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Sample records for probing intra-molecular mechanics

  1. 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

  2. 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

  3. Deployment mechanisms on Pioneer Venus probes

    NASA Technical Reports Server (NTRS)

    Townsend, W. L.; Miyakawa, R. H.; Meadows, F. R.

    1979-01-01

    Deployment mechanisms were developed to position scientific instruments during probe descent into the Venus atmosphere. Each mechanism includes a provision for pyrotechnic release of the enclosure door, negator springs for positive deployment torque, and an active damper using a shunted dc motor. The deployment time requirement is under 2 seconds, and the deployment shock must be less than 100 g's. The mechanism is completely dry lubricated and constructed mainly of titanium for high strength and high temperature stability. The mechanism was qualified for descent decelerations up to 565 g's and for instrument alignment up to 940 F. The mechanism requirements, the hardware design details, the analytical simulations, and the qualification testing are described.

  4. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

    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.

  6. Mechanisms and Molecular Probes of Sirtuins

    PubMed Central

    Smith, Brian C.; Hallows, William C.; Denu, John M.

    2008-01-01

    Summary Sirtuins are critical regulators of many cellular processes including insulin secretion, the cell cycle, and apoptosis. Sirtuins are associated with a variety of age-associated diseases such as type II diabetes, obesity, and Alzheimer’s disease. A thorough understanding of sirtuin chemical mechanisms will aid toward developing novel therapeutics that regulate metabolic disorders and combat associated diseases. In this review, we discuss the unique deacetylase mechanism of sirtuins and how this information might be employed to develop inhibitors and other molecular probes for therapeutic and basic research applications. We also cover physiological regulation of sirtuin activity and how these modes of regulation may be exploited to manipulate sirtuin activity in live cells. Development of molecular probes and drugs that specifically target sirtuins will further understanding of sirtuin biology and potentially afford new treatments of several human diseases. PMID:18940661

  7. 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.

  8. Intra-molecular enantiomerism in R-(+)-Limonene as evidenced by the differential bond polarizabilities

    NASA Astrophysics Data System (ADS)

    Shen, Hongxia; Wu, Guozhen; Wang, Peijie

    2014-07-01

    We propose an algorithm to obtain the differential bond polarizabilities from the Raman and Raman optical activity (ROA) spectral intensities. The signs of the differential bond polarizabilities of R-Limonene demonstrate that there is intra-molecular enantiomerism in its six membered ring structure. That is, the signs of the differential bond polarizabilities around the six membered ring are inversed under an intra-molecular mirror reflection. This is similar to what happens in the right and left handed chiral isomers under a mirror conversion.

  9. Elastic mechanism design of a CMM contact probe

    NASA Astrophysics Data System (ADS)

    Li, Rui-Jun; Fan, Kuang-Chao; Zhou, Hao; Wang, Na; Huang, Qiang-xian

    2013-10-01

    The measurement of miniature components with a micro- or nano-coordinate measuring machine requires a high precision contact scanning probe. The elastic mechanism of low stiffness is a major component of the contact scanning probe. A new elastic mechanism is analyzed by the theory of elasticity and finite element analysis in this paper. It is to realize the probe's mechanical behavior and stiffness when designing an elastic mechanism for a contact scanning probe. The contact scanning probe is composed of a tungsten stylus with a ruby ball tip, a mechanism of floating plate suspended by four V-shaped leaf springs, and a 3D optical sensor. The leaf spring experiences elastic deformation when a contact force is applied. Uniform stiffness model is analyzed. Simulation and experimental results verify the correctness of the analysis.

  10. 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.

  11. 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.

  12. 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.

  13. Dynamics of the chemical bond: inter- and intra-molecular hydrogen bond.

    PubMed

    Arunan, Elangannan; Mani, Devendra

    2015-01-01

    In this discussion, we show that a static definition of a 'bond' is not viable by looking at a few examples for both inter- and intra-molecular hydrogen bonding. This follows from our earlier work (Goswami and Arunan, Phys. Chem. Chem. Phys. 2009, 11, 8974) which showed a practical way to differentiate 'hydrogen bonding' from 'van der Waals interaction'. We report results from ab initio and atoms in molecules theoretical calculations for a series of Rg∙∙∙HX complexes (Rg=He/Ne/Ar and X=F/Cl/Br) and ethane-1,2-diol. Results for the Rg∙∙∙HX/DX complexes show that Rg∙∙∙DX could have a 'deuterium bond' even when Rg∙∙∙HX is not 'hydrogen bonded', according to the practical criterion given by Goswami and Arunan. Results for ethane-1,2-diol show that an 'intra-molecular hydrogen bond' can appear during a normal mode vibration which is dominated by the OO stretching, though a 'bond' is not found in the equilibrium structure. This dynamical 'bond' formation may nevertheless be important in ensuring the continuity of electron density across a molecule. In the former case, a vibration 'breaks' an existing bond and in the later case, a vibration leads to 'bond' formation. In both cases, the molecule/complex stays bound irrespective of what happens to this 'hydrogen bond'. Both these cases push the borders on the recent IUPAC recommendation on hydrogen bonding (Arunan et al. Pure. Appl. Chem. 2011, 83 1637) and justify the inclusive nature of the definition. PMID:25627627

  14. 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. PMID:25172112

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

    PubMed

    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

  16. 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

  17. 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

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

    PubMed

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

    2012-07-10

    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

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

    PubMed

    Novak, Petr; Kruppa, Gary H

    2008-01-01

    Intra-molecular cross-linking has been suggested as a method of obtaining distance constraints that would help to develop structural models of proteins. Recent work published on intra-molecular cross-linking for protein structural studies has employed commercially available primary amine (lysine, the amino terminus) selective reagents. 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 side chains 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 side chains can react to form "zero-length" cross-links with nearby primary amine containing residues, lysines (K) and the amino terminus (X), via the formation of a new amide bond. We also show that the EDC-activated DEO side chains can be cross-linked to each other using dihydrazides, two hydrazide moieties connected by an alkyl cross-linker arm 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 two 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 A. These results show that additional structural information can be obtained by exploiting new cross-linker chemistry

  20. 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

  1. SNR Observations as Probes of Explosion Mechanism(s)

    NASA Astrophysics Data System (ADS)

    Laming, J. Martin

    We review how observations of supernova remnants can be used to provide constraints and insights into the mechanism(s) of explosion of core-collapse supernovae. The key example is provided by Cassiopeia A, where the reverse shock has propagated a substantial distance into the ejecta. The remnant itself is detected in almost all wavebands from the radio to TeV gamma rays. Shocked ejecta may be studied by X-ray observations, and unshocked ejecta are visible in the infra-red. More recently, decays of the radioactive nucleus 44Ti, produced by nucleosynthesis at the heart of the explosion, have been imaged in hard X-rays. Optical observations reveal a variety of dense ejecta and circumstellar medium knots. Deprojecting the ejecta knot velocities allows a precise reconstruction of the supernova center of explosion. Other analyses tightly constrain fundamental parameters such as the distance and forward and reverse shock speeds and positions. These allow us to make quantitative statements about explosion energetics and element abundances and locations within the ejecta, to compare with the expectations from explosion models. In Cassiopeia A, we find a much stronger apparent inversion of the element stratification than expected. A significant fraction of the total Fe expected is visible in X-rays in the outer regions of the remnant, while infra-red spectra of the unshocked inner ejecta show essentially none. We will review the assumptions made in these analyses, and discuss the extent to which more sophisticated treatments might alter this conclusion, as well as the implications it might have for explosion models. Work supported by basic research funds of the Office of Naval Research and by NASA ADAP.

  2. Protein docking using an ensemble of spin labels optimized by intra-molecular paramagnetic relaxation enhancement.

    PubMed

    Schilder, Jesika; Liu, Wei-Min; Kumar, Pravin; Overhand, Mark; Huber, Martina; Ubbink, Marcellus

    2016-02-17

    Paramagnetic NMR is a useful technique to study proteins and protein complexes and the use of paramagnetic relaxation enhancement (PRE) for this purpose has become wide-spread. PREs are commonly generated using paramagnetic spin labels (SLs) that contain an unpaired electron in the form of a nitroxide radical, with 1-oxyl-2,2,5,5-tetramethyl-2,5-dihydropyrrol-3-ylmethyl methane thiosulfonate (MTSL) being the most popular tag. The inherent flexibility of the SL causes sampling of several conformations in solution, which can be problematic as over- or underestimation of the spatial distribution of the unpaired electron in structural calculations will lead to errors in the distance restraints. We investigated the effect of this mobility on the accuracy of protein-protein docking calculations using intermolecular PRE data by comparing MTSL and the less mobile 3-methanesulfonilthiomethyl-4-(pyridin-3-yl)-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-1-yloxyl (pyMTSL) on the dynamic complex of cytochrome c and cytochrome c peroxidase. No significant differences were found between the two SLs. Docking was performed using either single or multiple conformers and either fixed or flexible SLs. It was found that mobility of the SLs is the limiting factor for obtaining accurate solutions. Optimization of SL conformer orientations using intra-molecular PRE improves the accuracy of docking. PMID:26356049

  3. 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.

  4. 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.

  5. Molecular dynamics and principal components of potassium binding with human telomeric intra-molecular G-quadruplex.

    PubMed

    Wang, Zhiguo; Chen, Ruping; Hou, Ling; Li, Jianfeng; Liu, Jun-Ping

    2015-06-01

    Telomere assumes intra-molecular G-quadruplex that is a significant drug target for inhibiting telomerase maintenance of telomeres in cancer. Metal cations have been recognized as playing important roles in stabilizing G-quadruplex, but their binding processes to human telomeric G-quadruplex remain uncharacterized. To investigate the detailed binding procedures, molecular dynamics simulations were conducted on the hybrid [3 + 1] form-one human telomeric intra-molecular G-quadruplex. We show here that the binding of a potassium ion to a G-tetrad core is mediated by two alternative pathways. Principal component analysis illustrated the dominant concerted motions of G-quadruplex occurred at the loop domains. MM-PBSA calculations revealed that binding was energetically favorable and driven by the electrostatic interactions. The lower binding site was found more constructive favorable for binding. Our data provide useful information on a potassium-mediated stable structure of human telomeric intra-molecular G-quadruplex, implicating in ion disorder associated conformational changes and targeted drug design. PMID:25894091

  6. 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.

  7. Mass Spectrometry Profiles Superoxide-Induced Intra-molecular Disulfide in the FMN-binding Subunit of Mitochondrial Complex I

    PubMed Central

    Zhang, Liwen; Xu, Hua; Chen, Chwen-Lih; Green-Church, Kari B.; Freitas, Michael A.; Chen, Yeong-Renn

    2008-01-01

    Protein thiols with regulatory functions play a critical role in maintaining the homeostasis of the redox state in mitochondria. One major host of regulatory cysteines in mitochondria is complex I, with the thiols primarily located on its 51 kDa FMN-binding subunit. In response to oxidative stress, these thiols are expected to form intra-molecular disulfide bridges as one of their oxidative post-translational modifications. Here, to test this hypothesis and gain insights into the molecular pattern of disulfide in complex I, the isolated bovine complex I was prepared. Superoxide (O2•−) is generated by complex I under the conditions of enzyme turnover. O2•−-induced intra-molecular disulfide formation at the 51 kDa subunit was determined by tandem mass spectrometry and database searching, with the latter accomplished by adaptation of the in-house developed database search engine, MassMatrix [Xu H., et. al J. Proteome Res. (2008) 7, 138–44]. LC/MS/MS analysis of tryptic/chymotryptic digests of the 51 kDa subunit from alkylated complex I revealed that four specific cysteines (C125, C142, C187, and C206) of the 51 kDa subunit were involved in the formation of mixed intra-molecular disulfide linkages. In all, three cysteine pairs were observed: C125/C142, C187/C206, and C142/C206. The formation of disulfide bond was subsequently inhibited by superoxide dismutase, indicating the involvement of O2•−. These results elucidated by mass spectrometry indicates that the residues of C125, C142, C187, and C206 are the specific regulatory cysteines of complex I, and they participate in the oxidative modification with disulfide formation under the physiological or pathophysiological conditions of oxidative stress. PMID:18789718

  8. Probing mechanical properties of liposomes using acoustic sensors.

    PubMed

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

    2008-08-19

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

  9. 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

  10. In search of the cochlear amplifier: New mechanical and molecular tools to probe transduction channel function

    NASA Astrophysics Data System (ADS)

    Karavitaki, K. Domenica; Indzhykulian, Artur A.; Zhang, Duan-Sun; Corey, David P.

    2015-12-01

    The study of mechanotransduction in cochlear hair cells requires stimulus methods that mimic the in-vivo stimulation. We have developed a new mechanical probe to better mimic the physiological stimulus delivered to cochlear hair cells through the overlying tectorial membrane. We combine these new probes with electroporation to study the contribution of different components of the transduction apparatus.

  11. 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

  12. 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. PMID:25638003

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    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 1nN 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.

  15. 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.

  16. 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.

  17. Probing mechanical quantum coherence with an ultracold-atom meter

    SciTech Connect

    Lo Gullo, N.; Busch, Th.; Palma, G. M.; Paternostro, M.

    2011-12-15

    We propose a scheme to probe quantum coherence in the state of a nanocantilever based on its magnetic coupling (mediated by a magnetic tip) with a spinor Bose Einstein condensate (BEC). By mapping the BEC into a rotor, its coupling with the cantilever results in a gyroscopic motion whose properties depend on the state of the cantilever: the dynamics of one of the components of the rotor angular momentum turns out to be strictly related to the presence of quantum coherence in the state of the cantilever. We also suggest a detection scheme relying on Faraday rotation, which produces only a very small back-action on the BEC and is thus suitable for a continuous detection of the cantilever's dynamics.

  18. Probing mechanics and activity of cytoskeletal networks using carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Fakhri, Nikta

    2013-03-01

    We use single-walled carbon nanotubes (SWNTs) as multi-scale micro-probes to monitor transport and fluctuations in cytoskeletal networks. SWNTs are nanometer-diameter hollow carbon filaments with micrometer lengths and a tunable bending stiffness. Their persistence length varies between 20-100 microns. We study the motion of individual SWNTs in reconstituted actin networks by near-infrared fluorescence microscopy. At long times, SWNTs reptate through the networks. At short times, SWNTs sample the spectrum of thermal fluctuations in the networks. We can calculate complex shear moduli from recorded fluctuations and observe power-law scaling in equilibrium actin networks. In the non-equilibrium cytoskeleton of cells we have targeted SWNTs to kinesin motors and thereby to their microtubule tracks. We observe both transport along the tracks as well as active fluctuations of the tracks themselves. Human Frontier Science Program Cross-Disciplinary Fellow

  19. Spectroscopic Monitoring of Mechanical Forces during Protein Folding by using Molecular Force Probes.

    PubMed

    Stauch, Tim; Hoffmann, Marvin T; Dreuw, Andreas

    2016-05-18

    Detailed folding pathways of proteins are still largely unknown. Real-time monitoring of mechanical forces acting in proteins during structural transitions would provide deep insights into these highly complex processes. Here, we propose two molecular force probes that can be incorporated into the protein backbone to gain insight into the magnitude and direction of mechanical forces acting in proteins during natural folding and unfolding through their optical spectroscopic response. In fact, changes in the infrared and Raman spectra are proportional to the mechanical force deforming the force probes, and the relevant bands can be intensified and shifted to a transparent window in the protein spectrum by isotopic substitution. As a result, the proposed molecular force probes can act as "force rulers", allowing the spectroscopic observation and measurement of mechanical forces acting within the proteins under natural conditions without external perturbation. PMID:26928925

  20. 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.

  1. Probing mechanical properties of living cells by magnetopneumography.

    PubMed

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

    1997-01-01

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

  2. Probing embryonic tissue mechanics with laser hole drilling.

    PubMed

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

    2009-01-01

    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. PMID:19411738

  3. Probing embryonic tissue mechanics with laser hole drilling

    NASA Astrophysics Data System (ADS)

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

    2009-09-01

    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.

  4. 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.

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

    PubMed

    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

  6. 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

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

    PubMed

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

    2008-11-14

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

  8. 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].

  9. 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.

  10. [Derivative fluorescence probe recognition results of the light physical mechanism of metal ions].

    PubMed

    Dai, Yu-mei; Hu, Xiao-jun; Li, Fu-jun; Xie, Yu-meng; Zhao, Yang-yang; Zhou, Qiao

    2015-02-01

    As people deeply study the electronic spectra of fluorescent compounds and photophysical behavior, enormous progress has been made in the aspect of changes and states of different systems in the use of fluorescent molecules as probes. PTC-DA is a kind of typical fluorescent molecular probe that is highly sensitive and selective in water environment. This paper makes a research on the physical mechanism of light of PTCDA by TDF (Density Functional Theory), calculates the optimal configuration the charge population and excitation spectra of PTCDA molecules under ideal condition and acquires PTCDA fluorescence emission spectra then analyses that PTCDA is a kind of quenching and dual colorimetric signal probe response. Its optical signal response mechanism belongs to ICT (Intramolecular Charge Transfer) mechanism. According to the results, this perylene derivatives is fitted with Cu2+ excited state absorption spectra. Before and after the combination with Cu2+, the peak shape of absorption spectrum is similar. When copper is added, the overall absorption peak position occurred redshift, quenching discoloration happens. By comparing with experimental values, the calculated molecular configuration is reasonable and effective and the peak of excitation spectra is realistic. Analysis shows that: PTCDA molecules divalent copper ions have better fluorescence detection activity, the optical signal response mechanisms are intramolecular charge transfer (ICT) mechanisms. When a molecule receives divalent copper ions, the absorption spectrum peak position redshifts, intramolecular charge transfer direction and intensity changes. There occur both quenching signal and discoloration signal. It is a kind of fluorescent probe material with double quenching and discoloration fluorescent signal, which has great potential for development. This paper makes an early-stage exploration of the physical mechanism of light response mechanism analysis in molecular fluorescent probe field and

  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. Probing Hydrothermal Organic Reaction Mechanisms with Hydrothermal Photochemistry

    NASA Astrophysics Data System (ADS)

    Yang, Z.; Gould, I.; Shock, E.

    2013-12-01

    favorable and rapid at hydrothermal conditions [1]. These results show that several relatively stable hydrothermal products from DBK are derived from the radical-coupled intermediates, and that these intermediates can be successfully captured using the tool of hydrothermal photolysis. Analysis of the product distributions and the quantum yields for the hydrothermal photolysis also provides convincing evidence for the previously proposed radical cleavage mechanism for the thermal reactions of DBK. [1] Yang et al. (2012) Geochim. Cosmochim. Acta 98, 48-65.

  13. A comparison of excimer laser, thermal probe, and mechanical devices for recanalizing occluded human arteries.

    PubMed

    Moriuchi, M; Tobis, J M; Mcrae, M; Mallery, J A; Macleay, L; Moussabeck, O; Berns, M; Henry, W L

    1991-06-01

    To evaluate the mechanism of excimer laser recanalization and compare the results with those of laser-assisted thermal probe recanalization and mechanical recanalization, a total of 42 human atherosclerotic totally occluded arterial segments (2-15 cm long) were recanalized by excimer laser with a 400-800 micron quartz fiber pulsed at 20 Hz with 50 mJ/mm2 of energy (n = 21), an Argon heated thermal probe at 10-12 watts (n = 11), a guidewire directed through a 6 Fr multipurpose catheter, or an angioplasty balloon catheter (n = 10). On histologic examination, the excimer laster created a single round lumen or multiple lumens ("Swiss-cheese" like appearance) with no evidence of thermal injury at the perimeter of the lumen. The incidence of perforation in vitro was less with an excimer laser catherter (8/21 or 38%) than with the thermal prove (10/11 or 91%) (p less than 0.01). However, serial histologic cross-sectional examination showed that the pathway of the devices were essentially the same in all recanalization procedures. The pathway of the device was located outside the atheroma but proximal to the internal elastic membrane in 13 arteries with the excimer laser (62%), in 10 arteries with the thermal probe (91%), and 8 arteries with mechanical devices (80%). These results indicate that although the eximer laser could recanalize human atherosclerotic arteries without thermal injury, the fiber frequently deflected around firm atherosclerotic plaque and advanced in a dissection plane between the plaque and media. A similar course was noted for the thermal probe or during mechanical recanalization with a guidewire and catheter. To insure the safety of an excimer fiber or a thermal probe to reopen complete occlusions, better guidance systems must be developed. PMID:1875527

  14. 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

  15. 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

  16. 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.

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

    PubMed

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

    2005-08-01

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

  18. 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

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

    PubMed

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

    2016-05-19

    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

  20. Mechanical anisotropy and adaptation of metastatic cells probed by magnetic microbeads

    NASA Astrophysics Data System (ADS)

    Zhang, Zhipeng; Shi, Yanhui; Jhiang, Sissy M.; Menq, Chia-Hsiang

    2010-02-01

    Metastatic cells have the ability to break through the basal lamina, enter the blood vessels, circulate through the vasculature, exit at distant sites, and form secondary tumors. This multi-step process, therefore, clearly indicates the inherent ability of metastatic cells to sense, process, and adapt to the mechanical forces in different surrounding environments. We describe a magnetic probing device that is useful in characterizing the mechanical properties of cells along arbitrary two-dimensional directions. Magnetic force, with the advantages of biocompatibility and specificity, was produced by magnetic poles placed in an octupole configuration and applied to fibronectin-coated magnetic microbeads attached on cell membrane. Cell deformation in response to the applied force was then recorded through the displacement of the microbeads. The motion of the beads was measured by computer processing the video images acquired by a high-speed CMOS camera. Rotating force vectors with constant magnitude while pointing to directions of all 360 degrees were applied to study the mechanical anisotropy of metastatic breast cancer cells MDA-MB-231. The temporal changes in magnitude and directionality of the cellular responses were then analyzed to investigate the cellular adaptation to force stimulation. This probing technology thus has the potential to provide us a better understanding of the mechano-signatures of cells.

  1. An Engineered Kinetic Amplification Mechanism for Single Nucleotide Variant Discrimination by DNA Hybridization Probes.

    PubMed

    Chen, Sherry Xi; Seelig, Georg

    2016-04-20

    Even a single-nucleotide difference between the sequences of two otherwise identical biological nucleic acids can have dramatic functional consequences. Here, we use model-guided reaction pathway engineering to quantitatively improve the performance of selective hybridization probes in recognizing single nucleotide variants (SNVs). Specifically, we build a detection system that combines discrimination by competition with DNA strand displacement-based catalytic amplification. We show, both mathematically and experimentally, that the single nucleotide selectivity of such a system in binding to single-stranded DNA and RNA is quadratically better than discrimination due to competitive hybridization alone. As an additional benefit the integrated circuit inherits the property of amplification and provides at least 10-fold better sensitivity than standard hybridization probes. Moreover, we demonstrate how the detection mechanism can be tuned such that the detection reaction is agnostic to the position of the SNV within the target sequence. in contrast, prior strand displacement-based probes designed for kinetic discrimination are highly sensitive to position effects. We apply our system to reliably discriminate between different members of the let-7 microRNA family that differ in only a single base position. Our results demonstrate the power of systematic reaction network design to quantitatively improve biotechnology. PMID:27010123

  2. A Monte Carlo-quantum mechanics study of a solvatochromic π* probe.

    PubMed

    Domínguez, Moisés; Rezende, Marcos Caroli

    2016-09-01

    The solvation and the solvatochromic behavior of 5-(dimethylamino)-5'-nitro-2,2'-bithiophene 1, the basis of a π* scale of solvent polarities, was investigated theoretically in toluene, dichloromethane, methanol and formamide with a Monte Carlo and quantum mechanics (QM/MM) iterative approach. The calculated transition energies of the solvatochromic band of 1, obtained as averages of statistically uncorrelated configurations, including the solute and explicit solvent molecules of the first solvation layer, besides showing good agreement with the experimental transitions, reproduced very well the positive solvatochromism of this probe in various solvents. PMID:27553303

  3. Intra-molecular mobility of charge carriers along oligogermane backbones studied by flash photolysis time-resolved microwave conductivity and transient optical spectroscopy techniques

    NASA Astrophysics Data System (ADS)

    Seki, Shu; Saeki, Akinori; Acharya, Anjali; Koizumi, Yoshiko; Tagawa, Seiichi; Mochida, Kunio

    2008-10-01

    Time-resolved microwave conductivity (TRMC) measurement has been performed for fullerene-doped thin films of oligo (dimethylgermane) at different excitation energies to evaluate the intra-molecular mobility of holes along their Ge backbones. Photo-induced electron transfer reaction between oligogermane and fullerene has been observed in the solution with a variety of solvent polarity using transient optical spectroscopy (TOS). The transient spectrum at 391 nm can be attributed to the radical cation of the oligomer under an excitation at 532-nm light, whereas the same spectrum (391 nm) is the overlapping of absorptions of radical cations and neutral radicals of oligogermanes upon exposure of 355-nm light in polar solvent. A combined TRMC and TOS experiments on the solutions of oligomer confirms the conductive transients originate from the radical cations on the backbone chains.

  4. Towards highly efficient red thermally activated delayed fluorescence materials by the control of intra-molecular π-π stacking interactions

    NASA Astrophysics Data System (ADS)

    Zhang, Yunge; Zhang, Dongdong; Cai, Minghan; Li, Yilang; Zhang, Deqiang; Qiu, Yong; Duan, Lian

    2016-03-01

    Thermally activated delayed fluorescence (TADF) materials have attracted much attention as they can achieve 100% theoretical internal quantum efficiency without using expensive noble metals. However, efficient red TADF emitters are hard to realize according to the energy gap law. Here, three donor-acceptor-donor type TADF emitters with the same acceptor of o-phthalodinitrile (PN) but different donors (9, 9-dimethyl-9, 10-dihydroacridine (DMAC), phenoxazine (PXZ), and phenothiazine (PTZ) for DMAC-PN, PXZ-PN, and PTZ-PN, respectively) have been synthesized, and it is observed that the performance of the emitters can be improved by reducing the intra-molecular π-π stacking. DMAC-PN with reduced intra-molecular π-π stacking shows a photoluminescence quantum yield (PLQY) of 20.2% in degassed toluene solution, much higher than those of PXZ-PN, and PTZ-PN (0.8%, 0.2%, respectively). An organic light-emitting diode (OLED) employing DMAC-PN doped into 4,4‧-bis(9H-carbazol-9-yl)biphenyl (CBP) as the emitting layer exhibits a maximum external quantum efficiency (EQE) of 10.2% with the emission peak at 564 nm. Moreover, when DMAC-PN is doped into a polar host, bis[2-(diphenylphosphino)phenyl] ether oxide (DPEPO), the OLED shows a large redshift of the emission maximum to 594 nm, while maintaining a peak EQE as high as 7.2%, indicating that efficient red TADF OLEDs can be fabricated by doping orange TADF emitters into hosts with proper polarity.

  5. Towards highly efficient red thermally activated delayed fluorescence materials by the control of intra-molecular π-π stacking interactions.

    PubMed

    Zhang, Yunge; Zhang, Dongdong; Cai, Minghan; Li, Yilang; Zhang, Deqiang; Qiu, Yong; Duan, Lian

    2016-03-01

    Thermally activated delayed fluorescence (TADF) materials have attracted much attention as they can achieve 100% theoretical internal quantum efficiency without using expensive noble metals. However, efficient red TADF emitters are hard to realize according to the energy gap law. Here, three donor-acceptor-donor type TADF emitters with the same acceptor of o-phthalodinitrile (PN) but different donors (9, 9-dimethyl-9, 10-dihydroacridine (DMAC), phenoxazine (PXZ), and phenothiazine (PTZ) for DMAC-PN, PXZ-PN, and PTZ-PN, respectively) have been synthesized, and it is observed that the performance of the emitters can be improved by reducing the intra-molecular π-π stacking. DMAC-PN with reduced intra-molecular π-π stacking shows a photoluminescence quantum yield (PLQY) of 20.2% in degassed toluene solution, much higher than those of PXZ-PN, and PTZ-PN (0.8%, 0.2%, respectively). An organic light-emitting diode (OLED) employing DMAC-PN doped into 4,4'-bis(9H-carbazol-9-yl)biphenyl (CBP) as the emitting layer exhibits a maximum external quantum efficiency (EQE) of 10.2% with the emission peak at 564 nm. Moreover, when DMAC-PN is doped into a polar host, bis[2-(diphenylphosphino)phenyl] ether oxide (DPEPO), the OLED shows a large redshift of the emission maximum to 594 nm, while maintaining a peak EQE as high as 7.2%, indicating that efficient red TADF OLEDs can be fabricated by doping orange TADF emitters into hosts with proper polarity. PMID:26821694

  6. Mechanism of Fluorescence Switching in One ESIPT-Based Al(3+) Probe.

    PubMed

    Budzák, Šimon; Jacquemin, Denis

    2016-07-14

    A recently synthesized Schiff base used as a probe for aluminum cations was studied with ab initio models. The primary reason for the lack of fluorescence in aprotic solvents was found to be the presence of an efficient conical intersection (CI) between the ground-states and the first singlet excited-states close to the Franck-Condon geometry. The excited-state pathway leading to this CI is barrierless but implies large amplitude motions, explaining why the fluorescence was observed in frozen acetonitrile matrix. Our calculations suggest that constraining the molecule by impending the rotation around the imino bond enables excited-state intramolecular proton transfer. A similar stiffening mechanism is responsible for the strong fluorescence turn-on after formation of complexes between Al(3+) cations and dehydrogenated Schiff base. Finally, the analysis of the possible fluorescence mechanisms in water indicates that the anion of 1 is the likely fluorescence source. Overall, this work allows one to disentangle the various origins of fluorescence switching in a probe. PMID:27281545

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

    PubMed

    Põder, Endel

    2014-01-01

    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. PMID:25378369

  8. Membrane mechanics as a probe of ion-channel gating mechanisms

    PubMed Central

    Reeves, Daniel; Ursell, Tristan; Sens, Pierre; Kondev, Jane; Phillips, Rob

    2012-01-01

    The details of conformational changes undergone by transmembrane ion channels in response to stimuli, such as electric fields and membrane tension, remain controversial. We approach this problem by considering how the conformational changes impose deformations in the lipid bilayer. We focus on the role of bilayer deformations in the context of voltage-gated channels because we hypothesize that such deformations are relevant in this case as well as for channels that are explicitly mechanosensitive. As a result of protein conformational changes, we predict that the lipid bilayer suffers deformations with a characteristic free-energy scale of 10kBT. This free energy is comparable to the voltage-dependent part of the total gating energy, and we argue that these deformations could play an important role in the overall free-energy budget of gating. As a result, channel activity will depend upon mechanical membrane parameters such as tension and leaflet thickness. We further argue that the membrane deformation around any channel can be divided into three generic classes of deformation that exhibit different mechanosensitive properties. Finally, we provide the theoretical framework that relates conformational changes during gating to tension and leaflet thickness dependence in the critical gating voltage. This line of investigation suggests experiments that could discern the dominant deformation imposed upon the membrane as a result of channel gating, thus providing clues as to the channel deformation induced by the stimulus. PMID:18999449

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

    PubMed

    Melzak, Kathryn; Tsortos, Achilleas; Gizeli, Electra

    2009-01-01

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

  10. Probing the protein-folding mechanism using denaturant and temperature effects on rate constants

    PubMed Central

    Guinn, Emily J.; Kontur, Wayne S.; Tsodikov, Oleg V.; Shkel, Irina; Record, M. Thomas

    2013-01-01

    Protein folding has been extensively studied, but many questions remain regarding the mechanism. Characterizing early unstable intermediates and the high–free-energy transition state (TS) will help answer some of these. Here, we use effects of denaturants (urea, guanidinium chloride) and temperature on folding and unfolding rate constants and the overall equilibrium constant as probes of surface area changes in protein folding. We interpret denaturant kinetic m-values and activation heat capacity changes for 13 proteins to determine amounts of hydrocarbon and amide surface buried in folding to and from TS, and for complete folding. Predicted accessible surface area changes for complete folding agree in most cases with structurally determined values. We find that TS is advanced (50–90% of overall surface burial) and that the surface buried is disproportionately amide, demonstrating extensive formation of secondary structure in early intermediates. Models of possible pre-TS intermediates with all elements of the native secondary structure, created for several of these proteins, bury less amide and hydrocarbon surface than predicted for TS. Therefore, we propose that TS generally has both the native secondary structure and sufficient organization of other regions of the backbone to nucleate subsequent (post-TS) formation of tertiary interactions. The approach developed here provides proof of concept for the use of denaturants and other solutes as probes of amount and composition of the surface buried in coupled folding and other large conformational changes in TS and intermediates in protein processes. PMID:24043778

  11. Carbon nanotubes as mechanical probes of equilibrium and non-equilibrium cytoskeletal networks

    NASA Astrophysics Data System (ADS)

    Fakhri, Nikta; Pasquali, Matteo; Mackintosh, Frederick C.; Schmidt, Christoph F.

    2012-02-01

    Networks of filamentous proteins underlie the mechanics of cells. The activity of motor proteins typically creates strong fluctuations that drive the system out of equilibrium. Understanding the behavior of such networks requires probes that ideally span the characteristic length-scales, from nanometers to micrometers. Single-walled carbon nanotubes (SWNTs) are nanometer-diameter filaments with micrometer length and tunable bending stiffness. On a Brownian energy scale they have persistence lengths of about 20-100 micrometers and show significant thermal fluctuations on the cellular scale of a few microns. Diffusive motion and local bending dynamics of SWNTs embedded in an active polymeric network reflect forces and fluctuations of the embedding medium. We study the motion of individual SWNTs in equilibrium and non-equilibrium networks by near infrared fluorescence microscopy. We show that SWNTs reptate in the network. We will discuss the possibility of using SWNTs as multi-scale probes relating their local dynamic behavior to the viscoelastic properties of the surrounding network.

  12. Mechanics of interaction and atomic-scale wear of amplitude modulation atomic force microscopy probes.

    PubMed

    Vahdat, Vahid; Grierson, David S; Turner, Kevin T; Carpick, Robert W

    2013-04-23

    Wear is one of the main factors that hinders the performance of probes for atomic force microscopy (AFM), including for the widely used amplitude modulation (AM-AFM) mode. Unfortunately, a comprehensive scientific understanding of nanoscale wear is lacking. We have developed a protocol for conducting consistent and quantitative AM-AFM wear experiments. The protocol involves controlling the tip-sample interaction regime during AM-AFM scanning, determining the tip-sample contact geometry, calculating the peak repulsive force and normal stress over the course of the wear test, and quantifying the wear volume using high-resolution transmission electron microscopy imaging. The peak repulsive tip-sample interaction force is estimated from a closed-form equation accompanied by an effective tip radius measurement procedure, which combines transmission electron microscopy and blind tip reconstruction. The contact stress is estimated by applying Derjaguin-Müller-Toporov contact mechanics model and also numerically solving a general contact mechanics model recently developed for the adhesive contact of arbitrary axisymmetric punch shapes. We discuss the important role that the assumed tip shape geometry plays in calculating both the interaction forces and the contact stresses. Contact stresses are significantly affected by the tip geometry while the peak repulsive force is mainly determined by experimentally controlled parameters, specifically, the free oscillation amplitude and amplitude ratio. The applicability of this protocol is demonstrated experimentally by assessing the performance of diamond-like carbon-coated and silicon-nitride-coated silicon probes scanned over ultrananocrystalline diamond substrates in repulsive mode AM-AFM. There is no sign of fracture or plastic deformation in the case of diamond-like carbon; wear could be characterized as a gradual atom-by-atom process. In contrast, silicon nitride wears through removal of the cluster of atoms and plastic

  13. 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

  14. 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.

  15. Elucidating protein inter- and intra-molecular interacting domains using chemical cross-linking and MALDI-TOF/TOF mass spectrometry

    PubMed Central

    Pottiez, Gwënaël; Ciborowski, Pawel

    2012-01-01

    Among many methods used to investigate proteins/protein interactions, chemical cross-linking combined with mass spectrometry remains a vital experimental approach. Mapping peptides modified by cross-linker provides clues about proteins’ interacting domains. One complication is that such modification may result from intra- but not intermolecular interactions. Therefore, for overall data interpretation, a combination of results from various platforms is necessary. It is postulated that the secretory isoform of gelsolin regulates several biological processes through interactions with proteins such as actin, fibronectin, vitamin D binding protein and unidentified receptors on the surface of eukaryotic; it also has been shown to self-assemble eventually leading to the formation of homo-multimers. As such, it is an excellent model for this study. We used four cross-linkers with arm length ranging from 7.7Å to 21.7Å and MALDI-TOF/TOF mass spectrometry as the analytical platform. Results of this study show that MALDI based mass spectrometry generates high quality data to show lysine residues modified by cross-linkers and combined with existing data based on crystallography (Protein Data Bank, PDB) can be used to discriminate between inter- and intra-molecular linking. PMID:22226790

  16. 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.

  17. Space Science Education by Mathematica Demonstrations: Interactive Design of Moving Space Probe Elements Mechanics by Foldable and Extendable Structures for Space Applications

    NASA Astrophysics Data System (ADS)

    Kabai, S.; Bérczi, Sz.

    2010-03-01

    By the interactive Mathematica Demonstrations of the Wolfram Research several mechanics for space probe operation and motion simulations were studied as space robotics and science educational program.

