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Sample records for flexible catalytic loop

  1. A flexible loop as a functional element in the catalytic mechanism of nucleoside hydrolase from Trypanosoma vivax.

    PubMed

    Vandemeulebroucke, An; De Vos, Stefan; Van Holsbeke, Els; Steyaert, Jan; Versées, Wim

    2008-08-08

    The nucleoside hydrolase of Trypanosoma vivax hydrolyzes the N-glycosidic bond of purine nucleosides. Structural and kinetic studies on this enzyme have suggested a catalytic role for a flexible loop in the vicinity of the active sites. Here we present the analysis of the role of this flexible loop via the combination of a proline scan of the loop, loop deletion mutagenesis, steady state and pre-steady state analysis, and x-ray crystallography. Our analysis reveals that this loop has an important role in leaving group activation and product release. The catalytic role involves the entire loop and could only be perturbed by deletion of the entire loop and not by single site mutagenesis. We present evidence that the loop closes over the active site during catalysis, thereby ordering a water channel that is involved in leaving group activation. Once chemistry has taken place, the loop dynamics determine the rate of product release.

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

    PubMed Central

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

    2016-01-01

    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. PMID:26879383

  3. 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.

  4. 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).

  5. 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.

  6. 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.

  7. 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.

  8. The pepsin residue glycine-76 contributes to active-site loop flexibility and participates in catalysis.

    PubMed Central

    Okoniewska, M; Tanaka, T; Yada, R Y

    2000-01-01

    Glycine residues are known to contribute to conformational flexibility of polypeptide chains, and have been found to contribute to flexibility of some loops associated with enzymic catalysis. A comparison of porcine pepsin in zymogen, mature and inhibited forms revealed that a loop (a flap), consisting of residues 71--80, located near the active site changed its position upon substrate binding. The loop residue, glycine-76, has been implicated in the catalytic process and thought to participate in a hydrogen-bond network aligning the substrate. This study investigated the role of glycine-76 using site-directed mutagenesis. Three mutants, G76A, G76V and G76S, were constructed to increase conformational restriction of a polypeptide chain. In addition, the serine mutant introduced a hydrogen-bonding potential at position 76 similar to that observed in human renin. All the mutants, regardless of amino acid size and polarity, had lower catalytic efficiency and activated more slowly than the wild-type enzyme. The slower activation process was associated directly with altered proteolytic activity. Consequently, it was proposed that a proteolytic cleavage represents a limiting step of the activation process. Lower catalytic efficiency of the mutants was explained as a decrease in the flap flexibility and, therefore, a different pattern of hydrogen bonds responsible for substrate alignment and flap conformation. The results demonstrated that flap flexibility is essential for efficient catalytic and activation processes. PMID:10861225

  9. Dynamics of closed-loop systems containing flexible bodies

    NASA Technical Reports Server (NTRS)

    Tadikonda, Sivakumar S. K.; Singh, Ramendra P.

    1991-01-01

    An important characteristic of flexible multibody systems containing closed-loop topologies is that the component modes used to describe individual bodies will no longer be independent because of loop closure constraints. Thus, the issue of component modal selection becomes even more complicated. In addition, the foreshortening effect that has been studied extensively in the literature in the context of open-loop topologies will also be present in these constraint equations. Simulation results presented demonstrate the effects of modal selection and foreshortening on the dynamic response of closed-loop flexible systems.

  10. Efficient algorithms to explore conformation spaces of flexible protein loops.

    PubMed

    Yao, Peggy; Dhanik, Ankur; Marz, Nathan; Propper, Ryan; Kou, Charles; Liu, Guanfeng; van den Bedem, Henry; Latombe, Jean-Claude; Halperin-Landsberg, Inbal; Altman, Russ Biagio

    2008-01-01

    Several applications in biology - e.g., incorporation of protein flexibility in ligand docking algorithms, interpretation of fuzzy X-ray crystallographic data, and homology modeling - require computing the internal parameters of a flexible fragment (usually, a loop) of a protein in order to connect its termini to the rest of the protein without causing any steric clash. One must often sample many such conformations in order to explore and adequately represent the conformational range of the studied loop. While sampling must be fast, it is made difficult by the fact that two conflicting constraints - kinematic closure and clash avoidance - must be satisfied concurrently. This paper describes two efficient and complementary sampling algorithms to explore the space of closed clash-free conformations of a flexible protein loop. The "seed sampling" algorithm samples broadly from this space, while the "deformation sampling" algorithm uses seed conformations as starting points to explore the conformation space around them at a finer grain. Computational results are presented for various loops ranging from 5 to 25 residues. More specific results also show that the combination of the sampling algorithms with a functional site prediction software (FEATURE) makes it possible to compute and recognize calcium-binding loop conformations. The sampling algorithms are implemented in a toolkit (LoopTK), which is available at https://simtk.org/home/looptk.

  11. Two tandem flexible loops in a viscous flow

    NASA Astrophysics Data System (ADS)

    Ye, Huilin; Wei, Heng; Huang, Haibo; Lu, Xi-yun

    2017-02-01

    Interaction between two tandem flexible loops with tension and bending stiffness in a viscous flow is investigated by numerical simulations. In most cases, the heads of the loops facing the oncoming flow are fixed but flapping around the head is allowed. The effect of the gap distance between the two passive flapping loops (G) on the drag coefficient is investigated in detail. Here, for the first time, the sudden drag force reduction at a specific G, i.e., Gc for the downstream loop has been found in the two tandem flexible loops system. It is different from the drag "jump" behavior in the two tandem rigid cylinder system. Although the drag is partially associated with the flapping amplitude, the drag force reduction of the downstream loop may be mainly attributed to flow regimes transition or vortices merging mode transition. The vortices merging is also analysed from a Lagrangian viewpoint, which gives insight into the mechanism. The effects of Reynolds number (20 ≤ Re ≤100 ) , bending coefficient (10-4≤K ≤2 ×10-2 ) , and tension coefficient (10 ≤S ≤1000 ) are also investigated and the relevant mechanism is explored. If the head of the downstream loop is set free to move laterally, the critical distance (Gc) where the sudden drag reduction occurs would further decrease compared to the fixed case, which is due to the early shedding regime transition.

  12. Two strategies to engineer flexible loops for improved enzyme thermostability

    PubMed Central

    Yu, Haoran; Yan, Yihan; Zhang, Cheng; Dalby, Paul A.

    2017-01-01

    Flexible sites are potential targets for engineering the stability of enzymes. Nevertheless, the success rate of the rigidifying flexible sites (RFS) strategy is still low due to a limited understanding of how to determine the best mutation candidates. In this study, two parallel strategies were applied to identify mutation candidates within the flexible loops of Escherichia coli transketolase (TK). The first was a “back to consensus mutations” approach, and the second was computational design based on ΔΔG calculations in Rosetta. Forty-nine single variants were generated and characterised experimentally. From these, three single-variants I189H, A282P, D143K were found to be more thermostable than wild-type TK. The combination of A282P with H192P, a variant constructed previously, resulted in the best all-round variant with a 3-fold improved half-life at 60 °C, 5-fold increased specific activity at 65 °C, 1.3-fold improved kcat and a Tm increased by 5 °C above that of wild type. Based on a statistical analysis of the stability changes for all variants, the qualitative prediction accuracy of the Rosetta program reached 65.3%. Both of the two strategies investigated were useful in guiding mutation candidates to flexible loops, and had the potential to be used for other enzymes. PMID:28145457

  13. Two strategies to engineer flexible loops for improved enzyme thermostability

    NASA Astrophysics Data System (ADS)

    Yu, Haoran; Yan, Yihan; Zhang, Cheng; Dalby, Paul A.

    2017-02-01

    Flexible sites are potential targets for engineering the stability of enzymes. Nevertheless, the success rate of the rigidifying flexible sites (RFS) strategy is still low due to a limited understanding of how to determine the best mutation candidates. In this study, two parallel strategies were applied to identify mutation candidates within the flexible loops of Escherichia coli transketolase (TK). The first was a “back to consensus mutations” approach, and the second was computational design based on ΔΔG calculations in Rosetta. Forty-nine single variants were generated and characterised experimentally. From these, three single-variants I189H, A282P, D143K were found to be more thermostable than wild-type TK. The combination of A282P with H192P, a variant constructed previously, resulted in the best all-round variant with a 3-fold improved half-life at 60 °C, 5-fold increased specific activity at 65 °C, 1.3-fold improved kcat and a Tm increased by 5 °C above that of wild type. Based on a statistical analysis of the stability changes for all variants, the qualitative prediction accuracy of the Rosetta program reached 65.3%. Both of the two strategies investigated were useful in guiding mutation candidates to flexible loops, and had the potential to be used for other enzymes.

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. Role of enzyme-substrate flexibility in catalytic activity: an evolutionary perspective.

    PubMed

    Demetrius, L

    1998-09-21

    Site-directed mutagenesis has proved an effective experimental technique to investigate catalytic mechanisms and to determine relations between enzyme structure and function. This article invokes an analytical model based on evolution by mutation and natural selection-Nature's analogue of site-directed mutagenesis-to derive a set of general rules relating enzyme structure and activity. The catalysts are described in terms of the structural parameters, rigidity and flexibility, and the functional variables, reaction rate and substrate specificity. The evolutionary model predicts the following structure-activity relations: (a) rigid enzyme-flexible substrate: large variation in reaction rates, broad substrate specificity; (b) rigid enzyme-rigid substrate: diffusion controlled rates, absolute specificity; (c) flexible enzyme-rigid substrate: intermediate reaction rates, group specificity; (d) flexible enzyme-flexible substrate: slow rates, absolute specificity. Spectroscopic methods and X-ray crystallography now yield important characteristics of enzyme-substrate complexes such as molecular flexibility. The evolutionary analysis we have exploited provides general principles for inferring catalytic activity from structural studies of enzyme-substrate complexes.

  19. Closed loop control of a robot assisted smart flexible needle for percutaneous intervention.

    PubMed

    Maria Joseph, F O; Hutapea, P; Dicker, A; Yu, Y; Podder, T

    2015-08-01

    This paper presents the experimental evaluation of a coordinated control system for a robot and robot-driven shape memory alloy (SMA) actuated smart flexible needle capable of following a curved path for percutaneous intervention. The robot driving the needle is considered the outer loop and the non-linear SMA actuated flexible needle system comprises the inner loop. The two feedback control loops are coordinated in such a way that the robot drives the needle while monitoring the needle's actual deflection against a preplanned ideal trajectory, so that the needle tip reaches the target location within an acceptable accuracy. In air and in water experimental results are presented to validate the ability of the proposed coordinated controller to track the overall desired trajectory which includes the combined trajectory of the robot driver and the needle.

  20. 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

  1. 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

    2015-10-23

    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.

  2. Effects of FGFR2 kinase activation loop dynamics on catalytic activity.

    PubMed

    Karp, Jerome M; Sparks, Samuel; Cowburn, David

    2017-02-01

    The structural mechanisms by which receptor tyrosine kinases (RTKs) regulate catalytic activity are diverse and often based on subtle changes in conformational dynamics. The regulatory mechanism of one such RTK, fibroblast growth factor receptor 2 (FGFR2) kinase, is still unknown, as the numerous crystal structures of the unphosphorylated and phosphorylated forms of the kinase domains show no apparent structural change that could explain how phosphorylation could enable catalytic activity. In this study, we use several enhanced sampling molecular dynamics (MD) methods to elucidate the structural changes to the kinase's activation loop that occur upon phosphorylation. We show that phosphorylation favors inward motion of Arg664, while simultaneously favoring outward motion of Leu665 and Pro666. The latter structural change enables the substrate to bind leading to its resultant phosphorylation. Inward motion of Arg664 allows it to interact with the γ-phosphate of ATP as well as the substrate tyrosine. We show that this stabilizes the tyrosine and primes it for the catalytic phosphotransfer, and it may lower the activation barrier of the phosphotransfer reaction. Our work demonstrates the value of including dynamic information gleaned from computer simulation in deciphering RTK regulatory function.

  3. Effects of FGFR2 kinase activation loop dynamics on catalytic activity

    PubMed Central

    2017-01-01

    The structural mechanisms by which receptor tyrosine kinases (RTKs) regulate catalytic activity are diverse and often based on subtle changes in conformational dynamics. The regulatory mechanism of one such RTK, fibroblast growth factor receptor 2 (FGFR2) kinase, is still unknown, as the numerous crystal structures of the unphosphorylated and phosphorylated forms of the kinase domains show no apparent structural change that could explain how phosphorylation could enable catalytic activity. In this study, we use several enhanced sampling molecular dynamics (MD) methods to elucidate the structural changes to the kinase’s activation loop that occur upon phosphorylation. We show that phosphorylation favors inward motion of Arg664, while simultaneously favoring outward motion of Leu665 and Pro666. The latter structural change enables the substrate to bind leading to its resultant phosphorylation. Inward motion of Arg664 allows it to interact with the γ-phosphate of ATP as well as the substrate tyrosine. We show that this stabilizes the tyrosine and primes it for the catalytic phosphotransfer, and it may lower the activation barrier of the phosphotransfer reaction. Our work demonstrates the value of including dynamic information gleaned from computer simulation in deciphering RTK regulatory function. PMID:28151998

  4. The central loop of Escherichia coli glutamine synthetase is flexible and functionally passive.

    PubMed

    Pearson, Josh T; Dabrowski, Michael J; Kung, Irene; Atkins, William M

    2005-04-15

    Bacterial glutamine synthetases (GSs) are dodecameric aggregates comprised of two face-to-face hexameric rings, which form a cylindrical aqueous channel. Available crystal structures indicate that each subunit provides a 'central loop' that protrudes into this channel. Residues on either side of this loop contribute directly to substrate or metal ion cofactor binding. Although it has been suggested that this conspicuous structural feature may be functionally important, a systematic structure-function analysis of this loop has not been done. Here, we examine the behavior of a cysteine mutant, E165C, which yields inter-subunit disulfide bonds connecting the central loops. The inter-subunit disulfide bonds are readily detected by electrospray ionization mass spectrometry. Based on molecular models, the disulfide bonds would form only if the engineered cysteines on adjacent subunits moved approximately 5 A. Surprisingly, inter-subunit disulfide bonds between the central loops caused no detectable changes in the KMs for glutamate or ATP, nor the KD for either ATP or the transition state analog (L)-methionine sulfoximine (MSOX). Furthermore, covalent and quantitative adduction of the E165C mutant with iodo-acetamido-pyrene yielded nearly fully active enzyme bearing fluorescent pyrene excimers. The relative contribution of pyrene monomers to excimers in the steady state fluorescence is temperature dependent, suggesting thermal equilibrium between loop conformational states. However, the monomer-excimer ratio is independent of ligands such as MSOX, glutamate, or Mn2+. These results validate the suspected flexibility of the central loop, but raise significant doubt about its direct functional role in GS catalysis via conformational switching, including the proposed regulation of GS via ADP-ribosylation within this loop.

  5. Characterizing Solution Surface Loop Conformational Flexibility of the GM2 Activator Protein

    PubMed Central

    2015-01-01

    GM2AP has a β-cup topology with numerous X-ray structures showing multiple conformations for some of the surface loops, revealing conformational flexibility that may be related to function, where function is defined as either membrane binding associated with ligand binding and extraction or interaction with other proteins. Here, site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy and molecular dynamic (MD) simulations are used to characterize the mobility and conformational flexibility of various structural regions of GM2AP. A series of 10 single cysteine amino acid substitutions were generated, and the constructs were chemically modified with the methanethiosulfonate spin label. Continuous wave (CW) EPR line shapes were obtained and subsequently simulated using the microscopic order macroscopic disorder (MOMD) program. Line shapes for sites that have multiple conformations in the X-ray structures required two spectral components, whereas spectra of the remaining sites were adequately fit with single-component parameters. For spin labeled sites L126C and I66C, spectra were acquired as a function of temperature, and simulations provided for the determination of thermodynamic parameters associated with conformational change. Binding to GM2 ligand did not alter the conformational flexibility of the loops, as evaluated by EPR and NMR spectroscopies. These results confirm that the conformational flexibility observed in the surface loops of GM2AP crystals is present in solution and that the exchange is slow on the EPR time scale (>ns). Furthermore, MD simulation results are presented and agree well with the conformational heterogeneity revealed by SDSL. PMID:25127419

  6. Promotion of enzyme flexibility by dephosphorylation and coupling to the catalytic mechanism of a phosphohexomutase.

    PubMed

    Lee, Yingying; Villar, Maria T; Artigues, Antonio; Beamer, Lesa J

    2014-02-21

    The enzyme phosphomannomutase/phosphoglucomutase (PMM/PGM) from Pseudomonas aeruginosa catalyzes an intramolecular phosphoryl transfer across its phosphosugar substrates, which are precursors in the synthesis of exoproducts involved in bacterial virulence. Previous structural studies of PMM/PGM have established a key role for conformational change in its multistep reaction, which requires a dramatic 180° reorientation of the intermediate within the active site. Here hydrogen-deuterium exchange by mass spectrometry and small angle x-ray scattering were used to probe the conformational flexibility of different forms of PMM/PGM in solution, including its active, phosphorylated state and the unphosphorylated state that occurs transiently during the catalytic cycle. In addition, the effects of ligand binding were assessed through use of a substrate analog. We found that both phosphorylation and binding of ligand produce significant effects on deuterium incorporation. Phosphorylation of the conserved catalytic serine has broad effects on residues in multiple domains and is supported by small angle x-ray scattering data showing that the unphosphorylated enzyme is less compact in solution. The effects of ligand binding are generally manifested near the active site cleft and at a domain interface that is a site of conformational change. These results suggest that dephosphorylation of the enzyme may play two critical functional roles: a direct role in the chemical step of phosphoryl transfer and secondly through propagation of structural flexibility. We propose a model whereby increased enzyme flexibility facilitates the reorientation of the reaction intermediate, coupling changes in structural dynamics with the unique catalytic mechanism of this enzyme.

  7. 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.

  8. 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.

  9. 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.

  10. Design and Measurements of a Hybrid RF-MEMS Reconfigurable Loop Antenna on a Flexible Substrate (PREPRINT)

    DTIC Science & Technology

    2010-06-01

    AFRL-RY-WP-TP-2010-1147 DESIGN AND MEASUREMENTS OF A HYBRID RF-MEMS RECONFIGURABLE LOOP ANTENNA ON A FLEXIBLE SUBSTRATE (PREPRINT) Nelson... Antenna on a Flexible Substrate Nelson Sepulveda(1), Dimitrios E. Anagnostou* (2), Rafael A. Rodriguez-Solis(1), and John L. Ebel(3) (1... antenna was designed, fabricated (on a flexible substrate) and measured. The design concepts and measurement results are presented and discussed

  11. Crystal structure of Deinococcus radiodurans RecQ helicase catalytic core domain: the interdomain flexibility.

    PubMed

    Chen, Sheng-Chia; Huang, Chi-Hung; Yang, Chia Shin; Way, Tzong-Der; Chang, Ming-Chung; Chen, Yeh

    2014-01-01

    RecQ DNA helicases are key enzymes in the maintenance of genome integrity, and they have functions in DNA replication, recombination, and repair. In contrast to most RecQs, RecQ from Deinococcus radiodurans (DrRecQ) possesses an unusual domain architecture that is crucial for its remarkable ability to repair DNA. Here, we determined the crystal structures of the DrRecQ helicase catalytic core and its ADP-bound form, revealing interdomain flexibility in its first RecA-like and winged-helix (WH) domains. Additionally, the WH domain of DrRecQ is positioned in a different orientation from that of the E. coli RecQ (EcRecQ). These results suggest that the orientation of the protein during DNA-binding is significantly different when comparing DrRecQ and EcRecQ.

  12. Chloroperoxidase-Catalyzed Epoxidation of Cis-β-Methylstyrene:Distal Pocket Flexibility Tunes Catalytic Reactivity

    PubMed Central

    Morozov, Alexander N.; Chatfield, David C.

    2012-01-01

    Chloroperoxidase, the most versatile heme protein, has a hybrid active site pocket that shares structural features with peroxidases and cytochrome P450s. The simulation studies presented here show that the enzyme possesses a remarkable ability to efficiently utilize its hybrid structure, assuming structurally different peroxidase-like and P450-like distal pocket faces and thereby enhancing the inherent catalytic capability of the active center. We find that during epoxidation of cis-β-methylstyrene (CBMS), the native peroxidase-like aspect of the distal pocket is diminished as the polar Glu183 side chain is displaced away from the active center and the distal pocket takes on a more hydrophobic, P450-like, aspect. The P450-like distal pocket provides a significant enthalpic stabilization of ~4 kcal/mol of the 14 kcal/mol reaction barrier for gas-phase epoxidation of CMBS by an oxyferryl heme-thiolate species. This stabilization comes from breathing of the distal pocket. As until recently the active site of chloroperoxidase was postulated to be inflexible, these results suggest a new conceptual understanding of the enzyme’s versatility: catalytic reactivity is tuned by flexibility of the distal pocket. PMID:23020548

  13. 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.

  14. 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.

  15. 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.

  16. Substitutions in a flexible loop of horse liver alcohol dehydrogenase hinder the conformational change and unmask hydrogen transfer.

    PubMed

    Ramaswamy, S; Park, D H; Plapp, B V

    1999-10-19

    When horse liver alcohol dehydrogenase binds coenzyme, a rotation of about 10 degrees brings the catalytic domain closer to the coenzyme binding domain and closes the active site cleft. The conformational change requires that a flexible loop containing residues 293-298 in the coenzyme binding domain rearranges so that the coenzyme and some amino acid residues from the catalytic domain can be accommodated. The change appears to control the rate of dissociation of the coenzyme and to be necessary for installation of the proton relay system. In this study, directed mutagenesis produced the activated Gly293Ala/Pro295Thr enzyme. X-ray crystallography shows that the conformations of both free and complexed forms of the mutated enzyme and wild-type apoenzyme are very similar. Binding of NAD(+) and 2,2, 2-trifluoroethanol do not cause the conformational change, but the nicotinamide ribose moiety and alcohol are not in a fixed position. Although the Gly293Ala and Pro295Thr substitutions do not disturb the apoenzyme structure, molecular modeling shows that the new side chains cannot be accommodated in the closed native holoenzyme complex without steric alterations. The mutated enzyme may be active in the "open" conformation. The turnover numbers with ethanol and acetaldehyde increase 1.5- and 5.5-fold, respectively, and dissociation constants for coenzymes and other kinetic constants increase 40-2,000-fold compared to those of the native enzyme. Substrate deuterium isotope effects on the steady state V or V/K(m) parameters of 4-6 with ethanol or benzyl alcohol indicate that hydrogen transfer is a major rate-limiting step in catalysis. Steady state oxidation of benzyl alcohol is most rapid above a pK of about 9 for V and V/K(m) and is 2-fold faster in D(2)O than in H(2)O. The results are consistent with hydride transfer from a ground state zinc alkoxide that forms a low-barrier hydrogen bond with the hydroxyl group of Ser48.

  17. Removing the invariant salt bridge of parvalbumin increases flexibility in the AB-loop structure.

    PubMed

    Hoh, François; Cavé, Adrien; Strub, Marie Paule; Banères, Jean Louis; Padilla, André

    2009-08-01

    Parvalbumins (PVs) are calcium-buffer proteins that belong to the EF-hand family. Their N-terminal domain consists of two antiparallel helices A and B that make up a flat hydrophobic surface that is associated with the opposite side of the CD and EF binding sites. A single conserved Arg75-Glu81 salt bridge is buried in this hydrophobic interface. The structure of a rat PV mutant in which Arg75 was replaced by alanine was solved by molecular replacement. Unexpectedly, a large distance deviation of 7.8 A was observed for the AB loop but not for the residues that flank the R75A mutation. The thermal stability of the calcium-loaded form is lower (T(m) = 352.0 K; DeltaT(m) = -11.4 K) than that of the wild-type protein and the apo mutant is unfolded at room temperature. Weaker calcium or magnesium affinities were also measured for the R75A mutant (Ca(2+): K(1) = 4.21 x 10(7) M(-1), K(2) = 6.18 x 10(6) M(-1); Mg(2+): K(1) = 2.98 x 10(4) M(-1), K(2) = 3.09 x 10(3) M(-1)). Finally, comparison of the B factors showed an increase in the flexibility of the AB loop that is consistent with this region being more exposed to solvent in the mutant. The mutant structure therefore demonstrates the role of the salt bridge in attaching the nonbinding AB domain to the remaining protein core. Normal-mode analysis indeed indicated an altered orientation of the AB domain with regard to the CD-EF binding domains.

  18. Effect of charge distribution in a flexible loop on the bioluminescence color of firefly luciferases.

    PubMed

    Moradi, Ali; Hosseinkhani, Saman; Naderi-Manesh, Hossein; Sadeghizadeh, Majid; Alipour, Bagher Said

    2009-01-27

    Firefly luciferase is a monooxygenase that catalyzes the ATP-dependent conversion of firefly luciferin into a luciferyl-adenylate, which is oxidized to an electronically excited oxyluciferin in a multistep reaction and produces visible light with a remarkable quantum yield. The bioluminescence color of firefly luciferases is determined by the luciferase structure and assay conditions. Among different beetles, only luciferase from Phrixotrix railroad worm (Ph(RE)) emits red bioluminescence, naturally. The presence of Arg353 in Ph(RE) luciferase, which corresponds to the deleted residue in the other luciferases, is an important distinctive structural feature of it. Insertion of Arg356 into a green-emitter luciferase (Lampyris turkestanicus), corresponding to Arg353 in Phrixotrix hirtus, changed the emitted light from green to red. To further clarify the effect of this position on the light shift mechanism, four residues with similar sizes but different charges (Arg, Lys, Glu, and Gln) were inserted into Photinus pyralis luciferase, using site-specific insertion mutagenesis. Insertion of a residue with a positive side chain (Arg356 and Lys356) changed the light color to red, while insertion of a residue with a negative side chain (Glu356) had little effect on color. Insertion of a neutral residue (Gln356) at this position was performed without any change in bioluminescence spectra. Insertion of positively charged residues in this loop took place with a series of structural changes which were confirmed by fluorescence spectroscopy and homology modeling. Homology modeling reveals the appearance of a bulge in a flexible loop (T352-P359) upon mutation which shifts to the left side with a color change from green to red.

  19. Crystallographic and NMR evidence for flexibility in oligosaccharyltransferases and its catalytic significance.

    PubMed

    Nyirenda, James; Matsumoto, Shunsuke; Saitoh, Takashi; Maita, Nobuo; Noda, Nobuo N; Inagaki, Fuyuhiko; Kohda, Daisuke

    2013-01-08

    Oligosaccharyltransferase (OST) is a membrane-bound enzyme that catalyzes the transfer of an oligosaccharide to an asparagine residue in glycoproteins. It possesses a binding pocket that recognizes Ser and Thr residues at the +2 position in the N-glycosylation consensus, Asn-X-Ser/Thr. We determined the crystal structures of the C-terminal globular domains of the catalytic subunits of two archaeal OSTs. A comparison with previously determined structures identified a segment with remarkable conformational plasticity, induced by crystal contact effects. We characterized its dynamic properties in solution by (15)N NMR relaxation analyses. Intriguingly, the mobile region contains the +2 Ser/Thr-binding pocket. In agreement, the flexibility restriction forced by an engineered disulfide crosslink abolished the enzymatic activity, and its cleavage fully restored activity. These results suggest the necessity of multiple conformational states in the reaction. The dynamic nature of the Ser/Thr pocket could facilitate the efficient scanning of N-glycosylation sequons along nascent polypeptide chains.

  20. 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.

  1. On the modeling, and open loop control of a rotating thin flexible beam

    NASA Astrophysics Data System (ADS)

    Choura, Slim; Jayasuriya, Suhada; Medick, Matthew A.

    1989-12-01

    A set of governing differential equations is derived for the inplane motion of a rotating thin flexible beam. The beam is assumed to be linearly elastic and is connected to a rigid hub driven by a torque motor. Both flexural and extensional effects are included in the derivation. This coupling due to flexure and extension is usually neglected in studies dealing with the control of such a system. Models for typical control studies are often derived by utilizing an assumed mode approach where the mode shapes are obtained by solving the Euler-Bernoulli beam equation for flexural vibrations, with clamped-free or pinned-free boundary conditions. The coupled equations developed in this paper are used to demonstrate that typical models in control studies give satisfactory results up to a critical rotational speed. For the case where these coupled equations are specialized to simple flexure only, valid for low angular speeds, a unique feedforward control strategy can be derived. This is an open loop control strategy that enables total elimination of an a priori specified vibratory mode from the gross motion in a finite critical time.

  2. Automated stopped-in-dual-loop flow analysis system for catalytic determination of vanadium in drinking water.

    PubMed

    Teshima, Norio; Kuno, Masami; Ueda, Minoru; Ueda, Hisashi; Ohno, Shinsuke; Sakai, Tadao

    2009-07-15

    An automated stopped-in-dual-loop flow analysis (SIDL-FA) system is proposed for the determination of vanadium in drinking water. The chemistry is based on the vanadium-catalyzed oxidation reaction of p-anisidine by bromate in the presence of Tiron as an activator to produce a dye (lambda(max)=510 nm). A SIDL-FA system basically consists of a selection valve, three pumps (one is for delivering of standard/sample, and others are for reagents), two six-way injection valves, a spectrophotometric detector and a data acquisition device. A 100-microL coiled loop around a heated device is fitted onto each six-way injection valve. A well-mixed solution containing reagents and standard/sample is loaded into the first loop on a six-way valve, and then the same solution is loaded into the second loop on another six-way valve. The solutions are isolated by switching these two six-way valves, so that the catalytic reaction can be promoted. The net waste can be zero in this stage, because all pumps are turned off. Then each resulting solution is dispensed to the detector with suitable time lag. A touchscreen controller is developed to automatically carry out the original SIDL-FA protocol. The proposed SIDL-FA method allows vanadium to be quantified in the range of 0.1-2 microg L(-1) and is applied to the determination of vanadium in drinking water samples.

  3. 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

  4. Increasing the conformational entropy of the Ω-loop lid domain in PEPCK impairs catalysis and decreases catalytic fidelity†

    PubMed Central

    Johnson, Troy A.; Holyoak, Todd

    2010-01-01

    Many studies have shown that the dynamic motions of individual protein segments can play an important role in enzyme function. Recent structural studies on the gluconeogenic enzyme PEPCK demonstrate that PEPCK contains a 10-residue Ω-loop domain that acts as an active site lid. Based upon these structural studies we have previously proposed a model for the mechanism of PEPCK catalysis in which the conformation of this mobile lid-domain is energetically coupled to ligand binding resulting in the closed conformation of the lid, necessary for correct substrate positioning, becoming more energetically favorable as ligands associate with the enzyme. Here we test this model by the introduction of a point mutation (A467G) into the center of the Ω-loop lid that is designed to increase the entropic penalty for lid closure. Structural and kinetic characterization of this mutant enzyme demonstrates that the mutation has decreased the favorability of the enzyme adapting the closed lid conformation. As a consequence of this shift in the equilibrium defining the conformation of the active site lid, the enzyme’s ability to stabilize the reaction intermediate is reduced resulting in catalytic defect. This stabilization is initially surprising, as the lid domain makes no direct contacts with the enolate intermediate formed during the reaction. Furthermore, during the conversion of OAA to PEP, the destabilization of the lid closed conformation results in the reaction becoming decoupled as the enolate intermediate is protonated rather than phosphorylated resulting in the formation of pyruvate. Taken together, the structural and kinetic characterization of A467G-PEPCK support our model of the role of the active site lid in catalytic function and demonstrate that the shift in the lowest energy conformation between open and closed lid states is a function of the free energy available to the enzyme through ligand binding and the entropic penalty for ordering of the ten-residue Ω-loop

  5. Increasing the conformational entropy of the Omega-loop lid domain in phosphoenolpyruvate carboxykinase impairs catalysis and decreases catalytic fidelity .

