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Sample records for flexible catalytic loop

  1. Computational investigation of the pH dependence of loop flexibility and catalytic function in glycoside hydrolases.

    PubMed

    Bu, Lintao; Crowley, Michael F; Himmel, Michael E; Beckham, Gregg T

    2013-04-26

    Cellulase enzymes cleave glycosidic bonds in cellulose to produce cellobiose via either retaining or inverting hydrolysis mechanisms, which are significantly pH-dependent. Many fungal cellulases function optimally at pH ~5, and their activities decrease dramatically at higher or lower pH. To understand the molecular-level implications of pH in cellulase structure, we use a hybrid, solvent-based, constant pH molecular dynamics method combined with pH-based replica exchange to determine the pK(a) values of titratable residues of a glycoside hydrolase (GH) family 6 cellobiohydrolase (Cel6A) and a GH family 7 cellobiohydrolase (Cel7A) from the fungus Hypocrea jecorina. For both enzymes, we demonstrate that a bound substrate significantly affects the pKa values of the acid residues at the catalytic center. The calculated pK(a) values of catalytic residues confirm their proposed roles from structural studies and are consistent with the experimentally measured apparent pKa values. Additionally, GHs are known to impart a strained pucker conformation in carbohydrate substrates in active sites for catalysis, and results from free energy calculations combined with constant pH molecular dynamics suggest that the correct ring pucker is stable near the optimal pH for both Cel6A and Cel7A. Much longer molecular dynamics simulations of Cel6A and Cel7A with fixed protonation states based on the calculated pK(a) values suggest that pH affects the flexibility of tunnel loops, which likely affects processivity and substrate complexation. Taken together, this work demonstrates several molecular-level effects of pH on GH enzymes important for cellulose turnover in the biosphere and relevant to biomass conversion processes. PMID:23504310

  2. Conformational Flexibility of a Short Loop near the Active Site of the SARS-3CLpro is Essential to Maintain Catalytic Activity

    NASA Astrophysics Data System (ADS)

    Li, Chunmei; Teng, Xin; Qi, Yifei; Tang, Bo; Shi, Hailing; Ma, Xiaomin; Lai, Luhua

    2016-02-01

    The SARS 3C-like proteinase (SARS-3CLpro), which is the main proteinase of the SARS coronavirus, is essential to the virus life cycle. This enzyme has been shown to be active as a dimer in which only one protomer is active. However, it remains unknown how the dimer structure maintains an active monomer conformation. It has been observed that the Ser139-Leu141 loop forms a short 310-helix that disrupts the catalytic machinery in the inactive monomer structure. We have tried to disrupt this helical conformation by mutating L141 to T in the stable inactive monomer G11A/R298A/Q299A. The resulting tetra-mutant G11A/L141T/R298A/Q299A is indeed enzymatically active as a monomer. Molecular dynamics simulations revealed that the L141T mutation disrupts the 310-helix and helps to stabilize the active conformation. The coil-310-helix conformational transition of the Ser139-Leu141 loop serves as an enzyme activity switch. Our study therefore indicates that the dimer structure can stabilize the active conformation but is not a required structure in the evolution of the active enzyme, which can also arise through simple mutations.

  3. Deployable radiator with flexible line loop

    NASA Technical Reports Server (NTRS)

    Keeler, Bryan V. (Inventor); Lehtinen, Arthur Mathias (Inventor); McGee, Billy W. (Inventor)

    2003-01-01

    Radiator assembly (10) for use on a spacecraft (12) is provided including at least one radiator panel assembly (26) repeatably movable between a panel stowed position (28) and a panel deployed position (36), at least two flexible lines (40) in fluid communication with the at least one radiator panel assembly (26) and repeatably movable between a stowage loop (42) and a flattened deployed loop (44).

  4. Catalytic Combustor for Fuel-Flexible Turbine

    SciTech Connect

    W. R. Laster; E. Anoshkina

    2008-01-31

    Under the sponsorship of the U. S. Department of Energy's National Energy Technology Laboratory, Siemens Westinghouse has conducted a three-year program to develop an ultra low NOx, fuel flexible catalytic combustor for gas turbine application in IGCC. The program is defined in three phases: Phase 1 - Implementation Plan, Phase 2 - Validation Testing and Phase 3 - Field Testing. Both Phase 1 and Phase 2 of the program have been completed. In IGCC power plants, the gas turbine must be capable of operating on syngas as a primary fuel and an available back-up fuel such as natural gas. In this program the Rich Catalytic Lean (RCLTM) technology is being developed as an ultra low NOx combustor. In this concept, ultra low NOx is achieved by stabilizing a lean premix combustion process by using a catalytic reactor to oxidize a portion of the fuel, increasing the temperature of fuel/air mixture prior to the main combustion zone. In Phase 1, the feasibility of the catalytic concept for syngas application has been evaluated and the key technology issues identified. In Phase II the technology necessary for the application of the catalytic concept to IGCC fuels was developed through detailed design and subscale testing. Phase III (currently not funded) will consist of full-scale combustor basket testing on natural gas and syngas.

  5. Catalytic Combustor for Fuel-Flexible Turbine

    SciTech Connect

    Laster, W. R.; Anoshkina, E.

    2008-01-31

    Under the sponsorship of the U. S. Department of Energy’s National Energy Technology Laboratory, Siemens Westinghouse has conducted a three-year program to develop an ultra low NOx, fuel flexible catalytic combustor for gas turbine application in IGCC. The program is defined in three phases: Phase 1- Implementation Plan, Phase 2- Validation Testing and Phase 3 – Field Testing. Both Phase 1 and Phase 2 of the program have been completed. In IGCC power plants, the gas turbine must be capable of operating on syngas as a primary fuel and an available back-up fuel such as natural gas. In this program the Rich Catalytic Lean (RCLTM) technology is being developed as an ultra low NOx combustor. In this concept, ultra low NOx is achieved by stabilizing a lean premix combustion process by using a catalytic reactor to oxidize a portion of the fuel, increasing the temperature of fuel/air mixture prior to the main combustion zone. In Phase 1, the feasibility of the catalytic concept for syngas application has been evaluated and the key technology issues identified. In Phase II the technology necessary for the application of the catalytic concept to IGCC fuels was developed through detailed design and subscale testing. Phase III (currently not funded) will consist of full-scale combustor basket testing on natural gas and syngas.

  6. Catalytic Combustor for Fuel-Flexible Turbine

    SciTech Connect

    W. R. Laster; E. Anoshkina; P. Szedlacsek

    2006-03-31

    Under the sponsorship of the U.S. Department of Energy's National Energy Technology Laboratory, Siemens Westinghouse is conducting a three-year program to develop an ultra low NOx, fuel flexible catalytic combustor for gas turbine application in IGCC. The program is defined in three phases: Phase 1-Implementation Plan, Phase 2-Validation Testing and Phase 3-Field Testing. The Phase 1 program has been completed. Phase II was initiated in October 2004. In IGCC power plants, the gas turbine must be capable of operating on syngas as a primary fuel and an available back-up fuel such as natural gas. In this program the Rich Catalytic Lean (RCL{trademark}) technology is being developed as an ultra low NOx combustor. In this concept, ultra low NOx is achieved by stabilizing a lean premix combustion process by using a catalytic reactor to react part of the fuel, increasing the fuel/air mixture temperature. In Phase 1, the feasibility of the catalytic concept for syngas application has been evaluated and the key technology issues identified. In Phase II the catalytic concept will be demonstrated through subscale testing. Phase III will consist of full-scale combustor basket testing on natural gas and syngas.

  7. New Insights into the Role of T3 Loop in Determining Catalytic Efficiency of GH28 Endo-Polygalacturonases

    PubMed Central

    Tu, Tao; Meng, Kun; Luo, Huiying; Turunen, Ossi; Zhang, Lujia; Cheng, Yanli; Su, Xiaoyun; Ma, Rui; Shi, Pengjun; Wang, Yaru; Yang, Peilong; Yao, Bin

    2015-01-01

    Intramolecular mobility and conformational changes of flexible loops have important roles in the structural and functional integrity of proteins. The Achaetomium sp. Xz8 endo-polygalacturonase (PG8fn) of glycoside hydrolase (GH) family 28 is distinguished for its high catalytic activity (28,000 U/mg). Structure modeling indicated that PG8fn has a flexible T3 loop that folds partly above the substrate in the active site, and forms a hydrogen bond to the substrate by a highly conserved residue Asn94 in the active site cleft. Our research investigates the catalytic roles of Asn94 in T3 loop which is located above the catalytic residues on one side of the substrate. Molecular dynamics simulation performed on the mutant N94A revealed the loss of the hydrogen bond formed by the hydroxyl group at O34 of pentagalacturonic acid and the crucial ND2 of Asn94 and the consequent detachment and rotation of the substrate away from the active site, and that on N94Q caused the substrate to drift away from its place due to the longer side chain. In line with the simulations, site-directed mutagenesis at this site showed that this position is very sensitive to amino acid substitutions. Except for the altered Km values from 0.32 (wild type PG8fn) to 0.75–4.74 mg/ml, all mutants displayed remarkably lowered kcat (~3–20,000 fold) and kcat/Km (~8–187,500 fold) values and significantly increased △(△G) values (5.92–33.47 kJ/mol). Taken together, Asn94 in the GH28 T3 loop has a critical role in positioning the substrate in a correct way close to the catalytic residues. PMID:26327390

  8. Computational evaluation of the dynamic fluctuations of peripheral loops enclosing the catalytic tunnel of a family 7 cellobiohydrolase.

    PubMed

    Granum, David M; Schutt, Timothy C; Maupin, C Mark

    2014-05-22

    The size and character of the peripheral loops enclosing the active site for cellulase enzymes is believed to play a major role in dictating many critical enzymatic properties. For many cellulases it is observed that fully enclosed active sites forming a tunnel are more conducive to cellobiohydrolase activity and the ability to processively move along the substrate. Conversely, a more open active site groove is indicative of endoglucanase activity. For both cellobiohydrolases and endoglucanases, the loop regions have been implicated in the ability of the enzyme to bind substrate, influence the pKa of active site residues, modulate the catalytic activity, and influence thermal stability. Reported here are constant pH molecular dynamics (CpHMD) simulations that investigate the role of dynamic fluctuations, substrate interactions, and residue pKa values for the peripheral loops enclosing the active site of the cellobiohydrolase Melanocarpus albomyces Cel7B. Two highly flexible loop regions in the free enzyme have been identified, which impact the overall dynamical motions of the enzyme. Charge interactions between Asp198 and Asp367, which reside on two adjacent loops, were found to influence the overall loop conformations and dynamics. In the presence of a substrate the protonation of Asp367, Asp198, and Tyr370 were found to stabilize substrate binding and control the movement of two peripheral loops onto the active site containing the substrate (i.e., clamping down). The substrate-induced response of the loop regions secures the cellulose polymer in the catalytic tunnel and creates an environment that is conducive to hydrolysis of the glycosidic bond. PMID:24669967

  9. The active site loop of S-adenosylmethionine synthetase modulates catalytic efficiency.

    PubMed

    Taylor, John C; Takusagawa, Fusao; Markham, George D

    2002-07-30

    Crystallographic studies of Escherichia coli S-adenosylmethionine synthetase (ATP:L-methionine S-adenosyltransferase, MAT) have defined a flexible polypeptide loop that can gate access to the active site without contacting the substrates. The influence of the length and sequence of this active site loop on catalytic efficiency has been characterized in a mutant in which the E. coli MAT sequence (DRADPLEQ) has been replaced with the distinct sequence of the corresponding region of the otherwise highly homologous rat liver enzyme (HDLRNEEDV). Four additional mutants in which the entire DRADPLEQ sequence was replaced by five, six, seven, or eight glycines have been studied to unveil the effects of loop length and the influence of side chains. In all of the mutants, the maximal rate of S-adenosylmethionine formation (k(cat)) is diminished by more than 200-fold whereas the rate of hydrolysis of the tripolyphosphate intermediate is decreased by less than 3-fold. Thus, the function of the loop is localized to the first step in the overall reaction. The K(m) for methionine increases in all of the oligoglycine mutants, whereas the K(m) values for ATP are not substantially different. The k(cat) for the wild-type enzyme is decreased by increases in solution microviscosity with 55% of the maximal dependence. Thus, a diffusional event is coupled to the chemical step of AdoMet formation, which is known to be rate-limiting. The results indicate that a conformational change, possibly loop closure, is associated with AdoMet synthesis. The data integrate a previously discovered conformational change associated with PPP(i) binding to the E x AdoMet complex into the reaction sequence, reflecting a difference in protein conformation in the E x AdoMet x PPP(i) complex whether it is formed from the E x ATP x methionine complex or from binding of exogenous PPP(i). The temperature dependence of the k(cat) for S-adenosylmethionine formation shows that the removal of the side chains in the

  10. Fuel Flexible, Low Emission Catalytic Combustor for Opportunity Fuel Applications

    SciTech Connect

    Eteman, Shahrokh

    2013-06-30

    Limited fuel resources, increasing energy demand and stringent emission regulations are drivers to evaluate process off-gases or process waste streams as fuels for power generation. Often these process waste streams have low energy content and/or highly reactive components. Operability of low energy content fuels in gas turbines leads to issues such as unstable and incomplete combustion. On the other hand, fuels containing higher-order hydrocarbons lead to flashback and auto-ignition issues. Due to above reasons, these fuels cannot be used directly without modifications or efficiency penalties in gas turbine engines. To enable the use of these wide variety of fuels in gas turbine engines a rich catalytic lean burn (RCL®) combustion system was developed and tested in a subscale high pressure (10 atm.) rig. The RCL® injector provided stability and extended turndown to low Btu fuels due to catalytic pre-reaction. Previous work has shown promise with fuels such as blast furnace gas (BFG) with LHV of 85 Btu/ft3 successfully combusted. This program extends on this work by further modifying the combustor to achieve greater catalytic stability enhancement. Fuels containing low energy content such as weak natural gas with a Lower Heating Value (LHV) of 6.5 MJ/m3 (180 Btu/ft3 to natural gas fuels containing higher hydrocarbon (e.g ethane) with LHV of 37.6 MJ/m3 (1010 Btu/ft3) were demonstrated with improved combustion stability; an extended turndown (defined as the difference between catalytic and non-catalytic lean blow out) of greater than 250oF was achieved with CO and NOx emissions lower than 5 ppm corrected to 15% O2. In addition, for highly reactive fuels the catalytic region preferentially pre-reacted the higher order hydrocarbons with no events of flashback or auto-ignition allowing a stable and safe operation with low NOx and CO emissions.

  11. Catalytic roles of flexible regions at the active site of ribulose-bisphosphate carboxylase/oxygenase (Rubisco)

    SciTech Connect

    Hartman, F.C.; Harpel, M.R.; Chen, Yuh-Ru; Larson, E.M.; Larimer, F.W.

    1995-12-31

    Chemical and mutagenesis studies of Rubisco have identified Lys329 and Glu48 as active-site residues that are located in distinct, interacting domains from adjacent subunits. Crystallographic analyses have shown that Lys329 is the apical residue in a 12-residue flexible loop (loop 6) of the {Beta},{alpha}-barrel domain of the active site and that Glu48 resides at the end of helix B of the N-terminal domain of the active site. When phosphorylated ligands are bound by the enzyme, loop 6 adopts a closed conformation and, in concert with repositioning of helix B, thereby occludes the active site from the external environment. In this closed conformation, the {gamma}-carboxylate of Glu48 and the {epsilon}-amino group of Lys329 engage in intersubunit electrostatic interaction. By use of appropriate site-directed mutants of Rhodospirillum rubrum Rubisco, we are addressing several issues: the catalytic roles of Lys329 and Glu48, the functional significance of the intersubunit salt bridge comprised of these two residues, and the roles of loop 6 and helix B in stabilizing labile reaction intermediates. Characterization of novel products derived from misprocessing of D-ribulose-1,5-bisphosphate (RuBP) by the mutant proteins have illuminated the structure of the key intermediate in the normal oxygenase pathway.

  12. Fuel-Flexible, Low-Emissions Catalytic Combustor for Opportunity Fuels

    SciTech Connect

    2009-11-01

    Precision Combustion, Inc. will develop a unique, fuel-flexible Rich Catalytic Lean-Burn (RCL®) injector with catalytic combustor capable of enabling ultralow-emission, lean premixed combustion of a wide range of gaseous opportunity fuels. This will broaden the range of opportunity fuels that can be utilized to include low- and ultralow-Btu gases, such as digester and blast furnace gases, and fuels containing reactive species, such as refinery, wellhead, and industrial byproduct gases.

  13. Flexible macrocycles as versatile supports for catalytically active metal clusters.

    PubMed

    Ryan, Jason D; Gagnon, Kevin J; Teat, Simon J; McIntosh, Ruaraidh D

    2016-07-12

    Here we present three structurally diverse clusters stabilised by the same macrocyclic polyphenol; t-butylcalix[8]arene. This work demonstrates the range of conformations the flexible ligand is capable of adopting, highlighting its versatility in metal coordination. In addition, a Ti complex displays activity for the ring-opening polymerisation of lactide. PMID:26892948

  14. Exploring the energy landscapes of flexible molecular loops using higher-dimensional continuation.

    PubMed

    Porta, Josep M; Jaillet, Léonard

    2013-01-30

    The conformational space of a flexible molecular loop includes the set of conformations fulfilling the geometric loop-closure constraints and its energy landscape can be seen as a scalar field defined on this implicit set. Higher-dimensional continuation tools, recently developed in dynamical systems and also applied to robotics, provide efficient algorithms to trace out implicitly defined sets. This article describes these tools and applies them to obtain full descriptions of the energy landscapes of short molecular loops that, otherwise, can only be partially explored, mainly via sampling. Moreover, to deal with larger loops, this article exploits the higher-dimensional continuation tools to find local minima and minimum energy transition paths between them, without deviating from the loop-closure constraints. The proposed techniques are applied to previously studied molecules revealing the intricate structure of their energy landscapes. PMID:23015474

  15. HIPK2 catalytic activity and subcellular localization are regulated by activation-loop Y354 autophosphorylation.

    PubMed

    Siepi, Francesca; Gatti, Veronica; Camerini, Serena; Crescenzi, Marco; Soddu, Silvia

    2013-06-01

    HIPK2 (homeodomain-interacting protein kinase-2) binds to and phosphorylates, at Ser and Thr residues, a large number of targets involved in cell division and cell fate decision in response to different physiological or stress stimuli. Inactivation of HIPK2 has been observed in human and mouse cancers supporting its role as a tumor suppressor. Despite the biological relevance of this kinase, very little is known on how HIPK2 becomes catalytically active. Based on sequence homologies, HIPK2 has been taxonomically classified as a subfamily member of the dual-specificity tyrosine-regulated kinases (DYRKs) and the activation-loop Y354 of HIPK2 has been found phosphorylated in different cells; however, the relevance of this Y phosphorylation is presently unknown. Here, we show that HIPK2, which is extensively phosphorylated at S/T sites throughout its functional domains, becomes catalytically active by autophosphorylation at the activation-loop Y354. In particular, we found that, in analogy to DYRKs, HIPK2-Y354 phosphorylation is an autocatalytic event and its prevention, through Y354 substitution with non-phosphorylatable amino acids or by using the kinase inhibitor purvalanol A, induces a strong reduction of the HIPK2 S/T-kinase activity on different substrates. Interestingly, at variance from DYRKs, inhibition of HIPK2-Y354 phosphorylation induces a strong out-of-target Y-kinase activity in cis and a strong cytoplasmic relocalization of the kinase. Together, these results demonstrate that the catalytic activity, substrate specificity, and subcellular localization of HIPK2 are regulated by autophosphorylation of its activation-loop Y354. PMID:23485397

  16. HIPK2 catalytic activity and subcellular localization are regulated by activation-loop Y354 autophosphorylation

    PubMed Central

    Siepi, Francesca; Gatti, Veronica; Camerini, Serena; Crescenzi, Marco; Soddu, Silvia

    2013-01-01

    HIPK2 (homeodomain-interacting protein kinase-2) binds to and phosphorylates, at Ser and Thr residues, a large number of targets involved in cell division and cell fate decision in response to different physiological or stress stimuli. Inactivation of HIPK2 has been observed in human and mouse cancers supporting its role as a tumor suppressor. Despite the biological relevance of this kinase, very little is known on how HIPK2 becomes catalytically active. Based on sequence homologies, HIPK2 has been taxonomically classified as a subfamily member of the dual-specificity tyrosine-regulated kinases (DYRKs) and the activation-loop Y354 of HIPK2 has been found phosphorylated in different cells; however, the relevance of this Y phosphorylation is presently unknown. Here, we show that HIPK2, which is extensively phosphorylated at S/T sites throughout its functional domains, becomes catalytically active by autophosphorylation at the activation-loop Y354. In particular, we found that, in analogy to DYRKs, HIPK2-Y354 phosphorylation is an autocatalytic event and its prevention, through Y354 substitution with non-phosphorylatable amino acids or by using the kinase inhibitor purvalanol A, induces a strong reduction of the HIPK2 S/T-kinase activity on different substrates. Interestingly, at variance from DYRKs, inhibition of HIPK2-Y354 phosphorylation induces a strong out-of-target Y-kinase activity in cis and a strong cytoplasmic relocalization of the kinase. Together, these results demonstrate that the catalytic activity, substrate specificity, and subcellular localization of HIPK2 are regulated by autophosphorylation of its activation-loop Y354. PMID:23485397

  17. Differential utilization of binding loop flexibility in T cell receptor ligand selection and cross-reactivity.

    PubMed

    Ayres, Cory M; Scott, Daniel R; Corcelli, Steven A; Baker, Brian M

    2016-01-01

    Complementarity determining region (CDR) loop flexibility has been suggested to play an important role in the selection and binding of ligands by T cell receptors (TCRs) of the cellular immune system. However, questions remain regarding the role of loop motion in TCR binding, and crystallographic structures have raised questions about the extent to which generalizations can be made. Here we studied the flexibility of two structurally well characterized αβ TCRs, A6 and DMF5. We found that the two receptors utilize loop motion very differently in ligand binding and cross-reactivity. While the loops of A6 move rapidly in an uncorrelated fashion, those of DMF5 are substantially less mobile. Accordingly, the mechanisms of binding and cross-reactivity are very different between the two TCRs: whereas A6 relies on conformational selection to select and bind different ligands, DMF5 uses a more rigid, permissive architecture with greater reliance on slower motions or induced-fit. In addition to binding site flexibility, we also explored whether ligand-binding resulted in common dynamical changes in A6 and DMF5 that could contribute to TCR triggering. Although binding-linked motional changes propagated throughout both receptors, no common features were observed, suggesting that changes in nanosecond-level TCR structural dynamics do not contribute to T cell signaling. PMID:27118724

  18. Differential utilization of binding loop flexibility in T cell receptor ligand selection and cross-reactivity

    PubMed Central

    Ayres, Cory M.; Scott, Daniel R.; Corcelli, Steven A.; Baker, Brian M.

    2016-01-01

    Complementarity determining region (CDR) loop flexibility has been suggested to play an important role in the selection and binding of ligands by T cell receptors (TCRs) of the cellular immune system. However, questions remain regarding the role of loop motion in TCR binding, and crystallographic structures have raised questions about the extent to which generalizations can be made. Here we studied the flexibility of two structurally well characterized αβ TCRs, A6 and DMF5. We found that the two receptors utilize loop motion very differently in ligand binding and cross-reactivity. While the loops of A6 move rapidly in an uncorrelated fashion, those of DMF5 are substantially less mobile. Accordingly, the mechanisms of binding and cross-reactivity are very different between the two TCRs: whereas A6 relies on conformational selection to select and bind different ligands, DMF5 uses a more rigid, permissive architecture with greater reliance on slower motions or induced-fit. In addition to binding site flexibility, we also explored whether ligand-binding resulted in common dynamical changes in A6 and DMF5 that could contribute to TCR triggering. Although binding-linked motional changes propagated throughout both receptors, no common features were observed, suggesting that changes in nanosecond-level TCR structural dynamics do not contribute to T cell signaling. PMID:27118724

  19. Distributed flow sensing for closed-loop speed control of a flexible fish robot.

    PubMed

    Zhang, Feitian; Lagor, Francis D; Yeo, Derrick; Washington, Patrick; Paley, Derek A

    2015-12-01

    Flexibility plays an important role in fish behavior by enabling high maneuverability for predator avoidance and swimming in turbulent flow. This paper presents a novel flexible fish robot equipped with distributed pressure sensors for flow sensing. The body of the robot is molded from soft, hyperelastic material, which provides flexibility. Its Joukowski-foil shape is conducive to modeling the fluid analytically. A quasi-steady potential-flow model is adopted for real-time flow estimation, whereas a discrete-time vortex-shedding flow model is used for higher-fidelity simulation. The dynamics for the flexible fish robot yield a reduced model for one-dimensional swimming. A recursive Bayesian filter assimilates pressure measurements to estimate flow speed, angle of attack, and foil camber. The closed-loop speed-control strategy combines an inverse-mapping feedforward controller based on an average model derived for periodic actuation of angle-of-attack and a proportional-integral feedback controller utilizing the estimated flow information. Simulation and experimental results are presented to show the effectiveness of the estimation and control strategy. The paper provides a systematic approach to distributed flow sensing for closed-loop speed control of a flexible fish robot by regulating the flapping amplitude. PMID:26495855

  20. Glutamate Racemase Dimerization Inhibits Dynamic Conformational Flexibility and Reduces Catalytic Rates

    SciTech Connect

    Mehboob, Shahila; Guo, Liang; Fu, Wentao; Mittal, Anuradha; Yau, Tiffany; Truong, Kent; Johlfs, Mary; Long, Fei; Fung, Leslie W.-M.; Johnson, Michael E.

    2009-09-15

    Glutamate racemase (RacE) is a bacterial enzyme that converts L-glutamate to D-glutamate, an essential precursor for peptidoglycan synthesis. In prior work, we have shown that both isoforms cocrystallize with D-glutamate as dimers, and the enzyme is in a closed conformation with limited access to the active site [May, M., et al. (2007) J. Mol. Biol. 371, 1219-1237]. The active site of RacE2 is especially restricted. We utilize several computational and experimental approaches to understand the overall conformational dynamics involved during catalysis when the ligand enters and the product exits the active site. Our steered molecular dynamics simulations and normal-mode analysis results indicate that the monomeric form of the enzyme is more flexible than the native dimeric form. These results suggest that the monomeric enzyme might be more active than the dimeric form. We thus generated site-specific mutations that disrupt dimerization and find that the mutants exhibit significantly higher catalytic rates in the D-Glu to L-Glu reaction direction than the native enzyme. Low-resolution models restored from solution X-ray scattering studies correlate well with the first six normal modes of the dimeric form of the enzyme, obtained from NMA. Thus, along with the local active site residues, global domain motions appear to be implicated in the catalytically relevant structural dynamics of this enzyme and suggest that increased flexibility may accelerate catalysis. This is a novel observation that residues distant from the catalytic site restrain catalytic activity through formation of the dimer structure.

  1. Understanding the function of conserved variations in the catalytic loops of fungal glycoside hydrolase family 12.

    PubMed

    Damásio, André R L; Rubio, Marcelo V; Oliveira, Leandro C; Segato, Fernando; Dias, Bruno A; Citadini, Ana P; Paixão, Douglas A; Squina, Fabio M

    2014-08-01

    Enzymes that cleave the xyloglucan backbone at unbranched glucose residues have been identified in GH families 5, 7, 12, 16, 44, and 74. Fungi produce enzymes that populate 20 of 22 families that are considered critical for plant biomass deconstruction. We searched for GH12-encoding genes in 27 Eurotiomycetes genomes. After analyzing 50 GH12-related sequences, the conserved variations of the amino acid sequences were examined. Compared to the endoglucanases, the endo-xyloglucanase-associated YSG deletion at the negative subsites of the catalytic cleft with a SST insertion at the reducing end of the substrate-binding crevice is highly conserved. In addition, a highly conserved alanine residue was identified in all xyloglucan-specific enzymes, and this residue is substituted by arginine in more promiscuous glucanases. To understand the basis for the xyloglucan specificity displayed by certain GH12 enzymes, two fungal GH12 endoglucanases were chosen for mutagenesis and functional studies: an endo-xyloglucanase from Aspergillus clavatus (AclaXegA) and an endoglucanase from A. terreus (AtEglD). Comprehensive molecular docking studies and biochemical analyses were performed, revealing that mutations at the entrance of the catalytic cleft in AtEglD result in a wider binding cleft and the alteration of the substrate-cleavage pattern, implying that a trio of residues coordinates the interactions and binding to linear glycans. The loop insertion at the crevice-reducing end of AclaXegA is critical for catalytic efficiency to hydrolyze xyloglucan. The understanding of the structural elements governing endo-xyloglucanase activity on linear and branched glucans will facilitate future enzyme modifications with potential applications in industrial biotechnology. PMID:24578305

  2. Heterodimer Autorepression Loop: A Robust and Flexible Pulse-Generating Genetic Module

    NASA Astrophysics Data System (ADS)

    Lannoo, B.; Carlon, E.; Lefranc, M.

    2016-07-01

    We investigate the dynamics of the heterodimer autorepression loop (HAL), a small genetic module in which a protein A acts as an autorepressor and binds to a second protein B to form an A B dimer. For suitable values of the rate constants, the HAL produces pulses of A alternating with pulses of B . By means of analytical and numerical calculations, we show that the duration of A pulses is extremely robust against variation of the rate constants while the duration of the B pulses can be flexibly adjusted. The HAL is thus a minimal genetic module generating robust pulses with a tunable duration, an interesting property for cellular signaling.

  3. Crystal Structures of Trypanosoma cruzi UDP-Galactopyranose Mutase Implicate Flexibility of the Histidine Loop in Enzyme Activation

    SciTech Connect

    Dhatwalia, Richa; Singh, Harkewal; Oppenheimer, Michelle; Sobrado, Pablo; Tanner, John J.

    2012-11-01

    Chagas disease is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi. Here we report crystal structures of the galactofuranose biosynthetic enzyme UDP-galactopyranose mutase (UGM) from T. cruzi, which are the first structures of this enzyme from a protozoan parasite. UGM is an attractive target for drug design because galactofuranose is absent in humans but is an essential component of key glycoproteins and glycolipids in trypanosomatids. Analysis of the enzyme-UDP noncovalent interactions and sequence alignments suggests that substrate recognition is exquisitely conserved among eukaryotic UGMs and distinct from that of bacterial UGMs. This observation has implications for inhibitor design. Activation of the enzyme via reduction of the FAD induces profound conformational changes, including a 2.3 {angstrom} movement of the histidine loop (Gly60-Gly61-His62), rotation and protonation of the imidazole of His62, and cooperative movement of residues located on the si face of the FAD. Interestingly, these changes are substantially different from those described for Aspergillus fumigatus UGM, which is 45% identical to T. cruzi UGM. The importance of Gly61 and His62 for enzymatic activity was studied with the site-directed mutant enzymes G61A, G61P, and H62A. These mutations lower the catalytic efficiency by factors of 10-50, primarily by decreasing k{sub cat}. Considered together, the structural, kinetic, and sequence data suggest that the middle Gly of the histidine loop imparts flexibility that is essential for activation of eukaryotic UGMs. Our results provide new information about UGM biochemistry and suggest a unified strategy for designing inhibitors of UGMs from the eukaryotic pathogens.

  4. On the dynamics and control of flexible multibody systems with closed loops

    SciTech Connect

    Damaren, C.J.

    2000-03-01

    The motion control problem for cooperating flexible robot arms manipulating a large rigid payload is considered. An output that depends on the payload position and contributions form the joint motion of each arm is constructed whose rate yields the passivity property with respect to a special input. The input is a combination of the torques from each arm and contains a free load-sharing parameter. The passivity property is shown to depend on the payload mass properties, and in cases where the payload is large, a passivity-based controller combining feedforward and feedback as elements is devised, which yields tracking. An experimental facility consisting of two planar 3-DoF arms is used to implement the strategies. Good tracking is observed and compared with simulation predictions for closed-loop flexible multibody systems.

  5. Experimental Study of Flexible Plate Vibration Control by Using Two-Loop Sliding Mode Control Strategy

    NASA Astrophysics Data System (ADS)

    Yang, Jingyu; Lin, Jiahui; Liu, Yuejun; Yang, Kang; Zhou, Lanwei; Chen, Guoping

    2016-06-01

    It is well known that intelligent control theory has been used in many research fields, novel modeling method (DROMM) is used for flexible rectangular active vibration control, and then the validity of new model is confirmed by comparing finite element model with new model. In this paper, taking advantage of the dynamics of flexible rectangular plate, a two-loop sliding mode (TSM) MIMO approach is introduced for designing multiple-input multiple-output continuous vibration control system, which can overcome uncertainties, disturbances or unstable dynamics. An illustrative example is given in order to show the feasibility of the method. Numerical simulations and experiment confirm the effectiveness of the proposed TSM MIMO controller.

  6. Trains, tails and loops of partially adsorbed semi-flexible filaments.

    PubMed

    Welch, David; Lettinga, M P; Ripoll, Marisol; Dogic, Zvonimir; Vliegenthart, Gerard A

    2015-10-14

    Polymer adsorption is a fundamental problem in statistical mechanics that has direct relevance to diverse disciplines ranging from biological lubrication to stability of colloidal suspensions. We combine experiments with computer simulations to investigate depletion induced adsorption of semi-flexible polymers onto a hard-wall. Three dimensional filament configurations of partially adsorbed F-actin polymers are visualized with total internal reflection fluorescence microscopy. This information is used to determine the location of the adsorption/desorption transition and extract the statistics of trains, tails and loops of partially adsorbed filament configurations. In contrast to long flexible filaments which primarily desorb by the formation of loops, the desorption of stiff, finite-sized filaments is largely driven by fluctuating filament tails. Simulations quantitatively reproduce our experimental data and allow us to extract universal laws that explain scaling of the adsorption-desorption transition with relevant microscopic parameters. Our results demonstrate how the adhesion strength, filament stiffness, length, as well as the configurational space accessible to the desorbed filament can be used to design the characteristics of filament adsorption and thus engineer properties of composite biopolymeric materials. PMID:26279011

  7. Mutations in the Catalytic Loop HRD Motif Alter the Activity and Function of Drosophila Src64

    PubMed Central

    Strong, Taylor C.; Kaur, Gurvinder; Thomas, Jeffrey H.

    2011-01-01

    The catalytic loop HRD motif is found in most protein kinases and these amino acids are predicted to perform functions in catalysis, transition to, and stabilization of the active conformation of the kinase domain. We have identified mutations in a Drosophila src gene, src64, that alter the three HRD amino acids. We have analyzed the mutants for both biochemical activity and biological function during development. Mutation of the aspartate to asparagine eliminates biological function in cytoskeletal processes and severely reduces fertility, supporting the amino acid's critical role in enzymatic activity. The arginine to cysteine mutation has little to no effect on kinase activity or cytoskeletal reorganization, suggesting that the HRD arginine may not be critical for coordinating phosphotyrosine in the active conformation. The histidine to leucine mutant retains some kinase activity and biological function, suggesting that this amino acid may have a biochemical function in the active kinase that is independent of its side chain hydrogen bonding interactions in the active site. We also describe the phenotypic effects of other mutations in the SH2 and tyrosine kinase domains of src64, and we compare them to the phenotypic effects of the src64 null allele. PMID:22132220

  8. Flexibility in Surface-Exposed Loops in a Virus Capsid Mediates Escape from Antibody Neutralization

    PubMed Central

    Kolawole, Abimbola O.; Li, Ming; Xia, Chunsheng; Fischer, Audrey E.; Giacobbi, Nicholas S.; Rippinger, Christine M.; Proescher, Jody B. G.; Wu, Susan K.; Bessling, Seneca L.; Gamez, Monica; Yu, Chenchen; Zhang, Rebecca; Mehoke, Thomas S.; Pipas, James M.; Wolfe, Joshua T.; Lin, Jeffrey S.; Feldman, Andrew B.

    2014-01-01

    ABSTRACT New human norovirus strains emerge every 2 to 3 years, partly due to mutations in the viral capsid that allow escape from antibody neutralization and herd immunity. To understand how noroviruses evolve antibody resistance, we investigated the structural basis for the escape of murine norovirus (MNV) from antibody neutralization. To identify specific residues in the MNV-1 protruding (P) domain of the capsid that play a role in escape from the neutralizing monoclonal antibody (MAb) A6.2, 22 recombinant MNVs were generated with amino acid substitutions in the A′B′ and E′F′ loops. Six mutations in the E′F′ loop (V378F, A382K, A382P, A382R, D385G, and L386F) mediated escape from MAb A6.2 neutralization. To elucidate underlying structural mechanisms for these results, the atomic structure of the A6.2 Fab was determined and fitted into the previously generated pseudoatomic model of the A6.2 Fab/MNV-1 virion complex. Previously, two distinct conformations, A and B, of the atomic structures of the MNV-1 P domain were identified due to flexibility in the two P domain loops. A superior stereochemical fit of the A6.2 Fab to the A conformation of the MNV P domain was observed. Structural analysis of our observed escape mutants indicates changes toward the less-preferred B conformation of the P domain. The shift in the structural equilibrium of the P domain toward the conformation with poor structural complementarity to the antibody strongly supports a unique mechanism for antibody escape that occurs via antigen flexibility instead of direct antibody-antigen binding. IMPORTANCE Human noroviruses cause the majority of all nonbacterial gastroenteritis worldwide. New epidemic strains arise in part by mutations in the viral capsid leading to escape from antibody neutralization. Herein, we identify a series of point mutations in a norovirus capsid that mediate escape from antibody neutralization and determine the structure of a neutralizing antibody. Fitting of

  9. The Catalytic Activity of Protein-Disulfide Isomerase Requires a Conformationally Flexible Molecule

    SciTech Connect

    Tian, G.; Kober, F; Lewandrowski, U; Sickmann, A; Lennarz, W; Schindelin, H

    2008-01-01

    Protein-disulfide isomerase (PDI) catalyzes the formation of the correct pattern of disulfide bonds in secretory proteins. A low resolution crystal structure of yeast PDI described here reveals large scale conformational changes compared with the initially reported structure, indicating that PDI is a highly flexible molecule with its catalytic domains, a and a?, representing two mobile arms connected to a more rigid core composed of the b and b? domains. Limited proteolysis revealed that the linker between the a domain and the core is more susceptible to degradation than that connecting the a? domain to the core. By restricting the two arms with inter-domain disulfide bonds, the molecular flexibility of PDI, especially that of its a domain, was demonstrated to be essential for the enzymatic activity in vitro and in vivo. The crystal structure also featured a PDI dimer, and a propensity to dimerize in solution and in the ER was confirmed by cross-linking experiments and the split green fluorescent protein system. Although sedimentation studies suggested that the self-association of PDI is weak, we hypothesize that PDI exists as an interconvertible mixture of monomers and dimers in the endoplasmic reticulum due to its high abundance in this compartment.

  10. Identifying Functional Requirements for Flexible Airspace Management Concept Using Human-In-The-Loop Simulations

    NASA Technical Reports Server (NTRS)

    Lee, Paul U.; Bender, Kim; Pagan, Danielle

    2011-01-01

    Flexible Airspace Management (FAM) is a mid- term Next Generation Air Transportation System (NextGen) concept that allows dynamic changes to airspace configurations to meet the changes in the traffic demand. A series of human-in-the-loop (HITL) studies have identified procedures and decision support requirements needed to implement FAM. This paper outlines a suggested FAM procedure and associated decision support functionality based on these HITL studies. A description of both the tools used to support the HITLs and the planned NextGen technologies available in the mid-term are presented and compared. The mid-term implementation of several NextGen capabilities, specifically, upgrades to the Traffic Management Unit (TMU), the initial release of an en route automation system, the deployment of a digital data communication system, a more flexible voice communications network, and the introduction of a tool envisioned to manage and coordinate networked ground systems can support the implementation of the FAM concept. Because of the variability in the overall deployment schedule of the mid-term NextGen capabilities, the dependency of the individual NextGen capabilities are examined to determine their impact on a mid-term implementation of FAM. A cursory review of the different technologies suggests that new functionality slated for the new en route automation system is a critical enabling technology for FAM, as well as the functionality to manage and coordinate networked ground systems. Upgrades to the TMU are less critical but important nonetheless for FAM to be fully realized. Flexible voice communications network and digital data communication system could allow more flexible FAM operations but they are not as essential.

  11. Disparate Degrees of Hypervariable Loop Flexibility Control T-Cell Receptor Cross-Reactivity, Specificity, and Binding Mechanism

    SciTech Connect

    Scott, Daniel R.; Borbulevych, Oleg Y.; Piepenbrink, Kurt H.; Corcelli, Steven A.; Baker, Brian M.

    2012-06-19

    {alpha}{beta} T-cell receptors (TCRs) recognize multiple antigenic peptides bound and presented by major histocompatibility complex molecules. TCR cross-reactivity has been attributed in part to the flexibility of TCR complementarity-determining region (CDR) loops, yet there have been limited direct studies of loop dynamics to determine the extent of its role. Here we studied the flexibility of the binding loops of the {alpha}{beta} TCR A6 using crystallographic, spectroscopic, and computational methods. A significant role for flexibility in binding and cross-reactivity was indicated only for the CDR3{alpha} and CDR3{beta} hypervariable loops. Examination of the energy landscapes of these two loops indicated that CDR3{beta} possesses a broad, smooth energy landscape, leading to rapid sampling in the free TCR of a range of conformations compatible with different ligands. The landscape for CDR3{alpha} is more rugged, resulting in more limited conformational sampling that leads to specificity for a reduced set of peptides as well as the major histocompatibility complex protein. In addition to informing on the mechanisms of cross-reactivity and specificity, the energy landscapes of the two loops indicate a complex mechanism for TCR binding, incorporating elements of both conformational selection and induced fit in a manner that blends features of popular models for TCR recognition.

  12. Efficient Computation of Closed-loop Frequency Response for Large Order Flexible Systems

    NASA Technical Reports Server (NTRS)

    Maghami, Peiman G.; Giesy, Daniel P.

    1997-01-01

    An efficient and robust computational scheme is given for the calculation of the frequency response function of a large order, flexible system implemented with a linear, time invariant control system. Advantage is taken of the highly structured sparsity of the system matrix of the plant based on a model of the structure using normal mode coordinates. The computational time per frequency point of the new computational scheme is a linear function of system size, a significant improvement over traditional, full-matrix techniques whose computational times per frequency point range from quadratic to cubic functions of system size. This permits the practical frequency domain analysis of systems of much larger order than by traditional, full-matrix techniques. Formulations are given for both open and closed loop loop systems. Numerical examples are presented showing the advantages of the present formulation over traditional approaches, both in speed and in accuracy. Using a model with 703 structural modes, a speed-up of almost two orders of magnitude was observed while accuracy improved by up to 5 decimal places.

  13. The active site histidines of creatine kinase. A critical role of His 61 situated on a flexible loop.

    PubMed Central

    Forstner, M.; Müller, A.; Stolz, M.; Wallimann, T.

    1997-01-01

    A histidine residue with a pKa of 7 has been inferred to act as a general acid-base catalyst for the reaction of creatine kinase (CK), catalyzing the reversible phosphorylation of creatine by ATP. The chicken sarcomeric muscle mitochondrial isoenzyme Mib-CK contains several histidine residues that are conserved throughout the family of creatine kinases. By X-ray crystal structure analysis, three of them (His 61, His 92, and His 186) were recently shown to be located close to the active site of the enzyme. These residues were exchanged against alanine or aspartate by in vitro mutagenesis, and the six mutant proteins were expressed in E. coli and purified. Structural integrity of the mutant proteins was checked by small-angle X-ray scattering. Kinetic analysis showed the mutant His 61 Asp to be completely inactive in the direction of ATP consumption while exhibiting a residual activity of 1.7% of the wild-type (wt) activity in the reverse direction. The respective His to Ala mutant of residue 61 showed approximately 1% wt activity in the forward and 10% wt activity in the reverse reaction. All other mutants showed near wt activities. Changes in the kinetic parameters K(m) or Vmax, as well as a significant loss of synergism in substrate binding, could be observed with all active mutants. These effects were most pronounced for the binding of creatine and phosphocreatine, whereas ATP or ADP binding were less severely affected. Based on our results, we assume that His 92 and His 186 are involved in the binding of creatine and ATP in the active site, whereas His 61 is of importance for the catalytic reaction but does not serve as an acid-base catalyst in the transphosphorylation of creatine and ATP. In addition, our data support the idea that the flexible loop bearing His 61 is able to move towards the active site and to participate in catalysis. PMID:9041634

  14. Mutational analysis of sclerostin shows importance of the flexible loop and the cystine-knot for Wnt-signaling inhibition.

    PubMed

    Boschert, Verena; van Dinther, Maarten; Weidauer, Stella; van Pee, Katharina; Muth, Eva-Maria; Ten Dijke, Peter; Mueller, Thomas D

    2013-01-01

    The cystine-knot containing protein Sclerostin is an important negative regulator of bone growth and therefore represents a promising therapeutic target. It exerts its biological task by inhibiting the Wnt (wingless and int1) signaling pathway, which participates in bone formation by promoting the differentiation of mesenchymal stem cells to osteoblasts. The core structure of Sclerostin consists of three loops with the first and third loop (Finger 1 and Finger 2) forming a structured β-sheet and the second loop being unstructured and highly flexible. Biochemical data showed that the flexible loop is important for binding of Sclerostin to Wnt co-receptors of the low-density lipoprotein related-protein family (LRP), by interacting with the Wnt co-receptors LRP5 or -6 it inhibits Wnt signaling. To further examine the structural requirements for Wnt inhibition, we performed an extensive mutational study within all three loops of the Sclerostin core domain involving single and multiple mutations as well as truncation of important regions. By this approach we could confirm the importance of the second loop and especially of amino acids Asn92 and Ile94 for binding to LRP6. Based on a Sclerostin variant found in a Turkish family suffering from Sclerosteosis we generated a Sclerostin mutant with cysteines 84 and 142 exchanged thereby removing the third disulfide bond of the cystine-knot. This mutant binds to LRP6 with reduced binding affinity and also exhibits a strongly reduced inhibitory activity against Wnt1 thereby showing that also elements outside the flexible loop are important for inhibition of Wnt by Sclerostin. Additionally, we examined the effect of the mutations on the inhibition of two different Wnt proteins, Wnt3a and Wnt1. We could detect clear differences in the inhibition of these proteins, suggesting that the mechanism by which Sclerostin antagonizes Wnt1 and Wnt3a is fundamentally different. PMID:24312339

  15. Structural Study of a Flexible Active Site Loop in Human Indoleamine 2,3-Dioxygenase and Its Functional Implications.

    PubMed

    Álvarez, Lucía; Lewis-Ballester, Ariel; Roitberg, Adrián; Estrin, Darío A; Yeh, Syun-Ru; Marti, Marcelo A; Capece, Luciana

    2016-05-17

    Human indoleamine 2,3-dioxygenase catalyzes the oxidative cleavage of tryptophan to N-formyl kynurenine, the initial and rate-limiting step in the kynurenine pathway. Additionally, this enzyme has been identified as a possible target for cancer therapy. A 20-amino acid protein segment (the JK loop), which connects the J and K helices, was not resolved in the reported hIDO crystal structure. Previous studies have shown that this loop undergoes structural rearrangement upon substrate binding. In this work, we apply a combination of replica exchange molecular dynamics simulations and site-directed mutagenesis experiments to characterize the structure and dynamics of this protein region. Our simulations show that the JK loop can be divided into two regions: the first region (JK loop(C)) displays specific and well-defined conformations and is within hydrogen bonding distance of the substrate, while the second region (JK loop(N)) is highly disordered and exposed to the solvent. The peculiar flexible nature of JK loop(N) suggests that it may function as a target for post-translational modifications and/or a mediator for protein-protein interactions. In contrast, hydrogen bonding interactions are observed between the substrate and Thr379 in the highly conserved "GTGG" motif of JK loop(C), thereby anchoring JK loop(C) in a closed conformation, which secures the appropriate substrate binding mode for catalysis. Site-directed mutagenesis experiments confirm the key role of this residue, highlighting the importance of the JK loop(C) conformation in regulating the enzymatic activity. Furthermore, the existence of the partially and totally open conformations in the substrate-free form suggests a role of JK loop(C) in controlling substrate and product dynamics. PMID:27112409

  16. Intrinsic flexibility of snRNA hairpin loops facilitates protein binding.

    PubMed

    Rau, Michael; Stump, W Tom; Hall, Kathleen B

    2012-11-01

    Stem-loop II of U1 snRNA and Stem-loop IV of U2 snRNA typically have 10 or 11 nucleotides in their loops. The fluorescent nucleobase 2-aminopurine was used as a substitute for the adenines in each loop to probe the local and global structures and dynamics of these unusually long loops. Using steady-state and time-resolved fluorescence, we find that, while the bases in the loops are stacked, they are able to undergo significant local motion on the picosecond/nanosecond timescale. In addition, the loops have a global conformational change at low temperatures that occurs on the microsecond timescale, as determined using laser T-jump experiments. Nucleobase and loop motions are present at temperatures far below the melting temperature of the hairpin stem, which may facilitate the conformational change required for specific protein binding to these RNA loops. PMID:23012481

  17. The Role of Active Site Flexible Loops in Catalysis and of Zinc in Conformational Stability of Bacillus cereus 569/H/9 β-Lactamase.

    PubMed

    Montagner, Caroline; Nigen, Michaël; Jacquin, Olivier; Willet, Nicolas; Dumoulin, Mireille; Karsisiotis, Andreas Ioannis; Roberts, Gordon C K; Damblon, Christian; Redfield, Christina; Matagne, André

    2016-07-29

    Metallo-β-lactamases catalyze the hydrolysis of most β-lactam antibiotics and hence represent a major clinical concern. The development of inhibitors for these enzymes is complicated by the diversity and flexibility of their substrate-binding sites, motivating research into their structure and function. In this study, we examined the conformational properties of the Bacillus cereus β-lactamase II in the presence of chemical denaturants using a variety of biochemical and biophysical techniques. The apoenzyme was found to unfold cooperatively, with a Gibbs free energy of stabilization (ΔG(0)) of 32 ± 2 kJ·mol(-1) For holoBcII, a first non-cooperative transition leads to multiple interconverting native-like states, in which both zinc atoms remain bound in an apparently unaltered active site, and the protein displays a well organized compact hydrophobic core with structural changes confined to the enzyme surface, but with no catalytic activity. Two-dimensional NMR data revealed that the loss of activity occurs concomitantly with perturbations in two loops that border the enzyme active site. A second cooperative transition, corresponding to global unfolding, is observed at higher denaturant concentrations, with ΔG(0) value of 65 ± 1.4 kJ·mol(-1) These combined data highlight the importance of the two zinc ions in maintaining structure as well as a relatively well defined conformation for both active site loops to maintain enzymatic activity. PMID:27235401

  18. Switch-Loop Flexibility Affects Transport of Large Drugs by the Promiscuous AcrB Multidrug Efflux Transporter

    PubMed Central

    Cha, Hi-jea; Müller, Reinke T.

    2014-01-01

    Multidrug efflux transporters recognize a variety of structurally unrelated compounds for which the molecular basis is poorly understood. For the resistance nodulation and cell division (RND) inner membrane component AcrB of the AcrAB-TolC multidrug efflux system from Escherichia coli, drug binding occurs at the access and deep binding pockets. These two binding areas are separated by an 11-amino-acid-residue-containing switch loop whose conformational flexibility is speculated to be essential for drug binding and transport. A G616N substitution in the switch loop has a distinct and local effect on the orientation of the loop and on the ability to transport larger drugs. Here, we report a distinct phenotypical pattern of drug recognition and transport for the G616N variant, indicating that drug substrates with minimal projection areas of >70 Å2 are less well transported than other substrates. PMID:24914123

  19. Flexibility.

    ERIC Educational Resources Information Center

    Humphrey, L. Dennis

    1981-01-01

    Flexibility is an important aspect of all sports and recreational activities. Flexibility can be developed and maintained by stretching exercises. Exercises designed to develop flexibility in ankle joints, knees, hips, and the lower back are presented. (JN)

  20. A Catalytically Essential Motif in External Loop 5 of the Bacterial Oligosaccharyltransferase PglB*

    PubMed Central

    Lizak, Christian; Gerber, Sabina; Zinne, Daria; Michaud, Gaëlle; Schubert, Mario; Chen, Fan; Bucher, Monika; Darbre, Tamis; Zenobi, Renato; Reymond, Jean-Louis; Locher, Kaspar P.

    2014-01-01

    Asparagine-linked glycosylation is a post-translational protein modification that is conserved in all domains of life. The initial transfer of a lipid-linked oligosaccharide (LLO) onto acceptor asparagines is catalyzed by the integral membrane protein oligosaccharyltransferase (OST). The previously reported structure of a single-subunit OST enzyme, the Campylobacter lari protein PglB, revealed a partially disordered external loop (EL5), whose role in catalysis was unclear. We identified a new and functionally important sequence motif in EL5 containing a conserved tyrosine residue (Tyr293) whose aromatic side chain is essential for catalysis. A synthetic peptide containing the conserved motif can partially but specifically rescue in vitro activity of mutated PglB lacking Tyr293. Using site-directed disulfide cross-linking, we show that disengagement of the structurally ordered part of EL5 is an essential step of the glycosylation reaction, probably by allowing sequon binding or glyco-product release. Our findings define two distinct mechanistic roles of EL5 in OST-catalyzed glycosylation. These functions, exerted by the two halves of EL5, are independent, because the loop can be cleaved by specific proteolysis with only slight reduction in activity. PMID:24275651

  1. A catalytically essential motif in external loop 5 of the bacterial oligosaccharyltransferase PglB.

    PubMed

    Lizak, Christian; Gerber, Sabina; Zinne, Daria; Michaud, Gaëlle; Schubert, Mario; Chen, Fan; Bucher, Monika; Darbre, Tamis; Zenobi, Renato; Reymond, Jean-Louis; Locher, Kaspar P

    2014-01-10

    Asparagine-linked glycosylation is a post-translational protein modification that is conserved in all domains of life. The initial transfer of a lipid-linked oligosaccharide (LLO) onto acceptor asparagines is catalyzed by the integral membrane protein oligosaccharyltransferase (OST). The previously reported structure of a single-subunit OST enzyme, the Campylobacter lari protein PglB, revealed a partially disordered external loop (EL5), whose role in catalysis was unclear. We identified a new and functionally important sequence motif in EL5 containing a conserved tyrosine residue (Tyr293) whose aromatic side chain is essential for catalysis. A synthetic peptide containing the conserved motif can partially but specifically rescue in vitro activity of mutated PglB lacking Tyr293. Using site-directed disulfide cross-linking, we show that disengagement of the structurally ordered part of EL5 is an essential step of the glycosylation reaction, probably by allowing sequon binding or glyco-product release. Our findings define two distinct mechanistic roles of EL5 in OST-catalyzed glycosylation. These functions, exerted by the two halves of EL5, are independent, because the loop can be cleaved by specific proteolysis with only slight reduction in activity. PMID:24275651

  2. Donor-driven conformational flexibility in a real-life catalytic dicopper(ii) peroxo complex.

    PubMed

    Hoffmann, A; Herres-Pawlis, S

    2016-03-01

    The conformers of the real-life tyrosinase model [Cu2O2{HC(3-tBuPz)2(Py)}2](2+) which displays catalytic hydroxylation reactivity were investigated by density functional theory (DFT) studies including second-order perturbation theory and charge decomposition analysis (CDA). We elucidated the donor competition between pyrazolyl and pyridinyl moieties and found that pyrazolyl units are the stronger donors in bis(pyrazolyl)pyridinylmethane copper complexes. Geometry optimisations and TD-DFT calculations on all conformers proved to be robust in the prediction of the experimental data: the XAS distances and both charge-transfer bands are well reproduced. The CDA analyses gave insights into the electronic structure of the real-life peroxo dicopper species. The donor interplay as well as the multitude of interactions within two prototypical conformers have now been dissected in detail for the first time for a catalytic real-life system without simplifications. We find that the N donor interactions to the core are extremely stabilising and that in the conformer with both pyrazolyl units in equatorial position, these interactions are more stabilising than the axial ones. In the conformer with pyridinyl/pyrazolyl equator, the picture is more mixed but the general trend keeps consistent. We relate the extraordinary catalytic activity of the [Cu2O2{HC(3-tBuPz)2(Py)}2](2+) system to the subtle interplay of the different donor moieties. PMID:26688471

  3. The importance of hinge sequence for loop function and catalytic activity in the reaction catalyzed by triosephosphate isomerase.

    PubMed

    Xiang, J; Sun, J; Sampson, N S

    2001-04-01

    We have determined the sequence requirements for the N-terminal protein hinge of the active-site lid of triosephosphate isomerase. The codons for the hinge (PVW) were replaced with a genetic library of all possible 8000 amino acid combinations. The most active of these 8000 mutants were selected using in vivo complementation of a triosephosphate isomerase-deficient strain of Escherichia coli, DF502. Approximately 0.3 % of the mutants complement DF502 with an activity that is between 10 and 70 % of wild-type activity. They all contain Pro at the first position. Furthermore, the sequences of these hinge mutants reveal that hydrophobic packing is very important for efficient formation of the enediol intermediate. However, the reduced catalytic activities observed are not due to increased rates of loop opening. To explore the relationship between the N-terminal and C-terminal hinges, three semi-active mutants from the N-terminal hinge selection experiment (PLH, PHS and PTF), and six active C-terminal hinge mutants from previous work (NSS, LWA, YSL, KTK, NPN, KVA) were combined to form 18 "double-hinge" mutants. The activities of these mutants suggest that the N-terminal and C-terminal hinge structures affect one another. It appears that specific side-chain interactions are important for forming a catalytically active enzyme, but not for preventing release of the unstable enediol intermediate from the active site of the enzyme. The independence of intermediate release on amino acid sequence is consistent with the absence of a "universal" hinge sequence in structurally related enzymes. PMID:11286559

  4. Structure analysis and catalytic property of a microporous framework based on a flexible tripodal ligand with novel conformations

    NASA Astrophysics Data System (ADS)

    Shi, Xianju; Zhang, Xinhai; Li, Xiaoxia; Hou, Hongwei; Fan, Yaoting

    2011-06-01

    A microporous metal-organic framework {[Cu 3Cl 6(ttmb) 4]·6H 2O} n ( 1) (ttmb = 1,3,5-tris(1,2,4-triazol-1-ylmethyl)-benzene) with tetranodal (3,4)-connected topological type was prepared by the self-assembly reaction of the flexible tripodal ligand ttmb with CuCl 2·2H 2O. The ligand exhibits two infrequent coordination conformations in complex 1, and the framework has a large pore volume (remove the solvent molecules) of 1781.6 Å 3 (36.3% of the total). The test of 1 as the catalyst in the oxidative coupling reaction of 2,6-dimethylphenol indicates that it is catalytically active by showing high conversion of DMP under the optimized reaction condition.

  5. Coupled rotor-flexible fuselage vibration reduction using open loop higher harmonic control

    NASA Technical Reports Server (NTRS)

    Papavassiliou, I.; Friedmann, P. P.; Venkatesan, C.

    1991-01-01

    A fundamental study of vibration prediction and vibration reduction in helicopters using active controls was performed. The nonlinear equations of motion for a coupled rotor/flexible fuselage system have been derived using computer algebra on a special purpose symbolic computer facility. The trim state and vibratory response of the helicopter are obtained in a single pass by applying the harmonic balance technique and simultaneously satisfying the trim and the vibratory response of the helicopter for all rotor and fuselage degrees of freedom. The influence of the fuselage flexibility on the vibratory response is studied. It is shown that the conventional single frequency higher harmonic control is capable of reducing either the hub loads or only the fuselage vibrations but not both simultaneously. It is demonstrated that for simultaneous reduction of hub shears and fuselae vibrations a new scheme called multiple higher harmonic control is required.

  6. Modal domain fiber optic sensor for closed loop vibration control of a flexible beam

    NASA Technical Reports Server (NTRS)

    Cox, D.; Thomas, D.; Reichard, K.; Lindner, D.; Claus, R. O.

    1990-01-01

    The use of a modal domain sensor in a vibration control experiment is described. An optical fiber is bonded along the length of a flexible beam. A control signal derived from the output of the modal domain sensor is used to suppress vibrations induced in the beam. A distributed effect model for the modal domain sensor is developed and combined with models of the beam and actuator dynamics to produce a system suitable for control design.