  18. Probing the transcription mechanisms of reovirus cores with molecules that alter RNA duplex stability.

    PubMed

    Demidenko, Alexander A; Nibert, Max L

    2009-06-01

    The mammalian reovirus (MRV) genome comprises 10 double-stranded RNA (dsRNA) segments, packaged along with transcriptase complexes inside each core particle. Effects of four small molecules on transcription by MRV cores were studied for this report, chosen for their known capacities to alter RNA duplex stability. Spermidine and spermine, which enhance duplex stability, inhibited transcription, whereas dimethyl sulfoxide and trimethylglycine, which attenuate duplex stability, stimulated transcription. Different mechanisms were identified for inhibition or activation by these molecules. With spermidine, one round of transcription occurred normally, but subsequent rounds were inhibited. Thus, inhibition occurred at the transition between the end of elongation in one round and initiation in the next round of transcription. Dimethyl sulfoxide or trimethylglycine, on the other hand, had no effect on transcription by a constitutively active fraction of cores in each preparation but activated transcription in another fraction that was otherwise silent for the production of elongated transcripts. Activation of this other fraction occurred at the transition between transcript initiation and elongation, i.e., at promoter escape. These results suggest that the relative stability of RNA duplexes is most important for certain steps in the particle-associated transcription cycles of dsRNA viruses and that small molecules are useful tools for probing these and probably other steps. PMID:19297468

  19. Asphaltene adsorption mechanism under shear flow probed by in situ neutron reflectivity measurements

    NASA Astrophysics Data System (ADS)

    Corvis, Y.; Barré, L.; Jestin, J.; Gummel, J.; Cousin, F.

    2012-11-01

    We propose here a method to adapt a rheometer with a cone/plate geometry to a neutron reflectometer in order to perform in situ reflectivity measurements. This study allowed us to probe the influence of the shear rate on the mechanism of asphaltenes adsorption, the heaviest and most polar compounds of crude oil, using bad solvent conditions. Such experiment aims at describing at a local scale the surface modifications induced by flowing crude oils (pipe transportation or production through porous media). Without shearing, in a 34%/66% xylene/dodecane mixture for which the asphaltenes flocculation is achieved in bulk, the nanoaggregates are able to be adsorbed on a hydrophilic surface as multilayers, with a surface excess much larger than for good solvent conditions. Moreover, the thickness of these multilayers increases almost linearly with time, in accordance with QCM experiments. In shear rate conditions, the adsorption process is however strongly limited since the surface excess of the adsorbed layers is around twice lower at 2600 s-1 than at 1200 s-1.

  20. 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. PMID:27455091

  1. 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

  2. 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.

  3. Probing Binding Sites and Mechanisms of Action of an IKs Activator by Computations and Experiments

    PubMed Central

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

    2015-01-01

    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. PMID:25564853

  4. Mechanically tunable organic vertical-cavity surface emitting lasers (VCSELs) for highly sensitive stress probing in dual-modes.

    PubMed

    Yang, Yu; Zhou, Yuan; Liao, Zhifu; Yu, Jiancan; Cui, Yuanjing; Garcia-Moreno, Inmaculada; Wang, Zhiyu; Costela, Angel; Qian, Guodong

    2015-02-23

    Herein, we report a straight forward stress probing method based on mechanically tunable organic VCSELs via dual detecting-modes. By designing the active layer thickness, uploaded stress was measured simultaneously by the laser wavelength and mode separations, facilitating highly sensitive stress detection in broad ranges. Single-mode laser emission with low threshold and narrow line-width was characterized, which could be tuned continuously within 8 nm. The probing sensitivity and resolution were estimated to be 60 Pa and 5.6 nm/KPa respectively, which were ~160-folds higher than previous results. PMID:25836475

  5. 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

  6. High-resolution HDX-MS reveals distinct mechanisms of RNA recognition and activation by RIG-I and MDA5

    PubMed Central

    Zheng, Jie; Yong, Hui Yee; Panutdaporn, Nantika; Liu, Chuanfa; Tang, Kai; Luo, Dahai

    2015-01-01

    RIG-I and MDA5 are the major intracellular immune receptors that recognize viral RNA species and undergo a series of conformational transitions leading to the activation of the interferon-mediated antiviral response. However, to date, full-length RLRs have resisted crystallographic efforts and a molecular description of their activation pathways remains hypothetical. Here we employ hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) to probe the apo states of RIG-I and MDA5 and to dissect the molecular details with respect to distinct RNA species recognition, ATP binding and hydrolysis and CARDs activation. We show that human RIG-I maintains an auto-inhibited resting state owing to the intra-molecular HEL2i-CARD2 interactions while apo MDA5 lacks the analogous intra-molecular interactions and therefore adopts an extended conformation. Our work demonstrates that RIG-I binds and responds differently to short triphosphorylated RNA and long duplex RNA and that sequential addition of RNA and ATP triggers specific allosteric effects leading to RIG-I CARDs activation. We also present a high-resolution protein surface mapping technique that refines the cooperative oligomerization model of neighboring MDA5 molecules on long duplex RNA. Taken together, our data provide a high-resolution view of RLR activation in solution and offer new evidence for the molecular mechanism of RLR activation. PMID:25539915

  7. Probing the Failure Mechanism of SnO{sub 2} Nanowires for Sodium-Ion Batteries

    SciTech Connect

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

    2013-09-30

    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 SnO{sub 2} 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 SnO{sub 2}, a displacement reaction occurs, leading to the formation of amorphous Na{sub x}Sn nanoparticles dispersed in Na{sub 2}O matrix. With further Na insertion, the Na{sub x}Sn crystallized into Na{sub 15}Sn{sub 4} (x = 3.75). Upon extraction of Na (desodiation), the Na{sub x}Sn 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 Na{sub 2}O. These pores greatly increase electrical impedance, therefore accounting for the poor cyclability of SnO{sub 2}. DFT calculations indicate that Na{sup +} diffuses 30 times slower than Li{sup +} in SnO{sub 2}, 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 SnO{sub 2} 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.

  8. 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. PMID:26901396

  9. 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.

  10. 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

  11. Study the friction behaviour of poly[2-(dimethylamino)ethyl methacrylate] brush with AFM probes in contact mechanics

    NASA Astrophysics Data System (ADS)

    Raftari, Maryam; Zhang, Zhenyu; Leggett, Graham J.; Geoghegan, Mark

    2011-10-01

    We have studied the frictional behaviour of grafted poly[2-(dimethylamino)ethyl methacrylate] (PDMAEMA) films using friction force microscopy (FFM). The films were prepared on native oxide-terminated silicon substrates using the technique of atom transfer radical polymerization (ATRP). We show that single asperity contact mechanics (Johnson-Kendall-Roberts(JKR) and Derjaguin-Muller-Toporov(DMT)) as well as a linear (Amontons) relation between applied load and frictional load depending on the pH of the FFM probe. Measurements were made using functionalized and unfunctionalized silicon nitride triangular probes. Functionalized probes included gold-coated probes, and ones coated with a self-assembled monolayer of dodecanethiol (DDT). The frictional behaviour between PDMAEMA and all tips immersed in pH from 3 to 11 are corresponded to the DMT or JKR model and are linear in pH=1, 2, and 12. These results show that contact mechanics of polyelectrolytes in water is complex and strongly dependent on the environmental pH.

  12. 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. PMID:21896383

  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. Mechanical characterization of conducting polymer actuated neural probes under physiological settings

    NASA Astrophysics Data System (ADS)

    Daneshvar, Eugene D.; Smela, Elisabeth; Kipke, Daryl R.

    2010-04-01

    Most implantable chronic neural probes have fixed electrode sites on the shank of the probe. Neural probe shapes and insertion methods have been shown to have considerable effects on the resulting chronic reactive tissue response that encapsulates probes. We are developing probes with controllable articulated electrode projections, which are expected to provoke less reactive tissue response due to the projections being minimally sized, as well as to permit a degree of independence from the probe shank allowing the recording sites to "float" within the brain. The objective of this study was to predict and analyze the force-generating capability of conducting polymer bilayer actuators under physiological settings. Custom parylene beams 21 μm thick, 1 cm long, and of varying widths (200 - 1000 μm) were coated with Cr/Au. Electroplated weights were fabricated at the ends of the beams to apply known forces. Polypyrrole was potentiostatically polymerized to varying thicknesses onto the Au at 0.5 V in a solution of 0.1 M pyrrole and 0.1 M dodecylbenzenesulfonate (DBS). Using cyclic voltammetry, the bilayer beams were cycled in artificial cerebrospinal fluid (aCSF) at 37 °C, as well as in aqueous NaDBS as a control. Digital images and video were analyzed to quantify the deflections. The images and the cyclic voltammograms showed that divalent cations in the aCSF interfered with polymer reduction. By integrating polypyrrole-based conducting polymer actuators, we present a type novel neural probe. We demonstrate that actuating PPy(DBS) under physiological settings is possible, and that the technique of microfabricating weights onto the actuators is a useful tool for studying actuation forces.

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

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

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

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

    PubMed

    Gadalla, Atef; Dehoux, Thomas; Audoin, Bertrand

    2014-05-01

    Probing the mechanical properties of plant cell wall is crucial to understand tissue dynamics. However, the exact symmetry of the mechanical properties of this anisotropic fiber-reinforced composite remains uncertain. For this reason, biologically relevant measurements of the stiffness coefficients on individual living cells are a challenge. For this purpose, we have developed the single-cell optoacoustic nanoprobe (SCOPE) technique, which uses laser-generated acoustic waves to probe the stiffness, thickness and viscosity of live single-cell subcompartments. This all-optical technique offers a sub-micrometer lateral resolution, nanometer in-depth resolution, and allows the non-contact measurement of the mechanical properties of live turgid tissues without any assumption of mechanical symmetry. SCOPE experiments reveal that single-cell wall transverse stiffness in the direction perpendicular to the epidermis layer of onion cells is close to that of cellulose. This observation demonstrates that cellulose microfibrils are the main load-bearing structure in this direction, and suggests strong bonding of microfibrils by hemicelluloses. Altogether our measurement of the viscosity at high frequencies suggests that the rheology of the wall is dominated by glass-like dynamics. From a comparison with literature, we attribute this behavior to the influence of the pectin matrix. SCOPE's ability to unravel cell rheology and cell anisotropy defines a new class of experiments to enlighten cell nano-mechanics. PMID:24615232

  17. 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.

  18. 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…

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

    PubMed

    Kruse, Holger; Grimme, Stefan

    2012-04-21

    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

  20. 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.

  1. An atom probe investigation of the influence of trace impurities on the mechanical behavior of NiAl

    SciTech Connect

    Jayaram, R.; Liu, C.T.; Miller, M.K.

    1993-11-01

    Atom probe field ion microscopy (APFIM) and transmission electron microscopy (TEM) have been used to investigate the influence of trace metallic impurities on the enormous increase in the yield stress of boron-doped NiAl. Previous atom probe studies of NiAl containing 0.12 at. % boron had demonstrated that 0.026 at. % of the boron was in solid solution. The remainder reacted with trace metallic impurities, presumably present in high purity Ni, to form ultrafine MB{sub 2} precipitates ranging in size from less than 2 nm to 20 nm. Atom probe measurements had shown that their number densities were significant enough to make the dominant contribution to the observed increase in yield stress. An attempt was made in the present work to minimize the effect of these precipitates by an additional aging treatment. Field ion microscope (FIM) and TEM micrographs revealed that 2 nm precipitates coarsened significantly during aging. Microstructure of aged NiAl was consistent with observed mechanical behavior showing a significantly smaller increase in the yield stress. An approximate value of the Orowan stress, based on TEM estimates of the size and number density of the precipitates, is in reasonable agreement with the measured value. This APFIM/TEM investigation has indicated a practical approach to minimize the detrimental role of trace impurities in NiAl.

  2. 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.

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

    DOE PAGESBeta

    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 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

  4. Thiol Probes To Detect Electrophilic Natural Products Based on Their Mechanism of Action.

    PubMed

    Castro-Falcón, Gabriel; Hahn, Dongyup; Reimer, Daniela; Hughes, Chambers C

    2016-08-19

    New methods are urgently needed to find novel natural products as structural leads for the development of new drugs against emerging diseases such as cancer and multiresistant bacterial infections. Here we introduce a reactivity-guided drug discovery approach for electrophilic natural products, a therapeutically relevant class of natural products that covalently modify their cellular targets, in crude extracts. Using carefully designed halogenated aromatic reagents, the process furnishes derivatives that are UV-active and highly conspicuous via mass spectrometry by virtue of an isotopically unique bromine or chlorine tag. In addition to the identification of high-value metabolites, the process facilitates the difficult task of structure elucidation by providing derivatives that are primed for X-ray crystallographic analysis. We show that a cysteine probe efficiently and chemoselectively labels enone-, β-lactam-, and β-lactone-based electrophilic natural products (parthenolide, andrographolide, wortmannin, penicillin G, salinosporamide), while a thiophenol probe preferentially labels epoxide-based electrophilic natural products (triptolide, epoxomicin, eponemycin, cyclomarin, salinamide). Using the optimized method, we were able to detect and isolate the epoxide-bearing natural product tirandalydigin from Salinispora and thereby link an orphan gene cluster to its gene product. PMID:27294329

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2008-05-01

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

  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. PMID:25984833

  8. 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.

  9. 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. PMID:25167244

  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. Probing the mechanism of non-linear growth of polyelectrolyte multilayers

    NASA Astrophysics Data System (ADS)

    Selin, Victor; Ankner, John; Sukhishvili, Svetlana A.

    We report a study of the non-linear growth of electrostatically assembled polyelectrolyte multilayer films (PEM). PEM films were assembled by the layer-by-layer (LbL) technique using poly(methacrylic acid) as a polyanion and quaternized poly-2-(dimethylamino)ethyl methacrylate as a polycation. During film build-up, the thickness evolution as well as water uptake of PEM films were measured by in situ ellipsometry, whereas neutron reflectometry was used to probe the evolution of film internal structure as a function of deposition time. First, we found that during non-linear growth, films remain in a highly swollen hydrogel-like state, but the swelling ratio demonstrated an odd/even effect, with much larger hydration of the PEM when the terminal layer was the polycation. Second, while polycation chains were able to diffuse into the bulk of the film with a diffusion constant several orders of magnitude lower than in their free, unbound state, polyanion invasion was limited to the film surface. The amounts of the polycation and the polyanion adsorbed per deposition cycle were also drastically different. We quantify chemical composition and water content in the film, and correlate these data with the depth polyelectrolyte chains penetrate within the film during PEM construction.

  12. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

    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. Use of isotope effects as a probe of enzyme reaction mechanisms

    SciTech Connect

    Weiss, P.M.K.

    1987-01-01

    The use of multiple isotope effects has been extended to include both the variation of /sup 15/N isotope effects with deuterated and unlabeled substrates, and the use of solvent isotope effects in conjunction with /sup 13/C or /sup 15/N isotope effects. The deuterium isotope effect on the inhibition constant, /sup D/K/sub i/, of a competitive inhibitor has also been used to identify an active-site catalytic base. Phenylalanine ammonia lyase has been shown to catalyze the elimination of ammonia from the slow alternate substrate dihydrophenylalanine by an E1cb mechanism with a carbanion intermediate. This conclusion resulted from comparison of /sup 15/N isotope effects with 3-dideuterated and unlabeled substrates, and a deuterium isotope effect of 2.0 from dideuteration at C-3, with the equations for concerted, carbanion and carbonium ion mechanisms. Isotope effects with phenylalanine itself were smaller, but are also consistent with a carbanion mechanism, but with drastically increased commitments

  15. 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. PMID:27329353

  16. 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.

  17. A reconsideration for forming mechanism of optic fiber probe fabricated by static chemical etching

    NASA Astrophysics Data System (ADS)

    Chen, Yiru; Shen, Ruiqi

    2016-07-01

    The studies on the mechanism of static chemical etching are supplemented in this paper. Surface tension and diffusion effect are both taken into account. Theoretical analysis and data fitting show that the slant angle of the liquid-liquid interface leads to the maximum liquid rising, when diffusion effect is negligible.

  18. 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

  19. 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.

  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. Improved imaging of the carotid artery in the short-axis plane by a mechanical scanning ultrasonic probe.

    PubMed

    Kudo, Kazuki; Hasegawa, Hideyuki; Kanai, Hiroshi

    2007-03-01

    To image the intima-media complex of the carotid artery in a wider region, a method for measuring cross-sectional images in the arterial short-axis plane is presented. Using the proposed mechanical scanning system for an ultrasonic probe, cross-sectional images of a silicon rubber tube and a human carotid artery are measured in basic experiments and in in vivo experiments, respectively. These experiments show that this method successfully images the short-axis cross sections. Using the method proposed in this article, B-mode images in the short-axis plane can be accurately measured in a wider region than is possible with conventional methods. PMID:27278176

  2. 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}.

  3. 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.

  4. Mechanically activated switching of Si-based single-molecule junction as imaged with three-dimensional dynamic probe.

    PubMed

    Nakamura, Miki; Yoshida, Shoji; Katayama, Tomoki; Taninaka, Atsushi; Mera, Yutaka; Okada, Susumu; Takeuchi, Osamu; Shigekawa, Hidemi

    2015-01-01

    Understanding and extracting the full functions of single-molecule characteristics are key factors in the development of future device technologies, as well as in basic research on molecular electronics. Here we report a new methodology for realizing a three-dimensional (3D) dynamic probe of single-molecule conductance, which enables the elaborate 3D analysis of the conformational effect on molecular electronics, by the formation of a Si/single molecule/Si structure using scanning tunnelling microscopy (STM). The formation of robust covalent bonds between a molecule and Si electrodes, together with STM-related techniques, enables the stable and repeated control of the conformational modulation of the molecule. By 3D imaging of the conformational effect on a 1,4-diethynylbenzene molecule, a binary change in conductance with hysteresis is observed for the first time, which is considered to originate from a mechanically activated conformational change. PMID:26439280

  5. Mechanically activated switching of Si-based single-molecule junction as imaged with three-dimensional dynamic probe

    NASA Astrophysics Data System (ADS)

    Nakamura, Miki; Yoshida, Shoji; Katayama, Tomoki; Taninaka, Atsushi; Mera, Yutaka; Okada, Susumu; Takeuchi, Osamu; Shigekawa, Hidemi

    2015-10-01

    Understanding and extracting the full functions of single-molecule characteristics are key factors in the development of future device technologies, as well as in basic research on molecular electronics. Here we report a new methodology for realizing a three-dimensional (3D) dynamic probe of single-molecule conductance, which enables the elaborate 3D analysis of the conformational effect on molecular electronics, by the formation of a Si/single molecule/Si structure using scanning tunnelling microscopy (STM). The formation of robust covalent bonds between a molecule and Si electrodes, together with STM-related techniques, enables the stable and repeated control of the conformational modulation of the molecule. By 3D imaging of the conformational effect on a 1,4-diethynylbenzene molecule, a binary change in conductance with hysteresis is observed for the first time, which is considered to originate from a mechanically activated conformational change.

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

    PubMed Central

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

    2016-01-01

    One approach to improve contraction in the failing heart is the administration of calcium (Ca2 +) 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 Ca2 + 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 Ca2 + sensitivity of cardiac muscle. We conclude that i9 enhances Ca2 + sensitivity by stabilizing the open conformation of cTnC. These findings provide new insights into the in vivo mechanism of Ca2 + sensitization and demonstrate that directly targeting cTnC has significant potential in cardiovascular therapy. PMID:26853943

  7. 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. PMID:26795489

  8. 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.

  9. 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. PMID:16935884

  10. 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

  11. 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.

  12. 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

  13. Probing bactericidal mechanisms induced by cold atmospheric plasmas with Escherichia coli mutants

    SciTech Connect

    Perni, Stefano; Shama, Gilbert; Hobman, J. L.; Lund, P. A.; Kershaw, C. J.; Hidalgo-Arroyo, G. A.; Penn, C. W.; Deng, X. T.; Walsh, J. L.; Kong, M. G.

    2007-02-12

    Mechanisms of plasma-induced microbial inactivation have commonly been studied with physicochemical techniques. In this letter, Escherichia coli K-12 and its {delta}recA, {delta}rpoS, and {delta}soxS mutants are employed to discriminate effects of UV photons, OH radicals, and reactive oxygen species produced in atmospheric discharges. This microbiological approach exploits the fact that these E. coli mutants are defective in their resistance against various external stresses. By interplaying bacterial inactivation kinetics with optical emission spectroscopy, oxygen atoms are identified as a major contributor in plasma inactivation with minor contributions from UV photons, OH radicals, singlet oxygen metastables, and nitric oxide.

  14. 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.

  15. Probing bactericidal mechanisms induced by cold atmospheric plasmas with Escherichia coli mutants

    NASA Astrophysics Data System (ADS)

    Perni, Stefano; Shama, Gilbert; Hobman, J. L.; Lund, P. A.; Kershaw, C. J.; Hidalgo-Arroyo, G. A.; Penn, C. W.; Deng, X. T.; Walsh, J. L.; Kong, M. G.

    2007-02-01

    Mechanisms of plasma-induced microbial inactivation have commonly been studied with physicochemical techniques. In this letter, Escherichia coli K-12 and its ΔrecA, ΔrpoS, and ΔsoxS mutants are employed to discriminate effects of UV photons, OH radicals, and reactive oxygen species produced in atmospheric discharges. This microbiological approach exploits the fact that these E. coli mutants are defective in their resistance against various external stresses. By interplaying bacterial inactivation kinetics with optical emission spectroscopy, oxygen atoms are identified as a major contributor in plasma inactivation with minor contributions from UV photons, OH radicals, singlet oxygen metastables, and nitric oxide.

  16. Probing the Reaction Mechanism of Aluminum/Poly(vinylidene fluoride) Composites.

    PubMed

    DeLisio, Jeffery B; Hu, Xiuli; Wu, Tao; Egan, Garth C; Young, Gregory; Zachariah, Michael R

    2016-06-23

    Energetic thin films with high mass loadings of nanosized components have been recently fabricated using electrospray deposition. These films are composed of aluminum nanoparticles (nAl) homogeneously dispersed in an energetic fluoropolymer binder, poly(vinylidene fluoride) (PVDF). The nascent oxide shell of the nAl has been previously shown to undergo a preignition reaction (PIR) with fluoropolymers such as polytetrafluoroethylene (PTFE). This work examines the PIR between alumina and PVDF to further explain the reaction mechanism of the Al/PVDF system. Temperature jump (T-jump) ignition experiments in air, argon, and vacuum environments showed that the nAl is fluorinated by gas phase species due to a decrease in reactivity in a vacuum. Thermogravimetric analysis coupled with differential scanning calorimetry (TGA/DSC) was used to confirm the occurrence of a PIR, and gas phase products during the PIR and fluorination of nAl were investigated with temperature jump time-of-flight mass spectrometry (T-jump TOFMS). Results show a direct correlation between the amount of alumina in the PVDF film and the relative signal intensity of hydrogen fluoride release (HF). Although the PIR between alumina and PVDF plays an important role in the Al/PVDF reaction mechanism, burn speeds of Al/PVDF films containing additional pure alumina particles showed no burn speed enhancement. PMID:27228361

  17. Isotopically labeled chlorobenzenes as probes for the mechanism of cytochrome P-450 catalyzed aromatic hydroxylation

    SciTech Connect

    Korzekwa, K.R.; Swinney, D.C.; Trager, W.F. )

    1989-11-14

    Noncompetitive and competitive intermolecular deuterium isotope effects were measured for the cytochrome P-450 catalyzed hydroxylation of a series of selectively deuterated chlorobenzenes. An isotope effect of 1.27 accompanied the meta hydroxylation of chlorobenzene-2H5 as determined by two totally independent methods (EC-LC and GC-MS assays). All isotope effects associated with the meta hydroxylation of chlorobenzenes-3,5-2H2 and -2,4,6-2H3 were approximately 1.1. In contrast, competitive isotope studies on the ortho and para hydroxylation of chlorobenzenes-4-2H1, -3,5-2H2, and -2,4,6-2H3 resulted in significant inverse isotope effects (approximately 0.95) when deuterium was substituted at the site of oxidation whereas no isotope effect was observed for the oxidation of protio sites. These results eliminate initial epoxide formation and initial electron abstraction (charge transfer) as viable mechanisms for the cytochrome P-450 catalyzed hydroxylation of chlorobenzene. The results, however, can be explained by a mechanism in which an active triplet-like oxygen atom adds to the pi system in a manner analogous to that for olefin oxidation. The resulting tetrahedral intermediate can then rearrange to phenol directly or via epoxide or ketone intermediates.

  18. Probing the mechanical properties of brain cancer cells using a microfluidic cell squeezer device

    PubMed Central

    Khan, Z. S.; Vanapalli, S. A.

    2013-01-01

    Despite being invasive within surrounding brain tissues and the central nervous system, little is known about the mechanical properties of brain tumor cells in comparison with benign cells. Here, we present the first measurements of the peak pressure drop due to the passage of benign and cancerous brain cells through confined microchannels in a “microfluidic cell squeezer” device, as well as the elongation, speed, and entry time of the cells in confined channels. We find that cancerous and benign brain cells cannot be differentiated based on speeds or elongation. We have found that the entry time into a narrow constriction is a more sensitive indicator of the differences between malignant and healthy glial cells than pressure drops. Importantly, we also find that brain tumor cells take a longer time to squeeze through a constriction and migrate more slowly than benign cells in two dimensional wound healing assays. Based on these observations, we arrive at the surprising conclusion that the prevailing notion of extraneural cancer cells being more mechanically compliant than benign cells may not apply to brain cancer cells. PMID:24403988

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

    DOE PAGESBeta

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

    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

  20. 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

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

    SciTech Connect

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

    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 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

    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 and electron energy loss spectroscopy 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 can guide the design and improvement of LiFePO4 cathode for high-energy and high-power rechargeable battery for electric transportation.

  3. Non-Gilbert-damping Mechanism in a Ferromagnetic Heusler Compound Probed by Nonlinear Spin Dynamics.

    PubMed

    Pirro, P; Sebastian, T; Brächer, T; Serga, A A; Kubota, T; Naganuma, H; Oogane, M; Ando, Y; Hillebrands, B

    2014-11-28

    The nonlinear decay of propagating spin waves in the low-Gilbert-damping Heusler film Co_{2}Mn_{0.6}Fe_{0.4}Si is reported. Here, two initial magnons with frequency f_{0} scatter into two secondary magnons with frequencies f_{1} and f_{2}. The most remarkable observation is that f_{1} stays fixed if f_{0} is changed. This indicates, that the f_{1} magnon mode has the lowest instability threshold, which, however, cannot be understood if only Gilbert damping is present. We show that the observed behavior is caused by interaction of the magnon modes f_{1} and f_{2} with the thermal magnon bath. This evidences a significant contribution of the intrinsic magnon-magnon scattering mechanisms to the magnetic damping in high-quality Heusler compounds. PMID:25494091

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

    DOE PAGESBeta

    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 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

  5. Probing phase-space noncommutativity through quantum mechanics and thermodynamics of free particles and quantum rotors

    NASA Astrophysics Data System (ADS)

    Santos, Jonas F. G.; Bernardini, Alex E.; Bastos, Catarina

    2015-11-01

    Novel quantization properties related to the state vectors and the energy spectrum of a two-dimensional system of free particles are obtained in the framework of noncommutative (NC) quantum mechanics (QM) supported by the Weyl-Wigner formalism. Besides reproducing the magnetic field aspect of a Zeeman-like effect, the momentum space NC parameter introduces mutual information properties quantified by the quantum purity related to the relevant coordinates of the corresponding Hilbert space. Supported by the QM in the phase-space, the thermodynamic limit is obtained, and the results are extended to three-dimensional systems. The noncommutativity imprints on the thermodynamic variables related to free particles are identified and, after introducing some suitable constraints to fix an axial symmetry, the analysis is extended to two- and- three dimensional quantum rotor systems, for which the quantization aspects and the deviation from standard QM results are verified.

  6. 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. PMID:26478837

  7. 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

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

    PubMed

    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

  9. 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.

  10. 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.

  11. Probing the reaction mechanism of IspH protein by x-ray structure analysis

    PubMed Central

    Gräwert, Tobias; Span, Ingrid; Eisenreich, Wolfgang; Rohdich, Felix; Eppinger, Jörg; Bacher, Adelbert; Groll, Michael

    2010-01-01

    Isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) represent the two central intermediates in the biosynthesis of isoprenoids. The recently discovered deoxyxylulose 5-phosphate pathway generates a mixture of IPP and DMAPP in its final step by reductive dehydroxylation of 1-hydroxy-2-methyl-2-butenyl 4-diphosphate. This conversion is catalyzed by IspH protein comprising a central iron-sulfur cluster as electron transfer cofactor in the active site. The five crystal structures of IspH in complex with substrate, converted substrate, products and PPi reported in this article provide unique insights into the mechanism of this enzyme. While IspH protein crystallizes with substrate bound to a [4Fe-4S] cluster, crystals of IspH in complex with IPP, DMAPP or inorganic pyrophosphate feature [3Fe-4S] clusters. The IspH:substrate complex reveals a hairpin conformation of the ligand with the C(1) hydroxyl group coordinated to the unique site in a [4Fe-4S] cluster of aconitase type. The resulting alkoxide complex is coupled to a hydrogen-bonding network, which serves as proton reservoir via a Thr167 proton relay. Prolonged x-ray irradiation leads to cleavage of the C(1)-O bond (initiated by reducing photo electrons). The data suggest a reaction mechanism involving a combination of Lewis-acid activation and proton coupled electron transfer. The resulting allyl radical intermediate can acquire a second electron via the iron-sulfur cluster. The reaction may be terminated by the transfer of a proton from the β-phosphate of the substrate to C(1) (affording DMAPP) or C(3) (affording IPP). PMID:20080550

  12. Probing the self-assembly mechanism of diphenylalanine-based peptide nanovesicles and nanotubes.

    PubMed

    Guo, Cong; Luo, Yin; Zhou, Ruhong; Wei, Guanghong

    2012-05-22

    Nanostructures, particularly those from peptide self-assemblies, have attracted great attention lately due to their potential applications in nanotemplating and nanotechnology. Recent experimental studies reported that diphenylalanine-based peptides can self-assemble into highly ordered nanostructures such as nanovesicles and nanotubes. However, the molecular mechanism of the self-organization of such well-defined nanoarchitectures remains elusive. In this study, we investigate the assembly pathway of 600 diphenylalanine (FF) peptides at different peptide concentrations by performing extensive coarse-grained molecular dynamics (MD) simulations. Based on forty 0.6-1.8 μs trajectories at 310 K starting from random configurations, we find that FF dipeptides not only spontaneously assemble into spherical vesicles and nanotubes, consistent with previous experiments, but also form new ordered nanoarchitectures, namely, planar bilayers and a rich variety of other shapes of vesicle-like structures including toroid, ellipsoid, discoid, and pot-shaped vesicles. The assembly pathways are concentration-dependent. At low peptide concentrations, the self-assembly involves the fusion of small vesicles and bilayers, whereas at high concentrations, it occurs through the formation of a bilayer first, followed by the bending and closure of the bilayer. Energetic analysis suggests that the formation of different nanostructures is a result of the delicate balance between peptide-peptide and peptide-water interactions. Our all-atom MD simulation shows that FF nanostructures are stabilized by a combination of T-shaped aromatic stacking, interpeptide head-to-tail hydrogen-bonding, and peptide-water hydrogen-bonding interactions. This study provides, for the first time to our knowledge, the self-assembly mechanism and the molecular organization of FF dipeptide nanostructures. PMID:22468743

  13. Isotope exchange as a probe of the kinetic mechanism of pyrophosphate-dependent phosphofructokinase

    SciTech Connect

    Cho, Y.K.; Matsunaga, T.O.; Kenyon, G.I.; Bertagnolli, B.L.; Cook, P.F.

    1988-05-03

    Data obtained from isotope exchange at equilibrium, exchange of inorganic phosphate against forward reaction flux, and positional isotope exchange of /sup 18/O from the bridge position of pyrophosphate to a nonbridge position all indicate that the pyrophosphate-dependent phosphofructokinase fromPropionibacterium freudenreichii has a rapid equilibrium random kinetic mechanism. The maximum rates of isotope exchange at equilibrium for the (/sup 14/C)fructose 1,6-bisphosphate in equilibrium fructose 6-phosphate, (/sup 32/P)P/sub i/ in equilibrium MgPP/sub i/, and Mg(/sup 32/P)PP/sub i/ in equilibrium fructose, 1,6-bisphosphate exchange reactions increasing all four possible substrate-product pairs in constant ratio are identical, consistent with a rapid equilibrium mechanism. All exchange reactions are strongly inhibited at high concentrations of the fructose 6-phosphate (F6P)P/sub i/ and MgPP/sub i/P/sub i/ substrate-product pairs and weakly inhibited at high concentrations of the MgPP/sub i/fructose 1,6-bisphosphate (FBP) pair suggesting three dead-end complexes, E:F6P:P/sub i/, E:MgPP/sub i/:P/sub i/, and E:FBP:MgPP/sub i/, in agreement with initial velocity studies. Neither back-exchange by (/sup 32/P)P/sub i/ nor positional isotope exchange of /sup 18/O-bridge-labeled pyrophosphate was observed under any conditions, suggesting that either the chemical interconversion step or a step prior to it limits the overall rate of the reaction.

  14. Selective Probing of Gaseous Ammonia Using Red-Emitting Carbon Dots Based on an Interfacial Response Mechanism.

    PubMed

    Jiang, Bang-Ping; Zhou, Bo; Shen, Xing-Can; Yu, Yun-Xiang; Ji, Shi-Chen; Wen, Chang-Chun; Liang, Hong

    2015-12-21

    Solid-state fluorescence sensing is one of the most appealing detection techniques because of its simplicity and convenience in practical operation. Herein, we report the development of a red-emitting carbon dots (RCDs)-based material as a solid-state fluorescence sensor for the selective probing of gaseous ammonia. The RCDs were prepared by a low-cost, one-step carbonization method using sugar cane bagasse as the carbon precursor. The pristine RCDs were then directly coated on polyvinylidene fluoride membrane to produce a new fluorescence sensor capable of selectively distinguishing toxic gaseous ammonia from other analyte vapors through sensitive fluorescence quenching with a low detection limit. More importantly, the interfacial response mechanism occurring on the surface of the RCDs has been studied by X-ray photoelectron spectroscopy, Fourier-transform infrared spectroscopy, and Raman measurements. The results indicate that fluorescence quenching in the RCDs might result from ammonia-induced Michael addition through insertion of N into the C=C group and deprotonation of the carboxyl group. To the best of our knowledge, this is the first report that provides clear insight into the mechanism of surface chemistry on CDs in the solid state. PMID:26514914

  15. 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

  16. Mechanical properties of poly(dimethylsiloxane)-block-poly(2-methyloxazoline) polymersomes probed by atomic force microscopy.

    PubMed

    Jaskiewicz, Karmena; Makowski, Marcin; Kappl, Michael; Landfester, Katharina; Kroeger, Anja

    2012-08-28

    Poly(dimethylsiloxane)-block-poly(2-methyloxazoline) (PDMS-b-PMOXA) vesicles were characterized by a combination of dynamic light scattering (DLS), cryogenic transmission electron microscopy (cryo-TEM), and atomic force microscopy imaging and force spectroscopy (AFM). From DLS data, a hydrodynamic radius of ~150 nm was determined, and cryo-TEM micrographs revealed a bilayer thickness of ~16 nm. In AFM experiments on a silicon wafer substrate, adsorption led to a stable spherical caplike conformation of the polymersomes, whereas on mica, adsorption resulted also in vesicle fusion and formation of bilayer patches or multilayer stacks. This indicates a delicate balance between the mechanical stability of PDMS-b-PMOXA polymersomes on one hand and the driving forces for spreading on the other. A Young's modulus of 17 ± 11 MPa and a bending modulus of 7 ± 5 × 10(-18) J were derived from AFM force spectroscopy measurements. Therefore, the elastic response of the PDMS-b-PMOXA polymersomes to external stimuli is much closer to that of lipid vesicles compared to other types of polymersomes, such as polystyrene-block-poly(acrylic acid) (PS-b-PAA). PMID:22860888

  17. 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

    2015-11-01

    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. PMID:26538041

  18. Probing Energy and Electron Transfer Mechanisms in Fluorescence Quenching of Biomass Carbon Quantum Dots.

    PubMed

    Liang, Zicheng; Kang, Mijeong; Payne, Gregory F; Wang, Xiaohui; Sun, Runcang

    2016-07-13

    The recent discovery of biomass-derived carbon quantum dots (CQDs) offers the potential to extend the sensing and imaging capabilities of quantum dots (QDs) to applications that require biocompatibility and environmental friendliness. Many studies have confirmed the exciting optical properties of CQDs and suggested a range of applications, but realizing the potential of CQDs will require a deeper fundamental understanding of their photophysical behavior. Here, biomass-derived CQDs were synthesized by hydrothermal processing methods from the aminopolysaccharide chitosan, and their fluorescence quenching behaviors were investigated. A family of nitroaromatics with different ring substituents was used to generate systematically varying CQD-quenching behaviors. Experimental evidence including a correlation between quenching constant and spectral overlap, fluorescence lifetime decay, and donor-acceptor distance all demonstrate that the primary mechanism for QCD-quenching is Förster resonance energy transfer (FRET) and not electron transfer. Spectroelectrochemical studies with redox-dependent quenching molecules and studies with complex dye molecules further support this conclusion. We envision this fundamental understanding of CQDs will facilitate the application of these emerging nanomaterials for sensing and imaging. PMID:27314592

  19. Relation between Thermal and Magnetic Properties of Active Regions as a Probe of Coronal Heating Mechanisms

    NASA Astrophysics Data System (ADS)

    Yashiro, Seiji; Shibata, Kazunari

    2001-03-01

    We study the relation between thermal and magnetic properties of active regions in the corona observed with the soft X-ray telescope aboard Yohkoh. We derive the mean temperature and pressure of 64 mature active regions using the filter ratio technique, and examine the relationship of region size with temperature and pressure. We find that the temperature T of active regions increases with increasing region size L as T~L0.28, while the pressure P slightly decreases with the region size as P~L-0.16. We confirm the scaling law T~(PL)1/3 for mature active regions found by R. Rosner, W. H. Tucker, & G. S. Vaiana. We examined the magnetic properties of active regions by analyzing 31 active regions observed with the Solar and Heliospheric Observatory/Michelson Doppler Imager and find the following empirical scaling law between thermal and magnetic properties,Uth~Φ1.33,P~B0.78,where Uth, Φ, and B are the total thermal energy content, total magnetic flux, and average magnetic flux density of active regions, respectively. The former is consistent with the results of L. Golub et al., but the latter is not. Implications of our findings for coronal heating mechanisms are discussed.

