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Sample records for reactive site loop

  1. Understanding Which Residues of the Active Site and Loop Structure of a Tyrosine Aminomutase Define Its Mutase and Lyase Activities.

    Science.gov (United States)

    Attanayake, Gayanthi; Walter, Tyler; Walker, Kevin D

    2018-05-30

    Site-directed mutations and substrate analogues were used to gain insights into the branch-point reaction of the 3,5-dihydro-5-methylidene-4 H-imidazol-4-one (MIO)-tyrosine aminomutase from Oryza sativa ( OsTAM). Exchanging the active residues of OsTAM (Y125C/N446K) for those in a phenylalanine aminomutase TcPAM altered its substrate specificity from tyrosine to phenylalanine. The aminomutase mechanism of OsTAM surprisingly changed almost exclusively to that of an ammonia lyase making cinnamic acid (>95%) over β-phenylalanine [Walter, T., et al. (2016) Biochemistry 55, 3497-3503]. We hypothesized that the missing electronics or sterics on the aryl ring of the phenylalanine substrate, compared with the sizable electron-donating hydroxyl of the natural tyrosine substrate, influenced the unexpected lyase reactivity of the OsTAM mutant. The double mutant was incubated with 16 α-phenylalanine substituent analogues of varying electronic strengths and sterics. The mutant converted each analogue principally to its acrylate with ∼50% conversion of the p-Br substrate, making only a small amount of the β-amino acid. The inner loop structure over the entrance to the active site was also mutated to assess how the lyase and mutase activities are affected. An OsTAM loop mutant, matching the loop residues of TcPAM, still chiefly made >95% of the acrylate from each substrate. A combined active site:loop mutant was most reactive but remained a lyase, making 10-fold more acrylates than other mutants did. While mutations within the active site changed the substrate specificity of OsTAM, continued exploration is needed to fully understand the interplay among the inner loop, the substrate, and the active site in defining the mutase and lyase activities.

  2. Reactive sites influence in PMMA oligomers reactivity: a DFT study

    Science.gov (United States)

    Paz, C. V.; Vásquez, S. R.; Flores, N.; García, L.; Rico, J. L.

    2018-01-01

    In this work, we present a theoretical study of methyl methacrylate (MMA) living anionic polymerization. The study was addressed to understanding two important experimental observations made for Michael Szwarc in 1956. The unexpected effect of reactive sites concentration in the propagation rate, and the self-killer behavior of MMA (deactivating of living anionic polymerization). The theoretical calculations were performed by density functional theory (DFT) to obtain the frontier molecular orbitals values. These values were used to calculate and analyze the chemical interaction descriptors in DFT-Koopmans’ theorem. As a result, it was observed that the longest chain-length species (related with low concentration of reactive sites) exhibit the highest reactivity (behavior associated with the increase of the propagation rate). The improvement in this reactivity was attributed to the crosslinking produced in the polymethyl methacrylate chains. Meanwhile, the self-killer behavior was associated with the intermolecular forces present in the reactive sites. This behavior was associated to an obstruction in solvation, since the active sites remained active through all propagation species. The theoretical results were in good agreement with the Szwarc experiments.

  3. DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations

    Science.gov (United States)

    Rusling, David A.; Laurens, Niels; Pernstich, Christian; Wuite, Gijs J. L.; Halford, Stephen E.

    2012-01-01

    Most restriction endonucleases, including FokI, interact with two copies of their recognition sequence before cutting DNA. On DNA with two sites they act in cis looping out the intervening DNA. While many restriction enzymes operate symmetrically at palindromic sites, FokI acts asymmetrically at a non-palindromic site. The directionality of its sequence means that two FokI sites can be bridged in either parallel or anti-parallel alignments. Here we show by biochemical and single-molecule biophysical methods that FokI aligns two recognition sites on separate DNA molecules in parallel and that the parallel arrangement holds for sites in the same DNA regardless of whether they are in inverted or repeated orientations. The parallel arrangement dictates the topology of the loop trapped between sites in cis: the loop from inverted sites has a simple 180° bend, while that with repeated sites has a convoluted 360° turn. The ability of FokI to act at asymmetric sites thus enabled us to identify the synapse geometry for sites in trans and in cis, which in turn revealed the relationship between synapse geometry and loop topology. PMID:22362745

  4. Active site loop conformation regulates promiscuous activity in a lactonase from Geobacillus kaustophilus HTA426.

    Directory of Open Access Journals (Sweden)

    Yu Zhang

    Full Text Available Enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. A phosphotriesterase-like lactonase (PLL from Geobacillus kaustophilus HTA426 (GkaP exhibits main lactonase and promiscuous phosphotriesterase activities. To understand its catalytic and evolutionary mechanisms, we investigated a "hot spot" in the active site by saturation mutagenesis as well as X-ray crystallographic analyses. We found that position 99 in the active site was involved in substrate discrimination. One mutant, Y99L, exhibited 11-fold improvement over wild-type in reactivity (kcat/Km toward the phosphotriesterase substrate ethyl-paraoxon, but showed 15-fold decrease toward the lactonase substrate δ-decanolactone, resulting in a 157-fold inversion of the substrate specificity. Structural analysis of Y99L revealed that the mutation causes a ∼6.6 Å outward shift of adjacent loop 7, which may cause increased flexibility of the active site and facilitate accommodation and/or catalysis of organophosphate substrate. This study provides for the PLL family an example of how the evolutionary route from promiscuity to specificity can derive from very few mutations, which promotes alteration in the conformational adjustment of the active site loops, in turn draws the capacity of substrate binding and activity.

  5. Experimental evaluation of reactivity constraints for the closed-loop control of reactor power

    International Nuclear Information System (INIS)

    Bernard, J.A.; Lanning, D.D.; Ray, A.

    1984-01-01

    General principles for the closed-loop, digital control of reactor power have been identified, quantitatively enumerated, and experimentally demonstrated on the 5 MWt Research Reactor, MITR-II. The basic concept is to restrict the net reactivity so that it is always possible to make the reactor period infinite at the desired termination point of a transient by reversing the direction of motion of whatever control mechanism is associated with the controller. This capability is formally referred to as ''feasibility of control''. A series of ten experiments have been conducted over a period of eighteen months to demonstrate the efficacy of this property for the automatic control of reactor power. It has been shown that a controller which possesses this property is capable of both raising and lowering power in a safe, efficient manner while using a control rod of varying differential worth, that the reactivity constraints are a sufficient condition for the automatic control of reactor power, and that the use of a controller based on reactivity constraints can prevent overshoots either due to attempts to control a transient with a control rod of insufficient differential worth or due to failure to properly estimate when to commence rod insertion. Details of several of the more significant tests are presented together with a discussion of the rationale for the development of closed-loop control in large commercial power systems. Specific consideration is given to the motivation for designing a controller based on feasibility of control and the associated licensing issues

  6. Transient voltage control of a DFIG-based wind power plant for suppressing overvoltage using a reactive current reduction loop

    Directory of Open Access Journals (Sweden)

    Geon Park

    2016-01-01

    Full Text Available This paper proposes a transient voltage control scheme of a doubly fed induction generator (DFIG-based wind power plant (WPP using a reactive current reduction loop to suppress the overvoltage at a point of interconnection (POI and DFIG terminal after a fault clearance. The change of terminal voltage of a DFIG is monitored at every predefined time period to detect the fault clearance. If the voltage change exceeds a set value, then the reactive current reduction loop reduces the reactive current reference in the DFIG controller using the step function. The reactive current injection of DFIGs in a WPP is rapidly reduced, and a WPP can rapidly suppress the overvoltage at a fault clearance because the reactive current reference is reduced. Using an electromagnetic transients program–released version (EMTP–RV simulator, the performance of the proposed scheme was validated for a model system comprising 20 units of a 5-MW DFIG considering various scenarios, such as fault and wind conditions. Test results show that the proposed scheme enables a WPP to suppress the overvoltage at the POI and DFIG terminal within a short time under grid fault conditions.

  7. ZED-2 experiments on the effect of a Co absorber rod on an NRU loop

    International Nuclear Information System (INIS)

    Arbique, G.M.; French, P.M.

    1983-02-01

    A series of experiments has been performed in ZED-2 to measure the perturbing effects of an NRU cobalt absorber rod on a simulated NRU loop site containing graded enrichment U0 2 fuel. The objective of the measurements was to provide data useful in validating NRU reactor physics codes. Using a simulated NRU lattice containing a simulated NRU loop site and an asymmetrically placed Co absorber rod, measurements were made of: (a) reactivity effects, as measured by critical height changes, associated with voiding the loop and stepped insertion of the Co absorber rod, (b) flux perturbations at the simulated loop site and throughout the lattice induced by the Co rod, (c) Westcott r√T/Tsub(o) values throughout the lattice

  8. Differential active site loop conformations mediate promiscuous activities in the lactonase SsoPox.

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    Julien Hiblot

    Full Text Available Enzymes are proficient catalysts that enable fast rates of Michaelis-complex formation, the chemical step and products release. These different steps may require different conformational states of the active site that have distinct binding properties. Moreover, the conformational flexibility of the active site mediates alternative, promiscuous functions. Here we focused on the lactonase SsoPox from Sulfolobus solfataricus. SsoPox is a native lactonase endowed with promiscuous phosphotriesterase activity. We identified a position in the active site loop (W263 that governs its flexibility, and thereby affects the substrate specificity of the enzyme. We isolated two different sets of substitutions at position 263 that induce two distinct conformational sampling of the active loop and characterized the structural and kinetic effects of these substitutions. These sets of mutations selectively and distinctly mediate the improvement of the promiscuous phosphotriesterase and oxo-lactonase activities of SsoPox by increasing active-site loop flexibility. These observations corroborate the idea that conformational diversity governs enzymatic promiscuity and is a key feature of protein evolvability.

  9. Summertime OH reactivity from a receptor coastal site in the Mediterranean Basin

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    N. Zannoni

    2017-10-01

    Full Text Available Total hydroxyl radical (OH reactivity, the total loss frequency of the hydroxyl radical in ambient air, provides the total loading of OH reactants in air. We measured the total OH reactivity for the first time during summertime at a coastal receptor site located in the western Mediterranean Basin. Measurements were performed at a temporary field site located in the northern cape of Corsica (France, during summer 2013 for the project CARBOSOR (CARBOn within continental pollution plumes: SOurces and Reactivity–ChArMEx (Chemistry and Aerosols Mediterranean Experiment. Here, we compare the measured total OH reactivity with the OH reactivity calculated from the measured reactive gases. The difference between these two parameters is termed missing OH reactivity, i.e., the fraction of OH reactivity not explained by the measured compounds. The total OH reactivity at the site varied between the instrumental LoD (limit of detection  =  3 s−1 to a maximum of 17 ± 6 s−1 (35 % uncertainty and was 5 ± 4 s−1 (1σ SD – standard deviation on average. It varied with air temperature exhibiting a diurnal profile comparable to the reactivity calculated from the concentration of the biogenic volatile organic compounds measured at the site. For part of the campaign, 56 % of OH reactivity was unexplained by the measured OH reactants (missing reactivity. We suggest that oxidation products of biogenic gas precursors were among the contributors to missing OH reactivity.

  10. Directional R-Loop Formation by the CRISPR-Cas Surveillance Complex Cascade Provides Efficient Off-Target Site Rejection

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    Marius Rutkauskas

    2015-03-01

    Full Text Available CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against foreign nucleic acids. In type I CRISPR-Cas systems, invading DNA is detected by a large ribonucleoprotein surveillance complex called Cascade. The crRNA component of Cascade is used to recognize target sites in foreign DNA (protospacers by formation of an R-loop driven by base-pairing complementarity. Using single-molecule supercoiling experiments with near base-pair resolution, we probe here the mechanism of R-loop formation and detect short-lived R-loop intermediates on off-target sites bearing single mismatches. We show that R-loops propagate directionally starting from the protospacer-adjacent motif (PAM. Upon reaching a mismatch, R-loop propagation stalls and collapses in a length-dependent manner. This unambiguously demonstrates that directional zipping of the R-loop accomplishes efficient target recognition by rapidly rejecting binding to off-target sites with PAM-proximal mutations. R-loops that reach the protospacer end become locked to license DNA degradation by the auxiliary Cas3 nuclease/helicase without further target verification.

  11. Closed-Loop Targeted Memory Reactivation during Sleep Improves Spatial Navigation.

    Science.gov (United States)

    Shimizu, Renee E; Connolly, Patrick M; Cellini, Nicola; Armstrong, Diana M; Hernandez, Lexus T; Estrada, Rolando; Aguilar, Mario; Weisend, Michael P; Mednick, Sara C; Simons, Stephen B

    2018-01-01

    Sounds associated with newly learned information that are replayed during non-rapid eye movement (NREM) sleep can improve recall in simple tasks. The mechanism for this improvement is presumed to be reactivation of the newly learned memory during sleep when consolidation takes place. We have developed an EEG-based closed-loop system to precisely deliver sensory stimulation at the time of down-state to up-state transitions during NREM sleep. Here, we demonstrate that applying this technology to participants performing a realistic navigation task in virtual reality results in a significant improvement in navigation efficiency after sleep that is accompanied by increases in the spectral power especially in the fast (12-15 Hz) sleep spindle band. Our results show promise for the application of sleep-based interventions to drive improvement in real-world tasks.

  12. Electrocoagulation/electroflotation of reactive, disperse and mixture dyes in an external-loop airlift reactor

    International Nuclear Information System (INIS)

    Balla, Wafaa; Essadki, A.H.; Gourich, B.; Dassaa, A.; Chenik, H.; Azzi, M.

    2010-01-01

    This paper studied the efficiency of electrocoagulation/electroflotation in removing colour from synthetic and real textile wastewater by using aluminium and iron electrodes in an external-loop airlift reactor of 20 L. The disperse dye is a mixture of Yellow terasil 4G, Red terasil 343 150% and Blue terasil 3R02, the reactive dye is a mixture of Red S3B 195, Yellow SPD, Blue BRFS. For disperse dye, the removal efficiency was better using aluminium electrodes, whereas, the iron electrodes showed more efficiency for removing colour for reactive dye and mixed synthetic dye. Both for disperse, reactive and mixed dye, 40 mA cm -2 and 20 min were respectively the optimal current density and electrolysis time. 7.5 was an optimal initial pH for both reactive and mixed synthetic dye and 6.2 was an optimal initial pH for disperse dye. The colour efficiency reached in general 90%. The results showed also that Red and Blue disappeared quickly comparatively to the Yellow component both for reactive and disperse dyes. The real textile wastewater was then used. Three effluents were also used: disperse, reactive and the mixture. The colour efficiency is between 70 and 90% and COD efficiency reached 78%. The specific electrical energy consumption per kg dye removed (E dye ) in optimal conditions for real effluent was calculated. 170 kWh/kg dye was required for a reactive dye, 120 kWh/kg dye for disperse and 50 kWh/kg dye for the mixture.

  13. Electrocoagulation/electroflotation of reactive, disperse and mixture dyes in an external-loop airlift reactor

    Energy Technology Data Exchange (ETDEWEB)

    Balla, Wafaa [Ecole Superieure de Technologie, Laboratoire Genie des Procedes et Environnement, B.P. 8012, Oasis, Casablanca (Morocco); Faculte des sciences Ain Chock, Laboratoire d' Electrochimie et chimie de l' environnement, B.P. 5366, Maarif, Casablanca (Morocco); Essadki, A.H., E-mail: essadki@est-uh2c.ac.ma [Ecole Superieure de Technologie, Laboratoire Genie des Procedes et Environnement, B.P. 8012, Oasis, Casablanca (Morocco); Gourich, B. [Ecole Superieure de Technologie, Laboratoire Genie des Procedes et Environnement, B.P. 8012, Oasis, Casablanca (Morocco); Dassaa, A. [Faculte des sciences Ain Chock, Laboratoire d' Electrochimie et chimie de l' environnement, B.P. 5366, Maarif, Casablanca (Morocco); Chenik, H. [Ecole Superieure de Technologie, Laboratoire Genie des Procedes et Environnement, B.P. 8012, Oasis, Casablanca (Morocco); Faculte des sciences Ain Chock, Laboratoire d' Electrochimie et chimie de l' environnement, B.P. 5366, Maarif, Casablanca (Morocco); Azzi, M. [Faculte des sciences Ain Chock, Laboratoire d' Electrochimie et chimie de l' environnement, B.P. 5366, Maarif, Casablanca (Morocco)

    2010-12-15

    This paper studied the efficiency of electrocoagulation/electroflotation in removing colour from synthetic and real textile wastewater by using aluminium and iron electrodes in an external-loop airlift reactor of 20 L. The disperse dye is a mixture of Yellow terasil 4G, Red terasil 343 150% and Blue terasil 3R02, the reactive dye is a mixture of Red S3B 195, Yellow SPD, Blue BRFS. For disperse dye, the removal efficiency was better using aluminium electrodes, whereas, the iron electrodes showed more efficiency for removing colour for reactive dye and mixed synthetic dye. Both for disperse, reactive and mixed dye, 40 mA cm{sup -2} and 20 min were respectively the optimal current density and electrolysis time. 7.5 was an optimal initial pH for both reactive and mixed synthetic dye and 6.2 was an optimal initial pH for disperse dye. The colour efficiency reached in general 90%. The results showed also that Red and Blue disappeared quickly comparatively to the Yellow component both for reactive and disperse dyes. The real textile wastewater was then used. Three effluents were also used: disperse, reactive and the mixture. The colour efficiency is between 70 and 90% and COD efficiency reached 78%. The specific electrical energy consumption per kg dye removed (E{sub dye}) in optimal conditions for real effluent was calculated. 170 kWh/kg{sub dye} was required for a reactive dye, 120 kWh/kg{sub dye} for disperse and 50 kWh/kg{sub dye} for the mixture.

  14. Closed-Loop Targeted Memory Reactivation during Sleep Improves Spatial Navigation

    Directory of Open Access Journals (Sweden)

    Renee E. Shimizu

    2018-02-01

    Full Text Available Sounds associated with newly learned information that are replayed during non-rapid eye movement (NREM sleep can improve recall in simple tasks. The mechanism for this improvement is presumed to be reactivation of the newly learned memory during sleep when consolidation takes place. We have developed an EEG-based closed-loop system to precisely deliver sensory stimulation at the time of down-state to up-state transitions during NREM sleep. Here, we demonstrate that applying this technology to participants performing a realistic navigation task in virtual reality results in a significant improvement in navigation efficiency after sleep that is accompanied by increases in the spectral power especially in the fast (12–15 Hz sleep spindle band. Our results show promise for the application of sleep-based interventions to drive improvement in real-world tasks.

  15. Variation of wave speed determined by the PU-loop with proximity to a reflection site.

    Science.gov (United States)

    Li, Ye; Borlotti, Alessandra; Parker, Kim H; Khir, Ashraf W

    2011-01-01

    Wave speed is directly related to arterial distensibility and is widely used by clinicians to assess arterial stiffness. The PU-loop method for determining wave speed is based on the water hammer equation for flow in flexible tubes and artery using the method of characteristics. This technique determines wave speed using simultaneous measurements of pressure and velocity at a single point. The method shows that during the early part of systole, the relationship between pressure and velocity is generally linear, and the initial slope of the PU-loop is proportional to wave speed. In this work, we designed an in-vitro experiment to investigate the effect of proximity to a reflection site on the wave speed determined by the PU-loop through varying the distance between the measurement and reflection sites. Measurements were made in a flexible tube with a reflection site at the distal end formed by joining the tube to another tube with a different diameter and material properties. Six different flexible tubes were used to generate both positive and negative reflection coefficients of different magnitudes. We found that the wave speed determined by the PU-loop did not change when the measurement site was far from the reflection site but did change as the distance to the reflection site decreased. The calculated wave speed increased with positive reflections and decreased with negative reflections. The magnitude of the change in wave speed at a fixed distance from the reflection site increased with increasing the value of the reflection coefficient.

  16. Reactivity-flooding effect of the MNSR inner irradiation sites

    International Nuclear Information System (INIS)

    Khamis, I.; Khattab, K.

    1999-01-01

    For the purpose of safety assessments, evaluation of the reactivity effects of inner irradiation sites, being flooded with water in the MNSR reactor was conducted both numerically and experimentally. Measured and calculated effect of different combination of inner irradiation sites being flooded with water was evaluated numerically and experimentally. Good agreement between measurement and calculated results were obtained

  17. Description of the two-loop RELAP5 model of the L-Reactor at the Savannah River Site

    International Nuclear Information System (INIS)

    Cozzuol, J.M.; Davis, C.B.

    1989-12-01

    A two-loop RELAP5 input model of the L-Reactor at the Savannah River Site (SRS) was developed to support thermal-hydraulic analysis of SRS reactors. The model was developed to economically evaluate potential design changes. The primary simplifications in the model were in the number of loops and the detail in the moderator tank. The six loops in the reactor were modeled with two loops, one representing a single loop and the other representing five combined loops. The model has undergone a quality assurance review. This report describes the two-loop model, its limitations, and quality assurance. 29 refs., 18 figs., 10 tabs

  18. Mutations of the kissing-loop dimerization sequence influence the site specificity of murine leukemia virus recombination in vivo

    DEFF Research Database (Denmark)

    Mikkelsen, J G; Lund, Anders Henrik; Duch, M

    2000-01-01

    synthesis in newly infected cells. We have previously shown that template shifts within the 5' leader of murine leukemia viruses occur preferentially within the kissing stem-loop motif, a cis element crucial for in vitro RNA dimer formation. By use of a forced recombination approach based on single......-cycle transfer of Akv murine leukemia virus-based vectors harboring defective primer binding site sequences, we now report that modifications of the kissing-loop structure, ranging from a deletion of the entire sequence to introduction of a single point mutation in the loop motif, significantly disturb site...... specificity of recombination within the highly structured 5' leader region. In addition, we find that an intact kissing-loop sequence favors optimal RNA encapsidation and vector transduction. Our data are consistent with the kissing-loop dimerization model and suggest that a direct intermolecular RNA...

  19. Monoclonal antibodies to the reactive centre loop (RCL) of human corticosteroid-binding globulin (CBG) can protect against proteolytic cleavage.

    Science.gov (United States)

    Lewis, John G; Elder, Peter A

    2017-07-01

    Corticosteroid-binding globulin (CBG) binds most of the cortisol in circulation and is a non-functional member of the family of serine protease inhibitors (serpins) with an exposed elastase sensitive reactive centre loop (RCL). The RCL can be cleaved by human neutrophil elastase, released from activated neutrophils, and can also be cleaved at nearby site(s) by elastase released by Pseudomonas aeruginosa, and at two further sites, also within the RCL, by bovine chymotrypsin. Cleavage of the RCL results in a conformational change accompanied by a marked decrease in affinity for cortisol and hence its release at the site of proteolysis. These cleavages are irreversible and the similar half-lives of cleaved and intact CBG could mean that there may be some advantage in slowing the rate of CBG cleavage in acute inflammation thereby increasing the proportion of intact CBG in circulation. Here we show, for the first time, that pre-incubation of tethered human CBG with two monoclonal antibodies to the RCL of CBG protects against cleavage by all three enzymes. Furthermore, in plasma, pre-incubation with both RCL monoclonal antibodies delays neutrophil elastase cleavage of the RCL and one of these RCL monoclonal antibodies also delays bovine chymotrypsin cleavage of the RCL. These findings may provide a basis and rationale for the concept of the use of RCL antibodies as therapeutic agents to effectively increase the proportion of intact CBG in circulation which may be of benefit in acute inflammation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Half-of-the-sites reactivity of outer-membrane phospholipase A against an active-site-directed inhibitor.

    Science.gov (United States)

    Ubarretxena-Belandia, I; Cox, R C; Dijkman, R; Egmond, M R; Verheij, H M; Dekker, N

    1999-03-01

    The reaction of a novel active-site-directed phospholipase A1 inhibitor with the outer-membrane phospholipase A (OMPLA) was investigated. The inhibitor 1-p-nitrophenyl-octylphosphonate-2-tridecylcarbamoyl-3-et hanesulfonyl -amino-3-deoxy-sn-glycerol irreversibly inactivated OMPLA. The inhibition reaction did not require the cofactor calcium or an unprotonated active-site His142. The inhibition of the enzyme solubilized in hexadecylphosphocholine micelles was characterized by a rapid (t1/2 = 20 min) and complete loss of enzymatic activity, concurrent with the covalent modification of 50% of the active-site serines, as judged from the amount of p-nitrophenolate (PNP) released. Modification of the remaining 50% occurred at a much lower rate, indicative of half-of-the-sites reactivity against the inhibitor of this dimeric enzyme. Inhibition of monomeric OMPLA solubilized in hexadecyl-N,N-dimethyl-1-ammonio-3-propanesulfonate resulted in an equimolar monophasic release of PNP, concurrent with the loss of enzymatic activity (t1/2 = 14 min). The half-of-the-sites reactivity is discussed in view of the dimeric nature of this enzyme.

  1. Detection of radiation-induced changes in electrochemical properties of austenitic stainless steels using miniaturized specimens and the single-loop electrochemical potentiokinetic reactivation method

    International Nuclear Information System (INIS)

    Inazumi, T.; Bell, G.E.C.; Kenik, E.A.; Kiuchi, K.

    1993-01-01

    Single-loop electrochemical potentiokinetic reactivation testing of miniaturized (TEM) specimens can provide reliable data comparable to data obtained with larger specimens. Significant changes in electrochemical properties (increased reactivation current and Flade potential) were detected for PCA and type 316 stainless steels irradiated at 200--420 degrees C up to 7--9 dpa. Irradiations in the FFTF Materials Open Test Assembly and in the Oak Ridge Research Reactor are reported on. 45 figs., 5 tabs., 52 refs

  2. Morphological Changes of Limestone Sorbent Particles during Carbonation/Calcination Looping Cycles in a Thermogravimetric Analyzer (TGA) and Reactivation with Steam

    KAUST Repository

    Wu, Y.

    2010-04-15

    Carbonation and calcination looping cycles were carried out on four limestones in a thermogravimetric analyzer (TGA). The CO2 carrying capacity of a limestone particle decays very quickly in the first 10 cycles, reducing to about 20% of its original uptake capacity after 10 cycles for the four limestones studied in this work, and it decreases further to 6-12% after 50 cycles. A new steam reactivation method was applied on the spent sorbent to recover the loss of reactivity. The steam reactivation of multi-cycled samples was conducted at atmospheric pressure. Steam reactivation for 5 min at 130 °C of particles that had undergone 10 cycles resulted in an immediate increase (by 45-60% points) in carrying capacity. The morphological changes of limestone particles during the cycling and steam reactivation were studied using both an optical microscope and scanning electron microscopy (SEM). The diameters of limestone particles shrank by about 2-7% after 10 carbonation/calcination cycles, and the particle diameters swelled significantly (12-22% increase) after steam reactivation. These size changes are important for studies of attrition and mathematical modeling of carbonation. © 2010 American Chemical Society.

  3. Active Site Loop Dynamics of a Class IIa Fructose 1,6-Bisphosphate Aldolase from Mycobacterium tuberculosis

    Energy Technology Data Exchange (ETDEWEB)

    Pegan, Scott D. [Univ. of Denver, CO (United States); Rukseree, Kamolchanok [National Center for Genetic Engineering and Biotechnology (BIOTEC), Tha Khlong (Thailand); Capodagli, Glenn C. [Univ. of Denver, CO (United States); Baker, Erica A. [Univ. of Denver, CO (United States); Krasnykh, Olga [Univ. of Illinois, Chicago, IL (United States); Franzblau, Scott G. [Univ. of Illinois, Chicago, IL (United States); Mesecar, Andrew D. [Purdue Univ., West Lafayette, IN (United States)

    2013-01-08

    The class II fructose 1,6-bisphosphate aldolases (FBAs, EC 4.1.2.13) comprises one of two families of aldolases. Instead of forming a Schiff base intermediate using an ε-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate, forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs have been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies of class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria, and protozoa have been reported, the structure of the active site loop responsible for catalyzing the protonation–deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI- and DHAP-bound form of the enzyme and determined the X-ray structure of the MtFBA–PGH complex to 1.58 Å. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information and site-directed mutagenesis and kinetic studies conducted on a series of residues within the active site loop revealed that E169 facilitates a water-mediated deprotonation–protonation step of the MtFBA reaction mechanism. Furthermore, solvent isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form.

  4. Innovative hybrid pile oscillator technique in the Minerve reactor: open loop vs. closed loop

    Science.gov (United States)

    Geslot, Benoit; Gruel, Adrien; Bréaud, Stéphane; Leconte, Pierre; Blaise, Patrick

    2018-01-01

    Pile oscillator techniques are powerful methods to measure small reactivity worth of isotopes of interest for nuclear data improvement. This kind of experiments has long been implemented in the Mineve experimental reactor, operated by CEA Cadarache. A hybrid technique, mixing reactivity worth estimation and measurement of small changes around test samples is presented here. It was made possible after the development of high sensitivity miniature fission chambers introduced next to the irradiation channel. A test campaign, called MAESTRO-SL, took place in 2015. Its objective was to assess the feasibility of the hybrid method and investigate the possibility to separate mixed neutron effects, such as fission/capture or scattering/capture. Experimental results are presented and discussed in this paper, which focus on comparing two measurements setups, one using a power control system (closed loop) and another one where the power is free to drift (open loop). First, it is demonstrated that open loop is equivalent to closed loop. Uncertainty management and methods reproducibility are discussed. Second, results show that measuring the flux depression around oscillated samples provides valuable information regarding partial neutron cross sections. The technique is found to be very sensitive to the capture cross section at the expense of scattering, making it very useful to measure small capture effects of highly scattering samples.

  5. Immunological Reactivity Using Monoclonal and Polyclonal Antibodies of Autoimmune Thyroid Target Sites with Dietary Proteins

    Directory of Open Access Journals (Sweden)

    Datis Kharrazian

    2017-01-01

    Full Text Available Many hypothyroid and autoimmune thyroid patients experience reactions with specific foods. Additionally, food interactions may play a role in a subset of individuals who have difficulty finding a suitable thyroid hormone dosage. Our study was designed to investigate the potential role of dietary protein immune reactivity with thyroid hormones and thyroid axis target sites. We identified immune reactivity between dietary proteins and target sites on the thyroid axis that includes thyroid hormones, thyroid receptors, enzymes, and transport proteins. We also measured immune reactivity of either target specific monoclonal or polyclonal antibodies for thyroid-stimulating hormone (TSH receptor, 5′deiodinase, thyroid peroxidase, thyroglobulin, thyroxine-binding globulin, thyroxine, and triiodothyronine against 204 purified dietary proteins commonly consumed in cooked and raw forms. Dietary protein determinants included unmodified (raw and modified (cooked and roasted foods, herbs, spices, food gums, brewed beverages, and additives. There were no dietary protein immune reactions with TSH receptor, thyroid peroxidase, and thyroxine-binding globulin. However, specific antigen-antibody immune reactivity was identified with several purified food proteins with triiodothyronine, thyroxine, thyroglobulin, and 5′deiodinase. Laboratory analysis of immunological cross-reactivity between thyroid target sites and dietary proteins is the initial step necessary in determining whether dietary proteins may play a potential immunoreactive role in autoimmune thyroid disease.

  6. DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics

    Science.gov (United States)

    Laurens, Niels; Rusling, David A.; Pernstich, Christian; Brouwer, Ineke; Halford, Stephen E.; Wuite, Gijs J. L.

    2012-01-01

    Protein-induced DNA looping is crucial for many genetic processes such as transcription, gene regulation and DNA replication. Here, we use tethered-particle motion to examine the impact of DNA bending and twisting rigidity on loop capture and release, using the restriction endonuclease FokI as a test system. To cleave DNA efficiently, FokI bridges two copies of an asymmetric sequence, invariably aligning the sites in parallel. On account of the fixed alignment, the topology of the DNA loop is set by the orientation of the sites along the DNA. We show that both the separation of the FokI sites and their orientation, altering, respectively, the twisting and the bending of the DNA needed to juxtapose the sites, have profound effects on the dynamics of the looping interaction. Surprisingly, the presence of a nick within the loop does not affect the observed rigidity of the DNA. In contrast, the introduction of a 4-nt gap fully relaxes all of the torque present in the system but does not necessarily enhance loop stability. FokI therefore employs torque to stabilise its DNA-looping interaction by acting as a ‘torsional’ catch bond. PMID:22373924

  7. Deposition of chemically reactive and repellent sites on biosensor chips for reduced non-specific binding.

    Science.gov (United States)

    Gandhiraman, R P; Gubala, V; Le, N C H; Nam, Le Cao Hoai; Volcke, C; Doyle, C; James, B; Daniels, S; Williams, D E

    2010-08-01

    The performances of new polymeric materials with excellent optical properties and good machinability have led the biomedical diagnostics industry to develop cheap disposable biosensor platforms appropriate for point of care applications. Zeonor, a type of cycloolefin polymer (COP), is one such polymer that presents an excellent platform for biosensor chips. These polymer substrates have to be modified to have suitable physico-chemical properties for immobilizing proteins. In this work, we have demonstrated the amine functionalization of COP substrates, by plasma enhanced chemical vapour deposition (PECVD), through codeposition of ethylene diamine and 3-aminopropyltriethoxysilane precursors, for building chemistries on the plastic chip. The elemental composition, adhesion, ageing and reactivity of the plasma polymerized film were examined. The Si-O functionality present in amino silane contributed for a good interfacial adhesion of the coating to COP substrates and also acted as a network building layer for plasma polymerization. Wet chemical modification was then carried out on the amine functionalized chips to create chemically reactive isothiocyanate sites and protein repellent fluorinated sites on the same chip. The density of the reactive and repellent sites was altered by choosing appropriate mixtures of homofunctional phenyldiisothiocyanate (PDITC), pentafluoroisothiocyanate (5FITC) and phenylisothiocyanate (PITC) compounds. By tailoring the density of reactive binding sites and protein repellent sites, the non-specific binding of ssDNA has been decreased to a significant extent. Copyright 2010 Elsevier B.V. All rights reserved.

  8. A complete closed loop control system for MNSR

    International Nuclear Information System (INIS)

    Wang Liyu

    1988-01-01

    The MNSR (Miniature Neutron Source Reactor), a 27 kW reactor, was built in 1984 in the Institute of Atomic Energy, Beijing, China. A microcomputer closed-loop control system has been developed for the MNSR using an IBM PC-XT. This system not only controls the reactor, but it is also a data acquisition system and a reactivity monitor for the reactor. A closed-loop control system can be used for reactors such as the MNSR, in which the power is self-limited and the reactivity is limited to less than 5mk (∼0.7$). As a data acquisition system or a reactivity monitor, it is applicable for any nuclear reactor. This paper describes the hardware and software in detail. 4 refs, 11 figs

  9. Innovative hybrid pile oscillator technique in the Minerve reactor: open loop vs. closed loop

    Directory of Open Access Journals (Sweden)

    Geslot Benoit

    2018-01-01

    Full Text Available Pile oscillator techniques are powerful methods to measure small reactivity worth of isotopes of interest for nuclear data improvement. This kind of experiments has long been implemented in the Mineve experimental reactor, operated by CEA Cadarache. A hybrid technique, mixing reactivity worth estimation and measurement of small changes around test samples is presented here. It was made possible after the development of high sensitivity miniature fission chambers introduced next to the irradiation channel. A test campaign, called MAESTRO-SL, took place in 2015. Its objective was to assess the feasibility of the hybrid method and investigate the possibility to separate mixed neutron effects, such as fission/capture or scattering/capture. Experimental results are presented and discussed in this paper, which focus on comparing two measurements setups, one using a power control system (closed loop and another one where the power is free to drift (open loop. First, it is demonstrated that open loop is equivalent to closed loop. Uncertainty management and methods reproducibility are discussed. Second, results show that measuring the flux depression around oscillated samples provides valuable information regarding partial neutron cross sections. The technique is found to be very sensitive to the capture cross section at the expense of scattering, making it very useful to measure small capture effects of highly scattering samples.

  10. The role of autolysis loop in determining the specificity of coagulation proteases.

    Science.gov (United States)

    Yang, L; Manithody, C; Rezaie, A R

    2007-08-01

    We recently demonstrated that the substitution of the autolysis loop (residues 143 to 154 in the chymotrypsin numbering system) of activated protein C (APC) with the corresponding loop of factor Xa (fXa) renders the APC mutant (APC/fX143-154) susceptible to inhibition by antithrombin (AT) in the presence of pentasaccharide. Our recent results further indicated, that in addition to an improvement in the reactivity of APC/fX143-154 with AT, both the amidolytic and anti-factor Va activities of the mutant APC have also been significantly increased. Since the autolysis loop of APC is five residues longer than the autolysis loop of fXa, it could not be ascertained whether this loop in the mutant APC specifically interacts with the activated conformation of AT or if a shorter autolysis loop is responsible for a global improvement in the catalytic activity of the mutant protease. To answer this question, we prepared another APC mutant in which the autolysis loop of the protease was replaced with the corresponding loop of trypsin (APC/Tryp143-154). Unlike an approximately 500-fold improvement in the reactivity of APC/fX143-154 with AT in the presence of pentasaccharide, the reactivity of APC/Tryp143-154 with the serpin was improved approximately 10-fold. These results suggest that both the length and structure of residues of the autolysis loop are critical for the specificity of the coagulation protease interaction with AT. Further factor Va inactivation studies with the APC mutants revealed a similar role for the autolysis loop of APC in the interaction with its natural substrate.

  11. The role of autolysis loop in determining the specificity of coagulation proteases

    Directory of Open Access Journals (Sweden)

    L. Yang

    2007-08-01

    Full Text Available We recently demonstrated that the substitution of the autolysis loop (residues 143 to 154 in the chymotrypsin numbering system of activated protein C (APC with the corresponding loop of factor Xa (fXa renders the APC mutant (APC/fX143-154 susceptible to inhibition by antithrombin (AT in the presence of pentasaccharide. Our recent results further indicated, that in addition to an improvement in the reactivity of APC/fX143-154 with AT, both the amidolytic and anti-factor Va activities of the mutant APC have also been significantly increased. Since the autolysis loop of APC is five residues longer than the autolysis loop of fXa, it could not be ascertained whether this loop in the mutant APC specifically interacts with the activated conformation of AT or if a shorter autolysis loop is responsible for a global improvement in the catalytic activity of the mutant protease. To answer this question, we prepared another APC mutant in which the autolysis loop of the protease was replaced with the corresponding loop of trypsin (APC/Tryp143-154. Unlike an ~500-fold improvement in the reactivity of APC/fX143-154 with AT in the presence of pentasaccharide, the reactivity of APC/Tryp143-154 with the serpin was improved ~10-fold. These results suggest that both the length and structure of residues of the autolysis loop are critical for the specificity of the coagulation protease interaction with AT. Further factor Va inactivation studies with the APC mutants revealed a similar role for the autolysis loop of APC in the interaction with its natural substrate.

  12. The Australian national reactive phosphate rock project - Aims, experimental approach, and site characteristics

    International Nuclear Information System (INIS)

    McLaughlin, M.J.

    2002-01-01

    Field-based cutting trials were established across Australia in a range of environments to evaluate the agronomic effectiveness of 5 phosphate rocks, and 1 partially acidulated phosphate rock, relative to either single super-phosphate or triple superphosphate. The phosphate rocks differed in reactivity, as determined by the degree of carbonate substitution for phosphate in the apatite structure and solubility of phosphorus present in the fertilizers in 2% formic acid, 2% citric acid and neutral ammonium citrate. Sechura (Bayovar) and North Carolina phosphate rocks were highly reactive (>70% solubility in 2% formic acid), whilst Khouribja (Moroccan) and Hamrawein (Egypt) phosphate rock were moderately reactive. Duchess phosphate rock from Queensland was relatively unreactive ( 2 , from 4.0 to 5.1, and Colwell extractable phosphorus ranged from 3 to 47 μg/g prior to fertilizer application. Two core experiments were established at each site. The first measured the effects of phosphate rock reactivity on agronomic effectiveness, while the second core experiment measured the effects of the degree of water solubility of the phosphorus source on agronomic effectiveness. The National Reactive Phosphate Rock Project trials provided the opportunity to confirm the suitability of accepted procedures to model fertilizer response and to develop new approaches for comparing different fertilizer responses. The Project also provided the framework for subsidiary studies such as the effect of fertilizer source on soil phosphorus extractability; cadmium and fluorine concentrations in herbage; evaluation of soil phosphorus tests; and the influence of particle size on phosphate rock effectiveness. The National Reactive Phosphate Rock Project presents a valuable model for a large, Australia-wide, collaborative team approach to an important agricultural issue. The use of standard and consistent experimental methodologies at every site ensured that maximum benefit was obtained from data

  13. Investigation on reactivity of iron nickel oxides in chemical looping dry reforming

    International Nuclear Information System (INIS)

    Huang, Zhen; He, Fang; Chen, Dezhen; Zhao, Kun; Wei, Guoqiang; Zheng, Anqing; Zhao, Zengli; Li, Haibin

    2016-01-01

    Iron nickel oxides as oxygen carriers were investigated to clarify the reaction mechanism of NiFe_2O_4 material during the chemical looping dry reforming (CLDR) process. The thermodynamic analysis showed that metallic Fe can be oxidized into Fe_3O_4 by CO_2, but metallic Ni cannot. The oxidizability of the four oxygen carriers was in the order of NiO > synthetic NiFe_2O_4 spinel > NiO-Fe_2O_3 mixed oxides > Fe_2O_3, and the reducibility sequence of their reduced products was synthetic NiFe_2O_4 spinel > NiO-Fe_2O_3 mixed oxides > Fe_2O_3 > NiO. The NiO showed the best oxidizability but it was easy to cause CH_4 cracking and its reduced product (Ni) did not recover lattice oxygen under CO_2 atmosphere. It only produced 74 mL CO for 1 g Fe_2O_3 during the CO_2 reforming because of its weak oxidizability. The Redox ability of synthetic NiFe_2O_4 was obvious higher than that of NiO-Fe_2O_3 mixed oxides due to the synergistic effect of metallic Fe-Ni in the spinel structure. 1 g synthetic NiFe_2O_4 can produce 238 mL CO, which was twice higher than that of 1 g NiO-Fe_2O_3 mixed oxides (111 mL). A part of Fe element was divorced from the NiFe_2O_4 spinel structure after one cycle, which was the major reason for degradation of reactivity of NiFe_2O_4 oxygen carrier. - Highlights: • A synergistic effect of Fe/Ni can improve the reactivity of oxygen carrier (OC). • The oxidizability sequence of four OCs is NiO > NiFe_2O_4 > mixed NiO + Fe_2O_3 > Fe_2O_3. • The reducibility sequence of four OCs is NiFe_2O_4 > mixed NiO + Fe_2O_3 > Fe_2O_3 > NiO. • The formation of Fe (Ni) alloy phase facilitates more CO_2 reduced into CO. • Part of Fe is divorced from the spinel structure, leading to the degeneration of OC reactivity.

  14. Integrated Process Design and Control of Reactive Distillation Processes

    DEFF Research Database (Denmark)

    Mansouri, Seyed Soheil; Sales-Cruz, Mauricio; Huusom, Jakob Kjøbsted

    2015-01-01

    on the element concept, which is used to translate a system of compounds into elements. The operation of the reactive distillation column at the highest driving force and other candidate points is analyzed through analytical solution as well as rigorous open-loop and closed-loop simulations. By application...... of this approach, it is shown that designing the reactive distillation process at the maximum driving force results in an optimal design in terms of controllability and operability. It is verified that the reactive distillation design option is less sensitive to the disturbances in the feed at the highest driving...

  15. Multi-site exploration of sex differences in brain reactivity to smoking cues: Consensus across sites and methodologies.

    Science.gov (United States)

    Dumais, Kelly M; Franklin, Teresa R; Jagannathan, Kanchana; Hager, Nathan; Gawrysiak, Michael; Betts, Jennifer; Farmer, Stacey; Guthier, Emily; Pater, Heather; Janes, Amy C; Wetherill, Reagan R

    2017-09-01

    Biological sex influences cigarette smoking behavior. More men than women smoke, but women have a harder time quitting. Sex differences in smoking cue (SC) reactivity may underlie such behavioral differences. However, the influence of sex on brain reactivity to SCs has yielded inconsistent findings suggesting the need for continued study. Here, we investigated the effect of sex on SC reactivity across two sites using different imaging modalities and SC stimulus types. Pseudo-continuous arterial spin-labeled (pCASL) perfusion functional magnetic resonance imaging (fMRI) was used to assess brain responses to SC versus non-SC videos in 40 smokers (23 females) at the University of Pennsylvania. BOLD fMRI was used to assess brain responses to SC versus non-SC still images in 32 smokers (18 females) at McLean Hospital. Brain reactivity to SCs was compared between men and women and was correlated with SC-induced craving. In both cohorts, males showed higher SC versus non-SC reactivity compared to females in reward-related brain regions (i.e., ventral striatum/ventral pallidum, ventral medial prefrontal cortex). Brain activation during SC versus non-SC exposure correlated positively with SC-induced subjective craving in males, but not females. The current work provides much needed replication and validation of sex differences in SC-reactivity. These findings also add to a body of literature showing that men have greater reward-related brain activation to drug cues across drug classes. Such sex differences confirm the need to consider sex not only when evaluating SC-reactivity but when examining nicotine dependence etiology and treatment. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Advancements in Development of Chemical-Looping Combustion: A Review

    Directory of Open Access Journals (Sweden)

    He Fang

    2009-01-01

    Full Text Available Chemical-looping combustion (CLC is a novel combustion technology with inherent separation of greenhouse CO2. Extensive research has been performed on CLC in the last decade with respect to oxygen carrier development, reaction kinetics, reactor design, system efficiencies, and prototype testing. Transition metal oxides, such as Ni, Fe, Cu, and Mn oxides, were reported as reactive species in the oxygen carrier particles. Ni-based oxygen carriers exhibited the best reactivity and stability during multiredox cycles. The performance of the oxygen carriers can be improved by changing preparation method or by making mixedoxides. The CLC has been demonstrated successfully in continuously operated prototype reactors based on interconnected fluidized-bed system in the size range of 0.3–50 kW. High fuel conversion rates and almost 100%  CO2 capture efficiencies were obtained. The CLC system with two interconnected fluidized-bed reactors was considered the most suitable reactor design. Development of oxygen carriers with excellent reactivity and stability is still one of the challenges for CLC in the near future. Experiences of building and operating the large-scale CLC systems are needed before this technology is used commercially. Chemical-looping reforming (CLR and chemical-looping hydrogen (CLH are novel chemical-looping techniques to produce synthesis gas and hydrogen deserving more attention and research.

  17. Thermal inactivation of ileal loop-reactive Clostridium perfringens type A strains in phosphate buffer and beef gravy.

    Science.gov (United States)

    Bradshaw, J G; Peeler, J T; Twedt, R M

    1977-09-01

    The thermal resistance of spore crops produced from each of two ileal loop-reactive strains of Clostridium perfringens type A was determined in two suspending vehicles consisting of 0.067 M (pH 7.0) phosphate buffer and a commercial beef gravy. D115.6 values obtained in buffer and enumerated after pretreatment with sodium ethylenediaminetetraacetate and recovery in plating medium containing lysozyme were two- to threefold greater than those obtained without this treatment. D115.6 values obtained with beef gravy were less than those obtained in buffer with or without lysozyme; however, the D98.9 and D104.4 values were 1.3 to 2 times greater than those obtained in buffer with lysozyme. The z values were within the ranges reported by previous investigators.

  18. Investigation of reactivity changes due to flooding the irradiation sites of the MNSR reactor using the MCNP code and comparison with experimental results

    Directory of Open Access Journals (Sweden)

    A Shirani

    2010-06-01

    Full Text Available In this work, the Isfahan Miniature Neutron Source Reactor (MNSR has been simulated using the MCNP code, and reactivity worth of flooding the inner irradiation sites of this reactor in an accident has been calculated. Also, by inserting polyethylene capsules containing water inside the inner irradiation sites, reactivity changes of this reactor in same such accident have been measured, the results of which are in good agreements with the calculated results. In this work, the reactivity worth due to flooding one inner irradiation site is 0.53mk , and reactivity worth due to flooding of the whole 5 inner irradiation sites is 2.61 mk.

  19. Evaluation of a loop-mediated isothermal amplification (LAMP) method for rapid on-site detection of horse meat

    NARCIS (Netherlands)

    Aartse, Aafke; Scholtens-Toma, Ingrid; A, van der Hans J.G.; Boersma-Greve, Monique M.; Prins, Theo W.; Ginkel, van Leen A.; Kok, Esther J.; Bovee, Toine F.H.

    2017-01-01

    Detection of horse DNA by loop-mediated isothermal amplification (LAMP) seems one of the most promising methods to meet the criteria of fast, robust, cost efficient, specific, and sensitive on-site detection. In the present study an assessment of the specificity and sensitivity of the LAMP horse

  20. The functional significance of the autolysis loop in protein C and activated protein C.

    Science.gov (United States)

    Yang, Likui; Manithody, Chandrashekhara; Rezaie, Alireza R

    2005-07-01

    The autolysis loop of activated protein C (APC) is five residues longer than the autolysis loop of other vitamin K-dependent coagulation proteases. To investigate the role of this loop in the zymogenic and anticoagulant properties of the molecule, a protein C mutant was constructed in which the autolysis loop of the protein was replaced with the corresponding loop of factor X. The protein C mutant was activated by thrombin with approximately 5-fold higher rate in the presence of Ca2+. Both kinetics and direct binding studies revealed that the Ca2+ affinity of the mutant has been impaired approximately 3-fold. The result of a factor Va degradation assay revealed that the anticoagulant function of the mutant has been improved 4-5-fold in the absence but not in the presence of protein S. The improvement was due to a better recognition of both the P1-Arg506 and P1-Arg306 cleavage sites by the mutant protease. However, the plasma half-life of the mutant was markedly shortened due to faster inactivation by plasma serpins. These results suggest that the autolysis loop of protein C is critical for the Ca(2+)-dependence of activation by thrombin. Moreover, a longer autolysis loop in APC is not optimal for interaction with factor Va in the absence of protein S, but it contributes to the lack of serpin reactivity and longer half-life of the protease in plasma.

  1. Epicardial left ventricular lead placement for cardiac resynchronization therapy: optimal pace site selection with pressure-volume loops.

    Science.gov (United States)

    Dekker, A L A J; Phelps, B; Dijkman, B; van der Nagel, T; van der Veen, F H; Geskes, G G; Maessen, J G

    2004-06-01

    Patients in heart failure with left bundle branch block benefit from cardiac resynchronization therapy. Usually the left ventricular pacing lead is placed by coronary sinus catheterization; however, this procedure is not always successful, and patients may be referred for surgical epicardial lead placement. The objective of this study was to develop a method to guide epicardial lead placement in cardiac resynchronization therapy. Eleven patients in heart failure who were eligible for cardiac resynchronization therapy were referred for surgery because of failed coronary sinus left ventricular lead implantation. Minithoracotomy or thoracoscopy was performed, and a temporary epicardial electrode was used for biventricular pacing at various sites on the left ventricle. Pressure-volume loops with the conductance catheter were used to select the best site for each individual patient. Relative to the baseline situation, biventricular pacing with an optimal left ventricular lead position significantly increased stroke volume (+39%, P =.01), maximal left ventricular pressure derivative (+20%, P =.02), ejection fraction (+30%, P =.007), and stroke work (+66%, P =.006) and reduced end-systolic volume (-6%, P =.04). In contrast, biventricular pacing at a suboptimal site did not significantly change left ventricular function and even worsened it in some cases. To optimize cardiac resynchronization therapy with epicardial leads, mapping to determine the best pace site is a prerequisite. Pressure-volume loops offer real-time guidance for targeting epicardial lead placement during minimal invasive surgery.

  2. Identification of cisplatin-binding sites on the large cytoplasmic loop of the Na+/K+-ATPase.

    Science.gov (United States)

    Šeflová, Jaroslava; Čechová, Petra; Štenclová, Tereza; Šebela, Marek; Kubala, Martin

    2018-12-01

    Cisplatin is the most widely used chemotherapeutic drug for the treatment of various types of cancer; however, its administration brings also numerous side effects. It was demonstrated that cisplatin can inhibit the Na + /K + -ATPase (NKA), which can explain a large part of the adverse effects. In this study, we have identified five cysteinyl residues (C452, C456, C457, C577, and C656) as the cisplatin binding sites on the cytoplasmic loop connecting transmembrane helices 4 and 5 (C45), using site-directed mutagenesis and mass spectrometry experiments. The identified residues are known to be susceptible to glutathionylation indicating their involvement in a common regulatory mechanism.

  3. Post Audit of a Field Scale Reactive Transport Model of Uranium at a Former Mill Site

    Science.gov (United States)

    Curtis, G. P.

    2015-12-01

    Reactive transport of hexavalent uranium (U(VI)) in a shallow alluvial aquifer at a former uranium mill tailings site near Naturita CO has been monitored for nearly 30 years by the US Department of Energy and the US Geological Survey. Groundwater at the site has high concentrations of chloride, alkalinity and U(VI) as a owing to ore processing at the site from 1941 to 1974. We previously calibrated a multicomponent reactive transport model to data collected at the site from 1986 to 2001. A two dimensional nonreactive transport model used a uniform hydraulic conductivity which was estimated from observed chloride concentrations and tritium helium age dates. A reactive transport model for the 2km long site was developed by including an equilibrium U(VI) surface complexation model calibrated to laboratory data and calcite equilibrium. The calibrated model reproduced both nonreactive tracers as well as the observed U(VI), pH and alkalinity. Forward simulations for the period 2002-2015 conducted with the calibrated model predict significantly faster natural attenuation of U(VI) concentrations than has been observed by the persistent high U(VI) concentrations at the site. Alternative modeling approaches are being evaluating evaluated using recent data to determine if the persistence can be explained by multirate mass transfer models developed from experimental observations at the column scale(~0.2m), the laboratory tank scale (~2m), the field tracer test scale (~1-4m) or geophysical observation scale (~1-5m). Results of this comparison should provide insight into the persistence of U(VI) plumes and improved management options.

  4. Evaluation of a permeable reactive barrier technology for use at Rocky Flats Environmental Technology Site (RFETS)

    International Nuclear Information System (INIS)

    Dwyer, Brian P.

    2000-01-01

    Three reactive materials were evaluated at laboratory scale to identify the optimum treatment reagent for use in a Permeable Reactive Barrier Treatment System at Rocky Flats Environmental Technology Site (RFETS). The contaminants of concern (COCS) are uranium, TCE, PCE, carbon tetrachloride, americium, and vinyl chloride. The three reactive media evaluated included high carbon steel iron filings, an iron-silica alloy in the form of a foam aggregate, and a peculiar humic acid based sorbent (Humasorb from Arctech) mixed with sand. Each material was tested in the laboratory at column scale using simulated site water. All three materials showed promise for the 903 Mound Site however, the iron filings were determined to be the least expensive media. In order to validate the laboratory results, the iron filings were further tested at a pilot scale (field columns) using actual site water. Pilot test results were similar to laboratory results; consequently, the iron filings were chosen for the fill-scale demonstration of the reactive barrier technology. Additional design parameters including saturated hydraulic conductivity, treatment residence time, and head loss across the media were also determined and provided to the design team in support of the final design. The final design was completed by the Corps of Engineers in 1997 and the system was constructed in the summer of 1998. The treatment system began fill operation in December, 1998 and despite a few problems has been operational since. Results to date are consistent with the lab and pilot scale findings, i.e., complete removal of the contaminants of concern (COCs) prior to discharge to meet RFETS cleanup requirements. Furthermore, it is fair to say at this point in time that laboratory developed design parameters for the reactive barrier technology are sufficient for fuel scale design; however,the treatment system longevity and the long-term fate of the contaminants are questions that remain unanswered. This

  5. Sites of reactive oxygen species generation by mitochondria oxidizing different substrates

    Directory of Open Access Journals (Sweden)

    Casey L. Quinlan

    2013-01-01

    Full Text Available Mitochondrial radical production is important in redox signaling, aging and disease, but the relative contributions of different production sites are poorly understood. We analyzed the rates of superoxide/H2O2 production from different defined sites in rat skeletal muscle mitochondria oxidizing a variety of conventional substrates in the absence of added inhibitors: succinate; glycerol 3-phosphate; palmitoylcarnitine plus carnitine; or glutamate plus malate. In all cases, the sum of the estimated rates accounted fully for the measured overall rates. There were two striking results. First, the overall rates differed by an order of magnitude between substrates. Second, the relative contribution of each site was very different with different substrates. During succinate oxidation, most of the superoxide production was from the site of quinone reduction in complex I (site IQ, with small contributions from the flavin site in complex I (site IF and the quinol oxidation site in complex III (site IIIQo. However, with glutamate plus malate as substrate, site IQ made little or no contribution, and production was shared between site IF, site IIIQo and 2-oxoglutarate dehydrogenase. With palmitoylcarnitine as substrate, the flavin site in complex II (site IIF was a major contributor (together with sites IF and IIIQo, and with glycerol 3-phosphate as substrate, five different sites all contributed, including glycerol 3-phosphate dehydrogenase. Thus, the relative and absolute contributions of specific sites to the production of reactive oxygen species in isolated mitochondria depend very strongly on the substrates being oxidized, and the same is likely true in cells and in vivo.

  6. Alternative Mode of E-Site tRNA Binding in the Presence of a Downstream mRNA Stem Loop at the Entrance Channel.

    Science.gov (United States)

    Zhang, Yan; Hong, Samuel; Ruangprasert, Ajchareeya; Skiniotis, Georgios; Dunham, Christine M

    2018-03-06

    Structured mRNAs positioned downstream of the ribosomal decoding center alter gene expression by slowing protein synthesis. Here, we solved the cryo-EM structure of the bacterial ribosome bound to an mRNA containing a 3' stem loop that regulates translation. Unexpectedly, the E-site tRNA adopts two distinct orientations. In the first structure, normal interactions with the 50S and 30S E site are observed. However, in the second structure, although the E-site tRNA makes normal interactions with the 50S E site, its anticodon stem loop moves ∼54 Å away from the 30S E site to interact with the 30S head domain and 50S uL5. This position of the E-site tRNA causes the uL1 stalk to adopt a more open conformation that likely represents an intermediate state during E-site tRNA dissociation. These results suggest that structured mRNAs at the entrance channel restrict 30S subunit movement required during translation to slow E-site tRNA dissociation. Copyright © 2018 Elsevier Ltd. All rights reserved.

  7. Osmotic mechanism of the loop extrusion process

    Science.gov (United States)

    Yamamoto, Tetsuya; Schiessel, Helmut

    2017-09-01

    The loop extrusion theory assumes that protein factors, such as cohesin rings, act as molecular motors that extrude chromatin loops. However, recent single molecule experiments have shown that cohesin does not show motor activity. To predict the physical mechanism involved in loop extrusion, we here theoretically analyze the dynamics of cohesin rings on a loop, where a cohesin loader is in the middle and unloaders at the ends. Cohesin monomers bind to the loader rather frequently and cohesin dimers bind to this site only occasionally. Our theory predicts that a cohesin dimer extrudes loops by the osmotic pressure of cohesin monomers on the chromatin fiber between the two connected rings. With this mechanism, the frequency of the interactions between chromatin segments depends on the loading and unloading rates of dimers at the corresponding sites.

  8. Current control loop of 3-phase grid-connected inverter

    International Nuclear Information System (INIS)

    Jabbar, A F; Mansor, M

    2013-01-01

    This paper presents a comparative study of current control loop in 3-phase inverter which is used to control the active and reactive output power. Generally, current control loop, power control loop and phase lock-loop are the conventional parameters that can be found in an inverter system controlled by the conventional linear control type, for instance proportional (P), integral (I) and derivative (D). If the grid remains stable throughout the day, PID control can be use. However variation of magnitude, frequency, voltage dips, transient, and other related power quality issues occur in a 3-phase grid often affects the control loop. This paper aims to provide an overall review on the available current control techniques used in grid connected system.

  9. A conserved mechanism of autoinhibition for the AMPK kinase domain: ATP-binding site and catalytic loop refolding as a means of regulation

    International Nuclear Information System (INIS)

    Littler, Dene R.; Walker, John R.; Davis, Tara; Wybenga-Groot, Leanne E.; Finerty, Patrick J. Jr; Newman, Elena; Mackenzie, Farell; Dhe-Paganon, Sirano

    2010-01-01

    A 1.9 Å resolution crystal structure of the isolated kinase domain from the α2 subunit of human AMPK, the first from a multicellular organism, is presented. The AMP-activated protein kinase (AMPK) is a highly conserved trimeric protein complex that is responsible for energy homeostasis in eukaryotic cells. Here, a 1.9 Å resolution crystal structure of the isolated kinase domain from the α2 subunit of human AMPK, the first from a multicellular organism, is presented. This human form adopts a catalytically inactive state with distorted ATP-binding and substrate-binding sites. The ATP site is affected by changes in the base of the activation loop, which has moved into an inhibited DFG-out conformation. The substrate-binding site is disturbed by changes within the AMPKα2 catalytic loop that further distort the enzyme from a catalytically active form. Similar structural rearrangements have been observed in a yeast AMPK homologue in response to the binding of its auto-inhibitory domain; restructuring of the kinase catalytic loop is therefore a conserved feature of the AMPK protein family and is likely to represent an inhibitory mechanism that is utilized during function

  10. The determination and analysis of site-specific rates of mitochondrial reactive oxygen species production

    DEFF Research Database (Denmark)

    Quinlan, Casey L; Perevoschikova, Irina V; Goncalves, Renata L S

    2013-01-01

    Mitochondrial reactive oxygen species (ROS) are widely implicated in physiological and pathological pathways. We propose that it is critical to understand the specific sites of mitochondrial ROS production and their mechanisms of action. Mitochondria possess at least eight distinct sites of ROS...... production in the electron transport chain and matrix compartment. In this chapter, we describe the nature of the mitochondrial ROS-producing machinery and the relative capacities of each site. We provide detailed methods for the measurement of H2O2 release and the conditions under which maximal rates from...

  11. The kissing-loop motif is a preferred site of 5' leader recombination during replication of SL3-3 murine leukemia viruses in mice

    DEFF Research Database (Denmark)

    Lund, Anders Henrik; Mikkelsen, J G; Schmidt, J

    1999-01-01

    , and the upstream part of the 5' untranslated region, enabled us to map recombination sites, guided by distinct scattered nucleotide differences. In 30 of 44 analyzed sequences, recombination was mapped to a 33-nucleotide similarity window coinciding with the kissing-loop stem-loop motif implicated in dimerization...... of the diploid genome. Interestingly, the recombination pattern preference found in replication-competent viruses from T-cell tumors is very similar to the pattern previously reported for retroviral vectors in cell culture experiments. The data therefore sustain the hypothesis that the kissing loop, presumably...

  12. Loop-Loop Interactions Regulate KaiA-Stimulated KaiC Phosphorylation in the Cyanobacterial KaiABC Circadian Clock

    Energy Technology Data Exchange (ETDEWEB)

    Egli, Martin [Vanderbilt Univ., Nashville, TN (United States); Pattanayek, Rekha [Vanderbilt Univ., Nashville, TN (United States); Sheehan, Jonathan H. [Vanderbilt Univ., Nashville, TN (United States); Xu, Yao [Vanderbilt Univ., Nashville, TN (United States); Mori, Tetsuya [Vanderbilt Univ., Nashville, TN (United States); Smith, Jarrod A. [Vanderbilt Univ., Nashville, TN (United States); Johnson, Carl H. [Vanderbilt Univ., Nashville, TN (United States)

    2013-01-25

    We found that the Synechococcus elongatus KaiA, KaiB, and KaiC proteins in the presence of ATP generate a post-translational oscillator that runs in a temperature-compensated manner with a period of 24 h. KaiA dimer stimulates phosphorylation of KaiC hexamer at two sites per subunit, T432 and S431, and KaiB dimers antagonize KaiA action and induce KaiC subunit exchange. Neither the mechanism of KaiA-stimulated KaiC phosphorylation nor that of KaiB-mediated KaiC dephosphorylation is understood in detail at present. We demonstrate here that the A422V KaiC mutant sheds light on the former mechanism. It was previously reported that A422V is less sensitive to dark pulse-induced phase resetting and has a reduced amplitude of the KaiC phosphorylation rhythm in vivo. A422 maps to a loop (422-loop) that continues toward the phosphorylation sites. By pulling on the C-terminal peptide of KaiC (A-loop), KaiA removes restraints from the adjacent 422-loop whose increased flexibility indirectly promotes kinase activity. We found in the crystal structure that A422V KaiC lacks phosphorylation at S431 and exhibits a subtle, local conformational change relative to wild-type KaiC. Molecular dynamics simulations indicate higher mobility of the 422-loop in the absence of the A-loop and mobility differences in other areas associated with phosphorylation activity between wild-type and mutant KaiCs. Finally, the A-loop–422-loop relay that informs KaiC phosphorylation sites of KaiA dimer binding propagates to loops from neighboring KaiC subunits, thus providing support for a concerted allosteric mechanism of phosphorylation.

  13. Half-of-the-Sites Reactivity of the Castor Δ9-18:0-Acyl Carrier Protein Desaturase.

    Science.gov (United States)

    Liu, Qin; Chai, Jin; Moche, Martin; Guy, Jodie; Lindqvist, Ylva; Shanklin, John

    2015-09-01

    Fatty acid desaturases regulate the unsaturation status of cellular lipids. They comprise two distinct evolutionary lineages, a soluble class found in the plastids of higher plants and an integral membrane class found in plants, yeast (Saccharomyces cerevisiae), animals, and bacteria. Both classes exhibit a dimeric quaternary structure. Here, we test the functional significance of dimeric organization of the soluble castor Δ9-18:0-acyl carrier protein desaturase, specifically, the hypothesis that the enzyme uses an alternating subunit half-of-the-sites reactivity mechanism whereby substrate binding to one subunit is coordinated with product release from the other subunit. Using a fluorescence resonance energy transfer assay, we demonstrated that dimers stably associate at concentrations typical of desaturase assays. An active site mutant T104K/S202E, designed to occlude the substrate binding cavity, was expressed, purified, and its properties validated by x-ray crystallography, size exclusion chromatography, and activity assay. Heterodimers comprising distinctly tagged wild-type and inactive mutant subunits were purified at 1:1 stoichiometry. Despite having only one-half the number of active sites, purified heterodimers exhibit equivalent activity to wild-type homodimers, consistent with half-of-the-sites reactivity. However, because multiple rounds of turnover were observed, we conclude that substrate binding to one subunit is not required to facilitate product release from the second subunit. The observed half-of-the-sites reactivity could potentially buffer desaturase activity from oxidative inactivation. That soluble desaturases require only one active subunit per dimer for full activity represents a mechanistic difference from the membrane class of desaturases such as the Δ9-acyl-CoA, Ole1p, from yeast, which requires two catalytically competent subunits for activity. © 2015 American Society of Plant Biologists. All Rights Reserved.

  14. Dynamic Performance of the ITER Reactive Power Compensation System

    International Nuclear Information System (INIS)

    Sheng Zhicai; Fu Peng; Xu Liuwei

    2011-01-01

    Dynamic performance of a reactive power compensation (RPC) system for the international thermonuclear experimental reactor (ITER) power supply is presented. Static var compensators (SVCs) are adopted to mitigate voltage fluctuation and reduce the reactive power down to a level acceptable for the French/European 400 kV grid. A voltage feedback and load power feedforward controller for SVC is proposed, with the feedforward loop intended to guarantee short response time and the feedback loop ensuring good dynamics and steady characteristics of SVC. A mean filter was chosen to measure the control signals to improve the dynamic response. The dynamic performance of the SVC is verified by simulations using PSCAD/EMTDC codes.

  15. Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops.

    Science.gov (United States)

    Phan, Andy; Mailey, Katherine; Saeki, Jessica; Gu, Xiaobo; Schroeder, Susan J

    2017-05-01

    Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased toward small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with >6 nucleotides (nt) that occur frequently in viral RNA. This article presents new thermodynamic data for 40 pyrimidine loops, many of which can form UU or protonated CC base pairs. Uracil and protonated cytosine base pairs stabilize asymmetric internal loops. Accurate prediction rules are presented that account for all thermodynamic measurements of RNA asymmetric internal loops. New loop initiation terms for loops with >6 nt are presented that do not follow previous assumptions that increasing asymmetry destabilizes loops. Since the last 2004 update, 126 new loops with asymmetry or sizes greater than 2 × 2 have been measured. These new measurements significantly deepen and diversify the thermodynamic database for RNA. These results will help better predict internal loops that are larger, pyrimidine-rich, and occur within viral structures such as internal ribosome entry sites. © 2017 Phan et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  16. Characterization of Site for Installing Open Loop Ground Source Heat Pump System

    Science.gov (United States)

    Yun, S. W.; Park, Y.; Lee, J. Y.; Yi, M. J.; Cha, J. H.

    2014-12-01

    This study was conducted to understand hydrogeological properties of site where open loop ground source heat pump system will be installed and operated. Groundwater level and water temperature were hourly measured at the well developed for usage of open loop ground source heat pump system from 11 October 2013 to 8 January 2014. Groundwater was sampled in January and August 2013 and its chemical and isotopic compositions were analyzed. The bedrock of study area is the Jurassic granodiorite that mainly consists of quartz (27.9 to 46.8%), plagioclase (26.0 to 45.5%), and alkali feldspar (9.5 to 18.7%). The groundwater level ranged from 68.30 to 68.94 m (above mean sea level). Recharge rate was estimated using modified watertable fluctuation method and the recharge ratios was 9.1%. The water temperature ranged from 14.8 to 15.0oC. The vertical Increase rates of water temperature were 1.91 to 1.94/100 m. The water temperature showed the significant seasonal variation above 50 m depth, but had constant value below 50 m depth. Therefore, heat energy of the groundwater can be used securely in open loop ground source heat pump system. Electrical conductivity ranged from 120 to 320 µS/cm in dry season and from 133 to 310 µS/cm in wet season. The electrical conductivity gradually decreased with depth. In particular, electrical conductivity in approximately 30 m depth decreased dramatically (287 to 249 µS/cm) in wet season. The groundwater was Ca-HCO3 type. The concentrations of dissolved components did not show the vertically significant variations from 0 to 250 m depth. The δ18O and δD ranged from -9.5 to -9.4‰ and from -69 to -68‰. This work is supported by the New and Renewable Energy of the Korea Institute of Energy Technology Evaluation and Planning (KETEP) grant funded by the Korea government Ministry of Knowledge Economy (No.20123040110010).

  17. Identification of critical residues in loop E in the 5-HT3ASR binding site

    Directory of Open Access Journals (Sweden)

    Muthalagi Mani

    2002-06-01

    Full Text Available Abstract Background The serotonin type 3 receptor (5-HT3R is a member of a superfamily of ligand gated ion channels. All members of this family share a large degree of sequence homology and presumably significant structural similarity. A large number of studies have explored the structure-function relationships of members of this family, particularly the nicotinic and GABA receptors. This information can be utilized to gain additional insights into specific structural and functional features of other receptors in this family. Results Thirteen amino acids in the mouse 5-HT3ASR that correspond to the putative E binding loop of the nicotinic α7 receptor were chosen for mutagenesis. Due to the presence of a highly conserved glycine in this region, it has been suggested that this binding loop is comprised of a hairpin turn and may form a portion of the ligand-binding site in this ion channel family. Mutation of the conserved glycine (G147 to alanine eliminated binding of the 5-HT3R antagonist [3H]granisetron. Three tyrosine residues (Y140, Y142 and Y152 also significantly altered the binding of 5-HT3R ligands. Mutations in neighboring residues had little or no effect on binding of these ligands to the 5-HT3ASR. Conclusion Our data supports a role for the putative E-loop region of the 5-HT3R in the binding of 5-HT, mCPBG, d-tc and lerisetron. 5-HT and mCPBG interact with Y142, d-tc with Y140 and lerisetron with both Y142 and Y152. Our data also provides support for the hypothesis that this region of the receptor is present in a loop structure.