  7. A flexible loop-type flow modulator for comprehensive two-dimensional gas chromatography.

    PubMed

    Tranchida, Peter Quinto; Purcaro, Giorgia; Visco, Alessandro; Conte, Lanfranco; Dugo, Paola; Dawes, Peter; Mondello, Luigi

    2011-05-27

    The present investigation is focused on a simple flow modulator (FM), for comprehensive two-dimensional gas chromatography (GC×GC). The interface is stable at high temperatures, and consists of a metallic disc (located inside the GC oven) with seven ports, which are connected to an auxiliary pressure source via two branches, to the first and second dimension, to a waste branch (linked to a needle valve) and to an exchangeable modulation loop (2 ports). The ports are connected via micro-channels, etched on one of the inner surfaces of the disc. Modulation is achieved using a two-way electrovalve, connected on one side to the additional pressure source, and to the two metal branches, on the other. An FM enantio-GC×polar-GC method (using a flame ionization detector) was optimized (a 40-μL loop was employed), for the analysis of essential oils. As an example, an application on spearmint oil is shown; the method herein proposed was subjected to validation. Finally, an FM GC×GC diesel experiment was carried out, using an apolar-polar column combination, to demonstrate the effectiveness of the modulator in the analysis of a totally different sample-type. PMID:21256493

  8. Flexible Airspace Management (FAM) Research 2010 Human-in-the-Loop Simulation

    NASA Technical Reports Server (NTRS)

    Lee, Paul U.; Brasil, Connie; Homola, Jeffrey; Kessell, Angela; Prevot, Thomas; Smith, Nancy

    2011-01-01

    A human-in-the-Ioop (HITL) simulation was conducted to assess potential user and system benefits of Flexible Airspace Management (FAM) concept, as well as designing role definitions, procedures, and tools to support the FAM operations in the mid-term High Altitude Airspace (HAA) environment. The study evaluated the benefits and feasibility of flexible airspace reconfiguration in response to traffic overload caused by weather deviations, and compared them to those in a baseline condition without the airspace reconfiguration. The test airspace consisted of either four sectors in one Area of Specialization or seven sectors across two Areas. The test airspace was assumed to be at or above FL340 and fully equipped Vvith data communications (Data Comm). Other assumptions were consistent with those of the HAA concept. Overall, results showed that FAM operations with multiple Traffic Management Coordinators, Area Supervisors, and controllers worked remarkably well. The results showed both user and system benefits, some of which include the increased throughput, decreased flight distance, more manageable sector loads, and better utilized airspace. Also, the roles, procedures, airspace designs, and tools were all very well received. Airspace configuration options that resulted from a combination of algorithm-generated airspace configurations with manual modifications were well acceptec and posed little difficuIty and/or workload during airspace reconfiguration process. The results suggest a positive impact of FAM operations in HAA. Further investigation would be needed to evaluate if the benefits and feasibility would extend in either non-HAA or mixed equipage environment.

  9. Pilot modeling and closed-loop analysis of flexible aircraft in the pitch tracking task

    NASA Technical Reports Server (NTRS)

    Schmidt, D. K.

    1983-01-01

    The issue addressed in the appropriate modeling technique for pilot vehicle analysis of large flexible aircraft, when the frequency separation between the rigid-body mode and the dynamic aeroelastic modes is reduced. This situation was shown to have significant effects on pitch-tracking performance and subjective rating of the task, obtained via fixed base simulation. Further, the dynamics in these cases are not well modeled with a rigid-body-like model obtained by including only 'static elastic' effects, for example. It is shown that pilot/vehicle analysis of this data supports the hypothesis that an appropriate pilot-model structure is an optimal-control pilot model of full order. This is in contrast to the contention that a representative model is of reduced order when the subject is controlling high-order dynamics as in a flexible vehicle. The key appears to be in the correct assessment of the pilot's objective of attempting to control 'rigid-body' vehicle response, a response that must be estimated by the pilot from observations contaminated by aeroelastic dynamics. Finally, a model-based metric is shown to correlate well with the pilot's subjective ratings.

  10. Looping dynamics of a flexible chain with internal friction at different degrees of compactness

    NASA Astrophysics Data System (ADS)

    Samanta, Nairhita; Chakrabarti, Rajarshi

    2015-10-01

    In recent times single molecule experiments have shown the importance of internal friction in biopolymer dynamics. Such studies also suggested that the internal friction although independent of solvent viscosity has a strong dependence on denaturant concentration. In addition, recent simulations showed that the weak interactions contribute to the internal friction in proteins. In this work we made an attempt to investigate how a single polymer chain with internal friction undergoes reconfiguration and looping dynamics in a confining potential that accounts for the presence of the denaturant, by using recently proposed "Compacted Rouse with internal friction". We also incorporated the effect of hydrodynamics by extending this further to "Compacted Zimm with internal friction". All the calculations are carried out within the Wilemski Fixman framework without invoking excluded-volume effect. By changing the strength of the confinement we mimicked chains with different degrees of compactness at different denaturant concentrations. While compared with experiments our results are found to be in good agreement.

  11. The Role of Flexible Loops in Folding, Trafficking and Activity of Equilibrative Nucleoside Transporters

    PubMed Central

    Aseervatham, Jaya; Tran, Lucky; Machaca, Khaled; Boudker, Olga

    2015-01-01

    Equilibrative nucleoside transporters (ENTs) are integral membrane proteins, which reside in plasma membranes of all eukaryotic cells and mediate thermodynamically downhill transport of nucleosides. This process is essential for nucleoside recycling, and also plays a key role in terminating adenosine-mediated cellular signaling. Furthermore, ENTs mediate the uptake of many drugs, including anticancer and antiviral nucleoside analogues. The structure and mechanism, by which ENTs catalyze trans-membrane transport of their substrates, remain unknown. To identify the core of the transporter needed for stability, activity, and for its correct trafficking to the plasma membrane, we have expressed human ENT deletion mutants in Xenopus laevis oocytes and determined their localization, transport properties and susceptibility to inhibition. We found that the carboxyl terminal trans-membrane segments are essential for correct protein folding and trafficking. In contrast, the soluble extracellular and intracellular loops appear to be dispensable, and must be involved in the fine-tuning of transport regulation. PMID:26406980

  12. The Role of Flexible Loops in Folding, Trafficking and Activity of Equilibrative Nucleoside Transporters.

    PubMed

    Aseervatham, Jaya; Tran, Lucky; Machaca, Khaled; Boudker, Olga

    2015-01-01

    Equilibrative nucleoside transporters (ENTs) are integral membrane proteins, which reside in plasma membranes of all eukaryotic cells and mediate thermodynamically downhill transport of nucleosides. This process is essential for nucleoside recycling, and also plays a key role in terminating adenosine-mediated cellular signaling. Furthermore, ENTs mediate the uptake of many drugs, including anticancer and antiviral nucleoside analogues. The structure and mechanism, by which ENTs catalyze trans-membrane transport of their substrates, remain unknown. To identify the core of the transporter needed for stability, activity, and for its correct trafficking to the plasma membrane, we have expressed human ENT deletion mutants in Xenopus laevis oocytes and determined their localization, transport properties and susceptibility to inhibition. We found that the carboxyl terminal trans-membrane segments are essential for correct protein folding and trafficking. In contrast, the soluble extracellular and intracellular loops appear to be dispensable, and must be involved in the fine-tuning of transport regulation. PMID:26406980

  13. Insights into the Recognition, Binding and Reactivity of Catalytic Metallodrugs Targeting Stem Loop IIb of Hepatitis C IRES RNA

    PubMed Central

    Bradford, Seth S.; Ross, Martin James; Fidai, Insiya; Cowan, J. A.

    2014-01-01

    Complex Cu-GGHYrFK-amide (1-Cu) was previously reported as a novel metallotherapeutic that catalytically inactivates stem loop IIb of the Hepatitis C Virus (HCV) Internal Ribosomal Entry Site (IRES) RNA and demonstrates significant antiviral activity in a cellular HCV replicon assay. Herein are described additional studies focused on understanding the cleavage mechanism, as well as the relationship of catalyst configuration to structural recognition and site-selective cleavage of the structured RNA motif. These are advanced by use of a combination of MALDI-TOF mass spectrometry, melting temperature determination, and computational analysis to develop a structural model for binding and reactivity toward SLIIb of the IRES RNA. In addition, the binding, reactivity, and structural chemistry of the all d-amino acid form of this metallopeptide, complex 2-Cu, is reported and compared to complex 1-Cu. In vitro RNA binding and cleavage assays for complex 2-Cu show a KD of 76 ± 3 nM, and Michaelis-Menten parameters of kcat of 0.14 ± 0.01 min−1 and KM of 7.9 ± 1.2 µM, with a turnover number exceeding 40. In a luciferase-based cellular replicon assay Cu-GGhyrfk-amide shows activity similar to the parent peptide, complex 1-Cu, with IC50 of 1.9 ± 0.4 µM and cytotoxicity exceeding 100 µM. RT-PCR experiments confirm a significant reduction in HCV RNA levels in replicon assays for up to nine days when treated with complex 1-Cu in three day dosing increments. This study shows the influence that the α-carbon stereocenter has for this the new class of compounds, while detailed mass spectrometry and computational analysis provide new insights into the mechanisms of recognition, binding, and reactivity. PMID:24756921

  14. Free-energy calculations for semi-flexible macromolecules: applications to DNA knotting and looping.

    PubMed

    Giovan, Stefan M; Scharein, Robert G; Hanke, Andreas; Levene, Stephen D

    2014-11-01

    We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases. PMID:25381542

  15. Free-energy calculations for semi-flexible macromolecules: Applications to DNA knotting and looping

    NASA Astrophysics Data System (ADS)

    Giovan, Stefan M.; Scharein, Robert G.; Hanke, Andreas; Levene, Stephen D.

    2014-11-01

    We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases.

  16. Free-energy calculations for semi-flexible macromolecules: Applications to DNA knotting and looping

    SciTech Connect

    Giovan, Stefan M.; Scharein, Robert G.; Hanke, Andreas; Levene, Stephen D.

    2014-11-07

    We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases.

  17. A smallest 6 kda metalloprotease, mini-matrilysin, in living world: a revolutionary conserved zinc-dependent proteolytic domain- helix-loop-helix catalytic zinc binding domain (ZBD)

    PubMed Central

    2012-01-01

    Background The Aim of this study is to study the minimum zinc dependent metalloprotease catalytic folding motif, helix B Met loop-helix C, with proteolytic catalytic activities in metzincin super family. The metzincin super family share a catalytic domain consisting of a twisted five-stranded β sheet and three long α helices (A, B and C). The catalytic zinc is at the bottom of the cleft and is ligated by three His residues in the consensus sequence motif, HEXXHXXGXXH, which is located in helix B and part of the adjacent Met turn region. An interesting question is - what is the minimum portion of the enzyme that still possesses catalytic and inhibitor recognition?” Methods We have expressed a 60-residue truncated form of matrilysin which retains only the helix B-Met turn-helix C region and deletes helix A and the five-stranded β sheet which form the upper portion of the active cleft. This is only 1/4 of the full catalytic domain. The E. coli derived 6 kDa MMP-7 ZBD fragments were purified and refolded. The proteolytic activities were analyzed by Mca-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2 peptide assay and CM-transferrin zymography analysis. SC44463, BB94 and Phosphoramidon were computationally docked into the 3day structure of the human MMP7 ZBD and TAD and thermolysin using the docking program GOLD. Results This minimal 6 kDa matrilysin has been refolded and shown to have proteolytic activity in the Mca-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2 peptide assay. Triton X-100 and heparin are important factors in the refolding environment for this mini-enzyme matrilysin. This minienzyme has the proteolytic activity towards peptide substrate, but the hexamer and octamer of the mini MMP-7 complex demonstrates the CM-transferrin proteolytic activities in zymographic analysis. Peptide digestion is inhibited by SC44463, specific MMP7 inhibitors, but not phosphorimadon. Interestingly, the mini MMP-7 can be processed by autolysis and producing ~ 6 ~ 7 kDa fragments. Thus

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

    SciTech Connect

    Castelli, Silvia; Stella, Lorenzo; Petrarca, Patrizia; Battistoni, Andrea; Desideri, Alessandro; Falconi, Mattia

    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. Characterization of the functional role of a flexible loop in the alpha-subunit of tryptophan synthase from Salmonella typhimurium by rapid-scanning, stopped-flow spectroscopy and site-directed mutagenesis.

    PubMed

    Brzović, P S; Hyde, C C; Miles, E W; Dunn, M F

    1993-10-01

    The function of a flexible loop (loop 6) in the alpha-subunit from the tryptophan synthase alpha 2 beta 2 bienzyme complex has been investigated utilizing rapid-scanning (RSSF) and single-wavelength (SWSF) stopped-flow spectroscopies. Loop 6 is an extended sequence of residues which connects beta-strand 6 with alpha-helix 6 in the beta/alpha-barrel fold of the alpha-subunit. Substitution of Leu for Arg179 near the base of loop 6 does not significantly affect either the association of the alpha- and beta-subunits to form the bienzyme complex or the kinetics of the reaction of indole with L-serine (L-Ser) to form L-tryptophan (L-Trp), the process catalyzed by the wild-type beta-subunit [Kawasaki, H., Bauerle, R., Zon, G., Ahmed, S., & Miles, E. W. (1987) J. Biol. Chem. 262, 10678-10683]. However, the alpha-subunit-specific ligand glycerol phosphate (GP), which is an inhibitor of the wild-type beta-reaction, is a much less effective inhibitor of the alpha R179L-catalyzed beta-reaction. Equilibrium titration studies show that the affinity of GP for the alpha-site when either L-Ser or glycine is bound at the beta-site has been reduced by nearly 100- and 200-fold, respectively. SWSF analysis of the reaction of IGP and L-Ser to form L-Trp catalyzed by the bienzyme complex revealed a 15-fold reduction in the binding affinity of the alpha-site substrate 3-indole-D-glycerol 3'-phosphate (IGP) in the reaction catalyzed by the alpha R179L mutant as compared to the wild-type enzyme. These studies show that loop 6 is important both for ligand binding to the alpha-site and for the ligand-induced conformational transition of the alpha-subunit from an "open" to a "closed" structure. Modeling studies, based on extensive structural homology of the alpha-subunit with the glycolytic enzyme triosephosphate isomerase (TIM), predict that closure of loop 6 induced by ligand binding at the alpha-active site would effectively sequester the bound substrate from the solvent and trap indole

  20. Modified conducting polymer films having high catalytic activity for use as counter electrodes in rigid and flexible dye-sensitized solar cells

    NASA Astrophysics Data System (ADS)

    Ke, Chun-Ren; Chang, Chih-Ching; Ting, Jyh-Ming

    2015-06-01

    We report replacing platinum based counter electrode (CE) in dye-sensitized solar cell (DSSC) with conducting polymer based CE. Conducting polymers are prepared through mixing poly-(3,4-ethylenedioxythio phene):poly-(styrene sulfonic acid) (PEDOT:PSS) with Triton. The polymer mixture is spin-coated on indium tin oxide (ITO)-coated glass substrate and ITO-coated polyethylene naphthalate plastic substrate to form a CE for use in both rigid and flexible DSSCs, respectively. The PEDOT:PSS-Triton polymer not only is transparent (up to 93%) and highly conductive but also exhibits better catalytic activity than the expensive platinum. The DSSC fabricated using the PEDOT:PSS-Triton conducting polymer CE shows better performance or higher power conversion efficiency than that using Pt-based CE, either rigid or flexible.

  1. Scalable Fabrication of Nanoporous Carbon Fiber Films as Bifunctional Catalytic Electrodes for Flexible Zn-Air Batteries.

    PubMed

    Liu, Qin; Wang, Yaobing; Dai, Liming; Yao, Jiannian

    2016-04-01

    A flexible nanoporous carbon-fiber film for wearable electronics is prepared by a facile and scalable method through pyrolysis of electrospun polyimide. It exhibits excellent bifunctional electrocatalytic activities for oxygen reduction and oxygen evolution. Flexible rechargeable zinc-air batteries based on the carbon-fiber film show high round-trip efficiency and mechanical stability. PMID:26914270

  2. The second-sphere residue T263 is important for the function and catalytic activity of PTP1B via interaction with the WPD-loop.

    PubMed

    Xiao, Peng; Wang, Xiao; Wang, Hong-Mei; Fu, Xiao-Lei; Cui, Fu-ai; Yu, Xiao; Wen, Shi-shuai; Bi, Wen-Xiang; Sun, Jin-Peng

    2014-12-01

    Protein tyrosine phosphatases have diverse substrate specificities and intrinsic activities that lay the foundations for the fine-tuning of a phosphorylation network to precisely regulate cellular signal transduction. All classical PTPs share common catalytic mechanisms, and the important catalytic residues in the first sphere of their active sites have been well characterized. However, little attention has been paid to the second-sphere residues that are potentially important in defining the intrinsic activity and substrate specificity of PTPs. Here, we find that a conserved second-sphere residue, Thr263, located in the surface Q-loop is important for both the function and activity of PTPs. Using PTP1B as a study model, we found that mutations of Thr263 impaired the negative regulation role of PTP1B in insulin signaling. A detailed mechanistic study utilizing steady-state kinetics, Brønsted analysis and pH dependence in the presence of pNPP or phosphopeptide substrates revealed that Thr263 is required for the stabilization of the leaving group during catalysis. Further crystallographic studies and structural comparison revealed that Thr263 regulates the general acid function through modulation of the WPD-loop by the T263:F182/Y/H interaction pair, which is conserved in 26 out of 32 classical PTPs. In addition, the hydrophobic interaction between Thr263 and Arg1159 of the insulin receptor contributes to the substrate specificity of PTP1B. Taken together, our findings demonstrate the general role of the second-sphere residue Thr263 in PTP catalysis. Our findings suggest that the second sphere residues of PTP active site may play important roles in PTP-mediated function in both normal and diseased states. PMID:25450460

  3. Exploring the effect of chain length of bridging ligands in cobalt(II) coordination polymers based on flexible bis(5,6-dimethylbenzimidazole) ligands: Synthesis, crystal structures, fluorescence and catalytic properties

    NASA Astrophysics Data System (ADS)

    Qin, Li; Li, Yue-Hua; Ma, Pei-Juan; Cui, Guang-Hua

    2013-11-01

    Two Co(II) coordination polymers derived from a dicarboxylate and two flexible bis(5,6-dimethylbenzimidazole) ligands with varying chain lengths equipped, namely [Co(bdmbmm)(nip)]n (1) and [Co2(bdmbmb)2(nip)2ṡH2O]n (2) (bdmbmm = 1,1'-bis(5,6-dimethylbenzimidazole)methane, H2nip = 5-nitroisophthalic acid, bdmbmb = 1,4-bis(5,6-dimethylbenzimidazole)butane), have been synthesized by hydrothermal methods and characterized by elemental analyses, IR spectra, thermogravimetric analysis (TGA), X-ray powder diffraction (XRPD) and single-crystal X-ray diffraction. Complex 1 forms a 1D looped-like chain consisting of two kinds of macrocycles, which is further arranged into a 2D supramolecular layer through face-to-face π-π stacking interactions; whereas complex 2 exhibits a 3D framework with a twofold interpenetrating diamondoid topology. The fluorescence and catalytic properties of the complexes for the degradation of methyl orange by sodium persulfate have been investigated.

  4. Intracellular segment between transmembrane helices S0 and S1 of BK channel α subunit contains two amphipathic helices connected by a flexible loop

    SciTech Connect

    Shi, Pan; Li, Dong; Lai, Chaohua; Zhang, Longhua; Tian, Changlin

    2013-08-02

    Highlights: •The loop between S0 and S1 of BK channel was overexpressed and purified in DPC. •NMR studies indicated BK-IS1 contained two helices connected by a flexible loop. •Mg{sup 2+} titration of BK-IS1 indicated two possible binding sites of divalent ions. -- Abstract: The BK channel, a tetrameric potassium channel with very high conductance, has a central role in numerous physiological functions. The BK channel can be activated by intracellular Ca{sup 2+} and Mg{sup 2+}, as well as by membrane depolarization. Unlike other tetrameric potassium channels, the BK channel has seven transmembrane helices (S0–S6) including an extra helix S0. The intracellular segment between S0 and S1 (BK-IS1) is essential to BK channel functions and Asp99 in BK-IS1 is reported to be responsible for Mg{sup 2+} coordination. In this study, BK-IS1 (44–113) was over-expressed using a bacterial system and purified in the presence of detergent micelles for multidimensional heteronuclear nuclear magnetic resonance (NMR) structural studies. Backbone resonance assignment and secondary structure analysis showed that BK-IS1 contains two amphipathic helices connected by a 36-residue loop. Amide {sup 1}H–{sup 15}N heteronuclear NOE analysis indicated that the loop is very flexible, while the two amphipathic helices are possibly stabilized through interaction with the membrane. A solution NMR-based titration assay of BK-IS1 was performed with various concentrations of Mg{sup 2+}. Two residues (Thr45 and Leu46) with chemical shift changes were observed but no, or very minor, chemical shift difference was observed for Asp99, indicating a possible site for binding divalent ions or other modulation partners.

  5. Critical Role of a Loop at C-Terminal Domain on the Conformational Stability and Catalytic Efficiency of Chondroitinase ABC I.

    PubMed

    Akram Shirdel, S; Khalifeh, Khosrow; Golestani, Abolfazl; Ranjbar, Bijan; Khajeh, Khosro

    2015-08-01

    We used a combination of protein engineering and spectroscopic methods to investigate the effect of a long length loop on the conformational stability and activity of chondroitinase ABC I. This study involves manipulation of interactions around Asp(689) as a key residue in the central region of the loop containing residues 681-695 located at C-terminal domain of the enzyme. According to the equilibrium unfolding experiments and considering thermodynamic m value and ΔG(H2O), we found that the folded state of H700N, L701T, and H700N/L701T are more compact relative to the folded state of wild-type protein and they become stabilized upon mutation. However, the compactness and stability of other variants are less than those of wild-type protein. According to enzyme activity measurements, we found that the catalytic efficiency of structurally stabilized variants is decreased, while that of destabilized mutants is improved. PMID:25808032

  6. Facile fabrication of all-solid-state flexible interdigitated MnO2 supercapacitor via in-situ catalytic solution route

    NASA Astrophysics Data System (ADS)

    Long, Xiao; Zeng, Zhigang; Guo, Erjuan; Shi, Xiaobo; Zhou, Haijun; Wang, Xiaohong

    2016-09-01

    With the rapid development of wearable and portable electronics, the demand for all-solid-state flexible energy storage devices with high performance, long-term cycling stability and bending stability has been aroused. Physical and chemical method for preparing thin-film materials has enabled planar flexible supercapacitors (SCs) to be fabricated for a variety of applications. In this work, we report on the facile fabrication of an all-solid-state flexible interdigitated supercapacitor with a convenient and efficient two-step method. 3-D nanostructured α-MnO2 has been prepared on the surface of interdigitated Pt metal pattern on polyethylene terephthalate (PET) substrate as high-performance electrode material via in-situ catalytic solution route without any assistance of template or surfactant. The SCs are fabricated with PVA/H3PO4 as solid-state electrolyte, which exhibited good electrochemical performance with areal capacitance as much as 20 mF cm-2 at a scan rate of 10 mV s-1, relatively high energy density (3.6 × 10-7 Wh cm-2-1.9 × 10-6 Wh cm-2) and power density (9 × 10-5 W cm-2-1.6 × 10-4 W cm-2), and excellent long-term cycling stability with capacitance retention of 82.2% (10,000 times charge and discharge), and bending stability with capacitance retention of 89.6%.

  7. Structure of stem-loop IV of Tetrahymena telomerase RNA

    PubMed Central

    Chen, Yu; Fender, Jessica; Legassie, Jason D; Jarstfer, Michael B; Bryan, Tracy M; Varani, Gabriele

    2006-01-01

    Conserved domains within the RNA component of telomerase provide the template for reverse transcription, recruit protein components to the holoenzyme and are required for enzymatic activity. Among the functionally essential domains in ciliate telomerase RNA is stem-loop IV, which strongly stimulates telomerase activity and processivity even when provided in trans. The NMR structure of Tetrahymena thermophila stem-loop IV shows a highly structured distal stem-loop linked to a conformationally flexible template-proximal region by a bulge that severely kinks the entire RNA. Through extensive structure–function studies, we identify residues that contribute to both these structural features and to enzymatic activity, with no apparent effect on the binding of TERT protein. We propose that the bending induced by the GA bulge and the flexibility of the template-proximal region allow positioning of the prestructured apical loop during the catalytic cycle. PMID:16778765

  8. Structure of the Neisserial Outer Membrane Protein Opa60: Loop Flexibility Essential to Receptor Recognition and Bacterial Engulfment

    PubMed Central

    2015-01-01

    The structure and dynamics of Opa proteins, which we report herein, are responsible for the receptor-mediated engulfment of Neisseria gonorrheae or Neisseria meningitidis by human cells and can offer deep understanding into the molecular recognition of pathogen–host receptor interactions. Such interactions are vital to understanding bacterial pathogenesis as well as the mechanism of foreign body entry to a human cell, which may provide insights for the development of targeted pharmaceutical delivery systems. The size and dynamics of the extracellular loops of Opa60 required a hybrid refinement approach wherein membrane and distance restraints were used to generate an initial NMR structural ensemble, which was then further refined using molecular dynamics in a DMPC bilayer. The resulting ensemble revealed that the extracellular loops, which bind host receptors, occupy compact conformations, interact with each other weakly, and are dynamic on the nanosecond time scale. We predict that this conformational sampling is critical for enabling diverse Opa loop sequences to engage a common set of receptors. PMID:24813921

  9. Structure of the Neisserial outer membrane protein Opa₆₀: loop flexibility essential to receptor recognition and bacterial engulfment.

    PubMed

    Fox, Daniel A; Larsson, Per; Lo, Ryan H; Kroncke, Brett M; Kasson, Peter M; Columbus, Linda

    2014-07-16

    The structure and dynamics of Opa proteins, which we report herein, are responsible for the receptor-mediated engulfment of Neisseria gonorrheae or Neisseria meningitidis by human cells and can offer deep understanding into the molecular recognition of pathogen-host receptor interactions. Such interactions are vital to understanding bacterial pathogenesis as well as the mechanism of foreign body entry to a human cell, which may provide insights for the development of targeted pharmaceutical delivery systems. The size and dynamics of the extracellular loops of Opa60 required a hybrid refinement approach wherein membrane and distance restraints were used to generate an initial NMR structural ensemble, which was then further refined using molecular dynamics in a DMPC bilayer. The resulting ensemble revealed that the extracellular loops, which bind host receptors, occupy compact conformations, interact with each other weakly, and are dynamic on the nanosecond time scale. We predict that this conformational sampling is critical for enabling diverse Opa loop sequences to engage a common set of receptors. PMID:24813921

  10. Conformational Flexibility and Dynamics of the Internal Loop and Helical Regions of the Kink-Turn Motif in the Glycine Riboswitch by Site-Directed Spin-Labeling.

    PubMed

    Esquiaqui, Jackie M; Sherman, Eileen M; Ye, Jing-Dong; Fanucci, Gail E

    2016-08-01

    Site-directed spin-labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy provides a means for a solution state description of site-specific dynamics and flexibility of large RNAs, facilitating our understanding of the effects of environmental conditions such as ligands and ions on RNA structure and dynamics. Here, the utility and capability of EPR line shape analysis and distance measurements to monitor and describe site-specific changes in the conformational dynamics of internal loop nucleobases as well as helix-helix interactions of the kink-turn motif in the Vibrio cholerae (VC) glycine riboswitch that occur upon sequential K(+)-, Mg(2+)-, and glycine-induced folding were explored. Spin-labels were incorporated into the 232-nucleotide sequence via splinted ligation strategies. Thiouridine nucleobase labeling within the internal loop reveals unambiguous differential dynamics for two successive sites labeled, with varied rates of motion reflective of base flipping and base stacking. EPR-based distance measurements for nitroxide spin-labels incorporated within the RNA backbone in the helical regions of the kink-turn motif are reflective of helical formation and tertiary interaction induced by ion stabilization. In both instances, results indicate that the structural formation of the kink-turn motif in the VC glycine riboswitch can be stabilized by 100 mM K(+) where the conformational flexibility of the kink-turn motif is not further tightened by subsequent addition of divalent ions. Although glycine binding is likely to induce structural and dynamic changes in other regions, SDSL indicates no impact of glycine binding on the local dynamics or structure of the kink-turn motif as investigated here. Overall, these results demonstrate the ability of SDSL to interrogate site-specific base dynamics and packing of helices in large RNAs and demonstrate ion-induced stability of the kink-turn fold of the VC riboswitch. PMID:27427937

  11. Nonlinear effects of a modal domain optical fiber sensor in a vibration suppression control loop for a flexible structure

    NASA Technical Reports Server (NTRS)

    Lindner, D. K.; Zvonar, G. A.; Baumann, W. T.; Delos, P. L.

    1993-01-01

    Recently, a modal domain optical fiber sensor has been demonstrated as a sensor in a control system for vibration suppression of a flexible cantilevered beam. This sensor responds to strain through a mechanical attachment to the structure. Because this sensor is of the interferometric type, the output of the sensor has a sinusoidal nonlinearity. For small levels of strain, the sensor can be operated in its linear region. For large levels of strain, the detection electronics can be configured to count fringes. In both of these configurations, the sensor nonlinearity imposes some restrictions on the performance of the control system. In this paper we investigate the effects of these sensor nonlinearities on the control system, and identify the region of linear operation in terms of the optical fiber sensor parameters.

  12. (1,3;1,4)-β-Glucan Biosynthesis by the CSLF6 Enzyme: Position and Flexibility of Catalytic Residues Influence Product Fine Structure.

    PubMed

    Dimitroff, George; Little, Alan; Lahnstein, Jelle; Schwerdt, Julian G; Srivastava, Vaibhav; Bulone, Vincent; Burton, Rachel A; Fincher, Geoffrey B

    2016-04-01

    Cellulose synthase-like F6 (CslF6) genes encode polysaccharide synthases responsible for (1,3;1,4)-β-glucan biosynthesis in cereal grains. However, it is not clear how both (1,3)- and (1,4)-linkages are incorporated into a single polysaccharide chain and how the frequency and arrangement of the two linkage types that define the fine structure of the polysaccharide are controlled. Through transient expression in Nicotiana benthamiana leaves, two CSLF6 orthologs from different cereal species were shown to mediate the synthesis of (1,3;1,4)-β-glucans with very different fine structures. Chimeric cDNA constructs with interchanged sections of the barley and sorghum CslF6 genes were developed to identify regions of the synthase enzyme responsible for these differences. A single amino acid residue upstream of the TED motif in the catalytic region was shown to dramatically change the fine structure of the polysaccharide produced. The structural basis of this effect can be rationalized by reference to a homology model of the enzyme and appears to be related to the position and flexibility of the TED motif in the active site of the enzyme. The region and amino acid residue identified provide opportunities to manipulate the solubility of (1,3;1,4)-β-glucan in grains and vegetative tissues of the grasses and, in particular, to enhance the solubility of dietary fibers that are beneficial to human health. PMID:26967377

  13. Managing Demand and Capacity Using Multi-Sector Planning and Flexible Airspace: Human-in-the-Loop Evaluation of NextGen

    NASA Technical Reports Server (NTRS)

    Lee, Paul U.; Smith, Nancy M.; Prevot, Thomas; Homola, Jeffrey R.

    2010-01-01

    When demand for an airspace sector exceeds capacity, the balance can be re-established by reducing the demand, increasing the capacity, or both. The Multi-Sector Planner (MSP) concept has been proposed to better manage traffic demand by modifying trajectories across multiple sectors. A complementary approach to MSP, called Flexible Airspace Management (FAM), reconfigures the airspace such that capacity can be reallocated dynamically to balance the traffic demand across multiple sectors, resulting in fewer traffic management initiatives. The two concepts have been evaluated with a series of human-in-the-loop simulations at the Airspace Operations Laboratory to examine and refine the roles of the human operators in these concepts, as well as their tools and procedural requirements. So far MSP and FAM functions have been evaluated individually but the integration of the two functions is desirable since there are significant overlaps in their goals, geographic/temporal scope of the problem space, and the implementation timeframe. Ongoing research is planned to refine the humans roles in the integrated concept.

  14. Cold adaptation of zinc metalloproteases in the thermolysin family from deep sea and arctic sea ice bacteria revealed by catalytic and structural properties and molecular dynamics: new insights into relationship between conformational flexibility and hydrogen bonding.

    PubMed

    Xie, Bin-Bin; Bian, Fei; Chen, Xiu-Lan; He, Hai-Lun; Guo, Jun; Gao, Xiang; Zeng, Yin-Xin; Chen, Bo; Zhou, Bai-Cheng; Zhang, Yu-Zhong

    2009-04-01

    Increased conformational flexibility is the prevailing explanation for the high catalytic efficiency of cold-adapted enzymes at low temperatures. However, less is known about the structural determinants of flexibility. We reported two novel cold-adapted zinc metalloproteases in the thermolysin family, vibriolysin MCP-02 from a deep sea bacterium and vibriolysin E495 from an Arctic sea ice bacterium, and compared them with their mesophilic homolog, pseudolysin from a terrestrial bacterium. Their catalytic efficiencies, k(cat)/K(m) (10-40 degrees C), followed the order pseudolysin < MCP-02 < E495 with a ratio of approximately 1:2:4. MCP-02 and E495 have the same optimal temperature (T(opt), 57 degrees C, 5 degrees C lower than pseudolysin) and apparent melting temperature (T(m) = 64 degrees C, approximately 10 degrees C lower than pseudolysin). Structural analysis showed that the slightly lower stabilities resulted from a decrease in the number of salt bridges. Fluorescence quenching experiments and molecular dynamics simulations showed that the flexibilities of the proteins were pseudolysin < MCP-02 < E495, suggesting that optimization of flexibility is a strategy for cold adaptation. Molecular dynamics results showed that the ordinal increase in flexibility from pseudolysin to MCP-02 and E495, especially the increase from MCP-02 to E495, mainly resulted from the decrease of hydrogen-bond stability in the dynamic structure, which was due to the increase in asparagine, serine, and threonine residues. Finally, a model for the cold adaptation of MCP-02 and E495 was proposed. This is the first report of the optimization of hydrogen-bonding dynamics as a strategy for cold adaptation and provides new insights into the structural basis underlying conformational flexibility. PMID:19181663

  15. Co-occurrence of analogous enzymes determines evolution of a novel (βα)8-isomerase sub-family after non-conserved mutations in flexible loop.

    PubMed

    Verduzco-Castro, Ernesto A; Michalska, Karolina; Endres, Michael; Juárez-Vazquez, Ana L; Noda-García, Lianet; Chang, Changsoo; Henry, Christopher S; Babnigg, Gyorgy; Joachimiak, Andrzej; Barona-Gómez, Francisco

    2016-05-01

    We investigate the evolution of co-occurring analogous enzymes involved in L-tryptophan and L-histidine biosynthesis in Actinobacteria Phylogenetic analysis of trpF homologues, a missing gene in certain clades of this lineage whose absence is complemented by a dual-substrate HisA homologue, termed PriA, found that they fall into three categories: (i) trpF-1, an L-tryptophan biosynthetic gene horizontally acquired by certain Corynebacterium species; (ii) trpF-2, a paralogue known to be involved in synthesizing a pyrrolopyrrole moiety and (iii) trpF-3, a variable non-conserved orthologue of trpF-1 We previously investigated the effect of trpF-1 upon the evolution of PriA substrate specificity, but nothing is known about the relationship between trpF-3 and priA After in vitro steady-state enzyme kinetics we found that trpF-3 encodes a phosphoribosyl anthranilate isomerase. However, mutation of this gene in Streptomyces sviceus did not lead to auxothrophy, as expected from the biosynthetic role of trpF-1 Biochemical characterization of a dozen co-occurring TrpF-2 or TrpF-3, with PriA homologues, explained the prototrophic phenotype, and unveiled an enzyme activity trade-off between TrpF and PriA. X-ray structural analysis suggests that the function of these PriA homologues is mediated by non-conserved mutations in the flexible L5 loop, which may be responsible for different substrate affinities. Thus, the PriA homologues that co-occur with TrpF-3 represent a novel enzyme family, termed PriB, which evolved in response to PRA isomerase activity. The characterization of co-occurring enzymes provides insights into the influence of functional redundancy on the evolution of enzyme function, which could be useful for enzyme functional annotation. PMID:26929404

  16. Conformational flexibility in the catalytic triad revealed by the high-resolution crystal structure of Streptomyces erythraeus trypsin in an unliganded state

    SciTech Connect

    Blankenship, Elise; Vukoti, Krishna; Miyagi, Masaru; Lodowski, David T.

    2014-03-01

    This work reports the first sub-angstrom resolution structure of S. erythraeus trypsin. The detailed model of a prototypical serine protease at a catalytically relevant pH with an unoccupied active site is presented and is compared with other high-resolution serine protease structures. With more than 500 crystal structures determined, serine proteases make up greater than one-third of all proteases structurally examined to date, making them among the best biochemically and structurally characterized enzymes. Despite the numerous crystallographic and biochemical studies of trypsin and related serine proteases, there are still considerable shortcomings in the understanding of their catalytic mechanism. Streptomyces erythraeus trypsin (SET) does not exhibit autolysis and crystallizes readily at physiological pH; hence, it is well suited for structural studies aimed at extending the understanding of the catalytic mechanism of serine proteases. While X-ray crystallographic structures of this enzyme have been reported, no coordinates have ever been made available in the Protein Data Bank. Based on this, and observations on the extreme stability and unique properties of this particular trypsin, it was decided to crystallize it and determine its structure. Here, the first sub-angstrom resolution structure of an unmodified, unliganded trypsin crystallized at physiological pH is reported. Detailed structural analysis reveals the geometry and structural rigidity of the catalytic triad in the unoccupied active site and comparison to related serine proteases provides a context for interpretation of biochemical studies of catalytic mechanism and activity.

  17. Laminated BEAM loops

    NASA Astrophysics Data System (ADS)

    Danisch, Lee A.

    1996-10-01

    BEAM sensors include treated loops of optical fiber that modulate optical throughput with great sensitivity and linearity, in response to curvature of the loop out of its plane. This paper describes BEAM sensors that have two loops treated in opposed fashion, hermetically sealed in flexible laminations. The sensors include an integrated optoelectronics package that extracts curvature information from the treated portion of the loops while rejecting common mode errors. The laminated structure is used to sense various parameters including displacement, force, pressure, flow, and acceleration.

  18. Homology modelling and structural analysis of human arylamine N-acetyltransferase NAT1: evidence for the conservation of a cysteine protease catalytic domain and an active-site loop.

    PubMed Central

    Rodrigues-Lima, F; Deloménie, C; Goodfellow, G H; Grant, D M; Dupret, J M

    2001-01-01

    Arylamine N-acetyltransferases (EC 2.3.1.5) (NATs) catalyse the biotransformation of many primary arylamines, hydrazines and their N-hydroxylated metabolites, thereby playing an important role in both the detoxification and metabolic activation of numerous xenobiotics. The recently published crystal structure of the Salmonella typhimurium NAT (StNAT) revealed the existence of a cysteine protease-like (Cys-His-Asp) catalytic triad. In the present study, a three-dimensional homology model of human NAT1, based upon the crystal structure of StNAT [Sinclair, Sandy, Delgoda, Sim and Noble (2000) Nat. Struct. Biol. 7, 560-564], is demonstrated. Alignment of StNAT and NAT1, together with secondary structure predictions, have defined a consensus region (residues 29-131) in which 37% of the residues are conserved. Homology modelling provided a good quality model of the corresponding region in human NAT1. The location of the catalytic triad was found to be identical in StNAT and NAT1. Comparison of active-site structural elements revealed that a similar length loop is conserved in both species (residues 122-131 in NAT1 model and residues 122-133 in StNAT). This observation may explain the involvement of residues 125, 127 and 129 in human NAT substrate selectivity. Our model, and the fact that cysteine protease inhibitors do not affect the activity of NAT1, suggests that human NATs may have adapted a common catalytic mechanism from cysteine proteases to accommodate it for acetyl-transfer reactions. PMID:11368758

  19. Accessibility of cysteine residues in a cytoplasmic loop of CitS of Klebsiella pneumoniae is controlled by the catalytic state of the transporter.

    PubMed

    Sobczak, Iwona; Lolkema, Juke S

    2003-08-19

    The citrate transporter CitS of Klebsiella pneumoniae is a secondary transporter that transports citrate in symport with two sodium ions and one proton. Treatment of CitS with the alkylating agent N-ethylmaleimide resulted in a complete loss of transport activity. Treatment of mutant proteins in which the five endogenous cysteine residues were mutated into serines in different combinations revealed that two cysteine residues located in the C-terminal cytoplasmic loop, Cys-398 and Cys-414, were responsible for the inactivation. Labeling with the membrane impermeable methanethiosulfonate derivatives MTSET and MTSES in right-side-out membrane vesicles showed that the cytoplasmic loop was accessible from the periplasmic side of the membrane. The membrane impermeable but more bulky maleimide AmdiS did not inactivate the transporter in right-side-out membrane vesicles. Inactivation by N-ethylmaleimide, MTSES, and MTSET was prevented by the presence of the co-ion Na(+). Protection was obtained upon binding 2 Na(+), which equals the transport stoichiometry. In the absence of Na(+), the substrate citrate had no effect on the inactivation by permeable or impermeable thiol reagents. In contrast, when subsaturating concentrations of Na(+) were present, citrate significantly reduced inactivation suggesting ordered binding of the substrate and co-ion; citrate is bound after Na(+). In the presence of the proton motive force, the reactivity of the Cys residues was increased significantly for the membrane permeable N-ethylmaleimide, while no difference was observed for the membrane impermeable thiol reagents. The results are discussed in the context of a model for the opening and closing of the translocation pore during turnover of the transporter. PMID:12911322

  20. Regulative Loops, Step Loops and Task Loops

    ERIC Educational Resources Information Center

    VanLehn, Kurt

    2016-01-01

    This commentary suggests a generalization of the conception of the behavior of tutoring systems, which the target article characterized as having an outer loop that was executed once per task and an inner loop that was executed once per step of the task. A more general conception sees these two loops as instances of regulative loops, which…

  1. A new crystal form of human tear lipocalin reveals high flexibility in the loop region and induced fit in the ligand cavity

    SciTech Connect

    Breustedt, Daniel A.; Chatwell, Lorenz; Skerra, Arne

    2009-10-01

    The crystal structure of tear lipocalin determined in space group P2{sub 1} revealed large structural deviations from the previously solved X-ray structure in space group C2, especially in the loop region and adjoining parts of the β-barrel which give rise to the ligand-binding site. These findings illustrate a novel mechanism for promiscuity in ligand recognition by the lipocalin protein family. Tear lipocalin (TLC) with the bound artificial ligand 1,4-butanediol has been crystallized in space group P2{sub 1} with four protein molecules in the asymmetric unit and its X-ray structure has been solved at 2.6 Å resolution. TLC is a member of the lipocalin family that binds ligands with diverse chemical structures, such as fatty acids, phospholipids and cholesterol as well as microbial siderophores and the antibiotic rifampin. Previous X-ray structural analysis of apo TLC crystallized in space group C2 revealed a rather large bifurcated ligand pocket and a partially disordered loop region at the entrace to the cavity. Analysis of the P2{sub 1} crystal form uncovered major conformational changes (i) in β-strands B, C and D, (ii) in loops 1, 2 and 4 at the open end of the β-barrel and (iii) in the extended C-terminal segment, which is attached to the β-barrel via a disulfide bridge. The structural comparison indicates high conformational plasticity of the loop region as well as of deeper parts of the ligand pocket, thus allowing adaptation to ligands that differ vastly in size and shape. This illustrates a mechanism for promiscuity in ligand recognition which may also be relevant for some other physiologically important members of the lipocalin protein family.

  2. Functional dichotomy in the 16S rRNA (m1A1408) methyltransferase family and control of catalytic activity via a novel tryptophan mediated loop reorganization

    PubMed Central

    Witek, Marta A.; Conn, Graeme L.

    2016-01-01

    Methylation of the bacterial small ribosomal subunit (16S) rRNA on the N1 position of A1408 confers exceptionally high-level resistance to a broad spectrum of aminoglycoside antibiotics. Here, we present a detailed structural and functional analysis of the Catenulisporales acidiphilia 16S rRNA (m1A1408) methyltransferase (‘CacKam’). The apo CacKam structure closely resembles other m1A1408 methyltransferases within its conserved SAM-binding fold but the region linking core β strands 6 and 7 (the ‘β6/7 linker’) has a unique, extended structure that partially occludes the putative 16S rRNA binding surface, and sequesters the conserved and functionally critical W203 outside of the CacKam active site. Substitution of conserved residues in the SAM binding pocket reveals a functional dichotomy in the 16S rRNA (m1A1408) methyltransferase family, with two apparently distinct molecular mechanisms coupling cosubstrate/ substrate binding to catalytic activity. Our results additionally suggest that CacKam exploits the W203-mediated remodeling of the β6/7 linker as a novel mechanism to control 30S substrate recognition and enzymatic turnover. PMID:26609134

  3. A new crystal form of human tear lipocalin reveals high flexibility in the loop region and induced fit in the ligand cavity

    PubMed Central

    Breustedt, Daniel A.; Chatwell, Lorenz; Skerra, Arne

    2009-01-01

    Tear lipocalin (TLC) with the bound artificial ligand 1,4-butanediol has been crystallized in space group P21 with four protein molecules in the asymmetric unit and its X-ray structure has been solved at 2.6 Å resolution. TLC is a member of the lipocalin family that binds ligands with diverse chemical structures, such as fatty acids, phospholipids and cholesterol as well as microbial siderophores and the antibiotic rifampin. Previous X-ray structural analysis of apo TLC crystallized in space group C2 revealed a rather large bifurcated ligand pocket and a partially disordered loop region at the entrace to the cavity. Analysis of the P21 crystal form uncovered major conformational changes (i) in β-strands B, C and D, (ii) in loops 1, 2 and 4 at the open end of the β-­barrel and (iii) in the extended C-terminal segment, which is attached to the β-­barrel via a disulfide bridge. The structural comparison indicates high conformational plasticity of the loop region as well as of deeper parts of the ligand pocket, thus allowing adaptation to ligands that differ vastly in size and shape. This illustrates a mechanism for promiscuity in ligand recognition which may also be relevant for some other physiologically important members of the lipocalin protein family. PMID:19770509

  4. Flexibility and enzymatic cold-adaptation: a comparative molecular dynamics investigation of the elastase family.

    PubMed

    Papaleo, Elena; Riccardi, Laura; Villa, Chiara; Fantucci, Piercarlo; De Gioia, Luca

    2006-08-01

    Molecular dynamics simulations of representative mesophilic and psycrophilic elastases have been carried out at different temperatures to explore the molecular basis of cold adaptation inside a specific enzymatic family. The molecular dynamics trajectories have been compared and analyzed in terms of secondary structure, molecular flexibility, intramolecular and protein-solvent interactions, unravelling molecular features relevant to rationalize the efficient catalytic activity of psychrophilic elastases at low temperature. The comparative molecular dynamics investigation reveals that modulation of the number of protein-solvent interactions is not the evolutionary strategy followed by the psycrophilic elastase to enhance catalytic activity at low temperature. In addition, flexibility and solvent accessibility of the residues forming the catalytic triad and the specificity pocket are comparable in the cold- and warm-adapted enzymes. Instead, loop regions with different amino acid composition in the two enzymes, and clustered around the active site or the specificity pocket, are characterized by enhanced flexibility in the cold-adapted enzyme. Remarkably, the psycrophilic elastase is characterized by reduced flexibility, when compared to the mesophilic counterpart, in some scattered regions distant from the functional sites, in agreement with hypothesis suggesting that local rigidity in regions far from functional sites can be beneficial for the catalytic activity of psychrophilic enzymes. PMID:16920043

  5. Loop Dynamics of the Extracellular Domain of Human Tissue Factor and Activation of Factor VIIa

    PubMed Central

    Minazzo, Agnese S.; Darlington, Reuben C.; Ross, J.B. Alexander

    2009-01-01

    Abstract In the crystal structure of the complex between the soluble extracellular domain of tissue factor (sTF) and active-site-inhibited VIIa, residues 91 and 92 in the Pro79-Pro92 loop of sTF interact with the catalytic domain of VIIa. It is not known, however, whether this loop has a role in allosteric activation of VIIa. Time-resolved fluorescence anisotropy measurements of probes covalently bound to sTF mutants E84C and T121C show that binding uninhibited Factor VIIa affects segmental motions in sTF. Glu84 resides in the Pro79-Pro92 loop, and Thr121 resides in the turn between the first and second antiparallel β-strands of the sTF subdomain that interacts with the Gla and EGF1 domains of VIIa; neither Glu84 nor Thr121 makes direct contact with VIIa. Probes bound to T121C report limited segmental flexibility in free sTF, which is lost after VIIa binding. Probes bound to E84C report substantial segmental flexibility in the Pro79-Pro92 loop in free sTF, which is greatly reduced after VIIa binding. Thus, VIIa binding reduces dynamic motions in sTF. In particular, the decrease in the Pro79-Pro92 loop motions indicates that loop entropy has a role in the thermodynamics of the protein-protein interactions involved in allosteric control of VIIa activation. PMID:19167313

  6. The Arg7Lys mutant of heat-labile enterotoxin exhibits great flexibility of active site loop 47-56 of the A subunit.

    PubMed

    van den Akker, F; Merritt, E A; Pizza, M; Domenighini, M; Rappuoli, R; Hol, W G

    1995-09-01

    The heat-labile enterotoxin from Escherichia coli (LT) is a member of the cholera toxin family. These and other members of the larger class of AB5 bacterial toxins act through catalyzing the ADP-ribosylation of various intracellular targets including Gs alpha. The A subunit is responsible for this covalent modification, while the B pentamer is involved in receptor recognition. We report here the crystal structure of an inactive single-site mutant of LT in which arginine 7 of the A subunit has been replaced by a lysine residue. The final model contains 103 residues for each of the five B subunits, 175 residues for the A1 subunit, and 41 residues for the A2 subunit. In this Arg7Lys structure the active site cleft within the A subunit is wider by approximately 1 A than is seen in the wild-type LT. Furthermore, a loop near the active site consisting of residues 47-56 is disordered in the Arg7Lys structure, even though the new lysine residue at position 7 assumes a position which virtually coincides with that of Arg7 in the wild-type structure. The displacement of residues 47-56 as seen in the mutant structure is proposed to be necessary for allowing NAD access to the active site of the wild-type LT. On the basis of the differences observed between the wild-type and Arg7Lys structures, we propose a model for a coordinated sequence of conformational changes required for full activation of LT upon reduction of disulfide bridge 187-199 and cleavage of the peptide loop between the two cysteines in the A subunit.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7669757

  7. Flexibility and mutagenic resiliency of glycosyltransferases.

    PubMed

    Bay, Marie Lund; Cuesta-Seijo, Jose A; Weadge, Joel T; Persson, Mattias; Palcic, Monica M

    2014-10-01

    The human blood group A and B antigens are synthesized by two highly homologous enzymes, glycosyltransferase A (GTA) and glycosyltransferase B (GTB), respectively. These enzymes catalyze the transfer of either GalNAc or Gal from their corresponding UDP-donors to αFuc1-2βGal-R terminating acceptors. GTA and GTB differ at only four of 354 amino acids (R176G, G235S, L266M, G268A), which alter the donor specificity from UDP-GalNAc to UDP-Gal. Blood type O individuals synthesize truncated or non-functional enzymes. The cloning, crystallization and X-ray structure elucidations for GTA and GTB have revealed key residues responsible for donor discrimination and acceptor binding. Structural studies suggest that numerous conformational changes occur during the catalytic cycle. Over 300 ABO alleles are tabulated in the blood group antigen mutation database (BGMUT) that provides a framework for structure-function studies. Natural mutations are found in all regions of GTA and GTB from the active site, flexible loops, stem region and surfaces remote from the active site. Our characterizations of natural mutants near a flexible loop (V175M), on a remote surface site (P156L), in the metal binding motif (M212V) and near the acceptor binding site (L232P) demonstrate the resiliency of GTA and GTB to mutagenesis. PMID:25117515

  8. The synthesis, structure, topology and catalytic application of a novel cubane-based copper(II) metal-organic framework derived from a flexible amido tripodal acid.

    PubMed

    Karmakar, Anirban; Oliver, Clive L; Roy, Somnath; Öhrström, Lars

    2015-06-14

    A novel chiral metal-organic framework, [Cu4(HL)2(H2O)4(MeO)4]n (), has been successfully synthesized from a tripodal flexible ligand (2S,2'S,2''S)-2,2',2''-(benzenetricarbonyltris(azanediyl))tripropanoic acid (H3L). Compound was characterized by IR and X-ray powder diffraction analysis. The structure was determined by X-ray single crystal diffraction analysis revealing that possesses a 3D network, featuring a tetranuclear cubane-type secondary building block [Cu4(MeO)4](4+), formed via the connection of four metal ions to four methoxide ions. These secondary building blocks are linked by four different HL(2-) ligands to construct a porous three dimensional framework of the dia topology with one-dimensional channels. Compound also acts as a heterogeneous catalyst for the diastereoselective nitroaldol (Henry) reaction, providing high yields (up to 91%) and good diastereoselectivities under ambient conditions. This catalyst can be recycled without significant loss of activity. PMID:25645371

  9. Modulation of HIV protease flexibility by the T80N mutation.

    PubMed

    Zhou, Hao; Li, Shangyang; Badger, John; Nalivaika, Ellen; Cai, Yufeng; Foulkes-Murzycki, Jennifer; Schiffer, Celia; Makowski, Lee

    2015-11-01

    The flexibility of HIV protease (HIVp) plays a critical role in enabling enzymatic activity and is required for substrate access to the active site. While the importance of flexibility in the flaps that cover the active site is well known, flexibility in other parts of the enzyme is also critical for function. One key region is a loop containing Thr 80, which forms the walls of the active site. Although not situated within the active site, amino acid Thr80 is absolutely conserved. The mutation T80N preserves the structure of the enzyme but catalytic activity is completely lost. To investigate the potential influence of the T80N mutation on HIVp flexibility, wide-angle X-ray scattering (WAXS) data was measured for a series of HIVp variants. Starting with a calculated WAXS pattern from a rigid atomic model, the modulations in the intensity distribution caused by structural fluctuations in the protein were predicted by simple analytic methods and compared with the experimental data. An analysis of T80N WAXS data shows that this variant is significantly more rigid than the WT across all length scales. The effects of this single point mutation extend throughout the protein, to alter the mobility of amino acids in the enzymatic core. These results support the contentions that significant protein flexibility extends throughout HIVp and is critical to catalytic function. PMID:25488402

  10. A conserved salt bridge in the G loop of multiple protein kinases is important for catalysis and for in vivo Lyn function.

    PubMed

    Barouch-Bentov, Rina; Che, Jianwei; Lee, Christian C; Yang, Yating; Herman, Ann; Jia, Yong; Velentza, Anastasia; Watson, James; Sternberg, Luise; Kim, Sunjun; Ziaee, Niusha; Miller, Andrew; Jackson, Carie; Fujimoto, Manabu; Young, Mike; Batalov, Serge; Liu, Yi; Warmuth, Markus; Wiltshire, Tim; Cooke, Michael P; Sauer, Karsten

    2009-01-16

    The glycine-rich G loop controls ATP binding and phosphate transfer in protein kinases. Here we show that the functions of Src family and Abl protein tyrosine kinases require an electrostatic interaction between oppositely charged amino acids within their G loops that is conserved in multiple other phylogenetically distinct protein kinases, from plants to humans. By limiting G loop flexibility, it controls ATP binding, catalysis, and inhibition by ATP-competitive compounds such as Imatinib. In WeeB mice, mutational disruption of the interaction results in expression of a Lyn protein with reduced catalytic activity, and in perturbed B cell receptor signaling. Like Lyn(-/-) mice, WeeB mice show profound defects in B cell development and function and succumb to autoimmune glomerulonephritis. This demonstrates the physiological importance of the conserved G loop salt bridge and at the same time distinguishes the in vivo requirement for the Lyn kinase activity from other potential functions of the protein. PMID:19150426

  11. Interface dynamics explain assembly dependency of influenza neuraminidase catalytic activity

    PubMed Central

    von Grafenstein, Susanne; Wallnoefer, Hannes G.; Kirchmair, Johannes; Fuchs, Julian E.; Huber, Roland G.; Schmidtke, Michaela; Sauerbrei, Andreas; Rollinger, Judith M.; Liedl, Klaus R.

    2015-01-01

    Influenza virus neuraminidase (iNA) is a homotetrameric surface protein of the influenza virus and an established target for antiviral drugs. In contrast to neuraminidases (NAs) of other biological systems (non-iNAs), enzymatic activity of iNA is only observed in a quaternary assembly and iNA needs the tetramerization to mediate enzymatic activity. Obviously, differences on a molecular level between iNA and non-iNAs are responsible for this intriguing observation. Comparison between protein structures and multiple sequence alignment allow the identification of differences in amino acid composition in crucial regions of the enzyme, such as next to the conserved D151 and the 150-loop. These differences in amino acid sequence and protein tetramerization are likely to alter the dynamics of the system. Therefore, we performed molecular dynamics simulations to investigate differences in the molecular flexibility of monomers, dimers, and tetramers of iNAs of subtype N1 (avian 2004, pandemic 1918 and pandemic 2009 iNA) and as comparison the non-iNA monomer from Clostridium perfringens. We show that conformational transitions of iNA are crucially influenced by its assembly state. The protein–protein interface induces a complex hydrogen-bonding network between the 110-helix and the 150-loop, which consequently stabilizes the structural arrangement of the binding site. Therefore, we claim that these altered dynamics are responsible for the dependence of iNA’s catalytic activity on the tetrameric assembly. Only the tetramerization-induced balance between stabilization and altered local flexibility in the binding site provides the appropriate arrangement of key residues for iNA’s catalytic activity. PMID:24279589

  12. Biopolymer hairpin loops sustained by polarons

    NASA Astrophysics Data System (ADS)

    Chakrabarti, B.; Piette, B. M. A. G.; Zakrzewski, W. J.

    2012-08-01

    We show that polarons can sustain looplike configurations in flexible biopolymers and that the size of the loops depend on both the flexural rigidity of the polymer and the electron-phonon coupling constant. In particular we show that for single stranded DNA (ssDNA) and polyacetylene such loops can have as few as seven monomers. We also show that these configurations are very stable under thermal fluctuations and so could facilitate the formation of hairpin loops of ssDNA.

  13. Negative Factor from SIV Binds to the Catalytic Subunit of the V-ATPase to Internalize CD4 and to Increase Viral Infectivity

    PubMed Central

    Mandic, Robert; Fackler, Oliver T.; Geyer, Matthias; Linnemann, Thomas; Zheng, Yong-Hui; Peterlin, B. Matija

    2001-01-01

    The accessory protein negative factor (Nef) from human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) is required for optimal viral infectivity and the progression to acquired immunodeficiency syndrome (AIDS). Nef interacts with the endocytic machinery, resulting in the down-regulation of cluster of differentiation antigen 4 (CD4) and major histocompatibility complex class I (MHCI) molecules on the surface of infected cells. Mutations in the C-terminal flexible loop of Nef result in a lower rate of internalization by this viral protein. However, no loop-dependent binding of Nef to adaptor protein-2 (AP-2), which is the adaptor protein complex that is required for the internalization of proteins from the plasma membrane, could be demonstrated. In this study we investigated the relevance of different motifs in Nef from SIVmac239 for its internalization, CD4 down-regulation, binding to components of the trafficking machinery, and viral infectivity. Our data suggest that the binding of Nef to the catalytic subunit H of the vacuolar membrane ATPase (V-ATPase) facilitates its internalization. This binding depends on the integrity of the whole flexible loop. Subsequent studies on Nef mutant viruses revealed that the flexible loop is essential for optimal viral infectivity. Therefore, our data demonstrate how Nef contacts the endocytic machinery in the absence of its direct binding to AP-2 and suggest an important role for subunit H of the V-ATPase in viral infectivity. PMID:11179428

  14. Flexibility and Stability Trade-Off in Active Site of Cold-Adapted Pseudomonas mandelii Esterase EstK.

    PubMed

    Truongvan, Ngoc; Jang, Sei-Heon; Lee, ChangWoo

    2016-06-28

    Cold-adapted enzymes exhibit enhanced conformational flexibility, especially in their active sites, as compared with their warmer-temperature counterparts. However, the mechanism by which cold-adapted enzymes maintain their active site stability is largely unknown. In this study, we investigated the role of conserved D308-Y309 residues located in the same loop as the catalytic H307 residue in the cold-adapted esterase EstK from Pseudomonas mandelii. Mutation of D308 and/or Y309 to Ala or deletion resulted in increased conformational flexibility. Particularly, the D308A or Y309A mutant showed enhanced substrate affinity and catalytic rate, as compared with wild-type EstK, via enlargement of the active site. However, all mutant EstK enzymes exhibited reduced thermal stability. The effect of mutation was greater for D308 than Y309. These results indicate that D308 is not preferable for substrate selection and catalytic activity, whereas hydrogen bond formation involving D308 is critical for active site stabilization. Taken together, conformation of the EstK active site is constrained via flexibility-stability trade-off for enzyme catalysis and thermal stability. Our study provides further insights into active site stabilization of cold-adapted enzymes. PMID:27259687

  15. Loop-to-loop coupling.

    SciTech Connect

    Warne, Larry Kevin; Lucero, Larry Martin; Langston, William L.; Salazar, Robert Austin; Coleman, Phillip Dale; Basilio, Lorena I.; Bacon, Larry Donald

    2012-05-01

    This report estimates inductively-coupled energy to a low-impedance load in a loop-to-loop arrangement. Both analytical models and full-wave numerical simulations are used and the resulting fields, coupled powers and energies are compared. The energies are simply estimated from the coupled powers through approximations to the energy theorem. The transmitter loop is taken to be either a circular geometry or a rectangular-loop (stripline-type) geometry that was used in an experimental setup. Simple magnetic field models are constructed and used to estimate the mutual inductance to the receiving loop, which is taken to be circular with one or several turns. Circuit elements are estimated and used to determine the coupled current and power (an equivalent antenna picture is also given). These results are compared to an electromagnetic simulation of the transmitter geometry. Simple approximate relations are also given to estimate coupled energy from the power. The effect of additional loads in the form of attached leads, forming transmission lines, are considered. The results are summarized in a set of susceptibility-type curves. Finally, we also consider drives to the cables themselves and the resulting common-to-differential mode currents in the load.