  20. Directly probing the mechanical properties of the spindle and its matrix

    PubMed Central

    Matov, Alexandre; Danuser, Gaudenz; Mitchison, Timothy J.; Salmon, Edward D.

    2010-01-01

    Several recent models for spindle length regulation propose an elastic pole to pole spindle matrix that is sufficiently strong to bear or antagonize forces generated by microtubules and microtubule motors. We tested this hypothesis using microneedles to skewer metaphase spindles in Xenopus laevis egg extracts. Microneedle tips inserted into a spindle just outside the metaphase plate resulted in spindle movement along the interpolar axis at a velocity slightly slower than microtubule poleward flux, bringing the nearest pole toward the needle. Spindle velocity decreased near the pole, which often split apart slowly, eventually letting the spindle move completely off the needle. When two needles were inserted on either side of the metaphase plate and rapidly moved apart, there was minimal spindle deformation until they reached the poles. In contrast, needle separation in the equatorial direction rapidly increased spindle width as constant length spindle fibers pulled the poles together. These observations indicate that an isotropic spindle matrix does not make a significant mechanical contribution to metaphase spindle length determination. PMID:20176922

  1. Substrate analogues as probes of the catalytic mechanism of L-mandelate dehydrogenase from Rhodotorula graminis.

    PubMed Central

    Smékal, O; Reid, G A; Chapman, S K

    1994-01-01

    A detailed kinetic analysis of the oxidation of mono-substituted mandelates catalysed by L-(+)-mandelate dehydrogenase (L-MDH) from Rhodotorula graminis has been carried out to elucidate the role of the substrate in the catalytic mechanism. Values of Km and kcat. (25 degrees C, pH 7.5) were determined for mandelate and eight substrate analogues. Values of the activation parameters, delta H++ and delta S++ (determined over the range 5-37 degrees C), for mandelate and all substrate analogues were compensatory resulting in similar low values for free energies of activation delta G++ (approx. 60 kJ.mol-1 at 298.15 K) in all cases. A kinetic-isotope-effect value of 1.1 +/- 0.1 was observed using D,L-[2-2H]mandelate as substrate and was invariant over the temperature range studied. The logarithm of kcat. values for the enzymic oxidation of mandelate and all substrate analogues (except 4-hydroxymandelate) showed good correlation with Taft's dual substituent constant omega (where omega = omega I + 0.64 omega +R) and gave a positive reaction constant value, rho, of 0.36 +/- 0.07. This linear free-energy relationship was verified by analysing the data using isokinetic methods. These findings support the hypothesis that the enzyme-catalysed reaction proceeds via the same transition state for each substrate and indicates that this transition state is relatively nonpolar but has an electron-rich centre at the alpha-carbon position. PMID:8110205

  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. 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

  4. Probing Selection Mechanism of the Most Favorable Conformation of a Dipeptide in Chaotropic and Kosmotropic Solution.

    PubMed

    Jas, Gouri S; Middaugh, C Russell; Kuczera, Krzysztof

    2016-07-21

    Chaotropes like urea and guanidinium chloride (GdmCl) tend to destabilize, and kosmotropes like proline tend to stabilize folded structures of peptides and proteins. Here, we combine fluorescence anisotropy decay measurements and molecular dynamics simulations to gain a microscopic understanding of the molecular mechanism for shifting conformational preferences in aqueous, GdmCl, urea, and proline solutions of a simple model dipeptide, N-acetyl-tryptophan-amide (NATA). Measured anisotropy decay of NATA as a function of temperature, pH, and cosolvent concentrations showed reorientations moderately slower in GdmCl and urea and substantially slower in proline compared to those of aqueous environment. A small change in pH significantly slows orientation time in water and GdmCl and less markedly in urea. Computationally, we use molecular dynamics with dihedral restraints to separately analyze the motions and interactions of the representative NATA conformers in the four different solvent environments. This novel analysis provides a dissection of the observed overall diffusion rates into contributions from individual dipeptide conformations. The variation of rotational diffusion rates with conformation are quite large. Population-weighted averaging or using properties of the major cluster reproduces the dynamical features of the full unrestrained dynamics. Additionally, we correlate the observable diffusion rates with microscopic features of conformer size, shape, and solvation. This analysis uncovered underlying differences in detailed atomistic behavior of the three cosolvents-urea, GdmCl, and proline. For both urea and the pure water system we find good agreement with hydrodynamic theory, with diffusion rates primarily correlated with conformer size and shape. In contrast, for GdmCl and proline solutions, the variation in conformer diffusion rates was mostly determined by specific interactions with the cosolvents. We also find preferences for different molecular

  5. Human Augmenter of Liver Regeneration; probing the catalytic mechanism of a flavin-dependent sulfhydryl oxidase†

    PubMed Central

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

    2013-01-01

    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

  6. 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

  7. 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. PMID:26130378

  8. Ultrafast pump-probe microscopy reveals the mechanism of selective fs laser structuring of transparent thin films for maskless micropatterning

    NASA Astrophysics Data System (ADS)

    Rapp, Stephan; Rosenberger, Janosch; Domke, Matthias; Heise, Gerhard; Huber, Heinz P.; Schmidt, Michael

    2014-01-01

    Maskless patterning of biocompatible Ta2O5/Pt/glass sensor chips can be realized by ultra-short laser pulse ablation. At a fluence of 0.2 J/cm2, the thin Ta2O5 film is selectively lifted-off by indirectly-induced ablation at laser wavelenghts where the Ta2O5 is transparent and the Pt absorbing. This enables precise and very fast structuring. Here, 660 fs laser pulses at a center wavelength of 1053 nm are applied. The driving physical effects of this ablation mechanism are revealed by pump-probe microscopy. This technique allows the observation of the whole ablation process ranging temporally from femtoseconds to microseconds. An ultrafast heat-expansion in the absorbing Pt, initiating a shock-wave to the Ta2O5 within the first 10 ps, bulges the Ta2O5 film after some nanoseconds. Bulging velocities of 750 m/s are determined corresponding to an extreme acceleration of about 1010 g. Exceeding the stress limit in the Ta2O5 causes film disintegration after 50 ns. A model, describing essential reaction steps, is developed. This model is also applicable to other industrial important layer systems, where thin transparent films have to be removed.

  9. Single Molecule Investigation of Glycine-Chlorite Interaction by Cross-Correlated Scanning Probe Microscopy and Quantum Mechanics Simulations.

    PubMed

    Moro, Daniele; Ulian, Gianfranco; Valdrè, Giovanni

    2015-04-21

    In this work, we studied the interaction of glycine with the (001) surface of chlorite mineral at a single molecule level by cross-correlating scanning probe microscopy (SPM) and ab initio quantum mechanics (QM) investigations. Chlorite mineral is particularly interesting and peculiar for the interaction with organic molecules because it presents an alternated stacking of brucite-like (hydrophobic) and talc-like (hydrophilic) layers of different polarities. Brucite-like is positive, whereas talc-like is negative. The experimental atomic force microscopy (AFM) observations show that glycine is stably and selectively adsorbed on the brucite-like layer, organized in monolayers with different patterns. The sizes of single molecules of glycine measured by AFM are in agreement with those calculated by QM. Glycine molecules were found to align both at the edges and on the terraces of the brucitic surface. QM simulations confirmed the AFM observations that glycine molecule is adsorbed with high adsorption energy preferentially with its plane parallel to the (001) brucite-like surface. QM also provided the geometry conformation of the molecule and the bonding scheme between glycine and brucite surface. This kind of data can be very helpful both to biotechnological applications of this substrate and to depict some important processes that might have been occurred in prebiotic environments. PMID:25830864

  10. Probing the Catalytic Mechanism Involved in the Isocitrate Lyase Superfamily: Hybrid Quantum Mechanical/Molecular Mechanical Calculations on 2,3-Dimethylmalate Lyase.

    PubMed

    Jongkon, Nathjanan; Chotpatiwetchkul, Warot; Gleeson, M Paul

    2015-09-01

    The isocitrate lyase (ICL) superfamily catalyzes the cleavage of the C(2)-C(3) bond of various α-hydroxy acid substrates. Members of the family are found in bacteria, fungi, and plants and include ICL itself, oxaloacetate hydrolase (OAH), 2-methylisocitrate lyase (MICL), and (2R,3S)-dimethylmalate lyase (DMML) among others. ICL and related targets have been the focus of recent studies to treat bacterial and fungal infections, including tuberculosis. The catalytic process by which this family achieves C(2)-C(3) bond breaking is still not clear. Extensive structural studies have been performed on this family, leading to a number of plausible proposals for the catalytic mechanism. In this paper, we have applied quantum mechanical/molecular mechanical (QM/MM) methods to the most recently reported family member, DMML, to assess whether any of the mechanistic proposals offers a clear energetic advantage over the others. Our results suggest that Arg161 is the general base in the reaction and Cys124 is the general acid, giving rise to a rate-determining barrier of approximately 10 kcal/mol. PMID:26224328

  11. Soybean epoxide hydrolase: identification of the catalytic residues and probing of the reaction mechanism with secondary kinetic isotope effects.

    PubMed

    Blée, Elizabeth; Summerer, Stephan; Flenet, Martine; Rogniaux, Hélène; Van Dorsselaer, Alain; Schuber, Francis

    2005-02-25

    Soybean epoxide hydrolase catalyzes the oxirane ring opening of 9,10-epoxystearate via a two-step mechanism involving the formation of an alkylenzyme intermediate, which, in contrast to most epoxide hydrolases studied so far, was found to be the rate-limiting step. We have probed residues potentially involved in catalysis by site-directed mutagenesis. Mutation of His(320), a residue predicted from sequence analysis to belong to the catalytic triad of the enzyme, considerably slowed down the second half-reaction. This kinetic manipulation provoked an accumulation of the reaction intermediate, which could be trapped and characterized by electrospray ionization mass spectrometry. As expected, mutation of Asp(126) totally abolished the activity of the enzyme from its crucial function as nucleophile involved in the formation of the alkylenzyme. In line with its role as the partner of His(320) in the "charge relay system," mutation of Asp(285) dramatically reduced the rate of catalysis. However, the mutant D285L still exhibited a very low residual activity, which, by structural analysis and mutagenesis, has been tentatively attributed to Glu(195), another acidic residue of the active site. Our studies have also confirmed the fundamental role of the conserved Tyr(175) and Tyr(255) residues, which are believed to activate the oxirane ring. Finally, we have determined the secondary tritium kinetic isotope effects on the epoxide opening step of 9,10-epoxystearate. The large observed values, i.e. (T)(V/K(m)) approximately 1.30, can be interpreted by the occurrence of a very late transition state in which the epoxide bond is broken before the nucleophilic attack by Asp(126) takes place. PMID:15596432

  12. 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.

  13. 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

  14. Probe assembly

    SciTech Connect

    Avera, C.J.

    1981-01-06

    A hand-held probe assembly, suitable for monitoring a radioactive fibrinogen tracer, is disclosed comprising a substantially cylindrically shaped probe handle having an open end. The probe handle is adapted to be interconnected with electrical circuitry for monitoring radioactivity that is sensed or detected by the probe assembly. Mounted within the probe handle is a probe body assembly that includes a cylindrically shaped probe body inserted through the open end of the probe handle. The probe body includes a photomultiplier tube that is electrically connected with a male connector positioned at the rearward end of the probe body. Mounted at the opposite end of the probe body is a probe head which supports an optical coupler therewithin. The probe head is interconnected with a probe cap which supports a detecting crystal. The probe body assembly, which consists of the probe body, the probe head, and the probe cap is supported within the probe handle by means of a pair of compressible o-rings which permit the probe assembly to be freely rotatable, preferably through 360*, within the probe handle and removable therefrom without requiring any disassembly.

  15. 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. PMID:26977372

  16. 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

  17. 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. PMID:26469730

  18. 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

  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. PMID:27258486

  20. Probing Kinetic Mechanisms of Protein Function and Folding with Time-Resolved Natural and Magnetic Chiroptical Spectroscopies

    PubMed Central

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

    2012-01-01

    Recent and ongoing developments in time-resolved spectroscopy have made it possible to monitor circular dichroism, magnetic circular dichroism, optical rotatory dispersion, and magnetic optical rotatory dispersion with nanosecond time resolution. These techniques have been applied to determine structural changes associated with the function of several proteins as well as to determine the nature of early events in protein folding. These studies have required new approaches in triggering protein reactions as well as the development of time-resolved techniques for polarization spectroscopies with sufficient time resolution and sensitivity to probe protein structural changes. PMID:22312279

  1. 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

  2. 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.

  3. 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.

  4. Nondestructive Complete Mechanical Characterization of Zinc Blende and Wurtzite GaAs Nanowires Using Time-Resolved Pump-Probe Spectroscopy.

    PubMed

    Mante, Pierre-Adrien; Lehmann, Sebastian; Anttu, Nicklas; Dick, Kimberly A; Yartsev, Arkady

    2016-08-10

    We have developed and demonstrated an experimental method, based on the picosecond acoustics technique, to perform nondestructive complete mechanical characterization of nanowires, that is, the determination of the complete elasticity tensor. By means of femtosecond pump-probe spectroscopy, coherent acoustic phonons were generated in an ensemble of nanowires and their dynamics was resolved. Specific phonon modes were identified and the detection mechanism was addressed via wavelength dependent experiments. We calculated the exact phonon dispersion relation of the nanowires by fitting the experimentally observed frequencies, thus allowing the extraction of the complete elasticity tensor. The elasticity tensor and the nanowire diameter were determined for zinc blende GaAs nanowires and were found to be in a good agreement with literature data and independent measurements. Finally, we have applied this technique to characterize wurtzite GaAs nanowires, a metastable phase in bulk, for which no experimental values of elastic constants are currently available. Our results agree well with previous first principle calculations. The proposed approach to the complete and nondestructive mechanical characterization of nanowires will allow the efficient mechanical study of new crystal phases emerging in nanostructures, as well as size-dependent properties of nanostructured materials. PMID:27352041

  5. Effect of Sequence Variation on the Mechanical Response of Amyloid Fibrils Probed by Steered Molecular Dynamics Simulation

    PubMed Central

    Ndlovu, Hlengisizwe; Ashcroft, Alison E.; Radford, Sheena E.; Harris, Sarah A.

    2012-01-01

    The mechanical failure of mature amyloid fibers produces fragments that act as seeds for the growth of new fibrils. Fragmentation may also be correlated with cytotoxicity. We have used steered atomistic molecular dynamics simulations to study the mechanical failure of fibrils formed by the amyloidogenic fragment of human amylin hIAPP20-29 subjected to force applied in a variety of directions. By introducing systematic variations to this peptide sequence in silico, we have also investigated the role of the amino-acid sequence in determining the mechanical stability of amyloid fibrils. Our calculations show that the force required to induce mechanical failure depends on the direction of the applied stress and upon the degree of structural order present in the β-sheet assemblies, which in turn depends on the peptide sequence. The results have implications for the importance of sequence-dependent mechanical properties on seeding the growth of new fibrils and the role of breakage events in cytotoxicity. PMID:22325282

  6. On the use of SPM to probe the interplay between polymer surface chemistry and polymer surface mechanics

    NASA Astrophysics Data System (ADS)

    Brogly, Maurice; Noel, Olivier; Awada, Houssein; Castelein, Gilles

    2007-03-01

    Adhesive properties of a polymer surface results from the complex contribution of surface chemistry and activation of sliding and dissipating mechanisms within the polymer surface layer. The purpose of this study is to dissociate the different contributions (chemical and mechanical) included in an AFM force-distance curve in order to establish relationships between the surface viscoelastic properties of the polymer, the surface chemistry of functionalized polymer surfaces and the adhesive forces, as determined by C-AFM experiments. Indeed we are interested in the measurements of local attractive or adhesive forces in AFM contact mode, of controlled chemical and mechanical model substrates. In order to investigate the interplay between mechanical or viscoelastic mechanisms and surface chemistry during the tip - polymer contact, we achieved force measurements on model PDMS polymer networks, whose surfaces are chemically controlled with the same functional groups as before (silicon substrates). On the basis of AFM nano-indentation experiments, surface Young moduli have been determined. The results show that the viscoelastic contribution is dominating in the adhesion force measurement. We propose an original model, which express the local adhesion force to the energy dissipated within the contact and the surface properties of the material (thermodynamic work of adhesion). Moreover we show that the dissipation function is related to Mc, the mass between crosslinks of the network.

  7. Photodetachment of Zwitterions: Probing Intramolecular Coulomb Repulsion and Attraction in the Gas Phase Using Mono- Decarboxylated Pyridinium Dicarboxylates. Implications on the Mechanism of Orotidine 5' -Monophosphate Decarboxylase

    SciTech Connect

    Wang, Xue B.; Dacres, J E.; Yang, Xin; Lis, Lev; Bedell, Victoria M.; Wang, Lai S.; Kass, Steven R.

    2003-11-11

    Negative ion photoelectron spectra resulting from the decarboxylation of nine zwitterionic pyridinium dicarboxylates (D(x,y)) are reported. Structural assignments are made on the basis of analogy to the spectra of related species, labeling experiments with C-13- or H-2-containing substrates, independent syntheses, and comparison to density functional theory and ab initio (B3LYP and CCSD(T), respectively) results. In some cases, an acid-catalyzed isomerization of the D(xy)-CO2 ions was found to take place. Adiabatic detachment energies of the resulting zwitterionic ions were measured and are well reproduced by theory. The relative stabilities of the D(x,Y)- CO2 decarboxylation products are largely determined by their intramolecular electrostatic interactions, which are directly probed by the photoelectron spectra and were analyzed in terms of the resulting Coulombic forces. Expulsion of carbon dioxide from the D(x,y) ions was also used as an electrostatic model to probe the mechanism of the enzyme-catalyzed conversion of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP). It was found that the loss of CO2 from these zwitterions; and from oxygen-protonated OMP is retarded by the presence of an additional anionic group. This suggests that the formation of a zwitterion intermediate in the enzyme-catalyzed transformation of OMP to UMP may have less of an energetic impact than commonly thought and could be a''red herring''. If so, the electrostatic stress mechanism proposed by Larsen et al. and Pai, Guo, and co-workers maybe followed.

  8. AFM probing of polymer/nanofiller interfacial adhesion and its correlation with bulk mechanical properties in a poly(ethylene terephthalate) nanocomposite.

    PubMed

    Aoyama, Shigeru; Park, Yong Tae; Macosko, Christopher W; Ougizawa, Toshiaki; Haugstad, Greg

    2014-11-01

    The interfacial adhesion between polymer and nanofiller plays an important role in affecting the properties of nanocomposites. The detailed relationship between interfacial adhesion and bulk properties, however, is unclear. In this work, we developed an atomic force microscopy (AFM)-based abrasive scanning methodology, as applied to model laminate systems, to probe the strength of interfacial adhesion relevant to poly(ethylene terephthalate) (PET)/graphene or clay nanocomposites. Graphite and mica substrates covered with ∼2 nm thick PET films were abrasively sheared by an AFM tip as a model measurement of interfacial strength between matrix PET and dispersed graphene and clay, respectively. During several abrasive raster-scan cycles, PET was shear-displaced from the scanned region. At temperatures below the PET glass transition, PET on graphite exhibited abrupt delamination (i.e., full adhesive failure), whereas PET on mica did not; rather, it exhibited a degree of cohesive failure within the shear-displaced layer. Moreover, 100-fold higher force scanning procedures were required to abrade through an ultimate "precursor" layer of PET only ∼0.2-0.5 nm thick, which must be largely disentangled from the matrix polymer. Thus, the adhesive interface of relevance to the strength of clay-filler nanocomposites is between matrix polymer and strongly bound polymer. At 90 °C, above the bulk PET glass transition temperature, the PET film exhibited cohesive failure on both graphite and mica. Our results suggest that there is little difference in the strength of the relevant interfacial adhesion in the two nanocomposites within the rubbery dynamic regime. Further, the bulk mechanical properties of melt mixed PET/graphene and PET/clay nanocomposites were evaluated by dynamic mechanical analysis. The glassy dynamic storage modulus of the PET/clay nanocomposite was higher than that of PET/graphene, correlating with the differences in interfacial adhesion probed by AFM. PMID

  9. Photodetachment of zwitterions: probing intramolecular Coulomb repulsion and attraction in the gas phase using mono-decarboxylated pyridinium dicarboxylates. Implications on the mechanism of orotidine 5'-monophosphate decarboxylase.

    PubMed

    Wang, Xue-Bin; Dacres, Jelena E; Yang, Xin; Lis, Lev; Bedell, Victoria M; Wang, Lai-Sheng; Kass, Steven R

    2003-06-01

    Negative ion photoelectron spectra resulting from the decarboxylation of nine zwitterionic pyridinium dicarboxylates (D(x,y)) are reported. Structural assignments are made on the basis of analogy to the spectra of related species, labeling experiments with (13)C- or (2)H-containing substrates, independent syntheses, and comparison to density functional theory and ab initio (B3LYP and CCSD(T), respectively) results. In some cases, an acid-catalyzed isomerization of the D(x,y)-CO(2) ions was found to take place. Adiabatic detachment energies of the resulting zwitterionic ions were measured and are well reproduced by theory. The relative stabilities of the D(x,y)-CO(2) decarboxylation products are largely determined by their intramolecular electrostatic interactions, which are directly probed by the photoelectron spectra and were analyzed in terms of the resulting Coulombic forces. Expulsion of carbon dioxide from the D(x,y) ions was also used as an electrostatic model to probe the mechanism of the enzyme-catalyzed conversion of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP). It was found that the loss of CO(2) from these zwitterions and from oxygen-protonated OMP is retarded by the presence of an additional anionic group. This suggests that the formation of a zwitterion intermediate in the enzyme-catalyzed transformation of OMP to UMP may have less of an energetic impact than commonly thought and could be a "red herring". If so, the electrostatic stress mechanism proposed by Larsen et al. and Pai, Guo, and co-workers maybe followed. PMID:12769593

  10. 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.

  11. 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. PMID:26476413

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  13. Mechanical unfolding of human telomere G-quadruplex DNA probed by integrated fluorescence and magnetic tweezers spectroscopy.

    PubMed

    Long, Xi; Parks, Joseph W; Bagshaw, Clive R; Stone, Michael D

    2013-02-01

    Single-molecule techniques facilitate analysis of mechanical transitions within nucleic acids and proteins. Here, we describe an integrated fluorescence and magnetic tweezers instrument that permits detection of nanometer-scale DNA structural rearrangements together with the application of a wide range of stretching forces to individual DNA molecules. We have analyzed the force-dependent equilibrium and rate constants for telomere DNA G-quadruplex (GQ) folding and unfolding, and have determined the location of the transition state barrier along the well-defined DNA-stretching reaction coordinate. Our results reveal the mechanical unfolding pathway of the telomere DNA GQ is characterized by a short distance (<1 nm) to the transition state for the unfolding reaction. This mechanical unfolding response reflects a critical contribution of long-range interactions to the global stability of the GQ fold, and suggests that telomere-associated proteins need only disrupt a few base pairs to destabilize GQ structures. Comparison of the GQ unfolded state with a single-stranded polyT DNA revealed the unfolded GQ exhibits a compacted non-native conformation reminiscent of the protein molten globule. We expect the capacity to interrogate macromolecular structural transitions with high spatial resolution under conditions of low forces will have broad application in analyses of nucleic acid and protein folding. PMID:23303789

  14. 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.

  15. Probing red blood cell mechanics, rheology and dynamics with a two-component multi-scale model

    PubMed Central

    Li, Xuejin; Peng, Zhangli; Lei, Huan; Dao, Ming; Karniadakis, George Em

    2014-01-01

    This study is partially motivated by the validation of a new two-component multi-scale cell model we developed recently that treats the lipid bilayer and the cytoskeleton as two distinct components. Here, the whole cell model is validated and compared against several available experiments that examine red blood cell (RBC) mechanics, rheology and dynamics. First, we investigated RBC deformability in a microfluidic channel with a very small cross-sectional area and quantified the mechanical properties of the RBC membrane. Second, we simulated twisting torque cytometry and compared predicted rheological properties of the RBC membrane with experimental measurements. Finally, we modelled the tank-treading (TT) motion of a RBC in a shear flow and explored the effect of channel width variation on the TT frequency. We also investigated the effects of bilayer–cytoskeletal interactions on these experiments and our simulations clearly indicated that they play key roles in the determination of cell membrane mechanical, rheological and dynamical properties. These simulations serve as validation tests and moreover reveal the capabilities and limitations of the new whole cell model. PMID:24982252

  16. Quantifying Energy-Time Dispersion of Relativistic Electron Microbursts to Constrain Their Generation Mechanism: Coordinated Studies Using FIREBIRD, Van Allen Probes, and BARREL

    NASA Astrophysics Data System (ADS)

    Spence, H. E.; Blake, J. B.; Crew, A. B.; Fennell, J. F.; Klumpar, D. M.; Larsen, B.; Millan, R. M.; Miyoshi, Y.; O'Brien, T. P., III; Reeves, G. D.; Smith, S. S.

    2015-12-01

    In this paper, we quantify properties of relativistic electron precipitation at low altitudes in order to constrain the mechanism(s) for microburst loss occurring in Earth's radiation belt. Though studied for decades, the physical mechanism(s) responsible for the loss of radiation belt particles through microburst precipitation to the atmosphere remains uncertain, and, unquantified in a global sense. Accordingly, we appeal to new measurements from the NSF FIREBIRD (Focused Investigation of Relativistic Electron Burst Intensity Range and Dynamics) mission. FIREBIRD comprises two 1.5U CubeSats launched in early 2015 into identical coplanar polar low altitude orbits; a small spring imparted a slow separation between the two spacecraft upon orbit insertion. Over the course of the mission, the orbits of the two identically-instrumented spacecraft slowly evolve, sampling spatial scales of electron precipitation measured simultaneously at separations of 10's to 1000's of kilometers. FIREBIRD provides electron energy spectra from ~250 keV to > 1MeV, with both high spectral resolution (6 to 12 energy channels) and high temporal resolution (principally operated at ~18 millisecond sampling). To do so, FIREBIRD employs two solid-state detectors on each CubeSat, one an uncollimated detector with a large geometric factor (optimized for weak events) and the other a collimated detector (optimized for intense events). While the primary goal of FIREBIRD is to establish the spatial/temporal coherence of microburst precipitation, it also provides the capability of quantifying on each spacecraft the dispersive properties of microbursts. In this work, we report on the energy-time dispersive qualities of individual bursts, which in turn provide a means for testing models and constraining where and how the bursts are generated. To test these models, we use measurements made near the magnetic equator by the Van Allen Probes mission during times when the two FIREBIRD and two Van Allen

  17. 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.

  18. Probing minimal supergravity in the type-I seesaw mechanism with lepton flavor violation at the CERN LHC

    SciTech Connect

    Hirsch, M.; Valle, J. W. F.; Porod, W.; Romao, J. C.; del Moral, A. Villanova

    2008-07-01

    The most general supersymmetric seesaw mechanism has too many parameters to be predictive and thus can not be excluded by any measurements of lepton flavor violating (LFV) processes. We focus on the simplest version of the type I seesaw mechanism assuming minimal supergravity boundary conditions. We compute branching ratios for the LFV scalar tau decays, {tau}-tilde{sub 2}{yields}(e,{mu})+{chi}{sub 1}{sup 0}, as well as loop-induced LFV decays at low energy, such as l{sub i}{yields}l{sub j}+{gamma} and l{sub i}{yields}3l{sub j}, exploring their sensitivity to the unknown seesaw parameters. We find some simple, extreme scenarios for the unknown right-handed parameters, where ratios of LFV branching ratios correlate with neutrino oscillation parameters. If the overall mass scale of the left neutrinos and the value of the reactor angle were known, the study of LFV allows, in principle, to extract information about the so-far unknown right-handed neutrino parameters.

  19. Ambient-temperature Conditioning as a Probe of Double-C Transformation Mechanisms in Pu-2.0 at. % Ga

    SciTech Connect

    Jeffries, J R; Blobaum, K M; Wall, M A; Schwartz, A J

    2008-04-02

    The gallium-stabilized Pu-2.0 at. % Ga alloy undergoes a partial or incomplete low-temperature martensitic transformation from the metastable {delta} phase to the gallium-containing, monoclinic {alpha}{prime} phase near -100 C. This transformation has been shown to occur isothermally and it displays anomalous double-C kinetics in a time-temperature-transformation (TTT) diagram, where two nose temperatures anchoring an upper- and lower-C describe minima in the time for the initiation of transformation. The underlying mechanisms responsible for the double-C behavior are currently unresolved, although recent experiments suggest that a conditioning treatment--wherein, following an anneal at 375 C, the sample is held at a sub-anneal temperature for a period of time--significantly influences the upper-C of the TTT diagram. As such, elucidating the effects of the conditioning treatment upon the {delta} {yields} {alpha}{prime} transformation can provide valuable insights into the fundamental mechanisms governing the double-C kinetics of the transition. Following a high-temperature anneal, a differential scanning calorimeter (DSC) was used to establish an optimal conditioning curve that depicts the amount of {alpha}{prime} formed during the transformation as a function of conditioning temperature for a specified time. With the optimal conditioning curve as a baseline, the DSC was used to explore the circumstances under which the effects of the conditioning treatment were destroyed, resulting in little or no transformation.

  20. Probing mechanical properties of thin film and ceramic materials in micro- and nano-scale using indentation techniques

    NASA Astrophysics Data System (ADS)

    Charitidis, Costas A.

    2010-10-01

    In this study, we report on the mechanical properties, failure and fracture modes in two cases of engineering materials; that is transparent silicon oxide thin films onto poly(ethylene terephthalate) (PET) membranes and glass-ceramic materials. The first system was studied by the quazi-static indentation technique at the nano-scale and the second by the static indentation technique at the micro-scale. Nanocomposite laminates of silicon oxide thin films onto PET were found to sustain higher scratch induced stresses and were effective as protective coating material for PET membranes. Glass-ceramic materials with separated crystallites of different morphologies sustained a mixed crack propagation pattern in brittle fracture mode.

  1. 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.

  2. 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

  3. Probing the reaction mechanism of spore photoproduct lyase (SPL) via diastereoselectively labeled dinucleotide SP TpT substrates

    PubMed Central

    Yang, Linlin; Lin, Gengjie; Liu, Degang; Dria, Karl J.; Telser, Joshua; Li, Lei

    2011-01-01

    5-thyminyl-5,6-dihydrothymine (commonly called spore photoproduct or SP) is the exclusive DNA photo-damage product in bacterial endospores. It is generated in the bacterial sporulation phase and repaired by a radical SAM enzyme, spore photoproduct lyase (SPL), at the early germination phase. SPL utilizes a special [4Fe-4S] cluster to reductively cleave S-adenosylmethionine (SAM) to generate a reactive 5′-dA radical. The 5′-dA radical is proposed to abstract one of the two H atoms at the C6 carbon of SP to initiate the repair process. Via organic synthesis and DNA photochemistry, we selectively labeled the 6-HproS or 6-HproR position with a deuterium in a dinucleotide SP TpT substrate. Monitoring the deuterium migration in enzyme catalysis (employing Bacillus subtilis SPL) revealed that it is the 6-HproR atom of SP that is abstracted by the 5′-dA radical. Surprisingly, the abstracted deuterium was not returned to the resulting TpT after enzymatic catalysis, an H atom from the aqueous buffer was incorporated into TpT instead. This result questions the currently hypothesized SPL mechanism which excludes the involvement of protein residue(s) in SPL reaction, suggesting that some protein residue(s), which is capable of exchanging a proton with the aqueous buffer, is involved in the enzyme catalysis. Moreover, evidence has been obtained for a possible SAM regeneration after each catalytic cycle; however, such a regeneration process is more complex than currently thought, with one or even more protein residues involved as well. These observations have enabled us to propose a modified reaction mechanism for this intriguing DNA repair enzyme. PMID:21671623

  4. 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

  5. Probing the spontaneous reduction mechanism of platinum ions confined in the nanospace by X-ray absorption fine structure spectroscopy.

    PubMed

    Jiang, Fangling; Li, Cheng; Fu, Haiying; Guo, Xiaojing; Wu, Guozhong; Chen, Shimou

    2016-07-28

    The reduction mechanism of Pt(4+) ions confined in the channel of multi-walled carbon nanotubes was mainly investigated using X-ray absorption fine structure (XAFS) spectroscopy, with the aid of TEM, Raman, XRD and ICP-AES studies. The XAFS spectra revealed the spontaneous formation of Pt nanoparticles when H2PtCl6 was confined in multi-walled carbon nanotubes (MWCNTs). The Pt L3-edge X-ray absorption near edge structure (XANES) coupled with the C K-edge NEXAFS results indicated that the reduction of Pt(4+) from tetravalent to zerovalent was attributed to the electron transfer from MWCNTs. The Fourier transform R-space of the Pt L3-edge XAFS data displayed that the nanoconfinement effect of MWCNTs promoted the formation of Pt nanoparticles. Moreover, the Pt-Pt bond length in confined Pt nanoparticles became shorter than that of Pt in the bulk state. Furthermore, by varying the inner diameter of MWCNTs from 15 nm to 10 nm and 5 nm, the Pt-Pt bond length of nanoconfined Pt nanoparticles decreased gradually. The results clearly revealed that MWCNTs acting as enriched electron donors can continuously reduce the confined Pt ions to Pt nanoparticles, thereby showing a great potential for the design of a new type of confined nanocatalysts. PMID:27373466

  6. Cys-scanning Disulfide crosslinking and Bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ

    PubMed Central

    Molnar, Kathleen S; Bonomi, Massimiliano; Pellarin, Riccardo; Clinthorne, Graham D; Gonzalez, Gabriel; Goldberg, Shalom D; Goulian, Mark; Sali, Andrej; DeGrado, William F

    2014-01-01

    Summary Bacteria transduce signals across the membrane using two-component systems (TCSs), consisting of a membrane-spanning sensor histidine kinase and a cytoplasmic response regulator. In Gram negative bacteria, the PhoPQ TCS senses cations and antimicrobial peptides, yet little is known about the structural changes involved in transmembrane signaling. We construct a model of PhoQ signal transduction using Bayesian inference, based on disulfide crosslinking data and homologous crystal structures. The data are incompatible with a single conformation but are instead consistent with two interconverting structures. These states differ in membrane depth of the periplasmic acidic patch and the reciprocal displacement of diagonal helices along the dimer interface. Studies of multiple histidine kinases suggest this repacking might be a common mode of signal transduction in sensor His-kinase receptors. Since a similar scissors model has been ruled out in CheA-linked chemoreceptors, the new evidence suggests that sensor His-kinase and CheA-linked receptors possess different signaling mechanisms. PMID:25087511

  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 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.

  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. PMID:26045566

  10. 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.

  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

    2015-01-01

    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

  12. Sensitive determination of norfloxacin by the fluorescence probe of terbium (III)- sodium dodecylbenzene sulfonate and its luminescence mechanism.

    PubMed

    Tong, Changlun; Xiang, Guanghong

    2006-11-01

    The fluorescence system of the norfloxacin-Tb3+- sodium dodecylbenzene sulfonate (SDBS) was investigated in this paper. The experiments indicated that the fluorescence intensity of the Tb3+-SDBS was greatly enhanced by the norfloxacin. On the basis of the above findings, a sensitive fluorimetric method for determining the norfloxacin was established. The fluorescence intensity was measured by a 1-cm quartz cell with the excitation wavelength of 290 nm and the emission wavelength of 545 nm. The enhanced fluorescence intensity of the system (Delta F) showed a good linear relationship with the concentration of norfloxacin in the range of 5.0x10(-9) mol L(-1)-2.0x10(-6) mol L-1, its correlation coefficient was 0.9991 and the detection limit (S/N=3) was 1.2x10(-9) mol L-1. The presented method was used to determine the norfloxacin in real pharmaceutical samples. The luminescence mechanism was also discussed in detail. In the fluorescence system of the norfloxacin-Tb3+-SDBS, the SDBS not only acted as the surfactant, but also acted as the energy donor. PMID:16983510

  13. Early Holocene volcanism in CKD (Kamchatka) as a mechanical probe of the stress level in the crust.

    NASA Astrophysics Data System (ADS)

    Simakin, Alexander; Shaposhnikova, Olga

    2016-04-01

    The last (late Pleistocene) glaciation in Kluychevskaya group of volcanoes (KGV) can be considered as a large scale mechanical experiment allowing evaluation of the level of the global geodynamic stresses in the crust of North Kamchatka. KGV is located in the Central Kamchatka depression (CKD). Formation of the CKD can be connected with accretion of Kronotsky paleoarc to the Kamchatka edge c.a. 5 Mys ago. At the compression stage zone of the contact was thickened so that lower part can reach PT parameters of basalt-eclogite transition. Suggested carbonates contamination of the mantle wedge during accretion (Simakin et al., 2015) can became a source of CO2 facilitating eclogite formation. Dense eclogitic keel and trench retreat following accretion can be the driving forces of the CKD rift formation. Extension is partially accommodated (several mm/yr eastward motion) on the eastern border of CKD in the zone of the normal faulting (Kozhurin et al., 2006). And partially extension is accommodated by the formation of the series of dykes of submeridional direction marked by monogenic cones on the surface. At the last phase of the Pleistocene glaciation KGV was covered by the ice cap with 80 km diameter and above 1000 m maximum thickness on the slopes. After the fast deglaciation surface uplift has produced horizontal compression (Simakin and Muravyev, 2015; Pagli and Sigmundsson, 2008). Addition of the deglacial compression to the geodynamic extension turns s1 direction to the horizontal latitudinal one. Due to the horizontal compression areal of eruptions was expanded towards edges of the former glacier. Numerical modeling demonstrates that maximum level of the glacial stress is proportional to the ice gravity load and is estimated to be 5.8-7.5 MPa. Initially principle compressive stress due to the deglaciation was higher than geodynamic one abs(s1,glac) > abs(s1,geod). Time of the volcanism return to the basic submeridional direction marked the moment of viscous

  14. 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

  15. 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.