  18. Remodeling of the AB site of rat parvalbumin and oncomodulin into a canonical EF-hand

    DEFF Research Database (Denmark)

    Cox, J A; Durussel, I; Scott, D J

    1999-01-01

    -residue canonical loop. To create an optical conformational probe we also expressed the homologs with a F102W replacement. Unexpectedly, in none of the proteins did the mutation reactivate the AB site. The AB-remodeled parvalbumins bind two Ca2+ ions with strong positive cooperativity (nH = 2......Parvalbumin (PV) and the homologous protein oncomodulin (OM) contain three EF-hand motifs, but the first site (AB) cannot bind Ca2+. Here we aimed to recreate the putative ancestral proteins [D19-28E]PV and [D19-28E]OM by replacing the 10-residue-long nonfunctional loop in the AB site by a 12...... conformations. The AB-remodeled oncomodulins also bind two Ca2+ with [Ca2+]0.5 = 43 microM and nH = 1.45. Mg2+ does not affect Ca2+ binding. Again the Ca2+ forms display two-thirds of the alpha-helical content in the wild-type, while their core is still strongly hydrophobic as monitored by Trp and Tyr...

  19. Concentration and length dependence of DNA looping in transcriptional regulation.

    Directory of Open Access Journals (Sweden)

    Lin Han

    2009-05-01

    Full Text Available In many cases, transcriptional regulation involves the binding of transcription factors at sites on the DNA that are not immediately adjacent to the promoter of interest. This action at a distance is often mediated by the formation of DNA loops: Binding at two or more sites on the DNA results in the formation of a loop, which can bring the transcription factor into the immediate neighborhood of the relevant promoter. These processes are important in settings ranging from the historic bacterial examples (bacterial metabolism and the lytic-lysogeny decision in bacteriophage, to the modern concept of gene regulation to regulatory processes central to pattern formation during development of multicellular organisms. Though there have been a variety of insights into the combinatorial aspects of transcriptional control, the mechanism of DNA looping as an agent of combinatorial control in both prokaryotes and eukaryotes remains unclear. We use single-molecule techniques to dissect DNA looping in the lac operon. In particular, we measure the propensity for DNA looping by the Lac repressor as a function of the concentration of repressor protein and as a function of the distance between repressor binding sites. As with earlier single-molecule studies, we find (at least two distinct looped states and demonstrate that the presence of these two states depends both upon the concentration of repressor protein and the distance between the two repressor binding sites. We find that loops form even at interoperator spacings considerably shorter than the DNA persistence length, without the intervention of any other proteins to prebend the DNA. The concentration measurements also permit us to use a simple statistical mechanical model of DNA loop formation to determine the free energy of DNA looping, or equivalently, the for looping.

  20. Engineered, highly reactive substrates of microbial transglutaminase enable protein labeling within various secondary structure elements.

    Science.gov (United States)

    Rachel, Natalie M; Quaglia, Daniela; Lévesque, Éric; Charette, André B; Pelletier, Joelle N

    2017-11-01

    Microbial transglutaminase (MTG) is a practical tool to enzymatically form isopeptide bonds between peptide or protein substrates. This natural approach to crosslinking the side-chains of reactive glutamine and lysine residues is solidly rooted in food and textile processing. More recently, MTG's tolerance for various primary amines in lieu of lysine have revealed its potential for site-specific protein labeling with aminated compounds, including fluorophores. Importantly, MTG can label glutamines at accessible positions in the body of a target protein, setting it apart from most labeling enzymes that react exclusively at protein termini. To expand its applicability as a labeling tool, we engineered the B1 domain of Protein G (GB1) to probe the selectivity and enhance the reactivity of MTG toward its glutamine substrate. We built a GB1 library where each variant contained a single glutamine at positions covering all secondary structure elements. The most reactive and selective variants displayed a >100-fold increase in incorporation of a recently developed aminated benzo[a]imidazo[2,1,5-cd]indolizine-type fluorophore, relative to native GB1. None of the variants were destabilized. Our results demonstrate that MTG can react readily with glutamines in α-helical, β-sheet, and unstructured loop elements and does not favor one type of secondary structure. Introducing point mutations within MTG's active site further increased reactivity toward the most reactive substrate variant, I6Q-GB1, enhancing MTG's capacity to fluorescently label an engineered, highly reactive glutamine substrate. This work demonstrates that MTG-reactive glutamines can be readily introduced into a protein domain for fluorescent labeling. © 2017 The Protein Society.

  1. Ab-Initio Modelling Of Surface Site Reactivity And Fluid Transport In Clay Minerals Case Study: Pyrophyllite

    International Nuclear Information System (INIS)

    Churakov, S.V.

    2005-01-01

    Pyrophyllite, Al 2 [Si 4 O 10 ](OH) 2 , is the simplest structural prototype for 2:1 dioctahedral phyllosilicate. Because the net electric charge in pyrophyllite is zero, it is the best candidate for investigating the non electrostatic contribution to sorption and transport phenomena in clays. Using ab-initio simulations, we have investigated the reactivity and structure of the water-solid interface on the basal plane and edge sites of pyrophyllite. The calculations predict slightly hydrophobic behaviour of the basal plane. For the high water coverage (100), (110) and (-110), lateral facets have a lower energy than for the (010), (130) and (-130) surfaces. Analysis of the surface reactivity reveals that the =Al-OH groups are most easily protonated on the (010), (130) and (-130) facets. The =Al-O-Si= sites will be protonated on the (100), (130), (110), (-110) and (-130) surfaces. The =Al-OH 2 complexes are more easily de-protonated than the =Si-OH and =Al-OH sites. A spontaneous, reversible exchange of the protons between the solution and the edge sites has been observed in ab-initio molecular dynamics simulations at 300 K. Such near-surface proton diffusion may result in a significant contribution to the diffusion coefficients measured in neutron scattering experiments. (author)

  2. Using the general-purpose reactivity indicator: challenging examples.

    Science.gov (United States)

    Anderson, James S M; Melin, Junia; Ayers, Paul W

    2016-03-01

    We elucidate the regioselectivity of nucleophilic attack on substituted benzenesulfonates, quinolines, and pyridines using a general-purpose reactivity indicator (GPRI) for electrophiles. We observe that the GPRI is most accurate when the incoming nucleophile resembles a point charge. We further observe that the GPRI often chooses reactive "dead ends" as the most reactive sites as well as sterically hindered reactive sites. This means that care must be taken to remove sites that are inherently unreactive. Generally, among sites where reactions actually occur, the GPRI identifies the sites in the molecule that lead to the kinetically favored product(s). Furthermore, the GPRI can discern which sites react with hard reagents and which sites react with soft reagents. Because it is currently impossible to use the mathematical framework of conceptual DFT to identify sterically inaccessible sites and reactive dead ends, the GPRI is primarily useful as an interpretative, not a predictive, tool.

  3. Principles of agonist recognition in Cys-loop receptors

    Directory of Open Access Journals (Sweden)

    Timothy eLynagh

    2014-04-01

    Full Text Available Cys-loop receptors are ligand-gated ion channels that are activated by a structurally diverse array of neurotransmitters, including acetylcholine, serotonin, glycine and GABA. After the term chemoreceptor emerged over 100 years ago, there was some wait until affinity labeling, molecular cloning, functional studies and X-ray crystallography experiments identified the extracellular interface of adjacent subunits as the principal site of agonist binding. The question of how subtle differences at and around agonist-binding sites of different Cys-loop receptors can accommodate transmitters as chemically diverse as glycine and serotonin has been subject to intense research over the last three decades. This review outlines the functional diversity and current structural understanding of agonist-binding sites, including those of invertebrate Cys-loop receptors. Together, this provides a framework to understand the atomic determinants involved in how these valuable therapeutic targets recognize and bind their ligands.

  4. Genome-wide identification of basic helix-loop-helix and NF-1 motifs underlying GR binding sites in male rat hippocampus

    DEFF Research Database (Denmark)

    Pooley, John R.; Flynn, Ben P.; Grøntved, Lars

    2017-01-01

    linked to structural and organizational roles, an absence of major tethering partners for GRs, and little or no evidence for binding at negative glucocorticoid response elements. A basic helix-loop-helix motif closely resembling a NeuroD1 or Olig2 binding site was found underlying a subset of GR binding......Glucocorticoids regulate hippocampal function in part by modulating gene expression through the glucocorticoid receptor (GR). GR binding is highly cell type specific, directed to accessible chromatin regions established during tissue differentiation. Distinct classes of GR binding sites...

  5. Identification of Bacillus thuringiensis Cry3Aa toxin domain II loop 1 as the binding site of Tenebrio molitor cadherin repeat CR12.

    Science.gov (United States)

    Zúñiga-Navarrete, Fernando; Gómez, Isabel; Peña, Guadalupe; Amaro, Itzel; Ortíz, Ernesto; Becerril, Baltazar; Ibarra, Jorge E; Bravo, Alejandra; Soberón, Mario

    2015-04-01

    Bacillus thuringiensis Cry toxins exert their toxic effect by specific recognition of larval midgut proteins leading to oligomerization of the toxin, membrane insertion and pore formation. The exposed domain II loop regions of Cry toxins have been shown to be involved in receptor binding. Insect cadherins have shown to be functionally involved in toxin binding facilitating toxin oligomerization. Here, we isolated a VHH (VHHA5) antibody by phage display that binds Cry3Aa loop 1 and competed with the binding of Cry3Aa to Tenebrio molitor brush border membranes. VHHA5 also competed with the binding of Cry3Aa to a cadherin fragment (CR12) that was previously shown to be involved in binding and toxicity of Cry3Aa, indicating that Cry3Aa binds CR12 through domain II loop 1. Moreover, we show that a loop 1 mutant, previously characterized to have increased toxicity to T. molitor, displayed a correlative enhanced binding affinity to T. molitor CR12 and to VHHA5. These results show that Cry3Aa domain II loop 1 is a binding site of CR12 T. molitor cadherin. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. FY1995 study of highly efficient power generation system based on chemical-looping combustion; 1995 nendo chemical loop nenshoho ni yoru kokoritsu hatsuden system no kaihatsu ni kansuru kenkyu

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-03-01

    Synthesis of highly efficient and low emission power generation plant with chemical-looping combustion using various fuels such as natural gas, coal gas and hydrogen. Development of new looping materials with suitable reactivity, regenerative ability, and avoidance of carbon deposition. To obtain the design data for demo-plant by using the current experiment high- pressure fixed bed reactor. From the viewpoint of application of the proposed power generation system with chemical-looping combustion, the following main results were obtained. 1. New looping materials: NiO/NiAl{sub 2}O{sub 4}, CoO-NiO/YSZ, and Co{sub 3}O{sub 4}/CoAl{sub 2}O{sub 4}. These materials have high reactivity, repeatability, and avoidance of carbon deposition which play important roles in application of this new combustor. 2. NO{sub x} formation can be completely avoided; both fuel NO{sub x} in reduction reactor for coal gas as fuel and thermal NO{sub x} in oxidation reactor. 3. It is identified from the experiment using fixed bed reactor with the elevated pressure that NiO/NiAl{sub 2}O{sub 4} is a suitable material for coal gas or hydrogen. These promising results have provided valuable data for industrial application. (NEDO)

  7. Half-of-the-Sites Reactivity of the Castor Δ9-18:0-Acyl Carrier Protein Desaturase1[OPEN

    Science.gov (United States)

    Liu, Qin; Chai, Jin; Moche, Martin; Guy, Jodie; Lindqvist, Ylva; Shanklin, John

    2015-01-01

    Fatty acid desaturases regulate the unsaturation status of cellular lipids. They comprise two distinct evolutionary lineages, a soluble class found in the plastids of higher plants and an integral membrane class found in plants, yeast (Saccharomyces cerevisiae), animals, and bacteria. Both classes exhibit a dimeric quaternary structure. Here, we test the functional significance of dimeric organization of the soluble castor Δ9-18:0-acyl carrier protein desaturase, specifically, the hypothesis that the enzyme uses an alternating subunit half-of-the-sites reactivity mechanism whereby substrate binding to one subunit is coordinated with product release from the other subunit. Using a fluorescence resonance energy transfer assay, we demonstrated that dimers stably associate at concentrations typical of desaturase assays. An active site mutant T104K/S202E, designed to occlude the substrate binding cavity, was expressed, purified, and its properties validated by x-ray crystallography, size exclusion chromatography, and activity assay. Heterodimers comprising distinctly tagged wild-type and inactive mutant subunits were purified at 1:1 stoichiometry. Despite having only one-half the number of active sites, purified heterodimers exhibit equivalent activity to wild-type homodimers, consistent with half-of-the-sites reactivity. However, because multiple rounds of turnover were observed, we conclude that substrate binding to one subunit is not required to facilitate product release from the second subunit. The observed half-of-the-sites reactivity could potentially buffer desaturase activity from oxidative inactivation. That soluble desaturases require only one active subunit per dimer for full activity represents a mechanistic difference from the membrane class of desaturases such as the Δ9-acyl-CoA, Ole1p, from yeast, which requires two catalytically competent subunits for activity. PMID:26224800

  8. Fabrication and processing of next-generation oxygen carrier materials for chemical looping combustion

    Energy Technology Data Exchange (ETDEWEB)

    Nadarajah, Arunan [Univ. of Toledo, OH (United States)

    2017-04-26

    Among numerous methods of controlling the global warming effect, Chemical Looping Combustion is known to be the most viable option currently. A key factor to a successful chemical looping process is the presence of highly effective oxygen carriers that enable fuel combustion by going through oxidation and reduction in the presence of air and fuel respectively. In this study, CaMnO3-δ was used as the base material and doped on the A-site (Sr or La) and B-site (Fe, Ti, Zn and Al) by 10 mol % of dopants. Solid state reaction followed by mechanical extrusion (optimized paste formula) was used as the preparation method A series of novel doped perovskite-type oxygen carrier particles (CaxLa (Or Sa)1-x Mn1-yByO3-δ (B-site = Fe, Ti, Al, or Zr)) were synthesized by the proposed extrusion formula. The produced samples were characterized with XRD, SEM, BET and TGA techniques. According to the results obtained from TGA analysis, the oxygen capacity of the samples ranged between 1.2 for CLMZ and 1.75 for CSMF. Reactivity and oxygen uncoupling behaviors of the prepared samples were also evaluated using a fluidized bed chemical looping reactor using methane as the fuel at four different temperatures (800, 850, 900, 950 °C). All of the oxygen carriers showed oxygen uncoupling behavior and they were able to capture and release oxygen. Mass-based conversion of the perovskites was calculated and temperature increase proved to increase the mass-based conversion rate in all of the samples under study. Gas yield was calculated at 950 °C as well, and results showed that CLMZ, CM and CSMF showed 100% gas yields and CLMF and CSMZ showed approximately 85% yield in fluidized bed reactor, which is a high and acceptable quantity. Based on extended reactor tests the modified calcium manganese perovskite structures (CSMF) can be a good candidate for future pilot tests.

  9. Long-Term Groundwater Monitoring Optimization, Clare Water Supply Superfund Site, Permeable Reactive Barrier and Soil Remedy Areas, Clare, Michigan

    Science.gov (United States)

    This report contains a review of the long-term groundwater monitoring network for the Permeable Reactive Barrier (PRB) and Soil Remedy Areas at the Clare Water Supply Superfund Site in Clare, Michigan.

  10. A highly tilted binding mode by a self-reactive T cell receptor results in altered engagement of peptide and MHC

    Energy Technology Data Exchange (ETDEWEB)

    Sethi, D.K.; Heroux, A.; Schubert, D. A.; Anders, A.-K.; Bonsor, D. A.; Thomas, C. P.; Sundberg, E. J.; Pyrdol, J.; Wucherpfennig, K. W.

    2011-01-17

    Self-reactive T cells that escape elimination in the thymus can cause autoimmune pathology, and it is therefore important to understand the structural mechanisms of self-antigen recognition. We report the crystal structure of a T cell receptor (TCR) from a patient with relapsing-remitting multiple sclerosis that engages its self-peptide-major histocompatibility complex (pMHC) ligand in an unusual manner. The TCR is bound in a highly tilted orientation that prevents interaction of the TCR-{alpha} chain with the MHC class II {beta} chain helix. In this structure, only a single germline-encoded TCR loop engages the MHC protein, whereas in most other TCR-pMHC structures all four germline-encoded TCR loops bind to the MHC helices. The tilted binding mode also prevents peptide contacts by the short complementarity-determining region (CDR) 3{beta} loop, and interactions that contribute to peptide side chain specificity are focused on the CDR3{alpha} loop. This structure is the first example in which only a single germline-encoded TCR loop contacts the MHC helices. Furthermore, the reduced interaction surface with the peptide may facilitate TCR cross-reactivity. The structural alterations in the trimolecular complex are distinct from previously characterized self-reactive TCRs, indicating that there are multiple unusual ways for self-reactive TCRs to bind their pMHC ligand.

  11. A Highly Tilted Binding Mode by a Self-Reactive T Cell Receptor Results in Altered Engagement of Peptide and MHC

    Energy Technology Data Exchange (ETDEWEB)

    D Sethi; D Schubert; A Anders; A Heroux; D Bonsor; C Thomas; E Sundberg; J Pyrdol; K Wucherpfennig

    2011-12-31

    Self-reactive T cells that escape elimination in the thymus can cause autoimmune pathology, and it is therefore important to understand the structural mechanisms of self-antigen recognition. We report the crystal structure of a T cell receptor (TCR) from a patient with relapsing-remitting multiple sclerosis that engages its self-peptide-major histocompatibility complex (pMHC) ligand in an unusual manner. The TCR is bound in a highly tilted orientation that prevents interaction of the TCR-{alpha} chain with the MHC class II {beta} chain helix. In this structure, only a single germline-encoded TCR loop engages the MHC protein, whereas in most other TCR-pMHC structures all four germline-encoded TCR loops bind to the MHC helices. The tilted binding mode also prevents peptide contacts by the short complementarity-determining region (CDR) 3{beta} loop, and interactions that contribute to peptide side chain specificity are focused on the CDR3{alpha} loop. This structure is the first example in which only a single germline-encoded TCR loop contacts the MHC helices. Furthermore, the reduced interaction surface with the peptide may facilitate TCR cross-reactivity. The structural alterations in the trimolecular complex are distinct from previously characterized self-reactive TCRs, indicating that there are multiple unusual ways for self-reactive TCRs to bind their pMHC ligand.

  12. Closed loop auto control system software for Miniature Neutron Source Reactors (MNSRs)

    International Nuclear Information System (INIS)

    Iqbal, Masood; Qadir, Javed

    2009-01-01

    A closed loop auto control system has been developed and implemented at the Pakistan Research Reactor-2 (PARR-2). For interfacing of the site signals with a computer, a data acquisition card was employed. The system utilizes nine signals and, on their basis, carries out continuous on-line analysis, maintaining safe operation. On-line reactivity measurement is included in this software. Also, it generates control signals for keeping the reactor at the desired power level in auto-mode round-the-clock without human intervention. In case of abnormal conditions for either power or temperature or radiation level, alarms are initiated and if their levels reach beyond prescribed safe operation regime, automatic shutdown sequence is initiated. The control system has been thoroughly tested for various postulated scenarios. The test results have been in good agreement with the expected response. (orig.)

  13. Inhibitory plant serpins with a sequence of three glutamine residues in the reactive center

    DEFF Research Database (Denmark)

    Hejgaard, Jørn

    2005-01-01

    Serpins appear to be ubiquitous in eukaryotes, except fungi, and are also present in some bacteria, archaea and viruses. Inhibitory serpins with a glutamine as the reactive-center P1 residue have been identified exclusively in a few plant species. Unique serpins with a reactive center sequence...... of three Gln residues at P3-P1 or P2-P1' were isolated from barley and wheat grain, respectively. Barley BSZ3 was an irreversible inhibitor of chymotrypsin, with a second-order association rate constant for complex formation k(a)' of the order of 10(4) M-1 s(-1) ; however, only a minor fraction...... of the serpin molecules reacted with chymotrypsin, with the majority insensitive to cleavage in the reactive center loop. Wheat WSZ3 was cleaved specifically at P8 Thr and was not an inhibitor of chymotrypsin. These reactive-center loops may have evolved conformations that are optimal as inhibitory baits...

  14. Two-loop controller for maximizing performance of a grid-connected photovoltaic - fuel cell hybrid power plant

    Science.gov (United States)

    Ro, Kyoungsoo

    The study started with the requirement that a photovoltaic (PV) power source should be integrated with other supplementary power sources whether it operates in a stand-alone or grid-connected mode. First, fuel cells for a backup of varying PV power were compared in detail with batteries and were found to have more operational benefits. Next, maximizing performance of a grid-connected PV-fuel cell hybrid system by use of a two-loop controller was discussed. One loop is a neural network controller for maximum power point tracking, which extracts maximum available solar power from PV arrays under varying conditions of insolation, temperature, and system load. A real/reactive power controller (RRPC) is the other loop. The RRPC meets the system's requirement for real and reactive powers by controlling incoming fuel to fuel cell stacks as well as switching control signals to a power conditioning subsystem. The RRPC is able to achieve more versatile control of real/reactive powers than the conventional power sources since the hybrid power plant does not contain any rotating mass. Results of time-domain simulations prove not only effectiveness of the proposed computer models of the two-loop controller, but also their applicability for use in transient stability analysis of the hybrid power plant. Finally, environmental evaluation of the proposed hybrid plant was made in terms of plant's land requirement and lifetime COsb2 emissions, and then compared with that of the conventional fossil-fuel power generating forms.

  15. Biosphere-atmosphere exchange of reactive nitrogen and greenhouse gases at the NitroEurope core flux measurement sites: Measurement strategy and first data sets

    DEFF Research Database (Denmark)

    Skiba, U.; Drewer, J.; Tang, Y.S.

    2009-01-01

    The NitroEurope project aims to improve understanding of the nitrogen (N) cycle at the continental scale and quantify the major fluxes of reactive N by a combination of reactive N measurements and modelling activities. As part of the overall measurement strategy, a network of 13 flux ‘super sites...

  16. An accurate reactive power control study in virtual flux droop control

    Science.gov (United States)

    Wang, Aimeng; Zhang, Jia

    2017-12-01

    This paper investigates the problem of reactive power sharing based on virtual flux droop method. Firstly, flux droop control method is derived, where complicated multiple feedback loops and parameter regulation are avoided. Then, the reasons for inaccurate reactive power sharing are theoretically analyzed. Further, a novel reactive power control scheme is proposed which consists of three parts: compensation control, voltage recovery control and flux droop control. Finally, the proposed reactive power control strategy is verified in a simplified microgrid model with two parallel DGs. The simulation results show that the proposed control scheme can achieve accurate reactive power sharing and zero deviation of voltage. Meanwhile, it has some advantages of simple control and excellent dynamic and static performance.

  17. LoopIng: a template-based tool for predicting the structure of protein loops.

    KAUST Repository

    Messih, Mario Abdel

    2015-08-06

    Predicting the structure of protein loops is very challenging, mainly because they are not necessarily subject to strong evolutionary pressure. This implies that, unlike the rest of the protein, standard homology modeling techniques are not very effective in modeling their structure. However, loops are often involved in protein function, hence inferring their structure is important for predicting protein structure as well as function.We describe a method, LoopIng, based on the Random Forest automated learning technique, which, given a target loop, selects a structural template for it from a database of loop candidates. Compared to the most recently available methods, LoopIng is able to achieve similar accuracy for short loops (4-10 residues) and significant enhancements for long loops (11-20 residues). The quality of the predictions is robust to errors that unavoidably affect the stem regions when these are modeled. The method returns a confidence score for the predicted template loops and has the advantage of being very fast (on average: 1 min/loop).www.biocomputing.it/loopinganna.tramontano@uniroma1.itSupplementary data are available at Bioinformatics online.

  18. Nonequilibrium Chromosome Looping via Molecular Slip Links

    Science.gov (United States)

    Brackley, C. A.; Johnson, J.; Michieletto, D.; Morozov, A. N.; Nicodemi, M.; Cook, P. R.; Marenduzzo, D.

    2017-09-01

    We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of molecules like cohesin, which, along with the CTCF protein, stabilize loops which contribute to organizing the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable nonequilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favor of convergent CTCF-mediated chromosome loops observed experimentally. We also find that the diffusive motion of multiple slip links along chromatin is rectified by an intriguing ratchet effect that arises if slip links bind to the chromatin at a preferred "loading site." This emergent collective behavior favors the extrusion of loops which are much larger than the ones formed by single slip links.

  19. Proteins mediating DNA loops effectively block transcription.

    Science.gov (United States)

    Vörös, Zsuzsanna; Yan, Yan; Kovari, Daniel T; Finzi, Laura; Dunlap, David

    2017-07-01

    Loops are ubiquitous topological elements formed when proteins simultaneously bind to two noncontiguous DNA sites. While a loop-mediating protein may regulate initiation at a promoter, the presence of the protein at the other site may be an obstacle for RNA polymerases (RNAP) transcribing a different gene. To test whether a DNA loop alters the extent to which a protein blocks transcription, the lac repressor (LacI) was used. The outcome of in vitro transcription along templates containing two LacI operators separated by 400 bp in the presence of LacI concentrations that produced both looped and unlooped molecules was visualized with scanning force microscopy (SFM). An analysis of transcription elongation complexes, moving for 60 s at an average of 10 nt/s on unlooped DNA templates, revealed that they more often surpassed LacI bound to the lower affinity O2 operator than to the highest affinity Os operator. However, this difference was abrogated in looped DNA molecules where LacI became a strong roadblock independently of the affinity of the operator. Recordings of transcription elongation complexes, using magnetic tweezers, confirmed that they halted for several minutes upon encountering a LacI bound to a single operator. The average pause lifetime is compatible with RNAP waiting for LacI dissociation, however, the LacI open conformation visualized in the SFM images also suggests that LacI could straddle RNAP to let it pass. Independently of the mechanism by which RNAP bypasses the LacI roadblock, the data indicate that an obstacle with looped topology more effectively interferes with transcription. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

  20. Observations of speciated atmospheric mercury at three sites in Nevada: Evidence for a free tropospheric source of reactive gaseous mercury

    OpenAIRE

    Weiss-Penzias, Peter; Gustin, Mae Sexauer; Lyman, Seth

    2009-01-01

    Air mercury (Hg) speciation was measured for 11 weeks (June–August 2007) at three sites simultaneously in Nevada, USA. Mean reactive gaseous Hg (RGM) concentrations were elevated at all sites relative to those reported for locations not directly influenced by known point sources. RGM concentrations at all sites displayed a regular diel pattern and were positively correlated with ozone (O3) and negatively correlated with elemental Hg (Hg0) and dew point temperature (Tdp). Superimposed on the d...

  1. The Pt site reactivity of the molecular graphs of Au6Pt isomers

    Science.gov (United States)

    Xu, Tianlv; Jenkins, Samantha; Xiao, Chen-Xia; Maza, Julio R.; Kirk, Steven R.

    2013-12-01

    Within the framework of the theory of atoms in molecules (QTAIM), in an exploratory study we propose a new measure of site reactivity equivalent to the atomic coordination number based purely on the electronic structure. It was found that the number of ring critical points (NNRCPs) positioned on the boundary of the atomic basin of the dopant (Pt) nucleus correlated very well with the relative zero point energy (ZPE) corrected energies. A weaker condition (i.e. than the number of associated bond paths) for the association of the dopant Pt nucleus with the Au6Pt molecular graph is found for NNRCP = 0.

  2. Principles of agonist recognition in Cys-loop receptors

    DEFF Research Database (Denmark)

    Lynagh, Timothy Peter; Pless, Stephan Alexander

    2014-01-01

    , functional studies, and X-ray crystallography experiments identified the extracellular interface of adjacent subunits as the principal site of agonist binding. The question of how subtle differences at and around agonist-binding sites of different Cys-loop receptors can accommodate transmitters as chemically...

  3. A revision of sensitivity analysis for small reactivity effects in ZPRs

    International Nuclear Information System (INIS)

    Ros, Paul; Blaise, Patrick; Gruel, Adrien; Leconte, Pierre

    2017-01-01

    Sensitivity analysis appears to be an important element for nuclear data improvement experiments. Indeed, it brings significant information on the contribution of the isotopes involved in the measurements performed in Zero Power Reactors (ZPRs), particularly oscillation measurements like in MINERVE, and its successor ZEPHYR (Zero power Experimental PHYsics Reactor), currently being designed at CEA. Oscillation measurements consist in oscillating a small sample made of separated isotopes (or irradiated fuels) in the core center. Then, two perturbations occur: a local one corresponding to the flux modification around the sample, and a global one which corresponds to the induced variation of reactivity. This variation of reactivity is either uncontrolled (open loop) or automatically compensated by an external pilot rod (closed loop) to keep the configuration in its critical state. Representativity studies are used in order to evaluate the pertinence of an experiment configuration versus a targeted application. For oscillation experiments, sensitivity of the reactivity effects to nuclear data is needed to obtain such coefficients. The Equivalent Generalized Perturbation Theory (EGPT) method, based on an approximation of the Generalized Perturbation. Theory, is currently applied in the ERANOS code for control rod insertions and other important variations of reactivity. However, such reactivity insertions induce consequent reactivity changes and variations of the flux, whereas oscillations induce maximal reactivity effects of 10 pcm (10 10 -5 Δk/k ) and consequently very local variations of the flux surrounding the sample. Therefore, such numerical methods are not necessarily adapted to the calculation of small reactivity effect sensitivities to nuclear data. The influence of peripheral isotopes (through their cross-sections) to central measurements is evaluated thanks to the deterministic EGPT method and the Monte-Carlo technique of correlated samples. Large

  4. Reactive power control with CHP plants - A demonstration

    DEFF Research Database (Denmark)

    Nyeng, Preben; Østergaard, Jacob; Andersen, Claus A.

    2010-01-01

    power rating of 7.3 MW on two synchronous generators. A closed-loop control is implemented, that remote controls the CHP plant to achieve a certain reactive power flow in a near-by substation. The solution communicates with the grid operator’s existing SCADA system to obtain measurements from...... lines to underground cables has changed the reactive power balance, and third, the TSO has introduced restrictions in the allowed exchange of reactive power between the transmission system and distribution grids (known as the Mvar-arrangement). The demonstration includes a CHP plant with an electric......In this project the potential for ancillary services provision by distributed energy resources is investigated. Specifically, the provision of reactive power control by combined heat and power plants is examined, and the application of the new standard for DER communication systems, IEC 61850...

  5. Chemical-Looping Combustion and Gasification of Coals and Oxygen Carrier Development: A Brief Review

    Directory of Open Access Journals (Sweden)

    Ping Wang

    2015-09-01

    Full Text Available Chemical-looping technology is one of the promising CO2 capture technologies. It generates a CO2 enriched flue gas, which will greatly benefit CO2 capture, utilization or sequestration. Both chemical-looping combustion (CLC and chemical-looping gasification (CLG have the potential to be used to generate power, chemicals, and liquid fuels. Chemical-looping is an oxygen transporting process using oxygen carriers. Recently, attention has focused on solid fuels such as coal. Coal chemical-looping reactions are more complicated than gaseous fuels due to coal properties (like mineral matter and the complex reaction pathways involving solid fuels. The mineral matter/ash and sulfur in coal may affect the activity of oxygen carriers. Oxygen carriers are the key issue in chemical-looping processes. Thermogravimetric analysis (TGA has been widely used for the development of oxygen carriers (e.g., oxide reactivity. Two proposed processes for the CLC of solid fuels are in-situ Gasification Chemical-Looping Combustion (iG-CLC and Chemical-Looping with Oxygen Uncoupling (CLOU. The objectives of this review are to discuss various chemical-looping processes with coal, summarize TGA applications in oxygen carrier development, and outline the major challenges associated with coal chemical-looping in iG-CLC and CLOU.

  6. A chromate-contaminated site in southern Switzerland – Part 2: Reactive transport modeling to optimize remediation options

    International Nuclear Information System (INIS)

    Wanner, Christoph; Eggenberger, Urs; Mäder, Urs

    2012-01-01

    A 2D horizontal reactive transport model of a chromate-contaminated site near Rivera, Switzerland, was developed using the computer code CrunchFlow to evaluate site remediation strategies. Transport processes were defined according to the results of an existing hydrological model, and the definition of geochemical (reactive) processes is based on the results of a detailed mineralogical and geochemical site characterization leading to a comprehensive conceptual site model. Kinetics of naturally occurring Cr(VI) reduction by Fe(II) and natural solid organic matter is quantified by fitting measured Cr isotope ratios to a modeled 1D section along the best constrained flow line. The simulation of Cr isotope fractionation was also incorporated into the 2D model. Simulation of the measured present day Cr(VI) plume and δ 53 Cr value distribution was used for the 2D model calibration and corresponds to a situation where only monitored natural attenuation (MNA) is occurring. Other 2D model runs simulate alternate excavation scenarios. The simulations show that with an excavation of the top 2–4 m the groundwater Cr(VI) plume can be minimized, and that a deeper excavation depth only diminishes the plume if all the contaminants can be removed. A combination of an excavation of the top 2–4 m and monitoring of the ongoing natural Cr(VI) reduction is suggested as the most ecological and economical remediation strategy, even though a remaining time period with ongoing subsoil Cr(VI) contamination in the order of 1 ka is predicted.

  7. Internal mobility of reactive-site-hydrolyzed recombinant Cucurbita maxima trypsin inhibitor-V characterized by NMR spectroscopy: evidence for differential stabilization of newly formed C- and N-termini.

    Science.gov (United States)

    Liu, J; Prakash, O; Huang, Y; Wen, L; Wen, J J; Huang, J K; Krishnamoorthi, R

    1996-09-24

    The solution structure and internal dynamics of the reactive-site (Lys44-Asp45 peptide bond) hydrolyzed form of recombinant Cucurbita maxima trypsin inhibitor-V (rCMTI-V*) were characterized by the application of two-dimensional 1H-15N NMR methods to the uniformly 15N-labeled protein. The 1H-15N chemical shift correlation spectra of rCMTI-V* were assigned, and the chemical shift data were compared with those available for rCMTI-V [Liu, J., Prakash, O., Cai, M., Gong, Y., Huang, Y., Wen, L., Wen, J. J., Huang, J.-K., & Krishnamoorthi, R. (1996) Biochemistry 35, 1516-1524] and CMTI-V* [Cai, M., Gong, Y., Prakash, O., & Krishnamoorthi, R. (1995) Biochemistry 34, 12087-12094] for which three-dimensional solution structures have been determined. It was deduced that the solution structure of rCMTI-V* was almost the same as that of CMTI-V*. 15N spin-lattice and spin-spin relaxation rate constants (R1 and R2, respectively) and ¿1H¿-15N steady-state heteronuclear Overhauser effects were measured for the peptide NH units and arginine and tryptophan N epsilon H groups in rCMTI-V*, and the model-free parameters [Lipari, G., & Szabo, A. (1982) J. Am. Chem. Soc. 104, 4546-4559, 4559-4570] were computed. Most of the backbone of rCMTI-V* is found to be highly constrained (S2 = 0.85), including the N-terminal residues 3-6 (S2 = 0.77). Residues 39-44, forming the C-terminal fragment of the binding loop, exhibit increased mobility (S2 = 0.51); however, the N-terminal segment (residues 46-48) retains rigidity as in the intact form (S2 = 0.83). The S2 values, 0.78 and 0.59, respectively, of Arg50 and Arg52 side chain NHs provide evidence not only for the conservation of the Arg hydrogen-bonds with the binding loop segments but also for the difference in strength between them. This is consistent with the earlier observation made from a study of rCMTI-V at two different pHs and its R50 and R52 mutants [Cai, M., Huang, Y., Prakash, O., Wen, L., Dunkelbarger, S. P., Huang, J.-K., Liu, J

  8. Markets in real electric networks require reactive prices

    International Nuclear Information System (INIS)

    Hogan, W.W.

    1996-01-01

    Extending earlier seminal work, the author finds that locational spot price differences in an electric network provide the natural measure of the appropriate internodal transport charge. However, the problem of loop flow requires different economic intuition for interpreting the implications of spot pricing. The Direct Current model, which is the usual approximation for estimating spot prices, ignores reactive power effects; this approximation is best when thermal constraints create network congestion. However, when voltage constraints are problematic, the DC Load model is insufficient; a full AC Model is required to determine both real and reactive spot prices. 16 figs., 3 tabs., 22 refs

  9. A Hybrid Estimator for Active/Reactive Power Control of Single-Phase Distributed Generation Systems with Energy Storage

    DEFF Research Database (Denmark)

    Pahlevani, Majid; Eren, Suzan; Guerrero, Josep M.

    2016-01-01

    This paper presents a new active/reactive power closed-loop control system for a hybrid renewable energy generation system used for single-phase residential/commercial applications. The proposed active/reactive control method includes a hybrid estimator, which is able to quickly and accurately es...

  10. Role of Loop-Clamping Side Chains in Catalysis by Triosephosphate Isomerase.

    Science.gov (United States)

    Zhai, Xiang; Amyes, Tina L; Richard, John P

    2015-12-09

    The side chains of Y208 and S211 from loop 7 of triosephosphate isomerase (TIM) form hydrogen bonds to backbone amides and carbonyls from loop 6 to stabilize the caged enzyme-substrate complex. The effect of seven mutations [Y208T, Y208S, Y208A, Y208F, S211G, S211A, Y208T/S211G] on the kinetic parameters for TIM catalyzed reactions of the whole substrates dihydroxyacetone phosphate and d-glyceraldehyde 3-phosphate [(k(cat)/K(m))(GAP) and (k(cat)/K(m))DHAP] and of the substrate pieces glycolaldehyde and phosphite dianion (k(cat)/K(HPi)K(GA)) are reported. The linear logarithmic correlation between these kinetic parameters, with slope of 1.04 ± 0.03, shows that most mutations of TIM result in an identical change in the activation barriers for the catalyzed reactions of whole substrate and substrate pieces, so that the transition states for these reactions are stabilized by similar interactions with the protein catalyst. The second linear logarithmic correlation [slope = 0.53 ± 0.16] between k(cat) for isomerization of GAP and K(d)(⧧) for phosphite dianion binding to the transition state for wildtype and many mutant TIM-catalyzed reactions of substrate pieces shows that ca. 50% of the wildtype TIM dianion binding energy, eliminated by these mutations, is expressed at the wildtype Michaelis complex, and ca. 50% is only expressed at the wildtype transition state. Negative deviations from this correlation are observed when the mutation results in a decrease in enzyme reactivity at the catalytic site. The main effect of Y208T, Y208S, and Y208A mutations is to cause a reduction in the total intrinsic dianion binding energy, but the effect of Y208F extends to the catalytic site.

  11. High-temperature helium-loop facility

    International Nuclear Information System (INIS)

    Tokarz, R.D.

    1981-09-01

    The high-temperature helium loop is a facility for materials testing in ultrapure helium gas at high temperatures. The closed loop system is capable of recirculating high-purity helium or helium with controlled impurities. The gas loop maximum operating conditions are as follows: 300 psi pressure, 500 lb/h flow rate, and 2100 0 F temperature. The two test sections can accept samples up to 3.5 in. diameter and 5 ft long. The gas loop is fully instrumented to continuously monitor all parameters of loop operation as well as helium impurities. The loop is fully automated to operate continuously and requires only a daily servicing by a qualified operator to replenish recorder charts and helium makeup gas. Because of its versatility and high degree of parameter control, the helium loop is applicable to many types of materials research. This report describes the test apparatus, operating parameters, peripheral systems, and instrumentation system. The experimental capabilities and test conand presents the results that have been obtained. The study has been conducted using a four-phase approach. The first phase develops the solution to the steady-state radon-diffusion equation in one-dimensieered barriers; disposal charge analysis; analysis of spent fuel policy implementation; spent f water. Field measurements and observations are reported for each site. Analytical data and field measurements are presented in tables and maps. Uranium concentrations in the sediments which were above detection limits ranged from 0.10 t 51.2 ppM. The mean of the logarithms of the uranium concentrations was 0.53. A group of high uranium concentrations occurs near the junctions of quadrangles AB, AC, BB, a 200 mK. In case 2), x-ray studies of isotopic phase separation in 3 He-- 4 He bcc solids were carried out by B. A. Fraass

  12. Estimation of dynamic reactivity using an H∞ optimal filter with a nonlinear term

    International Nuclear Information System (INIS)

    Suzuki, Katsuo; Watanabe, Koiti

    1996-01-01

    A method of nonlinear filtering is applied to the problem of estimating the dynamic reactivity of a nonlinear reactor system. The nonlinear filtering algorithm developed is a simple modification of a linear H ∞ optimal filter with a nonlinear feedback loop added. The linear filter is designed on the basis of a linearized dynamical system model that consists of linearized point reactor kinetic equations and a reactivity state equation driven by a fictitious signal. The latter is artificially introduced to deal with the reactivity as a state variable. The results of the computer simulation show that the nonlinear filtering algorithm can be applied to estimate the dynamic reactivity of the nonlinear reactor system, even under relatively large reactivity disturbances

  13. Loop Transfer Matrix and Loop Quantum Mechanics

    International Nuclear Information System (INIS)

    Savvidy, George K.

    2000-01-01

    The gonihedric model of random surfaces on a 3d Euclidean lattice has equivalent representation in terms of transfer matrix K(Q i ,Q f ), which describes the propagation of loops Q. We extend the previous construction of the loop transfer matrix to the case of nonzero self-intersection coupling constant κ. We introduce the loop generalization of Fourier transformation which allows to diagonalize transfer matrices, that depend on symmetric difference of loops only and express all eigenvalues of 3d loop transfer matrix through the correlation functions of the corresponding 2d statistical system. The loop Fourier transformation allows to carry out the analogy with quantum mechanics of point particles, to introduce conjugate loop momentum P and to define loop quantum mechanics. We also consider transfer matrix on 4d lattice which describes propagation of memebranes. This transfer matrix can also be diagonalized by using the generalized Fourier transformation, and all its eigenvalues are equal to the correlation functions of the corresponding 3d statistical system. In particular the free energy of the 4d membrane system is equal to the free energy of 3d gonihedric system of loops and is equal to the free energy of 2d Ising model. (author)

  14. A study of temperature coefficients of reactivity for a Savannah River Site tritium-producing charge

    International Nuclear Information System (INIS)

    George, D.L.; Frost, R.L.

    1991-01-01

    Temperature coefficients of reactivity have been calculated for the Mark 22 assembly in the K-14 charge at the Savannah River Site. Temperature coefficients are the most important reactivity feedback mechanism in SRS reactors; they are used in all safety analyses performed in support of the Safety Analysis Report, and in operations to predict reactivity changes with control rod moves. The effects of the radial location of the assembly in the reactor, isotope depletion, and thermal expansion of the metal components on the temperature coefficients have also been investigated. With the exception of the dead space coefficient, all of the regional temperature coefficients were found to be negative or zero. All of the temperature coefficients become more negative with isotopic depletion over the fuel cycle. Coefficients also become more negative with increasing radial distance of the assembly from the center of the core; this is proven from first principles and confirmed by calculations. It was found that axial and radial thermal expansion effects on the metal fuel and target tubes counteract one another, indicating these effects do not need to be considered in future temperature coefficient calculations for the Mark 22 assembly. The moderator coefficient was found to be nonlinear with temperature; thus, the values derived for accidents involving increases in moderator temperature are significantly different than those for decreases in moderator temperature, although the moderator coefficient is always negative

  15. Programme of CABRI start-up measurements with the Zircaloy loop

    International Nuclear Information System (INIS)

    Kussmaul, G.; Rongier, P.

    1981-06-01

    After installation and operational tests of the CABRI Zircaloy loop, a start-up test programme will be carried out to determine the new coupling value between the driver core and the test pin and the reactivity dependent driver core energy release for transients from different power levels and modified injection rates. The purpose of the tests and the test programme itself are described in the report

  16. Evaluation by the Double Loop Electrochemical Potentiokinetic Reactivation Test of Aged Ferritic Stainless Steel Intergranular Corrosion Susceptibility

    Science.gov (United States)

    Sidhom, H.; Amadou, T.; Braham, C.

    2010-12-01

    An experimental design method was used to determine the effect of factors that significantly affect the response of the double loop-electrochemical potentiokinetic reactivation (DL-EPR) test in controlling the susceptibility to intergranular corrosion (IGC) of UNS S43000 (AISI 430) ferritic stainless steel. The test response is expressed in terms of the reactivation/activation current ratio ( I r / I a pct). Test results analysed by the analysis of variance (ANOVA) method show that the molarity of the H2SO4 electrolyte and the potential scanning rate have a more significant effect on the DL-EPR test response than the temperature and the depassivator agent concentration. On the basis of these results, a study was conducted in order to determine the optimal operating conditions of the test as a nondestructive technique for evaluating IGC resistance of ferritic stainless steel components. Three different heat treatments are considered in this study: solution annealing (nonsensitized), aging during 3 hours at 773 K (500 °C) (slightly sensitized), and aging during 2 hours at 873 K (600 °C) (highly sensitized). The aim is to find the operating conditions that simultaneously ensure the selectivity of the attack (intergranular and chromium depleted zone) and are able to detect the effect of low dechromization. It is found that a potential scanning rate of 2.5 mV/s in an electrolyte composed of H2SO4 3 M solution without depassivator, at a temperature around 293 K (20 °C), is the optimal operating condition for the DL-EPR test. Using this condition, it is possible to assess the degree of sensitization (DOS) to the IGC of products manufactured in ferritic stainless steels rapidly, reliably, and quantitatively. A time-temperature-start of sensitization (TTS) diagram for the UNS S43000 (France Inox, Villepinte, France) stainless steel was obtained with acceptable accuracy by this method when the IGC sensitization criterion was set to I r / I a > 1 pct. This diagram is in

  17. Droop Control with an Adjustable Complex Virtual Impedance Loop based on Cloud Model Theory

    DEFF Research Database (Denmark)

    Li, Yan; Shuai, Zhikang; Xu, Qinming

    2016-01-01

    Droop control framework with an adjustable virtual impedance loop is proposed in this paper, which is based on the cloud model theory. The proposed virtual impedance loop includes two terms: a negative virtual resistor and an adjustable virtual inductance. The negative virtual resistor term...... sometimes. The cloud model theory is applied to get online the changing line impedance value, which relies on the relevance of the reactive power responding the changing line impedance. The verification of the proposed control strategy is done according to the simulation in a low voltage microgrid in Matlab....

  18. Natural abundance 15N NMR assignments delineate structural differences between intact and reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III.

    Science.gov (United States)

    Krishnamoorthi, R; Nemmers, S; Tobias, B

    1992-06-15

    15N NMR assignments were made to the backbone amide nitrogen atoms at natural isotopic abundance of intact and reactive-site (Arg5-Ile6) hydrolyzed Cucurbita maxima trypsin inhibitor III (CMTI-III and CMTI-III*, respectively) by means of 2D proton-detected heteronuclear single bond chemical shift correlation (HSBC) spectroscopy, utilizing the previously made sequence-specific 1H NMR assignments (Krishnamoorthi et al. (1992) Biochemistry 31, 898-904). Comparison of the 15N chemical shifts of the two forms of the inhibitor molecule revealed significant changes not only for residues located near the reactive-site region, but also for those distantly located. Residues Cys3, Arg5, Leu7, Met8, Cys10, Cys16, Glu19, His25, Tyr27, Cys28 and Gly29 showed significant chemical shift changes ranging from 0.3 to 6.1 ppm, thus indicating structural perturbations that were transmitted throughout the molecule. These findings confirm the earlier conclusions based on 1H NMR investigations.

  19. Amino-acid composition after loop deletion drives domain swapping.

    Science.gov (United States)

    Nandwani, Neha; Surana, Parag; Udgaonkar, Jayant B; Das, Ranabir; Gosavi, Shachi

    2017-10-01

    Rational engineering of a protein to enable domain swapping requires an understanding of the sequence, structural and energetic factors that favor the domain-swapped oligomer over the monomer. While it is known that the deletion of loops between β-strands can promote domain swapping, the spliced sequence at the position of the loop deletion is thought to have a minimal role to play in such domain swapping. Here, two loop-deletion mutants of the non-domain-swapping protein monellin, frame-shifted by a single residue, were designed. Although the spliced sequence in the two mutants differed by only one residue at the site of the deletion, only one of them (YEIKG) promoted domain swapping. The mutant containing the spliced sequence YENKG was entirely monomeric. This new understanding that the domain swapping propensity after loop deletion may depend critically on the chemical composition of the shortened loop will facilitate the rational design of domain swapping. © 2017 The Protein Society.

  20. Loop kinematics

    International Nuclear Information System (INIS)

    Migdal, A.A.

    1982-01-01

    Basic operators acting in the loop space are introduced. The topology of this space and properties of the Stokes type loop functionals are discussed. The parametrically invariant loop calculus developed here is used in the loop dynamics

  1. Analyzing relationships between surface perturbations and local chemical reactivity of metal sites: Alkali promotion of O2 dissociation on Ag(111)

    Science.gov (United States)

    Xin, Hongliang; Linic, Suljo

    2016-06-01

    Many commercial heterogeneous catalysts are complex structures that contain metal active sites promoted by multiple additives. Developing fundamental understanding about the impact of these perturbations on the local surface reactivity is crucial for catalyst development and optimization. In this contribution, we develop a general framework for identifying underlying mechanisms that control the changes in the surface reactivity of a metal site (more specifically the adsorbate-surface interactions) upon a perturbation in the local environment. This framework allows us to interpret fairly complex interactions on metal surfaces in terms of specific, physically transparent contributions that can be evaluated independently of each other. We use Cs-promoted dissociation of O2 as an example to illustrate our approach. We concluded that the Cs adsorbate affects the outcome of the chemical reaction through a strong alkali-induced electric field interacting with the static dipole moment of the O2/Ag(111) system.

  2. Experimental study of flux depressions and anti-reactivities created by irradiation loops; Etude experimentale des depressions de flux et antireactivites creees par les dispositifs d'irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Roche, D [Commissariat a l' Energie Atomique, Grenoble (France). Centre d' Etudes Nucleaires

    1967-07-01

    Methods for fast computing of thermal flux depressions and reactivities created by irradiation-loops in natural water reactors are studied in this report. The classical methods of approximation which have been used are: diffusion theory or absorption-probability calculations for the flux-depression and perturbation theory for the anti-reactivities. Pertinent formulae are compiled together with graphs from theoretical calculations. These formulae and graphs have been checked from numerous experiments which show that the approximations used here are quite close to the actual physical situation, even when the theories are based from assumptions which cannot be verified here. (author) [French] Ce rapport propose aux experimentateurs des piles a eau legere des methodes de determination rapide des depressions de flux thermique et antireactivites creees par les dispositifs d'irradiation. Les methodes classiques d'approximation sont utilisees, a savoir: theorie de diffusion ou calcul de probabilites d'absorption pour les depressions de flux, theorie des perturbations pour les antireactivites. Un formulaire pratique, accompagne d'abaques est deduit des calculs theoriques et verifie par de nombreuses experiences qui montrent que les evaluations faites sont tres proches de la realite, meme dans le cas ou les hypotheses relatives aux theories utilisees ne sont pas respectees. (auteur)

  3. Structure of TSA2 reveals novel features of the active-site loop of peroxiredoxins

    DEFF Research Database (Denmark)

    Nielsen, Maja Holch; Kidmose, Rune Thomas; Jenner, Lasse Bohl

    2016-01-01

    Saccharomyces cerevisiae TSA2 belongs to the family of typical 2-Cys peroxiredoxins, a ubiquitously expressed family of redox-active enzymes that utilize a conserved peroxidatic cysteine to reduce peroxides. Typical 2-Cys peroxiredoxins have been shown to be involved in protection against oxidative...... stress and in hydrogen peroxide signalling. Furthermore, several 2-Cys peroxiredoxins, including S. cerevisiae TSA1 and TSA2, are able to switch to chaperone activity upon hyperoxidation of their peroxidatic cysteine. This makes the sensitivity to hyperoxidation of the peroxidatic cysteine a very....... This requires a local unfolding of the active site and the C-terminus. The balance between the fully folded and locally unfolded conformations is of key importance for the reactivity and sensitivity to hyperoxidation of the different peroxiredoxins. Here, the structure of a C48S mutant of TSA2 from S...

  4. In situ closed-loop bioremediation: Rapid closure in a northern climate

    International Nuclear Information System (INIS)

    Weymann, D.F.; Hammerbeck, L.M.

    1995-01-01

    In situ closed-loop bioremediation was employed to achieve site closure at a former railyard in Minneapolis, Minnesota. Soil and groundwater were contaminated with gasoline. The closed-loop remediation system design incorporated three downgradient groundwater recovery wells and a low-pressure pipe infiltration gallery. Aboveground treatment of recovered groundwater was provided by a fixed-film bioreactor. The total reported benzene, toluene, ethylbenzene, and xylenes (BTEX)-removal efficiency of the bioreactor ranged from 98.8% to 100%. Concentrations of BTEX components in groundwater wells were reduced by 45% to 98%. The cleanup goals set by the Minnesota Pollution Control Agency were met within the first 6 months of treatment, and the remediation system was shut down after 20 months of operation. This project further demonstrates the effectiveness of reactor-based, closed-loop in situ bioremediation at sites with favorable conditions

  5. Study of the absorbers and gaps influence on the reactor reactivity, IZ-061-0071-1961

    International Nuclear Information System (INIS)

    Martinc, R.

    1961-12-01

    It has been foreseen by the contract to study theoretically and experimentally the influence of the absorbers and gaps on the reactivity of the reactor. Within theoretical study it was planned to develop a method and find the approximation methods for calculations of these effects. Experimental part include development of equipment and performing the experiment at the RB reactor. Since it has not been possible to perform the experiment due to lack of heavy water, only the theoretical part of the task was completed with additional theoretical study of the VISA-1 experimental loop. This report includes the following annexes: influence of absorbers and gaps on the reactivity of the reactor, and calculation of flux depression in the VISA-1 loop [sr

  6. Brain network dynamics in the human articulatory loop.

    Science.gov (United States)

    Nishida, Masaaki; Korzeniewska, Anna; Crone, Nathan E; Toyoda, Goichiro; Nakai, Yasuo; Ofen, Noa; Brown, Erik C; Asano, Eishi

    2017-08-01

    The articulatory loop is a fundamental component of language function, involved in the short-term buffer of auditory information followed by its vocal reproduction. We characterized the network dynamics of the human articulatory loop, using invasive recording and stimulation. We measured high-gamma activity 70-110 Hz recorded intracranially when patients with epilepsy either only listened to, or listened to and then reproduced two successive tones by humming. We also conducted network analyses, and analyzed behavioral responses to cortical stimulation. Presentation of the initial tone elicited high-gamma augmentation bilaterally in the superior-temporal gyrus (STG) within 40ms, and in the precentral and inferior-frontal gyri (PCG and IFG) within 160ms after sound onset. During presentation of the second tone, high-gamma augmentation was reduced in STG but enhanced in IFG. The task requiring tone reproduction further enhanced high-gamma augmentation in PCG during and after sound presentation. Event-related causality (ERC) analysis revealed dominant flows within STG immediately after sound onset, followed by reciprocal interactions involving PCG and IFG. Measurement of cortico-cortical evoked-potentials (CCEPs) confirmed connectivity between distant high-gamma sites in the articulatory loop. High-frequency stimulation of precentral high-gamma sites in either hemisphere induced speech arrest, inability to control vocalization, or forced vocalization. Vocalization of tones was accompanied by high-gamma augmentation over larger extents of PCG. Bilateral PCG rapidly and directly receives feed-forward signals from STG, and may promptly initiate motor planning including sub-vocal rehearsal for short-term buffering of auditory stimuli. Enhanced high-gamma augmentation in IFG during presentation of the second tone may reflect high-order processing of the tone sequence. The articulatory loop employs sustained reciprocal propagation of neural activity across a network of

  7. Two-dimensional NMR studies of squash family inhibitors. Sequence-specific proton assignments and secondary structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III

    Energy Technology Data Exchange (ETDEWEB)

    Krisnamoorthi, R.; Yuxi Gong; Chanlan Sun Lin (Kansas State Univ., Manhattan (United States)); VanderVelde, D. (Univ. of Kansas, Lawrence (United States))

    1992-01-28

    The solution structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III (CMTI-III*) was investigated by two-dimensional proton nuclear magnetic resonance (2D NMR) spectroscopy. CMTI-III*, prepared by reacting CMTI-III with trypsin which cleaved the Arg5-Ile6 peptide bond, had the two fragments held together by a disulfide linkage. Sequence-specific {sup 1}H NMR resonance assignments were made for all the 29 amino acid residues of the protein. The secondary structure of CMTI-III*, as deduced from NOESY cross peaks and identification of slowly exchanging hydrogens, contains two turns, a 3{sub 10}-helix, and a triple-stranded {beta}-sheet. Sequential proton assignments were also made for the virgin inhibitor, CMTI-III, at pH 4.71, 30C. Comparison of backbone hydrogen chemical shifts of CMTI-III and CMTI-III* revealed significant changes for residues located far away from the reactive-site region as well as for those located near it, indicating tertiary structural changes that are transmitted through most of the 29 residues of the inhibitor protein. These chemical shift changes were relatively small compared to changes that occurred upon hydrolysis of the reactive-site peptide bond between Arg 5 and Ile6 in CMTI-III.

  8. Atmospheric photochemical reactivity and ozone production at two sites in Hong Kong: Application of a Master Chemical Mechanism-photochemical box model

    Science.gov (United States)

    Ling, Z. H.; Guo, H.; Lam, S. H. M.; Saunders, S. M.; Wang, T.

    2014-09-01

    A photochemical box model incorporating the Master Chemical Mechanism (v3.2), constrained with a full suite of measurements, was developed to investigate the photochemical reactivity of volatile organic compounds at a semirural site (Mount Tai Mo Shan (TMS)) and an urban site (Tsuen Wan (TW)) in Hong Kong. The levels of ozone (O3) and its precursors, and the magnitudes of the reactivity of O3 precursors, revealed significant differences in the photochemistry at the two sites. Simulated peak hydroperoxyl radical (HO2) mixing ratios were similar at TW and TMS (p = 0.05), while the simulated hydroxyl radical (OH) mixing ratios were much higher at TW (p TMS, but at TW, both HCHO and O3 photolyses were found to be major contributors. By contrast, radical-radical reactions governed HOx radical losses at TMS, while at TW, the OH + NO2 reaction was found to dominate in the morning and the radical-radical reactions at noon. Overall, the conversion of NO to NO2 by HO2 dictated the O3 production at the two sites, while O3 destruction was dominated by the OH + NO2 reaction at TW, and at TMS, O3 photolysis and the O3 + HO2 reaction were the major mechanisms. The longer OH chain length at TMS indicated that more O3 was produced for each radical that was generated at this site.

  9. PONDEROMOTIVE ACCELERATION IN CORONAL LOOPS

    International Nuclear Information System (INIS)

    Dahlburg, R. B.; Obenschain, K.; Laming, J. M.; Taylor, B. D.

    2016-01-01

    Ponderomotive acceleration has been asserted to be a cause of the first ionization potential (FIP) effect, the well-known enhancement in abundance by a factor of 3–4 over photospheric values of elements in the solar corona with FIP less than about 10 eV. It is shown here by means of numerical simulations that ponderomotive acceleration occurs in solar coronal loops, with the appropriate magnitude and direction, as a “by-product” of coronal heating. The numerical simulations are performed with the HYPERION code, which solves the fully compressible three-dimensional magnetohydrodynamic equations including nonlinear thermal conduction and optically thin radiation. Numerical simulations of coronal loops with an axial magnetic field from 0.005 to 0.02 T and lengths from 25,000 to 75,000 km are presented. In the simulations the footpoints of the axial loop magnetic field are convected by random, large-scale motions. There is a continuous formation and dissipation of field-aligned current sheets, which act to heat the loop. As a consequence of coronal magnetic reconnection, small-scale, high-speed jets form. The familiar vortex quadrupoles form at reconnection sites. Between the magnetic footpoints and the corona the reconnection flow merges with the boundary flow. It is in this region that the ponderomotive acceleration occurs. Mirroring the character of the coronal reconnection, the ponderomotive acceleration is also found to be intermittent.

  10. PONDEROMOTIVE ACCELERATION IN CORONAL LOOPS

    Energy Technology Data Exchange (ETDEWEB)

    Dahlburg, R. B.; Obenschain, K. [LCP and FD, Naval Research Laboratory, Washington, DC 20375 (United States); Laming, J. M. [Space Science Division, Naval Research Laboratory, Washington, DC 20375 (United States); Taylor, B. D. [AFRL Eglin AFB, Pensacola, FL 32542 (United States)

    2016-11-10

    Ponderomotive acceleration has been asserted to be a cause of the first ionization potential (FIP) effect, the well-known enhancement in abundance by a factor of 3–4 over photospheric values of elements in the solar corona with FIP less than about 10 eV. It is shown here by means of numerical simulations that ponderomotive acceleration occurs in solar coronal loops, with the appropriate magnitude and direction, as a “by-product” of coronal heating. The numerical simulations are performed with the HYPERION code, which solves the fully compressible three-dimensional magnetohydrodynamic equations including nonlinear thermal conduction and optically thin radiation. Numerical simulations of coronal loops with an axial magnetic field from 0.005 to 0.02 T and lengths from 25,000 to 75,000 km are presented. In the simulations the footpoints of the axial loop magnetic field are convected by random, large-scale motions. There is a continuous formation and dissipation of field-aligned current sheets, which act to heat the loop. As a consequence of coronal magnetic reconnection, small-scale, high-speed jets form. The familiar vortex quadrupoles form at reconnection sites. Between the magnetic footpoints and the corona the reconnection flow merges with the boundary flow. It is in this region that the ponderomotive acceleration occurs. Mirroring the character of the coronal reconnection, the ponderomotive acceleration is also found to be intermittent.

  11. Hardware-in-the-loop grid simulator system and method

    Science.gov (United States)

    Fox, John Curtiss; Collins, Edward Randolph; Rigas, Nikolaos

    2017-05-16

    A hardware-in-the-loop (HIL) electrical grid simulation system and method that combines a reactive divider with a variable frequency converter to better mimic and control expected and unexpected parameters in an electrical grid. The invention provides grid simulation in a manner to allow improved testing of variable power generators, such as wind turbines, and their operation once interconnected with an electrical grid in multiple countries. The system further comprises an improved variable fault reactance (reactive divider) capable of providing a variable fault reactance power output to control a voltage profile, therein creating an arbitrary recovery voltage. The system further comprises an improved isolation transformer designed to isolate zero-sequence current from either a primary or secondary winding in a transformer or pass the zero-sequence current from a primary to a secondary winding.

  12. Chemical Looping Combustion Reactions and Systems

    Energy Technology Data Exchange (ETDEWEB)

    Sarofim, Adel; Lighty, JoAnn; Smith, Philip; Whitty, Kevin; Eyring, Edward; Sahir, Asad; Alvarez, Milo; Hradisky, Michael; Clayton, Chris; Konya, Gabor; Baracki, Richard; Kelly, Kerry

    2014-03-01

    Chemical Looping Combustion (CLC) is one promising fuel-combustion technology, which can facilitate economic CO{sub 2} capture in coal-fired power plants. It employs the oxidation/reduction characteristics of a metal, or oxygen carrier, and its oxide, the oxidizing gas (typically air) and the fuel source may be kept separate. This topical report discusses the results of four complementary efforts: (5.1) the development of process and economic models to optimize important design considerations, such as oxygen carrier circulation rate, temperature, residence time; (5.2) the development of high-performance simulation capabilities for fluidized beds and the collection, parameter identification, and preliminary verification/uncertainty quantification; (5.3) the exploration of operating characteristics in the laboratoryscale bubbling bed reactor, with a focus on the oxygen carrier performance, including reactivity, oxygen carrying capacity, attrition resistance, resistance to deactivation, cost and availability; and (5.4) the identification of kinetic data for copper-based oxygen carriers as well as the development and analysis of supported copper oxygen carrier material. Subtask 5.1 focused on the development of kinetic expressions for the Chemical Looping with Oxygen Uncoupling (CLOU) process and validating them with reported literature data. The kinetic expressions were incorporated into a process model for determination of reactor size and oxygen carrier circulation for the CLOU process using ASPEN PLUS. An ASPEN PLUS process model was also developed using literature data for the CLC process employing an iron-based oxygen carrier, and the results of the process model have been utilized to perform a relative economic comparison. In Subtask 5.2, the investigators studied the trade-off between modeling approaches and available simulations tools. They quantified uncertainty in the high-performance computing (HPC) simulation tools for CLC bed applications. Furthermore

  13. Application of a Virtual Reactivity Feedback Control Loop in Non-Nuclear Testing of a Fast Spectrum Reactor

    International Nuclear Information System (INIS)

    Bragg-Sitton, Shannon M.; Forsbacka, Matthew

    2004-01-01

    For a compact, fast-spectrum reactor, reactivity feedback is dominated by core deformation at elevated temperature. Given the use of accurate deformation measurement techniques, it is possible to simulate nuclear feedback in non-nuclear electrically heated reactor tests. Implementation of simulated reactivity feedback in response to measured deflection is being tested at the Nasa Marshall Space Flight Center Early Flight Fission Test Facility (EFF-TF). During tests of the SAFE-100 reactor prototype, core deflection was monitored using a high resolution camera. 'Virtual' reactivity feedback was accomplished by applying the results of Monte Carlo calculations (MCNPX) to core deflection measurements; the computational analysis was used to establish the reactivity worth of various core deformations. The power delivered to the SAFE-100 prototype was then adjusted accordingly via kinetics calculations. The work presented in this paper will demonstrate virtual reactivity feedback as core power was increased from 1 kWt to 10 kWt, held approximately constant at 10 kWt, and then allowed to decrease based on the negative thermal reactivity coefficient. (authors)

  14. Two-loop polygon Wilson loops in N = 4 SYM

    International Nuclear Information System (INIS)

    Anastasiou, C.; Brandhuber, A.; Heslop, P.; Spence, B.; Travaglini, G.; Khoze, V.V.

    2009-01-01

    We compute for the first time the two-loop corrections to arbitrary n-gon lightlike Wilson loops in N = 4 supersymmetric Yang-Mills theory, using efficient numerical methods. The calculation is motivated by the remarkable agreement between the finite part of planar six-point MHV amplitudes and hexagon Wilson loops which has been observed at two loops. At n = 6 we confirm that the ABDK/BDS ansatz must be corrected by adding a remainder function, which depends only on conformally invariant ratios of kinematic variables. We numerically compute remainder functions for n = 7,8 and verify dual conformal invariance. Furthermore, we study simple and multiple collinear limits of the Wilson loop remainder functions and demonstrate that they have precisely the form required by the collinear factorisation of the corresponding two-loop n-point amplitudes. The number of distinct diagram topologies contributing to the n-gon Wilson loops does not increase with n, and there is a fixed number of 'master integrals', which we have computed. Thus we have essentially computed general polygon Wilson loops, and if the correspondence with amplitudes continues to hold, all planar n-point two-loop MHV amplitudes in the N = 4 theory.

  15. Afferent loop syndrome: Role of sonography and CT

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Dong Ho; Lim, Jae Hoon; Ko, Young Tae [Kyung Hee University Hospital, Seoul (Korea, Republic of)

    1992-03-15

    Afferent loop syndrome(ALS) is caused by obstruction of the afferent loop after subtotal gastrectomy with Billroth II gastrojejunostomy. Prompt diagnosis of ALS is important as perforation of the loop occurs. The aim of study is to ascertain the sonography and CT to diagnose ALS. We describe the radiologic findings in ten patients with ALS. The cause of ALS, established at surgery, included cancer recurrence (n=4), internal hernia (n=4), marginal ulcer (n=1), and development of cancer at the anastomosis site (n=1). Abdominal X-ray and sonography were performed in all cases, upper GI series in five cases and computed tomography in two cases. The dilated afferent loop was detected in only two cases out often patients in retrospective review of abdominal X-ray. ALS with recurrence of cancer was diagnosed in three cases by upper GI series. Of the cases that had sonography, the afferent loop was seen in the upper abdomen crossing transversely over the midline in all ten patients. The cause of ALS were predicated on the basis of the sonograms in three of the five patients. In two cases of computed tomography, the dilated afferent loop and recurrent cancer at the remnant stomach were seen.Our experience suggests that the diagnosis of afferent syndrome can be made on the basis of the typical anatomic location and shape of the dilated bowel loop in both sonography and computed tomography.

  16. GPR Imaging of Clastic Dikes at the Hanford Site, Hanford, Washington

    International Nuclear Information System (INIS)

    Clement, William P.; Murray, Christopher J.

    2007-01-01

    We use ground penetrating radar (GPR) data to help determine the spatial distribution and the subsurface geometry of clastic injection dikes at the Hanford site. This information will help to improve the understanding of the hydrological role of these ubiquitous clastic dikes at the Hanford Site. We collected 100 MHz ground penetrating radar (GPR) 3D surface reflection data at two sites, the S-16 Pond and the Army Loop Road sites, and 2D reflection data along a 6.9 km linear transect near the Army Loop Road site. The dikes are distinguished in the GPR data by a strongly attenuated zone, disruptions in the continuity of reflections, and diffractions where reflections are disrupted. In general, the data quality is better at the Army Loop Road and Traverse sites than at the S-16 Pond site, probably due to the presence of cobbles at the S-16 Pond site. A high-moisture, fine-grained unit probably causes the strong reflections at the Army Loop Road site and the Traverse survey site. The signal penetration varies between 5 to 12 m below the land surface

  17. Experimental study of flux depressions and anti-reactivities created by irradiation loops; Etude experimentale des depressions de flux et antireactivites creees par les dispositifs d'irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Roche, D. [Commissariat a l' Energie Atomique, Grenoble (France). Centre d' Etudes Nucleaires

    1967-07-01

    Methods for fast computing of thermal flux depressions and reactivities created by irradiation-loops in natural water reactors are studied in this report. The classical methods of approximation which have been used are: diffusion theory or absorption-probability calculations for the flux-depression and perturbation theory for the anti-reactivities. Pertinent formulae are compiled together with graphs from theoretical calculations. These formulae and graphs have been checked from numerous experiments which show that the approximations used here are quite close to the actual physical situation, even when the theories are based from assumptions which cannot be verified here. (author) [French] Ce rapport propose aux experimentateurs des piles a eau legere des methodes de determination rapide des depressions de flux thermique et antireactivites creees par les dispositifs d'irradiation. Les methodes classiques d'approximation sont utilisees, a savoir: theorie de diffusion ou calcul de probabilites d'absorption pour les depressions de flux, theorie des perturbations pour les antireactivites. Un formulaire pratique, accompagne d'abaques est deduit des calculs theoriques et verifie par de nombreuses experiences qui montrent que les evaluations faites sont tres proches de la realite, meme dans le cas ou les hypotheses relatives aux theories utilisees ne sont pas respectees. (auteur)

  18. Alternative loop rings

    CERN Document Server

    Goodaire, EG; Polcino Milies, C

    1996-01-01

    For the past ten years, alternative loop rings have intrigued mathematicians from a wide cross-section of modern algebra. As a consequence, the theory of alternative loop rings has grown tremendously. One of the main developments is the complete characterization of loops which have an alternative but not associative, loop ring. Furthermore, there is a very close relationship between the algebraic structures of loop rings and of group rings over 2-groups. Another major topic of research is the study of the unit loop of the integral loop ring. Here the interaction between loop rings and group ri

  19. Assessment of a Hydroxyapatite Permeable Reactive Barrier to Remediate Uranium at the Old Rifle Site Colorado

    International Nuclear Information System (INIS)

    Moore, Robert C.; Szecsody, James; Rigali, Mark J.; Vermuel, Vince; Leullen, Jon

    2016-01-01

    We have performed an initial evaluation and testing program to assess the effectiveness of a hydroxyapatite (Ca10(PO4)6(OH)2) permeable reactive barrier and source area treatment to decrease uranium mobility at the Department of Energy (DOE) former Old Rifle uranium mill processing site in Rifle, western Colorado. Uranium ore was processed at the site from the 1940s to the 1970s. The mill facilities at the site as well as the uranium mill tailings previously stored there have all been removed. Groundwater in the alluvial aquifer beneath the site still contains elevated concentrations of uranium, and is currently used for field tests to study uranium behavior in groundwater and investigate potential uranium remediation technologies. The technology investigated in this work is based on in situ formation of apatite in sediment to create a subsurface apatite PRB and also for source area treatment. The process is based on injecting a solution containing calcium citrate and sodium into the subsurface for constructing the PRB within the uranium plume. As the indigenous sediment micro-organisms biodegrade the injected citrate, the calcium is released and reacts with the phosphate to form hydroxyapatite (precipitate). This paper reports on proof-of-principle column tests with Old Rifle sediment and synthetic groundwater.

