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Sample records for fefe hydrogenase model

  1. Organometallic Complexes that Model the Active Sites of the [FeFe]- and [Fe]-Hydrogenases 

    E-print Network

    Liu, Tianbiao

    2011-02-22

    My research primarily focuses on biomimetics of the active sites of the [FeFe]- and [Fe]-hydrogenases (H2ase) and is classified into three parts. Part A: The one-electron oxidation of asymmetrically disubstituted FeIFeI models of the active site...

  2. Photoswitchable electrochemical behaviour of a [FeFe] hydrogenase model with a dithienylethene derivative.

    PubMed

    Wen, Hui-Min; Wang, Jin-Yun; Hu, Ming-Qiang; Li, Bin; Chen, Zhong-Ning; Chen, Chang-Neng

    2012-10-14

    A diiron dithiolate complex 1o with a dithienylethene (DTE) phosphine ligand has been elaborately designed and fully investigated by spectroscopic and DFT computational studies. Upon irradiation with UV light, the DTE moiety in complex 1o undergoes an excellent photocyclization reaction to attain ring-closed state 1c in high yield (>95%), accompanied by a colour change from orange to deep blue. On the other hand, upon irradiation with visible light (>460 nm), ring-closed form 1c in CH(3)CN solution reverts perfectly into ring-open form 1o. Both 1o and 1c were characterised by IR, (1)H, (31)P, (19)F NMR and electrochemical spectroscopy. The electrochemical behaviours of both the open and closed forms were investigated by cyclic voltammetry. Upon photocyclization reaction, a 290 mV (from -2.29 V to -2.00 V) positive shift is induced in the potential of electrochemical catalytic proton reduction, due to the electron-withdrawing effect of the ring-closed DTE moiety. Consequently, complex 1 can reversibly photoswitch the potential of proton reduction on the [FeFe] moiety. PMID:22907061

  3. Electronic structure of an [FeFe] hydrogenase model complex in solution revealed by X-ray absorption spectroscopy using narrow-band emission detection.

    PubMed

    Leidel, Nils; Chernev, Petko; Havelius, Kajsa G V; Schwartz, Lennart; Ott, Sascha; Haumann, Michael

    2012-08-29

    High-resolution X-ray absorption spectroscopy with narrow-band X-ray emission detection, supported by density functional theory calculations (XAES-DFT), was used to study a model complex, ([Fe(2)(?-adt)(CO)(4)(PMe(3))(2)] (1, adt = S-CH(2)-(NCH(2)Ph)-CH(2)-S), of the [FeFe] hydrogenase active site. For 1 in powder material (1(powder)), in MeCN solution (1'), and in its three protonated states (1H, 1Hy, 1HHy; H denotes protonation at the adt-N and Hy protonation of the Fe-Fe bond to form a bridging metal hydride), relations between the molecular structures and the electronic configurations were determined. EXAFS analysis and DFT geometry optimization suggested prevailing rotational isomers in MeCN, which were similar to the crystal structure or exhibited rotation of the (CO) ligands at Fe1 (1(CO), 1Hy(CO)) and in addition of the phenyl ring (1H(CO,Ph), 1HHy(CO,Ph)), leading to an elongated solvent-exposed Fe-Fe bond. Isomer formation, adt-N protonation, and hydride binding caused spectral changes of core-to-valence (pre-edge of the Fe K-shell absorption) and of valence-to-core (Kß(2,5) emission) electronic transitions, and of K? RIXS data, which were quantitatively reproduced by DFT. The study reveals (1) the composition of molecular orbitals, for example, with dominant Fe-d character, showing variations in symmetry and apparent oxidation state at the two Fe ions and a drop in MO energies by ~1 eV upon each protonation step, (2) the HOMO-LUMO energy gaps, of ~2.3 eV for 1(powder) and ~2.0 eV for 1', and (3) the splitting between iron d(z(2)) and d(x(2)-y(2)) levels of ~0.5 eV for the nonhydride and ~0.9 eV for the hydride states. Good correlations of reduction potentials to LUMO energies and oxidation potentials to HOMO energies were obtained. Two routes of facilitated bridging hydride binding thereby are suggested, involving ligand rotation at Fe1 for 1Hy(CO) or adt-N protonation for 1HHy(CO,Ph). XAES-DFT thus enables verification of the effects of ligand substitutions in solution for guided improvement of [FeFe] catalysts. PMID:22860512

  4. New Insights into [FeFe] Hydrogenase Activation and Maturase Function

    PubMed Central

    Kuchenreuther, Jon M.; Britt, R. David; Swartz, James R.

    2012-01-01

    [FeFe] hydrogenases catalyze H2 production using the H-cluster, an iron-sulfur cofactor that contains carbon monoxide (CO), cyanide (CN–), and a dithiolate bridging ligand. The HydE, HydF, and HydG maturases assist in assembling the H-cluster and maturing hydrogenases into their catalytically active form. Characterization of these maturases and in vitro hydrogenase activation methods have helped elucidate steps in the H-cluster biosynthetic pathway such as the HydG-catalyzed generation of the CO and CN– ligands from free tyrosine. We have refined our cell-free approach for H-cluster synthesis and hydrogenase maturation by using separately expressed and purified HydE, HydF, and HydG. In this report, we illustrate how substrates and protein constituents influence hydrogenase activation, and for the first time, we show that each maturase can function catalytically during the maturation process. With precise control over the biomolecular components, we also provide evidence for H-cluster synthesis in the absence of either HydE or HydF, and we further show that hydrogenase activation can occur without exogenous tyrosine. Given these findings, we suggest a new reaction sequence for the [FeFe] hydrogenase maturation pathway. In our model, HydG independently synthesizes an iron-based compound with CO and CN– ligands that is a precursor to the H-cluster [2Fe]H subunit, and which we have termed HydG-co. We further propose that HydF is a transferase that stabilizes HydG-co and also shuttles the complete [2Fe]H subcluster to the hydrogenase, a translocation process that may be catalyzed by HydE. In summary, this report describes the first example of reconstructing the [FeFe] hydrogenase maturation pathway using purified maturases and subsequently utilizing this in vitro system to better understand the roles of HydE, HydF, and HydG. PMID:23049878

  5. Process and genes for expression and overexpression of active [FeFe] hydrogenases

    DOEpatents

    Seibert, Michael; King, Paul W; Ghirardi, Maria Lucia; Posewitz, Matthew C; Smolinski, Sharon L

    2014-09-16

    A process for expression of active [FeFe]-hydrogenase in a host organism that does not contain either the structural gene(s) for [FeFe]-hydrogenases and/or homologues for the maturation genes HydE, HydF and HyG, comprising: cloning the structural hydrogenase gene(s) and/or the maturation genes HydE, HydF and HydG from an organisms that contains these genes into expression plasmids; transferring the plasmids into an organism that lacks a native [FeFe]-hydrogenase or that has a disrupted [FeFe]-hydrogenase and culturing it aerobically; and inducing anaerobiosis to provide [FeFe] hydrogenase biosynthesis and H?2#191 production.

  6. Structural Insight into the Complex of Ferredoxin and [FeFe] Hydrogenase from Chlamydomonas reinhardtii.

    PubMed

    Rumpel, Sigrun; Siebel, Judith F; Diallo, Mamou; Farès, Christophe; Reijerse, Edward J; Lubitz, Wolfgang

    2015-07-27

    The transfer of photosynthetic electrons by the ferredoxin PetF to the [FeFe] hydrogenase HydA1 in the microalga Chlamydomonas reinhardtii is a key step in hydrogen production. Electron delivery requires a specific interaction between PetF and HydA1. However, because of the transient nature of the electron-transfer complex, a crystal structure remains elusive. Therefore, we performed protein-protein docking based on new experimental data from a solution NMR spectroscopy investigation of native and gallium-substituted PetF. This provides valuable information about residues crucial for complex formation and electron transfer. The derived complex model might help to pinpoint residue substitution targets for improved hydrogen production. PMID:26010059

  7. A diferrous dithiolate as a model of the elusive H(ox)(inact) state of the [FeFe] hydrogenases: an electrochemical and theoretical dissection of its redox chemistry.

    PubMed

    Chouffai, Dounia; Capon, Jean-François; De Gioia, Luca; Pétillon, François Y; Schollhammer, Philippe; Talarmin, Jean; Zampella, Giuseppe

    2015-01-01

    The reduction of the Fe(II)Fe(II) complex [Fe2(CO)2{P(OMe)3}2(?(2)-IMe-CH2-IMe)(?-CO)(?-pdt)](2+) (2P(2+); pdt = S(CH2)3S), which is a synthetic model of the H cluster of the [FeFe] hydrogenases in its inactive state, has been investigated electrochemically and theoretically (by density functional theory, DFT) in order to determine the mechanisms, intermediates, and products of the related processes. The electrochemical reduction of 2P(2+) occurs according to an ECE-type reaction where the intervening chemical step is the loss of one P(OMe)3 ligand. This outcome, which is based on cyclic voltammetric experiments, is strongly supported by DFT calculations that provide additional information on the intermediates and the energetics of the reactions involved. The electrochemical reoxidation of the neutral product of the reduction follows an EEC process where the chemical step is the binding of P(OMe)3 to a dicationic intermediate. DFT calculations reveal that this intermediate has an unusual geometry wherein one of the two C-H bonds of a side methylene from the pdt group forms an agostic interaction with one Fe center. This interaction is crucial to stabilize the 32e(-) diferrous center and concomitantly to preserve Fe(II) from binding of weakly coordinating species. Nonetheless, it could be displaced by a relatively stronger electron donor such as H2, which could be relevant for the design of new oxidation catalysts. PMID:25496017

  8. NRVS and EPR Spectroscopy of 57Fe-enriched [FeFe] Hydrogenase Indicate Stepwise Assembly of the H-cluster†

    PubMed Central

    Kuchenreuther, Jon M.; Guo, Yisong; Wang, Hongxin; Myers, William K.; George, Simon J.; Boyke, Christine A.; Yoda, Yoshitaka; Alp, E. Ercan; Zhao, Jiyong; Britt, R. David; Swartz, James R.; Cramer, Stephen P.

    2013-01-01

    The [FeFe] hydrogenase from Clostridium pasteurianum (CpI) harbors four Fe–S clusters that facilitate electron transfer to the H-cluster, a ligand-coordinated six-iron prosthetic group that catalyzes the redox interconversion of protons and H2. Here, we have used 57Fe nuclear resonance vibrational spectroscopy (NRVS) to study the iron centers in CpI, and we compare our data to that for a [4Fe–4S] ferredoxin as well as a model complex resembling the [2Fe]H catalytic domain of the H-cluster. In order to enrich the hydrogenase with 57Fe nuclei, we used cell-free methods to post-translationally mature the enzyme. Specifically, inactive CpI apoprotein with 56Fe-labeled Fe–S clusters was activated in vitro using 57Fe-enriched maturation proteins. This approach enabled us to selectively label the [2Fe]H subcluster with 57Fe, which NRVS confirms by detecting 57Fe–CO and 57Fe–CN normal modes from the H-cluster nonprotein ligands. The NRVS and iron quantification results also suggest that the hydrogenase contains a second 57Fe–S cluster. EPR spectroscopy indicates that this 57Fe-enriched metal center is not the [4Fe– 4S]H subcluster of the H-cluster. This finding demonstrates that the CpI hydrogenase retained an 56Fe-enriched [4Fe–4S]H cluster during in vitro maturation, providing unambiguous evidence for stepwise assembly of the H-cluster. In addition, this work represents the first NRVS characterization of [FeFe] hydrogenases. PMID:23249091

  9. Patterns of [FeFe] hydrogenase diversity in the gut microbial communities of lignocellulose-feeding higher termites.

    PubMed

    Ballor, Nicholas R; Leadbetter, Jared R

    2012-08-01

    Hydrogen is the central free intermediate in the degradation of wood by termite gut microbes and can reach concentrations exceeding those measured for any other biological system. Degenerate primers targeting the largest family of [FeFe] hydrogenases observed in a termite gut metagenome have been used to explore the evolution and representation of these enzymes in termites. Sequences were cloned from the guts of the higher termites Amitermes sp. strain Cost010, Amitermes sp. strain JT2, Gnathamitermes sp. strain JT5, Microcerotermes sp. strain Cost008, Nasutitermes sp. strain Cost003, and Rhyncotermes sp. strain Cost004. Each gut sample harbored a more rich and evenly distributed population of hydrogenase sequences than observed previously in the guts of lower termites and Cryptocercus punctulatus. This accentuates the physiological importance of hydrogen for higher termite gut ecosystems and may reflect an increased metabolic burden, or metabolic opportunity, created by a lack of gut protozoa. The sequences were phylogenetically distinct from previously sequenced [FeFe] hydrogenases. Phylogenetic and UniFrac comparisons revealed congruence between host phylogeny and hydrogenase sequence library clustering patterns. This may reflect the combined influences of the stable intimate relationship of gut microbes with their host and environmental alterations in the gut that have occurred over the course of termite evolution. These results accentuate the physiological importance of hydrogen to termite gut ecosystems. PMID:22636002

  10. Cysteine as a ligand platform in the biosynthesis of the FeFe hydrogenase H cluster.

    PubMed

    Suess, Daniel L M; Bürstel, Ingmar; De La Paz, Liliana; Kuchenreuther, Jon M; Pham, Cindy C; Cramer, Stephen P; Swartz, James R; Britt, R David

    2015-09-15

    Hydrogenases catalyze the redox interconversion of protons and H2, an important reaction for a number of metabolic processes and for solar fuel production. In FeFe hydrogenases, catalysis occurs at the H cluster, a metallocofactor comprising a [4Fe-4S]H subcluster coupled to a [2Fe]H subcluster bound by CO, CN(-), and azadithiolate ligands. The [2Fe]H subcluster is assembled by the maturases HydE, HydF, and HydG. HydG is a member of the radical S-adenosyl-L-methionine family of enzymes that transforms Fe and L-tyrosine into an [Fe(CO)2(CN)] synthon that is incorporated into the H cluster. Although it is thought that the site of synthon formation in HydG is the "dangler" Fe of a [5Fe] cluster, many mechanistic aspects of this chemistry remain unresolved including the full ligand set of the synthon, how the dangler Fe initially binds to HydG, and how the synthon is released at the end of the reaction. To address these questions, we herein show that L-cysteine (Cys) binds the auxiliary [4Fe-4S] cluster of HydG and further chelates the dangler Fe. We also demonstrate that a [4Fe-4S]aux[CN] species is generated during HydG catalysis, a process that entails the loss of Cys and the [Fe(CO)2(CN)] fragment; on this basis, we suggest that Cys likely completes the coordination sphere of the synthon. Thus, through spectroscopic analysis of HydG before and after the synthon is formed, we conclude that Cys serves as the ligand platform on which the synthon is built and plays a role in both Fe(2+) binding and synthon release. PMID:26324916

  11. Spectroscopic Investigations of [FeFe] Hydrogenase Maturated with [(57)Fe2(adt)(CN)2(CO)4](2-).

    PubMed

    Gilbert-Wilson, Ryan; Siebel, Judith F; Adamska-Venkatesh, Agnieszka; Pham, Cindy C; Reijerse, Edward; Wang, Hongxin; Cramer, Stephen P; Lubitz, Wolfgang; Rauchfuss, Thomas B

    2015-07-22

    The preparation and spectroscopic characterization of a CO-inhibited [FeFe] hydrogenase with a selectively (57)Fe-labeled binuclear subsite is described. The precursor [(57)Fe2(adt)(CN)2(CO)4](2-) was synthesized from the (57)Fe metal, S8, CO, (NEt4)CN, NH4Cl, and CH2O. (Et4N)2[(57)Fe2(adt)(CN)2(CO)4] was then used for the maturation of the [FeFe] hydrogenase HydA1 from Chlamydomonas reinhardtii, to yield the enzyme selectively labeled at the [2Fe]H subcluster. Complementary (57)Fe enrichment of the [4Fe-4S]H cluster was realized by reconstitution with (57)FeCl3 and Na2S. The Hox-CO state of [2(57)Fe]H and [4(57)Fe-4S]H HydA1 was characterized by Mössbauer, HYSCORE, ENDOR, and nuclear resonance vibrational spectroscopy. PMID:26091969

  12. A radical intermediate in tyrosine scission to the CO and CN- ligands of FeFe hydrogenase.

    PubMed

    Kuchenreuther, Jon M; Myers, William K; Stich, Troy A; George, Simon J; Nejatyjahromy, Yaser; Swartz, James R; Britt, R David

    2013-10-25

    The radical S-adenosylmethionine (SAM) enzyme HydG lyses free l-tyrosine to produce CO and CN(-) for the assembly of the catalytic H cluster of FeFe hydrogenase. We used electron paramagnetic resonance spectroscopy to detect and characterize HydG reaction intermediates generated with a set of (2)H, (13)C, and (15)N nuclear spin-labeled tyrosine substrates. We propose a detailed reaction mechanism in which the radical SAM reaction, initiated at an N-terminal 4Fe-4S cluster, generates a tyrosine radical bound to a C-terminal 4Fe-4S cluster. Heterolytic cleavage of this tyrosine radical at the C?-C? bond forms a transient 4-oxidobenzyl (4OB(•)) radical and a dehydroglycine bound to the C-terminal 4Fe-4S cluster. Electron and proton transfer to this 4OB(•) radical forms p-cresol, with the conversion of this dehydroglycine ligand to Fe-bound CO and CN(-), a key intermediate in the assembly of the 2Fe subunit of the H cluster. PMID:24159045

  13. Electrochemical Measurements of the Kinetics of Inhibition of Two FeFe Hydrogenases by O2 Demonstrate That the Reaction Is Partly Reversible.

    PubMed

    Orain, Christophe; Saujet, Laure; Gauquelin, Charles; Soucaille, Philippe; Meynial-Salles, Isabelle; Baffert, Carole; Fourmond, Vincent; Bottin, Hervé; Léger, Christophe

    2015-10-01

    The mechanism of reaction of FeFe hydrogenases with oxygen has been debated. It is complex, apparently very dependent on the details of the protein structure, and difficult to study using conventional kinetic techniques. Here we build on our recent work on the anaerobic inactivation of the enzyme [Fourmond et al. Nat. Chem. 2014, 4, 336-342] to propose and apply a new method for studying this reaction. Using electrochemical measurements of the turnover rate of hydrogenase, we could resolve the first steps of the inhibition reaction and accurately determine their rates. We show that the two most studied FeFe hydrogenases, from Chlamydomonas reinhardtii and Clostridium acetobutylicum, react with O2 according to the same mechanism, despite the fact that the former is much more O2 sensitive than the latter. Unlike often assumed, both enzymes are reversibly inhibited by a short exposure to O2. This will have to be considered to elucidate the mechanism of inhibition, before any prediction can be made regarding which mutations will improve oxygen resistance. We hope that the approach described herein will prove useful in this respect. PMID:26352172

  14. Spectroscopic Characterization of the Bridging Amine in the Active Site of [FeFe] Hydrogenase Using Isotopologues of the H-Cluster.

    PubMed

    Adamska-Venkatesh, Agnieszka; Roy, Souvik; Siebel, Judith F; Simmons, Trevor R; Fontecave, Marc; Artero, Vincent; Reijerse, Edward; Lubitz, Wolfgang

    2015-10-14

    The active site of [FeFe] hydrogenase contains a catalytic binuclear iron subsite coordinated by CN(-) and CO ligands as well as a unique azadithiolate (adt(2-)) bridging ligand. It has been established that this binuclear cofactor is synthesized and assembled by three maturation proteins HydE, -F, and -G. By means of in vitro maturation in the presence of (15)N- and (13)C-labeled tyrosine it has been shown that the CN(-) and CO ligands originate from tyrosine. The source of the bridging adt(2-) ligand, however, remains unknown. In order to identify the nitrogen of the bridging amine using HYSCORE spectroscopy and distinguish its spectroscopic signature from that of the CN(-) nitrogens, we studied three isotope-labeled variants of the H-cluster ((15)N-adt(2-)/C(14)N(-), (15)N-adt(2-)/C(15)N(-), and (14)N-adt(2-)/C(15)N(-)) and extracted accurate values of the hyperfine and quadrupole couplings of both CN(-) and adt(2-) nitrogens. This will allow an evaluation of isotopologues of the H-cluster generated by in vitro bioassembly in the presence of various (15)N-labeled potential precursors as possible sources of the bridging ligand. PMID:26393426

  15. The HydG Enzyme Generates an Fe(CO)2(CN) Synthon in Assembly of the FeFe Hydrogenase H-Cluster

    PubMed Central

    Kuchenreuther, Jon M.; Myer, William K.; Suess, Daniel L. M.; Stich, Troy A.; Pelmenschikov, Vladimir; Shiigi, Stacey A.; Cramer, Stephen P.; Swartz, James R.; Britt, R. David; George, Simon J.

