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Sample records for flexible catalytic loop

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

    PubMed

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

    2013-04-26

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

  2. Computational Investigation of the pH Dependence of Loop Flexibility and Catalytic Function in Glycoside Hydrolases*

    PubMed Central

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

    2013-01-01

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

  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. A role for flexible loops in enzyme catalysis.

    PubMed

    Malabanan, M Merced; Amyes, Tina L; Richard, John P

    2010-12-01

    Triosephosphate isomerase (TIM), glycerol 3-phosphate dehydrogenase, and orotidine 5'-monophosphate decarboxylase each use the binding energy from the interaction of phosphite dianion with a flexible phosphate gripper loop to activate a second, phosphodianion-truncated, substrate towards enzyme-catalyzed proton transfer, hydride transfer, and decarboxylation, respectively. Studies on TIM suggest that the most important general effect of loop closure over the substrate phosphodianion, and the associated conformational changes, is to extrude water from the enzyme active site. This should cause a decrease in the effective active-site dielectric constant, and an increase in transition state stabilization from enhanced electrostatic interactions with polar amino acid side chains. The most important specific effect of these conformational changes is to increase the basicity of the carboxylate side chain of the active site glutamate base by its placement in a 'hydrophobic cage'.

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

    PubMed

    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

  12. 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

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

    PubMed

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

    2002-07-30

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

  14. Loops Adjacent to Catalytic Region and Molecular Stability of Man1312.

    PubMed

    Zhou, Haiyan; Yong, Jie; Gao, Han; Yuan, Zhihui; Yang, Wenjiao; Tian, Yun; Wu, Yongyao

    2016-09-01

    Hemicelluloses are the second major polysaccharides in nature and can be converted to ethanol product by a variety of enzymes including mannanases. Mannanase is an important enzyme that hydrolyses mannose-containing polysaccharides which are abundant in plants. An optimized mannanase could help to improve conversion process and make the technology efficiently and competitively. In this work, the effects of loops adjacent to active region on enzymic properties of Man1312 were investigated. Loop 6 and 10 are two loops neighboring to Man1312 catalytic region, and deletion mutagenesis and residue substitution were performed on both loops. Deletion on sites S145, Q148, N244, and S255 and substitution on sites N146, S147, S156, and T157 gave significant increased stability to enzyme. The quadruplet mutant ManD4I4 combined all the mutations and had higher optimal temperature and T m value by 5 and 4 °C than Man1312, respectively. From our data, we are able to conclude the loops of enzymes are important to design mutagenesis and obtain improved properties, especially the loops neighboring to catalytic region from tertiary structure. In our experiment, residue deletion and substitution on loops neighboring to catalytic region made significant improvement on enzyme properties.

  15. GABA production by glutamic acid decarboxylase is regulated by a dynamic catalytic loop.

    PubMed

    Fenalti, Gustavo; Law, Ruby H P; Buckle, Ashley M; Langendorf, Christopher; Tuck, Kellie; Rosado, Carlos J; Faux, Noel G; Mahmood, Khalid; Hampe, Christiane S; Banga, J Paul; Wilce, Matthew; Schmidberger, Jason; Rossjohn, Jamie; El-Kabbani, Ossama; Pike, Robert N; Smith, A Ian; Mackay, Ian R; Rowley, Merrill J; Whisstock, James C

    2007-04-01

    Gamma-aminobutyric acid (GABA) is synthesized by two isoforms of the pyridoxal 5'-phosphate-dependent enzyme glutamic acid decarboxylase (GAD65 and GAD67). GAD67 is constitutively active and is responsible for basal GABA production. In contrast, GAD65, an autoantigen in type I diabetes, is transiently activated in response to the demand for extra GABA in neurotransmission, and cycles between an active holo form and an inactive apo form. We have determined the crystal structures of N-terminal truncations of both GAD isoforms. The structure of GAD67 shows a tethered loop covering the active site, providing a catalytic environment that sustains GABA production. In contrast, the same catalytic loop is inherently mobile in GAD65. Kinetic studies suggest that mobility in the catalytic loop promotes a side reaction that results in cofactor release and GAD65 autoinactivation. These data reveal the molecular basis for regulation of GABA homeostasis.

  16. DNA twisting flexibility and the formation of sharply looped protein-DNA complexes

    NASA Astrophysics Data System (ADS)

    Cloutier, T. E.; Widom, J.

    2005-03-01

    Gene-regulatory complexes often require that pairs of DNA-bound proteins interact by looping-out short (often 100-bp) stretches of DNA. The loops can vary in detailed length and sequence and, thus, in total helical twist, which radically alters their geometry. How this variability is accommodated structurally is not known. Here we show that the inherent twistability of 89- to 105-bp DNA circles exceeds theoretical expectation by up to 400-fold. These results can be explained only by greatly enhanced DNA flexibility, not by permanent bends. They invalidate the use of classic theories of flexibility for understanding sharp DNA looping but support predictions of two recent theories. Our findings imply an active role for DNA flexibility in loop formation and suggest that variability in the detailed helical twist of regulatory loops is accommodated naturally by the inherent twistability of the DNA. activation | gene regulation | repression

  17. 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.

  18. 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.

  19. 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.

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

    PubMed

    Porta, Josep M; Jaillet, Léonard

    2013-01-30

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

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

    PubMed

    Porta, Josep M; Jaillet, Léonard

    2013-01-30

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

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

    PubMed Central

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

    2016-01-01

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

  3. 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.

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

    PubMed

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

    2015-12-01

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

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

    SciTech Connect

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

    2009-09-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    SciTech Connect

    Damaren, C.J.

    2000-03-01

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

  10. 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.

  11. Ternary complex structure of human HGPRTase, PRPP, Mg2+, and the inhibitor HPP reveals the involvement of the flexible loop in substrate binding.

    PubMed Central

    Balendiran, G. K.; Molina, J. A.; Xu, Y.; Torres-Martinez, J.; Stevens, R.; Focia, P. J.; Eakin, A. E.; Sacchettini, J. C.; Craig, S. P.

    1999-01-01

    Site-directed mutagenesis was used to replace Lys68 of the human hypoxanthine phosphoribosyltransferase (HGPRTase) with alanine to exploit this less reactive form of the enzyme to gain additional insights into the structure activity relationship of HGPRTase. Although this substitution resulted in only a minimal (one- to threefold) increase in the Km values for binding pyrophosphate or phosphoribosylpyrophosphate, the catalytic efficiencies (k(cat)/Km) of the forward and reverse reactions were more severely reduced (6- to 30-fold), and the mutant enzyme showed positive cooperativity in binding of alpha-D-5-phosphoribosyl-1-pyrophosphate (PRPP) and nucleotide. The K68A form of the human HGPRTase was cocrystallized with 7-hydroxy [4,3-d] pyrazolo pyrimidine (HPP) and Mg PRPP, and the refined structure reported. The PRPP molecule built into the [(Fo - Fc)phi(calc)] electron density shows atomic interactions between the Mg PRPP and enzyme residues in the pyrophosphate binding domain as well as in a long flexible loop (residues Leu101 to Gly111) that closes over the active site. Loop closure reveals the functional roles for the conserved SY dipeptide of the loop as well as the molecular basis for one form of gouty arthritis (S103R). In addition, the closed loop conformation provides structural information relevant to the mechanism of catalysis in human HGPRTase. PMID:10338013

  12. The combination of positive and negative feedback loops confers exquisite flexibility to biochemical switches

    NASA Astrophysics Data System (ADS)

    Pfeuty, Benjamin; Kaneko, Kunihiko

    2009-12-01

    A wide range of cellular processes require molecular regulatory pathways to convert a graded signal into a discrete response. One prevalent switching mechanism relies on the coexistence of two stable states (bistability) caused by positive feedback regulations. Intriguingly, positive feedback is often supplemented with negative feedback, raising the question of whether and how these two types of feedback can cooperate to control discrete cellular responses. To address this issue, we formulate a canonical model of a protein-protein interaction network and analyze the dynamics of a prototypical two-component circuit. The appropriate combination of negative and positive feedback loops can bring a bistable circuit close to the oscillatory regime. Notably, sharply activated negative feedback can give rise to a bistable regime wherein two stable fixed points coexist and may collide pairwise with two saddle points. This specific type of bistability is found to allow for separate and flexible control of switch-on and switch-off events, for example (i) to combine fast and reversible transitions, (ii) to enable transient switching responses and (iii) to display tunable noise-induced transition rates. Finally, we discuss the relevance of such bistable switching behavior, and the circuit topologies considered, to specific biological processes such as adaptive metabolic responses, stochastic fate decisions and cell-cycle transitions. Taken together, our results suggest an efficient mechanism by which positive and negative feedback loops cooperate to drive the flexible and multifaceted switching behaviors arising in biological systems.

  13. 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

  14. 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.

  15. 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.

  16. Dynamics of the SPRY domain–containing SOCS box protein 2: Flexibility of key functional loops

    PubMed Central

    Yao, Shenggen; Liu, Ming S.; Masters, Seth L.; Zhang, Jian-Guo; Babon, Jeffrey J.; Nicola, Nicos A.; Nicholson, Sandra E.; Norton, Raymond S.

    2006-01-01

    The SPRY domain was identified originally as a sequence repeat in the dual-specificity kinase splA and ryanodine receptors and subsequently found in many other distinct proteins, including more than 70 encoded in the human genome. It is a subdomain of the B30.2/SPRY domain and is believed to function as a protein–protein interaction module. Three-dimensional structures of several B30.2/SPRY domain–containing proteins have been reported recently: murine SSB-2 in solution by NMR spectroscopy, a Drosophila SSB (GUSTAVUS), and human PRYSPRY protein by X-ray crystallography. The three structures share a core of two antiparallel β-sheets for the B30.2/SPRY domain but show differences located mainly at one end of the β-sandwich. Analysis of SSB-2 residues required for interactions with its intracellular ligands has provided insights into B30.2/SPRY binding specificity and identified loop residues critical for the function of this domain. We have investigated the backbone dynamics of SSB-2 by means of Modelfree analysis of its backbone 15N relaxation parameters and carried out coarse-grained dynamics simulation of B30.2/SPRY domain–containing proteins using normal mode analysis. Translational self-diffusion coefficients of SSB-2 measured using pulsed field gradient NMR were used to confirm the monomeric state of SSB-2 in solution. These results, together with previously reported amide exchange data, highlight the underlying flexibility of the loop regions of B30.2/SPRY domain–containing proteins that have been shown to be important for protein–protein interactions. The underlying flexibility of certain regions of the B30.2/SPRY domain–containing proteins may also contribute to some apparent structural differences observed between GUSTAVUS or PRYSPRY and SSB-2. PMID:17088318

  17. 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.

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

    PubMed Central

    Cha, Hi-jea; Müller, Reinke T.

    2014-01-01

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

  19. Flexibility.

    ERIC Educational Resources Information Center

    Humphrey, L. Dennis

    1981-01-01

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

  20. Thermodynamic and structural consequences of flexible loop deletion by circular permutation in the streptavidin-biotin system.

    PubMed Central

    Chu, V.; Freitag, S.; Le Trong, I.; Stenkamp, R. E.; Stayton, P. S.

    1998-01-01

    A circularly permuted streptavidin (CP51/46) has been designed to remove the flexible polypeptide loop that undergoes an open to closed conformational change when biotin is bound. The original termini have been joined by a tetrapeptide linker, and four loop residues have been removed, resulting in the creation of new N- and C-termini. Isothermal titration calorimetric studies show that the association constant has been reduced approximately six orders of magnitude below that of wild-type streptavidin to 10(7) M(-1). The deltaH degrees of biotin association for CP51/46 is reduced by 11.1 kcal/mol. Crystal structures of CP51/46 and its biotin complex show no significant alterations in the binding site upon removal of the loop. A hydrogen bond between Ser45 and Ser52 found in the absence of biotin is broken in the closed conformation as the side-chain hydroxyl of Ser45 moves to hydrogen bond to a ureido nitrogen of biotin. This is true in both the wild-type and CP51/46 forms of the protein, and the hydrogen bonding interaction might thus help nucleate closure of the loop. The reduced entropic cost of binding biotin to CP51/46 is consistent with the removal of this loop and a reduction in entropic costs associated with loop closure and immobilization. The reduced enthalpic contribution to the free energy of binding is not readily explainable in terms of the molecular structure, as the binding contacts are nearly entirely conserved, and only small differences in solvent accessible surfaces are observed relative to wild-type streptavidin. PMID:9568892

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

    PubMed

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

    2001-04-01

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

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

    PubMed

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

    2001-04-01

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

  3. Site-directed mutagenesis of the glycine-rich loop of death associated protein kinase (DAPK) identifies it as a key structure for catalytic activity.

    PubMed

    McNamara, Laurie K; Brunzelle, Joseph S; Schavocky, James P; Watterson, D Martin; Grum-Tokars, Valerie

    2011-05-01

    Death associated protein kinase (DAPK) is a calmodulin (CaM)-regulated protein kinase that is a therapeutic target for central nervous system (CNS) disorders. We report here the results of studies that test the hypothesis of McNamara et al. (2009) that conformational selection in DAPK's glycine-rich region is key for catalytic activity. The hypothesis was tested by site-directed mutagenesis of glutamine-23 (Q23) in the middle of this loop. The glycine-rich loop exhibits localized differences in structure among DAPK conformations that correlate with different stages of the catalytic cycle. Changing the Q23 to a Valine (V23), found at the corresponding position in another CaM regulated protein kinase, results in a reduced catalytic efficiency. High resolution X-ray crystal structures of various conformations of the Q23V mutant DAPK and their superimposition with the corresponding conformations from wild type catalytic domain reveal localized changes in the glycine-rich region. The effect of the mutation on DAPK catalytic activity and the finding of only localized changes in the DAPK structure provide experimental evidence implicating conformational selection in this domain with activity. This article is part of a Special Issue entitled: 11th European Symposium on Calcium.

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

    NASA Astrophysics Data System (ADS)

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

    2011-06-01

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

  5. Closed-Loop Control Techniques for Active Vibration Suppression of a Flexible Mechanical System

    NASA Astrophysics Data System (ADS)

    Villaverde Huertas, Vladímir; Rohaľ-Ilkiv, Boris

    2012-12-01

    This paper investigates the problem of vibration attenuation of a lightly damped mechanical system using piezoelectric actuation. First of all, an explicit predictive controller will be designed using the Matlab multi-parametric toolbox. Then, we will explore the positive position feedback technique and test the discrete-time PPF controller using an xPC target real-time system. On the other hand, we will realize the modal analysis of the analyzed flexible system in order to determine the frequency corresponding to the first mode shape. This frequency will be utilized as PPF controller frequency. Moreover, the state-space model of the flexible mechanical system will be obtained using the Matlab system identification toolbox applying the subspace identification approach.

  6. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1990-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2011-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  10. 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.

  11. Specific residues in the connector loop of the human cytomegalovirus DNA polymerase accessory protein UL44 are crucial for interaction with the UL54 catalytic subunit.

    PubMed

    Loregian, Arianna; Appleton, Brent A; Hogle, James M; Coen, Donald M

    2004-09-01

    The human cytomegalovirus DNA polymerase includes an accessory protein, UL44, which has been proposed to act as a processivity factor for the catalytic subunit, UL54. How UL44 interacts with UL54 has not yet been elucidated. The crystal structure of UL44 revealed the presence of a connector loop analogous to that of the processivity subunit of herpes simplex virus DNA polymerase, UL42, which is crucial for interaction with its cognate catalytic subunit, UL30. To investigate the role of the UL44 connector loop, we replaced each of its amino acids (amino acids 129 to 140) with alanine. We then tested the effect of each substitution on the UL44-UL54 interaction by glutathione S-transferase pulldown and isothermal titration calorimetry assays, on the stimulation of UL54-mediated long-chain DNA synthesis by UL44, and on the binding of UL44 to DNA-cellulose columns. Substitutions that affected residues 133 to 136 of the connector loop measurably impaired the UL44-UL54 interaction without altering the ability of UL44 to bind DNA. One substitution, I135A, completely disrupted the binding of UL44 to UL54 and inhibited the ability of UL44 to stimulate long-chain DNA synthesis by UL54. Thus, similar to the herpes simplex virus UL30-UL42 interaction, a residue of the connector loop of the accessory subunit is crucial for UL54-UL44 interaction. However, while alteration of a polar residue of the UL42 connector loop only partially reduced binding to UL30, substitution of a hydrophobic residue of UL44 completely disrupted the UL54-UL44 interaction. This information may aid the discovery of small-molecule inhibitors of the UL44-UL54 interaction.

  12. Mapping the intrinsically disordered properties of the flexible loop domain of Bcl-2: a molecular dynamics simulation study.

    PubMed

    Ilizaliturri-Flores, Ian; Correa-Basurto, José; Bello, Martiniano; Rosas-Trigueros, Jorge L; Zamora-López, Beatriz; Benítez-Cardoza, Claudia G; Zamorano-Carrillo, Absalom

    2016-04-01

    Most of the B-cell lymphoma-2 (Bcl-2) protein structure has been elucidated; however, the conformation of its flexible loop domain (FLD) has not yet been experimentally predicted. Its high flexibility under physiological conditions is the reason. FLD behaves as an intrinsically disordered region (IDR) and can adopt regular structures in particular conditions associated with the control of Bcl-2's anti-apoptotic functions. In a previous contribution, we analyzed an engineered Bcl-2 construct (Bcl-2-Δ22Σ3) submitted to 25-ns MD and reported a disordered-to-helix transitions in a region of FLD (rFLD, residues 60-77). However, the conformational preferences in solution of rFLD in the nanosecond to microsecond scale were not analyzed. Herein, an average model was obtained for the native Bcl-2 protein by homology modeling and MD simulation techniques. From this, only the atomic coordinates corresponding to the rFLD were simulated for 1 μs by MD at 310 K. In concordance with previous studies, a disordered-to-helix transitions were exhibited, implying that this "interconversion of folding" in the rFLD suggest a possible set of conformations encoded in its sequence. Principal component analysis (PCA) showed that most of the conformational fluctuation of Bcl-2 is provided by rFLD. Dihedral PCA (dPCA) offered information about all the conformations of rFLD in the μs of the simulation, characterizing a dPCA-based free energy landscape of rFLD, and a conformational ensemble of fast interconverting conformations as other IDRs. Furthermore, despite the conformational heterogeneity of rFLD, the analysis of the dihedral angles (Φ, Ψ) showed that this region does not randomly explore the conformational space in solution.

  13. High resolution crystal structures of triosephosphate isomerase complexed with its suicide inhibitors: The conformational flexibility of the catalytic glutamate in its closed, liganded active site

    PubMed Central

    Venkatesan, Rajaram; Alahuhta, Markus; Pihko, Petri M; Wierenga, Rik K

    2011-01-01

    The key residue of the active site of triosephosphate isomerase (TIM) is the catalytic glutamate, which is proposed to be important (i) as a catalytic base, for initiating the reaction, as well as (ii) for the subsequent proton shuttling steps. The structural properties of this glutamate in the liganded complex have been investigated by studying the high resolution crystal structures of typanosomal TIM, complexed with three suicide inhibitors: (S)-glycidol phosphate ((S)-GOP, at 0.99 Å resolution), (R)-glycidol phosphate, ((R)-GOP, at 1.08 Å resolution), and bromohydroxyacetone phosphate (BHAP, at 1.97 Å resolution). The structures show that in the (S)-GOP active site this catalytic glutamate is in the well characterized, competent conformation. However, an unusual side chain conformation is observed in the (R)-GOP and BHAP complexes. In addition, Glu97, salt bridged to the catalytic lysine in the competent active site, adopts an unusual side chain conformation in these two latter complexes. The higher chemical reactivity of (S)-GOP compared with (R)-GOP, as known from solution studies, can be understood: the structures indicate that in the case of (S)-GOP, Glu167 can attack the terminal carbon of the epoxide in a stereoelectronically favored, nearly linear O–C–O arrangement, but this is not possible for the (R)-GOP isomer. These structures confirm the previously proposed conformational flexibility of the catalytic glutamate in its closed, liganded state. The importance of this conformational flexibility for the proton shuttling steps in the TIM catalytic cycle, which is apparently achieved by a sliding motion of the side chain carboxylate group above the enediolate plane, is also discussed. PMID:21633986

  14. 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.

  15. Structural and Catalytic Effects of Proline Substitution and Surface Loop Deletion in the Extended Active Site of Human Carbonic Anhydrase II

    PubMed Central

    Boone, Christopher D.; Rasi, Valerio; Tu, Chingkuang; McKenna, Robert

    2015-01-01

    The bioengineering of a thermophilic enzyme starting from a mesophilic scaffold has proven to be a significant challenge as several stabilizing elements have been proposed to be the foundation of thermal stability including disulfide bridges, surface loop reduction, ionic pair networks, proline substitutions, and aromatic clusters. This study emphasizes the impact of increasing the rigidity of human carbonic anhydrase II (HCA II) via incorporation of proline residues at positions 170 and 234, which are located in surface loops that are able to accommodate restrictive main-chain conformations without rearrangement of the surrounding peptide backbone. Additionally, the effect of compactness of HCA II was examined by way of deletion of a surface loop (residues 230 through 240), which had been previously identified as a possible source of thermal stability for the hyperthermophilic CA isolated from the bacterium Sulfurihydrogenibium yellowstonense YO3AOP1. Differential scanning calorimetry analysis of these HCA II variants revealed that these structural modifications had a minimum effect on the thermal stability of the enzyme while kinetic studies showed unexpected effects on the catalytic efficiency and proton transfer rates. X-ray crystallographic analysis of these HCA II variants showed the electrostatic potential and configuration of the highly acidic loop (residues 230 and 240) plays an important role in its high catalytic activity. Based on these observations and the literature, a picture is emerging of the various components within the general structural architecture of HCA II that are key to stability. These elements could provide the blueprints for the rational thermal stability engineering of other enzymes. PMID:25683338

  16. The Q-loop disengages from the first intracellular loop during the catalytic cycle of the multidrug ABC transporter BmrA.

    PubMed

    Dalmas, Olivier; Orelle, Cédric; Foucher, Anne-Emmanuelle; Geourjon, Christophe; Crouzy, Serge; Di Pietro, Attilio; Jault, Jean-Michel

    2005-11-01

    The ATP-binding cassette is the most abundant family of transporters including many medically relevant members and gathers both importers and exporters involved in the transport of a wide variety of substrates. Although three high resolution three-dimensional structures have been obtained for a prototypic exporter, MsbA, two have been subjected to much criticism. Here, conformational changes of BmrA, a multidrug bacterial transporter structurally related to MsbA, have been studied. A three-dimensional model of BmrA, based on the "open" conformation of Escherichia coli MsbA, was probed by simultaneously introducing two cysteine residues, one in the first intracellular loop of the transmembrane domain and the other in the Q-loop of the nucleotide-binding domain (NBD). Intramolecular disulfide bonds could be created in the absence of any effectors, which prevented both drug transport and ATPase activity. Interestingly, addition of ATP/Mg plus vanadate strongly prevented this bond formation in a cysteine double mutant, whereas ATP/Mg alone was sufficient when the ATPase-inactive E504Q mutation was also introduced, in agreement with additional BmrA models where the ATP-binding sites are positioned at the NBD/NBD interface. Furthermore, cross-linking between the two cysteine residues could still be achieved in the presence of ATP/Mg plus vanadate when homobifunctional cross-linkers separated by more than 13 Angstrom were added. Altogether, these results give support to the existence, in the resting state, of a monomeric conformation of BmrA similar to that found within the open MsbA dimer and show that a large motion is required between intracellular loop 1 and the nucleotide-binding domain for the proper functioning of a multidrug ATP-binding cassette transporter. PMID:16107340

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

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

    PubMed

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

    2014-12-01

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

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

    PubMed

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

    2016-04-20

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

  20. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

  2. 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%.

