiscale network model that consists of nodes, which represent molecular mediators, immune cells and lung tissues, and edges describing the interactions between the nodes. Our model study identifies several positive feedback loops and network elements playing a determinant role in the CS-induced immune response and COPD progression. The results are in agreement with clinic and laboratory measurements, offering novel insight into the cellular and molecular mechanisms of COPD. The study in this work also provides a rationale for targeted therapy and personalized medicine for the disease in future. PMID:27669518

  20. Probing Mechanisms of Axonopathy. Part II: Protein Targets of 2,5-Hexanedione, the Neurotoxic Metabolite of the Aliphatic Solvent n-Hexane

    PubMed Central

    Tshala-Katumbay, Desire; Monterroso, Victor; Kayton, Robert; Lasarev, Michael; Sabri, Mohammad; Spencer, Peter

    2009-01-01

    Neuroprotein changes in the spinal cord of rodents with aliphatic γ-diketone axonopathy induced by 2,5-hexanedione (2,5-HD) are compared with those reported previously in aromatic γ-diketone–like axonopathy induced by 1,2-diacetylbenzene (1,2-DAB). Sprague-Dawley rats were treated intraperitoneally with 500 mg/kg/day 2,5-HD, equimolar doses of 2,3-hexanedione (negative control), or an equivalent amount of saline containing 50% dimethyl sulfoxide (vehicle), 5 days a week, for 3 weeks. Analysis of the lumbosacral proteome by 2-dimensional differential in-gel electrophoresis and matrix-assisted laser desorption ionization time-of-flight/tandem mass spectrometry revealed 34 proteins markedly modified by 2,5-HD of which neurofilament triplet L, gelsolin, protein disulfide isomerase, glutathione S-transferase, nicotinamide adenine dinucleotide (reduced) dehydrogenase 1α, pyruvate kinase, and fatty acid synthase were also modified by 1,2-DAB. The expression of proteins involved in maintaining the physical integrity of the cytoskeleton or controlling the redox and protein-folding mechanisms was reduced, whereas that of proteins supporting energy metabolism was mainly increased. The similarity of the neuroproteomic patterns of 2,5-HD and 1,2-DAB axonopathy suggests common biomarkers and/or mechanisms of neurotoxicity associated with exposure to their parent chemicals, namely the industrial solvents n-hexane and 1,2-diethylbenzene, respectively. PMID:19033394

  1. Probing Cellular and Molecular Mechanisms of Cigarette Smoke-Induced Immune Response in the Progression of Chronic Obstructive Pulmonary Disease Using Multiscale Network Modeling.

    PubMed

    Pan, Zhichao; Yu, Haishan; Liao, Jie-Lou

    Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory disorder characterized by progressive destruction of lung tissues and airway obstruction. COPD is currently the third leading cause of death worldwide and there is no curative treatment available so far. Cigarette smoke (CS) is the major risk factor for COPD. Yet, only a relatively small percentage of smokers develop the disease, showing that disease susceptibility varies significantly among smokers. As smoking cessation can prevent the disease in some smokers, quitting smoking cannot halt the progression of COPD in others. Despite extensive research efforts, cellular and molecular mechanisms of COPD remain elusive. In particular, the disease susceptibility and smoking cessation effects are poorly understood. To address these issues in this work, we develop a multiscale network model that consists of nodes, which represent molecular mediators, immune cells and lung tissues, and edges describing the interactions between the nodes. Our model study identifies several positive feedback loops and network elements playing a determinant role in the CS-induced immune response and COPD progression. The results are in agreement with clinic and laboratory measurements, offering novel insight into the cellular and molecular mechanisms of COPD. The study in this work also provides a rationale for targeted therapy and personalized medicine for the disease in future.

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

    SciTech Connect

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

    2011-01-01

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

  3. Test probe for surface mounted leadless chip carrier

    DOEpatents

    Meyer, Kerry L.; Topolewski, John

    1989-05-23

    A test probe for a surface mounted leadless chip carrier is disclosed. The probed includes specially designed connector pins which allow size reductions in the probe. A thermoplastic housing provides spring action to ensure good mechanical and electrical contact between the pins and the contact strips of a leadless chip carrier. Other features include flexible wires molded into the housing and two different types of pins alternately placed in the housing. These features allow fabrication of a smaller and simpler test probe.

  4. Ultrafast scanning probe microscopy

    DOEpatents

    Weiss, Shimon; Chemla, Daniel S.; Ogletree, D. Frank; Botkin, David

    1995-01-01

    An ultrafast scanning probe microscopy method for achieving subpicosecond-temporal resolution and submicron-spatial resolution of an observation sample. In one embodiment of the present claimed invention, a single short optical pulse is generated and is split into first and second pulses. One of the pulses is delayed using variable time delay means. The first pulse is then directed at an observation sample located proximate to the probe of a scanning probe microscope. The scanning probe microscope produces probe-sample signals indicative of the response of the probe to characteristics of the sample. The second pulse is used to modulate the probe of the scanning probe microscope. The time delay between the first and second pulses is then varied. The probe-sample response signal is recorded at each of the various time delays created between the first and second pulses. The probe-sample response signal is then plotted as a function of time delay to produce a cross-correlation of the probe sample response. In so doing, the present invention provides simultaneous subpicosecond-temporal resolution and submicron-spatial resolution of the sample.

  5. Traversing probe system

    DOEpatents

    Mashburn, Douglas N.; Stevens, Richard H.; Woodall, Harold C.

    1977-01-01

    This invention comprises a rotatable annular probe-positioner which carries at least one radially disposed sensing probe, such as a Pitot tube having a right-angled tip. The positioner can be coaxially and rotatably mounted within a compressor casing or the like and then actuated to orient the sensing probe as required to make measurements at selected stations in the annulus between the positioner and compressor casing. The positioner can be actuated to (a) selectively move the probe along its own axis, (b) adjust the yaw angle of the right-angled probe tip, and (c) revolve the probe about the axis common to the positioner and casing. A cam plate engages a cam-follower portion of the probe and normally rotates with the positioner. The positioner includes a first-motor-driven ring gear which effects slidable movement of the probe by rotating the positioner at a time when an external pneumatic cylinder is actuated to engage the cam plate and hold it stationary. When the pneumatic cylinder is not actuated, this ring gear can be driven to revolve the positioner and thus the probe to a desired circumferential location about the above-mentioned common axis. A second motor-driven ring gear included in the positioner can be driven to rotate the probe about its axis, thus adjusting the yaw angle of the probe tip. The positioner can be used in highly corrosive atmosphere, such as gaseous uranium hexafluoride.

  6. Ultrafast scanning probe microscopy

    DOEpatents

    Weiss, S.; Chemla, D.S.; Ogletree, D.F.; Botkin, D.

    1995-05-16

    An ultrafast scanning probe microscopy method is described for achieving subpicosecond-temporal resolution and submicron-spatial resolution of an observation sample. In one embodiment of the present claimed invention, a single short optical pulse is generated and is split into first and second pulses. One of the pulses is delayed using variable time delay means. The first pulse is then directed at an observation sample located proximate to the probe of a scanning probe microscope. The scanning probe microscope produces probe-sample signals indicative of the response of the probe to characteristics of the sample. The second pulse is used to modulate the probe of the scanning probe microscope. The time delay between the first and second pulses is then varied. The probe-sample response signal is recorded at each of the various time delays created between the first and second pulses. The probe-sample response signal is then plotted as a function of time delay to produce a cross-correlation of the probe sample response. In so doing, the present invention provides simultaneous subpicosecond-temporal resolution and submicron-spatial resolution of the sample. 6 Figs.

  7. 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.

  8. Lighting-induced Electron Precipitation (LEP) Events versus Geomagnetic Activity: A Probe Tool to Re-Evaluate the Electron Radiation Belt Loss Mechanisms (P16)

    NASA Astrophysics Data System (ADS)

    Fernandez, J. H.; Raulin, J.-P.; Correia, E.; Brum, C. G. M.

    2006-11-01

    We present the first results of an incipient attempt to re-model the Van Allen electron radiation belts equilibrium mechanisms. During the 23rd cycle solar minimum period (1995-1997) the Lightning- induced Electron Precipitation (LEP) events (electron precipitation from the geo-space to the upper Earth atmosphere) occurrence at the Antarctica Peninsula region was collected and studied. With statistical techniques we have reproduced the pattern of the events incidence during that period. The year 1998 was also analyzed and two well-defined geomagnetic storms (01-07 May and 26-31 Aug) were studied in association with the Trimpi events data. We have confirmed the narrow relationship between events occurrence rate and geomagnetic activity. The next step, in order to carry on the model, will be the modeling of the solar maximum LEP occurrence and to compute these results in the present radiation belts population models.

  9. Molecular mechanics force field-based general map for the solvation effect on amide I probe of peptide in different micro-environments.

    PubMed

    Cai, Kaicong; Su, Tingting; Lin, Shen; Zheng, Renhui

    2014-01-03

    A general electrostatic potential map based on molecular mechanics force field for modeling the amide I frequency is presented. This map is applied to N-methylacetamide (NMA) and designed to be transferable in different micro-environments. The electrostatic potentials from solvent and peptide side chain are projected on the amide unit of NMA to induce the frequency shift of amide I mode. It is shown that the predicted amide I frequency reproduces the experimental data satisfactorily, especially when NMA in polar solvents. The amide I frequency shift is largely determined by the solvents in aqueous solution while it is dominated by the local structure of peptide in other solvent environments. The map parameters are further applied on NMA-MeOH system and the obtained IR spectra show doublet peak profile with negligible deviation from the experimental data, suggesting the usefulness of this general map for providing information about vibrational parameters of amide motions of peptide in different environments.

  10. Two-color spectroscopy of UV excited ssDNA complex with a single-wall nanotube (SWNT) probe: Fast nucleobase autoionization mechanism

    NASA Astrophysics Data System (ADS)

    Rotkin, Slava V.; Ignatova, Tetyana; Balaeff, Alexander; Zheng, Ming; Blades, Michael; Stoeckl, Peter

    DNA autoionization is a fundamental process wherein UV-photoexcited nucleobases dissipate energy to the environment without undergoing chemical damage. SWNT is shown to serve as a photoluminescent reporter for studying the mechanism and rates of DNA autoionization. Two-color photoluminescence (PL) spectroscopy revealed a strong SWNT PL quenching when the UV pump is resonant with the DNA absorption [Nano Research, 2015]. Semiempirical calculations of the DNA-SWNT electronic structure, combined with a Green's function theory for charge transfer, show a 20 fs autoionization rate, dominated by the hole transfer. Rate-equation analysis of the spectroscopy data confirms that the quenching rate is limited by the thermalization of the free charge carriers transferred to the nanotube reservoir. The developed approach has a great potential for monitoring DNA excitation, autoionization, and chemical damage both in vivo and in vitro. NSF ECCS-1509786 (S.V.R.,T.I.) and PHY-1359195 (P.S.), NIST and UCF facilities.

  11. Probing deep into the binding mechanisms of folic acid with α-amylase, pepsin and trypsin: An experimental and computational study.

    PubMed

    Shi, Weizhong; Wang, Yanqing; Zhang, Hongmei; Liu, Zhengming; Fei, Zhenghao

    2017-07-01

    The inhibitions of folic acid (FA) towards three digestive enzymes, including α-amylase, pepsin and trypsin, were examined. The results showed that FA was able to reduce the enzymatic activity of α-amylase, pepsin, and trypsin by the formation of FA-enzyme complexes. The fluorescence spectral data indicated that the binding of FA with α-amylase, pepsin and trypsin resulted in strong fluorescence quenching of Tyr and Trp residues by hydrophobic interactions, hydrogen bonding and electrostatic interactions. To identify the precise binding sites of FA on α-amylase, pepsin and trypsin, the molecular modeling studies were also performed in this work. These investigations may constitute meaningful work for further advances in the mechanisms behind the interactions between FA and digestive enzymes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Probing dynamics and mechanism of exchange process of quaternary ammonium dimeric surfactants, 14-s-14, in the presence of conventional surfactants.

    PubMed

    Liu, Jun; Jiang, Yan; Chen, Hong; Mao, Shi Zhen; Du, You Ru; Liu, Mai Li

    2012-12-27

    In this Article, we investigated effects of different types of conventional surfactants on exchange dynamics of quaternary ammonium dimeric surfactants, with chemical formula C(14)H(29)N(+)(CH(3))(2)- (CH(2))(s)-N(+)(CH(3))(2)C(14)H(29)·2Br(-), or 14-s-14 for short. Two nonionic surfactants, TritonX-100 (TX-100) and polyethylene glycol (23) laurylether (Brij-35), and one cationic surfactant, n-tetradecyltrimethyl ammonium bromide (TTAB), and one ionic surfactant, sodium dodecyl sulfate (SDS) were chosen as typical conventional surfactants. Exchange rates of 14-s-14 (s = 2, 3, and 4) between the micelle form and monomer in solution were detected by two NMR methods: one-dimensional (1D) line shape analysis and two-dimensional (2D) exchange spectroscopy (EXSY). Results show that the nonionic surfactants (TX-100 and Brij-35), the cationic surfactant (TTAB), and the ionic surfactant (SDS) respectively accelerated, barely influenced, and slowed the exchange rate of 14-s-14. The effect mechanism was investigated by the self-diffusion experiment, relaxation time measurements (T(2)/T(1)), the fluorescence experiment (I(1)/I(3)) and observed chemical shift variations. Results reveal that, nonionic conventional surfactants (TX-100 and Brij-35) loosened the molecule arrangement and decreased hydrophobic interactions in the micelle, and thus accelerated the exchange rate of 14-s-14. The cationic conventional surfactant (TTAB) barely changed the molecule arrangement and thus barely influenced the exchange rate of 14-s-14. The ionic conventional surfactant (SDS) introduced the electrostatic attraction effect, tightened the molecule arrangement, and increased hydrophobic interactions in the micelle, and thus slowed down the exchange rate of 14-s-14. Additionally, the two-step exchange mechanism of 14-s-14 in the mixed solution was revealed through interesting variation tendencies of exchange rates of 14-s-14.