  20. Assessment of a Hydroxyapatite Permeable Reactive Barrier to Remediate Uranium at the Old Rifle Site Colorado.

    Energy Technology Data Exchange (ETDEWEB)

    Moore, Robert C.; Szecsody, James (PNNL); Rigali, Mark J.; Vermuel, Vince (PNNL); Leullen, Jon (AECOM)

    2016-02-01

    We have performed an initial evaluation and testing program to assess the effectiveness of a hydroxyapatite (Ca10(PO4)6(OH)2) permeable reactive barrier and source area treatment to decrease uranium mobility at the Department of Energy (DOE) former Old Rifle uranium mill processing site in Rifle, western Colorado. Uranium ore was processed at the site from the 1940s to the 1970s. The mill facilities at the site as well as the uranium mill tailings previously stored there have all been removed. Groundwater in the alluvial aquifer beneath the site still contains elevated concentrations of uranium, and is currently used for field tests to study uranium behavior in groundwater and investigate potential uranium remediation technologies. The technology investigated in this work is based on in situ formation of apatite in sediment to create a subsurface apatite PRB and also for source area treatment. The process is based on injecting a solution containing calcium citrate and sodium into the subsurface for constructing the PRB within the uranium plume. As the indigenous sediment micro-organisms biodegrade the injected citrate, the calcium is released and reacts with the phosphate to form hydroxyapatite (precipitate). This paper reports on proof-of-principle column tests with Old Rifle sediment and synthetic groundwater.

  1. Spatially Resolved Quantification of the Surface Reactivity of Solid Catalysts.

    Science.gov (United States)

    Huang, Bing; Xiao, Li; Lu, Juntao; Zhuang, Lin

    2016-05-17

    A new property is reported that accurately quantifies and spatially describes the chemical reactivity of solid surfaces. The core idea is to create a reactivity weight function peaking at the Fermi level, thereby determining a weighted summation of the density of states of a solid surface. When such a weight function is defined as the derivative of the Fermi-Dirac distribution function at a certain non-zero temperature, the resulting property is the finite-temperature chemical softness, termed Fermi softness (SF ), which turns out to be an accurate descriptor of the surface reactivity. The spatial image of SF maps the reactive domain of a heterogeneous surface and even portrays morphological details of the reactive sites. SF analyses reveal that the reactive zones on a Pt3 Y(111) surface are the platinum sites rather than the seemingly active yttrium sites, and the reactivity of the S-dimer edge of MoS2 is spatially anisotropic. Our finding is of fundamental and technological significance to heterogeneous catalysis and industrial processes demanding rational design of solid catalysts. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Systematic Integrated Process Design and Control of Reactive Distillation Processes Involving Multi-elements

    DEFF Research Database (Denmark)

    Mansouri, Seyed Soheil; Sales-Cruz, Mauricio; Huusom, Jakob Kjøbsted

    2016-01-01

    driving force approach. Next, through analytical, steady-state and closed-loop dynamic analysis it is verified that the control structure, disturbance rejection and energy requirement of the reactive distillation column is better than any other operation point that is not at the maximum driving force...

  3. Redoable Tie-Over Dressing Using Multiple Loop Silk Threads

    Directory of Open Access Journals (Sweden)

    Hyeon Jong Jo

    2013-05-01

    Full Text Available After skin grafting, to prevent hematoma or seroma collection at the graft site, a tie-over dressing has been commonly used. However, although the conventional tie-over dressing by suture is a useful method for securing a graft site, refixation is difficult when repeated tie-over dressing is needed. Therefore, we recommend a redoable tie-over dressing technique with multiple loops threads and connecting silk threads. After the raw surface of each of our cases was covered with a skin graft, multiple loop silk thread attached with nylon at the skin graft margin. We applied the ointment gauze and wet cotton/fluffy gauze over the skin graft, then fixed the dressing by connecting cross-counter multiple loop thread with connecting silk threads. When we opened the tie-over dressing by cutting the connecting silk threads, we repeated the tie-over dressing with the same method. The skin graft was taken successfully without hematoma or seroma collection or any other complications. In conclusion, we report a novel tie-over dressing enabling simple fixation of the dressing to maintain proper tension for wounds that require repetitive fixation. Further, with this reliable method, the skin grafts were well taken.

  4. Redoable Tie-Over Dressing Using Multiple Loop Silk Threads

    Directory of Open Access Journals (Sweden)

    Hyeon Jong Jo

    2013-05-01

    Full Text Available After skin grafting, to prevent hematoma or seroma collection at the graft site, a tie-over dressing has been commonly used. However, although the conventional tie-over dressing by suture is a useful method for securing a graft site, refixation is difficult when repeated tieover dressing is needed. Therefore, we recommend a redoable tie-over dressing technique with multiple loops threads and connecting silk threads. After the raw surface of each of our cases was covered with a skin graft, multiple loop silk thread attached with nylon at the skin graft margin. We applied the ointment gauze and wet cotton/fluffy gauze over the skin graft, then fixed the dressing by connecting cross-counter multiple loop thread with connecting silk threads. When we opened the tie-over dressing by cutting the connecting silk threads, we repeated the tie-over dressing with the same method. The skin graft was taken successfully without hematoma or seroma collection or any other complications. In conclusion, we report a novel tie-over dressing enabling simple fixation of the dressing to maintain proper tension for wounds that require repetitive fixation. Further, with this reliable method, the skin grafts were well taken.

  5. Random walk loop soups and conformal loop ensembles

    NARCIS (Netherlands)

    van de Brug, T.; Camia, F.; Lis, M.

    2016-01-01

    The random walk loop soup is a Poissonian ensemble of lattice loops; it has been extensively studied because of its connections to the discrete Gaussian free field, but was originally introduced by Lawler and Trujillo Ferreras as a discrete version of the Brownian loop soup of Lawler and Werner, a

  6. Specificity of the photoreaction of 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen with ribonucleic acid. Identificaton of reactive sites in Escherichia coli phenylalanine-accepting transfer ribonucleic acid

    Energy Technology Data Exchange (ETDEWEB)

    Bachellerie, J.P.; Hearst, J.E.

    1982-03-16

    In order to test the potential of psoralen photo-addition for the probing of RNA conformation at sequence resolution, the specificity of the reaction of 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen (HMT) with Escherichia coli tRNA/sup Phe/ was analyzed. The sites of HMT covalent addition have been identified by a combination of analytical techniques involving chemical cleavage of the tRNA/sup Phe/ molecule at the m/sup 7/G site and gel electrophoresis of RNase T/sub 1/ digests together with paper electrophoretic characterization of HMT-modified nucleotides and oligonucleotides. HMT photoaddition shows a very high preference for uracil residues. However, important differences in HMT photoreactivity are observed for various U sites of the tRNA/sup Phe/ molecule. Reactivity of specific bases has been correlated with partial melting of the molecule. Data available so far indicate a strong preference of the photo-reactive probe for a ''loose'' helical conformation as compared with a tight helix, whereas a random coil appears poorly reactive. (JMT)

  7. Transition probability spaces in loop quantum gravity

    Science.gov (United States)

    Guo, Xiao-Kan

    2018-03-01

    We study the (generalized) transition probability spaces, in the sense of Mielnik and Cantoni, for spacetime quantum states in loop quantum gravity. First, we show that loop quantum gravity admits the structures of transition probability spaces. This is exemplified by first checking such structures in covariant quantum mechanics and then identifying the transition probability spaces in spin foam models via a simplified version of general boundary formulation. The transition probability space thus defined gives a simple way to reconstruct the discrete analog of the Hilbert space of the canonical theory and the relevant quantum logical structures. Second, we show that the transition probability space and in particular the spin foam model are 2-categories. Then we discuss how to realize in spin foam models two proposals by Crane about the mathematical structures of quantum gravity, namely, the quantum topos and causal sites. We conclude that transition probability spaces provide us with an alternative framework to understand various foundational questions of loop quantum gravity.

  8. Temporary loop ileostomy: prospective study of indications and complication

    International Nuclear Information System (INIS)

    Rajput, A.; Samad, A.; Khanzada, T.W.

    2007-01-01

    To asses the indications and complications of temporary loop ileostomy. This was a prospective cohort study conducted at Isra University Hospital, Hyderabad, Pakistan between February 2003 and August 2006. All patients who had temporary loop ileostomy during that period were included in this study. The indications and various postoperative complications were noted during postoperative hospital stay and subsequently during follow up till stoma were closed. Fifty six patients fulfilled the selection criteria during the study period. Typhoid (enteric) perforation was the most common indication of loop ileostomy accounting for about two thirds of all cases. Other indications were iatrogenic, covering ileostomy for rectal cancers, following resection anastomosis, tuberculosis, blunt abdominal trauma, anastomosis leak and rectovaginal fistula. Post operative skin excoriation was the most common complication while poor siting, transient edema, retraction and high output were other less common complications. Temporary loop ileostomy is the stoma of choice for temporary faecal diversion as most of its complications are manageable conservatively. (author)

  9. Renormalization of loop functions for all loops

    International Nuclear Information System (INIS)

    Brandt, R.A.; Neri, F.; Sato, M.

    1981-01-01

    It is shown that the vacuum expectation values W(C 1 ,xxx, C/sub n/) of products of the traces of the path-ordered phase factors P exp[igcontour-integral/sub C/iA/sub μ/(x)dx/sup μ/] are multiplicatively renormalizable in all orders of perturbation theory. Here A/sub μ/(x) are the vector gauge field matrices in the non-Abelian gauge theory with gauge group U(N) or SU(N), and C/sub i/ are loops (closed paths). When the loops are smooth (i.e., differentiable) and simple (i.e., non-self-intersecting), it has been shown that the generally divergent loop functions W become finite functions W when expressed in terms of the renormalized coupling constant and multiplied by the factors e/sup -K/L(C/sub i/), where K is linearly divergent and L(C/sub i/) is the length of C/sub i/. It is proved here that the loop functions remain multiplicatively renormalizable even if the curves have any finite number of cusps (points of nondifferentiability) or cross points (points of self-intersection). If C/sub γ/ is a loop which is smooth and simple except for a single cusp of angle γ, then W/sub R/(C/sub γ/) = Z(γ)W(C/sub γ/) is finite for a suitable renormalization factor Z(γ) which depends on γ but on no other characteristic of C/sub γ/. This statement is made precise by introducing a regularization, or via a loop-integrand subtraction scheme specified by a normalization condition W/sub R/(C-bar/sub γ/) = 1 for an arbitrary but fixed loop C-bar/sub γ/. Next, if C/sub β/ is a loop which is smooth and simple except for a cross point of angles β, then W(C/sub β/) must be renormalized together with the loop functions of associated sets S/sup i//sub β/ = ]C/sup i/ 1 ,xxx, C/sup i//sub p/i] (i = 2,xxx,I) of loops C/sup i//sub q/ which coincide with certain parts of C/sub β/equivalentC 1 1 . Then W/sub R/(S/sup i//sub β/) = Z/sup i/j(β)W(S/sup j//sub β/) is finite for a suitable matrix Z/sup i/j

  10. Laboratory and field scale demonstration of reactive barrier systems

    International Nuclear Information System (INIS)

    Dwyer, B.P.; Marozas, D.C.; Cantrell, K.; Stewart, W.

    1996-10-01

    In an effort to devise a cost efficient technology for remediation of uranium contaminated groundwater, the Department of Energy's Uranium Mill Tailings Remedial Action (DOE-UMTRA) Program through Sandia National Laboratories (SNL) fabricated a pilot scale research project utilizing reactive subsurface barriers at an UMTRA site in Durango, Colorado. A reactive subsurface barrier is produced by placing a reactant material (in this experiment, metallic iron) in the flow path of the contaminated groundwater. The reactive media then removes and/or transforms the contaminant(s) to regulatory acceptable levels. Experimental design and results are discussed with regard to other potential applications of reactive barrier remediation strategies at other sites with contaminated groundwater problems

  11. NHS-Esters As Versatile Reactivity-Based Probes for Mapping Proteome-Wide Ligandable Hotspots.

    Science.gov (United States)

    Ward, Carl C; Kleinman, Jordan I; Nomura, Daniel K

    2017-06-16

    Most of the proteome is considered undruggable, oftentimes hindering translational efforts for drug discovery. Identifying previously unknown druggable hotspots in proteins would enable strategies for pharmacologically interrogating these sites with small molecules. Activity-based protein profiling (ABPP) has arisen as a powerful chemoproteomic strategy that uses reactivity-based chemical probes to map reactive, functional, and ligandable hotspots in complex proteomes, which has enabled inhibitor discovery against various therapeutic protein targets. Here, we report an alkyne-functionalized N-hydroxysuccinimide-ester (NHS-ester) as a versatile reactivity-based probe for mapping the reactivity of a wide range of nucleophilic ligandable hotspots, including lysines, serines, threonines, and tyrosines, encompassing active sites, allosteric sites, post-translational modification sites, protein interaction sites, and previously uncharacterized potential binding sites. Surprisingly, we also show that fragment-based NHS-ester ligands can be made to confer selectivity for specific lysine hotspots on specific targets including Dpyd, Aldh2, and Gstt1. We thus put forth NHS-esters as promising reactivity-based probes and chemical scaffolds for covalent ligand discovery.

  12. Structural and reactivity models for copper oxygenases: cooperative effects and novel reactivities.

    Science.gov (United States)

    Serrano-Plana, Joan; Garcia-Bosch, Isaac; Company, Anna; Costas, Miquel

    2015-08-18

    Dioxygen is widely used in nature as oxidant. Nature itself has served as inspiration to use O2 in chemical synthesis. However, the use of dioxygen as an oxidant is not straightforward. Its triplet ground-state electronic structure makes it unreactive toward most organic substrates. In natural systems, metalloenzymes activate O2 by reducing it to more reactive peroxide (O2(2-)) or superoxide (O2(-)) forms. Over the years, the development of model systems containing transition metals has become a convenient tool for unravelling O2-activation mechanistic aspects and reproducing the oxidative activity of enzymes. Several copper-based systems have been developed within this area. Tyrosinase is a copper-based O2-activating enzyme, whose structure and reactivity have been widely studied, and that serves as a paradigm for O2 activation at a dimetal site. It contains a dicopper center in its active site, and it catalyzes the regioselective ortho-hydroxylation of phenols to catechols and further oxidation to quinones. This represents an important step in melanin biosynthesis and it is mediated by a dicopper(II) side-on peroxo intermediate species. In the present accounts, our research in the field of copper models for oxygen activation is collected. We have developed m-xylyl linked dicopper systems that mimick structural and reactivity aspects of tyrosinase. Synergistic cooperation of the two copper(I) centers results in O2 binding and formation of bis(μ-oxo)dicopper(III) cores. These in turn bind and ortho-hydroxylate phenolates via an electrophilic attack of the oxo ligand over the arene. Interestingly the bis(μ-oxo)dicopper(III) cores can also engage in ortho-hydroxylation-defluorination of deprotonated 2-fluorophenols, substrates that are well-known enzyme inhibitors. Analysis of Cu2O2 species with different binding modes show that only the bis(μ-oxo)dicopper(III) cores can mediate the reaction. Finally, the use of unsymmetric systems for oxygen activation is a field

  13. Closing the loop.

    Science.gov (United States)

    Dassau, E; Atlas, E; Phillip, M

    2010-02-01

    The dream of closing the loop is actually the dream of creating an artificial pancreas and freeing the patients from being involved with the care of their own diabetes. Insulin-dependent diabetes (type 1) is a chronic incurable disease which requires constant therapy without the possibility of any 'holidays' or insulin-free days. It means that patients have to inject insulin every day of their life, several times per day, and in order to do it safely they also have to measure their blood glucose levels several times per day. Patients need to plan their meals, their physical activities and their insulin regime - there is only very small room for spontaneous activities. This is why the desire for an artificial pancreas is so strong despite the fact that it will not cure the diabetic patients. Attempts to develop a closed-loop system started in the 1960s but never got to a clinical practical stage of development. In recent years the availability of continuous glucose sensors revived those efforts and stimulated the clinician and researchers to believe that closing the loop might be possible nowadays. Many papers have been published over the years describing several different ideas on how to close the loop. Most of the suggested systems have a sensing arm that measures the blood glucose repeatedly or continuously, an insulin delivery arm that injects insulin upon command and a computer that makes the decisions of when and how much insulin to deliver. The differences between the various published systems in the literature are mainly in their control algorithms. However, there are also differences related to the method and site of glucose measurement and insulin delivery. SC glucose measurements and insulin delivery are the most studied option but other combinations of insulin measurements and glucose delivery including intravascular and intraperitoneal (IP) are explored. We tried to select recent publications that we believe had influenced and inspired people interested

  14. COOH-terminal substitutions in the serpin C1 inhibitor that cause loop overinsertion and subsequent multimerization

    NARCIS (Netherlands)

    Eldering, E.; Verpy, E.; Roem, D.; Meo, T.; Tosi, M.

    1995-01-01

    The region COOH-terminal to the reactive center loop is highly conserved in the serine protease inhibitor (serpin) family. We have studied the structural consequences of three substitutions (Val451-->Met, Phe455-->Ser, and Pro476-->Ser) found in this region of C1 inhibitor in patients suffering from

  15. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

    Science.gov (United States)

    Sanborn, Adrian; Rao, Suhas; Huang, Su-Chen; Durand, Neva; Huntley, Miriam; Jewett, Andrew; Bochkov, Ivan; Chinnappan, Dharmaraj; Cutkosky, Ashok; Li, Jian; Geeting, Kristopher; McKenna, Doug; Stamenova, Elena; Gnirke, Andreas; Melnikov, Alexandre; Lander, Eric; Aiden, Erez

    Our recent kilobase-resolution genome-wide maps of DNA self-contacts demonstrated that mammalian genomes are organized into domains and loops demarcated by the DNA-binding protein CTCF. Here, we combine these maps with new Hi-C, microscopy, and genome-editing experiments to study the physical structure of chromatin fibers, domains, and loops. We find that domains are inconsistent with equilibrium and fractal models. Instead, we use physical simulations to study two models of genome folding. In one, intermonomer attraction during condensation leads to formation of an anisotropic ``tension globule.'' In the other, CTCF and cohesin act together to extrude unknotted loops. Both models are consistent with the observed domains and loops. However, the extrusion model explains a far wider array of observations, such as why the CTCF-binding motifs at pairs of loop anchors lie in the convergent orientation. Finally, we perform 13 genome-editing experiments examining the effect of altering CTCF-binding sites on chromatin folding. The extrusion model predicts in silico the experimental maps using only CTCF-binding sites. Thus, we show that it is possible to disrupt, restore, and move loops and domains using targeted mutations as small as a single base pair.

  16. Crystallographic and molecular dynamics analysis of loop motions unmasking the peptidoglycan-binding site in stator protein MotB of flagellar motor.

    Directory of Open Access Journals (Sweden)

    Cyril F Reboul

    Full Text Available BACKGROUND: The C-terminal domain of MotB (MotB-C shows high sequence similarity to outer membrane protein A and related peptidoglycan (PG-binding proteins. It is believed to anchor the power-generating MotA/MotB stator unit of the bacterial flagellar motor to the peptidoglycan layer of the cell wall. We previously reported the first crystal structure of this domain and made a puzzling observation that all conserved residues that are thought to be essential for PG recognition are buried and inaccessible in the crystal structure. In this study, we tested a hypothesis that peptidoglycan binding is preceded by, or accompanied by, some structural reorganization that exposes the key conserved residues. METHODOLOGY/PRINCIPAL FINDINGS: We determined the structure of a new crystalline form (Form B of Helicobacter pylori MotB-C. Comparisons with the existing Form A revealed conformational variations in the petal-like loops around the carbohydrate binding site near one end of the β-sheet. These variations are thought to reflect natural flexibility at this site required for insertion into the peptidoglycan mesh. In order to understand the nature of this flexibility we have performed molecular dynamics simulations of the MotB-C dimer. The results are consistent with the crystallographic data and provide evidence that the three loops move in a concerted fashion, exposing conserved MotB residues that have previously been implicated in binding of the peptide moiety of peptidoglycan. CONCLUSION/SIGNIFICANCE: Our structural analysis provides a new insight into the mechanism by which MotB inserts into the peptidoglycan mesh, thus anchoring the power-generating complex to the cell wall.

  17. Regenerable mixed copper-iron-inert support oxygen carriers for solid fuel chemical looping combustion process

    Energy Technology Data Exchange (ETDEWEB)

    Siriwardane, Ranjani V.; Tian, Hanjing

    2016-12-20

    The disclosure provides an oxygen carrier for a chemical looping cycle, such as the chemical looping combustion of solid carbonaceous fuels, such as coal, coke, coal and biomass char, and the like. The oxygen carrier is comprised of at least 24 weight % (wt %) CuO, at least 10 wt % Fe2O3, and an inert support, and is typically a calcine. The oxygen carrier exhibits a CuO crystalline structure and an absence of iron oxide crystalline structures under XRD crystallography, and provides an improved and sustained combustion reactivity in the temperature range of 600.degree. C.-1000.degree. C. particularly for solid fuels such as carbon and coal.

  18. Reactive barrier technologies for treatment of contaminated groundwater at Rocky Flats

    International Nuclear Information System (INIS)

    Marozas, D.C.; Bujewski, G.E.; Castaneda, N.

    1997-01-01

    The U.S. Department of Energy (DOE) Office of Science and Technology Subsurface Contaminants Focus Area is supporting the investigation of reactive barrier technologies to mitigate the risks associated with mixed organic/radioactive waste at several DOE sites. Groundwater from a small contaminated plume at the Rocky Flats Environmental Technology Site (RFETS) is being used to evaluate passive reactive material treatment. Permeable reactive barriers which intercept contaminants and destroy the VOC component while containing radionuclides are attractive for a number of reasons relating to public and regulatory acceptance. In situ treatment keeps contaminants away from the earth's surface, there is no above-ground treatment equipment that could expose workers and the public and operational costs are expected to be lower than currently used technologies. This paper will present results from preliminary site characterization and in-field small-scale column testing of reactive materials at RFETS. Successful demonstration is expected to lead to full-scale implementation of the technology at several DOE sites, including Rocky Flats

  19. Two-loop hard-thermal-loop thermodynamics with quarks

    International Nuclear Information System (INIS)

    Andersen, Jens O.; Petitgirard, Emmanuel; Strickland, Michael

    2004-01-01

    We calculate the quark contribution to the free energy of a hot quark-gluon plasma to two-loop order using hard-thermal-loop (HTL) perturbation theory. All ultraviolet divergences can be absorbed into renormalizations of the vacuum energy and the HTL quark and gluon mass parameters. The quark and gluon HTL mass parameters are determined self-consistently by a variational prescription. Combining the quark contribution with the two-loop HTL perturbation theory free energy for pure glue we obtain the total two-loop QCD free energy. Comparisons are made with lattice estimates of the free energy for N f =2 and with exact numerical results obtained in the large-N f limit

  20. LoopIng: a template-based tool for predicting the structure of protein loops.

    KAUST Repository

    Messih, Mario Abdel; Lepore, Rosalba; Tramontano, Anna

    2015-01-01

    ) and significant enhancements for long loops (11-20 residues). The quality of the predictions is robust to errors that unavoidably affect the stem regions when these are modeled. The method returns a confidence score for the predicted template loops and has

  1. Soft sensor based composition estimation and controller design for an ideal reactive distillation column.

    Science.gov (United States)

    Vijaya Raghavan, S R; Radhakrishnan, T K; Srinivasan, K

    2011-01-01

    In this research work, the authors have presented the design and implementation of a recurrent neural network (RNN) based inferential state estimation scheme for an ideal reactive distillation column. Decentralized PI controllers are designed and implemented. The reactive distillation process is controlled by controlling the composition which has been estimated from the available temperature measurements using a type of RNN called Time Delayed Neural Network (TDNN). The performance of the RNN based state estimation scheme under both open loop and closed loop have been compared with a standard Extended Kalman filter (EKF) and a Feed forward Neural Network (FNN). The online training/correction has been done for both RNN and FNN schemes for every ten minutes whenever new un-trained measurements are available from a conventional composition analyzer. The performance of RNN shows better state estimation capability as compared to other state estimation schemes in terms of qualitative and quantitative performance indices. Copyright © 2010 ISA. Published by Elsevier Ltd. All rights reserved.

  2. A DFIG Islanding Detection Scheme Based on Reactive Power Infusion

    Science.gov (United States)

    Wang, M.; Liu, C.; He, G. Q.; Li, G. H.; Feng, K. H.; Sun, W. W.

    2017-07-01

    A lot of research has been done on photovoltaic (the “PV”) power system islanding detection in recent years. As a comparison, much less attention has been paid to islanding in wind turbines. Meanwhile, wind turbines can work in islanding conditions for quite a long period, which can be harmful to equipments and cause safety hazards. This paper presents and examines a double fed introduction generation (the “DFIG”) islanding detection scheme based on feedback of reactive power and frequency and uses a trigger signal of reactive power infusion which can be obtained by dividing the voltage total harmonic distortion (the "THD") by the voltage THD of last cycle to avoid the deterioration of power quality. This DFIG islanding detection scheme uses feedback of reactive power current loop to amplify the frequency differences in islanding and normal conditions. Simulation results show that the DFIG islanding detection scheme is effective.

  3. Active site CP-loop dynamics modulate substrate binding, catalysis, oligomerization, stability, over-oxidation and recycling of 2-Cys Peroxiredoxins.

    Science.gov (United States)

    Kamariah, Neelagandan; Eisenhaber, Birgit; Eisenhaber, Frank; Grüber, Gerhard

    2018-04-01

    Peroxiredoxins (Prxs) catalyse the rapid reduction of hydrogen peroxide, organic hydroperoxide and peroxynitrite, using a fully conserved peroxidatic cysteine (C P ) located in a conserved sequence Pxxx(T/S)xxC P motif known as C P -loop. In addition, Prxs are involved in cellular signaling pathways and regulate several redox-dependent process related disease. The effective catalysis of Prxs is associated with alterations in the C P -loop between reduced, Fully Folded (FF), and oxidized, Locally Unfolded (LU) conformations, which are linked to dramatic changes in the oligomeric structure. Despite many studies, little is known about the precise structural and dynamic roles of the C P -loop on Prxs functions. Herein, the comprehensive biochemical and biophysical studies on Escherichia coli alkyl hydroperoxide reductase subunit C (EcAhpC) and the C P -loop mutants, EcAhpC-F45A and EcAhpC-F45P reveal that the reduced form of the C P -loop adopts conformational dynamics, which is essential for effective peroxide reduction. Furthermore, the point mutants alter the structure and dynamics of the reduced form of the C P -loop and, thereby, affect substrate binding, catalysis, oligomerization, stability and overoxidiation. In the oxidized form, due to restricted C P -loop dynamics, the EcAhpC-F45P mutant favours a decamer formation, which enhances the effective recycling by physiological reductases compared to wild-type EcAhpC. In addition, the study reveals that residue F45 increases the specificity of Prxs-reductase interactions. Based on these studies, we propose an evolution of the C P -loop with confined sequence conservation within Prxs subfamilies that might optimize the functional adaptation of Prxs into various physiological roles. Copyright © 2018 Elsevier Inc. All rights reserved.

  4. Reactivity of Ordinary Portland Cement (OPC) grout and various lithologies from the Harwell research site

    International Nuclear Information System (INIS)

    Milodowski, A.E.; George, I.A.; Bloodworth, A.J.; Robins, N.S.

    1985-08-01

    Ordinary Portland Cement (OPC) has been used in the completion of boreholes on the Harwell Research Site, AERE, Oxfordshire. The purpose of this study was to examine the effect of OPC and the alkaline pore fluids generated during its setting on the various lithological types encountered in the boreholes. To facilitate this, samples of core representing the various rock types were selected and cement-rock composites were prepared from these in the laboratory to simulate the borehole cements. After a curing period of 15 months the cores and associated cement plugs were examined for any signs of reactivity or bonding. The best cement-rock bonding was shown by naturally well-cemented sandstone and limestone lithologies. Although no significant chemical reaction was seen to have occurred between OPC and rock, the OPC appears able to bind onto the rock surface because of the rigidity of the rock surface. Therefore, the best cement rock bonding and seal with OPC may be expected in the limestones of the Great Oolite Group, Inferior Oolite Group and parts of the Corallian Beds. Because of the reactivity of OPC towards certain lithologies a better borehole seal in such a sedimentary sequence might be achieved using a bentonite backfill in those parts of the sequence which either react with or bond only weakly to OPC. (author)

  5. Reactivity of a Carbon-Supported Single-Site Molybdenum Dioxo Catalyst for Biodiesel Synthesis

    Energy Technology Data Exchange (ETDEWEB)

    Mouat, Aidan R.; Lohr, Tracy L.; Wegener, Evan C.; Miller, Jeffrey T.; Delferro, Massimiliano; Stair, Peter C.; Marks, Tobin J.

    2016-08-23

    A single-site molybdenum dioxo catalyst, (Oc)2Mo(=O)2@C, was prepared via direct grafting of MoO2Cl2(dme) (dme = 1,2-dimethoxyethane) on high-surface- area activated carbon. The physicochemical and chemical properties of this catalyst were fully characterized by N2 physisorption, ICP-AES/OES, PXRD, STEM, XPS, XAS, temperature-programmed reduction with H2 (TPR-H2), and temperature-programmed NH3 desorption (TPD-NH3). The single-site nature of the Mo species is corroborated by XPS and TPR-H2 data, and it exhibits the lowest reported MoOx Tmax of reduction reported to date, suggesting a highly reactive MoVI center. (Oc)2Mo(=O)2@C catalyzes the transesterification of a variety of esters and triglycerides with ethanol, exhibiting high activity at moderate temperatures (60-90 °C) and with negligible deactivation. (Oc)2Mo(=O)2@C is resistant to water and can be recycled at least three times with no loss of activity. The transesterification reaction is determined experimentally to be first order in [ethanol] and first order in [Mo] with ΔH = 10.5(8) kcal mol-1 and ΔS = -32(2) eu. The low energy of activation is consistent with the moderate conditions needed to achieve rapid turnover. This highly active carbon-supported single-site molybdenum dioxo species is thus an efficient, robust, and lowcost catalyst with significant potential for transesterification processes.

  6. A mutation in the envelope protein fusion loop attenuates mouse neuroinvasiveness of the NY99 strain of West Nile virus

    International Nuclear Information System (INIS)

    Zhang Shuliu; Li Li; Woodson, Sara E.; Huang, Claire Y.-H.; Kinney, Richard M.; Barrett, Alan D.T.; Beasley, David W.C.

    2006-01-01

    Substitutions were engineered individually and in combinations at the fusion loop, receptor-binding domain and a stem-helix structure of the envelope protein of a West Nile virus strain, NY99, and their effects on mouse virulence and presentation of epitopes recognized by monoclonal antibodies (MAbs) were assessed. A single substitution within the fusion loop (L107F) attenuated mouse neuroinvasiveness of NY99. No substitutions attenuated NY99 neurovirulence. The L107F mutation also abolished binding of a non-neutralizing MAb, 3D9, whose epitope had not been previously identified. MAb 3D9 was subsequently shown to be broadly cross-reactive with other flaviviruses, consistent with binding near the highly conserved fusion loop

  7. Neocortical electrical stimulation for epilepsy : Closed-loop versus open-loop

    NARCIS (Netherlands)

    Vassileva, Albena; van Blooijs, Dorien; Leijten, Frans; Huiskamp, Geertjan

    2018-01-01

    The aim of this review is to evaluate whether open-loop or closed-loop neocortical electrical stimulation should be the preferred approach to manage seizures in intractable epilepsy. Twenty cases of open-loop neocortical stimulation with an implanted device have been reported, in 5 case studies.

  8. The iodine reactivity

    International Nuclear Information System (INIS)

    2003-01-01

    The iodine is an important element because it has long life isotopes (such as iodine 129) and a great mobility in natural media. Iodine presents a complex chemistry because of its volatility and its strong redox reactivity. The S.E.C.R. works to better understand the reactivity of this element in different natural, industrial or biological environments. It plays a part in thermochemical sites as a possible way of hydrogen formation. This seminar gives some aspects relative to the chemical reactivity of iodine, since its thermochemistry in the I/S cycles to produce hydrogen to its reactivity in the natural medium and its potential radiological impact. This document includes 4 presentations transparencies) dealing with: the 129 I cycle rejected in the low radioactive gaseous and liquid effluents of the La Hague reprocessing plant (C. Frechou); a bibliographic review of iodine retention in soils (F. Bazer-Bachi); the hydrogen production and the iodine/sulfur thermochemical cycle (role of iodine in the process); and the direct characterization by electro-spray ionization mass spectroscopy of iodine fixation by fulvic acids (P. Reiller, B. Amekraz, C. Moulin, V. Moulin)

  9. A multiple-pass ring oscillator based dual-loop phase-locked loop

    International Nuclear Information System (INIS)

    Chen Danfeng; Ren Junyan; Deng Jingjing; Li Wei; Li Ning

    2009-01-01

    A dual-loop phase-locked loop (PLL) for wideband operation is proposed. The dual-loop architecture combines a coarse-tuning loop with a fine-tuning one, enabling a wide tuning range and low voltage-controlled oscillator (VCO) gain without poisoning phase noise and reference spur suppression performance. An analysis of the phase noise and reference spur of the dual-loop PLL is emphasized. A novel multiple-pass ring VCO is designed for the dual-loop application. It utilizes both voltage-control and current-control simultaneously in the delay cell. The PLL is fabricated in Jazz 0.18-μm RF CMOS technology. The measured tuning range is from 4.2 to 5.9 GHz. It achieves a low phase noise of -99 dBc/Hz - 1 MHz offset from a 5.5 GHz carrier.

  10. A multiple-pass ring oscillator based dual-loop phase-locked loop

    Energy Technology Data Exchange (ETDEWEB)

    Chen Danfeng; Ren Junyan; Deng Jingjing; Li Wei; Li Ning, E-mail: dfchen@fudan.edu.c [State Key Laboratory of ASIC and System, Fudan University, Shanghai 201203 (China)

    2009-10-15

    A dual-loop phase-locked loop (PLL) for wideband operation is proposed. The dual-loop architecture combines a coarse-tuning loop with a fine-tuning one, enabling a wide tuning range and low voltage-controlled oscillator (VCO) gain without poisoning phase noise and reference spur suppression performance. An analysis of the phase noise and reference spur of the dual-loop PLL is emphasized. A novel multiple-pass ring VCO is designed for the dual-loop application. It utilizes both voltage-control and current-control simultaneously in the delay cell. The PLL is fabricated in Jazz 0.18-{mu}m RF CMOS technology. The measured tuning range is from 4.2 to 5.9 GHz. It achieves a low phase noise of -99 dBc/Hz - 1 MHz offset from a 5.5 GHz carrier.

  11. Correlation of binding-loop internal dynamics with stability and function in potato I inhibitor family: relative contributions of Arg(50) and Arg(52) in Cucurbita maxima trypsin inhibitor-V as studied by site-directed mutagenesis and NMR spectroscopy.

    Science.gov (United States)

    Cai, Mengli; Gong, Yu-Xi; Wen, Lisa; Krishnamoorthi, Ramaswamy

    2002-07-30

    The side chains of Arg(50) and Arg(52) at positions P(6)' and P(8)', respectively, anchor the binding loop to the protein scaffold by means of hydrogen bonds in Cucurbita maxima trypsin inhibitor-V (CMTI-V), a potato I family member. Here, we have investigated the relative contributions of Arg(50) and Arg(52) to the binding-loop flexibility and stability by determining changes in structure, dynamics, and proteolytic stability as a consequence of individually mutating them into an alanine. We have compared chemical shift assignments of main-chain hydrogens and nitrogens, and (1)H-(1)H interresidue nuclear Overhauser effects (NOEs) for the two mutants with those of the wild-type protein. We have also measured NMR longitudinal and transverse relaxation rates and (15)N-(1)H NOE enhancements for all backbone and side-chain NH groups and calculated the model-free parameters for R50A-rCMTI-V and R52A-rCMTI-V. The three-dimensional structures and backbone dynamics of the protein scaffold region remain very similar for both mutants, relative to the wild-type protein. The flexibility of the binding loop is increased in both R50A- and R52A-rCMTI-V. In R52A-rCMTI-V, the mean generalized order parameter () of the P(6)-P(1) residues of the binding loop (39-44) decreases to 0.68 +/- 0.02 from 0.76 +/- 0.04 observed for the wild-type protein. However, in R50A-rCMTI-V, the flexibility of the whole binding loop increases, especially that of the P(1)'-P(3)' residues (45-47), whose value drops dramatically to 0.35 +/- 0.03 from 0.68 +/- 0.03 determined for rCMTI-V. More strikingly, S(2) values of side-chain N epsilon Hs reveal that, in the R50A mutant, removal of the R50 hydrogen bond results in the loss of the R52 hydrogen bond too, whereas in R52A, the R50 hydrogen bond remains unaffected. Kinetic data on trypsin-catalyzed hydrolysis of the reactive-site peptide bond (P(1)-P(1)') suggest that the activation free energy barrier of the reaction at 25 degrees C is reduced by 2.1 kcal

  12. Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.

    Science.gov (United States)

    Schudoma, Christian; May, Patrick; Nikiforova, Viktoria; Walther, Dirk

    2010-01-01

    The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence-structure relationships in loops. Loops differing by structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts.

  13. Identifying key controls on the behavior of an acidic-U(VI) plume in the Savannah River Site using reactive transport modeling.

    Science.gov (United States)

    Bea, Sergio A; Wainwright, Haruko; Spycher, Nicolas; Faybishenko, Boris; Hubbard, Susan S; Denham, Miles E

    2013-08-01

    Acidic low-level waste radioactive waste solutions were discharged to three unlined seepage basins at the F-Area of the Department of Energy (DOE) Savannah River Site (SRS), South Carolina, USA, from 1955 through 1989. Despite many years of active remediation, the groundwater remains acidic and contaminated with significant levels of U(VI) and other radionuclides. Monitored Natural Attenuation (MNA) is a desired closure strategy for the site, based on the premise that regional flow of clean background groundwater will eventually neutralize the groundwater acidity, immobilizing U(VI) through adsorption. An in situ treatment system is currently in place to accelerate this in the downgradient portion of the plume and similar measures could be taken upgradient if necessary. Understanding the long-term pH and U(VI) adsorption behavior at the site is critical to assess feasibility of MNA along with the in-situ remediation treatments. This paper presents a reactive transport (RT) model and uncertainty quantification (UQ) analyses to explore key controls on the U(VI)-plume evolution and long-term mobility at this site. Two-dimensional numerical RT simulations are run including the saturated and unsaturated (vadose) zones, U(VI) and H(+) adsorption (surface complexation) onto sediments, dissolution and precipitation of Al and Fe minerals, and key hydrodynamic processes are considered. UQ techniques are applied using a new open-source tool that is part of the developing ASCEM reactive transport modeling and analysis framework to: (1) identify the complex physical and geochemical processes that control the U(VI) plume migration in the pH range where the plume is highly mobile, (2) evaluate those physical and geochemical parameters that are most controlling, and (3) predict the future plume evolution constrained by historical, chemical and hydrological data. The RT simulation results show a good agreement with the observed historical pH and concentrations of U(VI), nitrates

  14. Fluoresceination of FepA during colicin B killing: effects of temperature, toxin and TonB.

    Science.gov (United States)

    Smallwood, Chuck R; Marco, Amparo Gala; Xiao, Qiaobin; Trinh, Vy; Newton, Salete M C; Klebba, Phillip E

    2009-06-01

    We studied the reactivity of 35 genetically engineered Cys sulphydryl groups at different locations in Escherichia coli FepA. Modification of surface loop residues by fluorescein maleimide (FM) was strongly temperature-dependent in vivo, whereas reactivity at other sites was much less affected. Control reactions with bovine serum albumin showed that the temperature dependence of loop residue reactivity was unusually high, indicating that conformational changes in multiple loops (L2, L3, L4, L5, L7, L8, L10) transform the receptor to a more accessible form at 37 degrees C. At 0 degrees C colicin B binding impaired or blocked labelling at 8 of 10 surface loop sites, presumably by steric hindrance. Overall, colicin B adsorption decreased the reactivity of more than half of the 35 sites, in both the N- and C- domains of FepA. However, colicin B penetration into the cell at 37 degrees C did not augment the chemical modification of any residues in FepA. The FM modification patterns were similarly unaffected by the tonB locus. FepA was expressed at lower levels in a tonB host strain, but when we accounted for this decrease its FM labelling was comparable whether TonB was present or absent. Thus we did not detect TonB-dependent structural changes in FepA, either alone or when it interacted with colicin B at 37 degrees C. The only changes in chemical modification were reductions from steric hindrance when the bacteriocin bound to the receptor protein. The absence of increases in the reactivity of N-domain residues argues against the idea that the colicin B polypeptide traverses the FepA channel.

  15. Structural studies on an internal loop from a hairpin ribozyme

    Energy Technology Data Exchange (ETDEWEB)

    Cai, Z.; SantaLucia, J. Jr.; Tinoco, I. Jr. [Univ. of California, Berkeley, CA (United States)

    1994-12-01

    Ribozymes, RNA enzymes, catalyze site-specific RNA cleavage and ligation reactions. We are studying the three-dimensional structure of a hairpin ribozyme derived from the minus strand of tobacco ring spot virus satellite RNA ((-)sTRSV), which has been engineering to specifically cleave the HIV-1 RNA. The minimum structure for the catalytic reaction involves a 50-nucleotide ribozyme and a 14-nucleotide substrate. The proposed secondary structure of the ribozyme-substrate complex consists of four short helices separated by two internal loops. The relatively large size (64-nucleotide) of the ribozyme-substrate complex presents formidable problems in solving the structure using NMR. Therefore we are studying smaller structural subunits of the complex. We are determining the high resolution structure of the symmetric internal loop involving the cleavage site and the flanking helices. One strand of the internal loop was selectively {sup 13}C-labeled at C8 of each purine and C6 of each pyrimidine. By using {sup 13}C-edited two-dimensional NMR, the proton NOESY spectrum was greatly simplified. This allowed unambiguous sequential proton resonance assignments along each strand. Three-dimensional {sup 1}-{sup 13}C HMQC-NOESY was used to further facilitate resonance assignments. We are also enzymatically synthesizing the entire 50-nucleotide ribozyme and will combine it with the {sup 13}C-labeled substrate. Through comparison of the NOE connectivities of the labeled nucleotides from the internal loop alone with those from the entire complex, the differences between the two structures can be elucidated.

  16. Use of reactivity constraints for the automatic control of reactor power

    International Nuclear Information System (INIS)

    Bernard, J.A.; Lanning, D.D.; Ray, A.

    1985-01-01

    A theoretical framework for the automatic control of reactor power has been developed and experimentally evaluated on the 5 MWt Research Reactor that is operated by the Massachusetts Institute of Technology. The controller functions by restricting the net reactivity so that it is always possible to make the reactor period infinite at the desired termination point of a transient by reversing the direction of motion of whatever control mechanism is associated with the controller. This capability is formally designated as ''feasibility of control''. It has been shown experimentally that maintenance of feasibility of control is a sufficient condition for the automatic control of reactor power. This research should be of value in the design of closed-loop controllers, in the creation of reactivity displays, in the provision of guidance to operators regarding the timing of reactivity changes, and as an experimental envelope within which alternate control strategies can be evaluated

  17. Study on LOOP and SBO Frequency for Multi-Unit PSA

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Kyung Ho; Heo, Gyun Young [Kyunghee University, Yongin (Korea, Republic of)

    2016-05-15

    In conventional single unit PSA, it was assumed that all accidents or events are independent and the risk of only one unit has been evaluated. In other words, the possibility that simultaneous events occur on multiple units was excluded because it was assumed that the probability of concurrent events were extremely low. After Fukushima accidents, however, it was found that external hazards such as tsunami may impact on multiple units; that means, for the sake of proper mitigation the risk of accidents in shared SSCs should be reevaluated. New risk metrics to improve conventional CDF (Core Damage frequency) based on reactor-year is needed to perform MUPSA (Multi-Unit Probabilistic Safety Assessment). IAEA suggested SCDF (Site CDF) as a risk metrics for MUPSA. The frequency based on reactor-year was converted to the frequency based on site-year. In addition, shared SSCs were modeled in single unit PSA as if those units have independent shared SSCs. Therefore, the risk of shared SSCs should be reevaluated. In this paper, the frequency of LOOP (Loss of Offsite Power), which is typically a multi-unit event, was evaluated and the frequency of SBO (Station Blackout) depending on LOOP frequency and emergency power systems such as EDG (Emergency Diesel Generator) and AAC (Alternate AC), that can mitigate SBO events, was modeled. This paper describes how to calculate LOOP and SBO frequency from the simple example for two-unit site with shared AAC. The events impacting on multiple units, which were excluded in conventional PSA, should be considered for MUPSA.

  18. MINI-FILAMENT ERUPTION AS THE INITIATION OF A JET ALONG CORONAL LOOPS

    International Nuclear Information System (INIS)

    Hong, Junchao; Jiang, Yunchun; Yang, Jiayan; Yang, Bo; Xu, Zhe; Xiang, Yongyuan

    2016-01-01

    Minifilament eruptions (MFEs) and coronal jets are different types of solar small-scale explosive events. We report an MFE observed at the New Vacuum Solar Telescope (NVST). As seen in the NVST H α images, during the rising phase, the minifilament erupts outward orthogonally to its length, accompanied with a flare-like brightening at the bottom. Afterward, dark materials are found to possibly extend along the axis of the expanded filament body. The MFE is analogous to large filament eruptions. However, a simultaneous observation of the Solar Dynamics Observatory shows that a jet is initiated and flows out along nearby coronal loops during the rising phase of the MFE. Meanwhile, small hot loops, which connect the original eruptive site of the minifilament to the footpoints of the coronal loops, are formed successively. A differential emission measure analysis demonstrates that, on the top of the new small loops, a hot cusp structure exists. We conjecture that the magnetic fields of the MFE interact with magnetic fields of the coronal loops. This interaction is interpreted as magnetic reconnection that produces the jet and the small hot loops.

  19. MINI-FILAMENT ERUPTION AS THE INITIATION OF A JET ALONG CORONAL LOOPS

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Junchao; Jiang, Yunchun; Yang, Jiayan; Yang, Bo; Xu, Zhe; Xiang, Yongyuan, E-mail: hjcsolar@ynao.ac.cn [Yunnan Observatories, Chinese Academy of Sciences, Kunming 650011 (China)

    2016-10-20

    Minifilament eruptions (MFEs) and coronal jets are different types of solar small-scale explosive events. We report an MFE observed at the New Vacuum Solar Telescope (NVST). As seen in the NVST H α images, during the rising phase, the minifilament erupts outward orthogonally to its length, accompanied with a flare-like brightening at the bottom. Afterward, dark materials are found to possibly extend along the axis of the expanded filament body. The MFE is analogous to large filament eruptions. However, a simultaneous observation of the Solar Dynamics Observatory shows that a jet is initiated and flows out along nearby coronal loops during the rising phase of the MFE. Meanwhile, small hot loops, which connect the original eruptive site of the minifilament to the footpoints of the coronal loops, are formed successively. A differential emission measure analysis demonstrates that, on the top of the new small loops, a hot cusp structure exists. We conjecture that the magnetic fields of the MFE interact with magnetic fields of the coronal loops. This interaction is interpreted as magnetic reconnection that produces the jet and the small hot loops.

  20. On-site detection of Xylella fastidiosa in host plants and in “spy insects” using the real-time loop-mediated isothermal amplification method

    Directory of Open Access Journals (Sweden)

    Thaer YASEEN

    2015-12-01

    Full Text Available A recent severe outbreak of Xylella fastidiosa associated with ‘olive quick decline syndrome’ (OQDS was reported in Apulia (Southern Italy. In this study an on-site real-time loop-mediated isothermal amplification (real-time LAMP was developed for detecting X. fastidiosa in host plants and insects. A marked simplification of the DNA extraction procedure was obtained by heating the samples in a portable Smart-Dart device and using an optimized enhancer reaction buffer. The connection to a tablet or Smartphone allowed to visualize the results of the reaction in real time. Compared to PCR and ELISA, with which it showed comparable results in terms of sensitivity and reliability in the X. fastidiosa detection, this simplified real-time LAMP procedure proved to be “user friendly”, displaying the advantages to be an on-site detection method of easy handling, rapid execution and low cost.

  1. Observations of speciated atmospheric mercury at three sites in Nevada: Evidence for a free tropospheric source of reactive gaseous mercury

    Science.gov (United States)

    Weiss-Penzias, Peter; Gustin, Mae Sexauer; Lyman, Seth N.

    2009-07-01

    Air mercury (Hg) speciation was measured for 11 weeks (June-August 2007) at three sites simultaneously in Nevada, USA. Mean reactive gaseous Hg (RGM) concentrations were elevated at all sites relative to those reported for locations not directly influenced by known point sources. RGM concentrations at all sites displayed a regular diel pattern and were positively correlated with ozone (O3) and negatively correlated with elemental Hg (Hg0) and dew point temperature (Tdp). Superimposed on the diel changes were 2- to 7-day periods when RGM concentrations increased across all three sites, producing significant intersite correlations of RGM daily means (r = 0.53-0.76, p distribution (GFD) plots and determine trajectory residence times (TRT) in specific source boxes. The GFD for the upper-quartile RGM daily means at one site showed a contributing airflow regime from the high-altitude subtropics with little precipitation, while that developed for the lower-quartile RGM concentrations indicated predominantly lower-altitude westerly flow and precipitation. Daily mean TRT in a subtropical high-altitude source box (>2 km and RGM at two sites (r2 = 0.37 and 0.27, p RGM from the free troposphere is a potentially important component of Hg input to rural areas of the western United States.

  2. Mutational epitope analysis of Pru av 1 and Api g 1, the major allergens of cherry (Prunus avium) and celery (Apium graveolens): correlating IgE reactivity with three-dimensional structure.

    Science.gov (United States)

    Neudecker, Philipp; Lehmann, Katrin; Nerkamp, Jörg; Haase, Tanja; Wangorsch, Andrea; Fötisch, Kay; Hoffmann, Silke; Rösch, Paul; Vieths, Stefan; Scheurer, Stephan

    2003-01-01

    Birch pollinosis is often accompanied by adverse reactions to food due to pollen-allergen specific IgE cross-reacting with homologous food allergens. The tertiary structure of Pru av 1, the major cherry (Prunus avium) allergen, for example, is nearly identical with Bet v 1, the major birch (Betula verrucosa) pollen allergen. In order to define cross-reactive IgE epitopes, we generated and analysed mutants of Pru av 1 and Api g 1.0101, the major celery (Apium graveolens) allergen, by immunoblotting, EAST (enzyme allergosorbent test), CD and NMR spectroscopy. The mutation of Glu45 to Trp45 in the P-loop region, a known IgE epitope of Bet v 1, significantly reduced IgE binding to Pru av 1 in a subgroup of cherry-allergic patients. The backbone conformation of Pru av 1 wild-type is conserved in the three-dimensional structure of Pru av 1 Trp45, demonstrating that the side chain of Glu45 is involved in a cross-reactive IgE epitope. Accordingly, for a subgroup of celery-allergic patients, IgE binding to the homologous celery allergen Api g 1.0101 was enhanced by the mutation of Lys44 to Glu. The almost complete loss of IgE reactivity to the Pru av 1 Pro112 mutant is due to disruption of its tertiary structure. Neither the mutation Ala112 nor deletion of the C-terminal residues 155-159 influenced IgE binding to Pru av 1. In conclusion, the structure of the P-loop partially explains the cross-reactivity pattern, and modulation of IgE-binding by site-directed mutagenesis is a promising approach to develop hypo-allergenic variants for patient-tailored specific immunotherapy. PMID:12943529

  3. LOOP CALCULUS AND BELIEF PROPAGATION FOR Q-ARY ALPHABET: LOOP TOWER

    Energy Technology Data Exchange (ETDEWEB)

    CHERTKOV, MICHAEL [Los Alamos National Laboratory; CHERNYAK, VLADIMIR [Los Alamos National Laboratory

    2007-01-10

    Loop calculus introduced in [1], [2] constitutes a new theoretical tool that explicitly expresses symbol Maximum-A-Posteriori (MAP) solution of a general statistical inference problem via a solution of the Belief Propagation (BP) equations. This finding brought a new significance to the BP concept, which in the past was thought of as just a loop-free approximation. In this paper they continue a discussion of the Loop Calculus, partitioning the results into three Sections. In Section 1 they introduce a new formulation of the Loop Calculus in terms of a set of transformations (gauges) that keeping the partition function of the problem invariant. The full expression contains two terms referred to as the 'ground state' and 'excited states' contributions. The BP equations are interpreted as a special (BP) gauge fixing condition that emerges as a special orthogonality constraint between the ground state and excited states, which also selects loop contributions as the only surviving ones among the excited states. In Section 2 they demonstrate how the invariant interpretation of the Loop Calculus, introduced in Section 1, allows a natural extension to the case of a general q-ary alphabet, this is achieved via a loop tower sequential construction. The ground level in the tower is exactly equivalent to assigning one color (out of q available) to the 'ground state' and considering all 'excited' states colored in the remaining (q-1) colors, according to the loop calculus rule. Sequentially, the second level in the tower corresponds to selecting a loop from the previous step, colored in (q-1) colors, and repeating the same ground vs excited states splitting procedure into one and (q-2) colors respectively. The construction proceeds till the full (q-1)-levels deep loop tower (and the corresponding contributions to the partition function) are established. In Section 3 they discuss an ultimate relation between the loop calculus and the Bethe

  4. Evaluation of the chemical reactivity in lignin precursors using the Fukui function.

    Science.gov (United States)

    Martinez, Carmen; Rivera, José L; Herrera, Rafael; Rico, José L; Flores, Nelly; Rutiaga, José G; López, Pablo

    2008-02-01

    The hydroxycinnamyl alcohols: p-coumarol, coniferol and sinapol are considered the basic units and precursors of lignins models. In this work, the specific reactivity of these molecules was studied. We investigate their intrinsic chemical reactivity in terms of the Fukui function, applying the principle of hard and soft acids and bases (HSAB) in the framework of the density functional theory (DFT). Comparisons of their nucleophilic, electrophilic and free radical reactivity show their most probably sites to form linkages among them. It is found that the most reactive sites, for reactions involving free radicals, are the carbons at the beta-position in the p-coumarol and sinapol molecules, whilst the regions around the carbon-oxygen bond of the phenoxyl group are the most reactive in coniferol.

  5. Differential Reactivity between Two Copper Sites in Peptidylglycine r-Hydroxylating Monooxygenase

    Energy Technology Data Exchange (ETDEWEB)

    E Chufan; S Prigge; X Siebert; B Eipper; R Mains; L Amzel

    2011-12-31

    Peptidylglycine {alpha}-hydroxylating monooxygenase (PHM) catalyzes the stereospecific hydroxylation of the C{alpha} of C-terminal glycine-extended peptides and proteins, the first step in the activation of many peptide hormones, growth factors, and neurotransmitters. The crystal structure of the enzyme revealed two nonequivalent Cu sites (Cu{sub M} and Cu{sub H}) separated by {approx}11 {angstrom}. In the resting state of the enzyme, Cu{sub M} is coordinated in a distorted tetrahedral geometry by one methionine, two histidines, and a water molecule. The coordination site of the water molecule is the position where external ligands bind. The Cu{sub H} has a planar T-shaped geometry with three histidines residues and a vacant position that could potentially be occupied by a fourth ligand. Although the catalytic mechanism of PHM and the role of the metals are still being debated, Cu{sub M} is identified as the metal involved in catalysis, while Cu{sub H} is associated with electron transfer. To further probe the role of the metals, we studied how small molecules such as nitrite (NO{sub 2}{sup -}), azide (N{sub 3}{sup -}), and carbon monoxide (CO) interact with the PHM copper ions. The crystal structure of an oxidized nitrite-soaked PHMcc, obtained by soaking for 20 h in mother liquor supplemented with 300 mM NaNO{sub 2}, shows that nitrite anion coordinates Cu{sub M} in an asymmetric bidentate fashion. Surprisingly, nitrite does not bind Cu{sub H}, despite the high concentration used in the experiments (nitrite/protein > 1000). Similarly, azide and carbon monoxide coordinate Cu{sub M} but not Cu{sub H} in the PHMcc crystal structures obtained by cocrystallization with 40 mM NaN{sub 3} and by soaking CO under 3 atm of pressure for 30 min. This lack of reactivity at the Cu{sub H} is also observed in the reduced form of the enzyme: CO binds Cu{sub M} but not Cu{sub H} in the structure of PHMcc obtained by exposure of a crystal to 3 atm CO for 15 min in the presence of 5

  6. Feedback stabilization of electrostatic reactive instabilities

    International Nuclear Information System (INIS)

    Richards, R.K.

    1976-01-01

    A general theory for the feedback stabilization of electrostatic reactive instabilities is developed which includes the effects of dissipation in the plasma and frequency dependence in the sensor-suppressor elements and in the external feedback circuit. This theory is compared to experiments involving particular reactive instability, an interchange mode, found in a magnetic mirror device; these results are found to be in good agreement with theory. One noteworthy result is that a frequency dependence in the overall gain and phase shift of the feedback loop can cause destabilization at large gain. Multimode feedback stabilization is studied using the spatial variation of two interchange modes to separate them such that each can be acted upon individually by the feedback system. The transfer function of the plasma is also examined. This analysis is used for mode identification and location of the pole positions. As an example of using feedback as a diagnostic tool, instability induced transport is studied. Here feedback is used to control the amplitude of fluctuations at saturation

  7. A New Way of Controlling Parallel-Connected Inverters by Using Synchronous-Reference-Frame Virtual Impedance Loop

    DEFF Research Database (Denmark)

    Guan, Yajuan; Guerrero, Josep M.; Zhao, Xin

    2016-01-01

    A novel simple and effective autonomous current-sharing controller for parallel three-phase inverters is proposed in this paper. The proposed controller provides faster response and better accuracy in contrast to the conventional droop control, since this novel approach does not require any active...... or reactive power calculations. Instead, a synchronous-reference-frame (SRF) virtual impedance loop and an SRF-based phase-locked loop are used. Stationary analysis is provided in order to identify the inherent mechanism of the direct and quadrature output currents in relation to the voltage amplitude...... from a setup with three parallel 2.2 kW inverters verify the effectiveness of the proposed control strategy in different scenarios....

  8. Introduction to Loop Heat Pipes

    Science.gov (United States)

    Ku, Jentung

    2015-01-01

    This is the presentation file for the short course Introduction to Loop Heat Pipes, to be conducted at the 2015 Thermal Fluids and Analysis Workshop, August 3-7, 2015, Silver Spring, Maryland. This course will discuss operating principles and performance characteristics of a loop heat pipe. Topics include: 1) pressure profiles in the loop; 2) loop operating temperature; 3) operating temperature control; 4) loop startup; 4) loop shutdown; 5) loop transient behaviors; 6) sizing of loop components and determination of fluid inventory; 7) analytical modeling; 8) examples of flight applications; and 9) recent LHP developments.

  9. Reactor loops at Chalk River

    International Nuclear Information System (INIS)

    Sochaski, R.O.

    1962-07-01

    This report describes broadly the nine in-reactor loops, and their components, located in and around the NRX and NRU reactors at Chalk River. First an introduction and general description is given of the loops and their function, supplemented with a table outlining some loop specifications and nine simplified flow sheets, one for each individual loop. The report then proceeds to classify each loop into two categories, the 'main loop circuit' and the 'auxiliary circuit', and descriptions are given of each circuit's components in turn. These components, in part, are comprised of the main loop pumps, the test section, loop heaters, loop coolers, delayed-neutron monitors, surge tank, Dowtherm coolers, loop piping. Here again photographs, drawings and tables are included to provide a clearer understanding of the descriptive literature and to include, in tables, some specifications of the more important components in each loop. (author)

  10. Differential modulation of binding loop flexibility and stability by Arg50 and Arg52 in Cucurbita maxima trypsin inhibitor-V deduced by trypsin-catalyzed hydrolysis and NMR spectroscopy.

    Science.gov (United States)

    Cai, M; Huang, Y; Prakash, O; Wen, L; Dunkelbarger, S P; Huang, J K; Liu, J; Krishnamoorthi, R

    1996-04-16

    The side chains of Arg50 and Arg52 iin Cucurbita maxima trypsin inhibitor-V (CMTI-V) anchor the binding loop to the scaffold region [Cai, M., Gong, Y., Kao, J.L-F., & Krishnamoorthi, R. (1995) Biochemistry 34, 5201-5211]. The consequences of these hydrogen-bonding and electrostatic interactions on the conformational flexibility and stability of the binding loop were evaluated by trypsin-catalyzed hydrolysis of CMTI-V mutants, in which each of the arginines was individually replaced with Ala, Lys, or Gln by genetic engineering methods. All mutants exhibited significantly increased vulnerability to the protease attack at many sites, including the reactive-site (Lys44-Asp45 peptide bond), with the R50 mutants showing much more pronounced effects than the R52 counterparts. For CmTI-V and the mutants studied, a qualitative correlation was inferred between binding loop flexibility and retention time on a reverse-phase high-pressure liquid chromatography C-18 column. The R50 mutants were found to be more flexible than the corresponding R52 versions. These results demonstrate that Arg50 contributes more to the stability and function of CMTI-V. The differing strengths of the hydrogen bonds made by Arg50 and Arg52 were characterized by determining the internal dynamics of their side chains at pH 5.0 and 2.5: 15N NMR longitudinal and transverse relaxation rates and 15N-1H nuclear Overhauser effect (NOE) enhancements were measured for the main-chain and side-chain NH groups in 15N-labeled recombinant CMTI-V (rCMTI-V) and the model-free parameters [Lipari, G., & Szabo, A.(1982) J. Am. Chem. Soc. 104, 4546-59; 4559-4570] were calculated. At both pH 5.0 and 2.5, the arginines at positions 26, 47, 58 and 66 are found to be highly mobile, as the caluculated general order parameters, S2 values, of their NepsilonH groups fall in the range 0.03-0.18. The corresponding values for Arg50 amd Arg52 are 0.73 and 0.63, respectively, at pH 5.0, thus confirming that the two arginines are

  11. NRU analysis support experiments performed in ZED-2

    International Nuclear Information System (INIS)

    Arbique, G.M.; French, P.M.

    1985-09-01

    A series of measurements have been performed in ZED-2 to investigate voiding in a simulated NRU loop site containing uniform and non-uniform UO 2 fuel strings. The objective of the measurements was to provide experimental data to validate NRU reactor physics codes. Using a simulated NRU loop site containing various UO 2 fuel strings, in a simulated NRU lattice in ZED-2, measurements were made of: a) reactivity effects, as measured by critical height changes, associated with the loop site and its contents, b) detailed and macroscopic flux shapes at the loop site and throughout the lattice, respectively, and c) Westcott spectral parameters. The report describes and presents the results of the experiments and is the second of a two part set of reports on this series of measurements. 6 refs

  12. Measurements of total OH reactivity during PROPHET-AMOS 2016

    Science.gov (United States)

    Rickly, P.; Sakowski, J.; Bottorff, B.; Lew, M.; Stevens, P. S.; Sklaveniti, S.; Locoge, N.; Dusanter, S.

    2017-12-01

    As one of the main oxidant in the atmosphere, the hydroxyl radical (OH) initiates the oxidation of volatile organic compounds that can lead to the formation of ozone and secondary organic aerosols. Understanding both the sources and sinks of OH is therefore important to address issues related to air quality and climate change. Measurements of total OH reactivity can provide an important test of our understanding of the OH radical budget. Recent measurements of total reactivity in many environments have been greater than calculated based on the measured concentration of VOCs, suggesting that important OH sinks in these environments are not well characterized. Measurements of total OH reactivity were performed in a forested environment during the PROPHET - AMOS field campaign (Program for Research on Oxidants: PHotochemisty, Emissions, and Transport - Atmospheric Measurements of Oxidants in Summer) using the Comparative Reactivity Method (CRM) and the Total OH Loss Rate Method (TOHLM). The site is characterized by large emissions of isoprene and monoterpenes and low anthropogenic influence. Measurements of total OH reactivity using these two techniques agree to within their respective uncertainties, giving confidence in the measured OH reactivity. In addition, measurements of trace gases (VOCs, NOx, O3) were used to perform a comprehensive apportionment of OH sinks. These measurements are used in a chemical model using the Master Chemical Mechanism to calculate the expected OH reactivity. The results will be compared to previous measurements of total OH reactivity at this site.

  13. The impact of closed-loop electronic medication management on time to first dose: a comparative study between paper and digital hospital environments.

    Science.gov (United States)

    Austin, Jodie A; Smith, Ian R; Tariq, Amina

    2018-01-22

    Closed-loop electronic medication management systems (EMMS) are recognised as an effective intervention to improve medication safety, yet evidence of their effectiveness in hospitals is limited. Few studies have compared medication turnaround time for a closed-loop electronic versus paper-based medication management environment. To compare medication turnaround times in a paper-based hospital environment with a digital hospital equipped with a closed-loop EMMS, consisting of computerised physician order entry, profiled automated dispensing cabinets packaged with unit dose medications and barcode medication administration. Data were collected during 2 weeks at three private hospital sites (one with closed-loop EMMS) within the same organisation network in Queensland, Australia. Time between scheduled and actual administration times was analysed for first dose of time-critical and non-critical medications located on the ward or sourced via pharmacy. Medication turnaround times at the EMMS site were less compared to the paper-based sites (median, IQR: 35 min, 8-57 min versus 120 min, 30-180 min, P medications, 77% were administered within 60 min of scheduled time at the EMMS site versus 38% for the paper-based sites. Similar difference was observed for non-critical medications, 80% were administered within 60 min of their scheduled time at the EMMS site versus 41% at the paper-based facilities. The study indicates medication turnaround times utilising a closed-loop EMMS are less compared to paper-based systems. This improvement may be attributable to increased accessibility of medications using automated dispensing cabinets and electronic medication administration records flagging tasks to nurses in real time. © 2018 Royal Pharmaceutical Society.

  14. Distribution of sizes of erased loops for loop-erased random walks

    OpenAIRE

    Dhar, Deepak; Dhar, Abhishek

    1997-01-01

    We study the distribution of sizes of erased loops for loop-erased random walks on regular and fractal lattices. We show that for arbitrary graphs the probability $P(l)$ of generating a loop of perimeter $l$ is expressible in terms of the probability $P_{st}(l)$ of forming a loop of perimeter $l$ when a bond is added to a random spanning tree on the same graph by the simple relation $P(l)=P_{st}(l)/l$. On $d$-dimensional hypercubical lattices, $P(l)$ varies as $l^{-\\sigma}$ for large $l$, whe...

  15. Safety report for the independent CO2 loop for cooling the samples irradiated in the vertical experimental channels of the RA reactor

    International Nuclear Information System (INIS)

    Pavlovic, A.; Zivkovic, S.; Milosevic, M.; Strugar, P.

    1969-01-01

    Independent CO 2 loop was designed for cooling the samples irradiated in the vertical experimental channels in the region of heavy water or in the graphite reflector. It is considered as a significant improvement of the RA reactor experimental possibilities. Six 'heads' are placed in vertical experimental channels and connected in parallel with the outer loop which contains out-of-reactor equipment. It is planned to irradiate samples in the 'heads' of the loop for the needs of Hot laboratory and Laboratory for reactor materials. Heat generated during sample irradiation is removed by CO 2 circulation. This report contains detailed description of the main loop, auxiliary systems, calculation results of anti reactivity and activation of construction materials of the low-temperature CO 2 loop. A separate chapter is devoted to control and regulation of temperature and pressure. Testing of the fundamental parameters of the coolant loop showed that it could fulfill more demanding tasks than designed by the project. Annex of this report includes results of leak testing for the loop 'heads' in vertical experimental channels VEK-6 and VEK-8 by helium leak detector [sr

  16. Structural consequences of the natural substitution, E9K, on reactive-site-hydrolyzed squash (Cucurbita maxima) trypsin inhibitor (CMTI), as studied by two-dimensional NMR.

    Science.gov (United States)

    Krishnamoorthi, R; Lin, C L; VanderVelde, D

    1992-06-02

    Sequence-specific hydrogen-1 NMR assignments were made to all of the 29 amino acid residues of reactive-site-hydrolyzed Cucurbita maxima trypsin inhibitor I (CMTI-I*) by the application of two-dimensional NMR (2D NMR) techniques, and its secondary structural elements (two tight turns, a 3(10)-helix, and a triple-stranded beta-sheet) were identified on the basis of short-range NOESY cross peaks and deuterium-exchange kinetics. These secondary structural elements are present in the intact inhibitor [Holak, T. A., Gondol, D., Otlewski, J., & Wilusz, T. (1989) J. Mol. Biol. 210, 635-648] and are unaffected by the hydrolysis of the reactive-site peptide bond between Arg5 and Ile6, in accordance with the earlier conclusion reached for CMTI-III* [Krishnamoorthi, R., Gong, Y.-X., Lin, C. S., & VanderVelde, D. (1992) Biochemistry 31, 898-904]. Chemical shifts of backbone hydrogen atoms, peptide NH's, and C alpha H's, of CMTI-I* were compared with those of the intact inhibitor, CMTI-I, and of the reactive-site-hydrolyzed, natural, E9K variant, CMTI-III*. Cleavage of the Arg5-Ile6 peptide bond resulted in changes of chemical shifts of most of the backbone atoms of CMTI-I, in agreement with the earlier results obtained for CMTI-III. Comparison of chemical shifts of backbone hydrogen atoms of CMTI-I* and CMTI-III* revealed no changes, except for residues Glu9 and His25. However, the intact forms of the same two proteins, CMTI-I and CMTI-III, showed small but significant perturbations of chemical shifts of residues that made up the secondary structural elements of the inhibitors.(ABSTRACT TRUNCATED AT 250 WORDS)

  17. PHOTOSPHERIC PROPERTIES OF WARM EUV LOOPS AND HOT X-RAY LOOPS

    Energy Technology Data Exchange (ETDEWEB)

    Kano, R. [National Astronomical Observatory of Japan, 2-21-1 Osawa, Mitaka, Tokyo 181-8588 (Japan); Ueda, K. [Department of Astronomy, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Tsuneta, S., E-mail: ryouhei.kano@nao.ac.jp [Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, 3-1-1 Yoshinodai, Chuo, Sagamihara, Kanagawa 252-5210 (Japan)

    2014-02-20

    We investigate the photospheric properties (vector magnetic fields and horizontal velocity) of a well-developed active region, NOAA AR 10978, using the Hinode Solar Optical Telescope specifically to determine what gives rise to the temperature difference between ''warm loops'' (1-2 MK), which are coronal loops observed in EUV wavelengths, and ''hot loops'' (>3 MK), coronal loops observed in X-rays. We found that outside sunspots, the magnetic filling factor in the solar network varies with location and is anti-correlated with the horizontal random velocity. If we accept that the observed magnetic features consist of unresolved magnetic flux tubes, this anti-correlation can be explained by the ensemble average of flux-tube motion driven by small-scale random flows. The observed data are consistent with a flux tube width of ∼77 km and horizontal flow at ∼2.6 km s{sup –1} with a spatial scale of ∼120 km. We also found that outside sunspots, there is no significant difference between warm and hot loops either in the magnetic properties (except for the inclination) or in the horizontal random velocity at their footpoints, which are identified with the Hinode X-Ray Telescope and the Transition Region and Coronal Explorer. The energy flux injected into the coronal loops by the observed photospheric motion of the magnetic fields is estimated to be 2 × 10{sup 6} erg s{sup –1} cm{sup –2}, which is the same for both warm and hot loops. This suggests that coronal properties (e.g., loop length) play a more important role in giving rise to temperature differences of active-region coronal loops than photospheric parameters.