    2015-01-01

    Three iron-sulfur proteins–HydE, HydF, and HydG–play a key role in the synthesis of the [2Fe]H component of the catalytic H-cluster of FeFe hydrogenase. The radical S-adenosyl-l-methionine enzyme HydG lyses free tyrosine to produce p-cresol and the CO and CN? ligands of the [2Fe]H cluster. Here, we applied stopped-flow Fourier transform infrared and electron-nuclear double resonance spectroscopies to probe the formation of HydG-bound Fe-containing species bearing CO and CN? ligands with spectroscopic signatures that evolve on the 1- to 1000-second time scale. Through study of the 13C, 15N, and 57Fe isotopologs of these intermediates and products, we identify the final HydG-bound species as an organometallic Fe(CO)2(CN) synthon that is ultimately transferred to apohydrogenase to form the [2Fe]H component of the H-cluster. PMID:24458644

  16. Solution-phase photochemistry of a [FeFe]hydrogenase model compound: Evidence of photoinduced isomerisation

    SciTech Connect

    Kania, Rafal; Hunt, Neil T.; Frederix, Pim W. J. M.; Wright, Joseph A.; Pickett, Christopher J.; Ulijn, Rein V.

    2012-01-28

    The solution-phase photochemistry of the [FeFe] hydrogenase subsite model ({mu}-S(CH{sub 2}){sub 3}S)Fe{sub 2}(CO){sub 4}(PMe{sub 3}){sub 2} has been studied using ultrafast time-resolved infrared spectroscopy supported by density functional theory calculations. In three different solvents, n-heptane, methanol, and acetonitrile, relaxation of the tricarbonyl intermediate formed by UV photolysis of a carbonyl ligand leads to geminate recombination with a bias towards a thermodynamically less stable isomeric form, suggesting that facile interconversion of the ligand groups at the Fe center is possible in the unsaturated species. In a polar or hydrogen bonding solvent, this process competes with solvent substitution leading to the formation of stable solvent adduct species. The data provide further insight into the effect of incorporating non-carbonyl ligands on the dynamics and photochemistry of hydrogenase-derived biomimetic compounds.

  17. Atomic resolution modeling of the ferredoxin:[FeFe] hydrogenase complex from Chlamydomonas reinhardtii.

    PubMed

    Chang, Christopher H; King, Paul W; Ghirardi, Maria L; Kim, Kwiseon

    2007-11-01

    The [FeFe] hydrogenases HydA1 and HydA2 in the green alga Chlamydomonas reinhardtii catalyze the final reaction in a remarkable metabolic pathway allowing this photosynthetic organism to produce H(2) from water in the chloroplast. A [2Fe-2S] ferredoxin is a critical branch point in electron flow from Photosystem I toward a variety of metabolic fates, including proton reduction by hydrogenases. To better understand the binding determinants involved in ferredoxin:hydrogenase interactions, we have modeled Chlamydomonas PetF1 and HydA2 based on amino-acid sequence homology, and produced two promising electron-transfer model complexes by computational docking. To characterize these models, quantitative free energy calculations at atomic resolution were carried out, and detailed analysis of the interprotein interactions undertaken. The protein complex model we propose for ferredoxin:HydA2 interaction is energetically favored over the alternative candidate by 20 kcal/mol. This proposed model of the electron-transfer complex between PetF1 and HydA2 permits a more detailed view of the molecular events leading up to H(2) evolution, and suggests potential mutagenic strategies to modulate electron flow to HydA2. PMID:17660315

  18. Extended X-ray absorption fine structure of the [Fe]-hydrogenase Hmd active site

    NASA Astrophysics Data System (ADS)

    Salomone-Stagni, Marco; Vogt, Sonja; Shima, Seigo; Meyer-Klaucke, Wolfram

    2009-11-01

    Hydrogenases are enzymes that catalyze the reversible oxidation of molecular hydrogen. Although their structure and catalytic mechanism are of considerable applied interest as models for the development of efficient catalysts for hydrogen fueled processes, the understanding of how hydrogenases react with H2 is only in its infancy. Two of the three known types of hydrogenases are iron-sulfur proteins that contain a dinuclear metal center, either [NiFe] or [FeFe]. In contrast, [Fe]-hydrogenase is the only mononuclear hydrogenase and thus a perfect system for studying the structural and electronic determinants of these enzymes. Here we summarize recent improvements in modeling based on the EXAFS signal and the geometric structure of this metalloenzyme in its as isolated or reconstituted form. The individual contributions to the EXAFS resulting in two different structural models are presented and discussed. Inspired by the new crystal structure, we show an advanced EXAFS model for the enzyme from Methanothermobacter marburgensis.

  19. [FeFe]-hydrogenase models assembled into vesicular structures.

    PubMed

    Menzel, Kristin; Apfel, Ulf-Peter; Wolter, Nonio; Rüger, Ronny; Alpermann, Theodor; Steiniger, Frank; Gabel, Detlef; Förster, Stephan; Weigand, Wolfgang; Fahr, Alfred

    2014-03-01

    Compartmentalization is a major prerequisite for the origin of life on earth according to Wächtershäuser "Iron-Sulfur-World". The hypothesis is mainly based on an autocatalytic inorganic energy reproducing redox system consisting of iron and sulfur as requirement for the subsequent synthesis of complex organic structures. Here, we modified [FeFe]-hydrogenase models by means of covalent coupling to either oleic acid or the amphiphilic block copolymer polybutadiene-polyethyleneoxide (PB-PEO) and incorporated those into the membranes of vesicles composed of phospholipids (liposomes) or the unmodified amphiphilic polymer (polymersomes). We employed a [2Fe-2S] cluster as a hydrogenase model, since these structures are known to be suitable catalysts for the generation of H2 in the presence of weak acids. Successful incorporation was confirmed by spectrophotometric iron quantification and the vesicles formed were characterized by size determination (photon correlation spectroscopy (PCS)), and zeta potential as well as by cryo-transmission electron microscopy (Cryo-TEM). The modified models could be incorporated into liposomes or polymersomes up to molar proportions of 3.15% and 28%, respectively. Due to the immobilization in vesicular bilayers the [FeFe]-hydrogenase models can even exhibit catalytic action under the particular conditions of the intravesicular microenvironment. Our results suggest that the vesicular systems described may be applied as a nanoreactor for the reduction of encapsulated substances by generating hydrogen and thus as a minimal cell model. PMID:24006843

  20. Microbial communities responsible for fixation of CO2 revealed by using mcrA, cbbM, cbbL, fthfs, fefe-hydrogenase genes as molecular biomarkers in petroleum reservoirs of different temperatures

    NASA Astrophysics Data System (ADS)

    Liu, J.-F.; Mbadinga, S. M.; Sun, X.-B.; Yang, G.-C.; Yang, S.-Z.; Gu, J.-D.; Mu, B.-Z.

    2015-01-01

    Sequestration of CO2 in oil reservoir is one of the feasible options for mitigating atmospheric CO2 building up. The in situ bioconversion of sequestrated CO2 to methane by microorganisms inhabiting oil reservoirs is feasible. To evaluate the potential of in situ microbial fixation and conversion of CO2 into CH4 in oil reservoirs, a comprehensive molecular survey was performed to reveal microbial communities inhabiting four oil reservoirs with different temperatures by analysis of functional genes involved in the biochemical pathways of CO2 fixation and CH4 synthesis (cbbM, cbbL, fthfs, [FeFe]-hydrogenase encoding gene, and mcrA). A rich diversity of these functional genes was found in all the samples with both high and low temperatures and they were affiliated to members of the Proteobacteria (cbbL and cbbM, fthfs), Firmicutes and Actinobacteria (fthfs), uncultured bacteria ([FeFe]-hydrogenase), and Methanomirobiales, Methanobacteriales and Methanosarcinales (mcrA). The predominant methanogens were all identified to be hydrogenotrophic CO2-reducing physiological types. These results showed that functional microbial communities capable of microbial fixation and bioconversion of CO2 into methane inhabit widely in oil reservoirs, which is helpful to microbial recycling of sequestrated CO2 to further new energy in oil reservoirs.

  1. Reconstitution of [Fe]-hydrogenase using model complexes.

    PubMed

    Shima, Seigo; Chen, Dafa; Xu, Tao; Wodrich, Matthew D; Fujishiro, Takashi; Schultz, Katherine M; Kahnt, Jörg; Ataka, Kenichi; Hu, Xile

    2015-12-01

    [Fe]-Hydrogenase catalyses the reversible hydrogenation of a methenyltetrahydromethanopterin substrate, which is an intermediate step during the methanogenesis from CO2 and H2. The active site contains an iron-guanylylpyridinol cofactor, in which Fe(2+) is coordinated by two CO ligands, as well as an acyl carbon atom and a pyridinyl nitrogen atom from a 3,4,5,6-substituted 2-pyridinol ligand. However, the mechanism of H2 activation by [Fe]-hydrogenase is unclear. Here we report the reconstitution of [Fe]-hydrogenase from an apoenzyme using two FeGP cofactor mimics to create semisynthetic enzymes. The small-molecule mimics reproduce the ligand environment of the active site, but are inactive towards H2 binding and activation on their own. We show that reconstituting the enzyme using a mimic that contains a 2-hydroxypyridine group restores activity, whereas an analogous enzyme with a 2-methoxypyridine complex was essentially inactive. These findings, together with density functional theory computations, support a mechanism in which the 2-hydroxy group is deprotonated before it serves as an internal base for heterolytic H2 cleavage. PMID:26587715

  2. Nitrogen heterocyclic carbene containing pentacoordinate iron dicarbonyl as a [Fe]-hydrogenase active site model.

    PubMed

    Jiang, Shuang; Zhang, Tianyong; Zhang, Xia; Zhang, Guanghui; Li, Bin

    2015-10-14

    A novel pentacoordinate mono iron dicarbonyl complex bearing a nitrogen heterocyclic carbene ligand was reported as a model of a [Fe]-hydrogenase active site, which exhibits interesting proton coupled CO binding reactivity, electro-catalytic proton reduction and catalytic transfer hydrogenation reactivity. PMID:26369379

  3. [NiFeSe]-Hydrogenase Chemistry

    E-print Network

    Wombwell, Claire; Caputo, Christine A.; Reisner, Erwin

    2015-10-21

    in exploring the unique ‘chemistry of [NiFeSe]-hydrogenases’ through biomimetic model chemistry and the ‘chemistry with [NiFeSe]-hydrogenases’ in semi-artificial, photosynthetic systems. We gain perspective from the structural, spectroscopic...

  4. Modeling the sublattice magnetizations for the layered bcc nanojunction … Fe[Fe1-cCoc ]? Fe … systems

    NASA Astrophysics Data System (ADS)

    Ashokan, V.; Abou Ghantous, M.; Khater, A.

    2015-12-01

    Ferromagnetic nanojunctions … Fe[Fe1-cCoc ]? Fe …, with ? is the number of layers which constitute the nanojunction, based on Fe/Co alloy are considered for the first time in this work. We model the salient magnetic properties of the layered ferromagnetic nanostructures between magnetically ordered iron leads. The effective field theory (EFT) Ising spin method is used to compute reliable Jav exchange values for the VCA Fe/Co alloy materials in comparison with experimental data and compared to existing DFT calculated exchange interactions. The new set of exchange interaction values between pairs of nearest neighbors atom in the alloy are deduced and agree with previous known measurement of lattice constant for this alloy. Using the combined EFT and mean field theory (MFT) spin methods, the sublattice magnetizations of the Fe and Co sites on the individual bcc basal planes of the layered nanostructures, are calculated and analyzed. The sublattice magnetizations, effective magnetic moments per site, and the possible ferromagnetic order of the layers [Fe1-cCoc ]? on the individual bcc atomic planes of the embedded nanostructures for all temperatures and in particular for TcFe ? T ?T? ? ? are presented as a function of temperature and thicknesses of the layered ferromagnetic nanostructures, for different stable concentrations c=0.25, 0.5 and 0.75. In the absence of first principles calculations for these basic physical variables for the layered nanostructures between iron leads, the combined EFT and MFT approach yields the only available information for them at present in the absence of a possible Curie temperature for these alloys. These variables are necessary for certain spin dynamic computations, as for the ballistic magnon transport across embedded nanojunctions in magnonics. The model is general, and may applied directly to other composite magnetic elements and embedded nanostructures.

  5. Micropatterns of [Fe-Fe]-Hydrogenase Active-Site Model Complexes Fabricated by Electro-Oxidative Lithography.

    PubMed

    Liu, He; Trautwein, Ralf; Schröter, Bernd; Ignaszak, Anna; Weigand, Wolfgang; Hoeppener, Stephanie; Schubert, Ulrich S

    2015-10-27

    [Fe-Fe]-hydrogenase active site model complexes ([Fe(CO)3]2[(?-SCH2)2C(CH2OH)2]) were immobilized on micropatterned n-octadecyltrichlorosilane (OTS) monolayers deposited on a Si substrate to form a microscale catalytic system. The micropatterns were generated by electro-oxidative lithography performed with a conductive TEM grid. The [Fe-Fe]-hydrogenase active-site complex molecules were selectively anchored in lithographic line areas with good coverage. Additionally, the biomimetic metal centers of the hydrogenase active-site complex molecules still maintained their catalytic activity and their redox-active properties after the immobilization process, which was proven by cyclic voltammetry. PMID:26465964

  6. Functional model for the [Fe] hydrogenase inspired by the frustrated Lewis pair concept.

    PubMed

    Kalz, Kai F; Brinkmeier, Alexander; Dechert, Sebastian; Mata, Ricardo A; Meyer, Franc

    2014-11-26

    [Fe] hydrogenase (Hmd) catalyzes the heterolytic splitting of H2 by using, in its active site, a unique organometallic iron-guanylylpyridinol (FeGP) cofactor and, as a hydride acceptor, the substrate methenyltetrahydromethanopterin (methenyl-H4MPT(+)). The combination FeGP/methenyl-H4MPT(+) and its reactivity bear resemblance to the concept of frustrated Lewis pairs (FLPs), some of which have been shown to heterolytically activate H2. The present work exploits this interpretation of Hmd reactivity by using the combination of Lewis basic ruthenium metalates, namely K[CpRu(CO)2] (KRp) and a related polymeric Cp/Ru/CO compound (Rs), with the new imidazolinium salt 1,3-bis(2,6-difluorophenyl)-2-(4-tolyl)imidazolinium bromide ([(Tol)Im(F4)](+)Br(-)) that was designed to emulate the hydride acceptor properties of methenyl-H4MPT(+). Solid-state structures of [(Tol)Im(F4)](+)Br(-) and the corresponding imidazolidine H(Tol)Im(F4) reveal that the heterocycle undergoes similar structural changes as in the biological substrate. DFT calculations indicate that heterolytic splitting of dihydrogen by the FLP Rp(-)/[(Tol)Im(F4)](+) is exothermic, but the formation of the initial Lewis pair should be unfavorable in polar solvents. Consequently the combination Rp(-)/[(Tol)Im(F4)](+) does not react with H2 but leads instead to side products from nucleophilic substitution (k = 4 × 10(-2) L mol (-1) s(-1) at room temperature). In contrast, the heterogeneous combination Rs/[(Tol)Im(F4)](+) does split H2 heterolytically to give H(Tol)Im(F4) and HRuCp(CO)2 (HRp) or D(Tol)Im(F4) and DRp when using D2. The reaction has been followed by (1)H/(2)H and (19)F NMR spectroscopy as well as by IR spectroscopy and reaches 96% conversion after 1 d. Formation of H(Tol)Im(F4) under these conditions demonstrates that superelectrophilic activation by protonation, which has been proposed for methenyl-H4MPT(+) to increase its carbocationic character, is not necessarily required for an imidazolinium ion to serve as a hydride acceptor. This unprecedented functional model for the [Fe] hydrogenase, using a Lewis acidic imidazolinium salt as a biomimetic hydride acceptor in combination with an organometallic Lewis base, may provide new inspiration for biomimetic H2 activation. PMID:25353322

  7. Fundamental Studies of Recombinant Hydrogenases

    SciTech Connect

    Adams, Michael W

    2014-01-25

    This research addressed the long term goals of understanding the assembly and organization of hydrogenase enzymes, of reducing them in size and complexity, of determining structure/function relationships, including energy conservation via charge separation across membranes, and in screening for novel H2 catalysts. A key overall goal of the proposed research was to define and characterize minimal hydrogenases that are produced in high yields and are oxygen-resistant. Remarkably, in spite of decades of research carried out on hydrogenases, it is not possible to readily manipulate or design the enzyme using molecular biology approaches since a recombinant form produced in a suitable host is not available. Such resources are essential if we are to understand what constitutes a “minimal” hydrogenase and design such catalysts with certain properties, such as resistance to oxygen, extreme stability and specificity for a given electron donor. The model system for our studies is Pyrococcus furiosus, a hyperthermophile that grows optimally at 100°C, which contains three different nickel-iron [NiFe-] containing hydrogenases. Hydrogenases I and II are cytoplasmic while the other, MBH, is an integral membrane protein that functions to both evolve H2 and pump protons. Three important breakthroughs were made during the funding period with P. furiosus soluble hydrogenase I (SHI). First, we produced an active recombinant form of SHI in E. coli by the co-expression of sixteen genes using anaerobically-induced promoters. Second, we genetically-engineered P. furiosus to overexpress SHI by an order of magnitude compared to the wild type strain. Third, we generated the first ‘minimal’ form of SHI, one that contained two rather than four subunits. This dimeric form was stable and active, and directly interacted with a pyruvate-oxidizing enzyme with any intermediate electron carrier. The research resulted in five peer-reviewed publications.

  8. [NiFeSe]-Hydrogenase Chemistry.