  13. Probing the mechanism of amyloidogenesis through a tandem repeat of the PI3-SH3 domain suggests a generic model for protein aggregation and fibril formation.

    PubMed

    Bader, Reto; Bamford, Richard; Zurdo, Jesús; Luisi, Ben F; Dobson, Christopher M

    2006-02-10

    Aggregation of the SH3 domain of the PI3 kinase, both as a single domain and as a tandem repeat in which the C terminus of one domain is linked to the N terminus of another by a flexible linker of ten glycine/serine residues, has been studied under a range of conditions in order to investigate the mechanism of protein aggregation and amyloid formation. The tandem repeat was found to form amyloid fibrils much more readily than the single domain under the acidic conditions used here, and the fibrils themselves have higher morphological homogeneity. The folding-unfolding transition of the PI3-SH3 domain shows two-state behaviour and is pH dependent; at pH 3.6, which is near the pH mid-point for folding and only slightly below the isoelectric point of the protein, both the single domain and the tandem repeat spontaneously form broad distributions of soluble oligomers without requirement for nucleation. Under prolonged incubation under these conditions, the oligomers convert into thin, curly fibrils that interact with thioflavin-T, suggesting that they contain an organised beta-sheet structure. Under more acidic conditions (pH 2.0) where the proteins are fully denatured and carry a positive net charge, long, straight fibrils are formed in a process having a pronounced lag phase. The latter was found to be reduced dramatically by the addition of oligomers exceeding a critical size of approximately 20 molecules. The results suggest that the process of aggregation of these SH3 domains can take place by a variety of mechanisms, ranging from downhill formation of relatively amorphous species to nucleated formation of highly organised structures, the relative importance of which varies greatly with solution conditions. Comparison with the behaviour of other amyloidogenic systems suggests that the general mechanistic features outlined here are likely to be common to at least a wide variety of peptides and proteins.

  14. In situ quantification and evaluation of ClO(-)/H2S homeostasis in inflammatory gastric tissue by applying a rationally designed dual-response fluorescence probe featuring a novel H(+)-activated mechanism.

    PubMed

    Fu, Qiang; Chen, Guang; Liu, Yuxia; Cao, Ziping; Zhao, Xianen; Li, Guoliang; Yu, Fabiao; Chen, Lingxin; Wang, Hua; You, Jinmao

    2017-05-02

    Homeostasis of ClO(-)/H2S plays a crucial role in the damage and repair of gastric tissue, but has rarely been investigated due to the challenge of in situ analysis in the highly acidic gastric environment. Herein, we designed a new H(+)-activated optical mechanism, involving controllable photoinduced electron transfer (PET) and switch of electron push-pull (SEPP), to develop the simple yet multifunctional probe (Z)-4-(2-benzylidenehydrazinyl)-7-nitrobenzo[c][1,2,5]oxadiazole (BNBD). First, the BNBD probe (Off) was protonated by the highly acidic media to trigger strong fluorescence (On). Then, the analytes ClO(-) and H2S reacted with the protonated BNBD, leading to ultrasensitive (ClO(-): 2.7 nM and H2S: 6.9 nM) fluorescence quenching via the rapid oxidation of C[double bond, length as m-dash]N (50 s) and nitro reduction (10 s), respectively. With the logical discrimination by absorbance/colour (ClO(-): 300 nm/colorless and H2S: 400 nm/orange), a strategy for the in situ quantification of ClO(-)/H2S in gastric mucosa and juice was developed. For the first time, the in situ quantitative monitoring of endogenous H2S and ClO(-)/H2S homeostasis as well as the pathologic manifestation in gastric mucosa were realized, thus overcoming the challenge of ClO(-)/H2S analysis under highly acidic conditions and enabling the in situ tissue quantification of ClO(-)/H2S. In combination with the assessment of mucosal damage, this study confirms the injurious/rehabilitative effects of ClO(-)/H2S on gastric mucosa (at 50-90 μm depth), which may facilitate the auxiliary diagnosis of stomach diseases induced by oxidative stress.

  15. Probing the mechanism of hypoxia selectivity of copper bis(thiosemicarbazonato) complexes: DFT calculation of redox potentials and absolute acidities in solution.

    PubMed

    Holland, Jason P; Green, Jennifer C; Dilworth, Jonathan R

    2006-02-14

    Density functional theory (DFT) calculations have been performed using the uB3LYP/6-31++G(d,p) model to calculate the solution phase one-electron reduction potentials (E(calc)) and absolute pKa values of a series of copper bis(thiosemicarbazonato) complexes. The effects of solvation in water and dimethylsulfoxide (DMSO) are incorporated as a self-consistent reaction field (SCRF) using the integral equation formalism polarisable continuum model (IEFPCM) and are found to be essential for quantitative agreement with an average error in E(calc) of -0.02 V compared to experiment. The bonding and spin densities are examined through the use of Natural Bond Order analysis and the results used to rationalise the calculated and observed reduction potentials. Calculated estimates of pKa values of several copper(II) species are presented and their implications for the mechanisms of transport and trapping within hypoxic cells are considered. Reduction is found to be a prerequisite for protonation of the complexes which suggests their transport in the blood stream as neutral species, and the mechanistic sequence is identified as a sequential electrochemical-chemical (EC) process. The complex equilibria of protonation, reoxidation and dissociation are discussed and the copper(I) diprotonated, cationic complex of diacetyl bis(4-methyl-3-thiosemicarbazonato)copper(II), Cu(I)ATSMH2(+), is identified as a possible candidate for the initial species trapped in hypoxic cells.

  16. Asphaltene adsorption mechanisms on the local scale probed by neutron reflectivity: transition from monolayer to multilayer growth above the flocculation threshold.

    PubMed

    Jouault, Nicolas; Corvis, Yohann; Cousin, Fabrice; Jestin, Jacques; Barré, Loïc

    2009-04-07

    We present here a study of the adsorption of asphaltenes on hydrophilic and hydrophobic solid surfaces by coupling measurements of adsorption isotherms on the macroscopic scale on silica powder with measurements of the structure of the adsorbed asphaltene layer on the microscopic scale obtained by neutron reflectivity on flat silicon wafers. Under good-solvent conditions, if adsorption isotherms reveal that the interaction potential between asphaltenes and the surface is slightly higher for the hydrophilic surface than for the hydrophobic one, then the mechanism of adsorption is similar in both cases because all samples exhibit the same local structure of the adsorbed asphaltene layer: it is a solvated monolayer with thickness of the same order of magnitude as the size of the asphaltene aggregates in the bulk. The surface excess, gamma, is thus always of the same order (approximately 3 mg/m2). The adsorption process induces a densification of the aggregates at the interface because the adsorbed monolayer is much less solvated than aggregates in bulk solution. When a bad solvent is progressively added, the asphaltene adsorbed layer keeps its monolayer structure as long as the bulk flocculation threshold is not reached. Above the threshold, the size of the asphaltene adsorbed layer grows and forms a multilayer structure.

  17. Probing Mechanisms of Photoreceptor Degeneration in a New Mouse Model of the Common Form of Autosomal Dominant Retinitis Pigmentosa due to P23H Opsin Mutations*♦

    PubMed Central

    Sakami, Sanae; Maeda, Tadao; Bereta, Grzegorz; Okano, Kiichiro; Golczak, Marcin; Sumaroka, Alexander; Roman, Alejandro J.; Cideciyan, Artur V.; Jacobson, Samuel G.; Palczewski, Krzysztof

    2011-01-01

    Rhodopsin, the visual pigment mediating vision under dim light, is composed of the apoprotein opsin and the chromophore ligand 11-cis-retinal. A P23H mutation in the opsin gene is one of the most prevalent causes of the human blinding disease, autosomal dominant retinitis pigmentosa. Although P23H cultured cell and transgenic animal models have been developed, there remains controversy over whether they fully mimic the human phenotype; and the exact mechanism by which this mutation leads to photoreceptor cell degeneration remains unknown. By generating P23H opsin knock-in mice, we found that the P23H protein was inadequately glycosylated with levels 1–10% that of wild type opsin. Moreover, the P23H protein failed to accumulate in rod photoreceptor cell endoplasmic reticulum but instead disrupted rod photoreceptor disks. Genetically engineered P23H mice lacking the chromophore showed accelerated photoreceptor cell degeneration. These results indicate that most synthesized P23H protein is degraded, and its retinal cytotoxicity is enhanced by lack of the 11-cis-retinal chromophore during rod outer segment development. PMID:21224384

  18. Evaluation of direct push probes: Sensor interface analysis of DC resistivity probes

    NASA Astrophysics Data System (ADS)

    Demuth, Daniel; Bumberger, Jan; Paasche, Hendrik

    2015-11-01

    In near surface sedimentary exploration direct push technology has become popular for geophysical logging. The method is thought to have great potential to offer accurate information about the variability of physical parameters since the region of disturbed sedimentary formation due to probe injection is considered to be smaller compared to disturbances by classical borehole measurements. Technical and experimental design of direct push probes follow often those of established borehole probes. A systematic appraisal of the suitability of such tools for direct push logging procedure exposing the probes to a very high mechanical stress and rapid aging process has been missing in the past. Following a recently developed general framework for direct push system decomposition we analyze two different DC resistivity direct push probes with regard to their sensor interface. Simple laboratory experiments validate the setup of a numerical simulation of both probes revealing significant differences on the suitability of the chosen electrode arrangement. Differences in robustness with regard to surface abrasion result in changing probe responses which could, depending on the experimental design of the probe, cause resistivity value changes of almost 25% within approximately 15 operational hours, which leaves severe doubts about the suitability of established direct push logging probes for quantitative geophysical probing.

  19. The use of electrostatic probes to characterize the discharge plasma structure and identify discharge cathode erosion mechanisms in ring-cusp ion thrusters

    NASA Astrophysics Data System (ADS)

    Herman, Daniel Andrew

    The erosion of the discharge cathode assembly (DCA) is currently one of the lifetime limiting factors of ion thruster operation and will play an even more important role for more ambitious, future ion thruster applications requiring more throughput at higher-power. Erosion of the DCA has been observed throughout the ground-based wear testing of the 30-cm NSTAR ion thruster. Energetic ions have been detected near the DCA, from Laser-Induced Fluorescence (LIF) measurements, that appear to be the cause of the DCA erosion, though a mechanism by which ions gain sufficient energy to sputter erode the DCA material has not been determined. This dissertation presents research aimed at characterizing the discharge chamber plasma near the DCA to determine the mechanism by which energetic ions are created and erode the DCA inside ring-cusp ion engines. A diagnostic technique is developed to interrogate the near-DCA regions of two ion thrusters: the 30-cm FMT2 NSTAR and 40-cm LM4 NEXT engines. Both engines contain similar plasma structures. Number densities are highest along cathode centerline as the axial magnetic field near the DCA effectively confines electrons to a narrow plume. Plasma potential mappings rule out the existence of a potential-hill that has been proposed as the cause of the DCA erosion. A free standing potential gradient structure is found to form the transition between the low-potential cathode plume and the high-potential bulk discharge plasma, termed a double layer. The field-aligned double layer accelerates ions from the bulk discharge plasma towards the DCA centerline. Measured plasma parameters and LIF velocimetry data are used to calculate an erosion rate utilizing near-threshold sputtering yield formulae. Singly-ionized xenon cannot solely account for the observed NSTAR erosion rates. Incorporation of double-ionized xenon from measured double-to-single current measurements in the plume of the 30-cm and 40-cm thrusters significantly increases the

  20. Immobilized Multifunctional Polymersomes on Solid Surfaces: Infrared Light-Induced Selective Photochemical Reactions, pH Responsive Behavior, and Probing Mechanical Properties under Liquid Phase.

    PubMed

    Iyisan, Banu; Janke, Andreas; Reichenbach, Philipp; Eng, Lukas M; Appelhans, Dietmar; Voit, Brigitte

    2016-06-22

    Fixing polymersomes onto surfaces is in high demand not only for the characterization with advanced microscopy techniques but also for designing specific compartments in microsystem devices in the scope of nanobiotechnology. For this purpose, this study reports the immobilization of multifunctional, responsive, and photo-cross-linked polymersomes on solid substrates by utilizing strong adamantane-β-cyclodextrin host-guest interactions. To reduce nonspecific binding and retain better spherical shape, the level of attractive forces acting on the immobilized polymersomes was tuned through poly(ethylene glycol) passivation as well as decreased β-cyclodextrin content on the corresponding substrates. One significant feature of this system is the pH responsivity of the polymersomes which has been demonstrated by swelling of the immobilized vesicles at acidic condition through in situ AFM measurements. Also, light responsivity has been provided by introducing nitroveratryloxycarbonyl (NVOC) protected amine molecules as photocleavable groups to the polymersome surface before immobilization. The subsequent low-energy femtosecond pulsed laser irradiation resulted in the cleavage of NVOC groups on immobilized polymersomes which in turn led to free amino groups as an additional functionality. The freed amines were further conjugated with a fluorescent dye having an activated ester that illustrates the concept of bio/chemo recognition for a potential binding of biological compounds. In addition to the responsive nature, the mechanical stability of the analyzed polymersomes was supported by computing Young's modulus and bending modulus of the membrane through force curves obtained by atomic force microscopy measurements. Overall, polymersomes with a robust and pH-swellable membrane combined with effective light responsive behavior are promising tools to design smart and stable compartments on surfaces for the development of microsystem devices such as chemo/biosensors.

  1. Nitric oxide physiological responses and delivery mechanisms probed by water-soluble Roussin's red ester and {Fe(NO)2}10 DNIC.