  3. 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

    2014-06-01

    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.

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

    PubMed Central

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

    2006-01-01

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

  5. 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.

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

    PubMed

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

    2014-07-16

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

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

    PubMed

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

    2014-07-16

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

  8. 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.

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

    SciTech Connect

    Lindner, D.K.; Zvonar, G.A.; Baumann, W.T.; Delos, P.L. . Bradley Dept. of Electrical Engineering)

    1993-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

  11. Step-wise addition of disulfide bridge in firefly luciferase controls color shift through a flexible loop: a thermodynamic perspective.

    PubMed

    Nazari, Mahboobeh; Hosseinkhani, Saman; Hassani, Leila

    2013-02-01

    Multi-color bioluminescence is developed using the introduction of single/double disulfide bridges in firefly luciferase. The bioluminescence reaction, which uses luciferin, Mg(2+)-ATP and molecular oxygen to yield an electronically excited oxyluciferin, is carried out by the luciferase and emits visible light. The bioluminescence color of firefly luciferases is determined by the luciferase sequence and assay conditions. It has been proposed that the stability of a protein may increase through the introduction of a disulfide bridge that decreases the configurational entropy of unfolding. Single and double disulfide bridges are introduced into Photinus pyralis firefly luciferase to make separate mutant enzymes with a single/double bridge (C(81)-A(105)C, L(306)C-L(309)C, P(451)C-V(469)C; C(81)-A(105)C/P(451)C-V(469)C, and A(296)C-A(326)C/P(451)C-V(469)C). By introduction of disulfide bridges using site-directed mutagenesis in Photinus pyralis luciferase the color of emitted light was changed to red or kept in different extents. The bioluminescence color shift occurred with displacement of a critical loop in the luciferase structure without any change in green emitter mutants. Thermodynamic analysis revealed that among mutants, L(306)C-L(309)C shows a remarkable stability against urea denaturation and also a considerable increase in kinetic stability and a clear shift in bioluminescence spectra towards red.

  12. 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.

  13. 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.

  14. (1,3;1,4)-β-Glucan Biosynthesis by the CSLF6 Enzyme: Position and Flexibility of Catalytic Residues Influence Product Fine Structure.

    PubMed

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

    2016-04-01

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

  15. 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.

  16. 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. PMID:25945585

  17. 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.

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

    PubMed Central

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

    2014-01-01

    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. PMID:24598752

  19. Catalytic molecular beacons.

    PubMed

    Stojanovic, M N; de Prada, P; Landry, D W

    2001-06-01

    We have constructed catalytic molecular beacons from a hammerhead-type deoxyribozyme by a modular design. The deoxyribozyme was engineered to contain a molecular beacon stem-loop module that, when closed, inhibits the deoxyribozyme module and is complementary to a target oligonucleotide. Binding of target oligonucleotides opens the beacon stem-loop and allosterically activates the deoxyribozyme module, which amplifies the recognition event through cleavage of a doubly labeled fluorescent substrate. The customized modular design of catalytic molecular beacons allows for any two single-stranded oligonucleotide sequences to be distinguished in homogenous solution in a single step. Our constructs demonstrate that antisense conformational triggers based on molecular beacons can be used to initiate catalytic events. The selectivity of the system is sufficient for analytical applications and has potential for the construction of deoxyribozyme-based drug delivery tools specifically activated in cells containing somatic mutations.

  20. The structure of truncated recombinant human bile salt-stimulated lipase reveals bile salt-independent conformational flexibility at the active-site loop and provides insights into heparin binding.

    PubMed

    Moore, S A; Kingston, R L; Loomes, K M; Hernell, O; Bläckberg, L; Baker, H M; Baker, E N

    2001-09-21

    Human bile salt-stimulated lipase (BSSL), which is secreted from the pancreas into the digestive tract and from the lactating mammary gland into human milk, is important for the effective absorption of dietary lipids. The dependence of BSSL on bile acids for activity with water-insoluble substrates differentiates it from other lipases. We have determined the crystal structure of a truncated variant of human BSSL (residues 1-5.8) and refined it at 2.60 A resolution, to an R-factor of 0.238 and R(free) of 0.275. This variant lacks the C-terminal alpha-helix and tandem C-terminal repeat region of native BSSL, but retains full catalytic activity. A short loop (residues 115-126) capable of occluding the active-site (the active site loop) is highly mobile and exists in two conformations, the most predominant of which leaves the active-site open for interactions with substrate. The bile salt analogue 3-[(3-cholamidopropyl)dimethylammonio]-1-propane sulfonic acid (CHAPS) was present in the crystallisation medium, but was not observed bound to the enzyme. However, the structure reveals a sulfonate group from the buffer piperizine ethane sulfonic acid (PIPES), making interactions with Arg63 and His115. His115 is part of the active-site loop, indicating that the loop could participate in the binding of a sulphate group from either the glycosaminoglycan heparin (known to bind BSSL) or a bile acid such as deoxycholate. Opening of the 115-126 active-site loop may be cooperatively linked to a sulphate anion binding at this site. The helix bundle domain of BSSL (residues 319-398) exhibits weak electron density and high temperature factors, indicating considerable structural mobility. This domain contains an unusual Asp:Glu pair buried in a hydrophobic pocket between helices alpha(H) and alpha(K) that may be functionally important. We have also solved the structure of full-length glycosylated human BSSL at 4.1 A resolution, using the refined coordinates of the truncated molecule as

  1. 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…

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed

    Witek, Marta A; Conn, Graeme L

    2016-01-01

    Methylation of the bacterial small ribosomal subunit (16S) rRNA on the N1 position of A1408 confers exceptionally high-level resistance to a broad spectrum of aminoglycoside antibiotics. Here, we present a detailed structural and functional analysis of the Catenulisporales acidiphilia 16S rRNA (m(1)A1408) methyltransferase ('CacKam'). The apo CacKam structure closely resembles other m(1)A1408 methyltransferases within its conserved SAM-binding fold but the region linking core β strands 6 and 7 (the 'β6/7 linker') has a unique, extended structure that partially occludes the putative 16S rRNA binding surface, and sequesters the conserved and functionally critical W203 outside of the CacKam active site. Substitution of conserved residues in the SAM binding pocket reveals a functional dichotomy in the 16S rRNA (m(1)A1408) methyltransferase family, with two apparently distinct molecular mechanisms coupling cosubstrate/ substrate binding to catalytic activity. Our results additionally suggest that CacKam exploits the W203-mediated remodeling of the β6/7 linker as a novel mechanism to control 30S substrate recognition and enzymatic turnover.

  4. Interaction of calcium with native and decarboxylated human factor X. Effect of proteolysis in the autolysis loop on catalytic efficiency and factor Va binding.

    PubMed

    Sabharwal, A K; Padmanabhan, K; Tulinsky, A; Mathur, A; Gorka, J; Bajaj, S P

    1997-08-29

    cleavage at Arg-332-Gln-333(150-151) in the protease domain autolysis loop. Des-44-Xa in which the autolysis loop was cleaved possessed loop-cleaved, active site-blocked native factor Xa was calculated to have approximately 10-fold reduced affinity for factor Va as compared with that of the noncleaved form. PMID:9268343

  5. Hydrogen bonds between the alpha and beta subunits of the F1-ATPase allow communication between the catalytic site and the interface of the beta catch loop and the gamma subunit.

    PubMed

    Boltz, Kathryn W; Frasch, Wayne D

    2006-09-19

    F(1)-ATPase mutations in Escherichia coli that changed the strength of hydrogen bonds between the alpha and beta subunits in a location that links the catalytic site to the interface between the beta catch loop and the gamma subunit were examined. Loss of the ability to form the hydrogen bonds involving alphaS337, betaD301, and alphaD335 lowered the k(cat) of ATPase and decreased its susceptibility to Mg(2+)-ADP-AlF(n) inhibition, while mutations that maintain or strengthen these bonds increased the susceptibility to Mg(2+)-ADP-AlF(n) inhibition and lowered the k(cat) of ATPase. These data suggest that hydrogen bonds connecting alphaS337 to betaD301 and betaR323 and connecting alphaD335 to alphaS337 are important to transition state stabilization and catalytic function that may result from the proper alignment of catalytic site residues betaR182 and alphaR376 through the VISIT sequence (alpha344-348). Mutations betaD301E, betaR323K, and alphaR282Q changed the rate-limiting step of the reaction as determined by an isokinetic plot. Hydrophobic mutations of betaR323 decreased the susceptibility to Mg(2+)-ADP-AlF(n)() inhibition and lowered the number of interactions required in the rate-limiting step yet did not affect the k(cat) of ATPase, suggesting that betaR323 is important to transition state formation. The decreased rate of ATP synthase-dependent growth and decreased level of lactate-dependent quenching observed with alphaD335, betaD301, and alphaE283 mutations suggest that these residues may be important to the formation of an alternative set of hydrogen bonds at the interface of the alpha and beta subunits that permits the release of intersubunit bonds upon the binding of ATP, allowing gamma rotation in the escapement mechanism. PMID:16964980

  6. Flexible long-range loops in the VH gene region of the Igh locus facilitate the generation of a diverse antibody repertoire.

    PubMed

    Medvedovic, Jasna; Ebert, Anja; Tagoh, Hiromi; Tamir, Ido M; Schwickert, Tanja A; Novatchkova, Maria; Sun, Qiong; Huis In 't Veld, Pim J; Guo, Chunguang; Yoon, Hye Suk; Denizot, Yves; Holwerda, Sjoerd J B; de Laat, Wouter; Cogné, Michel; Shi, Yang; Alt, Frederick W; Busslinger, Meinrad

    2013-08-22

    The immunoglobulin heavy-chain (Igh) locus undergoes large-scale contraction in pro-B cells, which facilitates VH-DJH recombination by juxtaposing distal VH genes next to the DJH-rearranged gene segment in the 3' proximal Igh domain. By using high-resolution mapping of long-range interactions, we demonstrate that local interaction domains established the three-dimensional structure of the extended Igh locus in lymphoid progenitors. In pro-B cells, these local domains engaged in long-range interactions across the Igh locus, which depend on the regulators Pax5, YY1, and CTCF. The large VH gene cluster underwent flexible long-range interactions with the more rigidly structured proximal domain, which probably ensures similar participation of all VH genes in VH-DJH recombination to generate a diverse antibody repertoire. These long-range interactions appear to be an intrinsic feature of the VH gene cluster, because they are still generated upon mutation of the Eμ enhancer, IGCR1 insulator, or 3' regulatory region in the proximal Igh domain.

  7. Rogowski Loop design for NSTX

    SciTech Connect

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

    2000-01-06

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

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

    PubMed

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

    2009-01-16

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

  9. 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.

  10. 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.

  11. Modulation of HIV Protease Flexibility by the T80N Mutation

    PubMed Central

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

    2015-01-01

    The flexibility of HIV protease 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 scattering (WAXS) data was measured for a series of HIV protease 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 to 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, so as to alter the mobility of amino acids in the enzymatic core. These results support the contentions that significant protein flexibility extends throughout HIV protease and is critical to catalytic function. PMID:25488402

  12. 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.

  13. Catalytic autothermal reforming increases fuel cell flexibility

    SciTech Connect

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

    1981-12-01

    To give a better understanding of autothermal reforming (ATR), a process which offers an advantageous alternative to steam reforming for H/sub 2/ production for fuel cells because of the wider range of fuels which can be converted, the conversion of individual fuel components was studied. Attempts have been made to characterize the chemical reactions of light and heavy paraffins and aromatics in ATR. Results of studies to determine the effects of operating parameters on the carbon-forming tendency of each hydrocarbon type are reported. The catalyst used for the ATR process was three-layers of supported nickel catalysts, Norton NC-100 spheres in the top zone, cylindrical G-56B tablets in the bottom one, and either ICI 46-I or ICI 46-4 Raschig rings in the middle zone. A summary of the experimental studies of the ATR of n-hexane, n-tetradecane, benzene, and benzene solutions of naphthalene is presented. (BLM)

  14. Catalytic autothermal reforming increases fuel cell flexibility

    SciTech Connect

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

    1981-12-01

    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.

  15. Torque transmission mechanism via DELSEED loop of F1-ATPase.

    PubMed

    Watanabe, Rikiya; Koyasu, Kazuma; You, Huijuan; Tanigawara, Mizue; Noji, Hiroyuki

    2015-03-10

    F1-ATPase (F1) is an ATP-driven rotary motor in which the three catalytic β subunits in the stator ring sequentially induce the unidirectional rotation of the rotary γ subunit. Many lines of evidence have revealed open-to-closed conformational transitions in the β subunit that swing the C-terminal domain inward. This conformational transition causes a C-terminal protruding loop with conserved sequence DELSEED to push the γ subunit. Previous work, where all residues of DELSEED were substituted with glycine to disrupt the specific interaction with γ and introduce conformational flexibility, showed that F1 still rotated, but that the torque was halved, indicating a remarkable impact on torque transmission. In this study, we conducted a stall-and-release experiment on F1 with a glycine-substituted DELSEED loop to investigate the impact of the glycine substitution on torque transmission upon ATP binding and ATP hydrolysis. The mutant F1 showed a significantly reduced angle-dependent change in ATP affinity, whereas there was no change in the equilibrium for ATP hydrolysis. These findings indicate that the DELSEED loop is predominantly responsible for torque transmission upon ATP binding but not for that upon ATP hydrolysis.

  16. Torque Transmission Mechanism via DELSEED Loop of F1-ATPase

    PubMed Central

    Watanabe, Rikiya; Koyasu, Kazuma; You, Huijuan; Tanigawara, Mizue; Noji, Hiroyuki

    2015-01-01

    F1-ATPase (F1) is an ATP-driven rotary motor in which the three catalytic β subunits in the stator ring sequentially induce the unidirectional rotation of the rotary γ subunit. Many lines of evidence have revealed open-to-closed conformational transitions in the β subunit that swing the C-terminal domain inward. This conformational transition causes a C-terminal protruding loop with conserved sequence DELSEED to push the γ subunit. Previous work, where all residues of DELSEED were substituted with glycine to disrupt the specific interaction with γ and introduce conformational flexibility, showed that F1 still rotated, but that the torque was halved, indicating a remarkable impact on torque transmission. In this study, we conducted a stall-and-release experiment on F1 with a glycine-substituted DELSEED loop to investigate the impact of the glycine substitution on torque transmission upon ATP binding and ATP hydrolysis. The mutant F1 showed a significantly reduced angle-dependent change in ATP affinity, whereas there was no change in the equilibrium for ATP hydrolysis. These findings indicate that the DELSEED loop is predominantly responsible for torque transmission upon ATP binding but not for that upon ATP hydrolysis. PMID:25762326

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

    PubMed Central

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

    2015-01-01

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

  18. Three critical hydrogen bonds determine the catalytic activity of the Diels–Alderase ribozyme

    PubMed Central

    Kraut, Stefanie; Bebenroth, Dirk; Nierth, Alexander; Kobitski, Andrei Y.; Nienhaus, G. Ulrich; Jäschke, Andres

    2012-01-01

    Compared to protein enzymes, our knowledge about how RNA accelerates chemical reactions is rather limited. The crystal structures of a ribozyme that catalyzes Diels–Alder reactions suggest a rich tertiary architecture responsible for catalysis. In this study, we systematically probe the relevance of crystallographically observed ground-state interactions for catalytic function using atomic mutagenesis in combination with various analytical techniques. The largest energetic contribution apparently arises from the precise shape complementarity between transition state and catalytic pocket: A single point mutant that folds correctly into the tertiary structure but lacks one H-bond that normally stabilizes the pocket is completely inactive. In the rate-limiting chemical step, the dienophile is furthermore activated by two weak H-bonds that contribute ∼7–8 kJ/mol to transition state stabilization, as indicated by the 25-fold slower reaction rates of deletion mutants. These H-bonds are also responsible for the tight binding of the Diels–Alder product by the ribozyme that causes product inhibition. For high catalytic activity, the ribozyme requires a fine-tuned balance between rigidity and flexibility that is determined by the combined action of one inter-strand H-bond and one magnesium ion. A sharp 360° turn reminiscent of the T-loop motif observed in tRNA is found to be important for catalytic function. PMID:21976731

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

    PubMed Central

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

    2001-01-01

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

  20. 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.

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

    PubMed

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

    2016-06-28

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

  2. Conformation-selective inhibitors reveal differences in the activation and phosphate-binding loops of the tyrosine kinases Abl and Src.

    PubMed

    Hari, Sanjay B; Perera, B Gayani K; Ranjitkar, Pratistha; Seeliger, Markus A; Maly, Dustin J

    2013-12-20

    Over the past decade, an increasingly diverse array of potent and selective inhibitors that target the ATP-binding sites of protein kinases have been developed. Many of these inhibitors, like the clinically approved drug imatinib (Gleevec), stabilize a specific catalytically inactive ATP-binding site conformation of their kinases targets. Imatinib is notable in that it is highly selective for its kinase target, Abl, over other closely related tyrosine kinases, such as Src. In addition, imatinib is highly sensitive to the phosphorylation state of Abl's activation loop, which is believed to be a general characteristic of all inhibitors that stabilize a similar inactive ATP-binding site conformation. In this report, we perform a systematic analysis of a diverse series of ATP-competitive inhibitors that stabilize a similar inactive ATP-binding site conformation as imatinib with the tyrosine kinases Src and Abl. In contrast to imatinib, many of these inhibitors have very similar potencies against Src and Abl. Furthermore, only a subset of this class of inhibitors is sensitive to the phosphorylation state of the activation loop of these kinases. In attempting to explain this observation, we have uncovered an unexpected correlation between Abl's activation loop and another flexible active site feature, called the phosphate-binding loop (p-loop). These studies shed light on how imatinib is able to obtain its high target selectivity and reveal how the conformational preference of flexible active site regions can vary between closely related kinases.

  3. 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.

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

    PubMed

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

    2013-02-01

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

  5. Exploring the conformational diversity of loops on conserved frameworks.

    PubMed

    Li, W; Liang, S; Wang, R; Lai, L; Han, Y

    1999-12-01

    Loops are structurally variable regions, but the secondary structural elements bracing loops are often conserved. Motifs with similar secondary structures exist in the same and different protein families. In this study, we made an all-PDB-based analysis and produced 495 motif families accessible from the Internet. Every motif family contains some variable loops spanning a common framework (a pair of secondary structures). The diversity of loops and the convergence of frameworks were examined. In addition, we also identified 119 loops with conformational changes in different PDB files. These materials can give some directions for functional loop design and flexible docking. PMID:10611401

  6. Flexible Scheduling.

    ERIC Educational Resources Information Center

    Davis, Harold S.; Bechard, Joseph E.

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

  7. Flexibility Program

    ERIC Educational Resources Information Center

    Connors, G. Patrick

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

  8. 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.

  9. Structure of the catalytic domain of the Clostridium thermocellum cellulase CelT.

    PubMed

    Kesavulu, Muppuru M; Tsai, Jia Yin; Lee, Hsiao Lin; Liang, Po Huang; Hsiao, Chwan Deng

    2012-03-01

    Cellulases hydrolyze cellulose, a major component of plant cell walls, to oligosaccharides and monosaccharides. Several Clostridium species secrete multi-enzyme complexes (cellulosomes) containing cellulases. C. thermocellum CelT, a family 9 cellulase, lacks the accessory module(s) necessary for activity, unlike most other family 9 cellulases. Therefore, characterization of the CelT structure is essential in order to understand its catalytic mechanism. Here, the crystal structure of free CelTΔdoc, the catalytic domain of CelT, is reported at 2.1 Å resolution. Its structure differs in several aspects from those of other family 9 cellulases. CelTΔdoc contains an additional α-helix, α-helices of increased length and two additional surface-exposed β-strands. It also contains three calcium ions instead of one as found in C. cellulolyticum Cel9M. CelTΔdoc also has two flexible loops at the open end of its active-site cleft. Movement of these loops probably allows the substrate to access the active site. CelT is stable over a wide range of pH and temperature conditions, suggesting that CelT could be used to convert cellulose biomass into biofuel.

  10. 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.

  11. Rollercoaster loop shapes

    NASA Astrophysics Data System (ADS)

    Pendrill, Ann-Marie

    2005-11-01

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

  12. 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.

  13. Water Stream "Loop-the-Loop"

    ERIC Educational Resources Information Center

    Jefimenko, Oleg

    1974-01-01

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

  14. 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.

  15. 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.

  16. Common hardware-in-the-loop development

    NASA Astrophysics Data System (ADS)

    Kim, Hajin J.; Moss, Stephen G.

    2010-04-01

    An approach to streamline the Hardware-In-the-Loop (HWIL) simulation development process is under evaluation. This Common HWIL technique will attempt to provide a more flexible, scalable system. The overall goal of the Common HWIL system will be to reduce cost by minimizing redundant development, operational labor and equipment expense. This paper will present current results and future plans of the development.

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

    PubMed

    Del Campo, Mark; Ofengand, James; Malhotra, Arun

    2004-02-01

    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 A 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 beta-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.

  18. Closed-Loop Neuromorphic Benchmarks.

    PubMed

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

    2015-01-01

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

  19. 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

  20. Look before You Loop.

    ERIC Educational Resources Information Center

    Bellis, Marilyn

    1999-01-01

    Explores looping, which involves one teacher staying with the same group of children for more than one year. Recognizes that, with today's changing demographics, looping can be a way to foster a family-like classroom atmosphere. Discusses advantages and disadvantages to looping. Includes a chart of looping opportunities and considerations;…

  1. 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.

  2. OPE for super loops

    NASA Astrophysics Data System (ADS)

    Sever, Amit; Vieira, Pedro; Wang, Tianheng

    2011-11-01

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

  3. The preprocessed doacross loop

    NASA Technical Reports Server (NTRS)

    Saltz, Joel H.; Mirchandaney, Ravi

    1990-01-01

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

  4. Asymmetric Flexible Supercapacitor Stack

    PubMed Central

    2008-01-01

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

  5. 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

  6. Switchable catalytic DNA catenanes.

    PubMed

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

    2015-03-11

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

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

    PubMed

    Taylor, John C; Markham, George D

    2003-07-15

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

  8. 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.