    PubMed

    Wombwell, Claire; Caputo, Christine A; Reisner, Erwin

    2015-11-17

    The development of technology for the inexpensive generation of the renewable energy vector H2 through water splitting is of immediate economic, ecological, and humanitarian interest. Recent interest in hydrogenases has been fueled by their exceptionally high catalytic rates for H2 production at a marginal overpotential, which is presently only matched by the nonscalable noble metal platinum. The mechanistic understanding of hydrogenase function guides the design of synthetic catalysts, and selection of a suitable hydrogenase enables direct applications in electro- and photocatalysis. [FeFe]-hydrogenases display excellent H2 evolution activity, but they are irreversibly damaged upon exposure to O2, which currently prevents their use in full water splitting systems. O2-tolerant [NiFe]-hydrogenases are known, but they are typically strongly biased toward H2 oxidation, while H2 production by [NiFe]-hydrogenases is often product (H2) inhibited. [NiFeSe]-hydrogenases are a subclass of [NiFe]-hydrogenases with a selenocysteine residue coordinated to the active site nickel center in place of a cysteine. They exhibit a combination of unique properties that are highly advantageous for applications in water splitting compared with other hydrogenases. They display a high H2 evolution rate with marginal inhibition by H2 and tolerance to O2. [NiFeSe]-hydrogenases are therefore one of the most active molecular H2 evolution catalysts applicable in water splitting. Herein, we summarize our recent progress in exploring the unique chemistry of [NiFeSe]-hydrogenases through biomimetic model chemistry and the chemistry with [NiFeSe]-hydrogenases in semiartificial photosynthetic systems. We gain perspective from the structural, spectroscopic, and electrochemical properties of the [NiFeSe]-hydrogenases and compare them with the chemistry of synthetic models of this hydrogenase active site. Our synthetic models give insight into the effects on the electronic properties and reactivity of the active site upon the introduction of selenium. We have utilized the exceptional properties of the [NiFeSe]-hydrogenase from Desulfomicrobium baculatum in a number of photocatalytic H2 production schemes, which are benchmark systems in terms of single site activity, tolerance toward O2, and in vitro water splitting with biological molecules. Each system comprises a light-harvesting component, which allows for light-driven electron transfer to the hydrogenase in order for it to catalyze H2 production. A system with [NiFeSe]-hydrogenase on a dye-sensitized TiO2 nanoparticle gives an enzyme-semiconductor hybrid for visible light-driven generation of H2 with an enzyme-based turnover frequency of 50 s(-1). A stable and inexpensive polymeric carbon nitride as a photosensitizer in combination with the [NiFeSe]-hydrogenase shows good activity for more than 2 days. Light-driven H2 evolution with the enzyme and an organic dye under high O2 levels demonstrates the excellent robustness and feasibility of water splitting with a hydrogenase-based scheme. This has led, most recently, to the development of a light-driven full water splitting system with a [NiFeSe]-hydrogenase wired to the water oxidation enzyme photosystem II in a photoelectrochemical cell. In contrast to the other systems, this photoelectrochemical system does not rely on a sacrificial electron donor and allowed us to establish the long sought after light-driven water splitting with an isolated hydrogenase. PMID:26488197

  9. Biomimetic peptide-based models of [FeFe]-hydrogenases: utilization of phosphine-containing peptides.

    PubMed

    Roy, Souvik; Nguyen, Thuy-Ai D; Gan, Lu; Jones, Anne K

    2015-09-01

    Two synthetic strategies for incorporating diiron analogues of [FeFe]-hydrogenases into short peptides via phosphine functional groups are described. First, utilizing the amine side chain of lysine as an anchor, phosphine carboxylic acids can be coupled via amide formation to resin-bound peptides. Second, artificial, phosphine-containing amino acids can be directly incorporated into peptides via solution phase peptide synthesis. The second approach is demonstrated using three amino acids each with a different phosphine substituent (diphenyl, diisopropyl, and diethyl phosphine). In total, five distinct monophosphine-substituted, diiron model complexes were prepared by reaction of the phosphine-peptides with diiron hexacarbonyl precursors, either (?-pdt)Fe2(CO)6 or (?-bdt)Fe2(CO)6 (pdt = propane-1,3-dithiolate, bdt = benzene-1,2-dithiolate). Formation of the complexes was confirmed by UV/Vis, FTIR and (31)P NMR spectroscopy. Electrocatalysis by these complexes is reported in the presence of acetic acid in mixed aqueous-organic solutions. Addition of water results in enhancement of the catalytic rates. PMID:26223293

  10. Synthetic Active Site Model of the [NiFeSe] Hydrogenase

    PubMed Central

    Wombwell, Claire; Reisner, Erwin

    2015-01-01

    A dinuclear synthetic model of the [NiFeSe] hydrogenase active site and a structural, spectroscopic and electrochemical analysis of this complex is reported. [NiFe(‘S2Se2’)(CO)3] (H2‘S2Se2’=1,2-bis(2-thiabutyl-3,3-dimethyl-4-selenol)benzene) has been synthesized by reacting the nickel selenolate complex [Ni(‘S2Se2’)] with [Fe(CO)3bda] (bda=benzylideneacetone). X-ray crystal structure analysis confirms that [NiFe(‘S2Se2’)(CO)3] mimics the key structural features of the enzyme active site, including a doubly bridged heterobimetallic nickel and iron center with a selenolate terminally coordinated to the nickel center. Comparison of [NiFe(‘S2Se2’)(CO)3] with the previously reported thiolate analogue [NiFe(‘S4’)(CO)3] (H2‘S4’=H2xbsms=1,2-bis(4-mercapto-3,3-dimethyl-2-thiabutyl)benzene) showed that the selenolate groups in [NiFe(‘S2Se2’)(CO)3] give lower carbonyl stretching frequencies in the IR spectrum. Electrochemical studies of [NiFe(‘S2Se2’)(CO)3] and [NiFe(‘S4’)(CO)3] demonstrated that both complexes do not operate as homogenous H2 evolution catalysts, but are precursors to a solid deposit on an electrode surface for H2 evolution catalysis in organic and aqueous solution. PMID:25847470

  11. Brownian Dynamics and Molecular Dynamics Study of the Association Between Hydrogenase and Ferredoxin from the Chlamydomonas reinhardtii

    SciTech Connect

    Long, H.; Chang, C. H.; King, P. W.; Ghirardi, M. L.; Kim, K.

    2008-10-01

    The [FeFe] hydrogenase from the green alga Chlamydomonas reinhardtii can catalyze the reduction of protons to hydrogen gas using electrons supplied from photosystem I and transferred via ferredoxin. To better understand the association of the hydrogenase and the ferredoxin, we have simulated the process over multiple timescales. A Brownian dynamics simulation method gave an initial thorough sampling of the rigid-body translational and rotational phase spaces, and the resulting trajectories were used to compute the occupancy and free-energy landscapes. Several important hydrogenase-ferredoxin encounter complexes were identified from this analysis, which were then individually simulated using atomistic molecular dynamics to provide more details of the hydrogenase and ferredoxin interaction. The ferredoxin appeared to form reasonable complexes with the hydrogenase in multiple orientations, some of which were good candidates for inclusion in a transition state ensemble of configurations for electron transfer.

  12. Hydrogen Activation by Biomimetic [NiFe]-Hydrogenase Model Containing Protected Cyanide Cofactors

    PubMed Central

    Manor, Brian C.; Rauchfuss, Thomas B.

    2013-01-01

    Described are experiments that allow incorporation of cyanide cofactors and hydride substrate into active site models [NiFe]-hydrogenases (H2ases). Complexes of the type (CO)2(CN)2Fe(pdt)Ni(dxpe), (dxpe = dppe, 1; dxpe = dcpe, 2) bind the Lewis acid B(C6F5)3 (BArF3) to give the adducts (CO)2(CNBArF3)2Fe(pdt)Ni(dxpe), (1(BArF3)2, 2(BArF3)2). Upon decarbonylation using amine oxides, these adducts react with H2 to give hydrido derivatives Et4N[(CO)(CNBArF3)2Fe(H)(pdt)Ni(dxpe)], (dxpe = dppe, Et4N[H3(BArF3)2]; dxpe = dcpe, Et4N[H4(BArF3)2]). Crystallographic analysis shows that Et4N[H3(BArF3)2] generally resembles the active site of the enzyme in the reduced, hydride-containing states (Ni-C/R). The Fe-H…Ni center is unsymmetrical with rFe-H = 1.51(3) and rNi-H = 1.71(3) Å. Both crystallographic and 19F NMR analysis show that the CNBArF3? ligands occupy basal and apical sites. Unlike cationic Ni-Fe hydrides, [H3(BArF3)2]? and [H4(BArF3)2]? oxidize at mild potentials, near the Fc+/0 couple. Electrochemical measurements indicate that in the presence of base, [H3(BArF3)2]? catalyzes the oxidation of H2. NMR evidence indicates dihydrogen bonding between these anionic hydrides and ammonium salts, which is relevant to the mechanism of hydrogenogenesis. In the case of Et4N[H3(BArF3)2], strong acids such as HCl induce H2 release to give the chloride Et4N[(CO)(CNBArF3)2Fe(pdt)(Cl)Ni(dppe)]. PMID:23899049

  13. Modelling NiFe hydrogenases: nickel-based electrocatalysts for hydrogen production.

    PubMed

    Canaguier, Sigolène; Artero, Vincent; Fontecave, Marc

    2008-01-21

    NiFe hydrogenases are unique enzymes that catalyze the H+/H2 interconversion with remarkable efficiency. The determination of the tridimensional structure of their active site (a sulfur-rich dinuclear nickel-iron cluster with diatomic cyanide and carbonyl ligands) has stimulated the synthesis of a variety of nickel-based complexes as potential electrocatalysts for hydrogen production. These catalysts may provide an adequate alternative to platinum. This paper gives an historical perspective of this biomimetic structural approach and then focusses on recently reported bio-inspired functional mimics displaying electrocatalytic activity for hydrogen production. PMID:18411840

  14. The Bioorganometallic Chemistry of Iron and the Diatomic Ligands CO and NO as Related to Hydrogenase Active Sites and Dinitrosyl Iron Complexes 

    E-print Network

    Bethel, Ryan D

    2014-08-20

    The discovery of a diiron organometallic active site, found in the [FeFe]-Hydrogenase (H2ase) enzyme, has led to a revisiting of the classic organometallic chemistry involving the Fe-Fe bond and bridging ligands. This diiron site is connected to a...

  15. Synthesis, Characterization, and Reactivity of Functionalized Trinuclear Iron–Sulfur Clusters – A New Class of Bioinspired Hydrogenase Models

    PubMed Central

    Kaiser, Manuel; Knör, Günther

    2015-01-01

    The air- and moisture-stable iron–sulfur carbonyl clusters Fe3S2(CO)7(dppm) (1) and Fe3S2(CO)7(dppf) (2) carrying the bisphosphine ligands bis(diphenylphosphanyl)methane (dppm) and 1,1?-bis(diphenylphosphanyl)ferrocene (dppf) were prepared and fully characterized. Two alternative synthetic routes based on different thionation reactions of triiron dodecacarbonyl were tested. The molecular structures of the methylene-bridged compound 1 and the ferrocene-functionalized derivative 2 were determined by single-crystal X-ray diffraction. The catalytic reactivity of the trinuclear iron–sulfur cluster core for proton reduction in solution at low overpotential was demonstrated. These deeply colored bisphosphine-bridged sulfur-capped iron carbonyl systems are discussed as promising candidates for the development of new bioinspired model compounds of iron-based hydrogenases. PMID:26512211

  16. Chemistry and the hydrogenases.

    PubMed

    Evans, David J; Pickett, Christopher J

    2003-09-01

    The reversible reduction protons to dihydrogen: 2H+ + 2e [symbol: see text] H2 is deceptively the simplest of reactions but one that requires multistep catalysis to proceed at practical rates. How the metal-sulfur clusters of the hydrogenases catalyse this interconversion is currently the subject of extensive structural, spectroscopic and mechanistic studies of the enzymes, of synthetic assemblies and of in silico models. This is driven both by curiosity and by the view that an understanding of the underlying chemistry may inform the design of new electrocatalytic systems for hydrogen production or uptake, pertinent to energy transduction technology in an 'Hydrogen Economy'. Can chemists design materials that replace the expensive platinum metal catalysts of fuel cells with metal-sulfur cluster assemblies utilising abundant Ni, Fe and S as in the natural systems? Here we review the state of the art. PMID:14518180

  17. Hydrogen Production Catalyzed by Bidirectional, Biomimetic Models of the [FeFe]-Hydrogenase Active Site

    PubMed Central

    2015-01-01

    Active site mimics of [FeFe]-hydrogenase are shown to be bidirectional catalysts, producing H2 upon treatment with protons and reducing equivalents. This reactivity complements the previously reported oxidation of H2 by these same catalysts in the presence of oxidants. The complex Fe2(adtBn)(CO)3(dppv)(PFc*Et2) ([1]0; adtBn = (SCH2)2NBn, dppv = cis-1,2-bis(diphenylphosphino)ethylene, PFc*Et2 = Et2PCH2C5Me4FeCp*) reacts with excess [H(OEt2)2]BArF4 (BArF4– = B(C6H3-3,5-(CF3)2)4–) to give ?0.5 equiv of H2 and [Fe2(adtBnH)(CO)3(dppv)(PFc*Et2)]2+ ([1H]2+). The species [1H]2+ consists of a ferrocenium ligand, an N-protonated amine, and an FeIFeI core. In the presence of additional reducing equivalents in the form of decamethylferrocene (Fc*), hydrogen evolution is catalytic, albeit slow. The related catalyst Fe2(adtBn)(CO)3(dppv)(PMe3) (3) behaves similarly in the presence of Fc*, except that in the absence of excess reducing agent it converts to the catalytically inactive ?-hydride derivative [?-H3]+. Replacement of the adt in [1]0 with propanedithiolate (pdt) results in a catalytically inactive complex. In the course of synthesizing [FeFe]-hydrogenase mimics, new routes to ferrocenylphosphine ligands and nonamethylferrocene were developed. PMID:25364093

  18. Studies of Hybrid Nano-Bio-System: Single-Walled Carbon Nanotubes and Hydrogenase

    SciTech Connect

    Svedruzic-Chang, D.; Blackburn, J. L.; McDonald, T. J.; Heben, M. J.; King, P. W.

    2008-01-01

    We have examined changes in single-walled carbon nanotubes (SWNT) optical signals upon addition of recombinant [FeFe] hydrogenases from Clostridium acetobutylicum or Chlamydomonas reinhardtii. We found evidence that novel and stable charge-transfer complexes are formed only under conditions of hydrogenase catalytic turnover. Formation of the complex sensitizes the nanotubes to the proton-to-hydrogen redox half-reaction. Thus, the experimental potential can be altered by changing the pH or molecular hydrogen concentration. In the presence of molecular hydrogen, hydrogenase mediates electron injection into the conduction band of semiconducting SWNT, which was observed as a quenching of the photoluminescence signals. Here, we will present recent Raman studies, which revealed that SWNTs in a complex with hydrogenase may undergo either oxidation or reduction, depending on the electronic structure of the SWNT and the oxidation state of the enzyme. In addition, we will describe our efforts to prepare stable, solubilized SWNT/hydrogenase complexes in the absence of detergent. This work shows that SWNT/hydrogenase complexes have potential applications as a component of an energy conversion device.

  19. Studies on hydrogenase

    PubMed Central

    YAGI, Tatsuhiko; HIGUCHI, Yoshiki

    2013-01-01

    Hydrogenases are microbial enzymes which catalyze uptake and production of H2. Hydrogenases are classified into 10 classes based on the electron carrier specificity, or into 3 families, [NiFe]-family (including [NiFeSe]-subfamily), [FeFe]-family and [Fe]-family, based on the metal composition of the active site. H2 is heterolytically cleaved on the enzyme (E) to produce EHaHb, where Ha and Hb have different rate constants for exchange with the medium hydron. X-ray crystallography unveiled the three-dimensional structures of hydrogenases. The simplest [NiFe]-hydrogenase is a heterodimer, in which the large subunit bears the Ni-Fe center buried deep in the protein, and the small subunit bears iron-sulfur clusters, which mediate electron transfer between the Ni-Fe center and the protein surface. Some hydrogenases have additional subunit(s) for interaction with their electron carriers. Various redox states of the enzyme were characterized by EPR, FTIR, etc. Based on the kinetic, structural and spectroscopic studies, the catalytic mechanism of [NiFe]-hydrogenase was proposed to explain H2-uptake, H2-production and isotopic exchange reactions. PMID:23318679

  20. Hydrogenases and Hydrogen Photoproduction in Oxygenic Photosynthetic Organisms

    SciTech Connect

    Ghirardi, M. L.; Posewitz, M. C.; Maness, P. C.; Dubini, A.; Yu, J.; Seibert, M.

    2007-01-01

    The photobiological production of H{sub 2} gas, using water as the only electron donor, is a property of two types of photosynthetic microorganisms: green algae and cyanobacteria. In these organisms, photosynthetic water splitting is functionally linked to H{sub 2} production by the activity of hydrogenase enzymes. Interestingly, each of these organisms contains only one of two major types of hydrogenases, [FeFe] or [NiFe] enzymes, which are phylogenetically distinct but perform the same catalytic reaction, suggesting convergent evolution. This idea is supported by the observation that each of the two classes of hydrogenases has a different metallo-cluster, is encoded by entirely different sets of genes (apparently under the control of different promoter elements), and exhibits different maturation pathways. The genetics, biosynthesis, structure, function, and O{sub 2} sensitivity of these enzymes have been the focus of extensive research in recent years. Some of this effort is clearly driven by the potential for using these enzymes in future biological or biohybrid systems to produce renewable fuel or in fuel cell applications.

  1. Combining acid-base, redox and substrate binding functionalities to give a complete model for the [FeFe]-hydrogenase

    NASA Astrophysics Data System (ADS)

    Camara, James M.; Rauchfuss, Thomas B.

    2012-01-01

    Some enzymes function by coupling substrate turnover with electron transfer from a redox cofactor such as ferredoxin. In the [FeFe]-hydrogenases, nature's fastest catalysts for the production and oxidation of H2, the one-electron redox by a ferredoxin complements the one-electron redox by the diiron active site. In this Article, we replicate the function of the ferredoxins with the redox-active ligand Cp*Fe(C5Me4CH2PEt2) (FcP*). FcP* oxidizes at mild potentials, in contrast to most ferrocene-based ligands, which suggests that it might be a useful mimic of ferredoxin cofactors. The specific model is Fe2[(SCH2)2NBn](CO)3(FcP*)(dppv) (1), which contains the three functional components of the active site: a reactive diiron centre, an amine as a proton relay and, for the first time, a one-electron redox module. By virtue of the synthetic redox cofactor, [1]2+ exhibits unique reactivity towards hydrogen and CO. In the presence of excess oxidant and base, H2 oxidation by [1]2+ is catalytic.

  2. Heterolytic Cleavage of Hydrogen by an Iron Hydrogenase Model: An Fe-H - - - H-N Dihydorgen Bond Characterized by Neutron Diffraction

    SciTech Connect

    Liu, Tianbiao L.; Wang, Xiaoping; Hoffmann, Christina; DuBois, Daniel L.; Bullock, R. Morris

    2014-05-19

    Use of hydrogen as a fuel by [FeFe]-hydrogenase enzymes in nature requires heterolytic cleavage of the H-H bond into a proton (H+) and hydride (H-), a reaction that is also a critical step in homogeneous catalysts for hydrogenation of C=O and C=N bonds. An understanding of the catalytic oxidation of H2 by hydrogenases provides insights into the design of synthetic catalysts that are sought as cost-effective alternatives to the use of the precious metal platinum in fuel cells. Crystallographic studies on the [FeFe]-hydrogenase enzyme were critical to understanding of its reactivity, but the key H-H cleavage step is not readily observed experimentally in natural hydrogenases. Synthetic biomimics have provided evidence for H2 cleavage leading to hydride transfer to the metal and proton transfer to an amine. Limitations on the precise location of hydrogen atoms by x-ray diffraction can be overcome by use of neutron diffraction, though its use is severely limited by the difficulty of obtaining suitable crystals and by the scarcity of neutron sources. Here we show that an iron complex with a pendant amine in the diphosphine ligand cleaves hydrogen heterolytically under mild conditions, leading to [CpC5F4NFeH(PtBu2NtBu2H)]+BArF4-, [PtBu2NtBu2 = 1,5-di(tert-butyl)-3,7-di(tert-butyl)-1,5-diaza-3,7-diphosphacyclooctane; ArF = 3,5-bis(trifluoromethyl)phenyl]. The Fe-H- - - H-N moiety has a strong dihydrogen bond, with a remarkably short H • • • H distance of 1.489(10) Å between the protic N-H?+ and hydridic Fe-H?-. The structural data for [CpC5F4NFeH(PtBu2NtBu2H)]+ provide a glimpse of how the H-H bond is oxidized or generated in hydrogenase enzymes, with the pendant amine playing a key role as a proton relay. The iron complex [CpC5F4NFeH(PtBu2NtBu2H)]+BArF4- is an electrocatalyst for oxidation of H2 (1 atm) at 22 °C, so the structural data are obtained on a complex that is a functional model for catalysis by [FeFe]-hydrogenase enzymes. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

  3. Steric effect of the dithiolato linker on the reduction mechanism of [Fe2(CO)6{?-(XCH2)2CRR'}] hydrogenase models (X = S, Se).

    PubMed

    Trautwein, Ralf; Almazahreh, Laith R; Görls, Helmar; Weigand, Wolfgang

    2015-10-27

    Studying the redox features of the [FeFe]-hydrogenase models is essential for understanding the function of the H cluster. The reduction of the [FeFe]-hydrogenase models of the type [Fe2(CO)6{?-(XCH2)2E}] (X = S, Se) is described to occur either via sequential transfer of two electrons at and for the first and the second reduction steps, respectively, where , or via transfer of two electrons at the same applied potential due to potential inversion of the two reduction steps, i.e.. Typically, the phenomenon of potential inversion is observed when a structural change intervenes in the cathodic process stabilizing the reduced species. In this report, we investigate the mechanism of the cathodic process of series of models [Fe2(CO)6{?-(XCH2)2E}] (X = S or Se and E = CH2, CHMe or CMe2) applying cyclic voltammetry. The studies herein show the remarkable influence of the steric bulk of E toward the cathodic process, such that only complexes with E = CMe2 are reduced with inverted potentials due to occurrence of an ECE mechanism (E = electrochemical process, C = chemical process) of reduction. Moreover, we describe the catalytic behaviour of these models toward reduction of protons using acetic acid, AcOH, as a proton source. PMID:26455379

  4. Biomimetic model for [FeFe]-hydrogenase: asymmetrically disubstituted diiron complex with a redox-active 2,2'-bipyridyl ligand.