  16. Mechanism-Based Inactivation of Cytochrome P450 2C9 by Tienilic Acid and (±)-Suprofen: A Comparison of Kinetics and Probe Substrate Selection

    PubMed Central

    Hutzler, J. Matthew; Balogh, Larissa M.; Zientek, Michael; Kumar, Vikas; Tracy, Timothy S.

    2009-01-01

    In vitro experiments were conducted to compare kinact, KI and inactivation efficiency (kinact/KI) of cytochrome P450 (P450) 2C9 by tienilic acid and (±)-suprofen using (S)-flurbiprofen, diclofenac, and (S)-warfarin as reporter substrates. Although the inactivation of P450 2C9 by tienilic acid when (S)-flurbiprofen and diclofenac were used as substrates was similar (efficiency of ∼9 ml/min/μmol), the inactivation kinetics were characterized by a sigmoidal profile. (±)-Suprofen inactivation of (S)-flurbiprofen and diclofenac hydroxylation was also described by a sigmoidal profile, although inactivation was markedly less efficient (∼1 ml/min/μmol). In contrast, inactivation of P450 2C9-mediated (S)-warfarin 7-hydroxylation by tienilic acid and (±)-suprofen was best fit to a hyperbolic equation, where inactivation efficiency was moderately higher (10 ml/min/μmol) and ∼3-fold higher (3 ml/min/μmol), respectively, relative to that of the other probe substrates, which argues for careful consideration of reporter substrate when mechanism-based inactivation of P450 2C9 is assessed in vitro. Further investigations into the increased inactivation seen with tienilic acid relative to that with (±)-suprofen revealed that tienilic acid is a higher affinity substrate with a spectral binding affinity constant (Ks) of 2 μM and an in vitro half-life of 5 min compared with a Ks of 21 μM and a 50 min in vitro half-life for (±)-suprofen. Lastly, a close analog of tienilic acid with the carboxylate functionality replaced by an oxirane ring was devoid of inactivation properties, which suggests that an ionic binding interaction with a positively charged residue in the P450 2C9 active site is critical for recognition and mechanism-based inactivation by these close structural analogs. PMID:18838506

  17. Mechanism of the bisphosphatase reaction of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase probed by (1)H-(15)N NMR spectroscopy.

    PubMed

    Okar, D A; Live, D H; Devany, M H; Lange, A J

    2000-08-15

    The histidines in the bisphosphatase domain of rat liver 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase were labeled with (15)N, both specifically at N1' and globally, for use in heteronuclear single quantum correlation (HSQC) NMR spectroscopic analyses. The histidine-associated (15)N resonances were assigned by correlation to the C2' protons which had been assigned previously [Okar et al., Biochemistry 38, 1999, 4471-79]. Acquisition of the (1)H-(15)N HSQC from a phosphate-free sample demonstrated that the existence of His-258 in the rare N1' tautomeric state is dependent upon occupation of the phosphate binding site filled by the O2 phosphate of the substrate, fructose-2,6-bisphosphate, and subsequently, the phosphohistidine intermediate. The phosphohistidine intermediate is characterized by two hydrogen bonds involving the catalytic histidines, His-258 and His-392, which are directly observed at the N1' positions of the imidazole rings. The N1' of phospho-His-258 is protonated ((1)H chemical shift, 14.0 ppm) and hydrogen bonded to the backbone carbonyl of Gly-259. The N1' of cationic His-392 is hydrogen bonded ((1)H chemical shift, 13.5 ppm) to the phosphoryl moiety of the phosphohistidine. The existence of a protonated phospho-His-258 intermediate and the observation of a fairly strong hydrogen bond to the same phosphohistidine implies that hydrolysis of the covalent intermediate proceeds without any requirement for an "activated" water. Using the labeled histidines as probes of the catalytic site mutation of Glu-327 to alanine revealed that, in addition to its function as the proton donor to fructose-6-phosphate during formation of the transient phosphohistidine intermediate at the N3' of His-258, this residue has a significant role in maintaining the structural integrity of the catalytic site. The (1)H-(15)N HSQC data also provide clear evidence that despite being a surface residue, His-446 has a very acidic pK(a), much less than 6.0. On the basis of

  18. Probing Allosteric Inhibition Mechanisms of the Hsp70 Chaperone Proteins Using Molecular Dynamics Simulations and Analysis of the Residue Interaction Networks.

    PubMed

    Stetz, Gabrielle; Verkhivker, Gennady M

    2016-08-22

    Although molecular mechanisms of allosteric regulation in the Hsp70 chaperones have been extensively studied at both structural and functional levels, the current understanding of allosteric inhibition of chaperone activities by small molecules is still lacking. In the current study, using a battery of computational approaches, we probed allosteric inhibition mechanisms of E. coli Hsp70 (DnaK) and human Hsp70 proteins by small molecule inhibitors PET-16 and novolactone. Molecular dynamics simulations and binding free energy analysis were combined with network-based modeling of residue interactions and allosteric communications to systematically characterize and compare molecular signatures of the apo form, substrate-bound, and inhibitor-bound chaperone complexes. The results suggested a mechanism by which the allosteric inhibitors may leverage binding energy hotspots in the interaction networks to stabilize a specific conformational state and impair the interdomain allosteric control. Using the network-based centrality analysis and community detection, we demonstrated that substrate binding may strengthen the connectivity of local interaction communities, leading to a dense interaction network that can promote an efficient allosteric communication. In contrast, binding of PET-16 to DnaK may induce significant dynamic changes and lead to a fractured interaction network and impaired allosteric communications in the DnaK complex. By using a mechanistic-based analysis of distance fluctuation maps and allosteric propensities of protein residues, we determined that the allosteric network in the PET-16 complex may be small and localized due to the reduced communication and low cooperativity of the substrate binding loops, which may promote the higher rates of substrate dissociation and the decreased substrate affinity. In comparison with the significant effect of PET-16, binding of novolactone to HSPA1A may cause only moderate network changes and preserve allosteric

  19. Conductivity Probe

    NASA Technical Reports Server (NTRS)

    2008-01-01

    The Thermal and Electrical Conductivity Probe (TECP) for NASA's Phoenix Mars Lander took measurements in Martian soil and in the air.

    The needles on the end of the instrument were inserted into the Martian soil, allowing TECP to measure the propagation of both thermal and electrical energy. TECP also measured the humidity in the surrounding air.

    The needles on the probe are 15 millimeters (0.6 inch) long.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  20. 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

  1. 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,…

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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 PAGESBeta

    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 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

  7. 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.

  8. 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.

  9. Thiol Reactive Probes and Chemosensors

    PubMed Central

    Peng, Hanjing; Chen, Weixuan; Cheng, Yunfeng; Hakuna, Lovemore; Strongin, Robert; Wang, Binghe

    2012-01-01

    Thiols are important molecules in the environment and in biological processes. Cysteine (Cys), homocysteine (Hcy), glutathione (GSH) and hydrogen sulfide (H2S) play critical roles in a variety of physiological and pathological processes. The selective detection of thiols using reaction-based probes and sensors is very important in basic research and in disease diagnosis. This review focuses on the design of fluorescent and colorimetric probes and sensors for thiol detection. Thiol detection methods include probes and labeling agents based on nucleophilic addition and substitution, Michael addition, disulfide bond or Se-N bond cleavage, metal-sulfur interactions and more. Probes for H2S are based on nucleophilic cyclization, reduction and metal sulfide formation. Thiol probe and chemosensor design strategies and mechanism of action are discussed in this review. PMID:23202239

  10. 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.

  11. 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.

  12. 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. PMID:27456500

  13. 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

  14. Mechanism of Interaction between the General Anesthetic Halothane and a Model Ion Channel Protein, II: Fluorescence and Vibrational Spectroscopy Using a Cyanophenylalanine Probe

    PubMed Central

    Liu, Jing; Strzalka, Joseph; Tronin, Andrey; Johansson, Jonas S.; Blasie, J. Kent

    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 α-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

  15. Two-body recombination in a quantum-mechanical lattice gas: Entropy generation and probing of short-range magnetic correlations

    SciTech Connect

    Baur, Stefan K.; Mueller, Erich J.

    2010-08-15

    We study entropy generation in a one-dimensional (1D) model of bosons in an optical lattice experiencing two-particle losses. Such heating is a major impediment to observing exotic low temperature states, and 'simulating' condensed matter systems. Developing intuition through numerical simulations, we present a simple empirical model for the entropy produced in this 1D setting. We also explore the time evolution of one- and two-particle correlation functions, showing that they are robust against two-particle loss. Because of this robustness, induced two-body losses can be used as a probe of short-range magnetic correlations.

  16. Two-body recombination in a quantum-mechanical lattice gas: Entropy generation and probing of short-range magnetic correlations

    NASA Astrophysics Data System (ADS)

    Baur, Stefan K.; Mueller, Erich J.

    2010-08-01

    We study entropy generation in a one-dimensional (1D) model of bosons in an optical lattice experiencing two-particle losses. Such heating is a major impediment to observing exotic low temperature states, and “simulating” condensed matter systems. Developing intuition through numerical simulations, we present a simple empirical model for the entropy produced in this 1D setting. We also explore the time evolution of one- and two-particle correlation functions, showing that they are robust against two-particle loss. Because of this robustness, induced two-body losses can be used as a probe of short-range magnetic correlations.

  17. 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.

  18. 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.

  19. 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

  20. 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. PMID:26738414

  1. Differences in the mechanisms that increase noradrenaline efflux after administration of d-amphetamine: a dual-probe microdialysis study in rat frontal cortex and hypothalamus.

    PubMed

    Géranton, Sandrine M; Heal, David J; Stanford, S Clare

    2003-08-01

    1. The extent to which impulse-independent release of noradrenaline and/or inhibition of its reuptake contribute to the response to d-amphetamine in vivo is unclear. Here, dual-probe microdialysis was used to investigate this question in the rat frontal cortex and hypothalamus. 2. After systemic administration of d-amphetamine (10 mg kg(-1)), or its local infusion (10 micro M), the increase in noradrenaline efflux in the hypothalamus was greater than in the frontal cortex. 3. In contrast, during local infusion of the noradrenaline reuptake inhibitor, BTS 54 354 (50 micro M), the noradrenaline response was similar in the frontal cortex and hypothalamus, even after systemic administration of the alpha(2)-antagonist, atipamezole, to block presynaptic inhibition of transmitter release and neuronal firing. 4. In the frontal cortex, but not the hypothalamus, the noradrenaline response to 10 micro M d-amphetamine was constrained by activation of alpha(2)-adrenoceptors. This suggests that, at this concentration, inhibition of reuptake of noradrenaline, following its impulse-dependent release, is evident in the frontal cortex, but that the noradrenaline response in the hypothalamus derives mostly from impulse-independent release (retrotransport). 5. Atipamezole did not affect the noradrenaline response to 100 micro M d-amphetamine in either brain region possibly because, at this higher concentration, retrotransport of noradrenaline masks any compensatory reduction in impulse-evoked release. 6. It is concluded that inhibition of reuptake and retrotransport make different contributions to the noradrenaline response to d-amphetamine in the frontal cortex and hypothalamus and that retrotransport increases with the concentration of d-amphetamine. PMID:12922931

  2. 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.

  3. 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.

  4. 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

  5. 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

    2015-01-01

    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

  6. 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

  7. Probing the molecular mechanism of cerium oxide nanoparticles in protecting against the neuronal cytotoxicity of Aβ1-42 with copper ions.

    PubMed

    Zhao, Yaqin; Xu, Qiming; Xu, Wei; Wang, Dandan; Tan, Jason; Zhu, Cuiqing; Tan, Xiangshi

    2016-07-13

    The molecular mechanism of CeONP in protecting against neuronal cytotoxicity from amyloid peptides and copper ions was investigated systematically by photoluminescence of [Ru(phen)2dppz](2+), morphology of TEM, mass spectroscopy, cell viability assay, ROS fluorescence assay, and EPR. The results revealed that CeONPs reduced Aβ1-42 aggregation, protected from neurotoxicity of ROS induced by Cu(2+) + Aβ1-42via blocking the production of free radicals and scavenging the radicals with Ce(3+)/Ce(4+) catalytic cycles, which provides a valuable insight into CeONPs as a therapeutic intervention in oxidative damage in Alzheimer's disease. PMID:26662372

  8. 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. PMID:27094449

  9. 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.

  10. 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

    2016-01-01

    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

  11. 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

  12. 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.

  13. 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. PMID:27259944

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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. PMID:21996591

  19. 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. PMID

  20. Mechanism of the Novel Prenylated Flavin-Containing Enzyme Ferulic Acid Decarboxylase Probed by Isotope Effects and Linear Free-Energy Relationships.

    PubMed

    Ferguson, Kyle L; Arunrattanamook, Nattapol; Marsh, E Neil G

    2016-05-24

    Ferulic acid decarboxylase from Saccharomyces cerevisiae catalyzes the decarboxylation of phenylacrylic acid to form styrene using a newly described prenylated flavin mononucleotide cofactor. A mechanism has been proposed, involving an unprecedented 1,3-dipolar cyclo-addition of the prenylated flavin with the α═β bond of the substrate that serves to activate the substrate toward decarboxylation. We measured a combination of secondary deuterium kinetic isotope effects (KIEs) at the α- and β-positions of phenylacrylic acid together with solvent deuterium KIEs. The solvent KIE is 3.3 on Vmax/KM but is close to unity on Vmax, indicating that proton transfer to the product occurs before the rate-determining step. The secondary KIEs are normal at both the α- and β-positions but vary in magnitude depending on whether the reaction is performed in H2O or D2O. In D2O, the enzyme catalyzed the exchange of deuterium into styrene; this reaction was dependent on the presence of bicarbonate. This observation implies that CO2 release must occur after protonation of the product. Further information was obtained from a linear free-energy analysis of the reaction through the use of a range of para- and meta-substituted phenylacrylic acids. Log(kcat/KM) for the reaction correlated well with the Hammett σ(-) parameter with ρ = -0.39 ± 0.03; r(2) = 0.93. The negative ρ value and secondary isotope effects are consistent with the rate-determining step being the formation of styrene from the prenylated flavin-product adduct through a cyclo-elimination reaction. PMID:27119435

  1. Heat pipe cooled probe

    NASA Technical Reports Server (NTRS)

    Camarda, C. J. (Inventor); Couch, L. M.

    1984-01-01

    The basic heat pipe principle is employed to provide a self-contained passively cooled probe that may be placed into a high temperature environment. The probe consists of an evaporator region of a heat pipe and a sensing instrument. Heat is absorbed as the working fluid evaporates in the probe. The vapor is transported to the vapor space of the condenser region. Heat is dissipated from the condenser region and fins causing condensation of the working fluid, which returns to the probe by gravity and the capillary action of the wick. Working fluid, wick and condenser configurations and structure materials can be selected to maintain the probe within an acceptable temperature range.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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. PMID:20446912

  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. 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

  9. 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.

  10. 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.

  11. Cone penetrometer fiber optic Raman spectroscopy probe assembly

    SciTech Connect

    Kyle, K.R.; Brown, S.B.

    2000-01-25

    A chemically and mechanically robust optical Raman spectroscopy probe assembly is described 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.

  12. Functional probes for scanning probe microscopy

    NASA Astrophysics Data System (ADS)

    Hasegawa, Yukio; Akiyama, Kotone; Hamada, Masayuki; Eguchi, Toyoaki; An, Toshu; Fujikawa, Yasunori; Sakurai, Toshio

    2008-03-01

    Inspite of importance of the probe in scanning probe microscopy (SPM), little attention was paid for the SPM probes for most of the measurements of SPM. We developed sharp metal-tip cantilevers with a typical curvature radius better than 5nm using focused ion beam (FIB) suitable for Kelvin probe force microscopy (KFM)^1. We obtained atomically resolved KFM images with an energy resolution less than 3meV with the probe^2. We also developed a glass-coated tungsten tip for synchrotron radiation-scanning tunneling microscopy with the FIB method^3 and obtained elementally resolved images in a resolution less than 20nm^4. We are now developing a precise atomic force microscope (AFM) lithography^5 with the FIB-milled tip attached to a quartz tuning fork controlled by noncontact AFM. We will present recent results of our AFM lithography, such as an Au line with a width of 20˜30 nm and characters drawn with Au nano dots on a Si surface. 1 K. Akiyama et al., RSI 76, 033705 (2005) 2 T. Eguchi, K. Akiyama et al., PRL 93, 266102 (2004) 3 K. Akiyama et al., RSI 76, 083711 (2005) 4 T. Eguchi, K. Akiyama et al., APL 89, 243119 (2006) 5 K. Akiyama et al., JP 61, 22 (2007).

  13. Periodontal probing: a review.

    PubMed

    Al Shayeb, Kwthar Nassar A; Turner, Wendy; Gillam, David G

    2014-08-01

    Periodontal probes are the main instruments that are used to assess the status of the periodontium, either for screening purposes or to evaluate periodontal changes throughout the treatment process. With increased knowledge and understanding of periodontal disease, the probes have evolved from a unidimensional manual shape into a more sophisticated computerised instrument. This is due to the need to increase the accuracy and reproducibility of readings and to improve efficiency (time, effort, money). Each probe has characteristic features that makes it unique and, in some cases, specific and limited to use. The aim of this paper is to present a brief introduction to periodontal disease and the methodology of measuring it, followed by probing limitations. The paper will also discuss the methodology of reducing probing error, examiner calibration and probing reproducibility. PMID:25198634

  14. 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.

  15. Titan Probe navigation analysis

    NASA Technical Reports Server (NTRS)

    Vijayaraghavan, A.; Wood, L. J.

    1986-01-01

    In the proposed Cassini mission, a combined Saturn Orbiter/Titan Probe spacecraft will be launched from the Space Shuttle to arrive at Saturn around 2002, by means of a delta-VEGA trajectory. After Saturn-orbit insertion and a pericrone raise maneuver, the probe will be released to enter the Titan atmosphere and impact onto its surface. During its descent phase and impact onto Titan, the probe will maintain radio contact with the orbiter. Since the Titan-probe experimental phase lasts for only about four hours, probe-orbiter geometry and probe-delivery accuracy are critical to successful completion of this part of the mission. From a preliminary navigation analysis for probe delivery accuracy, it seems feasible to deliver the probe within 50 km (1-sigma value) of the desired aim-point in the Titan B-plane. The covariance study, however, clearly indicates the need for optical data, in addition to radio metric data. A Monte Carlo study indicates that a Delta-V capability of 98 m/sec for trajectory correction maneuvers will be sufficient to cover 99 percent of all contingencies during the segment from Saturn-orbit insertion to Titan-probe release.

  16. Probing the Mechanical Unzipping of DNA

    NASA Astrophysics Data System (ADS)

    Voulgarakis, N. K.; Redondo, A.; Bishop, A. R.; Rasmussen, K. Ø.

    2006-06-01

    A study of the micromechanical unzipping of DNA in the framework of the Peyrard-Bishop-Dauxois model is presented. We introduce a Monte Carlo technique that allows accurate determination of the dependence of the unzipping forces on unzipping speed and temperature. Our findings agree quantitatively with experimental results for homogeneous DNA, and for λ-phage DNA we reproduce the recently obtained experimental force-temperature phase diagram. Finally, we argue that there may be fundamental differences between in vivo and in vitro DNA unzipping.

  17. 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.

  18. 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

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

    SciTech Connect

    Lee, Sang Heon

    2014-03-15

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

  20. Radio frequency-compensated Langmuir probe with auxiliary double probes

    SciTech Connect

    Oh, Se-Jin; Oh, Seung-Ju; Chung, Chin-Wook

    2010-09-15

    A radio frequency (rf) compensation design using auxiliary double probes connected in parallel with a main measurement probe was developed for Langmuir probe diagnostics. This probe structure can reduce the sheath impedance of the main probe. In our probe design, the sheath capacitance of the probe can be increased and its sheath resistance can be decreased with increasing dc bias differential voltage between the auxiliary double probes. The I-V characteristic curve and electron energy distribution functions measured by our probe system had sufficient rf compensation performance in inductively coupled plasmas.

  1. Radio frequency-compensated Langmuir probe with auxiliary double probes.

    PubMed

    Oh, Se-Jin; Oh, Seung-Ju; Chung, Chin-Wook

    2010-09-01

    A radio frequency (rf) compensation design using auxiliary double probes connected in parallel with a main measurement probe was developed for Langmuir probe diagnostics. This probe structure can reduce the sheath impedance of the main probe. In our probe design, the sheath capacitance of the probe can be increased and its sheath resistance can be decreased with increasing dc bias differential voltage between the auxiliary double probes. The I-V characteristic curve and electron energy distribution functions measured by our probe system had sufficient rf compensation performance in inductively coupled plasmas. PMID:20886976

  2. 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…

  3. Magnetically driven filament probe.

    PubMed

    Schmid, A; Herrmann, A; Rohde, V; Maraschek, M; Müller, H W

    2007-05-01

    A radially movable probe has been developed for studies of filamentary transport in ASDEX Upgrade during edge localized modes (ELMs) by means of Langmuir tips and magnetic pickup coils. The probe is permanently installed at the low field side in the ASDEX Upgrade vacuum vessel and is not subject to limitations in probe size, as, for example, probes on a shared manipulator are. The probe is moved by a magnetic drive, which allows for easy installation in the vessel, and has moderate machine requirements, as it will only require an electric feedthrough and an external power supply. The drive gives a linear motion with a radial range of 5 cm within 50 ms, where range and velocity can be largely scaled according to experimental requirements. The probe has been installed in the outer midplane of the ASDEX Upgrade vessel, where ELM filaments are expected to have their maximum amplitude. Filaments are coherent substructures within an ELM, carrying a fraction of the ELM released energy towards the wall. The new probe allows to measure the structure of these filaments, in particular, parameters such as filament rotation (by time delay measurements) and size (by peak width analysis). Activating the drive moves the probe from a safe position behind the limiter to a position in front of the limiters, i.e., exposes the Langmuir pins to the scrape-off layer plasma. PMID:17552815

  4. 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

  5. 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.

  6. 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.

  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. 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 PAGESBeta

    Yue, Chao; Li, Wen; Reeves, Geoffrey D.; Nishimura, Yukitoshi; Zong, Qiugang; Ma, Qianli; Bortnik, Jacob; Thorne, Richard M.; Spence, Harlan E.; Kletzing, Craig A.; et al

    2016-07-15

    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

  9. 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.

  10. 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.

  11. 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.

  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. Chemical sensing flow probe

    DOEpatents

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

    1999-01-01

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

  16. Chemical sensing flow probe

    DOEpatents

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

    1999-02-16

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

  17. Functional Probes for Scanning Probe Microscopy

    NASA Astrophysics Data System (ADS)

    Akiyama, Kotone; Eguchi, Toyoaki; An, Toshu; Fujikawa, Yasunori; Hasegawa, Yukio; Sakurai, Toshio

    2007-03-01

    For superior performance of scanning probe microscopy, we are working to fabricate functional probes. For Kelvin probe force microscopy, we fabricated a metal-tip cantilever by attaching a thin metal wire to a regular Si cantilever and milling it by focused ion beam (FIB)^1. By using the W tip with a curvature radius of 3.5 nm, we obtained the potential profile of Ge/Si(105) surface in atomic resolution with the energy resolution better than 3 meV^2. For synchrotron-radiation-light-irradiated scanning tunneling microscopy which aims at atomically resolved elemental analysis, we fabricated a glass-coated W tip using FIB^3. It is found that the glass coating blocks the unwanted secondary electrons, which come from large area of the sample, by a factor of 40 with respect to the case no coating. Using the tip to detect the electrons emitted just below the tip, we obtained element specific images with a spatial resolution better than 20 nm under the photo irradiation whose energy is just above the adsorption edge of the element^4. 1 K. Akiyama et al., RSI 76, 033705 (2005) 2 T. Eguchi, K. Akiyama et al., PRL 93, 266102 (2004) 3 K. Akiyama et al., RSI 76, 083711 (2005) 4 T. Eguchi, K. Akiyama et al., APL, in press

  18. 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.

  19. 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.

  20. Reflections on Electric Probes

    NASA Astrophysics Data System (ADS)

    Braithwaite, Nicholas

    2007-10-01

    One of the more immediate temptations for an experimental plasma physicist is to insert some kind of refractory, conducting material into a plasma, as a simple means of probing its charge composition. Irvine Langmuir tried it in the 1920s and was one of the first to develop an electrical probe method in his early work on electrical discharge plasmas. There are now numerous variations on the theme including planar, cylindrical and spherical geometry with single, double and triple probes. There are also probes that resonate, propagate and reciprocate. Some probes are electrostatic and others are electromagnetic; some are effectively wireless; most absorb but some emit. All types can be used in steady and transient plasmas, while special schemes have been devised for RF plasmas, using passive and active compensation. Magnetised plasmas pose further challenges. Each configuration is accompanied by assumptions that constrain both their applicability and the analytical methods that translate the measured currents and voltages variously into charge densities, space potentials, particle fluxes, energy distributions and measures of collisionality. This talk will take a broad look at the options and opportunities for electric probes, principally in the environment of non-equilibrium plasma.

  1. Development, physiochemical characterization and forming mechanism of Flammulina velutipes polysaccharide-based edible films.

    PubMed

    Du, Hengjun; Hu, Qiuhui; Yang, Wenjian; Pei, Fei; Kimatu, Benard Muinde; Ma, Ning; Fang, Yong; Cao, Chongjiang; Zhao, Liyan

    2016-11-01

    Edible films of Flammulina velutipes polysaccharide were prepared and characterized in terms of rheological, optical, morphologic, mechanical and barrier properties to evaluate their potential application in food packaging. Results suggested that FVP film prepared by the solution of 1:150 (w/v) had the optimal mechanical property, smooth and uniform surface, and good barrier property to water (37.92±2.00gmm/m(2)hkPa) and oxygen (37.92±2.01meq/kg). The capacity of film-formation might be related to inter-molecular and intra-molecular hydrogen bonds of FVP and formation of β-glycosidic bonds during the process of film-formation. These findings will contribute to a theoretical basis for the development of FVP film in food packaging. PMID:27516267

  2. Shock wave diagnostics using fluorescent dye probes

    NASA Astrophysics Data System (ADS)

    Banishev, Alexandr; Christensen, James; Dlott, Dana

    2015-06-01

    Fluorescent probes are highly developed, and have found increasing use in a wide variety of applications. We have studied shock compression of various materials with embedded dye probes used as high speed probes of pressure and temperature. Under the right conditions, dye emission can be used to make a map of the pressure distribution in shocked microstructured materials with high time (1 ns) and space (1 micrometer) resolution. In order to accomplish this goal, we started by studying shock compression of PMMA polymer with rhodamine 6G dye (R6G), as a function of shock pressure and shock duration. We observed the shock-induced spectral redshift and the shock-induced intensity loss. We investigated the fundamental mechanisms of R6G response to pressure. We showed that the time response of a dye probe is limited by its photophysical behavior under shock. We developed superemissive ultrafast dye probes by embedding R6G in a silica nanoparticle. More recently, we have searched for dye probes that have better responses. For instance, we have found that the dye Nile Red embedded in the right polymer matrix has 1.7 times larger pressure-induced redshift than R6G.

  3. Building versatile bipartite probes for quantum metrology

    NASA Astrophysics Data System (ADS)

    Farace, Alessandro; De Pasquale, Antonella; Adesso, Gerardo; Giovannetti, Vittorio

    2016-01-01

    We consider bipartite systems as versatile probes for the estimation of transformations acting locally on one of the subsystems. We investigate what resources are required for the probes to offer a guaranteed level of metrological performance, when the latter is averaged over specific sets of local transformations. We quantify such a performance via the average skew information (AvSk), a convex quantity which we compute in closed form for bipartite states of arbitrary dimensions, and which is shown to be strongly dependent on the degree of local purity of the probes. Our analysis contrasts and complements the recent series of studies focused on the minimum, rather than the average, performance of bipartite probes in local estimation tasks, which was instead determined by quantum correlations other than entanglement. We provide explicit prescriptions to characterize the most reliable states maximizing the AvSk, and elucidate the role of state purity, separability and correlations in the classification of optimal probes. Our results can help in the identification of useful resources for sensing, estimation and discrimination applications when complete knowledge of the interaction mechanism realizing the local transformation is unavailable, and access to pure entangled probes is technologically limited.

  4. Probe And Drogue For Quick Attachment And Detachment

    NASA Technical Reports Server (NTRS)

    Thomson, Mark; Gralewski, Mark; Young, Grant

    1992-01-01

    Prototype probe-and-drogue attachment mechanism connects and disconnects parts quickly and locks them together positively. Probe intended to be capturing stud, and drogue is mating recess in panel to be captured, as described in "Easy Attachment Of Panels To A Truss" (LAR-14478). Accommodates large alignment error when parts brought together.

  5. 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.

  6. 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.

  7. Galileo probe relay receiver - Acquisition and tracking

    NASA Technical Reports Server (NTRS)

    Von Der Embse, U. A.

    1983-01-01

    The probe-to-orbiter data link for the Jovian mission uses a Manchester encoded BPSK waveform which is demodulated by the Galileo probe relay receiver. Signal acquisition and tracking consists of a sequential probability ratio signal search, frequency acquisition with a least-squares estimator, wide-band phase lock acquisition, and a self-regulating mode control. A discrete Fourier transform serves as the basic mechanism to generate the algorithms that provide this orderly transition to phase tracking. Acquisition and tracking is addressed in this paper with emphasis on key algorithms, rationale, and theoretical/measured performance.

  8. 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.

  9. 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.

  10. 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.

  11. Pioneer III Probe

    NASA Technical Reports Server (NTRS)

    1961-01-01

    Looking more like surgeons, these technicians wearing 'cleanroom' attire inspect the Pioneer III probe before shipping it to Cape Canaveral, Florida. Pioneer III was launched on December 6, 1958 aboard a Juno II rocket at the Atlantic Missile Range, Cape Canaveral, Florida. The mission objectives were to measure the radiation intensity of the Van Allen radiation belt, test long range communication systems, the launch vehicle and other subsystems. The Juno II failed to reach proper orbital escape velocity. The probe re-entered the Earth's atmosphere on December 7th ending its brief mission.

  12. Probing from Both Sides: Reshaping the Graphene Landscape via Face-to-Face Dual-Probe Microscopy

    PubMed Central

    2013-01-01

    In two-dimensional samples, all atoms are at the surface and thereby exposed for probing and manipulation by physical or chemical means from both sides. Here, we show that we can access the same point on both surfaces of a few-layer graphene membrane simultaneously, using a dual-probe scanning tunneling microscopy (STM) setup. At the closest point, the two probes are separated only by the thickness of the graphene membrane. This allows us for the first time to directly measure the deformations induced by one STM probe on a free-standing membrane with an independent second probe. We reveal different regimes of stability of few-layer graphene and show how the STM probes can be used as tools to shape the membrane in a controlled manner. Our work opens new avenues for the study of mechanical and electronic properties of two-dimensional materials. PMID:23547751

  13. 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.

  14. 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.

  15. Cervical Neoplasia Probe Control

    Energy Science and Technology Software Center (ESTSC)

    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)

  16. 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. PMID:24795525

  17. 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.

  18. 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.

  19. 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.

  20. 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…

  1. 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)

  2. 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

  3. 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.

  4. Shielding of Piezoelectric Ultrasonic Probes in Hall Effect Imaging

    PubMed Central

    Wen, Han; Bennett, Eric; Wiesler, David G.

    2010-01-01

    This paper addresses significant sources of electromagnetic noise in Hall effect imaging. Hall effect imaging employs large electrical pulses for signal generation and high sensitivity ultrasonic probes for signal reception. Coherent noise arises through various coupling mechanisms between the excitation pulse and the probe. In this paper, the coupling mechanisms are experimentally isolated and theoretically analyzed. Several methods of shielding the probe from electromagnetic interference are devised and tested. These methods are able to reduce the noise to levels below the random thermal noise, thereby improving the signal-to-noise ratio in HEI by two orders of magnitude. PMID:9921620

  5. 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

  6. 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.

  7. Probing Inflation with CMB Polarization

    SciTech Connect

    Baumann, Daniel; Jackson, Mark G.; Adshead, Peter; Easther, Richard; Amblard, Alexandre; Cooray, Asantha; Ashoorioon, Amjad; Watson, Scott; Bartolo, Nicola; Matarrese, Sabino; Bean, Rachel; Beltran, Maria; Dvorkin, Cora; Bernardis, Francesco de; Melchiorri, Alessandro; Pagano, Luca; Bird, Simeon; Peiris, Hiranya V.; Chen Xingang; Hertzberg, Mark P.

    2009-06-09

    We summarize the utility of precise cosmic microwave background (CMB) polarization measurements as probes of the physics of inflation. We focus on the prospects for using CMB measurements to differentiate various inflationary mechanisms. In particular, a detection of primordial B-mode polarization would demonstrate that inflation occurred at a very high energy scale, and that the inflaton traversed a super-Planckian distance in field space. We explain how such a detection or constraint would illuminate aspects of physics at the Planck scale. Moreover, CMB measurements can constrain the scale-dependence and non-Gaussianity of the primordial fluctuations and limit the possibility of a significant isocurvature contribution. Each such limit provides crucial information on the underlying inflationary dynamics. Finally, we quantify these considerations by presenting forecasts for the sensitivities of a future satellite experiment to the inflationary parameters.

  8. The Scanning Theremin Microscope: A Model Scanning Probe Instrument for Hands-On Activities

    ERIC Educational Resources Information Center

    Quardokus, Rebecca C.; Wasio, Natalie A.; Kandel, S. Alex

    2014-01-01

    A model scanning probe microscope, designed using similar principles of operation to research instruments, is described. Proximity sensing is done using a capacitance probe, and a mechanical linkage is used to scan this probe across surfaces. The signal is transduced as an audio tone using a heterodyne detection circuit analogous to that used in…

  9. 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

  10. Novel rotating field probe for inspection of tubes

    NASA Astrophysics Data System (ADS)

    Xin, J.; Tarkleson, E.; Lei, N.; Udpa, L.; Udpa, S. S.

    2012-05-01

    Inspection of steam generator tubes in nuclear power plants is extremely critical for safe operation of the power plant. In the nuclear industry, steam generator tube inspection using eddy current techniques has evolved over the years from a single bobbin coil, to rotating probe coil (RPC) and array probe, in an attempt to improve the speed and reliability of inspection. The RPC probe offers the accurate spatial resolution but involves complex mechanical rotation. This paper presents a novel design of eddy current probes based on rotating fields produced by three identical coils excited by a balanced three-phase supply. The sensor thereby achieves rotating probe functionality by electronic means and eliminates the need for mechanical rotation. The field generated by the probe is largely radial that result in induced currents that flow circularly around the radial axis and rotating around the tube at a synchronous speed effectively producing induced eddy currents that are multidirectional. The probe will consequently be sensitive to cracks of all orientations in the tube wall. The finite element model (FEM) results of the rotating fields and induced currents are presented. A prototype probe is being built to validate simulation results.

  11. Novel rotating field probe for inspection of tubes

    SciTech Connect

    Xin, J.; Tarkleson, E.; Lei, N.; Udpa, L.; Udpa, S. S.

    2012-05-17

    Inspection of steam generator tubes in nuclear power plants is extremely critical for safe operation of the power plant. In the nuclear industry, steam generator tube inspection using eddy current techniques has evolved over the years from a single bobbin coil, to rotating probe coil (RPC) and array probe, in an attempt to improve the speed and reliability of inspection. The RPC probe offers the accurate spatial resolution but involves complex mechanical rotation. This paper presents a novel design of eddy current probes based on rotating fields produced by three identical coils excited by a balanced three-phase supply. The sensor thereby achieves rotating probe functionality by electronic means and eliminates the need for mechanical rotation. The field generated by the probe is largely radial that result in induced currents that flow circularly around the radial axis and rotating around the tube at a synchronous speed effectively producing induced eddy currents that are multidirectional. The probe will consequently be sensitive to cracks of all orientations in the tube wall. The finite element model (FEM) results of the rotating fields and induced currents are presented. A prototype probe is being built to validate simulation results.

  12. Molecular probes for cardiovascular imaging.

    PubMed

    Liang, Grace; Nguyen, Patricia K

    2016-08-01

    Molecular probes provide imaging signal and contrast for the visualization, characterization, and measurement of biological processes at the molecular level. These probes can be designed to target the cell or tissue of interest and must be retained at the imaging site until they can be detected by the appropriate imaging modality. In this article, we will discuss the basic design of molecular probes, differences among the various types of probes, and general strategies for their evaluation of cardiovascular disease. PMID:27189171

  13. 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.

  14. Molecular inversion probe assay.

    PubMed

    Absalan, Farnaz; Ronaghi, Mostafa

    2007-01-01

    We have described molecular inversion probe technologies for large-scale genetic analyses. This technique provides a comprehensive and powerful tool for the analysis of genetic variation and enables affordable, large-scale studies that will help uncover the genetic basis of complex disease and explain the individual variation in response to therapeutics. Major applications of the molecular inversion probes (MIP) technologies include targeted genotyping from focused regions to whole-genome studies, and allele quantification of genomic rearrangements. The MIP technology (used in the HapMap project) provides an efficient, scalable, and affordable way to score polymorphisms in case/control populations for genetic studies. The MIP technology provides the highest commercially available multiplexing levels and assay conversion rates for targeted genotyping. This enables more informative, genome-wide studies with either the functional (direct detection) approach or the indirect detection approach. PMID:18025701

  15. Fast Langmuir probe sweeping circuit

    SciTech Connect

    Milnes, K.A.; Ehlers, K.W.; Leung, K.N.; Owren, H.M.; Williams, M.D.

    1980-06-01

    An inexpensive, simple, and fast Langmuir probe sweeping circuit is presented. This sweeper completes a probe trace in 1.4 ms and has a maximum probe current capability of 5 A. It is suitable for pulsemode plasma operation with density greater than 10/sup 12/ ions/cm/sup 3/.