  9. 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.

  10. Rapid Deployment of Rich Catalytic Combustion

    SciTech Connect

    Richard S. Tuthill

    2004-06-10

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

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

    PubMed

    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.

  12. 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

  13. 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)

  14. Modification of residue 42 of the active site loop with a lysine-mimetic side chain rescues isochorismate-pyruvate lyase activity in Pseudomonas aeruginosa PchB.

    PubMed

    Olucha, José; Meneely, Kathleen M; Lamb, Audrey L

    2012-09-25

    PchB is an isochorismate-pyruvate lyase from Pseudomonas aeruginosa. A positively charged lysine residue is located in a flexible loop that behaves as a lid to the active site, and the lysine residue is required for efficient production of salicylate. A variant of PchB that lacks the lysine at residue 42 has a reduced catalytic free energy of activation of up to 4.4 kcal/mol. Construction of a lysine isosteric residue bearing a positive charge at the appropriate position leads to the recovery of 2.5-2.7 kcal/mol (about 60%) of the 4.4 kcal/mol by chemical rescue. Exogenous addition of ethylamine to the K42A variant leads to a neglible recovery of activity (0.180 kcal/mol, roughly 7% rescue), whereas addition of propylamine caused an additional modest loss in catalytic power (0.056 kcal/mol, or 2% loss). This is consistent with the view that (a) the lysine-42 residue is required in a specific conformation to stabilize the transition state and (b) the correct conformation is achieved for a lysine-mimetic side chain at site 42 in the course of loop closure, as expected for transition-state stabilization by the side chain ammonio function. That the positive charge is the main effector of transition state stabilization is shown by the construction of a lysine-isosteric residue capable of exerting steric effects and hydrogen bonding but not electrostatic effects, leading to a modest increase of catalytic power (0.267-0.505 kcal/mol of catalytic free energy, or roughly 6-11% rescue). PMID:22970849

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

    PubMed

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

    2014-07-29

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

  16. 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.

  17. 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.

  18. 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

  19. Multilayer coatings on flexible substrates

    SciTech Connect

    Martin, P.M.; Affinito, J.D.; Gross, M.E.; Coronado, C.A.; Bennett, W.D.; Stewart, D.C.

    1995-04-01

    Thin-film optical and non-optical multilayer coatings are deposited onto flexible substrates using a vacuum web coater developed at Pacific Northwest Laboratory. The coater`s primary application is rapid prototyping of multilayer (1) polymer coatings, (2) polymer/metal coatings, (3) ceramic/metal coatings, and (4) hybrid polymer, ceramic, and metal coatings. The coater is fully automated and incorporates polymer evaporation and extrusion heads, high-rate magnetron sputtering cathodes, and e-beam evaporation sources. Polymer electrolytes are deposited by extrusion techniques. Flexible plastic, metal, and ceramic substrates can be coated using roll-to-roll or closed-loop configurations. Examples of multilayer optical coatings demonstrated to date are solar reflectors, heat mirrors, Fabry-Perot filters, and alpha particle sensors. Nonoptical coatings include multilayer magnetic metal/ceramic and lamellar composites.

  20. Loop contributions to the folding thermodynamics of DNA straight hairpin loops and pseudoknots.

    PubMed

    Reiling, Calliste; Khutsishvili, Irine; Huang, Kai; Marky, Luis A

    2015-02-01

    Pseudoknots have diverse and important roles in many biological functions. We used a combination of UV spectroscopy and differential scanning calorimetry to investigate the effect of the loop length on the unfolding thermodynamics of three sets of DNA stem-loop motifs with the following sequences: (a) d(GCGCTnGCGC), where n = 3, 5, 7, 9; (b) d(CGCGCGT4GAAATTCGCGCGTnAATTTC), where n = 4, 6, and 8; and (c) d(TCTCTTnAAAAAAAAGAGAT5TTTTTTT), where n = 5, 7, 9, and 11. The increase in loop length of the first set of hairpins yielded decreasing TM's and constant unfolding enthalpies, resulting in an entropy driven decrease in the stability of the hairpin (ΔG° = -7.5 to -6.1 kcal/mol). In the second set, the increase in the length of the loops yielded similar TM's and slight increases in the unfolding enthalpies. This translated into more stable pseudoknots with an increasing ΔG° from -13.2 to -17.1 kcal/mol. This effect can be rationalized in terms of the increased flexibility of the pseudoknot with larger loops optimizing base-pair stacking interactions. In the last set of molecules, the increase in the length of one of the loops yielded an increase in the TM's and larger increases in the enthalpies, which stabilize the pseudoknot significantly increasing the ΔG° from -8.5 to -16.6 kcal/mol. In this set, the thymine loop is complementary to the stem of A·T base pairs and the longer loops are able to form T*A·T base triplets due to the partial folding of the thymine loop into the ceiling of the major groove of the duplex, thus yielding a net formation of 1-3 T*AT/T*AT base-triplet stacks at the middle of its stem, depending on the loop length. PMID:25584896

  1. 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.

  2. 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.

  3. 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.

  4. Structural backgrounds for the formation of a catalytically competent complex with NADP(H) during hydride transfer in ferredoxin-NADP(+) reductases.

    PubMed

    Sánchez-Azqueta, Ana; Musumeci, Matías A; Martínez-Júlvez, Marta; Ceccarelli, Eduardo A; Medina, Milagros

    2012-07-01

    The role of the highly conserved C266 and L268 of pea ferredoxin-NADP(+) reductase (FNR) in formation of the catalytically competent complex of the enzyme with NADP(H) was investigated. Previous studies suggest that the volume of these side-chains, situated facing the side of the C-terminal Y308 catalytic residue not stacking the flavin isoalloxazine ring, may be directly involved in the fine-tuning of the catalytic efficiency of the enzyme. Wild-type pea FNR as well as single and double mutants of C266 and L268 residues were analysed by fast transient-kinetic techniques and their midpoint reduction potentials were determined. For the C266A, C266M and C266A/L268A mutants a significant reduction in the overall hydride transfer (HT) rates was observed along with the absence of charge-transfer complex formation. The HT rate constants for NADPH oxidation were lower than those for NADP(+) reduction, reaching a 30-fold decrease in the double mutant. In agreement, these variants exhibited more negative midpoint potentials with respect to the wild-type enzyme. The three-dimensional structures of C266M and L268V variants were solved. The C266M mutant shows a displacement of E306 away from the relevant residue S90 to accommodate the bulky methionine introduced. The overall findings indicate that in FNR the volume of the residue at position 266 is essential to attain the catalytic architecture between the nicotinamide and isoalloxazine rings at the active site and, therefore, for an efficient HT process. In addition, flexibility of the 268-270 loop appears to be critical for FNR to achieve catalytically competent complexes with NADP(H).

  5. A fast loop-closure algorithm to accelerate residue matching in computational enzyme design.

    PubMed

    Xue, Jing; Huang, Xiaoqiang; Lin, Min; Zhu, Yushan

    2016-02-01

    Constructing an active site on an inert scaffold is still a challenge in chemical biology. Herein, we describe the incorporation of a Newton-direction-based fast loop-closure algorithm for catalytic residue matching into our enzyme design program ProdaMatch. This was developed to determine the sites and geometries of the catalytic residues as well as the position of the transition state with high accuracy in order to satisfy the geometric constraints on the interactions between catalytic residues and the transition state. Loop-closure results for 64,827 initial loops derived from 21 loops in the test set showed that 99.51% of the initial loops closed to within 0.05 Å in fewer than 400 iteration steps, while the large majority of the initial loops closed within 100 iteration steps. The revised version of ProdaMatch containing the novel loop-closure algorithm identified all native matches for ten scaffolds in the native active-site recapitulation test. Its high speed and accuracy when matching catalytic residues with a scaffold make this version of ProdaMatch potentially useful for scaffold selection through the incorporation of more complex theoretical enzyme models which may yield higher initial activities in de novo enzyme design.

  6. 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.

  7. The evolution of catalytic function

    NASA Astrophysics Data System (ADS)

    Maurel, Marie-Christine; Ricard, Jacques

    2006-03-01

    It is very likely that the main driving force of enzyme evolution is the requirement to improve catalytic and regulatory efficiency which results from the intrinsic performance as well as from the spatial and functional organization of enzymes in living cells. Kinetic co-operativity may occur in simple monomeric proteins if they display “slow” conformational transitions, at the cost of catalytic efficiency. Oligomeric enzymes on the other hand can be both efficient and co-operative. We speculate that the main reason for the emergence of co-operative oligomeric enzymes is the need for catalysts that are both cooperative and efficient. As it is not useful for an enzyme to respond to a change of substrate concentration in a complex kinetic way, the emergence of symmetry has its probable origin in a requirement for “functional simplicity”. In a living cell, enzyme are associated with other macromolecules and membranes. The fine tuning of their activity may also be reached through mutations of the microenvironment. Our hypothesis is that these mutations are related to the vectorial transport of molecules, to achieve the hysteresis loops of enzyme reactions generated by the coupling of reaction and diffusion, through the co-operativity brought about by electric interactions between a charged substrate and a membrane, and last but not least, through oscillations. As the physical origins of these effects are very simple and do not require complex molecular devices, it is very likely that the functional advantage generated by the spatial and functional organization of enzyme molecules within the cell have appeared in prebiotic catalysis or very early during the primeval stages of biological evolution. We shall began this paper by presenting the nature of the probable earliest catalysts in the RNA world.

  8. The importance of slow motions for protein functional loops

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

    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 (Cα 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Protein flexibility predictions using graph theory.

    PubMed

    Jacobs, D J; Rader, A J; Kuhn, L A; Thorpe, M F

    2001-08-01

    Techniques from graph theory are applied to analyze the bond networks in proteins and identify the flexible and rigid regions. The bond network consists of distance constraints defined by the covalent and hydrogen bonds and salt bridges in the protein, identified by geometric and energetic criteria. We use an algorithm that counts the degrees of freedom within this constraint network and that identifies all the rigid and flexible substructures in the protein, including overconstrained regions (with more crosslinking bonds than are needed to rigidify the region) and underconstrained or flexible regions, in which dihedral bond rotations can occur. The number of extra constraints or remaining degrees of bond-rotational freedom within a substructure quantifies its relative rigidity/flexibility and provides a flexibility index for each bond in the structure. This novel computational procedure, first used in the analysis of glassy materials, is approximately a million times faster than molecular dynamics simulations and captures the essential conformational flexibility of the protein main and side-chains from analysis of a single, static three-dimensional structure. This approach is demonstrated by comparison with experimental measures of flexibility for three proteins in which hinge and loop motion are essential for biological function: HIV protease, adenylate kinase, and dihydrofolate reductase.

  15. 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.

  16. Fault Accommodation in Control of Flexible Systems

    NASA Technical Reports Server (NTRS)

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

    1998-01-01

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

  17. 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.

  18. 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.

  19. 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.

  20. Thermal power loops

    NASA Technical Reports Server (NTRS)

    Gottschlich, Joseph M.; Richter, Robert

    1991-01-01

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

  1. 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.

  2. 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.

  3. Natively Unstructured Loops Differ from Other Loops

    PubMed Central

    Schlessinger, Avner; Liu, Jinfeng; Rost, Burkhard

    2007-01-01

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

  4. Natively unstructured loops differ from other loops.

    PubMed

    Schlessinger, Avner; Liu, Jinfeng; Rost, Burkhard

    2007-07-01

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

  5. 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.

  6. Catalytic combustion over hexaaluminates

    SciTech Connect

    Ramesh, K.S.; Kingsley, J.J.; Hubler, T.L.; McCready, D.E.; Cox, J.L.

    1997-12-31

    Combustion is the oldest and most extensively used process for the production of light, heat, and energy utilization. Mankind has sought to control combustion since prehistoric times to more effectively utilize the combustible material, control the products of combustion, and harness the energy released during combustion. Catalysts provide the means to control the reactions of combustion beyond what can be achieved in the homogeneous gas phase (1). Catalysts also enable operation outside the range of flammability limits and control atmospheric pollutants of combustion, mainly NO{sub x}, carbon monoxide, and particles of incomplete combustion (soot). The major technical difficulty that has hindered widespread application of catalytic combustion devices is their poor performance, particularly durability of their ceramic substrates and catalytically active phases in the high temperature environment. Catalytic combustion of hydrocarbons over metals and metal oxide catalysts has been explored extensively. Recent reviews of materials for high temperature catalytic combustion have been provided by Marcus et al. (2) and Trim (3). Hexaaluminates which show good thermal stability above 1200{degrees}C are one class of metal oxides receiving consideration for application in high temperature combustion devices. Matsuda et al. (4) have developed thermally stable La-hexaaluminates with the same layer structure as Ba-hexaaluminate and have investigated their catalytic application. Machida et al. (5-7) have investigated the catalytic properties of a number of hexaaluminates of BaMAl{sub 11}O{sub 19-{alpha}}(M=Cr, Mn,Fe,Co,Ni). Here we report the synthesis, properties and catalytic combustion of some new hexaaluminates.

  7. Blind loop syndrome

    MedlinePlus

    ... operations for extreme obesity As a complication of inflammatory bowel disease Diseases such as diabetes or scleroderma may slow down movement in a segment of the intestine, leading to blind loop syndrome.

  8. Rapid common hardware-in-the-loop development

    NASA Astrophysics Data System (ADS)

    Kim, Hajin J.; Moss, Stephen G.; Billings, Roger; Naumann, Charles B.

    2011-06-01

    An approach to streamline the Hardware-In-the-Loop (HWIL) simulation development process is under development. This Common HWIL technique will attempt to provide a more flexible, scalable system. The overall goal of the Common HWIL system will be to reduce communication latencies, minimize redundant development, operational labor and equipment expense. This paper will present current status and test results.

  9. Choking loops on surfaces.

    PubMed

    Feng, Xin; Tong, Yiying

    2013-08-01

    We present a method for computing "choking" loops--a set of surface loops that describe the narrowing of the volumes inside/outside of the surface and extend the notion of surface homology and homotopy loops. The intuition behind their definition is that a choking loop represents the region where an offset of the original surface would get pinched. Our generalized loops naturally include the usual 2g handles/tunnels computed based on the topology of the genus-g surface, but also include loops that identify chokepoints or bottlenecks, i.e., boundaries of small membranes separating the inside or outside volume of the surface into disconnected regions. Our definition is based on persistent homology theory, which gives a measure to topological structures, thus providing resilience to noise and a well-defined way to determine topological feature size. More precisely, the persistence computed here is based on the lower star filtration of the interior or exterior 3D domain with the distance field to the surface being the associated 3D Morse function. PMID:23744260

  10. 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

  11. 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.

  12. 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.

  13. Catalytic coherence transformations

    NASA Astrophysics Data System (ADS)

    Bu, Kaifeng; Singh, Uttam; Wu, Junde

    2016-04-01

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

  14. Closed Loop System Identification with Genetic Algorithms

    NASA Technical Reports Server (NTRS)

    Whorton, Mark S.

    2004-01-01

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

  15. Functional Loop Dynamics of the Streptavidin-Biotin Complex

    PubMed Central

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

    2015-01-01

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

  16. Control-structure interaction in precision pointing servo loops

    NASA Technical Reports Server (NTRS)

    Spanos, John T.

    1989-01-01

    The control-structure interaction problem is addressed via stability analysis of a generic linear servo loop model. With the plant described by the rigid body mode and a single elastic mode, structural flexibility is categorized into one of three types: (1) appendage, (2) in-the-loop minimum phase, and (3) in-the-loop nonminimum phase. Closing the loop with proportional-derivative (PD) control action and introducing sensor roll-off dynamics in the feedback path, stability conditions are obtained. Trade studies are conducted with modal frequency, modal participation, modal damping, loop bandwidth, and sensor bandwidth treated as free parameters. Results indicate that appendage modes are most likely to produce instability if they are near the sensor rolloff, whereas in-the-loop modes are most dangerous near the loop bandwidth. The main goal of this paper is to provide a fundamental understanding of the control-structure interaction problem so that it may benefit the design of complex spacecraft and pointing system servo loops. In this framework, the JPL Pathfinder gimbal pointer is considered as an example.

  17. 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.

  18. 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.

  19. 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.

  20. Fluid catalytic cracking

    SciTech Connect

    Bartley, B.H.; Petty, R.H.

    1982-08-17

    Gaseous sulfur compounds are removed from a sulfur-containing gas mixture by reacting sulfur oxides in the gas mixture with alumina in association with bismuth. The process is particularly useful in fluid catalytic cracking of sulfur-containing petroleum charge stocks wherein sulfur is contained in coke deposited on the fluidized cracking catalyst. By the process of this invention, sulfur oxides may be removed from regenerator off-gases from a fluidized catalytic cracking unit by incorporating particulate alumina impregnated with bismuth in particulate cracking catalyst whereby sulfur oxides generated in the regeneration of the catalyst are reacted with bismuth-impregnated alumina. Sulfur oxides produced during regeneration of the catalyst by burning the coke with air are captured and converted to hydrogen sulfide in the cracking reactor. The hydrogen sulfide so produced is readily separated from petroleum products of the catalytic cracking reaction process.

  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. 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.

  3. Fluid catalytic cracking

    SciTech Connect

    Petty, R.H.; Bartley, B.H.

    1984-05-01

    A fluid catalytic cracking process is disclosed for sulfur-containing petroleum charge stocks. Sulfur contained in coke deposited on the fluidized cracking catalyst in the reactor is converted to sulfur oxides in the regenerator and removed from regenerator off-gases by incorporating a composite of alumina and bismuth oxides in a particulate cracking catalyst. Sulfur oxides produced during regeneration of the catalyst by burning the coke with air in the regenerator are captured by the alumina-bismuth oxides composite and converted to hydrogen sulfide in the cracking reactor. The hydrogen sulfide so produced is readily separated from petroleum products of the catalytic cracking reaction process.

  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. Common hardware-in-the-loop development

    NASA Astrophysics Data System (ADS)

    Kim, Hajin J.; Moss, Stephen G.

    2009-05-01

    An approach to streamline the Hardware-In-the-Loop (HWIL) simulation development process is under evaluation. With increased microprocessor speed, FPGA capacity and increased bus bandwidth over the last decade, a common interface design may be able to support a large number of HWIL interfaces that were previously custom designed interfaces. The Common HWIL approach will attempt to provide a more flexible, scalable system. The overall goal of the Common HWIL system will be to reduce cost by minimizing redundant development and operational labor and equipment expenses. This paper will present current results and future plans of the development.

  6. High heat flux loop heat pipes

    NASA Technical Reports Server (NTRS)

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

    1997-01-01

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

  7. 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.

  8. 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.

  9. 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

  10. Catalytic efficiency of designed catalytic proteins.

    PubMed

    Korendovych, Ivan V; DeGrado, William F

    2014-08-01

    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.

  11. Structural Studies of Yeast Δ1-Pyrroline-5-carboxylate Dehydrogenase (ALDH4A1): Active Site Flexibility and Oligomeric State

    PubMed Central

    2015-01-01

    The proline catabolic enzyme Δ1-pyrroline-5-carboxylate dehydrogenase (ALDH4A1) catalyzes the NAD+-dependent oxidation of γ-glutamate semialdehyde to l-glutamate. In Saccharomyces cerevisiae, ALDH4A1 is encoded by the PUT2 gene and known as Put2p. Here we report the steady-state kinetic parameters of the purified recombinant enzyme, two crystal structures of Put2p, and the determination of the oligomeric state and quaternary structure from small-angle X-ray scattering and sedimentation velocity. Using Δ1-pyrroline-5-carboxylate as the substrate, catalytic parameters kcat and Km were determined to be 1.5 s–1 and 104 μM, respectively, with a catalytic efficiency of 14000 M–1 s–1. Although Put2p exhibits the expected aldehyde dehydrogenase superfamily fold, a large portion of the active site is disordered in the crystal structure. Electron density for the 23-residue aldehyde substrate-binding loop is absent, implying substantial conformational flexibility in solution. We furthermore report a new crystal form of human ALDH4A1 (42% identical to Put2p) that also shows disorder in this loop. The crystal structures provide evidence of multiple active site conformations in the substrate-free form of the enzyme, which is consistent with a conformational selection mechanism of substrate binding. We also show that Put2p forms a trimer-of-dimers hexamer in solution. This result is unexpected because human ALDH4A1 is dimeric, whereas some bacterial ALDH4A1s are hexameric. Thus, global sequence identity and domain of life are poor predictors of the oligomeric states of ALDH4A1. Mutation of a single Trp residue that forms knob-in-hole interactions across the dimer–dimer interface abrogates hexamer formation, suggesting that this residue is the center of a protein–protein association hot spot. PMID:24502590

  12. 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.

  13. The Anderson Current Loop

    NASA Technical Reports Server (NTRS)

    Anderson, Karl F.

    1994-01-01

    Four-wire-probe concept applied to electrical-resistance transducers. Anderson current loop is excitation-and-signal-conditioning circuit suitable for use with strain gauges, resistance thermometers, and other electrical-resistance transducers mounted in harsh environments. Used as alternative to Wheatstone bridge. Simplifies signal-conditioning problem, enabling precise measurement of small changes in resistance of transducer. Eliminates some uncertainties in Wheatstone-bridge resistance-change measurements in flight research. Current loop configuration makes effects of lead-wire and contact resistances insignificantly small. Also provides output voltage that varies linearly with change in gauge resistance, and does so at double sensitivity of Wheatstone bridge.

  14. 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.

  15. Loop quantum gravity

    NASA Astrophysics Data System (ADS)

    Chiou, Dah-Wei

    2015-12-01

    This paper presents an "in-a-nutshell" yet self-contained introductory review on loop quantum gravity (LQG) — a background-independent, nonperturbative approach to a consistent quantum theory of gravity. Instead of rigorous and systematic derivations, it aims to provide a general picture of LQG, placing emphasis on the fundamental ideas and their significance. The canonical formulation of LQG, as the central topic of the paper, is presented in a logically orderly fashion with moderate details, while the spin foam theory, black hole thermodynamics, and loop quantum cosmology are covered briefly. Current directions and open issues are also summarized.

  16. Livermore Compiler Analysis Loop Suite

    2013-03-01

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

  17. 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.

  18. 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.

  19. Sequence dependence of transcription factor-mediated DNA looping

    PubMed Central

    Johnson, Stephanie; Lindén, Martin; Phillips, Rob

    2012-01-01

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

  20. A graphene-based smart catalytic system with superior catalytic performances and temperature responsive catalytic behaviors.

    PubMed

    Qi, Junjie; Lv, Weipeng; Zhang, Guanghui; Li, Yang; Zhang, Guoliang; Zhang, Fengbao; Fan, Xiaobin

    2013-07-21

    We have successfully developed a unique graphene-based smart catalytic system which consists of the graphene supported Au-Pt bimetallic nanocatalyst with a well-defined core-shell structure and a dextran-based temperature-responsive polymer. The unique catalytic system possesses excellent catalytic performances and the catalytic activities could be readily switched on or off at different temperature windows. PMID:23740038

  1. 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)…

  2. Loop Quantum Gravity

    NASA Astrophysics Data System (ADS)

    Piguet, O.