  16. Loop statistics in polymers in crowded environment

    NASA Astrophysics Data System (ADS)

    Haydukivska, K.; Blavatska, V.

    2016-02-01

    We analyze the probability to find a single loop in a long flexible polymer chain in disordered environment in d dimensions. The structural defects are considered to be correlated on large distances r according to a power law ˜r-a. Working within the frames of continuous chain model and applying the direct polymer renormalization scheme, we obtain the values of critical exponents governing the scaling of probabilities to find the loops of various positions along the chain as function of loops' length. Our results quantitatively reveal that the presence of structural defects in environment decreases the probability of loop formation in polymer macromolecules.

  17. An extended loop in CE7 carbohydrate esterase family is dispensable for oligomerization but required for activity and thermostability.

    PubMed

    Singh, Mrityunjay K; Manoj, Narayanan

    2016-06-01

    The carbohydrate esterase family 7 (CE7) belonging to the α/β hydrolase superfamily contains a structurally conserved loop extension element relative to the canonical α/β hydrolase fold. This element called the β-interface loop contributes 20-30% of the total buried surface area at intersubunit interfaces of the functional hexameric state. To test whether this loop is an enabling region for the structure and function of the oligomeric assembly, we designed a truncation variant of the thermostable CE7 acetyl esterase from Thermotoga maritima (TmAcE). Although deletion of 26 out of 40 residues in the loop had little impact on the hexamer formation, the variant exhibited altered dynamics of the oligomeric assembly and a loss of thermal stability. Furthermore, the mutant lacked catalytic activity. Crystal structures of the variant and a new crystal form of the wild type protein determined at 2.75Å and 1.76Å, respectively, provide a rationale for the properties of the variant. The hexameric assembly in the variant is identical to that of the wild type and differed only in the lack of buried surface area interactions at the original intersubunit interfaces. This is accompanied by disorder in an extended region of the truncated loop that consequently induces disorder in the neighboring oxyanion hole loop. Overall, the results suggest that the β-interface loop in CE7 enzymes is dispensable for the oligomeric assembly. Rather, the loop extension event was evolutionarily selected to regulate activity, conformational flexibility and thermal stability. PMID:27085421

  18. Flexibility Program

    ERIC Educational Resources Information Center

    Connors, G. Patrick

    These brief guidelines for a muscular flexibility program state that the purpose of such a program is to increase the range of motion in order to avoid injuries and eliminate awkwardness in physical activities. A flexibility program is described as an extension of the warm-up period and should be an ongoing, permanent effort to lengthen muscles. A…

  19. Flexible Scheduling.

    ERIC Educational Resources Information Center

    Davis, Harold S.; Bechard, Joseph E.

    A flexible schedule allows teachers to change group size, group composition, and class length according to the purpose of the lesson. This pamphlet presents various "master" schedules for flexible scheduling: (1) Simple block schedules, (2) back-to-back schedules, (3) interdisciplinary schedules, (4) school-wide block schedules, (5) open-lab…

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

    SciTech Connect

    Pegan, Scott D.; Rukseree, Kamolchanok; Capodagli, Glenn C.; Baker, Erica A.; Krasnykh, Olga; Franzblau, Scott G.; Mesecar, Andrew D.

    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.

  1. Active site loop dynamics of a class IIa fructose 1,6-bisphosphate aldolase from Mycobacterium tuberculosis.

    PubMed

    Pegan, Scott D; Rukseree, Kamolchanok; Capodagli, Glenn C; Baker, Erica A; Krasnykh, Olga; Franzblau, Scott G; Mesecar, Andrew D

    2013-02-01

    Class II fructose 1,6-bisphosphate aldolases (FBAs, EC 4.1.2.13) comprise 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. Also, 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. PMID:23298222

  2. Active site loop dynamics of a class IIa fructose 1,6-bisphosphate aldolase from M. tuberculosis

    PubMed Central

    Pegan, Scott D.; Rukseree, Kamolchanok; Capodagli, Glenn C.; Baker, Erica A; Krasnykh, Olga; Franzblau, Scott G; Mesecar, Andrew D

    2014-01-01

    Class II fructose 1,6-bisphosphate aldolases (FBA; E.C. 4.1.2.13) comprise 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 has been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies on 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/DHAP bound form of the enzyme and determined the X-ray structure of 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 plus 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. Also, secondary 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. PMID:23298222

  3. Flexible spacecraft simulator

    NASA Technical Reports Server (NTRS)

    1987-01-01

    Verification of control algorithms for flexible spacecraft can be done only through simulation and test; these are necessary to understand control/structure interaction (C/SI) sufficiently to design robust controllers for future spacecraft. The objective persued is to develop a low-cost facility which simulates the fundamental problem of C/SI; and to provide accessibility for designs so that experience can be gained in applying various multivariable control design methods to an actual structure. A test facility is being constructed with test elements that provide 3 rigid body and 6 flexible modes, all in the horizontal plane, with frequencies below 2.5 Hz. The control force actuator are on/off air jets with sensing by optical displacement sensors. Loop closure is provided by a digital computer with control algorithms designed using the IAC and MATRIX-X.

  4. Catalytic reactor

    DOEpatents

    Aaron, Timothy Mark; Shah, Minish Mahendra; Jibb, Richard John

    2009-03-10

    A catalytic reactor is provided with one or more reaction zones each formed of set(s) of reaction tubes containing a catalyst to promote chemical reaction within a feed stream. The reaction tubes are of helical configuration and are arranged in a substantially coaxial relationship to form a coil-like structure. Heat exchangers and steam generators can be formed by similar tube arrangements. In such manner, the reaction zone(s) and hence, the reactor is compact and the pressure drop through components is minimized. The resultant compact form has improved heat transfer characteristics and is far easier to thermally insulate than prior art compact reactor designs. Various chemical reactions are contemplated within such coil-like structures such that as steam methane reforming followed by water-gas shift. The coil-like structures can be housed within annular chambers of a cylindrical housing that also provide flow paths for various heat exchange fluids to heat and cool components.

  5. Rigidification of the autolysis loop enhances Na[superscript +] binding to thrombin

    SciTech Connect

    Pozzi, Nicola; Chen, Raymond; Chen, Zhiwei; Bah, Alaji; Di Cera, Enrico

    2011-09-20

    Binding of Na{sup +} 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{sup +} is weak due to large heat capacity and enthalpy changes associated with binding, and the K{sub d} = 80 mM ensures only 64% saturation of the site at the concentration of Na{sup +} in the blood (140 mM). Residues controlling Na{sup +} binding and activation have been identified. Yet, attempts to improve the interaction of Na{sup +} 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{sup +} 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{sup +} 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.

  6. Synergize fuel and petrochemical processing plans with catalytic reforming

    SciTech Connect

    1997-03-01

    Depending on the market, refiner`s plans to produce clean fuels and higher value petrochemicals will weigh heavily on the catalytic reformer`s flexibility. It seems that as soon as a timely article related to catalytic reforming operations is published, a new {open_quotes}boutique{close_quotes} gasoline fuel specification is slapped on to existing fuel standards, affecting reformer operations and processing objectives. Just as importantly, the petrochemical market (such as aromatics) that refiners are targeting, can be very fickle. That`s why process engineers have endeavored to maintain an awareness of the flexibility that technology suppliers are building into modern catalytic reformers.

  7. Flexible cystoscopy.

    PubMed

    Kennedy, T J; Preminger, G M

    1988-08-01

    Flexible fiberoptic technology was first applied to cystoscopy in 1973, with greatly increased usage since 1982. Most procedures formerly performed with rigid cystoscopes can be done using flexible cystoscopes with minimal or no anesthesia. Patient positioning and precystocopy preparation and draping are simplified with the flexible fiberoptic instruments. Complete examination of the urethra and bladder can be performed with a single-lens system and with the patient in a variety of positions. Fiberoptic cystoscopy is limited in patients who are bleeding or have blood clots in their bladders. Withdrawal of irrigant or bladder drainage is cumbersome, and the fiberoptic image is currently not of the same caliber as that of the rigid-lens systems. Fiberoptic cystoscopy has become the procedure of choice for many urologists for ureteral stenting prior to extracorporeal shock-wave lithotripsy. With the advent of lithotripters that require no anesthesia, this application is likely to broaden. Future applications of flexible cystoscopy may include a flexible videocystoscope for use in diagnostic and therapeutic procedures. PMID:3407042

  8. Raney nickel catalytic device

    DOEpatents

    O'Hare, Stephen A.

    1978-01-01

    A catalytic device for use in a conventional coal gasification process which includes a tubular substrate having secured to its inside surface by expansion a catalytic material. The catalytic device is made by inserting a tubular catalytic element, such as a tubular element of a nickel-aluminum alloy, into a tubular substrate and heat-treating the resulting composite to cause the tubular catalytic element to irreversibly expand against the inside surface of the substrate.

  9. An RNA molecular switch: Intrinsic flexibility of 23S rRNA Helices 40 and 68 5’-UAA/5’-GAN internal loops studied by molecular dynamics methods

    PubMed Central

    Réblová, Kamila; Střelcová, Zora; Kulhánek, Petr; Beššeová, Ivana; Mathews, David H.; Nostrand, Keith Van; Yildirim, Ilyas; Turner, Douglas H.; Šponer, Jiří

    2010-01-01

    Functional RNA molecules such as ribosomal RNAs frequently contain highly conserved internal loops with a 5’-UAA/5’-GAN (UAA/GAN) consensus sequence. The UAA/GAN internal loops adopt distinctive structure inconsistent with secondary structure predictions. The structure has a narrow major groove and forms a trans Hoogsteen/Sugar edge (tHS) A/G base pair followed by an unpaired stacked adenine, a trans Watson-Crick/Hoogsteen (tWH) U/A base pair and finally by a bulged nucleotide (N). The structure is further stabilized by a three-adenine stack and base-phosphate interaction. In the ribosome, the UAA/GAN internal loops are involved in extensive tertiary contacts, mainly as donors of A-minor interactions. Further, this sequence can adopt an alternative 2D/3D pattern stabilized by a four-adenine stack involved in a smaller number of tertiary interactions. The solution structure of an isolated UAA/GAA internal loop shows substantially rearranged base pairing with three consecutive non-Watson-Crick base pairs. Its A/U base pair adopts an incomplete cis Watson-Crick/Sugar edge (cWS) A/U conformation instead of the expected Watson-Crick arrangement. We performed 3.1 µs of explicit solvent molecular dynamics (MD) simulations of the X-ray and NMR UAA/GAN structures, supplemented by MM-PBSA free energy calculations, locally enhanced sampling (LES) runs, targeted MD (TMD) and nudged elastic band (NEB) analysis. We compared parm99 and parmbsc0 force fields and net-neutralizing Na+ vs. excess salt KCl ion environments. Both force fields provide a similar description of the simulated structures, with the parmbsc0 leading to modest narrowing of the major groove. The excess salt simulations also cause a similar effect. While the NMR structure is entirely stable in simulations, the simulated X-ray structure shows considerable widening of the major groove, loss of base-phosphate interaction and other instabilities. The alternative X-ray geometry even undergoes conformational

  10. Rollercoaster Loop Shapes

    ERIC Educational Resources Information Center

    Pendrill, Ann-Marie

    2005-01-01

    Many modern rollercoasters feature loops. Although textbook loops are often circular, real rollercoaster loops are not. In this paper, we look into the mathematical description of various possible loop shapes, as well as their riding properties. We also discuss how a study of loop shapes can be used in physics education.

  11. Rollercoaster loop shapes

    NASA Astrophysics Data System (ADS)

    Pendrill, Ann-Marie

    2005-11-01

    Many modern rollercoasters feature loops. Although textbook loops are often circular, real rollercoaster loops are not. In this paper, we look into the mathematical description of various possible loop shapes, as well as their riding properties. We also discuss how a study of loop shapes can be used in physics education.

  12. Piping Flexibility

    NASA Technical Reports Server (NTRS)

    1978-01-01

    A NASA computer program aids Hudson Engineering Corporation, Houston, Texas, in the design and construction of huge petrochemical processing plants like the one shown, which is located at Ju'aymah, Saudi Arabia. The pipes handling the flow of chemicals are subject to a variety of stresses, such as weight and variations in pressure and temperature. Hudson Engineering uses a COSMIC piping flexibility analysis computer program to analyze stresses and unsure the necessary strength and flexibility of the pipes. This program helps the company realize substantial savings in reduced engineering time.

  13. Water Stream "Loop-the-Loop"

    ERIC Educational Resources Information Center

    Jefimenko, Oleg

    1974-01-01

    Discusses the design of a modified loop-the-loop apparatus in which a water stream is used to illustrate centripetal forces and phenomena of high-velocity hydrodynamics. Included are some procedures of carrying out lecture demonstrations. (CC)

  14. Improved activity and modulated action pattern obtained by random mutagenesis at the fourth beta-alpha loop involved in substrate binding to the catalytic (beta/alpha)8-barrel domain of barley alpha-amylase 1.

    PubMed

    Matsui, I; Svensson, B

    1997-09-01

    The functionality of the sequence Arg183-Gly184-Tyr185 of the substrate binding fourth beta-alpha loop in the (beta/alpha)8-barrel of barley alpha-amylase isozyme 1 (AMY1) was studied by random mutagenesis. A motif of polar Gly184 hydrophobic residues was present in active mutants, selected by starch plate screening of yeast transformants. Gly184 was important, probably due to the carbonyl group binding to Ca2+ and the spatial proximity of Phe181. Mutation of both flanking residues as in Ser183-Gly184-Met185 (SGM-) and TGL-AMY1 decreased the Ca2+ affinity. SGM-AMY1 has 2-fold increased activity for amylose but reduced activity on maltooligosaccharides, whereas KGY-AMY1 has up to 3-fold elevated activity toward the oligosaccharides. TGL-AMY1 has modest activity on all substrates. Shifted action pattern on maltooligosaccharides for NGY-, SGM-, and TGL-AMY1 support that Arg183 in wild type is located at subsites +1 and +2, accommodating two sugar rings toward the reducing end from the site of cleavage. In the crystal structure of barley alpha-amylase 2 (AMY2), Lys182 (equivalent to AMY1 Arg183) is hydrogen-bonded with sugar OH-3 in subsite +2. Higher Ki app for acarbose inhibition of KGY-AMY1 and parent AMY1 compared with the other mutants suggests favorable substrate interactions for Arg/Lys183. KGY-AMY1 was not inhibited by the AMY2-specific proteinaceous barley alpha-amylase/subtilisin inhibitor, although Lys182 of AMY2 is salt-linked to the inhibitor. PMID:9278396

  15. Closed-Loop Neuromorphic Benchmarks

    PubMed Central

    Stewart, Terrence C.; DeWolf, Travis; Kleinhans, Ashley; Eliasmith, Chris

    2015-01-01

    Evaluating the effectiveness and performance of neuromorphic hardware is difficult. It is even more difficult when the task of interest is a closed-loop task; that is, a task where the output from the neuromorphic hardware affects some environment, which then in turn affects the hardware's future input. However, closed-loop situations are one of the primary potential uses of neuromorphic hardware. To address this, we present a methodology for generating closed-loop benchmarks that makes use of a hybrid of real physical embodiment and a type of “minimal” simulation. Minimal simulation has been shown to lead to robust real-world performance, while still maintaining the practical advantages of simulation, such as making it easy for the same benchmark to be used by many researchers. This method is flexible enough to allow researchers to explicitly modify the benchmarks to identify specific task domains where particular hardware excels. To demonstrate the method, we present a set of novel benchmarks that focus on motor control for an arbitrary system with unknown external forces. Using these benchmarks, we show that an error-driven learning rule can consistently improve motor control performance across a randomly generated family of closed-loop simulations, even when there are up to 15 interacting joints to be controlled. PMID:26696820

  16. Closed-Loop Neuromorphic Benchmarks.

    PubMed

    Stewart, Terrence C; DeWolf, Travis; Kleinhans, Ashley; Eliasmith, Chris

    2015-01-01

    Evaluating the effectiveness and performance of neuromorphic hardware is difficult. It is even more difficult when the task of interest is a closed-loop task; that is, a task where the output from the neuromorphic hardware affects some environment, which then in turn affects the hardware's future input. However, closed-loop situations are one of the primary potential uses of neuromorphic hardware. To address this, we present a methodology for generating closed-loop benchmarks that makes use of a hybrid of real physical embodiment and a type of "minimal" simulation. Minimal simulation has been shown to lead to robust real-world performance, while still maintaining the practical advantages of simulation, such as making it easy for the same benchmark to be used by many researchers. This method is flexible enough to allow researchers to explicitly modify the benchmarks to identify specific task domains where particular hardware excels. To demonstrate the method, we present a set of novel benchmarks that focus on motor control for an arbitrary system with unknown external forces. Using these benchmarks, we show that an error-driven learning rule can consistently improve motor control performance across a randomly generated family of closed-loop simulations, even when there are up to 15 interacting joints to be controlled. PMID:26696820

  17. Structure of the catalytic domain of avian sarcoma virus integrase with a bound HIV-1 integrase-targeted inhibitor

    PubMed Central

    Lubkowski, Jacek; Yang, Fan; Alexandratos, Jerry; Wlodawer, Alexander; Zhao, He; Burke, Terrence R.; Neamati, Nouri; Pommier, Yves; Merkel, George; Skalka, Anna Marie

    1998-01-01

    The x-ray structures of an inhibitor complex of the catalytic core domain of avian sarcoma virus integrase (ASV IN) were solved at 1.9- to 2.0-Å resolution at two pH values, with and without Mn2+ cations. This inhibitor (Y-3), originally identified in a screen for inhibitors of the catalytic activity of HIV type 1 integrase (HIV-1 IN), was found in the present study to be active against ASV IN as well as HIV-1 IN. The Y-3 molecule is located in close proximity to the enzyme active site, interacts with the flexible loop, alters loop conformation, and affects the conformations of active site residues. As crystallized, a Y-3 molecule stacks against its symmetry-related mate. Preincubation of IN with metal cations does not prevent inhibition, and Y-3 binding does not prevent binding of divalent cations to IN. Three compounds chemically related to Y-3 also were investigated, but no binding was observed in the crystals. Our results identify the structural elements of the inhibitor that likely determine its binding properties. PMID:9560188

  18. Catalytic nanomotors: challenges and opportunities

    NASA Astrophysics Data System (ADS)

    Gibbs, John; Zhao, Yiping

    2011-06-01

    The fabrication of integrated nanomachinary systems can enable break-through applications in nanoelectronics, photonics, bioengineering, and drug delivery or disease treatment. Naturally occurring nanomotors are biological motor proteins powered by catalytic reactions, which convert the chemical energy from the environment into mechanical energy directly. It has been demonstrated recently that using a simple catalytic reaction and an asymmetric bimetallic nanorod, one can produce catalytic nanomotors that mimic the autonomous motions of bionanomotors. Yet the construction of artificial nanomachines remains a major contemporary challenge due to the lack of a flexible fabrication technique that can design the desired dynamic components. We use a design technique called dynamic shadowing growth that allows for the fabrication of a wide range of various geometries and the asymmetric placement of the catalyst is easily accomplished as well which is necessary for directed propulsion. Programming nanomotor behavior is possible through geometrically-focused design and by incorporating different materials into the nanomotor structure is a simple process as well. A propulsion mechanism based upon bubble ejection from the catalyst surface is introduced to explain the driving force, and the comparison of this driving mechanism with the self-electrophoresis mechanism is also studied. We have also successfully incorporated multiple parts to form complex nanomotor assemblies which exhibit motions not observed from individual parts by using magnetic interactions.

  19. Asymmetric Flexible Supercapacitor Stack

    PubMed Central

    2008-01-01

    Electrical double layer supercapacitor is very significant in the field of electrical energy storage which can be the solution for the current revolution in the electronic devices like mobile phones, camera flashes which needs flexible and miniaturized energy storage device with all non-aqueous components. The multiwalled carbon nanotubes (MWNTs) have been synthesized by catalytic chemical vapor deposition technique over hydrogen decrepitated Mischmetal (Mm) based AB3alloy hydride. The polymer dispersed MWNTs have been obtained by insitu polymerization and the metal oxide/MWNTs were synthesized by sol-gel method. Morphological characterizations of polymer dispersed MWNTs have been carried out using scanning electron microscopy (SEM), transmission electron microscopy (TEM and HRTEM). An assymetric double supercapacitor stack has been fabricated using polymer/MWNTs and metal oxide/MWNTs coated over flexible carbon fabric as electrodes and nafion®membrane as a solid electrolyte. Electrochemical performance of the supercapacitor stack has been investigated using cyclic voltammetry, galvanostatic charge-discharge, and electrochemical impedance spectroscopy.

  20. Control of flexible arms with friction in the joints

    SciTech Connect

    Feliu, V.; Rattan, K.S.; Brown, H.B. Jr.

    1993-08-01

    The control of flexible arms with friction in the joints is studied. A method to identify the dynamics of a flexible arm from its frequency response (which is strongly distorted by Coulomb`s friction) is proposed. A robust control scheme that minimizes the effects of this friction is presented. The scheme consists of two nested feedback loops: an inner loop to control the motor position and an outer loop to control the tip position. It is shown that a proper design of the inner loop eliminates the effect so friction while controlling the tip position and significantly simplifies the design of the outer loop. The proposed scheme is applied to a class of lightweight flexible arms, and the experiments show that the control scheme results in a simple controller. As a result, the computations are minimized and, thus, high sampling rates may be used.

  1. Alternative substrates reveal catalytic cycle and key binding events in the reaction catalysed by anthranilate phosphoribosyltransferase from Mycobacterium tuberculosis.

    PubMed

    Cookson, Tammie V M; Castell, Alina; Bulloch, Esther M M; Evans, Genevieve L; Short, Francesca L; Baker, Edward N; Lott, J Shaun; Parker, Emily J

    2014-07-01

    AnPRT (anthranilate phosphoribosyltransferase), required for the biosynthesis of tryptophan, is essential for the virulence of Mycobacterium tuberculosis (Mtb). AnPRT catalyses the Mg2+-dependent transfer of a phosphoribosyl group from PRPP (5'-phosphoribosyl-1'-pyrophosphate) to anthranilate to form PRA (5'-phosphoribosyl anthranilate). Mtb-AnPRT was shown to catalyse a sequential reaction and significant substrate inhibition by anthranilate was observed. Antimycobacterial fluoroanthranilates and methyl-substituted analogues were shown to act as alternative substrates for Mtb-AnPRT, producing the corresponding substituted PRA products. Structures of the enzyme complexed with anthranilate analogues reveal two distinct binding sites for anthranilate. One site is located over 8 Å (1 Å=0.1 nm) from PRPP at the entrance to a tunnel leading to the active site, whereas in the second, inner, site anthranilate is adjacent to PRPP, in a catalytically relevant position. Soaking the analogues for variable periods of time provides evidence for anthranilate located at transient positions during transfer from the outer site to the inner catalytic site. PRPP and Mg2+ binding have been shown to be associated with the rearrangement of two flexible loops, which is required to complete the inner anthranilate-binding site. It is proposed that anthranilate first binds to the outer site, providing an unusual mechanism for substrate capture and efficient transfer to the catalytic site following the binding of PRPP. PMID:24712732

  2. OPE for super loops

    NASA Astrophysics Data System (ADS)

    Sever, Amit; Vieira, Pedro; Wang, Tianheng

    2011-11-01

    We extend the Operator Product Expansion for Null Polygon Wilson loops to the Mason-Skinner-Caron-Huot super loop dual to non MHV gluon amplitudes. We explain how the known tree level amplitudes can be promoted into an infinite amount of data at any loop order in the OPE picture. As an application, we re-derive all one loop NMHV six gluon amplitudes by promoting their tree level expressions. We also present some new all loops predictions for these amplitudes.

  3. The preprocessed doacross loop

    NASA Technical Reports Server (NTRS)

    Saltz, Joel H.; Mirchandaney, Ravi

    1990-01-01

    Dependencies between loop iterations cannot always be characterized during program compilation. Doacross loops typically make use of a-priori knowledge of inter-iteration dependencies to carry out required synchronizations. A type of doacross loop is proposed that allows the scheduling of iterations of a loop among processors without advance knowledge of inter-iteration dependencies. The method proposed for loop iterations requires that parallelizable preprocessing and postprocessing steps be carried out during program execution.

  4. Fast flux locked loop

    DOEpatents

    Ganther, Jr., Kenneth R.; Snapp, Lowell D.

    2002-09-10

    A flux locked loop for providing an electrical feedback signal, the flux locked loop employing radio-frequency components and technology to extend the flux modulation frequency and tracking loop bandwidth. The flux locked loop of the present invention has particularly useful application in read-out electronics for DC SQUID magnetic measurement systems, in which case the electrical signal output by the flux locked loop represents an unknown magnetic flux applied to the DC SQUID.

  5. Switchable catalytic DNA catenanes.

    PubMed

    Hu, Lianzhe; Lu, Chun-Hua; Willner, Itamar

    2015-03-11

    Two-ring interlocked DNA catenanes are synthesized and characterized. The supramolecular catenanes show switchable cyclic catalytic properties. In one system, the catenane structure is switched between a hemin/G-quadruplex catalytic structure and a catalytically inactive state. In the second catenane structure the catenane is switched between a catalytically active Mg(2+)-dependent DNAzyme-containing catenane and an inactive catenane state. In the third system, the interlocked catenane structure is switched between two distinct catalytic structures that include the Mg(2+)- and the Zn(2+)-dependent DNAzymes. PMID:25642796

  6. Flexibility Correlation between Active Site Regions Is Conserved across Four AmpC β-Lactamase Enzymes

    PubMed Central

    Brown, Jenna R.; Livesay, Dennis R.

    2015-01-01

    β-lactamases are bacterial enzymes that confer resistance to β-lactam antibiotics, such as penicillins and cephalosporins. There are four classes of β-lactamase enzymes, each with characteristic sequence and structure properties. Enzymes from class A are the most common and have been well characterized across the family; however, less is known about how physicochemical properties vary across the C and D families. In this report, we compare the dynamical properties of four AmpC (class C) β-lactamases using our distance constraint model (DCM). The DCM reliably predicts thermodynamic and mechanical properties in an integrated way. As a consequence, quantitative stability/flexibility relationships (QSFR) can be determined and compared across the whole family. The DCM calculates a large number of QSFR metrics. Perhaps the most useful is the flexibility index (FI), which quantifies flexibility along the enzyme backbone. As typically observed in other systems, FI is well conserved across the four AmpC enzymes. Cooperativity correlation (CC), which quantifies intramolecular couplings within structure, is rarely conserved across protein families; however, it is in AmpC. In particular, the bulk of each structure is composed of a large rigid cluster, punctuated by three flexibly correlated regions located at the active site. These regions include several catalytic residues and the Ω-loop. This evolutionary conservation combined with active their site location strongly suggests that these coupled dynamical modes are important for proper functioning of the enzyme. PMID:26018804

  7. Large planar maneuvers for articulated flexible manipulators

    NASA Technical Reports Server (NTRS)

    Huang, Jen-Kuang; Yang, Li-Farn

    1988-01-01

    An articulated flexible manipulator carried on a translational cart is maneuvered by an active controller to perform certain position control tasks. The nonlinear dynamics of the articulated flexible manipulator are derived and a transformation matrix is formulated to localize the nonlinearities within the inertia matrix. Then a feedback linearization scheme is introduced to linearize the dynamic equations for controller design. Through a pole placement technique, a robust controller design is obtained by properly assigning a set of closed-loop desired eigenvalues to meet performance requirements. Numerical simulations for the articulated flexible manipulators are given to demonstrate the feasibility and effectiveness of the proposed position control algorithms.

  8. Rapid Deployment of Rich Catalytic Combustion

    SciTech Connect

    Richard S. Tuthill

    2004-06-10

    The overall objective of this research under the Turbines Program is the deployment of fuel flexible rich catalytic combustion technology into high-pressure ratio industrial gas turbines. The resulting combustion systems will provide fuel flexibility for gas turbines to burn coal derived synthesis gas or natural gas and achieve NO{sub x} emissions of 2 ppmvd or less (at 15 percent O{sub 2}), cost effectively. This advance will signify a major step towards environmentally friendly electric power generation and coal-based energy independence for the United States. Under Phase 1 of the Program, Pratt & Whitney (P&W) performed a system integration study of rich catalytic combustion in a small high-pressure ratio industrial gas turbine with a silo combustion system that is easily scalable to a larger multi-chamber gas turbine system. An implementation plan for this technology also was studied. The principal achievement of the Phase 1 effort was the sizing of the catalytic module in a manner which allowed a single reactor (rather than multiple reactors) to be used by the combustion system, a conclusion regarding the amount of air that should be allocated to the reaction zone to achieve low emissions, definition of a combustion staging strategy to achieve low emissions, and mechanical integration of a Ceramic Matrix Composite (CMC) combustor liner with the catalytic module.

  9. Conformational dynamics of the active site loop of S-adenosylmethionine synthetase illuminated by site-directed spin labeling.

    PubMed

    Taylor, John C; Markham, George D

    2003-07-15

    S-adenosylmethionine synthetase (ATP: L-methionine S-adenosyltransferase, methionine adenosyltransferase, a.k.a. MAT) is one of numerous enzymes that have a flexible polypeptide loop that moves to gate access to the active site in a motion that is closely coupled to catalysis. Crystallographic studies of this tetrameric enzyme have shown that the loop is closed in the absence of bound substrates. However, the loop must open to allow substrate binding and a variety of data indicate that the loop is closed during the catalytic steps. Previous kinetic studies indicate that during turnover loop motion occurs on a time scale of 10(-2)s, ca. 10-fold faster than chemical transformations and turnover. Site-directed spin labeling has been used to introduce nitroxide groups at two positions in the loop to illuminate how the motion of the loop is affected by substrate binding. The two loop mutants constructed, G105C and D107C, retain wild type levels of MAT activity; attachment of a methanethiosulfonate spin label to convert the cysteine to the "R1" residue reduced the k(cat) only for the labeled D107R1 form (7-fold). The K(m) value for methionine increased 2- to 4-fold for the cysteine mutants and 2- to 7-fold for the labeled proteins, whereas the K(m) for ATP was changed by at most 2-fold. EPR spectra for both labeled proteins are nearly identical and show the presence of two major spin label environments with rotational diffusion rates differing by approximately 10-fold; the slower rate is ca. 4-fold faster than the estimated protein rotational rate. The spectra are not altered by addition of substrates or products. At both positions the less mobile conformation constitutes ca. 65% of the total species, indicating an equilibrium that only slightly favors one form, that in which the label is more immobilized. The equilibrium constant that relates the two forms is comparable to the equilibrium constant of 1.5 for a conformational change that was previously deduced from the

  10. FLEXIBLE COUPLING

    DOEpatents

    Babelay, E.F.

    1962-02-13

    A flexible shaft coupling for operation at speeds in excess of 14,000 rpm is designed which requires no lubrication. A driving sleeve member and a driven sleeve member are placed in concentric spaced relationship. A torque force is transmitted to the driven member from the driving member through a plurality of nylon balls symmetrically disposed between the spaced sleeves. The balls extend into races and recesses within the respective sleeve members. The sleeve members have a suitable clearance therebetween and the balls have a suitable radial clearance during operation of the coupling to provide a relatively loose coupling. These clearances accommodate for both parallel and/or angular misalignments and avoid metal-tometal contact between the sleeve members during operation. Thus, no lubrication is needed, and a minimum of vibrations is transmitted between the sleeve members. (AEC)

  11. Impaired Acid Catalysis by Mutation of a Protein Loop Hinge Residue in a YopH Mutant Revealed by Crystal Structures

    SciTech Connect

    Brandao, T.; Robinson, H; Johnson, S; Hengge, A

    2009-01-01

    Catalysis by the Yersinia protein-tyrosine phosphatase YopH is significantly impaired by the mutation of the conserved Trp354 residue to Phe. Though not a catalytic residue, this Trp is a hinge residue in a conserved flexible loop (the WPD-loop) that must close during catalysis. To learn why this seemingly conservative mutation reduces catalysis by 2 orders of magnitude, we have solved high-resolution crystal structures for the W354F YopH in the absence and in the presence of tungstate and vanadate. Oxyanion binding to the P-loop in W354F is analogous to that observed in the native enzyme. However, the WPD-loop in the presence of oxyanions assumes a half-closed conformation, in contrast to the fully closed state observed in structures of the native enzyme. This observation provides an explanation for the impaired general acid catalysis observed in kinetic experiments with Trp mutants. A 1.4 Angstroms structure of the W354F mutant obtained in the presence of vanadate reveals an unusual divanadate species with a cyclic [VO]2 core, which has precedent in small molecules but has not been previously reported in a protein crystal structure.

  12. Blind loop syndrome

    MedlinePlus

    Blind loop syndrome occurs when digested food slows or stops moving through part of the intestines. This ... The name of this condition refers to the "blind loop" formed by part of the intestine that ...

  13. Single link flexible beam testbed project. Thesis

    NASA Technical Reports Server (NTRS)

    Hughes, Declan

    1992-01-01

    This thesis describes the single link flexible beam testbed at the CLaMS laboratory in terms of its hardware, software, and linear model, and presents two controllers, each including a hub angle proportional-derivative (PD) feedback compensator and one augmented by a second static gain full state feedback loop, based upon a synthesized strictly positive real (SPR) output, that increases specific flexible mode pole damping ratios w.r.t the PD only case and hence reduces unwanted residual oscillation effects. Restricting full state feedback gains so as to produce a SPR open loop transfer function ensures that the associated compensator has an infinite gain margin and a phase margin of at least (-90, 90) degrees. Both experimental and simulation data are evaluated in order to compare some different observer performance when applied to the real testbed and to the linear model when uncompensated flexible modes are included.

  14. Active Site Loop Conformation Regulates Promiscuous Activity in a Lactonase from Geobacillus kaustophilus HTA426

    PubMed Central

    Zhang, Yu; An, Jiao; Yang, Guang-Yu; Bai, Aixi; Zheng, Baisong; Lou, Zhiyong; Wu, Geng; Ye, Wei; Chen, Hai-Feng; Feng, Yan; Manco, Giuseppe

    2015-01-01

    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. PMID:25706379

  15. Two stage catalytic combustor

    NASA Technical Reports Server (NTRS)

    Alvin, Mary Anne (Inventor); Bachovchin, Dennis (Inventor); Smeltzer, Eugene E. (Inventor); Lippert, Thomas E. (Inventor); Bruck, Gerald J. (Inventor)

    2010-01-01

    A catalytic combustor (14) includes a first catalytic stage (30), a second catalytic stage (40), and an oxidation completion stage (49). The first catalytic stage receives an oxidizer (e.g., 20) and a fuel (26) and discharges a partially oxidized fuel/oxidizer mixture (36). The second catalytic stage receives the partially oxidized fuel/oxidizer mixture and further oxidizes the mixture. The second catalytic stage may include a passageway (47) for conducting a bypass portion (46) of the mixture past a catalyst (e.g., 41) disposed therein. The second catalytic stage may have an outlet temperature elevated sufficiently to complete oxidation of the mixture without using a separate ignition source. The oxidation completion stage is disposed downstream of the second catalytic stage and may recombine the bypass portion with a catalyst exposed portion (48) of the mixture and complete oxidation of the mixture. The second catalytic stage may also include a reticulated foam support (50), a honeycomb support, a tube support or a plate support.

  16. VOC Destruction by Catalytic Combustion Microturbine

    SciTech Connect

    Tom Barton

    2009-03-10

    This project concerned the application of a catalytic combustion system that has been married to a micro-turbine device. The catalytic combustion system decomposes the VOC's and transmits these gases to the gas turbine. The turbine has been altered to operate on very low-level BTU fuels equivalent to 1.5% methane in air. The performance of the micro-turbine for VOC elimination has some flexibility with respect to operating conditions, and the system is adaptable to multiple industrial applications. The VOC source that was been chosen for examination was the emissions from coal upgrading operations. The overall goal of the project was to examine the effectiveness of a catalytic combustion based system for elimination of VOCs while simultaneously producing electrical power for local consumption. Project specific objectives included assessment of the feasibility for using a Flex-Microturbine that generates power from natural gas while it consumes VOCs generated from site operations; development of an engineering plan for installation of the Flex-Microturbine system; operation of the micro-turbine through various changes in site and operation conditions; measurement of the VOC destruction quantitatively; and determination of the required improvements for further studies. The micro-turbine with the catalytic bed worked effectively to produce power on levels of fuel much lower than the original turbine design. The ability of the device to add or subtract supplemental fuel to augment the amount of VOC's in the inlet air flow made the device an effective replacement for a traditional flare. Concerns about particulates in the inlet flow and the presence of high sulfur concentrations with the VOC mixtures was identified as a drawback with the current catalytic design. A new microturbine design was developed based on this research that incorporates a thermal oxidizer in place of the catalytic bed for applications where particulates or contamination would limit the lifetime of

  17. Catalytic site interactions in yeast OMP synthase.

    PubMed

    Hansen, Michael Riis; Barr, Eric W; Jensen, Kaj Frank; Willemoës, Martin; Grubmeyer, Charles; Winther, Jakob R

    2014-01-15

    The enigmatic kinetics, half-of-the-sites binding, and structural asymmetry of the homodimeric microbial OMP synthases (orotate phosphoribosyltransferase, EC 2.4.2.10) have been proposed to result from an alternating site mechanism in these domain-swapped enzymes [R.W. McClard et al., Biochemistry 45 (2006) 5330-5342]. This behavior was investigated in the yeast enzyme by mutations in the conserved catalytic loop and 5-phosphoribosyl-1-diphosphate (PRPP) binding motif. Although the reaction is mechanistically sequential, the wild-type (WT) enzyme shows parallel lines in double reciprocal initial velocity plots. Replacement of Lys106, the postulated intersubunit communication device, produced intersecting lines in kinetic plots with a 2-fold reduction of kcat. Loop (R105G K109S H111G) and PRPP-binding motif (D131N D132N) mutant proteins, each without detectable enzymatic activity and ablated ability to bind PRPP, complemented to produce a heterodimer with a single fully functional active site showing intersecting initial velocity plots. Equilibrium binding of PRPP and orotidine 5'-monophosphate showed a single class of two binding sites per dimer in WT and K106S enzymes. Evidence here shows that the enzyme does not follow half-of-the-sites cooperativity; that interplay between catalytic sites is not an essential feature of the catalytic mechanism; and that parallel lines in steady-state kinetics probably arise from tight substrate binding. PMID:24262852

  18. Loop interactions during catalysis by dihydrofolate reductase from Moritella profunda.

    PubMed

    Behiry, Enas M; Evans, Rhiannon M; Guo, Jiannan; Loveridge, E Joel; Allemann, Rudolf K

    2014-07-29

    Dihydrofolate reductase (DHFR) is often used as a model system to study the relation between protein dynamics and catalysis. We have studied a number of variants of the cold-adapted DHFR from Moritella profunda (MpDHFR), in which the catalytically important M20 and FG loops have been altered, and present a comparison with the corresponding variants of the well-studied DHFR from Escherichia coli (EcDHFR). Mutations in the M20 loop do not affect the actual chemical step of transfer of hydride from reduced nicotinamide adenine dinucleotide phosphate to the substrate 7,8-dihydrofolate in the catalytic cycle in either enzyme; they affect the steady state turnover rate in EcDHFR but not in MpDHFR. Mutations in the FG loop also have different effects on catalysis by the two DHFRs. Despite the two enzymes most likely sharing a common catalytic cycle at pH 7, motions of these loops, known to be important for progression through the catalytic cycle in EcDHFR, appear not to play a significant role in MpDHFR. PMID:25014120

  19. Flexible Metal-Fabric Radiators

    NASA Technical Reports Server (NTRS)

    Cross, Cynthia; Nguyen, Hai D.; Ruemmele, Warren; Andish, Kambiz K.; McCalley, Sean

    2005-01-01

    Flexible metal-fabric radiators have been considered as alternative means of dissipating excess heat from spacecraft and space suits. The radiators also may be useful in such special terrestrial applications as rejecting heat from space-suit-like protective suits worn in hot work environments. In addition to flexibility and consequent ease of deployment and installation on objects of varying sizes and shapes, the main advantages of these radiators over conventional rigid radiators are that they weigh less and occupy less volume for a given amount of cooling capacity. A radiator of this type includes conventional stainless-steel tubes carrying a coolant fluid. The main radiating component consists of a fabric of interwoven aluminum-foil strips bonded to the tubes by use of a proprietary process. The strip/tube bonds are strong and highly thermally conductive. Coolant is fed to and from the tubes via flexible stainless-steel manifolds designed to accommodate flexing of, and minimize bending forces on, the fabric. The manifolds are sized to minimize pressure drops and distribute the flow of coolant evenly to all the tubes. The tubes and manifolds are configured in two independent flow loops for operational flexibility and protective redundancy.

  20. Isolated and coupled superquadric loop antennas for mobile communications applications

    NASA Technical Reports Server (NTRS)

    Jensen, Michael A.; Rahmat-Samii, Yahya

    1993-01-01

    This work provides an investigation of the performance of loop antennas for use in mobile communications applications. The analysis tools developed allow for high flexibility by representing the loop antenna as a superquadric curve, which includes the case of circular, elliptical, and rectangular loops. The antenna may be in an isolated environment, located above an infinite ground plane, or placed near a finite conducting plate or box. In cases where coupled loops are used, the two loops may have arbitrary relative positions and orientations. Several design examples are included to illustrate the versatility of the analysis capabilities. The performance of coupled loops arranged in a diversity scheme is also evaluated, and it is found that high diversity gain can be achieved even when the antennas are closely spaced.

  1. Catalytic distillation structure

    DOEpatents

    Smith, Jr., Lawrence A.

    1984-01-01

    Catalytic distillation structure for use in reaction distillation columns, a providing reaction sites and distillation structure and consisting of a catalyst component and a resilient component intimately associated therewith. The resilient component has at least about 70 volume % open space and being present with the catalyst component in an amount such that the catalytic distillation structure consist of at least 10 volume % open space.

  2. Catalytic cracking process

    DOEpatents

    Lokhandwala, Kaaeid A.; Baker, Richard W.

    2001-01-01

    Processes and apparatus for providing improved catalytic cracking, specifically improved recovery of olefins, LPG or hydrogen from catalytic crackers. The improvement is achieved by passing part of the wet gas stream across membranes selective in favor of light hydrocarbons over hydrogen.

  3. Putative implication of alpha-amylase loop 7 in the mechanism of substrate binding and reaction products release.

    PubMed

    André, G; Tran, V

    2004-10-01

    Alpha-amylases are widespread endo-enzymes involved in the hydrolysis of internal alpha-(1,4) glycosidic linkages of starch polymers. Molecular modeling of amylose-amylase interactions is a step toward enzymatic mechanism understanding and rational design of new enzymes. From the crystallographic complex of barley alpha-amylase AMY2-acarbose, the static aspects of amylose-amylase docking have been characterized with a model of maltododecaose (DP12) (G. André, A. Buléon, R. Haser, and V. Tran, Biopolymers 1999, Vol. 50, pp. 751-762; G. André and V. Tran, Special Publication no. 246 1999, The Royal Society of Chemistry, H. J. Gilbert, G. J. Davies, B. Henrissat, and B. Svensson, Eds., Cambridge, pp. 165-174). These studies, consistent with the experimental subsite mapping (K. Bak-Jensen, G. André, V. Tran, and B. Svensson, Journal of Biological Chemistry, to be published), propose a propagation scheme for an amylose chain in the active cleft of AMY2. The topographical overview of alpha-amylases identified loop 7 as a conserved segment flanking the active site. Since some crystallographic experiments suspected its high flexibility, its putative motion was explored through a robotic scheme, an alternate route to dynamics simulations that consume CPU time. The present article describes the characteristics of the flexibility of loop 7: location and motion in AMY2. A back-and-forth motion with a large amplitude of more than 0.6 nm was evaluated. This movement could be triggered by two hinge residues. It results in the loop flipping over the active site to enhance the docking of the native helical substrate through specific interactions, it positions the catalytic residues, it distorts the substrate towards its transition state geometry, and finally monitors the release of the products after hydrolysis. The residues involved in the process are now rational mutation points in the hands of molecular biologists. PMID:15356864

  4. Protein short loop prediction in terms of a structural alphabet.

    PubMed

    Tyagi, Manoj; Bornot, Aurélie; Offmann, Bernard; de Brevern, Alexandre G

    2009-08-01

    Loops connect regular secondary structures. In many instances, they are known to play crucial biological roles. To bypass the limitation of secondary structure description, we previously defined a structural alphabet composed of 16 structural prototypes, called Protein Blocks (PBs). It leads to an accurate description of every region of 3D protein backbones and has been used in local structure prediction. In the present study, we used our structural alphabet to predict the loops connecting two repetitive structures. Thus, we showed interest to take into account the flanking regions, leading to prediction rate improvement up to 19.8%, but we also underline the sensitivity of such an approach. This research can be used to propose different structures for the loops and to probe and sample their flexibility. It is a useful tool for ab initio loop prediction and leads to insights into flexible docking approach. PMID:19625218

  5. Loops and trees

    NASA Astrophysics Data System (ADS)

    Caron-Huot, S.

    2011-05-01

    We investigate relations between loop and tree amplitudes in quantum field theory that involve putting on-shell some loop propagators. This generalizes the so-called Feynman tree theorem which is satisfied at 1-loop. Exploiting retarded boundary conditions, we give a generalization to ℓ-loop expressing the loops as integrals over the on-shell phase space of exactly ℓ particles. We argue that the corresponding integrand for ℓ > 2 does not involve the forward limit of any physical tree amplitude, except in planar gauge theories. In that case we explicitly construct the relevant physical amplitude. Beyond the planar limit, abandoning direct integral representations, we propose that loops continue to be determined implicitly by the forward limit of physical connected trees, and we formulate a precise conjecture along this line. Finally, we set up technology to compute forward amplitudes in supersymmetric theories, in which specific simplifications occur.

  6. Loop residues and catalysis in OMP synthase.

    PubMed

    Wang, Gary P; Hansen, Michael Riis; Grubmeyer, Charles

    2012-06-01

    Residue-to-alanine mutations and a two-amino acid deletion have been made in the highly conserved catalytic loop (residues 100-109) of Salmonella typhimurium OMP synthase (orotate phosphoribosyltransferase, EC 2.4.2.10). As described previously, the K103A mutant enzyme exhibited a 10(4)-fold decrease in k(cat)/K(M) for PRPP; the K100A enzyme suffered a 50-fold decrease. Alanine mutations at His105 and Glu107 produced 40- and 7-fold decreases in k(cat)/K(M), respectively, and E101A, D104A, and G106A were slightly faster than the wild-type (WT) in terms of k(cat), with minor effects on k(cat)/K(M). Equilibrium binding of OMP or PRPP in binary complexes was affected little by loop mutation, suggesting that the energetics of ground-state binding have little contribution from the catalytic loop, or that a favorable binding energy is offset by costs of loop reorganization. Pre-steady-state kinetics for mutants showed that K103A and E107A had lost the burst of product formation in each direction that indicated rapid on-enzyme chemistry for WT, but that the burst was retained by H105A. Δ102Δ106, a loop-shortened enzyme with Ala102 and Gly106 deleted, showed a 10(4)-fold reduction of k(cat) but almost unaltered K(D) values for all four substrate molecules. The 20% (i.e., 1.20) intrinsic [1'-(3)H]OMP kinetic isotope effect (KIE) for WT is masked because of high forward and reverse commitment factors. K103A failed to express intrinsic KIEs fully (1.095 ± 0.013). In contrast, H105A, which has a smaller catalytic lesion, gave a [1'-(3)H]OMP KIE of 1.21 ± 0.0005, and E107A (1.179 ± 0.0049) also gave high values. These results are interpreted in the context of the X-ray structure of the complete substrate complex for the enzyme [Grubmeyer, C., Hansen, M. R., Fedorov, A. A., and Almo, S. C. (2012) Biochemistry 51 (preceding paper in this issue, DOI 10.1021/bi300083p )]. The full expression of KIEs by H105A and E107A may result from a less secure closure of the catalytic loop

  7. Observational Evidence for Loop-Loop Interaction

    NASA Astrophysics Data System (ADS)

    Guiping, W.; Guangli, H.; Yuhua, T.; Aoao, X.

    2004-01-01

    Through analysis of the data including the hard x-ray(BASTE) microwave(NoRP) and magnetogram(MDI from SOHO) as well as the images of soft x-ray(YHKOH) and EIT(SOHO) on Apr. 151998 solar flare in the active region 8203(N30W12) we found: (1) there are similar quasi period oscillation in the profile of hard x-ray flux (25-5050-100keV) and microwave flux(1GHz) with duration of 85+/-25s every peak includes two sub-peak structures; (2) in the preheat phase of the flare active magnetic field changes apparently and a s-pole spot emerges ; (3) several EIT and soft x-ray loops exist and turn into bright . All of these may suggest that loop-loop interaction indeed exist. Through reconnection the electrons may be accelerated and the hard x-ray and microwave emission take place.

  8. Conformational Sampling in Template-Free Protein Loop Structure Modeling: An Overview

    PubMed Central

    Li, Yaohang

    2013-01-01

    Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a “mini protein folding problem” under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increasing number of known structures available in PDB. This mini review provides an overview on the recent computational approaches for loop structure modeling. In particular, we focus on the approaches of sampling loop conformation space, which is a critical step to obtain high resolution models in template-free methods. We review the potential energy functions for loop modeling, loop buildup mechanisms to satisfy geometric constraints, and loop conformation sampling algorithms. The recent loop modeling results are also summarized. PMID:24688696

  9. Catalytic distillation process

    DOEpatents

    Smith, Jr., Lawrence A.

    1982-01-01

    A method for conducting chemical reactions and fractionation of the reaction mixture comprising feeding reactants to a distillation column reactor into a feed zone and concurrently contacting the reactants with a fixed bed catalytic packing to concurrently carry out the reaction and fractionate the reaction mixture. For example, a method for preparing methyl tertiary butyl ether in high purity from a mixed feed stream of isobutene and normal butene comprising feeding the mixed feed stream to a distillation column reactor into a feed zone at the lower end of a distillation reaction zone, and methanol into the upper end of said distillation reaction zone, which is packed with a properly supported cationic ion exchange resin, contacting the C.sub.4 feed and methanol with the catalytic distillation packing to react methanol and isobutene, and concurrently fractionating the ether from the column below the catalytic zone and removing normal butene overhead above the catalytic zone.

  10. Catalytic distillation process

    DOEpatents

    Smith, L.A. Jr.

    1982-06-22

    A method is described for conducting chemical reactions and fractionation of the reaction mixture comprising feeding reactants to a distillation column reactor into a feed zone and concurrently contacting the reactants with a fixed bed catalytic packing to concurrently carry out the reaction and fractionate the reaction mixture. For example, a method for preparing methyl tertiary butyl ether in high purity from a mixed feed stream of isobutene and normal butene comprising feeding the mixed feed stream to a distillation column reactor into a feed zone at the lower end of a distillation reaction zone, and methanol into the upper end of said distillation reaction zone, which is packed with a properly supported cationic ion exchange resin, contacting the C[sub 4] feed and methanol with the catalytic distillation packing to react methanol and isobutene, and concurrently fractionating the ether from the column below the catalytic zone and removing normal butene overhead above the catalytic zone.

  11. Evolution of catalytic function

    NASA Technical Reports Server (NTRS)

    Joyce, G. F.

    1993-01-01

    An RNA-based evolution system was constructed in the laboratory and used to develop RNA enzymes with novel catalytic function. By controlling the nature of the catalytic task that the molecules must perform in order to survive, it is possible to direct the evolving population toward the expression of some desired catalytic behavior. More recently, this system has been coupled to an in vitro translation procedure, raising the possibility of evolving protein enzymes in the laboratory to produce novel proteins with desired catalytic properties. The aim of this line of research is to reduce darwinian evolution, the fundamental process of biology, to a laboratory procedure that can be made to operate in the service of organic synthesis.

  12. Catalytic distillation structure

    DOEpatents

    Smith, L.A. Jr.

    1984-04-17

    Catalytic distillation structure is described for use in reaction distillation columns, and provides reaction sites and distillation structure consisting of a catalyst component and a resilient component intimately associated therewith. The resilient component has at least about 70 volume % open space and is present with the catalyst component in an amount such that the catalytic distillation structure consists of at least 10 volume % open space. 10 figs.

  13. Clean catalytic combustor program

    NASA Technical Reports Server (NTRS)

    Ekstedt, E. E.; Lyon, T. F.; Sabla, P. E.; Dodds, W. J.

    1983-01-01

    A combustor program was conducted to evolve and to identify the technology needed for, and to establish the credibility of, using combustors with catalytic reactors in modern high-pressure-ratio aircraft turbine engines. Two selected catalytic combustor concepts were designed, fabricated, and evaluated. The combustors were sized for use in the NASA/General Electric Energy Efficient Engine (E3). One of the combustor designs was a basic parallel-staged double-annular combustor. The second design was also a parallel-staged combustor but employed reverse flow cannular catalytic reactors. Subcomponent tests of fuel injection systems and of catalytic reactors for use in the combustion system were also conducted. Very low-level pollutant emissions and excellent combustor performance were achieved. However, it was obvious from these tests that extensive development of fuel/air preparation systems and considerable advancement in the steady-state operating temperature capability of catalytic reactor materials will be required prior to the consideration of catalytic combustion systems for use in high-pressure-ratio aircraft turbine engines.

  14. Hybrid nanomotor: a catalytically/magnetically powered adaptive nanowire swimmer.

    PubMed

    Gao, Wei; Manesh, Kalayil Manian; Hua, Joe; Sattayasamitsathit, Sirilak; Wang, Joseph

    2011-07-18

    A synthetic hybrid nanomotor, which combines chemically powered propulsion and magnetically driven locomotion, is described. The new catalytic-magnetic nanomotor consists of a flexible multisegment Pt-Au-Ag(flex)-Ni nanowire, with the Pt-Au and Au-Ag(flex)-Ni portions responsible for the catalytic and magnetic propulsion modes, respectively. The experimental data and theoretical considerations indicate that the hybrid design only minimally compromises the individual propulsion modes. Rapid and convenient switching from the catalytic to the magnetic mode is illustrated. The resulting catalytic-magnetic adaptive nanomotor can address the fuel depletion and salt limitation common to chemically powered motors by switching to magnetic propulsion. Reversal of the motion direction is also achieved upon applying the magnetic field. Such use of two sources to power a hybrid device offers a broader scope of operation and holds considerable promise for designing adaptive nanovehicles that reconfigure their operation in response to environmental changes or unexpected events. PMID:21626685

  15. Fault Accommodation in Control of Flexible Systems

    NASA Technical Reports Server (NTRS)

    Maghami, Peiman G.; Sparks, Dean W., Jr.; Lim, Kyong B.

    1998-01-01

    New synthesis techniques for the design of fault accommodating controllers for flexible systems are developed. Three robust control design strategies, static dissipative, dynamic dissipative and mu-synthesis, are used in the approach. The approach provides techniques for designing controllers that maximize, in some sense, the tolerance of the closed-loop system against faults in actuators and sensors, while guaranteeing performance robustness at a specified performance level, measured in terms of the proximity of the closed-loop poles to the imaginary axis (the degree of stability). For dissipative control designs, nonlinear programming is employed to synthesize the controllers, whereas in mu-synthesis, the traditional D-K iteration is used. To demonstrate the feasibility of the proposed techniques, they are applied to the control design of a structural model of a flexible laboratory test structure.

  16. Maneuvering and control of flexible space robots

    NASA Technical Reports Server (NTRS)

    Meirovitch, Leonard; Lim, Seungchul

    1994-01-01

    This paper is concerned with a flexible space robot capable of maneuvering payloads. The robot is assumed to consist of two hinge-connected flexible arms and a rigid end-effector holding a payload; the robot is mounted on a rigid platform floating in space. The equations of motion are nonlinear and of high order. Based on the assumption that the maneuvering motions are one order of magnitude larger than the elastic vibrations, a perturbation approach permits design of controls for the two types of motion separately. The rigid-body maneuvering is carried out open loop, but the elastic motions are controlled closed loop, by means of discrete-time linear quadratic regulator theory with prescribed degree of stability. A numerical example demonstrates the approach. In the example, the controls derived by the perturbation approach are applied to the original nonlinear system and errors are found to be relatively small.

  17. The Role of the β5-α11 Loop in the Active-Site Dynamics of Acylated Penicillin-Binding Protein A from Mycobacterium tuberculosis

    SciTech Connect

    Fedarovich, Alena; Nicholas, Robert A.; Davies, Christopher

    2013-04-22

    Penicillin-binding protein A (PBPA) is a class B penicillin-binding protein that is important for cell division in Mycobacterium tuberculosis. We have determined a second crystal structure of PBPA in apo form and compared it with an earlier structure of apoenzyme. Significant structural differences in the active site region are apparent, including increased ordering of a β-hairpin loop and a shift of the SxN active site motif such that it now occupies a position that appears catalytically competent. Using two assays, including one that uses the intrinsic fluorescence of a tryptophan residue, we have also measured the second-order acylation rate constants for the antibiotics imipenem, penicillin G, and ceftriaxone. Of these, imipenem, which has demonstrable anti-tubercular activity, shows the highest acylation efficiency. Crystal structures of PBPA in complex with the same antibiotics were also determined, and all show conformational differences in the β5–α11 loop near the active site, but these differ for each β-lactam and also for each of the two molecules in the crystallographic asymmetric unit. Overall, these data reveal the β5–α11 loop of PBPA as a flexible region that appears important for acylation and provide further evidence that penicillin-binding proteins in apo form can occupy different conformational states.

  18. The role of the β5-α11 loop in the active-site dynamics of acylated penicillin-binding protein A from Mycobacterium tuberculosis

    PubMed Central

    Fedarovich, Alena; Nicholas, Robert A.; Davies, Christopher

    2012-01-01

    Penicillin-binding protein A (PBPA) is a class B penicillin-binding protein that is important for cell division in M. tuberculosis. We have determined a second crystal structure of PBPA in apo form and compared it with an earlier structure of the apo enzyme. Significant structural differences in the active site region are apparent, including increased ordering of a β-hairpin loop and a shift of the SxN active site motif such that it now occupies a position that appears catalytically competent. Using two assays, including one that uses the intrinsic fluorescence of a tryptophan residue, we have also measured second-order acylation rate constants for the antibiotics, imipenem, penicillin G and ceftriaxone. Of these, imipenem, which has demonstrable antitubercular activity, shows the highest acylation efficiency. Crystal structures of PBPA in complex with the same antibiotics were also determined and all show conformational differences in the β5-α11 loop near the active site, but these differ for each β-lactam and also for each of the two molecules in the crystallographic asymmetric unit. Overall, these data reveal the β5-α11 loop of PBPA as a flexible region that appears important for acylation and provide further evidence that PBPs in apo form can occupy different conformational states. PMID:22365933

  19. One-Loop Helicity Amplitudes for tt Production at Hadron Colliders

    SciTech Connect

    Badger, Simon; Sattler, Ralf; Yundin, Valery

    2011-04-01

    We present compact analytic expressions for all one-loop helicity amplitudes contributing to tt production at hadron colliders. Using recently developed generalized unitarity methods and a traditional Feynman based approach we produce a fast and flexible implementation.

  20. Low and medium heating value coal gas catalytic combustor characterization

    NASA Technical Reports Server (NTRS)

    Schwab, J. A.

    1982-01-01

    Catalytic combustion with both low and medium heating value coal gases obtained from an operating gasifier was demonstrated. A practical operating range for efficient operation was determined, and also to identify potential problem areas were identified for consideration during stationary gas turbine engine design. The test rig consists of fuel injectors, a fuel-air premixing section, a catalytic reactor with thermocouple instrumentation and a single point, water cooled sample probe. The test rig included inlet and outlet transition pieces and was designed for installation into an existing test loop.