  16. Scanning Probe Microscopy and Spectroscopy

    NASA Astrophysics Data System (ADS)

    Wiesendanger, Roland

    1994-09-01

    Preface; List of acronyms; Introduction; Part I. Experimental Methods and Theoretical Background of Scanning Probe Microscopy and Spectroscopy: 1. Scanning tunnelling microscopy; 2. Scanning force microscopy; 3. Related scanning probe techniques; Part II. Applications of Scanning Probe Microscopy and Spectroscopy: 4. Condensed matter physics; 5. Chemistry; 6. Organic materials; 7. Metrology and standards; 8. Nanotechnology; References; Index.

  17. Properties of Broezel static probe

    NASA Astrophysics Data System (ADS)

    Gašparovič, Peter; Semrád, Karol; Cúttová, Miroslava

    2016-03-01

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

  18. Droplet monitoring probe

    NASA Technical Reports Server (NTRS)

    Baughman, J. R.; Thys, P. C.

    1973-01-01

    A droplet monitoring system is disclosed for analysis of mixed-phase fluid flow in development of gas turbines. The system uses a probe comprising two electrical wires spaced a known distance apart and connected at one end to means for establishing a dc potential between the wires. A drop in the fluid stream momentarily contacting both wires simultaneously causes and electrical signal which is amplified, detected and counted.

  19. Space Probe Launch

    NASA Technical Reports Server (NTRS)

    1970-01-01

    Managed by Marshall Space Flight Center, the Space Tug was a reusable multipurpose space vehicle designed to transport payloads to different orbital inclinations. Utilizing mission-specific combinations of its three primary modules (crew, propulsion, and cargo) and a variety of supplementary kits, the Space Tug was capable of numerous space applications. This 1970 artist's concept depicts the Tug's propulsion module launching a space probe into lunar orbit.

  20. Cosmological probes of gravity

    NASA Astrophysics Data System (ADS)

    Rassat, Anais Marie Melanie

    This Thesis is concerned with two cosmological probes of linear gravity. The first relates to Large Scale Structure (LSS) in the Universe, probed by galaxy surveys. The second to temperature anisotropics of the Cosmic Microwave Background (CMB), probed by the Wilkinson Microwave Anisotropy Map (WMAP). Both probe the matter and dark energy distributions in the Universe and can be used to test general relativity. The first part of this Thesis (Chapters 2 to 4) is concerned with the analysis of galaxy clustering in redshift space. The second part (Chapters 5 to 7) is concerned with the Integrated Sachs-Wolfe (ISW) effect using LSS-CMB cross-correlations. Chapter 1 introduces the cosmological theory and overviews the subsequent chapters. Chapter 2 gives a review of recent results from the 2 Micron All-Sky Survey (2MASS) and its Redshift Survey (2MRS). It includes work published in Erdogdu (a) et al. (2006) and Erdogdu (b) et al. (2006). Chapter 3 quantifies the clustering of 2MRS galaxies in redshift space. Chapter 4 uses results from Chapter 3 to constrain cosmological parameters. A selection of work from Chapters 3 and 4 will shortly become available in Rassat et al. (2008), entitled 'Redshift Space Analysis of 2MRS'. Chapter 5 overviews the late-time Integrated Sachs-Wolfe effect (ISW) and cross- correlations between the LSS and the CMB. Chapter 6 is also published in Rassat et al. (2007), entitled "Cross-correlation of 2MASS and WMAP3: Implications for the Integrated Sachs-Wolfe effect". It investigates a detection of the ISW effect and correlations which may affect statistical isotropy in the CMB ('Axis of Evil'). Chapter 7 uses the ISW effect to forecast constraints on dark energy parameters and general modifications of general relativity for the next generation of galaxy surveys, particularly the Dark UNiverse Explorer (DUNE) and the Dark Energy Survey (DES). Chapter 8 presents the overall conclusions of this Thesis. Chapter 9 discusses possible extensions to

  1. Ultrafast scanning probe microscopy

    SciTech Connect

    Botkin, D.; Weiss, S.; Ogletree, D.F.; Salmeron, M.; Chemla, D.S.

    1994-01-01

    The authors have developed a general technique which combines the temporal resolution of ultrafast laser spectroscopy with the spatial resolution of scanned probe microscopy (SPM). Using this technique with scanning tunneling microscopy (STM), they have obtained simultaneous 2 ps time resolution and 50 {angstrom} spatial resolution. This improves the time resolution currently attainable with STM by nine orders of magnitude. The potential of this powerful technique for studying ultrafast dynamical phenomena on surfaces with atomic resolution is discussed.

  2. Gravity Probe B Inspection

    NASA Technical Reports Server (NTRS)

    2000-01-01

    The space vehicle Gravity Probe B (GP-B) is the relativity experiment developed at Stanford University to test two extraordinary predictions of Albert Einstein's general theory of relativity. The experiment will measure, very precisely, the expected tiny changes in the direction of the spin axes of four gyroscopes contained in an Earth-orbiting satellite at a 400-mile altitude. So free are the gyroscopes from disturbance that they will provide an almost perfect space-time reference system. They will measure how space and time are very slightly warped by the presence of the Earth, and, more profoundly, how the Earth's rotation very slightly drags space-time around with it. These effects, though small for the Earth, have far-reaching implications for the nature of matter and the structure of the Universe. GP-B is among the most thoroughly researched programs ever undertaken by NASA. This is the story of a scientific quest in which physicists and engineers have collaborated closely over many years. Inspired by their quest, they have invented a whole range of technologies that are already enlivening other branches of science and engineering. In this photograph, engineer Gary Reynolds is inspecting the inside of the probe neck during probe thermal repairs. GP-B is scheduled for launch in April 2004 and managed for NASA by the Marshall Space Flight Center. Development of the GP-B is the responsibility of Stanford University along with major subcontractor Lockheed Martin Corporation. (Image credit to Russ Leese, Gravity Probe B, Stanford University)

  3. Phoenix Conductivity Probe

    NASA Technical Reports Server (NTRS)

    2008-01-01

    This image taken by the Surface Stereo Imager on Sol 49, or the 49th Martian day of the mission (July 14, 2008), shows thermal and electrical conductivity probe on NASA's Phoenix Mars Lander's Robotic Arm.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is led by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  4. Galileo probe relay receiver

    NASA Technical Reports Server (NTRS)

    Prouty, D. A.; Von Der Embse, U. A.

    1982-01-01

    For the Jovian mission, the data link from the Galileo probe to the orbiter uses suppressed-carrier Manchester encoded BPSK modulation and is protected with R = 1/2, K = 7 convolutional coding. The receiver closes the link by acquiring, tracking, and demodulating the data. It has to operate in a highly stressed environment with severe frequency offset, frequency rate, wind gust, and antenna spin conditions. Salient features are described and breadboard test data presented.

  5. Icing Sensor Probe

    NASA Technical Reports Server (NTRS)

    Emery, Edward; Kok, Gregory L.

    2002-01-01

    Aircraft icing is a serious safety problem for the general aviation and some commuter transport airplanes. There has been tremendous growth in the commuter aviation industry in the last few years, Since these type of aircraft generally operate at lower altitudes they consequently spend a far greater proportion of their time operating in icing conditions. For the past thirty years airborne and ground based facilities have relied primarily on two types of cloud physics instrumentation to measure the characteristics of icing clouds: hot wire liquid water content probes and laser based particle sizing probes for the measurement of water droplet size. The instrumentation is severely limited by the technology that was developed during the 1970's and is quite large in size. The goal of this research is to develop one instrument with a wide bandwidth, better response time, higher resolution, user selectability, and small and lightweight. NASA Glenn Research Center, Droplet Measurement Technology, and Meteorology Society of Canada have developed a collaborative effort to develop such an instrument. This paper describes the development and test results of the prototype Icing Sensor Probe.

  6. Einstein Inflationary Probe (EIP)

    NASA Technical Reports Server (NTRS)

    Hinshaw, Gary

    2004-01-01

    I will discuss plans to develop a concept for the Einstein Inflation Probe: a mission to detect gravity waves from inflation via the unique signature they impart to the cosmic microwave background (CMB) polarization. A sensitive CMB polarization satellite may be the only way to probe physics at the grand-unified theory (GUT) scale, exceeding by 12 orders of magnitude the energies studied at the Large Hadron Collider. A detection of gravity waves would represent a remarkable confirmation of the inflationary paradigm and set the energy scale at which inflation occurred when the universe was a fraction of a second old. Even a strong upper limit to the gravity wave amplitude would be significant, ruling out many common models of inflation, and pointing to inflation occurring at much lower energy, if at all. Measuring gravity waves via the CMB polarization will be challenging. We will undertake a comprehensive study to identify the critical scientific requirements for the mission and their derived instrumental performance requirements. At the core of the study will be an assessment of what is scientifically and experimentally optimal within the scope and purpose of the Einstein Inflation Probe.

  7. Nanoscale thermal probing

    PubMed Central

    Yue, Yanan; Wang, Xinwei

    2012-01-01

    Nanoscale novel devices have raised the demand for nanoscale thermal characterization that is critical for evaluating the device performance and durability. Achieving nanoscale spatial resolution and high accuracy in temperature measurement is very challenging due to the limitation of measurement pathways. In this review, we discuss four methodologies currently developed in nanoscale surface imaging and temperature measurement. To overcome the restriction of the conventional methods, the scanning thermal microscopy technique is widely used. From the perspective of measuring target, the optical feature size method can be applied by using either Raman or fluorescence thermometry. The near-field optical method that measures nanoscale temperature by focusing the optical field to a nano-sized region provides a non-contact and non-destructive way for nanoscale thermal probing. Although the resistance thermometry based on nano-sized thermal sensors is possible for nanoscale thermal probing, significant effort is still needed to reduce the size of the current sensors by using advanced fabrication techniques. At the same time, the development of nanoscale imaging techniques, such as fluorescence imaging, provides a great potential solution to resolve the nanoscale thermal probing problem. PMID:22419968

  8. Impedance Characteristics of the Plasma Absorption Probe

    NASA Astrophysics Data System (ADS)

    Yamazawa, Yohei

    2009-10-01

    The plasma absorption probe (PAP) is a diagnostics for determination of spatially resolved electron density.footnotetextH. Kokura, et al., Jpn. J. Appl. Phys. 38 5262 (1999). PAP has attracted considerable interest because of its applicability in a reactive plasma. The simple structure of the probe allows us a robust measurement while the mechanism of the absorption is complicated and there are still some uncertainty.footnotetextM. Lapke, et al., Appl. Phys. Lett. 90, 121502 (2007) In this study, we focus on the frequency characteristics of the impedance instead of the absorption spectrum. An electromagnetic field simulation reveals that there is only one parallel resonance in the impedance characteristics even in a case there are many peaks in absorption spectrum. Thus, the impedance characteristics provide a clue to understanding the mechanism.

  9. Comparative evaluation of probing depth and clinical attachment level using a manual probe and Florida probe

    PubMed Central

    Kour, Amandeep; Kumar, Ashish; Puri, Komal; Khatri, Manish; Bansal, Mansi; Gupta, Geeti

    2016-01-01

    Background: To compare and evaluate the intra- and inter-examiner efficacy and reproducibility of the first-generation manual (Williams) probe and the third-generation Florida probe in terms of measuring pocket probing depth (PD) and clinical attachment level (CAL). Materials and Methods: Forty subjects/4000 sites were included in this comparative, cross-sectional study. Group- and site-wise categorizations were done. Based on gingival index, PD, and CAL, patients were divided into four groups, i.e., periodontally healthy, gingivitis, mild to moderate periodontitis, and severe periodontitis. Further, based on these parameters, a total of 4000 sites, with 1000 sites in each category randomly selected from these 40 patients, were taken. Full mouth PD and CAL measurements were recorded with two probes, by Examiner 1 and on Ramfjord teeth by Examiner 2. Results: Full mouth and Ramfjord teeth group- and site-wise PD obtained with the manual probe by both the examiners were statistically significantly deeper than that obtained with the Florida probe. The full mouth and Ramfjord teeth mean CAL measurement by Florida probe was higher as compared to manual probe in mild to moderate periodontitis group and sites, whereas in severe periodontitis group and sites, manual probe recorded higher CAL as compared to Florida probe. Conclusion: Mean PD and CAL measurements were deeper with the manual probe as compared to the Florida probe in all the groups and sites, except for the mild-moderate periodontitis group and sites where the CAL measurements with the manual probe were less than the Florida probe. Manual probe was more reproducible and showed less interexaminer variability as compared to the Florida probe. PMID:27563204

  10. Probing the Higgs vacuum with general relativity

    NASA Technical Reports Server (NTRS)

    Mannheim, Philip D.; Kazanas, Demosthenes

    1991-01-01

    It is shown that the structure of the Higgs vacuum can be revealed in gravitational experiments which probe the Schwarzschild geometry to only one order in MG/r beyond that needed for the classical tests of general relativity. The possibility that deviations from the conventional geometry are at least theoretically conceivable is explored. The deviations obtained provide a diagnostic test for searching for the existence of macroscopic scalar fields and open up the possiblity for further exploring the Higgs mechanism.

  11. PROcess Based Diagnostics PROBE

    NASA Technical Reports Server (NTRS)

    Clune, T.; Schmidt, G.; Kuo, K.; Bauer, M.; Oloso, H.

    2013-01-01

    Many of the aspects of the climate system that are of the greatest interest (e.g., the sensitivity of the system to external forcings) are emergent properties that arise via the complex interplay between disparate processes. This is also true for climate models most diagnostics are not a function of an isolated portion of source code, but rather are affected by multiple components and procedures. Thus any model-observation mismatch is hard to attribute to any specific piece of code or imperfection in a specific model assumption. An alternative approach is to identify diagnostics that are more closely tied to specific processes -- implying that if a mismatch is found, it should be much easier to identify and address specific algorithmic choices that will improve the simulation. However, this approach requires looking at model output and observational data in a more sophisticated way than the more traditional production of monthly or annual mean quantities. The data must instead be filtered in time and space for examples of the specific process being targeted.We are developing a data analysis environment called PROcess-Based Explorer (PROBE) that seeks to enable efficient and systematic computation of process-based diagnostics on very large sets of data. In this environment, investigators can define arbitrarily complex filters and then seamlessly perform computations in parallel on the filtered output from their model. The same analysis can be performed on additional related data sets (e.g., reanalyses) thereby enabling routine comparisons between model and observational data. PROBE also incorporates workflow technology to automatically update computed diagnostics for subsequent executions of a model. In this presentation, we will discuss the design and current status of PROBE as well as share results from some preliminary use cases.

  12. Experimental probes of axions

    SciTech Connect

    Chou, Aaron S.; /Fermilab

    2009-10-01

    Experimental searches for axions or axion-like particles rely on semiclassical phenomena resulting from the postulated coupling of the axion to two photons. Sensitive probes of the extremely small coupling constant can be made by exploiting familiar, coherent electromagnetic laboratory techniques, including resonant enhancement of transitions using microwave and optical cavities, Bragg scattering, and coherent photon-axion oscillations. The axion beam may either be astrophysical in origin as in the case of dark matter axion searches and solar axion searches, or created in the laboratory from laser interactions with magnetic fields. This note is meant to be a sampling of recent experimental results.

  13. Vacuum probe surface sampler

    NASA Technical Reports Server (NTRS)

    Zahlava, B. A. (Inventor)

    1973-01-01

    A vacuum probe surface sampler is described for rapidly sampling relatively large surface areas which possess relatively light loading densities of micro-organism, drug particles or the like. A vacuum head with a hollow handle connected to a suitable vacuum source is frictionally attached to a cone assembly terminating in a flared tip adapted to be passed over the surface to be sampled. A fine mesh screen carried by the vacuum head provides support for a membrane filter which collects the microorganisms or other particles. The head assembly is easily removed from the cone assembly without contacting the cone assembly with human hands.

  14. Methods of and apparatus for levitating an eddy current probe

    DOEpatents

    Stone, William J.

    1988-05-03

    An eddy current probe is supported against the force of gravity with an air earing while being urged horizontally toward the specimen being examined by a spring and displaced horizontally against the force of the spring pneumatically. The pneumatic displacement is accomplished by flowing air between a plenum chamber fixed with respect to the probe and the surface of the specimen. In this way, the surface of the specimen can be examined without making mechanical contact therewith while precisely controlling the distance at which the probe stands-off from the surface of the specimen.

  15. Probing magnons with RIXS

    NASA Astrophysics Data System (ADS)

    Ament, Lucas; Ghiringhelli, Giacomo; Moretti Sala, Marco; Braicovich, Lucio; van den Brink, Jeroen

    2010-03-01

    Resonant Inelastic X-ray Scattering (RIXS) at the copper L and M edge can probe single spin-flips, which makes it possible to probe the dispersion of magnetic excitations (for instance magnons) of cuprates such as the high Tc superconductors [1]. The cross section factors into a local, atomic spin flip scattering amplitude and a momentum dependent factor describing the final state excitation. Recently, the single magnon dispersion has been measured and found to coincide with earlier neutron measurements [2]. For the cuprates, these results put RIXS as a technique on the same footing as neutron scattering, opening a new window for experiments on this class of materials. [1] L.J.P. Ament, G. Ghiringhelli, M. Moretti Sala, L. Braicovich, and J. van den Brink, PRL 103, 117003 (2009) [2] L. Braicovich, J. van den Brink, V. Bisogni, M. Moretti Sala, L.J.P. Ament, N.B. Brookes, G.M. De Luca, M. Salluzzo, T. Schmitt, and G. Ghiringhelli, arXiv:0911.0621

  16. Development and Application of Multiple-Probe Scanning Probe Microscopes

    SciTech Connect

    Nakayama, T.; Kubo, O.; Shingaya, Y.; Higuchi, S.; Hasegawa, T.; Jiang, C. S.; Okuda, T.; Kuwahara, Y.; Takami, K.; Aono, M.

    2012-04-03

    the research of advanced materials based on nanoscience and nanotechnology, it is often desirable to measure nanoscale local electrical conductivity at a designated position of a given sample. For this purpose, multiple-probe scanning probe microscopes (MP-SPMs), in which two, three or four scanning tunneling microscope (STM) or atomic force microscope (AFM) probes are operated independently, have been developed. Each probe in an MP-SPM is used not only for observing high-resolution STM or AFM images but also for forming an electrical contact enabling nanoscale local electrical conductivity measurement. The world's first double-probe STM (DP-STM) developed by the authors, which was subsequently modified to a triple-probe STM (TP-STM), has been used to measure the conductivities of one-dimensional metal nanowires and carbon nanotubes and also two-dimensional molecular films. A quadruple-probe STM (QP-STM) has also been developed and used to measure the conductivity of two-dimensional molecular films without the ambiguity of contact resistance between the probe and sample. Moreover, a quadruple-probe AFM (QP-AFM) with four conductive tuning-fork-type self-detection force sensing probes has been developed to measure the conductivity of a nanostructure on an insulating substrate. A general-purpose computer software to control four probes at the same time has also been developed and used in the operation of the QP-AFM. These developments and applications of MP-SPMs are reviewed in this paper.

  17. Automatic kelvin probe compatible with ultrahigh vacuum

    NASA Astrophysics Data System (ADS)

    Baikie, I. D.; van der Werf, K. O.; Oerbekke, H.; Broeze, J.; van Silfhout, A.

    1989-05-01

    This article describes a new type of in situ ultrahigh-vacuum compatible kelvin probe based on a voice-coil driving mechanism. This design exhibits several advantages over conventional mechanical feed-through and (in situ) piezoelectric devices in regard to the possibility of multiple probe geometry, flexibility of probe geometry, amplitude of oscillation, and pure parallel vibration. Automatic setup and constant spacing features are achieved using a digital-to-analog converter (DAC) steered offset potential. The combination of very low driver noise pick-up and data-acquisition system (DAS) signal processing techniques results in a work function (wf ) resolution, under optimal conditions, of <0.1 meV. Due to its high surface sensitivity and compatibility with standard sample cleaning and analysis techniques this design has numerous applications in surface studies, e.g., adsorption kinetics, sample topography and homogeneity, sputter profiles, etc. For semiconductor specimens the high wf resolution makes it eminently suitable for surface photovoltage (SPV) spectroscopy.

  18. Variable path length spectrophotometric probe

    DOEpatents

    O'Rourke, Patrick E.; McCarty, Jerry E.; Haggard, Ricky A.

    1992-01-01

    A compact, variable pathlength, fiber optic probe for spectrophotometric measurements of fluids in situ. The probe comprises a probe body with a shaft having a polished end penetrating one side of the probe, a pair of optic fibers, parallel and coterminous, entering the probe opposite the reflecting shaft, and a collimating lens to direct light from one of the fibers to the reflecting surface of the shaft and to direct the reflected light to the second optic fiber. The probe body has an inlet and an outlet port to allow the liquid to enter the probe body and pass between the lens and the reflecting surface of the shaft. A linear stepper motor is connected to the shaft to cause the shaft to advance toward or away from the lens in increments so that absorption measurements can be made at each of the incremental steps. The shaft is sealed to the probe body by a bellows seal to allow freedom of movement of the shaft and yet avoid leakage from the interior of the probe.

  19. Heat transfer probe

    DOEpatents

    Frank, Jeffrey I.; Rosengart, Axel J.; Kasza, Ken; Yu, Wenhua; Chien, Tai-Hsin; Franklin, Jeff

    2006-10-10

    Apparatuses, systems, methods, and computer code for, among other things, monitoring the health of samples such as the brain while providing local cooling or heating. A representative device is a heat transfer probe, which includes an inner channel, a tip, a concentric outer channel, a first temperature sensor, and a second temperature sensor. The inner channel is configured to transport working fluid from an inner inlet to an inner outlet. The tip is configured to receive at least a portion of the working fluid from the inner outlet. The concentric outer channel is configured to transport the working fluid from the inner outlet to an outer outlet. The first temperature sensor is coupled to the tip, and the second temperature sensor spaced apart from the first temperature sensor.

  20. Solar Probe Plus

    NASA Technical Reports Server (NTRS)

    Szabo, Adam

    2011-01-01

    The NASA Solar Probe Plus mission is planned to be launched in 2018 to study the upper solar corona with both.in-situ and remote sensing instrumentation. The mission will utilize 6 Venus gravity assist maneuver to gradually lower its perihelion to 9.5 Rs below the expected Alfven pOint to study the sub-alfvenic solar wind that is still at least partially co-rotates with the Sun. The detailed science objectives of this mission will be discussed. SPP will have a strong synergy with The ESA/NASA Solar orbiter mission to be launched a year ahead. Both missions will focus on the inner heliosphere and will have complimentary instrumentations. Strategies to exploit this synergy will be also presented.

  1. New probe of naturalness.

    PubMed

    Craig, Nathaniel; Englert, Christoph; McCullough, Matthew

    2013-09-20

    Any new scalar fields that perturbatively solve the hierarchy problem by stabilizing the Higgs boson mass also generate new contributions to the Higgs boson field-strength renormalization, irrespective of their gauge representation. These new contributions are physical, and in explicit models their magnitude can be inferred from the requirement of quadratic divergence cancellation; hence, they are directly related to the resolution of the hierarchy problem. Upon canonically normalizing the Higgs field, these new contributions lead to modifications of Higgs couplings that are typically great enough that the hierarchy problem and the concept of electroweak naturalness can be probed thoroughly within a precision Higgs boson program. Specifically, at a lepton collider this can be achieved through precision measurements of the Higgs boson associated production cross section. This would lead to indirect constraints on perturbative solutions to the hierarchy problem in the broadest sense, even if the relevant new fields are gauge singlets. PMID:24093250

  2. Trapping and Probing Antihydrogen

    SciTech Connect

    Wurtele, Jonathan

    2013-03-27

    Precision spectroscopy of antihydrogen is a promising path to sensitive tests of CPT symmetry. The most direct route to achieve this goal is to create and probe antihydrogen in a magnetic minimum trap. Antihydrogen has been synthesized and trapped for 1000s at CERN by the ALPHA Collaboration. Some of the challenges associated with achieving these milestones will be discussed, including mixing cryogenic positron and antiproton plasmas to synthesize antihydrogen with kinetic energy less than the trap potential of .5K. Recent experiments in which hyperfine transitions were resonantly induced with microwaves will be presented. The opportunity for gravitational measurements in traps based on detailed studies of antihydrogen dynamics will be described. The talk will conclude with a discussion future antihydrogen research that will use a new experimental apparatus, ALPHA-I.

  3. Nondestructive Test Probe

    NASA Technical Reports Server (NTRS)

    1996-01-01

    Under the Aircraft Structural Integrity program, Langley Research Center invented a device to detect fatigue cracks in aluminum alloy plates. Krautkramer Branson obtained an exclusive license and commercialized a hand-held device, the "CrackFinder," an electromagnetic probe for nondestructive evaluation, used to scan aircraft skins for surface breaks. The technology involves an eddy current, which is an electrical current induced by an alternating magnetic field. The CrackFinder also employs an innovative self-nulling feature, where the device automatically recalibrates to zero so that each flaw detected produces a reading. Compared to conventional testing systems, the CrackFinder is affordable, small, simple to use, and needs no calibration.

  4. Advanced Langmuir Probe (LP)

    NASA Technical Reports Server (NTRS)

    Voronka, N. R.; Block, B. P.; Carignan, G. R.

    1991-01-01

    The dynamic response of the MK-2 version of the Langmuir probe amplifier was studied. The settling time of the step response is increased by: (1) stray node-to-ground capacitance at series connections between high value feedback resistors; and (2) input capacitance due to the input cable, FET switches, and input source follower. The stray node-to-ground capacitances can be reduced to tolerable levels by elevating the string of feedback resistors above the printing board. A new feedback network was considered, with promising results. The design uses resistances having much lower nominal values, thereby minimizing the effect of stray capacitances. Faster settling times can be achieved by using an operational amplifier having a higher gain-bandwidth product.

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

    ERIC Educational Resources Information Center

    Bruce, Darryl

    1980-01-01

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

  6. Probing absolute spin polarization at the nanoscale.

    PubMed

    Eltschka, Matthias; Jäck, Berthold; Assig, Maximilian; Kondrashov, Oleg V; Skvortsov, Mikhail A; Etzkorn, Markus; Ast, Christian R; Kern, Klaus

    2014-12-10

    Probing absolute values of spin polarization at the nanoscale offers insight into the fundamental mechanisms of spin-dependent transport. Employing the Zeeman splitting in superconducting tips (Meservey-Tedrow-Fulde effect), we introduce a novel spin-polarized scanning tunneling microscopy that combines the probing capability of the absolute values of spin polarization with precise control at the atomic scale. We utilize our novel approach to measure the locally resolved spin polarization of magnetic Co nanoislands on Cu(111). We find that the spin polarization is enhanced by 65% when increasing the width of the tunnel barrier by only 2.3 Å due to the different decay of the electron orbitals into vacuum. PMID:25423049

  7. Small rocket tornado probe

    SciTech Connect

    Colgate, S.A.

    1982-01-01

    A (less than 1 lb.) paper rock tornado probe was developed and deployed in an attempt to measure the pressure, temperature, ionization, and electric field variations along a trajectory penetrating a tornado funnel. The requirements of weight and materials were set by federal regulations and a one-meter resolution at a penetration velocity of close to Mach 1 was desired. These requirements were achieved by telemetering a strain gage transducer for pressure, micro size thermister and electric field, and ionization sensors via a pulse time telemetry to a receiver on board an aircraft that digitizes a signal and presents it to a Z80 microcomputer for recording on mini-floppy disk. Recording rate was 2 ms for 8 channels of information that also includes telemetry rf field strength, magnetic field for orientation on the rocket, zero reference voltage for the sensor op amps as well as the previously mentioned items also. The absolute pressure was recorded. Tactically, over 120 h were flown in a Cessna 210 in April and May 1981, and one tornado was encountered. Four rockets were fired at this tornado, missed, and there were many equipment problems. The equipment needs to be hardened and engineered to a significant degree, but it is believed that the feasibility of the probe, tactics, and launch platform for future tornado work has been proven. The logistics of thunderstorm chasing from a remote base in New Mexico is a major difficulty and reliability of the equipment another. Over 50 dummy rockets have been fired to prove trajectories, stability, and photographic capability. Over 25 electronically equipped rockets have been fired to prove sensors transmission, breakaway connections, etc. The pressure recovery factor was calibrated in the Air Force Academy blow-down tunnel. There is a need for more refined engineering and more logistic support.

  8. Adaptive scanning probe microscopies

    SciTech Connect

    Swartzentruber, B.S.; Bouchard, A.M.; Osbourn, G.C.

    1997-02-01

    This work is comprised of two major sections. In the first section the authors develop multivariate image classification techniques to distinguish and identify surface electronic species directly from multiple-bias scanning tunneling microscope (STM) images. Multiple measurements at each site are used to distinguish and categorize inequivalent electronic or atomic species on the surface via a computerized classification algorithm. Then, comparison with theory or other suitably chosen experimental data enables the identification of each class. They demonstrate the technique by analyzing dual-polarity constant-current topographs of the Ge(111) surface. Just two measurements, negative- and positive-bias topography height, permit pixels to be separated into seven different classes. Labeling four of the classes as adatoms, first-layer atoms, and two inequivalent rest-atom sites, they find excellent agreement with the c(2 x 8) structure. The remaining classes are associated with structural defects and contaminants. This work represents a first step toward developing a general electronic/chemical classification and identification tool for multivariate scanning probe microscopy imagery. In the second section they report measurements of the diffusion of Si dimers on the Si(001) surface at temperatures between room temperature and 128 C using a novel atom-tracking technique that can resolve every diffusion event. The atom tracker employs lateral-positioning feedback to lock the STM probe tip into position above selected atoms with sub-Angstrom precision. Once locked the STM tracks the position of the atoms as they migrate over the crystal surface. By tracking individual atoms directly, the ability of the instrument to measure dynamic events is increased by a factor of {approximately} 1,000 over conventional STM imaging techniques.

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

    PubMed Central

    Staudinger, Christoph; Borisov, Sergey M

    2016-01-01

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

  10. The Gravity Probe B gyroscope

    NASA Astrophysics Data System (ADS)

    Buchman, S.; Lipa, J. A.; Keiser, G. M.; Muhlfelder, B.; Turneaure, J. P.

    2015-11-01

    The Gravity Probe B (GP-B) gyroscope, a unique cryogenically operated mechanical sensor, was used on-orbit to independently test two predictions of general relativity (GR). Here, we describe the development and performance of the GP-B gyroscope, its geometry and fabrication, spin-up and vacuum approach, magnetic considerations, and static charge management. The history of electrically suspended gyroscopes puts the current work in context. Fabrication and ground testing of the GP-B gyroscope are detailed, followed by a review of on-orbit initialization, calibration, operation, and performance. We find that the performance was degraded relative to the mission goals, but was still sufficient to provide excellent new tests of GR. The degradation is partially due to the existence of gyroscope torques due to an unanticipated interaction between patch potentials on the rotor and the housing. We discuss these patch potentials and describe the effect of related torques on gyro drift. It was essential to include models for the effects due to the patch potentials in the complete data analysis model to yield determinations of the two GR effects.

  11. Magnetic circuitry mutual coupling probe

    NASA Technical Reports Server (NTRS)

    Anthony, P. L.

    1972-01-01

    Development of magnetic probe for nondestructive testing of multilayer printed circuit boards to determine existence of opens or shorts is reported. Components of probe are described and procedures for operation are discussed. Two illustrations are provided to show magnetic circuits and principles of operation.

  12. Synergy Between probes and Orbiter

    NASA Technical Reports Server (NTRS)

    Young, Richard E.

    2005-01-01

    There are many ways in which the science return from a planetary mission is considerably enhanced by interactions between entry probes and a mission orbiter. Mission configuration aspects that are desirable include delivery of entry probes by the orbiter, and communication between probe and orbiter. Both of these mission aspects could greatly enhance access to key scientific sites that might not otherwise be accessible using delivery from say, a flyby, or employing direct communication from probes to Earth. Examples for Venus and Jupiter will be discussed. A second class of orbiter-probe interaction could better be termed direct probe-orbiter science collaboration. That would include, determining the global context of the entry probe sites from the orbiter, obtaining ground truth from the probe for remote sensing observations from the orbiter, observing the global and vertical distribution of key atmospheric trace species, and measuring the global and vertical distribution of clouds and winds. The importance of each of these items will be illustrated by particular examples.

  13. Cobra Probes Containing Replaceable Thermocouples

    NASA Technical Reports Server (NTRS)

    Jones, John; Redding, Adam

    2007-01-01

    A modification of the basic design of cobra probes provides for relatively easy replacement of broken thermocouples. Cobra probes are standard tube-type pressure probes that may also contain thermocouples and that are routinely used in wind tunnels and aeronautical hardware. They are so named because in side views, they resemble a cobra poised to attack. Heretofore, there has been no easy way to replace a broken thermocouple in a cobra probe: instead, it has been necessary to break the probe apart and then rebuild it, typically at a cost between $2,000 and $4,000 (2004 prices). The modified design makes it possible to replace the thermocouple, in minimal time and at relatively low cost, by inserting new thermocouple wire in a tube.

  14. Electrophoresis-mass spectrometry probe

    DOEpatents

    Andresen, B.D.; Fought, E.R.

    1987-11-10

    The invention involves a new technique for the separation of complex mixtures of chemicals, which utilizes a unique interface probe for conventional mass spectrometers which allows the electrophoretically separated compounds to be analyzed in real-time by a mass spectrometer. This new chemical analysis interface, which couples electrophoresis with mass spectrometry, allows complex mixtures to be analyzed very rapidly, with much greater specificity, and with greater sensitivity. The interface or probe provides a means whereby large and/or polar molecules in complex mixtures to be completely characterized. The preferred embodiment of the probe utilizes a double capillary tip which allows the probe tip to be continually wetted by the buffer, which provides for increased heat dissipation, and results in a continually operating interface which is more durable and electronically stable than the illustrated single capillary tip probe interface. 8 figs.

  15. Electrophoresis-mass spectrometry probe

    DOEpatents

    Andresen, Brian D.; Fought, Eric R.

    1987-01-01

    The invention involves a new technique for the separation of complex mixtures of chemicals, which utilizes a unique interface probe for conventional mass spectrometers which allows the electrophoretically separated compounds to be analyzed in real-time by a mass spectrometer. This new chemical analysis interface, which couples electrophoresis with mass spectrometry, allows complex mixtures to be analyzed very rapidly, with much greater specificity, and with greater sensitivity. The interface or probe provides a means whereby large and/or polar molecules in complex mixtures to be completely characterized. The preferred embodiment of the probe utilizes a double capillary tip which allows the probe tip to be continually wetted by the buffer, which provides for increased heat dissipation, and results in a continually operating interface which is more durable and electronically stable than the illustrated single capillary tip probe interface.

  16. Rotating concave eddy current probe

    DOEpatents

    Roach, Dennis P.; Walkington, Phil; Rackow, Kirk A.; Hohman, Ed

    2008-04-01

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

  17. Fluorogenic Probe for the Human Ether-a-Go-Go-Related Gene Potassium Channel Imaging

    PubMed Central

    2016-01-01

    The first small-molecule fluorogenic probe A1 for imaging the human Ether-a-go-go-Related Gene (hERG) potassium channel based on the photoinduced electron transfer (PET) off–on mechanism was described herein. After careful biological evaluation, this probe had the potential of detecting and imaging the hERG channel at the molecular and cellular level. Moreover, the competitive binding mechanism of this probe would presumably minimize the effects on the electrophysiological properties of the hERG channel. Therefore, this probe may serve as a powerful toolkit to the hERG-associated study. PMID:25665091

  18. Carbon nanotube scanning probe for imaging in aqueous environment

    NASA Technical Reports Server (NTRS)

    Stevens, Ramsey M.; Nguyen, Cattien V.; Meyyappan, M.

    2004-01-01

    Carbon nanotubes (CNTs) used as a probe for scanning probe microscopy has become one of the many potential usages of CNTs that is finding real applications in scientific research and industrial communities. It has been proposed that the unique mechanical buckling properties of the CNT would lessen the imaging force exerted on the sample and, thus, make CNT scanning probes ideal for imaging soft materials, including biological samples in liquid environments. The hydrophobic nature of the CNT graphitic sidewall is clearly chemically incompatible with the aqueous solution requirements in some biological imaging applications. In this paper, we present electron micrograph results demonstrating the instability of CNT scanning probes when submerged in aqueous solution. Moreover, we also introduce a novel approach to resolve this chemical incompatibility problem. By coating the CNT probe with ethylenediamine, thus rendering the CNT probe less hydrophobic, we demonstrate the liquid imaging capability of treated CNT probes. Experimental data for imaging in aqueous solutions are presented, which include an ultrathin Ir film and DNA molecules on a mica surface.

  19. Tuning the Spring Constant of Cantilever-free Probe Arrays

    NASA Astrophysics Data System (ADS)

    Eichelsdoerfer, Daniel J.; Brown, Keith A.; Boya, Radha; Shim, Wooyoung; Mirkin, Chad A.

    2013-03-01

    The versatility of atomic force microscope (AFM) based techniques such as scanning probe lithography is due in part to the utilization of a cantilever that can be fabricated to match a desired application. In contrast, cantilever-free scanning probe lithography utilizes a low cost array of probes on a compliant backing layer that allows for high throughput nanofabrication but lacks the tailorability afforded by the cantilever in traditional AFM. Here, we present a method to measure and tune the spring constant of probes in a cantilever-free array by adjusting the mechanical properties of the underlying elastomeric layer. Using this technique, we are able to fabricate large-area silicon probe arrays with spring constants that can be tuned in the range from 7 to 150 N/m. This technique offers an advantage in that the spring constant depends linearly on the geometry of the probe, which is in contrast to traditional cantilever-based lithography where the spring constant varies as the cube of the beam width and thickness. To illustrate the benefit of utilizing a probe array with a lower spring constant, we pattern a block copolymer on a delicate 50 nm thick silicon nitride window.