    PubMed

    Chen, Yi-Ju; Ku, Wei-Chi; Feng, Li-Ting; Tsai, Ming-Li; Hsieh, Chung-Hung; Hsu, Wen-Hwei; Liaw, Wen-Feng; Hung, Chen-Hsiung; Chen, Yu-Ju

    2008-08-20

    Dinitrosyl-iron complexes (DNICs) are stable carriers for nitric oxide (NO), an important biological signaling molecule and regulator. However, the insolubility of synthetic DNICs, such as Roussin's red ester (RRE), in water has impaired efforts to unravel their biological functions. Here, we report a water-soluble and structurally well-characterized RRE [Fe(mu-SC2H4COOH)(NO)2]2 (DNIC-1) and a {Fe(NO)2}(10) DNIC [(PPh2(Ph-3-SO3Na))2Fe(NO)2] (DNIC-2), their NO-induced protein regulation, and their cellular uptake mechanism using immortalized vascular endothelial cells as a model. Compared with the most common NO donor, S-nitroso-N-acetyl-penicillamine (SNAP), the in vitro NO release assay showed that both DNICs acted as much slower yet higher stoichiometric NO-release agents with low cytotoxicity (IC50 > 1 mM). Furthermore, L-cysteine facilitated NO release from SNAP and DNIC-1, but not DNIC-2, in a dose- and time-dependent manner. EPR spectroscopic analysis showed, for the first time, that intact DNIC-1 can either diffuse or be transported into cells independently and can transform to either paramagnetic protein bound DNIC in the presence of serum or [DNIC-(Cys)2] with excess L-cysteine under serum-free conditions. Both DNICs subsequently induced NO-dependent upregulation of cellular heat shock protein 70 and in vivo protein S-nitrosylation. We conclude that both novel water-soluble DNICs have potential to release physiologically relevant quantities of NO and can be a good model for deciphering how iron-sulfur-nitrosyl compounds permeate into the cell membrane and for elucidating their physiological significance.

  2. Probing into regional O3 and particulate matter pollution in the United States: 2. An examination of formation mechanisms through a process analysis technique and sensitivity study

    NASA Astrophysics Data System (ADS)

    Zhang, Yang; Wen, Xin-Yu; Wang, Kai; Vijayaraghavan, Krish; Jacobson, Mark Z.

    2009-11-01

    Following a comprehensive model evaluation in part 1, this part 2 paper describes results from 1 year process analysis and a number of sensitivity simulations using the Community Multiscale Air Quality (CMAQ) modeling system aimed to understand the formation mechanisms of O3 and PM2.5, their impacts on global environment, and implications for pollution control policies. Process analyses show that the most influential processes for O3 in the planetary boundary layer (PBL) are vertical and horizontal transport, gas-phase chemistry, and dry deposition and those for PM2.5 are primary PM emissions, horizontal transport, PM processes, and cloud processes. Exports of O3 and Ox from the U.S. PBL to free troposphere occur primarily in summer and at a rate of 0.16 and 0.65 Gmoles day-1, respectively. In contrast, export of PM2.5 is found to occur during all seasons and at rates of 25.68-34.18 Ggrams day-1, indicating a need to monitor and control PM2.5 throughout the year. Among nine photochemical indicators examined, the most robust include PH2O2/PHNO3, HCHO/NOy, and HCHO/NOz in winter and summer, H2O2/(O3 + NO2) in winter, and NOy in summer. They indicate a VOC-limited O3 chemistry in most areas in winter, but a NOx-limited O3 chemistry in most areas except for major cities in April-November, providing a rationale for nationwide NOx emission control and integrated control of NOx and VOCs emissions for large cities during high O3 seasons (May-September). For sensitivity of PM2.5 to its precursors, the adjusted gas ratio provides a more robust indicator than that without adjustment, especially for areas with insufficient sulfate neutralization in winter. NH4NO3 can be formed in most of the domain. Integrated control of emissions of PM precursors such as SO2, NOx, and NH3 are necessary for PM2.5 attainment. Among four types of VOCs examined, O3 formation is primarily affected by isoprene and low molecular weight anthropogenic VOCs, and PM2.5 formation is affected largely by

  3. High temperature probe

    DOEpatents

    Swan, Raymond A.

    1994-01-01

    A high temperature probe for sampling, for example, smokestack fumes, and is able to withstand temperatures of 3000.degree. F. The probe is constructed so as to prevent leakage via the seal by placing the seal inside the water jacket whereby the seal is not exposed to high temperature, which destroys the seal. The sample inlet of the probe is also provided with cooling fins about the area of the seal to provide additional cooling to prevent the seal from being destroyed. Also, a heated jacket is provided for maintaining the temperature of the gas being tested as it passes through the probe. The probe includes pressure sensing means for determining the flow velocity of an efficient being sampled. In addition, thermocouples are located in various places on the probe to monitor the temperature of the gas passing there through.

  4. Assessment of competitive and mechanism-based inhibition by clarithromycin: use of domperidone as a CYP3A probe-drug substrate and various enzymatic sources including a new cell-based assay with freshly isolated human hepatocytes.

    PubMed

    Michaud, Veronique; Turgeon, Jacques

    2010-04-01

    Clarithromycin is involved in a large number of clinically relevant drug-drug interactions. Discrepancies are observed between the magnitude of drug interactions predicted from in vitro competitive inhibition studies and changes observed clinically in the plasma levels of affected CYP3A substrates. The formation of metabolic-intermediate complexes has been proposed to explain these differences. The objectives of our study were: 1) to determine the competitive inhibition potency of clarithromycin on the metabolism of domperidone as a CYP3A probe drug using human recombinant CYP3A4 and CYP3A5 isoenzymes, human liver microsomes and cultured human hepatocytes; 2) to establish the modulatory role of cytochrome b5 on the competitive inhibition potency of clarithromycin; 3) to demonstrate the clarithromycin-induced formation of CYP450 metabolic-intermediate complexes in human liver microsomes; and 4) to determine the extent of CYP3A inhibition due to metabolic-intermediate complex formation using human liver microsomes and cultured human hepatocytes. At high concentrations (100 µM), clarithromycin had weak competitive inhibition potency towards CYP3A4 and CYP3A5. Inhibition potency was further decreased by the addition of cytochrome b5 (9-19%). Clarithromycin-induced metabolic-intermediate complexes were revealed by spectrophotometry analysis using human liver microsomes while time- and concentration-dependent mechanism-based inhibitions were quantified using isolated hepatocytes. These results indicate that mechanism-based but not competitive inhibition of CYP3As is the major underlying mechanism of drug-drug interactions observed clinically with clarithromycin. Drug interactions between clarithromycin and several CYP3A substrates are predicted to be insidious; the risk of severe adverse events should increase over time and persist for a few days after cessation of the drug.

  5. Multipressure and Temperature Probe

    NASA Technical Reports Server (NTRS)

    Raman, K. R.

    1982-01-01

    Aerodynamic probe is a small cylinder tube holding a network of tiny tubes leading to various ports. Six parameters are recorded simultaneously with little interference with aerodynamic flow. Two tubes connected by a hot-wire tungsten probe sense steady and fluctuating components of total and static pressures; the feedbacks from these tubes are input into differential-pressure sensors to measure fluctuating components of the pressures. Data are recorded by instruments at the back end of the probe.

  6. Advanced ultrasound probes for medical imaging

    NASA Astrophysics Data System (ADS)

    Wildes, Douglas G.; Smith, L. Scott

    2012-05-01

    New medical ultrasound probe architectures and materials build upon established 1D phased array technology and provide improved imaging performance and clinical value. Technologies reviewed include 1.25D and 1.5D arrays for elevation slice thickness control; electro-mechanical and 2D array probes for real-time 3D imaging; catheter probes for imaging during minimally-invasive procedures; single-crystal piezoelectric materials for greater frequency bandwidth; and cMUT arrays using silicon MEMS in place of piezo materials.

  7. Techniques for molecular imaging probe design.

    PubMed

    Reynolds, Fred; Kelly, Kimberly A

    2011-12-01

    Molecular imaging allows clinicians to visualize disease-specific molecules, thereby providing relevant information in the diagnosis and treatment of patients. With advances in genomics and proteomics and underlying mechanisms of disease pathology, the number of targets identified has significantly outpaced the number of developed molecular imaging probes. There has been a concerted effort to bridge this gap with multidisciplinary efforts in chemistry, proteomics, physics, material science, and biology--all essential to progress in molecular imaging probe development. In this review, we discuss target selection, screening techniques, and probe optimization with the aim of developing clinically relevant molecularly targeted imaging agents.

  8. Techniques for Molecular Imaging Probe Design

    PubMed Central

    Reynolds, Fred; Kelly, Kimberly A.

    2011-01-01

    Molecular imaging allows clinicians to visualize disease specific molecules, thereby providing relevant information in the diagnosis and treatment of patients. With advances in genomics and proteomics and underlying mechanisms of disease pathology, the number of targets identified has significantly outpaced the number of developed molecular imaging probes. There has been a concerted effort to bridge this gap with multidisciplinary efforts in chemistry, proteomics, physics, material science, and biology; all essential to progress in molecular imaging probe development. In this review, we will discuss target selection, screening techniques and probe optimization with the aim of developing clinically relevant molecularly targeted imaging agents. PMID:22201532

  9. Transient internal probe

    NASA Astrophysics Data System (ADS)

    Jarboe, Thomas R.; Mattick, Arthur T.

    1993-12-01

    The Transient Internal Probe (TIP) diagnostic is a novel method for probing the interior of hot magnetic fusion plasmas that are inaccessible with ordinary stationary probes. A small probe of magneto-optic (Verdet) material is fired through a plasma at speeds of several km/sec, illuminated by a laser beam. The beam's polarization is rotated in the probe by the local magnetic field and retroreflection back to a polarimetry detector allows determination of the B-field profile across the diameter of a plasma at a spatial resolution of better than 1-cm and an absolute B-field resolution of a few tens of Gauss. The principal components of a TIP diagnostic system were developed and tested. A two-stage light gas gun was constructed that accelerates 30-caliber projectiles to 3 km/sec, and methods were examined for stripping a lexan sabot from a probe prior to entry into a plasma. Probes of CdMnTe and FR-5 Verdet glass were fabricated, and a polarimetry system was constructed for resolving polarization to within 0.25 deg. The diagnostic was validated by measuring a static B-field with a moving (dropped) TIP probe, and finding agreement with Hall-probe measurements to within experimental accuracy (40 Gauss).

  10. Rocket exhaust probe

    NASA Astrophysics Data System (ADS)

    Kessel, P. A.

    1986-01-01

    Disclosed is a rocket exhaust probe for collecting particulates from a rocket exhaust plume. The probe comprises a tungsten nose tip, a tip holder, a probe body, and a tail section. Rocket exhaust gas enters the probe at the nose tip inlet and passes into a mixing chamber where the exhaust gas mixes with an inert cooling gas that cools and decelerates the exhaust gas. The mixture of exhaust gas and inert gas then passes into a diffusion chamber where it further cools and decelerates before passsing through a submicron particle collection filter.

  11. Raman tags: Novel optical probes for intracellular sensing and imaging.

    PubMed

    Li, Yuee; Wang, Zhong; Mu, Xijiao; Ma, Aning; Guo, Shu

    Optical labels are needed for probing specific target molecules in complex biological systems. As a newly emerging category of tags for molecular imaging in live cells, the Raman label attracts much attention because of the rich information obtained from targeted and untargeted molecules by detecting molecular vibrations. Here, we list three types of Raman probes based on different mechanisms: Surface Enhanced Raman Scattering (SERS) probes, bioorthogonal Raman probes, and Resonance Raman (RR) probes. We review how these Raman probes work for detecting and imaging proteins, nucleic acids, lipids, and other biomolecules in vitro, within cells, or in vivo. We also summarize recent noteworthy studies, expound on the construction of every type of Raman probe and operating principle, sum up in tables typically targeting molecules for specific binding, and provide merits, drawbacks, and future prospects for the three Raman probes. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Cone penetrometer fiber optic raman spectroscopy probe assembly

    DOEpatents

    Kyle, Kevin R.; Brown, Steven B.

    2000-01-01

    A chemically and mechanically robust optical Raman spectroscopy probe assembly that can be incorporated in a cone penetrometer (CPT) for subsurface deployment. This assembly consists of an optical Raman probe and a penetrometer compatible optical probe housing. The probe is intended for in-situ chemical analysis of chemical constituents in the surrounding environment. The probe is optically linked via fiber optics to the light source and the detection system at the surface. A built-in broadband light source provides a strobe method for direct measurement of sample optical density. A mechanically stable sapphire window is sealed directly into the side-wall of the housing using a metallic, chemically resistant, hermetic seal design. This window permits transmission of the interrogation light beam and the resultant signal. The spectroscopy probe assembly is capable of accepting Raman, Laser induced Fluorescence, reflectance, and other optical probes with collimated output for CPT deployment.