    PubMed

    Johnson, Troy A; Holyoak, Todd

    2010-06-29

    Many studies have shown that the dynamic motions of individual protein segments can play an important role in enzyme function. Recent structural studies of the gluconeogenic enzyme phosphoenolpyruvate carboxykinase (PEPCK) demonstrate that PEPCK contains a 10-residue Omega-loop domain that acts as an active site lid. On the basis of these structural studies, we have previously proposed a model for the mechanism of PEPCK catalysis in which the conformation of this mobile lid domain is energetically coupled to ligand binding, resulting in the closed conformation of the lid, necessary for correct substrate positioning, becoming more energetically favorable as ligands associate with the enzyme. Here we test this model by introducing a point mutation (A467G) into the center of the Omega-loop lid that is designed to increase the entropic penalty for lid closure. Structural and kinetic characterization of this mutant enzyme demonstrates that the mutation has decreased the favorability of the enzyme adapting the closed lid conformation. As a consequence of this shift in the equilibrium defining the conformation of the active site lid, the enzyme's ability to stabilize the reaction intermediate is weakened, resulting in catalytic defect. This stabilization is initially surprising, as the lid domain makes no direct contacts with the enolate intermediate formed during the reaction. Furthermore, during the conversion of OAA to PEP, the destabilization of the lid-closed conformation results in the reaction becoming decoupled as the enolate intermediate is protonated rather than phosphorylated, resulting in the formation of pyruvate. Taken together, the structural and kinetic characterization of A467G-PEPCK supports our model of the role of the active site lid in catalytic function and demonstrates that the shift in the lowest-energy conformation between open and closed lid states is a function of the free energy available to the enzyme through ligand binding and the entropic

  6. The Ω-loop lid domain of phosphoenolpyruvate carboxykinase is essential for catalytic function.

    PubMed

    Johnson, Troy A; Holyoak, Todd

    2012-11-27

    Phosphoenolpyruvate carboxykinase (PEPCK) is an essential metabolic enzyme operating in the gluconeogenesis and glyceroneogenesis pathways. Recent studies have demonstrated that the enzyme contains a mobile active site lid domain that undergoes a transition between an open, disorded conformation and a closed, ordered conformation as the enzyme progresses through the catalytic cycle. The understanding of how this mobile domain functions in catalysis is incomplete. Previous studies showed that the closure of the lid domain stabilizes the reaction intermediate and protects the reactive intermediate from spurious protonation and thus contributes to the fidelity of the enzyme. To more fully investigate the roles of the lid domain in PEPCK function, we introduced three mutations that replaced the 11-residue lid domain with one, two, and three glycine residues. Kinetic analysis of the mutant enzymes demonstrates that none of the enzyme constructs exhibit any measurable kinetic activity, resulting in a decrease in the catalytic parameters of at least 10(6). Structural characterization of the mutants in complexes representing the catalytic cycle suggests that the inactivity is due to a role for the lid domain in the formation of the fully closed state of the enzyme that is required for catalytic function. In the absence of the lid domain, the enzyme is unable to achieve the fully closed state and is rendered inactive despite possessing all of the residues and substrates required for catalytic function. This work demonstrates how enzyme catalytic function can be abolished through the alteration of conformational equilibria despite all the elements required for chemical conversion of substrates to products remaining intact.

  7. 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)

  8. Two Gd(III) coordination polymers based on a flexible tricarboxylate: Syntheses, structures, luminescence and catalytic properties

    NASA Astrophysics Data System (ADS)

    Zhu, Yu; Zhu, Min; Liu, Pan; Xia, Li; Wu, Yunlong; Xie, Jimin

    2017-02-01

    Two Gadolinium coordination polymers {[Gd·(TTTA)·(H2O)2]·2H2O}n (1) and [Gd·(TTTA)·DMF]n (2) have been synthesized based on Gd(NO3)3·6H2O and the flexible tripodal ligand 2,2‧,2″-[1,3,5-triazine-2,4,6-triyltris(thio)]tris-acetic acid (H3TTTA) under hydrothermal conditions. In the structure of 1, the tridentate TTTA3- ligands connect the dimeric metal centers into an infinite one dimensional chain. While 2 shows a two dimensional network with tridentate TTTA3- ligands. The two complexes all quench the emission spectra after coordinated to the Gd3+ ions. The catalytic results indicate that two complexes show excellent activities for the cyanosilylation of benzaldehyde and its derivatives. Besides, 2 is better than 1 in the catalytic reactions due to more possibility of metal open sites.

  9. Flexible non-nucleotide linkers as loop replacements in short double helical RNAs

    PubMed Central

    Pils, Werner; Micura, Ronald

    2000-01-01

    Ethylene glycol oligomers have been studied systematically as non-nucleotide loop replacements in short hairpin oligoribonucleotides. Structural optimization concerns the length of the linkers and is based on the thermodynamic stabilities of the corresponding duplexes. The optimum linker is derived from heptakis (ethylene glycol) provided that the duplex end to be bridged comprises solely the terminal base pair; the optimum linker is derived from hexakis(ethylene glycol) if a dangling unpaired nucleotide is incorporated into the loop. Moreover, these linkers have been compared to other commonly used linker types which consist of repeating units of tris- or tetrakis(ethylene glycol) phosphate, or of 3-hydroxypropane-1-phosphate. In all cases, the correlation between linker length and duplex stability is independent of the kind of counter ions used (Na+, Na+/Mg2+, K+ or Li+). Furthermore, all duplexes with non-nucleotide loop replacements are less stable than those with the corresponding standard nucleotide loop. The results corroborate that the linkers are solvent-exposed and do not specifically interfere with the terminal nucleotides at the bridged duplex end. PMID:10756183

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

    PubMed

    Hoffmann, A; Herres-Pawlis, S

    2016-03-07

    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.

  11. Enhanced complexity and catalytic efficiency in the hydrolysis of phosphate diesters by rationally designed helix-loop-helix motifs.

    PubMed

    Razkin, Jesus; Lindgren, Johan; Nilsson, Helena; Baltzer, Lars

    2008-08-11

    HJ1, a 42-residue peptide that folds into a helix-loop-helix motif and dimerizes to form a four-helix bundle, successfully catalyzes the cleavage of "early stage" DNA model substrates in an aqueous solution at pH 7.0, with a rate enhancement in the hydrolysis of heptyl 4-nitrophenyl phosphate of over three orders of magnitude over that of the imidazole-catalyzed reaction, k(2)(HJ1)/k(2)(Im) = 3135. The second-order rate constant, k(2)(HJ1) was determined to be 1.58x10(-4) M(-1) s(-1). The catalyst successfully assembles residues that in a single elementary reaction step are capable of general-acid and general-base catalysis as well as transition state stabilization and proximity effects. The reactivity achieved with the HJ1 polypeptide, rationally designed to catalyze the hydrolysis of phosphodiesters, is based on two histidine residues flanked by four arginines and two adjacent tyrosine residues, all located on the surface of a helix-loop-helix motif. The introduction of Tyr residues close to the catalytic site improves efficiency, in the cleavage of activated aryl alkyl phosphates as well as less activated dialkyl phosphates. HJ1 is also effective in the cleavage of an RNA-mimic substrate, uridine-3'-2,2,2-trichloroethyl phosphate (leaving group pK(a) = 12.3) with a second-order rate constant of 8.23x10(-4) M(-1) s(-1) in aqueous solution at pH 7.0, some 500 times faster than the reaction catalyzed by imidazole, k(2)(HJ1)/k(2)(Im) = 496.

  12. Synthesis and evaluation of novel 3-C-alkylated-Neu5Ac2en derivatives as probes of influenza virus sialidase 150-loop flexibility.

    PubMed

    Rudrawar, Santosh; Kerry, Philip S; Rameix-Welti, Marie-Anne; Maggioni, Andrea; Dyason, Jeffrey C; Rose, Faith J; van der Werf, Sylvie; Thomson, Robin J; Naffakh, Nadia; Russell, Rupert J M; von Itzstein, Mark

    2012-11-21

    Novel 3-C-alkylated-Neu5Ac2en derivatives have been designed to target the expanded active site cavity of influenza virus sialidases with an open 150-loop, currently seen in X-ray crystal structures of influenza A virus group-1 (N1, N4, N5, N8), but not group-2 (N2, N9), sialidases. The compounds show selectivity for inhibition of H5N1 and pdm09 H1N1 sialidases over an N2 sialidase, providing evidence of the relative 150-loop flexibility of these sialidases. In a complex with N8 sialidase, the C3 substituent of 3-phenylally-Neu5Ac2en occupies the 150-cavity while the central ring and the remaining substituents bind the active site as seen for the unsubstituted template. This new class of inhibitors, which can 'trap' the open 150-loop form of the sialidase, should prove useful as probes of 150-loop flexibility.

  13. 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.

  14. 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.

  15. 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.

  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. 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.

  18. 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

  19. A Continuous-Adaptive DDRx Interface with Flexible Round-Trip-Time and Full Self Loop-Backed AC Test

    NASA Astrophysics Data System (ADS)

    Haraguchi, Masaru; Osawa, Tokuya; Yamazaki, Akira; Morishima, Chikayoshi; Morihara, Toshinori; Morooka, Yoshikazu; Okuno, Yoshihiro; Arimoto, Kazutami

    This paper describes new DDRx SDRAM interface architecture suitable for system-on-chip (SOC) implementation. Our test chip fabricated in a 90-nm CMOS process adopts three key schemes and achieves 960 Mb/s/pin operations with 32 bits width. One of new schemes is to suppress timing skew with rising-edge signal transmission I/O circuit and look-up table type impedance calibration circuit. DQS round-trip-time, propagation delay from rising edge of system clock in SOC to arrival of DQS at input PAD of SOC during read operation, becomes longer than one clock cycle time as for DDR2 interface and beyond. Flexible DQS round-trip-time scheme can allow wide range up to N/2 cycles in N bits burst read operation. In addition, full self loop-backed test scheme is also proposed to measure AC timing parameters without high-end tester. The architecture reported in this paper can be continuously adaptive to realize higher data-rate and cost-efficient DDRx-SDRAM interface for various kinds of SOC.

  20. 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.

  1. 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.

  2. Improving the reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase through stabilizing a long loop in domain B

    PubMed Central

    Li, Zhu; Duan, Xuguo; Chen, Sheng; Wu, Jing

    2017-01-01

    The reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase were improved through site-directed mutagenesis. By using multiple sequence alignment and PoPMuSiC algorithm, Ser187 and Asn188, which located within a long loop in Domain B of Bacillus licheniformis α-amylase, were selected for mutation. In addition, Ala269, which is adjacent to Ser187 and Asn188, was also investigated. Seven mutants carrying the mutations S187D, N188T, N188S, A269K, A269K/S187D, S187D/N188T, and A269K/S187D/N188T were generated and characterized. The most thermostable mutant, A269K/S187D/N188T, exhibited a 9-fold improvement in half-life at 95°C and pH 5.5, compared with that of the wild-type enzyme. Mutant A269K/S187D/N188T also exhibited improved catalytic efficiency. The catalytic efficiency of mutant A269K/S187D/N188T reached 5.87×103±0.17 g·L-1·s-1 at pH 5.5, which is 1.84-fold larger than the corresponding value determined for the wild-type enzyme. Furthermore, the structure analysis showed that immobilization of the loop containing Ser187 and Asn188 plays a significant role in developing the properties of Bacillus licheniformis α-amylase. PMID:28253342

  3. Structural analysis of the PP2C phosphatase tPphA from Thermosynechococcus elongatus: a flexible flap subdomain controls access to the catalytic site.

    PubMed

    Schlicker, Christine; Fokina, Oleksandra; Kloft, Nicole; Grüne, Tim; Becker, Stefan; Sheldrick, George M; Forchhammer, Karl

    2008-02-15

    The homologue of the phosphoprotein PII phosphatase PphA from Thermosynechococcus elongatus, termed tPphA, was identified and its structure was resolved in two different space groups, C222(1) and P4(1)2(1)2, at a resolution of 1.28 and 3.05 A, respectively. tPphA belongs to a large and widely distributed subfamily of Mg(2+)/Mn(2+)-dependent phosphatases of the PPM superfamily characterized by the lack of catalytic and regulatory domains. The core structure of tPphA shows a high degree of similarity to the two PPM structures identified so far. In contrast to human PP2C, but similar to Mycobacterium tuberculosis phosphatase PstP, the catalytic centre exhibits a third metal ion in addition to the dinuclear metal centre universally conserved in all PPM members. The fact that the third metal is only liganded by amino acids, which are universally conserved in all PPM members, implies that the third metal could be general for all members of this family. As a specific feature of tPphA, a flexible subdomain, previously recognized as a flap domain, could be revealed. Comparison of different structural isomers of tPphA as well as site-specific mutagenesis implied that the flap domain is involved in substrate binding and catalytic activity. The structural arrangement of the flap domain was accompanied by a large side-chain movement of an Arg residue (Arg169) at the basis of the flap. Mutation of this residue strongly impaired protein stability as well as catalytic activity, emphasizing the importance of this amino acid for the regional polysterism of the flap subdomain and confirming the assumption that flap domain flexibility is involved in catalysis.

  4. Numerical Analysis of a Flexible Dual Loop Coil and its Experimental Validation for pre-Clinical Magnetic Resonance Imaging of Rodents at 7 T

    NASA Astrophysics Data System (ADS)

    Solis-Najera, S.; Vazquez, F.; Hernandez, R.; Marrufo, O.; Rodriguez, A. O.

    2016-12-01

    A surface radio frequency coil was developed for small animal image acquisition in a pre-clinical magnetic resonance imaging system at 7 T. A flexible coil composed of two circular loops was developed to closely cover the object to be imaged. Electromagnetic numerical simulations were performed to evaluate its performance before the coil construction. An analytical expression of the mutual inductance for the two circular loops as a function of the separation between them was derived and used to validate the simulations. The RF coil is composed of two circular loops with a 5 cm external diameter and was tuned to 300 MHz and 50 Ohms matched. The angle between the loops was varied and the Q factor was obtained from the S11 simulations for each angle. B1 homogeneity was also evaluated using the electromagnetic simulations. The coil prototype was designed and built considering the numerical simulation results. To show the feasibility of the coil and its performance, saline-solution phantom images were acquired. A correlation of the simulations and imaging experimental results was conducted showing a concordance of 0.88 for the B1 field. The best coil performance was obtained at the 90° aperture angle. A more realistic phantom was also built using a formaldehyde-fixed rat phantom for ex vivo imaging experiments. All images showed a good image quality revealing clearly defined anatomical details of an ex vivo rat.

  5. 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.

  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. The 1.59Å resolution structure of the minor pseudopilin EpsH of Vibrio cholerae reveals a long flexible loop.

    PubMed

    Raghunathan, Kannan; Vago, Frank S; Grindem, David; Ball, Terry; Wedemeyer, William J; Bagdasarian, Michael; Arvidson, Dennis N

    2014-02-01

    The type II secretion complex exports folded proteins from the periplasm to the extracellular milieu. It is used by the pathogenic bacterium Vibrio cholerae to export several proteins, including its major virulence factor, cholera toxin. The pseudopilus is an essential component of the type II secretion system and likely acts as a piston to push the folded proteins across the outer membrane through the secretin pore. The pseudopilus is composed of the major pseudopilin, EpsG, and four minor pseudopilins, EpsH, EpsI, EpsJ and EpsK. We determined the x-ray crystal structure of the head domain of EpsH at 1.59Å resolution using molecular replacement with the previously reported EpsH structure, 2qv8, as the template. Three additional N-terminal amino acids present in our construct prevent an artifactual conformation of residues 160-166, present in one of the two monomers of the 2qv8 structure. Additional crystal contacts stabilize a long flexible loop comprised of residues 104-135 that is more disordered in the 2qv8 structure but is partially observed in our structure in very different positions for the two EpsH monomers in the asymmetric unit. In one of the conformations the loop is highly extended. Modeling suggests the highly charged loop is capable of contacting EpsG and possibly secreted protein substrates, suggesting a role in specificity of pseudopilus assembly or secretion function.

  8. Alteration of the flexible loop in 1-deoxy-D-xylulose-5-phosphate reductoisomerase boosts enthalpy-driven inhibition by fosmidomycin.

    PubMed

    Kholodar, Svetlana A; Tombline, Gregory; Liu, Juan; Tan, Zhesen; Allen, C Leigh; Gulick, Andrew M; Murkin, Andrew S

    2014-06-03

    1-Deoxy-d-xylulose-5-phosphate reductoisomerase (DXR), which catalyzes the first committed step in the 2-C-methyl-d-erythritol 4-phosphate pathway of isoprenoid biosynthesis used by Mycobacterium tuberculosis and other infectious microorganisms, is absent in humans and therefore an attractive drug target. Fosmidomycin is a nanomolar inhibitor of DXR, but despite great efforts, few analogues with comparable potency have been developed. DXR contains a strictly conserved residue, Trp203, within a flexible loop that closes over and interacts with the bound inhibitor. We report that while mutation to Ala or Gly abolishes activity, mutation to Phe and Tyr only modestly impacts kcat and Km. Moreover, pre-steady-state kinetics and primary deuterium kinetic isotope effects indicate that while turnover is largely limited by product release for the wild-type enzyme, chemistry is significantly more rate-limiting for W203F and W203Y. Surprisingly, these mutants are more sensitive to inhibition by fosmidomycin, resulting in Km/Ki ratios up to 19-fold higher than that of wild-type DXR. In agreement, isothermal titration calorimetry revealed that fosmidomycin binds up to 11-fold more tightly to these mutants. Most strikingly, mutation strongly tips the entropy-enthalpy balance of total binding energy from 50% to 75% and 91% enthalpy in W203F and W203Y, respectively. X-ray crystal structures suggest that these enthalpy differences may be linked to differences in hydrogen bond interactions involving a water network connecting fosmidomycin's phosphonate group to the protein. These results confirm the importance of the flexible loop, in particular Trp203, in ligand binding and suggest that improved inhibitor affinity may be obtained against the wild-type protein by introducing interactions with this loop and/or the surrounding structured water network.

  9. Structure of Trypanosoma brucei glutathione synthetase: Domain and loop alterations in the catalytic cycle of a highly conserved enzyme

    PubMed Central

    Fyfe, Paul K.; Alphey, Magnus S.; Hunter, William N.

    2010-01-01

    Glutathione synthetase catalyses the synthesis of the low molecular mass thiol glutathione from l-γ-glutamyl-l-cysteine and glycine. We report the crystal structure of the dimeric enzyme from Trypanosoma brucei in complex with the product glutathione. The enzyme belongs to the ATP-grasp family, a group of enzymes known to undergo conformational changes upon ligand binding. The T. brucei enzyme crystal structure presents two dimers in the asymmetric unit. The structure reveals variability in the order and position of a small domain, which forms a lid for the active site and serves to capture conformations likely to exist during the catalytic cycle. Comparisons with orthologous enzymes, in particular from Homo sapiens and Saccharomyces cerevisae, indicate a high degree of sequence and structure conservation in part of the active site. Structural differences that are observed between the orthologous enzymes are assigned to different ligand binding states since key residues are conserved. This suggests that the molecular determinants of ligand recognition and reactivity are highly conserved across species. We conclude that it would be difficult to target the parasite enzyme in preference to the host enzyme and therefore glutathione synthetase may not be a suitable target for antiparasitic drug discovery. PMID:20045436

  10. Stopped-in-loop flow analysis system for successive determination of trace vanadium and iron in drinking water using their catalytic reactions.

    PubMed

    Ayala Quezada, Alejandro; Ohara, Keisuke; Ratanawimarnwong, Nuanlaor; Nacapricha, Duangjai; Murakami, Hiroya; Teshima, Norio; Sakai, Tadao

    2015-11-01

    An automated stopped-in-loop flow analysis (SILFA) system is proposed for the successive catalytic determination of vanadium and iron. The determination of vanadium was based on the p-anisidine oxidation by potassium bromate in the presence of Tiron as an activator to form a reddish dye, which has an absorption maximum at 510 nm. The selectivity of the vanadium determination was greatly improved by adding diphosphate as a masking agent of iron. For the iron determination, an iron-catalyzed oxidative reaction of p-anisidine by hydrogen peroxide with 1,10-phenanthroline as an activator to produce a reddish dye (510 nm) was employed. The SILFA system consisted of two peristaltic pumps, two six-port injection valves, a four-port selection valve, a heater device, a spectrophotometric detector and a data acquisition device. One six-port injection valve was used for the isolation of a mixed solution of standard/sample and reagent to promote each catalytic reaction, and another six-port injection valve was used for switching the reagent for vanadium or iron to achieve selective determination of each analyte. The above mentioned four-port selection valve was used to select standard solutions or sample. These three valves and the two peristaltic pumps were controlled by a built-in programmable logic controller in a touchscreen controller. The obtained results showed that the proposed SILFA monitoring system constituted an effective approach for the selective determination of vanadium and iron. The limits of detection, 0.052 and 0.55 µg L(-1), were obtained for vanadium and iron, respectively. The proposed system was successfully applied to drinking water samples without any preconcentration procedures.

  11. The regulatory subunit of Escherichia coli aspartate carbamoyltransferase may influence homotropic cooperativity and heterotropic interactions by a direct interaction with the loop containing residues 230-245 of the catalytic chain.

    PubMed Central

    Newton, C J; Kantrowitz, E R

    1990-01-01

    A recent x-ray structure of aspartate carbamoyltransferase (carbamoyl-phosphate: L-aspartate carbamoyl-transferase, EC 2.1.3.2) with phosphonoacetamide bound [Gouaux, J. E. & Lipscomb, W. N. (1990) Biochemistry 29, 389-402] shows an interaction between Asp-236 of the catalytic chain and Lys-143 of the regulatory chain. Asp-236 is part of the loop containing residues 230-245 (240s) of the catalytic chain that undergoes a significant conformational change between the tight and the relaxed states of the enzyme. Furthermore, side-chain interactions between the 240s loop and other portions of the enzyme have been shown to be important for the low activity and low affinity of the tight state and the high activity and high affinity of the relaxed state. To determine whether the intersubunit link between Lys-143 of the regulatory chain and Asp-236 of the catalytic chain is important for either homotropic cooperativity and/or the heterotropic interactions in aspartate carbamoyltransferase, site-specific mutagenesis was used to replace Asp-236 with alanine. The mutant enzyme exhibits full activity and a loss of both homotropic cooperativity and heterotropic interactions. Furthermore, the aspartate concentration at half the maximal observed specific activity is reduced by approximately 8-fold. The mutant enzyme exhibits normal thermal stability but drastically altered reactivity toward p-hydroxymercuribenzoate. The catalytic subunit of the mutant and wild-type enzymes have very similar properties. These results, in conjunction with previous experiments, suggest that the intersubunit link involving Asp-236 is involved in the stabilization of the 240s loop in its tight-state position and that the regulatory subunits exert their effect on the catalytic subunits by influencing the position of the 240s loop. PMID:2179954

  12. 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

  13. Decoupled and linear quadratic regulator control of a large, flexible space antenna with an observer in the control loop

    NASA Technical Reports Server (NTRS)

    Hamer, H. A.; Johnson, K. G.; Young, J. W.

    1985-01-01

    An analysis is performed to compare decoupled and linear quadratic regulator (LQR) procedures for the control of a large, flexible space antenna. Control objectives involve: (1) commanding changes in the rigid-body modes, (2) nulling initial disturbances in the rigid-body modes, or (3) nulling initial disturbances in the first three flexible modes. Control is achieved with two three-axis control-moment gyros located on the antenna column. Results are presented to illustrate various effects on control requirements for the two procedures. These effects include errors in the initial estimates of state variables, variations in the type, number, and location of sensors, and deletions of state-variable estimates for certain flexible modes after control activation. The advantages of incorporating a time lag in the control feedback are also illustrated. In addition, the effects of inoperative-control situations are analyzed with regard to control requirements and resultant modal responses. Comparisons are included which show the effects of perfect state feedback with no residual modes (ideal case). Time-history responses are presented to illustrate the various effects on the control procedures.

  14. Porphyrin Binding to Gun4 Protein, Facilitated by a Flexible Loop, Controls Metabolite Flow through the Chlorophyll Biosynthetic Pathway.

    PubMed

    Kopečná, Jana; Cabeza de Vaca, Israel; Adams, Nathan B P; Davison, Paul A; Brindley, Amanda A; Hunter, C Neil; Guallar, Victor; Sobotka, Roman

    2015-11-20

    In oxygenic phototrophs, chlorophylls, hemes, and bilins are synthesized by a common branched pathway. Given the phototoxic nature of tetrapyrroles, this pathway must be tightly regulated, and an important regulatory role is attributed to magnesium chelatase enzyme at the branching between the heme and chlorophyll pathway. Gun4 is a porphyrin-binding protein known to stimulate in vitro the magnesium chelatase activity, but how the Gun4-porphyrin complex acts in the cell was unknown. To address this issue, we first performed simulations to determine the porphyrin-docking mechanism to the cyanobacterial Gun4 structure. After correcting crystallographic loop contacts, we determined the binding site for magnesium protoporphyrin IX. Molecular modeling revealed that the orientation of α6/α7 loop is critical for the binding, and the magnesium ion held within the porphyrin is coordinated by Asn-211 residue. We also identified the basis for stronger binding in the Gun4-1 variant and for weaker binding in the W192A mutant. The W192A-Gun4 was further characterized in magnesium chelatase assay showing that tight porphyrin binding in Gun4 facilitates its interaction with the magnesium chelatase ChlH subunit. Finally, we introduced the W192A mutation into cells and show that the Gun4-porphyrin complex is important for the accumulation of ChlH and for channeling metabolites into the chlorophyll biosynthetic pathway.

  15. Porphyrin Binding to Gun4 Protein, Facilitated by a Flexible Loop, Controls Metabolite Flow through the Chlorophyll Biosynthetic Pathway*

    PubMed Central

    Kopečná, Jana; Cabeza de Vaca, Israel; Adams, Nathan B. P.; Davison, Paul A.; Brindley, Amanda A.; Hunter, C. Neil; Guallar, Victor; Sobotka, Roman

    2015-01-01

    In oxygenic phototrophs, chlorophylls, hemes, and bilins are synthesized by a common branched pathway. Given the phototoxic nature of tetrapyrroles, this pathway must be tightly regulated, and an important regulatory role is attributed to magnesium chelatase enzyme at the branching between the heme and chlorophyll pathway. Gun4 is a porphyrin-binding protein known to stimulate in vitro the magnesium chelatase activity, but how the Gun4-porphyrin complex acts in the cell was unknown. To address this issue, we first performed simulations to determine the porphyrin-docking mechanism to the cyanobacterial Gun4 structure. After correcting crystallographic loop contacts, we determined the binding site for magnesium protoporphyrin IX. Molecular modeling revealed that the orientation of α6/α7 loop is critical for the binding, and the magnesium ion held within the porphyrin is coordinated by Asn-211 residue. We also identified the basis for stronger binding in the Gun4-1 variant and for weaker binding in the W192A mutant. The W192A-Gun4 was further characterized in magnesium chelatase assay showing that tight porphyrin binding in Gun4 facilitates its interaction with the magnesium chelatase ChlH subunit. Finally, we introduced the W192A mutation into cells and show that the Gun4-porphyrin complex is important for the accumulation of ChlH and for channeling metabolites into the chlorophyll biosynthetic pathway. PMID:26446792

  16. Experimental and Theoretical Study of the Movement of the Wpd Flexible Loop of Human Protein Tyrosine Phosphatase PTP1B in Complex with Halide Ions

    NASA Astrophysics Data System (ADS)

    Katz, Aline; Saenz-Méndez, Patricia; Cousido-Siah, Alexandra; Podjarny, Alberto D.; Ventura, Oscar N.

    2012-11-01

    Protein tyrosine phosphorylation is a post-translational modification mechanism, crucial for the regulation of nearly all aspects of cell life. This dynamic, reversible process is regulated by the balanced opposing activity of protein tyrosine kinases and protein tyrosine phosphatases. In particular, the protein tyrosine phosphatase 1B (PTP1B) is implicated in the regulation of the insulin-receptor activity, leptin-stimulated signal transduction pathways and other clinically relevant metabolic routes, and it has been found overexpressed or overregulated in human breasts, colon and ovary cancers. The WPD loop of the enzyme presents an inherent flexibility, and it plays a fundamental role in the enzymatic catalysis, turning it into a potential target in the design of new efficient PTP1B inhibitors. In order to determine the interactions that control the spatial conformation adopted by the WPD loop, complexes between the enzyme and halide ions (Br- and I- in particular) were crystallized and their crystallographic structure determined, and the collective movements of the aforementioned complexes were studied through Molecular Dynamics (MD) simulations. Both studies yielded concordant results, indicating the existence of a relationship between the identity of the ion present in the complex and the strength of the interactions it establishes with the surrounding protein residues.

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

    PubMed

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

    2013-08-02

    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(2+) and Mg(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(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 (1)H-(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(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.

  18. Emerging Behavioral Flexibility in Loop Writing: A longitudinal study in 7- to 9-Year-Old Primary School Children.

    PubMed

    Bosga-Stork, Ida M; Bosga, Jurjen; Meulenbroek, Ruud G J

    2017-04-01

    The development of the ability to adapt one's motor performance to the constraints of a movement task was examined in a longitudinal study involving 7 to-9-year-old children who were asked to perform a preparatory handwriting task. The capacity for sensorimotor synchronization was captured by the standard deviation of the relative phase between pacing signals and writing movements and the capacity to adjust wrist-finger coordination while performing repetitive movements was analyzed by autocorrelations of the vertical pen-tip displacements. While the capacity for synchronization improved with age, the autocorrelations were positive at short time lags only and hardly changed with age. A measure of "the long-term memory" of time series (Hurst exponent) confirmed that the findings were systematic rather than noise. Collectively, the results indicate that flexible movement strategies emerge early on in the first 3 years of formal handwriting education. Implications for educational and clinical practice are considered.

  19. Syntheses, structures, molecular and cationic recognitions and catalytic properties of two lanthanide coordination polymers based on a flexible tricarboxylate

    NASA Astrophysics Data System (ADS)

    Zhu, Yu; Wang, Yan-Mei; Xu, Ji; Liu, Pan; Weththasinha, H. A. B. M. D.; Wu, Yun-Long; Lu, Xiao-Qing; Xie, Ji-Min

    2014-11-01

    Two lanthanide coordination polymers, namely, {[La(TTTA)(H2O)2]·2H2O}n (La-TTTA) and [Nd(TTTA)(H2O)2]·2H2O}n (Nd-TTTA) have been hydrothermally synthesized through the reaction of lanthanide ions (La3+ and Nd3+) with the flexible tripodal ligand 2,2‧,2″-[1,3,5-triazine-2,4,6-triyltris(thio)]tris-acetic acid (H3TTTA). La-TTTA and Nd-TTTA are isostructural and both show three dimensional structures. La-TTTA and Nd-TTTA show good recognition of amine molecules via quenching the luminescent intensities in amines emulsions. They can also recognize Fe3+, Cu2+, Mg2+, Cr3+ and Co2+ ions with the quenching the peak around 361 nm when the compounds immersed in ionic solutions. The two compounds act as efficient Lewis acid catalysts for the cyanosilylation of benzaldehyde and derivatives in high yields shortly due to the strong Lewis acidity and the possible open sites of the lanthanide ions.

  20. Syntheses, structures, molecular and cationic recognitions and catalytic properties of two lanthanide coordination polymers based on a flexible tricarboxylate

    SciTech Connect

    Zhu, Yu; Wang, Yan-Mei; Xu, Ji; Liu, Pan; Weththasinha, H.A.B.M.D.; Wu, Yun-Long; Lu, Xiao-Qing; Xie, Ji-Min

    2014-11-15

    Two lanthanide coordination polymers, namely, ([La(TTTA)(H{sub 2}O){sub 2}]·2H{sub 2}O){sub n} (La-TTTA) and [Nd(TTTA)(H{sub 2}O){sub 2}]·2H{sub 2}O){sub n} (Nd-TTTA) have been hydrothermally synthesized through the reaction of lanthanide ions (La{sup 3+} and Nd{sup 3+}) with the flexible tripodal ligand 2,2′,2″-[1,3,5-triazine-2,4,6-triyltris(thio)]tris-acetic acid (H{sub 3}TTTA). La-TTTA and Nd-TTTA are isostructural and both show three dimensional structures. La-TTTA and Nd-TTTA show good recognition of amine molecules via quenching the luminescent intensities in amines emulsions. They can also recognize Fe{sup 3+}, Cu{sup 2+}, Mg{sup 2+}, Cr{sup 3+} and Co{sup 2+} ions with the quenching the peak around 361 nm when the compounds immersed in ionic solutions. The two compounds act as efficient Lewis acid catalysts for the cyanosilylation of benzaldehyde and derivatives in high yields shortly due to the strong Lewis acidity and the possible open sites of the lanthanide ions. - Graphical abstract: We have synthesized two isostructural 3D compounds based on H{sub 3}TTTA. They are chemical sensor of amine solvents and cations. They have higher yields and TOFs to catalyze cyanosilylation reactions. - Highlights: • The compounds show recognition of amine molecules via quenching luminescent intensities. • The compounds recognize Fe{sup 3+}, Cu{sup 2+}, Mg{sup 2+}, Cr{sup 3+} and Co{sup 2+} ions via quenching the peak around 361 nm. • They act as efficient Lewis acid catalysts for the cyanosilylation reactions in high yields.

  1. 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.

  2. The structure of a dual-specificity tyrosine phosphorylation-regulated kinase 1A-PKC412 complex reveals disulfide-bridge formation with the anomalous catalytic loop HRD(HCD) cysteine.

    PubMed

    Alexeeva, Marina; Åberg, Espen; Engh, Richard A; Rothweiler, Ulli

    2015-05-01

    Dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a protein kinase associated with neuronal development and brain physiology. The DYRK kinases are very unusual with respect to the sequence of the catalytic loop, in which the otherwise highly conserved arginine of the HRD motif is replaced by a cysteine. This replacement, along with the proximity of a potential disulfide-bridge partner from the activation segment, implies a potential for redox control of DYRK family activities. Here, the crystal structure of DYRK1A bound to PKC412 is reported, showing the formation of the disulfide bridge and associated conformational changes of the activation loop. The DYRK kinases represent emerging drug targets for several neurological diseases as well as cancer. The observation of distinct activation states may impact strategies for drug targeting. In addition, the characterization of PKC412 binding offers new insights for DYRK inhibitor discovery.