  1. Catalytic coherence transformations

    NASA Astrophysics Data System (ADS)

    Bu, Kaifeng; Singh, Uttam; Wu, Junde

    2016-04-01

    Catalytic coherence transformations allow the otherwise impossible state transformations using only incoherent operations with the aid of an auxiliary system with finite coherence that is not being consumed in any way. Here we find the necessary and sufficient conditions for the deterministic and stochastic catalytic coherence transformations between a pair of pure quantum states. In particular, we show that the simultaneous decrease of a family of Rényi entropies of the diagonal parts of the states under consideration is a necessary and sufficient condition for the deterministic catalytic coherence transformations. Similarly, for stochastic catalytic coherence transformations we find the necessary and sufficient conditions for achieving a higher optimal probability of conversion. We thus completely characterize the coherence transformations among pure quantum states under incoherent operations. We give numerous examples to elaborate our results. We also explore the possibility of the same system acting as a catalyst for itself and find that indeed self-catalysis is possible. Further, for the cases where no catalytic coherence transformation is possible we provide entanglement-assisted coherence transformations and find the necessary and sufficient conditions for such transformations.

  2. Catalytic nanoporous membranes

    DOEpatents

    Pellin, Michael J; Hryn, John N; Elam, Jeffrey W

    2013-08-27

    A nanoporous catalytic membrane which displays several unique features Including pores which can go through the entire thickness of the membrane. The membrane has a higher catalytic and product selectivity than conventional catalysts. Anodic aluminum oxide (AAO) membranes serve as the catalyst substrate. This substrate is then subjected to Atomic Layer Deposition (ALD), which allows the controlled narrowing of the pores from 40 nm to 10 nm in the substrate by deposition of a preparatory material. Subsequent deposition of a catalytic layer on the inner surfaces of the pores reduces pore sizes to less than 10 nm and allows for a higher degree of reaction selectivity. The small pore sizes allow control over which molecules enter the pores, and the flow-through feature can allow for partial oxidation of reactant species as opposed to complete oxidation. A nanoporous separation membrane, produced by ALD is also provided for use in gaseous and liquid separations. The membrane has a high flow rate of material with 100% selectivity. Also provided is a method for producing a catalytic membrane having flow-through pores and discreet catalytic clusters adhering to the inside surfaces of the pores.

  3. Transient catalytic combustor model

    NASA Technical Reports Server (NTRS)

    Tien, J. S.

    1981-01-01

    A quasi-steady gas phase and thermally thin substrate model is used to analyze the transient behavior of catalytic monolith combustors in fuel lean operation. The combustor response delay is due to the substrate thermal inertia. Fast response is favored by thin substrate, short catalytic bed length, high combustor inlet and final temperatures, and small gas channel diameters. The calculated gas and substrate temperature time history at different axial positions provides an understanding of how the catalytic combustor responds to an upstream condition change. The computed results also suggest that the gas residence times in the catalytic bed in the after bed space are correlatable with the nondimensional combustor response time. The model also performs steady state combustion calculations; and the computed steady state emission characteristics show agreement with available experimental data in the range of parameters covered. A catalytic combustor design for automotive gas turbine engine which has reasonably fast response ( 1 second) and can satisfy the emission goals in an acceptable total combustor length is possible.

  4. Thermal power loops

    NASA Technical Reports Server (NTRS)

    Gottschlich, Joseph M.; Richter, Robert

    1991-01-01

    The concept of a thermal power loop (TPL) to transport thermal power over relatively large distances is presented as an alternative to heat pipes and their derivatives. The TPL is compared to heat pipes, and capillary pumped loops with respect to size, weight, conservation of thermal potential, start-up, and 1-g testing capability. Test results from a proof of feasibility demonstrator at the NASA JPL are discussed. This analysis demonstrates that the development of specific thermal power loops will result in substantial weight and cost savings for many spacecraft.

  5. Natively Unstructured Loops Differ from Other Loops

    PubMed Central

    Schlessinger, Avner; Liu, Jinfeng; Rost, Burkhard

    2007-01-01

    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 that long

  6. The Energy Landscape of Hyperstable LacI-DNA Loops

    NASA Astrophysics Data System (ADS)

    Kahn, Jason

    2009-03-01

    The Escherichia coli LacI protein represses transcription of the lac operon by blocking access to the promoter through binding at a promoter-proximal DNA operator. The affinity of tetrameric LacI (and therefore the repression efficiency) is enhanced by simultaneous binding to an auxiliary operator, forming a DNA loop. Hyperstable LacI-DNA loops were previously shown to be formed on DNA constructs that include a sequence-directed bend flanked by operators. Biochemical experiments showed that two such constructs (9C14 and 11C12) with different helical phasing between the operators and the DNA bend form different DNA loop shapes. The geometry and topology of the loops and the relevance of alternative conformations suggested by probable flexible linkers in LacI remain unclear. Bulk and single molecule fluorescence resonance energy transfer (SM-FRET, with D. English) experiments on a dual fluorophore-labeled 9C14-LacI loop demonstrate that it adopts a single, stable, rigid closed-form loop conformation. Here, we characterize the LacI-9C14 loop by SM-FRET as a function of inducer isopropyl-β,D-thiogalactoside (IPTG) concentration. Energy transfer measurements reveal partial but incomplete destabilization of loop formation by IPTG. Surprisingly, there is no change in the energy transfer efficiency of the remaining looped population. Models for the regulation of the lac operon often assume complete disruption of LacI-operator complexes upon inducer binding to LacI. Our work shows that even at saturating IPTG there is still a significant population of LacI-DNA complexes in a looped state, in accord with previous in vivo experiments that show incomplete induction (with J. Maher). Finally, we will report progress on characterizing the ``energy landscape'' for DNA looping upon systematic variation of the DNA linkers between the operators and the bending locus. Rod mechanics simulations (with N. Perkins) provide testable predictions on loop stability, topology, and FRET.

  7. Introduction to Loop Heat Pipes

    NASA Technical Reports Server (NTRS)

    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.

  8. Catalytic hydrotreating process

    DOEpatents

    Karr, Jr., Clarence; McCaskill, Kenneth B.

    1978-01-01

    Carbonaceous liquids boiling above about 300.degree. C such as tars, petroleum residuals, shale oils and coal-derived liquids are catalytically hydrotreated by introducing the carbonaceous liquid into a reaction zone at a temperature in the range of 300.degree. to 450.degree. C and a pressure in the range of 300 to 4000 psig for effecting contact between the carbonaceous liquid and a catalytic transition metal sulfide in the reaction zone as a layer on a hydrogen permeable transition metal substrate and then introducing hydrogen into the reaction zone by diffusing the hydrogen through the substrate to effect the hydrogenation of the carbonaceous liquid in the presence of the catalytic sulfide layer.

  9. Catalytic membranes beckon

    SciTech Connect

    Caruana, C.M.

    1994-11-01

    Chemical engineers here and abroad are finding that the marriage of catalysts and membranes holds promise for faster and more specific reactions, although commercialization of this technology is several years away. Catalytic membrane reactors (CMRs) combine a heterogeneous catalyst and a permselective membrane. Reactions performed by CMRs provide higher yields--sometimes as much as 50% higher--because of better reaction selectivity--as opposed to separation selectivity. CMRs also can work at very high temperatures, using ceramic materials that would not be possible with organic membranes. Although the use of CMRs is not widespread presently, the development of new membranes--particularly porous ceramic and zeolite membranes--will increase the potential to improve yields of many catalytic processes. The paper discusses ongoing studies, metal and advanced materials for membranes, the need for continued research, hydrogen recovery from coal-derived gases, catalytic oxidation of sulfides, CMRs for water purification, and oxidative coupling of methane.

  10. Steam reformer with catalytic combustor

    DOEpatents

    Voecks, Gerald E.

    1990-03-20

    A steam reformer is disclosed having an annular steam reforming catalyst bed formed by concentric cylinders and having a catalytic combustor located at the center of the innermost cylinder. Fuel is fed into the interior of the catalytic combustor and air is directed at the top of the combustor, creating a catalytic reaction which provides sufficient heat so as to maintain the catalytic reaction in the steam reforming catalyst bed. Alternatively, air is fed into the interior of the catalytic combustor and a fuel mixture is directed at the top. The catalytic combustor provides enhanced radiant and convective heat transfer to the reformer catalyst bed.

  11. Steam reformer with catalytic combustor

    NASA Technical Reports Server (NTRS)

    Voecks, Gerald E. (Inventor)

    1990-01-01

    A steam reformer is disclosed having an annular steam reforming catalyst bed formed by concentric cylinders and having a catalytic combustor located at the center of the innermost cylinder. Fuel is fed into the interior of the catalytic combustor and air is directed at the top of the combustor, creating a catalytic reaction which provides sufficient heat so as to maintain the catalytic reaction in the steam reforming catalyst bed. Alternatively, air is fed into the interior of the catalytic combustor and a fuel mixture is directed at the top. The catalytic combustor provides enhanced radiant and convective heat transfer to the reformer catalyst bed.

  12. Vibration and Control of Flexible Rotor Supported by Magnetic Bearings

    NASA Technical Reports Server (NTRS)

    Nonami, Kenzou

    1988-01-01

    Active vibration control of flexible rotors supported by magnetic bearings is discussed. Using a finite-element method for a mathematical model of the flexible rotor, the eigenvalue problem is formulated taking into account the interaction between a mechanical system of the flexible rotor and an electrical system of the magnetic bearings and the controller. However, for the sake of simplicity, gyroscopic effects are disregarded. It is possible to adapt this formulation to a general flexible rotor-magnetic bearing system. Controllability with and without collocation sensors and actuators located at the same distance along the rotor axis is discussed for the higher order flexible modes of the test rig. In conclusion, it is proposed that it is necessary to add new active control loops for the higher flexible modes even in the case of collocation. Then it is possible to stabilize for the case of uncollocation by means of this method.

  13. Flexibility and Muscular Strength.

    ERIC Educational Resources Information Center

    Liemohn, Wendell

    1988-01-01

    This definition of flexibility and muscular strength also explores their roles in overall physical fitness and focuses on how increased flexibility and muscular strength can help decrease or eliminate lower back pain. (CB)

  14. Closed Loop System Identification with Genetic Algorithms

    NASA Technical Reports Server (NTRS)

    Whorton, Mark S.

    2004-01-01

    High performance control design for a flexible space structure is challenging since high fidelity plant models are di.cult to obtain a priori. Uncertainty in the control design models typically require a very robust, low performance control design which must be tuned on-orbit to achieve the required performance. Closed loop system identi.cation is often required to obtain a multivariable open loop plant model based on closed-loop response data. In order to provide an accurate initial plant model to guarantee convergence for standard local optimization methods, this paper presents a global parameter optimization method using genetic algorithms. A minimal representation of the state space dynamics is employed to mitigate the non-uniqueness and over-parameterization of general state space realizations. This control-relevant system identi.cation procedure stresses the joint nature of the system identi.cation and control design problem by seeking to obtain a model that minimizes the di.erence between the predicted and actual closed-loop performance.

  15. Functional Loop Dynamics of the Streptavidin-Biotin Complex

    PubMed Central

    Song, Jianing; Li, Yongle; Ji, Changge; Zhang, John Z. H.

    2015-01-01

    Accelerated molecular dynamics (aMD) simulation is employed to study the functional dynamics of the flexible loop3-4 in the strong-binding streptavidin-biotin complex system. Conventional molecular (cMD) simulation is also performed for comparison. The present study reveals the following important properties of the loop dynamics: (1) The transition of loop3-4 from open to closed state is observed in 200 ns aMD simulation. (2) In the absence of biotin binding, the open-state streptavidin is more stable, which is consistent with experimental evidences. The free energy (ΔG) difference is about 5 kcal/mol between two states. But with biotin binding, the closed state is more stable due to electrostatic and hydrophobic interactions between the loop3-4 and biotin. (3) The closure of loop3-4 is concerted to the stable binding of biotin to streptavidin. When the loop3-4 is in its open-state, biotin moves out of the binding pocket, indicating that the interactions between the loop3-4 and biotin are essential in trapping biotin in the binding pocket. (4) In the tetrameric streptavidin system, the conformational change of the loop3-4 in each monomer is independent of each other. That is, there is no cooperative binding for biotin bound to the four subunits of the tetramer. PMID:25601277

  16. Functional Loop Dynamics of the Streptavidin-Biotin Complex

    NASA Astrophysics Data System (ADS)

    Song, Jianing; Li, Yongle; Ji, Changge; Zhang, John Z. H.

    2015-01-01

    Accelerated molecular dynamics (aMD) simulation is employed to study the functional dynamics of the flexible loop3-4 in the strong-binding streptavidin-biotin complex system. Conventional molecular (cMD) simulation is also performed for comparison. The present study reveals the following important properties of the loop dynamics: (1) The transition of loop3-4 from open to closed state is observed in 200 ns aMD simulation. (2) In the absence of biotin binding, the open-state streptavidin is more stable, which is consistent with experimental evidences. The free energy (ΔG) difference is about 5 kcal/mol between two states. But with biotin binding, the closed state is more stable due to electrostatic and hydrophobic interactions between the loop3-4 and biotin. (3) The closure of loop3-4 is concerted to the stable binding of biotin to streptavidin. When the loop3-4 is in its open-state, biotin moves out of the binding pocket, indicating that the interactions between the loop3-4 and biotin are essential in trapping biotin in the binding pocket. (4) In the tetrameric streptavidin system, the conformational change of the loop3-4 in each monomer is independent of each other. That is, there is no cooperative binding for biotin bound to the four subunits of the tetramer.

  17. Hollow fiber catalytic membranes

    SciTech Connect

    Ma, Yi Hua; Moser, W.; Shelekhin, A.; Pien, Shyhing

    1993-09-01

    The objective of the present research is to investigate the possibility of the enhancement of the H{sub 2}S thermal decomposition in the IGCC system by employing the hollow fiber catalytic membrane reactor. To accomplish the objective, the following major components in the analysis of the high temperature membrane reactor must be investigated: high-temperature stability of the porous glass membrane; catalytic properties of MoS{sub 2} and of the porous glass membrane; catalytic decomposition of H{sub 2}S in a packed bed reactor; catalytic decomposition of 100%, 8.6%, and 1.1% H{sub 2}S gas mixtures in the membrane reactor. The study has been shown that the conversion of the H{sub 2}S can be increased in the packed bed membrane reactor compared to the equilibrium conversion on the shell side. The development of a mathematical model for the proposed process is in progress. The model will enable optimization of the H{sub 2}S decomposition. These conditions include selectivity factors and pressure drop across the membrane.

  18. Monolithic catalytic igniters

    NASA Technical Reports Server (NTRS)

    La Ferla, R.; Tuffias, R. H.; Jang, Q.

    1993-01-01

    Catalytic igniters offer the potential for excellent reliability and simplicity for use with the diergolic bipropellant oxygen/hydrogen as well as with the monopropellant hydrazine. State-of-the-art catalyst beds - noble metal/granular pellet carriers - currently used in hydrazine engines are limited by carrier stability, which limits the hot-fire temperature, and by poor thermal response due to the large thermal mass. Moreover, questions remain with regard to longevity and reliability of these catalysts. In this work, Ultramet investigated the feasibility of fabricating monolithic catalyst beds that overcome the limitations of current catalytic igniters via a combination of chemical vapor deposition (CVD) iridium coatings and chemical vapor infiltration (CVI) refractory ceramic foams. It was found that under all flow conditions and O2:H2 mass ratios tested, a high surface area monolithic bed outperformed a Shell 405 bed. Additionally, it was found that monolithic catalytic igniters, specifically porous ceramic foams fabricated by CVD/CVI processing, can be fabricated whose catalytic performance is better than Shell 405 and with significantly lower flow restriction, from materials that can operate at 2000 C or higher.

  19. Catalytic coal liquefaction process

    DOEpatents

    Garg, D.; Sunder, S.

    1986-12-02

    An improved process for catalytic solvent refining or hydroliquefaction of non-anthracitic coal at elevated temperatures under hydrogen pressure in a solvent comprises using as catalyst a mixture of a 1,2- or 1,4-quinone and an alkaline compound, selected from ammonium, alkali metal, and alkaline earth metal oxides, hydroxides or salts of weak acids. 1 fig.

  20. Catalytic coal liquefaction process

    DOEpatents

    Garg, Diwakar; Sunder, Swaminathan

    1986-01-01

    An improved process for catalytic solvent refining or hydroliquefaction of non-anthracitic coal at elevated temperatures under hydrogen pressure in a solvent comprises using as catalyst a mixture of a 1,2- or 1,4-quinone and an alkaline compound, selected from ammonium, alkali metal, and alkaline earth metal oxides, hydroxides or salts of weak acids.

  1. High heat flux loop heat pipes

    NASA Technical Reports Server (NTRS)

    North, Mark T.; Sarraf, David B.; Rosenfeld, John H.; Maidanik, Yuri F.; Vershinin, Sergey

    1997-01-01

    Loop heat pipes (LHPs) can transport very large thermal power loads over long distances, through flexible, small diameter tubes against gravitational heads. In order to overcome the evaporator limit of LHPs, which is of about 0.07 MW/sq m, work was carried out to improve the efficiency by threefold to tenfold. The vapor passage geometry for the high heat flux conditions is shown. A bidisperse wick material within the circumferential vapor passages was used. Along with heat flux enhancement, several underlying issues were demonstrated, including the fabrication of bidisperse powder with controlled properties and the fabrication of a device geometry capable of replacing vapor passages with bidisperse powder.

  2. Simulation of catalytic oxidation and selective catalytic NOx reduction in lean-exhaust hybrid vehicles

    SciTech Connect

    Gao, Zhiming; Daw, C Stuart; Chakravarthy, Veerathu K

    2012-01-01

    We utilize physically-based models for diesel exhaust catalytic oxidation and urea-based selective catalytic NOx reduction to study their impact on drive cycle performance of hypothetical light-duty diesel powered hybrid vehicles. The models have been implemented as highly flexible SIMULINK block modules that can be used to study multiple engine-aftertreatment system configurations. The parameters of the NOx reduction model have been adjusted to reflect the characteristics of Cu-zeolite catalysts, which are of widespread current interest. We demonstrate application of these models using the Powertrain System Analysis Toolkit (PSAT) software for vehicle simulations, along with a previously published methodology that accounts for emissions and temperature transients in the engine exhaust. Our results illustrate the potential impact of DOC and SCR interactions for lean hybrid electric and plug-in hybrid electric vehicles.

  3. Mitsunobu Reactions Catalytic in Phosphine and a Fully Catalytic System

    PubMed Central

    Buonomo, Joseph A; Aldrich, Courtney C

    2015-01-01

    The Mitsunobu reaction is renowned for its mild reaction conditions and broad substrate tolerance, but has limited utility in process chemistry and industrial applications due to poor atom economy and the generation of stoichiometric phosphine oxide and hydrazine by-products that complicate purification. A catalytic Mitsunobu reaction using innocuous reagents to recycle these by-products would overcome both of these shortcomings. Herein we report a protocol that is catalytic in phosphine (1-phenylphospholane) employing phenylsilane to recycle the catalyst. Integration of this phosphine catalytic cycle with Taniguchi’s azocarboxylate catalytic system provided the first fully catalytic Mitsunobu reaction. PMID:26347115

  4. Mitsunobu Reactions Catalytic in Phosphine and a Fully Catalytic System.

    PubMed

    Buonomo, Joseph A; Aldrich, Courtney C

    2015-10-26

    The Mitsunobu reaction is renowned for its mild reaction conditions and broad substrate tolerance, but has limited utility in process chemistry and industrial applications due to poor atom economy and the generation of stoichiometric phosphine oxide and hydrazine by-products that complicate purification. A catalytic Mitsunobu reaction using innocuous reagents to recycle these by-products would overcome both of these shortcomings. Herein we report a protocol that is catalytic in phosphine (1-phenylphospholane) employing phenylsilane to recycle the catalyst. Integration of this phosphine catalytic cycle with Taniguchi's azocarboxylate catalytic system provided the first fully catalytic Mitsunobu reaction. PMID:26347115

  5. A decoupled recursive approach for constrained flexible multibody system dynamics

    NASA Technical Reports Server (NTRS)

    Lai, Hao-Jan; Kim, Sung-Soo; Haug, Edward J.; Bae, Dae-Sung

    1989-01-01

    A variational-vector calculus approach is employed to derive a recursive formulation for dynamic analysis of flexible multibody systems. Kinematic relationships for adjacent flexible bodies are derived in a companion paper, using a state vector notation that represents translational and rotational components simultaneously. Cartesian generalized coordinates are assigned for all body and joint reference frames, to explicitly formulate deformation kinematics under small deformation kinematics and an efficient flexible dynamics recursive algorithm is developed. Dynamic analysis of a closed loop robot is performed to illustrate efficiency of the algorithm.

  6. Wilson-loop instantons

    NASA Technical Reports Server (NTRS)

    Lee, Kimyeong; Holman, Richard; Kolb, Edward W.

    1987-01-01

    Wilson-loop symmetry breaking is considered on a space-time of the form M4 x K, where M4 is a four-dimensional space-time and K is an internal space with nontrivial and finite fundamental group. It is shown in a simple model that the different vacua obtained by breaking a non-Abelian gauge group by Wilson loops are separated in the space of gauge potentials by a finite energy barrier. An interpolating gauge configuration is then constructed between these vacua and shown to have minimum energy. Finally some implications of this construction are discussed.

  7. Automatic one-loop calculations with Sherpa+OpenLoops

    NASA Astrophysics Data System (ADS)

    Cascioli, F.; Höche, S.; Krauss, F.; Maierhöfer, P.; Pozzorini, S.; Siegert, F.

    2014-06-01

    We report on the OpenLoops generator for one-loop matrix elements and its application to four-lepton production in association with up to one jet. The open loops algorithm uses a numerical recursion to construct the numerator of one-loop Feynman diagrams as functions of the loop momentum. In combination with tensor integrals this results in a highly efficient and numerically stable matrix element generator. In order to obtain a fully automated setup for the simulation of next-to-leading order scattering processes we interfaced OpenLoops to the Sherpa Monte Carlo event generator.

  8. Catalytic Antioxidants and Neurodegeneration

    PubMed Central

    Golden, Tamara R.

    2009-01-01

    Abstract Oxidative stress, resulting from mitochondrial dysfunction, excitotoxicity, or neuroinflammation, is implicated in numerous neurodegenerative conditions. Damage due to superoxide, hydroxyl radical, and peroxynitrite has been observed in diseases such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis, as well as in acute conditions that lead to neuronal death, such as stroke and epilepsy. Antioxidant therapies to remove these toxic compounds have been of great interest in treating these disorders. Catalytic antioxidants mimic the activities of superoxide dismutase or catalase or both, detoxifying superoxide and hydrogen peroxide, and in some cases, peroxynitrite and other toxic species as well. Several compounds have demonstrated efficacy in in vitro and in animal models of neurodegeneration, leading to optimism that catalytic antioxidants may prove to be useful therapies in human disease. Antioxid. Redox Signal. 11, 555–569. PMID:18754709

  9. Catalytic, hollow, refractory spheres

    NASA Technical Reports Server (NTRS)

    Wang, Taylor G. (Inventor); Elleman, Daniel D. (Inventor); Lee, Mark C. (Inventor); Kendall, Jr., James M. (Inventor)

    1987-01-01

    Improved, heterogeneous, refractory catalysts are in the form of gas-impervious, hollow, thin-walled spheres (10) suitable formed of a shell (12) of refractory such as alumina having a cavity (14) containing a gas at a pressure greater than atmospheric pressure. The wall material may be itself catalytic or a catalytically active material coated onto the sphere as a layer (16), suitably platinum or iron, which may be further coated with a layer (18) of activator or promoter. The density of the spheres (30) can be uniformly controlled to a preselected value within .+-.10 percent of the density of the fluid reactant such that the spheres either remain suspended or slowly fall or rise through the liquid reactant.

  10. Catalytic thermal barrier coatings

    DOEpatents

    Kulkarni, Anand A.; Campbell, Christian X.; Subramanian, Ramesh

    2009-06-02

    A catalyst element (30) for high temperature applications such as a gas turbine engine. The catalyst element includes a metal substrate such as a tube (32) having a layer of ceramic thermal barrier coating material (34) disposed on the substrate for thermally insulating the metal substrate from a high temperature fuel/air mixture. The ceramic thermal barrier coating material is formed of a crystal structure populated with base elements but with selected sites of the crystal structure being populated by substitute ions selected to allow the ceramic thermal barrier coating material to catalytically react the fuel-air mixture at a higher rate than would the base compound without the ionic substitutions. Precious metal crystallites may be disposed within the crystal structure to allow the ceramic thermal barrier coating material to catalytically react the fuel-air mixture at a lower light-off temperature than would the ceramic thermal barrier coating material without the precious metal crystallites.

  11. Catalytic reforming catalyst

    SciTech Connect

    Buss, W.C.; Kluksdahl, H.E.

    1980-12-09

    An improved catalyst, having a reduced fouling rate when used in a catalytic reforming process, said catalyst comprising platinum disposed on an alumina support wherein the alumina support is obtained by removing water from aluminum hydroxide produced as a by-product from a ziegler higher alcohol synthesis reaction, and wherein the alumina is calcined at a temperature of 1100-1400/sup 0/F so as to have a surface area of 165 to 215 square meters per gram.

  12. Catalytic combustion nears application

    SciTech Connect

    1994-11-01

    This article is a brief review of efforts to develope a catalytic combustion system with emissions levels less than 10 ppm. Two efforts are discussed: (1) tests by General Electric using a GE Frame 7E/9E and 7F/9F gas turbine, and (2) tests by AES using a Kawasaki M1A-13A industrial gas turbine. The latter also employs a heat recovery steam generator and produces 3 MWe and 28,000 lbm/hr of steam.

  13. Molecular Dynamics Studies on the HIV-1 Integrase Catalytic Domain

    SciTech Connect

    Lins, Roberto D.; Briggs, J. M.; Straatsma, TP; Carlson, Heather A.; Greenwald, Jason; Choe, Senyon; Mccammon, Andy

    1999-06-30

    The HIV-1 integrase, which is essential for viral replication, catalyzes the insertion of viral DNA into the host chromosome, thereby recruiting host cell machinery into making viral proteins. It represents the third main HIV enzyme target for inhibitor design, the first two being the reverse transcriptase and the protease. Two 1-ns molecular dynamics simulations have been carried out on completely hydrated models of the HIV-1 integrase catalytic domain, one with no metal ions and another with one magnesium ion in the catalytic site. The simulations predict that the region of the active site that is missing in the published crystal structures has (at the time of this work) more secondary structure than previously thought. The flexibility of this region has been discussed with respect to the mechanistic function of the enzyme. The results of these simulations will be used as part of inhibitor design projects directed against the catalytic domain of the enzyme.

  14. Catalytic nanoporous membranes

    DOEpatents

    Pellin, Michael J.; Hryn, John N.; Elam, Jeffrey W.

    2009-12-01

    A nanoporous catalytic membrane which displays several unique features including pores which can go through the entire thickness of the membrane. The membrane has a higher catalytic and product selectivity than conventional catalysts. Anodic aluminum oxide (AAO) membranes serve as the catalyst substrate. This substrate is then subjected to Atomic Layer Deposition (ALD), which allows the controlled narrowing of the pores from 40 nm to 10 nm in the substrate by deposition of a preparatory material. Subsequent deposition of a catalytic layer on the inner surfaces of the pores reduces pore sizes to less than 10 nm and allows for a higher degree of reaction selectivity. The small pore sizes allow control over which molecules enter the pores, and the flow-through feature can allow for partial oxidation of reactant species as opposed to complete oxidation. A nanoporous separation membrane, produced by ALD is also provided for use in gaseous and liquid separations. The membrane has a high flow rate of material with 100% selectivity.

  15. Livermore Compiler Analysis Loop Suite

    Energy Science and Technology Software Center (ESTSC)

    2013-03-01

    LCALS is designed to evaluate compiler optimizations and performance of a variety of loop kernels and loop traversal software constructs. Some of the loop kernels are pulled directly from "Livermore Loops Coded in C", developed at LLNL (see item 11 below for details of earlier code versions). The older suites were used to evaluate floating-point performances of hardware platforms prior to porting larger application codes. The LCALS suite is geared toward assissing C++ compiler optimizationsmore » and platform performance related to SIMD vectorization, OpenMP threading, and advanced C++ language features. LCALS contains 20 of 24 loop kernels from the older Livermore Loop suites, plus various others representative of loops found in current production appkication codes at LLNL. The latter loops emphasize more diverse loop constructs and data access patterns than the others, such as multi-dimensional difference stencils. The loops are included in a configurable framework, which allows control of compilation, loop sampling for execution timing, which loops are run and their lengths. It generates timing statistics for analysis and comparing variants of individual loops. Also, it is easy to add loops to the suite as desired.« less

  16. Livermore Compiler Analysis Loop Suite

    SciTech Connect

    Hornung, R. D.

    2013-03-01

    LCALS is designed to evaluate compiler optimizations and performance of a variety of loop kernels and loop traversal software constructs. Some of the loop kernels are pulled directly from "Livermore Loops Coded in C", developed at LLNL (see item 11 below for details of earlier code versions). The older suites were used to evaluate floating-point performances of hardware platforms prior to porting larger application codes. The LCALS suite is geared toward assissing C++ compiler optimizations and platform performance related to SIMD vectorization, OpenMP threading, and advanced C++ language features. LCALS contains 20 of 24 loop kernels from the older Livermore Loop suites, plus various others representative of loops found in current production appkication codes at LLNL. The latter loops emphasize more diverse loop constructs and data access patterns than the others, such as multi-dimensional difference stencils. The loops are included in a configurable framework, which allows control of compilation, loop sampling for execution timing, which loops are run and their lengths. It generates timing statistics for analysis and comparing variants of individual loops. Also, it is easy to add loops to the suite as desired.

  17. [Prediction of short loops in the proteins with internal disorder].

    PubMed

    Deriusheva, E I; Galzitskaia, O V; Serdiuk, I N

    2008-01-01

    New possibility of the FoldUnfold program for prediction of short disordered regions (loops), which appears by using the short window width (3 amino acid residues), was described. For three representatives of the proteins G family the FoldUnfold program predicted almost all short loops and yield results are well compatible with the X-ray structure data. We have classified the loops predicted in the protein Ras-p21 structure in two types. In the first type, loops have high values of the Debye-Waller factor typical of the so-called functional loops (flexible loops). In the other type, loops have lower values of the Debye-Waller factor and can be considered as loops connecting secondary structure elements (rigid loops). When the results of prediction with the use of our program are compared with the results of other programs (PONDR, RONN, DisEMBL, PreLINK, IUPred, GlobPlot 2, FoldIndex), it is seen that the first enables far better prediction of short loop positions. Use of FoldUnfold for ubiquitin-like domain h-PLIC-2 allows to resolve such task as definition of boundary between the structured and unstructured regions in proteins with a big portion of disordered regions. The FoldUnfold program defines a clear boundary between the structured and unstructured regions at amino acid residues 30-31,whereas each of the other programs outlines the boundary from the 28-th amino acid residues through the 70th. PMID:19140328

  18. Sequence dependence of transcription factor-mediated DNA looping

    PubMed Central

    Johnson, Stephanie; Lindén, Martin; Phillips, Rob

    2012-01-01

    DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes and DNA looping in transcriptional regulation in both prokaryotes and eukaryotes. These kinds of regulatory problems are now becoming amenable to systematic quantitative dissection with a powerful dialogue between theory and experiment. Here, we use a single-molecule experiment in conjunction with a statistical mechanical model to test quantitative predictions for the behavior of DNA looping at short length scales and to determine how DNA sequence affects looping at these lengths. We calculate and measure how such looping depends upon four key biological parameters: the strength of the transcription factor binding sites, the concentration of the transcription factor, and the length and sequence of the DNA loop. Our studies lead to the surprising insight that sequences that are thought to be especially favorable for nucleosome formation because of high flexibility lead to no systematically detectable effect of sequence on looping, and begin to provide a picture of the distinctions between the short length scale mechanics of nucleosome formation and looping. PMID:22718983

  19. NETL - Chemical Looping Reactor

    SciTech Connect

    2013-07-24

    NETL's Chemical Looping Reactor unit is a high-temperature integrated CLC process with extensive instrumentation to improve computational simulations. A non-reacting test unit is also used to study solids flow at ambient temperature. The CLR unit circulates approximately 1,000 pounds per hour at temperatures around 1,800 degrees Fahrenheit.

  20. NETL - Chemical Looping Reactor

    ScienceCinema

    None

    2014-06-26

    NETL's Chemical Looping Reactor unit is a high-temperature integrated CLC process with extensive instrumentation to improve computational simulations. A non-reacting test unit is also used to study solids flow at ambient temperature. The CLR unit circulates approximately 1,000 pounds per hour at temperatures around 1,800 degrees Fahrenheit.

  1. Loops: Twisting and Scaling

    NASA Astrophysics Data System (ADS)

    Walsh, R. W.

    2004-01-01

    Loop-like structures are the fundamental magnetic building blocks of the solar atmosphere. Recent space-based EUV and X-ray satellite observations (from Yohkoh SOHO and TRACE) have challenged the view that these features are simply static gravitationally stratified plasma pipes. Rather it is now surmised that each loop may consist of a bundle of fine plasma threads that are twisted around one another and can brighten independently. This invited review will outline the latest developments in ""untangling"" the topology of these features through three dimensional magnetohydrodynamic modelling and how their properties are being deduced through spectroscopic observations coupled to theoretical scaling laws. In particular recent interest has centred on how the observed thermal profile along loops can be employed as a tool to diagnose any localised energy input to the structure and hence constrain the presence of a particular coronal heating mechanism. The dynamic nature of loops will be highlighted and the implications of superior resolution plasma thread observations (whether spatial temporal or spectral) from future space missions (SolarB STEREO SDO and Solar Orbiter) will be discussed.

  2. RNA in the Loop

    PubMed Central

    Kung, Johnny T.Y.; Lee, Jeannie T.

    2013-01-01

    Long noncoding RNAs (lncRNAs) have been implicated in a variety of biological roles, particularly as cis or trans gene expression regulators. Reporting recently in Nature, Lai et al. (2013) show that a class of gene-activating lncRNAs combines two gene regulation paradigms: enhancer-directed chromosomal looping and RNA-mediated protein effector recruitment. PMID:23537627

  3. Closing the Loop Sampler.

    ERIC Educational Resources Information Center

    California Integrated Waste Management Board, Sacramento.

    Closing the Loop (CTL) is a science curriculum designed to introduce students to integrated waste management through awareness. This document presents five lesson plans focusing on developing an understanding of natural resources, solid wastes, conservation, and the life of landfills. Contents include: (1) "What Are Natural Resources?"; (2)…

  4. Input shaped control of 3-dimensional maneuvers of flexible spacecraft

    NASA Technical Reports Server (NTRS)

    Singh, T.; Vadali, S. R.

    1992-01-01

    This paper deals with the control of three dimensional rotational maneuvers of flexible spacecraft. A spacecraft with a spherical hub and six symmetric appendages is considered here as a model. The appendages are long and flexible leading to low frequency vibration under any control action. To provide a comprehensive treatment of input shaped controllers, both open loop and closed loop controllers are considered. The minimum-time bang-bang and the near-minimum-time controller, used in conjunction with the shaped input technique are studied. In addition, a combination of a Liapunov controller with the shaped input control technique is proposed to take advantage of the simple feedback control strategy and augment it with a technique that can eliminate the vibratory motion of the flexible appendages more efficiently.

  5. Robotic Simulation of Flexible-Body Spacecraft Dynamics

    NASA Technical Reports Server (NTRS)

    Brannan, Justin C.; Carignan, Craig R.

    2016-01-01

    A robotic testbed has been developed to conduct hardware-in-the-loop simulations of a robotic servicer interacting with a client satellite on-orbit. By creating an analytical model of a satellite with flexible appendages, it is possible to simulate the system response to external force and torque inputs and compare the predicted system motion to a robot mass simulator outfitted with physical appendages. This validation effort includes multiple test cases that encompass the types of interaction forces a satellite might experience during a nominal on-orbit servicing mission and aims to show the simulation's ability to capture the physical system response. After incorporating the flexible-body dynamics into the robotic mass simulator at NASA Goddard Space Flight Center (GSFC), a hardware-in-the-loop simulation can be used to characterize the potential impact of structural flexibility on an end-to-end satellite servicing mission.

  6. COLD TEST LOOP INTEGRATED TEST LOOP RESULTS

    SciTech Connect

    Abraham, TJ

    2003-10-22

    A testing facility (Cold Test Loop) was constructed and operated to demonstrate the efficacy of the Accelerated Waste Retrieval (AWR) Project's planned sluicing approach to the remediation of Silos 1 and 2 at the Fernald Environmental Management Project near Cincinnati, Ohio. The two silos contain almost 10,000 tons of radium-bearing low-level waste, which consists primarily of solids of raffinates from processing performed on ores from the Democratic Republic of Congo (commonly referred to as ''Belgium Congo ores'') for the recovery of uranium. These silos are 80 ft in diameter, 36 ft high to the center of the dome, and 26.75 ft to the top of the vertical side walls. The test facility contained two test systems, each designed for a specific purpose. The first system, the Integrated Test Loop (ITL), a near-full-scale plant including the actual equipment to be installed at the Fernald Site, was designed to demonstrate the sluicing operation and confirm the selection of a slurry pump, the optimal sluicing nozzle operation, and the preliminary design material balance. The second system, the Component Test Loop (CTL), was designed to evaluate many of the key individual components of the waste retrieval system over an extended run. The major results of the initial testing performed during July and August 2002 confirmed that the AWR approach to sluicing was feasible. The ITL testing confirmed the following: (1) The selected slurry pump (Hazleton 3-20 type SHW) performed well and is suitable for AWR application. However, the pump's motor should be upgraded to a 200-hp model and be driven by a 150-hp variable-frequency drive (VFD). A 200-hp VFD is not much more expensive and would allow the pump to operate at full speed. (2) The best nozzle performance was achieved by using 15/16-in. nozzles operated alternately. This configuration appeared to most effectively mine the surrogate. (3) The Solartron densitometer, which was tested as an alternative mass flow measurement

  7. Flexibility, Is That All?

    ERIC Educational Resources Information Center

    Renes, Wim M.

    This paper discusses the design of flexible and intelligent library buildings. The first section addresses how flexibility, as one of the requirements of a library building, that has high priority in the planning process. Intelligent libraries are considered in the second section, and functionality is stressed. The third section examines…

  8. Shear flexibility for structures

    NASA Technical Reports Server (NTRS)

    Stangeland, Maynard L. (Inventor)

    1976-01-01

    This device comprises a flexible sheet member having cross convolutions oriented 45.degree. to the shear vector with spherical reliefs at the convolution junctions. The spherical reliefs are essential to the shear flexibility by interrupting the principal stress lines that act along the ridges of the convolutions. The spherical reliefs provide convolutions in both directions in the plane of the cross-convolution ridges.

  9. Shear flexibility for structures

    NASA Technical Reports Server (NTRS)

    Stangeland, Maynard L. (Inventor)

    1977-01-01

    This device comprises a flexible sheet member having cross convolutions oriented 45.degree. to the shear vector with spherical reliefs at the convolution junctions. The spherical reliefs are essential to the shear flexibility by interrupting the principal stress lines that act along the ridges of the convolutions. The spherical reliefs provide convolutions in both directions in the plane of the cross-convolution ridges.

  10. Flexible Learning Opportunities.

    ERIC Educational Resources Information Center

    Further Education Unit, London (England).

    One way for colleges to meet the demand for a wider range of learning opportunities for adults in Great Britain is to provide more flexibility within the further education system. The concept of flexible learning involves the modification of delivery systems, specific providing agencies, target populations, specific determinants such as geographic…

  11. Flexible Heat Pipe

    NASA Technical Reports Server (NTRS)

    Bienert, W. B.; Wolf, D. A.

    1985-01-01

    Narrow Tube carries 10 watts or more to moving parts. Heat pipe 12 inches long and diameter of 0.312 inch (7.92mm). Bent to minimum radius of 2.5 blocks. Flexible section made of 321 stainless steel tubing (Cajon Flexible Tubing or equivalent). Evaporator and condenser made of oxygen free copper. Working fluid methanol.

  12. Flexible Animation Computer Program

    NASA Technical Reports Server (NTRS)

    Stallcup, Scott S.

    1990-01-01

    FLEXAN (Flexible Animation), computer program animating structural dynamics on Evans and Sutherland PS300-series graphics workstation with VAX/VMS host computer. Typical application is animation of spacecraft undergoing structural stresses caused by thermal and vibrational effects. Displays distortions in shape of spacecraft. Program displays single natural mode of vibration, mode history, or any general deformation of flexible structure. Written in FORTRAN 77.

  13. Flexibility within Fidelity

    ERIC Educational Resources Information Center

    Kendall, Philip C.; Gosch, Elizabeth; Furr, Jami M.; Sood, Erica

    2008-01-01

    The authors address concerns regarding manual-based treatments, highlighting the role of flexibility and creativity. A cognitive-behavioral therapy for youth anxiety called the Coping Cat program demonstrates the flexible application of manuals and emphasizes the importance of a child-centered, personalized approach that involves the child in the…

  14. Shield For Flexible Pipe

    NASA Technical Reports Server (NTRS)

    Ponton, Michael K.; Williford, Clifford B.; Lagen, Nicholas T.

    1995-01-01

    Cylindrical shield designed to fit around flexible pipe to protect nearby workers from injury and equipment from damage if pipe ruptures. Designed as pressure-relief device. Absorbs impact of debris ejected radially from broken flexible pipe. Also redirects flow of pressurized fluid escaping from broken pipe onto flow path allowing for relief of pressure while minimizing potential for harm.

  15. L2′ loop is critical for caspase-7 active site formation

    PubMed Central

    Witkowski, Witold A; Hardy, Jeanne A

    2009-01-01

    The active sites of caspases are composed of four mobile loops. A loop (L2) from one half of the dimer interacts with a loop (L2′) from the other half of the dimer to bind substrate. In an inactive form, the two L2′ loops form a cross-dimer hydrogen-bond network over the dimer interface. Although the L2′ loop has been implicated as playing a central role in the formation of the active-site loop bundle, its precise role in catalysis has not been shown. A detailed understanding of the active and inactive conformations is essential to control the caspase function. We have interrogated the contributions of the residues in the L2′ loop to catalytic function and enzyme stability. In wild-type and all mutants, active-site binding results in substantial stabilization of the complex. One mutation, P214A, is significantly destabilized in the ligand-free conformation, but is as stable as wild type when bound to substrate, indicating that caspase-7 rests in different conformations in the absence and presence of substrate. Residues K212 and I213 in the L2′ loop are shown to be essential for substrate-binding and thus proper catalytic function of the caspase. In the crystal structure of I213A, the void created by side-chain deletion is compensated for by rearrangement of tyrosine 211 to fill the void, suggesting that the requirements of substrate-binding are sufficiently strong to induce the active conformation. Thus, although the L2′ loop makes no direct contacts with substrate, it is essential for buttressing the substrate-binding groove and is central to native catalytic efficiency. PMID:19530232

  16. Inner mappings of Bruck loops

    NASA Astrophysics Data System (ADS)

    Kreuzer, Alexander

    1998-01-01

    K-loops have their origin in the theory of sharply 2-transitive groups. In this paper a proof is given that K-loops and Bruck loops are the same. For the proof it is necessary to show that in a (left) Bruck loop the left inner mappings L(b)L(a) L(ab)[minus sign]1 are automorphisms. This paper generalizes results of Glauberman [3], Kist [8] and Kreuzer [9].

  17. Catalytic reforming methods

    DOEpatents

    Tadd, Andrew R; Schwank, Johannes

    2013-05-14

    A catalytic reforming method is disclosed herein. The method includes sequentially supplying a plurality of feedstocks of variable compositions to a reformer. The method further includes adding a respective predetermined co-reactant to each of the plurality of feedstocks to obtain a substantially constant output from the reformer for the plurality of feedstocks. The respective predetermined co-reactant is based on a C/H/O atomic composition for a respective one of the plurality of feedstocks and a predetermined C/H/O atomic composition for the substantially constant output.

  18. Role of connecting loop I in catalysis and allosteric regulation of human glucokinase

    PubMed Central

    Martinez, Juliana A; Larion, Mioara; Conejo, Maria S; Porter, Carol M; Miller, Brian G

    2014-01-01

    Glucokinase (GCK, hexokinase IV) is a monomeric enzyme with a single glucose binding site that displays steady-state kinetic cooperativity, a functional characteristic that affords allosteric regulation of GCK activity. Structural evidence suggests that connecting loop I, comprised of residues 47–71, facilitates cooperativity by dictating the rate and scope of motions between the large and small domains of GCK. Here we investigate the impact of varying the length and amino acid sequence of connecting loop I upon GCK cooperativity. We find that sequential, single amino acid deletions from the C-terminus of connecting loop I cause systematic decreases in cooperativity. Deleting up to two loop residues leaves the kcat value unchanged; however, removing three or more residues reduces kcat by 1000-fold. In contrast, the glucose K0.5 and KD values are unaffected by shortening the connecting loop by up to six residues. Substituting alanine or glycine for proline-66, which adopts a cis conformation in some GCK crystal structures, does not alter cooperativity, indicating that cis/trans isomerization of this loop residue does not govern slow conformational reorganizations linked to hysteresis. Replacing connecting loop I with the corresponding loop sequence from the catalytic domain of the noncooperative isozyme human hexokinase I (HK-I) eliminates cooperativity without impacting the kcat and glucose K0.5 values. Our results indicate that catalytic turnover requires a minimal length of connecting loop I, whereas the loop has little impact upon the binding affinity of GCK for glucose. We propose a model in which the primary structure of connecting loop I affects cooperativity by influencing conformational dynamics, without altering the equilibrium distribution of GCK conformations. PMID:24723372

  19. Role of connecting loop I in catalysis and allosteric regulation of human glucokinase.

    PubMed

    Martinez, Juliana A; Larion, Mioara; Conejo, Maria S; Porter, Carol M; Miller, Brian G

    2014-07-01

    Glucokinase (GCK, hexokinase IV) is a monomeric enzyme with a single glucose binding site that displays steady-state kinetic cooperativity, a functional characteristic that affords allosteric regulation of GCK activity. Structural evidence suggests that connecting loop I, comprised of residues 47-71, facilitates cooperativity by dictating the rate and scope of motions between the large and small domains of GCK. Here we investigate the impact of varying the length and amino acid sequence of connecting loop I upon GCK cooperativity. We find that sequential, single amino acid deletions from the C-terminus of connecting loop I cause systematic decreases in cooperativity. Deleting up to two loop residues leaves the kcat value unchanged; however, removing three or more residues reduces kcat by 1000-fold. In contrast, the glucose K0.5 and KD values are unaffected by shortening the connecting loop by up to six residues. Substituting alanine or glycine for proline-66, which adopts a cis conformation in some GCK crystal structures, does not alter cooperativity, indicating that cis/trans isomerization of this loop residue does not govern slow conformational reorganizations linked to hysteresis. Replacing connecting loop I with the corresponding loop sequence from the catalytic domain of the noncooperative isozyme human hexokinase I (HK-I) eliminates cooperativity without impacting the kcat and glucose K0.5 values. Our results indicate that catalytic turnover requires a minimal length of connecting loop I, whereas the loop has little impact upon the binding affinity of GCK for glucose. We propose a model in which the primary structure of connecting loop I affects cooperativity by influencing conformational dynamics, without altering the equilibrium distribution of GCK conformations. PMID:24723372

  20. Loop Heat Pipes and Capillary Pumped Loops: An Applications Perspective

    NASA Technical Reports Server (NTRS)

    Butler, Dan; Ku, Jentung; Swanson, Theodore; Obenschain, Arthur F. (Technical Monitor)

    2001-01-01

    Capillary pumped loops (CPLS) and loop heat pipes (LHPS) are versatile two-phase heat transfer devices which have recently gained increasing acceptance in space applications. Both systems work based on the same principles and have very similar designs. Nevertheless, some differences exist in the construction of the evaporator and the hydro-accumulator, and these differences lead to very distinct operating characteristics for each loop. This paper presents comparisons of the two loops from an applications perspective, and addresses their impact on spacecraft design, integration, and test. Some technical challenges and issues for both loops are also addressed.

  1. Adaptive control strategies for flexible robotic arm

    NASA Technical Reports Server (NTRS)

    Bialasiewicz, Jan T.

    1993-01-01

    The motivation of this research came about when a neural network direct adaptive control scheme was applied to control the tip position of a flexible robotic arm. Satisfactory control performance was not attainable due to the inherent non-minimum phase characteristics of the flexible robotic arm tip. Most of the existing neural network control algorithms are based on the direct method and exhibit very high sensitivity if not unstable closed-loop behavior. Therefore a neural self-tuning control (NSTC) algorithm is developed and applied to this problem and showed promising results. Simulation results of the NSTC scheme and the conventional self-tuning (STR) control scheme are used to examine performance factors such as control tracking mean square error, estimation mean square error, transient response, and steady state response.

  2. Closed-loop anesthesia.

    PubMed

    LE Guen, Morgan; Liu, Ngai; Chazot, Thierry; Fischler, Marc

    2016-05-01

    Automated anesthesia which may offer to the physician time to control hemodynamic and to supervise neurological outcome and which may offer to the patient safety and quality was until recently consider as a holy grail. But this field of research is now increasing in every component of general anesthesia (hypnosis, nociception, neuromuscular blockade) and literature describes some successful algorithms - single or multi closed-loop controller. The aim of these devices is to control a predefined target and to continuously titrate anesthetics whatever the patients' co morbidities and surgical events to reach this target. Literature contains many randomized trials comparing manual and automated anesthesia and shows feasibility and safety of this system. Automation could quickly concern other aspects of anesthesia as fluid management and this review proposes an overview of closed-loop systems in anesthesia. PMID:26554614

  3. Catalytic considerations in temperature measurement.

    NASA Technical Reports Server (NTRS)

    Ash, R. L.; Crossman, G. R.; Chitnis, R. V.

    1972-01-01

    Literature discussing catalytic activity in platinum group temperature sensors is surveyed. Methods for the determination and/or elimination of catalytic activity are reported. A particular application of the literature is discussed in which it is possible to infer that a shielded platinum total temperature probe does not experience significant catalytic activity in the wake of a supersonic hydrogen burner, while a bare iridium plus rhodium, iridium thermocouple does. It is concluded that catalytic data corrections are restricted and that it is preferable to coat the temperature sensor with a noncatalytic coating. Furthermore, the desirability of transparent coatings is discussed.

  4. A control system design approach for flexible spacecraft

    NASA Technical Reports Server (NTRS)

    Silverberg, L. M.

    1985-01-01

    A control system design approach for flexible spacecraft is presented. The control system design is carried out in two steps. The first step consists of determining the ideal control system in terms of a desirable dynamic performance. The second step consists of designing a control system using a limited number of actuators that possess a dynamic performance that is close to the ideal dynamic performance. The effects of using a limited number of actuators is that the actual closed-loop eigenvalues differ from the ideal closed-loop eigenvalues. A method is presented to approximate the actual closed-loop eigenvalues so that the calculation of the actual closed-loop eigenvalues can be avoided. Depending on the application, it also may be desirable to apply the control forces as impulses. The effect of digitizing the control to produce the appropriate impulses is also examined.

  5. Verification of Loop Diagnostics

    NASA Technical Reports Server (NTRS)

    Winebarger, A.; Lionello, R.; Mok, Y.; Linker, J.; Mikic, Z.

    2014-01-01

    Many different techniques have been used to characterize the plasma in the solar corona: density-sensitive spectral line ratios are used to infer the density, the evolution of coronal structures in different passbands is used to infer the temperature evolution, and the simultaneous intensities measured in multiple passbands are used to determine the emission measure. All these analysis techniques assume that the intensity of the structures can be isolated through background subtraction. In this paper, we use simulated observations from a 3D hydrodynamic simulation of a coronal active region to verify these diagnostics. The density and temperature from the simulation are used to generate images in several passbands and spectral lines. We identify loop structures in the simulated images and calculate the loop background. We then determine the density, temperature and emission measure distribution as a function of time from the observations and compare with the true temperature and density of the loop. We find that the overall characteristics of the temperature, density, and emission measure are recovered by the analysis methods, but the details of the true temperature and density are not. For instance, the emission measure curves calculated from the simulated observations are much broader than the true emission measure distribution, though the average temperature evolution is similar. These differences are due, in part, to inadequate background subtraction, but also indicate a limitation of the analysis methods.

  6. Chemical Looping Combustion Kinetics

    SciTech Connect

    Edward Eyring; Gabor Konya

    2009-03-31

    One of the most promising methods of capturing CO{sub 2} emitted by coal-fired power plants for subsequent sequestration is chemical looping combustion (CLC). A powdered metal oxide such as NiO transfers oxygen directly to a fuel in a fuel reactor at high temperatures with no air present. Heat, water, and CO{sub 2} are released, and after H{sub 2}O condensation the CO{sub 2} (undiluted by N{sub 2}) is ready for sequestration, whereas the nickel metal is ready for reoxidation in the air reactor. In principle, these processes can be repeated endlessly with the original nickel metal/nickel oxide participating in a loop that admits fuel and rejects ash, heat, and water. Our project accumulated kinetic rate data at high temperatures and elevated pressures for the metal oxide reduction step and for the metal reoxidation step. These data will be used in computational modeling of CLC on the laboratory scale and presumably later on the plant scale. The oxygen carrier on which the research at Utah is focused is CuO/Cu{sub 2}O rather than nickel oxide because the copper system lends itself to use with solid fuels in an alternative to CLC called 'chemical looping with oxygen uncoupling' (CLOU).

  7. Loops of Jupiter

    NASA Astrophysics Data System (ADS)

    Opolski, Antoni

    2014-12-01

    Professor Antoni Opolski was actively interested in astronomy after his retirement in 1983. He especially liked to study the works of the famous astronomer Copernicus getting inspiration for his own work. Opolski started his work on planetary loops in 2011 continuing it to the end of 2012 . During this period calculations, drawings, tables, and basic descriptions of all the planets of the Solar System were created with the use of a piece of paper and a pencil only. In 2011 Antoni Opolski asked us to help him in editing the manuscript and preparing it for publication. We have been honored having the opportunity to work on articles on planetary loops with Antoni Opolski in his house for several months. In the middle of 2012 the detailed material on Jupiter was ready. However, professor Opolski improved the article by smoothing the text and preparing new, better drawings. Finally the article ''Loops of Jupiter'', written by the 99- year old astronomer, was published in the year of his 100th birthday.

  8. Novel Catalytic Membrane Reactors

    SciTech Connect

    Stuart Nemser, PhD

    2010-10-01

    There are many industrial catalytic organic reversible reactions with amines or alcohols that have water as one of the products. Many of these reactions are homogeneously catalyzed. In all cases removal of water facilitates the reaction and produces more of the desired chemical product. By shifting the reaction to right we produce more chemical product with little or no additional capital investment. Many of these reactions can also relate to bioprocesses. Given the large number of water-organic compound separations achievable and the ability of the Compact Membrane Systems, Inc. (CMS) perfluoro membranes to withstand these harsh operating conditions, this is an ideal demonstration system for the water-of-reaction removal using a membrane reactor. Enhanced reaction synthesis is consistent with the DOE objective to lower the energy intensity of U.S. industry 25% by 2017 in accord with the Energy Policy Act of 2005 and to improve the United States manufacturing competitiveness. The objective of this program is to develop the platform technology for enhancing homogeneous catalytic chemical syntheses.

  9. Catalytic cracking process

    SciTech Connect

    Gladrow, E.M.; Winter, W.E.

    1980-04-29

    The octane number of a cracked naphtha can be significantly improved in a catalytic cracking unit, without significant decrease in naphtha yield, by maintaining certain critical concentrations of metals on the catalyst, suitably by blending or adding a heavy metals-containing component to the gas oil feed. Suitably, in a catalytic cracking process unit wherein a gas oil feed is cracked in a cracking reactor (Zone) at an elevated temperature in the presence of a cracking catalyst, the cracking catalyst is regenerated in a regenerator (Regeneration zone) by burning coke off the catalyst, and catalyst is circulated between the reactor and regenerator, sufficient of a metals-containing heavy feedstock is admixed, intermittantly or continuously, with the gas oil feed to deposit metals on said catalyst and raise the metals-content of said catalyst to a level of from about 1500 to about 6000 parts per million, preferably from about 2500 to about 4000 parts per million expressed as equivalent nickel, base the weight of the catalyst, and said metals level is maintained on the catalyst throughout the operation by withdrawing high metals-containing catalyst and adding low metals-containing catalyst to the regenerator.

  10. Control of nonlinear flexible space structures

    NASA Astrophysics Data System (ADS)

    Shi, Jianjun

    With the advances made in computer technology and efficiency of numerical algorithms over last decade, the MPC strategies have become quite popular among control community. However, application of MPC or GPC to flexible space structure control has not been explored adequately in the literature. The work presented in this thesis primarily focuses on application of GPC to control of nonlinear flexible space structures. This thesis is particularly devoted to the development of various approximate dynamic models, design and assessment of candidate controllers, and extensive numerical simulations for a realistic multibody flexible spacecraft, namely, Jupiter Icy Moons Orbiter (JIMO)---a Prometheus class of spacecraft proposed by NASA for deep space exploratory missions. A stable GPC algorithm is developed for Multi-Input-Multi-Output (MIMO) systems. An end-point weighting (penalty) is used in the GPC cost function to guarantee the nominal stability of the closed-loop system. A method is given to compute the desired end-point state from the desired output trajectory. The methodologies based on Fake Algebraic Riccati Equation (FARE) and constrained nonlinear optimization, are developed for synthesis of state weighting matrix. This makes this formulation more practical. A stable reconfigurable GPC architecture is presented and its effectiveness is demonstrated on both aircraft as well as spacecraft model. A representative in-orbit maneuver is used for assessing the performance of various control strategies using various design models. Different approximate dynamic models used for analysis include linear single body flexible structure, nonlinear single body flexible structure, and nonlinear multibody flexible structure. The control laws evaluated include traditional GPC, feedback linearization-based GPC (FLGPC), reconfigurable GPC, and nonlinear dissipative control. These various control schemes are evaluated for robust stability and robust performance in the presence of

  11. Creating stable stem regions for loop elongation in Fcabs — Insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations

    PubMed Central

    Hasenhindl, Christoph; Lai, Balder; Delgado, Javier; Traxlmayr, Michael W.; Stadlmayr, Gerhard; Rüker, Florian; Serrano, Luis; Oostenbrink, Chris; Obinger, Christian

    2014-01-01

    Fcabs (Fc antigen binding) are crystallizable fragments of IgG where the C-terminal structural loops of the CH3 domain are engineered for antigen binding. For the design of libraries it is beneficial to know positions that will permit loop elongation to increase the potential interaction surface with antigen. However, the insertion of additional loop residues might impair the immunoglobulin fold. In the present work we have probed whether stabilizing mutations flanking the randomized and elongated loop region improve the quality of Fcab libraries. In detail, 13 libraries were constructed having the C-terminal part of the EF loop randomized and carrying additional residues (1, 2, 3, 5 or 10, respectively) in the absence and presence of two flanking mutations. The latter have been demonstrated to increase the thermal stability of the CH3 domain of the respective solubly expressed proteins. Assessment of the stability of the libraries expressed on the surface of yeast cells by flow cytometry demonstrated that loop elongation was considerably better tolerated in the stabilized libraries. By using in silico loop reconstruction and mimicking randomization together with MD simulations the underlying molecular dynamics were investigated. In the presence of stabilizing stem residues the backbone flexibility of the engineered EF loop as well as the fluctuation between its accessible conformations were decreased. In addition the CD loop (but not the AB loop) and most of the framework regions were rigidified. The obtained data are discussed with respect to the design of Fcabs and available data on the relation between flexibility and affinity of CDR loops in Ig-like molecules. PMID:24792385

  12. Rolling cuff flexible bellows

    DOEpatents

    Lambert, Donald R.

    1985-01-01

    A flexible connector apparatus used to join two stiff non-deformable members, such as piping. The apparatus is provided with one or more flexible sections or assemblies each utilizing a bellows of a rolling cuff type connected between two ridge members, with the bellows being supported by a back-up ring, such that only the curved end sections of the bellows are unsupported. Thus, the bellows can be considered as being of a tube-shaped configuration and thus have high pressure resistance. The components of the flexible apparatus are sealed or welded one to another such that it is fluid tight.

  13. Rolling cuff flexible bellows

    SciTech Connect

    Lambert, D. R.

    1985-09-10

    A flexible connector apparatus used to join two stiff non-deformable members, such as piping. The apparatus is provided with one or more flexible sections or assemblies each utilizing a bellows of a rolling cuff type connected between two ridge members, with the bellows being supported by a back-up ring, such that only the curved end sections of the bellows are unsupported. Thus, the bellows can be considered as being of a tube-shaped configuration and thus have high pressure resistance. The components of the flexible apparatus are sealed or welded one to another such that it is fluid tight.

  14. Utilization of Substrate Intrinsic Binding Energy for Conformational Change and Catalytic Function in Phosphoenolpyruvate Carboxykinase.