  13. Metalloprotein-based MRI probes

    PubMed Central

    Matsumoto, Yuri; Jasanoff, Alan

    2013-01-01

    Metalloproteins have long been recognized as key determinants of endogenous contrast in magnetic resonance imaging (MRI) of biological subjects. More recently, both natural and engineered metalloproteins have been harnessed as biotechnological tools to probe gene expression, enzyme activity, and analyte concentrations by MRI. Metalloprotein MRI probes are paramagnetic and function by analogous mechanisms to conventional gadolinium or iron oxide-based MRI contrast agents. Compared with synthetic agents, metalloproteins typically offer worse sensitivity, but the possibilities of using protein engineering and targeted gene expression approaches in conjunction with metalloprotein contrast agents are powerful and sometimes definitive strengths. This review summarizes theoretical and practical aspects of metalloprotein-based contrast agents, and discusses progress in the exploitation of these proteins for molecular imaging applications. PMID:23376346

  14. Cyclodextrin-Based Metal-Organic Nanotube as Fluorescent Probe for Selective Turn-On Detection of Hydrogen Sulfide in Living Cells Based on H2S-Involved Coordination Mechanism

    PubMed Central

    Xin, Xuelian; Wang, Jingxin; Gong, Chuanfang; Xu, Hai; Wang, Rongming; Ji, Shijie; Dong, Hanxiao; Meng, Qingguo; Zhang, Liangliang; Dai, Fangna; Sun, Daofeng

    2016-01-01

    Hydrogen sulfide (H2S) has been considered as the third biologically gaseous messenger (gasotransmitter) after nitric oxide (NO) and carbon monoxide (CO). Fluorescent detection of H2S in living cells is very important to human health because it has been found that the abnormal levels of H2S in human body can cause Alzheimer’s disease, cancers and diabetes. Herein, we develop a cyclodextrin-based metal-organic nanotube, CD-MONT-2, possessing a {Pb14} metallamacrocycle for efficient detection of H2S. CD-MONT-2′ (the guest-free form of CD-MONT-2) exhibits turn-on detection of H2S with high selectivity and moderate sensitivity when the material was dissolved in DMSO solution. Significantly, CD-MONT-2′ can act as a fluorescent turn-on probe for highly selective detection of H2S in living cells. The sensing mechanism in the present work is based on the coordination of H2S as the auxochromic group to the central Pb(II) ion to enhance the fluorescence intensity, which is studied for the first time. PMID:26911657

  15. Cyclodextrin-Based Metal-Organic Nanotube as Fluorescent Probe for Selective Turn-On Detection of Hydrogen Sulfide in Living Cells Based on H2S-Involved Coordination Mechanism.

    PubMed

    Xin, Xuelian; Wang, Jingxin; Gong, Chuanfang; Xu, Hai; Wang, Rongming; Ji, Shijie; Dong, Hanxiao; Meng, Qingguo; Zhang, Liangliang; Dai, Fangna; Sun, Daofeng

    2016-02-25

    Hydrogen sulfide (H2S) has been considered as the third biologically gaseous messenger (gasotransmitter) after nitric oxide (NO) and carbon monoxide (CO). Fluorescent detection of H2S in living cells is very important to human health because it has been found that the abnormal levels of H2S in human body can cause Alzheimer's disease, cancers and diabetes. Herein, we develop a cyclodextrin-based metal-organic nanotube, CD-MONT-2, possessing a {Pb14} metallamacrocycle for efficient detection of H2S. CD-MONT-2' (the guest-free form of CD-MONT-2) exhibits turn-on detection of H2S with high selectivity and moderate sensitivity when the material was dissolved in DMSO solution. Significantly, CD-MONT-2' can act as a fluorescent turn-on probe for highly selective detection of H2S in living cells. The sensing mechanism in the present work is based on the coordination of H2S as the auxochromic group to the central Pb(II) ion to enhance the fluorescence intensity, which is studied for the first time.

  16. Cyclodextrin-Based Metal-Organic Nanotube as Fluorescent Probe for Selective Turn-On Detection of Hydrogen Sulfide in Living Cells Based on H2S-Involved Coordination Mechanism

    NASA Astrophysics Data System (ADS)

    Xin, Xuelian; Wang, Jingxin; Gong, Chuanfang; Xu, Hai; Wang, Rongming; Ji, Shijie; Dong, Hanxiao; Meng, Qingguo; Zhang, Liangliang; Dai, Fangna; Sun, Daofeng

    2016-02-01

    Hydrogen sulfide (H2S) has been considered as the third biologically gaseous messenger (gasotransmitter) after nitric oxide (NO) and carbon monoxide (CO). Fluorescent detection of H2S in living cells is very important to human health because it has been found that the abnormal levels of H2S in human body can cause Alzheimer’s disease, cancers and diabetes. Herein, we develop a cyclodextrin-based metal-organic nanotube, CD-MONT-2, possessing a {Pb14} metallamacrocycle for efficient detection of H2S. CD-MONT-2‧ (the guest-free form of CD-MONT-2) exhibits turn-on detection of H2S with high selectivity and moderate sensitivity when the material was dissolved in DMSO solution. Significantly, CD-MONT-2‧ can act as a fluorescent turn-on probe for highly selective detection of H2S in living cells. The sensing mechanism in the present work is based on the coordination of H2S as the auxochromic group to the central Pb(II) ion to enhance the fluorescence intensity, which is studied for the first time.

  17. Probing Skills for Tutors.

    ERIC Educational Resources Information Center

    Brown, Beryl E.

    The Office of Academic Support and Instructional Services (OASIS) at the University of California at San Diego sponsors a workshop that teaches tutors to use five types of probing skills. The use of the skills is fundamental to the student learner's acquisition of complex relationships and problem solving skills. The five types of probes are:…

  18. Formative Assessment Probes

    ERIC Educational Resources Information Center

    Eberle, Francis; Keeley, Page

    2008-01-01

    Formative assessment probes can be effective tools to help teachers build a bridge between students' initial ideas and scientific ones. In this article, the authors describe how using two formative assessment probes can help teachers determine the extent to which students make similar connections between developing a concept of matter and a…

  19. Formative Assessment Probes

    ERIC Educational Resources Information Center

    Eberle, Francis; Keeley, Page

    2008-01-01

    Formative assessment probes can be effective tools to help teachers build a bridge between students' initial ideas and scientific ones. In this article, the authors describe how using two formative assessment probes can help teachers determine the extent to which students make similar connections between developing a concept of matter and a…

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

    SciTech Connect

    Lee, Sang Heon

    2014-03-15

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

  1. PDV Probe Alignment Technique

    SciTech Connect

    Whitworth, T L; May, C M; Strand, O T

    2007-10-26

    This alignment technique was developed while performing heterodyne velocimetry measurements at LLNL. There are a few minor items needed, such as a white card with aperture in center, visible alignment laser, IR back reflection meter, and a microscope to view the bridge surface. The work was performed on KCP flyers that were 6 and 8 mils wide. The probes used were Oz Optics manufactured with focal distances of 42mm and 26mm. Both probes provide a spot size of approximately 80?m at 1550nm. The 42mm probes were specified to provide an internal back reflection of -35 to -40dB, and the probe back reflections were measured to be -37dB and -33dB. The 26mm probes were specified as -30dB and both measured -30.5dB. The probe is initially aligned normal to the flyer/bridge surface. This provides a very high return signal, up to -2dB, due to the bridge reflectivity. A white card with a hole in the center as an aperture can be used to check the reflected beam position relative to the probe and launch beam, and the alignment laser spot centered on the bridge, see Figure 1 and Figure 2. The IR back reflection meter is used to measure the dB return from the probe and surface, and a white card or similar object is inserted between the probe and surface to block surface reflection. It may take several iterations between the visible alignment laser and the IR back reflection meter to complete this alignment procedure. Once aligned normal to the surface, the probe should be tilted to position the visible alignment beam as shown in Figure 3, and the flyer should be translated in the X and Y axis to reposition the alignment beam onto the flyer as shown in Figure 4. This tilting of the probe minimizes the amount of light from the bridge reflection into the fiber within the probe while maintaining the alignment as near normal to the flyer surface as possible. When the back reflection is measured after the tilt adjustment, the level should be about -3dB to -6dB higher than the probes

  2. Circumferential pressure probe

    NASA Technical Reports Server (NTRS)

    Holmes, Harlan K. (Inventor); Moore, Thomas C. (Inventor); Fantl, Andrew J. (Inventor)

    1989-01-01

    A probe for measuring circumferential pressure inside a body cavity is disclosed. In the preferred embodiment, a urodynamic pressure measurement probe for evaluating human urinary sphincter function is disclosed. Along the length of the probe are disposed a multiplicity of deformable wall sensors which typically comprise support tube sections with flexible side wall areas. These are arranged along the length of the probe in two areas, one just proximal to the tip for the sensing of fluid pressure inside the bladder, and five in the sensing section which is positioned within the urethra at the point at which the urinary sphincter constricts to control the flow of urine. The remainder of the length of the probe comprises multiple rigid support tube sections interspersed with flexible support tube sections in the form of bellows to provide flexibility.

  3. Inflatable traversing probe seal

    NASA Technical Reports Server (NTRS)

    Trimarchi, Paul A.

    1991-01-01

    An inflatable seal acts as a pressure-tight zipper to provide traversing capability for instrumentation rakes and probes. A specially designed probe segment with a teardrop cross-section in the vicinity of the inflatable seal minimizes leakage at the interface. The probe is able to travel through a lengthwise slot in a pressure vessel or wind tunnel section, while still maintaining pressure integrity. The design uses two commercially available inflatable seals, opposing each other, to cover the probe slot in a wind tunnel wall. Proof-of-concept tests were conducted at vessel pressures up to 30 psig, with seals inflated to 50 psig, showing no measurable leakage along the seal's length or around the probe teardrop cross-section. This seal concept can replace the existing technology of sliding face plate/O-ring systems in applications where lengthwise space is limited.

  4. Application of probe manipulator to repair probe cards

    NASA Astrophysics Data System (ADS)

    Konno, Takeshi; Kobayashi, Mikihiko; Egashira, Mitsuru; Machida, Kazumichi; Urata, Atsuo

    2006-03-01

    We fabricated an apparatus for manipulation and welding of fine metal objects using a probe. The apparatus is composed of a work probe of a tungsten alloy needle, stages, a DC power supply, and an observation system. The work probe is held vertically above a gold substrate placed on stages to control the relative position against the work probe. The DC power supply is equipped to apply voltage of 0-10kV between the work probe and the substrate. One application of the apparatus is to repair probe cards. Thousands of contact probes (needles) are mounted on the printed circuit board (PCB) in the probe card. The contact probes are mounted one by one by the hands. Recently, an array of the contact probe on the PCB is produced by the LIGA process in response to narrower semiconductor pitch length. The problem is that there are no methods to repair a wrong contact probe. Whole of the contact probes should be a waste owing to one wrong contact probe. We propose to replace a wrong contact probe with a good one using our apparatus. Experiments to remove a contact probe by the apparatus is carried out using the specimen of a mimic probe card, where a cantilever type contact probes are arranged with a pitch of 25 micrometers. Removal of the wrong contact probe is carried out by a non-contact discharge and a contact discharge using the apparatus. High voltage of about 1-2kV is applied after the work probe is moved to above the target contact probe for the non-contact discharge. While high voltage of about10kV is applied after the work probe is positioned in contact with the target contact probe for the contact discharge. The target contact probe is removed by both methods, though the neighboring contact probes are damaged. The latter method is hopeful for removal for repair of the probe card.

  5. Probing the mechanical unzipping of DNA

    NASA Astrophysics Data System (ADS)

    Voulgarakis, Nikos K.; Bishop, Alan R.; Rasmussen, Kim O.

    2006-03-01

    Recent advances in single-molecule force spectroscopy have made a systematic study of local melting in DNA possible. This provide new insight into important biological processes as replication and transcription. In this work, we present an extensive study of the micromechanical unzipping of DNA in the framework of the Peyrard-Bishop-Dauxois (PBD) model. The force required to separate the doubled strand is derived through analysis of the force-extension curve, while an estimation of the nucleation bubble size of the unzipping process is obtained by the distribution of the rapture force. Our findings are in very good agreement with existing experimental results; for example the force-temperature phase diagram obtained by the PBD model agrees excellently with recent constant-force experimental measurements of the lambda-phage DNA. Fundamental differences between the in vivo and vitro DNA unzipping, as predicted by the PBD model, are also discussed.

  6. Probing Mechanism of Evolution of Simple Genomes

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; Ditzler, Mark; Popovic, Milena; Wei, Chenyu

    2016-01-01

    Our overarching goal is to discover how the structure of the genotypic space of RNA polymers affects their ability to evolve. Specifically, we will address several fundamental questions that, so far, have remained largely unanswered. Was the genotypic space explored globally or only locally? Was the outcome of early evolution predictable or was it, instead, govern by chance? What was the role of neutral mutations in the evolution of increasing complex systems? As the first step, we study the problem in the example of RNA ligases. We obtain the complete, empirical fitness landscapes for short ligases and examine possible evolutionary paths for RNA molecules that are sufficiently long to preclude exhaustive search of the genotypic space.

  7. Pioneer Jupiter orbiter probe mission 1980, probe description

    NASA Technical Reports Server (NTRS)

    Defrees, R. E.

    1974-01-01

    The adaptation of the Saturn-Uranus Atmospheric Entry Probe (SUAEP) to a Jupiter entry probe is summarized. This report is extracted from a comprehensive study of Jovian missions, atmospheric model definitions and probe subsystem alternatives.

  8. Constrained photophysics of partially and fully encapsulated charge transfer probe (E)-3-(4-Methylaminophenyl) acrylic acid methyl ester inside cyclodextrin nano-cavities: Evidence of cyclodextrins cavity dependent complex stoichiometry

    NASA Astrophysics Data System (ADS)

    Ghosh, Shalini; Jana, Sankar; Guchhait, Nikhil

    2011-12-01

    The polarity sensitive intra-molecular charge transfer (ICT) emission from (E)-3-(4-Methylaminophenyl) acrylic acid methyl ester (MAPAME) is found to show distinct changes once introduced into the nano-cavities of cyclodextrins in aqueous environment. Movement of the molecule from the more polar aqueous environment to the less polar, hydrophobic cyclodextrin interior is marked by the blue shift of the CT emission band with simultaneous fluorescence intensity enhancement. The emission spectral changes on complexation with the α- and β-CD show different stoichiometries as observed from the Benesi-Hildebrand plots. Fluorescence anisotropy and lifetime measurements were performed to probe the different behaviors of MAPAME in aqueous α- and β-CD solutions.

  9. Constrained photophysics of partially and fully encapsulated charge transfer probe (E)-3-(4-Methylaminophenyl) acrylic acid methyl ester inside cyclodextrin nano-cavities: evidence of cyclodextrins cavity dependent complex stoichiometry.