    PubMed

    Roy, Souvik; Groy, Thomas L; Jones, Anne K

    2013-03-21

    [FeFe]-hydrogenases feature a unique active site in which the primary catalytic unit is directly coordinated via a bridging cysteine thiolate to a secondary, redox active [4Fe4S] unit. The goal of this study was to evaluate the impact of a bidentate, redox non-innocent ligand on the electrocatalytic properties of the (?-S(CH(2))(3)S)Fe(2)(CO)(4)L(2) family of [FeFe]-hydrogenase models as a proxy for the iron-sulfur cluster. Reaction of the redox non-innocent ligand 2,2'-bipyridyl (bpy) with (?-S(CH(2))(3)S)Fe(2)(CO)(6) leads to substitution of two carbonyls to form the asymmetric complex (?-S(CH(2))(3)S)Fe(2)(CO)(4)(?(2)-bpy) which was structurally characterized by single crystal X-ray crystallography. This complex can be protonated by HBF(4)·OEt(2) to form a bridging hydride. Furthermore, electrochemical investigation shows that, at slow scan rates, the complex undergoes a two electron reduction at -2.06 V vs. Fc(+)/Fc that likely involves reduction of both the bpy ligand and the metal. Electrocatalytic reduction of protons is observed in the presence of three distinct acids of varying strengths: HBF(4)·OEt(2), AcOH, and p-TsOH. The catalytic mechanism depends on the strength of the acid. PMID:23307026

  5. Computational Investigation of [FeFe]-Hydrogenase Models: Characterization of Singly and Doubly Protonated Intermediates and Mechanistic Insights

    PubMed Central

    2015-01-01

    The [FeFe]-hydrogenase enzymes catalyze hydrogen oxidation and production efficiently with binuclear Fe metal centers. Recently the bioinspired H2-producing model system Fe2(adt)(CO)2(dppv)2 (adt=azadithiolate and dppv=diphosphine) was synthesized and studied experimentally. In this system, the azadithiolate bridge facilitates the formation of a doubly protonated ammonium-hydride species through a proton relay. Herein computational methods are utilized to examine this system in the various oxidation states and protonation states along proposed mechanistic pathways for H2 production. The calculated results agree well with the experimental data for the geometries, CO vibrational stretching frequencies, and reduction potentials. The calculations illustrate that the NH···HFe dihydrogen bonding distance in the doubly protonated species is highly sensitive to the effects of ion-pairing between the ammonium and BF4– counterions, which are present in the crystal structure, in that the inclusion of BF4– counterions leads to a significantly longer dihydrogen bond. The non-hydride Fe center was found to be the site of reduction for terminal hydride species and unsymmetric bridging hydride species, whereas the reduced symmetric bridging hydride species exhibited spin delocalization between the Fe centers. According to both experimental measurements and theoretical calculations of the relative pKa values, the Fed center of the neutral species is more basic than the amine, and the bridging hydride species is more thermodynamically stable than the terminal hydride species. The calculations implicate a possible pathway for H2 evolution that involves an intermediate with H2 weakly bonded to one Fe, a short H2 distance similar to the molecular bond length, the spin density delocalized over the two Fe centers, and a nearly symmetrically bridged CO ligand. Overall, this study illustrates the mechanistic roles of the ammonium-hydride interaction, flexibility of the bridging CO ligand, and intramolecular electron transfer between the Fe centers in the catalytic cycle. Such insights will assist in the design of more effective bioinspired catalysts for H2 production. PMID:25207842

  6. Production and Engineering of Hydrogenase as a Biocatalyst for Hydrogen Fuel

    SciTech Connect

    Wang, Guangyi

    2010-04-09

    Hydrogenases are fascinating redox proteins, showing tremendous promise in the utilization of hydrogen fuel as a bioelectrocatalyst. They play critical roles in both biohydrogen production and hydrogen oxidation. Specifically, the recently-established comparability of the oxidative activity of the [NiFe]-hydrogenase active site to that of the fuel cell catalyst platinum marks a significant milestone for the potential application of hydrogenase in hydrogen fuel cells to replace platinum. However, the ability of producing hydrogenase in heterologous expression hosts and the sensitivity of hydrogenases to oxygen and carbon monoxide, etc. have seriously limited the viable macroscale utilization and production of hydrogen from the renewable source. A new technology for the production of up-take hydrogenase is being developed for the utilization of hydrogenase as a hydrogen catalyst. The development of this new technology integrates knowledge of structural biology, molecular biology, and principles of metabolic engineering to produce and engineer a stable hydrogenase as a hydrogen bioelectrocatalyst. It contributes to the critical issues of “expensive noble metal catalysts (i.e., platinum) and their limited reserves threatening the long-term sustainability of a hydrogen economy”. It also provides a model to “design natural materials and enzyme catalyst” for “efficient and cost-effective technologies” for a clean and sustainable energy in 21st century. This new technology includes 3 major components. The first component is the synthetic operons, which carry hydrogenase maturation pathways of Ralstonia eutropha. These synthetic operons are engineered to produce RH hydrogenase in the Escherichia coli strains based on our current molecular and genetic information of hydrogenase maturation mechanisms and pathways of R. eutropha. It presents the first example of producing hydrogenase in the conventional expression host using synthetic biology principles and tool kits. For the high-yield production of the hydrogenase, protein degradation pathways are altered to prevent hydrogenase degradation. This part of the new technology provides a frame work for the design of hydrogenase production pathways for desirable bioengineering purposes. The results of this work are significantly beneficial to research in the areas of enzyme fuel cells, bioelectrocatalyst production, and biohydrogen production as well as basic research in hydrogenase structure biology. The second component of the new technology includes the stable hydrogenase with the improved electrochemical and catalytic properties. With the guidance of the current information on [NiFe] hydrogenase structure, hydrogenase mutants and mutant libraries are generated using protein engineering approaches. The resulting mutants are screened for better hydrogenase stability and catalytic activities. This part of the research results in the identification of new hydrogenase mutants with improved catalytic properties, which can be used for the future studies on enzyme full cells and the catalytic mechanism of hydrogenase. The third component is the optimized production of the selected hydrogenase mutant using current fermentation and metabolic engineering strategies. Metabolic burdens and biomass is balanced using different induction conditions for the optimum production of the engineered hydrogenase in genetically engineered E. coli strains. The success of this work presents a good example of the application of modern fermentation technologies in bioelectrocatalyst production.

  7. Hydrogenase/ferredoxin charge-transfer complexes: effect of hydrogenase mutations on the complex association.

    PubMed

    Long, Hai; King, Paul W; Ghirardi, Maria L; Kim, Kwiseon

    2009-04-23

    The [FeFe]-hydrogenases in the green alga Chlamydomonas reinhardtii utilize photogenerated electrons to reduce protons into hydrogen gas. The electrons are supplied from photosystem I and transferred to the [FeFe]-hydrogenase through specific hydrogenase-ferredoxin association. To understand how structural and kinetic factors control the association better, we used Brownian dynamics simulation methods to simulate the charge-transfer complex formation between both native and in silico mutants of the [FeFe]-hydrogenase HYDA2 and the [2Fe2S]-ferredoxin FDX1 from C. reinhardtii . The changes in binding free energy between different HYDA2 mutants and the native FDX1 were calculated by the free-energy perturbation method. Within the limits of our current models, we found that two HYDA2 mutations, T99K(H) and D102K(H), led to lower binding free energies and higher association rate with FDX1 and are thus promising targets for improving hydrogen production rates in engineered organisms. PMID:19317477

  8. Intramolecular C?H Activation and Metallacycle Aromaticity in the Photochemistry of [FeFe]-Hydrogenase Model Compounds in Low-Temperature Frozen Matrices.

    PubMed

    Thornley, Wyatt A; Bitterwolf, Thomas E

    2015-12-01

    The [FeFe]-hydrogenase model complexes [(?-pdt){Fe(CO)3 }2 ], [(?-edt){Fe(CO)3 }2 ], and [(?-mdt){Fe(CO)3 }2 ], where pdt=1,3-propanedithiolate, edt=1,2-ethanedithiolate, and mdt=methanedithiolate, undergo wavelength dependent photodecarbonylation in hydrocarbon matrices at 85?K resulting in multiple decarbonylation isomers. As previously reported in time-resolved solution photolysis experiments, the major photoproduct is attributed to a basal carbonyl-loss species. Apical carbonyl-loss isomers are also generated and may undergo secondary photolysis, resulting in ?-hydride activation of the alkyldithiolate bridge, as well as formation of bridging carbonyl isomers. For [(?-bdt){Fe(CO)3 }2 ], (bdt=1,2-benzenedithiolate), apical photodecarbonylation results in generation of a 10??-electron aromatic FeS2 C6 H4 metallacycle that coordinates the remaining iron through an ?(5) mode. PMID:26541102

  9. Cyanobacterial Hydrogenases and Hydrogen Metabolism Revisited: Recent Progress and Future Prospects

    PubMed Central

    Khanna, Namita; Lindblad, Peter

    2015-01-01

    Cyanobacteria have garnered interest as potential cell factories for hydrogen production. In conjunction with photosynthesis, these organisms can utilize inexpensive inorganic substrates and solar energy for simultaneous biosynthesis and hydrogen evolution. However, the hydrogen yield associated with these organisms remains far too low to compete with the existing chemical processes. Our limited understanding of the cellular hydrogen production pathway is a primary setback in the potential scale-up of this process. In this regard, the present review discusses the recent insight around ferredoxin/flavodoxin as the likely electron donor to the bidirectional Hox hydrogenase instead of the generally accepted NAD(P)H. This may have far reaching implications in powering solar driven hydrogen production. However, it is evident that a successful hydrogen-producing candidate would likely integrate enzymatic traits from different species. Engineering the [NiFe] hydrogenases for optimal catalytic efficiency or expression of a high turnover [FeFe] hydrogenase in these photo-autotrophs may facilitate the development of strains to reach target levels of biohydrogen production in cyanobacteria. The fundamental advancements achieved in these fields are also summarized in this review. PMID:26006225

  10. Elimination of hydrogenase post-translational modification blocks H2 production and increases ethanol yield in Clostridium thermocellum

    SciTech Connect

    Biswas, Ranjita; Zheng, Tianyong; Olson, Daniel G.; Lynd, Lee R; Guss, Adam M

    2015-01-01

    The native ability of Clostridium thermocellum to rapidly consume cellulose and produce ethanol makes it a leading candidate for a consolidated bioprocessing (CBP) biofuel production strategy. C. thermocellum also synthesizes lactate, formate, acetate, H2, and amino acids that compete with ethanol production for carbon and electrons. Elimination of H2 production could redirect carbon flux towards ethanol production by making more electrons available for acetyl-CoA reduction to ethanol. C. thermocellum encodes four hydrogenases and rather than delete each individually, we targeted a hydrogenase maturase gene (hydG), involved in converting the three [FeFe] hydrogenase apoenzymes into holoenzymes. Further deletion of the [NiFe] hydrogenase (ech) resulted in a mutant that functionally lacks all four hydrogenases. H2 production in hydG ech was undetectable and ethanol yield increased nearly 2-fold compared to wild type. Interestingly, mutant growth improved upon the addition of acetate, which led to increased expression of genes related to sulfate metabolism, suggesting these mutants may use sulfate as a terminal electron acceptor to balance redox reactions. Genomic analysis of hydG revealed a mutation in adhE, resulting in a strain with both NADH- and NADPH-dependent alcohol dehydrogenase activities. While this same adhE mutation is found in ethanol tolerant C. thermocellum strain E50C, hydG and hydG ech are not more ethanol tolerant than wild type, illustrating the complicated interactions between redox balancing and ethanol tolerance in C. thermocellum. The dramatic increase in ethanol production here suggests that targeting protein post-translational modification is a promising new approach for inactivation of multiple enzymes simultaneously for metabolic engineering.

  11. Characterization of the Fe Site in Iron-Sulfur-Cluster-Free Hydrogenase (Hmd) and of a Model Compound via Nuclear Resonance Vibrational Spectroscopy (NRVS)

    PubMed Central

    Guo, Yisong; Wang, Hongxin; Xiao, Yuming; vogt, Sonja; Shima, Seigo; Volkers, Phillip I.; Pelmentschikov, Vladimir; Alp, Ercan E.; Sturhahn, Wolfgang; Yada, Yoshitaka

    2009-01-01

    We have used 57Fe nuclear resonance vibrational spectroscopy (NRVS) to study the iron site in the iron-sulfur-cluster-free hydrogenase Hmd from the methanogenic archaeon Methanothermobacter marburgensis. The spectra have been interpreted by comparison with a cis-(CO)2-ligated Fe model compound, Fe(S2C2H4)(CO)2(PMe3)2, as well as by normal mode simulations of plausible active site structures. For this model complex, normal mode analyses both from an optimized Urey-Bradley force field and from complementary density functional theory (DFT) calculations produced consistent results. Previous IR spectroscopic studies found strong CO stretching modes at 1944 and 2011 cm?1, interpreted as evidence for cis-Fe(CO)2 ligation. The NRVS data provide further insight into the dynamics of the Fe site, revealing Fe-CO stretch and Fe-CO bend modes at 494, 562, 590, and 648 cm?1, consistent with the proposed cis-Fe(CO)2 ligation. The NRVS also reveals a band assigned to Fe-S stretching motion at ~311 cm?1, and another reproducible feature at ~380 cm?1. The 57Fe partial vibrational densities of states (PVDOS) for Hmd can be reasonably well simulated by a normal mode analysis based on a Urey-Bradley force field for a 5-coordinate cis-(CO)2-ligated Fe site with additional cysteine, water, and pyridone cofactor ligands. A final interpretation of the Hmd NRVS data, including DFT analysis, awaits a 3-dimensional structure for the active site. PMID:18407624

  12. Diversity and transcription of proteases involved in the maturation of hydrogenases in Nostoc punctiforme ATCC 29133 and Nostoc sp. strain PCC 7120

    PubMed Central

    2009-01-01

    Background The last step in the maturation process of the large subunit of [NiFe]-hydrogenases is a proteolytic cleavage of the C-terminal by a hydrogenase specific protease. Contrary to other accessory proteins these hydrogenase proteases are believed to be specific whereby one type of hydrogenases specific protease only cleaves one type of hydrogenase. In cyanobacteria this is achieved by the gene product of either hupW or hoxW, specific for the uptake or the bidirectional hydrogenase respectively. The filamentous cyanobacteria Nostoc punctiforme ATCC 29133 and Nostoc sp strain PCC 7120 may contain a single uptake hydrogenase or both an uptake and a bidirectional hydrogenase respectively. Results In order to examine these proteases in cyanobacteria, transcriptional analyses were performed of hupW in Nostoc punctiforme ATCC 29133 and hupW and hoxW in Nostoc sp. strain PCC 7120. These studies revealed numerous transcriptional start points together with putative binding sites for NtcA (hupW) and LexA (hoxW). In order to investigate the diversity and specificity among hydrogeanse specific proteases we constructed a phylogenetic tree which revealed several subgroups that showed a striking resemblance to the subgroups previously described for [NiFe]-hydrogenases. Additionally the proteases specificity was also addressed by amino acid sequence analysis and protein-protein docking experiments with 3D-models derived from bioinformatic studies. These studies revealed a so called "HOXBOX"; an amino acid sequence specific for protease of Hox-type which might be involved in docking with the large subunit of the hydrogenase. Conclusion Our findings suggest that the hydrogenase specific proteases are under similar regulatory control as the hydrogenases they cleave. The result from the phylogenetic study also indicates that the hydrogenase and the protease have co-evolved since ancient time and suggests that at least one major horizontal gene transfer has occurred. This co-evolution could be the result of a close interaction between the protease and the large subunit of the [NiFe]-hydrogenases, a theory supported by protein-protein docking experiments performed with 3D-models. Finally we present data that may explain the specificity seen among hydrogenase specific proteases, the so called "HOXBOX"; an amino acid sequence specific for proteases of Hox-type. This opens the door for more detailed studies of the specificity found among hydrogenase specific proteases and the structural properties behind it. PMID:19284580

  13. Discovery of [NiFe] hydrogenase genes in metagenomic DNA: cloning and heterologous expression in Thiocapsa roseopersicina.

    PubMed

    Maróti, Gergely; Tong, Yingkai; Yooseph, Shibu; Baden-Tillson, Holly; Smith, Hamilton O; Kovács, Kornél L; Frazier, Marvin; Venter, J Craig; Xu, Qing

    2009-09-01

    Using a metagenomics approach, we have cloned a piece of environmental DNA from the Sargasso Sea that encodes an [NiFe] hydrogenase showing 60% identity to the large subunit and 64% to the small subunit of a Thiocapsa roseopersicina O2-tolerant [NiFe] hydrogenase. The DNA sequence of the hydrogenase identified by the metagenomic approach was subsequently found to be 99% identical to the hyaA and hyaB genes of an Alteromonas macleodii hydrogenase, indicating that it belongs to the Alteromonas clade. We were able to express our new Alteromonas hydrogenase in T. roseopersicina. Expression was accomplished by coexpressing only two accessory genes, hyaD and hupH, without the need to express any of the hyp accessory genes (hypABCDEF). These results suggest that the native accessory proteins in T. roseopersicina could substitute for the Alteromonas counterparts that are absent in the host to facilitate the assembly of a functional Alteromonas hydrogenase. To further compare the complex assembly machineries of these two [NiFe] hydrogenases, we performed complementation experiments by introducing the new Alteromonas hyaD gene into the T. roseopersicina hynD mutant. Interestingly, Alteromonas endopeptidase HyaD could complement T. roseopersicina HynD to cleave endoproteolytically the C-terminal end of the T. roseopersicina HynL hydrogenase large subunit and activate the enzyme. This study refines our knowledge on the selectivity and pleiotropy of the elements of the [NiFe] hydrogenase assembly machineries. It also provides a model for functionally analyzing novel enzymes from environmental microbes in a culture-independent manner. PMID:19633107

  14. Influence of Escherichia coli hydrogenases on hydrogen fermentation from glycerol

    E-print Network

    Wood, Thomas K.

    Influence of Escherichia coli hydrogenases on hydrogen fermentation from glycerol Viviana Sanchez xxx Keywords: Hydrogen Glycerol metabolism Fermentation Hydrogenases Escherichia coli a b s t r a c t Since the actual role of Escherichia coli hydrogenases on fermentation from glycerol has not been clear

  15. Electrocatalytic mechanism of reversible hydrogen cycling by enzymes and distinctions between the major classes of hydrogenases.

    PubMed

    Hexter, Suzannah V; Grey, Felix; Happe, Thomas; Climent, Victor; Armstrong, Fraser A

    2012-07-17

    The extraordinary ability of Fe- and Ni-containing enzymes to catalyze rapid and efficient H(+)/H(2) interconversion--a property otherwise exclusive to platinum metals--has been investigated in a series of experiments combining variable-temperature protein film voltammetry with mathematical modeling. The results highlight important differences between the catalytic performance of [FeFe]-hydrogenases and [NiFe]-hydrogenases and justify a simple model for reversible catalytic electron flow in enzymes and electrocatalysts that should be widely applicable in fields as diverse as electrochemistry, catalysis, and bioenergetics. The active site of [FeFe]-hydrogenases, an intricate Fe-carbonyl complex known as the "H cluster," emerges as a supreme catalyst. PMID:22802675

  16. Electrocatalytic mechanism of reversible hydrogen cycling by enzymes and distinctions between the major classes of hydrogenases

    PubMed Central

    Hexter, Suzannah V.; Grey, Felix; Happe, Thomas; Climent, Victor; Armstrong, Fraser A.