  18. TREAT MK III Loop Thermoelastoplastic Stress Analysis for the L03 Experiment

    Energy Technology Data Exchange (ETDEWEB)

    Kennedy, James M.

    1981-03-01

    The STRAW code was used to analyze the static response of a TREAT MK III loop subjected to thermal and mechanical loadings arising from an accident situation for the purpose of determining the defiections and stresses. This analysis provides safety support for the L03 reactivity accident study. The analysis was subdivided into two tasks: (1) an analysis of a flow blockage accident (Cases A and B), where all the energy is assumed deposited in the test leg, resulting in a temperature increase from 530°F to 1720°F, with a small internal pressure throughout the loop and (2) an analysis of a second flow blockage accident (Cases C and D), where again, all the energy is assumed to he deposited in the test leg, resulting in a temperature rise from 530°F to 1845°F, with a small internal pressure throughout the loop. The purpose of these two tasks was to determine if loop failure can occur with the thermal differential across the pump and test legs. Also of interest is whether an undesirable amount of loop lateral deflection will be caused by the thermal differential. A two dimensional analysis of the TREAT MK III loop was performed. The analysis accounted for material nonlinearities, both as a function of temperature and stress, and geometric nonlinearities arising from large deflections. Straight beam elements with annular cross sections were used to model the loop. The analyses show that the maximum strains are less than 21% of their failure strains for all subcases of Cases A and B. For all subcases of cases C and D, the maximum strains are less than 53% of their failure strains. The failure strain is 27.9% for the material at 530°F, 38.1% at 1720°F and 17.8% at 1845°F. Large lateral deflections are observed when the loop is not constrained except at its clamped support--as much as 8.6 inches. However, by accounting for the constraint of the concrete biological shield, the maximum lateral deflection was reduced to less than 0.05 inches at the points of concern.

  19. Mining protein loops using a structural alphabet and statistical exceptionality

    Directory of Open Access Journals (Sweden)

    Martin Juliette

    2010-02-01

    Full Text Available Abstract Background Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. Results We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times. Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words. These structural words have low structural variability (mean RMSd of 0.85 Å. As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues and long loops. Moreover, half of

  20. Mining protein loops using a structural alphabet and statistical exceptionality.

    Science.gov (United States)

    Regad, Leslie; Martin, Juliette; Nuel, Gregory; Camproux, Anne-Claude

    2010-02-04

    Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 A). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of

  1. CTCF Binding Sites in the Herpes Simplex Virus 1 Genome Display Site-Specific CTCF Occupation, Protein Recruitment, and Insulator Function.

    Science.gov (United States)

    Washington, Shannan D; Musarrat, Farhana; Ertel, Monica K; Backes, Gregory L; Neumann, Donna M

    2018-04-15

    There are seven conserved CTCF binding domains in the herpes simplex virus 1 (HSV-1) genome. These binding sites individually flank the latency-associated transcript (LAT) and the immediate early (IE) gene regions, suggesting that CTCF insulators differentially control transcriptional domains in HSV-1 latency. In this work, we show that two CTCF binding motifs in HSV-1 display enhancer blocking in a cell-type-specific manner. We found that CTCF binding to the latent HSV-1 genome was LAT dependent and that the quantity of bound CTCF was site specific. Following reactivation, CTCF eviction was dynamic, suggesting that each CTCF site was independently regulated. We explored whether CTCF sites recruit the polycomb-repressive complex 2 (PRC2) to establish repressive domains through a CTCF-Suz12 interaction and found that Suz12 colocalized to the CTCF insulators flanking the ICP0 and ICP4 regions and, conversely, was removed at early times postreactivation. Collectively, these data support the idea that CTCF sites in HSV-1 are independently regulated and may contribute to lytic-latent HSV-1 control in a site-specific manner. IMPORTANCE The role of chromatin insulators in DNA viruses is an area of interest. It has been shown in several beta- and gammaherpesviruses that insulators likely control the lytic transcriptional profile through protein recruitment and through the formation of three-dimensional (3D) chromatin loops. The ability of insulators to regulate alphaherpesviruses has been understudied to date. The alphaherpesvirus HSV-1 has seven conserved insulator binding motifs that flank regions of the genome known to contribute to the establishment of latency. Our work presented here contributes to the understanding of how insulators control transcription of HSV-1. Copyright © 2018 American Society for Microbiology.

  2. Studies on reactivity of coal surfaces at low temperature; Teion ni okeru sekitan hyomen no hannosei no kento

    Energy Technology Data Exchange (ETDEWEB)

    Yasuda, H.; Kaiho, M.; Yamada, O.; Soneda, Y.; Kobayashi, M.; Makino, M. [National Institute for Resources and Environment, Tsukuba (Japan)

    1996-10-28

    With an objective to learn reactivity of coal at its surface, surfaces of oxidized coal samples were investigated. Miike coal was oxidized by using {sup 18}O2 in a closed loop system. As the reaction progresses, proportion of CO2 including isotopes increased rapidly as a result of oxidation of CO sites existing in the coal and the newly generated C{sup 18}O sites. The oxidizing reaction progressed via oxygen adsorbing sites generated near the surface, and oxygen containing groups. An FT-IR analysis estimated the depth of the oxidized layer to be 10{mu}m or less from particle surface. The oxidized coal was pulverized to see its surface condition. Functional groups introduced by the oxidation enter into the vicinity of the surface in a form to desorb as CO. CO2 is trapped in inner pores. The coal surface was observed by using an atomic force microscope. No observable openings in the pore structure were discerned on the surface before the oxidation, and the structure agrees with a closed pore model. Surface image oxidized in-situ by oxygen for one hour had slight roundness, which led to a supposition of structural change, and changes in the functional group and adsorption species. 7 refs., 5 figs.

  3. Formation of reactive oxygen by N2O decomposition over binuclear cationic sites of Fe-ferrierite zeolite: Periodic DFT + U study

    Science.gov (United States)

    Avdeev, Vasilii I.; Bedilo, Alexander F.

    2018-03-01

    The electronic nature of sites over Fe-ferrierite zeolite stabilizing active α-oxygen is analyzed by the periodic DFT + U approach. It is shown that two antiferromagnetically coupled Fe2+ cations with bridging OH-bonds form a stable bi-nuclear site of the [Fe2+Fe2+] doped FER complex. Frontier orbitals of this complex populated by two electrons with minority spins are localized in the bandgap. As a result, [Fe2+Fe2+] unit acquires the properties of a binuclear Lewis acid dipolarophile for 1,3-dipole N2O. First reaction step of N2O decomposition follows the Huisgen‧s concept of the 1,3-dipolar cycloaddition concept followed by the formation of reactive oxygen species Fesbnd O.

  4. Looping and clustering model for the organization of protein-DNA complexes on the bacterial genome

    Science.gov (United States)

    Walter, Jean-Charles; Walliser, Nils-Ole; David, Gabriel; Dorignac, Jérôme; Geniet, Frédéric; Palmeri, John; Parmeggiani, Andrea; Wingreen, Ned S.; Broedersz, Chase P.

    2018-03-01

    The bacterial genome is organized by a variety of associated proteins inside a structure called the nucleoid. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the looping and clustering model, which employs a statistical physics approach to describe protein-DNA complexes. The looping and clustering model accounts for the extrusion of DNA loops from a cluster of interacting DNA-bound proteins that is organized around a single high-affinity binding site. Conceptually, the structure of the protein-DNA complex is determined by a competition between attractive protein interactions and loop closure entropy of this protein-DNA cluster on the one hand, and the positional entropy for placing loops within the cluster on the other. Indeed, we show that the protein interaction strength determines the ‘tightness’ of the loopy protein-DNA complex. Thus, our model provides a theoretical framework for quantitatively computing the binding profiles of ParB-like proteins around a cognate (parS) binding site.

  5. Multiple Flow Loop SCADA System Implemented on the Production Prototype Loop

    Energy Technology Data Exchange (ETDEWEB)

    Baily, Scott A. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Dalmas, Dale Allen [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Wheat, Robert Mitchell [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Woloshun, Keith Albert [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Dale, Gregory E. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-11-16

    The following report covers FY 15 activities to develop supervisory control and data acquisition (SCADA) system for the Northstar Moly99 production prototype gas flow loop. The goal of this effort is to expand the existing system to include a second flow loop with a larger production-sized blower. Besides testing the larger blower, this system will demonstrate the scalability of our solution to multiple flow loops.

  6. Chemical looping coal gasification with calcium ferrite and barium ferrite via solid–solid reactions

    International Nuclear Information System (INIS)

    Siriwardane, Ranjani; Riley, Jarrett; Tian, Hanjing; Richards, George

    2016-01-01

    Highlights: • BaFe 2 O 4 and CaFe 2 O 4 are excellent for chemical looping coal gasification. • BaFe 2 O 4 and CaFe 2 O 4 have minimal reactivity with synthesis gas. • Steam enhances the gasification process with these oxygen carriers. • Reaction rates of steam gasification of coal with CaFe 2 O 4 was better than with gaseous oxygen. • Coal gasification appears to be via solid–solid interaction with the oxygen carrier. - Abstract: Coal gasification to produce synthesis gas by chemical looping was investigated with two oxygen carriers, barium ferrite (BaFe 2 O 4 ) and calcium ferrite (CaFe 2 O 4 ). Thermo-gravimetric analysis (TGA) and fixed-bed flow reactor data indicated that a solid–solid interaction occurred between oxygen carriers and coal to produce synthesis gas. Both thermodynamic analysis and experimental data indicated that BaFe 2 O 4 and CaFe 2 O 4 have high reactivity with coal but have a low reactivity with synthesis gas, which makes them very attractive for the coal gasification process. Adding steam increased the production of hydrogen (H 2 ) and carbon monoxide (CO), but carbon dioxide (CO 2 ) remained low because these oxygen carriers have minimal reactivity with H 2 and CO. Therefore, the combined steam–oxygen carrier produced the highest quantity of synthesis gas. It appeared that neither the water–gas shift reaction nor the water splitting reaction promoted additional H 2 formation with the oxygen carriers when steam was present. Wyodak coal, which is a sub-bituminous coal, had the best gasification yield with oxygen carrier–steam while Illinois #6 coal had the lowest. The rate of gasification and selectivity for synthesis gas production was significantly higher when these oxygen carriers were present during steam gasification of coal. The rates and synthesis gas yields during the temperature ramps of coal–steam with oxygen carriers were better than with gaseous oxygen.

  7. Design aspects of commercial open-loop heat pump systems

    Energy Technology Data Exchange (ETDEWEB)

    Rafferty, Kevin

    2000-01-01

    Open loop (or groundwater heat pump systems are the oldest of the ground-source systems. Common design variations include direct (groundwater used directly in the heat pump units), indirect (building loop isolated with a plate heat exchanger), and standing column (water produced and returned to the same well). Direct systems are typically limited to the smallest applications. Standing column systems are employed in hard rock geology sites where it is not possible to produce sufficient water for a conventional system. Due to its greater potential application, this paper reviews key design aspects of the indirect approach. The general design procedure is reviewed, identification of optimum groundwater flow, heat exchanger selection guidelines, well pump control, disposal options, well spacing, piping connections and related issues.

  8. Design Aspects of Commerical Open-Loop Heat Pump Systems

    Energy Technology Data Exchange (ETDEWEB)

    Rafferty, Kevin

    2001-03-01

    Open loop (or groundwater heat pump systems are the oldest of the ground-source systems. Common design variations include direct (groundwater used directly in the heat pump units), indirect (building loop isolated with a plate heat exchanger), and standing column (water produced and returned to the same well). Direct systems are typically limited to the smallest applications. Standing column systems are employed in hard rock geology sites where it is not possible to produce sufficient water for a conventional system. Due to its greater potential application, this paper reviews key design aspects of the indirect approach. The general design procedure is reviewed, identification of optimum groundwater flow, heat exchanger selection guidelines, well pump control, disposal options, well spacing, piping connections and related issues.

  9. Recovery Act: Novel Oxygen Carriers for Coal-fueled Chemical Looping

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Wei-Ping; Cao, Yan

    2012-11-30

    Chemical Looping Combustion (CLC) could totally negate the necessity of pure oxygen by using oxygen carriers for purification of CO{sub 2} stream during combustion. It splits the single fuel combustion reaction into two linked reactions using oxygen carriers. The two linked reactions are the oxidation of oxygen carriers in the air reactor using air, and the reduction of oxygen carriers in the fuel reactor using fuels (i.e. coal). Generally metal/metal oxides are used as oxygen carriers and operated in a cyclic mode. Chemical looping combustion significantly improves the energy conversion efficiency, in terms of the electricity generation, because it improves the reversibility of the fuel combustion process through two linked parallel processes, compared to the conventional combustion process, which is operated far away from its thermo-equilibrium. Under the current carbon-constraint environment, it has been a promising carbon capture technology in terms of fuel combustion for power generation. Its disadvantage is that it is less mature in terms of technological commercialization. In this DOE-funded project, accomplishment is made by developing a series of advanced copper-based oxygen carriers, with properties of the higher oxygen-transfer capability, a favorable thermodynamics to generate high purity of CO{sub 2}, the higher reactivity, the attrition-resistance, the thermal stability in red-ox cycles and the achievement of the auto-thermal heat balance. This will be achieved into three phases in three consecutive years. The selected oxygen carriers with final-determined formula were tested in a scaled-up 10kW coal-fueled chemical looping combustion facility. This scaled-up evaluation tests (2-day, 8-hour per day) indicated that, there was no tendency of agglomeration of copper-based oxygen carriers. Only trace-amount of coke or carbon deposits on the copper-based oxygen carriers in the fuel reactor. There was also no evidence to show the sulphidization of oxygen

  10. On loop extensions and cohomology of loops

    OpenAIRE

    Benítez, Rolando Jiménez; Meléndez, Quitzeh Morales

    2015-01-01

    In this paper are defined cohomology-like groups that classify loop extensions satisfying a given identity in three variables for association identities, and in two variables for the case of commutativity. It is considered a large amount of identities. This groups generalize those defined in works of Nishigori [2] and of Jhonson and Leedham-Green [4]. It is computed the number of metacyclic extensions for trivial action of the quotient on the kernel in one particular case for left Bol loops a...

  11. Binding of C-reactive protein to human polymorphonuclear leukocytes: evidence for association of binding sites with Fc receptors

    International Nuclear Information System (INIS)

    Mueller, H.; Fehr, J.

    1986-01-01

    The functional similarities between C-reactive protein (CRP) and IgG raised the question as to whether human phagocytes are stimulated by CRP in the same way as by binding of antigen-complexes or aggregated IgG to their Fc receptors. Studies with the use of highly purified 125 I-labeled CRP showed specific and saturable binding to human polymorphonuclear leukocytes (PNM) with a K/sub D/ of 10.5 +/- 5.7 x 10 -8 M only when carried out in heat-inactivated plasma. The number of specific binding sites per cell was estimated at 1 to 3 x 10 6 . Competitive inhibition of CRP binding by antigen-complexed or aggregated IgG suggests CRP binding sites to be associated IgG suggests CRP binding sites to be associated with PMN Fc receptors. Only when assayed in heat-inactivated plasma did CRP binding induce adherence of cells to tissue culture dishes. However, no metabolic and potentially cytotoxic simulation of PMN was detected during CRP plasma-dependent attachment to surfaces: induction of aggregation, release of secondary granule constituents, and activation of the hexose monophosphate pathway were not observed. These results imply that CRP-PMN interactions is dependent on an additional factor present in heat-inactivated plasma and is followed only by a complement-independent increase in PMN attachment to surfaces. Because CRP was found to be deposits at sites of tissue injury, the CRP-mediated adherence of PMN may be an important step in localizing an inflammatory focus

  12. Site of mitochondrial reactive oxygen species production in skeletal muscle of chronic obstructive pulmonary disease and its relationship with exercise oxidative stress.

    Science.gov (United States)

    Puente-Maestu, Luis; Tejedor, Alberto; Lázaro, Alberto; de Miguel, Javier; Alvarez-Sala, Luis; González-Aragoneses, Federico; Simón, Carlos; Agustí, Alvar

    2012-09-01

    Exercise triggers skeletal muscle oxidative stress in patients with chronic obstructive pulmonary disease (COPD). The objective of this research was to study the specific sites of reactive oxygen species (ROS) production in mitochondria isolated from skeletal muscle of patients with COPD and its relationship with local oxidative stress induced by exercise. Vastus lateralis biopsies were obtained in 16 patients with COPD (66 ± 10 yr; FEV(1), 54 ± 12% ref) and in 14 control subjects with normal lung function who required surgery because of lung cancer (65 ± 7 yr; FEV(1), 91 ± 14% ref) at rest and after exercise. In these biopsies we isolated mitochondria and mitochondrial membrane fragments and determined in vitro mitochondrial oxygen consumption (Mit$$\\stackrel{.}{\\hbox{ V }}$$o(2)) and ROS production before and after inhibition of complex I (rotenone), complex II (stigmatellin), and complex III (antimycin-A). We related the in vitro ROS production during state 3 respiration), which mostly corresponds to the mitochondria respiratory state during exercise, with skeletal muscle oxidative stress after exercise, as measured by thiobarbituric acid reactive substances.State 3 Mit$$\\stackrel{.}{\\hbox{ V }}$$o(2) was similar in patients with COPD and control subjects (191 ± 27 versus 229 ± 46 nmol/min/mg; P = 0.058), whereas H(2)O(2) production was higher in the former (147 ± 39 versus 51 ± 8 pmol/mg/h; P release by mitochondria in patients with COPD and in control subjects. The mitochondrial production of H(2)O(2) in state 3 respiration was related (r = 0.69; P < 0.001) to postexercise muscle thiobarbituric acid reactive substance levels. Our results show that complex III is the main site of the enhanced mitochondrial H(2)O(2) production that occurs in skeletal muscle of patients with COPD, and the latter appears to contribute to muscle oxidative damage.

  13. Rapid Simulation of Flat Knitting Loops Based On the Yarn Texture and Loop Geometrical Model

    Directory of Open Access Journals (Sweden)

    Lu Zhiwen

    2017-06-01

    Full Text Available In order to create realistic loop primitives suitable for the fast computer-aided design (CAD of the flat knitted fabric, we have a research on the geometric model of the loop as well as the variation of the loop surface. Establish the texture variation model based on the changing process from the normal yarn to loop that provides the realistic texture of the simulative loop. Then optimize the simulative loop based on illumination variation. This paper develops the computer program with the optimization algorithm and achieves the loop simulation of different yarns to verify the feasibility of the proposed algorithm. Our work provides a fast CAD of the flat knitted fabric with loop simulation, and it is not only more realistic but also material adjustable. Meanwhile it also provides theoretical value for the flat knitted fabric computer simulation.

  14. Density functional theory and surface reactivity study of bimetallic AgnYm (n+m = 10) clusters

    Science.gov (United States)

    Hussain, Riaz; Hussain, Abdullah Ijaz; Chatha, Shahzad Ali Shahid; Hussain, Riaz; Hanif, Usman; Ayub, Khurshid

    2018-06-01

    Density functional theory calculations have been performed on pure silver (Agn), yttrium (Ym) and bimetallic silver yttrium clusters AgnYm (n + m = 2-10) for reactivity descriptors in order to realize sites for nucleophilic and electrophilic attack. The reactivity descriptors of the clusters, studied as a function of cluster size and shape, reveal the presence of different type of reactive sites in a cluster. The size and shape of the pure silver, yttrium and bimetallic silver yttrium cluster (n = 2-10) strongly influences the number and position of active sites for an electrophilic and/or nucleophilic attack. The trends of reactivities through reactivity descriptors are confirmed through comparison with experimental data for CO binding with silver clusters. Moreover, the adsorption of CO on bimetallic silver yttrium clusters is also evaluated. The trends of binding energies support the reactivity descriptors values. Doping of pure cluster with the other element also influence the hardness, softness and chemical reactivity of the clusters. The softness increases as we increase the number of silver atoms in the cluster, whereas the hardness decreases. The chemical reactivity increases with silver doping whereas it decreases by increasing yttrium concentration. Silver atoms are nucleophilic in small clusters but changed to electrophilic in large clusters.

  15. Reactive dual magnetron sputtering for large area application

    International Nuclear Information System (INIS)

    Struempfel, J.

    2002-01-01

    Production lines for large area coating demand high productivity of reactive magnetron sputtering processes. Increased dynamic deposition rates for oxides and nitrides were already obtained by using of highly powered magnetrons in combination with advanced sputter techniques. However, besides high deposition rates the uniformity of such coatings has to be carefully considered. First the basics of reactive sputtering processes and dual magnetron sputtering are summarized. Different methods for process stabilization and control are commonly used for reactive sputtering. The Plasma Emission Monitor (PE M) offers the prerequisite for fast acting process control derived from the in-situ intensity measurements of a spectral line of the sputtered target material. Combined by multiple Plasma Emission Monitor control loops segmented gas manifolds are able to provide excellent thin film uniformity at high deposition rates. The Dual Magnetron allows a broad range of processing by different power supply modes. Medium frequency, DC and pulsed DC power supplies can be used for high quality layers. Whereas the large area coating of highly isolating layers like TiO 2 or SiO 2 is dominated by MF sputtering best results for coating with transparent conductive oxides are obtained by dual DC powering of the dual magnetron arrangement. (Author)

  16. Identification of a highly reactive threonine residue at the active site of γ-glutamyl transpeptidase

    International Nuclear Information System (INIS)

    Stole, E.; Seddon, A.P.; Wellner, D.; Meister, A.

    1990-01-01

    γ-Glutamyl transpeptidase an enzyme of major importance in glutathione metabolism, was inactivated by treating it with L-(αS,5S)-α-amino-3-chloro-4,5-dihydro-5-[3- 14 C]isoxazoleacetic acid. This selective reagent binds stoichiometrically to the enzyme; more than 90% of the label was bound to its light subunit. Enzymatic digestion of the light subunit gave a 14 C-labeled peptide that corresponds to amino acid residues 517-527 of the enzyme and two incomplete digestion products that contain this labeled peptide moiety. The radioactivity associated with this peptide was released with threonine-523 during sequencing by the automated gas-phase Edman method. The light subunit contains 14 other threonine residues and a total of 19 serine residues; these were not labeled. Threonine-523 is situated in the enzyme in an environment that greatly increases its reactivity, indicating that other amino acid residues of the enzyme must also participate in the active-site chemistry of the enzyme

  17. Multi-loop PWR modeling and hardware-in-the-loop testing using ACSL

    International Nuclear Information System (INIS)

    Thomas, V.M.; Heibel, M.D.; Catullo, W.J.

    1989-01-01

    Westinghouse has developed an Advanced Digital Feedwater Control System (ADFCS) which is aimed at reducing feedwater related reactor trips through improved control performance for pressurized water reactor (PWR) power plants. To support control system setpoint studies and functional design efforts for the ADFCS, an ACSL based model of the nuclear steam supply system (NSSS) of a Westinghouse (PWR) was generated. Use of this plant model has been extended from system design to system testing through integration of the model into a Hardware-in-Loop test environment for the ADFCS. This integration includes appropriate interfacing between a Gould SEL 32/87 computer, upon which the plant model executes in real time, and the Westinghouse Distributed Processing family (WDPF) test hardware. A development program has been undertaken to expand the existing ACSL model to include capability to explicitly model multiple plant loops, steam generators, and corresponding feedwater systems. Furthermore, the program expands the ADFCS Hardware-in-Loop testing to include the multi-loop plant model. This paper provides an overview of the testing approach utilized for the ADFCS with focus on the role of Hardware-in-Loop testing. Background on the plant model, methodology and test environment is also provided. Finally, an overview is presented of the program to expand the model and associated Hardware-in-Loop test environment to handle multiple loops

  18. Random walk loop soup

    OpenAIRE

    Lawler, Gregory F.; Ferreras, José A. Trujillo

    2004-01-01

    The Brownian loop soup introduced in Lawler and Werner (2004) is a Poissonian realization from a sigma-finite measure on unrooted loops. This measure satisfies both conformal invariance and a restriction property. In this paper, we define a random walk loop soup and show that it converges to the Brownian loop soup. In fact, we give a strong approximation result making use of the strong approximation result of Koml\\'os, Major, and Tusn\\'ady. To make the paper self-contained, we include a proof...

  19. Structure-function paradigm in human myoglobin: how a single-residue substitution affects NO reactivity at low pO2.

    Science.gov (United States)

    Scorciapino, Mariano Andrea; Spiga, Enrico; Vezzoli, Alessandra; Mrakic-Sposta, Simona; Russo, Rosaria; Fink, Bruno; Casu, Mariano; Gussoni, Maristella; Ceccarelli, Matteo

    2013-05-22

    This work is focused on the two more expressed human myoglobin isoforms. In the literature, their different overexpression in high-altitude natives was proposed to be related to alternative/complementary functions in hypoxia. Interestingly, they differ only at residue-54, lysine or glutamate, which is external and far from the main binding site. In order to ascertain whether these two almost identical myoglobins might exert different functions and to contribute to a deeper understanding about myoglobin's oxygen-level dependent functioning, they have been compared with respect to dynamics, heme electronic structure, and NO reactivity at different O2 levels. Electron paramagnetic resonance (EPR) spectroscopy was employed to investigate the electronic structure of the nitrosyl-form, obtaining fundamental clues about a different bond interaction between the heme-iron and the proximal histidine and highlighting striking differences in NO reactivity, especially at a very low pO2. The experimental results well matched with the information provided by molecular dynamics simulations, which showed a significantly different dynamics for the two proteins only in the absence of O2. The single mutation differentiating the two myoglobins resulted in strongly affecting the plasticity of the CD-region (C-helix-loop-D-helix), whose fluctuations, being coupled to the solvent, were found to be correlated with the dynamics of the distal binding site. In the absence of O2, on the one hand a significantly different probability for the histidine-gate opening has been shown by MD simulations, and on the other a different yield of myoglobin-NO formation was experimentally observed through EPR.

  20. Ni2+-binding RNA motifs with an asymmetric purine-rich internal loop and a G-A base pair.

    Science.gov (United States)

    Hofmann, H P; Limmer, S; Hornung, V; Sprinzl, M

    1997-01-01

    RNA molecules with high affinity for immobilized Ni2+ were isolated from an RNA pool with 50 randomized positions by in vitro selection-amplification. The selected RNAs preferentially bind Ni2+ and Co2+ over other cations from first series transition metals. Conserved structure motifs, comprising about 15 nt, were identified that are likely to represent the Ni2+ binding sites. Two conserved motifs contain an asymmetric purine-rich internal loop and probably a mismatch G-A base pair. The structure of one of these motifs was studied with proton NMR spectroscopy and formation of the G-A pair at the junction of helix and internal loop was demonstrated. Using Ni2+ as a paramagnetic probe, a divalent metal ion binding site near this G-A base pair was identified. Ni2+ ions bound to this motif exert a specific stabilization effect. We propose that small asymmetric purine-rich loops that contain a G-A interaction may represent a divalent metal ion binding site in RNA. PMID:9409620

  1. Neutron transport in irradiation loops (IRENE loop)

    International Nuclear Information System (INIS)

    Sarsam, Maher.

    1980-09-01

    This thesis is composed of two parts with different aspects. Part one is a technical description of the loop and its main ancillary facilities as well as of the safety and operational regulations. The measurement methods on the model of the ISIS reactor and on the loop in the OSIRIS reactor are described. Part two deals with the possibility of calculating the powers dissipated by each rod of the fuel cluster, using appropriate computer codes, not only in the reflector but also in the core and to suggest a method of calculation [fr

  2. Exploring the surface reactivity of 3d metal endofullerenes: a density-functional theory study.

    Science.gov (United States)

    Estrada-Salas, Rubén E; Valladares, Ariel A

    2009-09-24

    Changes in the preferential sites of electrophilic, nucleophilic, and radical attacks on the pristine C60 surface with endohedral doping using 3d transition metal atoms were studied via two useful reactivity indices, namely the Fukui functions and the molecular electrostatic potential. Both of these were calculated at the density functional BPW91 level of theory with the DNP basis set. Our results clearly show changes in the preferential reactivity sites on the fullerene surface when it is doped with Mn, Fe, Co, or Ni atoms, whereas there are no significant changes in the preferential reactivity sites on the C60 surface upon endohedral doping with Cu and Zn atoms. Electron affinities (EA), ionization potentials (IP), and HOMO-LUMO gaps (Eg) were also calculated to complete the study of the endofullerene's surface reactivity. These findings provide insight into endofullerene functionalization, an important issue in their application.

  3. Loop space representation of quantum general relativity and the group of loops

    International Nuclear Information System (INIS)

    Gambini, R.

    1991-01-01

    The action of the constraints of quantum general relativity on a general state in the loop representation is coded in terms of loop derivatives. These differential operators are related to the infinitesimal generators of the group of loops and generalize the area derivative first considered by Mandelstam. A new sector of solutions of the physical states space of nonperturbative quantum general relativity is found. (orig.)

  4. R-loops and initiation of DNA replication in human cells: a missing link?

    Directory of Open Access Journals (Sweden)

    Rodrigo eLombraña

    2015-04-01

    Full Text Available The unanticipated widespread occurrence of stable hybrid DNA/RNA structures (R-loops in human cells and the increasing evidence of their involvement in several human malignancies have invigorated the research on R-loop biology in recent years. Here we propose that physiological R-loop formation at CpG island promoters can contribute to DNA replication origin specification at these regions, the most efficient replication initiation sites in mammalian cells. Quite likely, this occurs by the strand-displacement reaction activating the formation of G-quadruplex structures that target the Origin Recognition Complex (ORC in the single-stranded conformation. In agreement with this, we found that R-loops co-localize with the ORC within the same CpG island region in a significant fraction of these efficient replication origins, precisely at the position displaying the highest density of G4 motifs. This scenario builds on the connection between transcription and replication in human cells and suggests that R-loop dysregulation at CpG island promoter-origins might contribute to the phenotype of DNA replication abnormalities and loss of genome integrity detected in cancer cells.

  5. Fermions and loops on graphs: I. Loop calculus for determinants

    International Nuclear Information System (INIS)

    Chernyak, Vladimir Y; Chertkov, Michael

    2008-01-01

    This paper is the first in a series devoted to evaluation of the partition function in statistical models on graphs with loops in terms of the Berezin/fermion integrals. The paper focuses on a representation of the determinant of a square matrix in terms of a finite series, where each term corresponds to a loop on the graph. The representation is based on a fermion version of the loop calculus, previously introduced by the authors for graphical models with finite alphabets. Our construction contains two levels. First, we represent the determinant in terms of an integral over anti-commuting Grassmann variables, with some reparametrization/gauge freedom hidden in the formulation. Second, we show that a special choice of the gauge, called the BP (Bethe–Peierls or belief propagation) gauge, yields the desired loop representation. The set of gauge fixing BP conditions is equivalent to the Gaussian BP equations, discussed in the past as efficient (linear scaling) heuristics for estimating the covariance of a sparse positive matrix

  6. Dechanneling by dislocation loops

    International Nuclear Information System (INIS)

    Chalant, Gerard.

    1976-09-01

    Ion implantation always induces the creation of dislocation loops. When the damage profile is determined by a backscattering technique, the dechanneling by these loops is implicitely at the origin of these measurements. The dechanneling of alpha particles by dislocation loops produced by the coalescence of quenched-in vacancies in aluminium is studied. The dechanneling and the concentration of loops were determined simultaneously. The dechanneling width around dislocation was found equal to lambda=6A, both for perfect and imperfect loops having a mean diameter d=250A. In the latter case, a dechanneling probability chi=0.34 was determined for the stacking fault, in good agreement with previous determination in gold. A general formula is proposed which takes into account the variation of lambda with the curvature (or the diameter d) of the loops. Finally, by a series of isothermal anneals, the self-diffusion energy ΔH of aluminium was measured. The value obtained ΔH=1.32+-0.10eV is in good agreement with the values obtained by other methods [fr

  7. Assessment of solid reactive mixtures for the development of biological permeable reactive barriers

    International Nuclear Information System (INIS)

    Pagnanelli, Francesca; Viggi, Carolina Cruz; Mainelli, Sara; Toro, Luigi

    2009-01-01

    Solid reactive mixtures were tested as filling material for the development of biological permeable reactive barriers for the treatment of heavy metals contaminated waters. Mixture selection was performed by taking into account the different mechanisms operating in sulphate and cadmium removal with particular attention to bioprecipitation and sorption onto the organic matrices in the mixtures. Suspensions of eight reactive mixtures were tested for sulphate removal (initial concentration 3 g L -1 ). Each mixture was made up of four main functional components: a mix of organic sources for bacterial growth, a neutralizing agent, a porous medium and zero-valent iron. The best mixture among the tested ones (M8: 6% leaves, 9% compost, 3% zero-valent iron, 30% silica sand, 30% perlite, 22% limestone) presented optimal conditions for SRB growth (pH 7.8 ± 0.1; E h = -410 ± 5 mV) and 83% sulphate removal in 22 days (25% due to bioreduction, 32% due to sorption onto compost and 20% onto leaves). M8 mixture allowed the complete abatement of cadmium with a significant contribution of sorption over bioprecipitation (6% Cd removal due to SRB activity). Sorption properties, characterised by potentiometric titrations and related modelling, were mainly due to carboxylic sites of organic components used in reactive mixtures.

  8. Distribution of u.v.-induced repair events in higher-order chromatin loops in human and hamster fibroblasts

    International Nuclear Information System (INIS)

    Mullenders, L.H.F.; Zeeland, A.A. van; Natarajan, A.T.; Kesteren, A.C. van; Bussmann, C.J.M.

    1986-01-01

    The repair of u.v.-induced damage in human and rodent cells was investigated at the level of DNA loops attached to the nuclear matrix. After 2 h post-u.v. incubation, DNase I digestion studies revealed a 3- to 4-fold enrichment of repair-labeled DNA at the nuclear matrix in four xeroderma pigmentosum cell strains belonging to complementation group C. Two xeroderma pigmentosum cell strains of complementation group D and Syrian hamster embryonic cells, as well as in HeLa cells and normal human fibroblasts, no enrichment of repair-labeled DNA at the nuclear matrix was observed. Visualization of repair events in DNA loops by autoradiography of DNA halo - matrix structures confirmed the biochemical observations. The presence or absence of preferential repair of nuclear matrix-associated DNA paralleled the presence or absence of inhomogeneity in the distribution of T4 endonuclease-V-sensitive sites. In xeroderma pigmentosum cells of complementation group C showed that after 2 h post-u.v. incubation, repair events were found at both attachment sites in a limited number of loops and that large domains of loops were not subjected to repair. (author)

  9. The Brownian loop soup

    OpenAIRE

    Lawler, Gregory F.; Werner, Wendelin

    2003-01-01

    We define a natural conformally invariant measure on unrooted Brownian loops in the plane and study some of its properties. We relate this measure to a measure on loops rooted at a boundary point of a domain and show how this relation gives a way to ``chronologically add Brownian loops'' to simple curves in the plane.

  10. Permeable bio-reactive barriers for hydrocarbon remediation in Antarctica

    Energy Technology Data Exchange (ETDEWEB)

    Mumford, K.A.; Stevens, G.W.; Gore, D.B. [Melbourne Univ., Victoria (Australia). Dept. of Chemical and Biomoleculuar Engineering, Particulate Fluids Processing Centre; Snape, I.; Rayner, J.L. [Australian Antarctic Div., Kingston, Tasmania (Australia); Gore, D.B. [Macquarie Univ., Sydney, NSW (Australia). Dept. of Environmental Science

    2010-07-01

    This study assessed the performance of a permeable bio-reactive barrier designed to treat contaminated water. The bio-reactive barrier was installed at a fuel spill site located in the Windmill Islands, Antarctica. A funnel and gate design was used to prevent contaminant migration beyond the barrier location as well as to ensure controlled nutrient delivery. The study also investigated the performance of the bio-reactive barrier in regions with freeze-thaw conditions. The 4-year project was also conducted to assess optimal conditions for enhancing the barrier's ability to degrade hydrocarbons.

  11. Multivariable model predictive control design of reactive distillation column for Dimethyl Ether production

    Science.gov (United States)

    Wahid, A.; Putra, I. G. E. P.

    2018-03-01

    Dimethyl ether (DME) as an alternative clean energy has attracted a growing attention in the recent years. DME production via reactive distillation has potential for capital cost and energy requirement savings. However, combination of reaction and distillation on a single column makes reactive distillation process a very complex multivariable system with high non-linearity of process and strong interaction between process variables. This study investigates a multivariable model predictive control (MPC) based on two-point temperature control strategy for the DME reactive distillation column to maintain the purities of both product streams. The process model is estimated by a first order plus dead time model. The DME and water purity is maintained by controlling a stage temperature in rectifying and stripping section, respectively. The result shows that the model predictive controller performed faster responses compared to conventional PI controller that are showed by the smaller ISE values. In addition, the MPC controller is able to handle the loop interactions well.

  12. A binding-site barrier affects imaging efficiency of high affinity amyloid-reactive peptide radiotracers in vivo.

    Science.gov (United States)

    Wall, Jonathan S; Williams, Angela; Richey, Tina; Stuckey, Alan; Huang, Ying; Wooliver, Craig; Macy, Sallie; Heidel, Eric; Gupta, Neil; Lee, Angela; Rader, Brianna; Martin, Emily B; Kennel, Stephen J

    2013-01-01

    Amyloid is a complex pathology associated with a growing number of diseases including Alzheimer's disease, type 2 diabetes, rheumatoid arthritis, and myeloma. The distribution and extent of amyloid deposition in body organs establishes the prognosis and can define treatment options; therefore, determining the amyloid load by using non-invasive molecular imaging is clinically important. We have identified a heparin-binding peptide designated p5 that, when radioiodinated, was capable of selectively imaging systemic visceral AA amyloidosis in a murine model of the disease. The p5 peptide was posited to bind effectively to amyloid deposits, relative to similarly charged polybasic heparin-reactive peptides, because it adopted a polar α helix secondary structure. We have now synthesized a variant, p5R, in which the 8 lysine amino acids of p5 have been replaced with arginine residues predisposing the peptide toward the α helical conformation in an effort to enhance the reactivity of the peptide with the amyloid substrate. The p5R peptide had higher affinity for amyloid and visualized AA amyloid in mice by using SPECT/CT imaging; however, the microdistribution, as evidenced in micro-autoradiographs, was dramatically altered relative to the p5 peptide due to its increased affinity and a resultant "binding site barrier" effect. These data suggest that radioiodinated peptide p5R may be optimal for the in vivo detection of discreet, perivascular amyloid, as found in the brain and pancreatic vasculature, by using molecular imaging techniques; however, peptide p5, due to its increased penetration, may yield more quantitative imaging of expansive tissue amyloid deposits.

  13. Mutation of mapped TIA-1/TIAR binding sites in the 3' terminal stem-loop of West Nile virus minus-strand RNA in an infectious clone negatively affects genomic RNA amplification.

    Science.gov (United States)

    Emara, Mohamed M; Liu, Hsuan; Davis, William G; Brinton, Margo A

    2008-11-01

    Previous data showed that the cellular proteins TIA-1 and TIAR bound specifically to the West Nile virus 3' minus-strand stem-loop [WNV3'(-)SL] RNA (37) and colocalized with flavivirus replication complexes in WNV- and dengue virus-infected cells (21). In the present study, the sites on the WNV3'(-)SL RNA required for efficient in vitro T-cell intracellular antigen-related (TIAR) and T-cell intracellular antigen-1 (TIA-1) protein binding were mapped to short AU sequences (UAAUU) located in two internal loops of the WNV3'(-)SL RNA structure. Infectious clone RNAs with all or most of the binding site nucleotides in one of the 3' (-)SL loops deleted or substituted did not produce detectable virus after transfection or subsequent passage. With one exception, deletion/mutation of a single terminal nucleotide in one of the binding sequences had little effect on the efficiency of protein binding or virus production, but mutation of a nucleotide in the middle of a binding sequence reduced both the in vitro protein binding efficiency and virus production. Plaque size, intracellular genomic RNA levels, and virus production progressively decreased with decreasing in vitro TIAR/TIA-1 binding activity, but the translation efficiency of the various mutant RNAs was similar to that of the parental RNA. Several of the mutant RNAs that inefficiently interacted with TIAR/TIA-1 in vitro rapidly reverted in vivo, indicating that they could replicate at a low level and suggesting that an interaction between TIAR/TIA-1 and the viral 3'(-)SL RNA is not required for initial low-level symmetric RNA replication but instead facilitates the subsequent asymmetric amplification of genome RNA from the minus-strand template.

  14. Absence of correlation between serum CRP levels and mitochondrial D-loop DNA mutations in gastro-oesophageal adenocarcinoma

    Directory of Open Access Journals (Sweden)

    Benjamin H. L. Tan

    2014-01-01

    Full Text Available Introduction: Both inflammation and mitochondrial DNA (mtDNA mutation are thought to play a role in the many human cancers. The aim of this study was to evaluate the relationship between inflammation and accumulation of mitochondrial DNA (mtDNA mutations in the D-loop region in carcinogenesis of gastro-oesophageal adenocarcinomas. Materials and Methods: Blood samples of 20 patients with gastro-oesophageal adenocarcinoma were taken for measurement of serum C-reactive protein (CRP concentration. Direct sequencing of mtDNA in the D-loop region was done in the 20 adenocarcinoma samples and their corresponding surrounding non-cancerous tissue. Sequences were compared with existing mtDNA databases to identify mutations. Results: mtDNA mutations in the D-loop region occur commonly with almost identical frequency in both non-cancerous tissue (3.0 ΁ 1.6 and adenocarcinoma (3.1 ΁ 1.9 (P = 0.916, paired t-test. CRP levels are not predictive of the number of D-loop mutations in both adenocarcinoma (β: -0.131; 95% CI: -2.354-1.364; P = 0.583 and non-cancerous tissue samples (β: 0.130; 95% CI: -1.125-1.933; P = 0.586. Five new mutations were identified that were not recorded previously in mtDNA databases. Conclusion: D-loop mtDNA mutations are common in both gastro-oesophageal adenocarcinoma and surrounding non-cancerous tissue. However, the accumulation of such mutations appears to occur independent of systemic inflammation. The frequency of D-loop mutations is likely not useful as a marker for carcinogenesis in gastro-oesophageal adenocarcinoma.

  15. Reactor recirculation pump test loop

    International Nuclear Information System (INIS)

    Taka, Shusei; Kato, Hiroyuki

    1979-01-01

    A test loop for a reactor primary loop recirculation pumps (PLR pumps) has been constructed at Ebara's Haneda Plant in preparation for production of PLR pumps under license from Byron Jackson Pump Division of Borg-Warner Corporation. This loop can simulate operating conditions for test PLR pumps with 130 per cent of the capacity of pumps for a 1100 MWe BWR plant. A main loop, primary cooling system, water demineralizer, secondary cooling system, instrumentation and control equipment and an electric power supply system make up the test loop. This article describes the test loop itself and test results of two PLR pumps for Fukushima No. 2 N.P.S. Unit 1 and one main circulation pump for HAZ Demonstration Test Facility. (author)

  16. Wilson loops in minimal surfaces

    International Nuclear Information System (INIS)

    Drukker, Nadav; Gross, David J.; Ooguri, Hirosi

    1999-01-01

    The AdS/CFT correspondence suggests that the Wilson loop of the large N gauge theory with N = 4 supersymmetry in 4 dimensions is described by a minimal surface in AdS 5 x S 5 . The authors examine various aspects of this proposal, comparing gauge theory expectations with computations of minimal surfaces. There is a distinguished class of loops, which the authors call BPS loops, whose expectation values are free from ultra-violet divergence. They formulate the loop equation for such loops. To the extent that they have checked, the minimal surface in AdS 5 x S 5 gives a solution of the equation. The authors also discuss the zig-zag symmetry of the loop operator. In the N = 4 gauge theory, they expect the zig-zag symmetry to hold when the loop does not couple the scalar fields in the supermultiplet. They will show how this is realized for the minimal surface

  17. Wilson loops and minimal surfaces

    International Nuclear Information System (INIS)

    Drukker, Nadav; Gross, David J.; Ooguri, Hirosi

    1999-01-01

    The AdS-CFT correspondence suggests that the Wilson loop of the large N gauge theory with N=4 supersymmetry in four dimensions is described by a minimal surface in AdS 5 xS 5 . We examine various aspects of this proposal, comparing gauge theory expectations with computations of minimal surfaces. There is a distinguished class of loops, which we call BPS loops, whose expectation values are free from ultraviolet divergence. We formulate the loop equation for such loops. To the extent that we have checked, the minimal surface in AdS 5 xS 5 gives a solution of the equation. We also discuss the zigzag symmetry of the loop operator. In the N=4 gauge theory, we expect the zigzag symmetry to hold when the loop does not couple the scalar fields in the supermultiplet. We will show how this is realized for the minimal surface. (c) 1999 The American Physical Society

  18. The one-loop partition function of N=4 super-Yang-Mills theory on RxS3

    International Nuclear Information System (INIS)

    Spradlin, Marcus; Volovich, Anastasia

    2005-01-01

    We study weakly coupled SU(N)N=4 super-Yang-Mills theory on RxS 3 at infinite N, which has interesting thermodynamics, including a Hagedorn transition, even at zero Yang-Mills coupling. We calculate the exact one-loop partition function below the Hagedorn temperature. Our calculation employs the representation of the one-loop dilatation operator as a spin chain Hamiltonian acting on neighboring sites and a generalization of Polya's counting of necklaces (gauge-invariant operators) to include necklaces with a 'pendant' (an operator which acts on neighboring beads). We find that the one-loop correction to the Hagedorn temperature is δlnT H =+λ/8π 2

  19. BPS Wilson loops and Bremsstrahlung function in ABJ(M): a two loop analysis

    Energy Technology Data Exchange (ETDEWEB)

    Bianchi, Marco S. [Institut für Physik, Humboldt-Universität zu Berlin,Newtonstraße 15, 12489 Berlin (Germany); Griguolo, Luca [Dipartimento di Fisica e Scienze della Terra, Università di Parmaand INFN Gruppo Collegato di Parma,Viale G.P. Usberti 7/A, 43100 Parma (Italy); Leoni, Matias [Physics Department, FCEyN-UBA & IFIBA-CONICETCiudad Universitaria, Pabellón I, 1428, Buenos Aires (Argentina); Penati, Silvia [Dipartimento di Fisica, Università di Milano-Bicoccaand INFN, Sezione di Milano-Bicocca,Piazza della Scienza 3, I-20126 Milano (Italy); Seminara, Domenico [Dipartimento di Fisica, Università di Firenzeand INFN Sezione di Firenze,via G. Sansone 1, 50019 Sesto Fiorentino (Italy)

    2014-06-19

    We study a family of circular BPS Wilson loops in N=6 super Chern-Simons-matter theories, generalizing the usual 1/2-BPS circle. The scalar and fermionic couplings depend on two deformation parameters and these operators can be considered as the ABJ(M) counterpart of the DGRT latitudes defined in N=4 SYM. We perform a complete two-loop analysis of their vacuum expectation value, discuss the appearance of framing-like phases and propose a general relation with cohomologically equivalent bosonic operators. We make an all-loop proposal for computing the Bremsstrahlung function associated to the 1/2-BPS cusp in terms of these generalized Wilson loops. When applied to our two-loop result it reproduces the known expression. Finally, we comment on the generalization of this proposal to the bosonic 1/6-BPS case.

  20. Recombination in the 5' leader of murine leukemia virus is accurate and influenced by sequence identity with a strong bias toward the kissing-loop dimerization region

    DEFF Research Database (Denmark)

    Mikkelsen, J G; Lund, Anders Henrik; Duch, M

    1998-01-01

    during minus-strand DNA synthesis occurred within defined areas of the genome and did not lead to misincorporations at the crossover site. The nonrandom distribution of recombination sites did not reflect a bias for specific sites due to selection at the level of marker gene expression. We address...... whether template switching is affected by the length of sequence identity, by palindromic sequences, and/or by putative stem-loop structures. Sixteen of 24 sites of recombination colocalized with the kissing-loop dimerization region, and we propose that RNA-RNA interactions between palindromic sequences...

  1. Long-period Intensity Pulsations in Coronal Loops Explained by Thermal Non-equilibrium Cycles

    Energy Technology Data Exchange (ETDEWEB)

    Froment, C.; Auchère, F.; Bocchialini, K.; Buchlin, E.; Solomon, J. [Institut d’Astrophysique Spatiale, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Bât. 121, F-91405 Orsay cedex (France); Aulanier, G. [LESIA, Observatoire de Paris, PSL Research University, CNRS, Sorbonne Universités, UPMC Univ. Paris 06, Univ. Paris Diderot, Sorbonne Paris Cité, 5 place Jules Janssen, F-92195 Meudon (France); Mikić, Z., E-mail: clara.froment@astro.uio.no [Predictive Science, Inc., San Diego, CA 92121 (United States)

    2017-02-01

    In solar coronal loops, thermal non-equilibrium (TNE) is a phenomenon that can occur when the heating is both highly stratified and quasi-constant. Unambiguous observational identification of TNE would thus permit us to strongly constrain heating scenarios. While TNE is currently the standard interpretation of coronal rain, the long-term periodic evolution predicted by simulations has never been observed. However, the detection of long-period intensity pulsations (periods of several hours) has been recently reported with the Solar and Heliospheric Observatory /EIT, and this phenomenon appears to be very common in loops. Moreover, the three intensity-pulsation events that we recently studied with the Solar Dynamics Observatory /Atmospheric Imaging Assembly (AIA) show strong evidence for TNE in warm loops. In this paper, a realistic loop geometry from linear force-free field (LFFF) extrapolations is used as input to 1D hydrodynamic simulations. Our simulations show that, for the present loop geometry, the heating has to be asymmetrical to produce TNE. We analyze in detail one particular simulation that reproduces the average thermal behavior of one of the pulsating loop bundle observed with AIA. We compare the properties of this simulation with those deduced from the observations. The magnetic topology of the LFFF extrapolations points to the presence of sites of preferred reconnection at one footpoint, supporting the presence of asymmetric heating. In addition, we can reproduce the temporal large-scale intensity properties of the pulsating loops. This simulation further strengthens the interpretation of the observed pulsations as signatures of TNE. This consequently provides important information on the heating localization and timescale for these loops.

  2. Peripheral site ligand conjugation to a non-quaternary oxime enhances reactivation of nerve agent-inhibited human acetylcholinesterase

    NARCIS (Netherlands)

    Koning, M.C. de; Grol, M. van; Noort, D.

    2011-01-01

    Commonly employed pyridinium-oxime (charged) reactivators of nerve agent inhibited acetylcholinesterase (AChE) do not readily pass the blood brain barrier (BBB) because of the presence of charge(s). Conversely, non-ionic oxime reactivators often suffer from a lack of reactivating potency due to a

  3. Jordan cells of periodic loop models

    International Nuclear Information System (INIS)

    Morin-Duchesne, Alexi; Saint-Aubin, Yvan

    2013-01-01

    Jordan cells in transfer matrices of finite lattice models are a signature of the logarithmic character of the conformal field theories that appear in their thermodynamical limit. The transfer matrix of periodic loop models, T N , is an element of the periodic Temperley–Lieb algebra EPTL N (β,α), where N is the number of sites on a section of the cylinder, and β = −q − q −1 = 2cos λ and α the weights of contractible and non-contractible loops. The thermodynamic limit of T N is believed to describe a conformal field theory of central charge c = 1 − 6λ 2 /(π(λ − π)). The abstract element T N acts naturally on (a sum of) spaces V-tilde N d , similar to those upon which the standard modules of the (classical) Temperley–Lieb algebra act. These spaces known as sectors are labeled by the numbers of defects d and depend on a twist parameter v that keeps track of the winding of defects around the cylinder. Criteria are given for non-trivial Jordan cells of T N both between sectors with distinct defect numbers and within a given sector. (paper)

  4. Activation loop targeting strategy for design of receptor-interacting protein kinase 2 (RIPK2) inhibitors.

    Science.gov (United States)

    Suebsuwong, Chalada; Pinkas, Daniel M; Ray, Soumya S; Bufton, Joshua C; Dai, Bing; Bullock, Alex N; Degterev, Alexei; Cuny, Gregory D

    2018-02-15

    Development of selective kinase inhibitors remains a challenge due to considerable amino acid sequence similarity among family members particularly in the ATP binding site. Targeting the activation loop might offer improved inhibitor selectivity since this region of kinases is less conserved. However, the strategy presents difficulties due to activation loop flexibility. Herein, we report the design of receptor-interacting protein kinase 2 (RIPK2) inhibitors based on pan-kinase inhibitor regorafenib that aim to engage basic activation loop residues Lys169 or Arg171. We report development of CSR35 that displayed >10-fold selective inhibition of RIPK2 versus VEGFR2, the target of regorafenib. A co-crystal structure of CSR35 with RIPK2 revealed a resolved activation loop with an ionic interaction between the carboxylic acid installed in the inhibitor and the side-chain of Lys169. Our data provides principle feasibility of developing activation loop targeting type II inhibitors as a complementary strategy for achieving improved selectivity. Copyright © 2018 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  5. Structure of the Cpf1 endonuclease R-loop complex after target DNA cleavage

    DEFF Research Database (Denmark)

    Stella, Stefano; Alcón, Pablo; Montoya, Guillermo

    2017-01-01

    involved in DNA unwinding to form a CRISPR RNA (crRNA)-DNA hybrid and a displaced DNA strand. The protospacer adjacent motif (PAM) is recognized by the PAM-interacting domain. The loop-lysine helix-loop motif in this domain contains three conserved lysine residues that are inserted in a dentate manner...... and the crRNA-DNA hybrid, avoiding DNA re-annealing. Mutations in key residues reveal a mechanism linking the PAM and DNA nuclease sites. Analysis of the Cpf1 structures proposes a singular working model of RNA-guided DNA cleavage, suggesting new avenues for redesign of Cpf1....

  6. Lattice artifacts in the non-Abelian Debye screening mass in one-loop order

    International Nuclear Information System (INIS)

    Kaste, P.; Rothe, H.J.

    1997-01-01

    We compute the electric screening mass in lattice QCD with Wilson fermions at finite temperature and chemical potential to one-loop order, and show that lattice artifacts arising from a finite lattice spacing result in an enhancement of the screening mass as compared to the continuum. We discuss the magnitude of this enhancement as a function of the temperature and chemical potential for lattices with a different number of lattice sites in the temporal direction that can be implemented in lattice simulations. Most of the enhancement is found to be due to the fermion loop contribution. copyright 1997 The American Physical Society

  7. Molecular sites for the positive allosteric modulation of glycine receptors by endocannabinoids.

    Directory of Open Access Journals (Sweden)

    Gonzalo E Yévenes

    Full Text Available Glycine receptors (GlyRs are transmitter-gated anion channels of the Cys-loop superfamily which mediate synaptic inhibition at spinal and selected supraspinal sites. Although they serve pivotal functions in motor control and sensory processing, they have yet to be exploited as drug targets partly because of hitherto limited possibilities for allosteric control. Endocannabinoids (ECs have recently been characterized as direct allosteric GlyR modulators, but the underlying molecular sites have remained unknown. Here, we show that chemically neutral ECs (e.g. anandamide, AEA are positive modulators of α(1, α(2 and α(3 GlyRs, whereas acidic ECs (e.g. N-arachidonoyl-glycine; NA-Gly potentiate α(1 GlyRs but inhibit α(2 and α(3. This subunit-specificity allowed us to identify the underlying molecular sites through analysis of chimeric and mutant receptors. We found that alanine 52 in extracellular loop 2, glycine 254 in transmembrane (TM region 2 and intracellular lysine 385 determine the positive modulation of α(1 GlyRs by NA-Gly. Successive substitution of non-conserved extracellular and TM residues in α(2 converted NA-Gly-mediated inhibition into potentiation. Conversely, mutation of the conserved lysine within the intracellular loop between TM3 and TM4 attenuated NA-Gly-mediated potentiation of α(1 GlyRs, without affecting inhibition of α(2 and α(3. Notably, this mutation reduced modulation by AEA of all three GlyRs. These results define molecular sites for allosteric control of GlyRs by ECs and reveal an unrecognized function for the TM3-4 intracellular loop in the allosteric modulation of Cys-loop ion channels. The identification of these sites may help to understand the physiological role of this modulation and facilitate the development of novel therapeutic approaches to diseases such as spasticity, startle disease and possibly chronic pain.

  8. Computational stability appraisal of rectangular natural circulation loop: Effect of loop inclination

    International Nuclear Information System (INIS)

    Krishnani, Mayur; Basu, Dipankar N.

    2017-01-01

    Highlights: • Computational model developed for single-phase rectangular natural circulation loop. • Role of loop inclination to vertical on thermalhydraulic stability is explored. • Inclination has strong stabilizing effect due to lower effective gravitation force. • Increase in tilt angle reduces settling time and highest amplitude of oscillation. • An angle of 15° is suggested for the selected loop geometry. - Abstract: Controlling stability behavior of single-phase natural circulation loops, without significantly affecting its steady-state characteristics, is a topic of wide research interest. Present study explores the role of loop inclination on a particular loop geometry. Accordingly a 3D computational model of a rectangular loop is developed and transient conservation equations are solved to obtain the temporal variation in flow parameters. Starting from the quiescent state, simulations are performed for selected sets of operating conditions and also with a few selected inclination angles. System experiences instability at higher heater powers and also with higher sink temperatures. Inclination is found to have a strong stabilizing influence owing to the reduction in the effective gravitational acceleration and subsequent decline in local buoyancy effects. The settling time and highest amplitude of oscillations substantially reduces for a stable system with a small inclination. Typically-unstable systems can also suppress the oscillations, when subjected to tilting, within a reasonable period of time. It is possible to stabilize the loop within shorter time span by increasing the tilt angle, but at the expense of reduction in steady-state flow rate. Overall a tilt angle of 15° is suggested for the selected geometry. Results from the 3D model is compared with the predictions from an indigenous 1D code. While similar qualitative influence of inclination is observed, the 1D model predicts early appearance of the stability threshold and hence hints

  9. Blowout Surge due to Interaction between a Solar Filament and Coronal Loops

    Energy Technology Data Exchange (ETDEWEB)

    Li, Haidong; Jiang, Yunchun; Yang, Jiayan; Yang, Bo; Xu, Zhe; Bi, Yi; Hong, Junchao; Chen, Hechao [Yunnan Observatories, Chinese Academy of Sciences, 396 Yangfangwang, Guandu District, Kunming, 650216 (China); Qu, Zhining, E-mail: lhd@ynao.ac.cn [Department of Physics, School of Science, Sichuan University of Science and Engineering, Zigong 643000 (China)

    2017-06-20

    We present an observation of the interaction between a filament and the outer spine-like loops that produces a blowout surge within one footpoint of large-scale coronal loops on 2015 February 6. Based the observation of the AIA 304 and 94 Å, the activated filament is initially embedded below a dome of a fan-spine configuration. Due to the ascending motion, the erupting filament reconnects with the outer spine-like field. We note that the material in the filament blows out along the outer spine-like field to form the surge with a wider spire, and a two-ribbon flare appears at the site of the filament eruption. In this process, small bright blobs appear at the interaction region and stream up along the outer spine-like field and down along the eastern fan-like field. As a result, a leg of the filament becomes radial and the material in it erupts, while another leg forms the new closed loops. Our results confirm that the successive reconnection occurring between the erupting filament and the coronal loops may lead to a strong thermal/magnetic pressure imbalance, resulting in a blowout surge.

  10. Physics evaluation for testino. of RAPS and TAPS fuel pins in CIRUS pressurised water loop

    International Nuclear Information System (INIS)

    John, Benjamin; Paul, O.P.K.

    1976-01-01

    Relevant calculations carried out to assess the reactivity effect, heat generation and other parameters for testing of RAPS and TAPS fuel pins in the Cirus pressurised water loop are summarised. The Cirus neutron flux level being low, in order to simulate the RAPS design heat rating of ∫ Kdtheta = 40 w/cm, the required plutonium enrichment in mixed plutonium uranium oxide fuel pin was worked out. The results showed that a PuO 2 enrichment of 1.5 wt percent would be necessary to meet the above requirement. The analysis for the TAPS pin indicated that the desired heat flux of 115w/cm 2 cannot be obtained in the Cirus loop with either a 7 pin cluster geometry, or with a single pin with the enrichment level as used in TAPS pin. Lattice code DUMLAC and the core simulation code AECLHEX were used for these studies. (author)

  11. Structural consequences of cutting a binding loop: two circularly permuted variants of streptavidin

    International Nuclear Information System (INIS)

    Le Trong, Isolde; Chu, Vano; Xing, Yi; Lybrand, Terry P.; Stayton, Patrick S.; Stenkamp, Ronald E.

    2013-01-01

    The crystal structures of two circularly permuted streptavidins probe the role of a flexible loop in the tight binding of biotin. Molecular-dynamics calculations for one of the mutants suggests that increased fluctuations in a hydrogen bond between the protein and biotin are associated with cleavage of the binding loop. Circular permutation of streptavidin was carried out in order to investigate the role of a main-chain amide in stabilizing the high-affinity complex of the protein and biotin. Mutant proteins CP49/48 and CP50/49 were constructed to place new N-termini at residues 49 and 50 in a flexible loop involved in stabilizing the biotin complex. Crystal structures of the two mutants show that half of each loop closes over the binding site, as observed in wild-type streptavidin, while the other half adopts the open conformation found in the unliganded state. The structures are consistent with kinetic and thermodynamic data and indicate that the loop plays a role in enthalpic stabilization of the bound state via the Asn49 amide–biotin hydrogen bond. In wild-type streptavidin, the entropic penalties of immobilizing a flexible portion of the protein to enhance binding are kept to a manageable level by using a contiguous loop of medium length (six residues) which is already constrained by its anchorage to strands of the β-barrel protein. A molecular-dynamics simulation for CP50/49 shows that cleavage of the binding loop results in increased structural fluctuations for Ser45 and that these fluctuations destabilize the streptavidin–biotin complex

  12. Diffusion of Wilson loops

    International Nuclear Information System (INIS)

    Brzoska, A.M.; Lenz, F.; Thies, M.; Negele, J.W.

    2005-01-01

    A phenomenological analysis of the distribution of Wilson loops in SU(2) Yang-Mills theory is presented in which Wilson loop distributions are described as the result of a diffusion process on the group manifold. It is shown that, in the absence of forces, diffusion implies Casimir scaling and, conversely, exact Casimir scaling implies free diffusion. Screening processes occur if diffusion takes place in a potential. The crucial distinction between screening of fundamental and adjoint loops is formulated as a symmetry property related to the center symmetry of the underlying gauge theory. The results are expressed in terms of an effective Wilson loop action and compared with various limits of SU(2) Yang-Mills theory

  13. RNA polymerase gate loop guides the nontemplate DNA strand in transcription complexes.

    Science.gov (United States)

    NandyMazumdar, Monali; Nedialkov, Yuri; Svetlov, Dmitri; Sevostyanova, Anastasia; Belogurov, Georgiy A; Artsimovitch, Irina

    2016-12-27

    Upon RNA polymerase (RNAP) binding to a promoter, the σ factor initiates DNA strand separation and captures the melted nontemplate DNA, whereas the core enzyme establishes interactions with the duplex DNA in front of the active site that stabilize initiation complexes and persist throughout elongation. Among many core RNAP elements that participate in these interactions, the β' clamp domain plays the most prominent role. In this work, we investigate the role of the β gate loop, a conserved and essential structural element that lies across the DNA channel from the clamp, in transcription regulation. The gate loop was proposed to control DNA loading during initiation and to interact with NusG-like proteins to lock RNAP in a closed, processive state during elongation. We show that the removal of the gate loop has large effects on promoter complexes, trapping an unstable intermediate in which the RNAP contacts with the nontemplate strand discriminator region and the downstream duplex DNA are not yet fully established. We find that although RNAP lacking the gate loop displays moderate defects in pausing, transcript cleavage, and termination, it is fully responsive to the transcription elongation factor NusG. Together with the structural data, our results support a model in which the gate loop, acting in concert with initiation or elongation factors, guides the nontemplate DNA in transcription complexes, thereby modulating their regulatory properties.

  14. Mapping the structural and dynamical features of multiple p53 DNA binding domains: insights into loop 1 intrinsic dynamics.

    Directory of Open Access Journals (Sweden)

    Suryani Lukman

    Full Text Available The transcription factor p53 regulates cellular integrity in response to stress. p53 is mutated in more than half of cancerous cells, with a majority of the mutations localized to the DNA binding domain (DBD. In order to map the structural and dynamical features of the DBD, we carried out multiple copy molecular dynamics simulations (totaling 0.8 μs. Simulations show the loop 1 to be the most dynamic element among the DNA-contacting loops (loops 1-3. Loop 1 occupies two major conformational states: extended and recessed; the former but not the latter displays correlations in atomic fluctuations with those of loop 2 (~24 Å apart. Since loop 1 binds to the major groove whereas loop 2 binds to the minor groove of DNA, our results begin to provide some insight into the possible mechanism underpinning the cooperative nature of DBD binding to DNA. We propose (1 a novel mechanism underlying the dynamics of loop 1 and the possible tread-milling of p53 on DNA and (2 possible mutations on loop 1 residues to restore the transcriptional activity of an oncogenic mutation at a distant site.

  15. On some properties of conjugacy closed loops

    International Nuclear Information System (INIS)

    Adeniran, John Olusola

    2002-07-01

    It is shown that central loops are not conjugacy closed loops but instead are loops of units in their loop algebras that are conjugacy closed. It is also shown that certain inner mappings of a conjugacy closed loop are nuclear. Some invariants of left conjugacy closed loops are obtained. (author)

  16. Mirror symmetry and loop operators

    Energy Technology Data Exchange (ETDEWEB)

    Assel, Benjamin [Department of Mathematics, King’s College London,The Strand, London WC2R 2LS (United Kingdom); Gomis, Jaume [Perimeter Institute for Theoretical Physics,Waterloo, Ontario, N2L 2Y5 (Canada)

    2015-11-09

    Wilson loops in gauge theories pose a fundamental challenge for dualities. Wilson loops are labeled by a representation of the gauge group and should map under duality to loop operators labeled by the same data, yet generically, dual theories have completely different gauge groups. In this paper we resolve this conundrum for three dimensional mirror symmetry. We show that Wilson loops are exchanged under mirror symmetry with Vortex loop operators, whose microscopic definition in terms of a supersymmetric quantum mechanics coupled to the theory encode in a non-trivial way a representation of the original gauge group, despite that the gauge groups of mirror theories can be radically different. Our predictions for the mirror map, which we derive guided by branes in string theory, are confirmed by the computation of the exact expectation value of Wilson and Vortex loop operators on the three-sphere.

  17. A binding-site barrier affects imaging efficiency of high affinity amyloid-reactive peptide radiotracers in vivo.

    Directory of Open Access Journals (Sweden)

    Jonathan S Wall

    Full Text Available Amyloid is a complex pathology associated with a growing number of diseases including Alzheimer's disease, type 2 diabetes, rheumatoid arthritis, and myeloma. The distribution and extent of amyloid deposition in body organs establishes the prognosis and can define treatment options; therefore, determining the amyloid load by using non-invasive molecular imaging is clinically important. We have identified a heparin-binding peptide designated p5 that, when radioiodinated, was capable of selectively imaging systemic visceral AA amyloidosis in a murine model of the disease. The p5 peptide was posited to bind effectively to amyloid deposits, relative to similarly charged polybasic heparin-reactive peptides, because it adopted a polar α helix secondary structure. We have now synthesized a variant, p5R, in which the 8 lysine amino acids of p5 have been replaced with arginine residues predisposing the peptide toward the α helical conformation in an effort to enhance the reactivity of the peptide with the amyloid substrate. The p5R peptide had higher affinity for amyloid and visualized AA amyloid in mice by using SPECT/CT imaging; however, the microdistribution, as evidenced in micro-autoradiographs, was dramatically altered relative to the p5 peptide due to its increased affinity and a resultant "binding site barrier" effect. These data suggest that radioiodinated peptide p5R may be optimal for the in vivo detection of discreet, perivascular amyloid, as found in the brain and pancreatic vasculature, by using molecular imaging techniques; however, peptide p5, due to its increased penetration, may yield more quantitative imaging of expansive tissue amyloid deposits.

  18. PERMEABLE REACTIVE BARRIERS FOR IN-SITU TREATMENT OF ARSENIC-CONTAMINATED GROUNDWATER

    Science.gov (United States)

    Laboratory and field research has shown that permeable reactive barriers (PRBs) containing a variety of materials can treat arsenic (As) contaminated groundwater. Sites where these PRBs are located include a mine tailings facility, fertilizer and chemical manufacturing sites, a...

  19. Thermohydraulics in a high-temperature gas-cooled reactor primary loop during early phases of unrestricted core-heatup accidents

    International Nuclear Information System (INIS)

    Kroeger, P.G.; Colman, J.; Hsu, C.J.

    1983-01-01

    In High Temperature Gas Cooled Reactor (HTGR) siting considerations, the Unrestricted Core Heatup Accidents (UCHA) are considered as accidents of highest consequence, corresponding to core meltdown accidents in light water reactors. Initiation of such accidents can be, for instance, due to station blackout, resulting in scram and loss of all main loop forced circulation, with none of the core auxiliary cooling system loops being started. The result is a slow but continuing core heatup, extending over days. During the initial phases of such UCHA scenarios, the primary loop remains pressurized, with the system pressure slowly increasing until the relief valve setpoint is reached. The major objectives of the work described here were to determine times to depressurization as well as approximate loop component temperatures up to depressurization

  20. An optimal reactive power control strategy for a DFIG-based wind farm to damp the sub-synchronous oscillation of a power system

    DEFF Research Database (Denmark)

    Zhao, Bin; Li, Hui; Wang, Mingyu

    2014-01-01

    This study presents the auxiliary damping control with the reactive power loop on the rotor-side converter of doubly-fed induction generator (DFIG)-based wind farms to depress the sub-synchronous resonance oscillations in nearby turbogenerators. These generators are connected to a series capaciti...

  1. WWER type reactor primary loop imitation on large test loop facility in MARIA reactor

    International Nuclear Information System (INIS)

    Moldysh, A.; Strupchevski, A.; Kmetek, Eh.; Spasskov, V.P.; Shumskij, A.M.