  3. 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

    2009-04-03

    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.

  4. 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.

  5. Enhancement of surface nonwettability by grafting loops.

    PubMed

    Pei, Han-Wen; Liu, Xiao-Li; Liu, Hong; Zhu, You-Liang; Lu, Zhong-Yuan

    2017-02-08

    We present a computer simulation study on the nonwettability of a flat surface tethered with deformable looped polymer chains. Two kinds of loops are studied: monodispersed loops (loops with the same length) and polydispersed loops (loops with different lengths). Both kinds of loops include two arrangements: with regularly tethered sites and with randomly tethered sites. Regularly grafted loops form typical grooves on the surface, while randomly grafted loops form a more rugged surface. For monodispersed loops, we analyze the factors that influence the nonwettability when varying the rigidity of the loops. The loops are divided into two categories based on their rigidity according to our previous analysis procedure (Phys. Chem. Chem. Phys., 2016, 18, 18767-18775): rigid loops and flexible loops. It is found that the loop can partially form a re-entrant-like structure, which is helpful to increase the nonwettability of the surface. The surfaces with grafted loops have increased nonwettability, especially those grafted with flexible chains. However, the contact angle on the loop structure cannot further increase for the rigid chains due to a large top layer density (Phys. Chem. Chem. Phys., 2016, 18, 18767-18775). For polydispersed loops, the contact angle is highly related to the rigidity of the long loops that contact the droplet. Different from monodispersed loops, the mechanism of the nonwettability of polydispersed loops is attributed to the supporting ability (rigidity) of long loops.

  6. 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…

  7. 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.

  8. Stent-coil treatment of a distal internal carotid artery dissecting pseudoaneurysm on a redundant loop by use of a flexible, dedicated nitinol intracranial stent.

    PubMed

    Pride, G Lee; Replogle, Robert E; Rappard, George; Graybeal, Christopher L Taylor Dion; White, Jonathan; Purdy, Phillip

    2004-02-01

    Treatment of dissecting pseudoaneurysms of the distal cervical internal carotid artery with preservation of the parent artery by using stents or coils has become routine. Tortuosity remains a significant obstacle to successful endovascular treatment in some cases. We report the use of a stent-coil technique to treat a nonhealing dissecting pseudoaneurysm and associated stenosis with anatomic preservation of a redundant loop involving the stented arterial segment. This was accomplished by using a Neuroform dedicated intracranial stent.

  9. 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

  10. Flexibility of the P-loop of Pim-1 kinase: observation of a novel conformation induced by interaction with an inhibitor.

    PubMed

    Parker, Lorien J; Watanabe, Hisami; Tsuganezawa, Keiko; Tomabechi, Yuri; Handa, Noriko; Shirouzu, Mikako; Yuki, Hitomi; Honma, Teruki; Ogawa, Naoko; Nagano, Tetsuo; Yokoyama, Shigeyuki; Tanaka, Akiko

    2012-08-01

    The serine/threonine kinase Pim-1 is emerging as a promising target for cancer therapeutics. Much attention has recently been focused on identifying potential Pim-1 inhibitor candidates for the treatment of haematopoietic malignancies. The outcome of a rational drug-design project has recently been reported [Nakano et al. (2012), J. Med. Chem. 55, 5151-5156]. The report described the process of optimization of the structure-activity relationship and detailed from a medicinal chemistry perspective the development of a low-potency and nonselective compound initially identified from in silico screening into a potent, selective and metabolically stable Pim-1 inhibitor. Here, the structures of the initial in silico hits are reported and the noteworthy features of the Pim-1 complex structures are described. A particular focus was placed on the rearrangement of the glycine-rich P-loop region that was observed for one of the initial compounds, (Z)-7-(azepan-1-ylmethyl)-2-[(1H-indol-3-yl)methylidene]-6-hydroxy-1-benzofuran-3(2H)-one (compound 1), and was also found in all further derivatives. This novel P-loop conformation, which appears to be stabilized by an additional interaction with the β3 strand located above the binding site, is not usually observed in Pim-1 structures.

  11. Flexibility of the P-loop of Pim-1 kinase: observation of a novel conformation induced by interaction with an inhibitor

    PubMed Central

    Parker, Lorien J.; Watanabe, Hisami; Tsuganezawa, Keiko; Tomabechi, Yuri; Handa, Noriko; Shirouzu, Mikako; Yuki, Hitomi; Honma, Teruki; Ogawa, Naoko; Nagano, Tetsuo; Yokoyama, Shigeyuki; Tanaka, Akiko

    2012-01-01

    The serine/threonine kinase Pim-1 is emerging as a promising target for cancer therapeutics. Much attention has recently been focused on identifying potential Pim-1 inhibitor candidates for the treatment of haematopoietic malignancies. The outcome of a rational drug-design project has recently been reported [Nakano et al. (2012 ▶), J. Med. Chem. 55, 5151–5156]. The report described the process of optimization of the structure–activity relationship and detailed from a medicinal chemistry perspective the development of a low-potency and nonselective compound initially identified from in silico screening into a potent, selective and metabolically stable Pim-1 inhibitor. Here, the structures of the initial in silico hits are reported and the noteworthy features of the Pim-1 complex structures are described. A particular focus was placed on the rearrangement of the glycine-rich P-loop region that was observed for one of the initial compounds, (Z)-7-(azepan-1-ylmethyl)-2-[(1H-indol-3-­yl)methylidene]-6-hydroxy-1-benzofuran-3(2H)-one (compound 1), and was also found in all further derivatives. This novel P-loop conformation, which appears to be stabilized by an additional interaction with the β3 strand located above the binding site, is not usually observed in Pim-1 structures. PMID:22869110

  12. Loop quantization

    SciTech Connect

    Nicolau, A.

    1988-10-01

    Loop unwinding is a known technique for reducing loop overhead, exposing parallelism, and increasing the efficiency of pipelining. Traditional loop unwinding is limited to the innermost loop in a group of nested loops and the amount of unwinding either is fixed or must be specified by the user, on a case by case basis. In this paper the authors present a general technique for automatically unwinding multiply nested loops, explain its advantages over other transformation techniques, and illustrate its practical effectiveness. Lopp Quantization could be beneficial by itself or coupled with other loop transformations.

  13. 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.

  14. Linking conformational flexibility and kinetics: catalytic 1,4-type Friedel-Crafts reactions of phenols utilizing 1,3-diamine-tethered guanidine/bisthiourea organocatalysts.

    PubMed

    Sohtome, Yoshihiro; Shin, Bongki; Horitsugi, Natsuko; Noguchi, Keiichi; Nagasawa, Kazuo

    2011-09-05

    Herein, we present details of our conformationally flexible, 1,3-diamine-tethered guanidine/bisthiourea organocatalysts for chemo-, regio-, and enantioselective 1,4-type Friedel-Crafts reactions of phenols. These organocatalysts show a unique stereo-discrimination governed by the differential activation entropy (ΔΔS(≠)), rather than by the differential activation enthalpy (ΔΔH(≠)). Extensive kinetic analyses using Eyring plots for a series of guanidine/bisthiourea organocatalysts revealed the key structural motif in the catalysts associated with a large magnitude of differential activation entropy (ΔΔS(≠)). A plausible guanidine-thiourea cooperative mechanism for the enantioselective Friedel-Crafts reaction is proposed.

  15. Catalytic Reforming

    SciTech Connect

    Little, D.M.

    1985-01-01

    Don Little's Catalytic Reforming deals exclusively with reforming. With the increasing need for unleaded gasoline, the importance of this volume has escalated since it combines various related aspects of reforming technology into a single publication. For those with no practical knowledge of catalytic reforming, the chemical reactions, flow schemes and how the cat reformer fits into the overall refinery process will be of interest. Contents include: Catalytic reforming in refinery processing: How catalytic reformers work - chemical reactions; Process design; The catalyst, process variables and unit operation; Commercial processes; BTX operation; Feed preparation; naphtha hydrotreating and catalytic reforming; Index.

  16. Effect of DNA modifications on DNA processing by HIV-1 integrase and inhibitor binding: role of DNA backbone flexibility and an open catalytic site.

    PubMed

    Johnson, Allison A; Sayer, Jane M; Yagi, Haruhiko; Patil, Sachindra S; Debart, Françoise; Maier, Martin A; Corey, David R; Vasseur, Jean-Jacques; Burke, Terrence R; Marquez, Victor E; Jerina, Donald M; Pommier, Yves

    2006-10-27

    Integration of the viral cDNA into host chromosomes is required for viral replication. Human immunodeficiency virus integrase catalyzes two sequential reactions, 3'-processing (3'-P) and strand transfer (ST). The first integrase inhibitors are undergoing clinical trial, but interactions of inhibitors with integrase and DNA are not well understood in the absence of a co-crystal structure. To increase our understanding of integrase interactions with DNA, we examined integrase catalysis with oligonucleotides containing DNA backbone, base, and groove modifications placed at unique positions surrounding the 3'-processing site. 3'-Processing was blocked with substrates containing constrained sugars and alpha-anomeric residues, suggesting that integrase requires flexibility of the phosphodiester backbone at the 3'-P site. Of several benzo[a]pyrene 7,8-diol 9,10-epoxide (BaP DE) adducts tested, only the adduct in the minor groove at the 3'-P site inhibited 3'-P, suggesting the importance of the minor groove contacts for 3'-P. ST occurred in the presence of bulky BaP DE DNA adducts attached to the end of the viral DNA suggesting opening of the active site for ST. Position-specific effects of these BaP DE DNA adducts were found for inhibition of integrase by diketo acids. Together, these results demonstrate the importance of DNA structure and specific contacts with the viral DNA processing site for inhibition by integrase inhibitors.

  17. Inhibitors bound to Ca(2+)-free sarcoplasmic reticulum Ca(2+)-ATPase lock its transmembrane region but not necessarily its cytosolic region, revealing the flexibility of the loops connecting transmembrane and cytosolic domains.

    PubMed

    Montigny, Cédric; Picard, Martin; Lenoir, Guillaume; Gauron, Carole; Toyoshima, Chikashi; Champeil, Philippe

    2007-12-25

    Ca2+-free crystals of sarcoplasmic reticulum Ca2+-ATPase have, up until now, been obtained in the presence of inhibitors such as thapsigargin (TG), bound to the transmembrane region of this protein. Here, we examined the consequences of such binding for the protein. We found that, after TG binding, an active site ligand such as beryllium fluoride can still bind to the ATPase and change the conformation or dynamics of the cytosolic domains (as revealed by the protection afforded against proteolysis), but it becomes unable to induce any change in the transmembrane domain (as revealed by the intrinsic fluorescence of the membranous tryptophan residues). TG also obliterates the Trp fluorescence changes normally induced by binding of MgATP or metal-free ATP, as well as those induced by binding of Mg2+ alone. In the nucleotide binding domain, the environment of Lys515 (as revealed by fluorescein isothiocyanate fluorescence after specific labeling of this residue) is significantly different in the ATPase complex with aluminum fluoride and in the ATPase complex with beryllium fluoride, and in the latter case it is modified by TG. All these facts document the flexibility of the loops connecting the transmembrane and cytosolic domains in the ATPase. In the absence of active site ligands, TG protects the ATPase from cleavage by proteinase K at Thr242-Glu243, suggesting TG-induced reduction in the mobility of these loops. 2,5-Di-tert-butyl-1,4-dihydroxybenzene or cyclopiazonic acid, inhibitors which also bind in or near the transmembrane region, also produce similar overall effects on Ca2+-free ATPase.

  18. The remarkable efficiency of a Pin-II proteinase inhibitor sans two conserved disulfide bonds is due to enhanced flexibility and hydrogen bond density in the reactive site loop.

    PubMed

    Joshi, Rakesh S; Mishra, Manasi; Tamhane, Vaijayanti A; Ghosh, Anirban; Sonavane, Uddhavesh; Suresh, C G; Joshi, Rajendra; Gupta, Vidya S; Giri, Ashok P

    2014-01-01

    Capsicum annuum (L.) expresses diverse potato type II family proteinase inhibitors comprising of inhibitory repeat domain (IRD) as basic functional unit. Most IRDs contain eight conserved cysteines forming four disulfide bonds, which are indispensible for their stability and activity. We investigated the functional significance of evolutionary variations in IRDs and their role in mediating interaction between the inhibitor and cognate proteinase. Among the 18 IRDs encoded by C. annuum, IRD-7, -9, and -12 were selected for further characterization on the basis of variation in their reactive site loop, number of conserved cysteine residues, and higher theoretical ΔGbind for interaction with Helicoverpa armigera trypsin. Moreover, inhibition kinetics showed that IRD-9, despite loss of some of the disulfide bonds, was a more potent proteinase inhibitor among the three selected IRDs. Molecular dynamic simulations revealed that serine residues in the place of cysteines at seventh and eighth positions of IRD-9 resulted in an increase in the density of intramolecular hydrogen bonds and reactive site loop flexibility. Results of the serine residues chemical modification also supported this observation and provided a possible explanation for the remarkable inhibitory potential of IRD-9. Furthermore, this natural variant among IRDs showed special attributes like stability to proteolysis and synergistic inhibitory effect on other IRDs. It is likely that IRDs have coevolved selective specialization of their structure and function as a response towards specific insect proteases they encountered. Understanding the molecular mechanism of pest protease-plant proteinaceous inhibitor interaction will help in developing effective pest control strategies. An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:39.

  19. Selective disruption of disulphide bonds lowered activation energy and improved catalytic efficiency in TALipB from Trichosporon asahii MSR54: MD simulations revealed flexible lid and extended substrate binding area in the mutant.

    PubMed

    Singh, Yogesh; Gupta, Namita; Verma, Ved Vrat; Goel, Manisha; Gupta, Rani

    2016-03-25

    TALipB (33 kDa) is a solvent stable, enantioselective lipase from Trichosporon asahii MSR54. It is cysteine-rich and shows activation in presence of thiol reducing agents. DIANNA server predicted three disulphide bridges C53-C195 (S1), C89-C228 (S2) and C164-C254 (S3) in the enzyme. Selective disruption of disulphide bonds by cysteine to alanine mutations at Cys53 and Cys89 of S1 and S2 bonds resulted in enzyme activation. Mutant mTALipB (S1+S2) showed increase in specific activity by ∼4-fold (834 mM/mg) and improved Vmax of 6.27 μmol/ml/min at 40 °Con pNP caprate. Temperature optima of mTALipB shifted from 50 to 40 °C and activation energy decreased by 0.7 kcal mol(-1). However, the mutant was less thermostable with a t1/2 of 18 min at 60 °C as compared to t1/2 of 38 min for the native enzyme. Mutant also displayed an improved activity on all pNP esters and higher enantiomeric excess (61%) during esterification of (±) 1-phenylethanol. Far-UV CD analysis showed significant changes in secondary structure after S-S bridge disruption with 7.16% decrease in α-helices and 1.31% increase in β-sheets. In silico analysis predicted two lids (α5 and α9) in TALipB. Molecular dynamic simulations at 40 °C and 50 °C revealed that in the mTALipB, both the lids opened at 40 °C with clockwise and anticlockwise rotations in Lid1 and Lid2, respectively. In the native protein, however, the lid was only partially open even at 50 °C. Concomitant to lid flexibility, there was an extension of accessible catalytic triad surface area resulting in improved catalytic efficiency of the mutant enzyme.

  20. 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.

  1. Catalytic autothermal reforming increases fuel cell flexibility

    NASA Technical Reports Server (NTRS)

    Flytzani-Stephanopoulos, M.; Voecks, G. E.

    1981-01-01

    Experimental results are presented for the autothermal reforming (ATR) of n-hexane, n-tetradecane, benzene and benzene solutions of naphthalene. The tests were run at atmospheric pressure and at moderately high reactant preheat temperatures in the 800-900 K range. Carbon formation lines were determined for paraffinic and aromatic liquids. Profiles were determined for axial bed temperature and composition. Space velocity efforts were assessed, and the locations and types of carbon were recorded. Significant reactive differences between hydrocarbons were identified. Carbon formation characteristics were hydrocarbon specific. The differing behavior of paraffinic and aromatic fuels with respect to their carbon formation may be important in explaining the narrow range of carbon-free operating conditions found in the ATR of number two fuel oil.

  2. Function of the D-alanine:D-alanine ligase lid loop: a molecular modeling and bioactivity study.

    PubMed

    Hrast, Martina; Vehar, Blaž; Turk, Samo; Konc, Janez; Gobec, Stanislav; Janežič, Dušanka

    2012-08-09

    D-Alanine:D-alanine ligase (Ddl) is an essential ATP-dependent bacterial enzyme involved in peptidoglycan biosynthesis. Discovery of Ddl inhibitors not competitive with ATP has proven to be difficult because the Ddl bimolecular d-alanine binding pocket is very restricted, as is accessibility to the active site for larger molecules in the catalytically active closed conformation of Ddl. A molecular dynamics study of the opening and closing of the Ddl lid loop informs future structure-based design efforts that allow for the flexibility of Ddl. A virtual screen on generated enzyme conformations yielded some hit inhibitors whose bioactivity was determined.

  3. Identification of cytoplasmic subdomains that control pH-sensing of the Na+/H+ exchanger (NHE1): pH-maintenance, ATP-sensitive, and flexible loop domains.

    PubMed

    Ikeda, T; Schmitt, B; Pouysségur, J; Wakabayashi, S; Shigekawa, M

    1997-02-01

    To precisely identify the cytoplasmic subdomains that are responsible for the intracellular pH (pHi)-sensitivity, ATP depletion-induced inhibition and Ca2+ activation of the Na+/H+ exchanger (NHE1), we generated a set of deletion mutants of carboxyl-terminated cytoplasmic domain and expressed them in the exchanger-deficient cell line PS120. We evaluated pHi-sensitivity of these mutants by measuring the resting pHi in cells placed in an acidic medium (pH 6.0) and pHi-dependence of 5-(N-ethyl-N-isopropyl)amiloride-sensitive 22Na+ uptake. Detailed analysis revealed that the cytoplasmic domain of NHE1 is consists of at least four subdomains in terms of pHi-sensitivity of the unstimulated NHE1: I, aa 516-590/595; II, aa 596-635; III aa 636-659; and IV, aa 660-815. Subdomains II and IV were silent for pHi-sensitivity. Subdomain I had a pHi-maintenance function, preserving pHi-sensitivity in a physiological range, whereas subdomain III, overlapping with the high affinity calmodulin (CaM)-binding site, exhibited an autoinhibitory function. Deletion of subdomain I abolished the decrease of pHi-sensitivity induced by cell ATP depletion, indicating that domain I plays a crucial role in this phenomenon. Deletion of subdomain III rendered the inhibition by ATP depletion less efficient, suggesting the possible interaction between subdomains I and III. On the other hand, tandem elongation of subdomain II by insertion did not affect either the inhibitory function of domain III or the removal of this inhibition by ionomycin or thrombin. However, deletion of subdomain II partially abolished the inhibitory effect of subdomain III. Subdomain II thus seems to function as a mobile "flexible loop," permitting the CaM-binding subdomain III to exert its normal function. These findings, together with our previous data, support a concept that cell ATP, Ca2+, and growth factors regulate NHE1 via a mechanism involving direct or indirect interactions of specific cytoplasmic subdomains with the

  4. Rational design of ornithine decarboxylase with high catalytic activity for the production of putrescine.

    PubMed

    Choi, Hyang; Kyeong, Hyun-Ho; Choi, Jung Min; Kim, Hak-Sung

    2014-09-01

    Putrescine finds wide industrial applications in the synthesis of polymers, pharmaceuticals, agrochemicals, and surfactants. Owing to economic and environmental concerns, the microbial production of putrescine has attracted a great deal of attention, and ornithine decarboxylase (ODC) is known to be a key enzyme in the biosynthetic pathway. Herein, we present the design of ODC from Escherichia coli with high catalytic efficiency using a structure-based rational approach. Through a substrate docking into the model structure of the enzyme, we first selected residues that might lead to an increase in catalytic activity. Of the selected residues that are located in the α-helix and the loops constituting the substrate entry site, a mutational analysis of the single mutants identified two key residues, I163 and E165. A combination of two single mutations resulted in a 62.5-fold increase in the catalytic efficiency when compared with the wild-type enzyme. Molecular dynamics simulations of the best mutant revealed that the substrate entry site becomes more flexible through mutations, while stabilizing the formation of the dimeric interface of the enzyme. Our approach can be applied to the design of other decarboxylases with high catalytic efficiency for the production of various chemicals through bio-based processes.

  5. 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.

  6. Flexible Ablators

    NASA Technical Reports Server (NTRS)

    Stackpoole, Margaret M. (Inventor); Ghandehari, Ehson M. (Inventor); Thornton, Jeremy J. (Inventor); Covington, Melmoth Alan (Inventor)

    2017-01-01

    A low-density article comprising a flexible substrate and a pyrolizable material impregnated therein, methods of preparing, and devices using the article are disclosed. The pyrolizable material pyrolizes above 350 C and does not flow at temperatures below the pyrolysis temperature. The low-density article remains flexible after impregnation and continues to remain flexible when the pyrolizable material is fully pyrolized.

  7. Catalytic reforming

    SciTech Connect

    Aldag, A.W. Jr.

    1986-01-28

    This patent describes a process for the catalytic reforming of a feedstock which contains at least one reformable organic compound. The process consists of contacting the feedstock under suitable reforming conditions with a catalyst composition selected from the group consisting of a catalyst. The catalyst essentially consists of zinc oxide and a spinel structure alumina. Another catalyst consists essentially of a physical mixture of zinc titanate and a spinel structure alumina in the presence of sufficient added hydrogen to substantially prevent the formation of coke. Insufficient zinc is present in the catalyst composition for the formation of a bulk zinc aluminate.

  8. 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.

  9. 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.

  10. Conformational flexibility of the glycosidase NagZ allows it to bind structurally diverse inhibitors to suppress β-lactam antibiotic resistance.

    PubMed

    Vadlamani, Grishma; Stubbs, Keith A; Désiré, Jérôme; Blériot, Yves; Vocadlo, David J; Mark, Brian L

    2017-03-28

    NagZ is an N-acetyl-β-d-glucosaminidase that participates in the peptidoglycan (PG) recycling pathway of Gram-negative bacteria by removing N-acetyl-glucosamine (GlcNAc) from PG fragments that have been excised from the cell wall during growth. The 1,6-anhydromuramoyl-peptide products generated by NagZ activate β-lactam resistance in many Gram-negative bacteria by inducing the expression of AmpC β-lactamase. Blocking NagZ activity can thereby suppress β-lactam antibiotic resistance in these bacteria. The NagZ active site is dynamic and it accommodates distortion of the glycan substrate during catalysis using a mobile catalytic loop that carries a histidine residue which serves as the active site general acid/base catalyst. Here, we show that flexibility of this catalytic loop also accommodates structural differences in small molecule inhibitors of NagZ, which could be exploited to improve inhibitor specificity. X-ray structures of NagZ bound to the potent yet non-selective N-acetyl-β-glucosaminidase inhibitor PUGNAc (O-(2-acetamido-2-deoxy-d-glucopyranosylidene) amino-N-phenylcarbamate), and two NagZ-selective inhibitors - EtBuPUG, a PUGNAc derivative bearing a 2-N-ethylbutyryl group, and MM-156, a 3-N-butyryl trihydroxyazepane, revealed that the phenylcarbamate moiety of PUGNAc and EtBuPUG completely displaces the catalytic loop from the NagZ active site to yield a catalytically incompetent form of the enzyme. In contrast, the catalytic loop was found positioned in the catalytically active conformation within the NagZ active site when bound to MM-156, which lacks the phenylcarbamate extension. Displacement of the catalytic loop by PUGNAc and its N-acyl derivative EtBuPUG alters the active site conformation of NagZ, which presents an additional strategy to improve the potency and specificity of NagZ inhibitors.

  11. Catalytic reactor

    SciTech Connect

    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.

  12. Flexible Straws.

    ERIC Educational Resources Information Center

    Prentice, Gerard

    1989-01-01

    Discusses the use of flexible straws for teaching properties of figures and families of shapes. Describes a way to make various two- or three-dimensional geometric shapes. Lists eight advantages of the method. (YP)

  13. 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.

  14. Replacement and deletion mutations in the catalytic domain and belt region of Aspergillus awamori glucoamylase to enhance thermostability.

    PubMed

    Liu, H L; Doleyres, Y; Coutinho, P M; Ford, C; Reilly, P J

    2000-09-01

    Three single-residue mutations, Asp71-->Asn, Gln409-->Pro and Gly447-->Ser, two long-to-short loop replacement mutations, Gly23-Ala24-Asp25-Gly26-Ala27-Trp28- Val29-Ser30-->Asn-Pro-Pro (23-30 replacement) and Asp297-Ser298-Glu299-Ala300-Val301-->Ala-G ly-Ala (297-301 replacement) and one deletion mutation removing Glu439, Thr440 and Ser441 (Delta439-441), all based on amino acid sequence alignments, were made to improve Aspergillus awamori glucoamylase thermostability. The first and second single-residue mutations were designed to introduce a potential N:-glycosylation site and to restrict backbone bond rotation, respectively, and therefore to decrease entropy during protein unfolding. The third single-residue mutation was made to decrease flexibility and increase O:-glycosylation in the already highly O:-glycosylated belt region that extends around the globular catalytic domain. The 23-30 replacement mutation was designed to eliminate a very thermolabile extended loop on the catalytic domain surface and to bring the remainder of this region closer to the rest of the catalytic domain, therefore preventing it from unfolding. The 297-301 replacement mutant GA was made to understand the function of the random coil region between alpha-helices 9 and 10. Delta439-441 was constructed to decrease belt flexibility. All six mutations increased glucoamylase thermostability without significantly changing enzyme kinetic properties, with the 23-30 replacement mutation increasing the activation free energy for thermoinactivation by about 4 kJ/mol, which leads to a 4 degrees C increase in operating temperature at constant thermostability.

  15. On the structural context and identification of enzyme catalytic residues.

    PubMed

    Chien, Yu-Tung; Huang, Shao-Wei

    2013-01-01

    Enzymes play important roles in most of the biological processes. Although only a small fraction of residues are directly involved in catalytic reactions, these catalytic residues are the most crucial parts in enzymes. The study of the fundamental and unique features of catalytic residues benefits the understanding of enzyme functions and catalytic mechanisms. In this work, we analyze the structural context of catalytic residues based on theoretical and experimental structure flexibility. The results show that catalytic residues have distinct structural features and context. Their neighboring residues, whether sequence or structure neighbors within specific range, are usually structurally more rigid than those of noncatalytic residues. The structural context feature is combined with support vector machine to identify catalytic residues from enzyme structure. The prediction results are better or comparable to those of recent structure-based prediction methods.

  16. On the Structural Context and Identification of Enzyme Catalytic Residues

    PubMed Central

    Chien, Yu-Tung; Huang, Shao-Wei

    2013-01-01

    Enzymes play important roles in most of the biological processes. Although only a small fraction of residues are directly involved in catalytic reactions, these catalytic residues are the most crucial parts in enzymes. The study of the fundamental and unique features of catalytic residues benefits the understanding of enzyme functions and catalytic mechanisms. In this work, we analyze the structural context of catalytic residues based on theoretical and experimental structure flexibility. The results show that catalytic residues have distinct structural features and context. Their neighboring residues, whether sequence or structure neighbors within specific range, are usually structurally more rigid than those of noncatalytic residues. The structural context feature is combined with support vector machine to identify catalytic residues from enzyme structure. The prediction results are better or comparable to those of recent structure-based prediction methods. PMID:23484160

  17. Length of the active-site crossover loop defines the substrate specificity of ubiquitin C-terminal hydrolases for ubiquitin chains.

    PubMed

    Zhou, Zi-Ren; Zhang, Yu-Hang; Liu, Shuai; Song, Ai-Xin; Hu, Hong-Yu

    2012-01-01

    UCHs [Ub (ubiquitin) C-terminal hydrolases] are a family of deubiquitinating enzymes that are often thought to only remove small C-terminal peptide tails from Ub adducts. Among the four UCHs identified to date, neither UCH-L3 nor UCH-L1 can catalyse the hydrolysis of isopeptide Ub chains, but UCH-L5 can when it is present in the PA700 complex of the proteasome. In the present paper, we report that the UCH domain of UCH-L5, different from UCH-L1 and UCH-L3, by itself can process the K48-diUb (Lys48-linked di-ubiquitin) substrate by cleaving the isopeptide bond between two Ub units. The catalytic specificity of the four UCHs is dependent on the length of the active-site crossover loop. The UCH domain with a long crossover loop (usually >14 residues), such as that of UCH-L5 or BAP1 [BRCA1 (breast cancer early-onset 1)-associated protein 1], is able to cleave both small and large Ub derivatives, whereas the one with a short loop can only process small Ub derivatives. We also found that elongation of the crossover loop enables UCH-L1 to have isopeptidase activity for K48-diUb in a length-dependent manner. Thus the loop length of UCHs defines their substrate specificity for diUb chains, suggesting that the chain flexibility of the crossover loop plays an important role in determining its catalytic activity and substrate specificity for cleaving isopeptide Ub chains.

  18. 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)

  19. 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

  20. 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.

  1. 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

    1997-09-05

    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.

  2. Crystal structure of the catalytic domain of RluD, the only rRNA pseudouridine synthase required for normal growth of Escherichia coli

    PubMed Central

    DEL CAMPO, MARK; OFENGAND, JAMES; MALHOTRA, ARUN

    2004-01-01

    Escherichia coli pseudouridine synthase RluD makes pseudouridines 1911, 1915, and 1917 in the loop of helix 69 in 23S RNA. These are the most highly conserved ribosomal pseudouridines known. Of 11 pseudouridine synthases in E. coli, only cells lacking RluD have severe growth defects and abnormal ribosomes. We have determined the 2.0 Å structure of the catalytic domain of RluD (residues 77–326), the first structure of an RluA family member. The catalytic domain folds into a mainly antiparallel β-sheet flanked by several loops and helices. A positively charged cleft that presumably binds RNA leads to the conserved Asp 139. The RluD N-terminal S4 domain, connected by a flexible linker, is disordered in our structure. RluD is very similar in both catalytic domain structure and active site arrangement to the pseudouridine synthases RsuA, TruB, and TruA. We identify five sequence motifs, two of which are novel, in the RluA, RsuA, TruB, and TruA families, uniting them as one superfamily. These results strongly suggest that four of the five families of pseudouridine synthases arose by divergent evolution. The RluD structure also provides insight into its multisite specificity. PMID:14730022

  3. Flexible pile thermal barrier insulator

    NASA Technical Reports Server (NTRS)

    Anderson, G. E.; Fell, D. M.; Tesinsky, J. S. (Inventor)

    1978-01-01

    A flexible pile thermal barrier insulator included a plurality of upstanding pile yarns. A generally planar backing section supported the upstanding pile yarns. The backing section included a plurality of filler yarns forming a mesh in a first direction. A plurality of warp yarns were looped around said filler yarns and pile yarns in the backing section and formed a mesh in a second direction. A binder prevented separation of the yarns in the backing section.

  4. 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.

  5. Flexible flatfoot

    PubMed Central

    Atik, Aziz; Ozyurek, Selahattin

    2014-01-01

    While being one of the most frequent parental complained deformities, flatfoot does not have a universally accepted description. The reasons of flexible flatfoot are still on debate, but they must be differentiated from rigid flatfoot which occurs secondary to other pathologies. These children are commonly brought up to a physician without any complaint. It should be kept in mind that the etiology may vary from general soft tissue laxities to intrinsic foot pathologies. Every flexible flatfoot does not require radiological examination or treatment if there is no complaint. Otherwise further investigation and conservative or surgical treatment may necessitate. PMID:28058304

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. Gene repression by minimal lac loops in vivo.

    PubMed

    Bond, Laura M; Peters, Justin P; Becker, Nicole A; Kahn, Jason D; Maher, L James

    2010-12-01

    The inflexibility of double-stranded DNA with respect to bending and twisting is well established in vitro. Understanding apparent DNA physical properties in vivo is a greater challenge. Here, we exploit repression looping with components of the Escherichia coli lac operon to monitor DNA flexibility in living cells. We create a minimal system for testing the shortest possible DNA repression loops that contain an E. coli promoter, and compare the results to prior experiments. Our data reveal that loop-independent repression occurs for certain tight operator/promoter spacings. When only loop-dependent repression is considered, fits to a thermodynamic model show that DNA twisting limits looping in vivo, although the apparent DNA twist flexibility is 2- to 4-fold higher than in vitro. In contrast, length-dependent resistance to DNA bending is not observed in these experiments, even for the shortest loops constraining <0.4 persistence lengths of DNA. As observed previously for other looping configurations, loss of the nucleoid protein heat unstable (HU) markedly disables DNA looping in vivo. Length-independent DNA bending energy may reflect the activities of architectural proteins and the structure of the DNA topological domain. We suggest that the shortest loops are formed in apical loops rather than along the DNA plectonemic superhelix.