    2014-09-01

    In this talk, I give a short general introduction to Loop Quantum Gravity (LQG), beginning with some motivations for quantizing General Relativity, listing various attempts and then focusing on the case of LQG. Work supported in part by the Conselho Nacional de Desenvolvimento Científico e Tecnológico - CNPq (Brazil).

  3. 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.

  4. 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.

  5. A Looping Journey.

    ERIC Educational Resources Information Center

    Chapman, Janet

    1999-01-01

    Recounts a teacher's experiences staying with the same group of children for more than one year (looping) as they progress through kindergarten and first grade. Discusses advantages of more stability and less trauma for the child, and more instructional time and less stress for the teacher. Addresses possible disadvantages of children having…

  6. Enzyme Selectivity Fine-Tuned through Dynamic Control of a Loop.

    PubMed

    Vögeli, Beat; Bibow, Stefan; Chi, Celestine N

    2016-02-24

    Allostery has been revealed as an essential property of all proteins. For enzymes, shifting of the structural equilibrium distribution at one site can have substantial impacts on protein dynamics and selectivity. Promising sites of remotely shifting such a distribution by changing the dynamics would be at flexible loops because relatively large changes may be achieved with minimal modification of the protein. A ligand-selective change of binding affinity to the active site of cyclophilin is presented involving tuning of the dynamics of a highly flexible loop. Binding affinity is increased upon substitution of double Gly to Ala at the hinge regions of the loop. Quenching of the motional amplitudes of the loop slightly rearranges the active site. In particular, key residues for binding Phe60 and His126 adopt a more fixed orientation in the bound protein. Our system may serve as a model system for studying the effects of various time scales of loop motion on protein function tuned by mutations.

  7. 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.

  8. 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.

  9. Catalytic, hollow, refractory spheres

    NASA Technical Reports Server (NTRS)

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

    1987-01-01

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

  10. 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

  11. 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.

  12. Tunable microwave metamaterial absorbers using varactor-loaded split loops

    NASA Astrophysics Data System (ADS)

    Zhu, Jinfeng; Li, Delong; Yan, Shuang; Cai, Yijun; Huo Liu, Qing; Lin, Timothy

    2015-12-01

    Currently, implementation of active circuit elements within metamaterials is an effective way to make them electrically tunable. We combine varactors with split copper loops in a metamaterial absorber in order to obtain an electrically tunable microwave response. This absorber has a compact planar structure and a simplified back feeding network. Flexible frequency tunability of the microwave reflection in the range of 5-6 GHz is experimentally achieved. The design, simulation, and experimental results are systematically presented. The proposed method is scalable for developing active metamaterial absorbers based on metal loops, and shows a promising potential of active metamaterial absorbers for extensive microwave applications.

  13. Inner mappings of Bruck loops

    NASA Astrophysics Data System (ADS)

    Kreuzer, Alexander

    1998-01-01

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

  14. 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.

  15. 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.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-07-01

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

  18. Closed-loop anesthesia.

    PubMed

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

    2016-05-01

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

  19. Determinants of RNA hairpin loop-loop complex stability.

    PubMed

    Gregorian, R S; Crothers, D M

    1995-05-19

    Complexes formed by RNA hairpin loops with complementary loop sequences derived from Escherichia coli RNA I and RNA II, which are involved in the control of DNA replication of plasmid ColE1, have been analyzed to determine the sequence and structural elements required to achieve full affinity. Of particular interest is the origin of the enhanced stability of the complex formed by hairpin loops whose loop sequences have been inverted 5' to 3' with respect to wild-type sequences. Full complementarity of the two interacting loops is required to achieve full or enhanced affinity, while the stems of the two hairpins can differ. The major determinant of enhanced affinity lies in the base-pairs formed at positions 1 and 7 of the loops, together with the two base-pairs of each stem which are closest to the loop. Sequence variation in the middle of the loops, or further down the stem away from the loops, exerts only a modest influence on complex stability. We incorporate these results into a model for the loop-loop interaction which accounts for the importance of positions one and seven and the first two nucleotides of the stem, while providing potentially unique structures for recognition by the RNA one modulator protein. PMID:7539081

  20. Determinants of RNA hairpin loop-loop complex stability.

    PubMed

    Gregorian, R S; Crothers, D M

    1995-05-19

    Complexes formed by RNA hairpin loops with complementary loop sequences derived from Escherichia coli RNA I and RNA II, which are involved in the control of DNA replication of plasmid ColE1, have been analyzed to determine the sequence and structural elements required to achieve full affinity. Of particular interest is the origin of the enhanced stability of the complex formed by hairpin loops whose loop sequences have been inverted 5' to 3' with respect to wild-type sequences. Full complementarity of the two interacting loops is required to achieve full or enhanced affinity, while the stems of the two hairpins can differ. The major determinant of enhanced affinity lies in the base-pairs formed at positions 1 and 7 of the loops, together with the two base-pairs of each stem which are closest to the loop. Sequence variation in the middle of the loops, or further down the stem away from the loops, exerts only a modest influence on complex stability. We incorporate these results into a model for the loop-loop interaction which accounts for the importance of positions one and seven and the first two nucleotides of the stem, while providing potentially unique structures for recognition by the RNA one modulator protein.

  1. 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).

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

    PubMed Central

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

    2014-01-01

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

  3. Creating stable stem regions for loop elongation in Fcabs - insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations.

    PubMed

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

    2014-09-01

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

  4. 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.

  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. 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…

  7. Flexibility, Is That All?

    ERIC Educational Resources Information Center

    Renes, Wim M.

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

  8. Flexible Learning Opportunities.

    ERIC Educational Resources Information Center

    Further Education Unit, London (England).

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

  9. 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.

  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. 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

  12. Catalytic reforming methods

    DOEpatents

    Tadd, Andrew R; Schwank, Johannes

    2013-05-14

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

  13. Control of nonlinear flexible space structures

    NASA Astrophysics Data System (ADS)

    Shi, Jianjun

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

  14. 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.

  15. 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.

  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. Painful Flexible Flatfoot.

    PubMed

    Sheikh Taha, Abdel Majid; Feldman, David S

    2015-12-01

    Flatfoot is commonly encountered by pediatric orthopedic surgeons and pediatricians. A paucity of literature exists on how to define a flatfoot. The absence of the medial arch with a valgus hindfoot is the hallmark of this pathology. Flatfoot can be flexible or rigid. This review focuses on the diagnosis and treatment of the flexible flatfoot. Most flatfeet are flexible and clinically asymptomatic, and warrant little intervention. If feet are symptomatic, treatment is needed. Most patients who require treatment improve with foot orthotics and exercises. Only feet resistant to conservative modalities are deemed surgical candidates. The presence of a tight heel cord is often found in patients who fail conservative management.

  18. 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.

  19. Two loop divergences studied with one loop constrained differential renormalization

    SciTech Connect

    Seijas, Cesar . E-mail: cesar@fpaxp1.usc.es

    2007-08-15

    In the context of differential renormalization, using constrained differential renormalization rules at one-loop, we show how to obtain concrete results in two-loop calculations without making use of Ward identities. In order to do that, we obtain a list of integrals with overlapping divergences compatible with CDR that can be applied to various two-loop background field calculations. As an example, we obtain the two-loop coefficient of the beta function of QED, SuperQED and Yang-Mills theory.

  20. Accelerating the loop expansion

    SciTech Connect

    Ingermanson, R.

    1986-07-29

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

  1. 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.

  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. Technical Institute Stresses Flexibility

    ERIC Educational Resources Information Center

    Industrial Education, 1976

    1976-01-01

    At the Waukesha County Technical Institute in Wisconsin students benefit from individualized instruction and open entry/open exit system. The key to this flexibility is a series of audio-visual modules to support lecture presentations and demonstrations. (HD)

  4. 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.

  5. ``OPTICAL Catalytic Nanomotors''

    NASA Astrophysics Data System (ADS)

    Rosary-Oyong, Se, Glory

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

  6. 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.

  7. Catalytic hollow spheres

    NASA Technical Reports Server (NTRS)

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

    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.

  8. 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

  9. 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.

  10. 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,…

  11. Unsteady catalytic processes and sorption-catalytic technologies

    NASA Astrophysics Data System (ADS)

    Zagoruiko, A. N.

    2007-07-01

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

  12. Role of the omega loop in specificity determination in subsite 2 of the D-alanine:D-alanine (D-lactate) ligase from Leuconostoc mesenteroides: a molecular docking study.

    PubMed

    Neuhaus, Francis C

    2011-09-01

    The synthesis of D-ala-D-lactate in Leuconostoc mesenteroides is catalyzed by D-alanine:D-alanine (D-lactate) ligase (ADP). The ability to assemble this depsipeptide as well as D-ala-D-ala provides a mechanism for the organism's intrinsic resistance to vancomycin. Mutation of Phe261 to Tyr261 in the Ω-loop of this ligase showed a complete loss of the ability to make D-ala-D-lactate (Park and Walsh, J. Biol. Chem. 272 (1997) 9210-9214). Phe261 is a key specificity determinant in the α-helical cap of the Ω-loop when folded into the closed conformation. A molecular docking study of the closed ligase using AutoDock 4.2 defines additional specificity constraints promoted by the Ω-loop capping the catalytic center. Attaining productive orientations of D-lactate with favorable ligation chemistry requires the flexibilities of Phe261 and Arg301 in the docking protocol. These are in addition to the optimization of van der Waals contacts with Lys260, Met326, and Ser327. The location of Phe261 and Lys260 in the α-helical cap of the Ω-loop over subsite 2 is an essential part of the folding process ensuring depsipeptide formation in the hydrophobic environment of the catalytic center. The importance of the F261Y mutation suggests that the hydroxyl of Tyr261 plays an instrumental role in determining non-productive docking orientations of D-lactate. Two of these are presented: (A) D-lactate-OH as an H-bond donor to the Tyr261-OH; (B) D-lactate as an H-bond donor to the phosphoryl of the intermediate D-alanyl phosphate, and the D-lactate-COO- as an H-bond acceptor for the Tyr261-OH. Neither orientation, A or B, show the bifurcated H-bonding with Arg301 recently proposed for the activation of the nucleophilic D-lactate for D-ala-D-lactate formation. Insights into the role of the Ω-loop and its K(F/Y) signature provide additional background for inhibitor design targeted to subsite 2 of the D-alanine:D-alanine (D-X) ligases.

  13. 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.

  14. 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.

  15. 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.

  16. The Loop Algorithm

    NASA Astrophysics Data System (ADS)

    Evertz, Hans Gerd

    1998-03-01

    Exciting new investigations have recently become possible for strongly correlated systems of spins, bosons, and fermions, through Quantum Monte Carlo simulations with the Loop Algorithm (H.G. Evertz, G. Lana, and M. Marcu, Phys. Rev. Lett. 70, 875 (1993).) (For a recent review see: H.G. Evertz, cond- mat/9707221.) and its generalizations. A review of this new method, its generalizations and its applications is given, including some new results. The Loop Algorithm is based on a formulation of physical models in an extended ensemble of worldlines and graphs, and is related to Swendsen-Wang cluster algorithms. It performs nonlocal changes of worldline configurations, determined by local stochastic decisions. It overcomes many of the difficulties of traditional worldline simulations. Computer time requirements are reduced by orders of magnitude, through a corresponding reduction in autocorrelations. The grand-canonical ensemble (e.g. varying winding numbers) is naturally simulated. The continuous time limit can be taken directly. Improved Estimators exist which further reduce the errors of measured quantities. The algorithm applies unchanged in any dimension and for varying bond-strengths. It becomes less efficient in the presence of strong site disorder or strong magnetic fields. It applies directly to locally XYZ-like spin, fermion, and hard-core boson models. It has been extended to the Hubbard and the tJ model and generalized to higher spin representations. There have already been several large scale applications, especially for Heisenberg-like models, including a high statistics continuous time calculation of quantum critical exponents on a regularly depleted two-dimensional lattice of up to 20000 spatial sites at temperatures down to T=0.01 J.

  17. 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

  18. Fast loop modeling for protein structures

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  19. Electrokinetic effects in catalytic platinum-insulator Janus swimmers

    NASA Astrophysics Data System (ADS)

    Ebbens, S.; Gregory, D. A.; Dunderdale, G.; Howse, J. R.; Ibrahim, Y.; Liverpool, T. B.; Golestanian, R.

    2014-06-01

    The effect of added salt on the propulsion of Janus platinum-polystyrene colloids in hydrogen peroxide solution is studied experimentally. It is found that micromolar quantities of potassium and silver nitrate salts reduce the swimming velocity by similar amounts, while leading to significantly different effects on the overall rate of catalytic breakdown of hydrogen peroxide. It is argued that the seemingly paradoxical experimental observations could be theoretically explained by using a generalised reaction scheme that involves charged intermediates and has the topology of two nested loops.

  20. Exploring local flexibility/rigidity in psychrophilic and mesophilic carbonic anhydrases.

    PubMed

    Chiuri, R; Maiorano, G; Rizzello, A; del Mercato, L L; Cingolani, R; Rinaldi, R; Maffia, M; Pompa, P P

    2009-02-18

    Molecular flexibility and rigidity are required to determine the function and specificity of protein molecules. Some psychrophilic enzymes demonstrate a higher catalytic efficiency at low temperatures, compared to the efficiency demonstrated by their meso/thermophilic homologous. The emerging picture suggests that such enzymes have an improved flexibility of the structural catalytic components, whereas other protein regions far from functional sites may be even more rigid than those of their mesophilic counterparts. To gain a deeper insight in the analysis of the activity-flexibility/rigidity relationship in protein structure, psychrophilic carbonic anhydrase of the Antarctic teleost Chionodraco hamatus has been compared with carbonic anhydrase II of Bos taurus through fluorescence studies, three-dimensional modeling, and activity analyses. Data demonstrated that the cold-adapted enzyme exhibits an increased catalytic efficiency at low and moderate temperatures and, more interestingly, a local flexibility in the region that controls the correct folding of the catalytic architecture, as well as a rigidity in the hydrophobic core. The opposite result was observed in the mesophilic counterpart. These results suggest a clear relationship between the activity and the presence of flexible and rigid protein substructures that may be useful in rational molecular and drug design of a class of enzymes playing a key role in pathologic processes.

  1. 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

  2. Flexible sucker rod unit

    SciTech Connect

    Allen, L.F.

    1987-02-03

    This patent describes a deep well having: a. an education tube with an inside diameter extending from the surface of the earth to far below the surface, b. a reciprocating pump housing attached to the bottom of the education tube, c. pump jack means at the surface for reciprocating the pump, d. a light sucker rod connected to the pump jack means and extending into the education tube, and e. a series of heavy sinker bars having a large cross sectional area in the education tube connecting the light sucker rod to the pump; f. an improved integral metal flexible rod unit interconnecting the sinker bars comprising in combination with the above: g. a coupling on each end of the integral metal flexible rod unit connecting the flexible rod unit to the contiguous sinker bar, h. a segment which is flexible as compared to the sinker bars connecting one of the couplings to i. an integral metal bearing adjacent to the other of the couplings, the bearing having j. a cylindrical surface with k. a diameter i. only slightly smaller than the inside diameter of the education tube thereby forming a sliding fit therewith, and ii. greater than the diameter of any other portion of the flexible rod unit and the sinker bar, and l. grooves in the cylindrical surface for the passage of fluid between in the education tube around the bearing.

  3. RCD+: Fast loop modeling server.

    PubMed

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

    2016-07-01

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

  4. 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

  5. Printed Microinductors for Flexible Substrates

    NASA Technical Reports Server (NTRS)

    Brandon, Erik; Whitacre, Jay; Wesseling, Emily

    2005-01-01

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

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

    SciTech Connect

    Huang, G.; Byrd, J. M.

    2006-11-20

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

  7. 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.

  8. Wilson Loop Diagrams and Positroids

    NASA Astrophysics Data System (ADS)

    Agarwala, Susama; Marin-Amat, Eloi

    2016-07-01

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

  9. 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.

  10. 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.

  11. 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.

  12. Flexible magnetoimpedance sensor

    NASA Astrophysics Data System (ADS)

    Li, Bodong; Kavaldzhiev, Mincho N.; Kosel, Jürgen

    2015-03-01

    Flexible magnetoimpedance (MI) sensors fabricated using a NiFe/Cu/NiFe tri-layer on Kapton substrate have been studied. A customized flexible microstrip transmission line was employed to investigate the MI sensors's magnetic field and frequency responses and their dependence on the sensors's deflection. For the first time, the impedance characteristic is obtained through reflection coefficient analysis over a wide range of frequencies from 0.1 MHz to 3 GHz and for deflections ranging from zero curvature to a radius of 7.2 cm. The sensor element maintains a high MI ratio of up to 90% and magnetic sensitivity of up to 9.2%/Oe over different bending curvatures. The relationship between the curvature and material composition is discussed based on the magnetostriction effect and stress simulations. The sensor's large frequency range, simple fabrication process and high sensitivity provide a great potential for flexible electronics and wireless applications.

  13. Natural flexible dermal armor.

    PubMed

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

    2013-01-01

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

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. Rationally designed coiled-coil DNA looping peptides control DNA topology.

    PubMed

    Gowetski, Daniel B; Kodis, Erin J; Kahn, Jason D

    2013-09-01

    Artificial DNA looping peptides were engineered to study the roles of protein and DNA flexibility in controlling the geometry and stability of protein-mediated DNA loops. These LZD (leucine zipper dual-binding) peptides were derived by fusing a second, C-terminal, DNA-binding region onto the GCN4 bZip peptide. Two variants with different coiled-coil lengths were designed to control the relative orientations of DNA bound at each end. Electrophoretic mobility shift assays verified formation of a sandwich complex containing two DNAs and one peptide. Ring closure experiments demonstrated that looping requires a DNA-binding site separation of 310 bp, much longer than the length needed for natural loops. Systematic variation of binding site separation over a series of 10 constructs that cyclize to form 862-bp minicircles yielded positive and negative topoisomers because of two possible writhed geometries. Periodic variation in topoisomer abundance could be modeled using canonical DNA persistence length and torsional modulus values. The results confirm that the LZD peptides are stiffer than natural DNA looping proteins, and they suggest that formation of short DNA loops requires protein flexibility, not unusual DNA bendability. Small, stable, tunable looping peptides may be useful as synthetic transcriptional regulators or components of protein-DNA nanostructures.

  19. 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.

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

    PubMed

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

    2015-10-01

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

  1. A matching algorithm for catalytic residue site selection in computational enzyme design.

    PubMed

    Lei, Yulin; Luo, Wenjia; Zhu, Yushan

    2011-09-01

    A loop closure-based sequential algorithm, PRODA_MATCH, was developed to match catalytic residues onto a scaffold for enzyme design in silico. The computational complexity of this algorithm is polynomial with respect to the number of active sites, the number of catalytic residues, and the maximal iteration number of cyclic coordinate descent steps. This matching algorithm is independent of a rotamer library that enables the catalytic residue to take any required conformation during the reaction coordinate. The catalytic geometric parameters defined between functional groups of transition state (TS) and the catalytic residues are continuously optimized to identify the accurate position of the TS. Pseudo-spheres are introduced for surrounding residues, which make the algorithm take binding into account as early as during the matching process. Recapitulation of native catalytic residue sites was used as a benchmark to evaluate the novel algorithm. The calculation results for the test set show that the native catalytic residue sites were successfully identified and ranked within the top 10 designs for 7 of the 10 chemical reactions. This indicates that the matching algorithm has the potential to be used for designing industrial enzymes for desired reactions.

  2. Flexible radiator system

    NASA Technical Reports Server (NTRS)

    Oren, J. A.

    1982-01-01

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

  3. Robust controller synthesis for large flexible space structures

    NASA Technical Reports Server (NTRS)

    Joshi, S. M.; Rowell, L. F.; Armstrong, E. S.

    1988-01-01

    The application of a multivariable frequency domain method for the attitude control and vibration suppression of large flexible space structures is discussed. Results of application of the linear-quadratic-Gaussian/loop transfer recovery method to the cases of a hop/column antenna, a wrap-rib antenna, and the Spacecraft Control Laboratory Experiment are presented. Controller order reduction is implemented using the balanced realization method, a Hankel-norm-based method, and a method based on stable factorization.

  4. 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.

  5. Fuel-Rich Catalytic Combustion

    NASA Technical Reports Server (NTRS)

    Brabbs, Theodore A.; Olson, Sandra L.

    1987-01-01

    Two-stage combustion system reduces particulate emissions. Program on catalytic oxidation of iso-octane demonstrates feasibility of two-stage combustion system for reducing particulate emissions. With fuel-rich (fuel/air equivalence ratios of 4.8 to 7.8) catalytic-combustion preburner as first stage, combustion process free of soot at reactor-outlet temperatures of 1,200 K or less.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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…

  11. 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…

  12. Diversity and Flexibility.

    ERIC Educational Resources Information Center

    Anastasi, Anne

    1990-01-01

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

  13. Designing Flexible Instruction

    ERIC Educational Resources Information Center

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

    2007-01-01

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

  14. Flexible electronics: Sophisticated skin

    NASA Astrophysics Data System (ADS)

    Bauer, Siegfried

    2013-10-01

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

  15. Flexible Mental Calculation.

    ERIC Educational Resources Information Center

    Threlfall, John

    2002-01-01

    Suggests that strategy choice is a misleading characterization of efficient mental calculation and that teaching mental calculation methods as a whole is not conducive to flexibility. Proposes an alternative in which calculation is thought of as an interaction between noticing and knowledge. Presents an associated teaching approach to promote…

  16. 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

  17. 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.

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

    PubMed

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

    2016-01-01

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

  19. 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

  20. 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...

  1. Automatic blocking of nested loops

    NASA Technical Reports Server (NTRS)

    Schreiber, Robert; Dongarra, Jack J.

    1990-01-01

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

  2. 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...

  3. 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 ...

  4. Number of cosmic string loops

    NASA Astrophysics Data System (ADS)

    Blanco-Pillado, Jose J.; Olum, Ken D.; Shlaer, Benjamin

    2014-01-01

    Using recent simulation results, we provide the mass and speed spectrum of cosmic string loops. This is the quantity of primary interest for many phenomenological signatures of cosmic strings, and it can be accurately predicted using recently acquired detailed knowledge of the loop production function. We emphasize that gravitational smoothing of long strings plays a negligible role in determining the total number of existing loops. We derive a bound on the string tension imposed by recent constraints on the stochastic gravitational wave background from pulsar timing arrays, finding Gμ ≤2.8×10-9. We also provide a derivation of the Boltzmann equation for cosmic string loops in the language of differential forms.

  5. 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

  6. Dynamical behaviour in coronal loops

    NASA Technical Reports Server (NTRS)

    Haisch, Bernhard M.