    1982-01-01

    At present in Poland in cooperation with USSR a nuclear water loop test facility (WL) in 'MARIA' reactor in Sverke is under construction. The program objective is to investigate processes occuring in WWER reactor under emergency conditions, first of all after the break of the mainprimary loop circulation pipe-line. WL with the power of about 600 kW consists of three major parts: 1) an active loop, imitating the undamaged loops of the WWER reactor; 2) a passive loop assignedfor modelling the broken loop of the WWER reactor; 3) the emergency core cooling system imitating the corresponding full-scale system. The fuel rod bundle consists of 18 1 m long rods. They were fabricated according to the standard WWER fuel technology. In the report some general principles of WWERbehaviour imitation under emergency conditions are given. They are based on the operation experience obtained from 'SEMISCALE' and 'LOFT' test facilities in the USA. A description of separate modelling factors and criteria effects on the development of 'LOCA'-type accident is presented (the break cross-section to the primary loop volume ratio, the pressure differential between inlet and outlet reactor chambers, the pressure drop rate in the loop, the coolant flow rate throuh the core etc.). As an example a comparison of calculated flow rate variations for the WWER-1000 reactor and the model during the loss-of-coolant accident with the main pipe-line break at the core inlet is given. Calculations have been carried out with the use of TECH'-M code [ru

  2. Natively unstructured loops differ from other loops.

    Directory of Open Access Journals (Sweden)

    Avner Schlessinger

    2007-07-01

    Full Text Available Natively unstructured or disordered protein regions may increase the functional complexity of an organism; they are particularly abundant in eukaryotes and often evade structure determination. Many computational methods predict unstructured regions by training on outliers in otherwise well-ordered structures. Here, we introduce an approach that uses a neural network in a very different and novel way. We hypothesize that very long contiguous segments with nonregular secondary structure (NORS regions differ significantly from regular, well-structured loops, and that a method detecting such features could predict natively unstructured regions. Training our new method, NORSnet, on predicted information rather than on experimental data yielded three major advantages: it removed the overlap between testing and training, it systematically covered entire proteomes, and it explicitly focused on one particular aspect of unstructured regions with a simple structural interpretation, namely that they are loops. Our hypothesis was correct: well-structured and unstructured loops differ so substantially that NORSnet succeeded in their distinction. Benchmarks on previously used and new experimental data of unstructured regions revealed that NORSnet performed very well. Although it was not the best single prediction method, NORSnet was sufficiently accurate to flag unstructured regions in proteins that were previously not annotated. In one application, NORSnet revealed previously undetected unstructured regions in putative targets for structural genomics and may thereby contribute to increasing structural coverage of large eukaryotic families. NORSnet found unstructured regions more often in domain boundaries than expected at random. In another application, we estimated that 50%-70% of all worm proteins observed to have more than seven protein-protein interaction partners have unstructured regions. The comparative analysis between NORSnet and DISOPRED2 suggested

  3. Analysis of boron dilution in a four-loop PWR

    International Nuclear Information System (INIS)

    Sun, J.G.; Sha, W.T.

    1995-03-01

    Thermal mixing and boron dilution in a pressurized water reactor were analyzed with COMMIX codes. The reactor system was the four-loop Zion reactor. Two boron dilution scenarios were analyzed. In the first scenario, the plant is in cold shutdown and the reactor coolant system has just been filled after maintenance on the steam generators. To flush the air out of the steam generator tubes, a reactor coolant pump (RCP) is started, with the water in the pump suction line devoid of boron and at the same temperature as the coolant in the system. In the second scenario, the plant is at hot standby and the reactor coolant system has been heated to operating temperature after a long outage. It is assumed that an RCP is started, with the pump suction line filled with cold unborated water, forcing a slug of diluted coolant down the downcomer and subsequently through the reactor core. The subsequent transient thermal mixing and boron dilution that would occur in the reactor system is simulated for these two scenarios. The reactivity insertion rate and the total reactivity are evaluated and a sensitivity study is performed to assess the accuracy of the numerical modeling of the geometry of the reactor coolant system

  4. YBCO coated conductors by reactive thermal co-evaporation

    Energy Technology Data Exchange (ETDEWEB)

    Schmatz, U.; Hoffmann, Ch.; Bauer, M.; Metzger, R.; Berberich, P.; Kinder, H. [Technische Univ. Muenchen, Garching (Germany). Physik-Department

    2001-12-01

    Coated tape conductors of YBCO require a deposition process allowing to obtain a high volume growth rate in order to produce long lengths of tape in a reasonable amount of time. We present our tape coating system where 15 parallel loops of travelling tape of 1 cm width can be coated simultaneously by reactive thermal co-evaporation. For high critical current densities, in-plane alignment of the YBCO film is necessary. Inclined substrate deposition (ISD) is a technique that allows to deposit in-plane oriented buffer layers suitable for YBCO growth at high deposition rates. We present results obtained for YBCO films grown on MgO-ISD buffer layers deposited by e-gun evaporation onto metallic tape substrates. (orig.)

  5. The composition dependence of the photochemical reactivity of strontium barium titanate

    Science.gov (United States)

    Bhardwaj, Abhilasha

    The efficiency of particulate water photolysis catalysts is impractically low due to the recombination of intermediate species and charge carriers. The back reaction can occur easily if the oxidation and reduction sites on the surface of the catalyst are not far enough apart. It is hypothesized that it will be possible to increase the separation of the sites of the two half reactions and reduce the recombination of photogenerated charge carriers by using a ferroelectric material with permanent internal dipolar fields. This separation of the reaction sites may significantly increase the efficiency of the process. The present work compares the photochemical reactivities of ferroelectric and nonferroelectric materials (SrxBa1-xTiO 3, 0.0≤ x ≤1.0) with similar composition and structure. The reactivities are compared by measuring the color change of methylene blue dye after the aqueous dye solution reacts on the surface of ceramic sample pellets as a result of exposure to UV light. The reactivities are also compared by measuring the amount of silver that is formed when an aqueous AgNO3 solution photochemically reacts on the surface. The change in the color of the dye is measured by diffuse reflectance spectroscopy and absorbance measurements. The amount of silver is measured by atomic force microscopy. The photochemical reactivity of SrxBa1-xTiO3 shows a local maximum at the composition of the ferroelectric to non-ferroelectric transition. Also, the reactivities decrease as BaTiO3 and SrTiO3 become less pure. The dominant factors causing this trend in reactivities of SrxBa1-xTiO3 are the dielectric constant and alloy scattering. It is found that higher values of the dielectric constant increase the photochemical reactivity by enlarging the space charge region. The increase in alloy scattering in SrxBa1-xTiO 3 solid solutions as x increases from zero or decreases from 1, has adverse effect on reactivity. There are other factors such as ferroelectric polarization

  6. Oxidized amino acid residues in the vicinity of Q(A and Pheo(D1 of the photosystem II reaction center: putative generation sites of reducing-side reactive oxygen species.

    Directory of Open Access Journals (Sweden)

    Laurie K Frankel

    Full Text Available Under a variety of stress conditions, Photosystem II produces reactive oxygen species on both the reducing and oxidizing sides of the photosystem. A number of different sites including the Mn4O5Ca cluster, P680, PheoD1, QA, QB and cytochrome b559 have been hypothesized to produce reactive oxygen species in the photosystem. In this communication using Fourier-transform ion cyclotron resonance mass spectrometry we have identified several residues on the D1 and D2 proteins from spinach which are oxidatively modified and in close proximity to QA (D1 residues (239F, (241Q, (242E and the D2 residues (238P, (239T, (242E and (247M and PheoD1 (D1 residues (130E, (133L and (135F. These residues may be associated with reactive oxygen species exit pathways located on the reducing side of the photosystem, and their modification may indicate that both QA and PheoD1 are sources of reactive oxygen species on the reducing side of Photosystem II.

  7. A type of loop algebra and the associated loop algebras

    International Nuclear Information System (INIS)

    Tam Honwah; Zhang Yufeng

    2008-01-01

    A higher-dimensional twisted loop algebra is constructed. As its application, a new Lax pair is presented, whose compatibility gives rise to a Liouville integrable hierarchy of evolution equations by making use of Tu scheme. One of the reduction cases of the hierarchy is an analogous of the well-known AKNS system. Next, the twisted loop algebra, furthermore, is extended to another higher dimensional loop algebra, from which a hierarchy of evolution equations with 11-potential component functions is obtained, whose reduction is just standard AKNS system. Especially, we prove that an arbitrary linear combination of the four Hamiltonian operators directly obtained from the recurrence relations is still a Hamiltonian operator. Therefore, the hierarchy with 11-potential functions possesses 4-Hamiltonian structures. Finally, an integrable coupling of the hierarchy is worked out

  8. Development of new design mechanical seal tester for Primary Loop Recirculation Pump (PLR Pump)

    International Nuclear Information System (INIS)

    Fukushima, Naoki; Koshiba, Koremutsu

    1995-01-01

    The mechanical seal for a Primary Loop Recirculation Pump (PLR Pump) is an important part of a BWR plant. This study describes a new mechanical seal tester developed to certify mechanical seal performance before installation in a PLR Pump on site. (author)

  9. Modeling of compact loop antennas

    International Nuclear Information System (INIS)

    Baity, F.W.

    1987-01-01

    A general compact loop antenna model which treats all elements of the antenna as lossy transmission lines has been developed. In addition to capacitively-tuned resonant double loop (RDL) antennas the model treats stub-tuned resonant double loop antennas. Calculations using the model have been compared with measurements on full-scale mockups of resonant double loop antennas for ATF and TFTR in order to refine the transmission line parameters. Results from the model are presented for RDL antenna designs for ATF, TFTR, Tore Supra, and for the Compact Ignition Tokamak

  10. Rogowski Loop design for NSTX

    International Nuclear Information System (INIS)

    McCormack, B.; Kaita, R.; Kugel, H.; Hatcher, R.

    2000-01-01

    The Rogowski Loop is one of the most basic diagnostics for tokamak operations. On the National Spherical Torus Experiment (NSTX), the plasma current Rogowski Loop had the constraints of the very limited space available on the center stack, 5,000 volt isolation, flexibility requirements as it remained a part of the Center Stack assembly after the first phase of operation, and a +120 C temperature requirement. For the second phase of operation, four Halo Current Rogowski Loops under the Center Stack tiles will be installed having +600 C and limited space requirements. Also as part of the second operational phase, up to ten Rogowski Loops will installed to measure eddy currents in the Passive Plate support structures with +350 C, restricted space, and flexibility requirements. This presentation will provide the details of the material selection, fabrication techniques, testing, and installation results of the Rogowski Loops that were fabricated for the high temperature operational and bakeout requirements, high voltage isolation requirements, and the space and flexibility requirements imposed upon the Rogowski Loops. In the future operational phases of NSTX, additional Rogowski Loops could be anticipated that will measure toroidal plasma currents in the vacuum vessel and in the Passive Plate assemblies

  11. Saturation Mutagenesis of the HIV-1 Envelope CD4 Binding Loop Reveals Residues Controlling Distinct Trimer Conformations.

    Directory of Open Access Journals (Sweden)

    Maria Duenas-Decamp

    2016-11-01

    Full Text Available The conformation of HIV-1 envelope (Env glycoprotein trimers is key in ensuring protection against waves of neutralizing antibodies generated during infection, while maintaining sufficient exposure of the CD4 binding site (CD4bs for viral entry. The CD4 binding loop on Env is an early contact site for CD4 while penetration of a proximal cavity by CD4 triggers Env conformational changes for entry. The role of residues in the CD4 binding loop in regulating the conformation of the trimer and trimer association domain (TAD was investigated using a novel saturation mutagenesis approach. Single mutations identified, resulted in distinct trimer conformations affecting CD4bs exposure, the glycan shield and the TAD across diverse HIV-1 clades. Importantly, mutations that improve access to the CD4bs without exposing the immunodominant V3 loop were identified. The different trimer conformations identified will affect the specificity and breadth of nabs elicited in vivo and are important to consider in design of Env immunogens for vaccines.

  12. Hybrid Combustion-Gasification Chemical Looping

    Energy Technology Data Exchange (ETDEWEB)

    Herbert Andrus; Gregory Burns; John Chiu; Gregory Lijedahl; Peter Stromberg; Paul Thibeault

    2009-01-07

    For the past several years Alstom Power Inc. (Alstom), a leading world-wide power system manufacturer and supplier, has been in the initial stages of developing an entirely new, ultra-clean, low cost, high efficiency power plant for the global power market. This new power plant concept is based on a hybrid combustion-gasification process utilizing high temperature chemical and thermal looping technology The process consists of the oxidation, reduction, carbonation, and calcination of calcium-based compounds, which chemically react with coal, biomass, or opportunity fuels in two chemical loops and one thermal loop. The chemical and thermal looping technology can be alternatively configured as (i) a combustion-based steam power plant with CO{sub 2} capture, (ii) a hybrid combustion-gasification process producing a syngas for gas turbines or fuel cells, or (iii) an integrated hybrid combustion-gasification process producing hydrogen for gas turbines, fuel cells or other hydrogen based applications while also producing a separate stream of CO{sub 2} for use or sequestration. In its most advanced configuration, this new concept offers the promise to become the technology link from today's Rankine cycle steam power plants to tomorrow's advanced energy plants. The objective of this work is to develop and verify the high temperature chemical and thermal looping process concept at a small-scale pilot facility in order to enable AL to design, construct and demonstrate a pre-commercial, prototype version of this advanced system. In support of this objective, Alstom and DOE started a multi-year program, under this contract. Before the contract started, in a preliminary phase (Phase 0) Alstom funded and built the required small-scale pilot facility (Process Development Unit, PDU) at its Power Plant Laboratories in Windsor, Connecticut. Construction was completed in calendar year 2003. The objective for Phase I was to develop the indirect combustion loop with CO{sub 2

  13. Thermal-hydraulic analyses for in-pile SCWR fuel qualification test loops and SCWR material loop

    Energy Technology Data Exchange (ETDEWEB)

    Vojacek, A.; Mazzini, G.; Zmitkova, J.; Ruzickova, M. [Research Centre Rez (Czech Republic)

    2014-07-01

    One of the R&D directions of Research Centre Rez is dedicated to the supercritical water-cooled reactor concept (SCWR). Among the developed experimental facilities and infrastructure in the framework of the SUSEN project (SUStainable ENergy) is construction and experimental operation of the supercritical water loop SCWL focusing on material tests. At the first phase, this SCWL loop is assembled and operated out-of-pile in the dedicated loop facilities hall. At this out-of-pile operation various operational conditions are tested and verified. After that, in the second phase, the SCWL loop will be situated in-pile, in the core of the research reactor LVR-15, operated at CVR. Furthermore, it is planned to carry out a test of a small scale fuel assembly within the SuperCritical Water Reactor Fuel Qualification Test (SCWR-FQT) loop, which is now being designed. This paper presents the results of the thermal-hydraulic analyses of SCWL loop out-of-pile operation using the RELAP5/MOD3.3. The thermal-hydraulic modeling and the performed analyses are focused on the SCWL loop model validation through a comparison of the calculation results with the experimental results obtained at various operation conditions. Further, the present paper focuses on the transient analyses for start-up and shut-down of the FQT loop, particularly to explore the ability of system codes ATHLET 3.0A to simulate the transient between subcritical conditions and supercritical conditions. (author)

  14. Active sites in char gasification: Final technical report

    Energy Technology Data Exchange (ETDEWEB)

    Wojtowicz, M.; Lilly, W.D.; Perkins, M.T.; Hradil, G.; Calo, J.M.; Suuberg, E.M.

    1987-09-01

    Among the key variables in the design of gasifiers and combustors is the reactivity of the chars which must be gasified or combusted. Significant loss of unburned char is unacceptable in virtually any process; the provision of sufficient residence time for complete conversion is essential. A very wide range of reactivities are observed, depending upon the nature of the char in a process. The current work focuses on furthering the understanding of gasification reactivities of chars. It has been well established that the reactivity of char to gasification generally depends upon three principal factors: (1) the concentration of ''active sites'' in the char; (2) mass transfer within the char; and (3) the type and concentration of catalytic impurities in the char. The present study primarily addresses the first factor. The subject of this research is the origin, nature, and fate of active sites in chars derived from parent hydrocarbons with coal-like structure. The nature and number of the active sites and their reactivity towards oxygen are examined in ''model'' chars derived from phenol-formaldehyde type resins. How the active sites are lost by the process of thermal annealing during heat treatment of chars are studied, and actual rate for the annealing process is derived. Since intrinsic char reactivities are of primary interest in the present study, a fair amount of attention was given to the model char synthesis and handling so that the effect of catalytic impurities and oxygen-containing functional groups in the chemical structure of the material were minimized, if not completely eliminated. The project would not be considered complete without comparing characteristic features of synthetic chars with kinetic behavior exhibited by natural chars, including coal chars.

  15. Structures of Receptor Complexes of a North American H7N2 Influenza Hemagglutinin with a Loop Deletion in the Receptor Binding Site

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Hua; Chen, Li-Mei; Carney, Paul J.; Donis, Ruben O.; Stevens, James (CDC)

    2012-02-21

    Human infections with subtype H7 avian influenza viruses have been reported as early as 1979. In 1996, a genetically stable 24-nucleotide deletion emerged in North American H7 influenza virus hemagglutinins, resulting in an eight amino acid deletion in the receptor-binding site. The continuous circulation of these viruses in live bird markets, as well as its documented ability to infect humans, raises the question of how these viruses achieve structural stability and functionality. Here we report a detailed molecular analysis of the receptor binding site of the North American lineage subtype H7N2 virus A/New York/107/2003 (NY107), including complexes with an avian receptor analog (3'-sialyl-N-acetyllactosamine, 3'SLN) and two human receptor analogs (6'-sialyl-N-acetyllactosamine, 6'SLN; sialyllacto-N-tetraose b, LSTb). Structural results suggest a novel mechanism by which residues Arg220 and Arg229 (H3 numbering) are used to compensate for the deletion of the 220-loop and form interactions with the receptor analogs. Glycan microarray results reveal that NY107 maintains an avian-type ({alpha}2-3) receptor binding profile, with only moderate binding to human-type ({alpha}2-6) receptor. Thus despite its dramatically altered receptor binding site, this HA maintains functionality and confirms a need for continued influenza virus surveillance of avian and other animal reservoirs to define their zoonotic potential.

  16. Structures of receptor complexes of a North American H7N2 influenza hemagglutinin with a loop deletion in the receptor binding site.

    Directory of Open Access Journals (Sweden)

    Hua Yang

    2010-09-01

    Full Text Available Human infections with subtype H7 avian influenza viruses have been reported as early as 1979. In 1996, a genetically stable 24-nucleotide deletion emerged in North American H7 influenza virus hemagglutinins, resulting in an eight amino acid deletion in the receptor-binding site. The continuous circulation of these viruses in live bird markets, as well as its documented ability to infect humans, raises the question of how these viruses achieve structural stability and functionality. Here we report a detailed molecular analysis of the receptor binding site of the North American lineage subtype H7N2 virus A/New York/107/2003 (NY107, including complexes with an avian receptor analog (3'-sialyl-N-acetyllactosamine, 3'SLN and two human receptor analogs (6'-sialyl-N-acetyllactosamine, 6'SLN; sialyllacto-N-tetraose b, LSTb. Structural results suggest a novel mechanism by which residues Arg220 and Arg229 (H3 numbering are used to compensate for the deletion of the 220-loop and form interactions with the receptor analogs. Glycan microarray results reveal that NY107 maintains an avian-type (alpha2-3 receptor binding profile, with only moderate binding to human-type (alpha2-6 receptor. Thus despite its dramatically altered receptor binding site, this HA maintains functionality and confirms a need for continued influenza virus surveillance of avian and other animal reservoirs to define their zoonotic potential.

  17. Algorithm for counting large directed loops

    Energy Technology Data Exchange (ETDEWEB)

    Bianconi, Ginestra [Abdus Salam International Center for Theoretical Physics, Strada Costiera 11, 34014 Trieste (Italy); Gulbahce, Natali [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, NM 87545 (United States)

    2008-06-06

    We derive a Belief-Propagation algorithm for counting large loops in a directed network. We evaluate the distribution of the number of small loops in a directed random network with given degree sequence. We apply the algorithm to a few characteristic directed networks of various network sizes and loop structures and compare the algorithm with exhaustive counting results when possible. The algorithm is adequate in estimating loop counts for large directed networks and can be used to compare the loop structure of directed networks and their randomized counterparts.

  18. Oscillation damping of chiral string loops

    International Nuclear Information System (INIS)

    Babichev, Eugeny; Dokuchaev, Vyacheslav

    2002-01-01

    Chiral cosmic string loops tend to the stationary (vorton) configuration due to energy loss into gravitational and electromagnetic radiation. We describe the asymptotic behavior of near stationary chiral loops and their fading to vortons. General limits on the gravitational and electromagnetic energy losses by near stationary chiral loops are found. For these loops we estimate the oscillation damping time. We present solvable examples of gravitational radiation energy loss by some chiral loop configurations. The analytical dependence of string energy with time is found in the case of the chiral ring with small amplitude radial oscillations

  19. LoopX: A Graphical User Interface-Based Database for Comprehensive Analysis and Comparative Evaluation of Loops from Protein Structures.

    Science.gov (United States)

    Kadumuri, Rajashekar Varma; Vadrevu, Ramakrishna

    2017-10-01

    Due to their crucial role in function, folding, and stability, protein loops are being targeted for grafting/designing to create novel or alter existing functionality and improve stability and foldability. With a view to facilitate a thorough analysis and effectual search options for extracting and comparing loops for sequence and structural compatibility, we developed, LoopX a comprehensively compiled library of sequence and conformational features of ∼700,000 loops from protein structures. The database equipped with a graphical user interface is empowered with diverse query tools and search algorithms, with various rendering options to visualize the sequence- and structural-level information along with hydrogen bonding patterns, backbone φ, ψ dihedral angles of both the target and candidate loops. Two new features (i) conservation of the polar/nonpolar environment and (ii) conservation of sequence and conformation of specific residues within the loops have also been incorporated in the search and retrieval of compatible loops for a chosen target loop. Thus, the LoopX server not only serves as a database and visualization tool for sequence and structural analysis of protein loops but also aids in extracting and comparing candidate loops for a given target loop based on user-defined search options.

  20. Modulation of constitutive activity and signaling bias of the ghrelin receptor by conformational constraint in the second extracellular loop

    DEFF Research Database (Denmark)

    Mokrosinski, Jacek; Frimurer, Thomas M; Sivertsen, Bjoern

    2012-01-01

    Based on a rare, natural Glu for Ala204(C+6) variant located six residues after the conserved Cys residue in extracellular loop 2 (ECL2b) associated with selective elimination of the high constitutive signaling of the ghrelin receptor, this loop was subjected to a detailed structure functional....... Moreover, the constitutive activity of the receptor was inhibited by Zn(2+) binding in an engineered metal-ion site stabilizing an a-helical conformation of this loop segment. It is concluded that the high constitutive activity of the ghrelin receptor is dependent upon flexibility in the C-terminal segment...

  1. Protein intercalation in DNA as one of main modes of fixation of the most stable chromatin loop domains

    Directory of Open Access Journals (Sweden)

    М. I. Chopei

    2014-08-01

    Full Text Available The main mechanism of DNA track formation during comet assay of nucleoids, obtained after removal of cell membranes and most of proteins, is the extension to anode of negatively supercoiled DNA loops attached to proteins, remaining in nucleoid after lysis treatment. The composition of these residual protein structures and the nature of their strong interaction with the loop ends remain poorly studied. In this work we investigated the influence of chloroquine intercalation and denaturation of nucleoid proteins on the efficiency of electrophoretic track formation during comet assay. The results obtained suggest that even gentle protein denaturation is sufficient to reduce considerably the effectiveness of the DNA loop migration due to an increase in the loops size. The same effect was observed under local DNA unwinding upon chloroquine intercalation around the sites of the attachment of DNA to proteins. The topological interaction (protein intercalation into the double helix between DNA loop ends and nucleoid proteins is discussed.

  2. Morphological Changes of Limestone Sorbent Particles during Carbonation/Calcination Looping Cycles in a Thermogravimetric Analyzer (TGA) and Reactivation with Steam

    KAUST Repository

    Wu, Y.; Blamey, J.; Anthony, E. J.; Fennell, P. S.

    2010-01-01

    Carbonation and calcination looping cycles were carried out on four limestones in a thermogravimetric analyzer (TGA). The CO2 carrying capacity of a limestone particle decays very quickly in the first 10 cycles, reducing to about 20% of its original

  3. Alkylation of deoxyribonucleic acid by carcinogens dimethyl sulphate, ethyl methanesulphonate, N-ethyl-N-nitrosourea and N-methyl-N-nitrosourea. Relative reactivity of the phosphodiester site thymidylyl(3'-5')thymidine.

    Science.gov (United States)

    Swenson, D H; Lawley, P D

    1978-01-01

    1. The ethyl phosphotriester of thymidylyl(3'-5')thymidine, dTp(Et)dT, was identified as a product from reaction of DNA with N-ethyl-N-nitrosourea, by procedures parallel to those reported previously for the methyl homologue produced by N-methyl-N-nitrosourea. 2. Enzymic degradation to yield alkyl phosphotriesters from DNA alkylated by these carcinogens and by dimethyl sulphate and ethyl methanesulphonate was studied quantitatively, and the relative yields of the triesters dTp(Alk)dT were determined. The relative reactivity of the phosphodiester group dTpdT to each of the four carcinogens was thus obtained, and compared with that of DNA overall, or with that of the N-7 atom of guanine in DNA. Relative reactivity of the phosphodiester group was lowest towards dimethyl sulphate, the least electrophilic of the reagents used, and was highest towards N-ethyl-N-nitrosourea, the most electrophilic reagent. 3. The nature of the alkyl group transferred also influenced reactivity of the phosphodiester site, since this site was relatively more reactive towards ethylation than would be predicted simply from the known Swain-Scott s values of the alkylating agents. It was therefore suggested that the steric accessibility of the weakly nucleophilic phosphodiester group on the outside of the DNA macromolecule favours its reaction with ethylating, as opposed to methylating, reagents. 4. Taking a value of the Swain-Scott nucleophilicity (n) of 2.5 for an average DNA nucleotide unit [Walles & Ehrenberg (1969) Acta Chem. Scand. 23, 1080-1084], a value of n of about 1 for the phosphodiester group was deduced, and this value was found to be 2-3 units less than that for the N-7 atom of guanine in DNA. 5. The reactivity of DNA overall was markedly high towards the alkylnitrosoureas, despite their relatively low s values. This was ascribed to an electrostatic factor that favoured reaction of the negatively charged polymer with alkyldiazonium cation intermediates. PMID:208508

  4. On the loop-loop scattering amplitudes in Abelian and non-Abelian gauge theories

    International Nuclear Information System (INIS)

    Meggiolaro, Enrico

    2005-01-01

    The high-energy elastic scattering amplitude of two colour-singlet qq-bar pairs is governed by the correlation function of two Wilson loops, which follow the classical straight lines for quark (antiquark) trajectories. This quantity is expected to be free of IR divergences, differently from what happens for the parton-parton elastic scattering amplitude, described, in the high-energy limit, by the expectation value of two Wilson lines. We shall explicitly test this IR finiteness by a direct non-perturbative computation of the loop-loop scattering amplitudes in the (pedagogic, but surely physically interesting) case of quenched QED. The results obtained for the Abelian case will be generalized to the case of a non-Abelian gauge theory with Nc colours, but stopping to the order O(g4) in perturbation theory. In connection with the above-mentioned IR finiteness, we shall also discuss some analytic properties of the loop-loop scattering amplitudes in both Abelian and non-Abelian gauge theories, when going from Minkowskian to Euclidean theory, which can be relevant to the still unsolved problem of the s-dependence of hadron-hadron total cross-sections

  5. Detection of siRNA Mediated Target mRNA Cleavage Activities in Human Cells by a Novel Stem-Loop Array RT-PCR Analysis

    Science.gov (United States)

    2016-09-07

    sequences of the target mRNA, and a double stranded stem at the 5′ end that forms a stem -loop to function as a forceps to stabilize the secondary...E-mjournal homepage: www.elsevier.com/locate/bbrepDetection of siRNA-mediated target mRNA cleavage activities in human cells by a novel stem -loop...challenges for the accurate and efficient detection and verification of cleavage sites on target mRNAs. Here we used a sensitive stem -loop array reverse

  6. Overlapping reactivations of herpes simplex virus type 2 in the genital and perianal mucosa.

    Science.gov (United States)

    Tata, Sunitha; Johnston, Christine; Huang, Meei-Li; Selke, Stacy; Magaret, Amalia; Corey, Lawrence; Wald, Anna

    2010-02-15

    Genital shedding of herpes simplex virus (HSV) type 2 occurs frequently. Anatomic patterns of genital HSV-2 reactivation have not been intensively studied. Four HSV-2-seropositive women with symptomatic genital herpes attended a clinic daily during a 30-day period. Daily samples were collected from 7 separate genital sites. Swab samples were assayed for HSV DNA by quantitative polymerase chain reaction. Anatomic sites of clinical HSV-2 recurrences were recorded. HSV was detected on 44 (37%) of 120 days and from 136 (16%) of 840 swab samples. Lesions were documented on 35 (29%) of 120 days. HSV was detected at >1 anatomic site on 25 (57%) of 44 days with HSV shedding (median, 2 sites; range, 1-7), with HSV detected bilaterally on 20 (80%) of the 25 days. The presence of a lesion was significantly associated with detectable HSV from any genital site (incident rate ratio [IRR], 5.41; 95% confidence interval [CI], 1.24-23.50; P= .02) and with the number of positive sites (IRR, 1.19; 95% CI, 1. 01-1.40; P=.03). The maximum HSV copy number detected was associated with the number of positive sites (IRR, 1.62; 95% CI, 1.44-1.82; Pgenital tract. To prevent HSV-2 reactivation, suppressive HSV-2 therapy must control simultaneous viral reactivations from multiple sacral ganglia.

  7. Characterization and reactivity of sodium aluminoborosilicate glass fiber surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Ortiz Rivera, Lymaris, E-mail: luo105@psu.edu [Materials Research Institute, Pennsylvania State University, University Park, PA 16802 (United States); Bakaev, Victor A.; Banerjee, Joy [Materials Research Institute, Pennsylvania State University, University Park, PA 16802 (United States); Mueller, Karl T. [Department of Chemistry, Pennsylvania State University, University Park, PA 16802 (United States); Pantano, Carlo G. [Materials Research Institute, Pennsylvania State University, University Park, PA 16802 (United States); Department of Materials Science and Engineering, Pennsylvania State University, University Park, PA 16802 (United States)

    2016-05-01

    Highlights: • XPS revealed that these fiber surfaces contain sodium carbonate weathering products. • IGC–MS data confirms the products of acetic acid reaction with sodium carbonate. • NMR data shows two closely spaced, but distinct sodium carboxylate peaks. • Acetic acid reacts with both sodium in the glass and sodium in the sodium carbonate. - Abstract: Multicomponent complex oxides, such as sodium aluminoborosilicate glass fibers, are important materials used for thermal insulation in buildings and homes. Although the surface properties of single oxides, such as silica, have been extensively studied, less is known about the distribution of reactive sites at the surface of multicomponent oxides. Here, we investigated the reactivity of sodium aluminoborosilicate glass fiber surfaces for better understanding of their interface chemistry and bonding with acrylic polymers. Acetic acid (with and without a {sup 13}C enrichment) was used as a probe representative of the carboxylic functional groups in many acrylic polymers and adhesives. Inverse gas chromatography coupled to a mass spectrometer (IGC–MS), and solid state nuclear magnetic resonance (NMR), were used to characterize the fiber surface reactions and surface chemical structure. In this way, we discovered that both sodium ions in the glass surface, as well as sodium carbonate salts that formed on the surface due to the intrinsic reactivity of this glass in humid air, are primary sites of interaction with the carboxylic acid. Surface analysis by X-ray photoelectron spectroscopy (XPS) confirmed the presence of sodium carbonates on these surfaces. Computer simulations of the interactions between the reactive sites on the glass fiber surface with acetic acid were performed to evaluate energetically favorable reactions. The adsorption reactions with sodium in the glass structure provide adhesive bonding sites, whereas the reaction with the sodium carbonate consumes the acid to form sodium-carboxylate, H

  8. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor (CMTI)-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family.

    Science.gov (United States)

    Liu, J; Gong, Y; Prakash, O; Wen, L; Lee, I; Huang, J K; Krishnamoorthi, R

    1998-01-01

    Serine proteinase protein inhibitors follow the standard mechanism of inhibition (Laskowski M Jr, Kato I, 1980, Annu Rev Biochem 49:593-626), whereby an enzyme-catalyzed equilibrium between intact (I) and reactive-site hydrolyzed inhibitor (I*) is reached. The hydrolysis constant, Khyd, is defined as [I*]/[I]. Here, we explore the role of internal dynamics in the resynthesis of the scissile bond by comparing the internal mobility data of intact and cleaved inhibitors belonging to two different families. The inhibitors studied are recombinant Cucurbita maxima trypsin inhibitor III (rCMTI-III; Mr 3 kDa) of the squash family and rCMTI-V (Mr approximately 7 kDa) of the potato I family. These two inhibitors have different binding loop-scaffold interactions and different Khyd values--2.4 (CMTI-III) and 9 (CMTI-V)--at 25 degrees C. The reactive-site peptide bond (P1-P1') is that between Arg5 and Ile6 in CMTI-III, and that between Lys44 and Asp45 in CMTI-V. The order parameters (S2) of backbone NHs of uniformly 15N-labeled rCMTI-III and rCMTI-III* were determined from measurements of 15N spin-lattice and spin-spin relaxation rates, and [1H]-15N steady-state heteronuclear Overhauser effects, using the model-free formalism, and compared with the data reported previously for rCMTI-V and rCMTI-V*. The backbones of rCMTI-III [(S2) = 0.71] and rCMTI-III* [(S2) = 0.63] are more flexible than those of rCMTI-V [(S2) = 0.83] and rCMTI-V* [(S2) = 0.85]. The binding loop residues, P4-P1, in the two proteins show the following average order parameters: 0.57 (rCMTI-III) and 0.44 (rCMTI-III*); 0.70 (rCMTI-V) and 0.40 (rCMTI-V*). The P1'-P4' residues, on the other hand, are associated with (S2) values of 0.56 (rCMTI-III) and 0.47 (rCMTI-III*); and 0.73 (rCMTI-V) and 0.83 (rCMTI-V*). The newly formed C-terminal (Pn residues) gains a smaller magnitude of flexibility in rCMTI-III* due to the Cys3-Cys20 crosslink. In contrast, the newly formed N-terminal (Pn' residues) becomes more flexible

  9. Whole-loop mitochondrial DNA D-loop sequence variability in Egyptian Arabian equine matrilines

    Science.gov (United States)

    Hudson, William

    2017-01-01

    Background Egyptian Arabian horses have been maintained in a state of genetic isolation for over a hundred years. There is only limited genetic proof that the studbook records of female lines of Egyptian Arabian pedigrees are reliable. This study characterized the mitochondrial DNA (mtDNA) signatures of 126 horses representing 14 matrilines in the Egyptian Agricultural Organization (EAO) horse-breeding program. Findings Analysis of the whole D-loop sequence yielded additional information compared to hypervariable region-1 (HVR1) analysis alone, with 42 polymorphic sites representing ten haplotypes compared to 16 polymorphic sites representing nine haplotypes, respectively. Most EAO haplotypes belonged to ancient haplogroups, suggesting origin from a wide geographical area over many thousands of years, although one haplotype was novel. Conclusions Historical families share haplotypes and some individuals from different strains belonged to the same haplogroup: the classical EAO strain designation is not equivalent to modern monophyletic matrilineal groups. Phylogenetic inference showed that the foundation mares of the historical haplotypes were highly likely to have the same haplotypes as the animals studied (p > 0.998 in all cases), confirming the reliability of EAO studbook records and providing the opportunity for breeders to confirm the ancestry of their horses. PMID:28859174

  10. PLASMOID EJECTIONS AND LOOP CONTRACTIONS IN AN ERUPTIVE M7.7 SOLAR FLARE: EVIDENCE OF PARTICLE ACCELERATION AND HEATING IN MAGNETIC RECONNECTION OUTFLOWS

    Energy Technology Data Exchange (ETDEWEB)

    Liu Wei [Lockheed Martin Solar and Astrophysics Laboratory, Building 252, 3251 Hanover Street, Palo Alto, CA 94304 (United States); Chen Qingrong; Petrosian, Vahe [Department of Physics, Stanford University, Stanford, CA 94305 (United States)

    2013-04-20

    Where particle acceleration and plasma heating take place in relation to magnetic reconnection is a fundamental question for solar flares. We report analysis of an M7.7 flare on 2012 July 19 observed by SDO/AIA and RHESSI. Bi-directional outflows in forms of plasmoid ejections and contracting cusp-shaped loops originate between an erupting flux rope and underlying flare loops at speeds of typically 200-300 km s{sup -1} up to 1050 km s{sup -1}. These outflows are associated with spatially separated double coronal X-ray sources with centroid separation decreasing with energy. The highest temperature is located near the nonthermal X-ray loop-top source well below the original heights of contracting cusps near the inferred reconnection site. These observations suggest that the primary loci of particle acceleration and plasma heating are in the reconnection outflow regions, rather than the reconnection site itself. In addition, there is an initial ascent of the X-ray and EUV loop-top source prior to its recently recognized descent, which we ascribe to the interplay among multiple processes including the upward development of reconnection and the downward contractions of reconnected loops. The impulsive phase onset is delayed by 10 minutes from the start of the descent, but coincides with the rapid speed increases of the upward plasmoids, the individual loop shrinkages, and the overall loop-top descent, suggestive of an intimate relation of the energy release rate and reconnection outflow speed.

  11. Higher dimensional loop quantum cosmology

    International Nuclear Information System (INIS)

    Zhang, Xiangdong

    2016-01-01

    Loop quantum cosmology (LQC) is the symmetric sector of loop quantum gravity. In this paper, we generalize the structure of loop quantum cosmology to the theories with arbitrary spacetime dimensions. The isotropic and homogeneous cosmological model in n + 1 dimensions is quantized by the loop quantization method. Interestingly, we find that the underlying quantum theories are divided into two qualitatively different sectors according to spacetime dimensions. The effective Hamiltonian and modified dynamical equations of n + 1 dimensional LQC are obtained. Moreover, our results indicate that the classical big bang singularity is resolved in arbitrary spacetime dimensions by a quantum bounce. We also briefly discuss the similarities and differences between the n + 1 dimensional model and the 3 + 1 dimensional one. Our model serves as a first example of higher dimensional loop quantum cosmology and offers the possibility to investigate quantum gravity effects in higher dimensional cosmology. (orig.)

  12. Hyperstaticity and loops in frictional granular packings

    Science.gov (United States)

    Tordesillas, Antoinette; Lam, Edward; Metzger, Philip T.

    2009-06-01

    The hyperstatic nature of granular packings of perfectly rigid disks is analyzed algebraically and through numerical simulation. The elementary loops of grains emerge as a fundamental element in addressing hyperstaticity. Loops consisting of an odd number of grains behave differently than those with an even number. For odd loops, the latent stresses are exterior and are characterized by the sum of frictional forces around each loop. For even loops, the latent stresses are interior and are characterized by the alternating sum of frictional forces around each loop. The statistics of these two types of loop sums are found to be Gibbsian with a "temperature" that is linear with the friction coefficient μ when μ<1.

  13. Loop Heat Pipe Startup Behaviors

    Science.gov (United States)

    Ku, Jentung

    2016-01-01

    A loop heat pipe must start successfully before it can commence its service. The startup transient represents one of the most complex phenomena in the loop heat pipe operation. This paper discusses various aspects of loop heat pipe startup behaviors. Topics include the four startup scenarios, the initial fluid distribution between the evaporator and reservoir that determines the startup scenario, factors that affect the fluid distribution between the evaporator and reservoir, difficulties encountered during the low power startup, and methods to enhance the startup success. Also addressed are the pressure spike and pressure surge during the startup transient, and repeated cycles of loop startup and shutdown under certain conditions.

  14. Synthetic strategies for efficient conjugation of organometallic complexes with pendant protein reactive markers

    KAUST Repository

    Jantke, Dominik; Marziale, Alexander N.; Reiner, Thomas; Kraus, Florian; Herdtweck, Eberhardt; Raba, Andreas; Eppinger, Jö rg

    2013-01-01

    Site-directed conjugation of metal centers to proteins is fundamental for biological and bioinorganic applications of transition metals. However, methods for the site-selective introduction of metal centers remain scarce. Herein, we present broadly applicable synthetic strategies for the conjugation of bioactive molecules with a range of organometallic complexes. Following three different synthetic strategies, we were able to synthesize a small library of metal conjugated protein markers featuring different types of protein reactive sites (epoxides, phenylphosphonates, fluorosulfonates and fluorophosphonate groups) as well as different late transition metals (iron, ruthenium, rhodium, palladium and platinum). The products were isolated in moderate to excellent yields and high purity. Furthermore, X-ray diffraction of the metalated protein markers corroborates structural integrity of the metal complex and the protein reactive site. © 2013 Elsevier B.V. All rights reserved.

  15. Synthetic strategies for efficient conjugation of organometallic complexes with pendant protein reactive markers

    KAUST Repository

    Jantke, Dominik

    2013-11-01

    Site-directed conjugation of metal centers to proteins is fundamental for biological and bioinorganic applications of transition metals. However, methods for the site-selective introduction of metal centers remain scarce. Herein, we present broadly applicable synthetic strategies for the conjugation of bioactive molecules with a range of organometallic complexes. Following three different synthetic strategies, we were able to synthesize a small library of metal conjugated protein markers featuring different types of protein reactive sites (epoxides, phenylphosphonates, fluorosulfonates and fluorophosphonate groups) as well as different late transition metals (iron, ruthenium, rhodium, palladium and platinum). The products were isolated in moderate to excellent yields and high purity. Furthermore, X-ray diffraction of the metalated protein markers corroborates structural integrity of the metal complex and the protein reactive site. © 2013 Elsevier B.V. All rights reserved.

  16. Conformal boundary loop models

    International Nuclear Information System (INIS)

    Jacobsen, Jesper Lykke; Saleur, Hubert

    2008-01-01

    We study a model of densely packed self-avoiding loops on the annulus, related to the Temperley-Lieb algebra with an extra idempotent boundary generator. Four different weights are given to the loops, depending on their homotopy class and whether they touch the outer rim of the annulus. When the weight of a contractible bulk loop x≡q+q -1 element of (-2,2], this model is conformally invariant for any real weight of the remaining three parameters. We classify the conformal boundary conditions and give exact expressions for the corresponding boundary scaling dimensions. The amplitudes with which the sectors with any prescribed number and types of non-contractible loops appear in the full partition function Z are computed rigorously. Based on this, we write a number of identities involving Z which hold true for any finite size. When the weight of a contractible boundary loop y takes certain discrete values, y r ≡([r+1] q )/([r] q ) with r integer, other identities involving the standard characters K r,s of the Virasoro algebra are established. The connection with Dirichlet and Neumann boundary conditions in the O(n) model is discussed in detail, and new scaling dimensions are derived. When q is a root of unity and y=y r , exact connections with the A m type RSOS model are made. These involve precise relations between the spectra of the loop and RSOS model transfer matrices, valid in finite size. Finally, the results where y=y r are related to the theory of Temperley-Lieb cabling

  17. Technical and economic feasibility study for the reactivation of the integral test facility of IPEN/CNEN Nuclear Engineering Center

    Energy Technology Data Exchange (ETDEWEB)

    Biaty, Flávia P.; Rocha, Marcelo da S.; Oliveira, Otávio L. de, E-mail: flavia.biaty@usp.br, E-mail: msrocha@ipen.br, E-mail: otavioluis@ipen.br [Instituto de Pesquisas Energéticas e Nucleares (IPEN/CNEN-SP), São Paulo, SP (Brazil)

    2017-07-01

    The Integral Test Facility of Nuclear Engineering Center (CEN/IPEN/CNEN-SP), known as 'Loop 70', is a semi-industrial thermal-hydraulic test facility and can operate as a BWR (Boiling Water Reactor) or a PWR (Pressurizing Water Reactor) mode. Designed and built in the 1980's, it is currently disabled. The experimental circuits ('test loop') are facilities that reproduce the thermohydraulic and fluid dynamic conditions that occur inside a reactor and are used to simulate the practical reality which it is not possible to be obtained through mathematical models. In this context, this research project aims the development of a Business Plan to analyze the technical and economic feasibility related to the reactivation of the facility. This methodology (adapted to the government sector) is a decision-making tool that will offer a wide perspective of the project, set the guidelines and actions that will define the future of the facility and provide a general rule to make investments on it. This paper presents the historic aspects to better understand the Loop 70's current situation. It also presents information about similar facilities around the world, services that can be offered (thermal-hydraulics parameters measurements, equipment qualification and transient analysis due accident situations), results of the strategic analysis (SWOT) performed, specific goals for each critical success or failure factor of the facility, financial aspects related to the reactivation and an overview of the facility's perspectives. (author)

  18. Technical and economic feasibility study for the reactivation of the integral test facility of IPEN/CNEN Nuclear Engineering Center

    International Nuclear Information System (INIS)

    Biaty, Flávia P.; Rocha, Marcelo da S.; Oliveira, Otávio L. de

    2017-01-01

    The Integral Test Facility of Nuclear Engineering Center (CEN/IPEN/CNEN-SP), known as 'Loop 70', is a semi-industrial thermal-hydraulic test facility and can operate as a BWR (Boiling Water Reactor) or a PWR (Pressurizing Water Reactor) mode. Designed and built in the 1980's, it is currently disabled. The experimental circuits ('test loop') are facilities that reproduce the thermohydraulic and fluid dynamic conditions that occur inside a reactor and are used to simulate the practical reality which it is not possible to be obtained through mathematical models. In this context, this research project aims the development of a Business Plan to analyze the technical and economic feasibility related to the reactivation of the facility. This methodology (adapted to the government sector) is a decision-making tool that will offer a wide perspective of the project, set the guidelines and actions that will define the future of the facility and provide a general rule to make investments on it. This paper presents the historic aspects to better understand the Loop 70's current situation. It also presents information about similar facilities around the world, services that can be offered (thermal-hydraulics parameters measurements, equipment qualification and transient analysis due accident situations), results of the strategic analysis (SWOT) performed, specific goals for each critical success or failure factor of the facility, financial aspects related to the reactivation and an overview of the facility's perspectives. (author)

  19. Large lithium loop experience

    International Nuclear Information System (INIS)

    Kolowith, R.; Owen, T.J.; Berg, J.D.; Atwood, J.M.

    1981-10-01

    An engineering design and operating experience of a large, isothermal, lithium-coolant test loop are presented. This liquid metal coolant loop is called the Experimental Lithium System (ELS) and has operated safely and reliably for over 6500 hours through September 1981. The loop is used for full-scale testing of components for the Fusion Materials Irradiation Test (FMIT) Facility. Main system parameters include coolant temperatures to 430 0 C and flow to 0.038 m 3 /s (600 gal/min). Performance of the main pump, vacuum system, and control system is discussed. Unique test capabilities of the ELS are also discussed

  20. Modular invariance and covariant loop calculus

    International Nuclear Information System (INIS)

    Petersen, J.L.; Roland, K.O.; Sidenius, J.R.

    1988-01-01

    The covariant loop calculus provides an efficient technique for computing explicit expressions for the density on moduli space corresponding to arbitrary (bosonic string) loop diagrams. Since modular invariance is not manifest, however, we carry out a detailed comparison with known explicit two- and three-loop results derived using analytic geometry (one loop is known to be okay). We establish identity to 'high' order in some moduli and exactly in others. Agreement is found as a result of various nontrivial cancellations, in part related to number theory. We feel our results provide very strong support for the correctness of the covariant loop calculus approach. (orig.)

  1. Modular invariance and covariant loop calculus

    International Nuclear Information System (INIS)

    Petersen, J.L.; Roland, K.O.; Sidenius, J.R.

    1988-01-01

    The covariant loop calculus provides and efficient technique for computing explicit expressions for the density on moduli space corresponding to arbitrary (bosonic string) loop diagrams. Since modular invariance is not manifest, however, we carry out a detailed comparison with known explicit 2- and 3- loop results derived using analytic geometry (1 loop is known to be ok). We establish identity to 'high' order in some moduli and exactly in others. Agreement is found as a result of various non-trivial cancellations, in part related to number theory. We feel our results provide very strong support for the correctness of the covariant loop calculus approach. (orig.)

  2. Preliminary reactive geochemical transport simulation study on CO2 geological sequestration at the Changhua Coastal Industrial Park Site, Taiwan

    Science.gov (United States)

    Sung, R.; Li, M.

    2013-12-01

    assumed throughout the simulation domain. Comparisons among simulated results with different mesh systems of nested meshes and non-nested meshes and considerations of multiphase reactive transport and physical transport were demonstrated in this study. Preliminary results of injection CO2 for 50 years are: (1) about 7 wt.% of injected CO2 was trapped as carbonate minerals mainly as ankerite; (2) porosities were decreased by 0.014 % and increased by 0.102 % at the injection point and beneath the cap rock, respectively, and were subsequently decreased with time due to minerals precipitation mostly as illite and ankerite; (3) differences of simulated aquifer responses between reactive transport and physical transport were insignificant; and (4) projected CO2 plumes with the nested meshes was smaller than those by the non-nested meshes after cease of CO2 injection. Keywords: CO2-Saline-Mineral Interaction, Reactive Geochemical Transport, TOUGHREACT, Mineral Trapping Assessment, Changhua Costal Industrial Park Site, Taiwan Reference: Marini, L., 2006, Geological Sequestration of Carbon Dioxide, Volume 11: Thermodynamics, Kinetics, and Reaction Path Modeling, Elsevier Science, pp.470. Xu, T., J. A. Apps and K. Pruess, 2004, Numerical simulation of CO2 disposal by mineral trapping in deep aquifers, Applied Geochemistry, Vol. 19:917-936.

  3. Computer modelling reveals new conformers of the ATP binding loop of Na+/K+-ATPase involved in the transphosphorylation process of the sodium pump.

    Science.gov (United States)

    Tejral, Gracian; Sopko, Bruno; Necas, Alois; Schoner, Wilhelm; Amler, Evzen

    2017-01-01

    Hydrolysis of ATP by Na + /K + -ATPase, a P-Type ATPase, catalyzing active Na + and K + transport through cellular membranes leads transiently to a phosphorylation of its catalytical α -subunit. Surprisingly, three-dimensional molecular structure analysis of P-type ATPases reveals that binding of ATP to the N-domain connected by a hinge to the P-domain is much too far away from the Asp 369 to allow the transfer of ATP's terminal phosphate to its aspartyl-phosphorylation site. In order to get information for how the transfer of the γ -phosphate group of ATP to the Asp 369 is achieved, analogous molecular modeling of the M 4 -M 5 loop of ATPase was performed using the crystal data of Na + /K + -ATPase of different species. Analogous molecular modeling of the cytoplasmic loop between Thr 338 and Ile 760 of the α 2 -subunit of Na + /K + -ATPase and the analysis of distances between the ATP binding site and phosphorylation site revealed the existence of two ATP binding sites in the open conformation; the first one close to Phe 475 in the N-domain, the other one close to Asp 369 in the P-domain. However, binding of Mg 2+ •ATP to any of these sites in the "open conformation" may not lead to phosphorylation of Asp 369 . Additional conformations of the cytoplasmic loop were found wobbling between "open conformation"  "semi-open conformation  "closed conformation" in the absence of 2Mg 2+ •ATP. The cytoplasmic loop's conformational change to the "semi-open conformation"-characterized by a hydrogen bond between Arg 543 and Asp 611 -triggers by binding of 2Mg 2+ •ATP to a single ATP site and conversion to the "closed conformation" the phosphorylation of Asp 369 in the P-domain, and hence the start of Na + /K + -activated ATP hydrolysis.

  4. Sodium Loop Safety Facility W-2 experiment fuel pin rupture detection system

    International Nuclear Information System (INIS)

    Hoffman, M.A.; Kirchner, T.L.; Meyers, S.C.

    1980-05-01

    The objective of the Sodium Loop Safety Facility (SLSF) W-2 experiment is to characterize the combined effects of a preconditioned full-length fuel column and slow transient overpower (TOP) conditions on breeder reactor (BR) fuel pin cladding failures. The W-2 experiment will meet this objective by providing data in two technological areas: (1) time and location of cladding failure, and (2) early post-failure test fuel behavior. The test involves a seven pin, prototypic full-length fast test reactor (FTR) fuel pin bundle which will be subjected to a simulated unprotected 5 cents/s reactivity transient overpower event. The outer six pins will provide the necessary prototypic thermal-hydraulic environment for the center pin

  5. Computational prediction of CTCF/cohesin-based intra-TAD loops that insulate chromatin contacts and gene expression in mouse liver.

    Science.gov (United States)

    Matthews, Bryan J; Waxman, David J

    2018-05-14

    CTCF and cohesin are key drivers of 3D-nuclear organization, anchoring the megabase-scale Topologically Associating Domains (TADs) that segment the genome. Here, we present and validate a computational method to predict cohesin-and-CTCF binding sites that form intra-TAD DNA loops. The intra-TAD loop anchors identified are structurally indistinguishable from TAD anchors regarding binding partners, sequence conservation, and resistance to cohesin knockdown; further, the intra-TAD loops retain key functional features of TADs, including chromatin contact insulation, blockage of repressive histone mark spread, and ubiquity across tissues. We propose that intra-TAD loops form by the same loop extrusion mechanism as the larger TAD loops, and that their shorter length enables finer regulatory control in restricting enhancer-promoter interactions, which enables selective, high-level expression of gene targets of super-enhancers and genes located within repressive nuclear compartments. These findings elucidate the role of intra-TAD cohesin-and-CTCF binding in nuclear organization associated with widespread insulation of distal enhancer activity. © 2018, Matthews et al.

  6. Functional mimicry of a discontinuous antigenic site by a designed synthetic peptide

    NARCIS (Netherlands)

    Villen, J.; Borras, E.; Schaaper, W.M.M.; Meloen, R.H.; Davila, M.; Domingo, E.; Giralt, E.; Andreu, D.

    2002-01-01

    Functional reproduction of the discontinuous antigenic site D of foot-and-mouth disease virus (FMDV) has been achieved by means of synthetic peptide constructions that integrate each of the three protein loops that define the antigenic site into a single molecule. The site D mimics were designed on

  7. Parallel tiled Nussinov RNA folding loop nest generated using both dependence graph transitive closure and loop skewing.

    Science.gov (United States)

    Palkowski, Marek; Bielecki, Wlodzimierz

    2017-06-02

    RNA secondary structure prediction is a compute intensive task that lies at the core of several search algorithms in bioinformatics. Fortunately, the RNA folding approaches, such as the Nussinov base pair maximization, involve mathematical operations over affine control loops whose iteration space can be represented by the polyhedral model. Polyhedral compilation techniques have proven to be a powerful tool for optimization of dense array codes. However, classical affine loop nest transformations used with these techniques do not optimize effectively codes of dynamic programming of RNA structure predictions. The purpose of this paper is to present a novel approach allowing for generation of a parallel tiled Nussinov RNA loop nest exposing significantly higher performance than that of known related code. This effect is achieved due to improving code locality and calculation parallelization. In order to improve code locality, we apply our previously published technique of automatic loop nest tiling to all the three loops of the Nussinov loop nest. This approach first forms original rectangular 3D tiles and then corrects them to establish their validity by means of applying the transitive closure of a dependence graph. To produce parallel code, we apply the loop skewing technique to a tiled Nussinov loop nest. The technique is implemented as a part of the publicly available polyhedral source-to-source TRACO compiler. Generated code was run on modern Intel multi-core processors and coprocessors. We present the speed-up factor of generated Nussinov RNA parallel code and demonstrate that it is considerably faster than related codes in which only the two outer loops of the Nussinov loop nest are tiled.

  8. Gauge theory loop operators and Liouville theory

    International Nuclear Information System (INIS)

    Drukker, Nadav; Teschner, Joerg

    2009-10-01

    We propose a correspondence between loop operators in a family of four dimensional N=2 gauge theories on S 4 - including Wilson, 't Hooft and dyonic operators - and Liouville theory loop operators on a Riemann surface. This extends the beautiful relation between the partition function of these N=2 gauge theories and Liouville correlators found by Alday, Gaiotto and Tachikawa. We show that the computation of these Liouville correlators with the insertion of a Liouville loop operator reproduces Pestun's formula capturing the expectation value of a Wilson loop operator in the corresponding gauge theory. We prove that our definition of Liouville loop operators is invariant under modular transformations, which given our correspondence, implies the conjectured action of S-duality on the gauge theory loop operators. Our computations in Liouville theory make an explicit prediction for the exact expectation value of 't Hooft and dyonic loop operators in these N=2 gauge theories. The Liouville loop operators are also found to admit a simple geometric interpretation within quantum Teichmueller theory as the quantum operators representing the length of geodesics. We study the algebra of Liouville loop operators and show that it gives evidence for our proposal as well as providing definite predictions for the operator product expansion of loop operators in gauge theory. (orig.)

  9. A True Open-Loop Synchronization Technique

    DEFF Research Database (Denmark)

    Golestan, Saeed; Vidal, Ana; Yepes, Alejandro G.

    2016-01-01

    Synchronization techniques can be broadly classified into two major categories: Closed-loop and open-loop methods. The open-loop synchronization (OLS) techniques, contrary to the closed-loop ones, are unconditionally stable and benefit from a fast dynamic response. Their performance, however, tends...... is to develop a true OLS (and therefore, unconditionally stable) technique without any need for the calculation of sine and cosine functions. The effectiveness of the proposed synchronization technique is confirmed through the simulation and experimental results....

  10. Epitaxial growth of indium oxyfluoride thin films by reactive pulsed laser deposition: Structural change induced by fluorine insertion into vacancy sites in bixbyite structure

    International Nuclear Information System (INIS)

    Okazaki, Sohei; Hirose, Yasushi; Nakao, Shoichiro; Yang, Chang; Harayama, Isao; Sekiba, Daiichiro; Hasegawa, Tetsuya

    2014-01-01

    InO x F y thin films were epitaxially grown on Y-stabilized ZrO 2 (111) substrates by reactive pulsed laser deposition. By changing the substrate temperature (T S ), we were able to control the fluorine content of the film. Phase-pure epitaxial thin films with bixbyite-like ordering in the anion-site occupancy were obtained at high T S (≥ 240 °C), where fluorine was inserted into the vacancy sites in the bixbyite lattice up to y / (x + y) ∼ 0.3. By decreasing T S , y / (x + y) increased and the bixbyite-like ordering disappeared; simultaneously, fluorine-rich and fluorine-poor subphases emerged. The films grown at T S ≤ 150 °C were amorphous and exhibited higher optical absorbance and electrical resistivity than the epitaxial films. - Highlights: • InO x F y epitaxial thin films with high fluorine concentration were grown on Y:ZrO 2 . • Anion composition and structural, optical and transport properties were studied. • Fluorine is topotactically inserted into the oxygen vacancy sites in bixbyite cell. • Bixbyite-like ordering of the anion site occupancy was conserved in y / (x + y) ≤ ∼ 0.3

  11. A kinematic view of loop closure.

    Science.gov (United States)

    Coutsias, Evangelos A; Seok, Chaok; Jacobson, Matthew P; Dill, Ken A

    2004-03-01

    We consider the problem of loop closure, i.e., of finding the ensemble of possible backbone structures of a chain segment of a protein molecule that is geometrically consistent with preceding and following parts of the chain whose structures are given. We reduce this problem of determining the loop conformations of six torsions to finding the real roots of a 16th degree polynomial in one variable, based on the robotics literature on the kinematics of the equivalent rotator linkage in the most general case of oblique rotators. We provide a simple intuitive view and derivation of the polynomial for the case in which each of the three pair of torsional axes has a common point. Our method generalizes previous work on analytical loop closure in that the torsion angles need not be consecutive, and any rigid intervening segments are allowed between the free torsions. Our approach also allows for a small degree of flexibility in the bond angles and the peptide torsion angles; this substantially enlarges the space of solvable configurations as is demonstrated by an application of the method to the modeling of cyclic pentapeptides. We give further applications to two important problems. First, we show that this analytical loop closure algorithm can be efficiently combined with an existing loop-construction algorithm to sample loops longer than three residues. Second, we show that Monte Carlo minimization is made severalfold more efficient by employing the local moves generated by the loop closure algorithm, when applied to the global minimization of an eight-residue loop. Our loop closure algorithm is freely available at http://dillgroup. ucsf.edu/loop_closure/. Copyright 2004 Wiley Periodicals, Inc. J Comput Chem 25: 510-528, 2004

  12. The Wilson loop and some applications

    International Nuclear Information System (INIS)

    Bezerra, V.B.

    1983-01-01

    A simple relation between the classical Wilson loop and the angular deviation in the parallel shift is found. An example of potential which given field copies and which give the same classical Wilson loop for a given trajectory is exchibited. Afterwards, the asymptotic behaviour of the Wilson loop for the BPST instanton and meron is discussed. Using the dimensional regularization technique to calculate the second order term of Quantum Wilson loop, the influence of geometrical factors for the residue in the polo due to contact points, cusp and intersections, in function of the upsilon dimension of the space-time is investigated. Finally, the charge renormalization in Quantum Electrodynamics using Quantum Wilson loop is calculated. (L.C.) [pt

  13. The Wilson loop and some applications

    International Nuclear Information System (INIS)

    Bezerra, V.B.

    1983-04-01

    A simple relation between the classical Wilson loop and the angular deviation in the parallel displacement is found. An example of potentials which give field copies and which suplly the same classical Wilson loop for a particular trajectory is exhibited. The asymptotic behaviour of the Wilson loop for the BPST instanton and the meron, is discussed. By using the dimensional regularization technique to calculate the second order term of the quantum Wilson loop, the influence of geometrical factors for the residue in the pole due to contact points, cuspides and intersections, in function of the space-time ν, is investigated. Charge renormalization in Quantum electrodynamics is finally calculated by using the quantum Wilson loop. (L.C.) [pt

  14. A novel mode for transcription inhibition mediated by PNA-induced R-loops with a model in vitro system.

    Science.gov (United States)

    D'Souza, Alicia D; Belotserkovskii, Boris P; Hanawalt, Philip C

    2018-02-01

    The selective inhibition of transcription of a chosen gene by an artificial agent has numerous applications. Usually, these agents are designed to bind a specific nucleotide sequence in the promoter or within the transcribed region of the chosen gene. However, since optimal binding sites might not exist within the gene, it is of interest to explore the possibility of transcription inhibition when the agent is designed to bind at other locations. One of these possibilities arises when an additional transcription initiation site (e.g. secondary promoter) is present upstream from the primary promoter of the target gene. In this case, transcription inhibition might be achieved by inducing the formation of an RNA-DNA hybrid (R-loop) upon transcription from the secondary promoter. The R-loop could extend into the region of the primary promoter, to interfere with promoter recognition by RNA polymerase and thereby inhibit transcription. As a sequence-specific R-loop-inducing agent, a peptide nucleic acid (PNA) could be designed to facilitate R-loop formation by sequestering the non-template DNA strand. To investigate this mode for transcription inhibition, we have employed a model system in which a PNA binding site is localized between the T3 and T7 phage RNA polymerase promoters, which respectively assume the roles of primary and secondary promoters. In accord with our model, we have demonstrated that with PNA-bound DNA substrates, transcription from the T7 promoter reduces transcription from the T3 promoter by 30-fold, while in the absence of PNA binding there is no significant effect of T7 transcription upon T3 transcription. Copyright © 2018 Elsevier B.V. All rights reserved.

  15. Role of the NC-loop in catalytic activity and stability in lipase from Fervidobacterium changbaicum.

    Directory of Open Access Journals (Sweden)

    Binchun Li

    Full Text Available Flexible NC-loops between the catalytic domain and the cap domain of the α/β hydrolase fold enzymes show remarkable diversity in length, sequence, and configuration. Recent investigations have suggested that the NC-loop might be involved in catalysis and substrate recognition in many enzymes from the α/β hydrolase fold superfamily. To foster a deep understanding of its role in catalysis, stability, and divergent evolution, we here systemically investigated the function of the NC-loop (residues 131-151 in a lipase (FClip1 from thermophilic bacterium Fervidobacterium changbaicum by loop deletion, alanine-scanning mutagenesis and site-directed mutagenesis. We found that the upper part of the NC-loop (residues 131-138 was of great importance to enzyme catalysis. Single substitutions in this region could fine-tune the activity of FClip1 as much as 41-fold, and any deletions from this region rendered the enzyme completely inactive. The lower part of the NC-loop (residues 139-151 was capable of enduring extensive deletions without loss of activity. The shortened mutants in this region were found to show both improved activity and increased stability simultaneously. We therefore speculated that the NC-loop, especially the lower part, would be a perfect target for enzyme engineering to optimize the enzymatic properties, and might present a hot zone for the divergent evolution of α/β hydrolases. Our findings may provide an opportunity for better understanding of the mechanism of divergent evolution in the α/β hydrolase fold superfamily, and may also guide the design of novel biocatalysts for industrial applications.

  16. An experimental study of dislocation loop nucleation

    International Nuclear Information System (INIS)

    Bounaud, J.Y.; Leteurtre, J.

    1975-01-01

    The nucleation of dislocation loops is experimentally studied by observing the demixion of the Burgers vectors of dislocation loops nucleated in copper whiskers irradiated in flexion by fission fragments at room temperature. The demixion of Burgers vectors is observed by the dimensional effects of dislocation loops: after irradiation, the applied stress is removed; the whisker shows a residual strain that is due to loops because, after an annealing treatment to evaporate dislocation loops, each whisker recovers its initial straight shape. Everywhere along the whisker, the radius of curvature is measured and plotted vs the max. applied stress. Estimations of the interstitial and vacancy dislocation loop nuclei are derived [fr

  17. Closed Loop Recycling of Plastic Housing for Flat Screen TVs

    OpenAIRE

    Peeters, Jef; Vanegas, Paul; Devoldere, Tom; Dewulf, Wim; Duflou, Joost

    2012-01-01

    The treatment of the rapidly increasing number of End-of-Life (EoL) Flat screen Televisions (FTVs) presents major challenges and opportunities. Closing loops in plastic housing material flows remains a particular technical challenge because of the presence of additives, such as Flame Retardants (FR) in recovered housings. In the framework of a collaborative project PRIME with TP Vision the TV development site for Philips TVs and a Van Gansewinkel first level recycling plant, series of experim...

  18. Coupling between feedback loops in autoregulatory networks affects bistability range, open-loop gain and switching times

    International Nuclear Information System (INIS)

    Tiwari, Abhinav; Igoshin, Oleg A

    2012-01-01

    Biochemical regulatory networks governing diverse cellular processes such as stress-response, differentiation and cell cycle often contain coupled feedback loops. We aim at understanding how features of feedback architecture, such as the number of loops, the sign of the loops and the type of their coupling, affect network dynamical performance. Specifically, we investigate how bistability range, maximum open-loop gain and switching times of a network with transcriptional positive feedback are affected by additive or multiplicative coupling with another positive- or negative-feedback loop. We show that a network's bistability range is positively correlated with its maximum open-loop gain and that both quantities depend on the sign of the feedback loops and the type of feedback coupling. Moreover, we find that the addition of positive feedback could decrease the bistability range if we control the basal level in the signal-response curves of the two systems. Furthermore, the addition of negative feedback has the capacity to increase the bistability range if its dissociation constant is much lower than that of the positive feedback. We also find that the addition of a positive feedback to a bistable network increases the robustness of its bistability range, whereas the addition of a negative feedback decreases it. Finally, we show that the switching time for a transition from a high to a low steady state increases with the effective fold change in gene regulation. In summary, we show that the effect of coupled feedback loops on the bistability range and switching times depends on the underlying mechanistic details. (paper)

  19. Gauge theory loop operators and Liouville theory

    Energy Technology Data Exchange (ETDEWEB)

    Drukker, Nadav [Humboldt Univ. Berlin (Germany). Inst. fuer Physik; Gomis, Jaume; Okuda, Takuda [Perimeter Inst. for Theoretical Physics, Waterloo, ON (Canada); Teschner, Joerg [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2009-10-15

    We propose a correspondence between loop operators in a family of four dimensional N=2 gauge theories on S{sup 4} - including Wilson, 't Hooft and dyonic operators - and Liouville theory loop operators on a Riemann surface. This extends the beautiful relation between the partition function of these N=2 gauge theories and Liouville correlators found by Alday, Gaiotto and Tachikawa. We show that the computation of these Liouville correlators with the insertion of a Liouville loop operator reproduces Pestun's formula capturing the expectation value of a Wilson loop operator in the corresponding gauge theory. We prove that our definition of Liouville loop operators is invariant under modular transformations, which given our correspondence, implies the conjectured action of S-duality on the gauge theory loop operators. Our computations in Liouville theory make an explicit prediction for the exact expectation value of 't Hooft and dyonic loop operators in these N=2 gauge theories. The Liouville loop operators are also found to admit a simple geometric interpretation within quantum Teichmueller theory as the quantum operators representing the length of geodesics. We study the algebra of Liouville loop operators and show that it gives evidence for our proposal as well as providing definite predictions for the operator product expansion of loop operators in gauge theory. (orig.)

  20. Relating loop quantum cosmology to loop quantum gravity: symmetric sectors and embeddings

    International Nuclear Information System (INIS)

    Engle, J

    2007-01-01

    In this paper we address the meaning of states in loop quantum cosmology (LQC), in the context of loop quantum gravity. First, we introduce a rigorous formulation of an embedding proposed by Bojowald and Kastrup, of LQC states into loop quantum gravity. Then, using certain holomorphic representations, a new class of embeddings, called b-embeddings, are constructed, following the ideas of Engle (2006 Quantum field theory and its symmetry reduction Class. Quantum Gravity 23 2861-94). We exhibit a class of operators preserving each of these embeddings, and show their consistency with the LQC quantization. In the b-embedding case, the classical analogues of these operators separate points in phase space. Embedding at the gauge and diffeomorphism invariant level is discussed briefly in the conclusions

  1. Goethite surface reactivity: III. Unifying arsenate adsorption behavior through a variable crystal face - Site density model

    Science.gov (United States)

    Salazar-Camacho, Carlos; Villalobos, Mario

    2010-04-01

    goethite, may be performed for each preparation either by experimental determination of site saturation by an index ion (e.g., chromate), or by achieving congruency of proton adsorption data with those of ideal goethites when plotted as percentage of proton-reactive ( lbond2 FeOH + lbond2 Fe 3OH) sites occupied. The surface arsenate complexes proposed additionally explained: (1) the higher affinity of goethite for As(V) than for Cr(VI) at high pH, and thus the gentle slope of the arsenate pH adsorption edges; and (2) the lower adsorption capacity for As(V) than for Cr(VI) at low pH on low-surface area goethites, through incomplete lbond2 FeOH site occupancy of As(V). The model is very promising as a practical means of predicting the adsorption behavior of arsenate on any goethite preparation, and may extend to predictive capabilities for adsorption behavior of many other relevant oxyanions, as well as for explaining differences in ligand-promoted surface transformation processes on goethite as a function of particle size.

  2. Reactivity of a Pt(100) cluster modified by adsorption of a nickel tetramer

    Energy Technology Data Exchange (ETDEWEB)

    Ortiz, E V; Lopez, M B [Centro de Investigaciones Fisicoquimicas, Teoricas y Aplicadas (CIFTA), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Catamarca, Av. Belgrano 300, (4700), Catamarca (Argentina); Castro, E A, E-mail: mblopez@fcasuser.unca.edu.a [INIFTA, CONICET, Universidad Nacional de la Plata, Diag. 113 y 64, Suc.4, C.C. 16, (1900), La Plata (Argentina)

    2009-05-01

    The aim of this paper is to report a study of the reactivity of Pt(100) cluster and the same system modified by a nickel tetramer towards the atomic hydrogen adsorption. This study was carried out in the framework of density functional theory which provides global and local indexes that can be used to characterize the reactivity. The analyzed reactivity descriptors were: chemical potential, chemical hardness, electrophilicity index and Fukui function. The results showed that the global reactivity descriptor predicts that the platinum cluster modified by nickel is more reactive than the pure platinum cluster and that the local Fukui function provides information about the most susceptible site to electrophilic attack in platinum cluster.