  11. 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.

  12. 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

  13. Large planar maneuvers for articulated flexible manipulators

    NASA Technical Reports Server (NTRS)

    Huang, Jen-Kuang; Yang, Li-Farn; Juang, Jer-Nan

    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 in the inertia matrix. Then a feeback 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.

  14. 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.

  15. High resolution crystal structure of the catalytic domain of MCR-1

    PubMed Central

    Ma, Guixing; Zhu, Yifan; Yu, Zhicheng; Ahmad, Ashfaq; Zhang, Hongmin

    2016-01-01

    The newly identified mobile colistin resistant gene (mcr-1) rapidly spread among different bacterial strains and confers colistin resistance to its host, which has become a global concern. Based on sequence alignment, MCR-1 should be a phosphoethanolamine transferase, members of the YhjW/YjdB/YijP superfamily and catalyze the addition of phosphoethanolamine to lipid A, which needs to be validated experimentally. Here we report the first high-resolution crystal structure of the C-terminal catalytic domain of MCR-1 (MCR-1C) in its native state. The active pocket of native MCR-1C depicts unphosphorylated nucleophilic residue Thr285 in coordination with two Zinc ions and water molecules. A flexible adjacent active site loop (aa: Lys348-365) pose an open conformation compared to its structural homologues, suggesting of an open substrate entry channel. Taken together, this structure sets ground for further study of substrate binding and MCR-1 catalytic mechanism in development of potential therapeutic agents. PMID:28000749

  16. Passivity Motivated Controller Design for Flexible Structures

    DTIC Science & Technology

    1993-01-18

    theoretical approach to the control of systems containing lumped joint flexibility is based on the exact linearization method. for a summary see [4...feedforward compensation (for the exact linearization ) and the feedback stabilization are intertwined and errors in the feedforward may affect the closed loop

  17. 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.

  18. Pseudonoise code tracking loop

    NASA Technical Reports Server (NTRS)

    Laflame, D. T. (Inventor)

    1980-01-01

    A delay-locked loop is presented for tracking a pseudonoise (PN) reference code in an incoming communication signal. The loop is less sensitive to gain imbalances, which can otherwise introduce timing errors in the PN reference code formed by the loop.

  19. 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

  20. 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)

  1. 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.

  2. Rich catalytic injection

    DOEpatents

    Veninger, Albert

    2008-12-30

    A gas turbine engine includes a compressor, a rich catalytic injector, a combustor, and a turbine. The rich catalytic injector includes a rich catalytic device, a mixing zone, and an injection assembly. The injection assembly provides an interface between the mixing zone and the combustor. The injection assembly can inject diffusion fuel into the combustor, provides flame aerodynamic stabilization in the combustor, and may include an ignition device.

  3. 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.

  4. 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.

  5. 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

  6. Aspartase/fumarase superfamily: a common catalytic strategy involving general base-catalyzed formation of a highly stabilized aci-carboxylate intermediate.

    PubMed

    Puthan Veetil, Vinod; Fibriansah, Guntur; Raj, Hans; Thunnissen, Andy-Mark W H; Poelarends, Gerrit J

    2012-05-29

    Members of the aspartase/fumarase superfamily share a common tertiary and quaternary fold, as well as a similar active site architecture; the superfamily includes aspartase, fumarase, argininosuccinate lyase, adenylosuccinate lyase, δ-crystallin, and 3-carboxy-cis,cis-muconate lactonizing enzyme (CMLE). These enzymes all process succinyl-containing substrates, leading to the formation of fumarate as the common product (except for the CMLE-catalyzed reaction, which results in the formation of a lactone). In the past few years, X-ray crystallographic analysis of several superfamily members in complex with substrate, product, or substrate analogues has provided detailed insights into their substrate binding modes and catalytic mechanisms. This structural work, combined with earlier mechanistic studies, revealed that members of the aspartase/fumarase superfamily use a common catalytic strategy, which involves general base-catalyzed formation of a stabilized aci-carboxylate (or enediolate) intermediate and the participation of a highly flexible loop, containing the signature sequence GSSxxPxKxN (named the SS loop), in substrate binding and catalysis.

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

    PubMed

    André, G; Tran, V

    2004-10-05

    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.

  8. Flexibility in substrate recognition by thimet oligopeptidase as revealed by denaturation studies.

    PubMed

    Sigman, Jeffrey A; Patwa, Tasneem H; Tablante, Ana V; Joseph, Calleen D; Glucksman, Marc J; Wolfson, Adele J

    2005-05-15

    Thimet oligopeptidase (TOP) is a soluble metalloendopeptidase belonging to a family of enzymes including neurolysin and neprilysin that utilize the HEXXH metal-binding motif. TOP is widely distributed among cell types and is able to cleave a number of structurally unrelated peptides. A recent focus of interest has been on structure-function relationships in substrate selectivity by TOP. The enzyme's structural fold comprises two domains that are linked at the bottom of a deep substrate-binding cleft via several flexible loop structures. In the present study, fluorescence spectroscopy has been used to probe structural changes in TOP induced by the chemical denaturant urea. Fluorescence emission, anisotropy and collisional quenching data support a two-step unfolding process for the enzyme in which complete loss of the tertiary structure occurs in the second step. Complete loss of activity and loss of catalytic Zn(II) from the active site, monitored by absorption changes of the metal chelator 4-(2-pyridylazo)-resorcinol, are also connected with the second step. In contrast, the first unfolding event, which is linked to changes in the non-catalytic domain, leads to a sharp increase in kcat towards a 9-residue substrate and a sharp decrease in kcat for a 5-residue substrate. Thus a conformational change in TOP has been directly correlated with a change in substrate selectivity. These results provide insight into how the enzyme can process the range of structurally unrelated peptides necessary for its many physiological roles.

  9. 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.

  10. 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.

  11. MD simulation of the Tat/Cyclin T1/CDK9 complex revealing the hidden catalytic cavity within the CDK9 molecule upon Tat binding

    PubMed Central

    Asamitsu, Kaori; Hirokawa, Takatsugu; Okamoto, Takashi

    2017-01-01

    In this study, we applied molecular dynamics (MD) simulation to analyze the dynamic behavior of the Tat/CycT1/CDK9 tri-molecular complex and revealed the structural changes of P-TEFb upon Tat binding. We found that Tat could deliberately change the local flexibility of CycT1. Although the structural coordinates of the H1 and H2 helices did not substantially change, H1ʹ, H2ʹ, and H3ʹ exhibited significant changes en masse. Consequently, the CycT1 residues involved in Tat binding, namely Tat-recognition residues (TRRs), lost their flexibility with the addition of Tat to P-TEFb. In addition, we clarified the structural variation of CDK9 in complex with CycT1 in the presence or absence of Tat. Interestingly, Tat addition significantly reduced the structural variability of the T-loop, thus consolidating the structural integrity of P-TEFb. Finally, we deciphered the formation of the hidden catalytic cavity of CDK9 upon Tat binding. MD simulation revealed that the PITALRE signature sequence of CDK9 flips the inactive kinase cavity of CDK9 into the active form by connecting with Thr186, which is crucial for its activity, thus presumably recruiting the substrate peptide such as the C-terminal domain of RNA pol II. These findings provide vital information for the development of effective novel anti-HIV drugs with CDK9 catalytic activity as the target. PMID:28178316

  12. 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

  13. CD and NMR conformational studies of a peptide encompassing the Mid Loop interface of Ship2-Sam.

    PubMed

    Mercurio, Flavia A; Scognamiglio, Pasqualina L; Di Natale, Concetta; Marasco, Daniela; Pellecchia, Maurizio; Leone, Marilisa

    2014-11-01

    The lipid phosphatase Ship2 is a protein that intervenes in several diseases such as diabetes, cancer, neurodegeneration, and atherosclerosis. It is made up of a catalytic domain and several protein docking modules such as a C-terminal Sam (Sterile alpha motif) domain. The Sam domain of Ship2 (Ship2-Sam) binds to the Sam domains of the EphA2 receptor (EphA2-Sam) and the PI3K effector protein Arap3 (Arap3-Sam). These heterotypic Sam-Sam interactions occur through formation of dimers presenting the canonical "Mid Loop/End Helix" binding mode. The central region of Ship2-Sam, spanning the C-terminal end of α2, the α3 and α4 helices together with the α2α3 and α3α4 interhelical loops, forms the Mid Loop surface that is needed to bind partners Sam domains. A peptide encompassing most of the Ship2-Sam Mid Loop interface (Shiptide) capable of binding to both EphA2-Sam and Arap3-Sam, was previously identified. Here we investigated the conformational features of this peptide, through solution CD and NMR studies in different conditions. These studies reveal that the peptide is highly flexible in aqueous buffer, while it adopts a helical conformation in presence of 2,2,2-trifluoroethanol. The discovered structural insights and in particular the identification of a helical motif, may lead to the design of more constrained and possibly cell permeable Shiptide analogs that could work as efficient antagonists of Ship2-Sam heterotypic interactions and embrace therapeutic applications.

  14. Conformational flexibility in biochemical regulation

    SciTech Connect

    Trewhella, J.

    1993-09-01

    Small-angle X-ray and neutron scattering have proven extremely useful for studying the evolutionarily related dumbbell-shaped Ca {sup 2+} -binding proteins calmodulin and troponin C and their interactions with the target proteins whose activity they regulate. Calmodulin contracts about target enzyme binding domains with the common characteristic of having a high propensity for forming a basic, amphipathic a-helix. The contraction is achieved via flexibility in the interconnecting helix region of the molecule that links its two globular domains. This flexibility allows calmodulin to optimize its binding to different arrangements of hydrophobic and charged residues important in forming these complexes. In contrast calmodulin remains extended in its interaction with the catalytic subunit of phosphorylase kinase. There are structural and functional similarities between this interaction and that of troponin C and troponin I. Our most recent neutron scattering experiments confirm our prediction that troponin C also remains extended in this complex. The ability of the dumbbell-shaped Ca {sup 2+} -binding proteins to modulate their conformations via flexibility in the interconnecting helix region in order to accommodate different target binding domains is a remarkable example nature building functional diversity as well as specificity into a compact and unusual shape.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. The importance of slow motions for protein functional loops.

    PubMed

    Skliros, Aris; Zimmermann, Michael T; Chakraborty, Debkanta; Saraswathi, Saras; Katebi, Ataur R; Leelananda, Sumudu P; Kloczkowski, Andrzej; Jernigan, Robert L

    2012-02-07

    Loops in proteins that connect secondary structures such as alpha-helix and beta-sheet, are often on the surface and may play a critical role in some functions of a protein. The mobility of loops is central for the motional freedom and flexibility requirements of active-site loops and may play a critical role for some functions. The structures and behaviors of loops have not been studied much in the context of the whole structure and its overall motions, especially how these might be coupled. Here we investigate loop motions by using coarse-grained structures (C(α) atoms only) to solve the motions of the system by applying Lagrange equations with elastic network models to learn about which loops move in an independent fashion and which move in coordination with domain motions, faster and slower, respectively. The normal modes of the system are calculated using eigen-decomposition of the stiffness matrix. The contribution of individual modes and groups of modes is investigated for their effects on all residues in each loop by using Fourier analyses. Our results indicate overall that the motions of functional sets of loops behave in similar ways as the whole structure. But overall only a relatively few loops move in coordination with the dominant slow modes of motion, and these are often closely related to function.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. A single mutation within a Ca(2+) binding loop increases proteolytic activity, thermal stability, and surfactant stability.

    PubMed

    Okuda, Mitsuyoshi; Ozawa, Tadahiro; Tohata, Masatoshi; Sato, Tsuyoshi; Saeki, Katsuhisa; Ozaki, Katsuya

    2013-03-01

    We improved the enzymatic properties of the oxidatively stable alkaline serine protease KP-43 through protein engineering to make it more suitable for use in laundry detergents. To enhance proteolytic activity, the gene encoding KP-43 was mutagenized by error-prone PCR. Screening identified a Tyr195Cys mutant enzyme that exhibited increased specific activity toward casein between pH 7 and 11. At pH 10, the mutant displayed 1.3-fold higher specific activity for casein compared to the wild-type enzyme, but the activity of the mutant was essentially unchanged toward several synthetic peptides. Furthermore, the Tyr195Cys mutation significantly increased thermal stability and surfactant stability of the enzyme under oxidizing conditions. Examination of the crystal structure of KP-43 revealed that Tyr195 is a solvent exposed residue that forms part of a flexible loop that binds a Ca(2+) ion. This residue lies 15-20Å away from the residues comprising the catalytic triad of the enzyme. These results suggest that the substitution at position 195 does not alter the structure of the active center, but instead may affect a substrate-enzyme interaction. We propose that the Tyr195Cys mutation enhances the interaction with Ca(2+) and affects the packing of the Ca(2+) binding loop, consequently increasing protein stability. The simultaneously increased proteolytic activity, thermal stability, and surfactant stability of the Tyr195Cys mutant enzyme make the protein an ideal candidate for laundry detergent application.

  5. 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.

  6. Multiprotein DNA Looping

    NASA Astrophysics Data System (ADS)

    Vilar, Jose M. G.; Saiz, Leonor

    2006-06-01

    DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve it analytically in the case of identical binding. We uncover a switchlike transition between looped and unlooped phases and identify the key parameters that control this transition. Our results establish the basis for the quantitative understanding of fundamental cellular processes like DNA recombination, gene silencing, and telomere maintenance.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Transient catalytic combustor model

    NASA Astrophysics Data System (ADS)

    Tien, J. S.

    1981-05-01

    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.

  12. Closed-Loop System Removes Contaminants From Inert Gas

    NASA Technical Reports Server (NTRS)

    Sharma, Pramod K.

    1995-01-01

    Concentration of oxygen in this closed-loop system kept low by use of heated catalytic sorbent bed in cartridge. Proposed to keep concentration of water vapor low by use of predried zeolite sorbent bed in another cartridge, and to remove particles smaller than 0.1 micrometer by use of porous metal filters. In specific application, chamber is one in which semiconducting materials processed. By virtue of closed-loop operation, limited supply of inert gas adequate to provide atmosphere for industrial processing of semiconductors.

  13. Explaining Warm Coronal Loops

    NASA Technical Reports Server (NTRS)

    Klimchuk, James A.; Karpen, Judy T.; Patsourakos, Spiros

    2008-01-01

    One of the great mysteries of coronal physics that has come to light in the last few years is the discovery that warn (- 1 INK) coronal loops are much denser than expected for quasi-static equilibrium. Both the excess densities and relatively long lifetimes of the loops can be explained with bundles of unresolved strands that are heated impulsively to very high temperatures. Since neighboring strands are at different stages of cooling, the composite loop bundle is multi-thermal, with the distribution of temperatures depending on the details of the "nanoflare storm." Emission hotter than 2 MK is predicted, but it is not clear that such emission is always observed. We consider two possible explanations for the existence of over-dense warm loops without corresponding hot emission: (1) loops are bundles of nanoflare heated strands, but a significant fraction of the nanoflare energy takes the form of a nonthermal electron beam rather then direct plasma heating; (2) loops are bundles of strands that undergo thermal nonequilibrium that results when steady heating is sufficiently concentrated near the footpoints. We present numerical hydro simulations of both of these possibilities and explore the observational consequences, including the production of hard X-ray emission and absorption by cool material in the corona.

  14. Loop-loop interactions govern multiple steps in indole-3-glycerol phosphate synthase catalysis.

    PubMed

    Zaccardi, Margot J; O'Rourke, Kathleen F; Yezdimer, Eric M; Loggia, Laura J; Woldt, Svenja; Boehr, David D

    2014-03-01

    Substrate binding, product release, and likely chemical catalysis in the tryptophan biosynthetic enzyme indole-3-glycerol phosphate synthase (IGPS) are dependent on the structural dynamics of the β1α1 active-site loop. Statistical coupling analysis and molecular dynamic simulations had previously indicated that covarying residues in the β1α1 and β2α2 loops, corresponding to Arg54 and Asn90, respectively, in the Sulfolobus sulfataricus enzyme (ssIGPS), are likely important for coordinating functional motions of these loops. To test this hypothesis, we characterized site mutants at these positions for changes in catalytic function, protein stability and structural dynamics for the thermophilic ssIGPS enzyme. Although there were only modest changes in the overall steady-state kinetic parameters, solvent viscosity and solvent deuterium kinetic isotope effects indicated that these amino acid substitutions change the identity of the rate-determining step across multiple temperatures. Surprisingly, the N90A substitution had a dramatic effect on the general acid/base catalysis of the dehydration step, as indicated by the loss of the descending limb in the pH rate profile, which we had previously assigned to Lys53 on the β1α1 loop. These changes in enzyme function are accompanied with a quenching of ps-ns and µs-ms timescale motions in the β1α1 loop as measured by nuclear magnetic resonance studies. Altogether, our studies provide structural, dynamic and functional rationales for the coevolution of residues on the β1α1 and β2α2 loops, and highlight the multiple roles that the β1α1 loop plays in IGPS catalysis. Thus, substitution of covarying residues in the active-site β1α1 and β2α2 loops of indole-3-glycerol phosphate synthase results in functional, structural, and dynamic changes, highlighting the multiple roles that the β1α1 loop plays in enzyme catalysis and the importance of regulating the structural dynamics of this loop through noncovalent

  15. 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.

  16. 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.

  17. 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.

  18. Functional loop dynamics of the streptavidin-biotin complex.

    PubMed

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

    2015-01-20

    Accelerated molecular dynamics (aMD) simulation is employed to study the functional dynamics of the flexible loop(3-4) 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 loop(3-4) 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 loop(3-4) and biotin. (3) The closure of loop(3-4) is concerted to the stable binding of biotin to streptavidin. When the loop(3-4) is in its open-state, biotin moves out of the binding pocket, indicating that the interactions between the loop(3-4) and biotin are essential in trapping biotin in the binding pocket. (4) In the tetrameric streptavidin system, the conformational change of the loop(3-4) 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Flexible thermal laminate

    NASA Technical Reports Server (NTRS)

    Dawn, F. S.; Sauers, D. G.

    1977-01-01

    Lightweight flexible laminate of interwoven conducting and insulating yarns, designed to provide localized controlled heating for propellant tanks on space vehicles, is useful for nonspace applications where weight, bulk, and flexibility are critical concerns.

  4. 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)

  5. Catalytic efficiency of designed catalytic proteins

    PubMed Central

    Korendovych, Ivan V; DeGrado, William F

    2014-01-01

    The de novo design of catalysts that mimic the affinity and specificity of natural enzymes remains one of the Holy Grails of chemistry. Despite decades of concerted effort we are still unable to design catalysts as efficient as enzymes. Here we critically evaluate approaches to (re)design of novel catalytic function in proteins using two test cases: Kemp elimination and ester hydrolysis. We show that the degree of success thus far has been modest when the rate enhancements seen for the designed proteins are compared with the rate enhancements by small molecule catalysts in solvents with properties similar to the active site. Nevertheless, there are reasons for optimism: the design methods are ever improving and the resulting catalyst can be efficiently improved using directed evolution. PMID:25048695

  6. 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.

  7. 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.

  8. Thinking about Flexibility

    ERIC Educational Resources Information Center

    Villa, Mario Diaz

    2009-01-01

    This article emphasizes the complexity of the term flexibility and discusses its meanings and political dimensions, along with its expressions or realizations within the field of higher education. It proposes a new principle of flexibility that overcomes an understanding of flexibility within higher education as the mere ability or versatility to…

  9. Reconstitution of active catalytic trimer of aspartate transcarbamoylase from proteolytically cleaved polypeptide chains.

    PubMed Central

    Powers, V. M.; Yang, Y. R.; Fogli, M. J.; Schachman, H. K.

    1993-01-01

    Treatment of the catalytic (C) trimer of Escherichia coli aspartate transcarbamoylase (ATCase) with alpha-chymotrypsin by a procedure similar to that used by Chan and Enns (1978, Can. J. Biochem. 56, 654-658) has been shown to yield an intact, active, proteolytically cleaved trimer containing polypeptide fragments of 26,000 and 8,000 MW. Vmax of the proteolytically cleaved trimer (CPC) is 75% that of the wild-type C trimer, whereas Km for aspartate and Kd for the bisubstrate analog, N-(phosphonacetyl)-L-aspartate, are increased about 7- and 15-fold, respectively. CPC trimer is very stable to heat denaturation as shown by differential scanning microcalorimetry. Amino-terminal sequence analyses as well as results from electrospray ionization mass spectrometry indicate that the limited chymotryptic digestion involves the rupture of only a single peptide bond leading to the production of two fragments corresponding to residues 1-240 and 241-310. This cleavage site involving the bond between Tyr 240 and Ala 241 is in a surface loop known to be involved in intersubunit contacts between the upper and lower C trimers in ATCase when it is in the T conformation. Reconstituted holoenzyme comprising two CPC trimers and three wild-type regulatory (R) dimers was shown by enzyme assays to be devoid of the homotropic and heterotropic allosteric properties characteristic of wild-type ATCase. Moreover, sedimentation velocity experiments demonstrate that the holoenzyme reconstituted from CPC trimers is in the R conformation. These results indicate that the intact flexible loop containing Tyr 240 is essential for stabilizing the T conformation of ATCase. Following denaturation of the CPC trimer in 4.7 M urea and dilution of the solution, the separate proteolytic fragments re-associate to form active trimers in about 60% yield. How this refolding of the fragments, docking, and association to form trimers are achieved is not known. PMID:8318885

  10. 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.

  11. Smart feedback loops

    NASA Astrophysics Data System (ADS)

    Chepurnov, A. S.; Gribov, I. V.; Gudkov, K. A.; Shumakov, A. V.; Shvedunov, V. I.

    1994-12-01

    It is necessary to find the golden mean in allocating the processing resources of a computer control system. Traditionally, feedback loops operate at the lower levels to ensure safe and stable operation of the accelerator. At present we use analogue and digital feedback loops. Some systems, such as the RF, require more complex algorithms. A possible way of providing these, using digital signal processors is described. The results of tests with the Race-Track Microtron Linac are given and the sources of the main internal and external disturbances have been analysed.

  12. Concentric Loop Surface Coil

    NASA Astrophysics Data System (ADS)

    Hernández-Flores, R.; Rodríguez-González, A. O.; Salgado-Lujambio, P.; Barrios-Alvarez, F. A.

    2002-08-01

    A surface coil for MRI consisted of two concentric loops was developed for brain imaging. Prior to build the coil prototype, the magnetic field (B1) generated by the coil was numerically simulated. This field simulation is based on the Biot-Savart law for the circular- and square-shaped loops. From these theoretical results, we can appreciate an improvement on the B1 homogeneity. Brain images obtained at 1.5 Tesla show a good sensitivity in a particular region of interest. Also, these images compared well against images obtained with a circular-shaped coil. This receiver coil can generate high quality brain images.

  13. 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.

  14. 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.

  15. Optimized input shaping for a single flexible robot link

    SciTech Connect

    Wilson, D.G.; Stokes, D.; Starr, G.; Robinett, R.D.

    1996-03-01

    This paper will discuss the design of an input shaped open-loop control for a single flexible robot link. The authors develop the equations of motion, including the first flexible mode shape and the actuator dynamics. Additional content includes the hardware system identification iterative runs used to update the model. Optimized input shaped commands for the flexible robot link to produce a rest-to-rest, residual vibration-free, 90 degree maneuver are developed. Correlation between both experimental and analytical results of the 90{degree} slew, using two different identification models, are reviewed.

  16. 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.

  17. 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.

  18. 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)…

  19. NETL - Chemical Looping Reactor

    ScienceCinema

    None

    2016-07-12

    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. 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.

  1. 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.

  2. A summary of the active flexible wing program

    NASA Technical Reports Server (NTRS)

    Perry, Boyd, III; Cole, Stanley R.; Miller, Gerald D.

    1992-01-01

    A summary of the NASA/Rockwell Active Flexible Wing Program is presented. Major elements of the program are presented. Key program accomplishments included single- and multiple-mode flutter suppression, load alleviation and load control during rapid roll maneuvers, and multi-input/multi-output multiple-function active controls tests above the open-loop flutter boundary.

  3. 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.

  4. Mutational analysis of the active site flap (20s loop) of mandelate racemase.

    PubMed

    Bourque, Jennifer R; Bearne, Stephen L

    2008-01-15

    Mandelate racemase from Pseudomonas putida catalyzes the Mg2+-dependent 1,1-proton transfer that interconverts the enantiomers of mandelate. Residues of the 20s and 50s loops determine, in part, the topology and polarity of the active site and hence the substrate specificity. Previously, we proposed that, during racemization, the phenyl ring of mandelate moves between an S-pocket comprised of residues from the 50s loop and an R-pocket comprised of residues from the 20s loop [Siddiqi, F., Bourque, J. R., Jiang, H., Gardner, M., St. Maurice, M., Blouin, C., and Bearne, S. L. (2005) Biochemistry 44, 9013-9021]. The 20s loop constitutes a mobile beta-meander flap that covers the active site cavity shielding it from solvent and controlling entry and egress of ligands. To understand the role of the 20s loop in catalysis and substrate specificity, we constructed a series of mutants (V22A, V22I, V22F, T24S, A25V, V26A, V26L, V26F, V29A, V29L, V29F, V26A/V29L, and V22I/V29L) in which the sizes of hydrophobic side chains of the loop residues were varied. Catalytic efficiencies (kcat/Km) for all mutants were reduced between 6- and 40-fold with the exception of those of V22I, V26A, V29L, and V22I/V29L which had near wild-type efficiencies with mandelate. Thr 24 and Ala 25, located at the tip of the 20s loop, were particularly sensitive to minor alterations in the size of their hydrophobic side chains; however, most mutations were tolerated quite well, suggesting that flap mobility could compensate for increases in the steric bulk of hydrophobic side chains. With the exception of V29L, with mandelate as the substrate, and V22F and V26A/V29L, with 2-naphthylglycolate (2-NG) as the substrate, the values of kcat and Km were not altered in a manner consistent with steric obstruction of the R-pocket, perhaps due to flap mobility compensating for the increased size of the hydrophobic side chains. Surprisingly, V22I and V29L catalyzed the racemization of the bulkier substrate 2-NG

  5. 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.

  6. Quenched catalytic cracking process

    SciTech Connect

    Krambeck, F.J.; Penick, J.E.; Schipper, P.H.

    1990-12-18

    This paper describes improvement in a fluidized catalytic cracking process wherein a fluidizable catalyst cracking catalyst and a hydrocarbon feed are charged to a reactor riser at catalytic riser cracking conditions to form catalytically cracked vapor product and spent catalyst which are discharged into a reactor vessel having a volume via a riser reactor outlet equipped with a separation means to produce a catalyst lean phase. It comprises: a majority of the cracked product, and a catalyst rich phase comprising a majority of the spend catalyst. The the catalyst rich phase is discharged into a dense bed of catalyst maintained below the riser outlet and the catalyst lean phase is discharged into the vessel for a time, and at a temperature, which cause unselective thermal cracking of the cracked product in the reactor volume before product is withdrawn from the vessel via a vessel outlet. The improvement comprises: addition, after riser cracking is completed, and after separation of cracked products from catalyst, of a quenching stream into the vessel above the dense bed of catalyst, via a quench stream addition point which allows the quench stream to contact at least a majority of the volume of the vessel above the dense bed.

  7. Joint X-ray crystallographic and molecular dynamics study of cellobiohydrolase I from Trichoderma harzianum: deciphering the structural features of cellobiohydrolase catalytic activity.

    PubMed

    Textor, Larissa C; Colussi, Francieli; Silveira, Rodrigo L; Serpa, Viviane; de Mello, Bruno L; Muniz, João Renato C; Squina, Fabio M; Pereira, Nei; Skaf, Munir S; Polikarpov, Igor

    2013-01-01

    Aiming to contribute toward the characterization of new, biotechnologically relevant cellulolytic enzymes, we report here the first crystal structure of the catalytic core domain of Cel7A (cellobiohydrolase I) from the filamentous fungus Trichoderma harzianum IOC 3844. Our structural studies and molecular dynamics simulations show that the flexibility of Tyr260, in comparison with Tyr247 from the homologous Trichoderma reesei Cel7A, is enhanced as a result of the short side-chains of adjacent Val216 and Ala384 residues and creates an additional gap at the side face of the catalytic tunnel. T. harzianum cellobiohydrolase I also has a shortened loop at the entrance of the cellulose-binding tunnel, which has been described to interact with the substrate in T. reesei Cel7A. These structural features might explain why T. harzianum Cel7A displays higher k(cat) and K(m) values, and lower product inhibition on both glucoside and lactoside substrates, compared with T. reesei Cel7A.

  8. 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

  9. 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.

  10. 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.

  11. Protein Loop Closure Using Orientational Restraints from NMR Data

    NASA Astrophysics Data System (ADS)

    Tripathy, Chittaranjan; Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

    Protein loops often play important roles in biological functions such as binding, recognition, catalytic activities and allosteric regulation. Modeling loops that are biophysically sensible is crucial to determining the functional specificity of a protein. A variety of algorithms ranging from robotics-inspired inverse kinematics methods to fragmentbased homology modeling techniques have been developed to predict protein loops. However, determining the 3D structures of loops using global orientational restraints on internuclear vectors, such as those obtained from residual dipolar coupling (RDC) data in solution Nuclear Magnetic Resonance (NMR) spectroscopy, has not been well studied. In this paper, we present a novel algorithm that determines the protein loop conformations using a minimal amount of RDC data. Our algorithm exploits the interplay between the sphero-conics derived from RDCs and the protein kinematics, and formulates the loop structure determination problem as a system of low-degree polynomial equations that can be solved exactly and in closed form. The roots of these polynomial equations, which encode the candidate conformations, are searched systematically, using efficient and provable pruning strategies that triage the vast majority of conformations, to enumerate or prune all possible loop conformations consistent with the data. Our algorithm guarantees completeness by ensuring that a possible loop conformation consistent with the data is never missed. This data-driven algorithm provides a way to assess the structural quality from experimental data with minimal modeling assumptions. We applied our algorithm to compute the loops of human ubiquitin, the FF Domain 2 of human transcription elongation factor CA150 (FF2), the DNA damage inducible protein I (DinI) and the third IgG-binding domain of Protein G (GB3) from experimental RDC data. A comparison of our results versus those obtained by using traditional structure determination protocols on the

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

    PubMed Central

    2010-01-01

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

  13. Aurora Australis, Sinuous Loop

    NASA Technical Reports Server (NTRS)

    1991-01-01

    This view of the Aurora Australis or Southern Lights (location unknown) shows a sinuous looping band of airglow above the Earth Limb. Calculated to be in the 80 - 120 km altitude region, auroral activity is due to exitation of atomic oxygen in the upper atmosphere by radiation from the van Allen Radiation Belts and is most common above the 65 degree north and south latitude range during the spring and fall of the year.

  14. Loop Quantum Cosmology.

    PubMed

    Bojowald, Martin

    2005-01-01

    Quantum gravity is expected to be necessary in order to understand situations where classical general relativity breaks down. In particular in cosmology one has to deal with initial singularities, i.e., the fact that the backward evolution of a classical space-time inevitably comes to an end after a finite amount of proper time. This presents a breakdown of the classical picture and requires an extended theory for a meaningful description. Since small length scales and high curvatures are involved, quantum effects must play a role. Not only the singularity itself but also the surrounding space-time is then modified. One particular realization is loop quantum cosmology, an application of loop quantum gravity to homogeneous systems, which removes classical singularities. Its implications can be studied at different levels. Main effects are introduced into effective classical equations which allow to avoid interpretational problems of quantum theory. They give rise to new kinds of early universe phenomenology with applications to inflation and cyclic models. To resolve classical singularities and to understand the structure of geometry around them, the quantum description is necessary. Classical evolution is then replaced by a difference equation for a wave function which allows to extend space-time beyond classical singularities. One main question is how these homogeneous scenarios are related to full loop quantum gravity, which can be dealt with at the level of distributional symmetric states. Finally, the new structure of space-time arising in loop quantum gravity and its application to cosmology sheds new light on more general issues such as time.

  15. Loop Quantum Cosmology.

    PubMed

    Bojowald, Martin

    2008-01-01

    Quantum gravity is expected to be necessary in order to understand situations in which classical general relativity breaks down. In particular in cosmology one has to deal with initial singularities, i.e., the fact that the backward evolution of a classical spacetime inevitably comes to an end after a finite amount of proper time. This presents a breakdown of the classical picture and requires an extended theory for a meaningful description. Since small length scales and high curvatures are involved, quantum effects must play a role. Not only the singularity itself but also the surrounding spacetime is then modified. One particular theory is loop quantum cosmology, an application of loop quantum gravity to homogeneous systems, which removes classical singularities. Its implications can be studied at different levels. The main effects are introduced into effective classical equations, which allow one to avoid the interpretational problems of quantum theory. They give rise to new kinds of early-universe phenomenology with applications to inflation and cyclic models. To resolve classical singularities and to understand the structure of geometry around them, the quantum description is necessary. Classical evolution is then replaced by a difference equation for a wave function, which allows an extension of quantum spacetime beyond classical singularities. One main question is how these homogeneous scenarios are related to full loop quantum gravity, which can be dealt with at the level of distributional symmetric states. Finally, the new structure of spacetime arising in loop quantum gravity and its application to cosmology sheds light on more general issues, such as the nature of time.