  20. Coating flexible probes with an ultra fast degrading polymer to aid in tissue insertion.

    PubMed

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

    2015-04-01

    We report a fabrication process for coating neural probes with an ultrafast degrading polymer to create consistent and reproducible devices for neural tissue insertion. The rigid polymer coating acts as a probe insertion aid, but resorbs within hours post-implantation. Despite the feasibility for short term neural recordings from currently available neural prosthetic devices, most of these devices suffer from long term gliosis, which isolates the probes from adjacent neurons, increasing the recording impedance and stimulation threshold. The size and stiffness of implanted probes have been identified as critical factors that lead to this long term gliosis. Smaller, more flexible probes that match the mechanical properties of brain tissue could allow better long term integration by limiting the mechanical disruption of the surrounding tissue during and after probe insertion, while being flexible enough to deform with the tissue during brain movement. However, these small flexible probes inherently lack the mechanical strength to penetrate the brain on their own. In this work, we have developed a micromolding method for coating a non-functional miniaturized SU-8 probe with an ultrafast degrading tyrosine-derived polycarbonate (E5005(2K)). Coated, non-functionalized probes of varying dimensions were reproducibly fabricated with high yields. The polymer erosion/degradation profiles of the probes were characterized in vitro. The probes were also mechanically characterized in ex vivo brain tissue models by measuring buckling and insertion forces during probe insertion. The results demonstrate the ability to produce polymer coated probes of consistent quality for future in vivo use, for example to study the effects of different design parameters that may affect tissue response during long term chronic intra-cortical microelectrode neural recordings. PMID:25681971

  1. Coating flexible probes with an ultra fast degrading polymer to aid in tissue insertion

    PubMed Central

    Wang, Shuwu; Singh, Sagar; Damodaran, Vinod B.; Kaplan, Hilton M.; Kohn, Joachim; Shreiber, David I.; Zahn, Jeffrey D.

    2016-01-01

    We report a fabrication process for coating neural probes with an ultrafast degrading polymer to create consistent and reproducible devices for neural tissue insertion. The rigid polymer coating acts as a probe insertion aid, but resorbs within hours post-implantation. Despite the feasibility for short term neural recordings from currently available neural prosthetic devices, most of these devices suffer from long term gliosis, which isolates the probes from adjacent neurons, increasing the recording impedance and stimulation threshold. The size and stiffness of implanted probes have been identified as critical factors that lead to this long term gliosis. Smaller, more flexible probes that match the mechanical properties of brain tissue could allow better long term integration by limiting the mechanical disruption of the surrounding tissue during and after probe insertion, while being flexible enough to deform with the tissue during brain movement. However, these small flexible probes inherently lack the mechanical strength to penetrate the brain on their own. In this work, we have developed a micromolding method for coating a non-functional miniaturized SU-8 probe with an ultrafast degrading tyrosine-derived polycarbonate (E5005(2K)). Coated, non-functionalized probes of varying dimensions were reproducibly fabricated with high yields. The polymer erosion/degradation profiles of the probes were characterized in vitro. The probes were also mechanically characterized in ex vivo brain tissue models by measuring buckling and insertion forces during probe insertion. The results demonstrate the ability to produce polymer coated probes of consistent quality for future in vivo use, for example to study the effects of different design parameters that may affect tissue response during long term chronic intra-cortical microelectrode neural recordings. PMID:25681971

  2. Fast reciprocating Langmuir probe for the DIII-D divertor

    SciTech Connect

    Watkins, J.G.; Hunter, J.; Tafoya, B.; Ulrickson, M.; Watson, R.D.; Moyer, R.A.; Cuthbertson, J.W.; Gunner, G.; Lehmer, R.; Luong, P.; Hill, D.N.; Mascaro, M.; Robinson, J.I.; Snider, R.; Stambaugh, R.

    1997-01-01

    A new reciprocating Langmuir probe was used to measure density and temperature profiles, ion flow, and potential fluctuation levels from the lower divertor floor up to the X point on the DIII-D Tokamak. This probe is designed to make fast (2 kHz swept, 20 kHz Mach, 500 kHz Vfloat) measurements with 2 mm spatial resolution in the region where the largest gradients on the plasma open flux tubes are found and therefore provide the best benchmarks for scrap-off layer and divertor numerical models. Profiles are constructed using the 300 ms time history of the probe measurements during the 25 cm reciprocating stroke. Both single and double null plasmas can be measured and compared with a 20 Hz divertor Thomson scattering system. The probe head is constructed of four different kinds of graphite to optimize the electrical and thermal characteristics. Electrically insulated pyrolytic graphite rings act as a heat shield to absorb the plasma heat flux on the probe shaft and are mounted on a carbon/carbon composite core for mechanical strength. The Langmuir probe sampling tips are made of a linear carbon fiber composite. The mechanical, electrical, data acquisition, and power supply systems will be described. Initial measurements will also be presented. {copyright} {ital 1997 American Institute of Physics.}

  3. Probing Nanoscale Pentacene Films by Resonant Raman Scattering

    NASA Astrophysics Data System (ADS)

    He, Rui; Dujovne, Irene; Chen, Liwei; Miao, Qian; Hirjibehedin, Cyrus F.; Pinczuk, Aron; Nuckolls, Colin; Kloc, Christian; Blanchet, Graciela B.

    2005-06-01

    Resonant enhancements of Raman scattering intensities offer the sensitivity required to study nanoscale pentacene films that reach into monolayer thickness. In the results reported here structural characterization of ultra-thin layers and of their fundamental optical properties are investigated by resonant Raman scattering from intra-molecular and inter-molecular vibrations. In this work Raman methods emerge as ideal tools for the study of physics and characterization of ultra-thin nanoscale films of molecular organic materials fabricated on diverse substrates of current and future devices.

  4. Chemical sensor with oscillating cantilevered probe

    DOEpatents

    Adams, Jesse D

    2013-02-05

    The invention provides a method of detecting a chemical species with an oscillating cantilevered probe. A cantilevered beam is driven into oscillation with a drive mechanism coupled to the cantilevered beam. A free end of the oscillating cantilevered beam is tapped against a mechanical stop coupled to a base end of the cantilevered beam. An amplitude of the oscillating cantilevered beam is measured with a sense mechanism coupled to the cantilevered beam. A treated portion of the cantilevered beam is exposed to the chemical species, wherein the cantilevered beam bends when exposed to the chemical species. A second amplitude of the oscillating cantilevered beam is measured, and the chemical species is determined based on the measured amplitudes.

  5. Long duration ash probe

    DOEpatents

    Hurley, John P.; McCollor, Don P.; Selle, Stanley J.

    1994-01-01

    A long duration ash probe includes a pressure shell connected to a port in a combustor with a sample coupon mounted on a retractable carriage so as to retract the sample coupon within the pressure shell during sootblowing operation of the combustor. A valve mounted at the forward end of the pressure shell is selectively closeable to seal the sample coupon within the shell, and a heating element in the shell is operable to maintain the desired temperature of the sample coupon while retracted within the shell. The carriage is operably mounted on a pair of rails within the shell for longitudinal movement within the shell. A hollow carrier tube connects the hollow cylindrical sample coupon to the carriage, and extends through the carriage and out the rearward end thereof. Air lines are connected to the rearward end of the carrier tube and are operable to permit coolant to pass through the air lines and thence through the carrier tube to the sample coupon so as to cool the sample coupon.

  6. Active Dynamic Frictional Probes

    NASA Astrophysics Data System (ADS)

    Steimel, Joshua; Aragones, Juan; Alexander-Katz, Alfredo

    2015-03-01

    In biological systems there are a myriad of interactions occurring instantaneously and these interactions can vary drastically in the strength of the interaction, the speed at which this interaction occurs, and the duration of the interaction. When multiple interactions occur any of these factors can determine which particular interaction is dominant. However, currently it is extremely difficult to measure binding affinity, Kon, and Koff rates in a relatively high throughput manner. Here we propose a novel and versatile system that will be able to detect differences in binding affinity of wide range of transient interactions and will be able to extract the relevant time scales of these interactions. Our system will utilize ferromagnetic particles that can be easily functionalized with a receptor of interest and the substrate will be coated in the corresponding ligand. A rotating magnetic field will cause particles, henceforth referred to as rollers, to rotate and this rotational motion will be converted into translational motion via the effective frictional force induced by interaction that is being probed. By measuring the translation of the rollers to a baseline, where only hydrodynamic friction occurs, we can measure the relative strength of the interactions. We can also potentially measure kinetic information by changing the frequency at which the magnetic field rotates, since changing the frequency at which the bead rotates is akin to changing the time allowed for bond formation. We will measure a wide range of interaction including ionic, metal-ion coordination, IgG-Protein A complex, and biotin-streptavidin complex.

  7. Gravity Probe B Encapsulated

    NASA Technical Reports Server (NTRS)

    2004-01-01

    In this photo, the Gravity Probe B (GP-B) space vehicle is being encapsulated atop the Delta II launch vehicle. The GP-B is the relativity experiment developed at Stanford University to test two extraordinary predictions of Albert Einstein's general theory of relativity. The experiment will measure, very precisely, the expected tiny changes in the direction of the spin axes of four gyroscopes contained in an Earth-orbiting satellite at a 400-mile altitude. So free are the gyroscopes from disturbance that they will provide an almost perfect space-time reference system. They will measure how space and time are very slightly warped by the presence of the Earth, and, more profoundly, how the Earth's rotation very slightly drags space-time around with it. These effects, though small for the Earth, have far-reaching implications for the nature of matter and the structure of the Universe. GP-B is among the most thoroughly researched programs ever undertaken by NASA. This is the story of a scientific quest in which physicists and engineers have collaborated closely over many years. Inspired by their quest, they have invented a whole range of technologies that are already enlivening other branches of science and engineering. Launched April 20, 2004 , the GP-B program was managed for NASA by the Marshall Space Flight Center. Development of the GP-B is the responsibility of Stanford University along with major subcontractor Lockheed Martin Corporation. (Image credit to Russ Underwood, Lockheed Martin Corporation).

  8. Long duration ash probe

    DOEpatents

    Hurley, J.P.; McCollor, D.P.; Selle, S.J.

    1994-07-26

    A long duration ash probe includes a pressure shell connected to a port in a combustor with a sample coupon mounted on a retractable carriage so as to retract the sample coupon within the pressure shell during soot blowing operation of the combustor. A valve mounted at the forward end of the pressure shell is selectively closeable to seal the sample coupon within the shell, and a heating element in the shell is operable to maintain the desired temperature of the sample coupon while retracted within the shell. The carriage is operably mounted on a pair of rails within the shell for longitudinal movement within the shell. A hollow carrier tube connects the hollow cylindrical sample coupon to the carriage, and extends through the carriage and out the rearward end thereof. Air lines are connected to the rearward end of the carrier tube and are operable to permit coolant to pass through the air lines and thence through the carrier tube to the sample coupon so as to cool the sample coupon. 8 figs.

  9. Scanning probe nanoimprint lithography

    NASA Astrophysics Data System (ADS)

    Dinelli, F.; Menozzi, C.; Baschieri, P.; Facci, P.; Pingue, P.

    2010-02-01

    The present paper reports on a novel lithographic approach at the nanoscale level, which is based on scanning probe microscopy (SPM) and nanoimprint lithography (NIL). The experimental set-up consists of an atomic force microscope (AFM) operated via software specifically developed for the purpose. In particular, this software allows one to apply a predefined external load for a given lapse of time while monitoring in real-time the relative distance between the tip and the sample as well as the normal and lateral force during the embossing process. Additionally, we have employed AFM tips sculptured by means of focused ion beam in order to create indenting tools of the desired shape. Anti-sticking layers can also be used to functionalize the tips if one needs to investigate the effects of different treatments on the indentation and de-molding processes. The lithographic capabilities of this set-up are demonstrated on a polystyrene NIL-patterned sample, where imprinted features have been obtained upon using different normal load values for increasing time intervals, and on a thermoplastic polymer film, where the imprint process has been monitored in real-time.

  10. Imaging and manipulation of nanoscale materials with coaxial and triaxial AFM probes

    NASA Astrophysics Data System (ADS)

    Brown, Keith A.; Westervelt, R. M.

    2011-03-01

    We present coaxial and triaxial Atomic Force Microscope (AFM) probes and demonstrate their applications to imaging and manipulating nanoscale materials. A coaxial probe with concentric electrodes at its tip creates a highly confined electric field that decays as a dipole field, making the coaxial probe useful for near field imaging of electrical properties. We show nearly an order of magnitude improvement in the step resolution of Kelvin probe force microscopy with coaxial probes. We further demonstrate that coaxial probes can image dielectric materials with the dielectrophoretic force. In addition to imaging, the capacitive structure that makes up the cantilever of a coaxial probe is used to locally mechanically drive the probe, making them self-driving probes. Finally, coaxial probes can create strong forces with dielectrophoresis (DEP) which we combine with the nanometer precision of the AFM to create a nanometer scale pick-and-place tool. We demonstrate 3D assembly of micrometer scale objects with coaxial probes using positive DEP and discuss the assembly of nanometer scale objects with triaxial probes using negative DEP.

  11. Morphological Computation of Haptic Perception of a Controllable Stiffness Probe

    PubMed Central

    Sornkarn, Nantachai; Dasgupta, Prokar; Nanayakkara, Thrishantha

    2016-01-01

    When people are asked to palpate a novel soft object to discern its physical properties such as texture, elasticity, and even non-homogeneity, they not only regulate probing behaviors, but also the co-contraction level of antagonistic muscles to control the mechanical impedance of fingers. It is suspected that such behavior tries to enhance haptic perception by regulating the function of mechanoreceptors at different depths of the fingertips and proprioceptive sensors such as tendon and spindle sensors located in muscles. In this paper, we designed and fabricated a novel two-degree of freedom variable stiffness indentation probe to investigate whether the regulation of internal stiffness, indentation, and probe sweeping velocity (PSV) variables affect the accuracy of the depth estimation of stiff inclusions in an artificial silicon phantom using information gain metrics. Our experimental results provide new insights into not only the biological phenomena of haptic perception but also new opportunities to design and control soft robotic probes. PMID:27257814

  12. Variable resolution imaging fiber probe using digital spatial light modulator

    NASA Astrophysics Data System (ADS)

    Shinde, Anant; Perinchery, Sandeep M.; Vadakke Matham, Murukeshan

    2015-07-01

    Flexible fiber optic imaging systems including fiber optic confocal probes have found tremendous significance in the recent past for its applications in high resolution imaging. However, motorized stage is required for scanning the sample or tip of the fiber in fiber based confocal probes. In this context, we propose a fiber probe confocal system using digital spatial light modulator devoid of using a mechanical scanning stage. Each fiberlet in the image fiber acts not only as a light conduit but also as a confocal pinhole. The paper also introduces the variation in the contrast by varying the number of illuminated fiberlets which effectively implies variation in the effective pinhole size. This approach has enabled the probe to act as an imaging unit with resolution that can be controlled and varied from a wide-field to a confocal.

  13. Morphological Computation of Haptic Perception of a Controllable Stiffness Probe.

    PubMed

    Sornkarn, Nantachai; Dasgupta, Prokar; Nanayakkara, Thrishantha

    2016-01-01

    When people are asked to palpate a novel soft object to discern its physical properties such as texture, elasticity, and even non-homogeneity, they not only regulate probing behaviors, but also the co-contraction level of antagonistic muscles to control the mechanical impedance of fingers. It is suspected that such behavior tries to enhance haptic perception by regulating the function of mechanoreceptors at different depths of the fingertips and proprioceptive sensors such as tendon and spindle sensors located in muscles. In this paper, we designed and fabricated a novel two-degree of freedom variable stiffness indentation probe to investigate whether the regulation of internal stiffness, indentation, and probe sweeping velocity (PSV) variables affect the accuracy of the depth estimation of stiff inclusions in an artificial silicon phantom using information gain metrics. Our experimental results provide new insights into not only the biological phenomena of haptic perception but also new opportunities to design and control soft robotic probes. PMID:27257814

  14. Probing lepton number violation on three frontiers

    SciTech Connect

    Deppisch, Frank F.

    2013-12-30

    Neutrinoless double beta decay constitutes the main probe for lepton number violation at low energies, motivated by the expected Majorana nature of the light but massive neutrinos. On the other hand, the theoretical interpretation of the (non-)observation of this process is not straightforward as the Majorana neutrinos can destructively interfere in their contribution and many other New Physics mechanisms can additionally mediate the process. We here highlight the potential of combining neutrinoless double beta decay with searches for Tritium decay, cosmological observations and LHC physics to improve the quantitative insight into the neutrino properties and to unravel potential sources of lepton number violation.

  15. Calibration of Langmuir probes against microwaves and plasma oscillation probes

    NASA Astrophysics Data System (ADS)

    Chen, Francis F.; Evans, John D.; Zawalski, Wade

    2012-10-01

    The use of Langmuir probes for measuring plasma density is subject to uncertainty because the theories commonly used to interpret the data give widely differing results. This is especially troublesome in partially ionized plasmas used, for instance, in the semiconductor industry, since no existing theory adequately treats the case when there are a few collisions between ions and neutral atoms. In this work, plasma densities measured by microwave interferometry and plasma-oscillation probes are compared with those from probe data analyzed with Langmuir's orbital motion limited (OML) theory, the Allen-Boyd-Reynolds (ABR) theory and the Bernstein-Rabinowitz-Laframboise (BRL) theory. It is found that ABR underestimates and BRL overestimates the density, the problems being the neglect of ion orbiting in ABR and the effect of ion-neutral collisions in BRL. The best theory is either OML or the geometric mean between the ABR and BRL results. For thicker probes, other methods are suggested.

  16. Design and fabrication of an actively cooled Langmuir probe for long pulse applications

    SciTech Connect

    Paterson, J.A.; Biagi, L.A.; Ehlers, K.W.; Koehler, G.W.

    1985-11-01

    The details of the mechanical design and fabrication for a Langmuir Probe for the continuous monitoring of plasma density are given. The probe was designed for use as a diagnostic tool in the development of long pulse positive ion plasma sources for use on neutral beam systems. The essential design feature of this probe is the incorporation of two electrically isolated cooling water circuits which actively cool the probe tip and probe jacket. The electrical isolation is required to prevent drain currents from the probe body disturbing the measurement of the probe tip current and thereby the plasma density measurement. The successful realization of the design requires precision components and vacuum tight ceramic to refractory metal brazes. To date this design has successfully operated in steady-state in plasma densities up to 250 mA/cmS and surface heat fluxes of 25 W/cmS.

  17. Optic probe for semiconductor characterization

    DOEpatents

    Sopori, Bhushan L.; Hambarian, Artak

    2008-09-02

    Described herein is an optical probe (120) for use in characterizing surface defects in wafers, such as semiconductor wafers. The optical probe (120) detects laser light reflected from the surface (124) of the wafer (106) within various ranges of angles. Characteristics of defects in the surface (124) of the wafer (106) are determined based on the amount of reflected laser light detected in each of the ranges of angles. Additionally, a wafer characterization system (100) is described that includes the described optical probe (120).

  18. Saturn orbiter dual probe mission

    NASA Technical Reports Server (NTRS)

    Rudd, R. P.

    1978-01-01

    The described Saturn orbiter dual probe mission and spacecraft combines three systems into a multi-purpose Saturn exploration package. The spacecraft consists of: (1) Saturn orbiter; (2) Saturn probe; and (3) Titan probe or lander. This single spacecraft provides the capability to conduct in situ measurements of the Saturn and Titan atmospheres, and, possibly the Titan surface, as well as a variety of remote sensing measurements. The remote sensing capabilities will be used to study the surfaces, interiors and environments of Saturn's satellites, the rings of Saturn, Saturn's magnetosphere, and synoptic properties of Saturn's atmosphere.

  19. ESA Venus Entry Probe Study

    NASA Technical Reports Server (NTRS)

    vandenBerg, M. L.; Falkner, P.; Phipps, A.; Underwood, J. C.; Lingard, J. S.; Moorhouse, J.; Kraft, S.; Peacock, A.

    2005-01-01

    The Venus Entry Probe is one of ESA s Technology Reference Studies (TRS). The purpose of the Technology Reference Studies is to provide a focus for the development of strategically important technologies that are of likely relevance for future scientific missions. The aim of the Venus Entry Probe TRS is to study approaches for low cost in-situ exploration of Venus and other planetary bodies with a significant atmosphere. In this paper, the mission objectives and an outline of the mission concept of the Venus Entry Probe TRS are presented.

  20. Atmospheric probes: needs and prospects

    NASA Astrophysics Data System (ADS)

    Owen, Tobias

    2004-02-01

    There is only one Rosetta Stone in the Solar System; it's in the British Museum. We cannot understand the inner planets by simply studying the Earth, nor can we apprehend the giants by examining only Jupiter. Despite the stunning successes of previous probes to Venus and the Galileo probe to Jupiter, our knowledge of the atmospheres of even these two planets remains tantalizingly incomplete. We must therefore return to Venus and consider the challenge of exploring all of the outer planets with a family of identical probes, a project that could commemorater the vision of multiple worlds championed by Giordano Bruno.

  1. Floating Potential Probe Langmuir Probe Data Reduction Results

    NASA Technical Reports Server (NTRS)

    Morton, Thomas L.; Minow, Joseph I.

    2002-01-01

    During its first five months of operations, the Langmuir Probe on the Floating Potential Probe (FPP) obtained data on ionospheric electron densities and temperatures in the ISS orbit. In this paper, the algorithms for data reduction are presented, and comparisons are made of FPP data with ground-based ionosonde and Incoherent Scattering Radar (ISR) results. Implications for ISS operations are detailed, and the need for a permanent FPP on ISS is examined.

  2. Fiberoptic probe and system for spectral measurements

    DOEpatents

    Dai, S.; Young, J.P.

    1998-10-13

    A fused fiberoptic probe, a system, method and embodiments thereof for conducting spectral measurements are disclosed. The fused fiberoptic probe comprises a probe tip having a specific geometrical configuration, an exciting optical fiber and at least one collection optical fiber fused within a housing, preferably silica. The specific geometrical configurations in which the probe tip can be shaped include a slanted probe tip with an angle greater than 0{degree}, an inverted cone-shaped probe tip, and a lens head. 12 figs.

  3. Fiberoptic probe and system for spectral measurements

    DOEpatents

    Dai, Sheng; Young, Jack P.

    1998-01-01

    A fused fiberoptic probe, a system, method and embodiments thereof for conducting spectral measurements are disclosed. The fused fiberoptic probe comprises a probe tip having a specific geometrical configuration, an exciting optical fiber and at least one collection optical fiber fused within a housing, preferrably silica. The specific geometrical configurations in which the probe tip can be shaped include a slanted probe tip with an angle greater than 0.degree., an inverted cone-shaped probe tip, and a lens head.

  4. Tetrapod nanocrystals as fluorescent stress probes of electrospun nanocomposites.

    PubMed

    Raja, Shilpa N; Olson, Andrew C K; Thorkelsson, Kari; Luong, Andrew J; Hsueh, Lillian; Chang, Guoqing; Gludovatz, Bernd; Lin, Liwei; Xu, Ting; Ritchie, Robert O; Alivisatos, A Paul

    2013-08-14

    A nanoscale, visible-light, self-sensing stress probe would be highly desirable in a variety of biological, imaging, and materials engineering applications, especially a device that does not alter the mechanical properties of the material it seeks to probe. Here we present the CdSe-CdS tetrapod quantum dot, incorporated into polymer matrices via electrospinning, as an in situ luminescent stress probe for the mechanical properties of polymer fibers. The mechanooptical sensing performance is enhanced with increasing nanocrystal concentration while causing minimal change in the mechanical properties even up to 20 wt % incorporation. The tetrapod nanoprobe is elastic and recoverable and undergoes no permanent change in sensing ability even upon many cycles of loading to failure. Direct comparisons to side-by-side traditional mechanical tests further validate the tetrapod as a luminescent stress probe. The tetrapod fluorescence stress-strain curve shape matches well with uniaxial stress-strain curves measured mechanically at all filler concentrations reported. PMID:23815586

  5. Integrated microfluidic probe station.

    PubMed

    Perrault, C M; Qasaimeh, M A; Brastaviceanu, T; Anderson, K; Kabakibo, Y; Juncker, D

    2010-11-01

    The microfluidic probe (MFP) consists of a flat, blunt tip with two apertures for the injection and reaspiration of a microjet into a solution--thus hydrodynamically confining the microjet--and is operated atop an inverted microscope that enables live imaging. By scanning across a surface, the microjet can be used for surface processing with the capability of both depositing and removing material; as it operates under immersed conditions, sensitive biological materials and living cells can be processed. During scanning, the MFP is kept immobile and centered over the objective of the inverted microscope, a few micrometers above a substrate that is displaced by moving the microscope stage and that is flushed continuously with the microjet. For consistent and reproducible surface processing, the gap between the MFP and the substrate, the MFP's alignment, the scanning speed, the injection and aspiration flow rates, and the image capture need all to be controlled and synchronized. Here, we present an automated MFP station that integrates all of these functionalities and automates the key operational parameters. A custom software program is used to control an independent motorized Z stage for adjusting the gap, a motorized microscope stage for scanning the substrate, up to 16 syringe pumps for injecting and aspirating fluids, and an inverted fluorescence microscope equipped with a charge-coupled device camera. The parallelism between the MFP and the substrate is adjusted using manual goniometer at the beginning of the experiment. The alignment of the injection and aspiration apertures along the scanning axis is performed using a newly designed MFP screw holder. We illustrate the integrated MFP station by the programmed, automated patterning of fluorescently labeled biotin on a streptavidin-coated surface. PMID:21133501

  6. Integrated microfluidic probe station

    NASA Astrophysics Data System (ADS)

    Perrault, C. M.; Qasaimeh, M. A.; Brastaviceanu, T.; Anderson, K.; Kabakibo, Y.; Juncker, D.

    2010-11-01

    The microfluidic probe (MFP) consists of a flat, blunt tip with two apertures for the injection and reaspiration of a microjet into a solution—thus hydrodynamically confining the microjet—and is operated atop an inverted microscope that enables live imaging. By scanning across a surface, the microjet can be used for surface processing with the capability of both depositing and removing material; as it operates under immersed conditions, sensitive biological materials and living cells can be processed. During scanning, the MFP is kept immobile and centered over the objective of the inverted microscope, a few micrometers above a substrate that is displaced by moving the microscope stage and that is flushed continuously with the microjet. For consistent and reproducible surface processing, the gap between the MFP and the substrate, the MFP's alignment, the scanning speed, the injection and aspiration flow rates, and the image capture need all to be controlled and synchronized. Here, we present an automated MFP station that integrates all of these functionalities and automates the key operational parameters. A custom software program is used to control an independent motorized Z stage for adjusting the gap, a motorized microscope stage for scanning the substrate, up to 16 syringe pumps for injecting and aspirating fluids, and an inverted fluorescence microscope equipped with a charge-coupled device camera. The parallelism between the MFP and the substrate is adjusted using manual goniometer at the beginning of the experiment. The alignment of the injection and aspiration apertures along the scanning axis is performed using a newly designed MFP screw holder. We illustrate the integrated MFP station by the programmed, automated patterning of fluorescently labeled biotin on a streptavidin-coated surface.

  7. Gravity Probe B Assembled

    NASA Technical Reports Server (NTRS)

    2000-01-01

    In this photo, the Gravity Probe B (GP-B) space vehicle is being assembled at the Sunnyvale, California location of the Lockheed Martin Corporation. The GP-B is the relativity experiment developed at Stanford University to test two extraordinary predictions of Albert Einstein's general theory of relativity. The experiment will measure, very precisely, the expected tiny changes in the direction of the spin axes of four gyroscopes contained in an Earth-orbiting satellite at a 400-mile altitude. So free are the gyroscopes from disturbance that they will provide an almost perfect space-time reference system. They will measure how space and time are very slightly warped by the presence of the Earth, and, more profoundly, how the Earth's rotation very slightly drags space-time around with it. These effects, though small for the Earth, have far-reaching implications for the nature of matter and the structure of the Universe. GP-B is among the most thoroughly researched programs ever undertaken by NASA. This is the story of a scientific quest in which physicists and engineers have collaborated closely over many years. Inspired by their quest, they have invented a whole range of technologies that are already enlivening other branches of science and engineering. Launched April 20, 2004 , the GP-B program was managed for NASA by the Marshall Space Flight Center. Development of the GP-B is the responsibility of Stanford University along with major subcontractor Lockheed Martin Corporation. (Image credit to Russ Underwood, Lockheed Martin Corporation).

  8. The mechanism of the reduction of [AnO2]2+ (An = U, Np, Pu) in aqueous solution, and by Fe(II) containing proteins and mineral surfaces, probed by DFT calculations.

    PubMed

    Sundararajan, Mahesh; Assary, Rajeev S; Hillier, Ian H; Vaughan, David J

    2011-11-14

    The fate of actinyl species in the environment is closely linked to oxidation state, since the reduction of An(VI) to An(IV) greatly decreases their mobility due to the precipitation of the relatively insoluble An(IV) species. Here we study the mechanism of the reduction of [AnO(2)](2+) (An = U, Np, Pu) both in aqueous solution and by Fe(II) containing proteins and mineral surfaces, using density functional theory calculations. We find a disproportionation mechanism involving a An(V)-An(V) cation-cation complex, and we have investigated how these complexes are formed in the different environments. We find that the behaviour of U and Pu complexes are similar, but the reduction of Np(V) to Np(IV) would seems to be more difficult, in line with the experimental finding that Np(V) is generally more stable than U(V) or Pu(V). Although the models we have used are somewhat idealised, our calculations suggest that there are strong similarities between the biotic and abiotic reduction pathways. PMID:21837318

  9. Design of a contact probe with high positioning accuracy for plasmonic lithography.

    PubMed

    Jang, Jinhee; Kim, Yongwoo; Kim, Seok; Jung, Howon; Hahn, Jae Won

    2011-01-01

    Plasmonic lithography with a contact probe records nano-meter scale features and has high-throughput owing to its capability to scan in contact mode. The probe is commonly based on a micrometer-scale cantilever, which leads to the tip-positioning problem due to force-deflection that induces lateral tip displacement. We propose a geometrically modified probe to achieve high positioning accuracy. Contrary to a conventional cantilever-tip probe, we designed a "circular probe" with arc-shaped arms that hold the tip in the center. The mechanism is based on the "fixed-fixed beam" concept in material mechanics. To confirm its positioning accuracy, we used a finite element method (FEM) to calculate the tip displacement for a circular probe and compared the results with those using a conventional cantilever-tip probe. The probe was designed considering a silicon-based micro-fabrication process. The designed probe has a square outline boundary with a length of 50 µm, four arms, and a pyramidal tip with a height of 5 µm. The ratio of the lateral tip displacement to the vertical deflection was evaluated to indicate the accuracy of the probe. The probe has higher positioning accuracy by a factor of 10(3) and 10 in its approach mode and scan mode, respectively, compared with a cantilever-tip probe. We expect that the probe is suitable for the applications that require high positioning accuracy, such as nanolithography in contact mode and applications based on multiple-probe arrays. PMID:21445985

  10. A colorimetric and fluorescent probe for fluoride ions based on 6-acetyl-2-naphthol.

    PubMed

    Hou, Peng; Chen, Song; Song, Xiangzhi

    2014-08-01

    A colorimetric and turn-on fluorescent probe for fluoride ions, tert-butyldimethylsilane 6-acetyl-2-naphtholate, was readily synthesized from 6-acetyl-2-naphthol and tert-butyldimethylchlorosilane (TBSCl). The probe exhibits high sensitivity and good selectivity for fluoride ions in acetonitrile. The inherent mechanism involves the cleavage of the Si-O bond in the probe, which induced yellow color formation and prominent fluorescence enhancement. PMID:23881573

  11. A new turn on coumarin-based fluorescence probe for Ga3 + detection in aqueous solution

    NASA Astrophysics Data System (ADS)

    Yan, Liqiang; Zhou, Yan; Du, Wenqi; Kong, Zhineng; Qi, Zhengjian

    2016-02-01

    The probe CT was synthesized and investigated as a novel label-free chemosensor for Ga3 + detection in water. Probe CT showed remarkable selectivity and sensitivity for Ga3 + in Tris-HCl aqueous buffer solution (pH 7.0). The chemosensor responded rapidly to Ga3 + with a 1:1 stoichiometry. Meanwhile, the unapparent changes of fluorescence lifetime decays suggest the turn-on process of probe CT by Ga3 + which appears to be a static mechanism.

  12. Study of alternative probe technologies

    NASA Technical Reports Server (NTRS)

    1977-01-01

    A number of implied technologies for a deep probe mission was examined; i.e., one that would provide the capability to scientifically examine planetary atmospheres at the 1000 bar level. Conditions imposed by current Jupiter, Saturn, and Uranus atmospheric models were considered. The major thrust of the measurements was to determine lower atmosphere composition, even to trace constituents of one part per billion. Two types of instruments having the necessary accuracy to meet the science objectives were considered and integrated into a deep probe configuration. One deep probe option that resulted was identified as a Minimum Technology Development approach. The significant feature of this option is that only three technology developments are required to enable the mission, i.e., (1) science instrument development, (2) advanced data processing, and (3) external high pressure/thermal insulation. It is concluded that a probe designed for a Jupiter mission could, with minor changes, be used for a Saturn or Uranus mission.

  13. The Radiation Belt Storm Probes

    NASA Video Gallery

    The Radiation Belt Storm Probe mission (RBSP) will explore the Van Allen Radiation Belts in the Earth's magnetosphere. The charge particles in these regions can be hazardous to both spacecraft and ...

  14. A three dimensional probe positioner

    SciTech Connect

    Intrator, T.; Sun, X.; Furno, I.; Dorf, L.; Lapenta, G.

    2008-10-15

    In order to sort out the physics that is important in many plasma experiments, data in three dimensions (3D) are becoming necessary. Access to the usual cylindrical vacuum vessel is typically restricted to radially or axially insertable probes that can pivot. The space that can be explored usually has significant restrictions either because probe travel must be along a travel path, or a 'wobbly' probe positioner requires one to map between a moveable coordinate system and a preferred laboratory coordinate system. This could for example introduce errors in measurements of vector quantities such as magnetic field or flow. We describe the design and implementation of a 3D probe positioner that slides in two dimensions on a double O-ring seal and radially inserts along the third dimension. The net result is that a 3D space can be explored in a laboratory Cartesian reference frame.

  15. Monitoring probe for groundwater flow

    DOEpatents

    Looney, B.B.; Ballard, S.

    1994-08-23

    A monitoring probe for detecting groundwater migration is disclosed. The monitor features a cylinder made of a permeable membrane carrying an array of electrical conductivity sensors on its outer surface. The cylinder is filled with a fluid that has a conductivity different than the groundwater. The probe is placed in the ground at an area of interest to be monitored. The fluid, typically saltwater, diffuses through the permeable membrane into the groundwater. The flow of groundwater passing around the permeable membrane walls of the cylinder carries the conductive fluid in the same general direction and distorts the conductivity field measured by the sensors. The degree of distortion from top to bottom and around the probe is precisely related to the vertical and horizontal flow rates, respectively. The electrical conductivities measured by the sensors about the outer surface of the probe are analyzed to determine the rate and direction of the groundwater flow. 4 figs.

  16. Monitoring probe for groundwater flow

    DOEpatents

    Looney, Brian B.; Ballard, Sanford

    1994-01-01

    A monitoring probe for detecting groundwater migration. The monitor features a cylinder made of a permeable membrane carrying an array of electrical conductivity sensors on its outer surface. The cylinder is filled with a fluid that has a conductivity different than the groundwater. The probe is placed in the ground at an area of interest to be monitored. The fluid, typically saltwater, diffuses through the permeable membrane into the groundwater. The flow of groundwater passing around the permeable membrane walls of the cylinder carries the conductive fluid in the same general direction and distorts the conductivity field measured by the sensors. The degree of distortion from top to bottom and around the probe is precisely related to the vertical and horizontal flow rates, respectively. The electrical conductivities measured by the sensors about the outer surface of the probe are analyzed to determine the rate and direction of the groundwater flow.

  17. Activatable Optical Probes for the Detection of Enzymes

    PubMed Central

    Drake, Christopher R.; Miller, David C.; Jones, Ella F.

    2013-01-01

    The early detection of many human diseases is crucial if they are to be treated successfully. Therefore, the development of imaging techniques that can facilitate early detection of disease is of high importance. Changes in the levels of enzyme expression are known to occur in many diseases, making their accurate detection at low concentrations an area of considerable active research. Activatable fluorescent probes show immense promise in this area. If properly designed they should exhibit no signal until they interact with their target enzyme, reducing the level of background fluorescence and potentially endowing them with greater sensitivity. The mechanisms of fluorescence changes in activatable probes vary. This review aims to survey the field of activatable probes, focusing on their mechanisms of action as well as illustrating some of the in vitro and in vivo settings in which they have been employed. PMID:23519774

  18. Foldback intercoil DNA and the mechanism of DNA transposition.

    PubMed

    Kim, Byung-Dong

    2014-09-01

    Foldback intercoil (FBI) DNA is formed by the folding back at one point of a non-helical parallel track of double-stranded DNA at as sharp as 180° and the intertwining of two double helixes within each other's major groove to form an intercoil with a diameter of 2.2 nm. FBI DNA has been suggested to mediate intra-molecular homologous recombination of a deletion and inversion. Inter-molecular homologous recombination, known as site-specific insertion, on the other hand, is mediated by the direct perpendicular approach of the FBI DNA tip, as the attP site, onto the target DNA, as the attB site. Transposition of DNA transposons involves the pairing of terminal inverted repeats and 5-7-bp tandem target duplication. FBI DNA configuration effectively explains simple as well as replicative transposition, along with the involvement of an enhancer element. The majority of diverse retrotransposable elements that employ a target site duplication mechanism is also suggested to follow the FBI DNA-mediated perpendicular insertion of the paired intercoil ends by non-homologous end-joining, together with gap filling. A genome-wide perspective of transposable elements in light of FBI DNA is discussed. PMID:25317106

  19. The Interstellar Heliopause Probe

    NASA Astrophysics Data System (ADS)

    Lyngvi, A.; Falkner, P.; Peacock, A.