    PubMed

    Johnson, Troy A; Mcleod, Matthew J; Holyoak, Todd

    2016-01-26

    Phosphoenolpyruvate carboxykinase (PEPCK) is an essential metabolic enzyme operating in the gluconeogenesis and glyceroneogenesis pathways. Previous work has demonstrated that the enzyme cycles between a catalytically inactive open state and a catalytically active closed state. The transition of the enzyme between these states requires the transition of several active site loops to shift from mobile, disordered structural elements to stable ordered states. The mechanism by which these disorder-order transitions are coupled to the ligation state of the active site however is not fully understood. To further investigate the mechanisms by which the mobility of the active site loops is coupled to enzymatic function and the transitioning of the enzyme between the two conformational states, we have conducted structural and functional studies of point mutants of E89. E89 is a proposed key member of the interaction network of mobile elements as it resides in the R-loop region of the enzyme active site. These new data demonstrate the importance of the R-loop in coordinating interactions between substrates at the OAA/PEP binding site and the mobile R- and Ω-loop domains. In turn, the studies more generally demonstrate the mechanisms by which the intrinsic ligand binding energy can be utilized in catalysis to drive unfavorable conformational changes, changes that are subsequently required for both optimal catalytic activity and fidelity. PMID:26709450

  15. ArchDB 2014: structural classification of loops in proteins

    PubMed Central

    Bonet, Jaume; Planas-Iglesias, Joan; Garcia-Garcia, Javier; Marín-López, Manuel A.; Fernandez-Fuentes, Narcis; Oliva, Baldo

    2014-01-01

    The function of a protein is determined by its three-dimensional structure, which is formed by regular (i.e. β-strands and α-helices) and non-periodic structural units such as loops. Compared to regular structural elements, non-periodic, non-repetitive conformational units enclose a much higher degree of variability—raising difficulties in the identification of regularities, and yet represent an important part of the structure of a protein. Indeed, loops often play a pivotal role in the function of a protein and different aspects of protein folding and dynamics. Therefore, the structural classification of protein loops is an important subject with clear applications in homology modelling, protein structure prediction, protein design (e.g. enzyme design and catalytic loops) and function prediction. ArchDB, the database presented here (freely available at http://sbi.imim.es/archdb), represents such a resource and has been an important asset for the scientific community throughout the years. In this article, we present a completely reworked and updated version of ArchDB. The new version of ArchDB features a novel, fast and user-friendly web-based interface, and a novel graph-based, computationally efficient, clustering algorithm. The current version of ArchDB classifies 149,134 loops in 5739 classes and 9608 subclasses. PMID:24265221

  16. Catalytic reactor with disposable cartridge

    NASA Technical Reports Server (NTRS)

    Mccullough, C. M.

    1973-01-01

    Catalytic reactor, disposable cartridge enclosing iron catalyst, acts as container for solid carbon formed by decomposition of carbon monoxide. Deposition of carbon in other parts of oxygen recovery system does not occur because of lack of catalytic activity; filters trap carbon particles and prevent their being transported outside reaction zone.

  17. Fast Protein Loop Sampling and Structure Prediction Using Distance-Guided Sequential Chain-Growth Monte Carlo Method

    PubMed Central

    Tang, Ke; Zhang, Jinfeng; Liang, Jie

    2014-01-01

    Loops in proteins are flexible regions connecting regular secondary structures. They are often involved in protein functions through interacting with other molecules. The irregularity and flexibility of loops make their structures difficult to determine experimentally and challenging to model computationally. Conformation sampling and energy evaluation are the two key components in loop modeling. We have developed a new method for loop conformation sampling and prediction based on a chain growth sequential Monte Carlo sampling strategy, called Distance-guided Sequential chain-Growth Monte Carlo (DiSGro). With an energy function designed specifically for loops, our method can efficiently generate high quality loop conformations with low energy that are enriched with near-native loop structures. The average minimum global backbone RMSD for 1,000 conformations of 12-residue loops is Å, with a lowest energy RMSD of Å, and an average ensemble RMSD of Å. A novel geometric criterion is applied to speed up calculations. The computational cost of generating 1,000 conformations for each of the x loops in a benchmark dataset is only about cpu minutes for 12-residue loops, compared to ca cpu minutes using the FALCm method. Test results on benchmark datasets show that DiSGro performs comparably or better than previous successful methods, while requiring far less computing time. DiSGro is especially effective in modeling longer loops (– residues). PMID:24763317

  18. Flexibility in insulin prescription

    PubMed Central

    Kalra, Sanjay; Gupta, Yashdeep; Unnikrishnan, Ambika Gopalakrishnan

    2016-01-01

    This communication explores the concept of flexibility, a propos insulin preparations and insulin regimes used in the management of type 2 diabetes. The flexibility of an insulin regime or preparation is defined as their ability to be injected at variable times, with variable injection-meal time gaps, in a dose frequency and quantum determined by shared decision making, with a minimal requirement of glucose monitoring and health professional consultation, with no compromise on safety, efficiency and tolerability. The relative flexibility of various basal, prandial and dual action insulins, as well as intensive regimes, is compared. The biopsychosocial model of health is used to assess the utility of different insulins while encouraging a philosophy of flexible insulin usage. PMID:27186563

  19. Modeling flexible active nematics

    NASA Astrophysics Data System (ADS)

    Varga, Michael; Selinger, Robin

    We study active nematic phases of self-propelled flexible chains in two dimensions using computer simulation, to investigate effects of chain flexibility. In a ``dry'' phase of self-propelled flexible chains, we find that increasing chain stiffness enhances orientational order and correlation length, narrows the distribution of turning angles, increases persistence length, and increases the magnitude of giant density fluctuations. We further adapt the simulation model to describe behavior of microtubules driven by kinesin molecular motors in two different environments: on a rigid substrate with kinesin immobilized on the surface; and on a lipid membrane where kinesin is bonded to lipid head groups and can diffuse. Results are compared to experiments by L. Hirst and J. Xu. Lastly, we consider active nematics of flexible particles enclosed in soft, deformable encapsulation in two dimensions, and demonstrate novel mechanisms of pattern formation that are fundamentally different from those observed in bulk. Supported by NSF-DMR 1409658.

  20. Composite flexible blanket insulation

    NASA Technical Reports Server (NTRS)

    Kourtides, Demetrius A. (Inventor); Lowe, David M. (Inventor)

    1994-01-01

    An improved composite flexible blanket insulation is presented comprising top silicon carbide having an interlock design, wherein the reflective shield is composed of single or double aluminized polyimide and wherein the polyimide film has a honeycomb pattern.

  1. Flexible memory networks.

    PubMed

    Curto, Carina; Degeratu, Anda; Itskov, Vladimir

    2012-03-01

    Networks of neurons in some brain areas are flexible enough to encode new memories quickly. Using a standard firing rate model of recurrent networks, we develop a theory of flexible memory networks. Our main results characterize networks having the maximal number of flexible memory patterns, given a constraint graph on the network's connectivity matrix. Modulo a mild topological condition, we find a close connection between maximally flexible networks and rank 1 matrices. The topological condition is H (1)(X;ℤ)=0, where X is the clique complex associated to the network's constraint graph; this condition is generically satisfied for large random networks that are not overly sparse. In order to prove our main results, we develop some matrix-theoretic tools and present them in a self-contained section independent of the neuroscience context. PMID:21826564

  2. Flexible Polyhedral Surfaces.

    ERIC Educational Resources Information Center

    Alexandrov, V. A.

    1998-01-01

    Discusses some questions connected with Cauchy's theorem which states that two convex closed polyhedral surfaces whose corresponding faces are congruent and whose faces adjoin each other in the same way are congruent. Describes how to construct a flexible polyhedron. (ASK)

  3. Flexibility in insulin prescription.

    PubMed

    Kalra, Sanjay; Gupta, Yashdeep; Unnikrishnan, Ambika Gopalakrishnan

    2016-01-01

    This communication explores the concept of flexibility, a propos insulin preparations and insulin regimes used in the management of type 2 diabetes. The flexibility of an insulin regime or preparation is defined as their ability to be injected at variable times, with variable injection-meal time gaps, in a dose frequency and quantum determined by shared decision making, with a minimal requirement of glucose monitoring and health professional consultation, with no compromise on safety, efficiency and tolerability. The relative flexibility of various basal, prandial and dual action insulins, as well as intensive regimes, is compared. The biopsychosocial model of health is used to assess the utility of different insulins while encouraging a philosophy of flexible insulin usage. PMID:27186563

  4. Top3-Rmi1 dissolve Rad51-mediated D-loops by a topoisomerase-based mechanism

    PubMed Central

    Fasching, Clare L.; Cejka, Petr; Kowalczykowski, Stephen C.; Heyer, Wolf-Dietrich

    2015-01-01

    Summary The displacement loop (D-loop) is the DNA strand invasion product formed during homologous recombination. Disruption of nascent D-loops represents a mechanism of anti-recombination. During Synthesis-Dependent Strand Annealing D-loop disruption after extension of the invading strand is an integral step of the pathway and ensures a non-crossover outcome. The proteins implicated in D-loop disruption are DNA motor proteins/helicases acting by migrating DNA junctions. Here we report an unanticipated mechanism of D-loop dissolution mediated by DNA topoisomerase 3 (Top3) and dependent on its catalytic activity. D-loop dissolution catalyzed by yeast Top3 is highly specific for yeast Rad51/Rad54-mediated D-loops, whereas protein-free D-loops or D-loop mediated by bacterial RecA protein or human RAD51/RAD54 resist dissolution. Also the human Topoisomerase IIIα-RMI1–RMI2 complex is capable of dissolving D-loops. Consistent with genetic data, we suggest that the extreme growth defect and hyper-recombination phenotype of Top3-deficient yeast cells is in part a result of unprocessed D-loops. PMID:25699708

  5. Flexible sliding seal

    NASA Technical Reports Server (NTRS)

    Wallenhorst, E. L.

    1980-01-01

    Circular seal both slides and flexes to accomodate relative motion between two sealed members. Originally developed for Space Shuttle orbiter, it contains sliding seal to accommodate engine gimbaling and flexible seal that absorbs forward motion at high thrust of engine heat shield relative to airframe. Other possible applications are in support structures of heavy machinery and vehicle engines. Flexible sliding seal is ring about 7 feet in diameter and can withstand temperatures up to 1,600 F.

  6. Catalytic conversions of chlorodecalin

    SciTech Connect

    Takhistov, U.V.; Kovyazin, V.E.

    1985-10-01

    This paper studies catalytic conversions of chlorinated decahydronaphthalene (chlorodecalin), since the introduction of chlorine into the hydrocarbon molecule would facilitate formation of the original carbonium ion required for conversion to adamantane. Analysis of the fractions obtained showed that two main products are formed: the tricyclic hydrocarbon C/sub 10/H/sub 16/ and the bicyclic hydrocarbon C/sub 10/H/sub 16/. Therefore, the C/sub 10/H/sub 17/ cation formed by removal of chlorine from chlorodecalin, C/sub 10/H/sub 17/CI, undergoes changes in two directions: addition of hydride ions from other chlorodecalin molecules to form Decalin, and loss of a proton to give a tricyclic system of the adamantane weries and its isomer. Introduction of a substituent (chlorine) into the Decalin molecule made it possible to conduct the process at low temperatures.

  7. Catalytic hollow spheres

    NASA Technical Reports Server (NTRS)

    Wang, Taylor G. (Inventor); Elleman, Daniel D. (Inventor); Lee, Mark C. (Inventor); Kendall, Jr., James M. (Inventor)

    1986-01-01

    The improved, heterogeneous catalysts are in the form of gas-impervious, hollow, thin-walled spheres (10) suitably formed of a shell (12) of metal such as aluminum having a cavity (14) containing a gas at a pressure greater than atmospheric pressure. The wall material may be, itself, catalytic or the catalyst can be coated onto the sphere as a layer (16), suitably platinum or iron, which may be further coated with a layer (18) of activator or promoter. The density of the spheres (30) can be uniformly controlled to a preselected value within .+-.10 percent of the density of the fluid reactant such that the spheres either remain suspended or slowly fall or rise through the liquid reactant.

  8. Catalytic hollow spheres

    NASA Technical Reports Server (NTRS)

    Wang, Taylor G. (Inventor); Elleman, Daniel D. (Inventor); Lee, Mark C. (Inventor); Kendall, Jr., James M. (Inventor)

    1989-01-01

    The improved, heterogeneous catalysts are in the form of gas-impervious, hollow, thin-walled spheres (10) suitably formed of a shell (12) of metal such as aluminum having a cavity (14) containing a gas at a pressure greater than atmospheric pressure. The wall material may be, itself, catalytic or the catalyst can be coated onto the sphere as a layer (16), suitably platinum or iron, which may be further coated with a layer (18) of activator or promoter. The density of the spheres (30) can be uniformly controlled to a preselected value within .+-.10 percent of the density of the fluid reactant such that the spheres either remain suspended or slowly fall or rise through the liquid reactant.

  9. ``OPTICAL Catalytic Nanomotors''

    NASA Astrophysics Data System (ADS)

    Rosary-Oyong, Se, Glory

    D. Kagan, et.al, 2009:'' a motion-based chemical sensing involving fuel-driven nanomotors is demonstrated. The new protocol relies on the use of an optical microscope for tracking charge in the speed of nanowire motors in the presence of target analyte''. Synthetic nanomotors are propelled by catalytic decomposition of .. they do not require external electric, magnetic or optical fields as energy... Accompanying Fig 2.6(a) of optical micrograph of a partial monolayer of silica microbeads [J.Gibbs, 2011 ] retrieves WF Paxton:''rods were characterized by transmission electron & dark-field optical microscopy..'' & LF Valadares:''dimer due to the limited resolution of optical microscopy, however the result..'. Acknowledged to HE. Mr. Prof. SEDIONO M.P. TJONDRONEGORO.

  10. Bifunctional catalytic electrode

    NASA Technical Reports Server (NTRS)

    Cisar, Alan (Inventor); Murphy, Oliver J. (Inventor); Clarke, Eric (Inventor)

    2005-01-01

    The present invention relates to an oxygen electrode for a unitized regenerative hydrogen-oxygen fuel cell and the unitized regenerative fuel cell having the oxygen electrode. The oxygen electrode contains components electrocatalytically active for the evolution of oxygen from water and the reduction of oxygen to water, and has a structure that supports the flow of both water and gases between the catalytically active surface and a flow field or electrode chamber for bulk flow of the fluids. The electrode has an electrocatalyst layer and a diffusion backing layer interspersed with hydrophilic and hydrophobic regions. The diffusion backing layer consists of a metal core having gas diffusion structures bonded to the metal core.

  11. Coupled dual loop absorption heat pump

    DOEpatents

    Sarkisian, Paul H.; Reimann, Robert C.; Biermann, Wendell J.

    1985-01-01

    A coupled dual loop absorption system which utilizes two separate complete loops. Each individual loop operates at three temperatures and two pressures. This low temperature loop absorber and condenser are thermally coupled to the high temperature loop evaporator, and the high temperature loop condenser and absorber are thermally coupled to the low temperature generator.

  12. Flexible production systems

    NASA Astrophysics Data System (ADS)

    Chudakov, A. D.; Shchetinin, D. D.

    1986-03-01

    Flexible production systems are a technological tool design to automate multiple product line manufacturing. Flexible production systems provide an efficient means of organizing combined equipment operations and bring the production organization nearer to an unmanned arrangement or one requiring a limited number of workers. This is achieved by intensifying and automating manufacturing processes; coordinating the automated processes involved in warehousing and materials transport to maintain a tight production path; and using computers to automate production preparation and production control. The prerequisites for a change to these new production structures include numerical control NC tools and machining centers, power connection points for robots, automated conveying and warehousing systems controlled by microelectronic devices and control computer complexes consisting primarily of microprocessor-based units capable of controlling equipment via a direct connection and on a real-time basis. The types of flexible production systems in operation are divided into three groups: (1) flexible automated lines (GAL), (2) flexible production modules (GPM); and (3) flexible production complexes (GPK).

  13. Closing the loop.

    PubMed

    Dassau, E; Atlas, E; Phillip, M

    2011-02-01

    Closed-loop algorithms can be found in every aspect of everyday modern life. Automation and control are used constantly to provide safety and to improve quality of life. Closed-loop systems and algorithms can be found in home appliances, automobiles, aviation and more. Can one imagine nowadays driving a car without ABS, cruise control or even anti-sliding control? Similar principles of automation and control can be used in the management of diabetes mellitus (DM). The idea of an algorithmic/technological way to control glycaemia is not new and has been researched for more than four decades. However, recent improvements in both glucose-sensing technology and insulin delivery together with advanced control and systems engineering made this dream of an artificial pancreas possible. The artificial pancreas may be the next big step in the treatment of DM since the use of insulin analogues. An artificial pancreas can be described as internal or external devices that use continuous glucose measurements to automatically manage exogenous insulin delivery with or without other hormones in an attempt to restore glucose regulation in individuals with DM using a control algorithm. This device as described can be internal or external; can use different types of control algorithms with bi-hormonal or uni-hormonal design; and can utilise different ways to administer them. The different designs and implementations have transitioned recently from in silico simulations to clinical evaluation stage with practical applications in mind. This may mark the beginning of a new era in diabetes management with the introduction of semi-closed-loop systems that can prevent or minimise nocturnal hypoglycaemia, to hybrid systems that will manage blood glucose (BG) levels with minimal user intervention to finally fully automated systems that will take the user out of the loop. More and more clinical trials will be needed for the artificial pancreas to become a reality but initial encouraging

  14. Unsteady catalytic processes and sorption-catalytic technologies

    NASA Astrophysics Data System (ADS)

    Zagoruiko, A. N.

    2007-07-01

    Catalytic processes that occur under conditions of the targeted unsteady state of the catalyst are considered. The highest efficiency of catalytic processes was found to be ensured by a controlled combination of thermal non-stationarity and unsteady composition of the catalyst surface. The processes based on this principle are analysed, in particular, catalytic selective reduction of nitrogen oxides, deep oxidation of volatile organic impurities, production of sulfur by the Claus process and by hydrogen sulfide decomposition, oxidation of sulfur dioxide, methane steam reforming and anaerobic combustion, selective oxidation of hydrocarbons, etc.

  15. Multiple copy sampling in protein loop modeling: computational efficiency and sensitivity to dihedral angle perturbations.

    PubMed Central

    Zheng, Q.; Rosenfeld, R.; DeLisi, C.; Kyle, D. J.

    1994-01-01

    Multiple copy sampling and the bond scaling-relaxation technique are combined to generate 3-dimensional conformations of protein loop segments. The computational efficiency and sensitivity to initial loop copy dispersion are analyzed. The multicopy loop modeling method requires approximately 20-50% of the computational time required by the single-copy method for the various protein segments tested. An analytical formula is proposed to estimate the computational gain prior to carrying out a multicopy simulation. When 7-residue loops within flexible proteins are modeled, each multicopy simulation can sample a set of loop conformations with initial dispersions up to +/- 15 degrees for backbone and +/- 30 degrees for side-chain rotatable dihedral angles. The dispersions are larger for shorter and smaller for longer and/or surface loops. The degree of convergence of loop copies during a simulation can be used to complement commonly used target functions (such as potential energy) for distinguishing between native and misfolded conformations. Furthermore, this convergence also reflects the conformational flexibility of the modeled protein segment. Application to simultaneously building all 6 hypervariable loops of an antibody is discussed. PMID:8019420

  16. Ekpyrotic loop quantum cosmology

    SciTech Connect

    Wilson-Ewing, Edward

    2013-08-01

    We consider the ekpyrotic paradigm in the context of loop quantum cosmology. In loop quantum cosmology the classical big-bang singularity is resolved due to quantum gravity effects, and so the contracting ekpyrotic branch of the universe and its later expanding phase are connected by a smooth bounce. Thus, it is possible to explicitly determine the evolution of scalar perturbations, from the contracting ekpyrotic phase through the bounce and to the post-bounce expanding epoch. The possibilities of having either one or two scalar fields have been suggested for the ekpyrotic universe, and both cases will be considered here. In the case of a single scalar field, the constant mode of the curvature perturbations after the bounce is found to have a blue spectrum. On the other hand, for the two scalar field ekpyrotic model where scale-invariant entropy perturbations source additional terms in the curvature perturbations, the power spectrum in the post-bounce expanding cosmology is shown to be nearly scale-invariant and so agrees with observations.

  17. Accelerating the loop expansion

    SciTech Connect

    Ingermanson, R.

    1986-07-29

    This thesis introduces a new non-perturbative technique into quantum field theory. To illustrate the method, I analyze the much-studied phi/sup 4/ theory in two dimensions. As a prelude, I first show that the Hartree approximation is easy to obtain from the calculation of the one-loop effective potential by a simple modification of the propagator that does not affect the perturbative renormalization procedure. A further modification then susggests itself, which has the same nice property, and which automatically yields a convex effective potential. I then show that both of these modifications extend naturally to higher orders in the derivative expansion of the effective action and to higher orders in the loop-expansion. The net effect is to re-sum the perturbation series for the effective action as a systematic ''accelerated'' non-perturbative expansion. Each term in the accelerated expansion corresponds to an infinite number of terms in the original series. Each term can be computed explicitly, albeit numerically. Many numerical graphs of the various approximations to the first two terms in the derivative expansion are given. I discuss the reliability of the results and the problem of spontaneous symmetry-breaking, as well as some potential applications to more interesting field theories. 40 refs.

  18. Measuring Pressure Volume Loops in the Mouse.

    PubMed

    Townsend, DeWayne

    2016-01-01

    Understanding the causes and progression of heart disease presents a significant challenge to the biomedical community. The genetic flexibility of the mouse provides great potential to explore cardiac function at the molecular level. The mouse's small size does present some challenges in regards to performing detailed cardiac phenotyping. Miniaturization and other advancements in technology have made many methods of cardiac assessment possible in the mouse. Of these, the simultaneous collection of pressure and volume data provides a detailed picture of cardiac function that is not available through any other modality. Here a detailed procedure for the collection of pressure-volume loop data is described. Included is a discussion of the principles underlying the measurements and the potential sources of error. Anesthetic management and surgical approaches are discussed in great detail as they are both critical to obtaining high quality hemodynamic measurements. The principles of hemodynamic protocol development and relevant aspects of data analysis are also addressed. PMID:27166576

  19. Catalytic Microtube Rocket Igniter

    NASA Technical Reports Server (NTRS)

    Schneider, Steven J.; Deans, Matthew C.

    2011-01-01

    Devices that generate both high energy and high temperature are required to ignite reliably the propellant mixtures in combustion chambers like those present in rockets and other combustion systems. This catalytic microtube rocket igniter generates these conditions with a small, catalysis-based torch. While traditional spark plug systems can require anywhere from 50 W to multiple kW of power in different applications, this system has demonstrated ignition at less than 25 W. Reactants are fed to the igniter from the same tanks that feed the reactants to the rest of the rocket or combustion system. While this specific igniter was originally designed for liquid methane and liquid oxygen rockets, it can be easily operated with gaseous propellants or modified for hydrogen use in commercial combustion devices. For the present cryogenic propellant rocket case, the main propellant tanks liquid oxygen and liquid methane, respectively are regulated and split into different systems for the individual stages of the rocket and igniter. As the catalyst requires a gas phase for reaction, either the stored boil-off of the tanks can be used directly or one stream each of fuel and oxidizer can go through a heat exchanger/vaporizer that turns the liquid propellants into a gaseous form. For commercial applications, where the reactants are stored as gases, the system is simplified. The resulting gas-phase streams of fuel and oxidizer are then further divided for the individual components of the igniter. One stream each of the fuel and oxidizer is introduced to a mixing bottle/apparatus where they are mixed to a fuel-rich composition with an O/F mass-based mixture ratio of under 1.0. This premixed flow then feeds into the catalytic microtube device. The total flow is on the order of 0.01 g/s. The microtube device is composed of a pair of sub-millimeter diameter platinum tubes connected only at the outlet so that the two outlet flows are parallel to each other. The tubes are each

  20. The double loop mattress suture

    PubMed Central

    Biddlestone, John; Samuel, Madan; Creagh, Terry; Ahmad, Tariq

    2014-01-01

    An interrupted stitch type with favorable tissue characteristics will reduce local wound complications. We describe a novel high-strength, low-tension repair for the interrupted closure of skin, cartilage, and muscle, the double loop mattress stitch, and compare it experimentally with other interrupted closure methods. The performance of the double loop mattress technique in porcine cartilage and skeletal muscle is compared with the simple, mattress, and loop mattress interrupted sutures in both a novel porcine loading chamber and mechanical model. Wound apposition is assessed by electron microscopy. The performance of the double loop mattress in vivo was confirmed using a series of 805 pediatric laparotomies/laparoscopies. The double loop mattress suture is 3.5 times stronger than the loop mattress in muscle and 1.6 times stronger in cartilage (p ≤ 0.001). Additionally, the double loop mattress reduces tissue tension by 66% compared with just 53% for the loop mattress (p ≤ 0.001). Wound gapping is equal, and wound eversion appears significantly improved (p ≤ 0.001) compared with the loop mattress in vitro. In vivo, the double loop mattress performs as well as the loop mattress and significantly better than the mattress stitch in assessments of wound eversion and dehiscence. There were no episodes of stitch extrusion in our series of patients. The mechanical advantage of its intrinsic pulley arrangement gives the double loop mattress its favorable properties. Wound dehiscence is reduced because this stitch type is stronger and exerts less tension on the tissue than the mattress stitch. We advocate the use of this novel stitch wherever a high-strength, low-tension repair is required. These properties will enhance wound repair, and its application will be useful to surgeons of all disciplines. PMID:24698436

  1. Genetically engineered immunoglobulins reveal structural features controlling segmental flexibility.

    PubMed Central

    Schneider, W P; Wensel, T G; Stryer, L; Oi, V T

    1988-01-01

    We have carried out nanosecond fluorescence polarization studies of genetically engineered immunoglobulins to determine the structural features controlling their segmental flexibility. The proteins studied were hybrids of a relatively rigid isotype (mouse IgG1) and a relatively flexible one (mouse IgG2a). They have identical light chains and heavy chain variable regions and have the same combining sites for epsilon-dansyl-L-lysine, a fluorescent hapten. The fluorescence of the bound dansyl chromophore was excited at 348 nm with subnanosecond laser pulses, and the emission in the nanosecond time range was measured with a single-photon-counting apparatus. The emission anisotropy kinetics of the hybrid antibodies revealed that segmental flexibility is controlled by the heavy chain constant region 1 (CH1) as well as by the hinge. In contrast, the CH2 and CH3 domains did not influence segmental flexibility. The hinge and CH1 domains must be properly matched to allow facile movement of the Fab units. Studies of hybrids of IgG1 and IgG2a within CH1 showed that the loop formed by residues 131-139 is important in controlling segmental flexibility. X-ray crystallographic studies by others of human IgG1 have shown that this loop makes several van der Waals contacts with the hinge. Images PMID:3128789

  2. Flexible transparent electrode

    NASA Astrophysics Data System (ADS)

    Demiryont, Hulya; Shannon, Kenneth C., III; Moorehead, David; Bratcher, Matthew

    2011-06-01

    This paper presents the properties of the EclipseTECTM transparent conductor. EclipseTECTM is a room temperature deposited nanostructured thin film coating system comprised of metal-oxide semiconductor elements. The system possesses metal-like conductivity and glass-like transparency in the visible region. These highly conductive TEC films exhibit high shielding efficiency (35dB at 1 to 100GHz). EclipseTECTM can be deposited on rigid or flexible substrates. For example, EclipseTECTM deposited on polyethylene terephthalate (PET) is extremely flexible that can be rolled around a 9mm diameter cylinder with little or no reduction in electrical conductivity and that can assume pre-extension states after an applied stress is relieved. The TEC is colorless and has been tailored to have high visible transmittance which matches the eye sensitivity curve and allows the viewing of true background colors through the coating. EclipseTECTM is flexible, durable and can be tailored at the interface for applications such as electron- or hole-injecting OLED electrodes as well as electrodes in flexible displays. Tunable work function and optical design flexibility also make EclipseTECTM well-suited as a candidate for grid electrode replacement in next-generation photovoltaic cells.

  3. Modeling of compact loop antennas

    SciTech Connect

    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 (CIT).

  4. Loop Heat Pipe Startup Behaviors

    NASA Technical Reports Server (NTRS)

    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.

  5. Heating Profiles of Coronal Loops

    NASA Astrophysics Data System (ADS)

    Plowman, Joseph; Kankelborg, Charles C.; Martens, Petrus C.

    2016-05-01

    We analyze the temperature and density profiles of coronal loops, as a function of their length, using data from SDO/AIA and Hinode/EIS. The analysis considers the location of the heating along the loop's length, and we conduct a more throrough investigation of our previous preliminary result that heating is concentrated near the loop footpoints. The work now features a larger selection of coronal loops, compared to our previous presentations, and examines their scale-height temperatures to ascertain the extent to which they are hydrostatic.

  6. Modeling of compact loop antennas

    NASA Astrophysics Data System (ADS)

    Baity, F. W.

    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 (CIT).

  7. Unstable anisotropic loop quantum cosmology

    SciTech Connect

    Nelson, William; Sakellariadou, Mairi

    2009-09-15

    We study stability conditions of the full Hamiltonian constraint equation describing the quantum dynamics of the diagonal Bianchi I model in the context of loop quantum cosmology. Our analysis has shown robust evidence of an instability in the explicit implementation of the difference equation, implying important consequences for the correspondence between the full loop quantum gravity theory and loop quantum cosmology. As a result, one may question the choice of the quantization approach, the model of lattice refinement, and/or the role of the ambiguity parameters; all these should, in principle, be dictated by the full loop quantum gravity theory.

  8. Equations for the vibration of a slewing flexible spacecraft

    NASA Technical Reports Server (NTRS)

    Quinn, R. D.; Meirovitch, L.

    1986-01-01

    The derivation of the equations describing the vibration of a flexible spacecraft is presented in the context of a perturbation method permitting a maneuver strategy independent of the vibration control. A straightforward open-loop minimum-time rotational maneuver strategy is developed for the spacecraft regarded as a rigid body. Actuator dynamics are considered in the formulation. A maneuver force distribution is developed which excites the least amount of elastic deformation of the flexible parts of the spacecraft. An efficient technique for simulating structural vibrations during a maneuver is presented. Numerical results demonstrate the maneuver strategy and highlight the vibration caused by rotational maneuvers.

  9. Printed Microinductors for Flexible Substrates

    NASA Technical Reports Server (NTRS)

    Brandon, Erik; Whitacre, Jay; Wesseling, Emily

    2005-01-01

    A method of fabricating planar, flexible microinductors that exhibit a relatively high quality factor (Q) between 1 and 10 MHz has been devised. These inductors are targeted for use in flexible, low-profile power-converter circuits. They could also be incorporated into electronic circuits integrated into flexible structures, including flexible antenna and solar-sail structures that are deployable.

  10. Improved Thin, Flexible Heat Pipes

    NASA Technical Reports Server (NTRS)

    Rosenfeld, John H.; Gernert, Nelson J.; Sarraf, David B.; Wollen, Peter J.; Surina, Frank C.; Fale, John E.

    2004-01-01

    Flexible heat pipes of an improved type are fabricated as layers of different materials laminated together into vacuum- tight sheets or tapes. In comparison with prior flexible heat pipes, these flexible heat pipes are less susceptible to leakage. Other advantages of these flexible heat pipes, relative to prior flexible heat pipes, include high reliability and greater ease and lower cost of fabrication. Because these heat pipes are very thin, they are highly flexible. When coated on outside surfaces with adhesives, these flexible heat pipes can be applied, like common adhesive tapes, to the surfaces of heat sinks and objects to be cooled, even if those surfaces are curved.

  11. Loop-the-Loop: Bringing Theory into Practice

    ERIC Educational Resources Information Center

    Suwonjandee, N.; Asavapibhop, B.

    2012-01-01

    During the Thai high-school physics teacher training programme, we used an aluminum loop-the-loop system built by the Institute for the Promotion of Teaching Science and Technology (IPST) to demonstrate a circular motion and investigate the concept of the conservation of mechanical energy. There were 27 high-school teachers from three provinces,…

  12. Natural flexible dermal armor.

    PubMed

    Yang, Wen; Chen, Irene H; Gludovatz, Bernd; Zimmermann, Elizabeth A; Ritchie, Robert O; Meyers, Marc A

    2013-01-01

    Fish, reptiles, and mammals can possess flexible dermal armor for protection. Here we seek to find the means by which Nature derives its protection by examining the scales from several fish (Atractosteus spatula, Arapaima gigas, Polypterus senegalus, Morone saxatilis, Cyprinius carpio), and osteoderms from armadillos, alligators, and leatherback turtles. Dermal armor has clearly been developed by convergent evolution in these different species. In general, it has a hierarchical structure with collagen fibers joining more rigid units (scales or osteoderms), thereby increasing flexibility without significantly sacrificing strength, in contrast to rigid monolithic mineral composites. These dermal structures are also multifunctional, with hydrodynamic drag (in fish), coloration for camouflage or intraspecies recognition, temperature and fluid regulation being other important functions. The understanding of such flexible dermal armor is important as it may provide a basis for new synthetic, yet bioinspired, armor materials. PMID:23161399

  13. Vortex loops and Majoranas

    SciTech Connect

    Chesi, Stefano; Jaffe, Arthur; Loss, Daniel; Pedrocchi, Fabio L.

    2013-11-15

    We investigate the role that vortex loops play in characterizing eigenstates of interacting Majoranas. We give some general results and then focus on ladder Hamiltonian examples as a test of further ideas. Two methods yield exact results: (i) A mapping of certain spin Hamiltonians to quartic interactions of Majoranas shows that the spectra of these two examples coincide. (ii) In cases with reflection-symmetric Hamiltonians, we use reflection positivity for Majoranas to characterize vortices in the ground states. Two additional methods suggest wider applicability of these results: (iii) Numerical evidence suggests similar behavior for certain systems without reflection symmetry. (iv) A perturbative analysis also suggests similar behavior without the assumption of reflection symmetry.

  14. Dynamic PID loop control

    SciTech Connect

    Pei, L.; Klebaner, A.; Theilacker, J.; Soyars, W.; Martinez, A.; Bossert, R.; DeGraff, B.; Darve, C.; /Fermilab

    2011-06-01

    The Horizontal Test Stand (HTS) SRF Cavity and Cryomodule 1 (CM1) of eight 9-cell, 1.3GHz SRF cavities are operating at Fermilab. For the cryogenic control system, how to hold liquid level constant in the cryostat by regulation of its Joule-Thompson JT-valve is very important after cryostat cool down to 2.0 K. The 72-cell cryostat liquid level response generally takes a long time delay after regulating its JT-valve; therefore, typical PID control loop should result in some cryostat parameter oscillations. This paper presents a type of PID parameter self-optimal and Time-Delay control method used to reduce cryogenic system parameters oscillation.

  15. A conserved P-loop anchor limits the structural dynamics that mediate nucleotide dissociation in EF-Tu

    PubMed Central

    Mercier, Evan; Girodat, Dylan; Wieden, Hans-Joachim

    2015-01-01

    The phosphate-binding loop (P-loop) is a conserved sequence motif found in mononucleotide-binding proteins. Little is known about the structural dynamics of this region and its contribution to the observed nucleotide binding properties. Understanding the underlying design principles is of great interest for biomolecular engineering applications. We have used rapid-kinetics measurements in vitro and molecular dynamics (MD) simulations in silico to investigate the relationship between GTP-binding properties and P-loop structural dynamics in the universally conserved Elongation Factor (EF) Tu. Analysis of wild type EF-Tu and variants with substitutions at positions in or adjacent to the P-loop revealed a correlation between P-loop flexibility and the entropy of activation for GTP dissociation. The same variants demonstrate more backbone flexibility in two N-terminal amino acids of the P-loop during force-induced EF-Tu·GTP dissociation in Steered Molecular Dynamics simulations. Amino acids Gly18 and His19 are involved in stabilizing the P-loop backbone via interactions with the adjacent helix C. We propose that these P-loop/helix C interactions function as a conserved P-loop anchoring module and identify the presence of P-loop anchors within several GTPases and ATPases suggesting their evolutionary conservation. PMID:25566871

  16. Catalytic Mechanisms for Phosphotriesterases

    PubMed Central

    Bigley, Andrew N.; Raushel, Frank M.

    2012-01-01

    Phosphotriesters are one class of highly toxic synthetic compounds known as organophosphates. Wide spread usage of organophosphates as insecticides as well as nerve agents has lead to numerous efforts to identify enzymes capable of detoxifying them. A wide array of enzymes has been found to have phosphotriesterase activity including phosphotriesterase (PTE), methyl parathion hydrolase (MPH), organophosphorus acid anhydrolase (OPAA), diisopropylfluorophosphatase (DFP), and paraoxonase 1 (PON1). These enzymes differ widely in protein sequence and three-dimensional structure, as well as in catalytic mechanism, but they also share several common features. All of the enzymes identified as phosphotriesterases are metal-dependent hydrolases that contain a hydrophobic active site with three discrete binding pockets to accommodate the substrate ester groups. Activation of the substrate phosphorus center is achieved by a direct interaction between the phosphoryl oxygen and a divalent metal in the active site. The mechanistic details of the hydrolytic reaction differ among the various enzymes with both direct attack of a hydroxide as well as covalent catalysis being found. PMID:22561533

  17. Catalytic Membrane Sensors

    SciTech Connect

    Boyle, T.J.; Brinker, C.J.; Gardner, T.J.; Hughes, R.C.; Sault, A.G.

    1998-12-01

    The proposed "catalytic membrane sensor" (CMS) was developed to generate a device which would selectively identify a specific reagent in a complex mixture of gases. This was to be accomplished by modifying an existing Hz sensor with a series of thin films. Through selectively sieving the desired component from a complex mixture and identifying it by decomposing it into Hz (and other by-products), a Hz sensor could then be used to detect the presence of the select component. The proposed "sandwich-type" modifications involved the deposition of a catalyst layered between two size selective sol-gel layers on a Pd/Ni resistive Hz sensor. The role of the catalyst was to convert organic materials to Hz and organic by-products. The role of the membraneo was to impart both chemical specificity by molecukir sieving of the analyte and converted product streams, as well as controlling access to the underlying Pd/Ni sensor. Ultimately, an array of these CMS elements encompassing different catalysts and membranes were to be developed which would enable improved selectivity and specificity from a compiex mixture of organic gases via pattern recognition methodologies. We have successfully generated a CMS device by a series of spin-coat deposited methods; however, it was determined that the high temperature required to activate the catalyst, destroys the sensor.

  18. Fast loop modeling for protein structures

    NASA Astrophysics Data System (ADS)

    Zhang, Jiong; Nguyen, Son; Shang, Yi; Xu, Dong; Kosztin, Ioan

    2015-03-01

    X-ray crystallography is the main method for determining 3D protein structures. In many cases, however, flexible loop regions of proteins cannot be resolved by this approach. This leads to incomplete structures in the protein data bank, preventing further computational study and analysis of these proteins. For instance, all-atom molecular dynamics (MD) simulation studies of structure-function relationship require complete protein structures. To address this shortcoming, we have developed and implemented an efficient computational method for building missing protein loops. The method is database driven and uses deep learning and multi-dimensional scaling algorithms. We have implemented the method as a simple stand-alone program, which can also be used as a plugin in existing molecular modeling software, e.g., VMD. The quality and stability of the generated structures are assessed and tested via energy scoring functions and by equilibrium MD simulations. The proposed method can also be used in template-based protein structure prediction. Work supported by the National Institutes of Health [R01 GM100701]. Computer time was provided by the University of Missouri Bioinformatics Consortium.

  19. Uranyl Nitrate Flow Loop

    SciTech Connect

    Ladd-Lively, Jennifer L

    2008-10-01

    The objectives of the work discussed in this report were to: (1) develop a flow loop that would simulate the purified uranium-bearing aqueous stream exiting the solvent extraction process in a natural uranium conversion plant (NUCP); (2) develop a test plan that would simulate normal operation and disturbances that could be anticipated in an NUCP; (3) use the flow loop to test commercially available flowmeters for use as safeguards monitors; and (4) recommend a flowmeter for production-scale testing at an NUCP. There has been interest in safeguarding conversion plants because the intermediate products [uranium dioxide (UO{sub 2}), uranium tetrafluoride (UF{sub 4}), and uranium hexafluoride (UF{sub 6})] are all suitable uranium feedstocks for producing special nuclear materials. Furthermore, if safeguards are not applied virtually any nuclear weapons program can obtain these feedstocks without detection by the International Atomic Energy Agency (IAEA). Historically, IAEA had not implemented safeguards until the purified UF{sub 6} product was declared as feedstock for enrichment plants. H. A. Elayat et al. provide a basic definition of a safeguards system: 'The function of a safeguards system on a chemical conversion plant is in general terms to verify that no useful nuclear material is being diverted to use in a nuclear weapons program'. The IAEA now considers all highly purified uranium compounds as candidates for safeguarding. DOE is currently interested in 'developing instruments, tools, strategies, and methods that could be of use to the IAEA in the application of safeguards' for materials found in the front end of the nuclear fuel cycle-prior to the production of the uranium hexafluoride or oxides that have been the traditional starting point for IAEA safeguards. Several national laboratories, including Oak Ridge, Los Alamos, Lawrence Livermore, and Brookhaven, have been involved in developing tools or techniques for safeguarding conversion plants. This study

  20. Flexible High-Energy Polymer-Electrolyte-Based Rechargeable Zinc-Air Batteries.

    PubMed

    Fu, Jing; Lee, Dong Un; Hassan, Fathy Mohamed; Yang, Lin; Bai, Zhengyu; Park, Moon Gyu; Chen, Zhongwei

    2015-10-01

    A thin-film, flexible, and rechargeable zinc-air battery having high energy density is reported particularly for emerging portable and wearable electronic applications. This freeform battery design is the first demonstrated by sandwiching a porous-gelled polymer electrolyte with a freestanding zinc film and a bifunctional catalytic electrode film. The flexibility of both the electrode films and polymer electrolyte membrane gives great freedom in tailoring the battery geometry and performance. PMID:26305154

  1. Loop-the-Loop: An Easy Experiment, A Challenging Explanation

    NASA Astrophysics Data System (ADS)

    Asavapibhop, B.; Suwonjandee, N.

    2010-07-01

    A loop-the-loop built by the Institute for the Promotion of Teaching Science and Technology (IPST) was used in Thai high school teachers training program to demonstrate a circular motion and investigate the concept of the conservation of mechanical energy. We took videos using high speed camera to record the motions of a spherical steel ball moving down the aluminum inclined track at different released positions. The ball then moved into the circular loop and underwent a projectile motion upon leaving the track. We then asked the teachers to predict the landing position of the ball if we changed the height of the whole loop-the-loop system. We also analyzed the videos using Tracker, a video analysis software. It turned out that most teachers did not realize the effect of the friction between the ball and the track and could not obtain the correct relationship hence their predictions were inconsistent with the actual landing positions of the ball.

  2. Flexible radiator system

    NASA Technical Reports Server (NTRS)

    Oren, J. A.

    1982-01-01

    The soft tube radiator subsystem is described including applicable system requirements, the design and limitations of the subsystem components, and the panel manufacturing method. The soft tube radiator subsystem is applicable to payloads requiring 1 to 12 kW of heat rejection for orbital lifetimes per mission of 30 days or less. The flexible radiator stowage volume required is about 60% and the system weight is about 40% of an equivalent heat rejection rigid panel. The cost should also be considerably less. The flexible radiator is particularly suited to shuttle orbiter sortie payloads and also whose mission lengths do not exceed the 30 day design life.

  3. Thin flexible intercalation anodes

    SciTech Connect

    Levy, S.C.; Cieslak, W.R.; Klassen, S.E.; Lagasse, R.R.

    1994-10-01

    Poly(acrylonitrile) fibers have been pyrolyzed under various conditions to form flexible carbon yarns capable of intercalating lithium ions. These fibers have also been formed into both woven and non woven cloths. Potentiostatic, potentiodynamic and galvanostatic tests have been conducted with these materials in several electrolytes. In some tests, a potential hold was used after each constant current charge and discharge. These tests have shown some of these flexible materials to reversibly intercalate lithium ions to levels that are suitable for use as a practical battery anode.

  4. Flexible manipulator control experiments and analysis

    NASA Technical Reports Server (NTRS)

    Yurkovich, S.; Ozguner, U.; Tzes, A.; Kotnik, P. T.

    1987-01-01

    Modeling and control design for flexible manipulators, both from an experimental and analytical viewpoint, are described. From the application perspective, an ongoing effort within the laboratory environment at the Ohio State University, where experimentation on a single link flexible arm is underway is described. Several unique features of this study are described here. First, the manipulator arm is slewed by a direct drive dc motor and has a rigid counterbalance appendage. Current experimentation is from two viewpoints: (1) rigid body slewing and vibration control via actuation with the hub motor, and (2) vibration suppression through the use of structure-mounted proof-mass actuation at the tip. Such an application to manipulator control is of interest particularly in design of space-based telerobotic control systems, but has received little attention to date. From an analytical viewpoint, parameter estimation techniques within the closed-loop for self-tuning adaptive control approaches are discussed. Also introduced is a control approach based on output feedback and frequency weighting to counteract effects of spillover in reduced-order model design. A model of the flexible manipulator based on experimental measurements is evaluated for such estimation and control approaches.

  5. Protein-protein docking with backbone flexibility.

    PubMed

    Wang, Chu; Bradley, Philip; Baker, David

    2007-10-19

    Computational protein-protein docking methods currently can create models with atomic accuracy for protein complexes provided that the conformational changes upon association are restricted to the side chains. However, it remains very challenging to account for backbone conformational changes during docking, and most current methods inherently keep monomer backbones rigid for algorithmic simplicity and computational efficiency. Here we present a reformulation of the Rosetta docking method that incorporates explicit backbone flexibility in protein-protein docking. The new method is based on a "fold-tree" representation of the molecular system, which seamlessly integrates internal torsional degrees of freedom and rigid-body degrees of freedom. Problems with internal flexible regions ranging from one or more loops or hinge regions to all of one or both partners can be readily treated using appropriately constructed fold trees. The explicit treatment of backbone flexibility improves both sampling in the vicinity of the native docked conformation and the energetic discrimination between near-native and incorrect models. PMID:17825317

  6. Invariant poles feedback control of flexible, highly variable spacecraft.

    NASA Technical Reports Server (NTRS)

    Mendel, J. M.

    1972-01-01

    This paper describes a technique for single-axis control of a model of a highly flexible Space Station. Active damping of lower frequency flexibility modes is employed. In the control technique, referred to as invariant poles feedback control (IPFC), feedback gains are adjusted so that the closed-loop system's characteristic equation is matched to that of a reference model; hence, closed-loop system's poles will not move - they will be invariant (provided bending frequencies and parameters can be identified accurately). This is accomplished by obtaining the system's characteristic equation in closed form; equating respective coefficients between terms of like powers in s in the system and reference model characteristic equations; and, solving for the feedback gains. The feedback gains are explicit functions of system plant parameters and the coefficients of the reference model's characteristic equation, and are easily programmed for the digital computer.

  7. Invariant poles feedback control of flexible highly variable spacecraft.

    NASA Technical Reports Server (NTRS)

    Mendel, J. M.

    1972-01-01

    Description of a technique for single-axis control of a model of a highly flexible space station. Active damping of lower frequency flexibility modes is employed. In the control technique, referred to as invariant poles feedback control, feedback gains are adjusted so that the closed-loop system characteristic equation is matched to that of a reference model. Hence closed-loop system poles will not move; they will be invariant (provided that bending frequencies and parameters can be identified accurately). This is accomplished by obtaining the system characteristic equation in closed form; equating respective coefficients between terms of like powers in s in the system and reference model characteristic equations; and solving for the feedback gains. The feedback gains are explicit functions of system plant parameters and the coefficients of the reference model characteristic equation, and are easily programmed for the digital computer.

  8. Evidence That GH115 α-Glucuronidase Activity, Which Is Required to Degrade Plant Biomass, Is Dependent on Conformational Flexibility*

    PubMed Central

    Rogowski, Artur; Baslé, Arnaud; Farinas, Cristiane S.; Solovyova, Alexandra; Mortimer, Jennifer C.; Dupree, Paul; Gilbert, Harry J.; Bolam, David N.

    2014-01-01

    The microbial degradation of the plant cell wall is an important biological process that is highly relevant to environmentally significant industries such as the bioenergy and biorefining sectors. A major component of the wall is glucuronoxylan, a β1,4-linked xylose polysaccharide that is decorated with α-linked glucuronic and/or methylglucuronic acid (GlcA/MeGlcA). Recently three members of a glycoside hydrolase family, GH115, were shown to hydrolyze MeGlcA side chains from the internal regions of xylan, an activity that has not previously been described. Here we show that a dominant member of the human microbiota, Bacteroides ovatus, contains a GH115 enzyme, BoAgu115A, which displays glucuronoxylan α-(4-O-methyl)-glucuronidase activity. The enzyme is significantly more active against substrates in which the xylose decorated with GlcA/MeGlcA is flanked by one or more xylose residues. The crystal structure of BoAgu115A revealed a four-domain protein in which the active site, comprising a pocket that abuts a cleft-like structure, is housed in the second domain that adopts a TIM barrel-fold. The third domain, a five-helical bundle, and the C-terminal β-sandwich domain make inter-chain contacts leading to protein dimerization. Informed by the structure of the enzyme in complex with GlcA in its open ring form, in conjunction with mutagenesis studies, the potential substrate binding and catalytically significant amino acids were identified. Based on the catalytic importance of residues located on a highly flexible loop, the enzyme is required to undergo a substantial conformational change to form a productive Michaelis complex with glucuronoxylan. PMID:24214982

  9. Catalytic Enantioselective Synthesis of Halocyclopropanes.

    PubMed

    Pons, Amandine; Ivashkin, Pavel; Poisson, Thomas; Charette, André B; Pannecoucke, Xavier; Jubault, Philippe

    2016-04-25

    A catalytic asymmetric synthesis of halocyclopropanes is described. The developed method is based on a carbenoid cyclopropanation of 2-haloalkenes with tert-butyl α-cyano-α-diazoacetate using a chiral rhodium catalyst that permits access to a broad range of highly functionalized chiral halocyclopropanes (F, Cl, Br, and I) in good yields, moderate diastereoselectivity, and excellent enantiomeric ratios. The reported methodology represents the first general catalytic enantioselective approach to halocyclopropanes. PMID:26945553

  10. RCD+: Fast loop modeling server

    PubMed Central

    López-Blanco, José Ramón; Canosa-Valls, Alejandro Jesús; Li, Yaohang; Chacón, Pablo

    2016-01-01

    Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards near-native conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbor-dependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop models are subsequently ranked using a fast distance-orientation dependent energy filter. Top ranked loops are refined with the Rosetta energy function to obtain accurate all-atom predictions that can be interactively inspected in an user-friendly web interface. Using standard benchmarks, the average root mean squared deviation (RMSD) is 0.8 and 1.4 Å for 8 and 12 residues loops, respectively, in the challenging modeling scenario in where the side chains of the loop environment are fully remodeled. These results are not only very competitive compared to those obtained with public state of the art methods, but also they are obtained ∼10-fold faster. PMID:27151199

  11. RCD+: Fast loop modeling server.

    PubMed

    López-Blanco, José Ramón; Canosa-Valls, Alejandro Jesús; Li, Yaohang; Chacón, Pablo

    2016-07-01

    Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards near-native conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbor-dependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop models are subsequently ranked using a fast distance-orientation dependent energy filter. Top ranked loops are refined with the Rosetta energy function to obtain accurate all-atom predictions that can be interactively inspected in an user-friendly web interface. Using standard benchmarks, the average root mean squared deviation (RMSD) is 0.8 and 1.4 Å for 8 and 12 residues loops, respectively, in the challenging modeling scenario in where the side chains of the loop environment are fully remodeled. These results are not only very competitive compared to those obtained with public state of the art methods, but also they are obtained ∼10-fold faster. PMID:27151199

  12. An improved output feedback control of flexible large space structures

    NASA Technical Reports Server (NTRS)

    Lin, Y. H.; Lin, J. G.

    1980-01-01

    A special output feedback control design technique for flexible large space structures is proposed. It is shown that the technique will increase both the damping and frequency of selected modes for more effective control. It is also able to effect integrated control of elastic and rigid-body modes and, in particular, closed-loop system stability and robustness to modal truncation and parameter variation. The technique is seen as marking an improvement over previous work concerning large space structures output feedback control.

  13. System Study of Rich Catalytic/Lean burn (RCL) Catalytic Combustion for Natural Gas and Coal-Derived Syngas Combustion Turbines

    SciTech Connect

    Shahrokh Etemad; Lance Smith; Kevin Burns

    2004-12-01

    Rich Catalytic/Lean burn (RCL{reg_sign}) technology has been successfully developed to provide improvement in Dry Low Emission gas turbine technology for coal derived syngas and natural gas delivering near zero NOx emissions, improved efficiency, extending component lifetime and the ability to have fuel flexibility. The present report shows substantial net cost saving using RCL{reg_sign} technology as compared to other technologies both for new and retrofit applications, thus eliminating the need for Selective Catalytic Reduction (SCR) in combined or simple cycle for Integrated Gasification Combined Cycle (IGCC) and natural gas fired combustion turbines.

  14. Implementing Audio Digital Feedback Loop Using the National Instruments RIO System

    SciTech Connect

    Huang, G.; Byrd, J. M.

    2006-11-20

    Development of system for high precision RF distribution and laser synchronization at Berkeley Lab has been ongoing for several years. Successful operation of these systems requires multiple audio bandwidth feedback loops running at relatively high gains. Stable operation of the feedback loops requires careful design of the feedback transfer function. To allow for flexible and compact implementation, we have developed digital feedback loops on the National Instruments Reconfigurable Input/Output (RIO) platform. This platform uses an FPGA and multiple I/Os that can provide eight parallel channels running different filters. We present the design and preliminary experimental results of this system.

  15. Flexible ceramic gasket for SOFC generator

    DOEpatents

    Zafred, Paolo; Prevish, Thomas

    2009-02-03

    A solid oxide fuel cell generator (10) contains stacks of hollow axially elongated fuel cells (36) having an open top end (37), an oxidant inlet plenum (52), a feed fuel plenum (11), a combustion chamber (94) for combusting reacted oxidant/spent fuel; and, optionally, a fuel recirculation chamber (106) below the combustion chamber (94), where the fuel recirculation chamber (94) is in part defined by semi-porous fuel cell positioning gasket (108), all within an outer generator enclosure (8), wherein the fuel cell gasket (108) has a laminate structure comprising at least a compliant fibrous mat support layer and a strong, yet flexible woven layer, which may contain catalytic particles facing the combustion chamber, where the catalyst, if used, is effective to further oxidize exhaust fuel and protect the open top end (37) of the fuel cells.

  16. Analysis of flexible aircraft longitudinal dynamics and handling qualities. Volume 1: Analysis methods

    NASA Technical Reports Server (NTRS)

    Waszak, M. R.; Schmidt, D. S.

    1985-01-01

    As aircraft become larger and lighter due to design requirements for increased payload and improved fuel efficiency, they will also become more flexible. For highly flexible vehicles, the handling qualities may not be accurately predicted by conventional methods. This study applies two analysis methods to a family of flexible aircraft in order to investigate how and when structural (especially dynamic aeroelastic) effects affect the dynamic characteristics of aircraft. The first type of analysis is an open loop model analysis technique. This method considers the effects of modal residue magnitudes on determining vehicle handling qualities. The second method is a pilot in the loop analysis procedure that considers several closed loop system characteristics. Volume 1 consists of the development and application of the two analysis methods described above.

  17. Flexible Classroom Furniture

    ERIC Educational Resources Information Center

    Kim Hassell,

    2011-01-01

    Classroom design for the 21st-century learning environment should accommodate a variety of learning skills and needs. The space should be large enough so it can be configured to accommodate a number of learning activities. This also includes furniture that provides flexibility and accommodates collaboration and interactive work among students and…

  18. Designing Flexible Instruction

    ERIC Educational Resources Information Center

    Harris, Clark R.; Kaff, Marilyn S.; Anderson, Mary Jo; Knackendoffel, Ann

    2007-01-01

    Principals and teachers need a framework that will allow school personnel to reach and teach all students within the general education setting. One such framework is universal design for learning (UDL). UDL is achieved by means of flexible curricular materials and activities that provide alternatives for students with disparities in abilities and…

  19. Flexible electronics: Sophisticated skin

    NASA Astrophysics Data System (ADS)

    Bauer, Siegfried

    2013-10-01

    Advances in materials science and layout design have enabled the realization of flexible and multifunctional electronic devices. Two demonstrations of electronic skins, which combine temperature and pressure sensing with integrated thermal actuators and organic displays, unveil the potential of these devices for robotics and clinical applications.

  20. Diversity and Flexibility.

    ERIC Educational Resources Information Center

    Anastasi, Anne

    1990-01-01

    Responds to five major articles by Duckworth, Goldman, Healy, Sampson, and Goodyear on issues pertaining to testing and assessment in counseling psychology. Suggests that such a diversity of approaches leads to a more comprehensive and flexible model of counseling, adaptable to differences in clients, context, and counselor personalities. (TE)

  1. Flexible photovoltaic device

    SciTech Connect

    Berman, E.

    1989-03-28

    A photovoltaic device is described comprising a transparent substrate, a transparent conductive layer adjacent to the transparent substrate, a TFS layer adjacent to the transparent conductive layer, and a conductive layer adjacent to the TFS layer, the transparent substrate being a tetrafluoroethyleneperfluoroalkooxy resin in the form of a flexible film.

  2. Flexible optical panel

    DOEpatents

    Veligdan, James T.

    2001-01-01

    A flexible optical panel includes laminated optical waveguides, each including a ribbon core laminated between cladding, with the core being resilient in the plane of the core for elastically accommodating differential movement thereof to permit winding of the panel in a coil.

  3. ESEA Flexibility. Updated

    ERIC Educational Resources Information Center

    US Department of Education, 2012

    2012-01-01

    In order to move forward with State and local reforms designed to improve academic achievement and increase the quality of instruction for all students in a manner that was not originally contemplated by the No Child Left Behind Act of 2001 (NCLB), a State educational agency (SEA) may request flexibility, on its own behalf and on behalf of its…

  4. Wilson Loop Diagrams and Positroids

    NASA Astrophysics Data System (ADS)

    Agarwala, Susama; Marin-Amat, Eloi

    2016-07-01

    In this paper, we study a new application of the positive Grassmannian to Wilson loop diagrams (or MHV diagrams) for scattering amplitudes in N= 4 Super Yang-Mill theory (N = 4 SYM). There has been much interest in studying this theory via the positive Grassmannians using BCFW recursion. This is the first attempt to study MHV diagrams for planar Wilson loop calculations (or planar amplitudes) in terms of positive Grassmannians. We codify Wilson loop diagrams completely in terms of matroids. This allows us to apply the combinatorial tools in matroid theory used to identify positroids (non-negative Grassmannians) to Wilson loop diagrams. In doing so, we find that certain non-planar Wilson loop diagrams define positive Grassmannians. While non-planar diagrams do not have physical meaning, this finding suggests that they may have value as an algebraic tool, and deserve further investigation.

  5. Higher dimensional loop quantum cosmology

    NASA Astrophysics Data System (ADS)

    Zhang, Xiangdong

    2016-07-01

    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.

  6. Loop-bed combustion apparatus

    DOEpatents

    Shang, Jer-Yu; Mei, Joseph S.; Slagle, Frank D.; Notestein, John E.

    1984-01-01

    The present invention is directed to a combustion apparatus in the configuration of a oblong annulus defining a closed loop. Particulate coal together with a sulfur sorbent such as sulfur or dolomite is introduced into the closed loop, ignited, and propelled at a high rate of speed around the loop. Flue gas is withdrawn from a location in the closed loop in close proximity to an area in the loop where centrifugal force imposed upon the larger particulate material maintains these particulates at a location spaced from the flue gas outlet. Only flue gas and smaller particulates resulting from the combustion and innerparticle grinding are discharged from the combustor. This structural arrangement provides increased combustion efficiency due to the essentially complete combustion of the coal particulates as well as increased sulfur absorption due to the innerparticle grinding of the sorbent which provides greater particle surface area.