  16. 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.

  17. 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.

  18. 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).

  19. Plasticity of 150-Loop in Influenza Neuraminidase Explored by Hamiltonian Replica Exchange Molecular Dynamics Simulations

    PubMed Central

    Han, Nanyu; Mu, Yuguang

    2013-01-01

    Neuraminidase (NA) of influenza is a key target for antiviral inhibitors, and the 150-cavity in group-1 NA provides new insight in treating this disease. However, NA of 2009 pandemic influenza (09N1) was found lacking this cavity in a crystal structure. To address the issue of flexibility of the 150-loop, Hamiltonian replica exchange molecular dynamics simulations were performed on different groups of NAs. Free energy landscape calculated based on the volume of 150-cavity indicates that 09N1 prefers open forms of 150-loop. The turn A (residues 147–150) of the 150-loop is discovered as the most dynamical motif which induces the inter-conversion of this loop among different conformations. In the turn A, the backbone dynamic of residue 149 is highly related with the shape of 150-loop, thus can function as a marker for the conformation of 150-loop. As a contrast, the closed conformation of 150-loop is more energetically favorable in N2, one of group-2 NAs. The D147-H150 salt bridge is found having no correlation with the conformation of 150-loop. Instead the intimate salt bridge interaction between the 150 and 430 loops in N2 variant contributes the stabilizing factor for the closed form of 150-loop. The clustering analysis elaborates the structural plasticity of the loop. This enhanced sampling simulation provides more information in further structural-based drug discovery on influenza virus. PMID:23593372

  20. Catalytic reforming process

    SciTech Connect

    Absil, R.P.; Huss, A. Jr.; McHale, W.D.; Partridge, R.D.

    1989-06-13

    This patent describes a catalytic reforming process which comprises contacting a naphtha range feed with a low acidity extrudate comprising an intermediate and/or a large pore acidic zeolite bound with a low acidity refractory oxide under reforming conditions to provide a reaction product of increased aromatic content, the extrudate having been prepared with at least an extrusion-facilitating amount of a low acidity refractory oxide in colloidal form and containing at least one metal species selected from the platinum group metals.

  1. Flexible aircraft flying and ride qualities

    NASA Technical Reports Server (NTRS)

    Ashkenas, I. L.; Magdaleno, R. E.; Mcruer, D. T.

    1984-01-01

    A brief analytic exposition is presented to illustrate a central principle in flexible mode control, some of the pertinent pilot centered requirements are listed and discussed. The desired features of the control methodology are exposed and the methodology to be used is selected. The example Boeing supplied characteristics are discussed and approximated with a reduced order model and a simplified treatment of unsteady aerodynamics. The closed loop flight control system design follows, along with first level assessments of resulting handling and ride quality characteristics. Some of these do not meet the postulated requirements and remain problems to be solved possibly by further analysis or future simulation.

  2. 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.

  3. 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.

  4. 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.

  5. TOWARDS AN ECONOMICAL FLEXIBILITY.

    ERIC Educational Resources Information Center

    CAUDILL, WILLIAM W.; RICHARDSON, L.S.

    AN ARCHITECT AND A SUPERINTENDENT OF SCHOOLS COLLABORATED ON THE DESIGN FOR A HIGH SCHOOL, WHICH STRESSED ECONOMY AND FLEXIBILITY. THEY CONSIDERED THREE ASPECTS OF FLEXIBILITY--(1) EXPANDABILITY, (2) CONVERTIBILITY, AND (3) VERSATILITY. EXPANDABILITY IS DISCUSSED IN TERMS OF SITE SELECTION AND PLANNING. CONVERTIBILITY FEATURES IDENTIFIED INCLUDE…

  6. Flexible 'zoning' aids adaptability.

    PubMed

    Corben, Simon

    2013-09-01

    Simon Corben, business development director at Capita Symonds' Health team, examines how 'clever use of zoning' when planning new healthcare facilities could improve hospital design, increase inherent flexibility, and reduce lifetime costs, and argues that a 'loose-fit, non-bespoke approach' to space planning will lead to 'more flexible buildings that are suitable for conversion to alternative uses'.

  7. 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…

  8. 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.

  9. Flexible ferroelectric organic crystals

    PubMed Central

    Owczarek, Magdalena; Hujsak, Karl A.; Ferris, Daniel P.; Prokofjevs, Aleksandrs; Majerz, Irena; Szklarz, Przemysław; Zhang, Huacheng; Sarjeant, Amy A.; Stern, Charlotte L.; Jakubas, Ryszard; Hong, Seungbum; Dravid, Vinayak P.; Stoddart, J. Fraser

    2016-01-01

    Flexible organic materials possessing useful electrical properties, such as ferroelectricity, are of crucial importance in the engineering of electronic devices. Up until now, however, only ferroelectric polymers have intrinsically met this flexibility requirement, leaving small-molecule organic ferroelectrics with room for improvement. Since both flexibility and ferroelectricity are rare properties on their own, combining them in one crystalline organic material is challenging. Herein, we report that trisubstituted haloimidazoles not only display ferroelectricity and piezoelectricity—the properties that originate from their non-centrosymmetric crystal lattice—but also lend their crystalline mechanical properties to fine-tuning in a controllable manner by disrupting the weak halogen bonds between the molecules. This element of control makes it possible to deliver another unique and highly desirable property, namely crystal flexibility. Moreover, the electrical properties are maintained in the flexible crystals. PMID:27734829

  10. Flexible ferroelectric organic crystals

    NASA Astrophysics Data System (ADS)

    Owczarek, Magdalena; Hujsak, Karl A.; Ferris, Daniel P.; Prokofjevs, Aleksandrs; Majerz, Irena; Szklarz, Przemysław; Zhang, Huacheng; Sarjeant, Amy A.; Stern, Charlotte L.; Jakubas, Ryszard; Hong, Seungbum; Dravid, Vinayak P.; Stoddart, J. Fraser

    2016-10-01

    Flexible organic materials possessing useful electrical properties, such as ferroelectricity, are of crucial importance in the engineering of electronic devices. Up until now, however, only ferroelectric polymers have intrinsically met this flexibility requirement, leaving small-molecule organic ferroelectrics with room for improvement. Since both flexibility and ferroelectricity are rare properties on their own, combining them in one crystalline organic material is challenging. Herein, we report that trisubstituted haloimidazoles not only display ferroelectricity and piezoelectricity--the properties that originate from their non-centrosymmetric crystal lattice--but also lend their crystalline mechanical properties to fine-tuning in a controllable manner by disrupting the weak halogen bonds between the molecules. This element of control makes it possible to deliver another unique and highly desirable property, namely crystal flexibility. Moreover, the electrical properties are maintained in the flexible crystals.

  11. Bifurcations of limit cycles in open and closed loop reverse flow reactors

    NASA Astrophysics Data System (ADS)

    Russo, Lucia; Crescitelli, Silvestro; Brasiello, Antonio

    2013-10-01

    The present work analyses the bifurcations of limit cycles in open and loop reverse flow reactors. The open loop system consists of a reactor where the flow direction is periodically forced whereas in the closed loop system, the flow inversion is dictated by a control law which activates when the temperature at the edge of catalytic bed falls below the set-point value. We performed the bifurcation analysis of the open loop system as the switch time is varied and we constructed the solution diagram through the application of continuation technique. Many Naimark-Sacker bifurcations leading to quasi-periodic regimes have been found on the limit cycles branches. Finally, we compared these limit cycles with those of the closed loop system where the flow inversion is dictated by a control system which acts if the temperature measured at the edge of reactor falls below a set-point value.

  12. 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.

  13. 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.

  14. Line Loss Minimization of Loop Distribution Systems Using UPFC

    NASA Astrophysics Data System (ADS)

    Sayed, Mahmoud A.; Inayoshi, Nobuyuki; Takeshita, Takaharu; Ueda, Fukashi

    This paper presents an elaborated mathematical analysis of the line loss minimum conditions of loop distribution systems. In order to achieve these conditions, the Unified Power Flow Controller (UPFC), a typical Flexible AC Transmission Systems (FACTS) device that is capable of instantaneous control of transmission and distribution power flow, is used. For minimizing the total line loss of the loop distribution system, the authors propose two control schemes, the Line Inductance Compensation control and the Line Voltage Compensation control. These control schemes can be applied for controlling the UPFC in the loop distribution system according to the line parameters. The effectiveness of the proposed control schemes has been verified experimentally using a laboratory prototype in a 200V, 6kVA system.

  15. Optical parametric loop mirror

    NASA Astrophysics Data System (ADS)

    Mori, K.; Morioka, T.; Saruwatari, M.

    1995-06-01

    A novel configuration for four-wave mixing (FWM) is proposed that offers the remarkable feature of inherently separating the FWM wave from the input pump and signal waves and suppressing their background amplified stimulated emission without optical filtering. In the proposed configuration, an optical parametric loop mirror, two counterpropagating FWM waves generated in a Sagnac interferometer interfere with a relative phase difference that is introduced deliberately. FWM frequency-conversion experiments in a polarization-maintaining fiber achieved more than 35 dB of input-wave suppression against the FWM wave.

  16. 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

  17. Chemistry and application of flexible porous coordination polymers*

    PubMed Central

    Bureekaew, Sareeya; Shimomura, Satoru; Kitagawa, Susumu

    2008-01-01

    Porous coordination polymers (PCPs), which are microporous materials, have been given much attention from both scientific and commercial aspects regarding their application to gas storage, gas separation and catalytic reaction because of the regularity of their pore shape and pore size, accompanied with the functionality. Moreover, in recent years, flexible PCPs, which are structurally transformable depending upon external stimuli, have been attractive because they provide unique properties, dissimilar to those of zeolites. In this review, the chemistry and application of flexible crystalline PCPs are summarized and discussed. PMID:27877934

  18. Flexible microstrip antennas

    NASA Astrophysics Data System (ADS)

    Cano Barrera, Camilo Antonio

    2013-05-01

    Actually the technological community has an interest in developing flexible circuits and antennas with particular characteristics e.g. robust, flexible, lightweight load-bearing, economical and efficient antennas for integrated millimeter wave systems. Microstrip antennas are an excellent solution because those have all the characteristics before mentioned, but they have the problem of being rigid antennas and this makes impossible that those antennas can be use in portable devices. A practical solution is developing flexible microstrip antennas that can be integrated to different devices. One axis of work is the analysis of the electromagnetic field to the microstrip antennas using Bessel function and after generalize for application inflexible microstrip antennas.

  19. 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.

  20. Flexible reusable mandrels

    NASA Technical Reports Server (NTRS)

    Willden, Kurtis S. (Inventor)

    1995-01-01

    A reusable laminate mandrel which is unaffected by extreme temperature changes. The flexible laminate mandrel is comprised of sheets stacked to produce the required configuration, a cover wrap that applies pressure to the mandrel laminate, maintaining the stack cross-section. Then after use, the mandrels can be removed, disassembled, and reused. In the method of extracting the flexible mandrel from one end of a composite stiffener, individual ones of the laminae of the flexible mandrel or all are extracted at the same time, depending on severity of the contour.

  1. Loop expansion and the bosonic representation of loop quantum gravity

    NASA Astrophysics Data System (ADS)

    Bianchi, E.; Guglielmon, J.; Hackl, L.; Yokomizo, N.

    2016-10-01

    We introduce a new loop expansion that provides a resolution of the identity in the Hilbert space of loop quantum gravity on a fixed graph. We work in the bosonic representation obtained by the canonical quantization of the spinorial formalism. The resolution of the identity gives a tool for implementing the projection of states in the full bosonic representation onto the space of solutions to the Gauss and area matching constraints of loop quantum gravity. This procedure is particularly efficient in the semiclassical regime, leading to explicit expressions for the loop expansions of coherent, heat kernel and squeezed states.

  2. High temperature storage loop :

    SciTech Connect

    Gill, David Dennis; Kolb, William J.

    2013-07-01

    A three year plan for thermal energy storage (TES) research was created at Sandia National Laboratories in the spring of 2012. This plan included a strategic goal of providing test capability for Sandia and for the nation in which to evaluate high temperature storage (>650ÀC) technology. The plan was to scope, design, and build a flow loop that would be compatible with a multitude of high temperature heat transfer/storage fluids. The High Temperature Storage Loop (HTSL) would be reconfigurable so that it was useful for not only storage testing, but also for high temperature receiver testing and high efficiency power cycle testing as well. In that way, HTSL was part of a much larger strategy for Sandia to provide a research and testing platform that would be integral for the evaluation of individual technologies funded under the SunShot program. DOEs SunShot program seeks to reduce the price of solar technologies to 6/kWhr to be cost competitive with carbon-based fuels. The HTSL project sought to provide evaluation capability for these SunShot supported technologies. This report includes the scoping, design, and budgetary costing aspects of this effort

  3. 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.

  4. Catalytic cracking of hydrocarbons

    SciTech Connect

    Absil, R.P.L.; Bowes, E.; Green, G.J.; Marler, D.O.; Shihabi, D.S.; Socha, R.F.

    1992-02-04

    This patent describes an improvement in a catalytic cracking process in which a hydrocarbon feed is cracked in a cracking zone in the absence of added hydrogen and in the presence of a circulating inventory of solid acidic cracking a catalyst which acquires a deposit of coke that contains chemically bound nitrogen while the cracking catalyst is in the cracking zone, the coke catalyst being circulated to t regeneration zone to convert the coke catalyst to a regenerated catalyst with the formation of a flue gas comprising nitrogen oxides: the improvement comprises incorporating into the circulating catalyst inventory an amount of additive particles comprising a synthetic porous crystalline material containing copper metal or cations, to reduce the content of nitrogen oxides in the flue gas.

  5. 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.

  6. 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.

  7. 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.

  8. Closed-loop active optical system control

    NASA Astrophysics Data System (ADS)

    Sparks, T. E.

    1980-01-01

    A control system, based on a real-time lateral shear interferometer has been developed for use in control during thermal tests and static error compensation experiments. The minicomputer which controls the interferometer and provides its service functions also controls the active system, thereby giving flexibility to the algorithm. The minicomputer system contains 288 K bytes of memory and 15 M bytes of disk storage. The interferometer system employed is composed of the measuring head and its support electronics, a video display on which wavefront contour maps are generated, and a DECwriter operator console. The versatility provided by the use of a general purpose interferometer system allows for interactive control of the closed-loop process. Various arithmetic capabilities such as the addition of wavefronts, division by a constant, and fitting of wavefront data with Zernike polynomials, allow for measurements to be averaged and for removal of alignment errors before correction is performed.

  9. 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.

  10. Flexibility of zeolite frameworks

    NASA Astrophysics Data System (ADS)

    Kapko, Vitaliy; Treacy, Michael; Thorpe, Michael

    2009-03-01

    Zeolites are an important class of industrial catalysts because of their large internal surfaces and molecular-sieving properties. Recent geometric simulations (1) show that almost all of the known zeolites can exist without distortion of their tetrahedra within some range of densities, which we call the flexibility window. Within this window, the framework accommodates density changes by rotations about the shared tetrahedral corners. We argue that the presence of a flexibility window can be used as a topological criterion to select potential candidates for synthesis from millions of hypothetical structures. We also investigate the exceptions to the rule, as well as the shape of the flexibility window and the symmetric properties of zeolites inside it. (1) A. Sartbaeva, S.A. Wells, M.M.J. Treacy and M.F. Thorpe The flexibility window in zeolites, Nature Materials 5, 962-965 (2006); I. Rivin, commentary 931-932.

  11. Are flexible designs sound?

    PubMed

    Burman, Carl-Fredrik; Sonesson, Christian

    2006-09-01

    Flexible designs allow large modifications of a design during an experiment. In particular, the sample size can be modified in response to interim data or external information. A standard flexible methodology combines such design modifications with a weighted test, which guarantees the type I error level. However, this inference violates basic inference principles. In an example with independent N(mu, 1) observations, the test rejects the null hypothesis of mu < or = 0 while the average of the observations is negative. We conclude that flexible design in its most general form with the corresponding weighted test is not valid. Several possible modifications of the flexible design methodology are discussed with a focus on alternative hypothesis tests.

  12. 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

  13. Catalytically Active Regenerative Sorbent beds (CARS) for airborne contaminants.

    PubMed

    Akse, J R; Thompson, J O

    1995-01-01

    The Pd on Al2O3 catalyst used in the projected Space Station's Trace Contaminant Control System (TCCS) catalytic oxidizer can be poisoned by volatile halogen-, sulfur-, and nitrogen-containing organic species. Catalytically Active Regenerable Sorbents (CARS) eliminate these problematic contaminants and the large carbon bed used for their elimination in a three-step process. Contaminants are conventionally adsorbed by the CARS bed. After saturation, the bed is connected to an off-line recirculation loop, filled with hydrogen, and then heated. At temperature, contaminants are hydrogenated on catalytic sites within the bed, forming simple alkanes and acid gases that are efficiently converted to innocuous salts in an in-line alkaline bed. The CARS bed is regenerated by this cycle and alkane gases are released to be safely oxidized in the catalytic oxidizer. A challenge mixture containing Freon-113, thiophene, trichloroethylene, Halon-1301, and dichloromethane at 1670, 75, 81, 68, and 83 mg/m3 was successfully treated using this technology, demonstrating the CARS feasibility.

  14. GROMACS: fast, flexible, and free.

    PubMed

    Van Der Spoel, David; Lindahl, Erik; Hess, Berk; Groenhof, Gerrit; Mark, Alan E; Berendsen, Herman J C

    2005-12-01

    This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.

  15. Optimization-based design of control systems for flexible structures

    NASA Technical Reports Server (NTRS)

    Polak, E.; Baker, T. E.; Wuu, T-L.; Harn, Y-P.

    1988-01-01

    The purpose of this presentation is to show that it is possible to use nonsmooth optimization algorithms to design both closed-loop finite dimensional compensators and open-loop optimal controls for flexible structures modeled by partial differential equations. An important feature of our approach is that it does not require modal decomposition and hence is immune to instabilities caused by spillover effects. Furthermore, it can be used to design control systems for structures that are modeled by mixed systems of coupled ordinary and partial differential equations.

  16. 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.

  17. 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.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

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

    2015-01-08

    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.

  20. 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,…

  1. 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.

  2. Pulse thermal loop

    NASA Technical Reports Server (NTRS)

    Weislogel, Mark M. (Inventor)

    2002-01-01

    A pulse thermal loop heat transfer system includes a means to use pressure rises in a pair of evaporators to circulate a heat transfer fluid. The system includes one or more valves that iteratively, alternately couple the outlets the evaporators to the condenser. While flow proceeds from one of the evaporators to the condenser, heating creates a pressure rise in the other evaporator, which has its outlet blocked to prevent fluid from exiting the other evaporator. When the flow path is reconfigured to allow flow from the other evaporator to the condenser, the pressure in the other evaporator is used to circulate a pulse of fluid through the system. The reconfiguring of the flow path, by actuating or otherwise changing the configuration of the one or more valves, may be triggered when a predetermined pressure difference between the evaporators is reached.

  3. 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.

  4. 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.

  5. Loop Quantum Gravity.

    PubMed

    Rovelli, Carlo

    2008-01-01

    The problem of describing the quantum behavior of gravity, and thus understanding quantum spacetime, is still open. Loop quantum gravity is a well-developed approach to this problem. It is a mathematically well-defined background-independent quantization of general relativity, with its conventional matter couplings. Today research in loop quantum gravity forms a vast area, ranging from mathematical foundations to physical applications. Among the most significant results obtained so far are: (i) The computation of the spectra of geometrical quantities such as area and volume, which yield tentative quantitative predictions for Planck-scale physics. (ii) A physical picture of the microstructure of quantum spacetime, characterized by Planck-scale discreteness. Discreteness emerges as a standard quantum effect from the discrete spectra, and provides a mathematical realization of Wheeler's "spacetime foam" intuition. (iii) Control of spacetime singularities, such as those in the interior of black holes and the cosmological one. This, in particular, has opened up the possibility of a theoretical investigation into the very early universe and the spacetime regions beyond the Big Bang. (iv) A derivation of the Bekenstein-Hawking black-hole entropy. (v) Low-energy calculations, yielding n-point functions well defined in a background-independent context. The theory is at the roots of, or strictly related to, a number of formalisms that have been developed for describing background-independent quantum field theory, such as spin foams, group field theory, causal spin networks, and others. I give here a general overview of ideas, techniques, results and open problems of this candidate theory of quantum gravity, and a guide to the relevant literature.

  6. 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

  7. 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

  8. Megawatt Scale Hardware-in-the-Loop Testing of a High Speed Generator

    DTIC Science & Technology

    2012-02-01

    measure the torque and speed on the high speed shaft . A flexible coupling with shear section, constructed by Coupling Corporation of America, is used...gearbox used to deliver up to 5 MW to the mechanical shaft of a generator at speeds of up to 24000 rpm. A rectifier using fast recovery diodes is...loop (HIL) simulation experiments provide a flexible and often cost effective way to exercise equipment and controllers in a realistic environment

  9. The Projectile Inside the Loop

    ERIC Educational Resources Information Center

    Varieschi, Gabriele U.

    2006-01-01

    The loop-the-loop demonstration can be easily adapted to study the kinematics of projectile motion, when the moving body falls inside the apparatus. Video capturing software can be used to reveal peculiar geometrical effects of this simple but educational experiment.

  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. Improved code-tracking loop

    NASA Technical Reports Server (NTRS)

    Laflame, D. T.

    1980-01-01

    Delay-locked loop tracks pseudonoise codes without introducing dc timing errors, because it is not sensitive to gain imbalance between signal processing arms. "Early" and "late" reference codes pass in combined form through both arms, and each arm acts on both codes. Circuit accomodates 1 dB weaker input signals with tracking ability equal to that of tau-dither loops.

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

    NASA Astrophysics Data System (ADS)

    Huang, G.; Byrd, J. M.

    2006-11-01

    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.

  13. 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.

  14. Catalytic gasification of biomass

    NASA Astrophysics Data System (ADS)

    Robertus, R. J.; Mudge, L. K.; Sealock, L. J., Jr.; Mitchell, D. H.; Weber, S. L.

    1981-12-01

    Methane and methanol synthesis gas can be produced by steam gasification of biomass in the presence of appropriate catalysts. This concept is to use catalysts in a fluidized bed reactor which is heated indirectly. The objective is to determine the technical and economic feasibility of the concept. Technically the concept has been demonstrated on a 50 lb per hr scale. Potential advantages over conventional processes include: no oxygen plant is needed, little tar is produced so gas and water treatment are simplified, and yields and efficiencies are greater than obtained by conventional gasification. Economic studies for a plant processing 2000 T/per day dry wood show that the cost of methanol from wood by catalytic gasification is competitive with the current price of methanol. Similar studies show the cost of methane from wood is competitive with projected future costs of synthetic natural gas. When the plant capacity is decreased to 200 T per day dry wood, neither product is very attractive in today's market.

  15. Wilson Loop Diagrams and Positroids

    NASA Astrophysics Data System (ADS)

    Agarwala, Susama; Marin-Amat, Eloi

    2017-03-01

    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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  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

    2015-10-07

    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.

  1. 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.

  2. 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

  3. Catalytic reforming of naphtha fractions

    SciTech Connect

    Bishop, K.C.; Vorhis, F.H.

    1980-09-16

    Production of motor gasoline and a btx-enriched reformate by fractionating a naphtha feedstock into a mid-boiling btxprecursor fraction, a relatively high-boiling fraction and a relatively low-boiling fraction; catalytically reforming the btxprecursor fraction in a first reforming zone; combining the relatively high-boiling and low-boiling fractions and catalytically reforming the combined fractions in a second reforming zone.

  4. Flexible Quantum Oblivious Transfer

    NASA Astrophysics Data System (ADS)

    Yang, Yu-Guang; Yang, Rui; Cao, Wei-Feng; Chen, Xiu-Bo; Zhou, Yi-Hua; Shi, Wei-Min

    2017-01-01

    We propose a flexible protocol for one-out-of- nquantum oblivious transfer (QOT) Compared with existing QOT protocols, our protocol is more flexible. We demonstrate that, by adjusting the value of 𝜃 the flexible one-out-of- nQOT is allowable where n can be located theoretically on any value the communicating parties wanted. Meanwhile, it also meets the rigorous security requirements of the oblivious transfer (OT) definition, which ensures Bob can receive on average one of n messages held by Alice, while Alice cannot know which one Bob has received. Finally, we analyze the security of our protocol and show that it is not based on quantum bit commitment and does not violate Lo's no-go theorem so that its security can be achieved.

  5. Flexible Quantum Oblivious Transfer

    NASA Astrophysics Data System (ADS)

    Yang, Yu-Guang; Yang, Rui; Cao, Wei-Feng; Chen, Xiu-Bo; Zhou, Yi-Hua; Shi, Wei-Min

    2017-04-01

    We propose a flexible protocol for one-out-of- nquantum oblivious transfer (QOT) Compared with existing QOT protocols, our protocol is more flexible. We demonstrate that, by adjusting the value of 𝜃 the flexible one-out-of- nQOT is allowable where n can be located theoretically on any value the communicating parties wanted. Meanwhile, it also meets the rigorous security requirements of the oblivious transfer (OT) definition, which ensures Bob can receive on average one of n messages held by Alice, while Alice cannot know which one Bob has received. Finally, we analyze the security of our protocol and show that it is not based on quantum bit commitment and does not violate Lo's no-go theorem so that its security can be achieved.

  6. A conserved loop in polynucleotide phosphorylase (PNPase) essential for both RNA and ADP/phosphate binding.

    PubMed

    Carzaniga, Thomas; Mazzantini, Elisa; Nardini, Marco; Regonesi, Maria Elena; Greco, Claudio; Briani, Federica; De Gioia, Luca; Dehò, Gianni; Tortora, Paolo

    2014-02-01

    Polynucleotide phosphorylase (PNPase) reversibly catalyzes RNA phosphorolysis and polymerization of nucleoside diphosphates. Its homotrimeric structure forms a central channel where RNA is accommodated. Each protomer core is formed by two paralogous RNase PH domains: PNPase1, whose function is largely unknown, hosts a conserved FFRR loop interacting with RNA, whereas PNPase2 bears the putative catalytic site, ∼20 Å away from the FFRR loop. To date, little is known regarding PNPase catalytic mechanism. We analyzed the kinetic properties of two Escherichia coli PNPase mutants in the FFRR loop (R79A and R80A), which exhibited a dramatic increase in Km for ADP/Pi binding, but not for poly(A), suggesting that the two residues may be essential for binding ADP and Pi. However, both mutants were severely impaired in shifting RNA electrophoretic mobility, implying that the two arginines contribute also to RNA binding. Additional interactions between RNA and other PNPase domains (such as KH and S1) may preserve the enzymatic activity in R79A and R80A mutants. Inspection of enzyme structure showed that PNPase has evolved a long-range acting hydrogen bonding network that connects the FFRR loop with the catalytic site via the F380 residue. This hypothesis was supported by mutation analysis. Phylogenetic analysis of PNPase domains and RNase PH suggests that such network is a unique feature of PNPase1 domain, which coevolved with the paralogous PNPase2 domain.

  7. Control of large flexible systems via eigenvalue relocation

    NASA Technical Reports Server (NTRS)

    Denman, E. D.; Jeon, G. J.

    1985-01-01

    For the vibration control of large flexible systems, a control scheme by which the eigenvalues of the closed-loop systems are assigned to predetermined locations within the feasible region through velocity-only feedback is presented. Owing to the properties of second-order lambda-matrices and an efficient model decoupling technique, the control scheme makes it possible that selected modes are damped with the rest of the modes unchanged.

  8. 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.

  9. 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.

  10. Flexible Heating Head

    NASA Technical Reports Server (NTRS)

    Fox, Robert L.; Johnson, Samuel D.; Coultrip, Robert H.; Phillips, W. Morris

    1994-01-01

    United States Air Force is investigating method of repairing aircraft by use of adhesive bonding with induction heating to cure adhesive. Fast-acting and reliable induction heating device that is lightweight, portable, and easy to use needed for such applications. Newly developed flexible heating head lightweight and conforms to complex, curved surfaces. Incorporates principles and circuitry of toroid joining gun described in "Toroid Joining Gun for Fittings and Couplings" (LAR-14278). Concentrates heat in local area through induction heating. Flexible heating head contains tank circuit, connected via cable to source of power.

  11. 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.

  12. 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.

  13. Modeling loop entropy.

    PubMed

    Chirikjian, Gregory S

    2011-01-01

    Proteins fold from a highly disordered state into a highly ordered one. Traditionally, the folding problem has been stated as one of predicting "the" tertiary structure from sequential information. However, new evidence suggests that the ensemble of unfolded forms may not be as disordered as once believed, and that the native form of many proteins may not be described by a single conformation, but rather an ensemble of its own. Quantifying the relative disorder in the folded and unfolded ensembles as an entropy difference may therefore shed light on the folding process. One issue that clouds discussions of "entropy" is that many different kinds of entropy can be defined: entropy associated with overall translational and rotational Brownian motion, configurational entropy, vibrational entropy, conformational entropy computed in internal or Cartesian coordinates (which can even be different from each other), conformational entropy computed on a lattice, each of the above with different solvation and solvent models, thermodynamic entropy measured experimentally, etc. The focus of this work is the conformational entropy of coil/loop regions in proteins. New mathematical modeling tools for the approximation of changes in conformational entropy during transition from unfolded to folded ensembles are introduced. In particular, models for computing lower and upper bounds on entropy for polymer models of polypeptide coils both with and without end constraints are presented. The methods reviewed here include kinematics (the mathematics of rigid-body motions), classical statistical mechanics, and information theory.

  14. 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.

  15. 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

  16. Wilson loops in minimal surfaces

    SciTech Connect

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

    1999-04-27

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

  17. 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.

  18. 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.

  19. Open loop distribution system design

    SciTech Connect

    Glamocanin, V. ); Filipovic, V. . Elektrotechnicki fakulet)

    1993-10-01

    The ability to supply consumers of an urban area, with minimum interruption during a feeder segment or substation transformer outage, is assured by a uniform cable size of the feeder segments along the entire loop. Based on the criterion of the uniform cable size, a loop configuration is obtained first by minimizing the installation costs, and then an open loop solution is found by minimizing the power losses. Heuristic rules are proposed and used to obtain an initial solution, as well as to improve current solutions.

  20. 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…

  1. 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.

  2. Retained Digital Flexible Ureteroscopes

    PubMed Central

    Huynh, Melissa; Telfer, Siobhan; Pautler, Stephen; Denstedt, John

    2017-01-01

    Abstract This report documents two instances of retained flexible ureteroscopes at the time of ureteroscopy and laser lithotripsy in a healthy 37-year-old male and a 53-year-old male with a pelvic kidney. We describe maneuvers to remove the ureteroscope endoscopically in the first case, while the second case required conversion to open surgery for ureteroscope extrication. PMID:28265593

  3. Split-Level Flexibility.

    ERIC Educational Resources Information Center

    Roberson, Kelly

    1997-01-01

    Presents photographs and the floor plan of a middle school whose split-level design separates "noisy" areas, such as the band room and gymnasium, from the academic wing. The design encourages teaming and flexibility through its classroom clustering and mobile partitions between classrooms. Additionally, all classrooms possess windows and…

  4. Flexibility: Ensuring Adaptability.

    ERIC Educational Resources Information Center

    Van Slyke, Paul; Goode, Chris

    2003-01-01

    Discusses how to collaborate with administrators, physical plant representatives, department heads, lawmakers, and design professionals to create flexible school facilities that adapt to changing needs, noting the importance of utilizing a programming process that determines the true needs of a facility, based on the potential activities that will…

  5. 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…

  6. Highly flexible, transparent and conducting CuS-nanosheet networks for flexible quantum-dot solar cells.

    PubMed

    Xu, Zijie; Li, Teng; Zhang, Fayin; Hong, Xiaodan; Xie, Shuyao; Ye, Meidan; Guo, Wenxi; Liu, Xiangyang

    2017-03-17

    The rapid development of modern electronics has given rise to a higher demand for flexible and wearable energy sources. Flexible transparent conducting electrodes (TCEs) are one of the essential components of flexible/wearable thin-film solar cells (SCs). In this regard, we present highly transparent and conducting CuS-nanosheet (NS) networks with an optimized sheet resistance (Rs) as low as 50 Ω sq(-1) at 85% transmittance as a counter electrode (CE) for flexible quantum-dot solar cells (QDSCs). The CuS NS network electrode exhibits remarkable mechanical flexibility under bending tests compared to traditional ITO/plastic substrates and sputtered CuS films. Herein, CuS NS networks not only served as conducting films for collecting electrons from the external circuit, but also served as superior catalysts for reducing polysulfide (S(2-)/Sx(2-)) electrolytes. A power conversion efficiency (PCE) up to 3.25% was achieved for the QDSCs employing CuS NS networks as CEs, which was much higher than those of the devices based on Pt networks and sputtered CuS films. We believe that such CuS network TCEs with high flexibility, transparency, conductivity and catalytic activity could be widely used in making wearable electronic products.