  3. Water loop for training

    International Nuclear Information System (INIS)

    Moeller, S.V.

    1983-02-01

    The procedures used to operate the water loop of the Institute of Nuclear Enginering (IEN) in Brazil are presented. The aim is to help future operators of the training water loop in the operation technique and in a better comprehension of the phenomena occured during the execution of an experience. (E.G.) [pt

  4. Environmental life cycle assessment of permeable reactive barriers: effects of construction methods, reactive materials and groundwater constituents.

    Science.gov (United States)

    Mak, Mark S H; Lo, Irene M C

    2011-12-01

    The effects of the construction methods, materials of reactive media and groundwater constituents on the environmental impacts of a permeable reactive barrier (PRB) were evaluated using life cycle assessment (LCA). The PRB is assumed to be installed at a simulated site contaminated by either Cr(VI) alone or Cr(VI) and As(V). Results show that the trench-based construction method can reduce the environmental impacts of the remediation remarkably compared to the caisson-based method due to less construction material consumption by the funnel. Compared to using the zerovalent iron (Fe(0)) and quartz sand mixture, the use of the Fe(0) and iron oxide-coated sand (IOCS) mixture can reduce the environmental impacts. In the presence of natural organic matter (NOM) in groundwater, the environmental impacts generated by the reactive media were significantly increased because of the higher usage of Fe(0). The environmental impacts are lower by using the Fe(0) and IOCS mixture in the groundwater with NOM, compared with using the Fe(0) and quartz sand mixture. Since IOCS can enhance the removal efficiency of Cr(VI) and As(V), the usage of the Fe(0) can be reduced, which in turn reduces the impacts induced by the reactive media.

  5. Reduced step edges on rutile TiO (110) as competing defects to oxygen vacancies on the terraces and reactive sites for ethanol dissociation

    DEFF Research Database (Denmark)

    Martinez, U.; Hansen, Jonas Ørbæk; Salazar, Estephania Lira

    2012-01-01

    microscopy studies, we here present experimental evidence for the existence of O vacancies along the ⟨11̅ 1⟩R step edges (OS vac.’s) on rutile TiO2(110). Both the distribution of bridging O vacancies on the terraces and temperature-programed reaction experiments of ethanol-covered TiO2(110) point...... to the existence of the OS vac.’s. Based on experiments and density functional theory calculations, we show that OS vac.’s are reactive sites for ethanol dissociation via O-H bond scission. Implications of these findings are discussed...

  6. Loop equations in the theory of gravitation

    International Nuclear Information System (INIS)

    Makeenko, Yu.M.; Voronov, N.A.

    1981-01-01

    Loop-space variables (matrices of parallel transport) for the theory of gravitation are described. Loop equations, which are equivalent to the Einstein equations, are derived in the classical case. Loop equations are derived for gravity with cosmological constant as well. An analogy with the loop-space approach in Yang-Mills theory is discussed [ru

  7. Electrostatic environment surrounding the activation loop phosphotyrosine in the oncoprotein v-Fps.

    Science.gov (United States)

    Leon, B C; Tsigelny, I; Adams, J A

    2001-08-28

    Autophosphorylation of Tyr-1073 in the activation loop of the oncoprotein v-Fps enhances the phosphoryl transfer reaction without influencing substrate, ATP, or metal ion binding affinities [Saylor, P., et al. (1998) Biochemistry 37, 17875-17881]. A structural model of v-Fps, generated from the insulin receptor, indicates that pTyr-1073 chelates two arginines. Mutation of these residues to alanine (R1042A and R1066A) results in weakly phosphorylated enzymes, indicating that one electropositive center is insufficient for attaining maximum loop phosphorylation and concomitant high catalytic activity. While the turnover rate for R1066A is similar to that for a mutant lacking a phosphorylatable residue in the activation loop, the rate for R1042A is 50-fold slower. While solvent perturbation studies suggest that the former is due to a slow phosphoryl transfer step, the latter effect results from a slow conformational change in the mutant, potentially linked to motions in the catalytic loop. Binding of a stoichiometric quantity of Mg(2+) is essential for ATP binding and catalysis, while binding of an additional Mg(2+) ion activates further the wild-type enzyme. The affinity of the R1066A enzyme for the second Mg(2+) ion is 23-fold higher than that of the phosphorylated or unphosphorylated form of wild-type v-Fps, with substrate binding unaffected. Conversely, the affinity of R1066A for a substrate mimic lacking a phosphorylation site is 12-fold higher than that for the phosphorylated or unphosphorylated form of wild-type v-Fps, with binding of the second Mg(2+) ion unaffected. A comparison of these enzyme-independent parameters indicates that Arg-1042 and Arg-1066 induce strain in the active site in the repressed form of the enzyme. While this strain is not relieved in the phosphorylated form, the improvements in catalysis in activated v-Fps compensate for reduced metal and substrate binding affinities.

  8. Tritium Management Loop Design Status

    Energy Technology Data Exchange (ETDEWEB)

    Rader, Jordan D. [ORNL; Felde, David K. [ORNL; McFarlane, Joanna [ORNL; Greenwood, Michael Scott [ORNL; Qualls, A L. [ORNL; Calderoni, Pattrick [Idaho National Laboratory (INL)

    2017-12-01

    This report summarizes physical, chemical, and engineering analyses that have been done to support the development of a test loop to study tritium migration in 2LiF-BeF2 salts. The loop will operate under turbulent flow and a schematic of the apparatus has been used to develop a model in Mathcad to suggest flow parameters that should be targeted in loop operation. The introduction of tritium into the loop has been discussed as well as various means to capture or divert the tritium from egress through a test assembly. Permeation was calculated starting with a Modelica model for a transport through a nickel window into a vacuum, and modifying it for a FLiBe system with an argon sweep gas on the downstream side of the permeation interface. Results suggest that tritium removal with a simple tubular permeation device will occur readily. Although this system is idealized, it suggests that rapid measurement capability in the loop may be necessary to study and understand tritium removal from the system.

  9. Criteria for saturated magnetization loop

    International Nuclear Information System (INIS)

    Harres, A.; Mikhov, M.; Skumryev, V.; Andrade, A.M.H. de; Schmidt, J.E.; Geshev, J.

    2016-01-01

    Proper estimation of magnetization curve parameters is vital in studying magnetic systems. In the present article, criteria for discrimination non-saturated (minor) from saturated (major) hysteresis loops are proposed. These employ the analysis of (i) derivatives of both ascending and descending branches of the loop, (ii) remanent magnetization curves, and (iii) thermomagnetic curves. Computational simulations are used in order to demonstrate their validity. Examples illustrating the applicability of these criteria to well-known real systems, namely Fe_3O_4 and Ni fine particles, are provided. We demonstrate that the anisotropy-field value estimated from a visual examination of an only apparently major hysteresis loop could be more than two times lower than the real one. - Highlights: • Proper estimation of hysteresis-loop parameters is vital in magnetic studies. • We propose criteria for discrimination minor from major hysteresis loops. • The criteria analyze magnetization, remanence and ZFC/FC curves and/or their derivatives. • Examples of their application on real nanoparticles systems are given. • Using the criteria could avoid twofold or bigger saturation-field underestimation errors.

  10. Criteria for saturated magnetization loop

    Energy Technology Data Exchange (ETDEWEB)

    Harres, A. [Departamento de Física, UFSM, Santa Maria, 97105-900 Rio Grande do Sul (Brazil); Mikhov, M. [Faculty of Physics, University of Sofia, 1164 Sofia (Bulgaria); Skumryev, V. [Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona (Spain); Departament de Física, Universitat Autònoma de Barcelona, 08193 Barcelona (Spain); Andrade, A.M.H. de; Schmidt, J.E. [Instituto de Física, UFRGS, Porto Alegre, 91501-970 Rio Grande do Sul (Brazil); Geshev, J., E-mail: julian@if.ufrgs.br [Departament de Física, Universitat Autònoma de Barcelona, 08193 Barcelona (Spain); Instituto de Física, UFRGS, Porto Alegre, 91501-970 Rio Grande do Sul (Brazil)

    2016-03-15

    Proper estimation of magnetization curve parameters is vital in studying magnetic systems. In the present article, criteria for discrimination non-saturated (minor) from saturated (major) hysteresis loops are proposed. These employ the analysis of (i) derivatives of both ascending and descending branches of the loop, (ii) remanent magnetization curves, and (iii) thermomagnetic curves. Computational simulations are used in order to demonstrate their validity. Examples illustrating the applicability of these criteria to well-known real systems, namely Fe{sub 3}O{sub 4} and Ni fine particles, are provided. We demonstrate that the anisotropy-field value estimated from a visual examination of an only apparently major hysteresis loop could be more than two times lower than the real one. - Highlights: • Proper estimation of hysteresis-loop parameters is vital in magnetic studies. • We propose criteria for discrimination minor from major hysteresis loops. • The criteria analyze magnetization, remanence and ZFC/FC curves and/or their derivatives. • Examples of their application on real nanoparticles systems are given. • Using the criteria could avoid twofold or bigger saturation-field underestimation errors.

  11. Increased Back-Bonding Explains Step-Edge Reactivity and Particle Size Effect for CO Activation on Ru Nanoparticles.

    Science.gov (United States)

    Foppa, Lucas; Copéret, Christophe; Comas-Vives, Aleix

    2016-12-28

    Carbon monoxide is a ubiquitous molecule, a key feedstock and intermediate in chemical processes. Its adsorption and activation, typically carried out on metallic nanoparticles (NPs), are strongly dependent on the particle size. In particular, small NPs, which in principle contain more corner and step-edge atoms, are surprisingly less reactive than larger ones. Hereby, first-principles calculations on explicit Ru NP models (1-2 nm) show that both small and large NPs can present step-edge sites (e.g., B 5 and B 6 sites). However, such sites display strong particle-size-dependent reactivity because of very subtle differences in local chemical bonding. State-of-the-art crystal orbital Hamilton population analysis allows a detailed molecular orbital picture of adsorbed CO on step-edges, which can be classified as flat (η 1 coordination) and concave (η 2 coordination) sites. Our analysis shows that the CO π-metal d π hybrid band responsible for the electron back-donation is better represented by an oxygen lone pair on flat sites, whereas it is delocalized on both C and O atoms on concave sites, increasing the back-bonding on these sites compared to flat step-edges or low-index surface sites. The bonding analysis also rationalizes why CO cleavage is easier on step-edge sites of large NPs compared to small ones irrespective of the site geometry. The lower reactivity of small NPs is due to the smaller extent of the Ru-O interaction in the η 2 adsorption mode, which destabilizes the η 2 transition-state structure for CO direct cleavage. Our findings provide a molecular understanding of the reactivity of CO on NPs, which is consistent with the observed particle size effect.

  12. Capillary-Condenser-Pumped Heat-Transfer Loop

    Science.gov (United States)

    Silverstein, Calvin C.

    1989-01-01

    Heat being transferred supplies operating power. Capillary-condenser-pumped heat-transfer loop similar to heat pipe and to capillary-evaporator-pumped heat-transfer loop in that heat-transfer fluid pumped by evaporation and condensation of fluid at heat source and sink, respectively. Capillary condenser pump combined with capillary evaporator pump to form heat exchanger circulating heat-transfer fluids in both loops. Transport of heat more nearly isothermal. Thermal stress in loop reduced, and less external surface area needed in condenser section for rejection of heat to heat sink.

  13. Quantum chromodynamics as dynamics of loops

    International Nuclear Information System (INIS)

    Makeenko, Yu.; Migdal, A.A.

    1980-01-01

    The problem of a possibility of reformulating quantum chromodynamics (QCD) in terms of colourless composite fields instead of coloured quarks and gluons is considered. The role of such fields is played by the gauge invariant loop functionals. The Shwinger equations of motion is derived in the loop space which completely describe dynamics of the loop fields. New manifestly gauge invariant diagram technique in the loop space is developed. These diagrams reproduce asymptotic freedom in the ultraviolet range and are consistent with the confinement law in the infrared range

  14. Abnormal duodenal loop demonstrated by X-ray

    International Nuclear Information System (INIS)

    Thommesen, P.; Funch-Jensen, P.

    1986-01-01

    The occurrence of dyspeptic symptoms has previously been correlated with the shape of the duodenal loop in patients with X-ray-negative dyspepsia. An abnormal duodenal loop was associated with a significantly higher incidence of symtoms provoked by meals, vomiting, regurgitations, heartburn, and the irritable bowel syndrome. 89% of these patients (26 patients with a normal duodenal loop and 39 patients with abnormal duodenal loop) were available for a 5-year follow-up study of symptomatic outcome. The incidence of symptoms provoked by meals was still significantly higher in patients with an abnormal duodenal loop, and there was also a significant difference concerning symptomatic outcome. Approximately 75% of the patients with a normal duodenal loop had improved, and 25% had unchanged clinical conditions. Approximately 50% of the patients with an abnormal duodenal loop had improved, and 50% had an unchanged or even deteriorated clinical condition

  15. Distal loop flexibility of a regulatory domain modulates dynamics and activity of C-terminal SRC kinase (csk.

    Directory of Open Access Journals (Sweden)

    Sulyman Barkho

    Full Text Available The Src family of tyrosine kinases (SFKs regulate numerous aspects of cell growth and differentiation and are under the principal control of the C-terminal Src Kinase (Csk. Csk and SFKs share a modular design with the kinase domain downstream of the N-terminal SH2 and SH3 domains that regulate catalytic function and membrane localization. While the function of interfacial segments in these multidomain kinases are well-investigated, little is known about how surface sites and long-range, allosteric coupling control protein dynamics and catalytic function. The SH2 domain of Csk is an essential component for the down-regulation of all SFKs. A unique feature of the SH2 domain of Csk is the tight turn in place of the canonical CD loop in a surface site far removed from kinase domain interactions. In this study, we used a combination of experimental and computational methods to probe the importance of this difference by constructing a Csk variant with a longer SH2 CD loop to mimic the flexibility found in homologous kinase SH2 domains. Our results indicate that while the fold and function of the isolated domain and the full-length kinase are not affected by loop elongation, native protein dynamics that are essential for efficient catalysis are perturbed. We also identify key motifs and routes through which the distal SH2 site might influence catalysis at the active site. This study underscores the sensitivity of intramolecular signaling and catalysis to native protein dynamics that arise from modest changes in allosteric regions while providing a potential strategy to alter intrinsic activity and signaling modulation.

  16. Kalman Orbit Optimized Loop Tracking

    Science.gov (United States)

    Young, Lawrence E.; Meehan, Thomas K.

    2011-01-01

    Under certain conditions of low signal power and/or high noise, there is insufficient signal to noise ratio (SNR) to close tracking loops with individual signals on orbiting Global Navigation Satellite System (GNSS) receivers. In addition, the processing power available from flight computers is not great enough to implement a conventional ultra-tight coupling tracking loop. This work provides a method to track GNSS signals at very low SNR without the penalty of requiring very high processor throughput to calculate the loop parameters. The Kalman Orbit-Optimized Loop (KOOL) tracking approach constitutes a filter with a dynamic model and using the aggregate of information from all tracked GNSS signals to close the tracking loop for each signal. For applications where there is not a good dynamic model, such as very low orbits where atmospheric drag models may not be adequate to achieve the required accuracy, aiding from an IMU (inertial measurement unit) or other sensor will be added. The KOOL approach is based on research JPL has done to allow signal recovery from weak and scintillating signals observed during the use of GPS signals for limb sounding of the Earth s atmosphere. That approach uses the onboard PVT (position, velocity, time) solution to generate predictions for the range, range rate, and acceleration of the low-SNR signal. The low- SNR signal data are captured by a directed open loop. KOOL builds on the previous open loop tracking by including feedback and observable generation from the weak-signal channels so that the MSR receiver will continue to track and provide PVT, range, and Doppler data, even when all channels have low SNR.

  17. The reactivity meter and core reactivity

    International Nuclear Information System (INIS)

    Siltanen, P.

    1999-01-01

    This paper discussed in depth the point kinetic equations and the characteristics of the point kinetic reactivity meter, particularly for large negative reactivities. From a given input signal representing the neutron flux seen by a detector, the meter computes a value of reactivity in dollars (ρ/β), based on inverse point kinetics. The prompt jump point of view is emphasised. (Author)

  18. Zinc ion coordination as a modulating factor of the ZnuA histidine-rich loop flexibility: A molecular modeling and fluorescence spectroscopy study

    Energy Technology Data Exchange (ETDEWEB)

    Castelli, Silvia [Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome (Italy); Stella, Lorenzo [Department of Chemical Sciences and Technologies, University of Roma Tor Vergata, Via della Ricerca Scientifica, 00133 Rome (Italy); Neuromed, IRCCS, Pozzilli 86077 (Italy); Petrarca, Patrizia [Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome (Italy); Battistoni, Andrea [Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome (Italy); Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), Viale delle Medaglie D' Oro 305, 00136 Rome (Italy); Desideri, Alessandro [Department of Biology, University of Rome Tor Vergata and CIBB, Center of Biostatistics and Bioinformatics, Via della Ricerca Scientifica, 00133 Rome (Italy); Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), Viale delle Medaglie D' Oro 305, 00136 Rome (Italy); Falconi, Mattia, E-mail: falconi@uniroma2.it [Department of Biology, University of Rome Tor Vergata and CIBB, Center of Biostatistics and Bioinformatics, Via della Ricerca Scientifica, 00133 Rome (Italy); Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), Viale delle Medaglie D' Oro 305, 00136 Rome (Italy)

    2013-01-11

    Highlights: Black-Right-Pointing-Pointer Fluorescence data indicate that the His-loop of ZnuA interacts with Zn{sup +2} ions. Black-Right-Pointing-Pointer The ZnuA structural model proposed validates these spectroscopic findings. Black-Right-Pointing-Pointer It is proposed that a zinc loaded His-loop may facilitate the ZnuA-ZnuB recognition. -- Abstract: ZnuA is the soluble component of the high-affinity ZnuABC zinc transporter belonging to the ATP-binding cassette-type periplasmic Zn-binding proteins. The zinc transporter ZnuABC is composed by three proteins: ZnuB, the membrane permease, ZnuC, the ATPase component and ZnuA, the soluble periplasmic metal-binding protein which captures Zn and delivers it to ZnuB. The ZnuA protein contains a charged flexible loop, rich in histidines and acidic residues, showing significant species-specific differences. Various studies have established that this loop contributes to the formation of a secondary zinc binding site, which has been proposed to be important in the acquisition of periplasmic Zn for its delivery to ZnuB or for regulation of zinc uptake. Due to its high mobility the structure of the histidine-rich loop has never been solved by X-ray diffraction studies. In this paper, through a combined use of molecular modeling, mutagenesis and fluorescence spectroscopy, we confirm the presence of two zinc binding sites characterized by different affinities for the metal ion and show that the flexibility of the loop is modulated by the binding of the zinc ions to the protein. The data obtained by fluorescence spectroscopy have then be used to validate a 3D model including the unsolved histidine-rich loop.

  19. LOOP: engineering marvel, economic calamity

    Energy Technology Data Exchange (ETDEWEB)

    Brossard, E B

    1985-01-01

    The Louisiana Offshore Oil Port (LOOP) is the first superport built in the Lower 48. The United States was the only major oil-importing country that did not have a superport, and therefore, could not offload very large crude carriers (VLCCs). Unfortunately, a number of factors changed after it was decided to build LOOP, and these, plus the onerous provisions of the Deepwater Ports Act of 1974, which authorized superports, prevented LOOP from operating economically. LOOP's facilities consist of an offshore platform complex with three single-point-mooring (SPM) system buoys, 19 miles offshore in 110 feet of water, as well as a 32-million-barrel storage terminal 31 miles inland at Clovelly Salt Dome, and connecting pipelines offshore and onshore. By the time LOOP was started-up in May 1981, demand for oil had declined, because of rises in the price of oil, and the source of US oil imports had shifted back to the western hemisphere, away from the eastern hemisphere, closer to the US. The refinery mix in the US also changed, because of up-grading of a number of big refineries, which further reduced demand and made heavier crudes from countries like Mexico and Venezuela more economical. Because of reduced oil imports and shorter hauls, oil shippers started using or continued to use smaller tankers. Smaller tankers are not economical for LOOP, nor do they need LOOP. The start-up of the Trans-Alaska Pipeline System (TAPS) in mid-1977 backed out 1.5 million bd/sup -1/ of foreign imports. TAPS' capacity coincides with LOOP's offloading capacity of 1.4 million bd/sup -1/. US decontrol of domestic crude in 1981 and increased drilling, plus general energy conservation further reduced US oil imports. US consumption declined to 15.1 million bd/sup -1/ in 1983, from 18.8 million bd/sup -1/ in 1978. This award-winning superport needed federal decontrol and increased oil imports along with more VLCCs, in order to operate economically.

  20. The massless two-loop two-point function

    International Nuclear Information System (INIS)

    Bierenbaum, I.; Weinzierl, S.

    2003-01-01

    We consider the massless two-loop two-point function with arbitrary powers of the propagators and derive a representation from which we can obtain the Laurent expansion to any desired order in the dimensional regularization parameter ε. As a side product, we show that in the Laurent expansion of the two-loop integral only rational numbers and multiple zeta values occur. Our method of calculation obtains the two-loop integral as a convolution product of two primitive one-loop integrals. We comment on the generalization of this product structure to higher loop integrals. (orig.)

  1. Open loop thanks to direct torque control (DTC). Motor control without feedback loop; Open loop dank direkter Drehmomentregelung (DTC). Hochwertige Motorregelung ohne Rueckfuehrung

    Energy Technology Data Exchange (ETDEWEB)

    Link, Michael [ABB Automation Products GmbH, Ladenburg (Germany)

    2009-07-01

    Servo drives are used in various applications. The range of applications is huge and thus also requirements to the drive system. Mainly, a fast torque and speed control is required. This is the domaine of direct torque control (DTC). In many applications DTC can meet this challenge to control the motor with full torque at zero speed. The servo converter based on DTC technology provides a control concept for synchronous and asynchronous motors for both closed loop and open loop control. DTC controlled drives support the whole range from open loop up to high performance motion control applications. (orig.)

  2. Targeting the autolysis loop of urokinase-type plasminogen activator with conformation-specific monoclonal antibodies.

    Science.gov (United States)

    Botkjaer, Kenneth A; Fogh, Sarah; Bekes, Erin C; Chen, Zhuo; Blouse, Grant E; Jensen, Janni M; Mortensen, Kim K; Huang, Mingdong; Deryugina, Elena; Quigley, James P; Declerck, Paul J; Andreasen, Peter A

    2011-08-15

    Tight regulation of serine proteases is essential for their physiological function, and unbalanced states of protease activity have been implicated in a variety of human diseases. One key example is the presence of uPA (urokinase-type plasminogen activator) in different human cancer types, with high levels correlating with a poor prognosis. This observation has stimulated efforts into finding new principles for intervening with uPA's activity. In the present study we characterize the so-called autolysis loop in the catalytic domain of uPA as a potential inhibitory target. This loop was found to harbour the epitopes for three conformation-specific monoclonal antibodies, two with a preference for the zymogen form pro-uPA, and one with a preference for active uPA. All three antibodies were shown to have overlapping epitopes, with three common residues being crucial for all three antibodies, demonstrating a direct link between conformational changes of the autolysis loop and the creation of a catalytically mature active site. All three antibodies are potent inhibitors of uPA activity, the two pro-uPA-specific ones by inhibiting conversion of pro-uPA to active uPA and the active uPA-specific antibody by shielding the access of plasminogen to the active site. Furthermore, using immunofluorescence, the conformation-specific antibodies mAb-112 and mAb-12E6B10 enabled us to selectively stain pro-uPA or active uPA on the surface of cultured cells. Moreover, in various independent model systems, the antibodies inhibited tumour cell invasion and dissemination, providing evidence for the feasibility of pharmaceutical intervention with serine protease activity by targeting surface loops that undergo conformational changes during zymogen activation. © The Authors Journal compilation © 2011 Biochemical Society

  3. A flexible loop at the dimer interface is a part of the active site of the adjacent monomer of Escherichia coli orotate phosphoribosyltransferase

    DEFF Research Database (Denmark)

    Henriksen, Annette; Aghajari, Nushin; Jensen, Kaj Frank

    1996-01-01

    structure is only traceable in one monomer. We expect that the mobility of this loop is important for catalysis, and, on the basis of the reported structure and the structure of Salmonella typhimurium OPRTase·OMP, we propose that the movement of this loop in association with the movement of OMP is vital...

  4. Stability, structure, and evolution of cool loops

    International Nuclear Information System (INIS)

    Cally, P.S.; Robb, T.D.

    1991-01-01

    The criteria for the existence and stability of cool loops are reexamined. It is found that the stability of the loops strongly depends on the form of the heating and radiative loss functions and that if the Ly-alpha peak which appears in most calculations of the radiative loss function is real, cool loops are almost certainly unstable. Removing the hydrogen contribution from the recent loss function Q(T) by Cook et al. (1989) does not produce the much-used result, Q proportional to T-cubed, which is so favorable to cool loop stability. Even using the probably unrealistically favorable loss function Q1 of Cook et al. with the hydrogen contribution removed, the maximum temperature attainable in stable cool loops is a factor of 2-3 too small to account for the excess emission observed in lower transition region lines. Dynamical simulations of cool loop instabilities reveal that the final state of such a model is the hot loop equilibrium. 26 refs

  5. Site-Specific Reactivity of Copper Chabazite Zeolites with Nitric Oxide, Ammonia, and Oxygen

    DEFF Research Database (Denmark)

    Godiksen, Anita; Isaksen, Oliver L.; Rasmussen, Søren B.

    2018-01-01

    In-situ electron paramagnetic resonance (EPR) spectroscopy was applied to dilute copper chabazite (CHA) zeolites under gas flows relevant for the selective catalytic reduction of NO with ammonia (NH3-SCR). Under both reducing and oxidizing conditions, we observed differences in reactivity between...

  6. Post-Pennsylvanian reactivation along the Washita Valley fault, southern Oklahoma

    International Nuclear Information System (INIS)

    VanArsdale, R.; Ward, C.; Cox, R.

    1989-06-01

    Surface exposures of faults of the Washita Valley fault (WVF) system in Garvin, Murray, Carter, and Johnston counties of southern Oklahoma were studied to determine if there has been post-Pennsylvanian fault reactivation and to determine if there has been any Quaternary fault movement. This was undertaken through field mapping, by dating alluvium which overlies the faults, and by logging trenches excavated across the WVF. In northern Murray County and southern Garvin County (site A), the WVF displaces Late-Pennsylvanian Oscar Group showing post-Pennsylvanian movement; however, no faulting was observed in 2000 year old alluvium of Wildhorse Creek along strike of the WVF. Three sites (B, C, and D) are located within the Arbuckle Mountains. Faulting of Virgilian age Vanoss Conglomerate and Vanoss Shale reveal post-Virgilian (Late Pennsylvanian) activity along a subsidiary fault in northern Murray County (site B). A 12000 to 15000 year old terrace at this site is unfaulted. Absence of any fault related features in paleosols which overly the WVF along the Washita River (site C) show that the fault has not been active during the last 1570 /+-/ 190 years in southern Murray County. Similarly, absence of any fault related features along Oil Creek (site D) indicates that the WVF has not been active during the last 1810 /+-/ 80 years in northern Carter and Johnston Counties. Faults in the Antlers Sandstone in southern Johnston County (site E) reveal post-Lower Cretaceous reactivation of the WVF. 49 refs., 28 figs., 1 tab

  7. Management of Animal Carcass Disposal Sites Using a Biochar Permeable Reactive Barrier and Fast Growth Tree (Populus euramericana: A Field Study in Korea

    Directory of Open Access Journals (Sweden)

    Jung-Hwan Yoon

    2017-03-01

    Full Text Available Among many disposal options of animal carcasses due to animal diseases including foot-and-mouth disease (FMD and avian influenza (AI, on-farm burial has been the most frequently used one in Korea. Animal carcasses generate contaminants such as ammonium-N and chloride. This study aimed at testing biochar (BC as a permeable reactive barrier (PRB material in combination with fast growing tree species (Populus euramericana to mitigate groundwater pollution from animal burial sites. For this, a PRB filled with BC was installed and 400 poplar tree (P. euramericana seedlings were planted. Tested BC was obtained from rice husk and its efficiency to mitigate contaminant migration from a burial site of pig carcasses was tested using ammonium-N, chloride, electrical conductivity (EC, and pH as monitoring parameters. Monitoring wells downstream from the burial site were used. Leachates from a monitoring well, three wells inside the burial site close to PRB and three wells outside the burial site close to PRB were sampled and analyzed for ammonium-N, Cl−, EC, and pH for four years from PRB installation. The pH, EC, and ammonium-N of leachate fluctuated during the test period depending on precipitation. pH, EC, and ammonium-N of the leachate samples collected from outside of the burial site close to PRB decreased compared to those from inside of the burial site close to PRB. The concentrations of ammonium-N in the leachate from the monitoring well kept under the threshold value of 10 mg·L−1 for two years from PRB construction. In addition, the growth of poplar plants appeared to be increased via uptaking available N and P released from the burial sites. Achieved results suggest that BC PRBs can be used to in situ mitigate contaminant release from buried animal carcasses.

  8. Conformal anomaly of super Wilson loop

    Energy Technology Data Exchange (ETDEWEB)

    Belitsky, A.V., E-mail: andrei.belitsky@asu.edu [Department of Physics, Arizona State University, Tempe, AZ 85287-1504 (United States)

    2012-09-11

    Classically supersymmetric Wilson loop on a null polygonal contour possesses all symmetries required to match it onto non-MHV amplitudes in maximally supersymmetric Yang-Mills theory. However, to define it quantum mechanically, one is forced to regularize it since perturbative loop diagrams are not well defined due to presence of ultraviolet divergences stemming from integration in the vicinity of the cusps. A regularization that is adopted by practitioners by allowing one to use spinor helicity formalism, on the one hand, and systematically go to higher orders of perturbation theory is based on a version of dimensional regularization, known as Four-Dimensional Helicity scheme. Recently it was demonstrated that its use for the super Wilson loop at one loop breaks both conformal symmetry and Poincare supersymmetry. Presently, we exhibit the origin for these effects and demonstrate how one can undo this breaking. The phenomenon is alike the one emerging in renormalization group mixing of conformal operators in conformal theories when one uses dimensional regularization. The rotation matrix to the diagonal basis is found by means of computing the anomaly in the Ward identity for the conformal boost. Presently, we apply this ideology to the super Wilson loop. We compute the one-loop conformal anomaly for the super Wilson loop and find that the anomaly depends on its Grassmann coordinates. By subtracting this anomalous contribution from the super Wilson loop we restore its interpretation as a dual description for reduced non-MHV amplitudes which are expressed in terms of superconformal invariants.

  9. Fundamental and Harmonic Oscillations in Neighboring Coronal Loops

    Science.gov (United States)

    Li, Hongbo; Liu, Yu; Vai Tam, Kuan

    2017-06-01

    We present observations of multimode (fundamental and harmonic) oscillations in a loop system, which appear to be simultaneously excited by a GOES C-class flare. Analysis of the periodic oscillations reveals that (1) the primary loop with a period of P a ≈ 4 minutes and a secondary loop with two periods of P a ≈ 4 minutes and P b ≈ 2 minutes are detected simultaneously in closely spaced loop strands; (2) both oscillation components have their peak amplitudes near the loop apex, while in the second loop the low-frequency component P a dominates in a loop segment that is two times larger than the high-frequency component P b ; (3) the harmonic mode P b shows the largest deviation from a sinusoidal loop shape at the loop apex. We conclude that multiple harmonic modes with different displacement profiles can be excited simultaneously even in closely spaced strands, similar to the overtones of a violin string.

  10. Power and reactive power simultaneous control by 0.5 MJ superconducting magnet energy storage

    International Nuclear Information System (INIS)

    Ise, Toshifumi; Tsuji, Kiichiro; Murakami, Yoshishige

    1984-01-01

    Superconducting magnet energy storage (SMES) is expected to be widely applied to the pulsed sources for fusion reactor research and to the energy storage substituting for pumping-up power stations, because of its fast energy storing and discharging and very high efficiency. Some results have been obtained so far. In this paper, however, the simultaneous control of power and reactive power is considered for an energy storage composed of two sets of thyristorized power conversion system and superconducting magnets in series connection, and a direct digital control system is described on the principle, design and configuration including the compensator, and on the experiment using the 0.5 MJ superconducting magnet energy storage installed in the Superconduction Engineering Experiment Center, Osaka University. The results obtained are as follows: (1) P control priority mode and Q control priority mode (in which power and reactive power control has priority, respectively) were proposed as the countermeasures when the simultaneous control of power and reactive power became impossible; (2) the design method was established, by which power and reactive power control loops can independently be designed as a result of simulation; (3) the achievement of the simultaneous control of power and reactive power was confirmed by using P-control priority mode and Q-control priority mode, in the experiment using the control system designed by simulation. The validity of simulation model was also confirmed by actual response waveforms. (Wakatsuki, Y.)

  11. Sodium Loop Safety Facility W-2 experiment fuel pin rupture detection system. [LMFBR

    Energy Technology Data Exchange (ETDEWEB)

    Hoffman, M.A.; Kirchner, T.L.; Meyers, S.C.

    1980-05-01

    The objective of the Sodium Loop Safety Facility (SLSF) W-2 experiment is to characterize the combined effects of a preconditioned full-length fuel column and slow transient overpower (TOP) conditions on breeder reactor (BR) fuel pin cladding failures. The W-2 experiment will meet this objective by providing data in two technological areas: (1) time and location of cladding failure, and (2) early post-failure test fuel behavior. The test involves a seven pin, prototypic full-length fast test reactor (FTR) fuel pin bundle which will be subjected to a simulated unprotected 5 cents/s reactivity transient overpower event. The outer six pins will provide the necessary prototypic thermal-hydraulic environment for the center pin.

  12. Sequential SO{sub 2}/CO{sub 2} capture enhanced by steam reactivation of a CaO-based sorbent

    Energy Technology Data Exchange (ETDEWEB)

    Vasilije Manovic; Edward J. Anthony [CANMET Energy Technology Centre-Ottawa, Ottawa, ON (Canada). Natural Resources Canada

    2008-07-15

    The steam hydration reactivation characteristics of three limestone samples after multiple CO{sub 2} looping cycles are presented here. The CO{sub 2} cycles were performed in a tube furnace (TF) and the resulting samples were hydrated by steam in a pressure reactor (PR). The reactivation was performed with spent samples after carbonation and calcination stages. The reactivation tests were done with a saturated steam pressure at 200{sup o}C and also at atmospheric pressure and 100 {sup o}C. The characteristics of the reactivation samples were examined using BET and BJH pore characterization (for the original and spent samples, and samples reactivated under different conditions) and also by means of a thermogravimetric analyzer (TGA). The levels of hydration achieved by the reactivated samples were determined as well as the conversions during sulphation and multiple carbonation cycles. It was found that the presence of a CaCO{sub 3} layer strongly hinders sorbent hydration and adversely affects the properties of the reactivated sorbent with regard to its behavior in sulphation and multiple carbonation cycles. Here, hydration of calcined samples under pressure is the most effective method to produce superior sulphur sorbents. However, reactivation of calcined samples under atmospheric conditions also produces sorbents with significantly better properties in comparison to those of the original sorbents. These results show that separate CO{sub 2} capture and SO{sub 2} retention in fluidized bed systems enhanced by steam reactivation is promising even for atmospheric conditions if the material for hydration is taken from the calciner. 49 refs., 5 figs., 3 tabs.

  13. Solution Structure of a Novel C2-Symmetrical Bifunctional Bicyclic Inhibitor Based on SFTI-1

    International Nuclear Information System (INIS)

    Jaulent, Agnes M.; Brauer, Arnd B. E.; Matthews, Stephen J.; Leatherbarrow, Robin J.

    2005-01-01

    A novel bifunctional bicyclic inhibitor has been created that combines features both from the Bowman-Birk inhibitor (BBI) proteins, which have two distinct inhibitory sites, and from sunflower trypsin inhibitor-1 (SFTI-1), which has a compact bicyclic structure. The inhibitor was designed by fusing together a pair of reactive loops based on a sequence derived from SFTI-1 to create a backbone-cyclized disulfide-bridged 16-mer peptide. This peptide has two symmetrically spaced trypsin binding sites. Its synthesis and biological activity have been reported in a previous communication [Jaulent and Leatherbarrow, 2004, PEDS 17, 681]. In the present study we have examined the three-dimensional structure of the molecule. We find that the new inhibitor, which has a symmetrical 8-mer half-cystine CTKSIPP'I' motif repeated through a C 2 symmetry axis also shows a complete symmetry in its three-dimensional structure. Each of the two loops adopts the expected canonical conformation common to all BBIs as well as SFTI-1. We also find that the inhibitor displays a strong and unique structural identity, with a notable lack of minor conformational isomers that characterise most reactive site loop mimics examined to date as well as SFTI-1. This suggests that the presence of the additional cyclic loop acts to restrict conformational mobility and that the deliberate introduction of cyclic symmetry may offer a general route to locking the conformation of β-hairpin structures

  14. Soft Neutrosophic Loops and Their Generalization

    Directory of Open Access Journals (Sweden)

    Mumtaz Ali

    2014-06-01

    Full Text Available Soft set theory is a general mathematical tool for dealing with uncertain, fuzzy, not clearly defined objects. In this paper we introduced soft neutrosophic loop,soft neutosophic biloop, soft neutrosophic N -loop with the discuission of some of their characteristics. We also introduced a new type of soft neutrophic loop, the so called soft strong neutrosophic loop which is of pure neutrosophic character. This notion also found in all the other corresponding notions of soft neutrosophic thoery. We also given some of their properties of this newly born soft structure related to the strong part of neutrosophic theory.

  15. Two- and three-loop amplitudes in covariant loop calculus

    International Nuclear Information System (INIS)

    Roland, K.

    1988-04-01

    We study 2- and 3-loop vacuum-amplitudes for the closed bosonic string. We compare two sets of expressions for the corresponding density on moduli space: One, based on the covariant Reggeon loop calculus (where modular invariance is not manifest). The other, based on analytic geometry. We want to prove identity between the two sets of expressions. Quite apart from demonstrating modular invariance of the Reggeon results, this would in itself be a remarkable mathematical feature. Identity is established to 'high' order in some moduli and exactly in others. The expansions reveal an essentially number-theoretical structure. Agreement is found only by exploiting the connection between the 4 Jacobi θ-functions and number theory. (orig.)

  16. Two- and three-loop amplitudes in covariant loop calculus

    International Nuclear Information System (INIS)

    Roland, K.

    1989-01-01

    We study two- and three-loop vacuum amplitudes for the closed bosonic string. We compare two sets of expressions for the corresponding density on moduli space. One is based on the covariant reggeon loop calculus (where modular invariance is not manifest). The other is based on analytic geometry. We want to prove identity between the two sets of expressions. Quite apart from demonstrating modular invariance of the reggeon results, this would in itself be a remarkable mathematical feature. Identity is established to ''high'' order in some moduli and exactly in others. The expansions reveal an essentially number-theoretic structure. Agreement is found only by exploiting the connection between the four Jacobi θ-functions and number theory. (orig.)

  17. Reactivation of latent herpes simplex virus infection by ultraviolet light: a human model

    International Nuclear Information System (INIS)

    Perna, J.J.; Mannix, M.L.; Rooney, J.F.; Notkins, A.L.; Straus, S.E.

    1987-01-01

    Infection with herpes simplex virus often results in a latent infection of local sensory ganglia and a disease characterized by periodic viral reactivation and mucocutaneous lesions. The factors that trigger reactivation in humans are still poorly defined. In our study, five patients with documented histories of recurrent herpes simplex virus infection on the buttocks or sacrum were exposed to three times their minimal erythema dose of ultraviolet light. Site-specific cutaneous herpes simplex virus infection occurred at 4.4 +/- 0.4 days after exposure to ultraviolet light in 8 of 13 attempts at reactivation. We conclude that ultraviolet light can reactivate herpes simplex virus under experimentally defined conditions. This model in humans should prove useful in evaluating the pathophysiology and prevention of viral reactivation

  18. Complete Genome Sequence of Germline Chromosomally Integrated Human Herpesvirus 6A and Analyses Integration Sites Define a New Human Endogenous Virus with Potential to Reactivate as an Emerging Infection.

    Science.gov (United States)

    Tweedy, Joshua; Spyrou, Maria Alexandra; Pearson, Max; Lassner, Dirk; Kuhl, Uwe; Gompels, Ursula A

    2016-01-15

    Human herpesvirus-6A and B (HHV-6A, HHV-6B) have recently defined endogenous genomes, resulting from integration into the germline: chromosomally-integrated "CiHHV-6A/B". These affect approximately 1.0% of human populations, giving potential for virus gene expression in every cell. We previously showed that CiHHV-6A was more divergent than CiHHV-6B by examining four genes in 44 European CiHHV-6A/B cardiac/haematology patients. There was evidence for gene expression/reactivation, implying functional non-defective genomes. To further define the relationship between HHV-6A and CiHHV-6A we used next-generation sequencing to characterize genomes from three CiHHV-6A cardiac patients. Comparisons to known exogenous HHV-6A showed CiHHV-6A genomes formed a separate clade; including all 85 non-interrupted genes and necessary cis-acting signals for reactivation as infectious virus. Greater single nucleotide polymorphism (SNP) density was defined in 16 genes and the direct repeats (DR) terminal regions. Using these SNPs, deep sequencing analyses demonstrated superinfection with exogenous HHV-6A in two of the CiHHV-6A patients with recurrent cardiac disease. Characterisation of the integration sites in twelve patients identified the human chromosome 17p subtelomere as a prevalent site, which had specific repeat structures and phylogenetically related CiHHV-6A coding sequences indicating common ancestral origins. Overall CiHHV-6A genomes were similar, but distinct from known exogenous HHV-6A virus, and have the capacity to reactivate as emerging virus infections.

  19. Targeted modulation of reactive oxygen species in the vascular endothelium

    OpenAIRE

    Shuvaev, Vladimir V.; Muzykantov, Vladimir R.

    2011-01-01

    Endothelial cells lining vascular luminal surface represent an important site of signaling and injurious effects of reactive oxygen species (ROS) produced by other cells and endothelium itself in ischemia, inflammation and other pathological conditions. Targeted delivery of ROS modulating enzymes conjugated with antibodies to endothelial surface molecules (vascular immunotargeting) provides site-specific interventions in the endothelial ROS, unattainable by other formulations including PEG-mo...

  20. Loop Quantum Gravity

    Directory of Open Access Journals (Sweden)

    Rovelli Carlo

    1998-01-01

    Full Text Available The problem of finding the quantum theory of the gravitational field, and thus understanding what is quantum spacetime, is still open. One of the most active of the current approaches is loop quantum gravity. Loop quantum gravity is a mathematically well-defined, non-perturbative and background independent quantization of general relativity, with its conventional matter couplings. Research in loop quantum gravity today forms a vast area, ranging from mathematical foundations to physical applications. Among the most significant results obtained are: (i The computation of the physical spectra of geometrical quantities such as area and volume, which yields quantitative predictions on Planck-scale physics. (ii A derivation of the Bekenstein-Hawking black hole entropy formula. (iii An intriguing physical picture of the microstructure of quantum physical space, characterized by a polymer-like Planck scale discreteness. This discreteness emerges naturally from the quantum theory and provides a mathematically well-defined realization of Wheeler's intuition of a spacetime ``foam''. Long standing open problems within the approach (lack of a scalar product, over-completeness of the loop basis, implementation of reality conditions have been fully solved. The weak part of the approach is the treatment of the dynamics: at present there exist several proposals, which are intensely debated. Here, I provide a general overview of ideas, techniques, results and open problems of this candidate theory of quantum gravity, and a guide to the relevant literature.

  1. Chemical reactivity of alkali lignin modified with laccase

    International Nuclear Information System (INIS)

    Sun, Yong; Qiu, Xueqing; Liu, Yunquan

    2013-01-01

    The modification of alkali lignin with laccase was investigated. The structural change of lignin was analyzed. The sulfonation reactivity was measured by the content of sulfonic group. The results showed the sulfonation reactivity increased to some extent under the condition of atmosphere pressure, but decreased under the condition of 0.3 MPa oxygen pressure. The analysis of Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance (NMR) and gel permeation chromatography (GPC) showed the cleavage of various ether linkages and demethylation took place in the structure of lignin to certain extent during modification with laccase, which contributed to the improvement of sulfonation reactivity. Under the condition of 0.3 MPa oxygen pressure, the ratio of s/g (guaiacyl/syringyl) increased after modification, which reduced the sulfonation reactivity of lignin. Simultaneously partial polymerization reaction, such as 4-O-5′, β-5, 5-5 and other reaction in the aromatic ring decreased the activity sites of C 2 , C 5 and C 6 . Abundant polymerization reaction of α-O increased steric hindrance of C 2 and C 6 in aromatic ring, resulting in low sulfonation reactivity of lignin. -- Highlights: ► The modification of alkali lignin with laccase was investigated. ► The sulfonation reactivity increased under the condition of atmosphere pressure. ► More content of guaiacyl and hydroxy, the less content of methoxyl, syringyl can enhance the sulfonation reactivity of lignin. ► Partial moieties polymerized each other with α-O linkgages during treatment with laccase under oxygen pressure. ► The steric hindrance on C 2 and C 6 in aromatic ring resulted in low sulfonation reaction reactivity of lignin

  2. A computational study of the Diels Alder reactions involving acenes: reactivity and aromaticity

    Science.gov (United States)

    Cheng, Mei-Fun; Li, Wai-Kee

    2003-01-01

    Ab initio and DFT methods have been used to study the Diels-Alder reactivity and the aromaticity of four linear acenes, namely, naphthalene, anthracene, tetracene and pentacene. In total, eight additional pathways between ethylene and four acenes have been studied and all of them are concerted and exothermic reactions. It is found that the most reactive sites on the acenes are the center ring's meso-carbons. Also, reactivity decreases along the series pentacene > tetracene > anthracene > naphthalene. In addition, the NICS results indicate that the most reactive rings in the acenes are those with the highest aromaticity. These results are consistent with those of other theoretical studies and experiments.

  3. Epitaxial growth of indium oxyfluoride thin films by reactive pulsed laser deposition: Structural change induced by fluorine insertion into vacancy sites in bixbyite structure

    Energy Technology Data Exchange (ETDEWEB)

    Okazaki, Sohei [Kanagawa Academy of Science and Technology (KAST), 3-2-1 Sakado, Takatsu-ku, Kawasaki 213-0012 (Japan); CREST, Japan Science and Technology Agency (JST), 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Hirose, Yasushi, E-mail: hirose@chem.s.u-tokyo.ac.jp [Kanagawa Academy of Science and Technology (KAST), 3-2-1 Sakado, Takatsu-ku, Kawasaki 213-0012 (Japan); CREST, Japan Science and Technology Agency (JST), 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Nakao, Shoichiro [Kanagawa Academy of Science and Technology (KAST), 3-2-1 Sakado, Takatsu-ku, Kawasaki 213-0012 (Japan); CREST, Japan Science and Technology Agency (JST), 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Yang, Chang [Kanagawa Academy of Science and Technology (KAST), 3-2-1 Sakado, Takatsu-ku, Kawasaki 213-0012 (Japan); CREST, Japan Science and Technology Agency (JST), 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Harayama, Isao; Sekiba, Daiichiro [Tandem Accelerator Complex, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8577 (Japan); Hasegawa, Tetsuya [Kanagawa Academy of Science and Technology (KAST), 3-2-1 Sakado, Takatsu-ku, Kawasaki 213-0012 (Japan); CREST, Japan Science and Technology Agency (JST), 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan)

    2014-05-30

    InO{sub x}F{sub y} thin films were epitaxially grown on Y-stabilized ZrO{sub 2} (111) substrates by reactive pulsed laser deposition. By changing the substrate temperature (T{sub S}), we were able to control the fluorine content of the film. Phase-pure epitaxial thin films with bixbyite-like ordering in the anion-site occupancy were obtained at high T{sub S} (≥ 240 °C), where fluorine was inserted into the vacancy sites in the bixbyite lattice up to y / (x + y) ∼ 0.3. By decreasing T{sub S}, y / (x + y) increased and the bixbyite-like ordering disappeared; simultaneously, fluorine-rich and fluorine-poor subphases emerged. The films grown at T{sub S} ≤ 150 °C were amorphous and exhibited higher optical absorbance and electrical resistivity than the epitaxial films. - Highlights: • InO{sub x}F{sub y} epitaxial thin films with high fluorine concentration were grown on Y:ZrO{sub 2}. • Anion composition and structural, optical and transport properties were studied. • Fluorine is topotactically inserted into the oxygen vacancy sites in bixbyite cell. • Bixbyite-like ordering of the anion site occupancy was conserved in y / (x + y) ≤ ∼ 0.3.

  4. Estimation of complex permittivity using loop antenna

    DEFF Research Database (Denmark)

    Lenler-Eriksen, Hans-Rudolph; Meincke, Peter

    2004-01-01

    A method for estimating the complex permittivity of materials in the vicinity of a loop antenna is proposed. The method is based on comparing measured and numerically calculated input admittances for the loop antenna.......A method for estimating the complex permittivity of materials in the vicinity of a loop antenna is proposed. The method is based on comparing measured and numerically calculated input admittances for the loop antenna....

  5. Local Chemical Reactivity of a Metal Alloy Surface

    DEFF Research Database (Denmark)

    Hammer, Bjørk; Scheffler, Matthias

    1995-01-01

    The chemical reactivity of a metal alloy surface is studied by density functional theory investigating the interaction of H2 with NiAl(110). The energy barrier for H2 dissociation is largely different over the Al and Ni sites without, however, reflecting the barriers over the single component metal...

  6. Closing the loop of deep brain stimulation

    Science.gov (United States)

    Carron, Romain; Chaillet, Antoine; Filipchuk, Anton; Pasillas-Lépine, William; Hammond, Constance

    2013-01-01

    High-frequency deep brain stimulation is used to treat a wide range of brain disorders, like Parkinson's disease. The stimulated networks usually share common electrophysiological signatures, including hyperactivity and/or dysrhythmia. From a clinical perspective, HFS is expected to alleviate clinical signs without generating adverse effects. Here, we consider whether the classical open-loop HFS fulfills these criteria and outline current experimental or theoretical research on the different types of closed-loop DBS that could provide better clinical outcomes. In the first part of the review, the two routes followed by HFS-evoked axonal spikes are explored. In one direction, orthodromic spikes functionally de-afferent the stimulated nucleus from its downstream target networks. In the opposite direction, antidromic spikes prevent this nucleus from being influenced by its afferent networks. As a result, the pathological synchronized activity no longer propagates from the cortical networks to the stimulated nucleus. The overall result can be described as a reversible functional de-afferentation of the stimulated nucleus from its upstream and downstream nuclei. In the second part of the review, the latest advances in closed-loop DBS are considered. Some of the proposed approaches are based on mathematical models, which emphasize different aspects of the parkinsonian basal ganglia: excessive synchronization, abnormal firing-rate rhythms, and a deficient thalamo-cortical relay. The stimulation strategies are classified depending on the control-theory techniques on which they are based: adaptive and on-demand stimulation schemes, delayed and multi-site approaches, stimulations based on proportional and/or derivative control actions, optimal control strategies. Some of these strategies have been validated experimentally, but there is still a large reservoir of theoretical work that may point to ways of improving practical treatment. PMID:24391555

  7. Closing the loop of deep brain stimulation.

    Science.gov (United States)

    Carron, Romain; Chaillet, Antoine; Filipchuk, Anton; Pasillas-Lépine, William; Hammond, Constance

    2013-12-20

    High-frequency deep brain stimulation is used to treat a wide range of brain disorders, like Parkinson's disease. The stimulated networks usually share common electrophysiological signatures, including hyperactivity and/or dysrhythmia. From a clinical perspective, HFS is expected to alleviate clinical signs without generating adverse effects. Here, we consider whether the classical open-loop HFS fulfills these criteria and outline current experimental or theoretical research on the different types of closed-loop DBS that could provide better clinical outcomes. In the first part of the review, the two routes followed by HFS-evoked axonal spikes are explored. In one direction, orthodromic spikes functionally de-afferent the stimulated nucleus from its downstream target networks. In the opposite direction, antidromic spikes prevent this nucleus from being influenced by its afferent networks. As a result, the pathological synchronized activity no longer propagates from the cortical networks to the stimulated nucleus. The overall result can be described as a reversible functional de-afferentation of the stimulated nucleus from its upstream and downstream nuclei. In the second part of the review, the latest advances in closed-loop DBS are considered. Some of the proposed approaches are based on mathematical models, which emphasize different aspects of the parkinsonian basal ganglia: excessive synchronization, abnormal firing-rate rhythms, and a deficient thalamo-cortical relay. The stimulation strategies are classified depending on the control-theory techniques on which they are based: adaptive and on-demand stimulation schemes, delayed and multi-site approaches, stimulations based on proportional and/or derivative control actions, optimal control strategies. Some of these strategies have been validated experimentally, but there is still a large reservoir of theoretical work that may point to ways of improving practical treatment.

  8. Closing the loop of deep brain stimulation

    Directory of Open Access Journals (Sweden)

    Romain eCARRON

    2013-12-01

    Full Text Available High-frequency deep brain stimulation is used to treat a wide range of brain disorders, like Parkinson's disease. The stimulated networks usually share common electrophysiological signatures, including hyperactivity and/or dysrhythmia. From a clinical perspective, HFS is expected to alleviate clinical signs without generating adverse effects. Here, we consider whether the classical open-loop HFS fulfils these criteria and outline current experimental or theoretical research on the different types of closed-loop DBS that could provide better clinical outcomes. In the first part of the review, the two routes followed by HFS-evoked axonal spikes are explored. In one direction, orthodromic spikes functionally de-afferent the stimulated nucleus from its downstream target networks. In the opposite direction, antidromic spikes prevent this nucleus from being influenced by its afferent networks. As a result, the pathological synchronized activity no longer propagates from the cortical networks to the stimulated nucleus. The overall result can be described as a reversible functional de-afferentation of the stimulated nucleus from its upstream and downstream nuclei. In the second part of the review, the latest advances in closed-loop DBS are considered. Some of the proposed approaches are based on mathematical models, which emphasize different aspects of the parkinsonian basal ganglia: excessive synchronization, abnormal firing-rate rhythms, and a deficient thalamo-cortical relay. The stimulation strategies are classified depending on the control-theory techniques on which they are based: adaptive and on-demand stimulation schemes, delayed and multi-site approaches, stimulations based on proportional and/or derivative control actions, optimal control strategies. Some of these strategies have been validated experimentally, but there is still a large reservoir of theoretical work that may point to ways of improving practical treatment.

  9. Global profiling of lysine reactivity and ligandability in the human proteome

    Science.gov (United States)

    Hacker, Stephan M.; Backus, Keriann M.; Lazear, Michael R.; Forli, Stefano; Correia, Bruno E.; Cravatt, Benjamin F.

    2017-12-01

    Nucleophilic amino acids make important contributions to protein function, including performing key roles in catalysis and serving as sites for post-translational modification. Electrophilic groups that target amino-acid nucleophiles have been used to create covalent ligands and drugs, but have, so far, been mainly limited to cysteine and serine. Here, we report a chemical proteomic platform for the global and quantitative analysis of lysine residues in native biological systems. We have quantified, in total, more than 9,000 lysines in human cell proteomes and have identified several hundred residues with heightened reactivity that are enriched at protein functional sites and can frequently be targeted by electrophilic small molecules. We have also discovered lysine-reactive fragment electrophiles that inhibit enzymes by active site and allosteric mechanisms, as well as disrupt protein-protein interactions in transcriptional regulatory complexes, emphasizing the broad potential and diverse functional consequences of liganding lysine residues throughout the human proteome.

  10. Global profiling of lysine reactivity and ligandability in the human proteome.

    Science.gov (United States)

    Hacker, Stephan M; Backus, Keriann M; Lazear, Michael R; Forli, Stefano; Correia, Bruno E; Cravatt, Benjamin F

    2017-12-01

    Nucleophilic amino acids make important contributions to protein function, including performing key roles in catalysis and serving as sites for post-translational modification. Electrophilic groups that target amino-acid nucleophiles have been used to create covalent ligands and drugs, but have, so far, been mainly limited to cysteine and serine. Here, we report a chemical proteomic platform for the global and quantitative analysis of lysine residues in native biological systems. We have quantified, in total, more than 9,000 lysines in human cell proteomes and have identified several hundred residues with heightened reactivity that are enriched at protein functional sites and can frequently be targeted by electrophilic small molecules. We have also discovered lysine-reactive fragment electrophiles that inhibit enzymes by active site and allosteric mechanisms, as well as disrupt protein-protein interactions in transcriptional regulatory complexes, emphasizing the broad potential and diverse functional consequences of liganding lysine residues throughout the human proteome.

  11. Enlarged symmetry algebras of spin chains, loop models, and S-matrices

    International Nuclear Information System (INIS)

    Read, N.; Saleur, H.

    2007-01-01

    The symmetry algebras of certain families of quantum spin chains are considered in detail. The simplest examples possess m states per site (m>=2), with nearest-neighbor interactions with U(m) symmetry, under which the sites transform alternately along the chain in the fundamental m and its conjugate representation m-bar. We find that these spin chains, even with arbitrary coefficients of these interactions, have a symmetry algebra A m much larger than U(m), which implies that the energy eigenstates fall into sectors that for open chains (i.e., free boundary conditions) can be labeled by j=0,1,...,L, for the 2L-site chain such that the degeneracies of all eigenvalues in the jth sector are generically the same and increase rapidly with j. For large j, these degeneracies are much larger than those that would be expected from the U(m) symmetry alone. The enlarged symmetry algebra A m (2L) consists of operators that commute in this space of states with the Temperley-Lieb algebra that is generated by the set of nearest-neighbor interaction terms; A m (2L) is not a Yangian. There are similar results for supersymmetric chains with gl(m+n|n) symmetry of nearest-neighbor interactions, and a richer representation structure for closed chains (i.e., periodic boundary conditions). The symmetries also apply to the loop models that can be obtained from the spin chains in a spacetime or transfer matrix picture. In the loop language, the symmetries arise because the loops cannot cross. We further define tensor products of representations (for the open chains) by joining chains end to end. The fusion rules for decomposing the tensor product of representations labeled j 1 and j 2 take the same form as the Clebsch-Gordan series for SU(2). This and other structures turn the symmetry algebra A m into a ribbon Hopf algebra, and we show that this is 'Morita equivalent' to the quantum group U q (sl 2 ) for m=q+q -1 . The open-chain results are extended to the cases vertical bar m vertical

  12. Adatom Fe(III on the hematite surface: Observation of a key reactive surface species

    Directory of Open Access Journals (Sweden)

    Rosso Kevin M

    2004-06-01

    Full Text Available The reactivity of a mineral surface is determined by the variety and population of different types of surface sites (e.g., step, kink, adatom, and defect sites. The concept of "adsorbed nutrient" has been built into crystal growth theories, and many other studies of mineral surface reactivity appeal to ill-defined "active sites." Despite their theoretical importance, there has been little direct experimental or analytical investigation of the structure and properties of such species. Here, we use ex-situ and in-situ scanning tunneling microcopy (STM combined with calculated images based on a resonant tunneling model to show that observed nonperiodic protrusions and depressions on the hematite (001 surface can be explained as Fe in an adsorbed or adatom state occupying sites different from those that result from simple termination of the bulk mineral. The number of such sites varies with sample preparation history, consistent with their removal from the surface in low pH solutions.

  13. Functional Fourier transforms and the loop equation

    International Nuclear Information System (INIS)

    Bershadskii, M.A.; Vaisburd, I.D.; Migdal, A.A.

    1986-01-01

    The Migdal-Makeenko momentum-space loop equation is investigated. This equation is derived from the ordinary loop equation by taking the Fourier transform of the Wilson functional. A perturbation theory is constructed for the new equation and it is proved that the action of the loop operator is determined by vertex functions which coincide with those of the previous equation. It is shown how the ghost loop arises in direct iterations of the momentum-space equation with respect to the coupling constant. A simple example is used to illustrate the mechanism of appearance of an integration in the interior loops in transition to observables

  14. Substantiation of operation limits of reactivity insertion during WWER-1000 reactors start-up; Obosnovanie ehkspluatatsionnykh predelov vvoda reaktivnosti pri puske reaktorov WWER-1000

    Energy Technology Data Exchange (ETDEWEB)

    Boev, I; Sabitov, A; Sal` kov, V; Sudarev, O; Yakovlev, A [ATOMTECHENERGO RF, Novovoronezh (Russian Federation)

    1996-12-31

    The methods and programmes used to define the tolerable rate of reactivity insertion during WWER-1000 start-up are presented. They include calculation of the neutron source power in the core during the sub-critical stage and calculation of the relative neutron density and reactor period during the critical stage. The need for optimisation and regulation of tolerable rates is discussed along with the tool parameters affecting the reactivity during start-up. The possibility of increasing the feed rate of pure condensate into the first loop during the time needed to reach critical stage is justified. 4 refs., 3 tabs.

  15. Evidence for an RNA pseudoknot loop-helix interaction essential for efficient -1 ribosomal frameshifting.

    Science.gov (United States)

    Liphardt, J; Napthine, S; Kontos, H; Brierley, I

    1999-05-07

    RNA pseudoknots are structural elements that participate in a variety of biological processes. At -1 ribosomal frameshifting sites, several types of pseudoknot have been identified which differ in their organisation and functionality. The pseudoknot found in infectious bronchitis virus (IBV) is typical of those that possess a long stem 1 of 11-12 bp and a long loop 2 (30-164 nt). A second group of pseudoknots are distinguishable that contain stems of only 5 to 7 bp and shorter loops. The NMR structure of one such pseudoknot, that of mouse mammary tumor virus (MMTV), has revealed that it is kinked at the stem 1-stem 2 junction, and that this kinked conformation is essential for efficient frameshifting. We recently investigated the effect on frameshifting of modulating stem 1 length and stability in IBV-based pseudoknots, and found that a stem 1 with at least 11 bp was needed for efficient frameshifting. Here, we describe the sequence manipulations that are necessary to bypass the requirement for an 11 bp stem 1 and to convert a short non-functional IBV-derived pseudoknot into a highly efficient, kinked frameshifter pseudoknot. Simple insertion of an adenine residue at the stem 1-stem 2 junction (an essential feature of a kinked pseudoknot) was not sufficient to create a functional pseudoknot. An additional change was needed: efficient frameshifting was recovered only when the last nucleotide of loop 2 was changed from a G to an A. The requirement for an A at the end of loop 2 is consistent with a loop-helix contact similar to those described in other RNA tertiary structures. A mutational analysis of both partners of the proposed interaction, the loop 2 terminal adenine residue and two G.C pairs near the top of stem 1, revealed that the interaction was essential for efficient frameshifting. The specific requirement for a 3'-terminal A residue was lost when loop 2 was increased from 8 to 14 nt, suggesting that the loop-helix contact may be required only in those

  16. Direct evidence that scorpion α-toxins (site-3 modulate sodium channel inactivation by hindrance of voltage-sensor movements.

    Directory of Open Access Journals (Sweden)

    Zhongming Ma

    Full Text Available The position of the voltage-sensing transmembrane segment, S4, in voltage-gated ion channels as a function of voltage remains incompletely elucidated. Site-3 toxins bind primarily to the extracellular loops connecting transmembrane helical segments S1-S2 and S3-S4 in Domain 4 (D4 and S5-S6 in Domain 1 (D1 and slow fast-inactivation of voltage-gated sodium channels. As S4 of the human skeletal muscle voltage-gated sodium channel, hNav1.4, moves in response to depolarization from the resting to the inactivated state, two D4S4 reporters (R2C and R3C, Arg1451Cys and Arg1454Cys, respectively move from internal to external positions as deduced by reactivity to internally or externally applied sulfhydryl group reagents, methane thiosulfonates (MTS. The changes in reporter reactivity, when cycling rapidly between hyperpolarized and depolarized voltages, enabled determination of the positions of the D4 voltage-sensor and of its rate of movement. Scorpion α-toxin binding impedes D4S4 segment movement during inactivation since the modification rates of R3C in hNav1.4 with methanethiosulfonate (CH3SO2SCH2CH2R, where R = -N(CH33 (+ trimethylammonium, MTSET and benzophenone-4-carboxamidocysteine methanethiosulfonate (BPMTS were slowed ~10-fold in toxin-modified channels. Based upon the different size, hydrophobicity and charge of the two reagents it is unlikely that the change in reactivity is due to direct or indirect blockage of access of this site to reagent in the presence of toxin (Tx, but rather is the result of inability of this segment to move outward to the normal extent and at the normal rate in the toxin-modified channel. Measurements of availability of R3C to internally applied reagent show decreased access (slower rates of thiol reaction providing further evidence for encumbered D4S4 movement in the presence of toxins consistent with the assignment of at least part of the toxin binding site to the region of D4S4 region of the voltage

  17. Comparison of energy expenditure and closed-loop performance of thermal and reactive distillation sequences coupled for biodiesel production; Comparacion de gasto energetico y desempeno a lazo cerrado de secuencias de destilacion reactiva y termicamente acopladas para produccion de biodiesel

    Energy Technology Data Exchange (ETDEWEB)

    Cornejo-Jacob, J.L [Universidad Michoacana de San Nicolas de Hidalgo, Morelia, Michoacan (Mexico); Vazquez-Ojeda, M; Segovia-Hernandez, J.G; Hernandez, S [Universidad de Guanajuato, Guanajuato, Guanajuato (Mexico); Maya-Yescas, R. [Universidad Michoacana de San Nicolas de Hidalgo, Morelia, Michoacan (Mexico)]. E-mail: rmayay@umich.mx

    2013-03-15

    Biodiesel is the common name for fatty acid methyl esters, obtained by esterification (basic catalysis) or trans-esterification (acid catalysis) of vegetable or animal oils with alcohols, and used as liquid fuel. Production involves the reaction, under mild conditions, between the oil and, typically, excess of methanol. Traditional production of biodiesel exhibits some handicaps, such as the shift of equilibrium to fatty acids by using excess of alcohol that must be separated and recycled. As alternative, it is possible to integrate reaction/separation operations into a single intensified unit, a reactive distillation column, followed by a second separation unit. These configurations exhibit several advantages such as shifting equilibrium in the reactive region and, because of the thermal integration with the second unit, energy savings during products separation. In order to design these production sequences taking advantage of steady state knowledge (energy savings) and considering dynamic performance, this work performs a controllability analysis for six possible configurations; open-loop control properties, evaluated by single value decomposition, are probed by implementing PI controllers to the system. The reactive distillation column coupled to a stripper, without reboilers, shows to be the best option in terms of closed-loop performance and energy savings. [Spanish] Biodiesel es el nombre comun dado a metil esteres de acidos grasos obtenidos por esterificacion (catalisis basica) o trans-esterificacion (catalisis acida) de aceites animales o vegetales con alcoholes, y usados como combustibles liquidos. Su produccion involucra la reaccion entre el aceite y, tipicamente, exceso de metanol a condiciones moderadas. La produccion tradicional de biodiesel exhibe algunas desventajas como el desplazamiento del equilibrio hacia acidos grasos debido al exceso de alcohol, que debe ser separado y reciclado. Alternativamente, es posible integrar las operaciones reaccion

  18. Loop Evolution Observed with AIA and Hi-C

    Science.gov (United States)

    Mulu-Moore, Fana; Winebarger, Amy R.; Cirtain, Jonathan W.; Kobayashi, Ken; Korreck, Kelly E.; Golub, Leon; Kuzin, Sergei; Walsh, Robert William; DeForest, Craig E.; De Pontieu, Bart; hide

    2012-01-01

    In the past decade, the evolution of EUV loops has been used to infer the loop substructure. With the recent launch of High Resolution Coronal Imager (Hi-C), this inference can be validated. In this presentation we discuss the first results of loop analysis comparing AIA and Hi-C data. In the past decade, the evolution of EUV loops has been used to infer the loop substructure. With the recent launch of High Resolution Coronal Imager (Hi-C), this inference can be validated. In this presentation we discuss the first results of loop analysis comparing AIA and Hi-C data.

  19. Attentional and non-attentional systems in the maintenance of verbal information in working memory: the executive and phonological loops.

    Science.gov (United States)

    Camos, Valérie; Barrouillet, Pierre

    2014-01-01

    Working memory is the structure devoted to the maintenance of information at short term during concurrent processing activities. In this respect, the question regarding the nature of the mechanisms and systems fulfilling this maintenance function is of particular importance and has received various responses in the recent past. In the time-based resource-sharing (TBRS) model, we suggest that only two systems sustain the maintenance of information at the short term, counteracting the deleterious effect of temporal decay and interference. A non-attentional mechanism of verbal rehearsal, similar to the one described by Baddeley in the phonological loop model, uses language processes to reactivate phonological memory traces. Besides this domain-specific mechanism, an executive loop allows the reconstruction of memory traces through an attention-based mechanism of refreshing. The present paper reviews evidence of the involvement of these two independent systems in the maintenance of verbal memory items.

  20. Attentional and non-attentional systems in the maintenance of verbal information in working memory: the executive and phonological loops

    Science.gov (United States)

    Camos, Valérie; Barrouillet, Pierre

    2014-01-01

    Working memory is the structure devoted to the maintenance of information at short term during concurrent processing activities. In this respect, the question regarding the nature of the mechanisms and systems fulfilling this maintenance function is of particular importance and has received various responses in the recent past. In the time-based resource-sharing (TBRS) model, we suggest that only two systems sustain the maintenance of information at the short term, counteracting the deleterious effect of temporal decay and interference. A non-attentional mechanism of verbal rehearsal, similar to the one described by Baddeley in the phonological loop model, uses language processes to reactivate phonological memory traces. Besides this domain-specific mechanism, an executive loop allows the reconstruction of memory traces through an attention-based mechanism of refreshing. The present paper reviews evidence of the involvement of these two independent systems in the maintenance of verbal memory items. PMID:25426049

  1. Attentional and non-attentional systems in the maintenance of verbal information in working memory: the executive and phonological loops.

    Directory of Open Access Journals (Sweden)

    Valerie eCamos

    2014-11-01

    Full Text Available Working memory is the structure devoted to the maintenance of information at short term during concurrent processing activities. In this respect, the question regarding the nature of the mechanisms and systems fulfilling this maintenance function is of particular importance and has received various responses in the recent past. In the time-based resource-sharing model, we suggest that only two systems sustain the maintenance of information at the short term, counteracting the deleterious effect of temporal decay and interference. A non-attentional mechanism of verbal rehearsal, similar to the one described by Baddeley in the phonological loop model, uses language processes to reactivate phonological memory traces. Besides this domain-specific mechanism, an executive loop allows the reconstruction of memory traces through an attention-based mechanism of refreshing. The present paper reviews evidence of the involvement of these two independent systems in the maintenance of verbal memory items.

  2. First cytoplasmic loop of glucagon-like peptide-1 receptor can function at the third cytoplasmic loop position of rhodopsin.