    1986-01-01

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

  7. 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

  8. 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.

  9. The Coronal Loop Inventory Project

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  10. Catalytic combustion with steam injection

    NASA Astrophysics Data System (ADS)

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

    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.

  11. 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.

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

    NASA Technical Reports Server (NTRS)

    Lanari, Leonardo; Wen, John T.

    1991-01-01

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

  13. 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.

  14. 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.

  15. 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)

  16. Ginga: Flexible FITS viewer

    NASA Astrophysics Data System (ADS)

    Jeschke, Eric

    2013-03-01

    Ginga is a viewer for astronomical data FITS (Flexible Image Transport System) files; the viewer centers around a FITS display widget which supports zooming and panning, color and intensity mapping, a choice of several automatic cut levels algorithms and canvases for plotting scalable geometric forms. In addition to this widget, the FITS viewer provides a flexible plugin framework for extending the viewer with many different features. A fairly complete set of "standard" plugins are provided for expected features of a modern viewer: panning and zooming windows, star catalog access, cuts, star pick/fwhm, thumbnails, and others. This viewer was written by software engineers at Subaru Telescope, National Astronomical Observatory of Japan, and is in use at that facility.

  17. Flexible Flapping Foils

    NASA Astrophysics Data System (ADS)

    Marais, Catherine; Godoy-Diana, Ramiro; Wesfreid, José. Eduardo

    2010-11-01

    Hydrodynamic tunnel experiments with flexible flapping foils of 4:1 span-to-chord aspect ratio are used in the present work to study the effect of foil compliance in the dynamical features of a propulsive wake. The average thrust force produced by the foil is estimated from 2D PIV measurements and the regime transitions in the wake are characterized according to a flapping frequency-amplitude phase diagram as in Godoy-Diana et al. (Phys. Rev. E 77, 016308, 2008). We show that the thrust production regime occurs on a broader region of the parameter space for flexible foils, with propulsive forces up to 3 times greater than for the rigid case. We examine in detail the vortex generation at the trailing edge of the foils, and propose a mechanism to explain how foil deformation leads to an optimization of propulsion.

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

    PubMed

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

    2015-11-01

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

  19. Analytic redundancy management for large flexible structures

    NASA Technical Reports Server (NTRS)

    Shenhar, J.; Montgomery, R. C.

    1992-01-01

    An analytic redundancy management approach for on-line component failure detection is described and illustrated using a simulation of the NASA Langley Spacecaft Control Laboratory Experiment (SCOLE) research facility. The SCOLE experimental apparatus simulated is a functional model of the Space Shuttle with a large, flexible, offset-feed antenna cantilevered from the payload bay. This approach uses a single, active, Kalman filter selected from a bank of filters, each element of which was previously designed to accommodate a specific failure condition. The residuals of this active filter are processed through a sequential probability ratio test (SPRT) filter to identify the failure state of the system and, hence, closing the failure accommodation loop, to select the active filter. Results are presented that illustrate the ability of the system to detect and recover from failures introduced in the angular rate and linear acceleration sensors on the SCOLE facility.

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

    PubMed

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

    2009-01-01

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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. High heat flux loop heat pipes

    NASA Astrophysics Data System (ADS)

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

    1997-01-01

    Loop Heat Pipes (LHPs) can transport very large thermal power loads, over long distances, through flexible, small diameter tubes and against high gravitational heads. While recent LHPs have transported as much as 1500 W, the peak heat flux through a LHP's evaporator has been limited to about 0.07 MW/m2. This limitation is due to the arrangement of vapor passages next to the heat load which is one of the conditions necessary to ensure self priming of the device. This paper describes work aimed at raising this limit by threefold to tenfold. Two approaches were pursued. One optimized the vapor passage geometry for the high heat flux conditions. The geometry improved the heat flow into the wick and working fluid. This approach also employed a finer pored wick to support higher vapor flow losses. The second approach used a bidisperse wick material within the circumferential vapor passages. The bidisperse material increased the thermal conductivity and the evaporative surface area in the region of highest heat flux, while providing a flow path for the vapor. Proof-of-concept devices were fabricated and tested for each approach. Both devices operated as designed and both demonstrated operation at a heat flux of 0.70 MW/m2. This performance exceeded the known state of the art by a factor of more than six for both conventional heat pipes and for loop heat pipes using ammonia. In addition, the bidisperse-wick device demonstrated boiling heat transfer coefficients up to 100,000 W/m2.K, and the fine pored device demonstrated an orientation independence with its performance essentially unaffected by whether its evaporator was positioned above, below or level with the condenser.

  7. 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…

  8. Flexible Scheduling: Making the Transition

    ERIC Educational Resources Information Center

    Creighton, Peggy Milam

    2008-01-01

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

  9. 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.

  10. Catalytic Enantioselective Carboannulation with Allylsilanes

    PubMed Central

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

    2015-01-01

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

  11. Catalytic enantioselective carboannulation with allylsilanes.

    PubMed

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

    2014-09-01

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

  12. 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.

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

    PubMed Central

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

    2011-01-01

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

  14. 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.

  15. Durability of ceramic catalytic converters for motorcycles

    SciTech Connect

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

    1995-12-31

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

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

    PubMed

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

    2012-09-11

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

  17. Catalytic strategy used by the myosin motor to hydrolyze ATP.

    PubMed

    Kiani, Farooq Ahmad; Fischer, Stefan

    2014-07-22

    Myosin is a molecular motor responsible for biological motions such as muscle contraction and intracellular cargo transport, for which it hydrolyzes adenosine 5'-triphosphate (ATP). Early steps of the mechanism by which myosin catalyzes ATP hydrolysis have been investigated, but still missing are the structure of the final ADP·inorganic phosphate (Pi) product and the complete pathway leading to it. Here, a comprehensive description of the catalytic strategy of myosin is formulated, based on combined quantum-classical molecular mechanics calculations. A full exploration of catalytic pathways was performed and a final product structure was found that is consistent with all experiments. Molecular movies of the relevant pathways show the different reorganizations of the H-bond network that lead to the final product, whose γ-phosphate is not in the previously reported HPγO4(2-) state, but in the H2PγO4(-) state. The simulations reveal that the catalytic strategy of myosin employs a three-pronged tactic: (i) Stabilization of the γ-phosphate of ATP in a dissociated metaphosphate (PγO3(-)) state. (ii) Polarization of the attacking water molecule, to abstract a proton from that water. (iii) Formation of multiple proton wires in the active site, for efficient transfer of the abstracted proton to various product precursors. The specific role played in this strategy by each of the three loops enclosing ATP is identified unambiguously. It explains how the precise timing of the ATPase activation during the force generating cycle is achieved in myosin. The catalytic strategy described here for myosin is likely to be very similar in most nucleotide hydrolyzing enzymes.

  18. Catalytic strategy used by the myosin motor to hydrolyze ATP

    PubMed Central

    Kiani, Farooq Ahmad; Fischer, Stefan

    2014-01-01

    Myosin is a molecular motor responsible for biological motions such as muscle contraction and intracellular cargo transport, for which it hydrolyzes adenosine 5'-triphosphate (ATP). Early steps of the mechanism by which myosin catalyzes ATP hydrolysis have been investigated, but still missing are the structure of the final ADP·inorganic phosphate (Pi) product and the complete pathway leading to it. Here, a comprehensive description of the catalytic strategy of myosin is formulated, based on combined quantum–classical molecular mechanics calculations. A full exploration of catalytic pathways was performed and a final product structure was found that is consistent with all experiments. Molecular movies of the relevant pathways show the different reorganizations of the H-bond network that lead to the final product, whose γ-phosphate is not in the previously reported HPγO42− state, but in the H2PγO4− state. The simulations reveal that the catalytic strategy of myosin employs a three-pronged tactic: (i) Stabilization of the γ-phosphate of ATP in a dissociated metaphosphate (PγO3−) state. (ii) Polarization of the attacking water molecule, to abstract a proton from that water. (iii) Formation of multiple proton wires in the active site, for efficient transfer of the abstracted proton to various product precursors. The specific role played in this strategy by each of the three loops enclosing ATP is identified unambiguously. It explains how the precise timing of the ATPase activation during the force generating cycle is achieved in myosin. The catalytic strategy described here for myosin is likely to be very similar in most nucleotide hydrolyzing enzymes. PMID:25006262

  19. Active control of buckling of flexible beams

    NASA Technical Reports Server (NTRS)

    Baz, A.; Tampe, L.

    1989-01-01

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

  20. Flexible DM-NRG

    NASA Astrophysics Data System (ADS)

    Legeza, Örs; Moca, Pascu; Tóth, Anna; Weymann, Ireneusz; Zaránd, Gergely

    2011-07-01

    This code combines the spectral sum-conserving methods of Weichselbaum and von Delft and of Peters, Pruschke and Anders (both relying upon the complete basis set construction of Anders and Schiller) with the use of non-Abelian symmetries in a flexible manner: Essentially any non-Abelian symmetry can be taught to the code, and any number of such symmetries can be used throughout the computation for any density of states, and to compute any local operators' correlation function's real and imaginary parts or any thermodynamical expectation value. The code works both at zero and finite temperatures.

  1. 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.

  2. 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.

  3. 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.

  4. Automatic and Flexible

    PubMed Central

    Hassin, Ran R.; Bargh, John A.; Zimerman, Shira

    2008-01-01

    Arguing from the nature of goal pursuit and from the economy of mental resources this paper suggests that automatic goal pursuit, much like its controlled counterpart, may be flexible. Two studies that employ goal priming procedures examine this hypothesis using the Wisconsin Card Sorting Test (Study 1) and a variation of the Iowa Gambling Task (Study 2). Implications of the results for our understanding of the dichotomy between automatic and controlled processes in general, and for our conception of automatic goal pursuit in particular, are discussed. PMID:19325712

  5. 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.

  6. 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.

  7. 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.

  8. Heterogeneous catalytic alcoholysis of benzonitrile

    SciTech Connect

    Kagarlitskii, A.D.; Dmumakaev, K.Kh.; Bekova, N.S.

    1986-04-01

    The authors investigate the possibility of the direct heterogeneous catalytic synthesis of ethylbenzoate from benzonitrile. The catalysts tested were oxides of aluminium, titanium, and vanadium. The main conversion product detected chromatographically was ethylbenzoate; benzaldehyde, benzamide, and benzanilide were also identified. Aluminium oxide was found to be the most effective catalyst.

  9. 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.

  10. Simple, chemoselective, catalytic olefin isomerization.

    PubMed

    Crossley, Steven W M; Barabé, Francis; Shenvi, Ryan A

    2014-12-01

    Catalytic amounts of Co(Sal(tBu,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.

  11. Social Entrepreneurs and Catalytic Change.

    ERIC Educational Resources Information Center

    Waddock, Sandra A.; Post, James E.

    1991-01-01

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

  12. 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.

  13. Waves in Solar Coronal Loops

    NASA Astrophysics Data System (ADS)

    Wang, T. J.

    2016-02-01

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

  14. Criteria for saturated magnetization loop

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

    Proper estimation of magnetization curve parameters is vital in studying magnetic systems. In the present article, criteria for discrimination non-saturated (minor) from saturated (major) hysteresis loops are proposed. These employ the analysis of (i) derivatives of both ascending and descending branches of the loop, (ii) remanent magnetization curves, and (iii) thermomagnetic curves. Computational simulations are used in order to demonstrate their validity. Examples illustrating the applicability of these criteria to well-known real systems, namely Fe3O4 and Ni fine particles, are provided. We demonstrate that the anisotropy-field value estimated from a visual examination of an only apparently major hysteresis loop could be more than two times lower than the real one.

  15. 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.

  16. Asymmetry of the active site loop conformation between subunits of glutamate-1-semialdehyde aminomutase in solution.

    PubMed

    Campanini, Barbara; Bettati, Stefano; di Salvo, Martino Luigi; Mozzarelli, Andrea; Contestabile, Roberto

    2013-01-01

    Glutamate-1-semialdehyde aminomutase (GSAM) is a dimeric, pyridoxal 5'-phosphate (PLP)- dependent enzyme catalysing in plants and some bacteria the isomerization of L-glutamate-1-semialdehyde to 5-aminolevulinate, a common precursor of chlorophyll, haem, coenzyme B12, and other tetrapyrrolic compounds. During the catalytic cycle, the coenzyme undergoes conversion from pyridoxamine 5'-phosphate (PMP) to PLP. The entrance of the catalytic site is protected by a loop that is believed to switch from an open to a closed conformation during catalysis. Crystallographic studies indicated that the structure of the mobile loop is related to the form of the cofactor bound to the active site, allowing for asymmetry within the dimer. Since no information on structural and functional asymmetry of the enzyme in solution is available in the literature, we investigated the active site accessibility by determining the cofactor fluorescence quenching of PMP- and PLP-GSAM forms. PLP-GSAM is partially quenched by potassium iodide, suggesting that at least one catalytic site is accessible to the anionic quencher and therefore confirming the asymmetry observed in the crystal structure. Iodide induces release of the cofactor from PMP-GSAM, apparently from only one catalytic site, therefore suggesting an asymmetry also in this form of the enzyme in solution, in contrast with the crystallographic data.

  17. Dynamics and control of flexible multibody structures

    NASA Astrophysics Data System (ADS)

    Stemple, Timothy John

    The goal of this study is to present a method for deriving equations of motion capable of modeling the controlled motion of an open loop multibody structure comprised of an arbitrary number of rigid bodies and slender beams. The procedure presented here for deriving equations of motion for flexible multibody systems is carried out by means of the Principle of Virtual Work (often referred to in the dynamics literature as d'Alembert's Principle). We first consider the motion of a general flexible body relative to the inertial space, and then derive specific formulas for both rigid bodies and slender beams. Next, we make a small motions assumption, with the end result being equations for a Rayleigh beam, which include terms which account for the axial motion, due to bending, of points on the beam central axis. This process includes a novel application of the exponential form of an orthogonal matrix, which is ideally suited for truncation. Then, the generalized coordinates and quasi-velocities used in the mathematical model, including those needed in the spatial discretization process of the beam equations are discussed. Furthermore, we develop a new set of recursive relations used to compute the inertial motion of a body in terms of the generalized coordinates and quasi-velocities. This research was motivated by the desire to model the controlled motion of a flexible space robot, and consequently, we use the multibody dynamics equations to simulate the motion of such a structure, providing a demonstration of the computer program. For this particular example we make use of a new sequence of shape functions, first used by Meirovitch and Stemple to model a two dimensional building frame subjected to earthquake excitations.

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. Force fluctuation in a semiflexible loop

    NASA Astrophysics Data System (ADS)

    Waters, James; Kim, Harold; Harold Kim Team

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

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

    PubMed

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

    2014-07-01

    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.

  4. 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.

  5. 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.

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

    PubMed Central

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

    2012-01-01

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

  7. 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.

  8. 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.

  9. Closing the Loop with Exercises

    ERIC Educational Resources Information Center

    Altizer, Andy

    2008-01-01

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

  10. 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.

  11. 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.

  12. Generalized flexibility-rigidity index

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  13. Flexible transformation plasmonics using graphene.

    PubMed

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

    2013-05-01

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

  14. Flexible transformation plasmonics using graphene.

    PubMed

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

    2013-05-01

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

  15. 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

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

    PubMed

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

    2016-08-26

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

  17. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  19. Conformational flexibility of aspartame.

    PubMed

    Toniolo, Claudio; Temussi, Pierandrea

    2016-05-01

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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Damped flexible seal

    DOEpatents

    DuBois, Neil J.; Amaral, Antonio M.

    1992-10-27

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

  5. The β Subunit Loop That Couples Catalysis and Rotation in ATP Synthase Has a Critical Length*

    PubMed Central

    Mnatsakanyan, Nelli; Kemboi, Silas K.; Salas, Jasmin; Weber, Joachim

    2011-01-01

    ATP synthase uses a unique rotational mechanism to convert chemical energy into mechanical energy and back into chemical energy. The helix-turn-helix structure in the C-terminal domain of the β subunit containing the conserved DELSEED motif, termed “DELSEED-loop,” was suggested to be involved in coupling between catalysis and rotation. If this is indeed the role of the loop, it must have a critical length, the minimum length required to sustain its function. Here, the critical length of the DELSEED-loop was determined by functional analysis of mutants of Bacillus PS3 ATP synthase that had 7–14 amino acids within the loop deleted. A 10 residue deletion lost the ability to catalyze ATP synthesis, but was still an active ATPase. Deletion of 14 residues abolished any enzymatic activity. Modeling indicated that in both deletion mutants the DELSEED-loop was shortened by ∼10 Å; fluorescence resonance energy transfer experiments confirmed the modeling results. This appears to define the minimum length for DELSEED-loop required for coupling of catalysis and rotation. In addition, we could demonstrate that the loss of high-affinity binding to the catalytic site(s) that had been observed previously in two deletion mutants with 3–4 residues removed was not due to the loss of negative charged residues of the DELSEED motif in these mutants. An AALSAAA mutant in which all negative charges of the DELSEED motif were removed showed a normal pattern for MgATP binding to the catalytic sites, with a clearly present high-affinity site. PMID:21705326

  6. 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.

  7. Catalytic combustion of residual fuels

    NASA Technical Reports Server (NTRS)

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

    1981-01-01

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

  8. 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.

  9. Catalytic asymmetric alkylation of acylsilanes.

    PubMed

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

    2015-03-01

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

  10. Homodimerization of the Death-Associated Protein Kinase Catalytic Domain: Development of a New Small Molecule Fluorescent Reporter

    PubMed Central

    Zimmermann, Michael; Atmanene, Cédric; Xu, Qingyan; Fouillen, Laetitia; Van Dorsselaer, Alain; Bonnet, Dominique; Marsol, Claire; Hibert, Marcel; Sanglier-Cianferani, Sarah; Pigault, Claire; McNamara, Laurie K.; Watterson, D. Martin; Haiech, Jacques; Kilhoffer, Marie-Claude

    2010-01-01

    Background Death-Associated Protein Kinase (DAPK) is a member of the Ca2+/calmodulin regulated serine/threonine protein kinases. Its biological function has been associated with induced cell death, and in vivo use of selective small molecule inhibitors of DAPK catalytic activity has demonstrated that it is a potential therapeutic target for treatment of brain injuries and neurodegenerative diseases. Methodology/Principal Findings In the in vitro study presented here, we describe the homodimerization of DAPK catalytic domain and the crucial role played by its basic loop structure that is part of the molecular fingerprint of death protein kinases. Nanoelectrospray ionization mass spectrometry of DAPK catalytic domain and a basic loop mutant DAPK protein performed under a variety of conditions was used to detect the monomer-dimer interchange. A chemical biological approach was used to find a fluorescent probe that allowed us to follow the oligomerization state of the protein in solution. Conclusions/Significance The use of this combined biophysical and chemical biology approach facilitated the elucidation of a monomer-dimer equilibrium in which the basic loop plays a key role, as well as an apparent allosteric conformational change reported by the fluorescent probe that is independent of the basic loop structure. PMID:21152427

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

    PubMed Central

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

    2015-01-01

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

  12. 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

  13. 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.

  14. Loop quantum cosmology from quantum reduced loop gravity

    NASA Astrophysics Data System (ADS)

    Alesci, Emanuele; Cianfrani, Francesco

    2015-08-01

    We show how loop quantum cosmology can be derived as an effective semiclassical description of loop quantum gravity. Using the tools of QRLG, a gauge fixed version of LQG, we take the coherent states of the fundamental microscopic theory suitable to describe a Bianchi I Universe and we find a mapping between the expectation value of the Hamiltonian and the dynamics of LQC. Our results are in agreement with a lattice refinement framework for LQC, thus the so-called “old” and “improved-dynamics” regularization schemes can be reproduced. These amount to different choices of relations between local variables and the smeared ones entering the definition of the coherent states. The leading order of the fundamental theory corresponds to LQC, but we also find different inverse volume corrections, that depend on a purely quantum observable, namely the number of nodes of the states.

  15. 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.

  16. Advantages of dynamic "closed loop" stable isotope flux phenotyping over static "open loop" clamps in detecting silent genetic and dietary phenotypes.

    PubMed

    Vaitheesvaran, Bhavapriya; Chueh, Fu-Yu; Xu, Jun; Trujillo, Chuck; Saad, M F; Lee, W N P; McGuinness, Owen P; Kurland, Irwin J

    2010-06-01

    In vivo insulin sensitivity can be assessed using "open loop" clamp or "closed loop" methods. Open loop clamp methods are static, and fix plasma glucose independently from plasma insulin. Closed loop methods are dynamic, and assess glucose disposal in response to a stable isotope labeled glucose tolerance test. Using PPARalpha(-/-) mice, open and closed loop assessments of insulin sensitivity/glucose disposal were compared. Indirect calorimetry done for the assessment of diurnal substrate utilization/metabolic flexibility showed that chow fed PPARalpha(-/-) mice had increased glucose utilization during the light (starved) cycle. Euglycemic clamps showed no differences in insulin stimulated glucose disposal, whether for chow or high fat diets, but did show differences in basal glucose clearance for chow fed PPARalpha(-/-) versus SV129J-wt mice. In contrast, the dynamic stable isotope labeled glucose tolerance tests reveal enhanced glucose disposal for PPARalpha(-/-) versus SV129J-wt, for chow and high fat diets. Area under the curve for plasma labeled and unlabeled glucose for PPARalpha(-/-) was approximately 1.7-fold lower, P < 0.01 during the stable isotope labeled glucose tolerance test for both diets. Area under the curve for plasma insulin was 5-fold less for the chow fed SV129J-wt (P < 0.01) but showed no difference on a high fat diet (0.30 +/- 0.1 for SV129J-wt vs. 0.13 +/- 0.10 for PPARalpha(-/-), P = 0.28). This study demonstrates that dynamic stable isotope labeled glucose tolerance test can assess "silent" metabolic phenotypes, not detectable by the static, "open loop", euglycemic or hyperglycemic clamps. Both open loop and closed loop methods may describe different aspects of metabolic inflexibility and insulin sensitivity. PMID:20445758

  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. 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...

  19. Noise Performance Of A Digital Tanlock Loop

    NASA Technical Reports Server (NTRS)

    Hurd, W. J.; Pomalaza-Raez, C. A.

    1988-01-01

    Slight improvement over sinusoidal phase-lock loop achieved. Report discusses theoretical studies and numerical simulations of performance of digital tangent phase-lock loop (DTL), in presence of noise.

  20. Dynamic modelling and analysis of a magnetically suspended flexible rotor. M.S. Thesis, 1988

    NASA Technical Reports Server (NTRS)

    Mccallum, Duncan C.