    2012-01-01

    The extraordinary ability of Fe- and Ni-containing enzymes to catalyze rapid and efficient H+/H2 interconversion—a property otherwise exclusive to platinum metals—has been investigated in a series of experiments combining variable-temperature protein film voltammetry with mathematical modeling. The results highlight important differences between the catalytic performance of [FeFe]-hydrogenases and [NiFe]-hydrogenases and justify a simple model for reversible catalytic electron flow in enzymes and electrocatalysts that should be widely applicable in fields as diverse as electrochemistry, catalysis, and bioenergetics. The active site of [FeFe]-hydrogenases, an intricate Fe-carbonyl complex known as the “H cluster,” emerges as a supreme catalyst. PMID:22802675

  17. CO and CN- syntheses by [FeFe]-hydrogenase maturase HydG are catalytically differentiated events.

    PubMed

    Pagnier, Adrien; Martin, Lydie; Zeppieri, Laura; Nicolet, Yvain; Fontecilla-Camps, Juan C

    2016-01-01

    The synthesis and assembly of the active site [FeFe] unit of [FeFe]-hydrogenases require at least three maturases. The radical S-adenosyl-l-methionine HydG, the best characterized of these proteins, is responsible for the synthesis of the hydrogenase CO and CN(-) ligands from tyrosine-derived dehydroglycine (DHG). We speculated that CN(-) and the CO precursor (-):CO2H may be generated through an elimination reaction. We tested this hypothesis with both wild type and HydG variants defective in second iron-sulfur cluster coordination by measuring the in vitro production of CO, CN(-), and (-):CO2H-derived formate. We indeed observed formate production under these conditions. We conclude that HydG is a multifunctional enzyme that produces DHG, CN(-), and CO at three well-differentiated catalytic sites. We also speculate that homocysteine, cysteine, or a related ligand could be involved in Fe(CO)x(CN)y transfer to the HydF carrier/scaffold. PMID:26699472

  18. Cobaloxime-based artificial hydrogenases.

    PubMed

    Bacchi, Marine; Berggren, Gustav; Niklas, Jens; Veinberg, Elias; Mara, Michael W; Shelby, Megan L; Poluektov, Oleg G; Chen, Lin X; Tiede, David M; Cavazza, Christine; Field, Martin J; Fontecave, Marc; Artero, Vincent

    2014-08-01

    Cobaloximes are popular H2 evolution molecular catalysts but have so far mainly been studied in nonaqueous conditions. We show here that they are also valuable for the design of artificial hydrogenases for application in neutral aqueous solutions and report on the preparation of two well-defined biohybrid species via the binding of two cobaloxime moieties, {Co(dmgH)2} and {Co(dmgBF2)2} (dmgH2 = dimethylglyoxime), to apo Sperm-whale myoglobin (SwMb). All spectroscopic data confirm that the cobaloxime moieties are inserted within the binding pocket of the SwMb protein and are coordinated to a histidine residue in the axial position of the cobalt complex, resulting in thermodynamically stable complexes. Quantum chemical/molecular mechanical docking calculations indicated a coordination preference for His93 over the other histidine residue (His64) present in the vicinity. Interestingly, the redox activity of the cobalt centers is retained in both biohybrids, which provides them with the catalytic activity for H2 evolution in near-neutral aqueous conditions. PMID:25029381

  19. Crystallographic studies of nitrogenase and hydrogenase

    NASA Astrophysics Data System (ADS)

    Bolin, J. T.

    The long term goal of this project is to obtain detailed knowledge of the structure and function of nitrogenase and hydrogenase through the analysis of physical, chemical, and biological data with reference to three-dimensional, atomic resolution crystal structures of components of the enzyme and/or complexes of the components. The current objectives to determine the crystal structure of wild-type Av1, the nitrogenase MoFe protein from Azotobacter vinelandii; to refine this structure at high resolution; and to initiate studies of mutant MoFe proteins that express altered chemical and physical properties. Further we seek to determine the crystal structure of the bi-directional all-Fe hydrogenase from C. pasteurianum, Cp-hydrI, and to initiate studies of the uptake hydrogenase from the same organism, Cp-hydrii.

  20. Evolutionary Significance of an Algal Gene Encoding an [FeFe]-Hydrogenase with F-Domain Homology and Hydrogenase Activity in Chlorella Variabilis NC64A

    SciTech Connect

    Meuser, J. E.; Boyd, E. S.; Ananyev, G.; Karns, D.; Radakovits, R.; Murthy, U. M. N.; Ghirardi, M. L.; Dismukes, G. C.; Peters, J. W.; Posewitz, M. C.

    2011-10-01

    [FeFe]-hydrogenases (HYDA) link the production of molecular H{sub 2} to anaerobic metabolism in many green algae. Similar to Chlamydomonas reinhardtii, Chlorella variabilis NC64A (Trebouxiophyceae, Chlorophyta) exhibits [FeFe]-hydrogenase (HYDA) activity during anoxia. In contrast to C. reinhardtii and other chlorophycean algae, which contain hydrogenases with only the HYDA active site (H-cluster), C. variabilis NC64A is the only known green alga containing HYDA genes encoding accessory FeS cluster-binding domains (F-cluster). cDNA sequencing confirmed the presence of F-cluster HYDA1 mRNA transcripts, and identified deviations from the in silico splicing models. We show that HYDA activity in C. variabilis NC64A is coupled to anoxic photosynthetic electron transport (PSII linked, as well as PSII-independent) and dark fermentation. We also show that the in vivo H{sub 2}-photoproduction activity observed is as O2 sensitive as in C. reinhardtii. The two C. variabilis NC64A HYDA sequences are similar to homologs found in more deeply branching bacteria (Thermotogales), diatoms, and heterotrophic flagellates, suggesting that an F-cluster HYDA is the ancestral enzyme in algae. Phylogenetic analysis indicates that the algal HYDA H-cluster domains are monophyletic, suggesting that they share a common origin, and evolved from a single ancestral F-cluster HYDA. Furthermore, phylogenetic reconstruction indicates that the multiple algal HYDA paralogs are the result of gene duplication events that occurred independently within each algal lineage. Collectively, comparative genomic, physiological, and phylogenetic analyses of the C. variabilis NC64A hydrogenase has provided new insights into the molecular evolution and diversity of algal [FeFe]-hydrogenases.

  1. Hydrogenase activity in catalase-positive strains of Campylobacter spp.

    PubMed Central

    Goodman, T G; Hoffman, P S

    1983-01-01

    A rapid hydrogenase assay has been developed which may be useful in separating the species Campylobacter jejuni and C. coli from the subspecies C. fetus subsp. fetus and C. fetus subsp. venerealis. This assay employs the impermeant redox dye benzyl viologen, and positive determinations can be made within 20 min. All strains of C. jejuni and C. coli were found to be strongly hydrogenase positive. All strains of C. fetus subsp. fetus and C. fetus subsp. venerealis were negative for hydrogenase when the assay was performed at a benzyl viologen concentration of 2 mM and an incubation temperature of 30 degrees C. Some strains of C. fetus had low levels of hydrogenase as determined with cell extracts but were hydrogenase negative by the benzyl viologen assay. Since there are few rapid diagnostic tests available for screening Campylobacter isolates, we hope that the rapid hydrogenase assay will prove useful. PMID:6355162

  2. Microstructure, mechanical property, biodegradation behavior, and biocompatibility of biodegradable Fe-Fe2O3 composites.

    PubMed

    Cheng, J; Huang, T; Zheng, Y F

    2014-07-01

    In this study, the effects of Fe2O3 (addition, 2, 5, 10, and 50 wt %) on the microstructure, mechanical properties, corrosion behaviors, and in vitro biocompatibility of Fe-Fe2O3 composites fabricated by spark plasma sintering were systematically investigated as a novel-structure biodegradable metallic material. The results of X-ray diffraction analysis and optical microscopy indicated that Fe-Fe2O3 composite is composed of ?-Fe and FeO instead of Fe2O3. Both eletrochemical measurements and immersion test showed a faster degradation rate of Fe-2Fe2O3 and Fe-5Fe2O3 composites than pure iron and Fe-5Fe2O3 exhibited the fastest corrosion rate among these composites. Besides, the effect of Fe2O3 on the corrosion behavior of Fe-Fe2O3 composites was discussed. The extracts of Fe-Fe2O3 composite exhibited no cytotoxicity to both ECV304 and L929 cells, whereas greatly reduced cell viabilities of vascular smooth muscle cells. In addition, good hemocompatibility of all Fe-Fe2O3 composites and pure iron was obtained. To sum up, Fe-5Fe2O3 composite is a promising alternative for biodegradable stent material with elevated corrosion rate, enhanced mechanical properties, as well as excellent biocompatibility. PMID:23894098

  3. A broad survey reveals substitution tolerance of residues ligating FeS clusters in [NiFe] hydrogenase

    PubMed Central

    2014-01-01

    Background In order to understand the effects of FeS cluster attachment in [NiFe] hydrogenase, we undertook a study to substitute all 12 amino acid positions normally ligating the three FeS clusters in the hydrogenase small subunit. Using the hydrogenase from Alteromonas macleodii “deep ecotype” as a model, we substituted one of four amino acids (Asp, His, Asn, Gln) at each of the 12 ligating positions because these amino acids are alternative coordinating residues in otherwise conserved-cysteine positions found in a broad survey of NiFe hydrogenase sequences. We also hoped to discover an enzyme with elevated hydrogen evolution activity relative to a previously reported “G1” (H230C/P285C) improved enzyme in which the medial FeS cluster Pro and the distal FeS cluster His were each substituted for Cys. Results Among all the substitutions screened, aspartic acid substitutions were generally well-tolerated, and examination suggests that the observed deficiency in enzyme activity may be largely due to misprocessing of the small subunit of the enzyme. Alignment of hydrogenase sequences from sequence databases revealed many rare substitutions; the five substitutions present in databases that we tested all exhibited measurable hydrogen evolution activity. Select substitutions were purified and tested, supporting the results of the screening assay. Analysis of these results confirms the importance of small subunit processing. Normalizing activity to quantity of mature small subunit, indicative of total enzyme maturation, weakly suggests an improvement over the “G1” enzyme. Conclusions We have comprehensively screened 48 amino acid substitutions of the hydrogenase from A. macleodii “deep ecotype”, to understand non-canonical ligations of amino acids to FeS clusters and to improve hydrogen evolution activity of this class of hydrogenase. Our studies show that non-canonical ligations can be functional and also suggests a new limiting factor in the production of active enzyme. PMID:24934472

  4. ASSESSING SHOOT-ROOT COMMUNICATION IN THE REGULATION OF IRON HOMEOSTASIS IN THE FEFE MELON MUTANT

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The fefe mutant of musk melon exhibits characteristics of iron deficiency such as interveinal chlorosis of leaves, retarded growth, and finally death unless supplemental Fe is provided. The seedlings have normal green cotyledons but the first true leaves are yellow with green veins. To determine the...

  5. Microstructure, mechanical property, biodegradation behavior, and biocompatibility of biodegradable FeFe2O3 composites

    E-print Network

    Zheng, Yufeng

    's Republic of China 2 Department of Materials Science and Engineering, State Key Laboratory for Turbulence is a promising alternative for biodegradable stent material with elevated corrosion rate, enhanced mechanical Fe­Fe2O3 composites J. Cheng,1 T. Huang,2 Y. F. Zheng1,2 1 Center for Biomedical Materials and Tissue

  6. Induction of Photosynthetic Carbon Fixation in Anoxia Relies on Hydrogenase Activity and Proton-Gradient Regulation-Like1-Mediated Cyclic Electron Flow in Chlamydomonas reinhardtii.

    PubMed

    Godaux, Damien; Bailleul, Benjamin; Berne, Nicolas; Cardol, Pierre

    2015-06-01

    The model green microalga Chlamydomonas reinhardtii is frequently subject to periods of dark and anoxia in its natural environment. Here, by resorting to mutants defective in the maturation of the chloroplastic oxygen-sensitive hydrogenases or in Proton-Gradient Regulation-Like1 (PGRL1)-dependent cyclic electron flow around photosystem I (PSI-CEF), we demonstrate the sequential contribution of these alternative electron flows (AEFs) in the reactivation of photosynthetic carbon fixation during a shift from dark anoxia to light. At light onset, hydrogenase activity sustains a linear electron flow from photosystem II, which is followed by a transient PSI-CEF in the wild type. By promoting ATP synthesis without net generation of photosynthetic reductants, the two AEF are critical for restoration of the capacity for carbon dioxide fixation in the light. Our data also suggest that the decrease in hydrogen evolution with time of illumination might be due to competition for reduced ferredoxins between ferredoxin-NADP(+) oxidoreductase and hydrogenases, rather than due to the sensitivity of hydrogenase activity to oxygen. Finally, the absence of the two alternative pathways in a double mutant pgrl1 hydrogenase maturation factor G-2 is detrimental for photosynthesis and growth and cannot be compensated by any other AEF or anoxic metabolic responses. This highlights the role of hydrogenase activity and PSI-CEF in the ecological success of microalgae in low-oxygen environments. PMID:25931521

  7. Biomimetic assembly and activation of [FeFe]-hydrogenases.

    PubMed

    Berggren, G; Adamska, A; Lambertz, C; Simmons, T R; Esselborn, J; Atta, M; Gambarelli, S; Mouesca, J-M; Reijerse, E; Lubitz, W; Happe, T; Artero, V; Fontecave, M

    2013-07-01

    Hydrogenases are the most active molecular catalysts for hydrogen production and uptake, and could therefore facilitate the development of new types of fuel cell. In [FeFe]-hydrogenases, catalysis takes place at a unique di-iron centre (the [2Fe] subsite), which contains a bridging dithiolate ligand, three CO ligands and two CN(-) ligands. Through a complex multienzymatic biosynthetic process, this [2Fe] subsite is first assembled on a maturation enzyme, HydF, and then delivered to the apo-hydrogenase for activation. Synthetic chemistry has been used to prepare remarkably similar mimics of that subsite, but it has failed to reproduce the natural enzymatic activities thus far. Here we show that three synthetic mimics (containing different bridging dithiolate ligands) can be loaded onto bacterial Thermotoga maritima HydF and then transferred to apo-HydA1, one of the hydrogenases of Chlamydomonas reinhardtii algae. Full activation of HydA1 was achieved only when using the HydF hybrid protein containing the mimic with an azadithiolate bridge, confirming the presence of this ligand in the active site of native [FeFe]-hydrogenases. This is an example of controlled metalloenzyme activation using the combination of a specific protein scaffold and active-site synthetic analogues. This simple methodology provides both new mechanistic and structural insight into hydrogenase maturation and a unique tool for producing recombinant wild-type and variant [FeFe]-hydrogenases, with no requirement for the complete maturation machinery. PMID:23803769

  8. Hydrogenase in actinorhizal root nodules and root nodule homogenates.

    PubMed Central

    Benson, D R; Arp, D J; Burris, R H

    1980-01-01

    Hydrogenases were measured in intact actinorhizal root nodules and from disrupted nodules of Alnus glutinosa, Alnus rhombifolia, Alnus rubra, and Myrica pensylvanica. Whole nodules took up H2 in an O2-dependent reaction. Endophyte preparations oxidized H2 through the oxyhydrogen reaction, but rates were enhanced when hydrogen uptake was coupled to artificial electron acceptors. Oxygen inhibited artifical acceptor-dependent H2 uptake. The hydrogenase system from M. pensylvanica had a different pattern of coupling to various electron acceptors than the hydrogenase systems from the alders; only the bayberry system evolved H2 from reduced viologen dyes. PMID:6989799

  9. Frankia KB5 possesses a hydrogenase immunologically related to membrane-bound.

    PubMed

    Mattsson, U; Johansson, L; Sandström, G; Sellstedt, A

    2001-06-01

    The immunological relationship of the hydrogenase in Frankia KB5 to hydrogenases in other microorganisms was investigated using antisera raised against holo-[NiFe]-hydrogenases isolated from Alcaligenes latus, Azotobacter vinelandii, Ralstonia eutropha, and the small and large hydrogenase subunits from Bradyrhizobium japonicum. The antisera raised against the A. latus, R. eutropha, and B. japonicum (large subunit) polypeptides were found to recognize two polypeptides, corresponding to the unprocessed and processed forms of the hydrogenase subunit in Frankia KB5. None of the antisera, including the antibodies produced against the small hydrogenase subunit isolated from B. japonicum, recognized any polypeptide related to the small hydrogenase subunit in Frankia KB5. An immunogold localization study of the intracellular distribution of hydrogenase in Frankia KB5, with the cryo-section technique, showed that labeling in the membrane of both hyphae and vesicles was positively correlated with hydrogenase activity. PMID:11381338

  10. Force Field Development and Molecular Dynamics of [NiFe] Hydrogenase

    SciTech Connect

    Smith, Dayle MA; Xiong, Yijia; Straatsma, TP; Rosso, Kevin M.; Squier, Thomas C.

    2012-05-09

    Classical molecular force-field parameters describing the structure and motion of metal clusters in [NiFe] hydrogenase enzymes can be used to compare the dynamics and thermodynamics of [NiFe] under different oxidation, protonation, and ligation circumstances. Using density functional theory (DFT) calculations of small model clusters representative of the active site and the proximal, medial, and distal Fe/S metal centers and their attached protein side chains, we have calculated classical force-field parameters for [NiFe] in reduced and oxidized states, including internal coordinates, force constants, and atom-centered charges. Derived force constants revealed that cysteinate ligands bound to the metal ions are more flexible in the Ni-B active site, which has a bridging hydroxide ligand, than in the Ni-C active site, which has a bridging hydride. Ten nanosecond all-atom, explicit-solvent MD simulations of [NiFe] hydrogenase in oxidized and reduced catalytic states established the stability of the derived force-field parameters in terms of C{alpha} and metal cluster fluctuations. Average active site structures from the protein MD simulations are consistent with [NiFe] structures from the Protein Data Bank, suggesting that the derived force-field parameters are transferrable to other hydrogenases beyond the structure used for testing. A comparison of experimental H{sub 2}-production rates demonstrated a relationship between cysteinate side chain rotation and activity, justifying the use of a fully dynamic model of [NiFe] metal cluster motion.

  11. Hydrogens detected by subatomic resolution protein crystallography in a [NiFe] hydrogenase.

    PubMed

    Ogata, Hideaki; Nishikawa, Koji; Lubitz, Wolfgang

    2015-04-23

    The enzyme hydrogenase reversibly converts dihydrogen to protons and electrons at a metal catalyst. The location of the abundant hydrogens is of key importance for understanding structure and function of the protein. However, in protein X-ray crystallography the detection of hydrogen atoms is one of the major problems, since they display only weak contributions to diffraction and the quality of the single crystals is often insufficient to obtain sub-ångström resolution. Here we report the crystal structure of a standard [NiFe] hydrogenase (?91.3 kDa molecular mass) at 0.89 Å resolution. The strictly anoxically isolated hydrogenase has been obtained in a specific spectroscopic state, the active reduced Ni-R (subform Ni-R1) state. The high resolution, proper refinement strategy and careful modelling allow the positioning of a large part of the hydrogen atoms in the structure. This has led to the direct detection of the products of the heterolytic splitting of dihydrogen into a hydride (H(-)) bridging the Ni and Fe and a proton (H(+)) attached to the sulphur of a cysteine ligand. The Ni-H(-) and Fe-H(-) bond lengths are 1.58 Å and 1.78Å, respectively. Furthermore, we can assign the Fe-CO and Fe-CN(-) ligands at the active site, and can obtain the hydrogen-bond networks and the preferred proton transfer pathway in the hydrogenase. Our results demonstrate the precise comprehensive information available from ultra-high-resolution structures of proteins as an alternative to neutron diffraction and other methods such as NMR structural analysis. PMID:25624102

  12. Synthesis of the H-cluster framework of iron-only hydrogenase.

    PubMed

    Tard, Cédric; Liu, Xiaoming; Ibrahim, Saad K; Bruschi, Maurizio; De Gioia, Luca; Davies, Siân C; Yang, Xin; Wang, Lai-Sheng; Sawers, Gary; Pickett, Christopher J

    2005-02-10

    The metal-sulphur active sites of hydrogenases catalyse hydrogen evolution or uptake at rapid rates. Understanding the structure and function of these active sites--through mechanistic studies of hydrogenases, synthetic assemblies and in silico models--will help guide the design of new materials for hydrogen production or uptake. Here we report the assembly of the iron-sulphur framework of the active site of iron-only hydrogenase (the H-cluster), and show that it functions as an electrocatalyst for proton reduction. Through linking of a di-iron subsite to a {4Fe4S} cluster, we achieve the first synthesis of a metallosulphur cluster core involved in small-molecule catalysis. In addition to advancing our understanding of the natural biological system, the availability of an active, free-standing analogue of the H-cluster may enable us to develop useful electrocatalytic materials for application in, for example, reversible hydrogen fuel cells. (Platinum is currently the preferred electrocatalyst for such applications, but is expensive, limited in availability and, in the long term, unsustainable.). PMID:15703741

  13. Structural and gene expression analyses of uptake hydrogenases and other proteins involved in nitrogenase protection in Frankia.