    PubMed

    Ghosh, Shalini; Jana, Sankar; Guchhait, Nikhil

    2011-12-15

    The polarity sensitive intra-molecular charge transfer (ICT) emission from (E)-3-(4-Methylaminophenyl) acrylic acid methyl ester (MAPAME) is found to show distinct changes once introduced into the nano-cavities of cyclodextrins in aqueous environment. Movement of the molecule from the more polar aqueous environment to the less polar, hydrophobic cyclodextrin interior is marked by the blue shift of the CT emission band with simultaneous fluorescence intensity enhancement. The emission spectral changes on complexation with the α- and β-CD show different stoichiometries as observed from the Benesi-Hildebrand plots. Fluorescence anisotropy and lifetime measurements were performed to probe the different behaviors of MAPAME in aqueous α- and β-CD solutions. Copyright © 2011 Elsevier B.V. All rights reserved.

  10. Mounting of molded AFM probes by soldering

    NASA Astrophysics Data System (ADS)

    Hantschel, Thomas; Pape, Uwe; Slesazeck, Stefan; Niedermann, Philippe; Vandervorst, Wilfried

    2000-08-01

    Electrical probes consisting of cantilever beams with integrated pyramidal metal or diamond tips have to be mounted to small holder chips before they can be used in electrical atomic force microscopy (AFM). Gluing procedures have been developed for this step but such a connection suffers mainly from low electrical conductivity and often also from low mechanical stability. Furthermore, it is not very suitable for massfabrication. Soldering is a well-established mounting method in microelectronics (e.g. surface mounted devices (SMD)) and could overcome these problems. Therefore, we have developed a soldering procedure for moulded AFM probes. This paper presents the optimized soldering procedure and demonstartes its use for probe mounting. Excellent results were obtained using a metallization system of Ti:W+Ni+Au and a SnBi58 solder paste in combination with a hotplate for the soldering step. The soldered probes are highly conductive and the mechanical connection between probe and holder chip is very rigid. They show clear resonance peaks in tapping mode AFM which we could not obtain with our glued probes before.

  11. Remote Adjustable focus Raman Spectroscopy Probe

    SciTech Connect

    Schmucker, John E.; Blasi, Raymond J.; Archer, William B.

    1998-07-28

    A remote adjustable focus Raman spectroscopy probe allows for analyzing Raman scattered light from a point of interest external to the probe. An environmental barrier including at least one window separates the probe from the point of interest. An optical tube is disposed adjacent to the environmental barrier and includes along working length compound lens objective next to the window. A beam splitter and a mirror are at the other end. A mechanical means is used to translate the probe body in the X, Y, and Z directions resulting in a variable focus optical apparatus. Laser light is reflected by the beam splitter and directed toward the compound lens objective, then through the window and focused on the point of interest. Raman scattered light is then collected by the compound lens objective and directed through the beam splitter to a mirror. A device for analyzing the light, such as a monochrometer, is coupled to the mirror.

  12. ALEX neutral beam probe

    SciTech Connect

    Pourrezaei, K.

    1982-01-01

    A neutral beam probe capable of measuring plasma space potential in a fully 3-dimensional magnetic field geometry has been developed. This neutral beam was successfully used to measure an arc target plasma contained within the ALEX baseball magnetic coil. A computer simulation of the experiment was performed to refine the experimental design and to develop a numerical model for scaling the ALEX neutral beam probe to other cases of fully 3-dimensional magnetic field. Based on this scaling a 30 to 50 keV neutral cesium beam probe capable of measuring space potential in the thermal barrier region of TMX Upgrade was designed.

  13. Foldable polymers as probes

    DOEpatents

    Li, Alexander D. Q.; Wang, Wei

    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.

  14. Foldable polymers as probes

    DOEpatents

    Li, Alexander D. Q.; Wang, Wei

    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.

  15. Focus: DNA probes

    SciTech Connect

    Not Available

    1986-11-01

    Progress in the development of DNA probes for the identification and quantitation of specific genetic sequences in biological samples is reviewed. Current research efforts in the development of DNA probes for the diagnosis of a wide variety of bacterial, viral, and other infectious diseases, such as herpes simplex and cytomegalovirus, and inherited genetic diseases such as cystic fibrosis and sickle cell anemia are discussed. Progress in development of DNA probe assays for cancer diagnosis, detection of Salmonella food poisoning, tissue typing (detection of histocompatibility antigens), mutagen screening, and animal diseases, among other applications is included.

  16. Jupiter probe heatshield configuration optimization

    NASA Technical Reports Server (NTRS)

    Dirling, R. B., Jr.; Binder, J. D.

    1978-01-01

    The effect of initial probe heatshield shape on the total probe mass loss during Jovian entry is considered. Modification of the aerothermal environment and probe entry trajectory due to changing probe heatshield shape is included in a computerized technique designed for rapid assessment of the effect of probe initial shape on heatshield mass loss. Results obtained indicate the importance of trajectory and heating distribution coupling with probe shape and mass change.

  17. Modeling an optical micromachine probe

    SciTech Connect

    Mittas, A.; Dickey, F.M.; Holswade, S.C.

    1997-08-01

    Silicon micromachines are fabricated using Surface Micro-Machining (SMM) techniques. Silicon micromachines include engines that consist of orthogonally oriented linear comb drive actuators mechanically connected to a rotating gear. These gears are as small a 50-{micro}m in diameter and can be driven at rotation rates exceeding 300,000-rpm. Measuring and analyzing microengine performance is basic to micromachine development and system applications. Optical techniques offer the potential for measuring long term statistical performance data and transient responses needed to optimize designs and manufacturing techniques. The authors describe the modeling of an optical probe developed at Sandia National Laboratories. Experimental data will be compared with output from the model.

  18. Scanning probe microscopy in catalysis.

    PubMed

    Yeung, King Lun; Yao, Nan

    2004-09-01

    This review discusses the recent progress in the application of scanning probe microscopy (SPM) in catalysis. SPM proves to be an invaluable technique for imaging catalytic surfaces and interfaces. Most SPM research is related to the structural and morphological transformation associated with catalyst preparation and use. Real-time SPM observation of surface dynamics including adsorption, diffusion and reaction, provides invaluable insights to the mechanism of catalysis. SPM is also used to shape and manipulate surfaces and surface processes. Fabrication of nanostructured catalysts, direct manipulation of adsorbed atoms and molecules and tip-mediated reactions are some examples of new SPM approach in catalyst research.

  19. Hands-Free Transcranial Color Doppler Probe

    NASA Technical Reports Server (NTRS)

    Chin, Robert; Madala, Srihdar; Sattler, Graham

    2012-01-01

    Current transcranial color Doppler (TCD) transducer probes are bulky and difficult to move in tiny increments to search and optimize TCD signals. This invention provides miniature motions of a TCD transducer probe to optimize TCD signals. The mechanical probe uses a spherical bearing in guiding and locating the tilting crystal face. The lateral motion of the crystal face as it tilts across the full range of motion was achieved by minimizing the distance between the pivot location and the crystal face. The smallest commonly available metal spherical bearing was used with an outer diameter of 12 mm, a 3-mm tall retaining ring, and 5-mm overall height. Small geared motors were used that would provide sufficient power in a very compact package. After confirming the validity of the basic positioning concept, optimization design loops were completed to yield the final design. A parallel motor configuration was used to minimize the amount of space wasted inside the probe case while minimizing the overall case dimensions. The distance from the front edge of the crystal to the edge of the case was also minimized to allow positioning of the probe very close to the ear on the temporal lobe. The mechanical probe is able to achieve a +/-20deg tip and tilt with smooth repeatable action in a very compact package. The enclosed probe is about 7 cm long, 4 cm wide, and 1.8 cm tall. The device is compact, hands-free, and can be adjusted via an innovative touchscreen. Positioning of the probe to the head is performed via conventional transducer gels and pillows. This device is amendable to having advanced software, which could intelligently focus and optimize the TCD signal.

  20. Atmospheric Probe Model: Construction and Wind Tunnel Tests

    NASA Technical Reports Server (NTRS)

    Vogel, Jerald M.

    1998-01-01

    The material contained in this document represents a summary of the results of a low speed wind tunnel test program to determine the performance of an atmospheric probe at low speed. The probe configuration tested consists of a 2/3 scale model constructed from a combination of hard maple wood and aluminum stock. The model design includes approximately 130 surface static pressure taps. Additional hardware incorporated in the baseline model provides a mechanism for simulating external and internal trailing edge split flaps for probe flow control. Test matrix parameters include probe side slip angle, external/internal split flap deflection angle, and trip strip applications. Test output database includes surface pressure distributions on both inner and outer annular wings and probe center line velocity distributions from forward probe to aft probe locations.

  1. Technology for Entry Probes

    NASA Technical Reports Server (NTRS)

    Cutts, James A.; Arnold, James; Venkatapathy, Ethiraj; Kolawa, Elizabeth; Munk, Michelle; Wercinski, Paul; Laub, Bernard

    2005-01-01

    A viewgraph describing technologies for entry probes is presented. The topics include: 1) Entry Phase; 2) Descent Phase; 3) Long duration atmospheric observations; 4) Survivability at high temperatures; and 5) Summary.

  2. Geological assessment probe

    NASA Astrophysics Data System (ADS)

    Collins, E. R.

    1980-04-01

    A probe is described which can be installed in a side hole that extends from a bore hole in the Earth, to assess the permeability of the strata surrounding the borehole. The probe is elongated and has a plurality of seals spaced therealong and sealed to the walls of the side hole to form a plurality of chambers sealed from one another. A tracer fluid injector on the probe can inject a tracer fluid into one of the chambers, while a tracer fluid detector located in another chamber can detect the tracer fluid, to thereby sense the permeability of the strata surrounding the side hole. The probe can include a train of modules, with each module having an inflatable packer which is inflated by the difference between the borehole pressure and the strata pressure.

  3. An Ultrasonographic Periodontal Probe

    NASA Astrophysics Data System (ADS)

    Bertoncini, C. A.; Hinders, M. K.

    2010-02-01

    Periodontal disease, commonly known as gum disease, affects millions of people. The current method of detecting periodontal pocket depth is painful, invasive, and inaccurate. As an alternative to manual probing, an ultrasonographic periodontal probe is being developed to use ultrasound echo waveforms to measure periodontal pocket depth, which is the main measure of periodontal disease. Wavelet transforms and pattern classification techniques are implemented in artificial intelligence routines that can automatically detect pocket depth. The main pattern classification technique used here, called a binary classification algorithm, compares test objects with only two possible pocket depth measurements at a time and relies on dimensionality reduction for the final determination. This method correctly identifies up to 90% of the ultrasonographic probe measurements within the manual probe's tolerance.

  4. Rapid enhancement of low energy (<100 eV) ion flux in response to interplanetary shocks based on two Van Allen Probes case studies: Implications for source regions and heating mechanisms

    SciTech Connect

    Yue, Chao; Li, Wen; Reeves, Geoffrey D.; Nishimura, Yukitoshi; Zong, Qiugang; Ma, Qianli; Bortnik, Jacob; Thorne, Richard M.; Spence, Harlan E.; Kletzing, Craig A.; Wygant, John R.; Nicolls, Michael J.

    2016-07-01

    Interactions between interplanetary (IP) shocks and the Earth's magnetosphere manifest many important space physics phenomena including low-energy ion flux enhancements and particle acceleration. In order to investigate the mechanisms driving shock-induced enhancement of low-energy ion flux, we have examined two IP shock events that occurred when the Van Allen Probes were located near the equator while ionospheric and ground observations were available around the spacecraft footprints. We have found that, associated with the shock arrival, electromagnetic fields intensified, and low-energy ion fluxes, including H+, He+, and O+, were enhanced dramatically in both the parallel and perpendicular directions. During the 2 October 2013 shock event, both parallel and perpendicular flux enhancements lasted more than 20 min with larger fluxes observed in the perpendicular direction. In contrast, for the 15 March 2013 shock event, the low-energy perpendicular ion fluxes increased only in the first 5 min during an impulse of electric field, while the parallel flux enhancement lasted more than 30 min. In addition, ionospheric outflows were observed after shock arrivals. From a simple particle motion calculation, we found that the rapid response of low-energy ions is due to drifts of plasmaspheric population by the enhanced electric field. Furthermore, the fast acceleration in the perpendicular direction cannot solely be explained by E × B drift but betatron acceleration also plays a role. Adiabatic acceleration may also explain the fast response of the enhanced parallel ion fluxes, while ion outflows may contribute to the enhanced parallel fluxes that last longer than the perpendicular fluxes.

  5. Rapid enhancement of low energy (<100 eV) ion flux in response to interplanetary shocks based on two Van Allen Probes case studies: Implications for source regions and heating mechanisms

    DOE PAGES

    Yue, Chao; Li, Wen; Reeves, Geoffrey D.; ...

    2016-07-01

    Interactions between interplanetary (IP) shocks and the Earth's magnetosphere manifest many important space physics phenomena including low-energy ion flux enhancements and particle acceleration. In order to investigate the mechanisms driving shock-induced enhancement of low-energy ion flux, we have examined two IP shock events that occurred when the Van Allen Probes were located near the equator while ionospheric and ground observations were available around the spacecraft footprints. We have found that, associated with the shock arrival, electromagnetic fields intensified, and low-energy ion fluxes, including H+, He+, and O+, were enhanced dramatically in both the parallel and perpendicular directions. During the 2more » October 2013 shock event, both parallel and perpendicular flux enhancements lasted more than 20 min with larger fluxes observed in the perpendicular direction. In contrast, for the 15 March 2013 shock event, the low-energy perpendicular ion fluxes increased only in the first 5 min during an impulse of electric field, while the parallel flux enhancement lasted more than 30 min. In addition, ionospheric outflows were observed after shock arrivals. From a simple particle motion calculation, we found that the rapid response of low-energy ions is due to drifts of plasmaspheric population by the enhanced electric field. Furthermore, the fast acceleration in the perpendicular direction cannot solely be explained by E × B drift but betatron acceleration also plays a role. Adiabatic acceleration may also explain the fast response of the enhanced parallel ion fluxes, while ion outflows may contribute to the enhanced parallel fluxes that last longer than the perpendicular fluxes.« less

  6. Rapid enhancement of low energy (<100 eV) ion flux in response to interplanetary shocks based on two Van Allen Probes case studies: Implications for source regions and heating mechanisms

    SciTech Connect

    Yue, Chao; Li, Wen; Reeves, Geoffrey D.; Nishimura, Yukitoshi; Zong, Qiugang; Ma, Qianli; Bortnik, Jacob; Thorne, Richard M.; Spence, Harlan E.; Kletzing, Craig A.; Wygant, John R.; Nicolls, Michael J.