    1991-01-01

    A 12-state lumped-element model is presented for a flexible rotor supported by two attractive force electromagnetic journal bearings. The rotor is modeled as a rigid disk with radial mass unbalance mounted on a flexible, massless shaft with internal damping (Jeffcott rotor). The disk is offset axially from the midspan of the shaft. Bearing dynamics in each radial direction are modeled as a parallel combination of a negative (unstable) spring and a linear current-to-force actuator. The model includes translation and rotation of the rigid mass and the first and second bending models of the flexible shaft, and it simultaneously includes internal shaft damping, gyroscopic effects, and the unstable nature of the attractive force magnetic bearings. The model is used to analyze the dependence of the system transmission zeros and open-loop poles on system parameters. The dominant open-loop poles occur in stable/unstable pairs with bandwidth dependent on the ratios of bearing (unstable) stiffnesses to rotor mass and damping dependent on the shaft spin rate. The zeros occur in complex conjugate pairs with bandwidth dependent on the ratios of shaft stiffness to rotor mass and damping dependent on the shaft spin rate. Some of the transmission zeros are non-minimum phase when the spin rate exceeds the shaft critical speed. The transmission zeros and open-loop poles impact the design of magnetic bearing control systems. The minimum loop cross-over frequency of the closed-loop system is the speed of the unstable open-loop poles. For the supercritical shaft spin rates, the presence of non-minimum phase zeros limits the distribution rejection achievable at frequencies near or above the shaft critical speed. Since non-minimum phase transmission zeros can only be changed by changing the system inputs and/or outputs, closed-loop performance is limited for supercritical spin rates unless additional force or torque actuators are added.

  1. On the feasibility of closed-loop control of intra-aortic balloon pumping

    NASA Technical Reports Server (NTRS)

    Clark, J. W., Jr.; Bourland, H. M.; Kane, G. R.

    1973-01-01

    A closed-loop control scheme for the control of intra-aortic balloon pumping has been developed and tested in dog experiments. A performance index reflecting the general objectives of balloon-assist pumping is developed and a modified steepest ascent control algorithm is utilized for the selection of a proper operating point for the balloon during its pumping cycle. This paper attempts to indicate the feasibility of closed-loop control of balloon pumping, and particularly its flexibility in achieving both diastolic augmentation of mean aortic pressure and control of the level of end-diastolic pressure (EDP) an important factor in reducing heart work.

  2. 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.

  3. Hard thermal loops in static external fields

    SciTech Connect

    Frenkel, J.; Takahashi, N.; Pereira, S. H.

    2009-04-15

    We examine, in the imaginary-time formalism, the high temperature behavior of n-point thermal loops in static Yang-Mills and gravitational fields. We show that in this regime, any hard thermal loop gives the same leading contribution as the one obtained by evaluating the loop integral at zero external energies and momenta.

  4. 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.

  5. Teacher Flexibility in Mathematical Discussion

    ERIC Educational Resources Information Center

    Leikin, Roza; Dinur, Sariga

    2007-01-01

    The significance of discussion in mathematics classes has been prominently debated in the research literature. Different studies have stressed the importance of teacher flexibility in orchestrating the discussion. We introduce an operational definition of teacher flexibility. In a case study with one secondary-school mathematics teacher, we…

  6. 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.

  7. Mutational analysis of the conserved TGES loop of sarcoplasmic reticulum Ca2+-ATPase.

    PubMed

    Anthonisen, Anne Nyholm; Clausen, Johannes D; Andersen, Jens Peter

    2006-10-20

    Crystal structures have shown that the conserved TGES loop of the Ca2+-ATPase is isolated in the Ca2E1 state but becomes inserted in the catalytic site in E2 states. Here, we have examined the kinetics of the partial reaction steps of the transport cycle and the binding of the phosphoryl analogs BeF, AlF, MgF, and vanadate in mutants with alterations to the TGES residues. The mutations encompassed variation of size, polarity, and charge of the side chains. Differential effects on the Ca2E1P --> E2P, E2P --> E2, and E2 --> Ca2E1 reactions and the binding of the phosphoryl analogs were observed. In the E183D mutant, the E2P --> E2 dephosphorylation reaction proceeded at a rate as high as one-third that of the wild type, whereas it was very slow in the other Glu183 mutants, including E183Q, thus demonstrating the need for a negatively charged carboxylate group to catalyze dephosphorylation. By contrast, the Ca2E1P --> E2P transition was accomplished at a reasonable rate with glutamine in place of Glu183, but not with aspartate, indicating that the length of the Glu183 side chain, in addition to its hydrogen bonding potential, is critical for Ca2E1P --> E2P. This transition was also slowed in mutants with alteration to other TGES residues. The data provide functional evidence in support of the proposed role of Glu183 in activating the water molecule involved in the E2P --> E2 dephosphorylation and suggest a direct participation of the side chains of the TGES loop in the control and facilitation of the insertion of the loop in the catalytic site. The interactions of the TGES loop furthermore seem to facilitate its disengagement from the catalytic site during the E2 --> Ca2E1 transition. PMID:16893884

  8. 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.

  9. The Statistical Loop Analyzer (SLA)

    NASA Technical Reports Server (NTRS)

    Lindsey, W. C.

    1985-01-01

    The statistical loop analyzer (SLA) is designed to automatically measure the acquisition, tracking and frequency stability performance characteristics of symbol synchronizers, code synchronizers, carrier tracking loops, and coherent transponders. Automated phase lock and system level tests can also be made using the SLA. Standard baseband, carrier and spread spectrum modulation techniques can be accomodated. Through the SLA's phase error jitter and cycle slip measurements the acquisition and tracking thresholds of the unit under test are determined; any false phase and frequency lock events are statistically analyzed and reported in the SLA output in probabilistic terms. Automated signal drop out tests can be performed in order to trouble shoot algorithms and evaluate the reacquisition statistics of the unit under test. Cycle slip rates and cycle slip probabilities can be measured using the SLA. These measurements, combined with bit error probability measurements, are all that are needed to fully characterize the acquisition and tracking performance of a digital communication system.

  10. Lock detection in Costas loops

    NASA Technical Reports Server (NTRS)

    Mileant, A.; Hinedi, S.

    1992-01-01

    Previous analyses of lock detector algorithms for Costas loops have ignored the effects of the inherent correlation between samples of the phase error process. In this paper, both analysis and simulations are used to quantify the effects of phase correlation on lock detection for the 'square law' and 'absolute value' type detectors. Results are obtained which depict the lock detection probability as a function of loop signal-to-noise ratio for a given false alarm rate. It is shown that the square law detector experiences less degradation due to phase jitter than the absolute value detector and that the degradation in detector signal-to-noise ratio is more pronounced for squarewave than for sinewave signals.

  11. Lock detection in Costas loops

    NASA Astrophysics Data System (ADS)

    Mileant, A.; Hinedi, S.

    1992-03-01

    Previous analyses of lock detector algorithms for Costas loops have ignored the effects of the inherent correlation between samples of the phase error process. In this paper, both analysis and simulations are used to quantify the effects of phase correlation on lock detection for the 'square law' and 'absolute value' type detectors. Results are obtained which depict the lock detection probability as a function of loop signal-to-noise ratio for a given false alarm rate. It is shown that the square law detector experiences less degradation due to phase jitter than the absolute value detector and that the degradation in detector signal-to-noise ratio is more pronounced for squarewave than for sinewave signals.

  12. Loop Diuretics in Clinical Practice.

    PubMed

    Oh, Se Won; Han, Sang Youb

    2015-06-01

    Diuretics are commonly used to control edema across various clinical fields. Diuretics inhibit sodium reabsorption in specific renal tubules, resulting in increased urinary sodium and water excretion. Loop diuretics are the most potent diuretics. In this article, we review five important aspects of loop diuretics, in particular furosemide, which must be considered when prescribing this medicine: (1) oral versus intravenous treatment, (2) dosage, (3) continuous versus bolus infusion, (4) application in chronic kidney disease patients, and (5) side effects. The bioavailability of furosemide differs between oral and intravenous therapy. Additionally, the threshold and ceiling doses of furosemide differ according to the particular clinical condition of the patient, for example in patients with severe edema or chronic kidney disease. To maximize the efficiency of furosemide, a clear understanding of how the mode of delivery will impact bioavailability and the required dosage is necessary.

  13. Loop Diuretics in Clinical Practice

    PubMed Central

    Oh, Se Won

    2015-01-01

    Diuretics are commonly used to control edema across various clinical fields. Diuretics inhibit sodium reabsorption in specific renal tubules, resulting in increased urinary sodium and water excretion. Loop diuretics are the most potent diuretics. In this article, we review five important aspects of loop diuretics, in particular furosemide, which must be considered when prescribing this medicine: (1) oral versus intravenous treatment, (2) dosage, (3) continuous versus bolus infusion, (4) application in chronic kidney disease patients, and (5) side effects. The bioavailability of furosemide differs between oral and intravenous therapy. Additionally, the threshold and ceiling doses of furosemide differ according to the particular clinical condition of the patient, for example in patients with severe edema or chronic kidney disease. To maximize the efficiency of furosemide, a clear understanding of how the mode of delivery will impact bioavailability and the required dosage is necessary. PMID:26240596

  14. Deconfinement and virtual quark loops

    NASA Astrophysics Data System (ADS)

    Çelik, T.; Engels, J.; Satz, H.

    1983-12-01

    We calculate paer Monte Carlo evaluation on an 83 × 3 lattice the energy density ɛG of the gluon sector of QCD, including virtual quark loops up to the fourth power in the hopping parameter expansion. For light quarks of one flavour, we observe at T/ΛL 95 +/- 10 a rapid variation of ɛG in T, accompanied by strong fluctuations from iteration to iteration. as clear signal of the deconfinement transition.

  15. 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.

  16. [The flexibility of family medicine].

    PubMed

    Minguet, C; Aubrege, A; Aubart, M; Cornuz, J; di Patrizio, P; Du Boullay, D; Farghadani, H; Flammang, M; Haas, N; Kacenelenbogen, N; Kopp, M; Leners, J C; Levêque, M; Mbengue, M; Paur, H; Paur, I; Raphaël, F; Rausch, S; Shetgen, M; Stein R; Tabouring, P; Thomas, J M; Vignon, G

    2015-01-01

    We are a European academic group of family doctors and we propose a definition of flexibility in family medicine. A review of the literature shows that flexibility and complexity are emerging concepts in the field of family practice. The outcomes of a workshop at the WONCA-Europe congress in 2014 are discussed. The flexibility is a capability of the general practitioner to deal with complex clinical situations in a biomedical and societal changing world. Flexibility is framed by ethics. It could improve the quality of care, be useful against burnout and used in medical research. In conclusion, family medicine should adopt a specific definition of the flexibility describing its specificity, a useful and teachable capacity. PMID:26946851

  17. Quantum reduced loop gravity and the foundation of loop quantum cosmology

    NASA Astrophysics Data System (ADS)

    Alesci, Emanuele; Cianfrani, Francesco

    2016-06-01

    Quantum reduced loop gravity is a promising framework for linking loop quantum gravity and the effective semiclassical dynamics of loop quantum cosmology. We review its basic achievements and its main perspectives, outlining how it provides a quantum description of the Universe in terms of a cuboidal graph which constitutes the proper framework for applying loop techniques in a cosmological setting.

  18. SOCMA study urges flexibility

    SciTech Connect

    Kirschner, E.

    1993-02-10

    In implementing the 1990 Pollution Prevention Act, regulators and legislators should hold off on cookie-cutter, numerical goal-based requirements to allow for site and process specific programs, says a study sponsored by the Synthetic Organic Chemicals Manufacturers Association (SOCMA; Washington). Companies should have that flexibility to target their resources toward those activities that reduce pollution cost effectively, says SOCMA environmental quality committee chairman Art Gillen, who is also BASF director of environmental regulatory affairs. The study - conducted by Woodward-Clyde Consultants (Denver) - examines four batch and custom chemical manufacturing films. As in the Clean Air Act, the batch processing of SOCMA-member plants should be considered in new regulations, Gillen says. For example, the study found that most wastes are from shutdowns and cleanouts, and there are frequent charges in waste streams and raw materials. Those characteristics do not lend themselves to annual reduction goals. Also, specific goals could have a wide range of costs: measures to reduce stack air emissions run from $18/lb to $1,106/lb. SOCMA says it will present the study to Congress and the Environmental Protection Agency.

  19. 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.

  20. Two-loop quantum gravity

    NASA Astrophysics Data System (ADS)

    van de Ven, Anton E. M.

    1992-07-01

    We prove the existence of a nonrenormalizable infinity in the two-loop effective action of perturbative quantum gravity by means of an explicit calculation. Our final result agrees with that obtained by earlier authors. We use the background-field method in coordinate space, combined with dimensional regularization and a heat kernel representation for the propagators. General covariance is manifestly preserved. Only vacuum graphs in the presence of an on-shell background metric need to be calculated. We extend the background covariant harmonic gauge to include terms nonlinear in the quantum gravitational fields and allow for general reparametrizations of those fields. For a particular gauge choice and field parametrization only two three-graviton and six four-graviton vertices are present in the action. Calculational labor is further reduced by restricting to backgrounds, which are not only Ricci-flat, but satisfy an additional constraint bilinear in the Weyl tensor. To handle the still formidable amount of algebra, we use the symbolic manipulation program FORM. We checked that the on-shell two-loop effective action is in fact independent of all gauge and field redefinition parameters. A two-loop analysis for Yang-Mills fields is included as well, since in that case we can give full details as well as simplify earlier analyses.

  1. 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.

  2. The Catalytic and Non-catalytic Functions of the Brahma Chromatin-Remodeling Protein Collaborate to Fine-Tune Circadian Transcription in Drosophila.

    PubMed

    Kwok, Rosanna S; Li, Ying H; Lei, Anna J; Edery, Isaac; Chiu, Joanna C

    2015-07-01

    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.

  3. 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

  4. Metabolic flexibility and insulin resistance.

    PubMed

    Galgani, Jose E; Moro, Cedric; Ravussin, Eric

    2008-11-01

    Metabolic flexibility is the capacity for the organism to adapt fuel oxidation to fuel availability. The inability to modify fuel oxidation in response to changes in nutrient availability has been implicated in the accumulation of intramyocellular lipid and insulin resistance. The metabolic flexibility assessed by the ability to switch from fat to carbohydrate oxidation is usually impaired during a hyperinsulinemic clamp in insulin-resistant subjects; however, this "metabolic inflexibility" is mostly the consequence of impaired cellular glucose uptake. Indeed, after controlling for insulin-stimulated glucose disposal rate (amount of glucose available for oxidation), metabolic flexibility is not altered in obesity regardless of the presence of type 2 diabetes. To understand how intramyocellular lipids accumulate and cause insulin resistance, the assessment of metabolic flexibility to high-fat diets is more relevant than metabolic flexibility during a hyperinsulinemic clamp. An impaired capacity to upregulate muscle lipid oxidation in the face of high lipid supply may lead to increased muscle fat accumulation and insulin resistance. Surprisingly, very few studies have investigated the response to high-fat diets. In this review, we discuss the role of glucose disposal rate, adipose tissue lipid storage, and mitochondrial function on metabolic flexibility. Additionally, we emphasize the bias of using the change in respiratory quotient to calculate metabolic flexibility and propose novel approaches to assess metabolic flexibility. On the basis of current evidence, one cannot conclude that impaired metabolic flexibility is responsible for the accumulation of intramyocellular lipid and insulin resistance. We propose to study metabolic flexibility in response to high-fat diets in individuals having contrasting degree of insulin sensitivity and/or mitochondrial characteristics. PMID:18765680

  5. Tackling Critical Catalytic Residues in Helicobacter pylori l-Asparaginase

    PubMed Central

    Maggi, Maristella; Chiarelli, Laurent R; Valentini, Giovanna; Scotti, Claudia

    2015-01-01

    Bacterial asparaginases (amidohydrolases, EC 3.5.1.1) are important enzymes in cancer therapy, especially for Acute Lymphoblastic Leukemia. They are tetrameric enzymes able to catalyze the deamination of l-ASN and, to a variable extent, of l-GLN, on which leukemia cells are dependent for survival. In contrast to other known l-asparaginases, Helicobacter pylori CCUG 17874 type II enzyme (HpASNase) is cooperative and has a low affinity towards l-GLN. In this study, some critical amino acids forming the active site of HpASNase (T16, T95 and E289) have been tackled by rational engineering in the attempt to better define their role in catalysis and to achieve a deeper understanding of the peculiar cooperative behavior of this enzyme. Mutations T16E, T95D and T95H led to a complete loss of enzymatic activity. Mutation E289A dramatically reduced the catalytic activity of the enzyme, but increased its thermostability. Interestingly, E289 belongs to a loop that is very variable in l-asparaginases from the structure, sequence and length point of view, and which could be a main determinant of their different catalytic features. PMID:25826146

  6. Gravitational radiation from realistic cosmic string loops

    NASA Astrophysics Data System (ADS)

    Casper, Paul; Allen, Bruce

    1995-10-01

    We examine the rates at which energy and momentum are radiated into gravitational waves by a large set of realistic cosmic string loops. The string loops are generated by numerically evolving parent loops with different initial conditions forward in time until they self-intersect, fragmenting into two child loops. The fragmentation of the child loops is followed recursively until only non-self-intersecting loops remain. The properties of the final non-self-intersecting loops are found to be independent of the initial conditions of the parent loops. We have calculated the radiated energy and momentum for a total of 11 625 stable child loops. We find that the majority of the final loops do not radiate significant amounts of spatial momentum. The velocity gained due to the rocket effect is typically small compared to the center-of-mass velocity of the fragmented loops. The distribution of gravitatoinal radiation rates in the center of mass frame of the loops, γ0≡(Gμ2)-1ΔE/Δτ, is strongly peaked in the range γ0=45-55 however, there are no loops found with γ0<40. Because the radiated spatial momentum is small, the distribution of gravitational radiation rates appears roughly the same in any reference frame. We conjecture that in the center-of-mass frame there is a lower bound γ0min>0 for the radiation rate from cosmic string loops. In a second conjecture, we identify a candidate for the loop with the minimal radiation rate and suggest that γ0min~=39.003.

  7. Force control for robotic manipulators with structurally flexible links

    NASA Astrophysics Data System (ADS)

    Latornell, Douglas John

    1992-01-01

    This thesis reports on the development of strategies for the control of contact forces exerted by a structurally flexible robotic manipulator on surfaces in its working environment. The controller is based on a multivariable, explicitly adaptive, long range predictive control algorithm. A static equilibrium bias term which is particularly applicable to the contact force control problem has been incorporated into the control algorithm cost function. A general formulation for the discrete time domain characteristic polynomial of the closed loop system has been derived and shown useful in tuning the controller. Kinematic and dynamic models of a robotic manipulator with structurally flexible links interacting with its working environment are derived. These models include inertia and damping effects in the contact dynamics in addition to the contact stiffness employed in most previous work. Linear analyses of the dynamic models for a variety of manipulator configurations reveal that the controlled variable, the contact force, is dominated by different open loop modes of the system depending on the effective stiffness of the contacting surfaces. This result has important implications for the selection of the controller parameters. The performance of the controller has been evaluated using computer simulation. A special purpose simulation program, TWOFLEX, which includes the dynamics models of the manipulator and the environment as well as the control algorithm was developed during the research. The configurations investigated using the simulation include a single flexible manipulator link, two link manipulators with both rigid and flexible links, and a two link prototype model of the Mobile Servicing System (MSS) manipulator for the proposed Space Station Freedom. The results show that the controller can be tuned to provide fast contact force step responses with minimal overshoot and zero steady-state error. The problem of maintaining control through the discontinuous

  8. Premeasured Chordal Loops for Mitral Valve Repair.

    PubMed

    Gillinov, Marc; Quinn, Reed; Kerendi, Faraz; Gaudiani, Vince; Shemin, Richard; Barnhart, Glenn; Raines, Edward; Gerdisch, Marc W; Banbury, Michael

    2016-09-01

    Premeasured expanded polytetrafluoroethylene chordal loops with integrated sutures for attachment to the papillary muscle and leaflet edges facilitate correction of mitral valve prolapse. Configured as a group of 3 loops (length range 12 to 24 mm), the loops are attached to a pledget that is passed through the papillary muscle and tied. Each of the loops has 2 sutures with attached needles; these needles are passed through the free edge of the leaflet and then the sutures are tied to each other, securing the chordal loop to the leaflet. PMID:27549563

  9. Influence of inflow angle on flexible flap aerodynamic performance

    NASA Astrophysics Data System (ADS)

    Y Zhao, H.; Ye, Z.; Li, Z. M.; Li, C.

    2013-12-01

    Large scale wind turbines have larger blade lengths and weights, which creates new challenges for blade design. This paper selects NREL S809 airfoil, and uses the parameterized technology to realize the flexible trailing edge deformation, researches the dynamic aerodynamic characteristics in the process of continuous flexible deformation, analyses the influence of inflow angle on flexible flap aerodynamic performance, in order to further realize the flexible wind turbine blade design and provides some references for the active control scheme. The results show that compared with the original airfoil, proper trailing edge deformation can improve the lift coefficient, reduce the drag coefficient, and thereby more efficiently realize flow field active control. With inflow angle increases, dynamic lift-drag coefficient hysteresis loop shape deviation occurs, even turns into different shapes. Appropriate swing angle can improve the flap lift coefficient, but may cause early separation of flow. To improve the overall performance of wind turbine blades, different angular control should be used at different cross sections, in order to achieve the best performance.

  10. 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.

  11. Rate-limiting domain and loop motions in arginine kinase.

    PubMed

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

    2011-05-17

    Arginine kinase catalyzes the reversible transfer of a phosphoryl group between ATP and arginine. It is the arthropod homologue of creatine kinase, buffering cellular ATP levels. Crystal structures of arginine kinase, in substrate-free and substrate-bound forms, have revealed large conformational changes associated with the catalytic cycle. Recent nuclear magnetic resonance identified movements of the N-terminal domain and a loop comprising residues I182--G209 with conformational exchange rates in the substrate-free enzyme similar to the turnover rate. Here, to understand whether these motions might be rate-limiting, we determined activation barriers for both the intrinsic dynamics and enzyme turnover using measurements over a temperature range of 15-30 °C. (15)N transverse relaxation dispersion yields activation barriers of 46 ± 8 and 34 ± 12 kJ/mol for the N-terminal domain and I182--G209 loop, respectively. An activation barrier of 34 ± 13 kJ/mol was obtained for enzyme turnover from steady-state kinetics. The similarity between the activation barriers is indeed consistent with turnover being limited by backbone conformational dynamics and pinpoints the locations of potentially rate-limiting motions.

  12. Size, shape, and flexibility of RNA structures

    NASA Astrophysics Data System (ADS)

    Hyeon, Changbong; Dima, Ruxandra I.; Thirumalai, D.