    PubMed

    Richau, K H; Kudahettige, R L; Pujic, P; Kudahettige, N P; Sellstedt, A

    2013-11-01

    The actinorhizal bacterium Frankia expresses nitrogenase and can therefore convert molecular nitrogen into ammonia and the by-product hydrogen. However, nitrogenase is inhibited by oxygen. Consequently, Frankia and its actinorhizal hosts have developed various mechanisms for excluding oxygen from their nitrogen-containing compartments. These include the expression of oxygen-scavenging uptake hydrogenases, the formation of hopanoid-rich vesicles, enclosed by multi-layered hopanoid structures, the lignification of hyphal cell walls, and the production of haemoglobins in the symbiotic nodule. In this work, we analysed the expression and structure of the so-called uptake hydrogenase (Hup), which catalyses the in vivo dissociation of hydrogen to recycle the energy locked up in this 'waste' product. Two uptake hydrogenase syntons have been identified in Frankia: synton 1 is expressed under freeliving conditions while synton 2 is expressed during symbiosis. We used qPCR to determine synton 1 hup gene expression in two Frankia strains under aerobic and anaerobic conditions. We also predicted the 3D structures of the Hup protein subunits based on multiple sequence alignments and remote homology modelling. Finally, we performed BLAST searches of genome and protein databases to identify genes that may contribute to the protection of nitrogenase against oxygen in the two Frankia strains. Our results show that in Frankia strain ACN14a, the expression patterns of the large (HupL1) and small (HupS1) uptake hydrogenase subunits depend on the abundance of oxygen in the external environment. Structural models of the membrane-bound hydrogenase subunits of ACN14a showed that both subunits resemble the structures of known [NiFe] hydrogenases (Volbeda et al. 1995), but contain fewer cysteine residues than the uptake hydrogenase of the Frankia DC12 and Eu1c strains. Moreover, we show that all of the investigated Frankia strains have two squalene hopane cyclase genes (shc1 and shc2). The only exceptions were CcI3 and the symbiont of Datisca glomerata, which possess shc1 but not shc2. Four truncated haemoglobin genes were identified in Frankia ACN14a and Eu1f, three in CcI3, two in EANpec1 and one in the Datisca glomerata symbiont (Dg). PMID:24287649

  14. Effect of exchange interaction in dumbbell Fe-Fe pairs on the curie temperature of the rhombohedral Gd2Fe17 phase

    NASA Astrophysics Data System (ADS)

    Medvedev, M. V.; Nekrasov, I. A.

    2015-05-01

    One of important problems of improving the magnetic properties of technologically promicing intermetallics R 2Fe17 ( R is rare-earth metal) with high Fe contents is related to the increase in the Curie temperature T C. There is a hypothesis on the possibility of a marked increase in T C of the alloys, which can be achieved via the synthesis of systems characterized by pairs of atoms coupled by strong exchange interaction similar to that for Fe-Fe pairs situated in the so-called dumbbell position in the R 2Fe17 systems. In the present study, based on an example of the rhombohedral Gd2Fe17 phase, it was shown in terms of a classical nearest-neighbor spin Heisenberg model that changes in the exchange interaction for a dimer pair of dumbbell Fe-Fe atoms from zero to infinitely large lead to no more than 10% increase in T C. Thus, the creation of ferromagnetic systems characterized by dimers of magnetic atoms coupled by strong short-range exchange interaction, which, in this case, do not form an infinite magnetic cluster, cannot increase radically the Curie temperature T C.

  15. BIOTECHNOLOGICALLY RELEVANT ENZYMES AND PROTEINS Escherichia coli hydrogenase 3 is a reversible enzyme

    E-print Network

    Wood, Thomas K.

    hydrogenase. Keywords E. coli hydrogenase 3 . Reversible hydrogenase . Hydrogen production . Hydrogen uptake no toxic by- products (Hansel and Lindblad 1998). The use of biological methods for hydrogen production ciliates, and anaerobic fungi (Horner et al. 2002). Biohydrogen may be produced through either

  16. Modeling the active site of [NiFe] hydrogenases and the [NiFeu] subsite of the C-cluster of carbon monoxide dehydrogenases: low-spin iron(II) versus high-spin iron(II).

    PubMed

    Weber, Katharina; Erdem, Özlen F; Bill, Eckhard; Weyhermüller, Thomas; Lubitz, Wolfgang

    2014-06-16

    A series of four [S2Ni(?-S)2FeCp*Cl] compounds with different tetradentate thiolate/thioether ligands bound to the Ni(II) ion is reported (Cp* = C5Me5). The {S2Ni(?-S)2Fe} core of these compounds resembles structural features of the active site of [NiFe] hydrogenases. Detailed analyses of the electronic structures of these compounds by Mössbauer and electron paramagnetic resonance spectroscopy, magnetic measurements, and density functional theory calculations reveal the oxidation states Ni(II) low spin and Fe(II) high spin for the metal ions. The same electronic configurations have been suggested for the Cred1 state of the C-cluster [NiFeu] subsite in carbon monoxide dehydrogenases (CODH). The Ni-Fe distance of ?3 Å excludes a metal-metal bond between nickel and iron, which is in agreement with the computational results. Electrochemical experiments show that iron is the redox active site in these complexes, performing a reversible one-electron oxidation. The four complexes are discussed with regard to their similarities and differences both to the [NiFe] hydrogenases and the C-cluster of Ni-containing CODH. PMID:24903610

  17. Distribution and activity of hydrogenase enzymes in subsurface sediments

    NASA Astrophysics Data System (ADS)

    Adhikari, R.; Nickel, J.; Glombitza, C.; Spivack, A. J.; D'Hondt, S. L.; Kallmeyer, J.

    2013-12-01

    Metabolically active microbial communities are present in a wide range of subsurface environments. Techniques like enumeration of microbial cells, activity measurements with radiotracer assays and the analysis of porewater constituents are currently being used to explore the subsurface biosphere, alongside with molecular biological analyses. However, many of these techniques reach their detection limits due to low microbial activity and abundance. Direct measurements of microbial turnover not just face issues of insufficient sensitivity, they only provide information about a single specific process rather than an overall microbial activity. Since hydrogenase enzymes are intracellular and ubiquitous in subsurface microbial communities, the enzyme activity represents a measure of total activity of the entire microbial community. A hydrogenase activity assay could quantify total metabolic activity without having to identify specific processes. This would be a major advantage in subsurface biosphere studies, where several metabolic processes can occur simultaneously. We quantified hydrogenase enzyme activity and distribution in sediment samples from different aquatic subsurface environments (Lake Van, Barents Sea, Equatorial Pacific and Gulf of Mexico) using a tritium-based assay. We found enzyme activity at all sites and depths. Volumetric hydrogenase activity did not show much variability between sites and sampling depths, whereas cell-specific activity ranged from 10-5 to 1 nmol H2 cell-1 d-1. Activity was lowest in sediment layers where nitrate was detected. Higher activity was associated with samples in which sulfate was the predominant electron acceptor. We found highest activity in samples from environments with >10 ppm methane in the pore water. The results show that cell-specific hydrogenase enzyme activity increases with decreasing energy yield of the electron acceptor used. It is not possible to convert volumetric or cell-specific hydrogenase activity into a turnover rate of a specific process like sulfate reduction. However, we can use the cell-specific hydrogenase activity to estimate the size of the metabolically active microbial population. The conversion factors vary according to the predominant electron-accepting process. In subsurface sediment standard methods for quantification of the metabolically active microbial population (e.g. CARD-FISH) are at their lower detection limit. The hydrogenase enzyme activity measurement provides an alternative and sensitive way of quantification.

  18. Rates and Routes of Electron Transfer of [NiFe]-Hydrogenase in an Enzymatic Fuel Cell.

    PubMed

    Petrenko, Alexander; Stein, Matthias

    2015-10-29

    Hydrogenase enzymes are being used in enzymatic fuel cells immobilized on a graphite or carbon electrode surface, for example. The enzyme is used for the anodic oxidation of molecular hydrogen (H2) to produce protons and electrons. The association and orientation of the enzyme at the anode electrode for a direct electron transfer is not completely resolved. The distal FeS-cluster in [NiFe]-hydrogenases contains a histidine residue which is known to play a critical role in the intermolecular electron transfer between the enzyme and the electrode surface. The [NiFe]-hydrogenase graphite electrode association was investigated using Brownian Dynamics simulations. Residues that were shown to be in proximity to the electrode surface were identified (His184, Ser196, Glu461, Glu464), and electron transfer routes connecting the distal FeS-cluster with the surface residues were investigated. Several possible pathways for electron transfer between the distal FeS-cluster and the terminal amino acid residues were probed in terms of their rates of electron transfer using DFT methods. The reorganization energies ? of the distal iron-sulfur cluster and coronene as a molecular model for graphite were calculated. The reorganization energy of the distal (His)(Cys)3 cluster was found to be not very different from that of a standard cubane clusters with a (Cys)4 coordination. Electronic coupling matrix elements and rates of electron transfer for the different pathways were calculated according to the Marcus equation. The rates for glutamate-mediated electrode binding were found to be incompatible with experimental data. A direct electron transfer from the histidine ligand of the distal FeS-cluster to the electrode yielded rates of electron transfer in excellent agreement with experiment. A second pathway, however, from the distal FeS-cluster to the Ser196 residue was found to be equally efficient and feasible. PMID:26218232

  19. ORIGINAL ARTICLE Hydrogenase-independent uptake and metabolism

    E-print Network

    ORIGINAL ARTICLE Hydrogenase-independent uptake and metabolism of electrons by the archaeon-derived electrons has been postulated as a novel mechanism of electron metabolism in some prokaryotes that may also implications for our understanding on the diversity of microbial electron uptake and metabolism. The ISME

  20. From enzyme maturation to synthetic chemistry: the case of hydrogenases.

    PubMed

    Artero, Vincent; Berggren, Gustav; Atta, Mohamed; Caserta, Giorgio; Roy, Souvik; Pecqueur, Ludovic; Fontecave, Marc

    2015-08-18

    Water splitting into oxygen and hydrogen is one of the most attractive strategies for storing solar energy and electricity. Because the processes at work are multielectronic, there is a crucial need for efficient and stable catalysts, which in addition have to be cheap for future industrial developments (electrolyzers, photoelectrochemicals, and fuel cells). Specifically for the water/hydrogen interconversion, Nature is an exquisite source of inspiration since this chemistry contributes to the bioenergetic metabolism of a number of living organisms via the activity of fascinating metalloenzymes, the hydrogenases. In this Account, we first briefly describe the structure of the unique dinuclear organometallic active sites of the two classes of hydrogenases as well as the complex protein machineries involved in their biosynthesis, their so-called maturation processes. This knowledge allows for the development of a fruitful bioinspired chemistry approach, which has already led to a number of interesting and original catalysts mimicking the natural active sites. More specifically, we describe our own attempts to prepare artificial hydrogenases. This can be achieved via the standard bioinspired approach using the combination of a synthetic bioinspired catalyst and a polypeptide scaffold. Such hybrid complexes provide the opportunity to optimize the system by manipulating both the catalyst through chemical synthesis and the protein component through mutagenesis. We also raise the possibility to reach such artificial systems via an original strategy based on mimicking the enzyme maturation pathways. This is illustrated in this Account by two examples developed in our laboratory. First, we show how the preparation of a lysozyme-{Mn(I)(CO)3} hybrid and its clean reaction with a nickel complex led us to generate a new class of binuclear Ni-Mn H2-evolving catalysts mimicking the active site of [NiFe]-hydrogenases. Then we describe how we were able to rationally design and prepare a hybrid system, displaying remarkable structural similarities to an [FeFe]-hydrogenase, and we show here for the first time that it is catalytically active for proton reduction. This system is based on the combination of HydF, a protein involved in the maturation of [FeFe]-hydrogenase (HydA), and a close mimic of the active site of this class of enzymes. Moreover, the synthetic [Fe2(adt)(CO)4(CN)2](2-) (adt(2-)= aza-propanedithiol) mimic, alone or within a HydF hybrid system, was shown to be able to maturate and activate a form of HydA itself lacking its diiron active site. We discuss the exciting perspectives this "synthetic maturation" opens regarding the "invention" of novel hydrogenases by the chemists. PMID:26165393

  1. Crystallographic studies of [NiFe]-hydrogenase mutants: towards consensus structures for the elusive unready oxidized states.

    PubMed

    Volbeda, Anne; Martin, Lydie; Barbier, Elodie; Gutiérrez-Sanz, Oscar; De Lacey, Antonio L; Liebgott, Pierre-Pol; Dementin, Sébastien; Rousset, Marc; Fontecilla-Camps, Juan C

    2015-01-01

    Catalytically inactive oxidized O2-sensitive [NiFe]-hydrogenases are characterized by a mixture of the paramagnetic Ni-A and Ni-B states. Upon O2 exposure, enzymes in a partially reduced state preferentially form the unready Ni-A state. Because partial O2 reduction should generate a peroxide intermediate, this species was previously assigned to the elongated Ni-Fe bridging electron density observed for preparations of [NiFe]-hydrogenases known to contain the Ni-A state. However, this proposition has been challenged based on the stability of this state to UV light exposure and the possibility of generating it anaerobically under either chemical or electrochemical oxidizing conditions. Consequently, we have considered alternative structures for the Ni-A species including oxidation of thiolate ligands to either sulfenate or sulfenic acid. Here, we report both new and revised [NiFe]-hydrogenases structures and conclude, taking into account corresponding characterizations by Fourier transform infrared spectroscopy (FTIR), that the Ni-A species contains oxidized cysteine and bridging hydroxide ligands instead of the peroxide ligand we proposed earlier. Our analysis was rendered difficult by the typical formation of mixtures of unready oxidized states that, furthermore, can be reduced by X-ray induced photoelectrons. The present study could be carried out thanks to the use of Desulfovibrio fructosovorans [NiFe]-hydrogenase mutants with special properties. In addition to the Ni-A state, crystallographic results are also reported for two diamagnetic unready states, allowing the proposal of a revised oxidized inactive Ni-SU model and a new structure characterized by a persulfide ion that is assigned to an Ni-'Sox' species. PMID:25315838

  2. Implementation of photobiological H2 production: the O 2 sensitivity of hydrogenases.

    PubMed

    Ghirardi, Maria L

    2015-09-01

    The search for the ultimate carbon-free fuel has intensified in recent years, with a major focus on photoproduction of H2. Biological sources of H2 include oxygenic photosynthetic green algae and cyanobacteria, both of which contain hydrogenase enzymes. Although algal and cyanobacterial hydrogenases perform the same enzymatic reaction through metallo-clusters, their hydrogenases have evolved separately, are expressed differently (transcription of algal hydrogenases is anaerobically induced, while bacterial hydrogenases are constitutively expressed), and display different sensitivity to O2 inactivation. Among various physiological factors, the sensitivity of hydrogenases to O2 has been one of the major factors preventing implementation of biological systems for commercial production of renewable H2. This review addresses recent strategies aimed at engineering increased O2 tolerance into hydrogenases (as of now mainly unsuccessful), as well as towards the development of methods to bypass the O2 sensitivity of hydrogenases (successful but still yielding low solar conversion efficiencies). The author concludes with a description of current approaches from various laboratories to incorporate multiple genetic traits into either algae or cyanobacteria to jointly address limiting factors other than the hydrogenase O2 sensitivity and achieve more sustained H2 photoproduction activity. PMID:26022106

  3. Oxygen-resistant hydrogenases and methods for designing and making same

    DOEpatents

    King, Paul; Ghirardi, Maria Lucia; Seibert, Michael

    2014-03-04

    The invention provides oxygen-resistant iron-hydrogenases ([Fe]-hydrogenases) for use in the production of H.sub.2. Methods used in the design and engineering of the oxygen-resistant [Fe]-hydrogenases are disclosed, as are the methods of transforming and culturing appropriate host cells with the oxygen-resistant [Fe]-hydrogenases. Finally, the invention provides methods for utilizing the transformed, oxygen insensitive, host cells in the bulk production of H.sub.2 in a light catalyzed reaction having water as the reactant.

  4. Oxygen-resistant hydrogenases and methods for designing and making same

    DOEpatents

    King, Paul (Golden, CO); Ghirardi, Maria L (Lakewood, CO); Seibert, Michael (Lakewood, CO)

    2009-03-10

    The invention provides oxygen- resistant iron-hydrogenases ([Fe]-hydrogenases) for use in the production of H2. Methods used in the design and engineering of the oxygen-resistant [Fe]-hydrogenases are disclosed, as are the methods of transforming and culturing appropriate host cells with the oxygen-resistant [Fe]-hydrogenases. Finally, the invention provides methods for utilizing the transformed, oxygen insensitive, host cells in the bulk production of H.sub.2 in a light catalyzed reaction having water as the reactant.

  5. Production and Application of a Soluble Hydrogenase from Pyrococcus furiosus

    PubMed Central

    Wu, Chang-Hao; McTernan, Patrick M.; Walter, Mary E.; Adams, Michael W. W.

    2015-01-01

    Hydrogen gas is a potential renewable alternative energy carrier that could be used in the future to help supplement humanity's growing energy needs. Unfortunately, current industrial methods for hydrogen production are expensive or environmentally unfriendly. In recent years research has focused on biological mechanisms for hydrogen production and specifically on hydrogenases, the enzyme responsible for catalyzing the reduction of protons to generate hydrogen. In particular, a better understanding of this enzyme might allow us to generate hydrogen that does not use expensive metals, such as platinum, as catalysts. The soluble hydrogenase I (SHI) from the hyperthermophile Pyrococcus furiosus, a member of the euryarchaeota, has been studied extensively and used in various biotechnological applications. This review summarizes the strategies used in engineering and characterizing three different forms of SHI and the properties of the recombinant enzymes. SHI has also been used in in vitro systems for hydrogen production and NADPH generation and these systems are also discussed. PMID:26543406

  6. Production and Application of a Soluble Hydrogenase from Pyrococcus furiosus

    DOE PAGESBeta

    Wu, Chang-Hao; McTernan, Patrick M.; Walter, Mary E.; Adams, Michael W. W.

    2015-01-01

    Hydrogen gas is a potential renewable alternative energy carrier that could be used in the future to help supplement humanity’s growing energy needs. Unfortunately, current industrial methods for hydrogen production are expensive or environmentally unfriendly. In recent years research has focused on biological mechanisms for hydrogen production and specifically on hydrogenases, the enzyme responsible for catalyzing the reduction of protons to generate hydrogen. In particular, a better understanding of this enzyme might allow us to generate hydrogen that does not use expensive metals, such as platinum, as catalysts. The soluble hydrogenase I (SHI) from the hyperthermophile Pyrococcus furiosus ,more »a member of the euryarchaeota, has been studied extensively and used in various biotechnological applications. This review summarizes the strategies used in engineering and characterizing three different forms of SHI and the properties of the recombinant enzymes. SHI has also been used in in vitro systems for hydrogen production and NADPH generation and these systems are also discussed. « less

  7. Production and Application of a Soluble Hydrogenase from Pyrococcus furiosus.

    PubMed

    Wu, Chang-Hao; McTernan, Patrick M; Walter, Mary E; Adams, Michael W W

    2015-01-01

    Hydrogen gas is a potential renewable alternative energy carrier that could be used in the future to help supplement humanity's growing energy needs. Unfortunately, current industrial methods for hydrogen production are expensive or environmentally unfriendly. In recent years research has focused on biological mechanisms for hydrogen production and specifically on hydrogenases, the enzyme responsible for catalyzing the reduction of protons to generate hydrogen. In particular, a better understanding of this enzyme might allow us to generate hydrogen that does not use expensive metals, such as platinum, as catalysts. The soluble hydrogenase I (SHI) from the hyperthermophile Pyrococcus furiosus, a member of the euryarchaeota, has been studied extensively and used in various biotechnological applications. This review summarizes the strategies used in engineering and characterizing three different forms of SHI and the properties of the recombinant enzymes. SHI has also been used in in vitro systems for hydrogen production and NADPH generation and these systems are also discussed. PMID:26543406

  8. Wiring of Photosystem II to Hydrogenase for Photoelectrochemical Water Splitting.

    PubMed

    Mersch, Dirk; Lee, Chong-Yong; Zhang, Jenny Zhenqi; Brinkert, Katharina; Fontecilla-Camps, Juan C; Rutherford, A William; Reisner, Erwin

    2015-07-01

    In natural photosynthesis, light is used for the production of chemical energy carriers to fuel biological activity. The re-engineering of natural photosynthetic pathways can provide inspiration for sustainable fuel production and insights for understanding the process itself. Here, we employ a semiartificial approach to study photobiological water splitting via a pathway unavailable to nature: the direct coupling of the water oxidation enzyme, photosystem II, to the H2 evolving enzyme, hydrogenase. Essential to this approach is the integration of the isolated enzymes into the artificial circuit of a photoelectrochemical cell. We therefore developed a tailor-made hierarchically structured indium-tin oxide electrode that gives rise to the excellent integration of both photosystem II and hydrogenase for performing the anodic and cathodic half-reactions, respectively. When connected together with the aid of an applied bias, the semiartificial cell demonstrated quantitative electron flow from photosystem II to the hydrogenase with the production of H2 and O2 being in the expected two-to-one ratio and a light-to-hydrogen conversion efficiency of 5.4% under low-intensity red-light irradiation. We thereby demonstrate efficient light-driven water splitting using a pathway inaccessible to biology and report on a widely applicable in vitro platform for the controlled coupling of enzymatic redox processes to meaningfully study photocatalytic reactions. PMID:26046591