  7. Optical loop framing

    SciTech Connect

    Kalibjian, R.; Chong, Y.P.; Prono, D.S.; Cavagnolo, H.R.

    1984-06-01

    The ATA provides an electron beam pulse of 70-ns duration at a 1-Hz rate. Our present optical diagnostics technique involve the imaging of the visible light generated by the beam incident onto the plant of a thin sheet of material. It has already been demonstrated that the light generated has a sufficiently fast temporal reponse in performing beam diagnostics. Notwithstanding possible beam emittance degradation due to scattering in the thin sheet, the observation of beam spatial profiles with relatively high efficiencies has provided data complementary to that obtained from beam wall current monitors and from various x-ray probes and other electrical probes. The optical image sensor consists of a gated, intensified television system. The gate pulse of the image intensifier can be appropriately delayed to give frames that are time-positioned from the head to the tail of the beam with a minimum gate time of 5-ns. The spatial correlation of the time frames from pulse to pulse is very good for a stable electron beam; however, when instabilities do occur, it is difficult to properly assess the spatial composition of the head and the tail of the beam on a pulse-to-pulse basis. Multiple gating within a pulse duration becomes desirable but cannot be performed because the recycle time (20-ms) of the TV system is much longer than the beam pulse. For this reason we have developed an optical-loop framing technique that will allow the recording of two frames within one pulse duration with our present gated/intensified TV system.

  8. Perspective on Catalytic Hydrodeoxygenation of Biomass Pyrolysis Oils: Essential Roles of Fe-Based Catalysts

    SciTech Connect

    Hong, Yongchun; Hensley, Alyssa; McEwen, Jean-Sabin; Wang, Yong

    2016-06-27

    Catalytic fast pyrolysis is the most promising approach for biofuel production, due to its simple process and versatility to handle lignocellulosic biomass feedstocks with varying and complex compositions. Compared with in situ catalytic fast pyrolysis, ex situ catalytic pyrolysis has the flexibility of optimizing the pyrolysis step and catalytic process individually to improve the quality of pyrolysis oil (stability, oxygen content, acid number, etc.) and to maximize the carbon efficiency in the conversion of biomass to pyrolysis oil. Hydrodeoxygenation is one of the key catalytic functions in ex situ catalytic fast pyrolysis. Recently, Fe-based catalysts have been reported to exhibit superior catalytic properties in hydrodeoxygenation of model compounds in pyrolysis oil, which potentially makes the ex situ pyrolysis of biomass commercially viable due to the abundance and low cost of Fe. Here, we briefly summarize the recent progress on Fe-based catalysts for hydrodeoxygenation of biomass, and provide perspectives on how to further improve Fe-based catalysts (activity and stability) for their potential applications in the emerging area of biomass conversion.

  9. A Redox 2-Cys Mechanism Regulates the Catalytic Activity of Divergent Cyclophilins1[W

    PubMed Central

    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; Leme, Adriana Franco Paes; Perez, Carlos Alberto; Whittaker, Sara Britt-Marie; Murakami, Mario Tyago; Zeri, Ana Carolina de Matos; Benedetti, Celso Eduardo

    2013-01-01

    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

  10. 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.

  11. Adding flexibility to physician training.

    PubMed

    Mahady, Suzanne E

    2011-05-02

    Demographic changes among junior doctors are driving demand for increased flexibility in advanced physician training, but flexible training posts are lacking. Suitable flexible training models include flexible full-time, job-share and part-time positions. Major barriers to establishing flexible training positions include difficulty in finding job-share partners, lack of funding for creating supernumerary positions, and concern over equivalence of educational quality compared with full-time training. Pilot flexible training positions should be introduced across the medical specialties and educational outcomes examined prospectively.

  12. F-actin structure destabilization and DNase I binding loop: fluctuations mutational cross-linking and electron microscopy analysis of loop states and effects on F-actin.

    PubMed

    Oztug Durer, Zeynep A; Diraviyam, Karthikeyan; Sept, David; Kudryashov, Dmitri S; Reisler, Emil

    2010-01-22

    The conformational dynamics of filamentous actin (F-actin) is essential for the regulation and functions of cellular actin networks. The main contribution to F-actin dynamics and its multiple conformational states arises from the mobility and flexibility of the DNase I binding loop (D-loop; residues 40-50) on subdomain 2. Therefore, we explored the structural constraints on D-loop plasticity at the F-actin interprotomer space by probing its dynamic interactions with the hydrophobic loop (H-loop), the C-terminus, and the W-loop via mutational disulfide cross-linking. To this end, residues of the D-loop were mutated to cysteines on yeast actin with a C374A background. These mutants showed no major changes in their polymerization and nucleotide exchange properties compared to wild-type actin. Copper-catalyzed disulfide cross-linking was investigated in equimolar copolymers of cysteine mutants from the D-loop with either wild-type (C374) actin or mutant S265C/C374A (on the H-loop) or mutant F169C/C374A (on the W-loop). Remarkably, all tested residues of the D-loop could be cross-linked to residues 374, 265, and 169 by disulfide bonds, demonstrating the plasticity of the interprotomer region. However, each cross-link resulted in different effects on the filament structure, as detected by electron microscopy and light-scattering measurements. Disulfide cross-linking in the longitudinal orientation produced mostly no visible changes in filament morphology, whereas the cross-linking of D-loop residues >45 to the H-loop, in the lateral direction, resulted in filament disruption and the presence of amorphous aggregates on electron microscopy images. A similar aggregation was also observed upon cross-linking the residues of the D-loop (>41) to residue 169. The effects of disulfide cross-links on F-actin stability were only partially accounted for by the simulations of current F-actin models. Thus, our results present evidence for the high level of conformational plasticity in

  13. 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 ...

  14. Integrated optical phase locked loop.

    SciTech Connect

    Lentine, Anthony L.; Kim, Jungwon; Trotter, Douglas Chandler; DeRose, Christopher T.; Kartner, Franz X.; Byun, Hyunil; Nejadmalayeri, Amir H.; Watts, Michael R.; Zortman, William A.

    2010-12-01

    A silicon photonics based integrated optical phase locked loop is utilized to synchronize a 10.2 GHz voltage controlled oscillator with a 509 MHz mode locked laser, achieving 32 fs integrated jitter over 300 kHz bandwidth.

  15. 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...

  16. 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...

  17. 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

  18. 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

  19. 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.

  20. LETS: An Expressional Loop Notation.

    DTIC Science & Technology

    1982-10-01

    r - ..’ -rI- x- - r ,11 V~ The Expressional Metaphor 2- Waters i "The Expressional Metaphor ’lhe key property of expressions which makes them...development of a notation which has the property of decomposability. Viewing Loops as Expressions Involving Sequences In order to represent loops as...a DEFUNS or LETS. For example, the function EPLIST takes in a discnbodied plist and returns two values: a sequence of the property names. and a

  1. Closed loop spray cooling apparatus

    NASA Technical Reports Server (NTRS)

    Alger, D. L.; Schwab, W. B.; Furman, E. R. (Inventor)

    1979-01-01

    A closed loop apparatus for jet spraying coolant against the back of a radiation target is described. The coolant is circulated through a closed loop with a bubble of inert gas being maintained around the spray. Mesh material is disposed between the bubble and the surface of the liquid coolant which is below the bubble at a predetermined level. In a second arrangement no inert gas is used, the bubble consists of vapor produced when the coolant is sprayed against the target.

  2. Point-to-Point Ultra-Remote Asymmetric Control with Flexible Linker.

    PubMed

    Kawasaki, Tsuneomi; Ishikawa, Yasuyuki; Minato, Yoshihiro; Otsuka, Takashi; Yonekubo, Shigeru; Sato, Itaru; Shibata, Takanori; Matsumoto, Arimasa; Soai, Kenso

    2017-01-05

    An ultra-remote intramolecular (point-to-point) asymmetric control through 38 bonds (1,39-asymmetric induction) has been achieved by using the principle of direct supramolecular orientation of catalytic and reactive moieties in asymmetric autocatalysis. We found the highly stereoselective diisopropylzinc addition reaction using designed molecules possessing pyrimidine sites at each terminal of a conformationally flexible simple methylene chain.

  3. High temperature loop heat pipes

    SciTech Connect

    Anderson, W.G.; Bland, J.J.; Fershtater, Y.; Goncharov, K.A.; Nikitkin, M.; Juhasz, A.

    1995-12-31

    Advantages of loop heat pipes over conventional heat pipes include self-priming during start-up, improved tolerance for noncondensible gas, and ability for ground testing in any orientation. The applications for high temperature, alkali-metal working fluid loop heat pipes include space radiators, and bimodal systems. A high temperature loop heat pipe was fabricated and tested at 850 K, using cesium as the working fluid. Previous loop heat pipes were tested with ambient temperature working fluids at temperatures below about 450 K. The loop heat pipe had a titanium envelope, and a titanium aluminide wick. The maximum cesium loop heat pipe power was only about 600 watts, which was lower the predicted 1,000 W power. The power limitation may be due to a wettability problem with the cesium not completely wetting the titanium aluminide wick. This would reduce the pumping capability of the wick, and the maximum power that the heat pipe could carry. This problem could be solved by using a refractory metal powder wick, since the alkali metals are known to wet refractory metal wicks.

  4. THE CORONAL LOOP INVENTORY PROJECT

    SciTech Connect

    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.

  5. Loop Models from SOHO Observations

    NASA Astrophysics Data System (ADS)

    Landini, M.; Brković , A.; Landi, E.; Rüedi, I.; Solanki, S.

    1999-01-01

    The Coronal Diagnostic Spectrometer (CDS) on SOHO is a grazing/normal incidence spectrograph, aimed to produce stigmatic spectra of selected regions of the solar surface in six spectral windows of the extreme ultraviolet from 150 Å to 785 Å (Harrison et al. 1995). In the present work, CDS, EIT, MDI and Yohkoh observations of active region lops have been analyzed. These observations are part of JOP 54. CDS monochromatic images from lines at different temperatures have been co-aligned with EIT and MDI images, and loop structures have been clearly identified using Fe XVI emission lines. Density sensitive lines and lines from adjacent stages of ionization of Fe ions have been used to measure electron density and temperature along the loop length; these measurements have been used to determine the electron pressure along the loop and test the constant pressure assumption commonly used in loop modeling. The observations have been compared with a static, isobaric loop model (Landini and Monsignori Fossi 1975) assuming a temperature-constant heating function in the energy balance equation. Good agreement is found for the temperature distribution along the loop at the coronal level. The model pressure is somewhat higher than obtained from density sensitive line ratios.

  6. General attitude maneuvers of spacecraft with flexible structures

    NASA Astrophysics Data System (ADS)

    Lin, Yiing-Yuh; Lin, Gern-Liang

    1995-03-01

    An efficient composite control strategy is proposed in this paper permitting simultaneous multi-axis reorientation of a spacecraft with flexible structures. The proposed control, separating large and small motions of the dynamic system, includes three parts that can be independently designed and tuned. For each maneuver, an open-loop referencing attitude control trajectory is derived by considering the spacecraft as rigid and executed by part 1. Flexural deformations of the structures are stabilized by part 2. Part 3, encompassing part 1 and part 2 control results and external disturbances, is an optimal guidance that tracks part 1 reference trajectory and achieves the specified final attitude in finite time. Three simulation cases are included in which a flexible model spacecraft is used. Collocated actuators and sensors are placed on the hub and on the flexible structures of the spacecraft.

  7. Engineering Bifunctional Laccase-Xylanase Chimeras for Improved Catalytic Performance*

    PubMed Central

    Ribeiro, Lucas F.; Furtado, Gilvan P.; Lourenzoni, Marcos R.; Costa-Filho, Antonio J.; Santos, Camila R.; Nogueira, Simone C. Peixoto; Betini, Jorge A.; Polizeli, Maria de Lourdes T. M.; Murakami, Mario T.; Ward, Richard J.

    2011-01-01

    Two bifunctional enzymes exhibiting combined xylanase and laccase activities were designed, constructed, and characterized by biochemical and biophysical methods. The Bacillus subtilis cotA and xynA genes were used as templates for gene fusion, and the xynA coding sequence was inserted into a surface loop of the cotA. A second chimera was built replacing the wild-type xynA gene by a thermostable variant (xynAG3) previously obtained by in vitro molecular evolution. Kinetic measurements demonstrated that the pH and temperature optima of the catalytic domains in the chimeras were altered by less than 0.5 pH units and 5 °C, respectively, when compared with the parental enzymes. In contrast, the catalytic efficiency (kcat/Km) of the laccase activity in both chimeras was 2-fold higher than for the parental laccase. Molecular dynamics simulations of the CotA-XynA chimera indicated that the two domains are in close contact, which was confirmed by the low resolution structure obtained by small angle x-ray scattering. The simulation also indicates that the formation of the inter-domain interface causes the dislocation of the loop comprising residues Leu-558 to Lys-573 in the laccase domain, resulting in a more accessible active site and exposing the type I Cu2+ ion to the solvent. These structural changes are consistent with the results from UV-visible electronic and EPR spectroscopy experiments of the type I copper between the native and chimeric enzymes and are likely to contribute to the observed increase in catalytic turnover number. PMID:22006920

  8. 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.

  9. 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.

  10. Expression studies of catalytic antibodies

    SciTech Connect

    Ulrich, H.D.; Patten, P.A.; Yang, P.L.

    1995-12-05

    We have examined the positive influence of human constant regions on the folding and bacterial expression of active soluble mouse immunoglobulin variable domains derived form a number of catalytic antibodies. Expression yields of eight hybridoma-and myeloma-derived chimeric Fab fragments are compared in both shake flasks and high-density fermentation. In addition the usefulness of this system for the generation of in vivo expression libraries is examined by constructing and expressing combinations of heavy and light chain variable regions that were not selected as a pair during an immune response. A mutagenesis study of one of the recombinant catalytic Fab fragments reveals that single amino acid substitutions can have dramatic effects on the expression yield. This system should be generally applicable to the production of Fab fragments of catalytic and other hybridoma-derived antibodies for crystallographic and structure-function studies. 41 refs., 4 figs., 1 tab.

  11. 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.

  12. 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.

  13. 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)

  14. 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.

  15. 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.

  16. 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

  17. Dynamics for flexible systems

    NASA Astrophysics Data System (ADS)

    Barraco, A.; Cuny, B.; Ishiomin, G.

    Analytical techniques for dynamic modeling of mechanical systems with deformable members are developed and demonstrated. Formulations for the rigid member and the flexible member are derived; the position of an arbitrary point is defined; and the construction of the complete model from these components is explained. Numerical results for the case of a planar four-bar parallelogram rotating about a fixed axis located in the same plane are presented in graphs and discussed.

  18. Flexible Data Link

    DTIC Science & Technology

    2015-04-01

    continuously-interleaved Reed- Solomon scheme with 8% overhead has the best trade-off of performance (net coding gain) and overhead. Therefore, this is...disparity between attenuation at sea level versus at a 9150 meter altitude. As the Flexible Data Link system is an airborne asset which may operate...Quadrature Amplitude Modulation QPSK Quadrature Phase Shift Key RF Radio Frequency RS Reed- Solomon S&E Scientist & Engineers SFP Small Form-factor

  19. 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.

  20. Flexible heliac configuration

    SciTech Connect

    Harris, J.H.; Cantrell, J.L.; Hender, T.C.; Carreras, B.A.; Morris, R.N.

    1985-04-01

    The addition of an l = 1 helical winding to the heliac central conductor adds a significant degree of flexibility to the configuration by making it possible to control the rotational transform and shear. Such control is essential for an experiment because the presence of low-order resonances in the rotational transform profile can cause breakup of the equilibrium magnetic surfaces. The use of the additional winding also permits reduction of the total central conductor current and can deepen the magnetic well.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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…

  6. 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.

  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. Orthogonal gene knock out and activation with a catalytically active Cas9 nuclease

    PubMed Central

    Dahlman, James E.; Abudayyeh, Omar O.; Joung, Julia; Gootenberg, Jonathan S.; Zhang, Feng; Konermann, Silvana

    2015-01-01

    We have developed a CRISPR-based method that uses catalytically active Cas9 and distinct sgRNA constructs to knock out and activate different genes in the same cell. These sgRNAs, with 14 15 bp target sequences and MS2 binding loops, can activate gene expression using an active Cas9 nuclease, without inducing DSBs. We use these ‘dead RNAs’ to perform orthogonal gene knockout and transcriptional activation in human cells. PMID:26436575

  9. HMG Proteins and DNA Flexibility in Transcription Activation

    PubMed Central

    Ross, Eric D.; Hardwidge, Philip R.; Maher, L. James

    2001-01-01

    The relative stiffness of naked DNA is evident from measured values of longitudinal persistence length (∼150 bp) and torsional persistence length (∼180 bp). These parameters predict that certain arrangements of eukaryotic transcription activator proteins in gene promoters should be much more effective than others in fostering protein-protein interactions with the basal RNA polymerase II transcription apparatus. Thus, if such interactions require some kind of DNA looping, DNA loop energies should depend sensitively on helical phasing of protein binding sites, loop size, and intrinsic DNA curvature within the loop. Using families of artificial transcription templates where these parameters were varied, we were surprised to find that the degree of transcription activation by arrays of Gal4-VP1 transcription activators in HeLa cell nuclear extract was sensitive only to the linear distance separating a basal promoter from an array of bound activators on DNA templates. We now examine the hypothesis that this unexpected result is due to factors in the extract that act to enhance apparent DNA flexibility. We demonstrate that HeLa cell nuclear extract is rich in a heat-resistant activity that dramatically enhances apparent DNA longitudinal and torsional flexibility. Recombinant mammalian high-mobility group 2 (HMG-2) protein can substitute for this activity. We propose that the abundance of HMG proteins in eukaryotic nuclei provides an environment in which DNA is made sufficiently flexible to remove many constraints on protein binding site arrangements that would otherwise limit efficient transcription activation to certain promoter geometries. PMID:11533247

  10. Study of the open loop and closed loop oscillator techniques

    SciTech Connect

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

    2015-07-01

    This paper presents some aspects 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 paper 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. (authors)

  11. Lattice calculation of the Polyakov loop and Polyakov loop correlators

    NASA Astrophysics Data System (ADS)

    Weber, Johannes Heinrich

    2017-03-01

    We discuss calculations of the Polyakov loop and of Polyakov loop correlators using lattice gauge theory. We simulate QCD with 2+1 flavors and almost physical quark masses using the highly improved staggered quark action (HISQ).We demonstrate that the entropy derived from the Polyakov loop is a good probe of color screening. In particular, it allows for scheme independent and quantitative conclusions about the deconfinement aspects of the crossover and for a rigorous study of the onset of weak-coupling behavior at high temperatures. We examine the correlators for small and large separations and identify vacuum-like and screening regimes in the thermal medium. We demonstrate that gauge-independent screening properties can be obtained even from gauge-fixed singlet correlators and that we can pin down the asymptotic regime.

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

    SciTech Connect

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

    2013-06-01

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

  14. Conformational sampling and structure prediction of multiple interacting loops in soluble and β-barrel membrane proteins using multi-loop distance-guided chain-growth Monte Carlo method

    PubMed Central

    Tang, Ke; Wong, Samuel W.K.; Liu, Jun S.; Zhang, Jinfeng; Liang, Jie

    2015-01-01

    Motivation: Loops in proteins are often involved in biochemical functions. Their irregularity and flexibility make experimental structure determination and computational modeling challenging. Most current loop modeling methods focus on modeling single loops. In protein structure prediction, multiple loops often need to be modeled simultaneously. As interactions among loops in spatial proximity can be rather complex, sampling the conformations of multiple interacting loops is a challenging task. Results: In this study, we report a new method called multi-loop Distance-guided Sequential chain-Growth Monte Carlo (M-DiSGro) for prediction of the conformations of multiple interacting loops in proteins. Our method achieves an average RMSD of 1.93 Å for lowest energy conformations of 36 pairs of interacting protein loops with the total length ranging from 12 to 24 residues. We further constructed a data set containing proteins with 2, 3 and 4 interacting loops. For the most challenging target proteins with four loops, the average RMSD of the lowest energy conformations is 2.35 Å. Our method is also tested for predicting multiple loops in β-barrel membrane proteins. For outer-membrane protein G, the lowest energy conformation has a RMSD of 2.62 Å for the three extracellular interacting loops with a total length of 34 residues (12, 12 and 10 residues in each loop). Availability and implementation: The software is freely available at: tanto.bioe.uic.edu/m-DiSGro. Contact: jinfeng@stat.fsu.edu or jliang@uic.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25861965

  15. Flatness based GPI Control for Flexible Robots

    NASA Astrophysics Data System (ADS)

    Becedas, Jonathan; Feliu, Vicente; Sira-Ramírez, Hebertt

    In this article, a new method to control a flexible robotic arm using a conventional direct current (DC) motor with a gear actuator strongly affected by non-linear friction torque is proposed. This control method does not require friction compensation and hence the estimation of this term because the control scheme is robust with respect to this effect. In addition, the only variables to measure are the motor shaft and tip angular positions. Velocity measurements, which always introduce errors and noises, are not required. The use of filters to estimate velocities and bounded derivatives are not needed. The Generalized Proportional Integral GPI controller is designed using a two-stage design procedure entitling an outer loop, designed under the assumption of no motor dynamics, and subsequently an inner loop which forces the motor response to track the control input position reference trajectory derived in the previous design stage. Velocity measurements, which always introduce errors and noises, are not required. Experimental results are presented.

  16. Loop coupled resonator optical waveguides.

    PubMed

    Song, Junfeng; Luo, Lian-Wee; Luo, Xianshu; Zhou, Haifeng; Tu, Xiaoguang; Jia, Lianxi; Fang, Qing; Lo, Guo-Qiang

    2014-10-06

    We propose a novel coupled resonator optical waveguide (CROW) structure that is made up of a waveguide loop. We theoretically investigate the forbidden band and conduction band conditions in an infinite periodic lattice. We also discuss the reflection- and transmission- spectra, group delay in finite periodic structures. Light has a larger group delay at the band edge in a periodic structure. The flat band pass filter and flat-top group delay can be realized in a non-periodic structure. Scattering matrix method is used to calculate the effects of waveguide loss on the optical characteristics of these structures. We also introduce a tunable coupling loop waveguide to compensate for the fabrication variations since the coupling coefficient of the directional coupler in the loop waveguide is a critical factor in determining the characteristics of a loop CROW. The loop CROW structure is suitable for a wide range of applications such as band pass filters, high Q microcavity, and optical buffers and so on.

  17. 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.

  18. Carbon Cloth Supports Catalytic Electrodes

    NASA Technical Reports Server (NTRS)

    Lu, W. T. P.; Ammon, R. L.

    1983-01-01

    Carbon cloth is starting material for promising new catalytic electrodes. Carbon-cloth electrodes are more efficient than sintered-carbon configuration previously used. Are also chemically stable and require less catalyst--an important economic advantage when catalyst is metal such as platinum.

  19. High temperature catalytic membrane reactors

    SciTech Connect

    Not Available

    1990-03-01

    Current state-of-the-art inorganic oxide membranes offer the potential of being modified to yield catalytic properties. The resulting modules may be configured to simultaneously induce catalytic reactions with product concentration and separation in a single processing step. Processes utilizing such catalytically active membrane reactors have the potential for dramatically increasing yield reactions which are currently limited by either thermodynamic equilibria, product inhibition, or kinetic selectivity. Examples of commercial interest include hydrogenation, dehydrogenation, partial and selective oxidation, hydrations, hydrocarbon cracking, olefin metathesis, hydroformylation, and olefin polymerization. A large portion of the most significant reactions fall into the category of high temperature, gas phase chemical and petrochemical processes. Microporous oxide membranes are well suited for these applications. A program is proposed to investigate selected model reactions of commercial interest (i.e. dehydrogenation of ethylbenzene to styrene and dehydrogenation of butane to butadiene) using a high temperature catalytic membrane reactor. Membranes will be developed, reaction dynamics characterized, and production processes developed, culminating in laboratory-scale demonstration of technical and economic feasibility. As a result, the anticipated increased yield per reactor pass economic incentives are envisioned. First, a large decrease in the temperature required to obtain high yield should be possible because of the reduced driving force requirement. Significantly higher conversion per pass implies a reduced recycle ratio, as well as reduced reactor size. Both factors result in reduced capital costs, as well as savings in cost of reactants and energy.

  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. Simple, Chemoselective, Catalytic Olefin Isomerization

    PubMed Central

    2015-01-01

    Catalytic amounts of Co(SaltBu,tBu)Cl and organosilane irreversibly isomerize terminal alkenes by one position. The same catalysts effect cycloisomerization of dienes and retrocycloisomerization of strained rings. Strong Lewis bases like amines and imidazoles, and labile functionalities like epoxides, are tolerated. PMID:25398144

  2. Catalytic Asymmetric Bromocyclization of Polyenes.

    PubMed

    Samanta, Ramesh C; Yamamoto, Hisashi

    2017-02-01

    The first catalytic asymmetric bromonium ion-induced polyene cyclization has been achieved by using a chiral BINOL-derived thiophosphoramide catalyst and 1,3-dibromo-5,5-dimethylhydantoin as an electrophilic bromine source. Bromocyclization products are obtained in high yields, with good enantiomeric ratios and high diastereoselectivity, and are abundantly found as scaffolds in natural products.

  3. 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.

  4. Process for Coating Substrates with Catalytic Materials

    NASA Technical Reports Server (NTRS)

    Klelin, Ric J. (Inventor); Upchurch, Billy T. (Inventor); Schryer, David R. (Inventor)

    2004-01-01

    A process for forming catalysts by coating substrates with two or more catalytic components, which comprises the following sequence of steps. First, the substrate is infused with an adequate amount of solution having a starting material comprising a catalytic component precursor, wherein the thermal decomposition product of the catalytic component precursor is a catalytic component. Second, the excess of the solution is removed from the substrate. thereby leaving a coating of the catalytic component precursor on the surface of the substrate. Third, the coating of the catalytic component precursor is converted to the catalytic component by thermal decomposition. Finally, the coated substance is etched to increase the surface area. The list three steps are then repeated for at least a second catalytic component. This process is ideally suited for application in producing efficient low temperature oxidation catalysts.

  5. Flexible graphene-PZT ferroelectric nonvolatile memory

    NASA Astrophysics Data System (ADS)

    Lee, Wonho; Kahya, Orhan; Tat Toh, Chee; Özyilmaz, Barbaros; Ahn, Jong-Hyun

    2013-11-01

    We report the fabrication of a flexible graphene-based nonvolatile memory device using Pb(Zr0.35,Ti0.65)O3 (PZT) as the ferroelectric material. The graphene and PZT ferroelectric layers were deposited using chemical vapor deposition and sol-gel methods, respectively. Such PZT films show a high remnant polarization (Pr) of 30 μC cm-2 and a coercive voltage (Vc) of 3.5 V under a voltage loop over ±11 V. The graphene-PZT ferroelectric nonvolatile memory on a plastic substrate displayed an on/off current ratio of 6.7, a memory window of 6 V and reliable operation. In addition, the device showed one order of magnitude lower operation voltage range than organic-based ferroelectric nonvolatile memory after removing the anti-ferroelectric behavior incorporating an electrolyte solution. The devices showed robust operation in bent states of bending radii up to 9 mm and in cycling tests of 200 times. The devices exhibited remarkable mechanical properties and were readily integrated with plastic substrates for the production of flexible circuits.

  6. Thermally activated transport of a dislocation loop within an elastic model

    NASA Astrophysics Data System (ADS)

    Ohsawa, Kazuhito; Kuramoto, Eiichi

    2007-08-01

    We report thermally activated transport of a dislocation loop in terms of a line tension model, where the dislocation line is assumed to be a flexible string. According to conventional rate theory, the features of thermal activation are determined by the saddle-point geometry in high dimensional configuration space. If the circumference of a dislocation loop L is longer than a critical length Lc, the selected saddle-point configuration is the well known double-kink type solution. On the other hand, the manner of the thermal activation of a dislocation loop shorter than Lc is rather point-defect-like. In the present work, we pay attention to the temperature dependence of transition rate which is represented such as ν0∗exp(-E/kT). The pre-exponential factor depends on temperature like ν0∗˜T for sufficiently long dislocation loops on the basis of the analysis.

  7. Severing of a hydrogen bond disrupts amino acid networks in the catalytically active state of the alpha subunit of tryptophan synthase

    PubMed Central

    Axe, Jennifer M; O'Rourke, Kathleen F; Kerstetter, Nicole E; Yezdimer, Eric M; Chan, Yan M; Chasin, Alexander; Boehr, David D

    2015-01-01

    Conformational changes in the β2α2 and β6α6 loops in the alpha subunit of tryptophan synthase (αTS) are important for enzyme catalysis and coordinating substrate channeling with the beta subunit (βTS). It was previously shown that disrupting the hydrogen bond interactions between these loops through the T183V substitution on the β6α6 loop decreases catalytic efficiency and impairs substrate channeling. Results presented here also indicate that the T183V substitution decreases catalytic efficiency in Escherchia coli αTS in the absence of the βTS subunit. Nuclear magnetic resonance (NMR) experiments indicate that the T183V substitution leads to local changes in the structural dynamics of the β2α2 and β6α6 loops. We have also used NMR chemical shift covariance analyses (CHESCA) to map amino acid networks in the presence and absence of the T183V substitution. Under conditions of active catalytic turnover, the T183V substitution disrupts long-range networks connecting the catalytic residue Glu49 to the αTS-βTS binding interface, which might be important in the coordination of catalytic activities in the tryptophan synthase complex. The approach that we have developed here will likely find general utility in understanding long-range impacts on protein structure and dynamics of amino acid substitutions generated through protein engineering and directed evolution approaches, and provide insight into disease and drug-resistance mutations. PMID:25377949

  8. 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.

  9. Flexible plasma linear antenna

    NASA Astrophysics Data System (ADS)

    Zhao, Jiansen; Wang, Shengzheng; Wu, Huafeng; Liu, Yue; Chang, Yongmeng; Chen, Xinqiang

    2017-02-01

    In this work, we introduce a type of plasma antenna that was fabricated using flexible materials and excited using a 5-20 kHz alternating current (ac) power supply. The results showed that the antenna characteristics, including the impedance, the reflection coefficient (S11), the radiation pattern, and the gain, can be controlled rapidly and easily by varying both the discharge parameters and the antenna shapes. The scope for reconfiguration is greatly enhanced when the antenna shape is changed from a monopole to a helix configuration. Additionally, the antenna polarization can also be adjusted by varying the antenna shapes.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  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. 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

  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. Reionization from cosmic string loops

    SciTech Connect

    Olum, Ken D.; Vilenkin, Alexander

    2006-09-15

    Loops formed from a cosmic string network at early times would act as seeds for early formation of halos, which would form galaxies and lead to early reionization. With reasonable guesses about astrophysical and string parameters, the cosmic string scale G{mu} must be no more than about 3x10{sup -8} to avoid conflict with the reionization redshift found by WMAP. The bound is much stronger for superstring models with a small string reconnection probability. For values near the bound, cosmic string loops may explain the discrepancy between the WMAP value and theoretical expectations.

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

    PubMed

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

    2002-05-14

    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.

  20. Decentralized control of flexible, multibody systems

    NASA Astrophysics Data System (ADS)

    Reisenauer, Brian Thomas

    1992-11-01

    The appearance of multibody flexible systems in robotics, telerobotics, and space application invites our study of a new method for closed-loop controller design. These systems differ substantially from standard rigid multibody structures. Active control in the presence of flexibility may induce system instability. Furthermore, multibody systems differ from flexible structures in that mode shapes and mode frequencies continually change as the orientation of one body about another varies. Our work brings together ideas from decentralized control and multibody dynamics to address this unique challenge. The composite system method applies decentralized control to interconnected systems and suggests analytic tools for assessing system stability. Multibody dynamics introduces the application of a moving reference frame to minimize the interconnection between gross body motion and elastic deformation. Together, the combination yields a decentralized design methodology. System modeling as well as control architecture benefit from substructure division and the application of a pseudo-rigid reference frame. Lyapunov based analysis presents proximate design goals, provides a template for redesign, and develops a sufficient condition for composite stability. Several examples help us further understand the control method. We concentrate on articulated structures as a primary type of multibody system and examine different models. A simplified rotational spring model enables a comprehensive study of the design method with analysis, as well as control performance. We see how analysis offers insight into the decentralized design and engenders a rather robust controller. A more complicated assumed mode model provides a further test-bed for design, while a finite element model outlines the application of the approach to much more complicated systems.

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

    PubMed

    Bouchard, Patricia; Legault, Pascale

    2014-09-01

    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.

  3. 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.