    2016-07-01

    Interactions between interplanetary (IP) shocks and the Earth's magnetosphere manifest many important space physics phenomena including low-energy ion flux enhancements and particle acceleration. In order to investigate the mechanisms driving shock-induced enhancement of low-energy ion flux, we have examined two IP shock events that occurred when the Van Allen Probes were located near the equator while ionospheric and ground observations were available around the spacecraft footprints. We have found that, associated with the shock arrival, electromagnetic fields intensified, and low-energy ion fluxes, including H+, He+, and O+, were enhanced dramatically in both the parallel and perpendicular directions. During the 2 October 2013 shock event, both parallel and perpendicular flux enhancements lasted more than 20 min with larger fluxes observed in the perpendicular direction. In contrast, for the 15 March 2013 shock event, the low-energy perpendicular ion fluxes increased only in the first 5 min during an impulse of electric field, while the parallel flux enhancement lasted more than 30 min. In addition, ionospheric outflows were observed after shock arrivals. From a simple particle motion calculation, we found that the rapid response of low-energy ions is due to drifts of plasmaspheric population by the enhanced electric field. Furthermore, the fast acceleration in the perpendicular direction cannot solely be explained by E × B drift but betatron acceleration also plays a role. Adiabatic acceleration may also explain the fast response of the enhanced parallel ion fluxes, while ion outflows may contribute to the enhanced parallel fluxes that last longer than the perpendicular fluxes.

  7. Rapid enhancement of low-energy (<100 eV) ion flux in response to interplanetary shocks based on two Van Allen Probes case studies: Implications for source regions and heating mechanisms

    NASA Astrophysics Data System (ADS)

    Yue, Chao; Li, Wen; Nishimura, Yukitoshi; Zong, Qiugang; Ma, Qianli; Bortnik, Jacob; Thorne, Richard M.; Reeves, Geoffrey D.; Spence, Harlan E.; Kletzing, Craig A.; Wygant, John R.; Nicolls, Michael J.

    2016-07-01

    Interactions between interplanetary (IP) shocks and the Earth's magnetosphere manifest many important space physics phenomena including low-energy ion flux enhancements and particle acceleration. In order to investigate the mechanisms driving shock-induced enhancement of low-energy ion flux, we have examined two IP shock events that occurred when the Van Allen Probes were located near the equator while ionospheric and ground observations were available around the spacecraft footprints. We have found that, associated with the shock arrival, electromagnetic fields intensified, and low-energy ion fluxes, including H+, He+, and O+, were enhanced dramatically in both the parallel and perpendicular directions. During the 2 October 2013 shock event, both parallel and perpendicular flux enhancements lasted more than 20 min with larger fluxes observed in the perpendicular direction. In contrast, for the 15 March 2013 shock event, the low-energy perpendicular ion fluxes increased only in the first 5 min during an impulse of electric field, while the parallel flux enhancement lasted more than 30 min. In addition, ionospheric outflows were observed after shock arrivals. From a simple particle motion calculation, we found that the rapid response of low-energy ions is due to drifts of plasmaspheric population by the enhanced electric field. However, the fast acceleration in the perpendicular direction cannot solely be explained by E × B drift but betatron acceleration also plays a role. Adiabatic acceleration may also explain the fast response of the enhanced parallel ion fluxes, while ion outflows may contribute to the enhanced parallel fluxes that last longer than the perpendicular fluxes.

  8. Cryogenic Optoelectronic Probe Station

    DTIC Science & Technology

    2012-08-01

    capability is very important for a few on- going projects under DOD support. Selected Examples of Research Using COPS Example 1: sheet resistance measurement...donor concentration of this thin film contact material, we need to know the sheet resistance . As shown in Fig. 1, four electric probes are landed...voltage of 62.4 mV across probe 2 and 3. Therefore we can determine the sheet resistance by using Eq: = ( ) . This gives the sheet

  9. Outer planets probe testing

    NASA Technical Reports Server (NTRS)

    Smittkamp, J. A.; Grote, M. G.; Edwards, T. M.

    1977-01-01

    An atmospheric entry Probe is being developed by NASA Ames Research Center (ARC) to conduct in situ scientific investigations of the outer planets' atmospheres. A full scale engineering model of an MDAC-E Probe configuration, was fabricated by NASA ARC. Proof-of-concept test validation of the structural and thermal design is being obtained at NASA ARC. The model was successfully tested for shock and dynamic loading and is currently in thermal vacuum testing.

  10. Adjustable Pitot Probe

    NASA Technical Reports Server (NTRS)

    Ashby, George C., Jr.; Robbins, W. Eugene; Horsley, Lewis A.

    1991-01-01

    Probe readily positionable in core of uniform flow in hypersonic wind tunnel. Formed of pair of mating cylindrical housings: transducer housing and pitot-tube housing. Pitot tube supported by adjustable wedge fairing attached to top of pitot-tube housing with semicircular foot. Probe adjusted both radially and circumferentially. In addition, pressure-sensing transducer cooled internally by water or other cooling fluid passing through annulus of cooling system.

  11. Huygens probe on target

    NASA Astrophysics Data System (ADS)

    1995-07-01

    In October 1997, a Titan/Centaur rocket lifting-off from Cape Canaveral will boost the spacecraft into a 6.7 year trajectory to reach Saturn. The trajectory will use two swing-bys of Venus in April 1998 and June 1999, followed by an Earth swing-by in August 1999 and a Jupiter swing-by in December 2000 to boost speed and reach Saturn in July 2004. A few months after going into orbit around Saturn, the Cassini spacecraft will release the Huygens probe for its descent through the atmosphere of Titan, the largest satellite of Saturn. The Huygens probe will measure the abundance of elements and compounds in Titan's atmosphere, the distribution of trace gases and aerosols, winds, temperature, pressure and surface state and its composition. A multi-spectral camera on the probe will provide images of the landscape of Titan. Titan is a unique planetary body in the solar system. It has an atmosphere which is primarily nitrogen. but is also rich in hydrocarbons. Due to the vast distance of the Saturnian system from the Sun, this atmosphere is at a very low temperature, thus greatly slowing down all the chemical processes. A study of this atmosphere will throw light on the development of our own atmosphere and contribute to our understanding of the origins of life on Earth. The Huygens probe is being developed by ESA with Aerospatiale (F) as the industrial prime contractor. Since the start of the programme in April 1990, very good progress has been made in design and hardware development. The entry into the Titan atmosphere will result in a very high surface temperature on the probe, generated as it decelerates due to the friction of the upper atmospheric layers. After the probe has slowed down sufficiently, a system of parachutes ensures a slow descent to the surface of Titan in approximately two and a half hours. The scientific measurements can only begin after the heat shield, which is needed to protect the probe during the high temperature entry phase, has been ejected

  12. Model for resonant plasma probe.

    SciTech Connect

    Warne, Larry Kevin; Johnson, William Arthur; Hebner, Gregory Albert; Jorgenson, Roy E.; Coats, Rebecca Sue

    2007-04-01

    This report constructs simple circuit models for a hairpin shaped resonant plasma probe. Effects of the plasma sheath region surrounding the wires making up the probe are determined. Electromagnetic simulations of the probe are compared to the circuit model results. The perturbing effects of the disc cavity in which the probe operates are also found.

  13. Titan atmospheric probe

    NASA Astrophysics Data System (ADS)

    Swenson, B. L.

    1984-08-01

    Increased scientific interest in the structure and composition of Titan's atmosphere, clouds and surface have led to the study of mission options to the Saturnian system with the main goal of placing a probe into the atmosphere of the satellite. Two probe concepts have been studied by NASA: the first concept, a slightly modified Galileo probe capable of withstanding approximately 50 earth G during atmospheric entry heating and deceleration, would consist of a blunted 53 degree, 136-cm-diameter half-angle cone with a hemispherical afterbody, and a descent module containing scientific instruments and a parachute; the second concept, a system designed to provide in situ atmospheric measurements of Titan's organic haze layer, would consist of a probe using a 165-cm deployable graphite fabric decelerator, a 50-cm-diameter cylindrical descent module containing five instruments and a 2.5 m-diameter parachute and a 50-cm-radius spherical nose cap. Although the modified Galileo probe is feasible, its scientific drawback includes its inability to obtain in situ measurements above approximately 100 km.

  14. Probing the Li Insertion Mechanism of ZnFe2O4 in Li-Ion Batteries: A Combined X-Ray Diffraction, Extended X-Ray Absorption Fine Structure, and Density Functional Theory Study [Probing the Li insertion mechanism of ZnFe2O4 in Li ion batteries: A combined XRD, EXAFS, and DFT study

    DOE PAGES

    Zhang, Yiman; Pelliccione, Christopher J.; Brady, Alexander B.; ...

    2017-04-24

    Here, we report an extensive study on fundamental properties that determine the functional electrochemistry of ZnFe2O4 spinel (theoretical capacity of 1000 mAh/g). For the first time, the reduction mechanism is followed through a combination of in situ X-ray diffraction data, synchrotron based powder diffraction, and ex-situ extended X-ray absorption fine structure allowing complete visualization of reduction products irrespective of their crystallinity. The first 0.5 electron equivalents (ee) do not significantly change the starting crystal structure. Subsequent lithiation results in migration of Zn2+ ions from 8a tetrahedral sites into vacant 16c sites. Density functional theory shows that Li+ ions insert intomore » 16c site initially and then 8a site with further lithiation. Fe metal is formed over the next eight ee of reduction with no evidence of concurrent Zn2+ reduction to Zn metal. Despite the expected formation of LiZn alloy from the electron count, we find no evidence for this phase under the tested conditions. Additionally, upon oxidation to 3 V, we observe an FeO phase with no evidence of Fe2O3. Electrochemistry data show higher electron equivalent transfer than can be accounted for solely based on ZnFe2O4 reduction indicating excess capacity ascribed to carbon reduction or surface electrolyte interphase formation.« less

  15. Dynamic scanned-probe lateral-force determination

    NASA Astrophysics Data System (ADS)

    Wetsel, G. C., Jr.; Drummond Roby, M. A.

    1995-10-01

    A continuum-mechanical model of the dynamics of a scanned probe is described that includes intrinsic losses as well as the effect of a lateral force on the end of the probe. A method for the determination of calibrated lateral force is experimentally evaluated and the sensitivity of the method is analyzed.

  16. 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

  17. Pressure measuring probe

    NASA Technical Reports Server (NTRS)

    Ashby, George C., Jr. (Inventor)

    1988-01-01

    The invention is a probe for measuring changes in pressure in a high velocity fluid stream over and adjacent to the surface of an object. The probe is formed of an exterior housing having a closed pressure chamber in which a piezoelectric pressure transducer is mounted. An open connector tube having a probe tip passes a portion of the fluid stream into the closed pressure chamber; any change of pressure within, which requires a settling-time to appear in the closed pressure chamber, is inversely proportional to the cross-sectional area of the connector tube. A cooling chamber formed around the pressure chamber is connected to a source of cooling fluid by means of inlet and outlet tubes.

  18. Multispectral imaging probe

    DOEpatents

    Sandison, D.R.; Platzbecker, M.R.; Descour, M.R.; Armour, D.L.; Craig, M.J.; Richards-Kortum, R.

    1999-07-27

    A multispectral imaging probe delivers a range of wavelengths of excitation light to a target and collects a range of expressed light wavelengths. The multispectral imaging probe is adapted for mobile use and use in confined spaces, and is sealed against the effects of hostile environments. The multispectral imaging probe comprises a housing that defines a sealed volume that is substantially sealed from the surrounding environment. A beam splitting device mounts within the sealed volume. Excitation light is directed to the beam splitting device, which directs the excitation light to a target. Expressed light from the target reaches the beam splitting device along a path coaxial with the path traveled by the excitation light from the beam splitting device to the target. The beam splitting device directs expressed light to a collection subsystem for delivery to a detector. 8 figs.

  19. Multispectral imaging probe

    SciTech Connect

    Sandison, D.R.; Platzbecker, M.R.; Descour, M.R.; Armour, D.L.; Craig, M.J.; Richards-Kortum, R.

    1999-07-27

    A multispectral imaging probe delivers a range of wavelengths of excitation light to a target and collects a range of expressed light wavelengths. The multispectral imaging probe is adapted for mobile use and use in confined spaces, and is sealed against the effects of hostile environments. The multispectral imaging probe comprises a housing that defines a sealed volume that is substantially sealed from the surrounding environment. A beam splitting device mounts within the sealed volume. Excitation light is directed to the beam splitting device, which directs the excitation light to a target. Expressed light from the target reaches the beam splitting device along a path coaxial with the path traveled by the excitation light from the beam splitting device to the target. The beam splitting device directs expressed light to a collection subsystem for delivery to a detector. 8 figs.

  20. Multispectral imaging probe

    SciTech Connect

    Sandison, David R.; Platzbecker, Mark R.; Descour, Michael R.; Armour, David L.; Craig, Marcus J.; Richards-Kortum, Rebecca

    1999-01-01

    A multispectral imaging probe delivers a range of wavelengths of excitation light to a target and collects a range of expressed light wavelengths. The multispectral imaging probe is adapted for mobile use and use in confined spaces, and is sealed against the effects of hostile environments. The multispectral imaging probe comprises a housing that defines a sealed volume that is substantially sealed from the surrounding environment. A beam splitting device mounts within the sealed volume. Excitation light is directed to the beam splitting device, which directs the excitation light to a target. Expressed light from the target reaches the beam splitting device along a path coaxial with the path traveled by the excitation light from the beam splitting device to the target. The beam splitting device directs expressed light to a collection subsystem for delivery to a detector.