  7. Loop Heat Pipe Startup Behaviors

    NASA Technical Reports Server (NTRS)

    Ku, Jentung

    2014-01-01

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

  8. Electro Catalytic Oxidation (ECO) Operation

    SciTech Connect

    Morgan Jones

    2011-03-31

    The power industry in the United States is faced with meeting many new regulations to reduce a number of air pollutants including sulfur dioxide, nitrogen oxides, fine particulate matter, and mercury. With over 1,000 power plants in the US, this is a daunting task. In some cases, traditional pollution control technologies such as wet scrubbers and SCRs are not feasible. Powerspan's Electro-Catalytic Oxidation, or ECO{reg_sign} process combines four pollution control devices into a single integrated system that can be installed after a power plant's particulate control device. Besides achieving major reductions in emissions of sulfur dioxide (SO{sub 2}), nitrogen oxides (NOx), fine particulate matter (PM2.5) and mercury (Hg), ECO produces a highly marketable fertilizer, which can help offset the operating costs of the process system. Powerspan has been operating a 50-MW ECO commercial demonstration unit (CDU) at FirstEnergy Corp.'s R.E. Burger Plant near Shadyside, Ohio, since February 2004. In addition to the CDU, a test loop has been constructed beside the CDU to demonstrate higher NOx removal rates and test various scrubber packing types and wet ESP configurations. Furthermore, Powerspan has developed the ECO{reg_sign}{sub 2} technology, a regenerative process that uses a proprietary solvent to capture CO{sub 2} from flue gas. The CO{sub 2} capture takes place after the capture of NOx, SO{sub 2}, mercury, and fine particulate matter. Once the CO{sub 2} is captured, the proprietary solution is regenerated to release CO{sub 2} in a form that is ready for geological storage or beneficial use. Pilot scale testing of ECO{sub 2} began in early 2009 at FirstEnergy's Burger Plant. The ECO{sub 2} pilot unit is designed to process a 1-MW flue gas stream and produce 20 tons of CO{sub 2} per day, achieving a 90% CO{sub 2} capture rate. The ECO{sub 2} pilot program provided the opportunity to confirm process design and cost estimates, and prepare for large scale capture and

  9. Analysis of flexible aircraft longitudinal dynamics and handling qualities. Volume 2: Data

    NASA Technical Reports Server (NTRS)

    Waszak, M. R.; Schmidt, D. K.

    1985-01-01

    Two analysis methods are applied to a family of flexible aircraft in order to investigate how and when structural (especially dynamic aeroelastic) effects affect the dynamic characteristics of aircraft. The first type of analysis is an open loop modal analysis technique. This method considers the effect of modal residue magnitudes on determining vehicle handling qualities. The second method is a pilot in the loop analysis procedure that considers several closed loop system characteristics. Both analyses indicated that dynamic aeroelastic effects caused a degradation in vehicle tracking performance, based on the evaluation of some simulation results. Volume 2 consists of the presentation of the state variable models of the flexible aircraft configurations used in the analysis applications mode shape plots for the structural modes, numerical results from the modal analysis frequency response plots from the pilot in the loop analysis and a listing of the modal analysis computer program.

  10. Computational Analysis of Looping of a Large Family of Highly Bent DNA by LacI

    PubMed Central

    Lillian, Todd D.; Goyal, Sachin; Kahn, Jason D.; Meyhöfer, Edgar; Perkins, N. C.

    2008-01-01

    Sequence-dependent intrinsic curvature of DNA influences looping by regulatory proteins such as LacI and NtrC. Curvature can enhance stability and control shape, as observed in LacI loops formed with three designed sequences with operators bracketing an A-tract bend. We explore geometric, topological, and energetic effects of curvature with an analysis of a family of highly bent sequences, using the elastic rod model from previous work. A unifying straight-helical-straight representation uses two phasing parameters to describe sequences composed of two straight segments that flank a common helically supercoiled segment. We exercise the rod model over this two-dimensional space of phasing parameters to evaluate looping behaviors. This design space is found to comprise two subspaces that prefer parallel versus anti-parallel binding topologies. The energetic cost of looping varies from 4 to 12 kT. Molecules can be designed to yield distinct binding topologies as well as hyperstable or hypostable loops and potentially loops that can switch conformations. Loop switching could be a mechanism for control of gene expression. Model predictions for linking numbers and sizes of LacI-DNA loops can be tested using multiple experimental approaches, which coupled with theory could address whether proteins or DNA provide the observed flexibility of protein-DNA loops. PMID:18931251

  11. Prediction of calcium-binding sites by combining loop-modeling with machine learning

    PubMed Central

    2009-01-01

    Background Protein ligand-binding sites in the apo state exhibit structural flexibility. This flexibility often frustrates methods for structure-based recognition of these sites because it leads to the absence of electron density for these critical regions, particularly when they are in surface loops. Methods for recognizing functional sites in these missing loops would be useful for recovering additional functional information. Results We report a hybrid approach for recognizing calcium-binding sites in disordered regions. Our approach combines loop modeling with a machine learning method (FEATURE) for structure-based site recognition. For validation, we compared the performance of our method on known calcium-binding sites for which there are both holo and apo structures. When loops in the apo structures are rebuilt using modeling methods, FEATURE identifies 14 out of 20 crystallographically proven calcium-binding sites. It only recognizes 7 out of 20 calcium-binding sites in the initial apo crystal structures. We applied our method to unstructured loops in proteins from SCOP families known to bind calcium in order to discover potential cryptic calcium binding sites. We built 2745 missing loops and evaluated them for potential calcium binding. We made 102 predictions of calcium-binding sites. Ten predictions are consistent with independent experimental verifications. We found indirect experimental evidence for 14 other predictions. The remaining 78 predictions are novel predictions, some with intriguing potential biological significance. In particular, we see an enrichment of beta-sheet folds with predicted calcium binding sites in the connecting loops on the surface that may be important for calcium-mediated function switches. Conclusion Protein crystal structures are a potentially rich source of functional information. When loops are missing in these structures, we may be losing important information about binding sites and active sites. We have shown that

  12. FSD- FLEXIBLE SPACECRAFT DYNAMICS

    NASA Technical Reports Server (NTRS)

    Fedor, J. V.

    1994-01-01

    The Flexible Spacecraft Dynamics and Control program (FSD) was developed to aid in the simulation of a large class of flexible and rigid spacecraft. FSD is extremely versatile and can be used in attitude dynamics and control analysis as well as in-orbit support of deployment and control of spacecraft. FSD has been used to analyze the in-orbit attitude performance and antenna deployment of the RAE and IMP class satellites, and the HAWKEYE, SCATHA, EXOS-B, and Dynamics Explorer flight programs. FSD is applicable to inertially-oriented spinning, earth oriented, or gravity gradient stabilized spacecraft. The spacecraft flexibility is treated in a continuous manner (instead of finite element) by employing a series of shape functions for the flexible elements. Torsion, bending, and three flexible modes can be simulated for every flexible element. FSD can handle up to ten tubular elements in an arbitrary orientation. FSD is appropriate for studies involving the active control of pointed instruments, with options for digital PID (proportional, integral, derivative) error feedback controllers and control actuators such as thrusters and momentum wheels. The input to FSD is in four parts: 1) Orbit Construction FSD calculates a Keplerian orbit with environmental effects such as drag, magnetic torque, solar pressure, thermal effects, and thruster adjustments; or the user can supply a GTDS format orbit tape for a particular satellite/time-span; 2) Control words - for options such as gravity gradient effects, control torques, and integration ranges; 3) Mathematical descriptions of spacecraft, appendages, and control systems- including element geometry, properties, attitudes, libration damping, tip mass inertia, thermal expansion, magnetic tracking, and gimbal simulation options; and 4) Desired state variables to output, i.e., geometries, bending moments, fast Fourier transform plots, gimbal rotation, filter vectors, etc. All FSD input is of free format, namelist construction. FSD

  13. Experimental demonstration of static shape control. [using flexible beam facility for large space structure development

    NASA Technical Reports Server (NTRS)

    Eldred, D.; Schaechter, D.

    1981-01-01

    Results of a microprocessor-controlled implementation of static shape control using a specially constructed flexible beam facility are presented. The discussion covers the development of shape control algorithms, adaptation of the algorithms for use with finite element models, construction of a flexible beam, characterization and calibration of the facility, development of a finite element model for the beam, and the development of computer hardware and software. It is shown that feedback control yields better results than open-loop control, and that the use of more than two sensors in the control loop has little effect on the system performance.

  14. Flexibility and molecular recognition in the immune system

    PubMed Central

    Jimenez, Ralph; Salazar, Georgina; Baldridge, Kim K.; Romesberg, Floyd E.

    2003-01-01

    Photon echo spectroscopy has been used to measure the response of three antibody-binding sites to perturbation from electronic excitation of a bound antigen, fluorescein. The three antibodies show motions that range in time scale from tens of femtoseconds to nanoseconds. Relative to the others, one antibody, 4-4-20, possesses a rigid binding site that likely results from a short and inflexible heavy chain complementarity-determining region 3 (HCDR3) loop and a critical Tyr that acts as a “molecular splint,” rigidifying the antigen across its most flexible internal degree of freedom. The remaining two antibodies, 34F10 and 40G4, despite being generated against the same antigen, possess binding sites that are considerably more flexible. The more flexible combining sites likely result from longer HCDR3 loops and a deletion in the light chain complementarity-determining region 1 (LCDR1) that removes the critical Tyr residue. The binding site flexibilities may result in varying mechanisms of antigen recognition including lock-and-key, induced-fit, and conformational selection. PMID:12518056

  15. Catalytic combustion with steam injection

    NASA Technical Reports Server (NTRS)

    Anderson, D. N.; Tacina, R. R.

    1982-01-01

    The effects of steam injection on (1) catalytic combustion performance, and (2) the tendency of residual fuel to burn in the premixing duct upstream of the catalytic reactor were determined. A petroleum residual, no. 2 diesel, and a blend of middle and heavy distillate coal derived fuels were tested. Fuel and steam were injected together into the preheated airflow entering a 12 cm diameter catalytic combustion test section. The inlet air velocity and pressure were constant at 10 m/s and 600 kPa, respectively. Steam flow rates were varied from 24 percent to 52 percent of the air flow rate. The resulting steam air mixture temperatures varied from 630 to 740 K. Combustion temperatures were in the range of 1200 to 1400 K. The steam had little effect on combustion efficiency or emissions. It was concluded that the steam acts as a diluent which has no adverse effect on catalytic combustion performance for no. 2 diesel and coal derived liquid fuels. Tests with the residual fuel showed that upstream burning could be eliminated with steam injection rates greater than 30 percent of the air flow rate, but inlet mixture temperatures were too low to permit stable catalytic combustion of this fuel.

  16. A redox 2-Cys mechanism regulates the catalytic activity of divergent cyclophilins.

    PubMed

    Campos, Bruna Medéia; Sforça, Mauricio Luis; Ambrosio, Andre Luis Berteli; Domingues, Mariane Noronha; Brasil de Souza, Tatiana de Arruda Campos; Barbosa, João Alexandre Ribeiro Gonçalvez; Paes Leme, Adriana Franco; Perez, Carlos Alberto; Whittaker, Sara Britt-Marie; Murakami, Mario Tyago; Zeri, Ana Carolina de Matos; Benedetti, Celso Eduardo

    2013-07-01

    The citrus (Citrus sinensis) cyclophilin CsCyp is a target of the Xanthomonas citri transcription activator-like effector PthA, required to elicit cankers on citrus. CsCyp binds the citrus thioredoxin CsTdx and the carboxyl-terminal domain of RNA polymerase II and is a divergent cyclophilin that carries the additional loop KSGKPLH, invariable cysteine (Cys) residues Cys-40 and Cys-168, and the conserved glutamate (Glu) Glu-83. Despite the suggested roles in ATP and metal binding, the functions of these unique structural elements remain unknown. Here, we show that the conserved Cys residues form a disulfide bond that inactivates the enzyme, whereas Glu-83, which belongs to the catalytic loop and is also critical for enzyme activity, is anchored to the divergent loop to maintain the active site open. In addition, we demonstrate that Cys-40 and Cys-168 are required for the interaction with CsTdx and that CsCyp binds the citrus carboxyl-terminal domain of RNA polymerase II YSPSAP repeat. Our data support a model where formation of the Cys-40-Cys-168 disulfide bond induces a conformational change that disrupts the interaction of the divergent and catalytic loops, via Glu-83, causing the active site to close. This suggests a new type of allosteric regulation in divergent cyclophilins, involving disulfide bond formation and a loop-displacement mechanism. PMID:23709667

  17. Digital phase-locked loop

    NASA Technical Reports Server (NTRS)

    Cliff, R. A. (Inventor)

    1975-01-01

    An digital phase-locked loop is provided for deriving a loop output signal from an accumulator output terminal. A phase detecting exclusive OR gate is fed by the loop digital input and output signals. The output of the phase detector is a bi-level digital signal having a duty cycle indicative of the relative phase of the input and output signals. The accumulator is incremented at a first rate in response to a first output level of the phase detector and at a second rate in response to a second output level of the phase detector.

  18. Flexible cryogenic conduit

    DOEpatents

    Brindza, Paul Daniel; Wines, Robin Renee; Takacs, James Joseph

    1999-01-01

    A flexible and relatively low cost cryogenic conduit is described. The flexible cryogenic conduit of the present invention comprises a first inner corrugated tube with single braided serving, a second outer corrugated tube with single braided serving concentric with the inner corrugated tube, and arranged outwardly about the periphery of the inner corrugated tube and between the inner and outer corrugated tubes: a superinsulation layer; a one half lap layer of polyester ribbon; a one half lap layer of copper ribbon; a spirally wound refrigeration tube; a second one half lap layer of copper ribbon; a second one half lap layer of polyester ribbon; a second superinsulation layer; a third one half lap layer of polyester ribbon; and a spirally wound stretchable and compressible filament.

  19. Flexible rotor dynamics analysis

    NASA Technical Reports Server (NTRS)

    Shen, F. A.

    1973-01-01

    A digital computer program was developed to analyze the general nonaxisymmetric and nonsynchronous transient and steady-state rotor dynamic performance of a bending- and shear-wise flexible rotor-bearing system under various operating conditions. The effects of rotor material mechanical hysteresis, rotor torsion flexibility, transverse effects of rotor axial and torsional loading and the anisotropic, in-phase and out-of-phase bearing stiffness and damping force and moment coefficients were included in the program to broaden its capability. An optimum solution method was found and incorporated in the computer program. Computer simulation of experimental data was made and qualitative agreements observed. The mathematical formulations, computer program verification, test data simulation, and user instruction was presented and discussed.

  20. Flexible cryogenic conduit

    SciTech Connect

    Brindza, P.D.; Wines, R.R.; Takacs, J.J.

    1999-12-21

    A flexible and relatively low cost cryogenic conduit is described. The flexible cryogenic conduit of the present invention comprises a first inner corrugated tube with single braided serving, a second outer corrugated tube with single braided serving concentric with the inner corrugated tube, and arranged outwardly about the periphery of the inner corrugated tube and between the inner and outer corrugated tubes: a superinsulation layer; a one half lap layer of polyester ribbon; a one half lap layer of copper ribbon; a spirally wound refrigeration tube; a second one half lap layer of copper ribbon; a second one half lap layer of polyester ribbon; a second superinsulation layer; a third one half lap layer of polyester ribbon; and a spirally wound stretchable and compressible filament.

  1. Control of flexible structures

    NASA Technical Reports Server (NTRS)

    Russell, R. A.

    1985-01-01

    The requirements for future space missions indicate that many of these spacecraft will be large, flexible, and in some applications, require precision geometries. A technology program that addresses the issues associated with the structure/control interactions for these classes of spacecraft is discussed. The goal of the NASA control of flexible structures technology program is to generate a technology data base that will provide the designer with options and approaches to achieve spacecraft performance such as maintaining geometry and/or suppressing undesired spacecraft dynamics. This technology program will define the appropriate combination of analysis, ground testing, and flight testing required to validate the structural/controls analysis and design tools. This work was motivated by a recognition that large minimum weight space structures will be required for many future missions. The tools necessary to support such design included: (1) improved structural analysis; (2) modern control theory; (3) advanced modeling techniques; (4) system identification; and (5) the integration of structures and controls.

  2. FLEXIBLE GEIGER COUNTER

    DOEpatents

    Richter, H.G.; Gillespie, A.S. Jr.

    1963-11-12

    A flexible Geiger counter constructed from materials composed of vinyl chloride polymerized with plasticizers or co-polymers is presented. The counter can be made either by attaching short segments of corrugated plastic sleeving together, or by starting with a length of vacuum cleaner hose composed of the above materials. The anode is maintained substantially axial Within the sleeving or hose during tube flexing by means of polystyrene spacer disks or an easily assembled polyethylene flexible cage assembly. The cathode is a wire spiraled on the outside of the counter. The sleeving or hose is fitted with glass end-pieces or any other good insulator to maintain the anode wire taut and to admit a counting gas mixture into the counter. Having the cathode wire on the outside of the counter substantially eliminates the objectional sheath effect of prior counters and permits counting rates up to 300,000 counts per minute. (AEC)

  3. PTFE films with improved flexibility

    NASA Technical Reports Server (NTRS)

    Muraca, R. F.; Koch, A. A.

    1972-01-01

    Development and application of flexible polytetrafluroethylene films for expulsion bladders in spacecraft propellant tanks are described. Flexibility of material is obtained by reducing crystallinity through annealing and quenching in water. Physical and mechanical properties of material are presented.

  4. Industrial Fuel Flexibility Workshop

    SciTech Connect

    none,

    2006-09-01

    On September 28, 2006, in Washington, DC, ITP and Booz Allen Hamilton conducted a fuel flexibility workshop with attendance from various stakeholder groups. Workshop participants included representatives from the petrochemical, refining, food and beverage, steel and metals, pulp and paper, cement and glass manufacturing industries; as well as representatives from industrial boiler manufacturers, technology providers, energy and waste service providers, the federal government and national laboratories, and developers and financiers.

  5. Flexible multiply towpreg

    NASA Technical Reports Server (NTRS)

    Muzzy, John D. (Inventor); Varughese, Babu (Inventor)

    1992-01-01

    This invention relates to an improved flexible towpreg and a method of production therefor. The improved flexible towpreg comprises a plurality of towpreg plies which comprise reinforcing filaments and matrix forming material; the reinforcing filaments being substantially wetout by the matrix forming material such that the towpreg plies are substantially void-free composite articles, and the towpreg plies having an average thickness less than about 100 microns. The method of production for the improved flexible towpreg comprises the steps of spreading the reinforcing filaments to expose individually substantially all of the reinforcing filaments; coating the reinforcing filaments with the matrix forming material in a manner causing interfacial adhesion of the matrix forming material to the reinforcing filaments; forming the towpreg plies by heating the matrix forming material contacting the reinforcing filaments until the matrix forming material liquifies and coats the reinforcing filaments; and cooling the towpreg plies in a manner such that substantial cohesion between neighboring towpreg plies is prevented until the matrix forming material solidifies.

  6. Flexible materials technology

    NASA Technical Reports Server (NTRS)

    Steurer, W. H.

    1980-01-01

    A survey of all presently defined or proposed large space systems indicated an ever increasing demand for flexible components and materials, primarily as a result of the widening disparity between the stowage space of launch vehicles and the size of advanced systems. Typical flexible components and material requirements were identified on the basis of recurrence and/or functional commonality. This was followed by the evaluation of candidate materials and the search for material capabilities which promise to satisfy the postulated requirements. Particular attention was placed on thin films, and on the requirements of deployable antennas. The assessment of the performance of specific materials was based primarily on the failure mode, derived from a detailed failure analysis. In view of extensive on going work on thermal and environmental degradation effects, prime emphasis was placed on the assessment of the performance loss by meteoroid damage. Quantitative data were generated for tension members and antenna reflector materials. A methodology was developed for the representation of the overall materials performance as related to systems service life. A number of promising new concepts for flexible materials were identified.

  7. Galactokinase promiscuity: a question of flexibility?

    PubMed

    McAuley, Megan; Kristiansson, Helena; Huang, Meilan; Pey, Angel L; Timson, David J

    2016-02-01

    Galactokinase catalyses the first committed step of the Leloir pathway, i.e. the ATP-dependent phosphorylation of α-D-galactose at C1-OH. Reduced galactokinase activity results in the inherited metabolic disease type II galactosaemia. However, inhibition of galactokinase is considered a viable approach to treating more severe forms of galactosaemia (types I and III). Considerable progress has been made in the identification of high affinity, selective inhibitors. Although the structure of galactokinase from a variety of species is known, its catalytic mechanism remains uncertain. Although the bulk of evidence suggests that the reaction proceeds via an active site base mechanism, some experimental and theoretical studies contradict this. The enzyme has potential as a biocatalyst in the production of sugar 1-phosphates. This potential is limited by its high specificity. A variety of approaches have been taken to identify galactokinase variants which are more promiscuous. These have broadened galactokinase's specificity to include a wide range of D- and L-sugars. Initial studies suggest that some of these alterations result in increased flexibility at the active site. It is suggested that modulation of protein flexibility is at least as important as structural modifications in determining the success or failure of enzyme engineering. PMID:26862196

  8. Olefin fractionation and catalytic conversion system with heat exchange means

    SciTech Connect

    Wright, B.S.; Owen, H.; Hsia, C.H

    1989-05-23

    This patent describes a continuous catalytic system for converting an olefinic feedstock comprising ethylene and C/sub 3/+ olefins to heavier liquid hydrocarbon product comprising: means for prefractionating the olefinic feedstock to obtain a gaseous stream rich in ethylene and a liquid stream containing C/sub 3/+ olefin; means for vaporizing and contacting the liquid stream from the prefractionating means with hydrocarbon conversion oligomerization catalyst in at least one exothermic catalytic reaction zone to provide a heavier hydrocarbon effluent stream comprising distillate, gasoline and lighter hydrocarbons; means for cooling and fractionating the effluent stream to recover distillate, gasoline and lighter hydrocarbons separately; means for recycling at least a portion of the recovered gasoline as a liquid sorbent stream to the prefractionating means thereby reacting the recycled gasoline together with sorbed C/sub 3/+ olefin in the catalytic reactor system; and means for exchanging heat between hot effluent from the exothermic reaction zone and fractionator liquid rich in C/sub 3/+ olefin in the prefractionator reboiler loop.

  9. Thrombomodulin Binding Selects the Catalytically Active Form of Thrombin.

    PubMed

    Handley, Lindsey D; Treuheit, Nicholas A; Venkatesh, Varun J; Komives, Elizabeth A

    2015-11-01

    Human α-thrombin is a serine protease with dual functions. Thrombin acts as a procoagulant, cleaving fibrinogen to make the fibrin clot, but when bound to thrombomodulin (TM), it acts as an anticoagulant, cleaving protein C. A minimal TM fragment consisting of the fourth, fifth, and most of the sixth EGF-like domain (TM456m) that has been prepared has much improved solubility, thrombin binding capacity, and anticoagulant activity versus those of previous TM456 constructs. In this work, we compare backbone amide exchange of human α-thrombin in three states: apo, D-Phe-Pro-Arg-chloromethylketone (PPACK)-bound, and TM456m-bound. Beyond causing a decreased level of amide exchange at their binding sites, TM and PPACK both cause a decreased level of amide exchange in other regions including the γ-loop and the adjacent N-terminus of the heavy chain. The decreased level of amide exchange in the N-terminus of the heavy chain is consistent with the historic model of activation of serine proteases, which involves insertion of this region into the β-barrel promoting the correct conformation of the catalytic residues. Contrary to crystal structures of thrombin, hydrogen-deuterium exchange mass spectrometry results suggest that the conformation of apo-thrombin does not yet have the N-terminus of the heavy chain properly inserted for optimal catalytic activity, and that binding of TM allosterically promotes the catalytically active conformation. PMID:26468766

  10. Flexible Multi-Shock Shield

    NASA Technical Reports Server (NTRS)

    Christiansen, Eric L. (Inventor); Crews, Jeanne L. (Inventor)

    2005-01-01

    Flexible multi-shock shield system and method are disclosed for defending against hypervelocity particles. The flexible multi-shock shield system and method may include a number of flexible bumpers or shield layers spaced apart by one or more resilient support layers, all of which may be encapsulated in a protective cover. Fasteners associated with the protective cover allow the flexible multi-shock shield to be secured to the surface of a structure to be protected.

  11. Robust fuel- and time-optimal control of uncertain flexible space structures

    NASA Technical Reports Server (NTRS)

    Wie, Bong; Sinha, Ravi; Sunkel, John; Cox, Ken

    1993-01-01

    The problem of computing open-loop, fuel- and time-optimal control inputs for flexible space structures in the face of modeling uncertainty is investigated. Robustified, fuel- and time-optimal pulse sequences are obtained by solving a constrained optimization problem subject to robustness constraints. It is shown that 'bang-off-bang' pulse sequences with a finite number of switchings provide a practical tradeoff among the maneuvering time, fuel consumption, and performance robustness of uncertain flexible space structures.

  12. A family of asymptotically stable control laws for flexible robots based on a passivity approach

    NASA Technical Reports Server (NTRS)

    Lanari, Leonardo; Wen, John T.

    1991-01-01

    A general family of asymptotically stabilizing control laws is introduced for a class of nonlinear Hamiltonian systems. The inherent passivity property of this class of systems and the Passivity Theorem are used to show the closed-loop input/output stability which is then related to the internal state space stability through the stabilizability and detectability condition. Applications of these results include fully actuated robots, flexible joint robots, and robots with link flexibility.

  13. Catalytic distillation water recovery subsystem

    NASA Technical Reports Server (NTRS)

    Budininkas, P.; Rasouli, F.

    1985-01-01

    An integrated engineering breadboard subsystem for the recovery of potable water from untreated urine based on the vapor phase catalytic ammonia removal was designed, fabricated and tested. Unlike other evaporative methods, this process catalytically oxidizes ammonia and volatile hydrocarbons vaporizing with water to innocuous products; therefore, no pretreatment of urine is required. Since the subsystem is fabricated from commercially available components, its volume, weight and power requirements are not optimized; however, it is suitable for zero-g operation. The testing program consists of parametric tests, one month of daily tests and a continuous test of 168 hours duration. The recovered water is clear, odorless, low in ammonia and organic carbon, and requires only an adjustment of its pH to meet potable water standards. The obtained data indicate that the vapor phase catalytic ammonia removal process, if further developed, would also be competitive with other water recovery systems in weight, volume and power requirements.

  14. Current Issues in Flexibility Fitness.

    ERIC Educational Resources Information Center

    Knudson, Duane V.; Magnusson, Peter; McHugh, Malachy

    2000-01-01

    Physical activity is extremely important in maintaining good health. Activity is not possible without a certain amount of flexibility. This report discusses issues related to flexibility fitness. Flexibility is a property of the musculoskeletal system that determines the range of motion achievable without injury to the joints. Static flexibility…

  15. Flexible Scheduling: Making the Transition

    ERIC Educational Resources Information Center

    Creighton, Peggy Milam

    2008-01-01

    Citing literature that supports the benefits of flexible scheduling on student achievement, the author exhorts readers to campaign for flexible scheduling in their library media centers. She suggests tips drawn from the work of Graziano (2002), McGregor (2006) and Stripling (1997) for making a smooth transition from fixed to flexible scheduling:…

  16. Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop.

    PubMed

    Tran, Huyen Thi; Hong, Myoung Ki; Ngo, Ho Phuong Thuy; Huynh, Kim Hung; Ahn, Yeh Jin; Wang, Zhong; Kang, Lin Woo

    2016-01-01

    D-Alanyl-D-alanine is an essential precursor of bacterial peptidoglycan and is synthesized by D-alanine-D-alanine ligase (DDL) with hydrolysis of ATP; this reaction makes DDL an important drug target for the development of antibacterial agents. Five crystal structures of DDL from Yersinia pestis (YpDDL) were determined at 1.7-2.5 Å resolution: apo, AMP-bound, ADP-bound, adenosine 5'-(β,γ-imido)triphosphate-bound, and D-alanyl-D-alanine- and ADP-bound structures. YpDDL consists of three domains, in which four loops, loop 1, loop 2 (the serine loop), loop 3 (the ω-loop) and loop 4, constitute the binding sites for two D-alanine molecules and one ATP molecule. Some of them, especially the serine loop and the ω-loop, show flexible conformations, and the serine loop is mainly responsible for the conformational change in substrate nucleotide phosphates. Enzyme-kinetics assays were carried out for both the D-alanine and ATP substrates and a substrate-binding mechanism was proposed for YpDDL involving conformational changes of the loops. PMID:26894530

  17. SDO Sees Brightening Magnetic Loops

    NASA Video Gallery

    Two active regions sprouted arches of bundled magnetic loops in this video from NASA’s Solar Dynamics Observatory taken on Nov. 11-12, 2015. Charged particles spin along the magnetic field, tracing...

  18. Automatic blocking of nested loops

    NASA Technical Reports Server (NTRS)

    Schreiber, Robert; Dongarra, Jack J.

    1990-01-01

    Blocked algorithms have much better properties of data locality and therefore can be much more efficient than ordinary algorithms when a memory hierarchy is involved. On the other hand, they are very difficult to write and to tune for particular machines. The reorganization is considered of nested loops through the use of known program transformations in order to create blocked algorithms automatically. The program transformations used are strip mining, loop interchange, and a variant of loop skewing in which invertible linear transformations (with integer coordinates) of the loop indices are allowed. Some problems are solved concerning the optimal application of these transformations. It is shown, in a very general setting, how to choose a nearly optimal set of transformed indices. It is then shown, in one particular but rather frequently occurring situation, how to choose an optimal set of block sizes.

  19. SDO Sees Flourishing Magnetic Loops

    NASA Video Gallery

    A bright set of loops near the edge of the sun’s face grew and shifted quickly after the magnetic field was disrupted by a small eruption on Nov. 25, 2015. Charged particles emitting light in extre...

  20. Loop Electrosurgical Excision Procedure (LEEP)

    MedlinePlus

    ... that acts like a scalpel (surgical knife). An electric current is passed through the loop, which cuts away ... A procedure in which an instrument works with electric current to destroy tissue. Local Anesthesia: The use of ...

  1. Observations of loops and prominences

    NASA Technical Reports Server (NTRS)

    Strong, Keith T.

    1994-01-01

    We review recent observations by the Yohkoh-SXT (Soft X-ray Telescope) in collaboration with other spacecraft and ground-based observatories of coronal loops and prominences. These new results point to problems that SoHO will be able to address. With a unique combination of rapid-cadence digital imaging (greater than or equal to 32 s full-disk and greater than or equal to 2 s partial-frame images), high spatial resolution (greater than or equal to 2.5 arcsec pixels), high sensitivity (EM less than or equal to 10(exp 42) cm(exp -3)), a low-scatter mirror, and large dynamic range, SXT can observe a vast range of targets on the Sun. Over the first 21 months of Yohkoh operations SXT has taken over one million images of the corona and so is building up an invaluable long-term database on the large-scale corona and loop geometry. The most striking thing about the SXT images is the range of loop sizes and shapes. The active regions are a bright tangle of magnetic field lines, surrounded by a network of large-scale quiet-Sun loops stretching over distances in excess of 105 km. The cross-section of most loops seems to be constant. Loops displaying significant Gamma's are the exception, not the rule, implying the presence of widespread currents in the corona. All magnetic structures show changes. Time scales range from seconds to months. The question of how these structures are formed, become filled with hot plasma, and are maintained is still open. While we see the propagation of brightenings along the length of active-region loops and in X-ray jets with velocities of several hundred km/s, much higher velocities are seen in the quiet Sun. In XBP flares, for example, velocities of over 1000 km/s are common. Active-region loops seem to be in constant motion, moving slowly outward, carrying plasma with them. During flares, loops often produce localized brightenings at the base and later at the apex of the loop. Quiescent filaments and prominences have been observed regularly

  2. Catalytic Enantioselective Carboannulation with Allylsilanes

    PubMed Central

    Ball-Jones, Nicolas R.; Badillo, Joseph J.; Tran, Ngon T.; Franz, Annaliese K.

    2015-01-01

    The first catalytic asymmetric carboannulation with allylsilanes is presented. The enantioselective [3+2] annulation is catalyzed using a Sc(III)-indapybox complex with tetrakis-[3,5-bis(trifluoromethyl)phenyl]-borate (BArF) to enhance catalytic activity and control stereoselectivity. Functionalized cyclopentanes containing a quaternary carbon are derived from alkylidene oxindole, coumarin, and malonate substrates with high stereoselectivity. The enantioselective 1,4-conjugate addition and enantioselective lactone formation (via trapping of the β-silyl carbocation) is also described. PMID:25045133

  3. Catalytic enantioselective carboannulation with allylsilanes.

    PubMed

    Ball-Jones, Nicolas R; Badillo, Joseph J; Tran, Ngon T; Franz, Annaliese K

    2014-09-01

    The first catalytic asymmetric carboannulation with allylsilanes is presented. The enantioselective [3+2] annulation is catalyzed using a scandium(III)/indapybox complex with tetrakis-[3,5-bis(trifluoromethyl)phenyl]-borate (BArF) to enhance catalytic activity and control stereoselectivity. Functionalized cyclopentanes containing a quaternary carbon center are derived from alkylidene oxindole, coumarin, and malonate substrates with high stereoselectivity. The enantioselective 1,4-conjugate addition and enantioselective lactone formation (by trapping of the β-silyl carbocation) is also described. PMID:25045133

  4. Perfluoropolyalkylether decomposition on catalytic aluminas

    NASA Technical Reports Server (NTRS)

    Morales, Wilfredo

    1994-01-01

    The decomposition of Fomblin Z25, a commercial perfluoropolyalkylether liquid lubricant, was studied using the Penn State Micro-oxidation Test, and a thermal gravimetric/differential scanning calorimetry unit. The micro-oxidation test was conducted using 440C stainless steel and pure iron metal catalyst specimens, whereas the thermal gravimetric/differential scanning calorimetry tests were conducted using catalytic alumina pellets. Analysis of the thermal data, high pressure liquid chromatography data, and x-ray photoelectron spectroscopy data support evidence that there are two different decomposition mechanisms for Fomblin Z25, and that reductive sites on the catalytic surfaces are responsible for the decomposition of Fomblin Z25.

  5. Dynamical behaviour in coronal loops

    NASA Technical Reports Server (NTRS)

    Haisch, Bernhard M.

    1986-01-01

    Rapid variability has been found in two active region coronal loops observed by the X-ray Polychromator (XRP) and the Hard X-ray Imaging Spectrometer (HXIS) onboard the Solar Maximum Mission (SMM). There appear to be surprisingly few observations of the short-time scale behavior of hot loops, and the evidence presented herein lends support to the hypothesis that coronal heating may be impulsive and driven by flaring.

  6. Digital tracking loops for a programmable digital modem

    NASA Technical Reports Server (NTRS)

    Poklemba, John J.

    1992-01-01

    In this paper, an analysis and hardware emulation of the tracking loops for a very flexible programmable digital modem (PDM) will be presented. The modem is capable of being programmed for 2, 4, 8, 16-PSK, 16-QAM, MSK, and Offset-QPSK modulation schemes over a range of data rates from 2.34 to 300 Mbps with programmable spectral occupancy from 1.2 to 1.8 times the symbol rate; these operational parameters are executable in burst or continuous mode. All of the critical processing in both the modulator and demodulator is done at baseband with very high-speed digital hardware and memory. Quadrature analog front-ends are used for translation between baseband and the IF center frequency. The modulator is based on a table lookup approach, where precomputed samples are stored in memory and clocked out according to the incoming data pattern. The sample values are predistorted to counteract the effects of the other filtering functions in the link as well as any transmission impairments. The demodulator architecture was adapted from a joint estimator-detector (JED) mathematical analysis. Its structure is applicable to most signalling formats that can be represented in a two-dimensional space. The JED realization uses interdependent, mutually aiding tracking loops with post-detection data feedback. To expedite and provide for more reliable synchronization, initial estimates for these loops are computed in a parallel acquisition processor. The cornerstone of the demodulator realization is the pre-averager received data filter which allows operation over a broad range of data rates without any hardware changes and greatly simplifies the implementation complexity. The emulation results confirmed tracking loop operation over the entire range of operational parameters listed above, as well as the capability of achieving and maintaining synchronization at BER's in excess of 10(exp -1). The emulation results also showed very close agreement with the tracking loop analysis, and

  7. Crystal structure of the catalytic domain of human bile salt activated lipase.

    PubMed Central

    Terzyan, S.; Wang, C. S.; Downs, D.; Hunter, B.; Zhang, X. C.

    2000-01-01

    Bile-salt activated lipase (BAL) is a pancreatic enzyme that digests a variety of lipids in the small intestine. A distinct property of BAL is its dependency on bile salts in hydrolyzing substrates of long acyl chains or bulky alcoholic motifs. A crystal structure of the catalytic domain of human BAL (residues 1-538) with two surface mutations (N186D and A298D), which were introduced in attempting to facilitate crystallization, has been determined at 2.3 A resolution. The crystal form belongs to space group P2(1)2(1)2(1) with one monomer per asymmetric unit, and the protein shows an alpha/beta hydrolase fold. In the absence of bound bile salt molecules, the protein possesses a preformed catalytic triad and a functional oxyanion hole. Several surface loops around the active site are mobile, including two loops potentially involved in substrate binding (residues 115-125 and 270-285). PMID:11045623

  8. The Coronal Loop Inventory Project

    NASA Astrophysics Data System (ADS)

    Schmelz, J. T.; Pathak, S.; Christian, G. M.; Dhaliwal, R. S. S.; Paul, K. S.

    2015-11-01

    Most coronal physicists now seem to agree that loops are composed of tangled magnetic strands and have both isothermal and multithermal cross-field temperature distributions. As yet, however, there is no information on the relative importance of each of these categories, and we do not know how common one is with respect to the other. In this paper, we investigate these temperature properties for all loop segments visible in the 171-Å image of AR 11294, which was observed by the Atmospheric Imaging Assembly (AIA) on 2011 September 15. Our analysis revealed 19 loop segments, but only 2 of these were clearly isothermal. Six additional segments were effectively isothermal, that is, the plasma emission to which AIA is sensitive could not be distinguished from isothermal emission, within measurement uncertainties. One loop had both isothermal transition region and multithermal coronal solutions. Another five loop segments require multithermal plasma to reproduce the AIA observations. The five remaining loop segments could not be separated reliably from the background in the crucial non-171-Å AIA images required for temperature analysis. We hope that the direction of coronal heating models and the efforts modelers spend on various heating scenarios will be influenced by these results.

  9. The Structure of Coronal Loops

    NASA Technical Reports Server (NTRS)

    Antiochos, Spiro K.

    2009-01-01

    It is widely believed that the simple coronal loops observed by XUV imagers, such as EIT, TRACE, or XRT, actually have a complex internal structure consisting of many (perhaps hundreds) of unresolved, interwoven "strands". According to the nanoflare model, photospheric motions tangle the strands, causing them to reconnect and release the energy required to produce the observed loop plasma. Although the strands, themselves, are unresolved by present-generation imagers, there is compelling evidence for their existence and for the nanoflare model from analysis of loop intensities and temporal evolution. A problem with this scenario is that, although reconnection can eliminate some of the strand tangles, it cannot destroy helicity, which should eventually build up to observable scales. we consider, therefore, the injection and evolution of helicity by the nanoflare process and its implications for the observed structure of loops and the large-scale corona. we argue that helicity does survive and build up to observable levels, but on spatial and temporal scales larger than those of coronal loops. we discuss the implications of these results for coronal loops and the corona, in general .

  10. Durability of ceramic catalytic converters for motorcycles

    SciTech Connect

    Reddy, K.P.; Scott, P.L.; Hwang, H.S.; Mooney, J.J.

    1995-12-31

    Motorcycle exhaust emission standards throughout the world are becoming more stringent. Emission control systems utilizing the catalytic converter are already in production in Taiwan for 2-stroke engine motorcycles. Catalysts designed for 2-stroke engines encounter a more severe exhaust environment than do those designed for 4-stroke engines. The two aspects of increased severity are the higher temperatures and higher stresses due to engine vibrations. Precious metal catalysts have been designed to operate in the thermal environment of 2-stroke engines and such catalysts have been successfully applied to both metal and ceramic substrates. However, until now, only the metal substrate catalysts have been utilized in motorcycle application. Ceramic based catalysts have not been considered because the mounting material that holds the catalyst substrate in place did not have enough durability to withstand the thermal/vibrational forces encountered in 2-stroke engine exhaust. Ceramic substrates have many advantages such as superior high temperature strength, which is especially important for the 2-stroke engine application, flexibility in cell shape and density, and lower cost. To realize these benefits, efforts were made in this study to develop better mounting systems. The results of this effort indicate that the durability requirements of 2-stroke engine can be met with the ceramic catalyst substrates if the improved mounting designs reported in the present study are employed.

  11. Multi-loop networked process control: a synchronized approach.

    PubMed

    Das, M; Ghosh, R; Goswami, B; Chandra, A K; Balasubramanian, R; Luksch, P; Gupta, A

    2009-01-01

    Modern day process control uses digital controllers which are based on the principle of distributed rather than centralized control. Distributing controllers, sensors and actuators across a plant entails considerable wiring which can be reduced substantially by integrating the components of a control loop over a network. The other advantages include greater flexibility and higher reliability with lower hardware redundancy. The controllers and sensors are on a network and can take over the function of a failed component automatically, without the need of manual reconfiguration, thus eliminating the need of having a redundant component for each and every component. Though elaborate techniques have been developed for Single Input Single Output (SISO) systems, the major challenge lies in extending these ideas to control a practical process plant where de-centralized control is actually achieved through control of individual SISO control loops derived through de-coupling of the original system. Multiple loops increase network load and hence the sampling times associated with the control loops and makes synchronization difficult. This paper presents a methodology by which network based process control can be applied to practical process plants, with a simple direct synchronization mechanism. PMID:19028386

  12. Coronal Loop Mapping to Infer the Best Magnetic Field Models for Active Region Prominences

    NASA Astrophysics Data System (ADS)

    Gary, G. Allen; Hu, Qiang; Lee, Jong Kwan

    2014-01-01

    This article comments on the results of a new, rapid, and flexible manual method to map on-disk individual coronal loops of a two-dimensional EUV image into the three-dimensional coronal loops. The method by Gary, Hu, and Lee (2013) employs cubic Bézier splines to map coronal loops using only four free parameters per loop. A set of 2D splines for coronal loops is transformed to the best 3D pseudo-magnetic field lines for a particular coronal model. The results restrict the magnetic field models derived from extrapolations of magnetograms to those admissible and inadmissible via a fitness parameter. This method uses the minimization of the misalignment angles between the magnetic field model and the best set of 3D field lines that match a set of closed coronal loops. We comment on the implication of the fitness parameter in connection with the magnetic free energy and comment on extensions of our earlier work by considering the issues of employing open coronal loops or employing partial coronal loop.

  13. Investigation of Inner Loop Flight Control Strategies for High-Speed Research

    NASA Technical Reports Server (NTRS)

    Newman, Brett; Kassem, Ayman

    1999-01-01

    This report describes the activities and findings conducted under contract NAS1-19858 with NASA Langley Research Center. Subject matter is the investigation of suitable flight control design methodologies and solutions for large, flexible high-speed vehicles. Specifically, methodologies are to address the inner control loops used for stabilization and augmentation of a highly coupled airframe system possibly involving rigid-body motion, structural vibrations, unsteady aerodynamics, and actuator dynamics. Techniques considered in this body of work are primarily conventional-based, and the vehicle of interest is the High-Speed Civil Transport (HSCT). Major findings include 1) current aeroelastic vehicle modeling procedures require further emphasis and refinement, 2) traditional and nontraditional inner loop flight control strategies employing a single feedback loop do not appear sufficient for highly flexible HSCT class vehicles, 3) inner loop flight control systems will, in all likelihood, require multiple interacting feedback loops, and 4) Ref. H HSCT configuration presents major challenges to designing acceptable closed-loop flight dynamics.

  14. Rotating flexible drag mill

    DOEpatents

    Pepper, W.B.

    1984-05-09

    A rotating parachute for decelerating objects travelling through atmosphere at subsonic or supersonic deployment speeds includes a circular canopy having a plurality of circumferentially arranged flexible panels projecting radially from a solid central disk. A slot extends radially between adjacent panels to the outer periphery of the canopy. Upon deployment, the solid disk diverts air radially to rapidly inflate the panels into a position of maximum diameter. Air impinging on the panels adjacent the panel slots rotates the parachute during its descent. Centrifugal force flattens the canopy into a constant maximum diameter during terminal descent for maximum drag and deceleration.

  15. Composite Flexible Blanket Insulation

    NASA Technical Reports Server (NTRS)

    Kourtides, Demetrius A. (Inventor); Pitts, William C. (Inventor); Goldstein, Howard E. (Inventor); Sawko, Paul M. (Inventor)

    1991-01-01

    Composite flexible multilayer insulation systems (MLI) were evaluated for thermal performance and compared with the currently used fibrous silica (baseline) insulation system. The systems described are multilayer insulations consisting of alternating layers of metal foil and scrim ceramic cloth or vacuum metallized polymeric films quilted together using ceramic thread. A silicon carbide thread for use in the quilting and the method of making it are also described. These systems are useful in providing lightweight insulation for a variety of uses, particularly on the surface of aerospace vehicles subject to very high temperatures during flight.

  16. A flexible business focus

    SciTech Connect

    Hennagir, T.

    1994-11-01

    The challenge of sourcing equipment to meet customer needs around the world remains a prerequisite for boiler and CFB manufacturers as they strive to maintain a strong business presence in key markets. Boiler vendors are learning to meet their targets based upon what the market is, not what they hope it will become. An elastic equipment supply strategy is bolstering new business activity for internationally active boiler and circulating fluidized bed combustion (CFB) vendors. Techniques such as flexible sourcing and expanded scope capability are helping suppliers gain market advantage in new global growth areas.

  17. Flexible composite radiation detector

    DOEpatents

    Cooke, D. Wayne; Bennett, Bryan L.; Muenchausen, Ross E.; Wrobleski, Debra A.; Orler, Edward B.

    2006-12-05

    A flexible composite scintillator was prepared by mixing fast, bright, dense rare-earth doped powdered oxyorthosilicate (such as LSO:Ce, LSO:Sm, and GSO:Ce) scintillator with a polymer binder. The binder is transparent to the scintillator emission. The composite is seamless and can be made large and in a wide variety of shapes. Importantly, the composite can be tailored to emit light in a spectral region that matches the optimum response of photomultipliers (about 400 nanometers) or photodiodes (about 600 nanometers), which maximizes the overall detector efficiency.

  18. Flexible Volumetric Structure

    NASA Technical Reports Server (NTRS)

    Cagle, Christopher M. (Inventor); Schlecht, Robin W. (Inventor)

    2014-01-01

    A flexible volumetric structure has a first spring that defines a three-dimensional volume and includes a serpentine structure elongatable and compressible along a length thereof. A second spring is coupled to at least one outboard edge region of the first spring. The second spring is a sheet-like structure capable of elongation along an in-plane dimension thereof. The second spring is oriented such that its in-plane dimension is aligned with the length of the first spring's serpentine structure.

  19. Flexible Material Systems Testing

    NASA Technical Reports Server (NTRS)

    Lin, John K.; Shook, Lauren S.; Ware, Joanne S.; Welch, Joseph V.

    2010-01-01

    An experimental program has been undertaken to better characterize the stress-strain characteristics of flexible material systems to support a NASA ground test program for inflatable decelerator material technology. A goal of the current study is to investigate experimental methods for the characterization of coated woven material stiffness. This type of experimental mechanics data would eventually be used to define the material inputs of fluid-structure interaction simulation models. The test methodologies chosen for this stress-strain characterization are presented along with the experimental results.

  20. Catalytic oxidation of waste materials

    NASA Technical Reports Server (NTRS)

    Jagow, R. B.

    1977-01-01

    Aqueous stream of human waste is mixed with soluble ruthenium salts and is introduced into reactor at temperature where ruthenium black catalyst forms on internal surfaces of reactor. This provides catalytically active surface to convert oxidizable wastes into breakdown products such as water and carbon dioxide.

  1. Social Entrepreneurs and Catalytic Change.

    ERIC Educational Resources Information Center

    Waddock, Sandra A.; Post, James E.

    1991-01-01

    Social entrepreneurs are private citizens who play critical roles in bringing about catalytic changes in the public sector agenda and the perception of social issues. Factors that make their projects--such as the Partnership for a Drug-Free America and Earth Day--successful include problem complexity, credibility, and a commitment to a collective…

  2. Catalytically enhanced packed tower scrubbing

    SciTech Connect

    Stitt, E.H.; Taylor, F.J.; Kelly, K.

    1996-12-31

    An enhanced wet scrubbing process for the treatment of gas streams containing odours and low level VOC`s is presented. It comprises essentially a single scrubbing column and a fixed bed catalytic reactor through which the dilute alkaline bleach scrubbing liquor is recirculated. The process has significant cost advantages over conventional chemical scrubbing technology, and copes well with peaks in odour levels. Traditional bleach scrubbing, and the improvements in process chemistry and the flowsheet afforded by inclusion of the catalyst, are discussed. The catalyst enables many of the well known problems associated with bleach scrubbing to be overcome, and facilitates odour removal efficiencies of greater than 99% in a single column. Pilot plant data from trials on sewage treatment works are presented. These show clearly the ability of the catalytically enhanced process to achieve sulphide and odour removals in excess of 99% in the single column. Case studies of some of the existing commercial installations are given, indicating the wide range of applications, industries and scale of the installed units. Comparative data are presented, measured on a commercial unit for the conventional operation of a bleach scrubber, and with the retrofitted catalyst in use. These data show clearly the benefits of the catalytic process in terms of removal efficiencies; and hence by inference also in equipment size and costs. The catalytic process is also shown to achieve very high removal efficiencies of organo-sulphides in a single column. 8 refs., 3 figs., 10 tabs.

  3. Induced fit and the catalytic mechanism of isocitrate dehydrogenase.

    PubMed

    Gonçalves, Susana; Miller, Stephen P; Carrondo, Maria A; Dean, Anthony M; Matias, Pedro M

    2012-09-11

    NADP(+) dependent isocitrate dehydrogenase (IDH; EC 1.1.1.42) belongs to a large family of α-hydroxyacid oxidative β-decarboxylases that catalyze similar three-step reactions, with dehydrogenation to an oxaloacid intermediate preceding β-decarboxylation to an enol intermediate followed by tautomerization to the final α-ketone product. A comprehensive view of the induced fit needed for catalysis is revealed on comparing the first "fully closed" crystal structures of a pseudo-Michaelis complex of wild-type Escherichia coli IDH (EcoIDH) and the "fully closed" reaction product complex of the K100M mutant with previously obtained "quasi-closed" and "open" conformations. Conserved catalytic residues, binding the nicotinamide ring of NADP(+) and the metal-bound substrate, move as rigid bodies during domain closure by a hinge motion that spans the central β-sheet in each monomer. Interactions established between Thr105 and Ser113, which flank the "phosphorylation loop", and the nicotinamide mononucleotide moiety of NADP(+) establish productive coenzyme binding. Electrostatic interactions of a Lys100-Leu103-Asn115-Glu336 tetrad play a pivotal role in assembling a catalytically competent active site. As predicted, Lys230* is positioned to deprotonate/reprotonate the α-hydroxyl in both reaction steps and Tyr160 moves into position to protonate C3 following β-decarboxylation. A proton relay from the catalytic triad Tyr160-Asp307-Lys230* connects the α-hydroxyl of isocitrate to the bulk solvent to complete the picture of the catalytic mechanism. PMID:22891681

  4. CATALYTIC COMBUSTION COMPONENT AND SYSTEM PROTOTYPE DEVELOPMENT

    EPA Science Inventory

    The report gives results of a project to develop the components required for catalytic combustion system operation and evaluation. The systems investigated (firetube boiler, watertube boiler, and gas turbine), when integrated with the catalytic combustor, have potential for both ...

  5. Active control of buckling of flexible beams

    NASA Technical Reports Server (NTRS)

    Baz, A.; Tampe, L.

    1989-01-01

    The feasibility of using the rapidly growing technology of the shape memory alloys actuators in actively controlling the buckling of large flexible structures is investigated. The need for such buckling control systems is becoming inevitable as the design trends of large space structures have resulted in the use of structural members that are long, slender, and very flexible. In addition, as these truss members are subjected mainly to longitudinal loading they become susceptible to structural instabilities due to buckling. Proper control of such instabilities is essential to the effective performance of the structures as stable platforms for communication and observation. Mathematical models are presented that simulate the dynamic characteristics of the shape memory actuator, the compressive structural members, and the associated active control system. A closed-loop computer-controlled system is designed, based on the developed mathematical models, and implemented to control the buckling of simple beams. The performance of the computer-controlled system is evaluated experimentally and compared with the theoretical predictions to validate the developed models. The obtained results emphasize the importance of buckling control and suggest the potential of the shape memory actuators as attractive means for controlling structural deformation in a simple and reliable way.

  6. Robust multivariable controller design for flexible spacecraft

    NASA Technical Reports Server (NTRS)

    Joshi, Suresh M.; Armstrong, Ernest S.

    1986-01-01

    Large, flexible spacecraft are typically characterized by a large number of significant elastic modes with very small inherent damping, low, closely spaced natural frequencies, and the lack of accurate knowledge of the structural parameters. Summarized here is some recent research on the design of robust controllers for such spacecraft, which will maintain stability, and possible performance, despite these problems. Two types of controllers are considered, the first being the linear-quadratic-Gaussian-(LQG)-type. The second type utilizes output feedback using collocated sensors and actuators. The problem of designing robust LQG-type controllers using the frequency domain loop transfer recovery (LTR) method is considered, and the method is applied to a large antenna model. Analytical results regarding the regions of stability for LQG-type controllers in the presence of actuator nonlinearities are also presented. The results obtained for the large antenna indicate that the LQG/LTR method is a promising approach for control system design for flexible spacecraft. For the second type of controllers (collocated controllers), it is proved that the stability is maintained in the presence of certain commonly encountered nonlinearities and first-order actuator dynamics. These results indicate that collocated controllers are good candidates for robust control in situations where model errors are large.

  7. Kalman Orbit Optimized Loop Tracking

    NASA Technical Reports Server (NTRS)

    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.

  8. Fabrication techniques for superconducting readout loops

    NASA Technical Reports Server (NTRS)

    Payne, J. E.

    1982-01-01

    Procedures for the fabrication of superconducting readout loops out of niobium on glass substrates were developed. A computer program for an existing fabrication system was developed. Both positive and negative resist procedures for the production of the readout loops were investigated. Methods used to produce satisfactory loops are described and the various parameters affecting the performance of the loops are analyzed.

  9. Filter for third order phase locked loops

    NASA Technical Reports Server (NTRS)

    Crow, R. B.; Tausworthe, R. C. (Inventor)

    1973-01-01

    Filters for third-order phase-locked loops are used in receivers to acquire and track carrier signals, particularly signals subject to high doppler-rate changes in frequency. A loop filter with an open-loop transfer function and set of loop constants, setting the damping factor equal to unity are provided.

  10. The DUSP–Ubl domain of USP4 enhances its catalytic efficiency by promoting ubiquitin exchange

    PubMed Central

    Clerici, Marcello; Luna-Vargas, Mark P. A.; Faesen, Alex C.; Sixma, Titia K.

    2014-01-01

    Ubiquitin-specific protease USP4 is emerging as an important regulator of cellular pathways, including the TGF-β response, NF-κB signalling and splicing, with possible roles in cancer. Here we show that USP4 has its catalytic triad arranged in a productive conformation. Nevertheless, it requires its N-terminal DUSP–Ubl domain to achieve full catalytic turnover. Pre-steady-state kinetics measurements reveal that USP4 catalytic domain activity is strongly inhibited by slow dissociation of ubiquitin after substrate hydrolysis. The DUSP–Ubl domain is able to enhance ubiquitin dissociation, hence promoting efficient turnover. In a mechanism that requires all USP4 domains, binding of the DUSP–Ubl domain promotes a change of a switching loop near the active site. This ‘allosteric regulation of product discharge’ provides a novel way of regulating deubiquitinating enzymes that may have relevance for other enzyme classes. PMID:25404403

  11. NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site

    PubMed Central

    Bonneau, Eric; Girard, Nicolas; Boisbouvier, Jérôme; Legault, Pascale

    2011-01-01

    The Neurospora VS ribozyme is a small nucleolytic ribozyme with unique primary, secondary and global tertiary structures, which displays mechanistic similarities to the hairpin ribozyme. Here, we determined the high-resolution NMR structure of a stem–loop VI fragment containing the A730 internal loop, which forms part of the active site. In the presence of magnesium ions, the A730 loop adopts a structure that is consistent with existing biochemical data and most likely reflects its conformation in the VS ribozyme prior to docking with the cleavage site internal loop. Interestingly, the A730 loop adopts an S-turn motif that is also present in loop B within the hairpin ribozyme active site. The S-turn appears necessary to expose the Watson–Crick edge of a catalytically important residue (A756) so that it can fulfill its role in catalysis. The A730 loop and the cleavage site loop of the VS ribozyme display structural similarities to internal loops found in the active site of the hairpin ribozyme. These similarities provided a rationale to build a model of the VS ribozyme active site based on the crystal structure of the hairpin ribozyme. PMID:21266483

  12. Study of the Open Loop and Closed Loop Oscillator Techniques

    SciTech Connect

    Imel, George R.; Baker, Benjamin; Riley, Tony; Langbehn, Adam; Aryal, Harishchandra; Benzerga, M. Lamine

    2015-04-11

    This report presents the progress and completion of a five-year study undertaken at Idaho State University of the measurement of very small worth reactivity samples comparing open and closed loop oscillator techniques.The study conclusively demonstrated the equivalency of the two techniques with regard to uncertainties in reactivity values, i.e., limited by reactor noise. As those results are thoroughly documented in recent publications, in this report we will concentrate on the support work that was necessary. For example, we describe in some detail the construction and calibration of a pilot rod for the closed loop system. We discuss the campaign to measure the required reactor parameters necessary for inverse-kinetics. Finally, we briefly discuss the transfer of the open loop technique to other reactor systems.

  13. Flexible ocean upwelling pipe

    DOEpatents

    Person, Abraham

    1980-01-01

    In an ocean thermal energy conversion facility, a cold water riser pipe is releasably supported at its upper end by the hull of the floating facility. The pipe is substantially vertical and has its lower end far below the hull above the ocean floor. The pipe is defined essentially entirely of a material which has a modulus of elasticity substantially less than that of steel, e.g., high density polyethylene, so that the pipe is flexible and compliant to rather than resistant to applied bending moments. The position of the lower end of the pipe relative to the hull is stabilized by a weight suspended below the lower end of the pipe on a flexible line. The pipe, apart from the weight, is positively buoyant. If support of the upper end of the pipe is released, the pipe sinks to the ocean floor, but is not damaged as the length of the line between the pipe and the weight is sufficient to allow the buoyant pipe to come to a stop within the line length after the weight contacts the ocean floor, and thereafter to float submerged above the ocean floor while moored to the ocean floor by the weight. The upper end of the pipe, while supported by the hull, communicates to a sump in the hull in which the water level is maintained below the ambient water level. The sump volume is sufficient to keep the pipe full during heaving of the hull, thereby preventing collapse of the pipe.

  14. Gluing hexagons at three loops

    NASA Astrophysics Data System (ADS)

    Basso, Benjamin; Goncalves, Vasco; Komatsu, Shota; Vieira, Pedro

    2016-06-01

    We perform extensive three-loop tests of the hexagon bootstrap approach for structure constants in planar N = 4 SYM theory. We focus on correlators involving two BPS operators and one non-BPS operator in the so-called SL (2) sector. At three loops, such correlators receive wrapping corrections from mirror excitations flowing in either the adjacent or the opposing channel. Amusingly, we find that the first type of correction coincides exactly with the leading wrapping correction for the spectrum (divided by the one-loop anomalous dimension). We develop an efficient method for computing the second type of correction for operators with any spin. The results are in perfect agreement with the recently obtained three-loop perturbative data by Chicherin, Drummond, Heslop, Sokatchev [2] and by Eden [3]. We also derive the integrand for general multi-particle wrapping corrections, which turns out to take a remarkably simple form. As an application we estimate the loop order at which various new physical effects are expected to kick-in.

  15. Catalytic multi-stage process for hydroconversion and refining hydrocarbon feeds

    DOEpatents

    Comolli, Alfred G.; Lee, Lap-Keung

    2001-01-01

    A multi-stage catalytic hydrogenation and hydroconversion process for heavy hydrocarbon feed materials such as coal, heavy petroleum fractions, and plastic waste materials. In the process, the feedstock is reacted in a first-stage, back-mixed catalytic reactor with a highly dispersed iron-based catalyst having a powder, gel or liquid form. The reactor effluent is pressure-reduced, vapors and light distillate fractions are removed overhead, and the heavier liquid fraction is fed to a second stage back-mixed catalytic reactor. The first and second stage catalytic reactors are operated at 700-850.degree. F. temperature, 1000-3500 psig hydrogen partial pressure and 20-80 lb./hr per ft.sup.3 reactor space velocity. The vapor and light distillates liquid fractions removed from both the first and second stage reactor effluent streams are combined and passed to an in-line, fixed-bed catalytic hydrotreater for heteroatom removal and for producing high quality naphtha and mid-distillate or a full-range distillate product. The remaining separator bottoms liquid fractions are distilled at successive atmospheric and vacuum pressures, low and intermediate-boiling hydrocarbon liquid products are withdrawn, and heavier distillate fractions are recycled and further upgraded to provide additional low-boiling hydrocarbon liquid products. This catalytic multistage hydrogenation process provides improved flexibility for hydroprocessing the various carbonaceous feedstocks and adjusting to desired product structures and for improved economy of operations.

  16. Bandwidth controller for phase-locked-loop

    NASA Technical Reports Server (NTRS)

    Brockman, Milton H. (Inventor)

    1992-01-01

    A phase locked loop utilizing digital techniques to control the closed loop bandwidth of the RF carrier phase locked loop in a receiver provides high sensitivity and a wide dynamic range for signal reception. After analog to digital conversion, a digital phase locked loop bandwidth controller provides phase error detection with automatic RF carrier closed loop tracking bandwidth control to accommodate several modes of transmission.