  4. Light and circadian regulation of clock components aids flexible responses to environmental signals

    PubMed Central

    Dixon, Laura E; Hodge, Sarah K; van Ooijen, Gerben; Troein, Carl; Akman, Ozgur E; Millar, Andrew J

    2014-01-01

    The circadian clock measures time across a 24 h period, increasing fitness by phasing biological processes to the most appropriate time of day. The interlocking feedback loop mechanism of the clock is conserved across species; however, the number of loops varies. Mathematical and computational analyses have suggested that loop complexity affects the overall flexibility of the oscillator, including its responses to entrainment signals. We used a discriminating experimental assay, at the transition between different photoperiods, in order to test this proposal in a minimal circadian network (in Ostreococcus tauri) and a more complex network (in Arabidopsis thaliana). Transcriptional and translational reporters in O. tauri primarily tracked dawn or dusk, whereas in A. thaliana, a wider range of responses were observed, consistent with its more flexible clock. Model analysis supported the requirement for this diversity of responses among the components of the more complex network. However, these and earlier data showed that the O. tauri network retains surprising flexibility, despite its simple circuit. We found that models constructed from experimental data can show flexibility either from multiple loops and/or from multiple light inputs. Our results suggest that O. tauri has adopted the latter strategy, possibly as a consequence of genomic reduction. PMID:24842166

  5. A Flexible Cloud Generator

    NASA Astrophysics Data System (ADS)

    Benassi, A.; Deguy, S.; Szczap, F.

    2001-05-01

    In this work we propose a flexible cloud generating model as well as a software. This model depends upon 5 quantities: -the cloud fractional coverage -the spectral slope -the mean value -the variance -the internal heterogeneity (intermittency). All these quantities are independantly identifiable on the base of mathematical proofs. This model also depends on a given function, called "morphlet", and on the law of a random variables family. In order to get a positive water contain inside the cloud,we ask the morphlet and the random variables to be positives. The structure of the model is hierarchycal. The vertebral column of this model is a tree: the basic encoding tree of the space where the cloud lives. At each edge of the tree is attached: -a Bernoulli random variable,this for tuning the fractional cover and the intermittency, -a rate of energy loose,giving the spectral slope, -a dilated morphlet. The word flexible is justified by the fact that we can choose to modify some objets on the basic tree in order to adjust the caracteristics of the desired cloud.

  6. 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.

  7. A flexible alternative

    SciTech Connect

    Dickenson, R.L.; Simbeck, D.R. )

    1994-01-01

    Coal gasification offers the efficiency and flexibility independent producers will need in an increasingly competitive power environment. It is difficult to make an economic case for coal-based power of any kind in the current market in most areas because of the low price and availability of natural gas. Furthermore, there is a large excess of baseload coal and nuclear capacity in the United States and Europe. New capacity requirements, for the time being, are necessary mainly for cycling and peaking service where coal is not economical compared with the much lower capital cost of gas- or oil-based combustion turbine systems. However, as erosion of the supply and demand balance drives natural gas prices up and new baseload capacity is required, coal-based power will again be widely economical. Based on recent technical and commercial successes coupled with current commercial demonstration programs, coal gasification will dramatically challenge direct-coal-fired power for this market. The advantages coal gasification has over direct coal-firing for power generation include environmental performance, efficiency and flexibility.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage

    PubMed Central

    Jiang, Fuguo; Taylor, David W.; Chen, Janice S.; Kornfeld, Jack E.; Zhou, Kaihong; Thompson, Aubri J.; Nogales, Eva; Doudna, Jennifer A.

    2016-01-01

    Bacterial adaptive immunity and genome engineering involving the CRISPR (clustered regularly interspaced short palindromic repeats)–associated (Cas) protein Cas9 begin with RNA-guided DNA unwinding to form an RNA-DNA hybrid and a displaced DNA strand inside the protein. The role of this R-loop structure in positioning each DNA strand for cleavage by the two Cas9 nuclease domains is unknown. We determine molecular structures of the catalytically active Streptococcus pyogenes Cas9 R-loop that show the displaced DNA strand located near the RuvC nuclease domain active site. These protein-DNA interactions, in turn, position the HNH nuclease domain adjacent to the target DNA strand cleavage site in a conformation essential for concerted DNA cutting. Cas9 bends the DNA helix by 30°, providing the structural distortion needed for R-loop formation. PMID:26841432

  13. Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage.

    PubMed

    Jiang, Fuguo; Taylor, David W; Chen, Janice S; Kornfeld, Jack E; Zhou, Kaihong; Thompson, Aubri J; Nogales, Eva; Doudna, Jennifer A

    2016-02-19

    Bacterial adaptive immunity and genome engineering involving the CRISPR (clustered regularly interspaced short palindromic repeats)-associated (Cas) protein Cas9 begin with RNA-guided DNA unwinding to form an RNA-DNA hybrid and a displaced DNA strand inside the protein. The role of this R-loop structure in positioning each DNA strand for cleavage by the two Cas9 nuclease domains is unknown. We determine molecular structures of the catalytically active Streptococcus pyogenes Cas9 R-loop that show the displaced DNA strand located near the RuvC nuclease domain active site. These protein-DNA interactions, in turn, position the HNH nuclease domain adjacent to the target DNA strand cleavage site in a conformation essential for concerted DNA cutting. Cas9 bends the DNA helix by 30°, providing the structural distortion needed for R-loop formation.

  14. 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.

  15. Telomeres thrown for a loop.

    PubMed

    Haber, James E

    2004-11-19

    A remarkable paper from the de Lange lab (Wang et al., 2004) in a recent issue of Cell reveals that homologous recombination can result in the abrupt shortening of telomeres in a process that appears to involve reciprocal crossing over within the t-loop structure that protects chromosome ends.

  16. 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.

  17. Ponderomotive Acceleration in Coronal Loops

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  18. Loop quantum cosmology gravitational baryogenesis

    NASA Astrophysics Data System (ADS)

    Odintsov, S. D.; Oikonomou, V. K.

    2016-11-01

    Loop quantum cosmology is an appealing quantum completion of classical cosmology, which brings along various theoretical features which in many cases offer a remedy for or modify various classical cosmology aspects. In this paper we address the gravitational baryogenesis mechanism in the context of loop quantum cosmology. As we demonstrate, when loop quantum cosmology effects are taken into account in the resulting Friedmann equations for a flat Friedmann-Robertson-Walker Universe, then even for a radiation-dominated Universe, the predicted baryon-to-entropy ratio from the gravitational baryogenesis mechanism is non-zero, in contrast to the Einstein-Hilbert case, in which case the baryon-to-entropy ratio is zero. We also discuss various other cases apart from the radiation domination case, and we discuss how the baryon-to-entropy ratio is affected from the parameters of the quantum theory. In addition, we use illustrative exact solutions of loop quantum cosmology and we investigate under which circumstances the baryon-to-entropy ratio can be compatible with the observational constraints.

  19. 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.

  20. 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

  1. 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.

  2. Protein flexibility as a biosignal.

    PubMed

    Zhao, Qinyi

    2010-01-01

    Dynamic properties of a protein are crucial for all protein functions, and those of signaling proteins are closely related to the biological function of living beings. The protein flexibility signal concept can be used to analyze this relationship. Protein flexibility controls the rate of protein conformational change and influences protein function. The modification of protein flexibility results in a change of protein activity. The logical nature of protein flexibility cannot be explained by applying the principles of protein three-dimensional structure theory or conformation concept. Signaling proteins show high protein flexibility. Many properties of signaling can be traced back to the dynamic natures of signaling protein. The action mechanism of volatile anesthetics and universal cellular reactions are related to flexibility in the change of signaling proteins. We conclude that protein dynamics is an enzyme-enhanced process, called dynamicase.

  3. The Flexibility Hypothesis of Healing.

    PubMed

    Hinton, Devon E; Kirmayer, Laurence J

    2017-03-01

    Theories of healing have attempted to identify general mechanisms that may work across different modalities. These include altering expectations, remoralization, and instilling hope. In this paper, we argue that many forms of healing and psychotherapy may work by inducing positive psychological states marked by flexibility or an enhanced ability to shift cognitive sets. Healing practices may induce these states of cognitive and emotional flexibility through specific symbolic interventions we term "flexibility primers" that can include images, metaphors, music, and other media. The flexibility hypothesis suggests that cognitive and emotional flexibility is represented, elicited, and enacted through multiple modalities in healing rituals. Identifying psychological processes and cultural forms that evoke and support cognitive and emotional flexibility provides a way to understand the cultural specificity and potential efficacy of particular healing practices and can guide the design of interventions that promote resilience and well-being.

  4. Flexible transformation plasmonics using graphene.

    PubMed

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

    2013-05-06

    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.

  5. Catalytic σ-Bond Metathesis

    NASA Astrophysics Data System (ADS)

    Reznichenko, Alexander L.; Hultzsch, Kai C.

    This account summarizes information on recently reported applications of organo-rare-earth metal complexes in various catalytic transformations of small molecules. The σ-bond metathesis at d0rare-earth metal centers plays a pivotal role in carbon-carbon and carbon-heteroatom bond forming processes. Relevant mechanistic details are discussed and the focus of the review lies in practical applications of organo-rare-earth metal complexes.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  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 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.

  12. 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.

  13. Damped flexible seal

    SciTech Connect

    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. Flexibility Matters: Cooperative Active Sites in Covalent Organic Framework and Threaded Ionic Polymer.

    PubMed

    Sun, Qi; Aguila, Briana; Perman, Jason; Nguyen, Nicholas; Ma, Shengqian

    2016-12-07

    The combination of two or more reactive centers working in concert on a substrate to facilitate the reaction is now considered state of the art in catalysis, yet there still remains a tremendous challenge. Few heterogeneous systems of this sort have been exploited, as the active sites spatially separated within the rigid framework are usually difficult to cooperate. It is now shown that this roadblock can be surpassed. The underlying principle of the strategy presented here is the integration of catalytic components with excellent flexibility and porous heterogeneous catalysts, as demonstrated by the placement of linear ionic polymers in close proximity to surface Lewis acid active sites anchored on the walls of a covalent organic framework (COF). Using the cycloaddition of the epoxides and CO2 as a model reaction, dramatic activity improvements have been achieved for the composite catalysts in relation to the individual catalytic component. Furthermore, they also clearly outperform the benchmark catalytic systems formed by the combination of the molecular organocatalysts and heterogeneous Lewis acid catalysts, while affording additional recyclability. The extraordinary flexibility and enriched concentration of the catalytically active moieties on linear polymers facilitate the concerted catalysis, thus leading to superior catalytic performance. This work therefore uncovers an entirely new strategy for designing bifunctional catalysts with double-activation behavior and opens a new avenue in the design of multicapable systems that mimic biocatalysis.

  15. A fragment-based approach applied to a highly flexible target: Insights and challenges towards the inhibition of HSP70 isoforms

    PubMed Central

    Jones, Alan M.; Westwood, Isaac M.; Osborne, James D.; Matthews, Thomas P.; Cheeseman, Matthew D.; Rowlands, Martin G.; Jeganathan, Fiona; Burke, Rosemary; Lee, Diane; Kadi, Nadia; Liu, Manjuan; Richards, Meirion; McAndrew, Craig; Yahya, Norhakim; Dobson, Sarah E.; Jones, Keith; Workman, Paul; Collins, Ian; van Montfort, Rob L. M.

    2016-01-01

    The heat shock protein 70s (HSP70s) are molecular chaperones implicated in many cancers and of significant interest as targets for novel cancer therapies. Several HSP70 inhibitors have been reported, but because the majority have poor physicochemical properties and for many the exact mode of action is poorly understood, more detailed mechanistic and structural insight into ligand-binding to HSP70s is urgently needed. Here we describe the first comprehensive fragment-based inhibitor exploration of an HSP70 enzyme, which yielded an amino-quinazoline fragment that was elaborated to a novel ATP binding site ligand with different physicochemical properties to known adenosine-based HSP70 inhibitors. Crystal structures of amino-quinazoline ligands bound to the different conformational states of the HSP70 nucleotide binding domain highlighted the challenges of a fragment-based approach when applied to this particular flexible enzyme class with an ATP-binding site that changes shape and size during its catalytic cycle. In these studies we showed that Ser275 is a key residue in the selective binding of ATP. Additionally, the structural data revealed a potential functional role for the ATP ribose moiety in priming the protein for the formation of the ATP-bound pre-hydrolysis complex by influencing the conformation of one of the phosphate binding loops. PMID:27708405

  16. A fragment-based approach applied to a highly flexible target: Insights and challenges towards the inhibition of HSP70 isoforms

    NASA Astrophysics Data System (ADS)

    Jones, Alan M.; Westwood, Isaac M.; Osborne, James D.; Matthews, Thomas P.; Cheeseman, Matthew D.; Rowlands, Martin G.; Jeganathan, Fiona; Burke, Rosemary; Lee, Diane; Kadi, Nadia; Liu, Manjuan; Richards, Meirion; McAndrew, Craig; Yahya, Norhakim; Dobson, Sarah E.; Jones, Keith; Workman, Paul; Collins, Ian; van Montfort, Rob L. M.

    2016-10-01

    The heat shock protein 70s (HSP70s) are molecular chaperones implicated in many cancers and of significant interest as targets for novel cancer therapies. Several HSP70 inhibitors have been reported, but because the majority have poor physicochemical properties and for many the exact mode of action is poorly understood, more detailed mechanistic and structural insight into ligand-binding to HSP70s is urgently needed. Here we describe the first comprehensive fragment-based inhibitor exploration of an HSP70 enzyme, which yielded an amino-quinazoline fragment that was elaborated to a novel ATP binding site ligand with different physicochemical properties to known adenosine-based HSP70 inhibitors. Crystal structures of amino-quinazoline ligands bound to the different conformational states of the HSP70 nucleotide binding domain highlighted the challenges of a fragment-based approach when applied to this particular flexible enzyme class with an ATP-binding site that changes shape and size during its catalytic cycle. In these studies we showed that Ser275 is a key residue in the selective binding of ATP. Additionally, the structural data revealed a potential functional role for the ATP ribose moiety in priming the protein for the formation of the ATP-bound pre-hydrolysis complex by influencing the conformation of one of the phosphate binding loops.

  17. 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.

  18. Deployable space manipulator closed-loop control, ideas and possibilities of using GPS as a sensor

    NASA Astrophysics Data System (ADS)

    Romero, I.; Vignjevic, R.

    2002-07-01

    In the area of study of the dynamics and control of large flexible spacecraft one of the most challenging areas is that of large space-based robotic manipulators. The Deployable Space Manipulator is a large manipulator concept for Low Earth Orbit operation with one rotational joint and one prismatic joint. In this paper the dynamics of the manipulator undergoing large rotational motion while carrying a payload and extending its length are developed and the need for closed loop control is discussed. An output feedback closed loop control approach is presented and a concept for using GPS antennas mounted on the structure as feedback sensor for the control law is presented and discussed.

  19. 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...

  20. Design and experimental evaluation of flexible manipulator control algorithms

    SciTech Connect

    Kwon, D.S.; Hwang, D.H.; Babcock, S.M.; Kress, R.L.; Lew, J.Y.; Evans, M.S.

    1995-04-01

    Within the Environmental Restoration and Waste Management Program of the US Department of Energy, the remediation of single-shell radioactive waste storage tanks is one of the areas that challenge state-of-the-art equipment and methods. The use of long-reach manipulators is being seriously considered for this task. Because of high payload capacity and high length-to-cross-section ratio requirements, these long-reach manipulator systems are expected to use hydraulic actuators and to exhibit significant structural flexibility. The controller has been designed to compensate for the hydraulic actuator dynamics by using a load-compensated velocity feedforward loop and to increase the bandwidth by using an inner pressure feedback loop. Shaping filter techniques have been applied as feedforward controllers to avoid structural vibrations during operation. Various types of shaping filter methods have been investigated. Among them, a new approach, referred to as a ``feedforward simulation filter`` that uses embedded simulation, has been presented.

  1. 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.

  2. Flexible space structure model reduction by modal cost analysis

    NASA Technical Reports Server (NTRS)

    Skelton, R. E.; Hughes, P. C.

    1979-01-01

    It is noted that reduced models and reduced controllers for flexible space structures are obtained by retaining those modes which make the greatest contribution to quadratic control objectives. Attention is given to the relative importance of damping, frequency and mode shapes in the mode truncation decisions for the following control objectives: attitude control, vibration suppression and figure control. It is also shown that using Modal Cost Analysis (MCA) on the closed loop modes of the optimally controlled system allows the construction of reduced control policies which feedback only those closed loop coordinates which are most critical to the quadratic control performance criterion. In this manner, the modes which need to be controlled are deduced from truncations of the optimal controller.

  3. 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.

  4. Optimum design of hybrid phase locked loops

    NASA Technical Reports Server (NTRS)

    Lee, P.; Yan, T.

    1981-01-01

    The design procedure of phase locked loops is described in which the analog loop filter is replaced by a digital computer. Specific design curves are given for the step and ramp input changes in phase. It is shown that the designed digital filter depends explicitly on the product of the sampling time and the noise bandwidth of the phase locked loop. This technique of optimization can be applied to the design of digital analog loops for other applications.

  5. 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.

  6. Teachers' Perception of Looping in Secondary Schools

    ERIC Educational Resources Information Center

    Chakey, Dennis J.

    2014-01-01

    The purpose of this qualitative study was to gain an understanding of secondary teachers' perception of the looping process. The research questions revealed teachers' opinions of the looping process and its impact on the overall educational experience. Participants within this study had experiences teaching within the looping process and within a…

  7. Data-aided carrier tracking loops

    NASA Technical Reports Server (NTRS)

    Lindsey, W. C.; Simon, M. K.

    1973-01-01

    Power in composite signal sidebands is used to enhance signal-to-noise ratio in carrier tracking loop, thereby reducing radio loss and decreasing probability of receiver error. By adding quadrature channel to phase-lock-loop detector circuit of receiver, dc component can be fed back into carrier tracking loop.

  8. Loop connectors in dentogenic diastema

    PubMed Central

    Nayar, Sanjna; Jayesh, Raghevendra; Venkateshwaran; Dinakarsamy, V.

    2015-01-01

    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

  9. 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.

  10. Grain boundary loops in graphene

    NASA Astrophysics Data System (ADS)

    Cockayne, Eric; Rutter, Gregory M.; Guisinger, Nathan P.; Crain, Jason N.; First, Phillip N.; Stroscio, Joseph A.

    2011-05-01

    Topological defects can affect the physical properties of graphene in unexpected ways. Harnessing their influence may lead to enhanced control of both material strength and electrical properties. Here we present a class of topological defects in graphene composed of a rotating sequence of dislocations that close on themselves, forming grain boundary loops that either conserve the number of atoms in the hexagonal lattice or accommodate vacancy or interstitial reconstruction, while leaving no unsatisfied bonds. One grain boundary loop is observed as a “flower” pattern in scanning tunneling microscopy studies of epitaxial graphene grown on SiC(0001). We show that the flower defect has the lowest energy per dislocation core of any known topological defect in graphene, providing a natural explanation for its growth via the coalescence of mobile dislocations.

  11. Loop Variables in String Theory

    NASA Astrophysics Data System (ADS)

    Sathiapalan, B.

    The loop variable approach is a proposal for a gauge-invariant generalization of the sigma-model renormalization group method of obtaining equations of motion in string theory. The basic guiding principle is space-time gauge invariance rather than world sheet properties. In essence it is a version of Wilson's exact renormalization group equation for the world sheet theory. It involves all the massive modes and is defined with a finite world sheet cutoff, which allows one to go off the mass-shell. On shell the tree amplitudes of string theory are reproduced. The equations are gauge-invariant off shell also. This paper is a self-contained discussion of the loop variable approach as well as its connection with the Wilsonian RG.

  12. Design of a Cascade Controller for a Flexible Spray Boom

    NASA Astrophysics Data System (ADS)

    Ramon, H.; De Baerdemaeker, J.; van Brussel, H.

    1996-03-01

    Longitudinal accelerations and yawning angular accelerations of a tractor induce horizontal flexible spray boom deformations which cannot be reduced sufficiently by simple structural adaptations. An electro-hydraulic control system has therefore been developed in order to attenuate the negative effect of longitudinal tractor accelerations on a spray boom. The linear quadratic Gaussian theory with loop transfer recovery has been used to design the compensator. Four different variants of the compensator are implemented in an experimental set-up to test the performance and the robustness of the feedback system and to investigate the applicability of the electro-hydraulic devices in active vibration control.

  13. An inverse dynamic method yielding flexible manipulator state trajectories

    NASA Technical Reports Server (NTRS)

    Kwon, Dong-Soo; Book, Wayne J.

    1990-01-01

    An inverse dynamic equation for a flexible manipulator is derived in a state form. By dividing the inverse system into the causal part and the anticausal part, torque is calculated in the time domain for a certain end point trajectory, as well as trajectories of all state variables. The open loop control of the inverse dynamic method shows an excellent result in simulation. For practical applications, a control strategy adapting feedback tracking control to the inverse dynamic feedforward control is illustrated, and its good experimental result is presented.

  14. Crystal structures of wild-type Trichoderma reesei Cel7A catalytic domain in open and closed states.

    PubMed

    Bodenheimer, Annette M; Meilleur, Flora

    2016-12-01

    Trichoderma reesei Cel7A efficiently hydrolyses cellulose. We report here the crystallographic structures of the wild-type TrCel7A catalytic domain (CD) in an open state and, for the first time, in a closed state. Molecular dynamics (MD) simulations indicate that the loops along the CD tunnel move in concerted motions. Together, the crystallographic and MD data suggest that the CD cycles between the tense and relaxed forms that are characteristic of work producing enzymes. Analysis of the interactions formed by R251 provides a structural rationale for the concurrent decrease in product inhibition and catalytic efficiency measured for product-binding site mutants.

  15. Flexible Calendar and Staff Development.

    ERIC Educational Resources Information Center

    Garlock, Jerry C.

    Three questionnaires were used at El Camino College to assess a flexible calendar that allowed ten days between semesters for staff development activities. A locally developed questionnaire on staff development drew responses from 245 instructors (68.6%), a state questionnaire on the flexible calendar was answered by 57% of full-time and 17% of…

  16. Active Flexible Wing (AFW) Technology

    DTIC Science & Technology

    1988-02-01

    copy of zeach of the fbllowing records: AD B253477, XV-8A Flexible Win& Aerial Utility Vehicle, by H-. Kredit . January 1964, 144 pages AD 13252433...Counterinsurgency Operations by R.A. Wise, Feb 0965, 74 pages - AD 461202. XV-8A Flexible Wing Aerial Utility Vehicle, H. Kredit , Feb. 1965. 100 pages _-AD

  17. Sensor Technologies on Flexible Substrates

    NASA Technical Reports Server (NTRS)

    Koehne, Jessica

    2016-01-01

    NASA Ames has developed sensor technologies on flexible substrates integrated into textiles for personalized environment monitoring and human performance evaluation. Current technologies include chemical sensing for gas leak and event monitoring and biological sensors for human health and performance monitoring. Targeted integration include next generation EVA suits and flexible habitats.

  18. 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

  19. DNA Looping, Supercoiling and Tension

    NASA Astrophysics Data System (ADS)

    Finzi, Laura

    2007-11-01

    In complex organisms, activation or repression of gene expression by proteins bound to enhancer or silencer elements located several kilobases away from the promoter is a well recognized phenomenon. However, a mechanistic understanding of any of these multiprotein interactions is still incomplete. Part of the difficulty in characterizing long-range interactions is the complexity of the regulatory systems and also an underestimation of the effect of DNA supercoiling and tension. Supercoiling is expected to promote interactions between DNA sites because it winds the DNA into compact plectonemes in which distant DNA segments more frequently draw close. The idea that DNA is also under various levels of tension is becoming more widely accepted. Forces that stretch the double helix in vivo are the electrostatic repulsion among the negatively charged phosphate groups along the DNA backbone, the action of motor enzymes perhaps acting upon a topologically constrained sequence of DNA or chromosome segregation during cell mitosis following DNA replication. Presently, little is known about the tension acting on DNA in vivo, but characterization of how physiological regulatory processes, such as loop formation, depend on DNA tension in vitro will indicate the stretching force regimes likely to exist in vivo. In this light, the well studied CI protein of bacteriophage l, which was recently found to cause a of 3.8 kbp loop in DNA, is an ideal system in which to characterize long-range gene regulation. The large size of the loop lends itself to single-molecule techniques, which allow characterization of the dynamics of CI-mediated l DNA looping under controlled levels of supercoiling and tension. Such experiments are being used to discover the principles of long-range interactions in l and in more complex systems.

  20. The role of proline substitutions within flexible regions on thermostability of luciferase.

    PubMed

    Yu, Haoran; Zhao, Yang; Guo, Chao; Gan, Yiru; Huang, He

    2015-01-01

    Improving the stability of firefly luciferase has been a critical issue for its wider industrial applications. Studies about hyperthermophile proteins show that flexibility could be an effective indicator to find out weak spots to engineering thermostability of proteins. However, the relationship among flexibility, activity and stability in most of proteins is unclear. Proline is the most rigid residue and can be introduced to rigidify flexible regions to enhance thermostability of proteins. We firstly apply three different methods, molecular dynamics (MD) simulation, B-FITTER and framework rigidity optimized dynamics algorithm (FRODA) to determine the flexible regions of Photinus pyralis luciferase: Fragment 197-207; Fragment 471-481 and Fragment 487-495. Then, introduction of proline is used to rigidify these flexible regions. Two mutants D476P and H489P within most flexible regions are finally designed. In the results, H489P mutant shows improved thermostability while maintaining its catalytic efficiency compared to that of wild type luciferase. Flexibility analysis confirms that the overall rigidity and local rigidity of H489P mutant are greatly strengthened. D476P mutant shows decreased thermosatbility and the reason for this is elucidated at the molecular level. S307P mutation is randomly chosen outside the flexible regions as a control. Thermostability analysis shows that S307P mutation has decreased kinetic stability and enhanced thermodynamic stability.

  1. 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.

  2. Image-guided Control of Flexible Bevel-Tip Needles

    PubMed Central

    Kallem, Vinutha; Cowan, Noah J.

    2010-01-01

    Physicians perform percutaneous therapies in many diagnostic and therapeutic procedures. Image guidance promises to improve targeting accuracy and broaden the scope of needle interventions. In this paper, we consider the possibility of automating the guidance of a flexible bevel-tip needle as it is inserted into human tissue. We build upon a previously proposed nonholonomic kinematic model to develop a nonlinear observer-based controller. As a first step for control, we show that flexible needles can be automatically controlled to remain within a planar slice of tissue as they are inserted by a physician; our approach keeps the physician in the loop to control insertion speed. In the proposed controller, the distance of the needle tip position from the plane of interest is used as a feedback signal. Numerical simulations demonstrate the stability and robustness of the controller in the face of parametric uncertainty. We also present results from pilot physical experiments with phantom tissue under stereo image guidance. PMID:21359170

  3. Loops in inflationary correlation functions

    NASA Astrophysics Data System (ADS)

    Tanaka, Takahiro; Urakawa, Yuko

    2013-12-01

    We review the recent progress regarding the loop corrections to the correlation functions in the inflationary universe. A naive perturbation theory predicts that the loop corrections generated during inflation suffer from various infrared (IR) pathologies. Introducing an IR cutoff by hand is neither satisfactory nor enough to fix the problem of a secular growth, which may ruin the predictive power of inflation models if the inflation lasts sufficiently long. We discuss the origin of the IR divergences and explore the regularity conditions of the loop corrections for the adiabatic perturbation, the iso-curvature perturbation, and the tensor perturbation, in turn. These three kinds of perturbations have qualitative differences, but in discussing the IR regularity there is a feature common to all cases, which is the importance of the proper identification of observable quantities. Genuinely, observable quantities should respect the gauge invariance from the view point of a local observer. Interestingly, we find that the requirement of the IR regularity restricts the allowed quantum states.

  4. Coupled nonlinear flight dynamics, aeroelasticity, and control of very flexible aircraft

    NASA Astrophysics Data System (ADS)

    Shearer, Christopher M.

    Flight dynamics and control of rigid aircraft motion coupled with linearized structural dynamics has been studied for several decades. However, new requirements for very flexible aircraft are challenging the validity of most rigid body coupled linearized structural motion formulations, due to the presence of large elastic motions. This dissertation presents, the flight dynamics, integration, and control of the six degree-of-freedom equations of motion of a reference point on a very flexible aircraft coupled with the aeroelastic equations which govern the geometrically nonlinear structural response of the vehicle. A low-order strain-based nonlinear structural analysis coupled with unsteady finite-state potential flow aerodynamics form the basis for the aeroelastic formulation. The nonlinear beam structural model is based upon the finite strain approach. Kinematic differential equations are used to provide orientation and position of the fixed reference point. The resulting governing differential equations are non-linear, first- and second-order differential algebraic equations and provide a low-order complete nonlinear aircraft formulation. The resulting equations are integrated using an implicit Modified Newmark Method. The method incorporates both first- and second-order nonlinear equations without the necessity of transforming second-order equations to first-order form. The method also incorporates a Newton-Raphson sub-iteration scheme to reduce residual error. Due to the inherent flexibility of these aircraft, the low order structural modes couple directly with the rigid body modes. This creates a system which cannot be separated as in traditional control schemes. Trajectory control techniques are developed based upon a combination of linear and nonlinear inner-loop tracking and an outer-loop nonlinear transformation from desired trajectories to reference frame velocities. Numerical simulations are presented validating the proposed integration scheme and the

  5. Orthogonal flexible Rydberg aggregates

    NASA Astrophysics Data System (ADS)

    Leonhardt, K.; Wüster, S.; Rost, J. M.

    2016-02-01

    We study the link between atomic motion and exciton transport in flexible Rydberg aggregates, assemblies of highly excited light alkali-metal atoms, for which motion due to dipole-dipole interaction becomes relevant. In two one-dimensional atom chains crossing at a right angle adiabatic exciton transport is affected by a conical intersection of excitonic energy surfaces, which induces controllable nonadiabatic effects. A joint exciton-motion pulse that is initially governed by a single energy surface is coherently split into two modes after crossing the intersection. The modes induce strongly different atomic motion, leading to clear signatures of nonadiabatic effects in atomic density profiles. We have shown how this scenario can be exploited as an exciton switch, controlling direction and coherence properties of the joint pulse on the second of the chains [K. Leonhardt et al., Phys. Rev. Lett. 113, 223001 (2014), 10.1103/PhysRevLett.113.223001]. In this article we discuss the underlying complex dynamics in detail, characterize the switch, and derive our isotropic interaction model from a realistic anisotropic one with the addition of a magnetic bias field.

  6. Flexible Foot Test Assembly

    SciTech Connect

    Kurita, C.H.; /Fermilab

    1987-04-27

    A test model of the flexible foot support was constructed early in the design stages to check its reactions to applied loads. The prototype was made of SS 304 and contained four vertical plates as opposed to the fourteen Inconel 718 plates which comprise the actual structure. Due to the fact that the prototype was built before the design of the support was finalized, the plate dimensions are different from those of the actual proposed design (i.e. model plate thickness is approximately one-half that of the actual plates). See DWG. 3740.210-MC-222376 for assembly details of the test model and DWG. 3740.210-MB-222377 for plate dimensions. This stanchion will be required to not only support the load of the inner vessel of the cryostat and its contents, but it must also allow for the movement of the vessel due to thermal contraction. Assuming that each vertical plate acts as a column, then the following formula from the Manual of Steel Construction (American Institute of Steel Construction, Inc., Eigth edition, 1980) can be applied to determine whether or not such columns undergoing simultaneous axial compression and transverse loading are considered safe for the given loading. The first term is representative of the axially compressive stress, and the second term, the bending stress. If the actual compressive stress is greater than 15% of the allowable compressive stress, then there are additional considerations which must be accounted for in the bending stress term.

  7. Flexible Computational Science Infrastructure

    SciTech Connect

    Bergen, Ben; Moss, Nicholas; Charest, Marc Robert Joseph

    2016-04-06

    FleCSI is a compile-time configurable framework designed to support multi-physics application development. As such, FleCSI attempts to provide a very general set of infrastructure design patterns that can be specialized and extended to suit the needs of a broad variety of solver and data requirements. Current support includes multi-dimensional mesh topology, mesh geometry, and mesh adjacency information, n-dimensional hashed-tree data structures, graph partitioning interfaces, and dependency closures. FleCSI also introduces a functional programming model with control, execution, and data abstractions that are consistent with both MPI and state-of-the-art task-based runtimes such as Legion and Charm++. The FleCSI abstraction layer provides the developer with insulation from the underlying runtime, while allowing support for multiple runtime systems, including conventional models like asynchronous MPI. The intent is to give developers a concrete set of user-friendly programming tools that can be used now, while allowing flexibility in choosing runtime implementations and optimizations that can be applied to architectures and runtimes that arise in the future. The control and execution models in FleCSI also provide formal nomenclature for describing poorly understood concepts like kernels and tasks.