    The Interstellar Heliopause Probe (IHP) is one of four Technology Reference Missions (TRM) introduced by the Planetary Exploration Studies Section of the Science Payload & Advanced Concepts Office (SCI-A) at ESA. The overall purpose of the TRMs is to focus the development of strategically important technologies of likely relevance to future science missions. This is accomplished through the study of several technologically demanding and scientifically interesting missions, which are currently not part of the ESA science programme. The TRM baseline uses small satellites (< 200kg), with highly miniaturized and highly integrated payload suites. The motivation for this is to use low resource spacecraft in a phased approach, which will reduce the risk and cost, compared to a single, high resource mission. Equipped with a Highly Integrated Payload Suite (HIPS) the IHP will answer scientific questions concerning the nature of the interstellar medium, how the interstellar medium affects our solar system and how the solar system impacts the interstellar medium. The HIPS, which is a standard element in all TRMs miniaturize through resource reduction, by using miniaturized components and sensors, and by sharing common structures and payload functionality. To achieve the scientific requirements of the mission the spacecraft is to leave the solar system as close to the heliosphere nose as possible and reach a distance of 200 AU from the Sun within 25 years. The requirement of all TRMs is to use a Souyz-Fregat version 2B or equivalent low cost launch vehicle. With this constraint no current propulsion system is capable of delivering the necessary mass to the final destination. Technologies are therefore needed to enable this mission. The current alternatives are using nuclear propulsion, either with radioisotope or reactor power system or solar sailing. All these alternatives are currently being investigated. Other challenges exist as well such as designing a communication link

  20. Temperature Correction in Probe Measurements

    NASA Astrophysics Data System (ADS)

    Gutsev, S. A.

    2015-09-01

    This work is devoted to experimental investigations of a decaying plasma using Langmuir probes. The gas pressure, the discharge current, and the moment of afterglow were selected to obtain probe characteristics in collisionless, intermediate, and drifting regimes of motion of charged particles. The manner in which the shape of the volt- ampere characteristics changes on passage from the collisionless motion to diffusion motion has been shown. A detailed analysis has been made of the source of errors arising when orbital-motion formulas or the logarithmic-operation method are applied to processing of the probe curves. It has been shown that neglect of collisions of charged particles in the probe layer leads to an ion-density value overstated more than three times, an electron-temperature value overstated two times, and an ion temperature overstated three to nine times. A model of interaction of charged particles in the probe layer has been proposed for correction of the procedure of determining temperature. Such an approach makes it possible to determine the space-charge layer in the probe, and also the value of the self-consistent field. The use of the developed procedures gives good agreement between experimental and theoretical results.

  1. Field measuring probe for SSC (Superconducting Super Collider) magnets

    SciTech Connect

    Ganetis, G.; Herrera, J.; Hogue, R.; Skaritka, J.; Wanderer, P.; Willen, E.

    1987-03-01

    The field probe developed for measuring the field in SSC dipole magnets is an adaptation of the rotating tangential coil system in use at Brookhaven for several years. Also known as the MOLE, it is a self-contained room-temperature mechanism that is pulled through the aperture of the magnet with regular stops to measure the local field. Several minutes are required to measure the field at each point. The probe measures the multipole components of the field as well as the field angle relative to gravity. The sensitivity of the coil and electronics is such that the field up to the full 6.6 T excitation of the magnet as well as the field when warm with only 0.01 T excitation can be measured. Tethers are attached to both ends of the probe to carry electrical connections and to supply dry nitrogen to the air motors that rotate the tangential windings as well as the gravity sensor. A small computer is attached to the probe for control and for data collection, analysis and storage. Digital voltmeters are used to digitize the voltages from the rotating coil and several custom circuits control motor speeds in the probe. The overall diameter of the probe is approximately 2 cm and its length is 2.4 m; the field sensitive windings are 0.6 m in length.

  2. Massively Multiplexed Cantilever-free Scanning Probe Lithography

    NASA Astrophysics Data System (ADS)

    Brown, Keith A.; Eichelsdoerfer, Daniel J.; Shim, Wooyoung; Boya, Radha; Schmucker, Abrin L.; Liu, Guoliang; Mirkin, Chad A.

    2013-03-01

    Cantilever-free scanning probe lithography has emerged as a low-cost technique for rapidly patterning nanoscale materials. In this architecture, an array of probes is fabricated on a soft backing layer that provides mechanical compliance to each probe while an underlying hard surface maintains the structural integrity of the array. One drawback of this technique is that each probe in the array acts simultaneously and thus generates a copy of the same pattern. Here, we discuss recent efforts to incorporate heaters into these probe arrays so that when a given heater is activated, the thermal expansion of the elastomer actuates a single tip. We find thermal actuation to be powerful enough to actuate individual tips over 4 μm with minimal crosstalk, fast enough to actuate on relevant time scales (20 ms), and scalable by virtue of being electrically addressable. Furthermore, tuning the individual heaters allows for variability in the arrays to be compensated for precisely, resulting in high quality nanopatterning. The addition of tunable actuators transforms cantilever-free scanning probe lithography into a technique capable of true desktop nanofabrication.

  3. Magnetomotive molecular probes for targeted contrast enhancement and therapy

    NASA Astrophysics Data System (ADS)

    Boppart, Stephen A.

    2011-03-01

    The diagnostic, interrogational, and therapeutic potential of molecular probes is rapidly being investigated and exploited across virtually every biomedical imaging modality. While many types of probes enhance contrast or delivery therapy by static localization to targeted sites, significant potential exists for utilizing dynamic molecular probes. Recent examples include molecular beacons, photoactivatable probes, or controlled switchable drug-releasing particles, to name a few. In this review, we describe a novel class of dynamic molecular probes that rely on the application and control of localized external magnetic fields. These magnetomotive molecular probes can provide optical image contrast through a modulated scattering signal, can interrogate the biomechanical properties of their viscoelastic microenvironment by tracking their underdamped oscillatory step-response to applied fields, and can potentially delivery therapy through nanometer-to-micrometer mechanical displacement or local hyperthermia. This class of magnetomotive agents includes not only magnetic iron-oxide nanoparticles, but also new magnetomotive microspheres or nanostructures with embedded iron-oxide agents. In vitro three-dimensional cell assays and in vivo targeting studies in animal tumor models have demonstrated the potential for multimodal detection and imaging, using magnetic resonance imaging for whole-body localization, and magnetomotive optical coherence tomography for high-resolution localization and imaging.

  4. Probe for high resolution NMR with sample reorientation

    DOEpatents

    Pines, A.; Samoson, A.

    1990-02-06

    An improved NMR probe and method are described which substantially improve the resolution of NMR measurements made on powdered or amorphous or otherwise orientationally disordered samples. The apparatus mechanically varies the orientation of the sample such that the time average of two or more sets of spherical harmonic functions are zero. 8 figs.

  5. Probe for high resolution NMR with sample reorientation

    DOEpatents

    Pines, Alexander; Samoson, Ago

    1990-01-01

    An improved NMR probe and method are described which substantially improve the resolution of NMR measurements made on powdered or amorphous or otherwise orientationally disordered samples. The apparatus mechanically varies the orientation of the sample such that the time average of two or more sets of spherical harmonic functions are zero.

  6. Novel Diubiquitin Probes Expand the Chemical Toolkit to Study DUBs.

    PubMed

    Kulathu, Yogesh

    2016-04-21

    Linkage-specific DUBs employ different mechanisms to recognize and cleave polyubiquitin chains of specific linkage types. In this issue of Cell Chemical Biology, Flierman et al. (2016) develop a new family of novel non-hydrolyzable diubiquitin probes that will be valuable tools to study how DUBs achieve specificity. PMID:27105279

  7. Electronic linearization of piezoelectric actuators and noise budget in scanning probe microscopy

    NASA Astrophysics Data System (ADS)

    Aloisi, G.; Santucci, A.; Carlà, M.; Dolci, D.; Lanzi, L.

    2006-07-01

    The maximum resolution achievable with a scanning probe microscope is limited by the probe size, by the mechanism of interaction with the sample, as is widely known, and by the electronic noise in the instrument. The evaluation of this noise for the three motion axes of a linearized high resolution scanning electrochemical microscope has been carried through and the intrinsic maximum resolution is discussed.

  8. Probe-Sample Coupling in the Magnetic Resonance Force Microscope

    NASA Astrophysics Data System (ADS)

    Suter, A.; Pelekhov, D. V.; Roukes, M. L.; Hammel, P. C.

    2002-02-01

    The magnetic resonance force microscope (MRFM) provides a route to achieving scanned probe magnetic resonance imaging with extremely high spatial resolution. Achieving this capability will require understanding the force exerted on a microscopic magnetic probe by a spatially extended sample over which the probe is scanned. Here we present a detailed analysis of this interaction between probe and sample. We focus on understanding the situation where the micromagnet mounted on the mechanical resonator generates a very inhomogeneous magnetic field and is scanned over a sample with at least one spatial dimension much larger than that of the micromagnet. This situation differs quite significantly from the conditions under which most MRFM experiments have been carried out where the sample is mounted on the mechanical resonator and placed in a rather weak magnetic field gradient. In addition to the concept of a sensitive slice (the spatial region where the magnetic resonance condition is met) it is valuable to map the forces exerted on the probe by spins at various locations; this leads to the concept of the force slice (the region in which spins exert force on the resonator). Results of this analysis, obtained both analytically and numerically, will be qualitatively compared with an initial experimental finding from an EPR-MRFM experiment carried out on DPPH at 4 K.

  9. Probe--sample coupling in the magnetic resonance force microscope.

    PubMed

    Suter, A; Pelekhov, D V; Roukes, M L; Hammel, P C

    2002-02-01

    The magnetic resonance force microscope (MRFM) provides a route to achieving scanned probe magnetic resonance imaging with extremely high spatial resolution. Achieving this capability will require understanding the force exerted on a microscopic magnetic probe by a spatially extended sample over which the probe is scanned. Here we present a detailed analysis of this interaction between probe and sample. We focus on understanding the situation where the micromagnet mounted on the mechanical resonator generates a very inhomogeneous magnetic field and is scanned over a sample with at least one spatial dimension much larger than that of the micromagnet. This situation differs quite significantly from the conditions under which most MRFM experiments have been carried out where the sample is mounted on the mechanical resonator and placed in a rather weak magnetic field gradient. In addition to the concept of a sensitive slice (the spatial region where the magnetic resonance condition is met) it is valuable to map the forces exerted on the probe by spins at various locations; this leads to the concept of the force slice (the region in which spins exert force on the resonator). Results of this analysis, obtained both analytically and numerically, will be qualitatively compared with an initial experimental finding from an EPR-MRFM experiment carried out on DPPH at 4 K. PMID:11846579

  10. Inter- and intra-molecular energy transfers of encapsulate dyes in dendrimers

    NASA Astrophysics Data System (ADS)

    Otomo, Akira; Zhou, Minniu; Furumi, Seiichi; Yokoyama, Shiyoshi; Mashiko, Shinro

    2002-12-01

    Dendrimers are capable to encapsulate small molecules inside them. Because three-dimensional structures of dendrimers are highly controllable, energy transfers among dye molecules encapsulated inside them can be controlled precisely. Electronic energy transfers from optical excited molecules are categorized into two classes, Forster and Dexter types. Inter-molecular interactions between encapsulated dyes can be expressed as the Forster (singlet-singlet) energy transfer, because the size of dendrimers extends to a few nanometers. We have evaluated time resolved optical responses in rhodamine-cored dendrimer films. Fast decay in fluorescent lifetime is observed and it depends on the dendrimer size. A low generation dendrimer shows lifetime as short as 10 psec without severe quenching of fluorescence. A quadratic dependence of the emission intensity on density of molecules indicates that the origin of the short lifetime is not only energy transfer, but also super-radiance. Since the Dexter (triplet-triplet) energy transfer occurs in short range of 1.0 nm, we attached both donor and acceptor molecules to a dendrimer for investigation. We demonstrated photocrosslinking via triplet-triplet energy transfer from donor molecules encapsulated to acceptors attached at the surface. This procedure of triplet-triplet energy transfer in dendritic molecules opens up way to design novel optical and electrical molecular devices.

  11. Identification of an intra-molecular disulfide bond in the sodium channel β1-subunit.

    PubMed

    Barbieri, Raffaella; Baroni, Debora; Moran, Oscar

    2012-04-01

    The sodium channel β1 subunit is non-covalently associated with the pore-forming α-subunits, and has been proposed to act as a modulator of channel activity, regulator of channel cell surface expression and cell adhesion molecule. Its importance is evident since mutations of the β1 subunit cause neurologic and cardiovascular disorders. The first described β1 subunit mutation is the C121W, that is related to generalized epilepsy with febrile seizures plus (GEFS+), a childhood genetic epilepsy syndrome. This mutation changed a conserved cysteine residue in position 121 into a tryptophan, putatively disrupting a disulfide bridge that should normally maintain the β1 extracellular immunoglobulin-like fold. Using the 2-D-diagonal-SDS-PAGE technique, we demonstrated the existence of this putative disulfide bridge in the Ig-like extracellular domain of the β1 subunit and its disruption in the epileptogenic C121W mutant. PMID:22425777

  12. Inter/intra molecular dynamics in gases and liquids studied by terahertz time-domain spectroscopy

    NASA Astrophysics Data System (ADS)

    Xin, Xuying

    This thesis presents a description of the low-frequency terahertz (THz) absorption spectrum of a variety of materials that are of interest to many biological and chemical processes. The work described here encompasses the development of time-domain THz spectrometers, based on amplified Ti: Sapphire lasers systems as well as mode-locked Erbium doped fiber lasers as the driving source. These systems were applied to characterize the absorption spectrum of liquid water and water vapor, heavy water vapor, methanol vapor and tryptophan in the 0.2-2.2THz frequency range. The absorption profiles observed are closely related to the intermolecular or intramolecular motions in the materials of interest. In liquid water, the absorption profile shows evidence for modes due to large-scale structure amongst individual water molecules. The effects on the overall absorption profile are further deduced by the addition of various solutes which can enhance or break the formation of molecule networks. Various solutions are examined such as KCl in liquid water. Ions can change the strength of hydrogen bond in liquid water in the similar way as temperature does. Both K+ and Cl- are considered to be strong "structure breakers" in terms of their functions as softening the strength of hydrogen bond in liquid water. Theoretically, this will cause a red shift of some mode frequencies, reducing the absorption intensity at those frequencies and, at the same time, increasing the absorption at non-mode frequencies toward the vicinity of the low frequencies. For liquid water, the vapor phase was also examined, where for varying concentrations (humidity) Beer's Law does not hold to explain the observed absorption profiles. Again the reduced absorption of certain modes is explained by interactions between water monomers and their nature due to hydrogen spins. There are two species of water molecules in terms of the nuclear spin effect of hydrogen atoms in water molecule, ortho-water and para-water. The two types of water molecules present significantly different properties, e.g. different surface adsorption on metals. The effects of para-water and ortho-water on the THz absorption profile are discussed. Finally, I discuss the absorption profile of methanol vapor and tryptophan. In methanol vapor we observe coherent echoes after absorption by a THz transient and attribute it to the relaxation of the molecule due to the regularly spaced rotational manifold. In tryptophan two distinct absorption modes are observed due to torsional modes. These "soft-modes" are calculated and attributed to intramolecular motions between various atoms. The results of this body of work are discussed in the context of applications ranging from medicine, pharmaceuticals and the cosmetics industries.

  13. Probing stem cell differentiation using atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Liang, Xiaobin; Shi, Xuetao; Ostrovidov, Serge; Wu, Hongkai; Nakajima, Ken

    2016-03-01

    A real-time method using atomic force microscopy (AFM) was developed to probe stem cell differentiation by measuring the mechanical properties of cells and the extracellular matrix (ECM). The mechanical properties of stem cells and their ECMs can be used to clearly distinguish specific stem cell-differentiated lineages. It is clear that AFM is a facile and useful tool for monitoring the differentiation of stem cells in a non-invasive manner.

  14. Probing the Probes: Fitness Factors For Small Molecule Tools

    PubMed Central

    Workman, Paul; Collins, Ian

    2010-01-01

    Chemical probes for interrogating biological processes are of considerable current interest. Cell permeable small molecule tools have a major role in facilitating the functional annotation of the human genome, understanding both physiological and pathological processes, and validating new molecular targets. To be valuable, chemical tools must satisfy necessary criteria and recent publications have suggested objective guidelines for what makes a useful chemical probe. Although recognizing that such guidelines may be valuable, we caution against overly restrictive rules that may stifle innovation in favor of a “fit-for-purpose” approach. Reviewing the literature and providing examples from the cancer field, we recommend a series of “fitness factors” to be considered when assessing chemical probes. We hope this will encourage innovative chemical biology research while minimizing the generation of poor quality and misleading biological data, thus increasing understanding of the particular biological area, to the benefit of basic research and drug discovery. PMID:20609406

  15. Probing deformed quantum commutators

    NASA Astrophysics Data System (ADS)

    Rossi, Matteo A. C.; Giani, Tommaso; Paris, Matteo G. A.

    2016-07-01

    Several quantum gravity theories predict a minimal length at the order of magnitude of the Planck length, under which the concepts of space and time lose their physical meaning. In quantum mechanics, the insurgence of such a minimal length can be described by introducing a modified position-momentum commutator, which in turn yields a generalized uncertainty principle, where the uncertainty on position measurements has a lower bound. The value of the minimal length is not predicted by theories and must be estimated experimentally. In this paper, we address the quantum bound to the estimability of the minimal uncertainty length by performing measurements on a harmonic oscillator, which is analytically solvable in the deformed algebra induced by the deformed commutation relations.

  16. Understanding of Jupiter's Atmosphere After the Galileo Probe Entry

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

    at least as deep as the probe made measurements, 22 bars. Models of hot spot dynamics raise the possibility that the variation with depth of the probe measured zonal winds between 0.4 and 4 bars reflect the dynamics of the hot spot rather than the global wind pattern. Galileo upper atmosphere measurements established that there is a sharp temperature rise with altitude between about 350 and 800 km above the 1 bar pressure level, with the upper atmosphere reaching, temperatures near 900 K. The energy sources for this upper atmosphere heating are not clearly established, but various mechanisms have been proposed. These and other aspects of the Galileo probe data will be discussed.

  17. Understanding of Jupiter's Atmosphere after the Galileo Probe Entry

    NASA Technical Reports Server (NTRS)

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

    2003-01-01

    at least as deep as the probe made measurements, 22 bars. Models of hot spot dynamics raise the possibility that the variation with depth of the probe measured zonal winds between 0.4 and 4 bars reflect the dynamics of the hot spot rather than the global wind pattern. Galileo upper atmosphere measurements established that there is a sharp temperature rise with altitude between about 350 and 800 km above the 1 bar pressure level, with the upper atmosphere reaching temperatures near 900 K. The energy sources for this upper atmosphere heating are not clearly established, but various mechanisms have been proposed. These and other aspects of the Galileo probe data will be discussed.

  18. Potent fluoro-oligosaccharide probes of adhesion in Toxoplasmosis.

    PubMed

    Allman, Sarah A; Jensen, Henrik H; Vijayakrishnan, Balakumar; Garnett, James A; Leon, Ester; Liu, Yan; Anthony, Daniel C; Sibson, Nicola R; Feizi, Ten; Matthews, Stephen; Davis, Benjamin G

    2009-10-12

    Unnatural, NMR- and MRI-active fluorinated sugar probes, designed and synthesised to bind to the pathogenic protein TgMIC1 from Toxoplasma gondii, were found to display binding potency equal to and above that of the natural ligand. Dissection of the binding mechanism and modes, including the first X-ray crystal structures of a fluoro-oligosaccharide bound to a lectin, demonstrate that it is possible to create effective fluorinated probe ligands for the study of, and perhaps intervention in, sugar-protein binding events. PMID:19750531

  19. Hand-held survey probe

    DOEpatents

    Young, Kevin L [Idaho Falls, ID; Hungate, Kevin E [Idaho Falls, ID

    2010-02-23

    A system for providing operational feedback to a user of a detection probe may include an optical sensor to generate data corresponding to a position of the detection probe with respect to a surface; a microprocessor to receive the data; a software medium having code to process the data with the microprocessor and pre-programmed parameters, and making a comparison of the data to the parameters; and an indicator device to indicate results of the comparison. A method of providing operational feedback to a user of a detection probe may include generating output data with an optical sensor corresponding to the relative position with respect to a surface; processing the output data, including comparing the output data to pre-programmed parameters; and indicating results of the comparison.

  20. Wake flowfields for Jovian probe

    NASA Technical Reports Server (NTRS)

    Engel, C. D.; Hair, L. M.

    1980-01-01

    The wake flow field developed by the Galileo probe as it enters the Jovian atmosphere was modeled. The wake produced by the probe is highly energetic, yielding both convective and radiative heat inputs to the base of the probe. A component mathematical model for the inviscid near and far wake, the viscous near and far wake, and near wake recirculation zone was developed. Equilibrium thermodynamics were used for both the ablation and atmospheric species. Flow fields for three entry conditions were calculated. The near viscous wave was found to exhibit a variable axial pressure distribution with the neck pressure approximately three times the base pressure. Peak wake flow field temperatures were found to be in proportion to forebody post shock temperatures.

  1. Oxide nanocrystal based nanocomposites for fabricating photoplastic AFM probes.

    PubMed

    Ingrosso, Chiara; Martin-Olmos, Cristina; Llobera, Andreu; Innocenti, Claudia; Sangregorio, Claudio; Striccoli, Marinella; Agostiano, Angela; Voigt, Anja; Gruetzner, Gabi; Brugger, Jürgen; Perez-Murano, Francesc; Curri, Maria Lucia

    2011-11-01

    We report on the synthesis, characterization and application of a novel nanocomposite made of a negative tone epoxy based photoresist modified with organic-capped Fe(2)O(3) nanocrystals (NCs). The mechanical properties of the nanocomposite drastically improve upon incorporation of a suitable concentration of NCs in the polymer, without deteriorating its photolithography performance. High aspect ratio 3D microstructures made of the nanocomposite have been fabricated with a uniform surface morphology and with a resolution down to few micrometres. The embedded organic-capped Fe(2)O(3) NCs drastically increase the stiffness and hardness of the epoxy based photoresist matrix, making the final material extremely interesting for manufacturing miniaturized polymer based mechanical devices and systems. In particular, the nanocomposite has been used as structural material for fabricating photoplastic Atomic Force Microscopy (AFM) probes with integrated tips showing outstanding mechanical response and high resolution imaging performance. The fabricated probes consist of straight cantilevers with low stress-gradient and high quality factors, incorporating sharp polymeric tips. They present considerably improved performance compared to pure epoxy based photoresist AFM probes, and to commercial silicon AFM probes. PMID:21858377

  2. A simple levulinate-based ratiometric fluorescent probe for sulfite with a large emission shift.

    PubMed

    Liu, Caiyun; Wu, Huifang; Yang, Wen; Zhang, Xiaoling

    2014-01-01

    A simple 4-hydroxynaphthalimide-derived colorimetric and ratiometric fluorescent probe (1) containing a receptor of levulinate moiety was designed and synthesized to monitor sulfite. Probe 1 could quantificationally detect sulfite by a ratiometric fluorescence spectroscopy method with high selectivity and sensitivity. Specially, probe 1 exhibited a 100 nm red-shifted absorption spectrum along with the color changes from colorless to yellow, and 103 nm red-shifted emission spectra upon the addition of sulfite. Thus, 1 can serve as a "naked-eye" probe for sulfite. Further, the recognition mechanism of probe 1 for sulfite was confirmed using nuclear magnetic resonance and electrospray ionization mass spectrometry. Also, the preliminary practical application demonstrated that our proposed probe provided a promising method for the determination of sulfite. PMID:24813958

  3. Development of a novel nanoindentation technique by utilizing a dual-probe AFM system

    PubMed Central

    Sahin, Ferat; Yablon, Dalia

    2015-01-01

    Summary A novel instrumentation approach to nanoindentation is described that exhibits improved resolution and depth sensing. The approach is based on a multi-probe scanning probe microscopy (SPM) tool that utilizes tuning-fork based probes for both indentation and depth sensing. Unlike nanoindentation experiments performed with conventional AFM systems using beam-bounce technology, this technique incorporates a second probe system with an ultra-high resolution for depth sensing. The additional second probe measures only the vertical movement of the straight indenter attached to a tuning-fork probe with a high spring constant and it can also be used for AFM scanning to obtain an accurate profiling. Nanoindentation results are demonstrated on silicon, fused silica, and Corning Eagle Glass. The results show that this new approach is viable in terms of accurately characterizing mechanical properties of materials through nanoindentation with high accuracy, and it opens doors to many other exciting applications in the field of nanomechanical characterization. PMID:26665072

  4. Electron Tunneling, a Quantum Probe for the Quantum World of Nanotechnology

    ERIC Educational Resources Information Center

    Hipps, K. W.; Scudiero, L.

    2005-01-01

    A quantum-mechanical probe is essential to study the quantum world, which is provided by electron tunneling. A spectroscopic mapping to image the electron-transport pathways on a sub-molecular scale is used.

  5. Rubidium pump-probe spectroscopy: Comparison between ab initio theory and experiment

    SciTech Connect

    Himsworth, M.; Freegarde, T.

    2010-02-15

    We present a simple, analytic model for pump-probe spectroscopy in dilute atomic gases. Our model treats multilevel atoms, takes several broadening mechanisms into account and, with no free parameters, shows excellent agreement with experimentally observed spectra.

  6. Local collective motion analysis for multi-probe dynamic imaging and microrheology.

    PubMed

    Khan, Manas; Mason, Thomas G

    2016-08-01

    Dynamical artifacts, such as mechanical drift, advection, and hydrodynamic flow, can adversely affect multi-probe dynamic imaging and passive particle-tracking microrheology experiments. Alternatively, active driving by molecular motors can cause interesting non-Brownian motion of probes in local regions. Existing drift-correction techniques, which require large ensembles of probes or fast temporal sampling, are inadequate for handling complex spatio-temporal drifts and non-Brownian motion of localized domains containing relatively few probes. Here, we report an analytical method based on local collective motion (LCM) analysis of as few as two probes for detecting the presence of non-Brownian motion and for accurately eliminating it to reveal the underlying Brownian motion. By calculating an ensemble-average, time-dependent, LCM mean square displacement (MSD) of two or more localized probes and comparing this MSD to constituent single-probe MSDs, we can identify temporal regimes during which either thermal or athermal motion dominates. Single-probe motion, when referenced relative to the moving frame attached to the multi-probe LCM trajectory, provides a true Brownian MSD after scaling by an appropriate correction factor that depends on the number of probes used in LCM analysis. We show that LCM analysis can be used to correct many different dynamical artifacts, including spatially varying drifts, gradient flows, cell motion, time-dependent drift, and temporally varying oscillatory advection, thereby offering a significant improvement over existing approaches. PMID:27269299

  7. Local collective motion analysis for multi-probe dynamic imaging and microrheology

    NASA Astrophysics Data System (ADS)

    Khan, Manas; Mason, Thomas G.

    2016-08-01

    Dynamical artifacts, such as mechanical drift, advection, and hydrodynamic flow, can adversely affect multi-probe dynamic imaging and passive particle-tracking microrheology experiments. Alternatively, active driving by molecular motors can cause interesting non-Brownian motion of probes in local regions. Existing drift-correction techniques, which require large ensembles of probes or fast temporal sampling, are inadequate for handling complex spatio-temporal drifts and non-Brownian motion of localized domains containing relatively few probes. Here, we report an analytical method based on local collective motion (LCM) analysis of as few as two probes for detecting the presence of non-Brownian motion and for accurately eliminating it to reveal the underlying Brownian motion. By calculating an ensemble-average, time-dependent, LCM mean square displacement (MSD) of two or more localized probes and comparing this MSD to constituent single-probe MSDs, we can identify temporal regimes during which either thermal or athermal motion dominates. Single-probe motion, when referenced relative to the moving frame attached to the multi-probe LCM trajectory, provides a true Brownian MSD after scaling by an appropriate correction factor that depends on the number of probes used in LCM analysis. We show that LCM analysis can be used to correct many different dynamical artifacts, including spatially varying drifts, gradient flows, cell motion, time-dependent drift, and temporally varying oscillatory advection, thereby offering a significant improvement over existing approaches.

  8. Large-Scale Fabrication of Carbon Nanotube Probe Tips For Atomic Force Microscopy Critical Dimension Imaging Applications

    NASA Technical Reports Server (NTRS)

    Ye, Qi Laura; Cassell, Alan M.; Stevens, Ramsey M.; Meyyappan, Meyya; Li, Jun; Han, Jie; Liu, Hongbing; Chao, Gordon

    2004-01-01

    Carbon nanotube (CNT) probe tips for atomic force microscopy (AFM) offer several advantages over Si/Si3N4 probe tips, including improved resolution, shape, and mechanical properties. This viewgraph presentation discusses these advantages, and the drawbacks of existing methods for fabricating CNT probe tips for AFM. The presentation introduces a bottom up wafer scale fabrication method for CNT probe tips which integrates catalyst nanopatterning and nanomaterials synthesis with traditional silicon cantilever microfabrication technology. This method makes mass production of CNT AFM probe tips feasible, and can be applied to the fabrication of other nanodevices with CNT elements.

  9. Direct and quantitative broadband absorptance spectroscopy with multilayer cantilever probes

    SciTech Connect

    Hsu, Wei-Chun; Tong, Jonathan Kien-Kwok; Liao, Bolin; Chen, Gang

    2015-04-21

    A system for measuring the absorption spectrum of a sample is provided that includes a broadband light source that produces broadband light defined within a range of an absorptance spectrum. An interferometer modulates the intensity of the broadband light source for a range of modulation frequencies. A bi-layer cantilever probe arm is thermally connected to a sample arm having at most two layers of materials. The broadband light modulated by the interferometer is directed towards the sample and absorbed by the sample and converted into heat, which causes a temperature rise and bending of the bi-layer cantilever probe arm. A detector mechanism measures and records the deflection of the probe arm so as to obtain the absorptance spectrum of the sample.

  10. Chemical Fluorescent Probe for Detection of Aβ Oligomers.

    PubMed

    Teoh, Chai Lean; Su, Dongdong; Sahu, Srikanta; Yun, Seong-Wook; Drummond, Eleanor; Prelli, Frances; Lim, Sulgi; Cho, Sunhee; Ham, Sihyun; Wisniewski, Thomas; Chang, Young-Tae

    2015-10-28

    Aggregation of amyloid β-peptide (Aβ) is implicated in the pathology of Alzheimer's disease (AD), with the soluble, Aβ oligomeric species thought to be the critical pathological species. Identification and characterization of intermediate species formed during the aggregation process is crucial to the understanding of the mechanisms by which oligomeric species mediate neuronal toxicity and following disease progression. Probing these species proved to be extremely challenging, as evident by the lack of reliable sensors, due to their heterogeneous and transient nature. We describe here an oligomer-specific fluorescent chemical probe, BoDipy-Oligomer (BD-Oligo), developed through the use of the diversity-oriented fluorescent library approach (DOFLA) and high-content, imaging-based screening. This probe enables dynamic oligomer monitoring during fibrillogenesis in vitro and shows in vivo Aβ oligomers staining possibility in the AD mice model. PMID:26218347

  11. Lipid-Targeting Peptide Probes for Extracellular Vesicles.

    PubMed

    Flynn, Aaron D; Yin, Hang

    2016-11-01

    Extracellular vesicles released from cells are under intense investigation for their roles in cell-cell communication and cancer progression. However, individual vesicles have been difficult to probe as their small size renders them invisible by conventional light microscopy. However, as a consequence of their small size these vesicles possess highly curved lipid membranes that offer an unconventional target for curvature-sensing probes. In this article, we present a strategy for using peptide-based biosensors to detect highly curved membranes and the negatively charged membrane lipid phosphatidylserine, we delineate several assays used to validate curvature- and lipid-targeting mechanisms, and we explore potential applications in probing extracellular vesicles released from sources such as apoptotic cells, cancer cells, or activated platelets. J. Cell. Physiol. 231: 2327-2332, 2016. © 2016 Wiley Periodicals, Inc. PMID:26909741

  12. Probing Dark Energy models with neutrons

    NASA Astrophysics Data System (ADS)

    Pignol, Guillaume

    2015-07-01

    There is a deep connection between cosmology — the science of the infinitely large — and particle physics — the science of the infinitely small. This connection is particularly manifest in neutron particle physics. Basic properties of the neutron — its Electric Dipole Moment and its lifetime — are intertwined with baryogenesis and nucleosynthesis in the early Universe. I will cover this topic in the first part, that will also serve as an introduction (or rather a quick recap) of neutron physics and Big Bang cosmology. Then, the rest of the paper will be devoted to a new idea: using neutrons to probe models of Dark Energy. In the second part, I will present the chameleon theory: a light scalar field accounting for the late accelerated expansion of the Universe, which interacts with matter in such a way that it does not mediate a fifth force between macroscopic bodies. However, neutrons can alleviate the chameleon mechanism and reveal the presence of the scalar field with properly designed experiments. In the third part, I will describe a recent experiment performed with a neutron interferometer at the Institut Laue Langevin that sets already interesting constraints on the chameleon theory. Last, the chameleon field can be probed by measuring the quantum states of neutrons bouncing over a mirror. In the fourth part, I will present the status and prospects of the GRANIT experiment at the ILL.

  13. Invited Review Article: Pump-probe microscopy

    NASA Astrophysics Data System (ADS)

    Fischer, Martin C.; Wilson, Jesse W.; Robles, Francisco E.; Warren, Warren S.

    2016-03-01

    Multiphoton microscopy has rapidly gained popularity in biomedical imaging and materials science because of its ability to provide three-dimensional images at high spatial and temporal resolution even in optically scattering environments. Currently the majority of commercial and home-built devices are based on two-photon fluorescence and harmonic generation contrast. These two contrast mechanisms are relatively easy to measure but can access only a limited range of endogenous targets. Recent developments in fast laser pulse generation, pulse shaping, and detection technology have made accessible a wide range of optical contrasts that utilize multiple pulses of different colors. Molecular excitation with multiple pulses offers a large number of adjustable parameters. For example, in two-pulse pump-probe microscopy, one can vary the wavelength of each excitation pulse, the detection wavelength, the timing between the excitation pulses, and the detection gating window after excitation. Such a large parameter space can provide much greater molecular specificity than existing single-color techniques and allow for structural and functional imaging without the need for exogenous dyes and labels, which might interfere with the system under study. In this review, we provide a tutorial overview, covering principles of pump-probe microscopy and experimental setup, challenges associated with signal detection and data processing, and an overview of applications.

  14. Invited Review Article: Pump-probe microscopy.

    PubMed

    Fischer, Martin C; Wilson, Jesse W; Robles, Francisco E; Warren, Warren S

    2016-03-01

    Multiphoton microscopy has rapidly gained popularity in biomedical imaging and materials science because of its ability to provide three-dimensional images at high spatial and temporal resolution even in optically scattering environments. Currently the majority of commercial and home-built devices are based on two-photon fluorescence and harmonic generation contrast. These two contrast mechanisms are relatively easy to measure but can access only a limited range of endogenous targets. Recent developments in fast laser pulse generation, pulse shaping, and detection technology have made accessible a wide range of optical contrasts that utilize multiple pulses of different colors. Molecular excitation with multiple pulses offers a large number of adjustable parameters. For example, in two-pulse pump-probe microscopy, one can vary the wavelength of each excitation pulse, the detection wavelength, the timing between the excitation pulses, and the detection gating window after excitation. Such a large parameter space can provide much greater molecular specificity than existing single-color techniques and allow for structural and functional imaging without the need for exogenous dyes and labels, which might interfere with the system under study. In this review, we provide a tutorial overview, covering principles of pump-probe microscopy and experimental setup, challenges associated with signal detection and data processing, and an overview of applications. PMID:27036751

  15. A quirky probe of neutral naturalness

    NASA Astrophysics Data System (ADS)

    Chacko, Zackaria; Curtin, David; Verhaaren, Christopher B.

    2016-07-01

    We consider the signals arising from top partner pair production at the LHC as a probe of theories of neutral naturalness. We focus on scenarios in which top partners carry electroweak charges, such as folded supersymmetry or the quirky little Higgs. In this class of theories the top partners are pair produced as quirky bound states, since they are charged under a mirror color group whose lightest states are hidden glueballs. The quirks promptly de-excite and annihilate into glueballs, which decay back to Standard Model fermions via Higgs mixing. This can give rise to spectacular signatures at the LHC, such displaced decays, or high-multiplicity prompt production of many hard b ¯b or τ+τ- pairs. We show that signals arising from top partner pair production constitute the primary discovery channel for this class of theories in most regions of parameter space, and might provide the only experimental probe of scenarios with sub-cm glueball decay lengths. The measurement of top partner masses and couplings, which could be used to test the neutral naturalness mechanism directly, is also a tantalizing possibility.

  16. Dynamic light scattering homodyne probe

    NASA Technical Reports Server (NTRS)

    Meyer, William V. (Inventor); Cannell, David S. (Inventor); Smart, Anthony E. (Inventor)

    2002-01-01

    An optical probe for analyzing a sample illuminated by a laser includes an input optical fiber operably connectable to the laser where the input optical fiber has an entrance end and an exit end. The probe also includes a first beam splitter where the first beam splitter is adapted to transmit an alignment portion of a light beam from the input fiber exit end and to reflect a homodyning portion of the light beam from the input fiber. The probe also includes a lens between the input fiber exit end and the first beam splitter and a first and a second output optical fiber, each having an entrance end and an exit end, each exit end being operably connectable to respective optical detectors. The probe also includes a second beam splitter which is adapted to reflect at least a portion of the reflected homodyning portion into the output fiber entrance ends and to transmit light from the laser scattered by the sample into the entrance ends.

  17. Probing the atmosphere with infrasound

    NASA Technical Reports Server (NTRS)

    Posmentier, E. S.; Donn, W. L.

    1969-01-01

    Recent studies are reported which have contributed to the knowledge of atmospheric structure and have established the practicality of infrasonic techniques for probing the atmosphere to heights of 120 km or more. Observations of a few types of infrasound are reviewed, and the theories used to account for the infrasound propagation and the deduced atmospheric structures are discussed.