    Science.gov (United States)

    Yamashita, Takahiro; Tose, Koji; Shichida, Yoshinori

    2008-01-01

    G protein-coupled receptors (GPCRs) are classified into several families based on their amino acid sequences. In family 1, GPCRs such as rhodopsin and adrenergic receptor, the structure-function relationship has been extensively investigated to demonstrate that exposure of the third cytoplasmic loop is essential for selective G protein activation. In contrast, much less is known about other families. Here we prepared chimeric mutants between Gt-coupled rhodopsin and Gi/Go- and Gs-coupled glucagon-like peptide-1 (GLP-1) receptor of family 2 and tried to identify the loop region that functions at the third cytoplasmic loop position of rhodopsin. We succeeded in expressing a mutant having the first cytoplasmic loop of GLP-1 receptor and found that this mutant activated Gi and Go efficiently but did not activate Gt. Moreover, the rhodopsin mutant having the first loop of Gs-coupled secretin receptor of family 2 decreased the Gi and Go activation efficiencies. Therefore, the first loop of GLP-1 receptor would share a similar role to the third loop of rhodopsin in G protein activation. This result strongly suggested that different families of GPCRs have maintained molecular architectures of their ancestral types to generate a common mechanism, namely exposure of the cytoplasmic loop, to activate peripheral G protein.

  3. High pressure experimental water loop

    International Nuclear Information System (INIS)

    Grenon, M.

    1958-01-01

    A high pressure experimental water loop has been made for studying the detection and evolution of cladding failure in a pressurized reactor. The loop has been designed for a maximum temperature of 360 deg. C, a maximum of 160 kg/cm 2 and flow rates up to 5 m 3 /h. The entire loop consists of several parts: a main circuit with a canned rotor circulation pump, steam pressurizer, heating tubes, two hydro-cyclones (one de-gasser and one decanter) and one tubular heat exchanger; a continuous purification loop, connected in parallel, comprising pressure reducing valves and resin pots which also allow studies of the stability of resins under pressure, temperature and radiation; following the gas separator is a gas loop for studying the recombination of the radiolytic gases in the steam phase. The preceding circuits, as well as others, return to a low pressure storage circuit. The cold water of the low pressure storage flask is continuously reintroduced into the high pressure main circuit by means of a return pump at a maximum head of 160 kg /cm 2 , and adjusted to the pressurizer level. This loop is also a testing bench for the tight high pressure apparatus. The circulating pump and the connecting flanges (Oak Ridge type) are water-tight. The feed pump and the pressure reducing valves are not; the un-tight ones have a system of leak recovery. To permanently check the tightness the circuit has been fitted with a leak detection system (similar to the HRT one). (author) [fr

  4. Intraspecific variations in Cyt b and D-loop sequences of Testudine species, Lissemys punctata from south Karnataka

    Directory of Open Access Journals (Sweden)

    R. Lalitha

    2018-01-01

    Full Text Available The freshwater Testudine species have gained importance in recent years, as most of their population is threatened due to exploitation for delicacy and pet trade. In this regard, Lissemys punctata, a freshwater terrapin, predominantly distributed in Asian countries has gained its significance for the study. A pilot study report on mitochondrial markers (Cyt b and D-loop conducted on L. punctata species from southern Karnataka, India was presented in this investigation. A complete region spanning 1.14 kb and ∼1 kb was amplified by HotStart PCR and sequenced by Sanger sequencing. The Cyt b sequence revealed 85 substitution sites, no indels and 17 parsimony informative sites, whereas D-loop showed 189 variable sites, 51 parsimony informative sites with 5′ functional domains TAS, CSB-F, CSBs (1, 2, 3 preceding tandem repeat at 3′ end. Current data highlights the intraspecific variations in these target regions and variations validated using suitable evolutionary models points out that the overall point mutations observed in the region are transitions leading to no structural and functional alterations. The mitochondrial data generated uncover the genetic diversity within species and conservationist can utilize the data to estimate the effective population size or for forensic identification of animal or its seizures during unlawful trade activities.

  5. Scoping erosion flow loop test results in support of Hanford WTP

    International Nuclear Information System (INIS)

    Duignan, M.; Imrich, K.; Fowley, M.; Restivo, M.; Reigel, M.

    2015-01-01

    The Waste Treatment and Immobilization Plant (WTP) will process Hanford Site tank waste by converting the waste into a stable glass form. Before the tank waste can be vitrified, the baseline plan is to process the waste through the Pretreatment (PT) Facility where it will be mixed in various process vessels using Pulse Jet Mixers (PJM) and transferred to the High Level Waste (HLW) or Low Activity Waste (LAW) vitrification facilities. The Department of Energy (DOE) and Defense Nuclear Facility Safety Board (DNFSB), as well as independent review groups, have raised concerns regarding the design basis for piping erosion in the PT Facility. Due to the complex nature of slurry erosion/corrosion wear and the unique conditions that exist within the PT Facility, additional testing has been recommended by these entities. Pipe loop testing is necessary to analyze the potential for localized wear at elbows and bends, close the outstanding PT and HLW erosion/corrosion technical issues, and underpin BNI's design basis for a 40-year operational life for black cell piping and vessels. SRNL is consulting with the DOE Office of River Protection (ORP) to resolve technical concerns related to piping erosion/corrosion (wear) design basis for PT. SRNL was tasked by ORP to start designing, building, and testing a flow loop to obtain long-term total-wear rate data using bounding simulant chemistry, operating conditions, and prototypical materials. The initial test involved a scoping paint loop to locate experimentally the potential high-wear locations. This information will provide a basis for the placement of the many sensitive wear measurement instruments in the appropriate locations so that the principal flow-loop test has the best chance to estimate long-term erosion and corrosion. It is important to note that the scoping paint loop test only utilized a bounding erosion simulant for this test. A full chemical simulant needs to be added for the complete test flow loop. The

  6. Automation of loop amplitudes in numerical approach

    International Nuclear Information System (INIS)

    Fujimoto, J.; Ishikawa, T.; Shimizu, Y.; Kato, K.; Nakazawa, N.; Kaneko, T.

    1997-01-01

    An automatic calculating system GRACE-L1 of one-loop Feynman amplitude is reviewed. This system can be applied to 2 to 2-body one-loop processes. A sample calculation of 2 to 3-body one-loop amplitudes is also presented. (orig.)

  7. Loop-quantum-gravity vertex amplitude.

    Science.gov (United States)

    Engle, Jonathan; Pereira, Roberto; Rovelli, Carlo

    2007-10-19

    Spin foam models are hoped to provide the dynamics of loop-quantum gravity. However, the most popular of these, the Barrett-Crane model, does not have the good boundary state space and there are indications that it fails to yield good low-energy n-point functions. We present an alternative dynamics that can be derived as a quantization of a Regge discretization of Euclidean general relativity, where second class constraints are imposed weakly. Its state space matches the SO(3) loop gravity one and it yields an SO(4)-covariant vertex amplitude for Euclidean loop gravity.

  8. THE CORONAL LOOP INVENTORY PROJECT: EXPANDED ANALYSIS AND RESULTS

    Energy Technology Data Exchange (ETDEWEB)

    Schmelz, J. T. [USRA, 7178 Columbia Gateway Drive, Columbia, MD 21046 (United States); Christian, G. M.; Chastain, R. A., E-mail: jschmelz@usra.edu [Physics Department, University of Memphis, Memphis, TN 38152 (United States)

    2016-11-10

    We have expanded upon earlier work that investigates the relative importance of coronal loops with isothermal versus multithermal cross-field temperature distributions. These results are important for determining if loops have substructure in the form of unresolved magnetic strands. We have increased the number of loops targeted for temperature analysis from 19 to 207 with the addition of 188 new loops from multiple regions. We selected all loop segments visible in the 171 Å images of the Atmospheric Imaging Assembly (AIA) that had a clean background. Eighty-six of the new loops were rejected because they could not be reliably separated from the background in other AIA filters. Sixty-one loops required multithermal models to reproduce the observations. Twenty-eight loops were effectively isothermal, that is, the plasma emission to which AIA is sensitive could not be distinguished from isothermal emission, within uncertainties. Ten loops were isothermal. Also, part of our inventory was one small flaring loop, one very cool loop whose temperature distribution could not be constrained by the AIA data, and one loop with inconclusive results. Our survey can confirm an unexpected result from the pilot study: we found no isothermal loop segments where we could properly use the 171-to-193 ratio method, which would be similar to the analysis done for many loops observed with TRACE and EIT. We recommend caution to observers who assume the loop plasma is isothermal, and hope that these results will influence the direction of coronal heating models and the effort modelers spend on various heating scenarios.

  9. Bootstrapping the Three-Loop Hexagon

    Energy Technology Data Exchange (ETDEWEB)

    Dixon, Lance J.; /CERN /SLAC; Drummond, James M.; /CERN /Annecy, LAPTH; Henn, Johannes M.; /Humboldt U., Berlin /Santa Barbara, KITP

    2011-11-08

    We consider the hexagonal Wilson loop dual to the six-point MHV amplitude in planar N = 4 super Yang-Mills theory. We apply constraints from the operator product expansion in the near-collinear limit to the symbol of the remainder function at three loops. Using these constraints, and assuming a natural ansatz for the symbol's entries, we determine the symbol up to just two undetermined constants. In the multi-Regge limit, both constants drop out from the symbol, enabling us to make a non-trivial confirmation of the BFKL prediction for the leading-log approximation. This result provides a strong consistency check of both our ansatz for the symbol and the duality between Wilson loops and MHV amplitudes. Furthermore, we predict the form of the full three-loop remainder function in the multi-Regge limit, beyond the leading-log approximation, up to a few constants representing terms not detected by the symbol. Our results confirm an all-loop prediction for the real part of the remainder function in multi-Regge 3 {yields} 3 scattering. In the multi-Regge limit, our result for the remainder function can be expressed entirely in terms of classical polylogarithms. For generic six-point kinematics other functions are required.

  10. Lattice QED in the loop space

    International Nuclear Information System (INIS)

    Fort, H.

    1994-01-01

    We present a survey on the state of the art in the formulation of lattice compact QED in the space of loops. In a first part we review our most recent Hamiltonian results which signal a second order transition for (3+1) compact QED. We devote the second part to the Lagrangian loop formalism, showing the equivalence of the recently proposed loop action with the Villain form. (orig.)

  11. Loop quantization as a continuum limit

    International Nuclear Information System (INIS)

    Manrique, Elisa; Oeckl, Robert; Weber, Axel; Zapata, Jose A

    2006-01-01

    We present an implementation of Wilson's renormalization group and a continuum limit tailored for loop quantization. The dynamics of loop-quantized theories is constructed as a continuum limit of the dynamics of effective theories. After presenting the general formalism we show as a first explicit example the 2D Ising field theory, an interacting relativistic quantum field theory with local degrees of freedom quantized by loop quantization techniques

  12. FLARE-GENERATED SHOCK WAVE PROPAGATION THROUGH SOLAR CORONAL ARCADE LOOPS AND AN ASSOCIATED TYPE II RADIO BURST

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Pankaj; Cho, Kyung-Suk [Korea Astronomy and Space Science Institute (KASI), Daejeon, 305-348 (Korea, Republic of); Innes, D. E., E-mail: pankaj@kasi.re.kr [Max-Planck Institut für Sonnensystemforschung, D-37077 Göttingen (Germany)

    2016-09-01

    This paper presents multiwavelength observations of a flare-generated type II radio burst. The kinematics of the shock derived from the type II burst closely match a fast extreme ultraviolet (EUV) wave seen propagating through coronal arcade loops. The EUV wave was closely associated with an impulsive M1.0 flare without a related coronal mass ejection, and was triggered at one of the footpoints of the arcade loops in active region NOAA 12035. It was initially observed in the 335 Å images from the Atmospheric Image Assembly with a speed of ∼800 km s{sup −1} and it accelerated to ∼1490 km s{sup −1} after passing through the arcade loops. A fan–spine magnetic topology was revealed at the flare site. A small, confined filament eruption (∼340 km s{sup −1}) was also observed moving in the opposite direction to the EUV wave. We suggest that breakout reconnection in the fan–spine topology triggered the flare and associated EUV wave that propagated as a fast shock through the arcade loops.

  13. FLARE-GENERATED SHOCK WAVE PROPAGATION THROUGH SOLAR CORONAL ARCADE LOOPS AND AN ASSOCIATED TYPE II RADIO BURST

    International Nuclear Information System (INIS)

    Kumar, Pankaj; Cho, Kyung-Suk; Innes, D. E.

    2016-01-01

    This paper presents multiwavelength observations of a flare-generated type II radio burst. The kinematics of the shock derived from the type II burst closely match a fast extreme ultraviolet (EUV) wave seen propagating through coronal arcade loops. The EUV wave was closely associated with an impulsive M1.0 flare without a related coronal mass ejection, and was triggered at one of the footpoints of the arcade loops in active region NOAA 12035. It was initially observed in the 335 Å images from the Atmospheric Image Assembly with a speed of ∼800 km s −1 and it accelerated to ∼1490 km s −1 after passing through the arcade loops. A fan–spine magnetic topology was revealed at the flare site. A small, confined filament eruption (∼340 km s −1 ) was also observed moving in the opposite direction to the EUV wave. We suggest that breakout reconnection in the fan–spine topology triggered the flare and associated EUV wave that propagated as a fast shock through the arcade loops.

  14. Flat Knitting Loop Deformation Simulation Based on Interlacing Point Model

    Directory of Open Access Journals (Sweden)

    Jiang Gaoming

    2017-12-01

    Full Text Available In order to create realistic loop primitives suitable for the faster CAD of the flat-knitted fabric, we have performed research on the model of the loop as well as the variation of the loop surface. This paper proposes an interlacing point-based model for the loop center curve, and uses the cubic Bezier curve to fit the central curve of the regular loop, elongated loop, transfer loop, and irregular deformed loop. In this way, a general model for the central curve of the deformed loop is obtained. The obtained model is then utilized to perform texture mapping, texture interpolation, and brightness processing, simulating a clearly structured and lifelike deformed loop. The computer program LOOP is developed by using the algorithm. The deformed loop is simulated with different yarns, and the deformed loop is applied to design of a cable stitch, demonstrating feasibility of the proposed algorithm. This paper provides a loop primitive simulation method characterized by lifelikeness, yarn material variability, and deformation flexibility, and facilitates the loop-based fast computer-aided design (CAD of the knitted fabric.

  15. Variational solution of the loop equation in QCD

    International Nuclear Information System (INIS)

    Agishtein, M.E.; Migdal, A.A.

    1988-01-01

    A new technique for the large N loop equation of QCD is worked out. The Wilson loop W(C) is approximated by a Gaussian functional. The parameters are fitted to the loop equation, after which the equation is statisfied up to 0.2%. The resulting Wilson loop corresponds to linearly rising Regge trajectories. The problem of tachyon is still present, but it could be cured by iteration of the loop equation starting from this variational solution. (orig.)

  16. Variational solution of the loop equation in QCD

    International Nuclear Information System (INIS)

    Agishtein, M.E.; Migdal, A.A.

    1988-01-01

    A new technique for the large N loop equation of QCD is worked out. The Wilson loop W(C) is approximated by a Gaussian functional. The parameters are fitted to the loop equation, after which the equation is satisfied up to 0.2%. The resulting Wilson loop corresponds to linearly rising Regge trajectories. The problem of tachyon is still present, but it could be cured by iteration of the loop equation starting from this variational solution

  17. Loop Quantum Cosmology

    Directory of Open Access Journals (Sweden)

    Bojowald Martin

    2008-07-01

    Full Text Available Quantum gravity is expected to be necessary in order to understand situations in which classical general relativity breaks down. In particular in cosmology one has to deal with initial singularities, i.e., the fact that the backward evolution of a classical spacetime inevitably comes to an end after a finite amount of proper time. This presents a breakdown of the classical picture and requires an extended theory for a meaningful description. Since small length scales and high curvatures are involved, quantum effects must play a role. Not only the singularity itself but also the surrounding spacetime is then modified. One particular theory is loop quantum cosmology, an application of loop quantum gravity to homogeneous systems, which removes classical singularities. Its implications can be studied at different levels. The main effects are introduced into effective classical equations, which allow one to avoid the interpretational problems of quantum theory. They give rise to new kinds of early-universe phenomenology with applications to inflation and cyclic models. To resolve classical singularities and to understand the structure of geometry around them, the quantum description is necessary. Classical evolution is then replaced by a difference equation for a wave function, which allows an extension of quantum spacetime beyond classical singularities. One main question is how these homogeneous scenarios are related to full loop quantum gravity, which can be dealt with at the level of distributional symmetric states. Finally, the new structure of spacetime arising in loop quantum gravity and its application to cosmology sheds light on more general issues, such as the nature of time.

  18. Loop Quantum Cosmology

    Directory of Open Access Journals (Sweden)

    Bojowald Martin

    2005-12-01

    Full Text Available Quantum gravity is expected to be necessary in order to understand situations where classical general relativity breaks down. In particular in cosmology one has to deal with initial singularities, i.e., the fact that the backward evolution of a classical space-time inevitably comes to an end after a finite amount of proper time. This presents a breakdown of the classical picture and requires an extended theory for a meaningful description. Since small length scales and high curvatures are involved, quantum effects must play a role. Not only the singularity itself but also the surrounding space-time is then modified. One particular realization is loop quantum cosmology, an application of loop quantum gravity to homogeneous systems, which removes classical singularities. Its implications can be studied at different levels. Main effects are introduced into effective classical equations which allow to avoid interpretational problems of quantum theory. They give rise to new kinds of early universe phenomenology with applications to inflation and cyclic models. To resolve classical singularities and to understand the structure of geometry around them, the quantum description is necessary. Classical evolution is then replaced by a difference equation for a wave function which allows to extend space-time beyond classical singularities. One main question is how these homogeneous scenarios are related to full loop quantum gravity, which can be dealt with at the level of distributional symmetric states. Finally, the new structure of space-time arising in loop quantum gravity and its application to cosmology sheds new light on more general issues such as time.

  19. High-rate reactive magnetron sputtering of zirconia films for laser optics applications

    International Nuclear Information System (INIS)

    Juskevicius, K.; Subacius, A.; Drazdys, R.; Juskenas, R.; Audronis, M.; Matthews, A.; Leyland, A.

    2014-01-01

    ZrO 2 exhibits low optical absorption in the near-UV range and is one of the highest laser-induced damage threshold (LIDT) materials; it is, therefore, very attractive for laser optics applications. This paper reports explorations of reactive sputtering technology for deposition of ZrO 2 films with low extinction coefficient k values in the UV spectrum region at low substrate temperature. A high deposition rate (64 % of the pure metal rate) process is obtained by employing active feedback reactive gas control which creates a stable and repeatable deposition processes in the transition region. Substrate heating at 200 C was found to have no significant effect on the optical ZrO 2 film properties. The addition of nitrogen to a closed-loop controlled process was found to have mostly negative effects in terms of deposition rate and optical properties. Open-loop O 2 gas-regulated ZrO 2 film deposition is slow and requires elevated (200 C) substrate temperature or post-deposition annealing to reduce absorption losses. Refractive indices of the films were distributed in the range n = 2.05-2.20 at 1,000 nm and extinction coefficients were in the range k = 0.6 x 10 -4 and 4.8 x 10 -3 at 350 nm. X-ray diffraction analysis showed crystalline ZrO 2 films consisted of monoclinic + tetragonal phases when produced in Ar/O 2 atmosphere and monoclinic + rhombohedral or a single rhombohedral phase when produced in Ar/O 2 + N 2 . Optical and physical properties of the ZrO 2 layers produced in this study are suitable for high-power laser applications in the near-UV range. (orig.)

  20. CHY loop integrands from holomorphic forms

    Energy Technology Data Exchange (ETDEWEB)

    Gomez, Humberto [Facultad de Ciencias Basicas, Universidad Santiago de Cali,Calle 5 62-00 Barrio Pampalinda, Cali, Valle (Colombia); Perimeter Institute for Theoretical Physics,31 Caroline Street N, Waterloo, ON N2L 2Y5 (Canada); Mizera, Sebastian; Zhang, Guojun [Perimeter Institute for Theoretical Physics,31 Caroline Street N, Waterloo, ON N2L 2Y5 (Canada); Department of Physics & Astronomy, University of Waterloo,Waterloo, ON N2L 3G1 (Canada)

    2017-03-16

    Recently, the Cachazo-He-Yuan (CHY) approach for calculating scattering amplitudes has been extended beyond tree level. In this paper, we introduce a way of constructing CHY integrands for Φ{sup 3} theory up to two loops from holomorphic forms on Riemann surfaces. We give simple rules for translating Feynman diagrams into the corresponding CHY integrands. As a complementary result, we extend the L-algorithm, originally introduced in https://arxiv.org/abs/1604.05373, to two loops. Using this approach, we are able to analytically verify our prescription for the CHY integrands up to seven external particles at two loops. In addition, it gives a natural way of extending to higher-loop orders.

  1. Supramolecular Recognition Allows Remote, Site-Selective C-H Oxidation of Methylenic Sites in Linear Amines.

    Science.gov (United States)

    Olivo, Giorgio; Farinelli, Giulio; Barbieri, Alessia; Lanzalunga, Osvaldo; Di Stefano, Stefano; Costas, Miquel

    2017-12-18

    Site-selective C-H functionalization of aliphatic alkyl chains is a longstanding challenge in oxidation catalysis, given the comparable relative reactivity of the different methylenes. A supramolecular, bioinspired approach is described to address this challenge. A Mn complex able to catalyze C(sp 3 )-H hydroxylation with H 2 O 2 is equipped with 18-benzocrown-6 ether receptors that bind ammonium substrates via hydrogen bonding. Reversible pre-association of protonated primary aliphatic amines with the crown ether selectively exposes remote positions (C8 and C9) to the oxidizing unit, resulting in a site-selective oxidation. Remarkably, such control of selectivity retains its efficiency for a whole series of linear amines, overriding the intrinsic reactivity of C-H bonds, no matter the chain length. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Mutations to a glycine loop in the catalytic site of human Lon changes its protease, peptidase and ATPase activities

    Czech Academy of Sciences Publication Activity Database

    Ambro, L.; Pevala, V.; Ondrovičová, G.; Bellová, J.; Kunová, N.; Kutejová, Eva; Bauer, J.

    2014-01-01

    Roč. 281, č. 7 (2014), s. 1784-1797 ISSN 1742-464X Institutional support: RVO:61388971 Keywords : ATP-dependent protease * glycine loop * human Lon protease Subject RIV: CE - Biochemistry Impact factor: 4.001, year: 2014

  3. Loop quantum cosmology and singularities.

    Science.gov (United States)

    Struyve, Ward

    2017-08-15

    Loop quantum gravity is believed to eliminate singularities such as the big bang and big crunch singularity. This belief is based on studies of so-called loop quantum cosmology which concerns symmetry-reduced models of quantum gravity. In this paper, the problem of singularities is analysed in the context of the Bohmian formulation of loop quantum cosmology. In this formulation there is an actual metric in addition to the wave function, which evolves stochastically (rather than deterministically as the case of the particle evolution in non-relativistic Bohmian mechanics). Thus a singularity occurs whenever this actual metric is singular. It is shown that in the loop quantum cosmology for a homogeneous and isotropic Friedmann-Lemaître-Robertson-Walker space-time with arbitrary constant spatial curvature and cosmological constant, coupled to a massless homogeneous scalar field, a big bang or big crunch singularity is never obtained. This should be contrasted with the fact that in the Bohmian formulation of the Wheeler-DeWitt theory singularities may exist.

  4. Liquid Lead-Bismuth Materials Test Loop

    International Nuclear Information System (INIS)

    Tcharnotskaia, Valentina; Ammerman, Curtt; Darling, Timothy; King, Joe; Li, Ning; Shaw, Don; Snodgrass, Leon; Woloshun, Keith

    2002-01-01

    We designed and built the Liquid Lead-Bismuth Materials Test Loop (MTL) to study the materials behavior in a flow of molten lead-bismuth eutectic (LBE). In this paper we present a description of the loop with main components and their functions. Stress distribution in the piping due to sustained, occasional and expansion loads is shown. The loop is designed so that a difference of 100 deg. C can be attained between the coldest and the hottest parts at a nominal flow rate of 8.84 GPM. Liquid LBE flow can be activated by a mechanical sump pump or by natural convection. In order to maintain a self-healing protective film on the surface of the stainless steel pipe, a certain concentration of oxygen has to be maintained in the liquid metal. We developed oxygen sensors and an oxygen control system to be implemented in the loop. The loop is outfitted with a variety of instruments that are controlled from a computer based data acquisition system. Initial experiments include preconditioning the loop, filling it up with LBE, running at uniform temperature and tuning the oxygen control system. We will present some preliminary results and discuss plans for the future tests. (authors)

  5. CO2 separation by calcium looping from full and partial fuel oxidation processes

    International Nuclear Information System (INIS)

    Sivalingam, Senthoorselvan

    2013-01-01

    This thesis work deals with the research and development of calcium looping process for CO 2 separation from full and partial fuel oxidation based power generation systems. CO 2 is the main greenhouse gas and undoubtedly a major contributor to the global warming. It is estimated that more than one third of the total anthropogenic CO 2 emissions come from fossil fuel based heat and power generation. Moreover, fossil fuels are unlikely to be phased out rapidly, since developing alternative energy sources not only take time but also require huge investments and infrastructure. An alternative way to reduce emissions in a medium term is to capture the CO 2 from fossil fueled power plants and store it away from the atmosphere. This process system combining a bunch of technologies is called carbon capture and storage (CCS). CO 2 capture is an important and costly part of CCS and an array of technologies is considered for this. Calcium looping (CaL) is one of such and seems to offer effective and efficient CO 2 separation from fuel oxidation processes. CaL process involves separation of CO 2 at high temperatures (600-700 C) by calcium sorbents (CaO). CO 2 reacts with CaO in a carbonation process and produces CaCO 3 . In a subsequent thermal regeneration (>850 C) called calcination, the CO 2 is released from CaCO 3 . By alternating carbonations and calcinations over multiple cycles, CO 2 is separated from a gas stream. Moreover, the CaL is realised in industrial scale with dual fluidised bed reactors for CO 2 capture (the carbonator) and sorbent regeneration (the calciner). As a process in the development, research is still required in many aspects from thermodynamic modeling to experimental studies. Research works have been carried out in process simulations, sorbent reactivity and optimisation studies in a controlled reactor environment and process parametric studies in a semi-pilot scale CaL test facility. ASPEN Plus power plant simulations integrating the CaL based CO 2

  6. Melioidosis: reactivation during radiation therapy

    International Nuclear Information System (INIS)

    Jegasothy, B.V.; Goslen, J.B.; Salvatore, M.A.

    1980-01-01

    Melioidosis is caused by Pseudomonas pseudomallei, a gram-negative, motile bacillus which is a naturally occurring soil saprophyte. The organism is endemic in Southeast Asia, the Philippines, Australia, and parts of Central and South America. Most human disease occurs from infection acquired in these countries. Infection with P pseudomallei may produce no apparent clinical disease. Acute pneumonitis or septicemia may result from inhalation of the organism, and inoculation into sites of trauma may cause localized skin abscesses, or the disease may remain latent and be reactivated months or years later by trauma, burns, or pneumococcal pneumonia, diabetic ketoacidosis, influenza, or bronchogenic carcinoma. The last is probably the commonest form of melioidosis seen in the United States. We present the first case of reactivation of melioidosis after radiation therapy for carcinoma of the lung, again emphasizing the need to consider melioidosis in a septic patient with a history of travel, especially to Southeast Asia

  7. Constructing QCD one-loop amplitudes

    International Nuclear Information System (INIS)

    Forde, D

    2008-01-01

    In the context of constructing one-loop amplitudes using a unitarity bootstrap approach we discuss a general systematic procedure for obtaining the coefficients of the scalar bubble and triangle integral functions of one-loop amplitudes. Coefficients are extracted after examining the behavior of the cut integrand as the unconstrained parameters of a specifically chosen parameterization of the cut loop momentum approach infinity. Measurements of new physics at the forthcoming experimental program at CERN's Large Hadron Collider (LHC) will require a precise understanding of processes at next-to-leading order (NLO). This places increased demands for the computation of new one-loop amplitudes. This in turn has spurred recent developments towards improved calculational techniques. Direct calculations using Feynman diagrams are in general inefficient. Developments of more efficient techniques have usually centered around unitarity techniques [1], where tree amplitudes are effectively 'glued' together to form loops. The most straightforward application of this method, in which the cut loop momentum is in D = 4, allows for the computation of 'cut-constructible' terms only, i.e. (poly)logarithmic containing terms and any related constants. QCD amplitudes contain, in addition to such terms, rational pieces which cannot be derived using such cuts. These 'missing' rational parts can be extracted using cut loop momenta in D = 4-2 (var e psilon). The greater difficulty of such calculations has restricted the application of this approach, although recent developments [3, 4] have provided new promise for this technique. Recently the application of on-shell recursion relations [5] to obtaining the 'missing' rational parts of one-loop processes [6] has provided an alternative very promising solution to this problem. In combination with unitarity methods an 'on-shell bootstrap' approach provides an efficient technique for computing complete one-loop QCD amplitudes [7]. Additionally

  8. Distinct pools of cdc25C are phosphorylated on specific TP sites and differentially localized in human mitotic cells.

    Directory of Open Access Journals (Sweden)

    Celine Franckhauser

    Full Text Available BACKGROUND: The dual specificity phosphatase cdc25C was the first human cdc25 family member found to be essential in the activation of cdk1/cyclin B1 that takes place at the entry into mitosis. Human cdc25C is phosphorylated on Proline-dependent SP and TP sites when it becomes active at mitosis and the prevalent model is that this phosphorylation/activation of cdc25C would be part of an amplification loop with cdk1/cyclin B1. METHODOLOGY/PRINCIPAL FINDINGS: Using highly specific antibodies directed against cdc25C phospho-epitopes, pT67 and pT130, we show here that these two phospho-forms of cdc25C represent distinct pools with differential localization during human mitosis. Phosphorylation on T67 occurs from prophase and the cdc25C-pT67 phospho-isoform closely localizes with condensed chromosomes throughout mitosis. The phospho-T130 form of cdc25C arises in late G2 and associates predominantly with centrosomes from prophase to anaphase B where it colocalizes with Plk1. As shown by immunoprecipitation of each isoform, these two phospho-forms are not simultaneously phosphorylated on the other mitotic TP sites or associated with one another. Phospho-T67 cdc25C co-precipitates with MPM2-reactive proteins while pT130-cdc25C is associated with Plk1. Interaction and colocalization of phosphoT130-cdc25C with Plk1 demonstrate in living cells, that the sequence around pT130 acts as a true Polo Box Domain (PBD binding site as previously identified from in vitro peptide screening studies. Overexpression of non-phosphorylatable alanine mutant forms for each isoform, but not wild type cdc25C, strongly impairs mitotic progression showing the functional requirement for each site-specific phosphorylation of cdc25C at mitosis. CONCLUSIONS/SIGNIFICANCE: These results show for the first time that in human mitosis, distinct phospho-isoforms of cdc25C exist with different localizations and interacting partners, thus implying that the long-standing model of a cdc25C

  9. Coupled hydrogeological and reactive transport modelling of the Simpevarp area (Sweden)

    International Nuclear Information System (INIS)

    Molinero, Jorge; Raposo, Juan R.; Galindez, Juan M.; Arcos, David; Guimera, Jordi

    2008-01-01

    The Simpevarp area is one of the alternative sites being considered for the deep geological disposal of high level radioactive waste in Sweden. In this paper, a coupled regional groundwater flow and reactive solute transport model of the Simpevarp area is presented that integrates current hydrogeological and hydrochemical data of the area. The model simulates the current hydrochemical pattern of the groundwater system in the area. To that aim, a conceptual hydrochemical model was developed in order to represent the dominant chemical processes. Groundwater flow conditions were reproduced by taking into account fluid-density-dependent groundwater flow and regional hydrogeologic boundary conditions. Reactive solute transport calculations were performed on the basis of the velocity field so obtained. The model was calibrated and sensitivity analyses were carried out in order to investigate the effects of heterogeneities of hydraulic conductivity in the subsurface medium. Results provided by the reactive transport model are in good agreement with much of the measured hydrochemical data. This paper emphasizes the appropriateness of the use of reactive solute transport models when water-rock interaction reactions are involved, and demonstrates what powerful tools they are for the interpretation of hydrogeological and hydrochemical data from site geological repository characterization programs, by providing a qualitative framework for data analysis and testing of conceptual assumptions in a process-oriented approach

  10. Diuretics in the treatment of hypertension. Part 2: loop diuretics and potassium-sparing agents.

    Science.gov (United States)

    Tamargo, Juan; Segura, Julian; Ruilope, Luis M

    2014-04-01

    Diuretics enhance the renal excretion of Na(+) and water due to a direct action at different tubular sites of the nephron where solute re-absorption occurs. This paper focuses on the mechanism of action, pharmacodynamics, antihypertensive effects, adverse effects, interactions and contraindications of loop diuretics and potassium-sparing agents (including mineralocorticoid receptor antagonists (MRAs) and epithelial Na(+) channel blockers). Loop diuretics are less effective than thiazide diuretics in lowering blood pressure, so that their major use is in edematous patients with congestive heart failure (HF), cirrhosis with ascites and nephritic edema. MRAs represent a major advance in the treatment of resistant hypertension, primary and secondary hyperaldosteronism and in patients with systolic HF to reduce the risks of hospitalization and of premature death. Potassium-sparing diuretics when coadministered with diuretics (thiazides and loop diuretics) working at more proximal nephron locations reduce the risk of hypokalemia and hypomagnesemia and the risk of cardiac arrhythmias. At the end of the article, the basis for the combination of diuretics with other antihypertensive drugs to achieve blood pressure targets is presented.

  11. Chemical reactivity of cation-exchanged zeolites

    OpenAIRE

    Pidko, E.A.

    2008-01-01

    Zeolites modified with metal cations have been extensively studied during the last two decades because of their wide application in different technologically important fields such as catalysis, adsorption and gas separation. Contrary to the well-understood mechanisms of chemical reactions catalyzed by Brønsted acid sites in the hydrogen forms of zeolites, the nature of chemical reactivity, and related, the structure of the metal-containing ions in cation-exchanged zeolites remains the subject...

  12. Two-phase Heating in Flaring Loops

    Science.gov (United States)

    Zhu, Chunming; Qiu, Jiong; Longcope, Dana W.

    2018-03-01

    We analyze and model a C5.7 two-ribbon solar flare observed by the Solar Dynamics Observatory, Hinode, and GOES on 2011 December 26. The flare is made of many loops formed and heated successively over one and half hours, and their footpoints are brightened in the UV 1600 Å before enhanced soft X-ray and EUV missions are observed in flare loops. Assuming that anchored at each brightened UV pixel is a half flaring loop, we identify more than 6700 half flaring loops, and infer the heating rate of each loop from the UV light curve at the footpoint. In each half loop, the heating rate consists of two phases: intense impulsive heating followed by a low-rate heating that is persistent for more than 20 minutes. Using these heating rates, we simulate the evolution of their coronal temperatures and densities with the model of the “enthalpy-based thermal evolution of loops.” In the model, suppression of thermal conduction is also considered. This model successfully reproduces total soft X-ray and EUV light curves observed in 15 passbands by four instruments GOES, AIA, XRT, and EVE. In this flare, a total energy of 4.9 × 1030 erg is required to heat the corona, around 40% of this energy is in the slow-heating phase. About two-fifths of the total energy used to heat the corona is radiated by the coronal plasmas, and the other three fifth transported to the lower atmosphere by thermal conduction.

  13. Reactivating dynamics for the susceptible-infected-susceptible model: a simple method to simulate the absorbing phase

    Science.gov (United States)

    Macedo-Filho, A.; Alves, G. A.; Costa Filho, R. N.; Alves, T. F. A.

    2018-04-01

    We investigated the susceptible-infected-susceptible model on a square lattice in the presence of a conjugated field based on recently proposed reactivating dynamics. Reactivating dynamics consists of reactivating the infection by adding one infected site, chosen randomly when the infection dies out, avoiding the dynamics being trapped in the absorbing state. We show that the reactivating dynamics can be interpreted as the usual dynamics performed in the presence of an effective conjugated field, named the reactivating field. The reactivating field scales as the inverse of the lattice number of vertices n, which vanishes at the thermodynamic limit and does not affect any scaling properties including ones related to the conjugated field.

  14. Control-structure interaction in precision pointing servo loops

    Science.gov (United States)

    Spanos, John T.

    1989-01-01

    The control-structure interaction problem is addressed via stability analysis of a generic linear servo loop model. With the plant described by the rigid body mode and a single elastic mode, structural flexibility is categorized into one of three types: (1) appendage, (2) in-the-loop minimum phase, and (3) in-the-loop nonminimum phase. Closing the loop with proportional-derivative (PD) control action and introducing sensor roll-off dynamics in the feedback path, stability conditions are obtained. Trade studies are conducted with modal frequency, modal participation, modal damping, loop bandwidth, and sensor bandwidth treated as free parameters. Results indicate that appendage modes are most likely to produce instability if they are near the sensor rolloff, whereas in-the-loop modes are most dangerous near the loop bandwidth. The main goal of this paper is to provide a fundamental understanding of the control-structure interaction problem so that it may benefit the design of complex spacecraft and pointing system servo loops. In this framework, the JPL Pathfinder gimbal pointer is considered as an example.

  15. Numerical evaluation of one-loop QCD amplitudes

    DEFF Research Database (Denmark)

    Badger, Simon David; Biedermann, Benedikt; Uwer, Peter

    2012-01-01

    We present the publicly available program NGluon allowing the numerical evaluation of primitive amplitudes at one-loop order in massless QCD. The program allows the computation of one-loop amplitudes for an arbitrary number of gluons. The focus of the present article is the extension to one-loop ...

  16. Vertically Polarized Omnidirectional Printed Slot Loop Antenna

    DEFF Research Database (Denmark)

    Kammersgaard, Nikolaj Peter Iversen; Kvist, Søren H.; Thaysen, Jesper

    2015-01-01

    A novel vertically polarized omnidirectional printed slot loop antenna has been designed, simulated, fabricated and measured. The slot loop works as a magnetic loop. The loop is loaded with inductors to insure uniform and in-phase fields in the slot in order to obtain an omnidirectional radiation...... pattern. The antenna is designed for the 2.45 GHz Industrial, Scientific and Medical band. Applications of the antenna are many. One is for on-body applications since it is ideal for launching a creeping waves due to the polarization....

  17. Complete Genome Sequence of Germline Chromosomally Integrated Human Herpesvirus 6A and Analyses Integration Sites Define a New Human Endogenous Virus with Potential to Reactivate as an Emerging Infection

    Science.gov (United States)

    Tweedy, Joshua; Spyrou, Maria Alexandra; Pearson, Max; Lassner, Dirk; Kuhl, Uwe; Gompels, Ursula A.

    2016-01-01

    Human herpesvirus-6A and B (HHV-6A, HHV-6B) have recently defined endogenous genomes, resulting from integration into the germline: chromosomally-integrated “CiHHV-6A/B”. These affect approximately 1.0% of human populations, giving potential for virus gene expression in every cell. We previously showed that CiHHV-6A was more divergent than CiHHV-6B by examining four genes in 44 European CiHHV-6A/B cardiac/haematology patients. There was evidence for gene expression/reactivation, implying functional non-defective genomes. To further define the relationship between HHV-6A and CiHHV-6A we used next-generation sequencing to characterize genomes from three CiHHV-6A cardiac patients. Comparisons to known exogenous HHV-6A showed CiHHV-6A genomes formed a separate clade; including all 85 non-interrupted genes and necessary cis-acting signals for reactivation as infectious virus. Greater single nucleotide polymorphism (SNP) density was defined in 16 genes and the direct repeats (DR) terminal regions. Using these SNPs, deep sequencing analyses demonstrated superinfection with exogenous HHV-6A in two of the CiHHV-6A patients with recurrent cardiac disease. Characterisation of the integration sites in twelve patients identified the human chromosome 17p subtelomere as a prevalent site, which had specific repeat structures and phylogenetically related CiHHV-6A coding sequences indicating common ancestral origins. Overall CiHHV-6A genomes were similar, but distinct from known exogenous HHV-6A virus, and have the capacity to reactivate as emerging virus infections. PMID:26784220

  18. Structural Characterization of the Loop at the Alpha-Subunit C-Terminus of the Mixed Lineage Leukemia Protein Activating Protease Taspase1.

    Directory of Open Access Journals (Sweden)

    Johannes van den Boom

    Full Text Available Type 2 asparaginases, a subfamily of N-terminal nucleophile (Ntn hydrolases, are activated by limited proteolysis. This activation yields a heterodimer and a loop region at the C-terminus of the α-subunit is released. Since this region is unresolved in all type 2 asparaginase crystal structures but is close to the active site residues, we explored this loop region in six members of the type 2 asparaginase family using homology modeling. As the loop model for the childhood cancer-relevant protease Taspase1 differed from the other members, Taspase1 activation as well as the conformation and dynamics of the 56 amino acids loop were investigated by CD and NMR spectroscopy. We propose a helix-turn-helix motif, which can be exploited as novel anticancer target to inhibit Taspase1 proteolytic activity.

  19. Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs.

    Science.gov (United States)

    Regad, Leslie; Martin, Juliette; Camproux, Anne-Claude

    2011-06-20

    One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet), which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P) and SAH/SAM. Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.

  20. Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs

    Directory of Open Access Journals (Sweden)

    Martin Juliette

    2011-06-01

    Full Text Available Abstract Background One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Results Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet, which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i ubiquitous motifs, shared by several superfamilies and (ii superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P and SAH/SAM. Conclusions Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.

  1. String breaking with Wilson loops?

    CERN Document Server

    Kratochvila, S; Kratochvila, Slavo; Forcrand, Philippe de

    2003-01-01

    A convincing, uncontroversial observation of string breaking, when the static potential is extracted from Wilson loops only, is still missing. This failure can be understood if the overlap of the Wilson loop with the broken string is exponentially small. In that case, the broken string ground state will only be seen if the Wilson loop is long enough. Our preliminary results show string breaking in the context of the 3d SU(2) adjoint static potential, using the L\\"uscher-Weisz exponential variance reduction approach. As a by-product, we measure the fundamental SU(2) static potential with improved accuracy and see clear deviations from Casimir scaling.

  2. BMN correlators by loop equations

    International Nuclear Information System (INIS)

    Eynard, Bertrand; Kristjansen, Charlotte

    2002-01-01

    In the BMN approach to N=4 SYM a large class of correlators of interest are expressible in terms of expectation values of traces of words in a zero-dimensional gaussian complex matrix model. We develop a loop-equation based, analytic strategy for evaluating such expectation values to any order in the genus expansion. We reproduce the expectation values which were needed for the calculation of the one-loop, genus one correction to the anomalous dimension of BMN-operators and which were earlier obtained by combinatorial means. Furthermore, we present the expectation values needed for the calculation of the one-loop, genus two correction. (author)

  3. A pepducin derived from the third intracellular loop of FPR2 is a partial agonist for direct activation of this receptor in neutrophils but a full agonist for cross-talk triggered reactivation of FPR2.

    Directory of Open Access Journals (Sweden)

    Michael Gabl

    Full Text Available We recently described a novel receptor cross-talk mechanism in neutrophils, unique in that the signals generated by the PAF receptor (PAFR and the ATP receptor (P2Y2R transfer formyl peptide receptor 1 (FPR1 from a desensitized (non-signaling state back to an actively signaling state (Forsman H et al., PLoS One, 8:e60169, 2013; Önnheim K, et al., Exp Cell Res, 323∶209, 2014. In addition to the G-protein coupled FPR1, neutrophils also express the closely related receptor FPR2. In this study we used an FPR2 specific pepducin, proposed to work as an allosteric modulator at the cytosolic signaling interface, to determine whether the cross-talk pathway is utilized also by FPR2. The pepducin used contains a fatty acid linked to a peptide sequence derived from the third intracellular loop of FPR2, and it activates as well as desensensitizes this receptor. We now show that neutrophils desensitized with the FPR2-specific pepducin display increased cellular responses to stimulation with PAF or ATP. The secondary PAF/ATP induced response was sensitive to FPR2-specific inhibitors, disclosing a receptor cross-talk mechanism underlying FPR2 reactivation. The pepducin induced an activity in naïve cells similar to that of a conventional FPR2 agonist, but with lower potency (partial efficacy, meaning that the pepducin is a partial agonist. The PAF- or ATP-induced reactivation was, however, much more pronounced when neutrophils had been desensitized to the pepducin as compared to cells desensitized to conventional agonists. The pepducin should thus in this respect be classified as a full agonist. In summary, we demonstrate that desensitized FPR2 can be transferred back to an actively signaling state by receptor cross-talk signals generated through PAFR and P2Y2R, and the difference in agonist potency with respect to pepducin-induced direct receptor activation and cross-talk reactivation of FPR2 puts the concept of functional selectivity in focus.

  4. Loop-space quantum formulation of free electromagnetism

    International Nuclear Information System (INIS)

    Di Bartolo, C.; Nori, F.; Gambini, R.; Trias, A.

    1983-01-01

    A procedure for direct quantization of free electromagnetism in the loop-space is proposed. Explicit solutions for the loop-dependent vacuum and the Wilson loop-average are given. It is shown that elementary lines of magnetic field appear as extremals in the vacuum state as a result of the regularization procedure

  5. A totally diverting loop colostomy.

    Science.gov (United States)

    Merrett, N. D.; Gartell, P. C.

    1993-01-01

    A technique is described where the distal limb of a loop colostomy is tied with nylon or polydioxanone. This ensures total faecal diversion and dispenses with the supporting rod, enabling early application of stoma appliances. The technique does not interfere with the traditional transverse closure of a loop colostomy. PMID:8379632

  6. Real-Time Control of Active and Reactive Power for Doubly Fed Induction Generator (DFIG-Based Wind Energy Conversion System

    Directory of Open Access Journals (Sweden)

    Aman Abdulla Tanvir

    2015-09-01

    Full Text Available This paper presents the modeling, rapid control prototyping, and hardware-in-the-loop testing for real-time simulation and control of a grid-connected doubly fed induction generator (DFIG in a laboratory-size wind turbine emulator for wind energy conversation systems. The generator is modeled using the direct-quadrature rotating reference frame circuit along with the aligned stator flux, and the field-oriented control approach is applied for independent control of the active and reactive power and the DC-link voltage at the grid side. The control of the active, reactive power and the DC-link voltage are performed using a back-to-back converter at sub- and super-synchronous as well as at variable speeds. The control strategy is experimentally validated on an emulated wind turbine driven by the Opal-RT real-time simulator (OP5600 for simultaneous control of the DC-link voltage, active and reactive power.

  7. On-the-fly reduction of open loops

    Energy Technology Data Exchange (ETDEWEB)

    Buccioni, Federico; Pozzorini, Stefano; Zoller, Max [Universitaet Zuerich, Physik-Institut, Zurich (Switzerland)

    2018-01-15

    Building on the open-loop algorithm we introduce a new method for the automated construction of one-loop amplitudes and their reduction to scalar integrals. The key idea is that the factorisation of one-loop integrands in a product of loop segments makes it possible to perform various operations on-the-fly while constructing the integrand. Reducing the integrand on-the-fly, after each segment multiplication, the construction of loop diagrams and their reduction are unified in a single numerical recursion. In this way we entirely avoid objects with high tensor rank, thereby reducing the complexity of the calculations in a drastic way. Thanks to the on-the-fly approach, which is applied also to helicity summation and for the merging of different diagrams, the speed of the original open-loop algorithm can be further augmented in a very significant way. Moreover, addressing spurious singularities of the employed reduction identities by means of simple expansions in rank-two Gram determinants, we achieve a remarkably high level of numerical stability. These features of the new algorithm, which will be made publicly available in a forthcoming release of the OpenLoops program, are particularly attractive for NLO multi-leg and NNLO real-virtual calculations. (orig.)

  8. On-the-fly reduction of open loops

    Science.gov (United States)

    Buccioni, Federico; Pozzorini, Stefano; Zoller, Max

    2018-01-01

    Building on the open-loop algorithm we introduce a new method for the automated construction of one-loop amplitudes and their reduction to scalar integrals. The key idea is that the factorisation of one-loop integrands in a product of loop segments makes it possible to perform various operations on-the-fly while constructing the integrand. Reducing the integrand on-the-fly, after each segment multiplication, the construction of loop diagrams and their reduction are unified in a single numerical recursion. In this way we entirely avoid objects with high tensor rank, thereby reducing the complexity of the calculations in a drastic way. Thanks to the on-the-fly approach, which is applied also to helicity summation and for the merging of different diagrams, the speed of the original open-loop algorithm can be further augmented in a very significant way. Moreover, addressing spurious singularities of the employed reduction identities by means of simple expansions in rank-two Gram determinants, we achieve a remarkably high level of numerical stability. These features of the new algorithm, which will be made publicly available in a forthcoming release of the OpenLoops program, are particularly attractive for NLO multi-leg and NNLO real-virtual calculations.

  9. Loop Quantum Cosmology.

    Science.gov (United States)

    Bojowald, Martin

    2008-01-01

    Quantum gravity is expected to be necessary in order to understand situations in which classical general relativity breaks down. In particular in cosmology one has to deal with initial singularities, i.e., the fact that the backward evolution of a classical spacetime inevitably comes to an end after a finite amount of proper time. This presents a breakdown of the classical picture and requires an extended theory for a meaningful description. Since small length scales and high curvatures are involved, quantum effects must play a role. Not only the singularity itself but also the surrounding spacetime is then modified. One particular theory is loop quantum cosmology, an application of loop quantum gravity to homogeneous systems, which removes classical singularities. Its implications can be studied at different levels. The main effects are introduced into effective classical equations, which allow one to avoid the interpretational problems of quantum theory. They give rise to new kinds of early-universe phenomenology with applications to inflation and cyclic models. To resolve classical singularities and to understand the structure of geometry around them, the quantum description is necessary. Classical evolution is then replaced by a difference equation for a wave function, which allows an extension of quantum spacetime beyond classical singularities. One main question is how these homogeneous scenarios are related to full loop quantum gravity, which can be dealt with at the level of distributional symmetric states. Finally, the new structure of spacetime arising in loop quantum gravity and its application to cosmology sheds light on more general issues, such as the nature of time. Supplementary material is available for this article at 10.12942/lrr-2008-4.

  10. Two-dimensional NMR studies of squash family inhibitors. Sequence-specific proton assignments and secondary structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III.

    Science.gov (United States)

    Krishnamoorthi, R; Gong, Y X; Lin, C L; VanderVelde, D

    1992-01-28

    The solution structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III (CMTI-III*) was investigated by two-dimensional proton nuclear magnetic resonance (2D NMR) spectroscopy. CMTI-III*, prepared by reacting CMTI-III with trypsin which cleaved the Arg5-Ile6 peptide bond, had the two fragments held together by a disulfide linkage. Sequence-specific 1H NMR resonance assignments were made for all the 29 amino acid residues of the protein. The secondary structure of CMTI-III*, as deduced from NOESY cross peaks and identification of slowly exchanging hydrogens, contains two turns (residues 8-12 and 24-27), a 3(10)-helix (residues 13-16), and a triple-stranded beta-sheet (residues 8-10, 29-27, and 21-25). This secondary structure is similar to that of CMTI-I [Holak, T. A., Gondol, D., Otlewski, J., & Wilusz, T. (1989) J. Mol. Biol. 210, 635-648], which has a Glu instead of a Lys at position 9. Sequential proton assignments were also made for the virgin inhibitor, CMTI-III, at pH 4.71, 30 degrees C. Comparison of backbone hydrogen chemical shifts of CMTI-III and CMTI-III* revealed significant changes for residues located far away from the reactive-site region as well as for those located near it, indicating tertiary structural changes that are transmitted through most of the 29 residues of the inhibitor protein. Many of these residues are functionally important in that they make contact with atoms of the enzyme in the trypsin-inhibitor complex, as revealed by X-ray crystallography [Bode, W., Greyling, H. J., Huber, R., Otlewski, J., & Wilusz, T. (1989) FEBS Lett. 242, 285-292].(ABSTRACT TRUNCATED AT 250 WORDS)

  11. Chemical Looping Combustion Reactions and Systems

    Energy Technology Data Exchange (ETDEWEB)

    Sarofim, Adel; Lighty, JoAnn; Smith, Philip; Whitty, Kevin; Eyring, Edward; Sahir, Asad; Alvarez, Milo; Hradisky, Michael; Clayton, Chris; Konya, Gabor; Baracki, Richard; Kelly, Kerry

    2011-07-01

    Chemical Looping Combustion (CLC) is one promising fuel-combustion technology, which can facilitate economic CO2 capture in coal-fired power plants. It employs the oxidation/reduction characteristics of a metal, or oxygen carrier, and its oxide, the oxidizing gas (typically air) and the fuel source may be kept separate. This work focused on two classes of oxygen carrier, one that merely undergoes a change in oxidation state, such as Fe3O4/Fe2O3 and one that is converted from its higher to its lower oxidation state by the release of oxygen on heating, i.e., CuO/Cu2O. This topical report discusses the results of four complementary efforts: (1) the development of process and economic models to optimize important design considerations, such as oxygen carrier circulation rate, temperature, residence time; (2) the development of high-performance simulation capabilities for fluidized beds and the collection, parameter identification, and preliminary verification/uncertainty quantification (3) the exploration of operating characteristics in the laboratory-scale bubbling bed reactor, with a focus on the oxygen carrier performance, including reactivity, oxygen carrying capacity, attrition resistance, resistance to deactivation, cost and availability (4) the identification of mechanisms and rates for the copper, cuprous oxide, and cupric oxide system using thermogravimetric analysis.

  12. Hydraulic loop: practices using open control systems

    International Nuclear Information System (INIS)

    Carrasco, J.A.; Alonso, L.; Sanchez, F.

    1998-01-01

    The Tecnatom Hydraulic Loop is a dynamic training platform. It has been designed with the purpose of improving the work in teams. With this system, the student can obtain a full scope vision of a system. The hydraulic Loop is a part of the Tecnatom Maintenance Centre. The first objective of the hydraulic Loop is the instruction in components, process and process control using open control system. All the personal of an electric power plant can be trained in the Hydraulic Loop with specific courses. The development of a dynamic tool for tests previous to plant installations has been an additional objective of the Hydraulic Loop. The use of this platform is complementary to the use of full-scope simulators in order to debug and to analyse advanced control strategies. (Author)

  13. Two-Loop Scattering Amplitudes from the Riemann Sphere

    CERN Document Server

    Geyer, Yvonne; Monteiro, Ricardo; Tourkine, Piotr

    2016-01-01

    The scattering equations give striking formulae for massless scattering amplitudes at tree level and, as shown recently, at one loop. The progress at loop level was based on ambitwistor string theory, which naturally yields the scattering equations. We proposed that, for ambitwistor strings, the standard loop expansion in terms of the genus of the worldsheet is equivalent to an expansion in terms of nodes of a Riemann sphere, with the nodes carrying the loop momenta. In this paper, we show how to obtain two-loop scattering equations with the correct factorization properties. We adapt genus-two integrands from the ambitwistor string to the nodal Riemann sphere and show that these yield correct answers, by matching standard results for the four-point two-loop amplitudes of maximal supergravity and super-Yang-Mills theory. In the Yang-Mills case, this requires the loop analogue of the Parke-Taylor factor carrying the colour dependence, which includes non-planar contributions.

  14. Free convection in a partially submerged fluid loop

    International Nuclear Information System (INIS)

    Britt, T.E.; Wood, D.C.

    1982-01-01

    Several natural convection loop systems are studied in order to determine the operational characteristics for a multiple loop container which is used to cool failed nuclear reactor assemblies. Both analytical and experimental studies were undertaken to examine flow in both circular and rectangular flow loops. It was found that when a circular loop is heated at the bottom and cooled at the top, recirculation cells form at all input power fluxes. At fluxes between 0.1 W/cm 2 and 0.7 W/cm 2 the cells caused flow oscillations and reversals. With the circular loop heated from the side, no recirculation cells were observed at the power fluxes up to 1.5 W/cm. Boiling did not occur in the circular loop. For a rectangular loop heated and cooled on its vertical sides, no recirculation cells or flow reversals were seen. At input power fluxes above 1.2 W/cm 2 , periodic boiling in the heated side caused flow oscillations

  15. Cooling Active Region Loops Observed With SXT and TRACE

    OpenAIRE

    Winebarger, Amy R.; Warren, Harry P.

    2005-01-01

    An Impulsive Heating Multiple Strand (IHMS) Model is able to reproduce the observational characteristics of EUV (~ 1 MK) active region loops. This model implies that some of the loops must reach temperatures where X-ray filters are sensitive (> 2.5 MK) before they cool to EUV temperatures. Hence, some bright EUV loops must be preceded by bright X-ray loops. Previous analysis of X-ray and EUV active region observations, however, have concluded that EUV loops are not preceded by X-ray loops. In...

  16. Quantum chromodynamics as dynamics of loops

    International Nuclear Information System (INIS)

    Makeenko, Yu.M.; Migdal, A.A.

    1981-01-01

    QCD is entirely reformulated in terms of white composite fields - the traces of the loop products. The 1/N expansion turns out to be the WKB (Hartree-Fock) approximation for these fields. The 'classical' equation describing the N = infinite case is reduced tp a bootstrap form. New, manifestly gauge-invariant perturbation theory in the loop space, reproducing asymptotic freedom, is developed by iterations of this equation. The area law appears to be a self-consistent solution at large loops. (orig.)

  17. Status of the INERI sulfur-iodine integrated-loop experiment

    International Nuclear Information System (INIS)

    Pickard, P.; Carles, Ph.; Buckingham, R.; Russ, B.; Besenbruch, G.

    2007-01-01

    The Sulfur-Iodine (S-I) thermochemical water-splitting cycle has been studied as a potential source of hydrogen on a large scale. Coupled to a nuclear reactor, an S-I hydrogen plant could efficiently produce hydrogen without greenhouse gas emissions. In the S-I cycle, iodine and sulfur dioxide are combined with water to create two immiscible acid phases - a light sulfuric acid phase, and a heavy hydriodic acid phase. The sulfuric acid phase is decomposed at temperatures near 850 C degrees, and the resulting sulfur dioxide is recycled back into the process. The hydriodic acid in the lower phase is separated from excess water and iodine, and is then decomposed into the product hydrogen and iodine. The water and iodine from these steps are also recycled. In an International Nuclear Energy Research Initiative (INERI) project supported by the US DOE Office of Nuclear Energy, Sandia National Labs (SNL) has teamed with Cea in France, and industrial partner General Atomics (GA) to construct and operate a closed-loop device for demonstration of hydrogen production by the S-I process. Previous work in Japan has demonstrated continuous closed-loop operation of the S-I cycle for up to one week using glass components at atmospheric pressure. This work will aim for operation under process conditions expected at the pilot plant-level and beyond pressures up to 20 bar using engineering materials of construction. Staff at Cea is responsible for the acid-generation step, known as the Bunsen reaction. SNL is handling the sulfuric acid decomposition step, and GA is providing equipment for decomposing hydriodic acid into the product hydrogen. All parties are assembling equipment at the GA site in San Diego, California. Operation of the closed-loop device is expected to commence in the second half of calendar year 2007. This paper will summarize project goals, work done to date, current status, and scheduled future work on the INERI S-I Integrated-Loop Experiment. (authors)

  18. Influence of char structure on reactivity and nitric oxide emissions

    Energy Technology Data Exchange (ETDEWEB)

    Arenillas, Ana; Rubiera, Fernando; Parra, Jose B.; Pis, Jose J. [Department of Energy and Environment, Instituto Nacional del Carbon, CSIC, Apartado 73, 33080 Oviedo (Spain)

    2002-06-20

    The aim of this study was to investigate the influence of coal rank and operating conditions during coal pyrolysis on the resultant char texture properties, morphology and reactivity. A range of bituminous coals were pyrolysed in a fixed bed reactor at different heating rates. It was found that the higher the heating rate and the lower the coal rank, the more microporous chars were obtained. Isothermal (500 C) gasification in 20% oxygen in argon of the chars was carried out using a differential thermogravimetric system (DTG). The results of this work indicated that the increase in the availability of char-active surface sites led to an increase in char reactivity, not only for oxygen but also for other reactive gases, in particular NO, diminishing emissions during the combustion process.

  19. The Universal One-Loop Effective Action

    CERN Document Server

    Drozd, Aleksandra; Quevillon, Jérémie; You, Tevong

    2016-01-01

    We present the universal one-loop effective action for all operators of dimension up to six obtained by integrating out massive, non-degenerate multiplets. Our general expression may be applied to loops of heavy fermions or bosons, and has been checked against partial results available in the literature. The broad applicability of this approach simplifies one-loop matching from an ultraviolet model to a lower-energy effective field theory (EFT), a procedure which is now reduced to the evaluation of a combination of matrices in our universal expression, without any loop integrals to evaluate. We illustrate the relationship of our results to the Standard Model (SM) EFT, using as an example the supersymmetric stop and sbottom squark Lagrangian and extracting from our universal expression the Wilson coefficients of dimension-six operators composed of SM fields.

  20. The universal one-loop effective action

    International Nuclear Information System (INIS)

    Drozd, Aleksandra; Ellis, John; Quevillon, Jérémie; You, Tevong

    2016-01-01

    We present the universal one-loop effective action for all operators of dimension up to six obtained by integrating out massive, non-degenerate multiplets. Our general expression may be applied to loops of heavy fermions or bosons, and has been checked against partial results available in the literature. The broad applicability of this approach simplifies one-loop matching from an ultraviolet model to a lower-energy effective field theory (EFT), a procedure which is now reduced to the evaluation of a combination of matrices in our universal expression, without any loop integrals to evaluate. We illustrate the relationship of our results to the Standard Model (SM) EFT, using as an example the supersymmetric stop and sbottom squark Lagrangian and extracting from our universal expression the Wilson coefficients of dimension-six operators composed of SM fields.

  1. Mathematical Modeling of Loop Heat Pipes

    Science.gov (United States)

    Kaya, Tarik; Ku, Jentung; Hoang, Triem T.; Cheung, Mark L.

    1998-01-01

    The primary focus of this study is to model steady-state performance of a Loop Heat Pipe (LHP). The mathematical model is based on the steady-state energy balance equations at each component of the LHP. The heat exchange between each LHP component and the surrounding is taken into account. Both convection and radiation environments are modeled. The loop operating temperature is calculated as a function of the applied power at a given loop condition. Experimental validation of the model is attempted by using two different LHP designs. The mathematical model is tested at different sink temperatures and at different elevations of the loop. Tbc comparison of the calculations and experimental results showed very good agreement (within 3%). This method proved to be a useful tool in studying steady-state LHP performance characteristics.

  2. Silica fractionation and reactivity in soils

    Science.gov (United States)

    Unzué Belmonte, Dácil; Barão, Lúcia; Vandevenne, Floor; Schoelynck, Jonas; Struyf, Eric; Meire, Patrick

    2014-05-01

    550°C burnings. The first results showed differences in silica fractions between treatments and between soil types. This project is a close collaboration with University of Dresden. -Fertilization. Humans use fertilizers to increase crops growth and to avoid plagues affecting soil biogeochemistry. We set up a greenhouse experiment where olivine (a relatively easily weatherable silicate mineral) fertilization is applied to two crops (barley and wheat), at two rain application regimes (daily rain and weekly heavy rain) and with different fertilizer grain sizes. The aim of this project is to investigate how olivine application affects Si fractionation and reactivity in the soil profile. Barão, L., Clymans, W., Vandevenne, F., Meire, P., Conley, D.J. and Struyf, E. Pedogenic and biogenic amorphous Si distribution along a temperate land use gradient. Submitted, European Journal of Soil Science, 2013. Koning, E., Epping, E., and Van Raaphorst, W.: Determining bio- genic silica in marine samples by tracking silicate and aluminium concentrations in alkaline leaching solutions, Aquat. Geochem., 8, 37-67, 2002. Vandevenne, F.I., Struyf, E., Clymans, W. & Meire, P. 2012. Agricultural silica harvest: have humans created a new and important loop in the global silica cycle? Frontiers in Ecology and the Environment 10: 243-248.

  3. Reactivity of Tic Observation Procedures to Situation and Setting

    Science.gov (United States)

    Piacentini, John; Himle, Michael B.; Chang, Susanna; Baruch, David E.; Buzzella, Brian A.; Pearlman, Amanda; Woods, Douglas W.

    2006-01-01

    Tic frequency was assessed and compared across home and clinic as well as three experimentally-manipulated situations in order to assess the phenomenon of tic reactivity. Forty-three youngsters with chronic tic disorder recruited from two geographically-distinct sites were videotaped over three weekly laboratory visits under each of the following…

  4. PNA binding to the non-template DNA strand interferes with transcription, suggesting a blockage mechanism mediated by R-loop formation.

    Science.gov (United States)

    Belotserkovskii, Boris P; Hanawalt, Philip C

    2015-11-01

    Peptide Nucleic Acids (PNAs) are artificial DNA mimics with superior nucleic acid binding capabilities. T7 RNA polymerase (T7 RNAP) transcription upon encountering PNA bound to the non-template DNA strand was studied in vitro. A characteristic pattern of blockage signals was observed, extending downstream from the PNA binding site, similar to that produced by G-rich homopurine-homopyrimidine (hPu-hPy) sequences and likely caused by R-loop formation. Since blocked transcription complexes in association with stable R-loops may interfere with replication and in some cases trigger apoptosis, targeted R-loop formation might be employed to inactivate selected cells, such as those in tumors, based upon their unique complement of expressed genes. © 2014 The Authors. Molecular Carcinogenesis published by Wiley Periodicals, Inc.

  5. Loop expansion in massless three-dimensional QED

    International Nuclear Information System (INIS)

    Guendelman, E.I.; Radulovic, Z.M.

    1983-01-01

    It is shown how the loop expansion in massless three-dimensional QED can be made finite, up to three loops, by absorbing the infrared divergences in a gauge-fixing term. The same method removes leading and first subleading singularities to all orders of perturbation theory, and all singularities of the fermion self-energy to four loops

  6. Zero-Valent Iron Permeable Reactive Barriers: A Review of Performance

    International Nuclear Information System (INIS)

    Korte, NE

    2001-01-01

    This report briefly reviews issues regarding the implementation of the zero-valent iron permeable reactive barrier (PRB) technology at sites managed by the U.S. Department of Energy (DOE). Initially, the PRB technology, using zero-valent iron for the reactive media, was received with great enthusiasm, and DOE invested millions of dollars testing and implementing PRBs. Recently, a negative perception of the technology has been building. This perception is based on the failure of some deployments to satisfy goals for treatment and operating expenses. The purpose of this report, therefore, is to suggest reasons for the problems that have been encountered and to recommend whether DOE should invest in additional research and deployments. The principal conclusion of this review is that the most significant problems have been the result of insufficient characterization, which resulted in poor engineering implementation. Although there are legitimate concerns regarding the longevity of the reactive media, the ability of zero-valent iron to reduce certain chlorinated hydrocarbons and to immobilize certain metals and radionuclides is well documented. The primary problem encountered at some DOE full-scale deployments has been an inadequate assessment of site hydrology, which resulted in misapplication of the technology. The result is PRBs with higher than expected flow velocities and/or incomplete plume capture

  7. Recombinant Envelope-Proteins with Mutations in the Conserved Fusion Loop Allow Specific Serological Diagnosis of Dengue-Infections.

    Directory of Open Access Journals (Sweden)

    Alexandra Rockstroh

    2015-11-01

    Full Text Available Dengue virus (DENV is a mosquito-borne flavivirus and a major international public health concern in many tropical and sub-tropical areas worldwide. DENV is divided into four major serotypes, and infection with one serotype leads to immunity against the same, but not the other serotypes. The specific diagnosis of DENV-infections via antibody-detection is problematic due to the high degree of cross-reactivity displayed by antibodies against related flaviviruses, such as West Nile virus (WNV, Yellow Fever virus (YFV or Tick-borne encephalitis virus (TBEV. Especially in areas where several flaviviruses co-circulate or in the context of vaccination e.g. against YFV or TBEV, this severely complicates diagnosis and surveillance. Most flavivirus cross-reactive antibodies are produced against the highly conserved fusion loop (FL domain in the viral envelope (E protein. We generated insect-cell derived recombinant E-proteins of the four DENV-serotypes which contain point mutations in the FL domain. By using specific mixtures of these mutant antigens, cross-reactivity against heterologous flaviviruses was strongly reduced, enabling sensitive and specific diagnosis of the DENV-infected serum samples in IgG and IgM-measurements. These results have indications for the development of serological DENV-tests with improved specificity.

  8. Atmospheric reactive nitrogen concentrations at ten sites with contrasting land use in an arid region of central Asia

    Directory of Open Access Journals (Sweden)

    K. H. Li

    2012-10-01

    Full Text Available Atmospheric concentrations of reactive nitrogen (Nr species from 2009 to 2011 are reported for ten sites in Xinjiang, China, an arid region of central Asia. Concentrations of NH3, NO2, particulate ammonium and nitrate (pNH4+ and pNO3 showed large spatial and seasonal variation and averaged 7.71, 9.68, 1.81 and 1.13 μg N m−3, and PM10 concentrations averaged 249.2 μg m−3 across all sites. Lower NH3 concentrations and higher NO2, pNH4+ and pNO3 concentrations were found in winter, reflecting serious air pollution due to domestic heating in winter and other anthropogenic sources such as increased emissions from motor traffic and industry. The increasing order of total concentrations of Nr species was alpine grassland; desert, desert-oasis ecotone; desert in an oasis; farmland; suburban and urban ecosystems. Lower ratios of secondary particles (NH4+ and NO3 were found in the desert and desert-oasis ecotone, while urban and suburban areas had higher ratios, which implied that anthropogenic activities have greatly influenced local air quality and must be controlled.

  9. A LabVIEW model incorporating an open-loop arterial impedance and a closed-loop circulatory system.

    Science.gov (United States)

    Cole, R T; Lucas, C L; Cascio, W E; Johnson, T A

    2005-11-01

    While numerous computer models exist for the circulatory system, many are limited in scope, contain unwanted features or incorporate complex components specific to unique experimental situations. Our purpose was to develop a basic, yet multifaceted, computer model of the left heart and systemic circulation in LabVIEW having universal appeal without sacrificing crucial physiologic features. The program we developed employs Windkessel-type impedance models in several open-loop configurations and a closed-loop model coupling a lumped impedance and ventricular pressure source. The open-loop impedance models demonstrate afterload effects on arbitrary aortic pressure/flow inputs. The closed-loop model catalogs the major circulatory waveforms with changes in afterload, preload, and left heart properties. Our model provides an avenue for expanding the use of the ventricular equations through closed-loop coupling that includes a basic coronary circuit. Tested values used for the afterload components and the effects of afterload parameter changes on various waveforms are consistent with published data. We conclude that this model offers the ability to alter several circulatory factors and digitally catalog the most salient features of the pressure/flow waveforms employing a user-friendly platform. These features make the model a useful instructional tool for students as well as a simple experimental tool for cardiovascular research.

  10. Total OH Reactivity Measurements in the Boreal Forest

    Science.gov (United States)

    Praplan, A. P.; Hellén, H.; Hakola, H.; Hatakka, J.