  17. Analysis of virtual passive controllers for flexible space structures

    NASA Technical Reports Server (NTRS)

    Williams, Trevor W.

    1992-01-01

    The dynamics of flexible spacecraft are not usually well known before launch. This makes it important to develop controllers for such systems that can never be destabilized by perturbations in the structural model. Virtual passive controllers, or active vibration absorbers, possess this guaranteed stability property; they mimic a fictitious flexible structure attached to the true physical one. This report analyzes the properties of such controllers, and shows that disturbance absorption behavior can be naturally described in terms of a set of virtual zeros that they introduce into the closed-loop dynamics of the system. Based on this analysis, techniques are then derived for selecting the active vibration absorber internal parameters, i.e., the gain matrices of such controllers, so as to achieve specified control objectives. Finally, the effects on closed-loop stability of small delays in the feedback loop are investigated. Such delays would typically be introduced by a digital implementation of an active vibration absorber. It is shown that these delays only affect the real parts of the eigenvalues of a lightly-damped structure. Furthermore, it is only the high-frequency modes that are destabilized by delays; low-frequency modes are actually made more heavily damped. Eigenvalue perturbation methods are used to obtain accurate predictions of the critical delay at which a given system will become unstable; these methods also determine which mode is critical.

  18. Refined molecular hinge between allosteric and catalytic domain determines allosteric regulation and stability of fungal chorismate mutase

    PubMed Central

    Helmstaedt, Kerstin; Heinrich, Gabriele; Lipscomb, William N.; Braus, Gerhard H.

    2002-01-01

    The yeast chorismate mutase is regulated by tyrosine as feedback inhibitor and tryptophan as crosspathway activator. The monomer consists of a catalytic and a regulatory domain covalently linked by the loop L220s (212–226), which functions as a molecular hinge. Two monomers form the active dimeric enzyme stabilized by hydrophobic interactions in the vicinity of loop L220s. The role of loop L220s and its environment for enzyme regulation, dimerization, and stability was analyzed. Substitution of yeast loop L220s in place of the homologous loop from the corresponding and similarly regulated Aspergillus enzyme (and the reverse substitution) changed tyrosine inhibition to activation. Yeast loop L220s substituted into the Aspergillus enzyme resulted in a tryptophan-inhibitable enzyme. Monomeric yeast chorismate mutases could be generated by substituting two hydrophobic residues in and near the hinge region. The resulting Thr-212→Asp–Phe-28→Asp enzyme was as stable as wild type, but lost allosteric regulation and showed reduced catalytic activity. These results underline the crucial role of this molecular hinge for inhibition, activation, quaternary structure, and stability of yeast chorismate mutase. PMID:11997452

  19. Solution-state structure of an intramolecular G-quadruplex with propeller, diagonal and edgewise loops

    PubMed Central

    Marušič, Maja; Šket, Primož; Bauer, Lubos; Viglasky, Viktor; Plavec, Janez

    2012-01-01

    We herein report on the formation and high-resolution NMR solution-state structure determination of a G-quadruplex adopted by d[G3ATG3ACACAG4ACG3] comprised of four G-tracts with the third one consisting of four guanines that are intervened with non-G streches of different lengths. A single intramolecular antiparallel (3+1) G-quadruplex exhibits three stacked G-quartets connected with propeller, diagonal and edgewise loops of different lengths. The propeller and edgewise loops are well structured, whereas the longer diagonal loop is more flexible. To the best of our knowledge, this is the first high-resolution G-quadruplex structure where all of the three main loop types are present. PMID:22532609

  20. Digital phase-lock loop

    NASA Technical Reports Server (NTRS)

    Thomas, Jr., Jess B. (Inventor)

    1991-01-01

    An improved digital phase lock loop incorporates several distinctive features that attain better performance at high loop gain and better phase accuracy. These features include: phase feedback to a number-controlled oscillator in addition to phase rate; analytical tracking of phase (both integer and fractional cycles); an amplitude-insensitive phase extractor; a more accurate method for extracting measured phase; a method for changing loop gain during a track without loss of lock; and a method for avoiding loss of sampled data during computation delay, while maintaining excellent tracking performance. The advantages of using phase and phase-rate feedback are demonstrated by comparing performance with that of rate-only feedback. Extraction of phase by the method of modeling provides accurate phase measurements even when the number-controlled oscillator phase is discontinuously updated.

  1. Criteria for saturated magnetization loop

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

    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 Fe3O4 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.

  2. Waves in Solar Coronal Loops

    NASA Astrophysics Data System (ADS)

    Wang, T. J.

    2016-02-01

    The corona is visible in the optical band only during a total solar eclipse or with a coronagraph. Coronal loops are believed to be plasma-filled closed magnetic flux anchored in the photosphere. Based on the temperature regime, they are generally classified into cool, warm, and hot loops. The magnetized coronal structures support propagation of various types of magnetohydrodynamics (MHD) waves. This chapter reviews the recent progress made in studies based on observations of four types of wave phenomena mainly occurring in coronal loops of active regions, including: flare-excited slow-mode waves; impulsively excited kink-mode waves; propagating slow magnetoacoustic waves; and ubiquitous propagating kink (Alfvénic) waves. This review not only comprehensively discusses these waves and coronal seismology but also topics that are newly emerging or hotly debated in order to provide the reader with useful guidance on further studies.

  3. Catalytic Combustion for Ultra-Low NOx Hydrogen Turbines

    SciTech Connect

    Etemad, Shahrokh; Baird, Benjamin; Alavandi, Sandeep

    2011-06-30

    Precision Combustion, Inc., (PCI) in close collaboration with Solar Turbines, Incorporated, has developed and demonstrated a combustion system for hydrogen fueled turbines that reduces NOx to low single digit level while maintaining or improving current levels of efficiency and eliminating emissions of carbon dioxide. Full scale Rich Catalytic Hydrogen (RCH1) injector was developed and successfully tested at Solar Turbines, Incorporated high pressure test facility demonstrating low single digit NOx emissions for hydrogen fuel in the range of 2200F-2750F. This development work was based on initial subscale development for faster turnaround and reduced cost. Subscale testing provided promising results for 42% and 52% H2 with NOx emissions of less than 2 ppm with improved flame stability. In addition, catalytic reactor element testing for substrate oxidation, thermal cyclic injector testing to simulate start-stop operation in a gas turbine environment, and steady state 15 atm. operation testing were performed successfully. The testing demonstrated stable and robust catalytic element component life for gas turbine conditions. The benefit of the catalytic hydrogen combustor technology includes capability of delivering near-zero NOx without costly post-combustion controls and without requirement for added sulfur control. In addition, reduced acoustics increase gas turbine component life. These advantages advances Department of Energy (DOE’s) objectives for achievement of low single digit NOx emissions, improvement in efficiency vs. postcombustion controls, fuel flexibility, a significant net reduction in Integrated Gasification Combined Cycle (IGCC) system net capital and operating costs, and a route to commercialization across the power generation field from micro turbines to industrial and utility turbines.

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

    PubMed Central

    Egli, Martin; Pattanayek, Rekha; Sheehan, Jonathan H.; Xu, Yao; Mori, Tetsuya; Smith, Jarrod A.; Johnson, Carl H.

    2013-01-01

    The Synechococcus elongatus KaiA, KaiB and KaiC proteins in the presence of ATP generate a post-translational oscillator (PTO) that runs in a temperature-compensated manner with a period of 24 hours. 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 the present time. 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. MD 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. 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. PMID:23351065

  5. Generalized flexibility-rigidity index

    NASA Astrophysics Data System (ADS)

    Nguyen, Duc Duy; Xia, Kelin; Wei, Guo-Wei

    2016-06-01

    Flexibility-rigidity index (FRI) has been developed as a robust, accurate, and efficient method for macromolecular thermal fluctuation analysis and B-factor prediction. The performance of FRI depends on its formulations of rigidity index and flexibility index. In this work, we introduce alternative rigidity and flexibility formulations. The structure of the classic Gaussian surface is utilized to construct a new type of rigidity index, which leads to a new class of rigidity densities with the classic Gaussian surface as a special case. Additionally, we introduce a new type of flexibility index based on the domain indicator property of normalized rigidity density. These generalized FRI (gFRI) methods have been extensively validated by the B-factor predictions of 364 proteins. Significantly outperforming the classic Gaussian network model, gFRI is a new generation of methodologies for accurate, robust, and efficient analysis of protein flexibility and fluctuation. Finally, gFRI based molecular surface generation and flexibility visualization are demonstrated.

  6. Flexible transformation plasmonics using graphene.

    PubMed

    Lu, Wei Bing; Zhu, Wei; Xu, Hong Ju; Ni, Zhen Hua; Dong, Zheng Gao; Cui, Tie Jun

    2013-05-01

    The flexible control of surface plasmon polaritons (SPPs) is important and intriguing due to its wide application in novel plasmonic devices. Transformation optics (TO) offers the capability either to confine the SPP propagation on rigid curved/uneven surfaces, or to control the flow of SPPs on planar surfaces. However, TO has not permitted us to confine, manipulate, and control SPP waves on flexible curved surfaces. Here, we propose to confine and freely control flexible SPPs using TO and graphene. We show that SPP waves can be naturally confined and propagate on curved or uneven graphene surfaces with little bending and radiation losses, and the confined SPPs are further manipulated and controlled using TO. Flexible plasmonic devices are presented, including the bending waveguides, wave splitter, and Luneburg lens on curved surfaces. Together with the intrinsic flexibility, graphene can be served as a good platform for flexible transformation plasmonics. PMID:23669904

  7. Catalytically active lead(ii)-imidazolium coordination assemblies with diversified lead(ii) coordination geometries.

    PubMed

    Naga Babu, Chatla; Suresh, Paladugu; Srinivas, Katam; Sathyanarayana, Arruri; Sampath, Natarajan; Prabusankar, Ganesan

    2016-05-10

    Five Pb(ii)-imidazolium carboxylate coordination assemblies with novel structural motifs were derived from the reaction between the corresponding flexible, semi flexible or rigid imidazolium carboxylic acid ligands and lead nitrate. The imidazolium linker present in these molecules likely plays a triple role such as the counter ion to balance the metal charge, the ligand being an integral part of the final product and the catalyst facilitating carbon-carbon bond formation reaction. These lead-imidazolium coordination assemblies exhibit, variable chemical and thermal stabilities, as well as catalytic activity. These newly prepared catalysts are highly active towards benzoin condensation reactions with good functional group tolerance. PMID:27093629

  8. Flexible Zirconium Metal-Organic Frameworks as Bioinspired Switchable Catalysts.

    PubMed

    Yuan, Shuai; Zou, Lanfang; Li, Haixia; Chen, Ying-Pin; Qin, Junsheng; Zhang, Qiang; Lu, Weigang; Hall, Michael B; Zhou, Hong-Cai

    2016-08-26

    Flexible metal-organic frameworks (MOFs) are highly desirable in host-guest chemistry owing to their almost unlimited structural/functional diversities and stimuli-responsive pore architectures. Herein, we designed a flexible Zr-MOF system, namely PCN-700 series, for the realization of switchable catalysis in cycloaddition reactions of CO2 with epoxides. Their breathing behaviors were studied by successive single-crystal X-ray diffraction analyses. The breathing amplitudes of the PCN-700 series were modulated through pre-functionalization of organic linkers and post-synthetic linker installation. Experiments and molecular simulations confirm that the catalytic activities of the PCN-700 series can be switched on and off upon reversible structural transformation, which is reminiscent of sophisticated biological systems such as allosteric enzymes. PMID:27346468

  9. Wireless Flexible Smart Bandage for Continuous Monitoring of Wound Oxygenation.

    PubMed

    Mostafalu, Pooria; Lenk, William; Dokmeci, Mehmet R; Ziaie, Babak; Khademhosseini, Ali; Sonkusale, Sameer R

    2015-10-01

    Current methods in treating chronic wounds have had limited success in large part due to the open loop nature of the treatment. We have created a localized 3D-printed smart wound dressing platform that will allow for real-time data acquisition of oxygen concentration, which is an important indicator of wound healing. This will serve as the first leg of a feedback loop for a fully optimized treatment mechanism tailored to the individual patient. A flexible oxygen sensor was designed and fabricated with high sensitivity and linear current output. With a series of off-the-shelf electronic components including a programmable-gain analog front-end, a microcontroller and wireless radio, an integrated electronic system with data readout and wireless transmission capabilities was assembled in a compact package. Using an elastomeric material, a bandage with exceptional flexibility and tensile strength was 3D-printed. The bandage contains cavities for both the oxygen sensor and the electronic systems, with contacts interfacing the two systems. Our integrated, flexible platform is the first step toward providing a self-operating, highly optimized remote therapy for chronic wounds. PMID:26552096

  10. Flexible retinal electrode array

    DOEpatents

    Okandan, Murat; Wessendorf, Kurt O.; Christenson, Todd R.

    2006-10-24

    An electrode array which has applications for neural stimulation and sensing. The electrode array can include a large number of electrodes each of which is flexibly attached to a common substrate using a plurality of springs to allow the electrodes to move independently. The electrode array can be formed from a combination of bulk and surface micromachining, with electrode tips that can include an electroplated metal (e.g. platinum, iridium, gold or titanium) or a metal oxide (e.g. iridium oxide) for biocompatibility. The electrode array can be used to form a part of a neural prosthesis, and is particularly well adapted for use in an implantable retinal prosthesis where the electrodes can be tailored to provide a uniform gentle contact pressure with optional sensing of this contact pressure at one or more of the electrodes.

  11. Flexible weapons architecture design

    NASA Astrophysics Data System (ADS)

    Pyant, William C., III

    Present day air-delivered weapons are of a closed architecture, with little to no ability to tailor the weapon for the individual engagement. The closed architectures require weaponeers to make the target fit the weapon instead of fitting the individual weapons to a target. The concept of a flexible weapons aims to modularize weapons design using an open architecture shell into which different modules are inserted to achieve the desired target fractional damage while reducing cost and civilian casualties. This thesis shows that the architecture design factors of damage mechanism, fusing, weapons weight, guidance, and propulsion are significant in enhancing weapon performance objectives, and would benefit from modularization. Additionally, this thesis constructs an algorithm that can be used to design a weapon set for a particular target class based on these modular components.

  12. Flexible cloth seal assembly

    DOEpatents

    Bagepalli, Bharat Sampathkumar; Taura, Joseph Charles; Aksit, Mahmut Faruk; Demiroglu, Mehmet; Predmore, Daniel Ross

    1999-01-01

    A seal assembly having a flexible cloth seal which includes a shim assemblage surrounded by a cloth assemblage. A first tubular end portion, such as a gas turbine combustor, includes a longitudinal axis and has smooth and spaced-apart first and second surface portions defining a notch therebetween which is wider at its top than at its bottom and which extends outward from the axis. The second surface portion is outside curved, and a first edge of the cloth seal is positioned in the bottom of the notch. A second tubular end portion, such as a first stage nozzle, is located near, spaced apart from, and coaxially aligned with, the first tubular end portion. The second tubular end portion has a smooth third surface portion which surrounds at least a portion of the first tubular end portion and which is contacted by the cloth seal.

  13. Damped flexible seal

    DOEpatents

    DuBois, Neil J.; Amaral, Antonio M.

    1992-10-27

    A damped flexible seal assembly for a torpedo isolates the tailcone thereof rom vibrational energy present in the drive shaft assembly. A pair of outside flanges, each of which include an inwardly facing groove and an O-ring constrained therein, provide a watertight seal against the outer non-rotating surface of the drive shaft assembly. An inside flange includes an outwardly-facing groove and an O-ring constrained therein, and provides a watertight seal against the inner surface of the tail cone. Two cast-in-place elastomeric seals provide a watertight seal between the flanges and further provide a damping barrier between the outside flanges and the inside flanges for damping vibrational energy present in the drive shaft assembly before the energy can reach the tailcone through the seal assembly.

  14. Flexible cloth seal assembly

    DOEpatents

    Bagepalli, B.S.; Taura, J.C.; Aksit, M.F.; Demiroglu, M.; Predmore, D.R.

    1999-06-29

    A seal assembly is described having a flexible cloth seal which includes a shim assemblage surrounded by a cloth assemblage. A first tubular end portion, such as a gas turbine combustor, includes a longitudinal axis and has smooth and spaced-apart first and second surface portions defining a notch there between which is wider at its top than at its bottom and which extends outward from the axis. The second surface portion is outside curved, and a first edge of the cloth seal is positioned in the bottom of the notch. A second tubular end portion, such as a first stage nozzle, is located near, spaced apart from, and coaxially aligned with, the first tubular end portion. The second tubular end portion has a smooth third surface portion which surrounds at least a portion of the first tubular end portion and which is contacted by the cloth seal. 7 figs.

  15. Flexible swivel connection

    DOEpatents

    Hoh, J.C.

    1985-02-19

    A flexible swivel boot connector for connecting a first boot shield section to a second boot shield section, both first and second boot sections having openings therethrough, the second boot section having at least two adjacent accordian folds at the end having the opening, the second boot section being positioned through the opening of the first boot section such that a first of the accordian folds is within the first boot section and a second of the accordian folds is outside of the first boot, includes first and second annular discs, the first disc being positioned within and across the first accordian fold, the second disc being positioned within and across the second accordian fold, such that the first boot section is moveably and rigidly connected between the first and second accordian folds of the second boot section.

  16. Conformational flexibility of aspartame.

    PubMed

    Toniolo, Claudio; Temussi, Pierandrea

    2016-05-01

    L-Aspartyl-L-phenylalanine methyl ester, better known as aspartame, is not only one of the most used artificial sweeteners, but also a very interesting molecule with respect to the correlation between molecular structure and taste. The extreme conformational flexibility of this dipeptide posed a huge difficulty when researchers tried to use it as a lead compound to design new sweeteners. In particular, it was difficult to take advantage of its molecular model as a mold to infer the shape of the, then unknown, active site of the sweet taste receptor. Here, we follow the story of the 3D structural aspects of aspartame from early conformational studies to recent docking into homology models of the receptor. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 376-384, 2016. PMID:27038223

  17. All digital pulsewidth control loop

    NASA Astrophysics Data System (ADS)

    Huang, Hong-Yi; Jan, Shiun-Dian; Pu, Ruei-Iun

    2013-03-01

    This work presents an all-digital pulsewidth control loop (ADPWCL). The proposed system accepts a wide range of input duty cycles and performs a fast correction to the target output pulsewidth. An all-digital delay-locked loop (DLL) with fast locking time using a simplified time to digital converter and a new differential two-step delay element is proposed. The area of the delay element is much smaller than that in conventional designs, while having the same delay range. A test chip is verified in a 0.18-µm CMOS process. The measured duty cycle ranges from 4% to 98% with 7-bit resolution.

  18. Loop quantum cosmology: an overview

    NASA Astrophysics Data System (ADS)

    Ashtekar, Abhay

    2009-04-01

    A brief overview of loop quantum cosmology of homogeneous isotropic models is presented with emphasis on the origin of and subtleties associated with the resolution of big bang and big crunch singularities. These results bear out the remarkable intuition that John Wheeler had. Discussion is organized at two levels. The the main text provides a bird’s eye view of the subject that should be accessible to non-experts. Appendices address conceptual and technical issues that are often raised by experts in loop quantum gravity and string theory.

  19. Modeling of compact loop antennas

    NASA Astrophysics Data System (ADS)

    Baity, F. W.

    1987-09-01

    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 sub-tuned RDL antennas. Calculations using the model have been compared with measurements on full-scale mock-ups of RDL 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 the Compact Ignition Tokamak (CIT).

  20. Many Ways to Loop DNA

    PubMed Central

    Griffith, Jack D.

    2013-01-01

    In the 1960s, I developed methods for directly visualizing DNA and DNA-protein complexes using an electron microscope. This made it possible to examine the shape of DNA and to visualize proteins as they fold and loop DNA. Early applications included the first visualization of true nucleosomes and linkers and the demonstration that repeating tracts of adenines can cause a curvature in DNA. The binding of DNA repair proteins, including p53 and BRCA2, has been visualized at three- and four-way junctions in DNA. The trombone model of DNA replication was directly verified, and the looping of DNA at telomeres was discovered. PMID:24005675

  1. A remarkably stable kissing-loop interaction defines substrate recognition by the Neurospora Varkud Satellite ribozyme

    PubMed Central

    Bouchard, Patricia; Legault, Pascale

    2014-01-01

    Kissing loops are tertiary structure elements that often play key roles in functional RNAs. In the Neurospora VS ribozyme, a kissing-loop interaction between the stem–loop I (SLI) substrate and stem–loop V (SLV) of the catalytic domain is known to play an important role in substrate recognition. In addition, this I/V kissing-loop interaction is associated with a helix shift in SLI that activates the substrate for catalysis. To better understand the role of this kissing-loop interaction in substrate recognition and activation by the VS ribozyme, we performed a thermodynamic characterization by isothermal titration calorimetry using isolated SLI and SLV stem–loops. We demonstrate that preshifted SLI variants have higher affinity for SLV than shiftable SLI variants, with an energetic cost of 1.8–3 kcal/mol for the helix shift in SLI. The affinity of the preshifted SLI for SLV is remarkably high, the interaction being more stable by 7–8 kcal/mol than predicted for a comparable duplex containing three Watson–Crick base pairs. The structural basis of this remarkable stability is discussed in light of previous NMR studies. Comparative thermodynamic studies reveal that kissing-loop complexes containing 6–7 Watson–Crick base pairs are as stable as predicted from comparable RNA duplexes; however, those with 2–3 Watson–Crick base pairs are more stable than predicted. Interestingly, the stability of SLI/ribozyme complexes is similar to that of SLI/SLV complexes. Thus, the I/V kissing loop interaction represents the predominant energetic contribution to substrate recognition by the trans-cleaving VS ribozyme. PMID:25051972

  2. Force fluctuation in a semiflexible loop

    NASA Astrophysics Data System (ADS)

    Waters, James; Kim, Harold; Harold Kim Team

    DNA-binding proteins can regulate genetic expression by holding two sites in close proximity, forming a closed loop. Such complexes may require strong bending of DNA segments on the order of one persistence length or less. Both this elastic bending and the thermal fluctuations of the DNA molecule are necessary to describe the resulting behavior. To explore this problem, we consider a discrete model of a wormlike chain, kept in the fixed extension ensemble. By using a novel method to sample conformations in both position and momentum space, we can obtain a distribution of constraint forces as a function of chain length, extension, and flexibility. Our coarse-grained model allows us to explore the space of these parameters more efficiently than a detailed molecular dynamics approach. We find that increasing contour length decreases average force by relieving bending stress, but that the additional freedom allows fluctuations in the constraint force to increase. This implies that the probability of large forces may go up even as the mean goes down, impacting the lifetime of such bound states in a way unforeseen by purely equilibrium methods.

  3. Catalytic combustion of residual fuels

    NASA Technical Reports Server (NTRS)

    Bulzan, D. L.; Tacina, R. R.

    1981-01-01

    A noble metal catalytic reactor was tested using two grades of petroleum derived residual fuels at specified inlet air temperatures, pressures, and reference velocities. Combustion efficiencies greater than 99.5 percent were obtained. Steady state operation of the catalytic reactor required inlet air temperatures of at least 800 K. At lower inlet air temperatures, upstream burning in the premixing zone occurred which was probably caused by fuel deposition and accumulation on the premixing zone walls. Increasing the inlet air temperature prevented this occurrence. Both residual fuels contained about 0.5 percent nitrogen by weight. NO sub x emissions ranged from 50 to 110 ppm by volume at 15 percent excess O2. Conversion of fuel-bound nitrogen to NO sub x ranged from 25 to 50 percent.

  4. Vapor Phase Catalytic Ammonia Reduction

    NASA Technical Reports Server (NTRS)

    Flynn, Michael T.; Harper, Lynn D. (Technical Monitor)

    1994-01-01

    This paper discusses the development of a Vapor Phase Catalytic Ammonia Reduction (VPCAR) teststand and the results of an experimental program designed to evaluate the potential of the technology as a water purification process. In the experimental program the technology is evaluated based upon product water purity, water recovery rate, and power consumption. The experimental work demonstrates that the technology produces high purity product water and attains high water recovery rates at a relatively high specific power consumption. The experimental program was conducted in 3 phases. In phase I an Igepon(TM) soap and water mixture was used to evaluate the performance of an innovative Wiped-Film Rotating-Disk evaporator and associated demister. In phase II a phenol-water solution was used to evaluate the performance of the high temperature catalytic oxidation reactor. In phase III a urine analog was used to evaluate the performance of the combined distillation/oxidation functions of the processor.

  5. Catalytic asymmetric alkylation of acylsilanes.

    PubMed

    Rong, Jiawei; Oost, Rik; Desmarchelier, Alaric; Minnaard, Adriaan J; Harutyunyan, Syuzanna R

    2015-03-01

    The highly enantioselective addition of Grignard reagents to acylsilanes is catalyzed by copper diphosphine complexes. This transformation affords α-silylated tertiary alcohols in up to 97% yield and 98:2 enantiomeric ratio. The competing Meerwein-Ponndorf-Verley reduction is suppressed by the use of a mixture of Lewis acid additives. The chiral catalyst can be recovered as a copper complex and used repeatedly without any loss of catalytic activity. PMID:25403641

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

    SciTech Connect

    Cai, Z.; SantaLucia, J. Jr.; Tinoco, I. Jr.

    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.

  7. Thermodynamics of catalytic nanoparticle morphology

    NASA Astrophysics Data System (ADS)

    Zwolak, Michael; Sharma, Renu; Lin, Pin Ann

    Metallic nanoparticles are an important class of industrial catalysts. The variability of their properties and the environment in which they act, from their chemical nature & surface modification to their dispersion and support, allows their performance to be optimized for many chemical processes useful in, e.g., energy applications and other areas. Their large surface area to volume ratio, as well as varying sizes and faceting, in particular, makes them an efficient source for catalytically active sites. These characteristics of nanoparticles - i.e., their morphology - can often display intriguing behavior as a catalytic process progresses. We develop a thermodynamic model of nanoparticle morphology, one that captures the competition of surface energy with other interactions, to predict structural changes during catalytic processes. Comparing the model to environmental transmission electron microscope images of nickel nanoparticles during carbon nanotube (and other product) growth demonstrates that nickel deformation in response to the nanotube growth is due to a favorable interaction with carbon. Moreover, this deformation is halted due to insufficient volume of the particles. We will discuss the factors that influence morphology and also how the model can be used to extract interaction strengths from experimental observations.

  8. Evolved Streptavidin Mutants Reveal Key Role of Loop Residue in High-affinity Binding

    SciTech Connect

    M Magalhaes; C Melo Czekster; R Guan; V Malashkevich; S Almo; M Levy

    2011-12-31

    We have performed a detailed analysis of streptavidin variants with altered specificity towards desthiobiotin. In addition to changes in key residues which widen the ligand binding pocket and accommodate the more structurally flexible desthiobiotin, the data revealed the role of a key, non-active site mutation at the base of the flexible loop (S52G) which slows dissociation of this ligand by approximately sevenfold. Our data suggest that this mutation results in the loss of a stabilizing contact which keeps this loop open and accessible in the absence of ligand. When this mutation was introduced into the wild-type protein, destabilization of the opened loop conferred a {approx}10-fold decrease in both the on-rate and off-rate for the ligand biotin-4-fluoroscein. A similar effect was observed when this mutation was added to a monomeric form of this protein. Our results provide key insight into the role of the streptavidin flexible loop in ligand binding and maintaining high affinity interactions.

  9. Thumb-loops up for catalysis: a structure/function investigation of a functional loop movement in a GH11 xylanase

    PubMed Central

    Paës, Gabriel; Cortés, Juan; Siméon, Thierry; O'Donohue, Michael J.; Tran, Vinh

    2012-01-01

    Dynamics is a key feature of enzyme catalysis. Unfortunately, current experimental and computational techniques do not yet provide a comprehensive understanding and description of functional macromolecular motions. In this work, we have extended a novel computational technique, which combines molecular modeling methods and robotics algorithms, to investigate functional motions of protein loops. This new approach has been applied to study the functional importance of the so-called thumb-loop in the glycoside hydrolase family 11 xylanase from Thermobacillus xylanilyticus (Tx-xyl). The results obtained provide new insight into the role of the loop in the glycosylation/deglycosylation catalytic cycle, and underline the key importance of the nature of the residue located at the tip of the thumb-loop. The effect of mutations predicted in silico has been validated by in vitro site-directed mutagenesis experiments. Overall, we propose a comprehensive model of Tx-xyl catalysis in terms of substrate and product dynamics by identifying the action of the thumb-loop motion during catalysis. PMID:24688637

  10. Structures of the CDK12/CycK complex with AMP-PNP reveal a flexible C-terminal kinase extension important for ATP binding

    PubMed Central

    Dixon-Clarke, Sarah E.; Elkins, Jonathan M.; Cheng, S.-W. Grace; Morin, Gregg B.; Bullock, Alex N.

    2015-01-01

    Cyclin-dependent kinase 12 (CDK12) promotes transcriptional elongation by phosphorylation of the RNA polymerase II C-terminal domain (CTD). Structure-function studies show that this activity is dependent on a C-terminal kinase extension, as well as the binding of cyclin K (CycK). To better define these interactions we determined the crystal structure of the human CDK12/CycK complex with and without the kinase extension in the presence of AMP-PNP. The structures revealed novel features for a CDK, including a large β4-β5 loop insertion that contributes to the N-lobe interaction with the cyclin. We also observed two different conformations of the C-terminal kinase extension that effectively open and close the ATP pocket. Most notably, bound AMP-PNP was only observed when trapped in the closed state. Truncation of this C-terminal structure also diminished AMP-PNP binding, as well as the catalytic activity of the CDK12/CycK complex. Further kinetic measurements showed that the full length CDK12/CycK complex was significantly more active than the two crystallised constructs suggesting a critical role for additional domains. Overall, these results demonstrate the intrinsic flexibility of the C-terminal extension in CDK12 and highlight its importance for both ATP binding and kinase activity. PMID:26597175

  11. Closing the Loop with Exercises

    ERIC Educational Resources Information Center

    Altizer, Andy

    2008-01-01

    Conducting exercises provides a critical bridge between the theory of an Emergency Action Plan and its effective implementation. When conducted properly, exercises can fill the gap between training and after-action review to close the preparedness loop--before an actual emergency occurs. Often exercises are planned and conducted on campus based on…

  12. Manchester transition tracking loop (MTTL)

    NASA Technical Reports Server (NTRS)

    Cellier, A.; Ma, L. N.; Huey, D. C.

    1977-01-01

    In new tracking loop, separate phase detection algorithm is incorporated for acquisition; programmed acquisition-to-track sequence includes automatic bandwidth switching. Additionally, system has very effective phase detection signal-to-noise ratio and can operate at any rate by changing master clock frequency. All system parameters remain constant.

  13. Bimodal loop-gap resonator

    NASA Astrophysics Data System (ADS)

    Piasecki, W.; Froncisz, W.; Hyde, James S.

    1996-05-01

    A bimodal loop-gap resonator for use in electron paramagnetic resonance (EPR) spectroscopy at S band is described. It consists of two identical one-loop-one-gap resonators in coaxial juxtaposition. In one mode, the currents in the two loops are parallel and in the other antiparallel. By introducing additional capacitors between the loops, the frequencies of the two modes can be made to coincide. Details are given concerning variable coupling to each mode, tuning of the resonant frequency of one mode to that of the other, and adjustment of the isolation between modes. An equivalent circuit is given and network analysis carried out both experimentally and theoretically. EPR applications are described including (a) probing of the field distributions with DPPH, (b) continuous wave (cw) EPR with a spin-label line sample, (c) cw electron-electron double resonance (ELDOR), (d) modulation of saturation, and (e) saturation-recovery (SR) EPR. Bloch induction experiments can be performed when the sample extends half way through the structure, but microwave signals induced by Mx and My components of magnetization cancel when it extends completely through. This latter situation is particularly favorable for SR, modulation of saturation, and ELDOR experiments, which depend on observing Mz indirectly using a second weak observing microwave source.

  14. Sensor enabled closed-loop bending control of soft beams

    NASA Astrophysics Data System (ADS)

    Case, Jennifer C.; White, Edward L.; Kramer, Rebecca K.

    2016-04-01

    Control of soft-bodied systems is challenging, as the absence of rigidity typically implies distributed deformations and infinite degrees-of-freedom. In this paper, we demonstrate closed-loop control of three elastomer beams that vary in bending stiffness. The most stiff beam is comprised of a single prismatic structure made from a single elastomer. In the next beam, increased flexibility is introduced via an indentation in the elastomer, forming a joint. The most flexible beam uses a softer elastomer in the joint section, along with an indentation. An antagonistic pair of actuators bend the joint while a pair of liquid-metal-embedded strain sensors provide angle feedback to a control loop. We were able to achieve control of the system with a proportional-integral-derivative control algorithm. The procedure we demonstrate in this work is not dependent on actuator and sensor choice and could be applied to to other hardware systems, as well as more complex multi-joint robotic structures in the future.

  15. Closed Loop Software Control of the MIDEX Power System

    NASA Technical Reports Server (NTRS)

    Castell, Karen; Hernandez-Pellerano, Amri; Wismer, Margaret

    1998-01-01

    The Microwave Anisotropy Probe (MAP) is a follow-on to the Differential Microwave Radiometer (DMR) instrument on the Cosmic Background Explorer (COBE) spacecraft. The design and analysis of the MAP attitude control system (ACS) have been refined since work previously reported. The full spacecraft and instrument flexible model was developed in NASTRAN, and the resulting flexible modes were plotted and reduced with the Modal Significance Analysis Package (MSAP). The reduced-order model was used to perform the linear stability analysis for each control mode, the results of which are presented in this paper. Although MAP is going to a relatively disturbance-free Lissajous orbit around the Earth-Sun L2 Lagrange point, a detailed disturbance-torque analysis is required because there are only a small number of opportunities for momentum unloading each year. Environmental torques, including solar pressure at L2, and aerodynamic and gravity gradient during phasing-loop orbits, were calculated and simulated. A simple model of fuel slosh was derived to model its effect on the motion of the spacecraft. In addition, a thruster mode linear impulse controller was developed to meet the accuracy requirements of the phasing loop burns. A dynamic attitude error limiter was added to improve the performance of the ACS during large attitude slews. The result of this analysis is a stable ACS subsystem that meets all of the mission's requirements.

  16. Boundary feedback stabilisation of a flexible robotic manipulator with constraint

    NASA Astrophysics Data System (ADS)

    He, Wei; Sun, Chen

    2016-03-01

    In this paper, the flexible robotic manipulator is modelled as a distributed parameter system, represented by a group of partial differential equations and ordinary differential equations. Control is designed at the boundary of the robotic manipulator based on integral-barrier Lyapunov function to suppress the vibration of the elastic deflection and track the desired angular position. With the proposed boundary control, the manipulator can be driven to the desired set-point with angular position and elastic deflection stay under the former setting constraint. Uniformed boundedness of the closed-loop system under the unknown time-varying disturbance is achieved. Stability analysis of the closed-loop system is given by employing the Lyapunov stability theory. Simulation results illustrate the effectiveness of the proposed boundary controller for ensuring output constraint and suppressing vibrations.

  17. Lac Repressor Mediated DNA Looping: Monte Carlo Simulation of Constrained DNA Molecules Complemented with Current Experimental Results

    PubMed Central

    Biton, Yoav Y.; Kumar, Sandip; Dunlap, David; Swigon, David

    2014-01-01

    Tethered particle motion (TPM) experiments can be used to detect time-resolved loop formation in a single DNA molecule by measuring changes in the length of a DNA tether. Interpretation of such experiments is greatly aided by computer simulations of DNA looping which allow one to analyze the structure of the looped DNA and estimate DNA-protein binding constants specific for the loop formation process. We here present a new Monte Carlo scheme for accurate simulation of DNA configurations subject to geometric constraints and apply this method to Lac repressor mediated DNA looping, comparing the simulation results with new experimental data obtained by the TPM technique. Our simulations, taking into account the details of attachment of DNA ends and fluctuations of the looped subsegment of the DNA, reveal the origin of the double-peaked distribution of RMS values observed by TPM experiments by showing that the average RMS value for anti-parallel loop types is smaller than that of parallel loop types. The simulations also reveal that the looping probabilities for the anti-parallel loop types are significantly higher than those of the parallel loop types, even for loops of length 600 and 900 base pairs, and that the correct proportion between the heights of the peaks in the distribution can only be attained when loops with flexible Lac repressor conformation are taken into account. Comparison of the in silico and in vitro results yields estimates for the dissociation constants characterizing the binding affinity between O1 and Oid DNA operators and the dimeric arms of the Lac repressor. PMID:24800809

  18. Teacher Flexibility in Mathematical Discussion

    ERIC Educational Resources Information Center

    Leikin, Roza; Dinur, Sariga

    2007-01-01

    The significance of discussion in mathematics classes has been prominently debated in the research literature. Different studies have stressed the importance of teacher flexibility in orchestrating the discussion. We introduce an operational definition of teacher flexibility. In a case study with one secondary-school mathematics teacher, we…

  19. Determinants of ligand binding and catalytic activity in the myelin enzyme 2',3'-cyclic nucleotide 3'-phosphodiesterase.

    PubMed

    Raasakka, Arne; Myllykoski, Matti; Laulumaa, Saara; Lehtimäki, Mari; Härtlein, Michael; Moulin, Martine; Kursula, Inari; Kursula, Petri

    2015-01-01

    2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) is an enzyme highly abundant in the central nervous system myelin of terrestrial vertebrates. The catalytic domain of CNPase belongs to the 2H phosphoesterase superfamily and catalyzes the hydrolysis of nucleoside 2',3'-cyclic monophosphates to nucleoside 2'-monophosphates. The detailed reaction mechanism and the essential catalytic amino acids involved have been described earlier, but the roles of many amino acids in the vicinity of the active site have remained unknown. Here, several CNPase catalytic domain mutants were studied using enzyme kinetics assays, thermal stability experiments, and X-ray crystallography. Additionally, the crystal structure of a perdeuterated CNPase catalytic domain was refined at atomic resolution to obtain a detailed view of the active site and the catalytic mechanism. The results specify determinants of ligand binding and novel essential residues required for CNPase catalysis. For example, the aromatic side chains of Phe235 and Tyr168 are crucial for substrate binding, and Arg307 may affect active site electrostatics and regulate loop dynamics. The β5-α7 loop, unique for CNPase in the 2H phosphoesterase family, appears to have various functions in the CNPase reaction mechanism, from coordinating the nucleophilic water molecule to providing a binding pocket for the product and being involved in product release. PMID:26563764

  20. Dynamic modelling and analysis of a magnetically suspended flexible rotor. M.S. Thesis, 1988

    NASA Technical Reports Server (NTRS)

    Mccallum, Duncan C.

    1991-01-01

    A 12-state lumped-element model is presented for a flexible rotor supported by two attractive force electromagnetic journal bearings. The rotor is modeled as a rigid disk with radial mass unbalance mounted on a flexible, massless shaft with internal damping (Jeffcott rotor). The disk is offset axially from the midspan of the shaft. Bearing dynamics in each radial direction are modeled as a parallel combination of a negative (unstable) spring and a linear current-to-force actuator. The model includes translation and rotation of the rigid mass and the first and second bending models of the flexible shaft, and it simultaneously includes internal shaft damping, gyroscopic effects, and the unstable nature of the attractive force magnetic bearings. The model is used to analyze the dependence of the system transmission zeros and open-loop poles on system parameters. The dominant open-loop poles occur in stable/unstable pairs with bandwidth dependent on the ratios of bearing (unstable) stiffnesses to rotor mass and damping dependent on the shaft spin rate. The zeros occur in complex conjugate pairs with bandwidth dependent on the ratios of shaft stiffness to rotor mass and damping dependent on the shaft spin rate. Some of the transmission zeros are non-minimum phase when the spin rate exceeds the shaft critical speed. The transmission zeros and open-loop poles impact the design of magnetic bearing control systems. The minimum loop cross-over frequency of the closed-loop system is the speed of the unstable open-loop poles. For the supercritical shaft spin rates, the presence of non-minimum phase zeros limits the distribution rejection achievable at frequencies near or above the shaft critical speed. Since non-minimum phase transmission zeros can only be changed by changing the system inputs and/or outputs, closed-loop performance is limited for supercritical spin rates unless additional force or torque actuators are added.

  1. Experimental Study of Non-Resonant Self Circulating Heat Transfer Loop Used in Thermoacoustic-Stirling Engines

    NASA Astrophysics Data System (ADS)

    Gao, B.; Luo, E. C.; Dai, W.; Chen, Y. Y.; Hu, J. Y.

    2010-04-01

    A novel heat transfer loop for thermoacoustic-Stirling engines which could substitute for a traditional heat exchanger was developed. This new heat transfer loop uses a pair of check valves to transform oscillating flow into steady flow that allows the oscillating flow system's own working gas to go through a physically remote high-temperature or cold-temperature heat source. Since the early principle experiment has achieved success, this paper explores the real operating performance of this heat transfer loop by coupling with thermoacoustic-Stirling engine. Furthermore, a new type water-cooled heat exchanger was developed in this paper to deduce the extra acoustic power dissipation. In addition, the influence of two kinds of check valves the heat transfer loop was discussed in this paper. The loop with 0.1 mm valve disc thickness shows that the heat transfer capacity is higher than the traditional heat exchanger. Our experiments have demonstrated its feasibility and flexibility for practical applications.

  2. Phosphorylation of Leukotriene C4 Synthase at Serine 36 Impairs Catalytic Activity.

    PubMed

    Ahmad, Shabbir; Ytterberg, A Jimmy; Thulasingam, Madhuranayaki; Tholander, Fredrik; Bergman, Tomas; Zubarev, Roman; Wetterholm, Anders; Rinaldo-Matthis, Agnes; Haeggström, Jesper Z

    2016-08-26

    Leukotriene C4 synthase (LTC4S) catalyzes the formation of the proinflammatory lipid mediator leukotriene C4 (LTC4). LTC4 is the parent molecule of the cysteinyl leukotrienes, which are recognized for their pathogenic role in asthma and allergic diseases. Cellular LTC4S activity is suppressed by PKC-mediated phosphorylation, and recently a downstream p70S6k was shown to play an important role in this process. Here, we identified Ser(36) as the major p70S6k phosphorylation site, along with a low frequency site at Thr(40), using an in vitro phosphorylation assay combined with mass spectrometry. The functional consequences of p70S6k phosphorylation were tested with the phosphomimetic mutant S36E, which displayed only about 20% (20 μmol/min/mg) of the activity of WT enzyme (95 μmol/min/mg), whereas the enzyme activity of T40E was not significantly affected. The enzyme activity of S36E increased linearly with increasing LTA4 concentrations during the steady-state kinetics analysis, indicating poor lipid substrate binding. The Ser(36) is located in a loop region close to the entrance of the proposed substrate binding pocket. Comparative molecular dynamics indicated that Ser(36) upon phosphorylation will pull the first luminal loop of LTC4S toward the neighboring subunit of the functional homotrimer, thereby forming hydrogen bonds with Arg(104) in the adjacent subunit. Because Arg(104) is a key catalytic residue responsible for stabilization of the glutathione thiolate anion, this phosphorylation-induced interaction leads to a reduction of the catalytic activity. In addition, the positional shift of the loop and its interaction with the neighboring subunit affect active site access. Thus, our mutational and kinetic data, together with molecular simulations, suggest that phosphorylation of Ser(36) inhibits the catalytic function of LTC4S by interference with the catalytic machinery. PMID:27365393

  3. Structural Insights into the Catalytic Active Site and Activity of Human Nit2/ω-Amidase

    PubMed Central

    Chien, Chin-Hsiang; Gao, Quan-Ze; Cooper, Arthur J. L.; Lyu, Jyun-Hong; Sheu, Sheh-Yi

    2012-01-01

    Human nitrilase-like protein 2 (hNit2) is a putative tumor suppressor, recently identified as ω-amidase. hNit2/ω-amidase plays a crucial metabolic role by catalyzing the hydrolysis of α-ketoglutaramate (the α-keto analog of glutamine) and α-ketosuccinamate (the α-keto analog of asparagine), yielding α-ketoglutarate and oxaloacetate, respectively. Transamination between glutamine and α-keto-γ-methiolbutyrate closes the methionine salvage pathway. Thus, hNit2/ω-amidase links sulfur metabolism to the tricarboxylic acid cycle. To elucidate the catalytic specificity of hNit2/ω-amidase, we performed molecular dynamics simulations on the wild type enzyme and its mutants to investigate enzyme-substrate interactions. Binding free energies were computed to characterize factors contributing to the substrate specificity. The predictions resulting from these computations were verified by kinetic analyses and mutational studies. The activity of hNit2/ω-amidase was determined with α-ketoglutaramate and succinamate as substrates. We constructed three catalytic triad mutants (E43A, K112A, and C153A) and a mutant with a loop 116–128 deletion to validate the role of key residues and the 116–128 loop region in substrate binding and turnover. The molecular dynamics simulations successfully verified the experimental trends in the binding specificity of hNit2/ω-amidase toward various substrates. Our findings have revealed novel structural insights into the binding of substrates to hNit2/ω-amidase. A catalytic triad and the loop residues 116–128 of hNit2 play an essential role in supporting the stability of the enzyme-substrate complex, resulting in the generation of the catalytic products. These observations are predicted to be of benefit in the design of new inhibitors or activators for research involving cancer and hyperammonemic diseases. PMID:22674578

  4. Flexible phosphorene devices and circuits

    NASA Astrophysics Data System (ADS)

    Zhu, Weinan; Yogeesh, Maruthi N.; Akinwande, Deji

    2015-05-01

    Two-dimensional (2D) semiconductors with high carrier mobilities and sizeable bandgap are desirable for future high-speed and low power mechanically flexible nanoelectronics. In this work, we report encapsulated bottom-gated black phosphorus (BP) field-effect transistors (FETs) on flexible polyimide affording maximum carrier mobility of about 310cm2/V•s and current on/off ratio exceeding 103. Essential circuits of flexible electronic systems enabled by the device ambipolar functionality, high-mobility and current saturation are demonstrated in this work, including digital inverter, frequency doubler, and analog amplifiers featuring a voltage gain of ~8.7, which is the state-of-the-art value for flexible 2D semiconductor based amplifiers. In addition, we demonstrate the single FET based flexible BP amplitude-modulated (AM) demodulator, an active stage in radio receivers.

  5. [The flexibility of family medicine].

    PubMed

    Minguet, C; Aubrege, A; Aubart, M; Cornuz, J; di Patrizio, P; Du Boullay, D; Farghadani, H; Flammang, M; Haas, N; Kacenelenbogen, N; Kopp, M; Leners, J C; Levêque, M; Mbengue, M; Paur, H; Paur, I; Raphaël, F; Rausch, S; Shetgen, M; Stein R; Tabouring, P; Thomas, J M; Vignon, G

    2015-01-01

    We are a European academic group of family doctors and we propose a definition of flexibility in family medicine. A review of the literature shows that flexibility and complexity are emerging concepts in the field of family practice. The outcomes of a workshop at the WONCA-Europe congress in 2014 are discussed. The flexibility is a capability of the general practitioner to deal with complex clinical situations in a biomedical and societal changing world. Flexibility is framed by ethics. It could improve the quality of care, be useful against burnout and used in medical research. In conclusion, family medicine should adopt a specific definition of the flexibility describing its specificity, a useful and teachable capacity. PMID:26946851

  6. Conformational flexibility of mephenesin.

    PubMed

    Écija, Patricia; Evangelisti, Luca; Vallejo, Montserrat; Basterretxea, Francisco J; Lesarri, Alberto; Castaño, Fernando; Caminati, Walther; Cocinero, Emilio J

    2014-05-22

    The mephenesin molecule (3-(2-methylphenoxy)propane-1,2-diol) serves as a test bank to explore several structural and dynamical issues, such as conformational flexibility, the orientation of the carbon linear chain relative to the benzene plane, or the effect of substituent position on the rotational barrier of a methyl group. The molecule has been studied by rotational spectroscopy in the 4-18 GHz frequency range by Fourier-transform methods in a supersonic expansion. The experiment has been backed by a previous conformational search plus optimization of the lowest energy structures by ab initio and density functional quantum calculations. The three lowest-lying conformers that can interconvert to each other by simple bond rotations have been detected in the jet. Rotational parameters for all structures have been obtained, and methyl torsional barriers have been determined for the two lowest-lying rotamers. The lowest-lying structure of mephenesin is highly planar, with all carbon atoms lying nearly in the benzene ring plane, and is stabilized by the formation of cooperative intramolecular hydrogen bonding. An estimation of the relative abundance of the detected conformers indicates that the energetically most stable conformer will have an abundance near 80% at temperatures relevant for biological activity. PMID:24754523

  7. Design and experimental validation of looped-tube thermoacoustic engine

    NASA Astrophysics Data System (ADS)

    Abduljalil, Abdulrahman S.; Yu, Zhibin; Jaworski, Artur J.

    2011-10-01

    The aim of this paper is to present the design and experimental validation process for a thermoacoustic looped-tube engine. The design procedure consists of numerical modelling of the system using DELTA EC tool, Design Environment for Low-amplitude ThermoAcoustic Energy Conversion, in particular the effects of mean pressure and regenerator configuration on the pressure amplitude and acoustic power generated. This is followed by the construction of a practical engine system equipped with a ceramic regenerator — a substrate used in automotive catalytic converters with fine square channels. The preliminary testing results are obtained and compared with the simulations in detail. The measurement results agree very well on the qualitative level and are reasonably close in the quantitative sense.

  8. On the feasibility of closed-loop control of intra-aortic balloon pumping

    NASA Technical Reports Server (NTRS)

    Clark, J. W., Jr.; Bourland, H. M.; Kane, G. R.

    1973-01-01

    A closed-loop control scheme for the control of intra-aortic balloon pumping has been developed and tested in dog experiments. A performance index reflecting the general objectives of balloon-assist pumping is developed and a modified steepest ascent control algorithm is utilized for the selection of a proper operating point for the balloon during its pumping cycle. This paper attempts to indicate the feasibility of closed-loop control of balloon pumping, and particularly its flexibility in achieving both diastolic augmentation of mean aortic pressure and control of the level of end-diastolic pressure (EDP) an important factor in reducing heart work.

  9. Control of a flexible planar truss using proof mass actuators

    NASA Technical Reports Server (NTRS)

    Minas, Constantinos; Garcia, Ephrahim; Inman, Daniel J.

    1989-01-01

    A flexible structure was modeled and actively controlled by using a single space realizable linear proof mass actuator. The NASA/UVA/UB actuator was attached to a flexible planar truss structure at an optimal location and it was considered as both passive and active device. The placement of the actuator was specified by examining the eigenvalues of the modified model that included the actuator dynamics, and the frequency response functions of the modified system. The electronic stiffness of the actuator was specified, such that the proof mass actuator system was tuned to the fourth structural mode of the truss by using traditional vibration absorber design. The active control law was limited to velocity feedback by integrating of the signals of two accelerometers attached to the structure. The two lower modes of the closed-loop structure were placed further in the LHS of the complex plane. The theoretically predicted passive and active control law was experimentally verified.

  10. Vibration control of a manipulator tip on a flexible body

    NASA Technical Reports Server (NTRS)

    Xu, J.; Bainum, P. M.; Li, F.

    1992-01-01

    Vibration control of a rigid manipulator tip on a main flexible uniform beam is examined. It is proposed to add a compensator between the manipulator and the beam to rotate and extend/retrieve the manipulator during the control period. The 2D station-keeping maneuvers within the linear range without gravity and damping are considered. The compensatory open-loop control law, which depends on the amplitudes of the beam's flexible deformations at the connection joint, is synthesized using linear quadratic regulator techniques. After introducing the compensatory control into the system, system control is still stable, and the tip coordinates of the manipulator can be made to closely follow the rigid beam motion, which is assumed to be a desired motion.

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

    SciTech Connect

    Egli, Martin; Pattanayek, Rekha; Sheehan, Jonathan H.; Xu, Yao; Mori, Tetsuya; Smith, Jarrod A.; Johnson, Carl H.

    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.

  12. The Catalytic and Non-catalytic Functions of the Brahma Chromatin-Remodeling Protein Collaborate to Fine-Tune Circadian Transcription in Drosophila

    PubMed Central

    Kwok, Rosanna S.; Li, Ying H.; Lei, Anna J.; Edery, Isaac; Chiu, Joanna C.

    2015-01-01

    Daily rhythms in gene expression play a critical role in the progression of circadian clocks, and are under regulation by transcription factor binding, histone modifications, RNA polymerase II (RNAPII) recruitment and elongation, and post-transcriptional mechanisms. Although previous studies have shown that clock-controlled genes exhibit rhythmic chromatin modifications, less is known about the functions performed by chromatin remodelers in animal clockwork. Here we have identified the Brahma (Brm) complex as a regulator of the Drosophila clock. In Drosophila, CLOCK (CLK) is the master transcriptional activator driving cyclical gene expression by participating in an auto-inhibitory feedback loop that involves stimulating the expression of the main negative regulators, period (per) and timeless (tim). BRM functions catalytically to increase nucleosome density at the promoters of per and tim, creating an overall restrictive chromatin landscape to limit transcriptional output during the active phase of cycling gene expression. In addition, the non-catalytic function of BRM regulates the level and binding of CLK to target promoters and maintains transient RNAPII stalling at the per promoter, likely by recruiting repressive and pausing factors. By disentangling its catalytic versus non-catalytic functions at the promoters of CLK target genes, we uncovered a multi-leveled mechanism in which BRM fine-tunes circadian transcription. PMID:26132408

  13. Tackling Critical Catalytic Residues in Helicobacter pylori l-Asparaginase

    PubMed Central

    Maggi, Maristella; Chiarelli, Laurent R; Valentini, Giovanna; Scotti, Claudia

    2015-01-01

    Bacterial asparaginases (amidohydrolases, EC 3.5.1.1) are important enzymes in cancer therapy, especially for Acute Lymphoblastic Leukemia. They are tetrameric enzymes able to catalyze the deamination of l-ASN and, to a variable extent, of l-GLN, on which leukemia cells are dependent for survival. In contrast to other known l-asparaginases, Helicobacter pylori CCUG 17874 type II enzyme (HpASNase) is cooperative and has a low affinity towards l-GLN. In this study, some critical amino acids forming the active site of HpASNase (T16, T95 and E289) have been tackled by rational engineering in the attempt to better define their role in catalysis and to achieve a deeper understanding of the peculiar cooperative behavior of this enzyme. Mutations T16E, T95D and T95H led to a complete loss of enzymatic activity. Mutation E289A dramatically reduced the catalytic activity of the enzyme, but increased its thermostability. Interestingly, E289 belongs to a loop that is very variable in l-asparaginases from the structure, sequence and length point of view, and which could be a main determinant of their different catalytic features. PMID:25826146

  14. Cation-specific structural accommodation within a catalytic RNA.

    PubMed

    Lambert, Dominic; Heckman, Joyce E; Burke, John M

    2006-01-24

    Metal ions facilitate the folding of the hairpin ribozyme but do not participate directly in catalysis. The metal complex cobalt(III) hexaammine supports folding and activity of the ribozyme and also mediates specific internucleotide photocrosslinks, several of which retain catalytic ability. These crosslinks imply that the active core structure organized by [Co(NH3)6]3+ is different from that organized by Mg2+ and that revealed in the crystal structure [Rupert, P. B., and Ferre-D'Amare, A. R. (2001) Nature 410, 780-786] (1). Residues U+2 and C+3 of the substrate, in particular, adopt different conformations in [Co(NH3)6]3+. U+2 is bulged out of loop A and stacked on residue G36, whereas the nucleotide at position +3 is stacked on G8, a nucleobase crucial for catalysis. Cleavage kinetics performed with +2 variants and a C+3 U variant correlate with the crosslinking observations. Variants that decreased cleavage rates in magnesium up to 70-fold showed only subtle decreases or even increases in observed rates when assayed in [Co(NH3)6]3+. Here, we propose a model of the [Co(NH3)6]3+-mediated catalytic core generated by MC-SYM that is consistent with these data. PMID:16411759

  15. Evolution in a Braided Loop Ensemble

    NASA Video Gallery

    This braided loop has several loops near the 'base' that appear to be unwinding with significant apparent outflow. This is evidence of untwisting, and the braided structure also seeming to unwind w...

  16. Sub-1 nm Nickel Molybdate Nanowires as Building Blocks of Flexible Paper and Electrochemical Catalyst for Water Oxidation.

    PubMed

    Liu, Huiling; Li, Haoyi; He, Peilei; Wang, Xun

    2016-02-24

    Sub-1 nm, extremely long nickel molybdate nanowires are synthesized based on a good/poor solvent system. The ultrathin nanowires can be hierarchically assembled into flexible, free-standing films with good mechanical properties. Compared with the large-size counterpart, nickel molybdate ultrathin nanowires display promising oxygen evolution reaction catalytic performance derived from the ultrathin feature. PMID:26724910

  17. Fragmentation of cosmic-string loops

    NASA Technical Reports Server (NTRS)

    York, Thomas

    1989-01-01

    The fragmentation of cosmic string loops is discussed, and the results of a simulation of this process are presented. The simulation can evolve any of a large class of loops essentially exactly, including allowing fragments that collide to join together. Such reconnection enhances the production of small fragments, but not drastically. With or without reconnections, the fragmentation process produces a collection of nonself-intersecting loops whose typical length is on the order of the persistence length of the initial loop.

  18. Force control for robotic manipulators with structurally flexible links

    NASA Astrophysics Data System (ADS)

    Latornell, Douglas John

    1992-01-01

    This thesis reports on the development of strategies for the control of contact forces exerted by a structurally flexible robotic manipulator on surfaces in its working environment. The controller is based on a multivariable, explicitly adaptive, long range predictive control algorithm. A static equilibrium bias term which is particularly applicable to the contact force control problem has been incorporated into the control algorithm cost function. A general formulation for the discrete time domain characteristic polynomial of the closed loop system has been derived and shown useful in tuning the controller. Kinematic and dynamic models of a robotic manipulator with structurally flexible links interacting with its working environment are derived. These models include inertia and damping effects in the contact dynamics in addition to the contact stiffness employed in most previous work. Linear analyses of the dynamic models for a variety of manipulator configurations reveal that the controlled variable, the contact force, is dominated by different open loop modes of the system depending on the effective stiffness of the contacting surfaces. This result has important implications for the selection of the controller parameters. The performance of the controller has been evaluated using computer simulation. A special purpose simulation program, TWOFLEX, which includes the dynamics models of the manipulator and the environment as well as the control algorithm was developed during the research. The configurations investigated using the simulation include a single flexible manipulator link, two link manipulators with both rigid and flexible links, and a two link prototype model of the Mobile Servicing System (MSS) manipulator for the proposed Space Station Freedom. The results show that the controller can be tuned to provide fast contact force step responses with minimal overshoot and zero steady-state error. The problem of maintaining control through the discontinuous

  19. A sustainable catalytic pyrrole synthesis

    NASA Astrophysics Data System (ADS)

    Michlik, Stefan; Kempe, Rhett

    2013-02-01

    The pyrrole heterocycle is a prominent chemical motif and is found widely in natural products, drugs, catalysts and advanced materials. Here we introduce a sustainable iridium-catalysed pyrrole synthesis in which secondary alcohols and amino alcohols are deoxygenated and linked selectively via the formation of C-N and C-C bonds. Two equivalents of hydrogen gas are eliminated in the course of the reaction, and alcohols based entirely on renewable resources can be used as starting materials. The catalytic synthesis protocol tolerates a large variety of functional groups, which includes olefins, chlorides, bromides, organometallic moieties, amines and hydroxyl groups. We have developed a catalyst that operates efficiently under mild conditions.

  20. Molecular catalytic coal liquid conversion

    SciTech Connect

    Stock, L.M.; Yang, Shiyong

    1995-12-31

    This research, which is relevant to the development of new catalytic systems for the improvement of the quality of coal liquids by the addition of dihydrogen, is divided into two tasks. Task 1 centers on the activation of dihydrogen by molecular basic reagents such as hydroxide ion to convert it into a reactive adduct (OH{center_dot}H{sub 2}){sup {minus}} that can reduce organic molecules. Such species should be robust withstanding severe conditions and chemical poisons. Task 2 is focused on an entirely different approach that exploits molecular catalysts, derived from organometallic compounds that are capable of reducing monocyclic aromatic compounds under very mild conditions. Accomplishments and conclusions are discussed.

  1. Catalytic Organometallic Reactions of Ammonia

    PubMed Central

    Klinkenberg, Jessica L.

    2012-01-01

    Until recently, ammonia had rarely succumbed to catalytic transformations with homogeneous catalysts, and the development of such reactions that are selective for the formation of single products under mild conditions has encountered numerous challenges. However, recently developed catalysts have allowed several classes of reactions to create products with nitrogen-containing functional groups from ammonia. These reactions include hydroaminomethylation, reductive amination, alkylation, allylic substitution, hydroamination, and cross-coupling. This Minireview describes examples of these processes and the factors that control catalyst activity and selectivity. PMID:20857466

  2. Modeling a Transient Catalytic Combustor

    NASA Technical Reports Server (NTRS)

    Tien, J. S.