  1. Recent advances in thiol and sulfide reactive probes.

    PubMed

    Wang, Ke; Peng, Hanjing; Wang, Binghe

    2014-06-01

    Because of the biological relevance of thiols and sulfides such as cysteine, homocysteine, glutathione and hydrogen sulfide, their detection has attracted a great deal of research interest. Fluorescent probes are emerging as a new strategy for thiol and hydrogen sulfide analysis due to their high sensitivity, low cost, and ability to detect and image thiols in biological samples. In this short review, we have summarized recent advances in the development of thiol and hydrogen sulfide reactive fluorescent probes. These probes are compared and contrasted with regard to their designing strategies, mechanisms, photophysical properties, and/or reaction kinetics. Biological applications of these probes are also discussed.

  2. Test probe for surface mounted leadless chip carrier

    DOEpatents

    Meyer, K.L.; Topolewski, J.

    1987-10-02

    A test probe for a surface mounted leadless chip carrier is disclosed. The probe includes specially designed connector pins which allow size reductions in the probe. A thermoplastic housing provides spring action to ensure good mechanical and electrical contact between the pins and the contact strips of a leadless chip carrier. Other features include flexible wires molded into the housing and two different types of pins alternately placed in the housing. These features allow fabrication of a smaller and simpler test probe. 1 fig.

  3. Imaging Probe Development Center: a National Institutes of Health core synthesis resource for imaging probes.

    PubMed

    Shi, Zhen-Dan; Wu, Haitao; Ruddy, Brian; Griffiths, Gary L

    2007-01-01

    The Imaging Probe Development Center (IPDC) has been set up under the auspices of the National Institutes of Health (NIH) Roadmap as part of the molecular libraries and imaging initiatives. It comprises a core synthesis facility dedicated to the preparation of imaging probes, initially for intramural NIH scientists, and later, for the extramural scientific community. The facility opened fully in late 2006, in refurbished laboratories in Rockville, Maryland, and a staff of around a dozen was recruited into place by early 2007; the director was hired in late 2005. The IPDC provides a mechanism for the production of sensitive probes for use by imaging scientists who cannot obtain such probes commercially. The probes to be made will encompass all major imaging modalities including radionuclide, magnetic resonance, and optical. The operation of the IPDC is outlined, together with the results of interim achievements while the IPDC maintained a small temporary laboratory in Bethesda. As of December 2006, a total of eleven probe compositions had been made, and several of these are described with particular mention of those probes intended for use in optical applications.

  4. Modeling Atom Probe Tomography: A review.

    PubMed

    Vurpillot, F; Oberdorfer, C

    2015-12-01

    Improving both the precision and the accuracy of Atom Probe Tomography reconstruction requires a correct understanding of the imaging process. In this aim, numerical modeling approaches have been developed for 15 years. The injected ingredients of these modeling tools are related to the basic physic of the field evaporation mechanism. The interplay between the sample nature and structure of the analyzed sample and the reconstructed image artefacts have pushed to gradually improve and make the model more and more sophisticated. This paper reviews the evolution of the modeling approach in Atom Probe Tomography and presents some future potential directions in order to improve the method.

  5. DAPI: a DNA-specific fluorescent probe.

    PubMed

    Kapuscinski, J

    1995-09-01

    DAPI (4',6-diamidino-2-phenylindole) is a DNA-specific probe which forms a fluorescent complex by attaching in the minor grove of A-T rich sequences of DNA. It also forms nonfluorescent intercalative complexes with double-stranded nucleic acids. The physicochemical properties of the dye and its complexes with nucleic acids and history of the development of this dye as a biological stain are described. The application of DAPI as a DNA-specific probe for flow cytometry, chromosome staining, DNA visualization and quantitation in histochemistry and biochemistry is reviewed. The mechanisms of DAPI-nucleic acid complex formation including minor groove binding, intercalation and condensation are discussed.

  6. Probing the Solar System

    ERIC Educational Resources Information Center

    Wilkinson, John

    2013-01-01

    Humans have always had the vision to one day live on other planets. This vision existed even before the first person was put into orbit. Since the early space missions of putting humans into orbit around Earth, many advances have been made in space technology. We have now sent many space probes deep into the Solar system to explore the planets and…

  7. Endocavity Ultrasound Probe Manipulators.

    PubMed

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

    2013-06-01

    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.

  8. The Phoenix Pluto Probe

    NASA Technical Reports Server (NTRS)

    Gunning, George R.; Spapperi, Jeff; Wilkinson, Jeffrey P.; Eldred, Jim; Labij, Dennis; Strinni, Meredith

    1990-01-01

    A design proposal for an unmanned probe to Pluto is presented. The topics covered include: (1) scientific instrumentation; (2) mission management, planning, and costing; (3) power and propulsion system; (4) structural subsystem; (5) command, control, and communication; and (6) attitude and articulation control.

  9. Laboratory plasma probe studies

    NASA Technical Reports Server (NTRS)

    Heikkila, W. J.

    1975-01-01

    Diagnostic experiments performed in a collisionless plasma using CO2 as the working gas are described. In particular, simultaneous measurements that have been performed by means of Langmuir- and RF-probes are presented. A resonance occurring above the parallel resonance in the frequency characteristic of a two electrode system is interpreted as being due to the resonant excitation of electroacoustic waves.

  10. Ultrasonic search wheel probe

    DOEpatents

    Mikesell, Charles R.

    1978-01-01

    A device is provided for reducing internal reflections from the tire of an ultrasonic search wheel probe or from within the material being examined. The device includes a liner with an anechoic chamber within which is an ultrasonic transducer. The liner is positioned within the wheel and includes an aperture through which the ultrasonic sound from the transducer is directed.

  11. Cervical Neoplasia Probe Control

    SciTech Connect

    Vargo, Timothy D.

    1997-01-24

    This software, which consists of a main executive and several subroutines, performs control of the optics, image acquisition, and Digital Signal Processing (DSP) of this image, of an optical based medical instrument that performs fluoresence detection of precancerous lesions (neoplasia) of the human cervix. The hardware portion of this medical instrument is known by the same name Cervical Neoplasia Probe (CNP)

  12. 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

  13. Experimenting with Temperature Probes.

    ERIC Educational Resources Information Center

    Roth, Wolff-Michael

    1989-01-01

    Presented are four activities which are designed to familiarize children with the multiple uses of computers and help them learn about heat and temperature using temperature probes. Included are the tempering effect of water, heat capacity, caloric content of foods, and weather. Hardware and software are discussed. (CW)

  14. Probing the Solar System

    ERIC Educational Resources Information Center

    Wilkinson, John

    2013-01-01

    Humans have always had the vision to one day live on other planets. This vision existed even before the first person was put into orbit. Since the early space missions of putting humans into orbit around Earth, many advances have been made in space technology. We have now sent many space probes deep into the Solar system to explore the planets and…

  15. Advanced oxidation scanning probe lithography.

    PubMed

    Ryu, Yu K; Garcia, Ricardo

    2017-04-07

    Force microscopy enables a variety of approaches to manipulate and/or modify surfaces. Few of those methods have evolved into advanced probe-based lithographies. Oxidation scanning probe lithography (o-SPL) is the only lithography that enables the direct and resist-less nanoscale patterning of a large variety of materials, from metals to semiconductors; from self-assembled monolayers to biomolecules. Oxidation SPL has also been applied to develop sophisticated electronic and nanomechanical devices such as quantum dots, quantum point contacts, nanowire transistors or mechanical resonators. Here, we review the principles, instrumentation aspects and some device applications of o-SPL. Our focus is to provide a balanced view of the method that introduces the key steps in its evolution, provides some detailed explanations on its fundamentals and presents current trends and applications. To illustrate the capabilities and potential of o-SPL as an alternative lithography we have favored the most recent and updated contributions in nanopatterning and device fabrication.

  16. Advanced oxidation scanning probe lithography

    NASA Astrophysics Data System (ADS)

    Ryu, Yu K.; Garcia, Ricardo

    2017-04-01

    Force microscopy enables a variety of approaches to manipulate and/or modify surfaces. Few of those methods have evolved into advanced probe-based lithographies. Oxidation scanning probe lithography (o-SPL) is the only lithography that enables the direct and resist-less nanoscale patterning of a large variety of materials, from metals to semiconductors; from self-assembled monolayers to biomolecules. Oxidation SPL has also been applied to develop sophisticated electronic and nanomechanical devices such as quantum dots, quantum point contacts, nanowire transistors or mechanical resonators. Here, we review the principles, instrumentation aspects and some device applications of o-SPL. Our focus is to provide a balanced view of the method that introduces the key steps in its evolution, provides some detailed explanations on its fundamentals and presents current trends and applications. To illustrate the capabilities and potential of o-SPL as an alternative lithography we have favored the most recent and updated contributions in nanopatterning and device fabrication.

  17. Mechanosensitive membrane probes.

    PubMed

    Dal Molin, Marta; Verolet, Quentin; Soleimanpour, Saeideh; Matile, Stefan

    2015-04-13

    This article assembles pertinent insights behind the concept of planarizable push-pull probes. As a response to the planarization of their polarized ground state, a red shift of their excitation maximum is expected to report on either the disorder, the tension, or the potential of biomembranes. The combination of chromophore planarization and polarization contributes to various, usually more complex processes in nature. Examples include the color change of crabs or lobsters during cooking or the chemistry of vision, particularly color vision. The summary of lessons from nature is followed by an overview of mechanosensitive organic materials. Although often twisted and sometimes also polarized, their change of color under pressure usually originates from changes in their crystal packing. Intriguing exceptions include the planarization of several elegantly twisted phenylethynyl oligomers and polymers. Also mechanosensitive probes in plastics usually respond to stretching by disassembly. True ground-state planarization in response to molecular recognition is best exemplified with the binding of thoughtfully twisted cationic polythiophenes to single- and double-stranded oligonucleotides. Molecular rotors, en vogue as viscosity sensors in cells, operate by deplanarization of the first excited state. Pertinent recent examples are described, focusing on λ-ratiometry and intracellular targeting. Complementary to planarization of the ground state with twisted push-pull probes, molecular rotors report on environmental changes with quenching or shifts in emission rather than absorption. The labeling of mechanosensitive channels is discussed as a bioengineering approach to bypass the challenge to create molecular mechanosensitivity and use biological systems instead to sense membrane tension. With planarizable push-pull probes, this challenge is met not with twistome screening, but with "fluorescent flippers," a new concept to insert large and bright monomers into oligomeric

  18. Remote adjustable focus Raman spectroscopy probe

    DOEpatents

    Schmucker, John E.; Blasi, Raymond J.; Archer, William B.

    1999-01-01

    A remote adjustable focus Raman spectroscopy probe allows for analyzing Raman scattered light from a point of interest external probe. An environmental barrier including at least one window separates the probe from the point of interest. An optical tube is disposed adjacent to the environmental barrier and includes a long working length compound lens objective next to the window. A beam splitter and a mirror are at the other end. A mechanical means is used to translated the prove body in the X, Y, and Z directions resulting in a variable focus optical apparatus. Laser light is reflected by the beam splitter and directed toward the compound lens objective, then through the window and focused on the point of interest. Raman scattered light is then collected by the compound lens objective and directed through the beam splitter to a mirror. A device for analyzing the light, such as a monochrometer, is coupled to the mirror.

  19. Hands-Free Transcranial Color Doppler Probe

    NASA Technical Reports Server (NTRS)

    Chin, Robert; Madala, Srihdar; Sattler, Graham

    2012-01-01

    Current transcranial color Doppler (TCD) transducer probes are bulky and difficult to move in tiny increments to search and optimize TCD signals. This invention provides miniature motions of a TCD transducer probe to optimize TCD signals. The mechanical probe uses spherical bearing in guiding and locating the tilting crystal face. The lateral motion of the crystal face as it tilts across the full range of motion was achieved by minimizing the distance between the pivot location and the crystal face. The smallest commonly available metal spherical bearing was used with an outer diameter of 12 mm, a 3-mm tall retaining ring, and 5-mm overall height. Small geared motors were used that would provide sufficient power in a very compact package. After confirming the validity of the basic positioning concept, optimization design loops were completed to yield the final design.

  20. 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.

  1. Computer simulations of local anesthetic mechanisms: Quantum chemical investigation of procaine

    SciTech Connect

    Smith, Jeremy C; Bondar, A.N.; Suhai, Sandor; Frangopol, P.T.

    2007-02-01

    A description at the atomic level of detail of the interaction between local anesthetics, lipid membranes and membrane proteins, is essential for understanding the mechanism of local anesthesia. The importance of performing computer simulations to decipher the mechanism of local anesthesia is discussed here in the context of the current status of understanding of the local anesthetics action. As a first step towards accurate simulations of the interaction between local anesthetics, proteins, lipid and water molecules, here we use quantum mechanical methods to assess the charge distribution and structural properties of procaine in the presence and in the absence of water molecules. The calculations indicate that, in the absence of hydrogen-bonding water molecules, protonated procaine strongly prefers a compact structure enabled by intramolecular hydrogen bonding. In the presence of water molecules the torsional energy pro?le of procaine is modified, and hydrogen bonding to water molecules is favored relative to intra-molecular hydrogen bonding.