  8. Flexible sparse regularization

    NASA Astrophysics Data System (ADS)

    Lorenz, Dirk A.; Resmerita, Elena

    2017-01-01

    The seminal paper of Daubechies, Defrise, DeMol made clear that {{\\ell }}p spaces with p\\in [1,2) and p-powers of the corresponding norms are appropriate settings for dealing with reconstruction of sparse solutions of ill-posed problems by regularization. It seems that the case p = 1 provides the best results in most of the situations compared to the cases p\\in (1,2). An extensive literature gives great credit also to using {{\\ell }}p spaces with p\\in (0,1) together with the corresponding quasi-norms, although one has to tackle challenging numerical problems raised by the non-convexity of the quasi-norms. In any of these settings, either superlinear, linear or sublinear, the question of how to choose the exponent p has been not only a numerical issue, but also a philosophical one. In this work we introduce a more flexible way of sparse regularization by varying exponents. We introduce the corresponding functional analytic framework, that leaves the setting of normed spaces but works with so-called F-norms. One curious result is that there are F-norms which generate the ℓ 1 space, but they are strictly convex, while the ℓ 1-norm is just convex.

  9. An update on catalytic reforming

    SciTech Connect

    Wei, D.H.; Moser, M.D.; Haizmann, R.S.

    1996-10-01

    The UOP Platforming process is a catalytic reforming process in widespread use throughout the petroleum and petrochemical industries. Since the first unit went onstream in 1949, the process has become a standard feature in refineries worldwide. Over the years, significant improvements have been made in process catalysts and process design. The most recent improvement is the combination of a catalyst called R-72 with a new patented flow scheme, R-72 staged loading, which gives significantly higher yields and provides increased catalyst stability. In this article, the authors describe two types of Platforming processes and the new R-72 staged loading scheme.

  10. 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.

  11. Catalytic cracking of heavy oils

    SciTech Connect

    Otterstedt, J.E.; Gevert, B.; Sterte, J. )

    1987-08-01

    Of the many factors which influence product yields in a fluid catalytic cracker, the feed stock quality and the catalyst composition are of particular interest as they can be controlled only to a limited extent by the refiner. In the past decade there has been a trend towards using heavier feedstocks in the FCC-unit, which is expected to continue in the foreseeable future. It is therefore important to study how molecular types, characteristic not only of heavy petroleum oil but also of e.g. coal liquid, shale oil and biomass oil, respond to cracking over catalysts of different compositions.

  12. 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.

  13. Catalytic membranes for fuel cells

    SciTech Connect

    Liu, Di-Jia; Yang, Junbing; Wang, Xiaoping

    2011-04-19

    A fuel cell of the present invention comprises a cathode and an anode, one or both of the anode and the cathode including a catalyst comprising a bundle of longitudinally aligned graphitic carbon nanotubes including a catalytically active transition metal incorporated longitudinally and atomically distributed throughout the graphitic carbon walls of said nanotubes. The nanotubes also include nitrogen atoms and/or ions chemically bonded to the graphitic carbon and to the transition metal. Preferably, the transition metal comprises at least one metal selected from the group consisting of Fe, Co, Ni, Mn, and Cr.

  14. 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.

  15. Modeling Phase-Locked Loops Using Verilog

    DTIC Science & Technology

    2007-11-01

    a charge pump, the phase detector has a tri-state output that can drive a opamp loop filter directly. This signal is conditioned by the charge pump...then it can directly drive an opamp based loop filter. Most loop filters are based upon an integrator loop. The integrator loop filter is advantageous...replaced with an accumulator. The opamp circuit can be replaced by a digital filter using Z-transform theory z=exp(jwT), where T is the sampling

  16. A dramatic synergistic effect of a flexible achiral linker on a rigid chiral cis-1,2-diamine bifunctional organocatalyst.

    PubMed

    Matsunaga, Hirofumi; Tajima, Daisuke; Kawauchi, Tetsuro; Yasuyama, Takuro; Ando, Shin; Ishizuka, Tadao

    2017-04-05

    The combination of a "rigid" chiral bicyclic cis-1,2-diamine skeleton with steric bulkiness and a "flexible" achiral linker was newly designed as a bifunctional organocatalyst framework and it showed excellent catalytic activity of up to 0.05 mol%, accompanied by the reversal of enantioselection depending on the position of the linker, in an amine-thiourea organocatalyzed asymmetric Michael reaction.

  17. Mechanisms and Kinetics of Catalytic Reactions

    DTIC Science & Technology

    1990-08-01

    CHEMICAL RESEARCH, r- DEVELOPMENT 5 N ENGINEERING CRDE-R-084 "" CENTER CENER(GC-TR-1728-008) ’ 04 N MECHANISMS AND KINETICS OF CATALYTIC REACTIONS Q...and Kinetics of Catalytic Reactions &AUTHOR(S) Garlick, Stephanie M. 7. PERFORMING ORGANIZATION NAME(S) AND ADORESS(ES) . PERFORMING ORGANIZATION...Tables........................87 vi MECHANISMS AND KINETICS OF CATALYTIC REACTIONS 1. INTRODUCTION The hydrolysis of phosphate esters in microemulsion

  18. 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.

  19. Rate limiting domain and loop motions in arginine kinase

    PubMed Central

    Davulcu, Omar; Skalicky, Jack J.; Chapman, Michael S.

    2011-01-01

    Arginine kinase catalyzes the reversible transfer of a phosphoryl group between ATP and arginine. It is the arthropod homolog 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 NMR 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, activation barriers for both the intrinsic dynamics and enzyme turnover are determined using measurements over a temperature range of 15 to 30°C. 15N transverse relaxation dispersion yields activation barriers of 46 ± 8 and 34 ± 12 kJ/mol for of 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

  20. 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.

  1. Spontaneous Helicity of a Polymer with Side Loops Confined to a Cylinder

    NASA Astrophysics Data System (ADS)

    Chaudhuri, Debasish; Mulder, Bela M.

    2012-06-01

    Inspired by recent experiments on the spatial organization of bacterial chromosomes, we consider a type of “bottle-brush” polymer consisting of a flexible backbone chain, to which flexible side loops are connected. We show that such a model with an open linear backbone spontaneously adopts a helical structure with a well-defined pitch when confined to small cylindrical volume. This helicity persists over a range of sizes and aspect ratios of the cylinder, provided the packing fraction of the chain is suitably large. We analyze these results in terms of the interplay between the effective stiffness and actual intrachain packing effects caused by the side loops in response to the confinement.

  2. Role of loop dynamics in thermal stability of mesophilic and thermophilic adenylosuccinate synthetase: a molecular dynamics and normal mode analysis study.

    PubMed

    Vemparala, Satyavani; Mehrotra, Sonali; Balaram, Hemalatha

    2011-05-01

    Enzymes from thermophiles are poorly active at temperatures at which their mesophilic homologs exhibit high activity and attain corresponding active states at high temperatures. In this study, comparative molecular dynamics (MD) simulations, supplemented by normal mode analysis, have been performed on an enzyme Adenylosuccinate synthetase (AdSS) from E. coli (mesophilic) and P. horikoshii (thermophilic) systems to understand the effects of loop dynamics on thermal stability of AdSS. In mesophilic AdSS, both ligand binding and catalysis are facilitated through the coordinated movement of five loops on the protein. The simulation results suggest that thermophilic P. horikoshii preserves structure and catalytic function at high temperatures by using the movement of only a subset of loops (two out of five) for ligand binding and catalysis unlike its mesophilic counterpart in E. coli. The pre-arrangement of the catalytic residues in P. horikoshii is well-preserved and salt bridges remain stable at high temperature (363K). The simulations suggest a general mechanism (including pre-arrangement of catalytic residues, increased polar residue content, stable salt bridges, increased rigidity, and fewer loop movements) used by thermophilic enzymes to preserve structure and be catalytically active at elevated temperatures.

  3. 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).

  4. Structures of native and complexed complement factor D: implications of the atypical His57 conformation and self-inhibitory loop in the regulation of specific serine protease activity.

    PubMed

    Jing, H; Babu, Y S; Moore, D; Kilpatrick, J M; Liu, X Y; Volanakis, J E; Narayana, S V

    1998-10-09

    Factor D is a serine protease essential for the activation of the alternative pathway of complement. The structures of native factor D and a complex formed with isatoic anhydride inhibitor were determined at resolution of 2.3 and 1.5 A, respectively, in an isomorphous monoclinic crystal form containing one molecule per asymmetric unit. The native structure was compared with structures determined previously in a triclinic cell containing two molecules with different active site conformations. The current structure shows greater similarity with molecule B in the triclinic cell, suggesting that this may be the dominant factor D conformation in solution. The major conformational differences with molecule A in the triclinic cell are located in four regions, three of which are close to the active site and include some of the residues shown to be critical for factor D catalytic activity. The conformational flexibility associated with these regions is proposed to provide a structural basis for the previously proposed substrate-induced reversible conformational changes in factor D. The high-resolution structure of the factor D/isatoic anhydride complex reveals the binding mode of the mechanism-based inhibitor. The higher specificity towards factor D over trypsin and thrombin is based on hydrophobic interactions between the inhibitor benzyl ring and the aliphatic side-chain of Arg218 that is salt bridged with Asp189 at the bottom of the primary specificity (S1) pocket. Comparison of factor D structural variants with other serine protease structures revealed the presence of a unique "self-inhibitory loop". This loop (214-218) dictates the resting-state conformation of factor D by (1) preventing His57 from adopting active tautomer conformation, (2) preventing the P1 to P3 residues of the substrate from forming anti-parallel beta-sheets with the non-specific substrate binding loop, and (3) blocking the accessibility of Asp189 to the positive1y charged P1 residue of the

  5. Catalytic microrotor driven by geometrical asymmetry.

    PubMed

    Yang, Mingcheng; Ripoll, Marisol; Chen, Ke

    2015-02-07

    An asymmetric gear with homogeneous surface properties is, here, presented as a prototype to fabricate catalytic microrotors. The driving torque arises from the diffusiophoretic effect induced by the concentration gradients generated by catalytic chemical reactions at the gear surface. This torque produces a spontaneous and unidirectional rotation of the asymmetric gear. By means of mesoscopic simulations, we prove and characterize this scenario. The gear rotational velocity is determined by the gear-solvent interactions, the gear geometry, the solvent viscosity, and the catalytic reaction ratio. Our work presents a simple way to design self-propelled microrotors, alternative to existing catalytic bi-component, or thermophoretic ones.

  6. Catalytic microrotor driven by geometrical asymmetry

    NASA Astrophysics Data System (ADS)

    Yang, Mingcheng; Ripoll, Marisol; Chen, Ke

    2015-02-01

    An asymmetric gear with homogeneous surface properties is, here, presented as a prototype to fabricate catalytic microrotors. The driving torque arises from the diffusiophoretic effect induced by the concentration gradients generated by catalytic chemical reactions at the gear surface. This torque produces a spontaneous and unidirectional rotation of the asymmetric gear. By means of mesoscopic simulations, we prove and characterize this scenario. The gear rotational velocity is determined by the gear-solvent interactions, the gear geometry, the solvent viscosity, and the catalytic reaction ratio. Our work presents a simple way to design self-propelled microrotors, alternative to existing catalytic bi-component, or thermophoretic ones.

  7. 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.

  8. High-temperature helium-loop facility

    SciTech Connect

    Tokarz, R.D.

    1981-09-01

    The high-temperature helium loop is a facility for materials testing in ultrapure helium gas at high temperatures. The closed loop system is capable of recirculating high-purity helium or helium with controlled impurities. The gas loop maximum operating conditions are as follows: 300 psi pressure, 500 lb/h flow rate, and 2100/sup 0/F temperature. The two test sections can accept samples up to 3.5 in. diameter and 5 ft long. The gas loop is fully instrumented to continuously monitor all parameters of loop operation as well as helium impurities. The loop is fully automated to operate continuously and requires only a daily servicing by a qualified operator to replenish recorder charts and helium makeup gas. Because of its versatility and high degree of parameter control, the helium loop is applicable to many types of materials research. This report describes the test apparatus, operating parameters, peripheral systems, and instrumentation system.

  9. Chemical Looping Technology: Oxygen Carrier Characteristics.

    PubMed

    Luo, Siwei; Zeng, Liang; Fan, Liang-Shih

    2015-01-01

    Chemical looping processes are characterized as promising carbonaceous fuel conversion technologies with the advantages of manageable CO2 capture and high energy conversion efficiency. Depending on the chemical looping reaction products generated, chemical looping technologies generally can be grouped into two types: chemical looping full oxidation (CLFO) and chemical looping partial oxidation (CLPO). In CLFO, carbonaceous fuels are fully oxidized to CO2 and H2O, as typically represented by chemical looping combustion with electricity as the primary product. In CLPO, however, carbonaceous fuels are partially oxidized, as typically represented by chemical looping gasification with syngas or hydrogen as the primary product. Both CLFO and CLPO share similar operational features; however, the optimum process configurations and the specific oxygen carriers used between them can vary significantly. Progress in both CLFO and CLPO is reviewed and analyzed with specific focus on oxygen carrier developments that characterize these technologies.

  10. 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.

  11. Flexible Blades for Wind Turbines

    NASA Astrophysics Data System (ADS)

    Collins, Madeline Carlisle; Macphee, David; Harris, Caleb

    2016-11-01

    Previous research has shown that windmills with flexible blades are more efficient than those with rigid blades. Flexibility offers passive pitch control, preferable to active pitch control which is costly and requires maintenance. Flexible blades morph such that the blade more closely resembles its design point at part load and over load. The lift-to-drag ratios on individual blades was investigated. A mold was designed and machined from an acrylic slab for the casting of blades with a NACA 0012 cross section. A flexible blade was cast from silicone and a rigid blade was cast from polyurethane. Each of these blades was tested in a wind tunnel, cantilever mounted, spanning the whole test section. The angle of attack was varied by rotating the mount. All tests were performed at the same wind speed. A load cell within the mount measured forces on the blade, from which the lift and drag forces were calculated. The stall point for the flexible blade occurred later than for the rigid blade, which agrees with previous research. Lift-to-drag ratios were larger for the flexible blade at all angles of attack tested. Flexible blades seem to be a viable option for passive pitch control. Future research will include different airfoil cross sections, wind speeds, and blade materials. Funding from NSF REU site Grant EEC 1358991 is greatly appreciated.

  12. 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

  13. 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).

  14. Evolution of a Catalytic Mechanism

    PubMed Central

    Rauwerdink, Alissa; Lunzer, Mark; Devamani, Titu; Jones, Bryan; Mooney, Joanna; Zhang, Zhi-Jun; Xu, Jian-He; Kazlauskas, Romas J.; Dean, Antony M.

    2016-01-01

    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

  15. 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.

  16. 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.

  17. 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…

  18. Voltage Regulation and Line Loss Minimization of Loop Distribution Systems Using UPFC

    NASA Astrophysics Data System (ADS)

    Sayed, Mahmoud A.; Takeshita, Takaharu

    This paper presents a new method for achieving line loss minimization and voltage regulation in the loop distribution systems, simultaneously. First, mathematical analysis of the line loss minimum conditions in the loop distribution systems is presented. Then, load voltage regulation is applied in the loop distribution system under line loss minimum condition. Reference angle of the desired load voltage is the main factor that can be used to minimize total line loss during load voltage control. In order to achieve these two objectives simultaneously, the UPFC (unified power flow controller), a typical FACTS (flexible AC transmission systems) device, that is capable of instantaneous control of transmission and distribution power flow, is used. Also, the UPFC control scheme to regulate the load voltage under line loss minimization is presented. The effectiveness of the proposed control scheme has been verified experimentally using laboratory prototype in a 200V, 6kVA system.

  19. Dirac Loops in Carbon Allotropes

    NASA Astrophysics Data System (ADS)

    Mullen, Kieran; Uchoa, Bruno; Glatzhofer, D.

    2015-03-01

    We propose a family of structures that have ``Dirac loops'': closed lines in momentum space with Dirac-like quasiparticles, on which the density of states vanishes linearly with energy. The structures all possess the planar trigonal connectivity present in graphene, but are three dimensional. We discuss the consequences of their multiply-connected Fermi surface for transport, including the presence of three dimensional Integer Quantum Hall effect. In the presence of spin-orbit coupling, we show that those structures may have topological surface states. We discuss the feasibility of realizing the structures as an allotrope of carbon. Work supported by NSF Grants DMR-1310407 and DMR-1352604.

  20. Singularities in loop quantum cosmology.

    PubMed

    Cailleteau, Thomas; Cardoso, Antonio; Vandersloot, Kevin; Wands, David

    2008-12-19

    We show that simple scalar field models can give rise to curvature singularities in the effective Friedmann dynamics of loop quantum cosmology (LQC). We find singular solutions for spatially flat Friedmann-Robertson-Walker cosmologies with a canonical scalar field and a negative exponential potential, or with a phantom scalar field and a positive potential. While LQC avoids big bang or big rip type singularities, we find sudden singularities where the Hubble rate is bounded, but the Ricci curvature scalar diverges. We conclude that the effective equations of LQC are not in themselves sufficient to avoid the occurrence of curvature singularities.

  1. 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

  2. Flexibility effects on the control system performance of large scale robotic manipulators

    NASA Technical Reports Server (NTRS)

    Cetinkunt, Sabri; Book, Wayne J.

    1990-01-01

    Structural flexibility of robotic manipulators becomes significant and limits the performance of a control system when manipulators are large structures, manipulating on large payloads, and/or operating at high speeds. The question of when a manipulator can be considered rigid or must be considered flexible is studied as a function of manipulator dynamics and task characteristics. Results are interpreted in simple quantitative forms which can be used as design and analysis tools to decide whether or not the manipulator flexibility will be a significant factor for a given task condition. The limitations imposed by the manipulator flexibility on the joint variable feedback control system performance is determined using linear and nonlinear methods. The closed loop eigenstructure behavior of finite dimensional models under joint variable feedback is studied and results are compared with the previously reported results.

  3. Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery

    NASA Astrophysics Data System (ADS)

    Fischer, Marcus; Coleman, Ryan G.; Fraser, James S.; Shoichet, Brian K.

    2014-07-01

    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 for which similar experimental information is available.

  4. Structural Insight into the Critical Role of the N-Terminal Region in the Catalytic Activity of Dual-Specificity Phosphatase 26

    PubMed Central

    Won, Eun-Young; Lee, Sang-Ok; Lee, Dong-Hwa; Lee, Daeyoup; Bae, Kwang-Hee; Lee, Sang Chul; Kim, Seung Jun; Chi, Seung-Wook

    2016-01-01

    Human dual-specificity phosphatase 26 (DUSP26) is a novel target for anticancer therapy because its dephosphorylation of the p53 tumor suppressor regulates the apoptosis of cancer cells. DUSP26 inhibition results in neuroblastoma cell cytotoxicity through p53-mediated apoptosis. Despite the previous structural studies of DUSP26 catalytic domain (residues 61–211, DUSP26-C), the high-resolution structure of its catalytically active form has not been resolved. In this study, we determined the crystal structure of a catalytically active form of DUSP26 (residues 39–211, DUSP26-N) with an additional N-terminal region at 2.0 Å resolution. Unlike the C-terminal domain-swapped dimeric structure of DUSP26-C, the DUSP26-N (C152S) monomer adopts a fold-back conformation of the C-terminal α8-helix and has an additional α1-helix in the N-terminal region. Consistent with the canonically active conformation of its protein tyrosine phosphate-binding loop (PTP loop) observed in the structure, the phosphatase assay results demonstrated that DUSP26-N has significantly higher catalytic activity than DUSP26-C. Furthermore, size exclusion chromatography-multiangle laser scattering (SEC-MALS) measurements showed that DUSP26-N (C152S) exists as a monomer in solution. Notably, the crystal structure of DUSP26-N (C152S) revealed that the N-terminal region of DUSP26-N (C152S) serves a scaffolding role by positioning the surrounding α7-α8 loop for interaction with the PTP-loop through formation of an extensive hydrogen bond network, which seems to be critical in making the PTP-loop conformation competent for phosphatase activity. Our study provides the first high-resolution structure of a catalytically active form of DUSP26, which will contribute to the structure-based rational design of novel DUSP26-targeting anticancer therapeutics. PMID:27583453

  5. 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.

  6. 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.

  7. Flexible fitting for fluid lines

    NASA Technical Reports Server (NTRS)

    Barajas, S. L.

    1976-01-01

    Tube fitting, consisting of movable tubular section containing two spring pressure Teflon actuated low friction seals, two standard connectors, and two hexagonal retaining nuts, provides flexible joint that allows axial and rotational motion.

  8. Flexible protection for metal bellows

    NASA Technical Reports Server (NTRS)

    Kimble, K. G.

    1970-01-01

    RTV silicone is used with a braided wire sheath surrounding the metal bellows in fluid transfer systems. It demonstrated best overall performance in flexibility and shock absorbing tests, high temperature, low temperature, and salt spray.

  9. Flexible sensors based on nanoparticles.

    PubMed

    Segev-Bar, Meital; Haick, Hossam

    2013-10-22

    Flexible sensors can be envisioned as promising components for smart sensing applications, including consumer electronics, robotics, prosthetics, health care, safety equipment, environmental monitoring, homeland security and space flight. The current review presents a concise, although admittedly nonexhaustive, didactic review of some of the main concepts and approaches related to the use of nanoparticles (NPs) in flexible sensors. The review attempts to pull together different views and terminologies used in the NP-based sensors, mainly those established via electrical transduction approaches, including, but, not confined to: (i) strain-gauges, (ii) flexible multiparametric sensors, and (iii) sensors that are unaffected by mechanical deformation. For each category, the review presents and discusses the common fabrication approaches and state-of-the-art results. The advantages, weak points, and possible routes for future research, highlighting the challenges for NP-based flexible sensors, are presented and discussed as well.

  10. 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.

  11. Engineering the thermostability of β-glucuronidase from Penicillium purpurogenum Li-3 by loop transplant.

    PubMed

    Feng, Xudong; Tang, Heng; Han, Beijia; Zhang, Liang; Lv, Bo; Li, Chun

    2016-12-01

    In this study, we proposed a loop transplant strategy to improve the thermostability of Penicillium purpurogenum Li-3 β-glucuronidase expressed in Escherichia coli (abbreviated to PGUS-E). Firstly, three unstable surface loops of PGUS-E to be replaced were identified with regards to B-factor values and in-depth structure analysis: loops 205-211, 258-263, and 25-31. Then, based on B-factor analysis, eight stable loops for substitution were selected from two typical thermophilic glycosidases which had low homology with PGUS-E (less than 25 %). By analyzing the common features of these stable loops, it was found that they shared a common residue skeleton DXXTX(X)R, based on this, three chimera loops were also manually designed: RSQTSND, RSSTQRD, and DDQTSR. All these loops were introduced to replace the unstable loops of PGUS-E by homology structure modeling, and only mutants with increased hydrogen bonds number and good compatibility with the local mutated region were further subjected to experimental verification. By using this strategy, 10 mutants were experimentally generated, among which three mutants, M1, M3, and M8, were obtained which showed 11.8, 3.3, and 9.4 times higher half-life at 70 °C than that of wild-type (8.5 min). Finally, the MD simulation indicated that the increased hydrogen bonds, decreased flexibility of N-terminal, and increased π-π stacking interaction were responsible for the improved thermostability.

  12. Structural Insights Into Substrate Recognition by the Neurospora Varkud Satellite Ribozyme: Importance of U-Turns at the Kissing-Loop Junction

    PubMed Central

    2013-01-01

    Substrate recognition by the Neurospora Varkud satellite ribozyme depends on the formation of a magnesium-dependent kissing-loop interaction between the stem-loop I (SLI) substrate and stem-loop V (SLV) of the catalytic domain. From mutagenesis studies, it has been established that this I/V kissing-loop interaction involves three Watson–Crick base pairs and is associated with a structural rearrangement of the SLI substrate that facilitates catalysis. Here, we report the NMR structural characterization of this I/V kissing-loop using isolated stem-loops. NMR studies were performed on different SLI/SLV complexes containing a common SLV and shiftable, preshifted, or double-stranded SLI variants. These studies confirm the presence of three Watson–Crick base pairs at the kissing-loop junction and provide evidence for the structural rearrangement of shiftable SLI variants upon SLV binding. NMR structure determination of an SLI/SLV complex demonstrates that both the SLI and SLV loops adopt U-turn structures, which facilitates intermolecular Watson–Crick base pairing. Several other interactions at the I/V interface, including base triples and base stacking, help create a continuously stacked structure. These NMR studies provide a structural basis to understand the stability of the I/V kissing-loop interaction and lead us to propose a kinetic model for substrate activation in the VS ribozyme. PMID:24325625

  13. Structural insights into substrate recognition by the Neurospora Varkud satellite ribozyme: importance of U-turns at the kissing-loop junction.

    PubMed

    Bouchard, Patricia; Legault, Pascale

    2014-01-14

    Substrate recognition by the Neurospora Varkud satellite ribozyme depends on the formation of a magnesium-dependent kissing-loop interaction between the stem-loop I (SLI) substrate and stem-loop V (SLV) of the catalytic domain. From mutagenesis studies, it has been established that this I/V kissing-loop interaction involves three Watson-Crick base pairs and is associated with a structural rearrangement of the SLI substrate that facilitates catalysis. Here, we report the NMR structural characterization of this I/V kissing-loop using isolated stem-loops. NMR studies were performed on different SLI/SLV complexes containing a common SLV and shiftable, preshifted, or double-stranded SLI variants. These studies confirm the presence of three Watson-Crick base pairs at the kissing-loop junction and provide evidence for the structural rearrangement of shiftable SLI variants upon SLV binding. NMR structure determination of an SLI/SLV complex demonstrates that both the SLI and SLV loops adopt U-turn structures, which facilitates intermolecular Watson-Crick base pairing. Several other interactions at the I/V interface, including base triples and base stacking, help create a continuously stacked structure. These NMR studies provide a structural basis to understand the stability of the I/V kissing-loop interaction and lead us to propose a kinetic model for substrate activation in the VS ribozyme.

  14. 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.

  15. Flexible packaging for PV modules

    NASA Astrophysics Data System (ADS)

    Dhere, Neelkanth G.

    2008-08-01

    Economic, flexible packages that provide needed level of protection to organic and some other PV cells over >25-years have not yet been developed. However, flexible packaging is essential in niche large-scale applications. Typical configuration used in flexible photovoltaic (PV) module packaging is transparent frontsheet/encapsulant/PV cells/flexible substrate. Besides flexibility of various components, the solder bonds should also be flexible and resistant to fatigue due to cyclic loading. Flexible front sheets should provide optical transparency, mechanical protection, scratch resistance, dielectric isolation, water resistance, UV stability and adhesion to encapsulant. Examples are Tefzel, Tedlar and Silicone. Dirt can get embedded in soft layers such as silicone and obscure light. Water vapor transmittance rate (WVTR) of polymer films used in the food packaging industry as moisture barriers are ~0.05 g/(m2.day) under ambient conditions. In comparison, light emitting diodes employ packaging components that have WVTR of ~10-6 g/(m2.day). WVTR of polymer sheets can be improved by coating them with dense inorganic/organic multilayers. Ethylene vinyl acetate, an amorphous copolymer used predominantly by the PV industry has very high O2 and H2O diffusivity. Quaternary carbon chains (such as acetate) in a polymer lead to cleavage and loss of adhesional strength at relatively low exposures. Reactivity of PV module components increases in presence of O2 and H2O. Adhesional strength degrades due to the breakdown of structure of polymer by reactive, free radicals formed by high-energy radiation. Free radical formation in polymers is reduced when the aromatic rings are attached at regular intervals. This paper will review flexible packaging for PV modules.

  16. Catalytic Leadership: Strategies for an Interconnected World.

    ERIC Educational Resources Information Center

    Luke, Jeffrey S.

    A catalytic leader brings together diverse individuals from multiple agencies to address intractable public problems. Strategies for promoting catalytic leadership are explored. The book opens with a review of the problems facing public leaders, emphasizing the complexity and interconnectedness of problems in the public sphere. The book highlights…

  17. Catalytic partial oxidation of pyrolysis oils

    NASA Astrophysics Data System (ADS)

    Rennard, David Carl

    2009-12-01

    details the catalytic partial oxidation of glycerol without preheat: droplets of glycerol are sprayed directly onto the top of the catalyst bed, where they react autothermally with contact times on the order of tau ≈ 30 ms. The reactive flash volatilization of glycerol results in equilibrium syngas production over Rh-Ce catalysts. In addition, water can be added to the liquid glycerol, resulting in true autothermal reforming. This highly efficient process can increase H2 yields and alter the H2 to CO ratio, allowing for flexibility in syngas quality depending on the purpose. Chapter 5 details the results of a time on stream experiment, in which optimal syngas conditions are chosen. Although conversion is 100% for 450 hours, these experiments demonstrate the deactivation of the catalyst over time. Deactivation is exhibited by decreases in H2 and CO 2 production accompanied by a steady increase in CO and temperature. These results are explained as a loss of water-gas shift equilibration. SEM images suggest catalyst sintering may play a role; EDS indicates the presence of impurities on the catalyst. In addition, the instability of quartz in the reactor is demonstrated by etching, resulting in a hole in the reactor tube at the end of the experiment. These results suggest prevaporization may be desirable in this application, and that quartz is not a suitable material for the reactive flash volatilization of oxygenated fuels. In Chapter 6, pyrolysis oil samples from three sources - poplar, pine, and hardwoods - are explored in the context of catalytic partial oxidation. Lessons derived from the tests with model compounds are applied to reactor design, resulting in the reactive flash vaporization of bio oils. Syngas is successfully produced, though deactivation due to coke and ash deposition keeps H2 below equlibrium. Coke formation is observed on the reactor walls, but is avoided between the fuel injection site and catalyst by increasing the proximity of these in the reactor

  18. Oxide Heteroepitaxy for Flexible Optoelectronics.

    PubMed

    Bitla, Yugandhar; Chen, Ching; Lee, Hsien-Chang; Do, Thi Hien; Ma, Chun-Hao; Qui, Le Van; Huang, Chun-Wei; Wu, Wen-Wei; Chang, Li; Chiu, Po-Wen; Chu, Ying-Hao

    2016-11-30

    The emerging technological demands for flexible and transparent electronic devices have compelled researchers to look beyond the current silicon-based electronics. However, fabrication of devices on conventional flexible substrates with superior performance are constrained by the trade-off between processing temperature and device performance. Here, we propose an alternative strategy to circumvent this issue via the heteroepitaxial growth of transparent conducting oxides (TCO) on the flexible mica substrate with performance comparable to that of their rigid counterparts. With the examples of ITO and AZO as a case study, a strong emphasis is laid upon the growth of flexible yet epitaxial TCO relying muscovite's superior properties compared to those of conventional flexible substrates and its compatibility with the present fabrication methods. Besides excellent optoelectro-mechanical properties, an additional functionality of high-temperature stability, normally lacking in the current state-of-the-art transparent flexitronics, is provided by these heterostructures. These epitaxial TCO electrodes with good chemical and thermal stabilities as well as mechanical durability can significantly contribute to the field of flexible, light-weight, and portable smart electronics.

  19. 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.

  20. Exploration of Alternate Catalytic Mechanisms and Optimization Strategies for Retroaldolase Design

    PubMed Central

    Bjelic, Sinisa; Kipnis, Yakov; Wang, Ling; Pianowski, Zbigniew; Vorobiev, Sergey; Su, Min; Seetharaman, Jayaraman; Xiao, Rong; Kornhaber, Gregory; Hunt, John F.; Tong, Liang; Hilvert, Donald; Baker, David

    2014-01-01

    Designed retroaldolases have utilized a nucleophilic lysine to promote carbon–carbon bond cleavage of β-hydroxy-ketones via a covalent Schiff base intermediate. Previous computational designs have incorporated a water molecule to facilitate formation and breakdown of the carbinolamine intermediate to give the Schiff base and to function as a general acid/base. Here we investigate an alternative active-site design in which the catalytic water molecule was replaced by the side chain of a glutamic acid. Five out of seven designs expressed solubly and exhibited catalytic efficiencies similar to previously designed retroaldolases for the conversion of 4-hydro-xy-4-(6-methoxy-2-naphthyl)-2-butanone to 6-methoxy-2-naphthaldehyde and acetone. After one round of site-directed saturation mutagenesis, improved variants of the two best designs, RA114 and RA117, exhibited among the highest kcat (>10−3 s−1) and kcat/KM (11–25 M−1 s−1) values observed for retroaldolase designs prior to comprehensive directed evolution. In both cases, the >105-fold rate accelerations that were achieved are within 1–3 orders of magnitude of the rate enhancements reported for the best catalysts for related reactions, including catalytic antibodies (kcat/kuncat = 106 to 108) and an extensively evolved computational design (kcat/kuncat > 107). The catalytic sites, revealed by X-ray structures of optimized versions of the two active designs, are in close agreement with the design models except for the catalytic lysine in RA114. We further improved the variants by computational remodeling of the loops and yeast display selection for reactivity of the catalytic lysine with a diketone probe, obtaining an additional order of magnitude enhancement in activity with both approaches. PMID:24161950