  9. Experimental approaches to kinetics of gas diffusion in hydrogenase

    PubMed Central

    Leroux, Fanny; Dementin, Sébastien; Burlat, Bénédicte; Cournac, Laurent; Volbeda, Anne; Champ, Stéphanie; Martin, Lydie; Guigliarelli, Bruno; Bertrand, Patrick; Fontecilla-Camps, Juan; Rousset, Marc; Léger, Christophe

    2008-01-01

    Hydrogenases, which catalyze H2 to H+ conversion as part of the bioenergetic metabolism of many microorganisms, are among the metalloenzymes for which a gas-substrate tunnel has been described by using crystallography and molecular dynamics. However, the correlation between protein structure and gas-diffusion kinetics is unexplored. Here, we introduce two quantitative methods for probing the rates of diffusion within hydrogenases. One uses protein film voltammetry to resolve the kinetics of binding and release of the competitive inhibitor CO; the other is based on interpreting the yield in the isotope exchange assay. We study structurally characterized mutants of a NiFe hydrogenase, and we show that two mutations, which significantly narrow the tunnel near the entrance of the catalytic center, decrease the rates of diffusion of CO and H2 toward and from the active site by up to 2 orders of magnitude. This proves the existence of a functional channel, which matches the hydrophobic cavity found in the crystal. However, the changes in diffusion rates do not fully correlate with the obstruction induced by the mutation and deduced from the x-ray structures. Our results demonstrate the necessity of measuring diffusion rates and emphasize the role of side-chain dynamics in determining these. PMID:18685111

  10. Mechanism of hydrogen activation by [NiFe] hydrogenases.

    PubMed

    Evans, Rhiannon M; Brooke, Emily J; Wehlin, Sara A M; Nomerotskaia, Elena; Sargent, Frank; Carr, Stephen B; Phillips, Simon E V; Armstrong, Fraser A

    2016-01-01

    The active site of [NiFe] hydrogenases contains a strictly conserved arginine that suspends a guanidine nitrogen atom <4.5 Å above the nickel and iron atoms. The guanidine headgroup interacts with the side chains of two conserved aspartic acid residues to complete an outer-shell canopy that has thus far proved intractable to investigation by site-directed mutagenesis. Using hydrogenase-1 from Escherichia coli, the strictly conserved residues R509 and D574 have been replaced by lysine (R509K) and asparagine (D574N) and the highly conserved D118 has been replaced by alanine (D118A) or asparagine (D118N/D574N). Each enzyme variant is stable, and their [(RS)2Ni?(SR)2Fe(CO)(CN)2] inner coordination shells are virtually unchanged. The R509K variant had >100-fold lower activity than native enzyme. Conversely, the variants D574N, D118A and D118N/D574N, in which the position of the guanidine headgroup is retained, showed 83%, 26% and 20% activity, respectively. The special kinetic requirement for R509 implicates the suspended guanidine group as the general base in H2 activation by [NiFe] hydrogenases. PMID:26619250

  11. Distribution Analysis of Hydrogenases in Surface Waters of Marine and Freshwater Environments

    PubMed Central

    Barz, Martin; Beimgraben, Christian; Staller, Torsten; Germer, Frauke; Opitz, Friederike; Marquardt, Claudia; Schwarz, Christoph; Gutekunst, Kirstin; Vanselow, Klaus Heinrich; Schmitz, Ruth; LaRoche, Julie; Schulz, Rüdiger; Appel, Jens

    2010-01-01

    Background Surface waters of aquatic environments have been shown to both evolve and consume hydrogen and the ocean is estimated to be the principal natural source. In some marine habitats, H2 evolution and uptake are clearly due to biological activity, while contributions of abiotic sources must be considered in others. Until now the only known biological process involved in H2 metabolism in marine environments is nitrogen fixation. Principal Findings We analyzed marine and freshwater environments for the presence and distribution of genes of all known hydrogenases, the enzymes involved in biological hydrogen turnover. The total genomes and the available marine metagenome datasets were searched for hydrogenase sequences. Furthermore, we isolated DNA from samples from the North Atlantic, Mediterranean Sea, North Sea, Baltic Sea, and two fresh water lakes and amplified and sequenced part of the gene encoding the bidirectional NAD(P)-linked hydrogenase. In 21% of all marine heterotrophic bacterial genomes from surface waters, one or several hydrogenase genes were found, with the membrane-bound H2 uptake hydrogenase being the most widespread. A clear bias of hydrogenases to environments with terrestrial influence was found. This is exemplified by the cyanobacterial bidirectional NAD(P)-linked hydrogenase that was found in freshwater and coastal areas but not in the open ocean. Significance This study shows that hydrogenases are surprisingly abundant in marine environments. Due to its ecological distribution the primary function of the bidirectional NAD(P)-linked hydrogenase seems to be fermentative hydrogen evolution. Moreover, our data suggests that marine surface waters could be an interesting source of oxygen-resistant uptake hydrogenases. The respective genes occur in coastal as well as open ocean habitats and we presume that they are used as additional energy scavenging devices in otherwise nutrient limited environments. The membrane-bound H2-evolving hydrogenases might be useful as marker for bacteria living inside of marine snow particles. PMID:21079771

  12. Magnetic properties of mechanochemically prepared iron-wüstite (Fe-Fe yO) nanocomposites

    NASA Astrophysics Data System (ADS)

    Mozaffari, M.; Gheisari, M.; Niyaifar, M.; Amighian, J.

    2009-10-01

    In this work, iron-wüstite (Fe-Fe yO) nanocomposites have been prepared via high-energy ball milling (HEBM), using high-purity hematite (?-Fe 2O 3) and iron (Fe) powders as the raw materials with different Fe/Fe 2O 3 mole ratios (MR)=0.6, 0.9, 1.0, 2.3, 4.9 and 13.6. X-ray diffraction studies of the as-milled powders show that a single-phase wüstite was formed for the lowest mole ratio (MR=0.6) and mixtures with MRs higher than 0.6 result in iron-wüstite nanocomposites, except for MR=13.6 that is dominantly a pure iron phase. The mean crystallite sizes of the iron and wüstite in the nanocomposites have been calculated by Scherrer's formula, which were 9±1 and 7±1 nm, respectively. Using the formula a=3.856+0.478 y, for Fe yO, where " a" is the lattice parameter of wüstite, it is possible to estimate the value of " y" for different nanocomposites and a composition of Fe 0.93O was estimated for the wüstite single phase (MR=0.6). In addition, a gradual decrease in " y" from 0.87 to 0.83 was obtained by increasing MR values from 0.9 to 4.9, respectively. The room-temperature Mössbauer spectrum of the single-phase wüstite shows considerable asymmetry due to two overlapping quadrupole doublets. For higher MRs, room-temperature Mössbauer spectra exhibit sextets, which confirm the existence of iron in the samples. The Mössbauer spectrum of the sample with the highest mole ratio (MR=13.6) shows only a sextet related to ?-Fe without any detection of wüstite, which is in agreement with the XRD results. The nanosized prepared wüstite shows ferrimagnetic like behavior, which was interpreted according to spinel-like defect clusters. The Ms values obtained from VSM measurements and those calculated based on the Mössbauer data and chemical reaction are in good agreement. By increasing MR from 0.6 to 2.3, the coercivity ( Hc) increases sharply to its maximum value at about MR=2.3, for which the value of Fe content is 45% and then drops off. This behavior is discussed based on ?-Fe contents in the nanocomposites and percolation threshold.

  13. Nanocrystalline Fe-Fe2O3 particle-deposited N-doped graphene as an activity-modulated Pt-free electrocatalyst for oxygen reduction reaction.

    PubMed

    Dhavale, Vishal M; Singh, Santosh K; Nadeema, Ayasha; Gaikwad, Sachin S; Kurungot, Sreekumar

    2015-12-21

    The size-controlled growth of nanocrystalline Fe-Fe2O3 particles (2-3 nm) and their concomitant dispersion on N-doped graphene (Fe-Fe2O3/NGr) could be attained when the mutually assisted redox reaction between NGr and Fe(3+) ions could be controlled within the aqueous droplets of a water-in-oil emulsion. The synergistic interaction existing between Fe-Fe2O3 and NGr helped the system to narrow down the overpotential for the oxygen reduction reaction (ORR) by bringing a significant positive shift to the reduction onset potential, which is just 15 mV higher than its Pt-counterpart. In addition, the half-wave potential (E1/2) of Fe-Fe2O3/NGr is found to be improved by a considerable amount of 135 mV in comparison to the system formed by dispersing Fe-Fe2O3 nanoparticles on reduced graphene oxide (Fe-Fe2O3/RGO), which indicates the presence of a higher number of active sites in Fe-Fe2O3/NGr. Despite this, the ORR kinetics of Fe-Fe2O3/NGr are found to be shifted significantly to the preferred 4-electron-transfer pathway compared to NGr and Fe-Fe2O3/RGO. Consequently, the H2O2% was found to be reduced by 78.3% for Fe-Fe2O3/NGr (13.0%) in comparison to Fe-Fe2O3/RGO (51.2%) and NGr (41.0%) at -0.30 V (vs. Hg/HgO). This difference in the yield of H2O2 formed between the systems along with the improvements observed in terms of the oxygen reduction onset and E1/2 in the case of Fe-Fe2O3/NGr reveals the activity modulation achieved for the latter is due to the coexistence of factors such as the presence of the mixed valancies of iron nanoparticles, small size and homogeneous distribution of Fe-Fe2O3 nanoparticles and the electronic modifications induced by the doped nitrogen in NGr. A controlled interplay of these factors looks like worked favorably in the case of Fe-Fe2O3/NGr. As a realistic system level validation, Fe-Fe2O3/NGr was employed as the cathode electrode of a single cell in a solid alkaline electrolyte membrane fuel cell (AEMFC). The system could display an open circuit voltage (OCV) of 0.73 V and maximum power and current densities of 54.40 mW cm(-2) and 200 mA cm(-2), respectively, which are comparable to the performance characteristics of a similar system derived by using 40 wt% Pt/C as the cathode electrode. PMID:26568372

  14. Enhancement of photoheterotrophic biohydrogen production at elevated temperatures by the expression of a thermophilic clostridial hydrogenase.

    PubMed

    Lo, Shou-Chen; Shih, Shau-Hua; Chang, Jui-Jen; Wang, Chun-Ying; Huang, Chieh-Chen

    2012-08-01

    The working temperature of a photobioreactor under sunlight can be elevated above the optimal growth temperature of a microorganism. To improve the biohydrogen productivity of photosynthetic bacteria at higher temperatures, a [FeFe]-hydrogenase gene from the thermophile Clostridium thermocellum was expressed in the mesophile Rhodopseudomonas palustris CGA009 (strain CGA-CThydA) using a log-phase expression promoter P( pckA ) to drive the expression of heterogeneous hydrogenase gene. In contrast, a mesophilic Clostridium acetobutylicum [FeFe]-hydrogenase gene was also constructed and expressed in R. palustris (strain CGA-CAhydA). Both transgenic strains were tested for cell growth, in vivo hydrogen production rate, and in vitro hydrogenase activity at elevated temperatures. Although both CGA-CThydA and CGA-CAhydA strains demonstrated enhanced growth over the vector control at temperatures above 38 °C, CGA-CThydA produced more hydrogen than the other strains. The in vitro hydrogenase activity assay, measured at 40 °C, confirmed that the activity of the CGA-CThydA hydrogenase was higher than the CGA-CAhydA hydrogenase. These results showed that the expression of a thermophilic [FeFe]-hydrogenase in R. palustris increased the growth rate and biohydrogen production at elevated temperatures. This transgenic strategy can be applied to a broad range of purple photosynthetic bacteria used to produce biohydrogen under sunlight. PMID:22460592

  15. A hidden reservoir of Fe/FeS in interstellar silicates?

    NASA Astrophysics Data System (ADS)

    Köhler, M.; Jones, A.; Ysard, N.

    2014-05-01

    Context. The depletion of iron and sulphur into dust in the interstellar medium and the exact nature of interstellar amorphous silicate grains is still an open question. Aims: We study the incorporation of iron and sulphur into amorphous silicates of olivine- and pyroxene-types and their effects on the dust spectroscopy and thermal emission. Methods: We used the Maxwell-Garnett effective-medium theory to construct the optical constants for a mixture of silicates, metallic iron, and iron sulphide. We also studied the effects of iron and iron sulphide in aggregate grains. Results: Iron sulphide inclusions within amorphous silicates that contain iron metal inclusions show no strong differences in the optical properties of the grains. A mix of amorphous olivine- and pyroxene-type silicate broadens the silicate features. An amorphous carbon mantle with a thickness of 10 nm on the silicate grains leads to an increase in absorption on the short-wavelength side of the 10 ?m silicate band. Conclusions: The assumption of amorphous olivine-type and pyroxene-type silicates and a 10 nm thick amorphous carbon mantle better matches the interstellar silicate band profiles. Including iron nano-particles leads to an increase in the mid-IR extinction, while up to 5 ppm of sulphur can be incorporated as Fe/FeS nano inclusions into silicate grains without leaving a significant trace of its presence.

  16. Hydrogenase synthesis in Bradyrhizobium japonicum Hupc mutants is altered in sensitivity to DNA gyrase inhibitors.

    PubMed Central

    Novak, P D; Maier, R J

    1989-01-01

    In the Hupc mutants of Bradyrhizobium japonicum SR, regulation of expression of hydrogenase is altered; the mutants synthesize hydrogenase constitutively in the presence of atmospheric levels of oxygen. The DNA gyrase inhibitors nalidixic acid, novobiocin, and coumermycin were used to inhibit growth of wild-type and mutant cells. For each inhibitor tested, growth of mutant and wild-type strains was equally sensitive. However, in contrast to the wild type, the Hupc mutants synthesized hydrogenase in the presence of high levels of any inhibitor. Cells were incubated with the drugs and simultaneously labeled with 14C-labeled amino acids, and hydrogenase was immunoprecipitated with antibody to the large subunit of the enzyme. Fluorograms of antibody blots then were scanned to determine the relative amount of hydrogenase (large subunit) synthesized in the presence or absence of the gyrase inhibitors. The amount of hydrogenase synthesized by the Hupc mutants in the presence of 300 micrograms of nalidixic acid per ml was near the level of enzyme synthesized in the absence of the inhibitor. No hydrogenase was detected in antibody blots of wild-type cultures which were derepressed for hydrogenase in the presence of 100 micrograms of coumermycin or novobiocin per ml. In contrast, hydrogenase was synthesized by the Hupc mutants in the presence of 100 micrograms of either drug per ml. The amount synthesized ranged from 5 to 32% and 20 to 49%, respectively, of that in the absence of those inhibitors, but nevertheless, hydrogenase synthesis was detected in all of the mutants examined.(ABSTRACT TRUNCATED AT 250 WORDS) Images PMID:2547335

  17. Structural and functional investigations of biological catalysts for optimization of solar-driven H II production systems

    NASA Astrophysics Data System (ADS)

    King, Paul W.; Svedruzic, Drazenka; Cohen, Jordi; Schulten, Klaus; Seibert, Michael; Ghirardi, Maria L.

    2006-08-01

    Research efforts to develop efficient systems for H II production encompass a variety of biological and chemical approaches. For solar-driven H II production we are investigating an approach that integrates biological catalysts, the [FeFe] hydrogenases, with a photoelectrochemical cell as a novel bio-hybrid system. Structurally the [FeFe] hydrogenases consist of an iron-sulfur catalytic site that in some instances is electronically wired to accessory iron-sulfur clusters proposed to function in electron transfer. The inherent structural complexity of most examples of these enzymes is compensated by characteristics desired for bio-hybrid systems (i.e., low activation energy, high catalytic activity and solubility) with the benefit of utilizing abundant, less costly non-precious metals. Redesign and modification of [FeFe] hydrogenases is being undertaken to reduce complexity and to optimize structural properties for various integration strategies. The least complex examples of [FeFe] hydrogenase are found in the species of photosynthetic green algae and are being studied as design models for investigating the effects of structural minimization on substrate transfer, catalytic activity and oxygen sensitivity. Redesigning hydrogenases for effective use in bio-hybrid systems requires a detailed understanding of the relationship between structure and catalysis. To achieve better mechanistic understanding of [FeFe] hydrogenases both structural and dynamic models are being used to identify potential substrate transfer mechanisms which are tested in an experimental system. Here we report on recent progress of our investigations in the areas of [FeFe] hydrogenase overexpression, minimization and biochemical characterization.

  18. Structure and magnetic properties of irradiated Fe/Fe oxide core-shell nanoclusters

    SciTech Connect

    McCloy, John S.; Jiang, Weilin; Sundararajan, Jennifer A.; Qiang, You; Burks, Edward; Liu, Kai

    2013-04-25

    A cluster deposition method was used to produce a film of loosely aggregated particles of Fe-Fe3O4 core-shell nanoclusters with an 8 nm iron core size and 2 nm oxide shell thickness. The film of particles on a silicon substrate was irradiated with 5.5 MeV Si2+ ions to a fluence of 1016 cm-2 near room temperature, and computer simulations based on the SRIM (Stopping and Range of Ions in Matter) code show that the implanted Si species stops near the film-substrate interface. The ion irradiation creates a structural change in the film with corresponding chemical and magnetic changes. X-ray diffraction shows that the core size and chemistry stay the same but the shell becomes FeO that grows to a thickness of 17 nm. Helium ion microscopy shows that the previously separate particles have densified into a nearly continuous film. Major loop magnetic hysteresis measurements show a decrease in saturation magnetization that we attribute to the presence of the antiferromagnetic (AFM) FeO shell. First-order reversal curve measurements on the irradiated film performed with a vibrating sample magnetometer show that the AFM shell prevents the particles from interacting magnetically, leading to low coercivity from the iron core and little bias field from the core interactions. These results, and others reported previously on different compositions (Fe3O4 or FeO+Fe3N nanoclusters), show that the ion irradiation behavior of nanocluster films such as these depends strongly on the initial nanostructure and chemistry.

  19. H, not O or pressure, causes eutectic T depression in the Fe-FeS System to 8 GPa

    NASA Astrophysics Data System (ADS)

    Buono, Antonio S.; Walker, David

    2015-04-01

    The Fe-FeS system maintains a eutectic temperature of 990 ± 10 °C to at least 8 GPa if starting materials and pressure media are rigorously dehydrated. Literature reports of pressure-induced freezing point depression of the eutectic for the Fe-FeS system are not confirmed. Modest addition of oxygen alone is confirmed to cause negligible freezing point depression at 6 GPa. Addition of H alone causes a progressive decrease in the eutectic temperature with P in the Fe-FeS-H system to below 965 °C at 6 GPa to below 950 °C at 8 GPa. It is our hypothesis that moisture contamination in unrigorously dried experiments may be an H source for freezing point depression. O released from H2O disproportionation reacts with Fe and is sequestered as ferropericlase along the sample capsules walls, leaving the H to escape the system and/or enter the Fe-FeS mixture. The observed occurrence of ferropericlase on undried MgO capsule margins is otherwise difficult to explain, because an alternate source for the oxygen in the ferropericlase layer is difficult to identify. This study questions the use of pressure-depressed Fe-S eutectic temperatures and suggests that the lower eutectic temperatures sometimes reported are achieved by moving into the ternary Fe-S-H system. These results adjust slightly the constraints on eutectic temperatures allowed for partly solidified cores on small planets. H substantially diminishes the temperature extent of the melting interval in Fe-S by reducing the melting points of the crystalline phases more than it depresses the eutectic.

  20. Turning Cellulose Waste Into Electricity: Hydrogen Conversion by a Hydrogenase Electrode

    PubMed Central

    Abramov, Sergey M.; Sadraddinova, Elmira R.; Shestakov, Andrey I.; Voronin, Oleg G.; Karyakin, Arkadiy A.; Zorin, Nikolay A.; Netrusov, Alexander I.

    2013-01-01

    Hydrogen-producing thermophilic cellulolytic microorganisms were isolated from cow faeces. Rates of cellulose hydrolysis and hydrogen formation were 0.2 mM L-1 h-1 and 1 mM L-1 h-1, respectively. An enzymatic fuel cell (EFC) with a hydrogenase anode was used to oxidise hydrogen produced in a microbial bioreactor. The hydrogenase electrode was exposed for 38 days (912 h) to a thermophilic fermentation medium. The hydrogenase activity remaining after continuous operation under load was 73% of the initial value. PMID:24312437

  1. Melting relations in the Fe-rich portion of the system FeFeS at 30 kb pressure

    USGS Publications Warehouse

    Brett, R.; Bell, P.M.