    2006-11-01

    Determination of sizes and flexibilities of RNA molecules is important in understanding the nature of packing in folded structures and in elucidating interactions between RNA and DNA or proteins. Using the coordinates of the structures of RNA in the Protein Data Bank we find that the size of the folded RNA structures, measured using the radius of gyration RG, follows the Flory scaling law, namely, RG=5.5N1/3Å, where N is the number of nucleotides. The shape of RNA molecules is characterized by the asphericity Δ and the shape S parameters that are computed using the eigenvalues of the moment of inertia tensor. From the distribution of Δ, we find that a large fraction of folded RNA structures are aspherical and the distribution of S values shows that RNA molecules are prolate (S>0). The flexibility of folded structures is characterized by the persistence length lp. By fitting the distance distribution function P(r ), that is computed using the coordinates of the folded RNA, to the wormlike chain model we extracted the persistence length lp. We find that lp≈1.5N0.33Å which might reflect the large separation between the free energies that stabilize secondary and tertiary structures. The dependence of lp on N implies that the average length of helices should increase as the size of RNA grows. We also analyze packing in the structures of ribosomes (30S, 50S, and 70S) in terms of RG, Δ, S, and lp. The 70S and the 50S subunits are more spherical compared to most RNA molecules. The globularity in 50S is due to the presence of an unusually large number (compared to 30S subunit) of small helices that are stitched together by bulges and loops. Comparison of the shapes of the intact 70S ribosome and the constituent particles suggests that folding of the individual molecules might occur prior to assembly.

  13. Modeling a Transient Catalytic Combustor

    NASA Technical Reports Server (NTRS)

    Tien, J. S.

    1985-01-01

    Transient model of monolith catalytic combustor presented in report done under NASA/DOE contract. Model assumes quasi-steady gas phase and thermally "thin" solid. In gas-phase treatment, several quasi-global chemical reactions assumed capable of describing CO and unburnt hydrocarbon emissions in fuel-lean operations. In steady-state computation presented, influence of selected operating and design parameters on minimum combustor length studied. When fast transient responses required, both steady and unsteady studies made to achieve meaningful compromise in design.

  14. Catalytic Organometallic Reactions of Ammonia

    PubMed Central

    Klinkenberg, Jessica L.

    2012-01-01

    Until recently, ammonia had rarely succumbed to catalytic transformations with homogeneous catalysts, and the development of such reactions that are selective for the formation of single products under mild conditions has encountered numerous challenges. However, recently developed catalysts have allowed several classes of reactions to create products with nitrogen-containing functional groups from ammonia. These reactions include hydroaminomethylation, reductive amination, alkylation, allylic substitution, hydroamination, and cross-coupling. This Minireview describes examples of these processes and the factors that control catalyst activity and selectivity. PMID:20857466

  15. 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.

  16. Catalytic membranes for fuel cells

    DOEpatents

    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.

  17. Swarming: flexible roaming plans.

    PubMed

    Partridge, Jonathan D; Harshey, Rasika M

    2013-03-01

    Movement over an agar surface via swarming motility is subject to formidable challenges not encountered during swimming. Bacteria display a great deal of flexibility in coping with these challenges, which include attracting water to the surface, overcoming frictional forces, and reducing surface tension. Bacteria that swarm on "hard" agar surfaces (robust swarmers) display a hyperflagellated and hyperelongated morphology. Bacteria requiring a "softer" agar surface (temperate swarmers) do not exhibit such a dramatic morphology. For polarly flagellated robust swarmers, there is good evidence that restriction of flagellar rotation somehow signals the induction of a large number of lateral flagella, but this scenario is apparently not relevant to temperate swarmers. Swarming bacteria can be further subdivided by their requirement for multiple stators (Mot proteins) or a stator-associated protein (FliL), secretion of essential polysaccharides, cell density-dependent gene regulation including surfactant synthesis, a functional chemotaxis signaling pathway, appropriate cyclic (c)-di-GMP levels, induction of virulence determinants, and various nutritional requirements such as iron limitation or nitrate availability. Swarming strategies are as diverse as the bacteria that utilize them. The strength of these numerous designs stems from the vantage point they offer for understanding mechanisms for effective colonization of surface niches, acquisition of pathogenic potential, and identification of environmental signals that regulate swarming. The signature swirling and streaming motion within a swarm is an interesting phenomenon in and of itself, an emergent behavior with properties similar to flocking behavior in diverse systems, including birds and fish, providing a convenient new avenue for modeling such behavior. PMID:23264580

  18. Swarming: flexible roaming plans.

    PubMed

    Partridge, Jonathan D; Harshey, Rasika M

    2013-03-01

    Movement over an agar surface via swarming motility is subject to formidable challenges not encountered during swimming. Bacteria display a great deal of flexibility in coping with these challenges, which include attracting water to the surface, overcoming frictional forces, and reducing surface tension. Bacteria that swarm on "hard" agar surfaces (robust swarmers) display a hyperflagellated and hyperelongated morphology. Bacteria requiring a "softer" agar surface (temperate swarmers) do not exhibit such a dramatic morphology. For polarly flagellated robust swarmers, there is good evidence that restriction of flagellar rotation somehow signals the induction of a large number of lateral flagella, but this scenario is apparently not relevant to temperate swarmers. Swarming bacteria can be further subdivided by their requirement for multiple stators (Mot proteins) or a stator-associated protein (FliL), secretion of essential polysaccharides, cell density-dependent gene regulation including surfactant synthesis, a functional chemotaxis signaling pathway, appropriate cyclic (c)-di-GMP levels, induction of virulence determinants, and various nutritional requirements such as iron limitation or nitrate availability. Swarming strategies are as diverse as the bacteria that utilize them. The strength of these numerous designs stems from the vantage point they offer for understanding mechanisms for effective colonization of surface niches, acquisition of pathogenic potential, and identification of environmental signals that regulate swarming. The signature swirling and streaming motion within a swarm is an interesting phenomenon in and of itself, an emergent behavior with properties similar to flocking behavior in diverse systems, including birds and fish, providing a convenient new avenue for modeling such behavior.

  19. 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

  20. 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.

  1. 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. PMID:25898071

  2. 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.

  3. 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.

  4. 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).

  5. Computational Introduction of Catalytic Activity into Proteins.

    PubMed

    Bertolani, Steve J; Carlin, Dylan Alexander; Siegel, Justin B

    2016-01-01

    Recently, there have been several successful cases of introducing catalytic activity into proteins. One method that has been used successfully to achieve this is the theozyme placement and enzyme design algorithms implemented in Rosetta Molecular Modeling Suite. Here, we illustrate how to use this software to recapitulate the placement of catalytic residues and ligand into a protein using a theozyme, protein scaffold, and catalytic constraints as input. PMID:27094294

  6. Effect of helix stability on the formation of loop-loop complexes.

    PubMed

    Sehdev, Preeti; Crews, Gordon; Soto, Ana Maria

    2012-12-01

    Kissing loop complexes are loop-loop complexes where two RNA hairpins interact through their complementary loops. In this work, we have investigated the role of the helical stems on the ability of hairpins derived from the ColE1 plasmid to associate as kissing loop complexes in the presence and absence of divalent cations. Our results show that although kissing loop complexes form more readily in the presence of Mg(2+), they are able to form in the presence of 850 mM NaCl, as long as their stems contain at least six base-pairs. Formation of the Na(+) loop-loop complexes is facilitated by changing the sequence at the stem-loop interface to include less stable AU base pairs. We suggest that the conformation at the stem-loop interface is critical in the formation of kissing loop complexes and that in the absence of Mg(2+) the conformation at the stem-loop interface is packed more loosely than with Mg(2+), to allow for a lower charge density. Consistent with this hypothesis, shortening the stems to five base pairs results in unfolding of the hairpins and formation of an extended duplex rather than a kissing loop complex because the short stems are not stable enough to tolerate the necessary conformation at the stem-loop interface to allow the formation of a kissing loop complex. PMID:23094588

  7. 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.

  8. Catalytic oxidizers and Title V requirements

    SciTech Connect

    Uberoi, M.; Rach, S.E.

    1999-07-01

    Catalytic oxidizers have been used to reduce VOC emissions from various industries including printing, chemical, paint, coatings, etc. A catalytic oxidizer uses a catalyst to reduce the operating temperature for combustion to approximately 600 F, which is substantially lower than thermal oxidation unit. Title V requirements have renewed the debate on the best methods to assure compliance of catalytic oxidizers, with some suggesting the need for continuous emission monitoring equipment. This paper will discuss the various aspects of catalytic oxidation and consider options such as monitoring inlet/outlet temperatures, delta T across the catalyst, periodic laboratory testing of catalyst samples, and preventive maintenance procedures as means of assuring continuous compliance.

  9. The C-terminal loop of aldehyde reductase determines the substrate and inhibitor specificity.

    PubMed

    Barski, O A; Gabbay, K H; Bohren, K M

    1996-11-12

    Human aldehyde reductase has a preference for carboxyl group-containing negatively charged substrates. It belongs to the NADPH-dependent aldo-keto reductase superfamily whose members are in part distinguished by unique C-terminal loops. To probe the role of the C-terminal loops in determining substrate specificities in these enzymes, two arginine residues, Arg308 and Arg311, located in the C-terminal loop of aldehyde reductase, and not found in any other C-terminal loop, were replaced with alanine residues. The catalytic efficiency of the R311A mutant for aldehydes containing a carboxyl group is reduced 150-250-fold in comparison to that of the wild-type enzyme, while substrates not containing a negative charge are unaffected. The R311A mutant is also significantly less sensitive to inhibition by dicarboxylic acids, indicating that Arg311 interacts with one of the carboxyl groups. The inhibition pattern indicates that the other carboxyl group binds to the anion binding site formed by Tyr49, His112, and the nicotinamide moiety of NADP+. The correlation between inhibitor potency and the length of the dicarboxylic acid molecules suggests a distance of approximately 10 A between the amino group of Arg311 and the anion binding site in the aldehyde reductase molecule. The sensitivity of inhibition of the R311A mutant by several commercially available aldose reductase inhibitors (ARIs) was variable, with tolrestat and zopolrestat becoming more potent inhibitors (30- and 5-fold, respectively), while others remained the same or became less potent. The catalytic properties, substrate specificity, and susceptibility to inhibition of the R308A mutant remained similar to that of the wild-type enzyme. The data provide direct evidence for C-terminal loop participation in determining substrate and inhibitor specificity of aldo-keto reductases and specifically identifies Arg311 as the basis for the carboxyl-containing substrate preference of aldehyde reductase. PMID:8916913

  10. Flexible sensors for biomedical technology.

    PubMed

    Vilela, Diana; Romeo, Agostino; Sánchez, Samuel

    2016-02-01

    Flexible sensing devices have gained a great deal of attention among the scientific community in recent years. The application of flexible sensors spans over several fields, including medicine, industrial automation, robotics, security, and human-machine interfacing. In particular, non-invasive health-monitoring devices are expected to play a key role in the improvement of patient life and in reducing costs associated with clinical and biomedical diagnostic procedures. Here, we focus on recent advances achieved in flexible devices applied on the human skin for biomedical and healthcare purposes. PMID:26675174

  11. Guideline Implementation: Processing Flexible Endoscopes.

    PubMed

    Bashaw, Marie A

    2016-09-01

    The updated AORN "Guideline for processing flexible endoscopes" provides guidance to perioperative, endoscopy, and sterile processing personnel for processing all types of reusable flexible endoscopes and accessories in all procedural settings. This article focuses on key points of the guideline to help perioperative personnel safely and effectively process flexible endoscopes to prevent infection transmission. The key points address verification of manual cleaning, mechanical cleaning and processing, storage in a drying cabinet, determination of maximum storage time before reprocessing is needed, and considerations for implementing a microbiologic surveillance program. Perioperative RNs should review the complete guideline for additional information and for guidance when writing and updating policies and procedures.

  12. Flexible sensors for biomedical technology.

    PubMed

    Vilela, Diana; Romeo, Agostino; Sánchez, Samuel

    2016-02-01

    Flexible sensing devices have gained a great deal of attention among the scientific community in recent years. The application of flexible sensors spans over several fields, including medicine, industrial automation, robotics, security, and human-machine interfacing. In particular, non-invasive health-monitoring devices are expected to play a key role in the improvement of patient life and in reducing costs associated with clinical and biomedical diagnostic procedures. Here, we focus on recent advances achieved in flexible devices applied on the human skin for biomedical and healthcare purposes.

  13. 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.

  14. Guideline Implementation: Processing Flexible Endoscopes.

    PubMed

    Bashaw, Marie A

    2016-09-01

    The updated AORN "Guideline for processing flexible endoscopes" provides guidance to perioperative, endoscopy, and sterile processing personnel for processing all types of reusable flexible endoscopes and accessories in all procedural settings. This article focuses on key points of the guideline to help perioperative personnel safely and effectively process flexible endoscopes to prevent infection transmission. The key points address verification of manual cleaning, mechanical cleaning and processing, storage in a drying cabinet, determination of maximum storage time before reprocessing is needed, and considerations for implementing a microbiologic surveillance program. Perioperative RNs should review the complete guideline for additional information and for guidance when writing and updating policies and procedures. PMID:27568535

  15. A Flexible Electrode Based on Iron Phosphide Nanotubes for Overall Water Splitting.

    PubMed

    Yan, Ya; Xia, Bao Yu; Ge, Xiaoming; Liu, Zhaolin; Fisher, Adrian; Wang, Xin

    2015-12-01

    The design of cheap and efficient water splitting systems for sustainable hydrogen production has attracted increasing attention. A flexible electrode, based on carbon cloth substrate and iron phosphide nanotubes coated with an iron oxide/phosphate layer, is shown to catalyze overall water splitting. The as-prepared flexible electrode demonstrates remarkable electrocatalytic activity for both the hydrogen evolution reaction (HER) and the oxygen evolution reaction (OER) at modest overpotentials. The surface iron oxide/phosphate, which is formed in situ, is proposed to improve the HER activity by facilitating the water-dissociation step and serves directly as the catalytically-active component for the OER process.

  16. 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).

  17. Flight Testing of a Cryogenic Capillary Pumped Loop

    NASA Technical Reports Server (NTRS)

    Ku, Jentung; Kobel, Mark; Bugby, David; Kroliczek, Edward; Baumann, Jane; Cullimore, Brent

    1999-01-01

    Future space-based cryogenic systems will require enhanced integration flexibility, lower weight reduced parasitic penalties, better vibration isolation, and a variety of other improvements to meet performance goals. Additionally, there is an increasing need to locate cooling sources remotely from cooled components. In the past flexible conductive links were used and worked well in most cases. However, as the transport lengths increase, conductive couplings become heavier and less effective, and must be replaced by higher performance systems. One available option, which can meet many of these future requirements, is the cryogenic capillary pumped loop (CCPL). The development of the CCPL technology started in 1992, following the success of the room temperature CPLS. The extrapolation of CCPL technology to cryogenic temperatures offers many performance benefits, which are not currently within the reach of traditional heat pipes or conductive links. Specific advantages of the CCPL technology pertaining to cryocooler integration include: (1) greater capillary pumping pressure for improved ground testability; (2) improved mechanical isolation; (3) faster diode shutdown and lower reverse heat leaks; (4) tighter control of detector temperature; (5) variable or fixed conductance operation; and (6) ease of integration due to their flexibility. The applications of CCPL technology are numerous. Military and commercial applications include surveillance satellites, earth observing satellites, deep space observation systems, medical devices, and many other cryogenic systems. Over the past few years, several breadboard and prototype CCPLs have been built and ground tested. A prototype CCPL has demonstrated successful operation between 80K and 110K with heat loads between O.5W and 12W using nitrogen as the working fluid, and 35K and 40K with head loads of 0.25W to 3.5W using neon. In order to verify CCPL performance in a microgravity environment, a flight unit, CCPL-5, was tested

  18. Capillary pumped loop application guide

    NASA Astrophysics Data System (ADS)

    Cullimore, Brent A.

    Capillary pumped loops (CPLs) have undergone extensive development since the late 1970's, and represent a maturing technology that is beginning to appear in spacecraft designs. Perhaps because most CPL literature is intended for CPL and heat pipe dedvelopers, or perhaps because of the myriad of component design and layout options available, many thermal control designers are either unfamiliar with the capabilities offered by CPLs, or are confused about their limitations. This survey paper is targeted toward thermal control designers who must decide when and where to use CPLs, or having chosen a CPL solution, must deal with system-level integration and test issues.

  19. Cygnus Loop: A double bubble?

    NASA Astrophysics Data System (ADS)

    West, J.; Safi-Harb, S.; Reichardt, I.; Stil, J.; Kothes, R.; Jaffe, T.; Galfacts Team

    2016-06-01

    The Cygnus Loop is a well-studied supernova remnant (SNR) that has been observed across the electromagnetic spectrum. Although widely believed to be an SNR shell with a blow-out region in the south, we consider the possibility that this object is two SNRs projected along the same line-of-sight by using multi-wavelength images and modelling. Our results show that a model of two objects including some overlap region/interaction between the two objects has the best match to the observed data.

  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. Interpolating gain-scheduled H∞ loop shaping design for high speed ball screw feed drives.

    PubMed

    Dong, Liang; Tang, WenCheng; Bao, DaFei

    2015-03-01

    This paper presents a method to design servo controllers for flexible ball screw drives with time-varying dynamics, which are mainly due to the time-varying table position and the workpiece mass. A gain-scheduled H∞ loop shaping controller is designed to achieve high tracking performance against the dynamic variations. H∞ loop shaping design procedure incorporates open loop shaping by a set of compensators to obtain performance/robust stability tradeoffs. The interpolating gain-scheduled controller is obtained by interpolating the state space model of the linear time-invariant (LTI) controllers estimated for fixed values of the scheduling parameters and a linear least squares problem can be solved. The proposed controller has been compared with P/PI with velocity and acceleration feedforward and adaptive backstepping sliding mode control experimentally. The experimental results indicate that the tracking performance has been improved and the robustness for time-varying dynamics has been achieved with the proposed scheme.

  2. Closed-Loop Neuroscience and Non-Invasive Brain Stimulation: A Tale of Two Loops.

    PubMed

    Zrenner, Christoph; Belardinelli, Paolo; Müller-Dahlhaus, Florian; Ziemann, Ulf

    2016-01-01

    Closed-loop neuroscience is receiving increasing attention with recent technological advances that enable complex feedback loops to be implemented with millisecond resolution on commodity hardware. We summarize emerging conceptual and methodological frameworks that are available to experimenters investigating a "brain in the loop" using non-invasive brain stimulation and briefly review the experimental and therapeutic implications. We take the view that closed-loop neuroscience in fact deals with two conceptually quite different loops: a "brain-state dynamics" loop, used to couple with and modulate the trajectory of neuronal activity patterns, and a "task dynamics" loop, that is the bidirectional motor-sensory interaction between brain and (simulated) environment, and which enables goal-directed behavioral tasks to be incorporated. Both loops need to be considered and combined to realize the full experimental and therapeutic potential of closed-loop neuroscience. PMID:27092055

  3. Flexible Transparent Electronic Gas Sensors.

    PubMed

    Wang, Ting; Guo, Yunlong; Wan, Pengbo; Zhang, Han; Chen, Xiaodong; Sun, Xiaoming

    2016-07-01

    Flexible and transparent electronic gas sensors capable of real-time, sensitive, and selective analysis at room-temperature, have gained immense popularity in recent years for their potential to be integrated into various smart wearable electronics and display devices. Here, recent advances in flexible transparent sensors constructed from semiconducting oxides, carbon materials, conducting polymers, and their nanocomposites are presented. The sensing material selection, sensor device construction, and sensing mechanism of flexible transparent sensors are discussed in detail. The critical challenges and future development associated with flexible and transparent electronic gas sensors are presented. Smart wearable gas sensors are believed to have great potential in environmental monitoring and noninvasive health monitoring based on disease biomarkers in exhaled gas.

  4. 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.

  5. Flexible Transparent Electronic Gas Sensors.

    PubMed

    Wang, Ting; Guo, Yunlong; Wan, Pengbo; Zhang, Han; Chen, Xiaodong; Sun, Xiaoming

    2016-07-01

    Flexible and transparent electronic gas sensors capable of real-time, sensitive, and selective analysis at room-temperature, have gained immense popularity in recent years for their potential to be integrated into various smart wearable electronics and display devices. Here, recent advances in flexible transparent sensors constructed from semiconducting oxides, carbon materials, conducting polymers, and their nanocomposites are presented. The sensing material selection, sensor device construction, and sensing mechanism of flexible transparent sensors are discussed in detail. The critical challenges and future development associated with flexible and transparent electronic gas sensors are presented. Smart wearable gas sensors are believed to have great potential in environmental monitoring and noninvasive health monitoring based on disease biomarkers in exhaled gas. PMID:27276698

  6. 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.

  7. Ultra-Thin, Flexible Electronics

    NASA Technical Reports Server (NTRS)

    Holland, Brian; McPherson, Ryan; Zhang, Tan; Hou, Zhenwei; Dean, Robert; Johnson, R. Wayne; DelCastillo, Linda; Moussessian, Alina

    2008-01-01

    Thinned die can be used to realize ultra-thin flexible electronics for applications such as conformal and wearable electronics. Three techniques have been developed to achieve this goal using thinned die: die flip chip bonded onto flexible substrates, die laminated onto LCP films, and die embedded in polyimide. A key to achieving each of these techniques is the thinning of die to a thickness of 50 microns or thinner. Conventional CMP processing can be used to thin to 50 microns. At 50 microns, the active die become flexible and must be handled by temporarily bonding them to a holder die, for further processing. Once bonded face down to the holder die, the active die can be further thinned by DRIE etching the exposed backside. The thinned die can then been packaged in or on the flexible substrate.

  8. Fuel Flexibility in Combustion

    SciTech Connect

    Freeman, M.C.; O'Dowd, W.J.; Mathur, M.P.; Walbert, G.F.

    2001-11-06

    This poster presents research findings from cofiring studies of various biomass feedstocks such as pentachlorophenol (PCP) and creosote-treated wood, lumber mill and furniture waste sawdusts, pallets, feedlot biomass (cattle manure), hybrid willow, and switchgrass with several bituminous and subbituminous coals. This research includes evaluation of advanced instrumentation and the study of interrelated combustion/emissions issues, such as char burnout, impacts on SO2, NOx, fine particulate (PM2.5), mercury (Hg) and other trace emissions, as well as issues impacting heat transfer, such as ash deposition slagging/fouling behavior. Biomass cofiring in large industrial and utility coal-fired boilers is a practical approach for increasing renewable energy given the wide availability, capital investment, and established performance of coal-fired boilers for providing efficient, low cost power. Although some utility biomass cofiring is successfully practiced in the U.S. and abroad, establishing long-term reliability and improving economics are still significant needs, along with research to support advanced combustion in future Vision 21 systems. Biomass cofiring in Vision 21 systems may reduce fossil CO2 emissions per MWe at capital and operations/maintenance cost savings relative to other technology options. Because an increasing number (currently 14) states have recently passed legislation establishing renewable portfolio standards (RPS), goals, or set-asides that will impact new power generation by 2009 and beyond, cofiring may broaden the appeal of Vision 21 systems to solve other environmental issues, including reducing landfill requirements. Legislation has been proposed to establish a federal RPS as well as extend IRS Section 29/45 tax credits (e.g., $0.005-0.010/kW-hr) for cofiring residues to supplement existing incentives, such as a $0.015/kW-hr tax credit for closed loop biomass (e.g., energy crops, such as switchgrass, hybrid willow) gasification. In addition

  9. Robust disturbance rejection for flexible mechanical structures

    NASA Astrophysics Data System (ADS)

    Enzmann, Marc R.; Doeschner, Christian

    2000-06-01

    Topic of the presentation is a procedure to determine controller parameters using principles from Internal Model Control (IMC) in combination with Quantitative Feedback Theory (QFT) for robust vibration control of flexible mechanical structures. IMC design is based on a parameterization of all controllers that stabilize a given nominal plant, called the Q-parameter or Youla-parameter. It will be shown that it is possible to choose the controller structure and the Q- parameter in a very straightforward manner, so that a low order controller results, which stabilizes the given nominal model. Additional constraints can be implemented, so that the method allows for a direct and transparent trade-off between control performance and controller complexity and facilitates the inclusion of low-pass filters. In order to test (and if necessary augment) the inherent robust performance of the resulting controllers, boundaries based on the work of Kidron and Yaniv are calculated in the Nichols-Charts of the open loop and the complementary sensitivity function. The application of these boundaries is presented. Very simple uncertainty models for resonant modes are used to assess the robustness of the design. Using a simply structured plant as illustrative example we will demonstrate the design process. This will illuminate several important features of the design process, e.g. trade-off between conflicting objectives, trade- off between controller complexity and achievable performance.