  18. A fluorescent probe for ecstasy.

    PubMed

    Masseroni, D; Biavardi, E; Genovese, D; Rampazzo, E; Prodi, L; Dalcanale, E

    2015-08-18

    A nanostructure formed by the insertion in silica nanoparticles of a pyrene-derivatized cavitand, which is able to specifically recognize ecstasy in water, is presented. The absence of effects from interferents and an efficient electron transfer process occurring after complexation of ecstasy, makes this system an efficient fluorescent probe for this popular drug. PMID:26166808

  19. Samara Probe For Remote Imaging

    NASA Technical Reports Server (NTRS)

    Burke, James D.

    1989-01-01

    Imaging probe descends through atmosphere of planet, obtaining images of ground surface as it travels. Released from aircraft over Earth or from spacecraft over another planet. Body and single wing shaped like samara - winged seed like those of maple trees. Rotates as descends, providing panoramic view of terrain below. Radio image obtained by video camera to aircraft or spacecraft overhead.

  20. SUB-SLAB PROBE INSTALLATION

    EPA Science Inventory

    Sub-slab sampling has become an integral part of vapor intrusion investigations. It is now recommended in guidance documents developed by EPA and most states. A method for sub-slab probe installation was devised in 2002, presented at conferences through 2005, and finally docume...

  1. Wind measurements by electromagnetic probes

    NASA Technical Reports Server (NTRS)

    Susko, Michael

    1988-01-01

    The emerging technology of electromagnetic probing of the atmosphere to measure winds used in a space vehicle ascent winds load calculations is presented. The frequency range, altitude, and resolution for the following probes are presented: lidars, microwave radars, and clear-air Doppler radars (popularly known as wind profilers). The electromagnetic probing of the atmosphere by clear-air radars and lasers is the new technology to supplement balloon-borne wind sensors used to determine ascent wind loads of space vehicles. The electromagnetic probes measure the wind velocity using the Doppler effect. This is the radar technology used in MSFC's Radar Wind Profiler, and is similar to the technology used in conventional Doppler systems except that the frequency is generally lower, antenna is bigger, and dwell time much longer. Designed for unattended and automated instrumentation in providing measurements of the wind in the troposphere, the profiler employs Doppler radar technology and is currently being put in operation at NASA Kennedy Space Center, Florida.

  2. Health. CEM Probe, January 1977.

    ERIC Educational Resources Information Center

    Billington, Roy

    The importance of health and its relationship to personal and community life are explored in this issue of PROBE. Designed to acquaint British secondary school youth with topical problems, the series contains discussion and case studies of national and world issues, followed by questions for student discussion and research. Nine chapters comprise…

  3. NASA Smart Surgical Probe Project

    NASA Technical Reports Server (NTRS)

    Mah, Robert W.; Andrews, Russell J.; Jeffrey, Stefanie S.; Guerrero, Michael; Papasin, Richard; Koga, Dennis (Technical Monitor)

    2002-01-01

    Information Technologies being developed by NASA to assist astronaut-physician in responding to medical emergencies during long space flights are being employed for the improvement of women's health in the form of "smart surgical probe". This technology, initially developed for neurosurgery applications, not only has enormous potential for the diagnosis and treatment of breast cancer, but broad applicability to a wide range of medical challenges. For the breast cancer application, the smart surgical probe is being designed to "see" a suspicious lump, determine by its features if it is cancerous, and ultimately predict how the disease may progress. A revolutionary early breast cancer detection tool based on this technology has been developed by a commercial company and is being tested in human clinical trials at the University of California at Davis, School of Medicine. The smart surgical probe technology makes use of adaptive intelligent software (hybrid neural networks/fuzzy logic algorithms) with the most advanced physiologic sensors to provide real-time in vivo tissue characterization for the detection, diagnosis and treatment of tumors, including determination of tumor microenvironment and evaluation of tumor margins. The software solutions and tools from these medical applications will lead to the development of better real-time minimally-invasive smart surgical probes for emergency medical care and treatment of astronauts on long space flights.

  4. CNP. Cervical Neoplasia Probe Control

    SciTech Connect

    Vargo, T.

    1995-05-17

    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)

  5. OCR Pace on Probes Quickens

    ERIC Educational Resources Information Center

    Maxwell, Lesli A.

    2011-01-01

    In the 21 months since U.S. Secretary of Education Arne Duncan stood on an iconic bridge in Selma, Alabama, and pledged to aggressively combat discrimination in the nation's schools, federal education officials have launched dozens of new probes in school districts and states that reach into civil rights issues that previously received little, if…

  6. Possible concepts for an in situ Saturn probe mission

    NASA Astrophysics Data System (ADS)

    Coustenis, Athena; Lebreton, Jean-Pierre; Mousis, Olivier; Atkinson, David H.; Lunine, Jonathan I.; Reh, Kim R.; Fletcher, Leigh N.; Simon-Miller, Amy A.; Atreya, Sushil; Brinckerhoff, William B.; Cavalie, Thibault; Colaprete, Anthony; Gautier, Daniel; Guillot, Tristan; Mahaffy, Paul R.; Marty, Bernard; Morse, Andy; Sims, Jon; Spilker, Tom; Spilker, Linda

    2014-05-01

    In situ exploration of Saturn's atmosphere would bring insights in two broad themes: the formation history of our solar system and the processes at play in planetary atmospheres. The science case for in situ measurements at Saturn are developed in [1] and two companion abstracts (see Mousis et al., and Atkinson et al.). They are summarized here. Measurements of Saturn's bulk chemical and isotopic composition would place important constraints on the volatile reservoirs in the protosolar nebula and hence on the formation mechanisms. An in situ probe, penetrating from the upper atmosphere (μbar level) into the convective weather layer to a minimum depth of 10 bar, would also contribute to our knowledge of Saturn's atmospheric structure, dynamics, composition, chemistry and cloud-forming processes. Different mission architectures are envisaged, all based on an entry probe that would descend through Saturn's stratosphere and troposphere under parachute down to a minimum of 10 bars [1]. Future studies will focus on the trade-offs between science return and the added design complexity of a probe that could operate at pressures larger than 10 bars. Accelerometry measurements may also be performed during the entry phase in the higher part of the stratosphere prior to starting measurements under parachute. A carrier system would be required to deliver the probe along its interplanetary trajectory to the desired atmospheric entry point at Saturn. The entry site would be carefully selected. Three possible mission configurations are currently under study (with different risk/cost trades): • Configuration 1: Probe + Carrier. After probe delivery, the carrier would follow its path and be destroyed during atmospheric entry, but could perform pre-entry science. The carrier would not be used as a radio relay, but the probe would transmit its data to the ground system via a direct-to-Earth (DTE) RF link; • Configuration 2: Probe + Carrier/Relay. The probe would detach from the

  7. ANTS-anchored Zn-Al-CO3-LDH particles as fluorescent probe for sensing of folic acid

    NASA Astrophysics Data System (ADS)

    Liu, Pengfei; Liu, Dan; Liu, Yanhuan; Li, Lei

    2016-09-01

    A novel fluorescent nanosensor for detecting folic acid (FA) in aqueous media has been developed based on 8-aminonaphthalene-1,3,6-trisulfonate (ANTS) anchored to the surface of Zn-Al-CO3-layered double hydroxides (LDH) particles. The nanosensor showed high fluorescence intensity and good photostability due to a strong coordination interaction between surface Zn2+ ions of Zn-Al-CO3-LDH and N atoms of ANTS, which were verified by result of X-ray photoelectron spectroscopy (XPS). ANTS-anchored on the surface of Zn-Al-CO3-LDH restricted the intra-molecular rotation leading to ANTS-anchored J-type aggregation emission enhancement. ANTS-anchored Zn-Al-CO3-LDH particles exhibited highly sensitive and selective response to FA over other common metal ions and saccharides present in biological fluids. The proposed mechanism was that oxygen atoms of -SO3 groups in ANTS-anchored on the surface of Zn-Al-CO3-LDH were easily collided by FA molecules to form potential hydrogen bonds between ANTS-anchored and FA molecules, which could effectively quench the ANTS-anchored fluorescence. Under the simulated physiological conditions (pH of 7.4), the fluorescence quenching was fitted to Stern-Volmer equation with a linear response in the concentration range of 1 μM to 200 μM with a limit of detection of 0.1 μM. The results indicate that ANTS-anchored Zn-Al-CO3-LDH particles can afford a very sensitive system for the sensing FA in aqueous solution.

  8. Nucleic acid probes in diagnostic medicine

    NASA Technical Reports Server (NTRS)

    Oberry, Phillip A.

    1991-01-01

    The need for improved diagnostic procedures is outlined and variations in probe technology are briefly reviewed. A discussion of the application of probe technology to the diagnosis of disease in animals and humans is presented. A comparison of probe versus nonprobe diagnostics and isotopic versus nonisotopic probes is made and the current state of sequence amplification is described. The current market status of nucleic acid probes is reviewed with respect to their diagnostic application in human and veterinary medicine. Representative product examples are described and information on probes being developed that offer promise as future products is discussed.

  9. High pressure optical combustion probe

    SciTech Connect

    Woodruff, S.D.; Richards, G.A.

    1995-06-01

    The Department of Energy`s Morgantown Energy Technology Center has developed a combustion probe for monitoring flame presence and heat release. The technology involved is a compact optical detector of the OH radical`s UV fluorescence. The OH Monitor/Probe is designed to determine the flame presence and provide a qualitative signal proportional to the flame intensity. The probe can be adjusted to monitor a specific volume in the combustion zone to track spatial fluctuations in the flame. The probe is capable of nanosecond time response and is usually slowed electronically to fit the flame characteristics. The probe is a sapphire rod in a stainless steel tube which may be inserted into the combustion chamber and pointed at the flame zone. The end of the sapphire rod is retracted into the SS tube to define a narrow optical collection cone. The collection cone may be adjusted to fit the experiment. The fluorescence signal is collected by the sapphire rod and transmitted through a UV transmitting, fused silica, fiber optic to the detector assembly. The detector is a side window photomultiplier (PMT) with a 310 run line filter. A Hamamatsu photomultiplier base combined with a integral high voltage power supply permits this to be a low voltage device. Electronic connections include: a power lead from a modular DC power supply for 15 VDC; a control lead for 0-1 volts to control the high voltage level (and therefore gain); and a lead out for the actual signal. All low voltage connections make this a safe and easy to use device while still delivering the sensitivity required.

  10. An evaluation of cleaning methods for micro-CMM probes

    NASA Astrophysics Data System (ADS)

    Kinnell, P. K.; Habeb, R. R.

    2013-08-01

    To support the manufacture of complex products made of multiple micro-parts, a traceable and accurate 3D-measurement system with sub-micron accuracy is required. This paper investigates the use of a micro electro mechanical system (MEMS) tactile-micro-probe for 3D-coordinate metrology on the micro-scale. It will show that probe-tip contamination may be a significant source of error for such tactile-probing systems. Even in a clean-room environment, there are many types of contaminants that may affect dimensional measurement accuracy. These mainly come from repeated contact between probe tip and artefact material. To address this issue a number of cleaning methods were utilized to remove contaminants from the MEMS tactile-micro-probe sensor. Scanning electron microscopy was used to assess the efficacy of each cleaning method. Initial findings on different cleaning methods including ultrasonic, plasma, micro-beam melting, electron beam melting and cryogenic cleaning have shown that the latter is a feasible process.

  11. Impact of probe compound in MRP2 vesicular transport assays.

    PubMed

    Kidron, Heidi; Wissel, Gloria; Manevski, Nenad; Häkli, Marika; Ketola, Raimo A; Finel, Moshe; Yliperttula, Marjo; Xhaard, Henri; Urtti, Arto

    2012-05-12

    MRP2 is an efflux transporter that is expressed mainly in the canalicular membrane of hepatocytes, where it expels polar and ionic compounds into the bile. MRP2 is also present in the apical membrane of enterocytes and epithelial cells of proximal tubules of the kidney. Inhibition of MRP2 transport can lead to the accumulation of metabolites and other MRP2 substrates up to toxic levels in these cells. The transport properties of MRP2 are frequently studied with the vesicular transport assay. The assay identifies compounds that interact with MRP2 by measuring the effect of a compound on the transport of a radioactively labeled or fluorescent probe. We have compared the effect of eight selected test compounds (quercetin, disopyramide, paracetamol, indomethacin, diclofenac, estrone-3-sulfate, budesonide, and thioridazine) on the MRP2-mediated transport of three commonly used probes: 5(6)-carboxy-2,7-dichlorofluorescein, leukotriene C4 and estradiol-17-β-d-glucuronide (E217βG). Five of the test compounds had different probe-dependent effects on the MRP2-mediated transport, suggesting differences in the transport mechanism of the probes. Our results underline the complexity of substrate recognition by these efflux transporters and the difficulties in directly comparing results obtained with different assays, especially when different probes are used. PMID:22406294

  12. Ultrahigh currents in dielectric-coated carbon nanotube probes.

    PubMed

    Lisunova, Yuliya; Levkivskyi, Ivan; Paruch, Patrycja

    2013-09-11

    Carbon nanotubes used as conductive atomic force microscopy probes are expected to withstand extremely high currents. However, in existing prototypes, significant self-heating results in rapid degradation of the nanotube probe. Here, we investigate an alternative probe design, fabricated by dielectric encapsulation of multiwalled carbon nanotubes, which can support unexpectedly high currents with extreme stability. We show that the dielectric coating acts as a reservoir for Joule heat removal, and as a chemical barrier against thermal oxidation, greatly enhancing transport properties. In contact with Au surfaces, these probes can carry currents of 0.12 mA at a power of 1.5 mW and show no measurable change in resistance at current densities of 10(12) A/m(2) over a time scale of 10(3) s. Our observations are in good agreement with theoretical modeling and exact numerical calculations, demonstrating that the enhanced transport characteristics of such probes are governed by their more effective heat removal mechanisms. PMID:23978224

  13. Probing Kibble-Zurek Mechanism in Quenched Elongated Bose Gases

    NASA Astrophysics Data System (ADS)

    Liu, I.-Kang; Gou, Shih-Chuan; Lamporesi, Giacomo; Donadello, Simone; Dalfovo, Franco; Ferrari, Gabriele; Proukakis, Nikolaos

    2016-05-01

    We report our numerical findings on the statistics and dynamics of spontaneous formation of defects during a gradual quench of an initially thermal atomic gas to below the critical temperature. Our study focuses on the Trento experiments, which showed the appearance of a few long-lived solitonic vortices, as measured sometime after the system crossed the transition temperature. Our simulations access both the initial quench-driven turbulent regime where a large number of randomly-distributed defects emerge during the condensation, and the subsequent relaxation of such defects towards a few long-lived solitonic vortices, similar to those observed experimentally. We analyze our findings in the context of the Kibble-Zurek scaling law, highlighting various subtle issues associated with this dynamical process, and characterize the transition through the critical region, by studying the corresponding first-order spatial correlation functions. Our simulations are based on the 3D stochastic projected Gross-Pitaevskii equation subjected to a linear temperature and chemical potential quench. Funding: MOST Taiwan, EPSRC, Provinza Autonoma di Trento.

  14. Probing the mechanisms underlying human diseases in making ribosomes.

    PubMed

    Farley, Katherine I; Baserga, Susan J

    2016-08-15

    Ribosomes are essential, highly complex machines responsible for protein synthesis in all growing cells. Because of their importance, the process of building these machines is intricately regulated. Although the proteins involved in regulating ribosome biogenesis are just beginning to be understood, especially in human cells, the consequences for dysregulating this process have been even less studied. Such interruptions in ribosome synthesis result in a collection of human disorders known as ribosomopathies. Ribosomopathies, which occur due to mutations in proteins involved in the global process of ribosome biogenesis, result in tissue-specific defects. The questions posed by this dichotomy and the steps taken to address these questions are therefore the focus of this review: How can tissue-specific disorders result from alterations in global processes? Could ribosome specialization account for this difference? PMID:27528749

  15. Single Molecule Mechanical Probing of the SNARE Protein Interactions

    PubMed Central

    Liu, W.; Montana, Vedrana; Bai, Jihong; Chapman, Edwin R.; Mohideen, U.; Parpura, Vladimir

    2006-01-01

    Exocytotic release of neurotransmitters is mediated by the ternary soluble N-ethyl maleimide-sensitive fusion protein attachment protein receptors (SNAREs) complex, comprised of syntaxin (Sx), synaptosome-associated protein of 25 kDa (SNAP25), and synaptobrevin 2 (Sb2). Since exocytosis involves the nonequilibrium process of association and dissociation of bonds between molecules of the SNARE complex, dynamic measurements at the single molecule level are necessary for a detailed understanding of these interactions. To address this issue, we used the atomic force microscope in force spectroscopy mode to show from single molecule investigations of the SNARE complex, that Sx1A and Sb2 are zippered throughout their entire SNARE domains without the involvement of SNAP25. When SNAP25B is present in the complex, it creates a local interaction at the 0 (ionic) layer by cuffing Sx1A and Sb2. Force loading rate studies indicate that the ternary complex interaction is more stable than the Sx1A-Sb2 interaction. PMID:16648158

  16. Probing the mechanism of material specific peptides for optical biosensors

    NASA Astrophysics Data System (ADS)

    Ramakrishnan, Sathish K.; Estephan, Elias; Martin, Marta; Cloitre, Thierry; Gergely, Csilla

    2013-05-01

    The possibility to engineer bio-nanomaterials with programmed synthesis and controlled immobilization of biomolecules through biomimetic molecular evolution approach has been demonstrated. Material specific peptides with exquisite molecular recognition function were used as a linker for the attachment of biomolecules. Exploring the origin of peptide material specificity not only opens up rational design approach with precise control over biomimetic bio-sensor design, but more importantly provides a new route of functionalizing for various material surfaces with enhanced sensitivity over classical grafting chemistry. To study the fine prints of experimentally obtained peptides, theoretical understanding of surface interactions may serve as important clues for further refinement. By taking advantage of classical molecular dynamics (MD) simulations and density functional theory (DFT), we investigated the origin of this smart recognition function through the strength of interaction of experimentally selected 12mer peptides revealing high binding affinity towards n+-Si(100). Here, we attempt for the very first time to model the interaction of the peptides (in buffer solution) with semiconductors and we calculate their binding energies at the atomic level, enabling thereby linking direct evidence to our experimental evidence. Several peptide conformations have been taken into account simultaneously upon the surface. Our studies demonstrate that the peptides possess certain recognition function and their high interaction energy with the surface makes them unique among the populations. Our work is a step towards the understanding of the interactions between peptides and semiconductor surfaces that is a highly relevant challenge in the development of novel devices with a high degree of biocompatibility as well.

  17. Coulomb chronometry to probe the decay mechanism of hot nuclei

    NASA Astrophysics Data System (ADS)

    Gruyer, D.; Frankland, J. D.; Bonnet, E.; Chbihi, A.; Ademard, G.; Boisjoli, M.; Borderie, B.; Bougault, R.; Galichet, E.; Gauthier, J.; Guinet, D.; Lautesse, P.; Le Neindre, N.; Legouée, E.; Lombardo, I.; Lopez, O.; Manduci, L.; Marini, P.; Mazurek, K.; Nadtochy, P. N.; Pârlog, M.; Rivet, M. F.; Roy, R.; Rosato, E.; Spadaccini, G.; Verde, G.; Vient, E.; Vigilante, M.; Wieleczko, J. P.; Indra Collaboration

    2015-12-01

    In 129Xe+natSn central collisions from 8 to 25 MeV/nucleon, the three-fragment exit channel occurs with a significant cross section. We show that these fragments arise from two successive binary splittings of a heavy composite system. The sequence of fragment production is determined. Strong Coulomb proximity effects are observed in the three-fragment final state. A comparison with Coulomb trajectory calculations shows that the time scale between the consecutive breakups decreases with increasing bombarding energy, becoming quasisimultaneous above excitation energy E*=4.0 ±0.5 MeV /nucleon . This transition from sequential to simultaneous breakup was interpreted as the signature of the onset of multifragmentation for the three-fragment exit channel in this system.

  18. Radiation Belt Storm Probe (RBSP) Mission

    NASA Technical Reports Server (NTRS)

    Sibeck, D. G.; Fox, N.; Grebowsky, J. M.; Mauk, B. H.

    2009-01-01

    Scheduled to launch in May 2012, NASA's dual spacecraft Living With a Star Radiation Belt Storm Probe mission carries the field and particle instrumentation needed to determine the processes that produce enhancements in radiation belt ion and electron fluxes, the dominant mechanisms that cause the loss of relativistic electrons, and the manner by which the ring current and other geomagnetic phenomena affect radiation belt behavior. The two spacecraft will operate in low-inclination elliptical lapping orbits around the Earth, within and immediately exterior to the Van Allen radiation belts. During course of their two year primary mission, they will cover the full range of local times, measuring both AC and DC electric and magnetic fields to 10kHz, as well as ions from 50 eV to 1 GeV and electrons with energies ranging from 50 eV to 10 MeV.

  19. Synergy Between Entry Probes and Orbiters

    NASA Technical Reports Server (NTRS)

    Young, Richard E.

    2005-01-01

    We identify two catagories of probe-orbiter interactions which benefit the science return from a particular mission. The first category is termed "Mission Design Aspects". This category is meant to describe those aspects of the mission design involving the orbiter that affect the science return from the probe(s). The second category of probe-orbiter interaction is termed "Orbiter-Probe Science Interactions", and is meant to include interactions between oribter and probe(s) that directly involve science measurements made from each platform. Two mission related aspects of probe-orbiter interactions are delivery of a probe(s) to the entry site(s) by an orbiter, and communication between each probe and the orbiter. We consider four general probe-orbiter science interactions that greatly enhance, or in certain cases are essential for, the mission science return. The four topics are, global context of the probe entry site(s), ground truth for remote sensing observations of an orbiter, atmospheric composition measurements, and wind measurements.

  20. The reference-probe model in avian magnetoreception

    NASA Astrophysics Data System (ADS)

    Procopio, Maria; Ritz, Thorsten

    2015-03-01

    The sensory mechanism that allows magneto-sensitive organisms to detect the direction of the geomagnetic field for navigation purposes is still largely unclear. One of the two leading hypothesis stipulates that photoindused radical-pair reactions in photoreceptor proteins act as the primary magnetic sensor in migratory birds. In recent years the radical-pair mechanism has been receiving considerable support, qualifying the avian compass for a place in the emerging field of quantum biology. Investigations on such a spin-based sensor have focussed on uncovering the design features for bioinspired technology. The reference-probe model has been suggested as an optimal radical-pair design. Radical-pairs with probe character have been shown to achieve not only optimal but also robust directional sensitivity to weak magnetic fields. However, the relevance of the reference character has not been studied yet. Here we introduce a method to investigate the contribution of the reference character to optimality and robustness. By analytical and computational studies, we find that the probe character is crucial for optimality, while the reference character captures robust features. Our results suggest the reference-probe model to contain both optimal and robust design features.

  1. Multifunctional hydrogel nano-probes for atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Lee, Jae Seol; Song, Jungki; Kim, Seong Oh; Kim, Seokbeom; Lee, Wooju; Jackman, Joshua A.; Kim, Dongchoul; Cho, Nam-Joon; Lee, Jungchul

    2016-05-01

    Since the invention of the atomic force microscope (AFM) three decades ago, there have been numerous advances in its measurement capabilities. Curiously, throughout these developments, the fundamental nature of the force-sensing probe--the key actuating element--has remained largely unchanged. It is produced by long-established microfabrication etching strategies and typically composed of silicon-based materials. Here, we report a new class of photopolymerizable hydrogel nano-probes that are produced by bottom-up fabrication with compressible replica moulding. The hydrogel probes demonstrate excellent capabilities for AFM imaging and force measurement applications while enabling programmable, multifunctional capabilities based on compositionally adjustable mechanical properties and facile encapsulation of various nanomaterials. Taken together, the simple, fast and affordable manufacturing route and multifunctional capabilities of hydrogel AFM nano-probes highlight the potential of soft matter mechanical transducers in nanotechnology applications. The fabrication scheme can also be readily utilized to prepare hydrogel cantilevers, including in parallel arrays, for nanomechanical sensor devices.

  2. Multifunctional hydrogel nano-probes for atomic force microscopy.

    PubMed

    Lee, Jae Seol; Song, Jungki; Kim, Seong Oh; Kim, Seokbeom; Lee, Wooju; Jackman, Joshua A; Kim, Dongchoul; Cho, Nam-Joon; Lee, Jungchul

    2016-01-01

    Since the invention of the atomic force microscope (AFM) three decades ago, there have been numerous advances in its measurement capabilities. Curiously, throughout these developments, the fundamental nature of the force-sensing probe-the key actuating element-has remained largely unchanged. It is produced by long-established microfabrication etching strategies and typically composed of silicon-based materials. Here, we report a new class of photopolymerizable hydrogel nano-probes that are produced by bottom-up fabrication with compressible replica moulding. The hydrogel probes demonstrate excellent capabilities for AFM imaging and force measurement applications while enabling programmable, multifunctional capabilities based on compositionally adjustable mechanical properties and facile encapsulation of various nanomaterials. Taken together, the simple, fast and affordable manufacturing route and multifunctional capabilities of hydrogel AFM nano-probes highlight the potential of soft matter mechanical transducers in nanotechnology applications. The fabrication scheme can also be readily utilized to prepare hydrogel cantilevers, including in parallel arrays, for nanomechanical sensor devices. PMID:27199165

  3. Neptune Polar Orbiter with Probes

    NASA Technical Reports Server (NTRS)

    Bienstock, Bernard; Atkinson, David; Baines, Kevin; Mahaffy, Paul; Steffes, Paul; Atreya, Sushil; Stern, Alan; Wright, Michael; Willenberg, Harvey; Smith, David; Frampton, Robert; Sichi, Steve; Peltz, Leora; Masciarelli, James; VanCleve, Jeffey

    2005-01-01

    The giant planets of the outer solar system divide into two distinct classes: the gas giants Jupiter and Saturn, which consist mainly of hydrogen and helium; and the ice giants Uranus and Neptune, which are believed to contain significant amounts of the heavier elements oxygen, nitrogen, and carbon and sulfur. Detailed comparisons of the internal structures and compositions of the gas giants with those of the ice giants will yield valuable insights into the processes that formed the solar system and, perhaps, other planetary systems. By 2012, Galileo, Cassini and possibly a Jupiter Orbiter mission with microwave radiometers, Juno, in the New Frontiers program, will have yielded significant information on the chemical and physical properties of Jupiter and Saturn. A Neptune Orbiter with Probes (NOP) mission would deliver the corresponding key data for an ice giant planet. Such a mission would ideally study the deep Neptune atmosphere to pressures approaching and possibly exceeding 1000 bars, as well as the rings, Triton, Nereid, and Neptune s other icy satellites. A potential source of power would be nuclear electric propulsion (NEP). Such an ambitious mission requires that a number of technical issues be investigated, however, including: (1) atmospheric entry probe thermal protection system (TPS) design, (2) probe structural design including seals, windows, penetrations and pressure vessel, (3) digital, RF subsystem, and overall communication link design for long term operation in the very extreme environment of Neptune's deep atmosphere, (4) trajectory design allowing probe release on a trajectory to impact Neptune while allowing the spacecraft to achieve a polar orbit of Neptune, (5) and finally the suite of science instruments enabled by the probe technology to explore the depths of the Neptune atmosphere. Another driving factor in the design of the Orbiter and Probes is the necessity to maintain a fully operational flight system during the lengthy transit time

  4. Further capacitive imaging experiments using modified probes

    NASA Astrophysics Data System (ADS)

    Yin, Xiaokang; Li, Zhen; Yan, An; Li, Wei; Chen, Guoming; Hutchins, David A.

    2016-02-01

    In recent years, capacitive imaging (CI) is growing in popularity within the NDE communities, as it has the potential to test materials and structures for defects that are not easily tested by other techniques. In previous work, The CI technique has been successfully used on a various types of materials, including concrete, glass/carbon fibre composite, steel, etc. In such CI experiments, the probes are normally with symmetric or concentric electrodes etched onto PCBs. In addition to these conventional coplanar PCB probes, modified geometries can be made and they can lead to different applications. A brief overview of these modified probes, including high resolution surface imaging probe, combined CI/eddy current probe, and CI probe using an oscilloscope probe as the sensing electrode, is presented in this work. The potential applications brought by these probes are also discussed.

  5. Cantilevered probe detector with piezoelectric element

    SciTech Connect

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

    2014-04-29

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

  6. Developing MR probes for molecular imaging.

    PubMed

    McMahon, Michael T; Chan, Kannie W Y

    2014-01-01

    Molecular imaging plays an important role in the era of personalized medicine, especially with recent advances in magnetic resonance (MR) probes. While the first generation of these probes focused on maximizing contrast enhancement, a second generation of probes has been developed to improve the accumulation within specific tissues or pathologies, and the newest generation of agents is also designed to report on changes in physiological status and has been termed "smart" agents. This represents a paradigm switch from the previously commercialized gadolinium and iron oxide probes to probes with new capabilities, and leads to new challenges as scanner hardware needs to be adapted for detecting these probes. In this chapter, we highlight the unique features for all five different categories of MR probes, including the emerging chemical exchange saturation transfer, (19)F, and hyperpolarized probes, and describe the key physical properties and features motivating their design. As part of this comparison, the strengths and weaknesses of each category are discussed. PMID:25287693

  7. Cantilevered probe detector with piezoelectric element

    DOEpatents

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

    2013-04-30

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

  8. Cantilevered probe detector with piezoelectric element

    DOEpatents

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

    2012-07-10

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

  9. Cantilevered probe detector with piezoelectric element

    DOEpatents

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

    2010-04-06

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

  10. Design Strategies for Bioorthogonal Smart Probes

    PubMed Central

    Shieh, Peyton; Bertozzi, Carolyn R.

    2014-01-01

    Bioorthogonal chemistry has enabled the selective labeling and detection of biomolecules in living systems. Bioorthogonal smart probes, which become fluorescent or deliver imaging or therapeutic agents upon reaction, allow for the visualization of biomolecules or targeted delivery even in the presence of excess unreacted probe. This review discusses the strategies used in the development of bioorthogonal smart probes and highlights the potential of these probes to further our understanding of biology. PMID:25315039

  11. Local Optical Probe of Motion and Stress in a NEMS

    NASA Astrophysics Data System (ADS)

    Reserbat-Plantey, Antoine; Marty, Laëtitia; Arcizet, Olivier; Bendiab, Nedjma; Bouchiat, Vincent

    2012-02-01

    Nanoelectromechanical systems (NEMSs) are emerging nanoscale elements at the crossroads between mechanics, optics and electronics, with significant potential for actuation and sensing applications. The reduction of dimensions compared to their micronic counterparts brings new effects including sensitivity to very low mass, resonant frequencies in the radiofrequency range, mechanical non-linearities and observation of quantum mechanical effects. An important issue of NEMS is the understanding of fundamental physical properties conditioning dissipation mechanisms, known to limit mechanical quality factors and to induce aging due to material degradation. There is a need for detection methods tailored for these systems which allow probing motion and stress at the nanometer scale. Here, we show a non-invasive local optical probe for the quantitative measurement of motion and stress within a multilayer graphene NEMS provided by a combination of Fizeau interferences, Raman spectroscopy and electrostatically actuated mirror. Interferometry provides a calibrated measurement of the motion, resulting from an actuation ranging from a quasi-static load up to the mechanical resonance while Raman spectroscopy allows a purely spectral detection of mechanical resonance at the nanoscale. Such spectroscopic detection reveals the coupling between a strained nano-resonator and the energy of an inelastically scattered photon, and thus offers a new approach for optomechanics.

  12. Fabrication of molecular tension probes.

    PubMed

    Kim, Sung Bae; Fujii, Rika

    2016-01-01

    A unique bioluminescent imaging probe is introduced for illuminating molecular tension appended by protein-protein interactions (PPIs) of interest. A full-length luciferase is sandwiched between two proteins of interest via minimal flexible linkers. The ligand-activated PPIs append intramolecular tension to the sandwiched luciferase, boosting or dropping the enzymatic activity in a quantitative manner. This method guides construction of a new lineage of bioassays for determining molecular tension appended by ligand-activated PPIs. The summary of the method is: •Molecular tension appended by protein-protein interactions (PPI) is visualized with a luciferase.•Estrogen activities are quantitatively illuminated with the molecular tension probes.•Full-length Renilla luciferase enhances the optical intensities after bending by PPI. PMID:27222821

  13. Underwater probing with laser radar

    NASA Technical Reports Server (NTRS)

    Carswell, A. I.; Sizgoric, S.

    1975-01-01

    Recent advances in laser and electro optics technology have greatly enhanced the feasibility of active optical probing techniques aimed at the remote sensing of water parameters. This paper describes a LIDAR (laser radar) that has been designed and constructed for underwater probing. The influence of the optical properties of water on the general design parameters of a LIDAR system is considered. Discussion of the specific details in the choice of the constructed LIDAR is given. This system utilizes a cavity dumped argon ion laser transmitter capable of 50 watt peak powers, 10 nanosecond pulses and megahertz pulse repetition rates at 10 different wavelengths in the blue green region of the spectrum. The performance of the system, in proving various types of water, is demonstrated by summarizing the results of initial laboratory and field experiments.

  14. Fabrication of molecular tension probes

    PubMed Central

    Kim, Sung Bae; Fujii, Rika

    2016-01-01

    A unique bioluminescent imaging probe is introduced for illuminating molecular tension appended by protein–protein interactions (PPIs) of interest. A full-length luciferase is sandwiched between two proteins of interest via minimal flexible linkers. The ligand-activated PPIs append intramolecular tension to the sandwiched luciferase, boosting or dropping the enzymatic activity in a quantitative manner. This method guides construction of a new lineage of bioassays for determining molecular tension appended by ligand-activated PPIs. The summary of the method is: • Molecular tension appended by protein–protein interactions (PPI) is visualized with a luciferase. • Estrogen activities are quantitatively illuminated with the molecular tension probes. • Full-length Renilla luciferase enhances the optical intensities after bending by PPI. PMID:27222821

  15. Improved double planar probe data analysis technique

    SciTech Connect

    Ghim, Young-chul; Hershkowitz, Noah

    2009-03-15

    Plasma electron number density and ion number density in a dc multidipole weakly collisional Ar plasma are measured with a single planar Langmuir probe and a double planar probe, respectively. A factor of two discrepancy between the two density measurements is resolved by applying Sheridan's empirical formula [T. E. Sheridan, Phys. Plasmas 7, 3084 (2000)] for sheath expansion to the double probe data.

  16. PROBE: Empowering the Individual (A Case Study).

    ERIC Educational Resources Information Center

    Towns, Kathryn; And Others

    The Potential Reentry Opportunities in Business and Education (PROBE) counseling and referral system is intended to help single parents and displaced homemakers gain greater control over their own lives, careers, and futures. PROBE began in 1975 as a campus-based program at Pennsylvania State University and became community based in 1977. PROBE,…

  17. Outer planet probe missions, designs and science

    NASA Technical Reports Server (NTRS)

    Colin, L.

    1978-01-01

    The similarities and differences of atmosphere entry probe mission designs and sciences appropriate to certain solar system objects, are reviewed. Candidate payloads for Saturn and Titan probes are suggested. Significant supporting research and technology efforts are required to develop mission-peculiar technology for probe exploration of the Saturnian system.

  18. Probe Follower for Moving Blood Vessels

    NASA Technical Reports Server (NTRS)

    Frazer, R. E.; Andrews, T. W.

    1985-01-01

    Probes track vessel expansion and contraction with minimal perturbation. Nozzle back-pressure changes at cuff on blood vessel basis for monitoring position of probe in blood vessel. Fluidic amplifiers use signals to control three-axis servo that centers measuring probe between sensing-nozzle pairs at cuff.

  19. Fiber-Optic Probe For Laser Velocimetry

    NASA Technical Reports Server (NTRS)

    Lynch, Dana H.; Mcalister, Kenneth W.; Gunter, William D., Jr.

    1992-01-01

    Size and weight of optics reduced considerably. Proposed fiber-optic probe in laser velocimeter smaller (and, therefore, lighter in weight and more maneuverable) than previous probe. Proposed configuration is product of calculations and experiments showing virtual waists serve same purpose. Laser-velocimeter lens brought close to transfer lenses to focus on virtual waists, thereby shortening probe head considerably.

  20. Mass Spectrometry for Planetary Probes: Past, Present and Future

    NASA Technical Reports Server (NTRS)

    Niemann, Hasso B.; Harpold, Dan N.; Jamieson, Brian G.; Mahaffy, Paul R.

    2005-01-01

    Atmospheric entry probes present a unique opportunity for performing quantitative analysis of extra-terrestrial atmospheres in cases where remote sensing alone may not be sufficient and measurements with balloons or aircraft is not practical. An entry probe can provide a complete vertical profile of atmospheric parameters including chemical composition, which cannot be obtained with most other techniques. There are, however, unique challenges associated with building instruments for an entry probe, as compared to orbiters, landers, or rovers. Conditions during atmospheric entry are extreme, there are inherent time constraints due to the short duration of the experiment, and the instrument experiences rapid environmental changes in temperature and pressure as it descends. In addition, there are resource limitations, i.e. mass, power, size and bandwidth. Finally, the demands on the instrument design are determined in large part by conditions (pressure, temperature, composition) unique to the particular body under study, and as a result there is no one-size-fits-all instrument for an atmospheric probe. Many of these requirements can be more easily met by miniaturizing the probe instrument. Our experience building mass spectrometers for atmospheric entry probes leads us to believe that the time is right for a fundamental change in the way spaceflight mass spectrometers are built. The emergence over the past twenty years of Micro-electro- mechanical Systems (MEMS), utilizing lithographic semiconductor fabrication techniques to produce instrument systems in miniature, holds great promise for application to spaceflight mass spectrometry. A highly miniaturized, high performance and low-power mass spectrometer would be an enormous benefit to future entry probe missions, allowing, for example, parallel measurements (e.g., multiple simultaneous gas chromatographic analyses and direct atmospheric leaks.) Such an instrument would also enable mass spectrometry on board small