  2. Gravity Probe B spacecraft description

    NASA Astrophysics Data System (ADS)

    Bennett, Norman R.; Burns, Kevin; Katz, Russell; Kirschenbaum, Jon; Mason, Gary; Shehata, Shawky

    2015-11-01

    The Gravity Probe B spacecraft, developed, integrated, and tested by Lockheed Missiles & Space Company and later Lockheed Martin Corporation, consisted of structures, mechanisms, command and data handling, attitude and translation control, electrical power, thermal control, flight software, and communications. When integrated with the payload elements, the integrated system became the space vehicle. Key requirements shaping the design of the spacecraft were: (1) the tight mission timeline (17 months, 9 days of on-orbit operation), (2) precise attitude and translational control, (3) thermal protection of science hardware, (4) minimizing aerodynamic, magnetic, and eddy current effects, and (5) the need to provide a robust, low risk spacecraft. The spacecraft met all mission requirements, as demonstrated by dewar lifetime meeting specification, positive power and thermal margins, precision attitude control and drag-free performance, reliable communications, and the collection of more than 97% of the available science data.

  3. Enabling interstellar probe

    NASA Astrophysics Data System (ADS)

    McNutt, Ralph L.; Wimmer-Schweingruber, Robert F.; International Interstellar Probe Team

    2011-04-01

    The scientific community has advocated a scientific probe to the interstellar medium for over 30 years. While the Voyager spacecraft have passed through the termination shock of the solar wind, they have limited lifetimes as their radioisotope power supplies decay. It remains unclear whether they can reach the heliopause, the boundary between shocked solar wind and interstellar plasmas, and, in any case, they will not reach the undisturbed interstellar medium. As with most exploratory space missions, their ongoing observations continue to raise even more questions about the nature of the interaction of our heliosphere and the interstellar medium. Scientific questions including: What is the nature of the nearby interstellar medium? How do the Sun and galaxy affect the dynamics of the heliosphere? What is the structure of the heliosphere? How did matter in the solar system and interstellar medium originate and evolve? can only be answered by an "interstellar precursor" probe. Such a mission is required to make in situ measurements in the interaction region and interstellar medium itself at distances far from the Sun, but in a finite mission lifetime. By launching a probe toward the incoming "interstellar wind," whose direction is known, the distance to be traveled can be minimized but is still large. The current consensus is that a scientifically compelling mission must function to at least a distance of 200 astronomical units (AU) from the Sun and return a reasonable stream of data during the voyage. The central problem is that of providing a means of propulsion to accelerate a probe from the Solar System. Even with a low-mass payload and spacecraft, achieving the high speeds needed, even with gravity assists, have remained problematic. Voyager 1, the fastest object ever to leave the system is now traveling ˜3.6 AU/yr, and a credible probe must reach at least 2-3 times this speed. The use of an Ares V is an approach for enabling a fast interstellar precursor

  4. Calibration Fixture For Anemometer Probes

    NASA Technical Reports Server (NTRS)

    Lewis, Charles R.; Nagel, Robert T.

    1993-01-01

    Fixture facilitates calibration of three-dimensional sideflow thermal anemometer probes. With fixture, probe oriented at number of angles throughout its design range. Readings calibrated as function of orientation in airflow. Calibration repeatable and verifiable.

  5. Calibration Fixture For Anemometer Probes

    NASA Technical Reports Server (NTRS)

    Lewis, Charles R.; Nagel, Robert T.

    1993-01-01

    Fixture facilitates calibration of three-dimensional sideflow thermal anemometer probes. With fixture, probe oriented at number of angles throughout its design range. Readings calibrated as function of orientation in airflow. Calibration repeatable and verifiable.

  6. Experiments with probe masses

    PubMed Central

    Braginsky, V. B.

    2007-01-01

    It is reasonable to regard the experiments performed by C. Coulomb and H. Cavendish in the end of the 18th century as the beginning of laboratory experimental physics. These outstanding scientists have measured forces (accelerations) produced by electric charges and by gravitational “charges” on probe masses that were attached to torque balance. Among the variety of different research programs and projects existing today, experiments with probe masses are still playing an important role. In this short review, the achieved and planned sensitivities of very challenging LIGO (Laser Interferometer Gravitational wave Observatory) and LISA (Laser Interferometer Space Antennae) projects are described, and a list of nonsolved problems is discussed as well. The role of quantum fluctuations in high precision measurements is also outlined. Apart from these main topics, the limitations of sensitivity caused by cosmic rays and the prospects of clock frequency stability are presented. PMID:17296944

  7. Temperature averaging thermal probe

    NASA Technical Reports Server (NTRS)

    Kalil, L. F.; Reinhardt, V. (Inventor)

    1985-01-01

    A thermal probe to average temperature fluctuations over a prolonged period was formed with a temperature sensor embedded inside a solid object of a thermally conducting material. The solid object is held in a position equidistantly spaced apart from the interior surfaces of a closed housing by a mount made of a thermally insulating material. The housing is sealed to trap a vacuum or mass of air inside and thereby prevent transfer of heat directly between the environment outside of the housing and the solid object. Electrical leads couple the temperature sensor with a connector on the outside of the housing. Other solid objects of different sizes and materials may be substituted for the cylindrically-shaped object to vary the time constant of the probe.

  8. Heavy ion beam probing

    SciTech Connect

    Hickok, R L

    1980-07-01

    This report consists of the notes distributed to the participants at the IEEE Mini-Course on Modern Plasma Diagnostics that was held in Madison, Wisconsin in May 1980. It presents an overview of Heavy Ion Beam Probing that briefly describes the principles and discuss the types of measurements that can be made. The problems associated with implementing beam probes are noted, possible variations are described, estimated costs of present day systems, and the scaling requirements for large plasma devices are presented. The final chapter illustrates typical results that have been obtained on a variety of plasma devices. No detailed calculations are included in the report, but a list of references that will provide more detailed information is included.

  9. Experiments with probe masses.

    PubMed

    Braginsky, V B

    2007-03-06

    It is reasonable to regard the experiments performed by C. Coulomb and H. Cavendish in the end of the 18th century as the beginning of laboratory experimental physics. These outstanding scientists have measured forces (accelerations) produced by electric charges and by gravitational "charges" on probe masses that were attached to torque balance. Among the variety of different research programs and projects existing today, experiments with probe masses are still playing an important role. In this short review, the achieved and planned sensitivities of very challenging LIGO (Laser Interferometer Gravitational wave Observatory) and LISA (Laser Interferometer Space Antennae) projects are described, and a list of nonsolved problems is discussed as well. The role of quantum fluctuations in high precision measurements is also outlined. Apart from these main topics, the limitations of sensitivity caused by cosmic rays and the prospects of clock frequency stability are presented.

  10. Gravity Probe B

    NASA Image and Video Library

    2003-07-12

    The Gravity Probe B experiment is lifted from its transporter in the spacecraft processing facility on North Vandenberg Air Force Base. Gravity Probe B will launch a payload of four gyroscopes into low-Earth polar orbit to test two extraordinary predictions of Albert Einstein’s general theory of relativity: the geodetic effect (how space and time are warped by the presence of the Earth) and frame dragging (how Earth’s rotation drags space and time around with it). Once in orbit, for 18 months each gyroscope’s spin axis will be monitored as it travels through local spacetime, observing and measuring these effects. The experiment was developed by Stanford University, Lockheed Martin and NASA’s Marshall Space Flight Center.

  11. Gravity Probe B

    NASA Image and Video Library

    2003-07-12

    The Gravity Probe B experiment is lowered onto an assembly and test stand in the spacecraft processing facility on North Vandenberg Air Force Base. Gravity Probe B will launch a payload of four gyroscopes into low-Earth polar orbit to test two extraordinary predictions of Albert Einstein’s general theory of relativity: the geodetic effect (how space and time are warped by the presence of the Earth) and frame dragging (how Earth’s rotation drags space and time around with it). Once in orbit, for 18 months each gyroscope’s spin axis will be monitored as it travels through local spacetime, observing and measuring these effects. The experiment was developed by Stanford University, Lockheed Martin and NASA’s Marshall Space Flight Center.

  12. Gravity Probe B

    NASA Image and Video Library

    2003-07-18

    In the spacecraft processing facility on North Vandenberg Air Force Base, workers conduct battery charge/discharge cycles as part of the battery conditioning process on Gravity Probe B. The Gravity Probe B will launch a payload of four gyroscopes into low-Earth polar orbit to test two extraordinary predictions of Albert Einstein’s general theory of relativity: the geodetic effect (how space and time are warped by the presence of the Earth) and frame dragging (how Earth’s rotation drags space and time around with it). Once in orbit, for 18 months each gyroscope’s spin axis will be monitored as it travels through local spacetime, observing and measuring these effects. The experiment was developed by Stanford University, Lockheed Martin and NASA’s Marshall Space Flight Center.

  13. Gravity Probe B

    NASA Image and Video Library

    2003-07-12

    The Gravity Probe B experiment enters the spacecraft processing facility on North Vandenberg Air Force Base. Gravity Probe B will launch a payload of four gyroscopes into low-Earth polar orbit to test two extraordinary predictions of Albert Einstein’s general theory of relativity: the geodetic effect (how space and time are warped by the presence of the Earth) and frame dragging (how Earth’s rotation drags space and time around with it). Once in orbit, for 18 months each gyroscope’s spin axis will be monitored as it travels through local spacetime, observing and measuring these effects. The experiment was developed by Stanford University, Lockheed Martin and NASA’s Marshall Space Flight Center.

  14. Gravity Probe B

    NASA Image and Video Library

    2003-07-12

    A transporter carrying the Gravity Probe B experiment backs into the spacecraft processing facility on North Vandenberg Air Force Base. Gravity Probe B will launch a payload of four gyroscopes into low-Earth polar orbit to test two extraordinary predictions of Albert Einstein’s general theory of relativity: the geodetic effect (how space and time are warped by the presence of the Earth) and frame dragging (how Earth’s rotation drags space and time around with it). Once in orbit, for 18 months each gyroscope’s spin axis will be monitored as it travels through local spacetime, observing and measuring these effects. The experiment was developed by Stanford University, Lockheed Martin and NASA’s Marshall Space Flight Center.

  15. Gravity Probe B

    NASA Image and Video Library

    2003-07-12

    Enclosed in a canister, the Gravity Probe B (GP-B) spacecraft arrives on Vandenberg Air Force Base, headed for the spacecraft processing facility. Gravity Probe B will launch a payload of four gyroscopes into low-Earth polar orbit to test two extraordinary predictions of Albert Einstein’s general theory of relativity: the geodetic effect (how space and time are warped by the presence of the Earth) and frame dragging (how Earth’s rotation drags space and time around with it). Once in orbit, for 18 months each gyroscope’s spin axis will be monitored as it travels through local spacetime, observing and measuring these effects. The experiment was developed by Stanford University, Lockheed Martin and NASA’s Marshall Space Flight Center.

  16. Gravity Probe B

    NASA Image and Video Library

    2003-07-12

    The Gravity Probe B experiment rests on an assembly and test stand in the spacecraft processing facility on North Vandenberg Air Force Base. Gravity Probe B will launch a payload of four gyroscopes into low-Earth polar orbit to test two extraordinary predictions of Albert Einstein’s general theory of relativity: the geodetic effect (how space and time are warped by the presence of the Earth) and frame dragging (how Earth’s rotation drags space and time around with it). Once in orbit, for 18 months each gyroscope’s spin axis will be monitored as it travels through local spacetime, observing and measuring these effects. The experiment was developed by Stanford University, Lockheed Martin and NASA’s Marshall Space Flight Center.

  17. Gravity Probe B

    NASA Image and Video Library

    2003-07-12

    At Vandenberg AFB, the canister enclosing the Gravity Probe B (GP-B) spacecraft is removed from the transporter. Gravity Probe B will launch a payload of four gyroscopes into low-Earth polar orbit to test two extraordinary predictions of Albert Einstein’s general theory of relativity: the geodetic effect (how space and time are warped by the presence of the Earth) and frame dragging (how Earth’s rotation drags space and time around with it). Once in orbit, for 18 months each gyroscope’s spin axis will be monitored as it travels through local spacetime, observing and measuring these effects. The experiment was developed by Stanford University, Lockheed Martin and NASA’s Marshall Space Flight Center.

  18. Gravity Probe B

    NASA Image and Video Library

    2003-07-18

    In the spacecraft processing facility on North Vandenberg Air Force Base, battery charge/discharge cycles are underway as part of the battery conditioning process on Gravity Probe B. The Gravity Probe B will launch a payload of four gyroscopes into low-Earth polar orbit to test two extraordinary predictions of Albert Einstein’s general theory of relativity: the geodetic effect (how space and time are warped by the presence of the Earth) and frame dragging (how Earth’s rotation drags space and time around with it). Once in orbit, for 18 months each gyroscope’s spin axis will be monitored as it travels through local spacetime, observing and measuring these effects. The experiment was developed by Stanford University, Lockheed Martin and NASA’s Marshall Space Flight Center.

  19. Subsurface Ice Probe

    NASA Technical Reports Server (NTRS)

    Hecht, Michael; Carsey, Frank

    2005-01-01

    The subsurface ice probe (SIPR) is a proposed apparatus that would bore into ice to depths as great as hundreds of meters by melting the ice and pumping the samples of meltwater to the surface. Originally intended for use in exploration of subsurface ice on Mars and other remote planets, the SIPR could also be used on Earth as an alternative to coring, drilling, and melting apparatuses heretofore used to sample Arctic and Antarctic ice sheets. The SIPR would include an assembly of instrumentation and electronic control equipment at the surface, connected via a tether to a compact assembly of boring, sampling, and sensor equipment in the borehole (see figure). Placing as much equipment as possible at the surface would help to attain primary objectives of minimizing power consumption, sampling with high depth resolution, and unobstructed imaging of the borehole wall. To the degree to which these requirements would be satisfied, the SIPR would offer advantages over the aforementioned ice-probing systems.

  20. Temperature averaging thermal probe

    NASA Astrophysics Data System (ADS)

    Kalil, L. F.; Reinhardt, V.

    1985-12-01

    A thermal probe to average temperature fluctuations over a prolonged period was formed with a temperature sen