  10. The incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery

    PubMed Central

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

    2014-01-01

    Proteins fluctuate between alternative conformations, which presents a challenge for ligand discovery because such flexibility is difficult to treat computationally owing to problems with conformational sampling and energy weighting. Here, we describe a flexible-docking method that samples and weights protein conformations using experimentally-derived conformations as a guide. The crystallographically refined occupancies of these conformations, which are observable in an apo receptor structure, define energy penalties for docking. In a large prospective library screen, we identified new ligands that target specific receptor conformations of a cavity in Cytochrome c Peroxidase, and we confirm both ligand pose and associated receptor conformation predictions by crystallography. The inclusion of receptor flexibility led to ligands with new chemotypes and physical properties. By exploiting experimental measures of loop and side chain flexibility, this method can be extended to the discovery of new ligands for hundreds of targets in the Protein Data Bank where similar experimental information is available. PMID:24950326

  11. 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.

  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. 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

  14. 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

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

    PubMed

    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

  16. Developmental constraints on behavioural flexibility

    PubMed Central

    Holekamp, Kay E.; Swanson, Eli M.; Van Meter, Page E.

    2013-01-01

    We suggest that variation in mammalian behavioural flexibility not accounted for by current socioecological models may be explained in part by developmental constraints. From our own work, we provide examples of constraints affecting variation in behavioural flexibility, not only among individuals, but also among species and higher taxonomic units. We first implicate organizational maternal effects of androgens in shaping individual differences in aggressive behaviour emitted by female spotted hyaenas throughout the lifespan. We then compare carnivores and primates with respect to their locomotor and craniofacial adaptations. We inquire whether antagonistic selection pressures on the skull might impose differential functional constraints on evolvability of skulls and brains in these two orders, thus ultimately affecting behavioural flexibility in each group. We suggest that, even when carnivores and primates would theoretically benefit from the same adaptations with respect to behavioural flexibility, carnivores may nevertheless exhibit less behavioural flexibility than primates because of constraints imposed by past adaptations in the morphology of the limbs and skull. Phylogenetic analysis consistent with this idea suggests greater evolutionary lability in relative brain size within families of primates than carnivores. Thus, consideration of developmental constraints may help elucidate variation in mammalian behavioural flexibility. PMID:23569298

  17. Developmental constraints on behavioural flexibility.

    PubMed

    Holekamp, Kay E; Swanson, Eli M; Van Meter, Page E

    2013-05-19

    We suggest that variation in mammalian behavioural flexibility not accounted for by current socioecological models may be explained in part by developmental constraints. From our own work, we provide examples of constraints affecting variation in behavioural flexibility, not only among individuals, but also among species and higher taxonomic units. We first implicate organizational maternal effects of androgens in shaping individual differences in aggressive behaviour emitted by female spotted hyaenas throughout the lifespan. We then compare carnivores and primates with respect to their locomotor and craniofacial adaptations. We inquire whether antagonistic selection pressures on the skull might impose differential functional constraints on evolvability of skulls and brains in these two orders, thus ultimately affecting behavioural flexibility in each group. We suggest that, even when carnivores and primates would theoretically benefit from the same adaptations with respect to behavioural flexibility, carnivores may nevertheless exhibit less behavioural flexibility than primates because of constraints imposed by past adaptations in the morphology of the limbs and skull. Phylogenetic analysis consistent with this idea suggests greater evolutionary lability in relative brain size within families of primates than carnivores. Thus, consideration of developmental constraints may help elucidate variation in mammalian behavioural flexibility. PMID:23569298

  18. 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.

  19. IRBIT Interacts with the Catalytic Core of Phosphatidylinositol Phosphate Kinase Type Iα and IIα through Conserved Catalytic Aspartate Residues

    PubMed Central

    Ando, Hideaki; Hirose, Matsumi; Gainche, Laura; Kawaai, Katsuhiro; Bonneau, Benjamin; Ijuin, Takeshi; Itoh, Toshiki; Takenawa, Tadaomi; Mikoshiba, Katsuhiko

    2015-01-01

    Phosphatidylinositol phosphate kinases (PIPKs) are lipid kinases that generate phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), a critical lipid signaling molecule that regulates diverse cellular functions, including the activities of membrane channels and transporters. IRBIT (IP3R-binding protein released with inositol 1,4,5-trisphosphate) is a multifunctional protein that regulates diverse target proteins. Here, we report that IRBIT forms signaling complexes with members of the PIPK family. IRBIT bound to all PIPK isoforms in heterologous expression systems and specifically interacted with PIPK type Iα (PIPKIα) and type IIα (PIPKIIα) in mouse cerebellum. Site-directed mutagenesis revealed that two conserved catalytic aspartate residues of PIPKIα and PIPKIIα are involved in the interaction with IRBIT. Furthermore, phosphatidylinositol 4-phosphate, Mg2+, and/or ATP interfered with the interaction, suggesting that IRBIT interacts with catalytic cores of PIPKs. Mutations of phosphorylation sites in the serine-rich region of IRBIT affected the selectivity of its interaction with PIPKIα and PIPKIIα. The structural flexibility of the serine-rich region, located in the intrinsically disordered protein region, is assumed to underlie the mechanism of this interaction. Furthermore, in vitro binding experiments and immunocytochemistry suggest that IRBIT and PIPKIα interact with the Na+/HCO3− cotransporter NBCe1-B. These results suggest that IRBIT forms signaling complexes with PIPKIα and NBCe1-B, whose activity is regulated by PI(4,5)P2. PMID:26509711

  20. Wilson loop from a Dyson equation

    SciTech Connect

    Pak, M.; Reinhardt, H.

    2009-12-15

    The Dyson equation proposed for planar temporal Wilson loops in the context of supersymmetric gauge theories is critically analyzed thereby exhibiting its ingredients and approximations involved. We reveal its limitations and identify its range of applicability in nonsupersymmetric gauge theories. In particular, we show that this equation is applicable only to strongly asymmetric planar Wilson loops (consisting of a long and a short pair of loop segments) and as a consequence the Wilsonian potential can be extracted only up to intermediate distances. By this equation the Wilson loop is exclusively determined by the gluon propagator. We solve the Dyson equation in Coulomb gauge for the temporal Wilson loop with the instantaneous part of the gluon propagator and for the spatial Wilson loop with the static gluon propagator obtained in the Hamiltonian approach to continuum Yang-Mills theory and on the lattice. In both cases we find a linearly rising color potential.

  1. 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

  2. Diesel engine catalytic combustor system. [aircraft engines

    NASA Technical Reports Server (NTRS)

    Ream, L. W. (Inventor)

    1984-01-01

    A low compression turbocharged diesel engine is provided in which the turbocharger can be operated independently of the engine to power auxiliary equipment. Fuel and air are burned in a catalytic combustor to drive the turbine wheel of turbine section which is initially caused to rotate by starter motor. By opening a flapper value, compressed air from the blower section is directed to catalytic combustor when it is heated and expanded, serving to drive the turbine wheel and also to heat the catalytic element. To start, engine valve is closed, combustion is terminated in catalytic combustor, and the valve is then opened to utilize air from the blower for the air driven motor. When the engine starts, the constituents in its exhaust gas react in the catalytic element and the heat generated provides additional energy for the turbine section.

  3. Catalytic ignition of hydrogen and oxygen propellants

    NASA Technical Reports Server (NTRS)

    Zurawski, Robert L.; Green, James M.

    1988-01-01

    An experimental program was conducted to evaluate the catalytic ignition of gaseous hydrogen and oxygen propellants. Shell 405 granular catalyst and a monolithic sponge catalyst were tested. Mixture ratio, mass flow rate, propellant temperature, and back pressure were varied parametrically in testing to determine the operational limits of the catalytic igniter. The test results show that the gaseous hydrogen and oxygen propellant combination can be ignited catalytically using Shell 405 catalyst over a wide range of mixture ratios, mass flow rates, and propellant injection temperatures. These operating conditions must be optimized to ensure reliable ignition for an extended period of time. A cyclic life of nearly 2000, 2 sec pulses at nominal operating conditions was demonstrated with the catalytic igniter. The results of the experimental program and the established operational limits for a catalytic igniter using the Shell 405 catalysts are presented.

  4. Method of fabricating a catalytic structure

    DOEpatents

    Rollins, Harry W.; Petkovic, Lucia M.; Ginosar, Daniel M.

    2009-09-22

    A precursor to a catalytic structure comprising zinc oxide and copper oxide. The zinc oxide has a sheet-like morphology or a spherical morphology and the copper oxide comprises particles of copper oxide. The copper oxide is reduced to copper, producing the catalytic structure. The catalytic structure is fabricated by a hydrothermal process. A reaction mixture comprising a zinc salt, a copper salt, a hydroxyl ion source, and a structure-directing agent is formed. The reaction mixture is heated under confined volume conditions to produce the precursor. The copper oxide in the precursor is reduced to copper. A method of hydrogenating a carbon oxide using the catalytic structure is also disclosed, as is a system that includes the catalytic structure.

  5. Catalytic ignition of hydrogen and oxygen propellants

    NASA Technical Reports Server (NTRS)

    Zurawski, Robert L.; Green, James M.

    1988-01-01

    An experimental program was conducted to evaluate the catalytic ignition of gaseous hydrogen and oxygen propellants. Shell 405 granular catalyst and a monolithic sponge catalyst were tested. Mixture ratio, mass flow rate, propellant temperature, and back pressure were varied parametrically in testing to determine the operational limits of the catalytic igniter. The test results show that the gaseous hydrogen and oxygen propellant combination can be ignited catalytically using Shell 405 catalyst over a wide range of mixture ratios, mass flow rates, and propellant injection temperatures. These operating conditions must be optimized to ensure reliable ignition for an extended period of time. A cyclic life of nearly 2000, 2 sec pulses at nominal operating conditions was demonstrated with the catalytic igniter. The results of the experimental program and the established operational limits for a catalytic igniter using the Shell 405 catalyst are presented.

  6. Catalytic ignition of hydrogen/oxygen

    NASA Technical Reports Server (NTRS)

    Green, James M.; Zurawski, Robert L.

    1988-01-01

    An experimental program was conducted to evaluate the catalytic ignition of gaseous hydrogen and oxygen. Shell 405 granular catalyst and a unique monolithic sponge catalyst were tested. Mixture ratio, mass flow rate, propellant inlet temperature, and back pressure were varied parametrically in testing to determine the operational limits of a catalytic igniter. The test results showed that the gaseous hydrogen/oxygen propellant combination can be ignited catalytically using Shell 405 catalyst over a wide range of mixture ratios, mass flow rates, and propellant injection temperatures. These operating conditions must be optimized to ensure reliable ignition for an extended period of time. The results of the experimental program and the established operational limits for a catalytic igniter using both the granular and monolithic catalysts are presented. The capabilities of a facility constructed to conduct the igniter testing and the advantages of a catalytic igniter over other ignition systems for gaseous hydrogen and oxygen are also discussed.

  7. Silver nanocluster catalytic microreactors for water purification

    NASA Astrophysics Data System (ADS)

    Da Silva, B.; Habibi, M.; Ognier, S.; Schelcher, G.; Mostafavi-Amjad, J.; Khalesifard, H. R. M.; Tatoulian, M.; Bonn, D.

    2016-07-01

    A new method for the elaboration of a novel type of catalytic microsystem with a high specific area catalyst is developed. A silver nanocluster catalytic microreactor was elaborated by doping a soda-lime glass with a silver salt. By applying a high power laser beam to the glass, silver nanoclusters are obtained at one of the surfaces which were characterized by BET measurements and AFM. A microfluidic chip was obtained by sealing the silver coated glass with a NOA 81 microchannel. The catalytic activity of the silver nanoclusters was then tested for the efficiency of water purification by using catalytic ozonation to oxidize an organic pollutant. The silver nanoclusters were found to be very stable in the microreactor and efficiently oxidized the pollutant, in spite of the very short residence times in the microchannel. This opens the way to study catalytic reactions in microchannels without the need of introducing the catalyst as a powder or manufacturing complex packed bed microreactors.

  8. Catalytic decarbonylation of biosourced substrates.

    PubMed

    Ternel, Jérémy; Lebarbé, Thomas; Monflier, Eric; Hapiot, Frédéric

    2015-05-11

    Linear α-olefins (LAO) are one of the main targets in the field of surfactants, lubricants, and polymers. With the depletion of petroleum resources, the production of LAO from renewable feedstocks has gained increasing interest in recent years. In the present study, we demonstrated that Ir catalysts were suitable to decarbonylate a wide range of biosourced substrates under rather mild conditions (160 °C, 5 h reaction time) in the presence of potassium iodide and acetic anhydride. The resulting LAO were obtained with good conversion and selectivity provided that the purity of the substrate, the nature of the ligand, and the amounts of the additives were controlled accurately. The catalytic system could be recovered efficiently by using a Kugelrohr distillation apparatus and recycled.

  9. Non-catalytic recuperative reformer

    SciTech Connect

    Khinkis, Mark J.; Kozlov, Aleksandr P.; Kurek, Harry

    2015-12-22

    A non-catalytic recuperative reformer has a flue gas flow path for conducting hot flue gas from a thermal process and a reforming mixture flow path for conducting a reforming mixture. At least a portion of the reforming mixture flow path is embedded in the flue gas flow path to permit heat transfer from the hot flue gas to the reforming mixture. The reforming mixture flow path contains substantially no material commonly used as a catalyst for reforming hydrocarbon fuel (e.g., nickel oxide, platinum group elements or rhenium), but instead the reforming mixture is reformed into a higher calorific fuel via reactions due to the heat transfer and residence time. In a preferred embodiment, extended surfaces of metal material such as stainless steel or metal alloy that are high in nickel content are included within at least a portion of the reforming mixture flow path.

  10. Catalytic Carbonylative Spirolactonization of Hydroxycyclopropanols.

    PubMed

    Davis, Dexter C; Walker, Katherine L; Hu, Chunhua; Zare, Richard N; Waymouth, Robert M; Dai, Mingji

    2016-08-24

    A palladium-catalyzed cascade carbonylative spirolactonization of hydroxycyclopropanols has been developed to efficiently synthesize oxaspirolactones common to many complex natural products of important therapeutic value. The mild reaction conditions, high atom economy, broad substrate scope, and scalability of this new method were highlighted in expedient total syntheses of the Turkish tobacco natural products α-levantanolide and α-levantenolide in two and four steps, respectively. The hydroxycyclopropanol substrates are readily available in one step via a Kulinkovich reaction of the corresponding lactones. Mechanistic studies utilizing high-resolution electrospray ionization mass spectrometry (ESI-MS) identified several key intermediates in the catalytic cycle, as well as those related to catalyst decomposition and competitive pathways. PMID:27459274

  11. APPARATUS FOR CATALYTICALLY COMBINING GASES

    DOEpatents

    Busey, H.M.

    1958-08-12

    A convection type recombiner is described for catalytically recombining hydrogen and oxygen which have been radiolytically decomposed in an aqueous homogeneous nuclear reactor. The device is so designed that the energy of recombination is used to circulate the gas mixture over the catalyst. The device consists of a vertical cylinder having baffles at its lower enda above these coarse screens having platinum and alumina pellets cemented thereon, and an annular passage for the return of recombined, condensed water to the reactor moderator system. This devicea having no moving parts, provides a simple and efficient means of removing the danger of accumulated hot radioactive, explosive gases, and restoring them to the moderator system for reuse.

  12. Wood stove having catalytic converter

    SciTech Connect

    Willson, A.C.

    1982-12-14

    A wood burning stove is formed with double front and rear side walls of heat conductive metal spaced apart by heat conductive spacer fins and providing air passageways by which room air is heated by conduction from the walls which are heated by the burning of wood deposited on a firebox floor supported in heat conducting relationship with the inner side walls. A catalytic converter is disposed over the fire area in the upper portion of the stove, and is arranged to receive preheated fresh secondary air which mixes with hot, incompletely combusted compounds from the fire and, in the presence of the catalyst, induces a secondary combustion of the substances. This mixture is channeled into a heat extraction chamber where the secondary combustion is completed and the resultant heat is transferred to the metal body of the stove. An exhaust passageway is provided for releasing the products of complete combustion into the atmosphere.

  13. Catalytic reactor with improved burner

    DOEpatents

    Faitani, Joseph J.; Austin, George W.; Chase, Terry J.; Suljak, George T.; Misage, Robert J.

    1981-01-01

    To more uniformly distribute heat to the plurality of catalyst tubes in a catalytic reaction furnace, the burner disposed in the furnace above the tops of the tubes includes concentric primary and secondary annular fuel and air outlets. The fuel-air mixture from the primary outlet is directed towards the tubes adjacent the furnace wall, and the burning secondary fuel-air mixture is directed horizontally from the secondary outlet and a portion thereof is deflected downwardly by a slotted baffle toward the tubes in the center of the furnace while the remaining portion passes through the slotted baffle to another baffle disposed radially outwardly therefrom which deflects it downwardly in the vicinity of the tubes between those in the center and those near the wall of the furnace.

  14. The dynamics and control of large flexible space structures, 8

    NASA Technical Reports Server (NTRS)

    Bainum, P. M.; Reddy, A. S. S. R.; Diarra, C. M.; Ananthakrishnan, S.

    1985-01-01

    A development of the in plane open loop rotational equations of motion for the proposed Spacecraft Control Laboratory Experiment (SCOLE) in orbit configuration is presented based on an Eulerian formulation. The mast is considered to be a flexible beam connected to the (rigid) shuttle and the reflector. Frequencies and mode shapes are obtained for the mast vibrational appendage modes (assumed to be decoupled) for different boundary conditions based on continuum approaches and also preliminary results are obtained using a finite element representation of the mast reflector system. The linearized rotational in plane equation is characterized by periodic coefficients and open loop system stability can be examined with an application of the Floquet theorem. Numerical results are presented to illustrate the potential instability associated with actuator time delays even for delays which represent only a small fraction of the natural period of oscillation of the modes contained in the open loop model of the system. When plant and measurement noise effects are added to the previously designed deterministic model of the hoop column system, it is seen that both the system transient and steady state performance are degraded. Mission requirements can be satisfied by appropriate assignment of cost function weighting elements and changes in the ratio of plant noise to measurement noise.

  15. Loop anomalies in the causal approach

    NASA Astrophysics Data System (ADS)

    Grigore, Dan-Radu

    2015-01-01

    We consider gauge models in the causal approach and study one-loop contributions to the chronological products and the anomalies they produce. We prove that in order greater than 4 there are no one-loop anomalies. Next we analyze one-loop anomalies in the second- and third-order of the perturbation theory. We prove that the even parity contributions (with respect to parity) do not produce anomalies; for the odd parity contributions we reobtain the well-known result.

  16. Magnetic monopole in the loop representation

    SciTech Connect

    Leal, Lorenzo; Lopez, Alexander

    2006-01-15

    We quantize, within the Loop Representation formalism, the electromagnetic field in the presence of a static magnetic pole. It is found that the loop-dependent physical wave functionals of the quantum Maxwell theory become multivalued, through a topological phase factor depending on the solid angle subtended at the monopole by a surface bounded by the loop. It is discussed how this fact generalizes what occurs in ordinary quantum mechanics in multiply connected spaces.

  17. Costas loop analysis for coherent optical receivers

    NASA Astrophysics Data System (ADS)

    Hodgkinson, T. G.

    1986-03-01

    A homodyne Costas loop receiver is analyzed taking both shot and laser phase noise sources into acount. The reciever performance is compared with that of a heterodyne receiver using an electrical Costas loop and that of a coherent receiver using a pilot carrier phase-locked loop. It is shown that, to avoid large performance penalties, beat linewidth to bit-rate ratios smaller than 0.05 percent and 0.5 percent are needed for PSK homodyne and heterodyne systems, respectively.

  18. LMFBR with booster pump in pumping loop

    DOEpatents

    Rubinstein, H.J.

    1975-10-14

    A loop coolant circulation system is described for a liquid metal fast breeder reactor (LMFBR) utilizing a low head, high specific speed booster pump in the hot leg of the coolant loop with the main pump located in the cold leg of the loop, thereby providing the advantages of operating the main pump in the hot leg with the reliability of cold leg pump operation.

  19. Wilson loops in open string theory

    SciTech Connect

    Shiraishi, K.

    1988-02-01

    Wilson loop elements on torus are introduced into the partition function of open strings as Polyakov's path integral at one-loop level. Mass spectra from compactification and expected symmetry breaking are illustrated by choosing the correct weight for the contributions from annulus and Mobius strip. The authors show that Jacobi's imaginary transformation connects the mass spectra with the Wilson loops. The application to thermo-partition function and cosmological implications are briefly discussed.

  20. Cosmic recall and the scattering picture of loop quantum cosmology

    SciTech Connect

    Kaminski, Wojciech; Pawlowski, Tomasz

    2010-04-15

    The global dynamics of a homogeneous Universe in loop quantum cosmology is viewed as a scattering process of its geometrodynamical equivalent. This picture is applied to build a flexible (easy to generalize) and not restricted just to exactly solvable models method of verifying the preservation of the semiclassicality through the bounce. The devised method is next applied to two simple examples: (i) the isotropic Friedmann-Robertson-Walker universe, and (ii) the isotropic sector of the Bianchi I model. For both of them we show that the dispersions in the logarithm of the volume ln(v) and scalar field momentum ln(p{sub {phi}}) in the distant future and past are related via strong triangle inequalities. This implies, in particular, a strict preservation of the semiclassicality (in considered degrees of freedom) in both the cases (i) and (ii). Derived inequalities are general: valid for all the physical states within the considered models.