    1985-01-01

    Transient model of monolith catalytic combustor presented in report done under NASA/DOE contract. Model assumes quasi-steady gas phase and thermally "thin" solid. In gas-phase treatment, several quasi-global chemical reactions assumed capable of describing CO and unburnt hydrocarbon emissions in fuel-lean operations. In steady-state computation presented, influence of selected operating and design parameters on minimum combustor length studied. When fast transient responses required, both steady and unsteady studies made to achieve meaningful compromise in design.

  3. Combined Electrolysis Catalytic Exchange (CECE)

    SciTech Connect

    Ellis, R.E.; Mills, T.K.; Rogers, M.L.

    1980-09-30

    Starting from an effort to control airborne emissions, the Mound tritium containment program has evolved to include development of the Combined Electrolysis Catalytic Exchange (CECE) process. This process separates tritiated aqueous streams into detritiated water and an enriched hydrogen stream that is suitable for use by other tritium recovery processes. Experimentation has shown that the process performs as predicted by bench-scale measurements, and that available process components exhibit acceptable resistance to damage by radiation from tritium exposure. Planned future efforts are concentrated on finalizing automatic control of the process and on developing feed treatment methods for the protection of process components.

  4. Swarming: flexible roaming plans.

    PubMed

    Partridge, Jonathan D; Harshey, Rasika M

    2013-03-01

    Movement over an agar surface via swarming motility is subject to formidable challenges not encountered during swimming. Bacteria display a great deal of flexibility in coping with these challenges, which include attracting water to the surface, overcoming frictional forces, and reducing surface tension. Bacteria that swarm on "hard" agar surfaces (robust swarmers) display a hyperflagellated and hyperelongated morphology. Bacteria requiring a "softer" agar surface (temperate swarmers) do not exhibit such a dramatic morphology. For polarly flagellated robust swarmers, there is good evidence that restriction of flagellar rotation somehow signals the induction of a large number of lateral flagella, but this scenario is apparently not relevant to temperate swarmers. Swarming bacteria can be further subdivided by their requirement for multiple stators (Mot proteins) or a stator-associated protein (FliL), secretion of essential polysaccharides, cell density-dependent gene regulation including surfactant synthesis, a functional chemotaxis signaling pathway, appropriate cyclic (c)-di-GMP levels, induction of virulence determinants, and various nutritional requirements such as iron limitation or nitrate availability. Swarming strategies are as diverse as the bacteria that utilize them. The strength of these numerous designs stems from the vantage point they offer for understanding mechanisms for effective colonization of surface niches, acquisition of pathogenic potential, and identification of environmental signals that regulate swarming. The signature swirling and streaming motion within a swarm is an interesting phenomenon in and of itself, an emergent behavior with properties similar to flocking behavior in diverse systems, including birds and fish, providing a convenient new avenue for modeling such behavior. PMID:23264580

  5. Swarming: Flexible Roaming Plans

    PubMed Central

    Partridge, Jonathan D.

    2013-01-01

    Movement over an agar surface via swarming motility is subject to formidable challenges not encountered during swimming. Bacteria display a great deal of flexibility in coping with these challenges, which include attracting water to the surface, overcoming frictional forces, and reducing surface tension. Bacteria that swarm on “hard” agar surfaces (robust swarmers) display a hyperflagellated and hyperelongated morphology. Bacteria requiring a “softer” agar surface (temperate swarmers) do not exhibit such a dramatic morphology. For polarly flagellated robust swarmers, there is good evidence that restriction of flagellar rotation somehow signals the induction of a large number of lateral flagella, but this scenario is apparently not relevant to temperate swarmers. Swarming bacteria can be further subdivided by their requirement for multiple stators (Mot proteins) or a stator-associated protein (FliL), secretion of essential polysaccharides, cell density-dependent gene regulation including surfactant synthesis, a functional chemotaxis signaling pathway, appropriate cyclic (c)-di-GMP levels, induction of virulence determinants, and various nutritional requirements such as iron limitation or nitrate availability. Swarming strategies are as diverse as the bacteria that utilize them. The strength of these numerous designs stems from the vantage point they offer for understanding mechanisms for effective colonization of surface niches, acquisition of pathogenic potential, and identification of environmental signals that regulate swarming. The signature swirling and streaming motion within a swarm is an interesting phenomenon in and of itself, an emergent behavior with properties similar to flocking behavior in diverse systems, including birds and fish, providing a convenient new avenue for modeling such behavior. PMID:23264580

  6. Influence of inflow angle on flexible flap aerodynamic performance

    NASA Astrophysics Data System (ADS)

    Y Zhao, H.; Ye, Z.; Li, Z. M.; Li, C.

    2013-12-01

    Large scale wind turbines have larger blade lengths and weights, which creates new challenges for blade design. This paper selects NREL S809 airfoil, and uses the parameterized technology to realize the flexible trailing edge deformation, researches the dynamic aerodynamic characteristics in the process of continuous flexible deformation, analyses the influence of inflow angle on flexible flap aerodynamic performance, in order to further realize the flexible wind turbine blade design and provides some references for the active control scheme. The results show that compared with the original airfoil, proper trailing edge deformation can improve the lift coefficient, reduce the drag coefficient, and thereby more efficiently realize flow field active control. With inflow angle increases, dynamic lift-drag coefficient hysteresis loop shape deviation occurs, even turns into different shapes. Appropriate swing angle can improve the flap lift coefficient, but may cause early separation of flow. To improve the overall performance of wind turbine blades, different angular control should be used at different cross sections, in order to achieve the best performance.

  7. Robust on-off pulse control of flexible space vehicles

    NASA Technical Reports Server (NTRS)

    Wie, Bong; Sinha, Ravi

    1993-01-01

    The on-off reaction jet control system is often used for attitude and orbital maneuvering of various spacecraft. Future space vehicles such as the orbital transfer vehicles, orbital maneuvering vehicles, and space station will extensively use reaction jets for orbital maneuvering and attitude stabilization. The proposed robust fuel- and time-optimal control algorithm is used for a three-mass spacing model of flexible spacecraft. A fuel-efficient on-off control logic is developed for robust rest-to-rest maneuver of a flexible vehicle with minimum excitation of structural modes. The first part of this report is concerned with the problem of selecting a proper pair of jets for practical trade-offs among the maneuvering time, fuel consumption, structural mode excitation, and performance robustness. A time-optimal control problem subject to parameter robustness constraints is formulated and solved. The second part of this report deals with obtaining parameter insensitive fuel- and time- optimal control inputs by solving a constrained optimization problem subject to robustness constraints. It is shown that sensitivity to modeling errors can be significantly reduced by the proposed, robustified open-loop control approach. The final part of this report deals with sliding mode control design for uncertain flexible structures. The benchmark problem of a flexible structure is used as an example for the feedback sliding mode controller design with bounded control inputs and robustness to parameter variations is investigated.

  8. FlexibleSUSY-A spectrum generator generator for supersymmetric models

    NASA Astrophysics Data System (ADS)

    Athron, Peter; Park, Jae-hyeon; Stöckinger, Dominik; Voigt, Alexander

    2015-05-01

    We introduce FlexibleSUSY, a Mathematica and C++ package, which generates a fast, precise C++ spectrum generator for any SUSY model specified by the user. The generated code is designed with both speed and modularity in mind, making it easy to adapt and extend with new features. The model is specified by supplying the superpotential, gauge structure and particle content in a SARAH model file; specific boundary conditions e.g. at the GUT, weak or intermediate scales are defined in a separate FlexibleSUSY model file. From these model files, FlexibleSUSY generates C++ code for self-energies, tadpole corrections, renormalization group equations (RGEs) and electroweak symmetry breaking (EWSB) conditions and combines them with numerical routines for solving the RGEs and EWSB conditions simultaneously. The resulting spectrum generator is then able to solve for the spectrum of the model, including loop-corrected pole masses, consistent with user specified boundary conditions. The modular structure of the generated code allows for individual components to be replaced with an alternative if available. FlexibleSUSY has been carefully designed to grow as alternative solvers and calculators are added. Predefined models include the MSSM, NMSSM, E6SSM, USSM, R-symmetric models and models with right-handed neutrinos.

  9. Inherent conformational flexibility of F1-ATPase α-subunit.

    PubMed

    Hahn-Herrera, Otto; Salcedo, Guillermo; Barril, Xavier; García-Hernández, Enrique

    2016-09-01

    The core of F1-ATPase consists of three catalytic (β) and three noncatalytic (α) subunits, forming a hexameric ring in alternating positions. A wealth of experimental and theoretical data has provided a detailed picture of the complex role played by catalytic subunits. Although major conformational changes have only been seen in β-subunits, it is clear that α-subunits have to respond to these changes in order to be able to transmit information during the rotary mechanism. However, the conformational behavior of α-subunits has not been explored in detail. Here, we have combined unbiased molecular dynamics (MD) simulations and calorimetrically measured thermodynamic signatures to investigate the conformational flexibility of isolated α-subunits, as a step toward deepening our understanding of its function inside the α3β3 ring. The simulations indicate that the open-to-closed conformational transition of the α-subunit is essentially barrierless, which is ideal to accompany and transmit the movement of the catalytic subunits. Calorimetric measurements of the recombinant α-subunit from Geobacillus kaustophilus indicate that the isolated subunit undergoes no significant conformational changes upon nucleotide binding. Simulations confirm that the nucleotide-free and nucleotide-bound subunits show average conformations similar to that observed in the F1 crystal structure, but they reveal an increased conformational flexibility of the isolated α-subunit upon MgATP binding, which might explain the evolutionary conserved capacity of α-subunits to recognize nucleotides with considerable strength. Furthermore, we elucidate the different dependencies that α- and β-subunits show on Mg(II) for recognizing ATP. PMID:27137408

  10. Electronic applications of flexible graphite

    NASA Astrophysics Data System (ADS)

    Luo, Xiangcheng; Chugh, Randy; Biller, Brian C.; Hoi, Yie Meng; Chung, D. D. L.

    2002-05-01

    Flexible graphite is effective for electronic applications, specifically electromagnetic interference (EMI) gasketing, resistive heating, thermoelectric-energy generation, and heat dissipation. It is comparable to or better than conductive-filled silicone materials for EMI gasketing. The shielding effectiveness reaches 125 dB. Flexible graphite as a heating element provides temperatures up to 980°C, response half-time down to 4 sec, and heat output at 60 sec up to 5600 J. The through-thickness, absolute thermoelectric power of flexible graphite is -2.6 µV/°C. Flexible graphite is effective as a thermal-interface material if the thickness is low (0.13 mm), the density is low (1.1 g/cm3), and the contact pressure is high (11.1 MPa). These applications make use of the flexibility and compliance of flexible graphite, in addition to its electronic and thermal behavior. Compliance is particularly important for the use of flexible graphite as interface materials, whether the interface is electrom agnetic, thermoelectric, or thermal.

  11. Chromosome Compaction by Active Loop Extrusion.

    PubMed

    Goloborodko, Anton; Marko, John F; Mirny, Leonid A

    2016-05-24

    During cell division, chromosomes are compacted in length by more than a 100-fold. A wide range of experiments demonstrated that in their compacted state, mammalian chromosomes form arrays of closely stacked consecutive ∼100 kb loops. The mechanism underlying the active process of chromosome compaction into a stack of loops is unknown. Here we test the hypothesis that chromosomes are compacted by enzymatic machines that actively extrude chromatin loops. When such loop-extruding factors (LEF) bind to chromosomes, they progressively bridge sites that are further away along the chromosome, thus extruding a loop. We demonstrate that collective action of LEFs leads to formation of a dynamic array of consecutive loops. Simulations and an analytically solved model identify two distinct steady states: a sparse state, where loops are highly dynamic but provide little compaction; and a dense state, where there are more stable loops and dramatic chromosome compaction. We find that human chromosomes operate at the border of the dense steady state. Our analysis also shows how the macroscopic characteristics of the loop array are determined by the microscopic properties of LEFs and their abundance. When the number of LEFs are used that match experimentally based estimates, the model can quantitatively reproduce the average loop length, the degree of compaction, and the general loop-array morphology of compact human chromosomes. Our study demonstrates that efficient chromosome compaction can be achieved solely by an active loop-extrusion process. PMID:27224481

  12. Hard thermal loops in static external fields

    SciTech Connect

    Frenkel, J.; Takahashi, N.; Pereira, S. H.

    2009-04-15

    We examine, in the imaginary-time formalism, the high temperature behavior of n-point thermal loops in static Yang-Mills and gravitational fields. We show that in this regime, any hard thermal loop gives the same leading contribution as the one obtained by evaluating the loop integral at zero external energies and momenta.

  13. The Statistical Loop Analyzer (SLA)

    NASA Technical Reports Server (NTRS)

    Lindsey, W. C.

    1985-01-01

    The statistical loop analyzer (SLA) is designed to automatically measure the acquisition, tracking and frequency stability performance characteristics of symbol synchronizers, code synchronizers, carrier tracking loops, and coherent transponders. Automated phase lock and system level tests can also be made using the SLA. Standard baseband, carrier and spread spectrum modulation techniques can be accomodated. Through the SLA's phase error jitter and cycle slip measurements the acquisition and tracking thresholds of the unit under test are determined; any false phase and frequency lock events are statistically analyzed and reported in the SLA output in probabilistic terms. Automated signal drop out tests can be performed in order to trouble shoot algorithms and evaluate the reacquisition statistics of the unit under test. Cycle slip rates and cycle slip probabilities can be measured using the SLA. These measurements, combined with bit error probability measurements, are all that are needed to fully characterize the acquisition and tracking performance of a digital communication system.

  14. Microgyroscope with closed loop output

    NASA Technical Reports Server (NTRS)

    Challoner, A. Dorian (Inventor); Gutierrez, Roman C. (Inventor); Tang, Tony K. (Inventor); Cargille, Donald R. (Inventor)

    2002-01-01

    A micro-gyroscope (10) having closed loop operation by a control voltage (V.sub.TY), that is demodulated by an output signal of the sense electrodes (S1, S2), providing Coriolis torque rebalance to prevent displacement of the micro-gyroscope (10) on the output axis (y-axis). The present invention provides wide-band, closed-loop operation for a micro-gyroscope (10) and allows the drive frequency to be closely tuned to a high Q sense axis resonance. A differential sense signal (S1-S2) is compensated and fed back by differentially changing the voltage on the drive electrodes to rebalance Coriolis torque. The feedback signal is demodulated in phase with the drive axis signal (K.sub..omega..crclbar..sub.x) to produce a measure of the Coriolis force.

  15. Loop connectors in dentogenic diastema.

    PubMed

    Nayar, Sanjna; Jayesh, Raghevendra; Venkateshwaran; Dinakarsamy, V

    2015-04-01

    Patients with a missing tooth along with diastema have limited treatment options to restore the edentulous space. The use of a conventional fixed partial denture (FPD) to replace the missing tooth may result in too wide anterior teeth leading to poor esthetics. Loss of anterior teeth with existing diastema may result in excess space available for pontic. This condition presents great esthetic challenge for prosthodontist. If implant supported prosthesis is not possible because of inadequate bone support, FPD along with loop connector may be a treatment option to maintain the diastema and provide optimal esthetic restoration. Here, we report a clinical case where FPD along with loop connector was used to achieve esthetic rehabilitation in maxillary anterior region in which midline diastema has been maintained. PMID:26015732

  16. Size, shape, and flexibility of RNA structures

    NASA Astrophysics Data System (ADS)

    Hyeon, Changbong; Dima, Ruxandra I.; Thirumalai, D.

    2006-11-01

    Determination of sizes and flexibilities of RNA molecules is important in understanding the nature of packing in folded structures and in elucidating interactions between RNA and DNA or proteins. Using the coordinates of the structures of RNA in the Protein Data Bank we find that the size of the folded RNA structures, measured using the radius of gyration RG, follows the Flory scaling law, namely, RG=5.5N1/3Å, where N is the number of nucleotides. The shape of RNA molecules is characterized by the asphericity Δ and the shape S parameters that are computed using the eigenvalues of the moment of inertia tensor. From the distribution of Δ, we find that a large fraction of folded RNA structures are aspherical and the distribution of S values shows that RNA molecules are prolate (S>0). The flexibility of folded structures is characterized by the persistence length lp. By fitting the distance distribution function P(r ), that is computed using the coordinates of the folded RNA, to the wormlike chain model we extracted the persistence length lp. We find that lp≈1.5N0.33Å which might reflect the large separation between the free energies that stabilize secondary and tertiary structures. The dependence of lp on N implies that the average length of helices should increase as the size of RNA grows. We also analyze packing in the structures of ribosomes (30S, 50S, and 70S) in terms of RG, Δ, S, and lp. The 70S and the 50S subunits are more spherical compared to most RNA molecules. The globularity in 50S is due to the presence of an unusually large number (compared to 30S subunit) of small helices that are stitched together by bulges and loops. Comparison of the shapes of the intact 70S ribosome and the constituent particles suggests that folding of the individual molecules might occur prior to assembly.

  17. Is the catalytic mechanism of bacteria, plant, and mammal copper-TPQ amine oxidases identical?

    PubMed

    Pietrangeli, P; Nocera, S; Mondovi, B; Morpurgo, L

    2003-04-11

    This short review is mostly concerned with the work carried out in Rome on the copper amine oxidase from bovine serum (BSAO). The first target was the copper oxidation state and its relationship with the organic cofactor. It was found that copper is not reduced on reaction with amines under anaerobic conditions or along the catalytic cycle and that it is not within bonding distance of the quinone cofactor. The copper stability in the oxidised state was supported by BSAO ability to oxidise benzylhydrazine, a slow substrate, in the presence of N,N-diethyldithiocarbamate (DDC) and by the substantial catalytic activity of Co(2+)-substituted BSAO. Parallel work established that only one subunit of the dimeric enzyme readily binds reagents of the carbonyl group. Flexible hydrazides with a long aromatic tail were found to be highly specific inhibitors, suggesting the presence of an extended hydrophobic region at the catalytic site. A study by stopped-flow transient spectroscopy and steady state kinetics led to the formulation of a simplified, yet complete and consistent, catalytic mechanism for BSAO that was compared with that available for lentil seedling amine oxidase (LSAO). As in other copper amine oxidases, BSAO is inactivated by H(2)O(2) produced in the catalytic reaction, while the cofactor is stabilised in its reduced state. A conserved tyrosine hydrogen-bonded to the cofactor might be oxidised. PMID:12686125

  18. Crystal Structure of the Catalytic Domain of a Serine Threonine Protein Phosphatase

    NASA Technical Reports Server (NTRS)

    Swinglel, Mark; Honkanel, Richard; Ciszak, Ewa

    2003-01-01

    Reversible phosphorylation of serine and threonine residues is a well-recognized mechanism in eukaryotic cells for the regulation of cell-cycle progression, cell growth and metabolism. Human serine/threonine phosphatases can be placed into two major families, PPP and PPM. To date the structure on one PPP family member (PPl) has been determined. Here we present the structure of a 323-residue catalytic domain of a second phosphatase belonging to the PPP family of enzyme. catalytic domain of the enzyme has been determined to 1.60Angstrom resolution and refined to R=17.5 and Rfree = 20.8%. The catalytic domain possesses a unique fold consisting of a largely monolithic structure, divisible into closely-associated helical and sheet regions. The catalytic site contains two manganese ions that are involved in substrate binding and catalysis. The enzyme crystallizes as a dimer that completely buries catalytic surfaces of both monomers, Also, the structure shows evidence of some flexibility around the active site cleft that may be related to substrate specificity of this enzyme.

  19. CATALYTIC CONVERSION OF HAZARDOUS AND TOXIC CHEMICALS: CATALYTIC HYDRODECHLORINATION OF POLYCHLORINATED PESTICIDES AND RELATED SUBSTANCES

    EPA Science Inventory

    A study has been undertaken of the catalytic conversion of chlorinated pesticides and other environmentally undesirable chlorinated materials into acceptable compounds. The results of this study show that chlorine can be catalytically removed and replaced by hydrogen to produce r...

  20. Two Loop Higgs Unitarity Constraints

    NASA Astrophysics Data System (ADS)

    Maher, Peter Noel

    The perturbative approximation in the Symmetry Breaking sector of the Standard Model is investigated to two loops. The breakdown of perturbative unitarity seen at one loop is only slightly postponed. Attention is restricted to the coupled elastic scattering matrix of the neutral channels W^+W ^-, ZZ, HH, ZH. The high energy limit s gg M_sp{H} {2} gg M_sp{W}{2} and the Equivalence Theorem are used to simplify the calculation. The theory is renormalized on mass shell, in a way that automatically sums the tadpole graphs. Calculation of the counterterms was the most difficult part of the entire work. The running coupling and anomalous dimensions are calculated. The Landau pole of the running coupling is not significantly affected by the two loop contributions unless the coupling is large. Similarly, the anomalous dimensions are small. The eigen-amplitudes of the partial wave projected scattering matrix are analysed for breakdown of perturbative unitarity using Argand diagrams, and for term-wise convergence. It is found that if the Standard Model is to hold true up to sqrt{s} ~ 2TeV, the theory is strongly coupled and perturbative approximations are no longer trustworthy if M_{H} _sp{~}{>} 350 - 450 GeV. If the Standard Model is embedded in a perturbative grand unified theory, and assumed to hold true up to sqrt{s} = 10^ {15} GeV, then the Higgs mass is bounded M_{H} _sp{~ }{<} 160 GeV.

  1. Polyhedra in loop quantum gravity

    SciTech Connect

    Bianchi, Eugenio; Speziale, Simone; Dona, Pietro

    2011-02-15

    Intertwiners are the building blocks of spin-network states. The space of intertwiners is the quantization of a classical symplectic manifold introduced by Kapovich and Millson. Here we show that a theorem by Minkowski allows us to interpret generic configurations in this space as bounded convex polyhedra in R{sup 3}: A polyhedron is uniquely described by the areas and normals to its faces. We provide a reconstruction of the geometry of the polyhedron: We give formulas for the edge lengths, the volume, and the adjacency of its faces. At the quantum level, this correspondence allows us to identify an intertwiner with the state of a quantum polyhedron, thus generalizing the notion of the quantum tetrahedron familiar in the loop quantum gravity literature. Moreover, coherent intertwiners result to be peaked on the classical geometry of polyhedra. We discuss the relevance of this result for loop quantum gravity. In particular, coherent spin-network states with nodes of arbitrary valence represent a collection of semiclassical polyhedra. Furthermore, we introduce an operator that measures the volume of a quantum polyhedron and examine its relation with the standard volume operator of loop quantum gravity. We also comment on the semiclassical limit of spin foams with nonsimplicial graphs.

  2. Two-loop quantum gravity

    NASA Astrophysics Data System (ADS)

    van de Ven, Anton E. M.

    1992-07-01

    We prove the existence of a nonrenormalizable infinity in the two-loop effective action of perturbative quantum gravity by means of an explicit calculation. Our final result agrees with that obtained by earlier authors. We use the background-field method in coordinate space, combined with dimensional regularization and a heat kernel representation for the propagators. General covariance is manifestly preserved. Only vacuum graphs in the presence of an on-shell background metric need to be calculated. We extend the background covariant harmonic gauge to include terms nonlinear in the quantum gravitational fields and allow for general reparametrizations of those fields. For a particular gauge choice and field parametrization only two three-graviton and six four-graviton vertices are present in the action. Calculational labor is further reduced by restricting to backgrounds, which are not only Ricci-flat, but satisfy an additional constraint bilinear in the Weyl tensor. To handle the still formidable amount of algebra, we use the symbolic manipulation program FORM. We checked that the on-shell two-loop effective action is in fact independent of all gauge and field redefinition parameters. A two-loop analysis for Yang-Mills fields is included as well, since in that case we can give full details as well as simplify earlier analyses.

  3. Polyhedra in loop quantum gravity

    NASA Astrophysics Data System (ADS)

    Bianchi, Eugenio; Doná, Pietro; Speziale, Simone

    2011-02-01

    Intertwiners are the building blocks of spin-network states. The space of intertwiners is the quantization of a classical symplectic manifold introduced by Kapovich and Millson. Here we show that a theorem by Minkowski allows us to interpret generic configurations in this space as bounded convex polyhedra in R3: A polyhedron is uniquely described by the areas and normals to its faces. We provide a reconstruction of the geometry of the polyhedron: We give formulas for the edge lengths, the volume, and the adjacency of its faces. At the quantum level, this correspondence allows us to identify an intertwiner with the state of a quantum polyhedron, thus generalizing the notion of the quantum tetrahedron familiar in the loop quantum gravity literature. Moreover, coherent intertwiners result to be peaked on the classical geometry of polyhedra. We discuss the relevance of this result for loop quantum gravity. In particular, coherent spin-network states with nodes of arbitrary valence represent a collection of semiclassical polyhedra. Furthermore, we introduce an operator that measures the volume of a quantum polyhedron and examine its relation with the standard volume operator of loop quantum gravity. We also comment on the semiclassical limit of spin foams with nonsimplicial graphs.

  4. Flexible sensors for biomedical technology.

    PubMed

    Vilela, Diana; Romeo, Agostino; Sánchez, Samuel

    2016-02-01

    Flexible sensing devices have gained a great deal of attention among the scientific community in recent years. The application of flexible sensors spans over several fields, including medicine, industrial automation, robotics, security, and human-machine interfacing. In particular, non-invasive health-monitoring devices are expected to play a key role in the improvement of patient life and in reducing costs associated with clinical and biomedical diagnostic procedures. Here, we focus on recent advances achieved in flexible devices applied on the human skin for biomedical and healthcare purposes. PMID:26675174

  5. Guideline Implementation: Processing Flexible Endoscopes.

    PubMed

    Bashaw, Marie A

    2016-09-01

    The updated AORN "Guideline for processing flexible endoscopes" provides guidance to perioperative, endoscopy, and sterile processing personnel for processing all types of reusable flexible endoscopes and accessories in all procedural settings. This article focuses on key points of the guideline to help perioperative personnel safely and effectively process flexible endoscopes to prevent infection transmission. The key points address verification of manual cleaning, mechanical cleaning and processing, storage in a drying cabinet, determination of maximum storage time before reprocessing is needed, and considerations for implementing a microbiologic surveillance program. Perioperative RNs should review the complete guideline for additional information and for guidance when writing and updating policies and procedures. PMID:27568535

  6. Rolling-cuff flexible bellows

    DOEpatents

    Lambert, D.R.

    1982-09-27

    A flexible connector apparatus used to join two stiff non-deformable members, such as piping, is described. The apparatus is provided with one or more flexible sections or assemblies each utilizing a bellows of a rolling cuff type connected between two ridge members, with the bellows being supported by a back-up ring, such that only the curved end sections of the bellows are unsupported. Thus, the bellows can be considered as being of a tube-shaped configuration and thus have high pressure resistance. The components of the flexible apparatus are sealed or welded one to another such that it is fluid tight.

  7. High performance flexible heat pipes

    NASA Technical Reports Server (NTRS)

    Shaubach, R. M.; Gernert, N. J.

    1985-01-01

    A Phase I SBIR NASA program for developing and demonstrating high-performance flexible heat pipes for use in the thermal management of spacecraft is examined. The program combines several technologies such as flexible screen arteries and high-performance circumferential distribution wicks within an envelope which is flexible in the adiabatic heat transport zone. The first six months of work during which the Phase I contract goal were met, are described. Consideration is given to the heat-pipe performance requirements. A preliminary evaluation shows that the power requirement for Phase II of the program is 30.5 kilowatt meters at an operating temperature from 0 to 100 C.

  8. A Flexible Electrode Based on Iron Phosphide Nanotubes for Overall Water Splitting.

    PubMed

    Yan, Ya; Xia, Bao Yu; Ge, Xiaoming; Liu, Zhaolin; Fisher, Adrian; Wang, Xin

    2015-12-01

    The design of cheap and efficient water splitting systems for sustainable hydrogen production has attracted increasing attention. A flexible electrode, based on carbon cloth substrate and iron phosphide nanotubes coated with an iron oxide/phosphate layer, is shown to catalyze overall water splitting. The as-prepared flexible electrode demonstrates remarkable electrocatalytic activity for both the hydrogen evolution reaction (HER) and the oxygen evolution reaction (OER) at modest overpotentials. The surface iron oxide/phosphate, which is formed in situ, is proposed to improve the HER activity by facilitating the water-dissociation step and serves directly as the catalytically-active component for the OER process. PMID:26493157

  9. Quantum reduced loop gravity and the foundation of loop quantum cosmology

    NASA Astrophysics Data System (ADS)

    Alesci, Emanuele; Cianfrani, Francesco

    2016-06-01

    Quantum reduced loop gravity is a promising framework for linking loop quantum gravity and the effective semiclassical dynamics of loop quantum cosmology. We review its basic achievements and its main perspectives, outlining how it provides a quantum description of the Universe in terms of a cuboidal graph which constitutes the proper framework for applying loop techniques in a cosmological setting.

  10. Catalytic conversion of light alkanes

    SciTech Connect

    Lyons, J.E.

    1992-06-30

    The second Quarterly Report of 1992 on the Catalytic Conversion of Light Alkanes reviews the work done between April 1, 1992 and June 31, 1992 on the Cooperative Agreement. The mission of this work is to devise a new catalyst which can be used in a simple economic process to convert the light alkanes in natural gas to oxygenate products that can either be used as clean-burning, high octane liquid fuels, as fuel components or as precursors to liquid hydrocarbon uwspomdon fuel. During the past quarter we have continued to design, prepare, characterize and test novel catalysts for the mild selective reaction of light hydrocarbons with air or oxygen to produce alcohols directly. These catalysts are designed to form active metal oxo (MO) species and to be uniquely active for the homolytic cleavage of the carbon-hydrogen bonds in light alkanes producing intermediates which can form alcohols. We continue to investigate three molecular environments for the active catalytic species that we are trying to generate: electron-deficient macrocycles (PHASE I), polyoxometallates (PHASE II), and regular oxidic lattices including zeolites and related structures as well as other molecular surface structures having metal oxo groups (PHASE I).

  11. Evolution of a Catalytic Mechanism.

    PubMed

    Rauwerdink, Alissa; Lunzer, Mark; Devamani, Titu; Jones, Bryan; Mooney, Joanna; Zhang, Zhi-Jun; Xu, Jian-He; Kazlauskas, Romas J; Dean, Antony M

    2016-04-01

    The means by which superfamilies of specialized enzymes arise by gene duplication and functional divergence are poorly understood. The escape from adaptive conflict hypothesis, which posits multiple copies of a gene encoding a primitive inefficient and highly promiscuous generalist ancestor, receives support from experiments showing that resurrected ancestral enzymes are indeed more substrate-promiscuous than their modern descendants. Here, we provide evidence in support of an alternative model, the innovation-amplification-divergence hypothesis, which posits a single-copied ancestor as efficient and specific as any modern enzyme. We argue that the catalytic mechanisms of plant esterases and descendent acetone cyanohydrin lyases are incompatible with each other (e.g., the reactive substrate carbonyl must bind in opposite orientations in the active site). We then show that resurrected ancestral plant esterases are as catalytically specific as modern esterases, that the ancestor of modern acetone cyanohydrin lyases was itself only very weakly promiscuous, and that improvements in lyase activity came at the expense of esterase activity. These observations support the innovation-amplification-divergence hypothesis, in which an ancestor gains a weak promiscuous activity that is improved by selection at the expense of the ancestral activity, and not the escape from adaptive conflict in which an inefficient generalist ancestral enzyme steadily loses promiscuity throughout the transition to a highly active specialized modern enzyme. PMID:26681154

  12. Flexible Learning in a Digital World.

    ERIC Educational Resources Information Center

    Collis, Betty; Moonen, Jef

    2002-01-01

    Defines flexible learning and describes components of flexible learning in higher education, including technology, pedagogy or instructional approach, implementation strategies, and institutional framework. Considers factors constraining learning flexibility; changing student characteristics; and the need for lifelong learning, particularly in the…

  13. Structural and kinetic contributions of the oxyanion binding site to the catalytic activity of acylaminoacyl peptidase.

    PubMed

    Kiss, András L; Palló, Anna; Náray-Szabó, Gábor; Harmat, Veronika; Polgár, László

    2008-05-01

    It is widely accepted that the catalytic activity of serine proteases depends primarily on the Asp-His-Ser catalytic triad and other residues within the vicinity of this motif. Some of these residues form the oxyanion binding site that stabilizes the tetrahedral intermediate by hydrogen bonding to the negatively charged oxyanion. In acylaminoacyl peptidase from the thermophile Aeropyrum pernix, the main chain NH group of Gly369 is one of the hydrogen bond donors forming the oxyanion binding site. The side chain of His367, a conserved residue in acylaminoacyl peptidases across all species, fastens the loop holding Gly369. Determination of the crystal structure of the H367A mutant revealed that this loop, including Gly369, moves away considerably, accounting for the observed three orders of magnitude decrease in the specificity rate constant. For the wild-type enzyme ln(k(cat)/K(m)) vs. 1/T deviates from linearity indicating greater rate enhancement with increasing temperature for the dissociation of the enzyme-substrate complex compared with its decomposition to product. In contrast, the H367A variant provided a linear Arrhenius plot, and its reaction was associated with unfavourable entropy of activation. These results show that a residue relatively distant from the active site can significantly affect the catalytic activity of acylaminoacyl peptidase without changing the overall structure of the enzyme. PMID:18325786

  14. Rate-limiting domain and loop motions in arginine kinase.

    PubMed

    Davulcu, Omar; Skalicky, Jack J; Chapman, Michael S

    2011-05-17

    Arginine kinase catalyzes the reversible transfer of a phosphoryl group between ATP and arginine. It is the arthropod homologue of creatine kinase, buffering cellular ATP levels. Crystal structures of arginine kinase, in substrate-free and substrate-bound forms, have revealed large conformational changes associated with the catalytic cycle. Recent nuclear magnetic resonance identified movements of the N-terminal domain and a loop comprising residues I182--G209 with conformational exchange rates in the substrate-free enzyme similar to the turnover rate. Here, to understand whether these motions might be rate-limiting, we determined activation barriers for both the intrinsic dynamics and enzyme turnover using measurements over a temperature range of 15-30 °C. (15)N transverse relaxation dispersion yields activation barriers of 46 ± 8 and 34 ± 12 kJ/mol for the N-terminal domain and I182--G209 loop, respectively. An activation barrier of 34 ± 13 kJ/mol was obtained for enzyme turnover from steady-state kinetics. The similarity between the activation barriers is indeed consistent with turnover being limited by backbone conformational dynamics and pinpoints the locations of potentially rate-limiting motions. PMID:21425868

  15. Premeasured Chordal Loops for Mitral Valve Repair.

    PubMed

    Gillinov, Marc; Quinn, Reed; Kerendi, Faraz; Gaudiani, Vince; Shemin, Richard; Barnhart, Glenn; Raines, Edward; Gerdisch, Marc W; Banbury, Michael

    2016-09-01

    Premeasured expanded polytetrafluoroethylene chordal loops with integrated sutures for attachment to the papillary muscle and leaflet edges facilitate correction of mitral valve prolapse. Configured as a group of 3 loops (length range 12 to 24 mm), the loops are attached to a pledget that is passed through the papillary muscle and tied. Each of the loops has 2 sutures with attached needles; these needles are passed through the free edge of the leaflet and then the sutures are tied to each other, securing the chordal loop to the leaflet. PMID:27549563

  16. Z-Sum approach to loop integrals

    NASA Astrophysics Data System (ADS)

    Rottmann, Paulo A.

    We study the applicability of the Z-Sum approach to multi-loop calculations with massive particles in perturbative quantum field theory. We systematically analyze the case of one-loop scalar integrals, which represent the building blocks of any higher-loop calculation. We focus in particular on triangle one-loop integrals and identify strengths and limitations of the Z-Sum approach, extending our results to the case of one-loop box integrals when appropriate. We conclude with the calculation of a specific physical example: the calculation of heavy flavor corrections to the renormalized scattering amplitude for deep inelastic scattering.

  17. Dynamic Aperture-based Solar Loop Segmentation

    NASA Technical Reports Server (NTRS)

    Lee, Jon Kwan; Newman, Timothy S.; Gary, G. Allen

    2006-01-01

    A new method to automatically segment arc-like loop structures from intensity images of the Sun's corona is introduced. The method constructively segments credible loop structures by exploiting the Gaussian-like shape of loop cross-sectional intensity profiles. The experimental results show that the method reasonably segments most of the well-defined loops in coronal images. The method is only the second published automated solar loop segmentation method. Its advantage over the other published method is that it operates independently of supplemental time specific data.

  18. Zinc enhancement of cytidine deaminase activity highlights a potential allosteric role of loop-3 in regulating APOBEC3 enzymes

    PubMed Central

    Marx, Ailie; Galilee, Meytal; Alian, Akram

    2015-01-01

    The strong association of APOBEC3 cytidine deaminases with somatic mutations leading to cancers accentuates the importance of their tight intracellular regulation to minimize cellular transformations. We reveal a novel allosteric regulatory mechanism of APOBEC3 enzymes showing that APOBEC3G and APOBEC3A coordination of a secondary zinc ion, reminiscent to ancestral deoxycytidylate deaminases, enhances deamination activity. Zinc binding is pinpointed to loop-3 which whilst highly variable harbors a catalytically essential and spatially conserved asparagine at its N-terminus. We suggest that loop-3 may play a general role in allosterically tuning the activity of zinc-dependent cytidine deaminase family members. PMID:26678087

  19. Zinc enhancement of cytidine deaminase activity highlights a potential allosteric role of loop-3 in regulating APOBEC3 enzymes.

    PubMed

    Marx, Ailie; Galilee, Meytal; Alian, Akram

    2015-01-01

    The strong association of APOBEC3 cytidine deaminases with somatic mutations leading to cancers accentuates the importance of their tight intracellular regulation to minimize cellular transformations. We reveal a novel allosteric regulatory mechanism of APOBEC3 enzymes showing that APOBEC3G and APOBEC3A coordination of a secondary zinc ion, reminiscent to ancestral deoxycytidylate deaminases, enhances deamination activity. Zinc binding is pinpointed to loop-3 which whilst highly variable harbors a catalytically essential and spatially conserved asparagine at its N-terminus. We suggest that loop-3 may play a general role in allosterically tuning the activity of zinc-dependent cytidine deaminase family members. PMID:26678087

  20. Photocatalytic reactor with flexible supports

    DOEpatents

    Jacoby, William A.; Blake, Daniel M.

    1995-01-01

    Organic pollutants and bioaerosols in a gaseous stream are oxidized by exposure to light (e.g., UV light) in the presence of semiconductor catalyst particles or coatings supported on flexible strips suspended in the gaseous stream.

  1. Photocatalytic reactor with flexible supports

    DOEpatents

    Jacoby, W.A.; Blake, D.M.

    1995-09-12

    Organic pollutants and bioaerosols in a gaseous stream are oxidized by exposure to light (e.g., UV light) in the presence of semiconductor catalyst particles or coatings supported on flexible strips suspended in the gaseous stream. 3 figs.

  2. Ultra-Thin, Flexible Electronics

    NASA Technical Reports Server (NTRS)

    Holland, Brian; McPherson, Ryan; Zhang, Tan; Hou, Zhenwei; Dean, Robert; Johnson, R. Wayne; DelCastillo, Linda; Moussessian, Alina

    2008-01-01

    Thinned die can be used to realize ultra-thin flexible electronics for applications such as conformal and wearable electronics. Three techniques have been developed to achieve this goal using thinned die: die flip chip bonded onto flexible substrates, die laminated onto LCP films, and die embedded in polyimide. A key to achieving each of these techniques is the thinning of die to a thickness of 50 microns or thinner. Conventional CMP processing can be used to thin to 50 microns. At 50 microns, the active die become flexible and must be handled by temporarily bonding them to a holder die, for further processing. Once bonded face down to the holder die, the active die can be further thinned by DRIE etching the exposed backside. The thinned die can then been packaged in or on the flexible substrate.

  3. Flexible Transparent Electronic Gas Sensors.

    PubMed

    Wang, Ting; Guo, Yunlong; Wan, Pengbo; Zhang, Han; Chen, Xiaodong; Sun, Xiaoming

    2016-07-01

    Flexible and transparent electronic gas sensors capable of real-time, sensitive, and selective analysis at room-temperature, have gained immense popularity in recent years for their potential to be integrated into various smart wearable electronics and display devices. Here, recent advances in flexible transparent sensors constructed from semiconducting oxides, carbon materials, conducting polymers, and their nanocomposites are presented. The sensing material selection, sensor device construction, and sensing mechanism of flexible transparent sensors are discussed in detail. The critical challenges and future development associated with flexible and transparent electronic gas sensors are presented. Smart wearable gas sensors are believed to have great potential in environmental monitoring and noninvasive health monitoring based on disease biomarkers in exhaled gas. PMID:27276698

  4. Marine Technology: Diversity and Flexibility

    ERIC Educational Resources Information Center

    Buck, Dale R.

    1973-01-01

    Training for a specific field must reflect the diversity of that field and also remain flexible enough to accommodate fluctuations in the job market and the field, as marine technology illustrates. (Editor)

  5. Efficient Tiled Loop Generation: D-Tiling

    NASA Astrophysics Data System (ADS)

    Kim, Daegon; Rajopadhye, Sanjay

    Tiling is an important loop optimization for exposing coarse-grained parallelism and enhancing data locality. Tiled loop generation from an arbitrarily shaped polyhedron is a well studied problem. Except for the special case of a rectangular iteration space, the tiled loop generation problem has been long believed to require heavy machinery such as Fourier-Motzkin elimination and projection, and hence to have an exponential complexity. In this paper we propose a simple and efficient tiled loop generation technique similar to that for a rectangular iteration space. In our technique, each loop bound is adjusted only once, syntactically and independently. Therefore, our algorithm runs linearly with the number of loop bounds. Despite its simplicity, we retain several advantages of recent tiled code generation schemes - unified generation for fixed, parameterized and hybrid tiled loops, scalability for multi-level tiled loop generation with the ability to separate full tiles at any levels, and compact code. We also explore various schemes for multi-level tiled loop generation. We formally prove the correctness of our scheme and experimentally validate that the efficiency of our technique is comparable to existing parameterized tiled loop generation approaches. Our experimental results also show that multi-level tiled loop generation schemes have an impact on performance of generated code. The fact that our scheme can be implemented without sophisticated machinery makes it well suited for autotuners and production compilers.

  6. Modern control design for flexible wind turbines

    NASA Astrophysics Data System (ADS)

    Wright, Alan Duane

    Control can improve energy capture and reduce dynamic loads in wind turbines. In the 1970s and 1980s wind turbines used classical control designs to regulate power and speed. The methods used, however, were not always successful. These systems often had bandwidths large enough to destabilize low-damped flexible modes leading to high dynamic load fatigue failures. Modern turbines are larger, mounted on taller towers, and are more dynamically active than their predecessors. Control systems to regulate turbine power and maintain stable closed-loop behavior in the presence of turbulent wind inflow will be critical for these designs. New advanced control approaches and paradigms must account for low-damped flexible modes in order to reduce structural dynamic loading and achieve the 20--25 year operational life required of today's machines. This thesis applies modern state-space control design methods to a two-bladed teetering hub upwind machine located at the National Wind Technology Center. The design objective is to regulate turbine speed and enhance damping in several low-damped flexible modes of the turbine. Starting with simple control algorithms based on linear models, complexity is added incrementally until the desired performance is firmly established. The controls approach is based on the Disturbance Accommodating Control (DAC) method and provides accountability for wind-speed fluctuations. First, controls are designed using the single control input rotor collective pitch to stabilize the 1st drive-train torsion as well as the tower 1st fore-aft bending modes. Generator torque is then incorporated as an additional control input. This reduces some of the demand placed on the rotor collective pitch control system and enhances 1st drive train torsion mode damping. Individual blade pitch control is then used to attenuate wind disturbances having spatial variation over the rotor and effectively reduces blade flap deflections due to wind shear. Finally, results from

  7. Flexible solar-array mechanism

    NASA Technical Reports Server (NTRS)

    Olson, M. C.

    1972-01-01

    One of the key elements of the flexible rolled-up solar array system is a mechanism to deploy, retract, and store the flexible solar-cell arrays. The selection of components, the design of the mechanism assembly, and the tests that were performed are discussed. During 6 months in orbit, all mission objectives were satisfied, and inflight performance has shown good correlation with preflight analyses and tests.

  8. Kinetic Cooperativity, Loop Dynamics, and Allostery from NMR and MD simulations

    NASA Astrophysics Data System (ADS)

    Bruschweiler, Rafael

    The hallmark of glucokinase (GCK), which catalyzes the phosphorylation of glucose during glycolysis, is its kinetic cooperativity whose understanding at atomic detail has remained open since its discovery over 40 years ago. I will discuss how the origin of kinetic cooperativity is rooted in intramolecular protein dynamics using NMR relaxation data of 17 isoleucines distributed over all parts of GCK. Residues of glucose-free GCK located in the small domain display a distinct exchange behavior involving multiple conformers that are substantially populated, whereas in the glucose-bound form these dynamic processes are quenched. The conformational exchange process directly competes with the enzymatic turnover at physiological glucose concentrations, thereby generating the sigmoidal rate dependence that defines kinetic cooperativity. The flexible nature of protein loops and the timescales of their dynamics are critical for many biologically important events at the molecular level, such as protein interaction and recognition processes. Based on a library of proteins, rules about loop dynamics in terms of amplitude and timescales can be derived using molecular dynamics (MD) simulations and NMR data. These rules have been implemented in the new web server ToeLoop (for Timescales Of Every Loop) that permits the prediction of loop dynamics based on an average 3D protein structure (http://spin.ccic.ohio-state.edu/index.php/loop/index).

  9. Enzymatic activation of autotaxin by divalent cations without EF-hand loop region involvement.

    PubMed

    Lee, J; Jung, I D; Nam, S W; Clair, T; Jeong, E M; Hong, S Y; Han, J W; Lee, H W; Stracke, M L; Lee, H Y

    2001-07-15

    Autotaxin (ATX) is a recently described member of the nucleotide pyrophosphatase/phosphodiesterase (NPP) family of proteins with potent tumor cell motility-stimulating activity. Like other NPPs, ATX is a glycoprotein with peptide sequences homologous to the catalytic site of bovine intestinal alkaline phosphodiesterase (PDE) and the loop region of an EF-hand motif. The PDE active site of ATX has been associated with the motility-stimulating activity of ATX. In this study, we examined the roles of the EF-hand loop region and of divalent cations on the enzymatic activities of ATX. Ca(2+) or Mg(2+) was each demonstrated to increase the PDE activity of ATX in a concentration-dependent manner, whereas incubation of ATX with chelating agents abolished this activity, indicating a requirement for divalent cations. Non-linear regression analysis of enzyme kinetic data indicated that addition of these divalent cations increases reaction velocity predominantly through an effect on V(max.) Three mutant proteins, Ala(740)-, Ala(742)-, and Ala(751)-ATX, in the EF-hand loop region of ATX had enzymatic activity comparable to that of the wild-type protein. A deletion mutation of the entire loop region resulted in slightly reduced PDE activity but normal motility-stimulating activity. However, the PDE activity of this same deletion mutant remained sensitive to augmentation by cations, strongly implying that cations exert their effect by interactions outside of the EF-hand loop region. PMID:11389881

  10. Hyperstaticity and loops in frictional granular packings

    NASA Astrophysics Data System (ADS)

    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.

  11. Developmental constraints on behavioural flexibility

    PubMed Central

    Holekamp, Kay E.; Swanson, Eli M.; Van Meter, Page E.

    2013-01-01

    We suggest that variation in mammalian behavioural flexibility not accounted for by current socioecological models may be explained in part by developmental constraints. From our own work, we provide examples of constraints affecting variation in behavioural flexibility, not only among individuals, but also among species and higher taxonomic units. We first implicate organizational maternal effects of androgens in shaping individual differences in aggressive behaviour emitted by female spotted hyaenas throughout the lifespan. We then compare carnivores and primates with respect to their locomotor and craniofacial adaptations. We inquire whether antagonistic selection pressures on the skull might impose differential functional constraints on evolvability of skulls and brains in these two orders, thus ultimately affecting behavioural flexibility in each group. We suggest that, even when carnivores and primates would theoretically benefit from the same adaptations with respect to behavioural flexibility, carnivores may nevertheless exhibit less behavioural flexibility than primates because of constraints imposed by past adaptations in the morphology of the limbs and skull. Phylogenetic analysis consistent with this idea suggests greater evolutionary lability in relative brain size within families of primates than carnivores. Thus, consideration of developmental constraints may help elucidate variation in mammalian behavioural flexibility. PMID:23569298

  12. Flexible metal-organic frameworks.

    PubMed

    Schneemann, A; Bon, V; Schwedler, I; Senkovska, I; Kaskel, S; Fischer, R A

    2014-08-21

    Advances in flexible and functional metal-organic frameworks (MOFs), also called soft porous crystals, are reviewed by covering the literature of the five years period 2009-2013 with reference to the early pertinent work since the late 1990s. Flexible MOFs combine the crystalline order of the underlying coordination network with cooperative structural transformability. These materials can respond to physical and chemical stimuli of various kinds in a tunable fashion by molecular design, which does not exist for other known solid-state materials. Among the fascinating properties are so-called breathing and swelling phenomena as a function of host-guest interactions. Phase transitions are triggered by guest adsorption/desorption, photochemical, thermal, and mechanical stimuli. Other important flexible properties of MOFs, such as linker rotation and sub-net sliding, which are not necessarily accompanied by crystallographic phase transitions, are briefly mentioned as well. Emphasis is given on reviewing the recent progress in application of in situ characterization techniques and the results of theoretical approaches to characterize and understand the breathing mechanisms and phase transitions. The flexible MOF systems, which are discussed, are categorized by the type of metal-nodes involved and how their coordination chemistry with the linker molecules controls the framework dynamics. Aspects of tailoring the flexible and responsive properties by the mixed component solid-solution concept are included, and as well examples of possible applications of flexible metal-organic frameworks for separation, catalysis, sensing, and biomedicine. PMID:24875583

  13. Developmental constraints on behavioural flexibility.

    PubMed

    Holekamp, Kay E; Swanson, Eli M; Van Meter, Page E

    2013-05-19

    We suggest that variation in mammalian behavioural flexibility not accounted for by current socioecological models may be explained in part by developmental constraints. From our own work, we provide examples of constraints affecting variation in behavioural flexibility, not only among individuals, but also among species and higher taxonomic units. We first implicate organizational maternal effects of androgens in shaping individual differences in aggressive behaviour emitted by female spotted hyaenas throughout the lifespan. We then compare carnivores and primates with respect to their locomotor and craniofacial adaptations. We inquire whether antagonistic selection pressures on the skull might impose differential functional constraints on evolvability of skulls and brains in these two orders, thus ultimately affecting behavioural flexibility in each group. We suggest that, even when carnivores and primates would theoretically benefit from the same adaptations with respect to behavioural flexibility, carnivores may nevertheless exhibit less behavioural flexibility than primates because of constraints imposed by past adaptations in the morphology of the limbs and skull. Phylogenetic analysis consistent with this idea suggests greater evolutionary lability in relative brain size within families of primates than carnivores. Thus, consideration of developmental constraints may help elucidate variation in mammalian behavioural flexibility. PMID:23569298

  14. The C-terminal loop of aldehyde reductase determines the substrate and inhibitor specificity.

    PubMed

    Barski, O A; Gabbay, K H; Bohren, K M

    1996-11-12

    Human aldehyde reductase has a preference for carboxyl group-containing negatively charged substrates. It belongs to the NADPH-dependent aldo-keto reductase superfamily whose members are in part distinguished by unique C-terminal loops. To probe the role of the C-terminal loops in determining substrate specificities in these enzymes, two arginine residues, Arg308 and Arg311, located in the C-terminal loop of aldehyde reductase, and not found in any other C-terminal loop, were replaced with alanine residues. The catalytic efficiency of the R311A mutant for aldehydes containing a carboxyl group is reduced 150-250-fold in comparison to that of the wild-type enzyme, while substrates not containing a negative charge are unaffected. The R311A mutant is also significantly less sensitive to inhibition by dicarboxylic acids, indicating that Arg311 interacts with one of the carboxyl groups. The inhibition pattern indicates that the other carboxyl group binds to the anion binding site formed by Tyr49, His112, and the nicotinamide moiety of NADP+. The correlation between inhibitor potency and the length of the dicarboxylic acid molecules suggests a distance of approximately 10 A between the amino group of Arg311 and the anion binding site in the aldehyde reductase molecule. The sensitivity of inhibition of the R311A mutant by several commercially available aldose reductase inhibitors (ARIs) was variable, with tolrestat and zopolrestat becoming more potent inhibitors (30- and 5-fold, respectively), while others remained the same or became less potent. The catalytic properties, substrate specificity, and susceptibility to inhibition of the R308A mutant remained similar to that of the wild-type enzyme. The data provide direct evidence for C-terminal loop participation in determining substrate and inhibitor specificity of aldo-keto reductases and specifically identifies Arg311 as the basis for the carboxyl-containing substrate preference of aldehyde reductase. PMID:8916913

  15. Robust disturbance rejection for flexible mechanical structures

    NASA Astrophysics Data System (ADS)

    Enzmann, Marc R.; Doeschner, Christian

    2000-06-01

    Topic of the presentation is a procedure to determine controller parameters using principles from Internal Model Control (IMC) in combination with Quantitative Feedback Theory (QFT) for robust vibration control of flexible mechanical structures. IMC design is based on a parameterization of all controllers that stabilize a given nominal plant, called the Q-parameter or Youla-parameter. It will be shown that it is possible to choose the controller structure and the Q- parameter in a very straightforward manner, so that a low order controller results, which stabilizes the given nominal model. Additional constraints can be implemented, so that the method allows for a direct and transparent trade-off between control performance and controller complexity and facilitates the inclusion of low-pass filters. In order to test (and if necessary augment) the inherent robust performance of the resulting controllers, boundaries based on the work of Kidron and Yaniv are calculated in the Nichols-Charts of the open loop and the complementary sensitivity function. The application of these boundaries is presented. Very simple uncertainty models for resonant modes are used to assess the robustness of the design. Using a simply structured plant as illustrative example we will demonstrate the design process. This will illuminate several important features of the design process, e.g. trade-off between conflicting objectives, trade- off between controller complexity and achievable performance.

  16. Cwc2 and its human homologue RBM22 promote an active conformation of the spliceosome catalytic centre

    PubMed Central

    Rasche, Nicolas; Dybkov, Olexandr; Schmitzová, Jana; Akyildiz, Berktan; Fabrizio, Patrizia; Lührmann, Reinhard

    2012-01-01

    RNA-structural elements play key roles in pre-mRNA splicing catalysis; yet, the formation of catalytically competent RNA structures requires the assistance of spliceosomal proteins. We show that the S. cerevisiae Cwc2 protein functions prior to step 1 of splicing, and it is not required for the Prp2-mediated spliceosome remodelling that generates the catalytically active B* complex, suggesting that Cwc2 plays a more sophisticated role in the generation of a functional catalytic centre. In active spliceosomes, Cwc2 contacts catalytically important RNA elements, including the U6 internal stem-loop (ISL), and regions of U6 and the pre-mRNA intron near the 5′ splice site, placing Cwc2 at/near the spliceosome's catalytic centre. These interactions are evolutionarily conserved, as shown by studies with Cwc2's human counterpart RBM22, indicating that Cwc2/RBM22–RNA contacts are functionally important. We propose that Cwc2 induces an active conformation of the spliceosome's catalytic RNA elements. Thus, the function of RNA–RNA tertiary interactions within group II introns, namely to induce an active conformation of domain V, may be fulfilled by proteins that contact the functionally analogous U6-ISL, within the spliceosome. PMID:22246180

  17. Voltage-dependent motion of the catalytic region of voltage-sensing phosphatase monitored by a fluorescent amino acid.

    PubMed

    Sakata, Souhei; Jinno, Yuka; Kawanabe, Akira; Okamura, Yasushi

    2016-07-01

    The cytoplasmic region of voltage-sensing phosphatase (VSP) derives the voltage dependence of its catalytic activity from coupling to a voltage sensor homologous to that of voltage-gated ion channels. To assess the conformational changes in the cytoplasmic region upon activation of the voltage sensor, we genetically incorporated a fluorescent unnatural amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (Anap), into the catalytic region of Ciona intestinalis VSP (Ci-VSP). Measurements of Anap fluorescence under voltage clamp in Xenopus oocytes revealed that the catalytic region assumes distinct conformations dependent on the degree of voltage-sensor activation. FRET analysis showed that the catalytic region remains situated beneath the plasma membrane, irrespective of the voltage level. Moreover, Anap fluorescence from a membrane-facing loop in the C2 domain showed a pattern reflecting substrate turnover. These results indicate that the voltage sensor regulates Ci-VSP catalytic activity by causing conformational changes in the entire catalytic region, without changing their distance from the plasma membrane. PMID:27330112

  18. Voltage-dependent motion of the catalytic region of voltage-sensing phosphatase monitored by a fluorescent amino acid

    PubMed Central

    Sakata, Souhei; Jinno, Yuka; Kawanabe, Akira; Okamura, Yasushi

    2016-01-01

    The cytoplasmic region of voltage-sensing phosphatase (VSP) derives the voltage dependence of its catalytic activity from coupling to a voltage sensor homologous to that of voltage-gated ion channels. To assess the conformational changes in the cytoplasmic region upon activation of the voltage sensor, we genetically incorporated a fluorescent unnatural amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (Anap), into the catalytic region of Ciona intestinalis VSP (Ci-VSP). Measurements of Anap fluorescence under voltage clamp in Xenopus oocytes revealed that the catalytic region assumes distinct conformations dependent on the degree of voltage-sensor activation. FRET analysis showed that the catalytic region remains situated beneath the plasma membrane, irrespective of the voltage level. Moreover, Anap fluorescence from a membrane-facing loop in the C2 domain showed a pattern reflecting substrate turnover. These results indicate that the voltage sensor regulates Ci-VSP catalytic activity by causing conformational changes in the entire catalytic region, without changing their distance from the plasma membrane. PMID:27330112

  19. The incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery

    PubMed Central

    Fischer, Marcus; Coleman, Ryan G.; Fraser, James S.; Shoichet, Brian K.

    2014-01-01

    Proteins fluctuate between alternative conformations, which presents a challenge for ligand discovery because such flexibility is difficult to treat computationally owing to problems with conformational sampling and energy weighting. Here, we describe a flexible-docking method that samples and weights protein conformations using experimentally-derived conformations as a guide. The crystallographically refined occupancies of these conformations, which are observable in an apo receptor structure, define energy penalties for docking. In a large prospective library screen, we identified new ligands that target specific receptor conformations of a cavity in Cytochrome c Peroxidase, and we confirm both ligand pose and associated receptor conformation predictions by crystallography. The inclusion of receptor flexibility led to ligands with new chemotypes and physical properties. By exploiting experimental measures of loop and side chain flexibility, this method can be extended to the discovery of new ligands for hundreds of targets in the Protein Data Bank where similar experimental information is available. PMID:24950326

  20. IRBIT Interacts with the Catalytic Core of Phosphatidylinositol Phosphate Kinase Type Iα and IIα through Conserved Catalytic Aspartate Residues

    PubMed Central

    Ando, Hideaki; Hirose, Matsumi; Gainche, Laura; Kawaai, Katsuhiro; Bonneau, Benjamin; Ijuin, Takeshi; Itoh, Toshiki; Takenawa, Tadaomi; Mikoshiba, Katsuhiko

    2015-01-01

    Phosphatidylinositol phosphate kinases (PIPKs) are lipid kinases that generate phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), a critical lipid signaling molecule that regulates diverse cellular functions, including the activities of membrane channels and transporters. IRBIT (IP3R-binding protein released with inositol 1,4,5-trisphosphate) is a multifunctional protein that regulates diverse target proteins. Here, we report that IRBIT forms signaling complexes with members of the PIPK family. IRBIT bound to all PIPK isoforms in heterologous expression systems and specifically interacted with PIPK type Iα (PIPKIα) and type IIα (PIPKIIα) in mouse cerebellum. Site-directed mutagenesis revealed that two conserved catalytic aspartate residues of PIPKIα and PIPKIIα are involved in the interaction with IRBIT. Furthermore, phosphatidylinositol 4-phosphate, Mg2+, and/or ATP interfered with the interaction, suggesting that IRBIT interacts with catalytic cores of PIPKs. Mutations of phosphorylation sites in the serine-rich region of IRBIT affected the selectivity of its interaction with PIPKIα and PIPKIIα. The structural flexibility of the serine-rich region, located in the intrinsically disordered protein region, is assumed to underlie the mechanism of this interaction. Furthermore, in vitro binding experiments and immunocytochemistry suggest that IRBIT and PIPKIα interact with the Na+/HCO3− cotransporter NBCe1-B. These results suggest that IRBIT forms signaling complexes with PIPKIα and NBCe1-B, whose activity is regulated by PI(4,5)P2. PMID:26509711