    2015-12-01

    INTRODUCTION Atmospheric total OH reactivity (Rtotal) can be measured (Kovacs and Brune, 2001; Sinha et al., 2008) or it can be calculated according to Rtotal = ∑i kOH+X_i [Xi] where kOH+X_i corresponds to the reaction rate coefficient for the reaction of OH with a given compound Xi and [Xi] its concentration. Studies suggest that in some environments a large fraction of missing reactivity, comparing calculated Rtotal with ambient total OH reactivity measurements (Di Carlo et al., 2004; Hofzumahaus et al., 2009). In this study Rtotal has been measured using the Comparative Reactivity Method (Sinha et al., 2008). Levels of the reference compound (pyrrole, C4H5N) are monitored by gas chromatography every 2 minutes and Rtotal is derived from the difference of reactivity between zero and ambient air. RESULTS Around 36 hours of preliminary total OH reactivity data (30 May until 2 June 2015) are presented in Fig. 1. Its range matches previous studies for this site (Nölscher et al., 2012; Sinha et al., 2010) and is similar to values in another pine forest (Nakashima et al., 2014). The setup used during the period presented here has been updated and more recent data will be presented, as well as a comparison with calculated OH reactivity from measured individual species. ACKNOWLEDGEMENTS This work was supported by Academy of Finland (Academy Research Fellowship No. 275608). The authors acknowledge Juuso Raine for technical support. REFERENCES Di Carlo et al. (2004). Science 304, 722-725.Hofzumahaus et al. (2009). Science 324, 1702-1704.Kovacs and Brune (2001). J. Atmos. Chem. 39, 105-122.Nakashima et al. (2014). Atmos. Env. 85, 1-8.Nölscher et al. (2012). Atmos. Chem. Phys. 12, 8257-8270.Sinha et al. (2008). Atmos. Chem. Phys. 8, 2213-2227.Sinha et al. (2010). Environ. Sci. Technol. 44, 6614-6620.

  11. Mechanical evaluation of space closure loops in orthodontics.

    Science.gov (United States)

    Rodrigues, Eduardo Uggeri; Maruo, Hiroshi; Guariza Filho, Odilon; Tanaka, Orlando; Camargo, Elisa Souza

    2011-01-01

    This study evaluated the mechanical performance of teardrop-shaped loops and teardrop-shaped loops with helix used in orthodontic space closure. Sixty retraction loops made with 0.019" x 0.025" stainless steel (SS) and beta-titanium (BT) wires were used. They were attached to a testing machine to measure the magnitudes of the sagittal force and the load-deflection ratio necessary for 1 mm, 2 mm and 3 mm activation. The results demonstrated that the BT alloy presented significantly smaller mean values (p < 0.01) of sagittal force and load-deflection than the SS alloy. The loop with the highest mean value of sagittal force and load-deflection was the teardrop-shaped loop (p < 0.01). Differences were observed in the mean values of sagittal force and load-deflection among activations, and the highest mean value was found in the activation of 3 mm, while the smallest mean value was evident in the activation of 1 mm (p < 0.01). It could be concluded that the metallic alloy used and the presence of a helix in configuration of the loops may have a strong influence on the sagittal force produced and on the load-deflection ratio; the teardrop-shaped loops and teardrop-shaped loops with helix in BT presented the release of lighter forces; the teardrop-shaped loop in SS generated a high load-deflection ratio, providing high magnitudes of horizontal force during its deactivation.

  12. Mechanical evaluation of space closure loops in Orthodontics

    Directory of Open Access Journals (Sweden)

    Eduardo Uggeri Rodrigues

    2011-02-01

    Full Text Available This study evaluated the mechanical performance of teardrop-shaped loops and teardrop-shaped loops with helix used in orthodontic space closure. Sixty retraction loops made with 0.019" x 0.025" stainless steel (SS and beta-titanium (BT wires were used. They were attached to a testing machine to measure the magnitudes of the sagittal force and the load-deflection ratio necessary for 1 mm, 2 mm and 3 mm activation. The results demonstrated that the BT alloy presented significantly smaller mean values (p < 0.01 of sagittal force and load-deflection than the SS alloy. The loop with the highest mean value of sagittal force and load-deflection was the teardrop-shaped loop (p < 0.01. Differences were observed in the mean values of sagittal force and load-deflection among activations, and the highest mean value was found in the activation of 3 mm, while the smallest mean value was evident in the activation of 1 mm (p < 0.01. It could be concluded that the metallic alloy used and the presence of a helix in configuration of the loops may have a strong influence on the sagittal force produced and on the load-deflection ratio; the teardrop-shaped loops and teardrop-shaped loops with helix in BT presented the release of lighter forces; the teardrop-shaped loop in SS generated a high load-deflection ratio, providing high magnitudes of horizontal force during its deactivation.

  13. Protein Loop Structure Prediction Using Conformational Space Annealing.

    Science.gov (United States)

    Heo, Seungryong; Lee, Juyong; Joo, Keehyoung; Shin, Hang-Cheol; Lee, Jooyoung

    2017-05-22

    We have developed a protein loop structure prediction method by combining a new energy function, which we call E PLM (energy for protein loop modeling), with the conformational space annealing (CSA) global optimization algorithm. The energy function includes stereochemistry, dynamic fragment assembly, distance-scaled finite ideal gas reference (DFIRE), and generalized orientation- and distance-dependent terms. For the conformational search of loop structures, we used the CSA algorithm, which has been quite successful in dealing with various hard global optimization problems. We assessed the performance of E PLM with two widely used loop-decoy sets, Jacobson and RAPPER, and compared the results against the DFIRE potential. The accuracy of model selection from a pool of loop decoys as well as de novo loop modeling starting from randomly generated structures was examined separately. For the selection of a nativelike structure from a decoy set, E PLM was more accurate than DFIRE in the case of the Jacobson set and had similar accuracy in the case of the RAPPER set. In terms of sampling more nativelike loop structures, E PLM outperformed E DFIRE for both decoy sets. This new approach equipped with E PLM and CSA can serve as the state-of-the-art de novo loop modeling method.

  14. Effect of Loop Diameter on the Steady State and Stability Behaviour of Single-Phase and Two-Phase Natural Circulation Loops

    Directory of Open Access Journals (Sweden)

    P. K. Vijayan

    2008-01-01

    Full Text Available In natural circulation loops, the driving force is usually low as it depends on the riser height which is generally of the order of a few meters. The heat transport capability of natural circulation loops (NCLs is directly proportional to the flow rate it can generate. With low driving force, the straightforward way to enhance the flow is to reduce the frictional losses. A simple way to do this is to increase the loop diameter which can be easily adopted in pressure tube designs such as the AHWR and the natural circulation boilers employed in fossil-fuelled power plants. Further, the loop diameter also plays an important role on the stability behavior. An extensive experimental and theoretical investigation of the effect of loop diameter on the steady state and stability behavior of single- and two-phase natural circulation loops have been carried out and the results of this study are presented in this paper.

  15. UPTF loop seal tests and their RELAP simulation

    International Nuclear Information System (INIS)

    Tuomainen, M.; Tuunanen, J.

    1997-01-01

    In a pressurized water reactor the loop seals have an effect on the natural circulation. If a loop seal is filled with water it can cause a flow stagnation in the loop during two-phase natural circulation. Also the pressure loss over a filled loop seal is high, which lowers the water level in the core. Tests to investigate the loop seal behaviour were performed on a German Upper Plenum Test Facility (UPTF). The purpose of the tests was to study the amount of water in the loop seal under different steam flow rates. The tests were simulated with RELAP5/MOD3.2. With high steam flow rates the code had problems in simulating the amount of the water remaining in the pump elbow, but in general the agreement between the calculated results and the experimental data was good. (orig.)

  16. SU(2) string tension from large Wilson loops

    International Nuclear Information System (INIS)

    Karsch, F.; Lang, C.B.

    1984-01-01

    We determine expectation values of Wilson loops and correlations of Polyakov loops on lattices of size 10 X 16 3 and 8 X 16 3 at β values 2.25 and 2.375. Utilizing a recently proposed method to reduce the variance of loop expectation values, we are able to measure loops up to 6 X 6. We find Λsub(L) = 0.0151 +- 0.0006√sub(K) at β = 2.375. (orig.)

  17. New Cinchona Oximes Evaluated as Reactivators of Acetylcholinesterase and Butyrylcholinesterase Inhibited by Organophosphorus Compounds

    Directory of Open Access Journals (Sweden)

    Maja Katalinić

    2017-07-01

    Full Text Available For the last six decades, researchers have been focused on finding efficient reactivators of organophosphorus compound (OP-inhibited acetylcholinesterase (AChE and butyrylcholinesterase (BChE. In this study, we have focused our research on a new oxime scaffold based on the Cinchona structure since it was proven to fit the cholinesterases active site and reversibly inhibit their activity. Three Cinchona oximes (C1, C2, and C3, derivatives of the 9-oxocinchonidine, were synthesized and investigated in reactivation of various OP-inhibited AChE and BChE. As the results showed, the tested oximes were more efficient in the reactivation of BChE and they reactivated enzyme activity to up to 70% with reactivation rates similar to known pyridinium oximes used as antidotes in medical practice today. Furthermore, the oximes showed selectivity towards binding to the BChE active site and the determined enzyme-oxime dissociation constants supported work on the future development of inhibitors in other targeted studies (e.g., in treatment of neurodegenerative disease. Also, we monitored the cytotoxic effect of Cinchona oximes on two cell lines Hep G2 and SH-SY5Y to determine the possible limits for in vivo application. The cytotoxicity results support future studies of these compounds as long as their biological activity is targeted in the lower micromolar range.

  18. Gamma reactivation using the spongy effect of KLF1-binding site sequence: an approach in gene therapy for beta-thalassemia

    Science.gov (United States)

    Heydari, Nasrin; Shariati, Laleh; Khanahmad, Hossein; Hejazi, Zahra; Shahbazi, Mansoureh; Salehi, Mansoor

    2016-01-01

    Objective(s): β-thalassemia is one of the most common genetic disorders in the world. As one of the promising treatment strategies, fetal hemoglobin (Hb F) can be induced. The present study was an attempt to reactivate the γ-globin gene by introducing a gene construct containing KLF1 binding sites to the K562 cell line. Materials and Methods: A plasmid containing a 192 bp sequence with two repeats of KLF1 binding sites on β-globin and BCL11A promoters was constructed and used to transfect the K562 cell line. Positive selection was performed under treatment with 150 μg/ml hygromycin B. The remaining cells were expanded and harvested on day 28, and genomic DNA was extracted. The PCR was carried out to verify insertion of DNA fragment to the genome of K562 cells. The cells were differentiated with 15 μg/ml cisplatin. Flowcytometry was performed to identify erythroid differentiation by detection of CD235a+ cells. Real-time RT-PCR was performed to evaluate γ-globin expression in the transfected cells. Results: A 1700 bp fragment was observed on agarose gel as expected and insertion of DNA fragment to the genome of K562 cells was verified. Totally, 84% of cells were differentiated. The transfected cells significantly increased γ-globin expression after differentiation compared to untransfected ones. Conclusion: The findings demonstrate that the spongy effect of KLF1-binding site on BCL11A and β-globin promoters can induce γ-globin expression in K562 cells. This novel strategy can be promising for the treatment of β-thalassemia and sickle cell disease. PMID:27872702

  19. Incremental Closed-loop Identification of Linear Parameter Varying Systems

    DEFF Research Database (Denmark)

    Bendtsen, Jan Dimon; Trangbæk, Klaus

    2011-01-01

    , closed-loop system identification is more difficult than open-loop identification. In this paper we prove that the so-called Hansen Scheme, a technique known from linear time-invariant systems theory for transforming closed-loop system identification problems into open-loop-like problems, can be extended...

  20. Studying DNA looping by single-molecule FRET.

    Science.gov (United States)

    Le, Tung T; Kim, Harold D

    2014-06-28

    Bending of double-stranded DNA (dsDNA) is associated with many important biological processes such as DNA-protein recognition and DNA packaging into nucleosomes. Thermodynamics of dsDNA bending has been studied by a method called cyclization which relies on DNA ligase to covalently join short sticky ends of a dsDNA. However, ligation efficiency can be affected by many factors that are not related to dsDNA looping such as the DNA structure surrounding the joined sticky ends, and ligase can also affect the apparent looping rate through mechanisms such as nonspecific binding. Here, we show how to measure dsDNA looping kinetics without ligase by detecting transient DNA loop formation by FRET (Fluorescence Resonance Energy Transfer). dsDNA molecules are constructed using a simple PCR-based protocol with a FRET pair and a biotin linker. The looping probability density known as the J factor is extracted from the looping rate and the annealing rate between two disconnected sticky ends. By testing two dsDNAs with different intrinsic curvatures, we show that the J factor is sensitive to the intrinsic shape of the dsDNA.

  1. Process/Equipment Co-Simulation on Syngas Chemical Looping Process

    Energy Technology Data Exchange (ETDEWEB)

    Zeng, Liang; Zhou, Qiang; Fan, Liang-Shih

    2012-09-30

    The chemical looping strategy for fossil energy applications promises to achieve an efficient energy conversion system for electricity, liquid fuels, hydrogen and/or chemicals generation, while economically separate CO{sub 2} by looping reaction design in the process. Chemical looping particle performance, looping reactor engineering, and process design and applications are the key drivers to the success of chemical looping process development. In order to better understand and further scale up the chemical looping process, issues such as cost, time, measurement, safety, and other uncertainties need to be examined. To address these uncertainties, advanced reaction/reactor modeling and process simulation are highly desired and the modeling efforts can accelerate the chemical looping technology development, reduce the pilot-scale facility design time and operating campaigns, as well as reduce the cost and technical risks. The purpose of this work is thus to conduct multiscale modeling and simulations on the key aspects of chemical looping technology, including particle reaction kinetics, reactor design and operation, and process synthesis and optimization.

  2. Perception as a closed-loop convergence process.

    Science.gov (United States)

    Ahissar, Ehud; Assa, Eldad

    2016-05-09

    Perception of external objects involves sensory acquisition via the relevant sensory organs. A widely-accepted assumption is that the sensory organ is the first station in a serial chain of processing circuits leading to an internal circuit in which a percept emerges. This open-loop scheme, in which the interaction between the sensory organ and the environment is not affected by its concurrent downstream neuronal processing, is strongly challenged by behavioral and anatomical data. We present here a hypothesis in which the perception of external objects is a closed-loop dynamical process encompassing loops that integrate the organism and its environment and converging towards organism-environment steady-states. We discuss the consistency of closed-loop perception (CLP) with empirical data and show that it can be synthesized in a robotic setup. Testable predictions are proposed for empirical distinction between open and closed loop schemes of perception.

  3. Feedback Loop Gains and Feedback Behavior (1996)

    DEFF Research Database (Denmark)

    Kampmann, Christian Erik

    2012-01-01

    Linking feedback loops and system behavior is part of the foundation of system dynamics, yet the lack of formal tools has so far prevented a systematic application of the concept, except for very simple systems. Having such tools at their disposal would be a great help to analysts in understanding...... large, complicated simulation models. The paper applies tools from graph theory formally linking individual feedback loop strengths to the system eigenvalues. The significance of a link or a loop gain and an eigenvalue can be expressed in the eigenvalue elasticity, i.e., the relative change...... of an eigenvalue resulting from a relative change in the gain. The elasticities of individual links and loops may be found through simple matrix operations on the linearized system. Even though the number of feedback loops can grow rapidly with system size, reaching astronomical proportions even for modest systems...

  4. Two-Loop Splitting Amplitudes

    International Nuclear Information System (INIS)

    Bern, Z.

    2004-01-01

    Splitting amplitudes govern the behavior of scattering amplitudes at the momenta of external legs become collinear. In this talk we outline the calculation of two-loop splitting amplitudes via the unitarity sewing method. This method retains the simple factorization properties of light-cone gauge, but avoids the need for prescriptions such as the principal value or Mandelstam-Leibbrandt ones. The encountered loop momentum integrals are then evaluated using integration-by-parts and Lorentz invariance identities. We outline a variety of applications for these splitting amplitudes

  5. Two-loop splitting amplitudes

    International Nuclear Information System (INIS)

    Bern, Z.; Dixon, L.J.; Kosower, D.A.

    2004-01-01

    Splitting amplitudes govern the behavior of scattering amplitudes at the momenta of external legs become collinear. In this talk we outline the calculation of two-loop splitting amplitudes via the unitarity sewing method. This method retains the simple factorization properties of light-cone gauge, but avoids the need for prescriptions such as the principal value or Mandelstam-Leibbrandt ones. The encountered loop momentum integrals are then evaluated using integration-by-parts and Lorentz invariance identities. We outline a variety of applications for these splitting amplitudes

  6. Reactive Kripke semantics

    CERN Document Server

    Gabbay, Dov M

    2013-01-01

    This text offers an extension to the traditional Kripke semantics for non-classical logics by adding the notion of reactivity. Reactive Kripke models change their accessibility relation as we progress in the evaluation process of formulas in the model. This feature makes the reactive Kripke semantics strictly stronger and more applicable than the traditional one. Here we investigate the properties and axiomatisations of this new and most effective semantics, and we offer a wide landscape of applications of the idea of reactivity. Applied topics include reactive automata, reactive grammars, rea

  7. Spatial distribution of soluble reactive silica (SRSi) in the Tanzanian ...

    African Journals Online (AJOL)

    Soluble reactive silica (SRSi) concentrations and diatom abundance were determined during four surveys in the Tanzanian waters of Lake Victoria between 2005 and 2008. The SRSi concentrations increased towards offshore sites, while the opposite was true for diatom abundance. The water directly above the sediment ...

  8. Results from GRACE/SUSY at one-loop

    International Nuclear Information System (INIS)

    Fujimoto, J.; Ishikawa, T.; Kurihara, Y.; Jimbo, M.; Yasui, Y.; Kaneko, T.; Kon, T.; Kuroda, M.; Shimizu, Y.

    2007-01-01

    We report the recent development on the SUSY calculations with the help of GRACE system. GRACE/SUSY/1LOOP is the computer code which can generate Feynman diagrams in the MSSM automatically and compute one-loop amplitudes in the numerical way. We present new results of various two-body widths and chargino pair production at ILC (international linear collider) at one-loop level. (author)

  9. LMFBR with booster pump in pumping loop

    International Nuclear Information System (INIS)

    Rubinstein, H.J.

    1975-01-01

    A loop coolant circulation system is described for a liquid metal fast breeder reactor (LMFBR) utilizing a low head, high specific speed booster pump in the hot leg of the coolant loop with the main pump located in the cold leg of the loop, thereby providing the advantages of operating the main pump in the hot leg with the reliability of cold leg pump operation

  10. Reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor-V: function, thermodynamic stability, and NMR solution structure.

    Science.gov (United States)

    Cai, M; Gong, Y; Prakash, O; Krishnamoorthi, R

    1995-09-26

    Reactive-site (Lys44-Asp45 peptide bond) hydrolyzed Cucurbita maxima trypsin inhibitor-V (CMTI-V*) was prepared and characterized: In comparison to the intact form, CMTI-V* exhibited markedly reduced inhibitory properties and binding affinities toward trypsin and human blood coagulation factor XIIa. The equilibrium constant of trypsin-catalyzed hydrolysis, Khyd, defined as [CMTI-V*]/[CMTI-V], was measured to be approximately 9.4 at 25 degrees C (delta G degrees = -1.3 kcal.mol-1). From the temperature dependence of delta G degrees, the following thermodynamic parameters were estimated: delta H degrees = 1.6 kcal.mol-1 and delta S degrees = 9.8 eu. In order to understand the functional and thermodynamic differences between the two forms, the three-dimensional solution structure of CMTI-V* was determined by a combined approach of NMR, distance geometry, and simulated annealing methods. Thus, following sequence-specific and stereospecific resonance assignments, including those of beta-, gamma-, delta-, and epsilon-hydrogens and valine methyl hydrogens, 809 interhydrogen distances and 123 dihedral angle constraints were determined, resulting in the computation and energy-minimization of 20 structures for CMTI-V*. The average root mean squared deviation in position for equivalent atoms between the 20 individual structures and the mean structure obtained by averaging their coordinates is 0.67 +/- 0.15 A for the main chain atoms and 1.19 +/- 0.23 A for all the non-hydrogen atoms of residues 5-40 and residues 48-67.(ABSTRACT TRUNCATED AT 250 WORDS)

  11. Computational advantages of reverberating loops for sensorimotor learning.

    Science.gov (United States)

    Fortney, Kristen; Tweed, Douglas B

    2012-03-01

    When we learn something new, our brain may store the information in synapses or in reverberating loops of electrical activity, but current theories of motor learning focus almost entirely on the synapses. Here we show that loops could also play a role and would bring advantages: loop-based algorithms can learn complex control tasks faster, with exponentially fewer neurons, and avoid the problem of weight transport. They do all this at a cost: in the presence of long feedback delays, loop algorithms cannot control very fast movements, but in this case, loop and synaptic mechanisms can complement each other-mixed systems quickly learn to make accurate but not very fast motions and then gradually speed up. Loop algorithms explain aspects of consolidation, the role of attention, and the relapses that are sometimes seen after a task has apparently been learned, and they make further predictions.

  12. Thermal instabilities in magnetically confined plasmas: Solar coronal loops

    International Nuclear Information System (INIS)

    Habbal, S.R.; Rosner, R.

    1979-01-01

    The thermal stability of confined solar coronal structures (''loops'') is investigated, following both normal mode and a new, global instability analysis. We demonstrate that: (a) normal mode analysis shows modes with size scales comparable to that of loops to be unstable, but to be strongly affected by the loop boundary conditions; (b) a global analysis, based upon variation of the total loop energy losses and gains, yields loop stability conditions for global modes dependent upon the coronal loop heating process, with magnetically coupled heating processes giving marginal stability. The connection between the present analysis and the minimum flux corona of Hearn is also discussed

  13. Human antibody recognition of antigenic site IV on Pneumovirus fusion proteins.

    Science.gov (United States)

    Mousa, Jarrod J; Binshtein, Elad; Human, Stacey; Fong, Rachel H; Alvarado, Gabriela; Doranz, Benjamin J; Moore, Martin L; Ohi, Melanie D; Crowe, James E

    2018-02-01

    Respiratory syncytial virus (RSV) is a major human pathogen that infects the majority of children by two years of age. The RSV fusion (F) protein is a primary target of human antibodies, and it has several antigenic regions capable of inducing neutralizing antibodies. Antigenic site IV is preserved in both the pre-fusion and post-fusion conformations of RSV F. Antibodies to antigenic site IV have been described that bind and neutralize both RSV and human metapneumovirus (hMPV). To explore the diversity of binding modes at antigenic site IV, we generated a panel of four new human monoclonal antibodies (mAbs) and competition-binding suggested the mAbs bind at antigenic site IV. Mutagenesis experiments revealed that binding and neutralization of two mAbs (3M3 and 6F18) depended on arginine (R) residue R429. We discovered two R429-independent mAbs (17E10 and 2N6) at this site that neutralized an RSV R429A mutant strain, and one of these mAbs (17E10) neutralized both RSV and hMPV. To determine the mechanism of cross-reactivity, we performed competition-binding, recombinant protein mutagenesis, peptide binding, and electron microscopy experiments. It was determined that the human cross-reactive mAb 17E10 binds to RSV F with a binding pose similar to 101F, which may be indicative of cross-reactivity with hMPV F. The data presented provide new concepts in RSV immune recognition and vaccine design, as we describe the novel idea that binding pose may influence mAb cross-reactivity between RSV and hMPV. Characterization of the site IV epitope bound by human antibodies may inform the design of a pan-Pneumovirus vaccine.

  14. Feedback loop compensates for rectifier nonlinearity

    Science.gov (United States)

    1966-01-01

    Signal processing circuit with two negative feedback loops rectifies two sinusoidal signals which are 180 degrees out of phase and produces a single full-wave rectified output signal. Each feedback loop incorporates a feedback rectifier to compensate for the nonlinearity of the circuit.

  15. Observing string breaking with Wilson loops

    CERN Document Server

    Kratochvila, S; Kratochvila, Slavo; Forcrand, Philippe de

    2003-01-01

    An uncontroversial observation of adjoint string breaking is proposed, while measuring the static potential from Wilson loops only. The overlap of the Wilson loop with the broken-string state is small, but non-vanishing, so that the broken-string groundstate can be seen if the Wilson loop is long enough. We demonstrate this in the context of the (2+1)d SU(2) adjoint static potential, using an improved version of the Luscher-Weisz exponential variance reduction. To complete the picture we perform the more usual multichannel analysis with two basis states, the unbroken-string state and the broken-string state (two so-called gluelumps). As by-products, we obtain the temperature-dependent static potential measured from Polyakov loop correlations, and the fundamental SU(2) static potential with improved accuracy. Comparing the latter with the adjoint potential, we see clear deviations from Casimir scaling.

  16. Near BPS Wilson loop in β-deformed theories

    International Nuclear Information System (INIS)

    Chu, C-S; Giataganas, Dimitrios

    2007-01-01

    We propose a definition of the Wilson loop operator in the N = 1 β-deformed supersymmetric Yang-Mills theory. Although the operator is not BPS, it has a finite expectation value at least up to order (g 2 N) 2 . This does not happen generally for a generic non-BPS Wilson loop whose expectation value is UV divergent. For this reason we call this a near-BPS Wilson loop. We derive the general form of the boundary condition satisfied by the dual string worldsheet and find that it is deformed. Finiteness of the expectation value of the Wilson loop fixes the boundary condition to be one which is characterized by the vielbein of the deformed supergravity metric. The Wilson loop operators provide natural candidates as dual descriptions to some of the existing D-brane configurations in the Lunin-Maldacena background. We also construct the string dual configuration for a near-1/4 BPS circular Wilson loop operator. The string lies on a deformed three-sphere instead of a two-sphere as in the undeformed case. The expectation value of the Wilson loop operator is computed using the AdS/CFT correspondence and is found to be independent of the deformation. We conjecture that the exact expectation value of the Wilson loop is given by the same matrix model as in the undeformed case

  17. The iodine reactivity; La reactivite de l'iode

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2003-07-01

    The iodine is an important element because it has long life isotopes (such as iodine 129) and a great mobility in natural media. Iodine presents a complex chemistry because of its volatility and its strong redox reactivity. The S.E.C.R. works to better understand the reactivity of this element in different natural, industrial or biological environments. It plays a part in thermochemical sites as a possible way of hydrogen formation. This seminar gives some aspects relative to the chemical reactivity of iodine, since its thermochemistry in the I/S cycles to produce hydrogen to its reactivity in the natural medium and its potential radiological impact. This document includes 4 presentations transparencies dealing with: the {sup 129}I cycle rejected in the low radioactive gaseous and liquid effluents of the La Hague reprocessing plant (C. Frechou); a bibliographic review of iodine retention in soils (F. Bazer-Bachi); the hydrogen production and the iodine/sulfur thermochemical cycle (role of iodine in the process); and the direct characterization by electro-spray ionization mass spectroscopy of iodine fixation by fulvic acids (P. Reiller, B. Amekraz, C. Moulin, V. Moulin)

  18. A virtual closed loop method for closed loop identification

    NARCIS (Netherlands)

    Agüero, J.C.; Goodwin, G.C.; Hof, Van den P.M.J.

    2011-01-01

    Indirect methods for the identification of linear plant models on the basis of closed loop data are based on the use of (reconstructed) input signals that are uncorrelated with the noise. This generally requires exact (linear) controller knowledge. On the other hand, direct identification requires

  19. Novel Phosphorylation and Ubiquitination Sites Regulate Reactive Oxygen Species-dependent Degradation of Anti-apoptotic c-FLIP Protein*

    Science.gov (United States)

    Wilkie-Grantham, Rachel P.; Matsuzawa, Shu-Ichi; Reed, John C.

    2013-01-01

    The cytosolic protein c-FLIP (cellular Fas-associated death domain-like interleukin 1β-converting enzyme inhibitory protein) is an inhibitor of death receptor-mediated apoptosis that is up-regulated in a variety of cancers, contributing to apoptosis resistance. Several compounds found to restore sensitivity of cancer cells to TRAIL, a TNF family death ligand with promising therapeutic potential, act by targeting c-FLIP ubiquitination and degradation by the proteasome. The generation of reactive oxygen species (ROS) has been implicated in c-FLIP protein degradation. However, the mechanism by which ROS post-transcriptionally regulate c-FLIP protein levels is not well understood. We show here that treatment of prostate cancer PPC-1 cells with the superoxide generators menadione, paraquat, or buthionine sulfoximine down-regulates c-FLIP long (c-FLIPL) protein levels, which is prevented by the proteasome inhibitor MG132. Furthermore, pretreatment of PPC-1 cells with a ROS scavenger prevented ubiquitination and loss of c-FLIPL protein induced by menadione or paraquat. We identified lysine 167 as a novel ubiquitination site of c-FLIPL important for ROS-dependent degradation. We also identified threonine 166 as a novel phosphorylation site and demonstrate that Thr-166 phosphorylation is required for ROS-induced Lys-167 ubiquitination. The mutation of either Thr-166 or Lys-167 was sufficient to stabilize c-FLIP protein levels in PPC-1, HEK293T, and HeLa cancer cells treated with menadione or paraquat. Accordingly, expression of c-FLIP T166A or K167R mutants protected cells from ROS-mediated sensitization to TRAIL-induced cell death. Our findings reveal novel ROS-dependent post-translational modifications of the c-FLIP protein that regulate its stability, thus impacting sensitivity of cancer cells to TRAIL. PMID:23519470

  20. Mass inflation in the loop black hole

    International Nuclear Information System (INIS)

    Brown, Eric G.; Mann, Robert; Modesto, Leonardo

    2011-01-01

    In classical general relativity the Cauchy horizon within a two-horizon black hole is unstable via a phenomenon known as mass inflation, in which the mass parameter (and the spacetime curvature) of the black hole diverges at the Cauchy horizon. Here we study this effect for loop black holes - quantum gravitationally corrected black holes from loop quantum gravity - whose construction alleviates the r=0 singularity present in their classical counterparts. We use a simplified model of mass inflation, which makes use of the generalized Dray-'t Hooft relation, to conclude that the Cauchy horizon of loop black holes indeed results in a curvature singularity similar to that found in classical black holes. The Dray-'t Hooft relation is of particular utility in the loop black hole because it does not directly rely upon Einstein's field equations. We elucidate some of the interesting and counterintuitive properties of the loop black hole, and corroborate our results using an alternate model of mass inflation due to Ori.

  1. A comparative approach to closed-loop computation.

    Science.gov (United States)

    Roth, E; Sponberg, S; Cowan, N J

    2014-04-01

    Neural computation is inescapably closed-loop: the nervous system processes sensory signals to shape motor output, and motor output consequently shapes sensory input. Technological advances have enabled neuroscientists to close, open, and alter feedback loops in a wide range of experimental preparations. The experimental capability of manipulating the topology-that is, how information can flow between subsystems-provides new opportunities to understand the mechanisms and computations underlying behavior. These experiments encompass a spectrum of approaches from fully open-loop, restrained preparations to the fully closed-loop character of free behavior. Control theory and system identification provide a clear computational framework for relating these experimental approaches. We describe recent progress and new directions for translating experiments at one level in this spectrum to predictions at another level. Operating across this spectrum can reveal new understanding of how low-level neural mechanisms relate to high-level function during closed-loop behavior. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. Decoding the Mobility and Time Scales of Protein Loops.

    Science.gov (United States)

    Gu, Yina; Li, Da-Wei; Brüschweiler, Rafael

    2015-03-10

    The flexible nature of protein loops and the time scales of their dynamics are critical for many biologically important events at the molecular level, such as protein interaction and recognition processes. In order to obtain a predictive understanding of the dynamic properties of loops, 500 ns molecular dynamics (MD) computer simulations of 38 different proteins were performed and validated using NMR chemical shifts. A total of 169 loops were analyzed and classified into three types, namely fast loops with correlation times Web server (http://spin.ccic.ohio-state.edu/index.php/loop). The results demonstrate that loop dynamics with their time scales can be predicted rapidly with reasonable accuracy, which will allow the screening of average protein structures to help better understand the various roles loops can play in the context of protein-protein interactions and binding.

  3. Shortening a loop can increase protein native state entropy.

    Science.gov (United States)

    Gavrilov, Yulian; Dagan, Shlomi; Levy, Yaakov

    2015-12-01

    Protein loops are essential structural elements that influence not only function but also protein stability and folding rates. It was recently reported that shortening a loop in the AcP protein may increase its native state conformational entropy. This effect on the entropy of the folded state can be much larger than the lower entropic penalty of ordering a shorter loop upon folding, and can therefore result in a more pronounced stabilization than predicted by polymer model for loop closure entropy. In this study, which aims at generalizing the effect of loop length shortening on native state dynamics, we use all-atom molecular dynamics simulations to study how gradual shortening a very long or solvent-exposed loop region in four different proteins can affect their stability. For two proteins, AcP and Ubc7, we show an increase in native state entropy in addition to the known effect of the loop length on the unfolded state entropy. However, for two permutants of SH3 domain, shortening a loop results only with the expected change in the entropy of the unfolded state, which nicely reproduces the observed experimental stabilization. Here, we show that an increase in the native state entropy following loop shortening is not unique to the AcP protein, yet nor is it a general rule that applies to all proteins following the truncation of any loop. This modification of the loop length on the folded state and on the unfolded state may result with a greater effect on protein stability. © 2015 Wiley Periodicals, Inc.

  4. Adsorption performance and mechanism in binding of Reactive Red 4 by coke waste

    International Nuclear Information System (INIS)

    Won, Sung Wook; Wu Guiping; Ma Hui; Liu Qiong; Yan Yao; Cui Longzhe; Liu Chengfu; Yun, Yeoung-Sang

    2006-01-01

    The protonated coke waste was used as a new type of adsorbent for the removal of Reactive Red 4. To identify the binding sites in the protonated coke waste, the waste was potentiometrically titrated. As a result, four types of functional groups were present in the waste, which was confirmed by FT-IR analysis. Among functional groups, primary amine groups (-NH 2 ) were likely the binding sites for anionic Reactive Red 4. It was also found that sulfonate, carboxyl and phosphonate groups played a role in electrostatic interference with the binding of dye molecules. The maximum adsorption capacities of the coke waste were 70.3 ± 11.1 and 24.9 ± 1.8 mg/g at pH 1 and 2, respectively. Kinetic study showed a pseudo-first-order rate of adsorption with respect to the solution. The uptake of Reactive Red 4 was not significantly affected by the high concentration of salts. These results of adsorption performance indicate the coke waste as a potentially economical adsorbent for dye removal

  5. Numerical approach to one-loop integrals

    International Nuclear Information System (INIS)

    Fujimoto, Junpei; Shimizu, Yoshimitsu; Kato, Kiyoshi; Oyanagi, Yoshio.

    1992-01-01

    Two numerical methods are proposed for the calculation of one-loop scalar integrals. In the first method, the singularity is cancelled by the symmetrization of the integrand and the integration is done by a Monte-Carlo method. In the second one, after the transform of the integrand into a standard form, the integral is reduced into a regular numerical integral. These methods provide us practical tools to evaluate one-loop Feynman diagrams with desired numerical accuracy. They are extended to the integral with numerator and the treatment of the one-loop virtual correction to the cross section is also presented. (author)

  6. Loop corrections to primordial non-Gaussianity

    Science.gov (United States)

    Boran, Sibel; Kahya, E. O.

    2018-02-01

    We discuss quantum gravitational loop effects to observable quantities such as curvature power spectrum and primordial non-Gaussianity of cosmic microwave background (CMB) radiation. We first review the previously shown case where one gets a time dependence for zeta-zeta correlator due to loop corrections. Then we investigate the effect of loop corrections to primordial non-Gaussianity of CMB. We conclude that, even with a single scalar inflaton, one might get a huge value for non-Gaussianity which would exceed the observed value by at least 30 orders of magnitude. Finally we discuss the consequences of this result for scalar driven inflationary models.

  7. Thermodynamics in Loop Quantum Cosmology

    International Nuclear Information System (INIS)

    Li, L.F.; Zhu, J.Y.

    2009-01-01

    Loop quantum cosmology (LQC) is very powerful to deal with the behavior of early universe. Moreover, the effective loop quantum cosmology gives a successful description of the universe in the semiclassical region. We consider the apparent horizon of the Friedmann-Robertson-Walker universe as a thermodynamical system and investigate the thermodynamics of LQC in the semiclassical region. The effective density and effective pressure in the modified Friedmann equation from LQC not only determine the evolution of the universe in LQC scenario but also are actually found to be the thermodynamic quantities. This result comes from the energy definition in cosmology (the Misner-Sharp gravitational energy) and is consistent with thermodynamic laws. We prove that within the framework of loop quantum cosmology, the elementary equation of equilibrium thermodynamics is still valid.

  8. A full-scale porous reactive wall for prevention of acid mine drainage

    International Nuclear Information System (INIS)

    Benner, S.G.; Blowes, D.W.; Ptacek, C.J.

    1997-01-01

    The generation and release of acidic drainage containing high concentrations of dissolved metals from decommissioned mine wastes is an environmental problem of international scale. A potential solution to many acid drainage problems is the installation of permeable reactive walls into aquifers affected by drainage water derived from mine waste materials. A permeable reactive wall installed into an aquifer impacted by low-quality mine drainage waters was installed in August 1995 at the Nickel Rim mine site near Sudbury, Ontario. The reactive mixture, containing organic matter, was designed to promote bacterially mediated sulfate reduction and subsequent metal sulfide precipitation. The reactive wall is installed to an average depth of 12 feet (3.6 m) and is 49 feet (15 m) long perpendicular to ground water flow. The wall thickness (flow path length) is 13 feet (4 m). Initial results, collected nine months after installation, indicate that sulfate reduction and metal sulfide precipitation is occurring. The reactive wall has effectively removed the capacity of the ground water to generate acidity on discharge to the surface. Calculations based on comparison to previously run laboratory column experiments indicate that the reactive wall has potential to remain effective for at least 15 years

  9. Five-loop Konishi in N=4 SYM

    International Nuclear Information System (INIS)

    Eden, Burkhard; Heslop, Paul; Korchemsky, Gregory P.; Smirnov, Vladimir A.; Sokatchev, Emery

    2012-01-01

    We present a new method for computing the Konishi anomalous dimension in N=4 SYM at weak coupling. It does not rely on the conventional Feynman diagram technique and is not restricted to the planar limit. It is based on the OPE analysis of the four-point correlation function of stress-tensor multiplets, which has been recently constructed up to six loops. The Konishi operator gives the leading contribution to the singlet SU(4) channel of this OPE. Its anomalous dimension is the coefficient of the leading single logarithmic singularity of the logarithm of the correlation function in the double short-distance limit, in which the operator positions coincide pairwise. We regularize the logarithm of the correlation function in this singular limit by a version of dimensional regularization. At any loop level, the resulting singularity is a simple pole whose residue is determined by a finite two-point integral with one loop less. This drastically simplifies the five-loop calculation of the Konishi anomalous dimension by reducing it to a set of known four-loop two-point integrals and two unknown integrals which we evaluate analytically. We obtain an analytic result at five loops in the planar limit and observe perfect agreement with the prediction based on integrability in AdS/CFT.

  10. Centrally Acting Oximes in Reactivation of Tabun-Phosphoramidated AChE

    Science.gov (United States)

    Kovarik, Zrinka; Maček, Nikolina; Sit, Rakesh K.; Radić, Zoran; Fokin, Valery V.; Sharpless, K. Barry; Taylor, Palmer

    2012-01-01

    Organophosphates (OP) inhibit acetylcholinesterase (AChE, E.C.3.1.1.7), both in peripheral tissues and central nervous system (CNS), causing adverse and sometimes fatal effects due to the accumulation of neurotransmitter acetylcholine (ACh). The currently used therapy, focusing on the reactivation of inhibited AChE, is limited to peripheral tissues because commonly used quaternary pyridinium oxime reactivators do not cross the blood brain barrier (BBB) at therapeutically relevant levels. A directed library of thirty uncharged oximes that contain tertiary amine or imidazole protonable functional groups that should cross the BBB as unionized species was tested as tabun-hAChE conjugate reactivators along with three reference oximes: DAM (diacetylmonoxime), MINA (monoisonitrosoacetone), and 2-PAM. The oxime RS150D [N-((1-(3-(2-((hydroxyimino)methyl)-1H-imidazol-1-yl)propyl)-1H-1,2,3-triazol-4-yl)methyl)benzamide] was highlighted as the most promising reactivator of the tabun-hAChE conjugate. We also observed that oximes RS194B [N-(2-(azepan-1-yl)ethyl)-2-(hydroxyimino)acetamide] and RS41A [2-(hydroxyimino)-N-(2-(pyrrolidin-1-yl)ethyl)acetamide], which emerged as lead uncharged reactivators of phosphylated hAChE with other OPs (sarin, cyclosarin and VX), exhibited only moderate reactivation potency for tabun inhibited hAChE. This implies that geometry of oxime access to the phosphorus atom conjugated to the active serine is an important criterion for efficient reactivation, along with the chemical nature of the conjugated moiety: phosphorate, phosphonate, or phosphoramidate. Moreover, modification of the active center through mutagenesis enhances the rates of reactivation. The phosphoramidated-hAChE choline-binding site mutant Y337A showed three-times enhanced reactivation capacity with non-triazole imidazole containing aldoximes (RS113B, RS113A and RS115A) and acetamide derivative (RS194B) than with 2PAM. PMID:22960624

  11. Horizontal and vertical structure of reactive bromine events probed by bromine monoxide MAX-DOAS

    Directory of Open Access Journals (Sweden)

    W. R. Simpson

    2017-08-01

    Full Text Available Heterogeneous photochemistry converts bromide (Br− to reactive bromine species (Br atoms and bromine monoxide, BrO that dominate Arctic springtime chemistry. This phenomenon has many impacts such as boundary-layer ozone depletion, mercury oxidation and deposition, and modification of the fate of hydrocarbon species. To study environmental controls on reactive bromine events, the BRomine, Ozone, and Mercury EXperiment (BROMEX was carried out from early March to mid-April 2012 near Barrow (Utqiaġvik, Alaska. We measured horizontal and vertical gradients in BrO with multiple-axis differential optical absorption spectroscopy (MAX-DOAS instrumentation at three sites, two mobile and one fixed. During the campaign, a large crack in the sea ice (an open lead formed pushing one instrument package ∼ 250 km downwind from Barrow (Utqiaġvik. Convection associated with the open lead converted the BrO vertical structure from a surface-based event to a lofted event downwind of the lead influence. The column abundance of BrO downwind of the re-freezing lead was comparable to upwind amounts, indicating direct reactions on frost flowers or open seawater was not a major reactive bromine source. When these three sites were separated by ∼ 30 km length scales of unbroken sea ice, the BrO amount and vertical distributions were highly correlated for most of the time, indicating the horizontal length scales of BrO events were typically larger than ∼ 30 km in the absence of sea ice features. Although BrO amount and vertical distribution were similar between sites most of the time, rapid changes in BrO with edges significantly smaller than this ∼ 30 km length scale episodically transported between the sites, indicating BrO events were large but with sharp edge contrasts. BrO was often found in shallow layers that recycled reactive bromine via heterogeneous reactions on snowpack. Episodically, these surface-based events propagated aloft when

  12. Closed Loop Supply Chains for Sustainable Mass Customization

    DEFF Research Database (Denmark)

    Nielsen, Kjeld; Brunø, Thomas Ditlev

    2013-01-01

    Closed loop supply chains reducing waste, energy consumption and natural resource depletion which all contribute to more sustainable production and products. For mass customization however, the challenges of closed loop supply chains are emphasized by the large variety of inbound end-of-life prod......Closed loop supply chains reducing waste, energy consumption and natural resource depletion which all contribute to more sustainable production and products. For mass customization however, the challenges of closed loop supply chains are emphasized by the large variety of inbound end...

  13. Design of diamagnetic loop on EAST superconducting tokamak

    International Nuclear Information System (INIS)

    Xi Weibin; Shen Biao; Qian Jinping; Wu Songtao; Wan Baonan

    2007-01-01

    The design of EAST diamagnetic measurement system including diamagnetic loop and compensation loop has been given. The advantage of this method is that, the compensation loop is applied for eliminating the change of toroidal flux produced by the toroidal coils and the adjustable structure can be used to decrease the error signals come from the poloidal field. On the other hand, the effect of the material and structure on the diamagnetic loop is detailedly checked during engineering design. Error analysis of the measurement system is given. (authors)

  14. Stepping out of homogeneity in loop quantum cosmology

    International Nuclear Information System (INIS)

    Rovelli, Carlo; Vidotto, Francesca

    2008-01-01

    We explore the extension of quantum cosmology outside the homogeneous approximation using the formalism of loop quantum gravity. We introduce a model where some of the inhomogeneous degrees of freedom are present, providing a tool for describing general fluctuations of quantum geometry near the initial singularity. We show that the dynamical structure of the model reduces to that of loop quantum cosmology in the Born-Oppenheimer approximation. This result corroborates the assumptions that ground loop cosmology sheds some light on the physical and mathematical relation between loop cosmology and full loop quantum gravity, and on the nature of the cosmological approximation. Finally, we show that the non-graph-changing Hamiltonian constraint considered in the context of algebraic quantum gravity provides a viable effective dynamics within this approximation

  15. Label-free fluorescence strategy for sensitive detection of adenosine triphosphate using a loop DNA probe with low background noise.

    Science.gov (United States)

    Lin, Chunshui; Cai, Zhixiong; Wang, Yiru; Zhu, Zhi; Yang, Chaoyong James; Chen, Xi

    2014-07-15

    A simple, rapid, label-free, and ultrasensitive fluorescence strategy for adenosine triphosphate (ATP) detection was developed using a loop DNA probe with low background noise. In this strategy, a loop DNA probe, which is the substrate for both ligation and digestion enzyme reaction, was designed. SYBR green I (SG I), a double-stranded specific dye, was applied for the readout fluorescence signal. Exonuclease I (Exo I) and exonuclease III (Exo III), sequence-independent nucleases, were selected to digest the loop DNA probe in order to minimize the background fluorescence signal. As a result, in the absence of ATP, the loop DNA was completely digested by Exo I and Exo III, leading to low background fluorescence owing to the weak electrostatic interaction between SG I and mononucleotides. On the other hand, ATP induced the ligation of the nicking site, and the sealed loop DNA resisted the digestion of Exo I and ExoIII, resulting in a remarkable increase of fluorescence response. Upon background noise reduction, the sensitivity of the ATP determination was improved significantly, and the detection limitation was found to be 1.2 pM, which is much lower than that in almost all the previously reported methods. This strategy has promise for wide application in the determination of ATP.

  16. LDB1-mediated enhancer looping can be established independent of mediator and cohesin.

    Science.gov (United States)

    Krivega, Ivan; Dean, Ann

    2017-08-21

    Mechanistic studies in erythroid cells indicate that LDB1, as part of a GATA1/TAL1/LMO2 complex, brings erythroid-expressed genes into proximity with enhancers for transcription activation. The role of co-activators in establishing this long-range interaction is poorly understood. Here we tested the contributions of the RNA Pol II pre-initiation complex (PIC), mediator and cohesin to establishment of locus control region (LCR)/β-globin proximity. CRISPR/Cas9 editing of the β-globin promoter to eliminate the RNA Pol II PIC by deleting the TATA-box resulted in loss of transcription, but enhancer-promoter interaction was unaffected. Additional deletion of the promoter GATA1 site eliminated LDB1 complex and mediator occupancy and resulted in loss of LCR/β-globin proximity. To separate the roles of LDB1 and mediator in LCR looping, we expressed a looping-competent but transcription-activation deficient form of LDB1 in LDB1 knock down cells: LCR/β-globin proximity was restored without mediator core occupancy. Further, Cas9-directed tethering of mutant LDB1 to the β-globin promoter forced LCR loop formation in the absence of mediator or cohesin occupancy. Moreover, ENCODE data and our chromatin immunoprecipitation results indicate that cohesin is almost completely absent from validated and predicted LDB1-regulated erythroid enhancer-gene pairs. Thus, lineage specific factors largely mediate enhancer-promoter looping in erythroid cells independent of mediator and cohesin. Published by Oxford University Press on behalf of Nucleic Acids Research 2017.

  17. Identification of a Novel EF-Loop in the N-terminus of TRPM2 Channel Involved in Calcium Sensitivity

    Directory of Open Access Journals (Sweden)

    Yuhuan Luo

    2018-06-01

    Full Text Available As an oxidative stress sensor, transient receptor potential melastatin 2 (TRPM2 channel is involved in many physiological and pathological processes including warmth sensing, ischemia injury, inflammatory diseases and diabetes. Intracellular calcium is critical for TRPM2 channel activation and the IQ-like motif in the N-terminus has been shown to be important by mediating calmodulin binding. Sequence analysis predicted two potential EF-loops in the N-terminus of TRPM2. Site-directed mutagenesis combining with functional assay showed that substitution with alanine of several residues, most of which are conserved in the typical EF-loop, including D267, D278, D288, and E298 dramatically reduced TRPM2 channel currents. By further changing the charges or side chain length of these conserved residues, our results indicate that the negative charge of D267 and the side chain length of D278 are critical for calcium-induced TRPM2 channel activation. G272I mutation also dramatically reduced the channel currents, suggesting that this site is critical for calcium-induced TRPM2 channel activation. Furthermore, D267A mutant dramatically reduced the currents induced by calcium alone compared with that by ADPR, indicating that D267 residue in D267–D278 motif is the most important site for calcium sensitivity of TRPM2. In addition, inside-out recordings showed that mutations at D267, G272, D278, and E298 had no effect on single-channel conductance. Taken together, our data indicate that D267–D278 motif in the N-terminus as a novel EF-loop is critical for calcium-induced TRPM2 channel activation.

  18. pH-regulated metal-ligand switching in the HM loop of ATP7A: a new paradigm for metal transfer chemistry.

    Science.gov (United States)

    Kline, Chelsey D; Gambill, Benjamin F; Mayfield, Mary; Lutsenko, Svetlana; Blackburn, Ninian J

    2016-08-01

    Cuproproteins such as PHM and DBM mature in late endosomal vesicles of the mammalian secretory pathway where changes in vesicle pH are employed for sorting and post-translational processing. Colocation with the P1B-type ATPase ATP7A suggests that the latter is the source of copper and supports a mechanism where selectivity in metal transfer is achieved by spatial colocation of partner proteins in their specific organelles or vesicles. In previous work we have suggested that a lumenal loop sequence located between trans-membrane helices TM1 and TM2 of the ATPase, and containing five histidines and four methionines, acts as an organelle-specific chaperone for metallation of the cuproproteins. The hypothesis posits that the pH of the vesicle regulates copper ligation and loop conformation via a mechanism which involves His to Met ligand switching induced by histidine protonation. Here we report the effect of pH on the HM loop copper coordination using X-ray absorption spectroscopy (XAS), and show via selenium substitution of the Met residues that the HM loop undergoes similar conformational switching to that found earlier for its partner PHM. We hypothesize that in the absence of specific chaperones, HM motifs provide a template for building a flexible, pH-sensitive transfer site whose structure and function can be regulated to accommodate the different active site structural elements and pH environments of its partner proteins.

  19. Tree-loop duality relation beyond single poles

    Energy Technology Data Exchange (ETDEWEB)

    Bierenbaum, Isabella [Hamburg Univ. (Germany). 2. Inst. fuer Theoretische Physik; Buchta, Sebastian; Draggiotis, Petros; Malamos, Ioannis; Rodrigo, German [Valencia Univ. Paterna (Spain). Inst. de Fisica Corpuscular

    2012-11-15

    We develop the Tree-Loop Duality Relation for two- and three-loop integrals with multiple identical propagators (multiple poles). This is the extension of the Duality Relation for single poles and multi-loop integrals derived in previous publications. We prove a generalization of the formula for single poles to multiple poles and we develop a strategy for dealing with higher-order pole integrals by reducing them to single pole integrals using Integration By Parts.

  20. Improvement of CaO-based sorbent performance for CO{sub 2} looping cycles

    Energy Technology Data Exchange (ETDEWEB)

    Vasilije Manovic; Edward J. Anthony [CANMET Energy Technology Centre-Ottawa, Ottawa, ON (Canada)

    2009-07-01

    This paper presents research on CO{sub 2} capture by lime-based looping cycles. This is a new and promising technology that may help in mitigation of global warming and climate change caused primarily by the use of fossil fuels. The intensity of the anticipated changes urgently requires solutions such as the developing technologies for CO{sub 2} capture, especially those based on CaO looping cycles. This technology is at the pilot plant demonstration stage and there are still significant challenges that require solutions. The technology is based on a dual fluidized bed reactor which contains a carbonator - a unit for CO{sub 2} capture, and a calciner - a unit for CaO regeneration. The major technology components are well known from other technologies and easily applicable. However, even though CaO is a very good candidate as a solid CO{sub 2} carrier, its performance in a practical system still has significant limitations. Thus, research on CaO performance is critical and this paper discusses some of the more important problems and potential solutions that are being examined at CETC-O. To date, the most promising methods were reactivation of spent sorbent by steam, thermal pretreatment of sorbent, and doping, most likely with Al{sub 2}O{sub 3}. The combination of these methods, including pelletization, should provide us with enhanced sorbent performance. 75 refs., 19 figs.

  1. On the Loop Current Penetration into the Gulf of Mexico

    Science.gov (United States)

    Weisberg, Robert H.; Liu, Yonggang

    2017-12-01

    The Gulf of Mexico Loop Current generally intrudes some distance into the Gulf of Mexico before shedding an anticyclonic eddy and retreating back to its more direct entry to exit pathway. The control of this aperiodic process remains only partially known. Here we describe the evolution of the Loop Current throughout the era of satellite altimetry, and offer a mechanistic hypothesis on Loop Current intrusion. As a complement to the known effects of Loop Current forcing on the west Florida shelf circulation, we argue that the west Florida shelf, in turn, impacts the Loop Current evolution. A Self-Organizing Map analysis shows that anomalous northward penetrations of the Loop Current into the Gulf of Mexico occur when the eastern side of Loop Current is positioned west from the southwest corner of the west Florida shelf, whereas the more direct inflow to outflow route occurs when the eastern side of the Loop Current comes in contact with the southwest corner of the west Florida shelf. In essence, we argue that the west Florida shelf anchors the Loop Current in its direct path configuration and that farther northward penetration into the Gulf of Mexico occurs when such anchoring is released. To test of this hypothesis heuristically, we estimate that the dissipation and buoyancy work due to known Loop Current forcing of the west Florida shelf circulation (when in contact with the southwest corner) may exceed the pressure work required for the Loop Current to advance against the ambient Gulf of Mexico fluid.Plain Language SummaryThe Gulf of Mexico Loop Current may intrude far into the Gulf of Mexico or take a more direct entry to exit pathway. Such Loop Current behaviors are described using remote observations by satellites, and a heuristic hypothesis on the control of Loop Current intrusion is presented. We argue that energy dissipation and buoyancy work by the west Florida shelf circulation, when the Loop Current contacts the southwest corner of the west Florida shelf

  2. Phylogenetic relationships of German heavy draught horse breeds inferred from mitochondrial DNA D-loop variation.

    Science.gov (United States)

    Aberle, K S; Hamann, H; Drögemüller, C; Distl, O

    2007-04-01

    We analysed a 610-bp mitochondrial (mt)DNA D-loop fragment in a sample of German draught horse breeds and compared the polymorphic sites with sequences from Arabian, Hanoverian, Exmoor, Icelandic, Sorraia and Przewalski's Horses as well as with Suffolk, Shire and Belgian horses. In a total of 65 horses, 70 polymorphic sites representing 47 haplotypes were observed. The average percentage of polymorphic sites was 11.5% for the mtDNA fragment analysed. In the nine different draught horse breeds including South German, Mecklenburg, Saxon Thuringa coldblood, Rhenisch German, Schleswig Draught Horse, Black Forest Horse, Shire, Suffolk and Belgian, 61 polymorphic sites and 24 haplotypes were found. The phylogenetic analysis failed to show monophyletic groups for the draught horses. The analysis indicated that the draught horse populations investigated consist of diverse genetic groups with respect to their maternal lineage.

  3. Newtonian gravity in loop quantum gravity

    OpenAIRE

    Smolin, Lee

    2010-01-01

    We apply a recent argument of Verlinde to loop quantum gravity, to conclude that Newton's law of gravity emerges in an appropriate limit and setting. This is possible because the relationship between area and entropy is realized in loop quantum gravity when boundaries are imposed on a quantum spacetime.

  4. Study of methyl bromide reactivity with human and mouse hemoglobin

    African Journals Online (AJOL)

    A study has been carried out on in-vitro reactivity of human and mouse hemoglobin spectrophotometrically at physiological pH, using different protein to reagent ratios. Hemoglobin side chains were modified with different concentrations of methyl bromide on agro-soil fumigant. To ascertain if the site of alkylation was the ...

  5. Two-loop off-shell QCD amplitudes in FDR

    CERN Document Server

    Page, Ben

    2015-01-01

    We link the FDR treatment of ultraviolet (UV) divergences to dimensional regularization up to two loops in QCD. This allows us to derive the one-loop and two-loop coupling constant and quark mass shifts necessary to translate infrared finite quantities computed in FDR to the MSbar renormalization scheme. As a by-product of our analysis, we solve a problem analogous to the breakdown of unitarity in the Four Dimensional Helicity (FDH) method beyond one loop. A fix to FDH is then presented that preserves the renormalizability properties of QCD without introducing evanescent quantities.

  6. Intercomparison of the comparative reactivity method (CRM) and pump-probe technique for measuring total OH reactivity in an urban environment

    Science.gov (United States)

    Hansen, R. F.; Blocquet, M.; Schoemaecker, C.; Léonardis, T.; Locoge, N.; Fittschen, C.; Hanoune, B.; Stevens, P. S.; Sinha, V.; Dusanter, S.

    2015-10-01

    up to 100 ppbv. The CRM technique has hitherto mainly been used in low-NOx environments, i.e. environments with ambient NOx mixing ratios lower than a few ppbv, due to a measurement artifact generated by ambient NO inside the sampling reactor. However, this study shows that this technique can also be used under NOx-rich conditions if a NOx-dependent correction is carefully applied on the OH reactivity measurements. A full suite of 52 VOCs, NOx, and other inorganic species were monitored during this intercomparison. An investigation of the OH reactivity budget for this urban site suggests that this suite of trace gases can account for the measured total OH reactivity.

  7. Engineering flat electronic bands in quasiperiodic and fractal loop geometries

    Energy Technology Data Exchange (ETDEWEB)

    Nandy, Atanu, E-mail: atanunandy1989@gmail.com; Chakrabarti, Arunava, E-mail: arunava_chakrabarti@yahoo.co.in

    2015-11-06

    Exact construction of one electron eigenstates with flat, non-dispersive bands, and localized over clusters of various sizes is reported for a class of quasi-one-dimensional looped networks. Quasiperiodic Fibonacci and Berker fractal geometries are embedded in the arms of the loop threaded by a uniform magnetic flux. We work out an analytical scheme to unravel the localized single particle states pinned at various atomic sites or over clusters of them. The magnetic field is varied to control, in a subtle way, the extent of localization and the location of the flat band states in energy space. In addition to this we show that an appropriate tuning of the field can lead to a re-entrant behavior of the effective mass of the electron in a band, with a periodic flip in its sign. - Highlights: • Exact construction of eigenstates with flat and dispersive bands is reported. • Competition between translational order and growth of aperiodicity is discussed. • The effect of magnetic field on the location of flat band states is shown. • Flux tunable re-entrant behavior of the effective mass of electron is studied.

  8. Rigidification of the autolysis loop enhances Na+ binding to thrombin

    Science.gov (United States)

    Pozzi, Nicola; Chen, Raymond; Chen, Zhiwei; Bah, Alaji; Di Cera, Enrico

    2011-01-01

    Binding of Na+ to thrombin ensures high activity toward physiological substrates and optimizes the procoagulant and prothrombotic roles of the enzyme in vivo. Under physiological conditions of pH and temperature, the binding affinity of Na+ is weak due to large heat capacity and enthalpy changes associated with binding, and the Kd=80 mM ensures only 64% saturation of the site at the concentration of Na+ in the blood (140 mM). Residues controlling Na+ binding and activation have been identified. Yet, attempts to improve the interaction of Na+ with thrombin and possibly increase catalytic activity under physiological conditions have so far been unsuccessful. Here we report how replacement of the flexible autolysis loop of human thrombin with the homologous rigid domain of the murine enzyme results in a drastic (up to 10-fold) increase in Na+ affinity and a significant improvement in the catalytic activity of the enzyme. Rigidification of the autolysis loop abolishes the heat capacity change associated with Na+ binding observed in the wild-type and also increases the stability of thrombin. These findings have general relevance to protein engineering studies of clotting proteases and trypsin-like enzymes. PMID:21536369

  9. Universality hypothesis breakdown at one-loop order

    Science.gov (United States)

    Carvalho, P. R. S.

    2018-05-01

    We probe the universality hypothesis by analytically computing the at least two-loop corrections to the critical exponents for q -deformed O (N ) self-interacting λ ϕ4 scalar field theories through six distinct and independent field-theoretic renormalization group methods and ɛ -expansion techniques. We show that the effect of q deformation on the one-loop corrections to the q -deformed critical exponents is null, so the universality hypothesis is broken down at this loop order. Such an effect emerges only at the two-loop and higher levels, and the validity of the universality hypothesis is restored. The q -deformed critical exponents obtained through the six methods are the same and, furthermore, reduce to their nondeformed values in the appropriated limit.

  10. LONG-TERM GEOCHEMICAL BEHAVIOR OF A ZEROVALENT IRON PERMEABLE REACTIVE BARRIER FOR THE TREATMENT OF HEXAVALENT CHROMIUM IN GROUNDWATER

    Science.gov (United States)

    Passive, in-situ reactive barriers have proven to be viable, cost-effective systems for the remediation of Cr-contaminated groundwater at some sites. Permeable reactive barriers (PRBs) are installed in the flow-path of groundwater, most typically as vertical treatment walls. Re...

  11. Electron acceleration and radiation signatures in loop coronal transients

    International Nuclear Information System (INIS)

    Vlahos, L.; Gergely, T.E.; Papadopoulos, K.

    1982-01-01

    A model for electron aceleration in loop coronal transients is suggested. We propose that in these transients an erupting loop moves away from the solar surface, with a velocity greater than the local Alfven speed, pushing against the overlying magnetic fields and driving a shock in the front of the moving part of the loop. We suggest that lower hybrid waves are excited at the shock front and propagate radially toward the center of the loop with phase velocity along the magnetic field which exceeds the thermal velocity. The lower hybrid waves stochastically accelerate the tail of the electron distribution inside the loop. We discuss how the accelerated electrons are trapped in the moving loop and give a rough estimate of their radiation signature. We find that plasma radiation can explain the power observed in stationary and moving type IV bursts. We discuss some of the conditions under which moving or stationary type IV bursts are expected to be associated with loop coronal transients

  12. Digital reactivity meter

    International Nuclear Information System (INIS)

    Akkus, B.; Anac, H.; Alsan, S.; Erk, S.

    1991-01-01

    Nowadays, various digital methods making use of microcomputers for neutron detector signals and determining the reactivity by numerical calculations are used in reactor control systems in place of classical reactivity meters. In this work, a calculation based on the ''The Time Dependent Transport Equation'' has been developed for determining the reactivity numerically. The reactivity values have been obtained utilizing a computer-based data acquisition and control system and compared with the analog reactivity meter values as well as the values calculated from the ''Inhour Equation''

  13. Mass transfer of steels for FBR in sodium loop

    International Nuclear Information System (INIS)

    Susukida, Hiroshi; Yonezawa, Toshio; Ueda, Mitsuo; Imazu, Takayuki; Kiyokawa, Teruyuki.

    1976-06-01

    In order to grasp quantitatively the corrosion and mass transfer of steels for FBR in sodium loop and to establish their allowable stress value and corrosion rate, a special sodium loop for material testing was designed and fabricated and the steels were given 3010 hours exposing test in the sodium loop. This paper gives the outline of the sodium loop and the results of the test. (1) Carburization and a slight increase in weight were observed in the specimens of type 304 stainless steel exposed in the sodium loop for 3010 hours, while decarburization was observed in the specimens of 2 1/4 Cr-1 Mo steel. It is considered that these phenomena were caused by the downstream factor of the sodium loop. (2) A remarkable decrease of Charpy absorbed energy was observed in the specimens of type 304 stainless steel exposed in the sodium loop. It is considered that this resulted from the weakening of the grain boundary due to heat history and mass transfer. (3) The specimens exposed in the sodium loop must be washed by ultrasonic waves in a water bath after washing in alcohol. (auth.)

  14. R-loops: targets for nuclease cleavage and repeat instability.

    Science.gov (United States)

    Freudenreich, Catherine H

    2018-01-11

    R-loops form when transcribed RNA remains bound to its DNA template to form a stable RNA:DNA hybrid. Stable R-loops form when the RNA is purine-rich, and are further stabilized by DNA secondary structures on the non-template strand. Interestingly, many expandable and disease-causing repeat sequences form stable R-loops, and R-loops can contribute to repeat instability. Repeat expansions are responsible for multiple neurodegenerative diseases, including Huntington's disease, myotonic dystrophy, and several types of ataxias. Recently, it was found that R-loops at an expanded CAG/CTG repeat tract cause DNA breaks as well as repeat instability (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Two factors were identified as causing R-loop-dependent breaks at CAG/CTG tracts: deamination of cytosines and the MutLγ (Mlh1-Mlh3) endonuclease, defining two new mechanisms for how R-loops can generate DNA breaks (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Following R-loop-dependent nicking, base excision repair resulted in repeat instability. These results have implications for human repeat expansion diseases and provide a paradigm for how RNA:DNA hybrids can cause genome instability at structure-forming DNA sequences. This perspective summarizes mechanisms of R-loop-induced fragility at G-rich repeats and new links between DNA breaks and repeat instability.

  15. Annealing of dislocation loops in neutron-irradiated copper investigated by positron annihilation

    International Nuclear Information System (INIS)

    Gauster, W.B.; Mantl, S.; Schober, T.; Triftshauser, W.

    1975-01-01

    Positron annihilation angular correlation measurements were carried out on neutron-irradiated copper as a function of annealing temperature. Two types of specimens were used: single crystals irradiated with fast neutrons, and 10 B-doped polycrystalline samples irradiated with thermal neutrons. All irradiations were at approximately 320 0 K. A structure in the annealing curve, not previously observed by other techniques, indicates that between 460 and 600 0 K the dislocation loops present after irradiation dissociate and more effective positron trapping sites are formed. (auth)

  16. Operation of the hot test loop facilities

    International Nuclear Information System (INIS)

    Cheong, Moon Ki; Park, Choon Kyeong; Won, Soon Yeon; Yang, Sun Kyu; Cheong, Jang Whan; Cheon, Se Young; Song, Chul Hwa; Jeon, Hyeong Kil; Chang, Suk Kyu; Jeong, Heung Jun; Cho, Young Ro; Kim, Bok Duk; Min, Kyeong Ho

    1994-12-01

    The objective of this project is to obtain the available experimental data and to develop the measuring techniques through taking full advantage of the facilities. The facilities operated by the thermal hydraulics department have been maintained and repaired in order to carry out the thermal hydraulics tests necessary for providing the available data. The performance tests for double grid type bottom end piece which was improved on the debris filtering effectivity were performed using the PWR-Hot Test Loop. The CANDU-Hot Test Loop was operated to carry out the pressure drop tests and strength tests of fuel. The Cold Test Loop was used to obtain the local velocity data in subchannel within fuel bundle and to understand the characteristic of pressure drop required for improving the nuclear fuel and to develop the advanced measuring techniques. RCS Loop, which is used to measure the CHF, is presently under design and construction. B and C Loop is designed and constructed to assess the automatic depressurization safety system behavior. 4 tabs., 79 figs., 7 refs. (Author) .new

  17. Design factors analyses of second-loop PRHRS

    Directory of Open Access Journals (Sweden)

    ZHANG Hongyan

    2017-05-01

    Full Text Available In order to study the operating characteristics of a second-loop Passive Residual Heat Removal System (PRHRS, the transient thermal analysis code RELAP5 is used to build simulation models of the main coolant system and second-loop PRHRS. Transient calculations and comparative analyses under station blackout accident and one-side feed water line break accident conditions are conducted for three critical design factors of the second-loop PRHRS:design capacity, emergency makeup tank and isolation valve opening speed. The impacts of the discussed design factors on the operating characteristics of the second-loop PRHRS are summarized based on calculations and analyses. The analysis results indicate that the system safety and cooling rate should be taken into consideration in designing PRHRS's capacity,and water injection from emergency makeup tank to steam generator can provide advantage to system cooling in the event of accident,and system startup performance can be improved by reducing the opening speed of isolation valve. The results can provide references for the design of the second-loop PRHRS in nuclear power plants.

  18. Long-term Performance of Permeable Reactive Barriers Using Zero-valent Iron: An Evaluation at Two Sites

    National Research Council Canada - National Science Library

    Wilkin, Richard T; Puls, Robert W; Sewell, Guy W

    2002-01-01

    Research described in this research brief explores the geochemical and microbiological processes occurring within zero-valent iron treatment zones in permeable reactive barriers that may contribute...

  19. Stability analysis for single-phase liquid metal rectangular natural circulation loops

    International Nuclear Information System (INIS)

    Lu, Daogang; Zhang, Xun; Guo, Chao

    2014-01-01

    Highlights: • The stability for asymmetric liquid metal natural circulation loops is analyzed. • The Na and NaK loops have higher critical Reynolds number than Pb and LBE loops. • Decreasing the ratio of height to width of loop can increase loop stability. • The length of heater would not affect the loop stability obviously. • Adding the length or heat transfer coefficient of cooler can increase loop stability. - Abstract: Natural circulation systems are preferred in some advanced nuclear power plants as they can simplify the designs and improve the inherent safety. The stability and steady-state characteristics of natural circulation are important for the applications of natural circulation loops (NCLs). A linear stability analysis method was used to study the stability behavior of liquid metal NCLs. The influences of the types of working fluids and loop geometry parameters on the stability of NCLs were evaluated. The liquid sodium (Na) loop and sodium–potassium alloy (NaK) loop would be more stable than lead bismuth eutectics (LBE) loop. The pressure drop could stabilize the loop behavior and also lead an increase of operating temperature for the loop. The NCL with a lower aspect ratio (ratio of vertical center distance between the heating and cooling section to the horizontal length of loop) is supposed to be more stable. It was found that the length of heating section would not have an obvious effect on the stability of NCL. However, the loop behavior could be stabilized by adding the length or heat transfer coefficient of the cooling section

  20. Structure-Reactivity Relationships in Multi-Component Transition Metal Oxide Catalysts FINAL Report

    Energy Technology Data Exchange (ETDEWEB)

    Altman, Eric I. [Yale Univ., New Haven, CT (United States)

    2015-10-06

    The focus of the project was on developing an atomic-level understanding of how transition metal oxide catalysts function. Over the course of several renewals the specific emphases shifted from understanding how local structure and oxidation state affect how molecules adsorb and react on the surfaces of binary oxide crystals to more complex systems where interactions between different transition metal oxide cations in an oxide catalyst can affect reactivity, and finally to the impact of cluster size on oxide stability and reactivity. Hallmarks of the work were the use of epitaxial growth methods to create surfaces relevant to catalysis yet tractable for fundamental surface science approaches, and the use of scanning tunneling microscopy to follow structural changes induced by reactions and to pinpoint adsorption sites. Key early findings included the identification of oxidation and reduction mechanisms on a tungsten oxide catalyst surface that determine the sites available for reaction, identification of C-O bond cleavage as the rate limiting step in alcohol dehydration reactions on the tungsten oxide surface, and demonstration that reduction does not change the favored reaction pathway but rather eases C-O bond cleavage and thus reduces the reaction barrier. Subsequently, a new reconstruction on the anatase phase of TiO2 relevant to catalysis was discovered and shown to create sites with distinct reactivity compared to other TiO2 surfaces. Building on this work on anatase, the mechanism by which TiO2 enhances the reactivity of vanadium oxide layers was characterized and it was found that the TiO2 substrate can force thin vanadia layers to adopt structures they would not ordinarily form in the bulk which in turn creates differences in reactivity between supported layers and bulk samples. From there, the work progressed to studying well-defined ternary oxides where synergistic effects between the two cations can induce