    1969-01-01

    The melting relations of FeFeS mixtures covering the composition range from Fe to Fe67S33 have been determined at 30 kb pressure. The phase relations are similar to those at low pressure. The eutectic has a composition of Fe72.9S27.1 and a temperature of 990??C. Solubility of S in Fe at elevated temperatures at 30 kb is of the same order of magnitude as at low pressure. Sulfur may have significantly lowered the melting point of iron in the upper mantle during the period of coalescence of metal prior to core formation in the primitive earth. ?? 1969.

  2. Effect of Hydrogenase and Mixed Sulfate-Reducing Bacterial Populations on the Corrosion of Steel

    PubMed Central

    Bryant, Richard D.; Jansen, Wayne; Boivin, Joe; Laishley, Edward J.; Costerton, J. William

    1991-01-01

    The importance of hydrogenase activity to corrosion of steel was assessed by using mixed populations of sulfate-reducing bacteria isolated from corroded and noncorroded oil pipelines. Biofilms which developed on the steel studs contained detectable numbers of sulfate-reducing bacteria (104 increasing to 107/0.5 cm2). However, the biofilm with active hydrogenase activity (i.e., corrosion pipeline organisms), as measured by a semiquantitative commercial kit, was associated with a significantly higher corrosion rate (7.79 mm/year) relative to noncorrosive biofilm (0.48 mm/year) with 105 sulfate-reducing bacteria per 0.5 cm2 but no measurable hydrogenase activity. The importance of hydrogenase and the microbial sulfate-reducing bacterial population making up the biofilm are discussed relative to biocorrosion. Images PMID:16348560

  3. Catalytic mechanism of hydrogenase from Azotobacter vinelandii. Final technical report, August 1, 1994--July 31, 1997

    SciTech Connect

    Arp, D.J.

    1997-10-01

    This project is focused on investigations of the catalytic mechanism of the hydrogenase found in the aerobic, N{sub 2}-fixing microorganism Azotobacter vinelandii. This report summarizes the progress during the first two years of the current project and include the anticipated course of the research for the remaining year of the current project. Because the current proposal represents a change in direction, the authors also include a brief progress report of prior DOE-sponsored research dealing with hydrogenases.

  4. Function of Periplasmic Hydrogenases in the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough? †

    PubMed Central

    Caffrey, Sean M.; Park, Hyung-Soo; Voordouw, Johanna K.; He, Zhili; Zhou, Jizhong; Voordouw, Gerrit

    2007-01-01

    The sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough possesses four periplasmic hydrogenases to facilitate the oxidation of molecular hydrogen. These include an [Fe] hydrogenase, an [NiFeSe] hydrogenase, and two [NiFe] hydrogenases encoded by the hyd, hys, hyn1, and hyn2 genes, respectively. In order to understand their cellular functions, we have compared the growth rates of existing (hyd and hyn1) and newly constructed (hys and hyn-1 hyd) mutants to those of the wild type in defined media in which lactate or hydrogen at either 5 or 50% (vol/vol) was used as the sole electron donor for sulfate reduction. Only strains missing the [Fe] hydrogenase were significantly affected during growth with lactate or with 50% (vol/vol) hydrogen as the sole electron donor. When the cells were grown at low (5% [vol/vol]) hydrogen concentrations, those missing the [NiFeSe] hydrogenase suffered the greatest impairment. The growth rate data correlated strongly with gene expression results obtained from microarray hybridizations and real-time PCR using mRNA extracted from cells grown under the three conditions. Expression of the hys genes followed the order 5% hydrogen > 50% hydrogen > lactate, whereas expression of the hyd genes followed the reverse order. These results suggest that growth with lactate and 50% hydrogen is associated with high intracellular hydrogen concentrations, which are best captured by the higher activity, lower affinity [Fe] hydrogenase. In contrast, growth with 5% hydrogen is associated with a low intracellular hydrogen concentration, requiring the lower activity, higher affinity [NiFeSe] hydrogenase. PMID:17601789

  5. Photosynthetic electron partitioning between [FeFe]-hydrogenase and ferredoxin:NADP+-oxidoreductase (FNR) enzymes in vitro.

    PubMed

    Yacoby, Iftach; Pochekailov, Sergii; Toporik, Hila; Ghirardi, Maria L; King, Paul W; Zhang, Shuguang

    2011-06-01

    Photosynthetic water splitting, coupled to hydrogenase-catalyzed hydrogen production, is considered a promising clean, renewable source of energy. It is widely accepted that the oxygen sensitivity of hydrogen production, combined with competition between hydrogenases and NADPH-dependent carbon dioxide fixation are the main limitations for its commercialization. Here we provide evidence that, under the anaerobic conditions that support hydrogen production, there is a significant loss of photosynthetic electrons toward NADPH production in vitro. To elucidate the basis for competition, we bioengineered a ferredoxin-hydrogenase fusion and characterized hydrogen production kinetics in the presence of Fd, ferredoxin:NADP(+)-oxidoreductase (FNR), and NADP(+). Replacing the hydrogenase with a ferredoxin-hydrogenase fusion switched the bias of electron transfer from FNR to hydrogenase and resulted in an increased rate of hydrogen photoproduction. These results suggest a new direction for improvement of biohydrogen production and a means to further resolve the mechanisms that control partitioning of photosynthetic electron transport. PMID:21606330

  6. (Catalytic mechanism of hydrogenase from aerobic N2-fixing microorganisms). [Azotobacter vinelandii:a1

    SciTech Connect

    Not Available

    1991-01-01

    The results of this DOE-sponsored project have contributed to our understanding of the catalytic mechanism of A. vinelandii hydrogenase. A group of inhibitors have been characterized. These provide information about the different types of redox clusters involved in catalysis and the roles of each. One group has already used acetylene in a study of three desulfovibrian hydrogenases and shown that onbly the NiFe hydrogenases are inhibited. The inhibitor studies are also being extended to other enzymes. We have characterized a number of special properties of A. vinelandii hydrogenase. While the NiFe dimeric hydrogenases are now recognized as a large group of similar enzymes, there are differences in the spectral and catalytic properties which are not explained by their similar redox inventories, identical subunit structures, immunological cross reactivity and conserved sequences. Surprisingly, we only see a significant EPR signal attributable to Ni after the enzyme has been inactivated with O{sub 2} and then re-reduced (though not reactivated). Acetylene, which does not substantially perterb the EPR signal of active hydrogenase, does result in a new absorption envelope in the UV-Vis spectrum. Overall, the results of this project have revealed the complex interactions of the redox clusters in catalysis through studies of inhibitor mechanisms and spectral properties. 14 refs., 9 figs.

  7. Hydrogenase Activity of Mineral-Associated and Suspended Populations of Desulfovibrio desulfuricans Essex 6

    SciTech Connect

    C.L. Reardon; T.S. Magnuson; E.S. Boyd; W.D. Leavitt; D.W. Reed; G.G. Geesey

    2014-02-01

    The interactions between sulfate-reducing microorganisms and iron oxides influence a number of important redox-sensitive biogeochemical processes including the formation of iron sulfides. Enzymes, such as hydrogenase which catalyze the reversible oxidation of molecular hydrogen, are known to mediate electron transfer to metals and may contribute to the formation and speciation of ferrous sulfides formed at the cell–mineral interface. In the present study, we compared the whole cell hydrogenase activity of Desulfovibrio desulfuricans strain Essex 6 growing as biofilms on hematite (hematite-associated) or as suspended populations using different metabolic pathways. Hematite-associated cells exhibited significantly greater hydrogenase activity than suspended populations during sulfate respiration but not during pyruvate fermentation. The enhanced activity of the hematite-associated, sulfate-grown cells appears to be dependent on iron availability rather than a general response to surface attachment since the activity of glass-associated cells did not differ from that of suspended populations. Hydrogenase activity of pyruvate-fermenting cells was stimulated by addition of iron as soluble Fe(II)Cl2 and, in the absence of added iron, both sulfate-reducing and pyruvate-fermenting cells displayed similar rates of hydrogenase activity. These data suggest that iron exerts a stronger influence on whole cell hydrogenase activity than either metabolic pathway or mode of growth. The location of hydrogenase to the cell envelope and the enhanced activity at the hematite surface in sulfate-reducing cells may influence the redox conditions that control the species of iron sulfides on the mineral surface.

  8. Identification of a locus within the hydrogenase gene cluster involved in intracellular nickel metabolism in Bradyrhizobium japonicum

    SciTech Connect

    Changlin Fu; Maier, R.J. )

    1991-12-01

    A 0.6-kb fragment of DNA involved in intracellular Ni metabolism was isolated and cloned from a cosmid containing 23.2 kb of hydrogenase-related genes of Bradyrhizobium japonicum. This locus is located 8.3 kb upstream of the hydrogenase structural genes. The hydrogenase activity of a mutant with a gene-directed mutation at this locus (strain JHK7) showed dependency on nickel provided during hydrogenase depression. The hydrogenase activity was only 20% of that in the wild-type strain, JH, at a concentration of 0.5 {mu}M NiCl{sub 2}. The hydrogenase activity in JH reached its maximum at 3 {mu}M NiCl{sub 2}, whereas the mutant (JHK7) reached wild-type levels of hydrogenase activity when derepressed in 50 {mu}M NiCl{sub 2}. Studies with the hup-lacZ transcriptional fusion plasmid pSY7 in JHK7 showed that the mutant JHK7 expressed less promoter activity under low-nickel conditions than did strain JH. The mutant accumulated less nickel during a 45-h hydrogenase under low-nickel conditions than did strain JH. The mutant accumulated less nickel during a 45-h hydrogenase derepression period than did the wild type. However, both JHK7 and the JH wild-type strain had the same short-term Ni transport rates, and the K{sub m}s for Ni of both strains were about 62 {mu}M. When incubated under non-hydrogenase-derepression conditions, the mutant accumulated Ni at the same rate as strain JH. However, this stored source of nickel was unable to restore hydrogenase expression ability of the mutant to wild-type levels during derepression without nickel. The results that the locus identified in B. japonicum is not involved in nickel-specific transport.

  9. Theoretical Studies of Structures and Mechanisms in Organometallic and Bioinorganic Chemistry: Heck Reaction with Palladium Phosphines, Active Sites of Superoxide Reductase and Cytochrome P450 Monooxygenase, and Tetrairon Hexathiolate Hydrogenase Model 

    E-print Network

    Surawatanawong, Panida

    2010-07-14

    The electronic structures and reaction mechanisms of transition-metal complexes can be calculated accurately by density functional theory (DFT) in cooperation with the continuum solvation model. The palladium catalyzed ...

  10. [NiFe]-hydrogenase is essential for cyanobacterium Synechocystis sp. PCC 6803 aerobic growth in the dark

    PubMed Central

    De Rosa, Edith; Checchetto, Vanessa; Franchin, Cinzia; Bergantino, Elisabetta; Berto, Paola; Szabò, Ildikò; Giacometti, Giorgio M.; Arrigoni, Giorgio; Costantini, Paola

    2015-01-01

    The cyanobacterium Synechocystis sp. PCC 6803 has a bidirectional [NiFe]-hydrogenase (Hox hydrogenase) which reversibly reduces protons to H2. This enzyme is composed of a hydrogenase domain and a diaphorase moiety, which is distinctly homologous to the NADH input module of mitochondrial respiratory Complex I. Hox hydrogenase physiological function is still unclear, since it is not required for Synechocystis fitness under standard growth conditions. We analyzed the phenotype under prolonged darkness of three Synechocystis knock-out strains, lacking either Hox hydrogenase (?HoxE-H) or one of the proteins responsible for the assembly of its NiFe active site (?HypA1 and ?HypB1). We found that Hox hydrogenase is required for Synechocystis growth under this condition, regardless of the functional status of its catalytic site, suggesting an additional role beside hydrogen metabolism. Moreover, quantitative proteomic analyses revealed that the expression levels of several subunits of the respiratory NADPH/plastoquinone oxidoreductase (NDH-1) are reduced when Synechocystis is grown in the dark. Our findings suggest that the Hox hydrogenase could contribute to electron transport regulation when both photosynthetic and respiratory pathways are down-regulated, and provide a possible explanation for the close evolutionary relationship between mitochondrial respiratory Complex I and cyanobacterial [NiFe]-hydrogenases. PMID:26215212

  11. Nickel-Iron Dithiolates Related to the Deactivated [NiFe]-Hydrogenases

    PubMed Central

    Schilter, David

    2012-01-01

    Described herein are preparations of synthetic models for the deactivated Ni(II)Fe(II) states of the [NiFe]-hydrogenases. Iodination of the S = ½ species [(dppe)Ni(pdt)Fe(CO)3]+ afforded the diamagnetic iodo complex [(dppe)Ni(pdt)IFe(CO)3]+. Crystallographic analysis of this species confirmed the presence of square-pyramidal Ni linked to an octahedral Fe centre. The Ni···Fe separation of 3.018 Å indicated the absence of metal-metal bonding. This complex could be reduced to give (dppe)Ni(pdt)Fe(CO)3 and, in the presence of iodide, decarbonylated to afford (dppe)Ni(pdt)FeI2. Derivatives of the type [(diphosphine)Ni(dithiolate)XFe(CO)2L]+ (X = Cl, Br, I) were prepared by halogenation of mixed-valence precursors [(diphosphine)Ni(dithiolate)Fe(CO)2L]+ (diphosphine = dppe, dcpe; L = tertiary phosphine or CO). The Fe(CO)2(PR3)-containing derivatives are more robust than the related tricarbonyl derivatives. Exploiting this greater stability, we characterised examples of chloride and bromide derivatives. Related fluorides could be prepared by F? abstraction from BF4?. Spectroscopic evidence is presented for the hydroperoxide [(diphosphine)Ni(dithiolate)(OOH)Fe(CO)2L]+, which was prepared by oxidation of a model for Ni-SU and Ni-SIr states. PMID:22992700

  12. Structural And Biological Analysis of the Metal Sites of Escherichia Coli Hydrogenase Accessory Protein

    SciTech Connect

    Dias, A.V.; Mulvihill, C.M.; Leach, M.R.; Pickering, I.J.; George, G.N.; Zamble, D.B.

    2009-05-12

    The [NiFe]-hydrogenase protein produced by many types of bacteria contains a dinuclear metal center that is required for enzymatic activity. Assembly of this metal cluster involves the coordinated activity of a number of helper proteins including the accessory protein, HypB, which is necessary for Ni(II) incorporation into the hydrogenase proteins. The HypB protein from Escherichia coli has two metal-binding sites, a high-affinity Ni(II) site that includes ligands from the N-terminal domain and a low-affinity metal site located within the C-terminal GTPase domain. In order to determine the physiological relevance of the two separate sites, hydrogenase production was assessed in strains of E. coli expressing wild-type HypB, the isolated GTPase domain, or site-directed mutants of metal-binding residues. These experiments demonstrate that both metal sites of HypB are critical for the maturation of the hydrogenase enzymes in E. coli. X-ray absorption spectroscopy of purified proteins was used to examine the detailed coordination spheres of each nickel-loaded site. In addition, because the low-affinity metal site has a stronger preference for Zn(II) than Ni(II), the ligands and geometry for this metal were also resolved. The results from these experiments are discussed in the context of a mechanism for Ni(II) insertion into the hydrogenase protein.

  13. Purification and characterization of the hydrogen uptake hydrogenase from the hyperthermpholic archaebacterium Pyrodictium brockii

    SciTech Connect

    Pihl, T.D. ); Maier, R.J. Univ. of Maryland, Baltimore )

    1991-03-01

    Pyrodictium brockii is a hyperthermophilic archaebacterium with an optimal growth temperature of 105C. P. brokii is also a chemolithotroph, requiring H{sub 2} and CO{sub 2} for growth. The authors have purified the hydrogen uptake hydrogenase from membranes of P. brockii by reactive red affinity chromatography and sucrose gradient centrifugation. Colorometric analysis of Fe and S content in reactive red-purified hydrogenase revealed 8.7 {plus minus} 0.6 mol of Fe and 6.2 {plus minus} 1.2 mol of S per mol of hydrogenase. Growth of cells in {sup 63} NiCl{sub 2} resulted in label incorporation into reactive red-purified hydrogenase. Temperature stability studies indicated that the membrane-bound form of the enzyme was more stable than the solubilized purified form over a period of minutes with respect to temperature. However, the membranes were not able to protect the enzyme from thermal inactivation over a period of hours. The artificial electron acceptor specificity of the pure enzyme was similar to that of the membrane-bound form, but the purified enzyme was able to evolve H{sub 2} in the presence of reduced methyl viologen. The K{sub m} of membrane-bound hydrogenase for H{sub 2} was approximately 19 {mu}M with methylene blue as the electron acceptor, whereas the purified enzyme had a higher K{sub m} value.

  14. Advances in the Function and Regulation of Hydrogenase in the Cyanobacterium Synechocystis PCC6803

    PubMed Central

    Cassier-Chauvat, Corinne; Veaudor, Théo; Chauvat, Franck

    2014-01-01

    In order to use cyanobacteria for the biological production of hydrogen, it is important to thoroughly study the function and the regulation of the hydrogen-production machine in order to better understand its role in the global cell metabolism and identify bottlenecks limiting H2 production. Most of the recent advances in our understanding of the bidirectional [Ni-Fe] hydrogenase (Hox) came from investigations performed in the widely-used model cyanobacterium Synechocystis PCC6803 where Hox is the sole enzyme capable of combining electrons with protons to produce H2 under specific conditions. Recent findings suggested that the Hox enzyme can receive electrons from not only NAD(P)H as usually shown, but also, or even preferentially, from ferredoxin. Furthermore, plasmid-encoded functions and glutathionylation (the formation of a mixed-disulfide between the cysteines residues of a protein and the cysteine residue of glutathione) are proposed as possible new players in the function and regulation of hydrogen production. PMID:25365180

  15. Evolutionary and biotechnological implications of robust hydrogenase activity in halophilic strains of Tetraselmis.

    PubMed

    D'Adamo, Sarah; Jinkerson, Robert E; Boyd, Eric S; Brown, Susan L; Baxter, Bonnie K; Peters, John W; Posewitz, Matthew C

    2014-01-01

    Although significant advances in H2 photoproduction have recently been realized in fresh water algae (e.g. Chlamydomonas reinhardtii), relatively few studies have focused on H2 production and hydrogenase adaptations in marine or halophilic algae. Salt water organisms likely offer several advantages for biotechnological H2 production due to the global abundance of salt water, decreased H2 and O2 solubility in saline and hypersaline systems, and the ability of extracellular NaCl levels to influence metabolism. We screened unialgal isolates obtained from hypersaline ecosystems in the southwest United States and identified two distinct halophilic strains of the genus Tetraselmis (GSL1 and QNM1) that exhibit both robust fermentative and photo H2-production activities. The influence of salinity (3.5%, 5.5% and 7.0% w/v NaCl) on H2 production was examined during anoxic acclimation, with the greatest in vivo H2-production rates observed at 7.0% NaCl. These Tetraselmis strains maintain robust hydrogenase activity even after 24 h of anoxic acclimation and show increased hydrogenase activity relative to C. reinhardtii after extended anoxia. Transcriptional analysis of Tetraselmis GSL1 enabled sequencing of the cDNA encoding the FeFe-hydrogenase structural enzyme (HYDA) and its maturation proteins (HYDE, HYDEF and HYDG). In contrast to freshwater Chlorophyceae, the halophilic Tetraselmis GSL1 strain likely encodes a single HYDA and two copies of HYDE, one of which is fused to HYDF. Phylogenetic analyses of HYDA and concatenated HYDA, HYDE, HYDF and HYDG in Tetraselmis GSL1 fill existing knowledge gaps in the evolution of algal hydrogenases and indicate that the algal hydrogenases sequenced to date are derived from a common ancestor. This is consistent with recent hypotheses that suggest fermentative metabolism in the majority of eukaryotes is derived from a common base set of enzymes that emerged early in eukaryotic evolution with subsequent losses in some organisms. PMID:24465722

  16. Novel, Oxygen-Insensitive Group 5 [NiFe]-Hydrogenase in Ralstonia eutropha

    PubMed Central

    Schäfer, Caspar; Friedrich, Bärbel

    2013-01-01

    Recently, a novel group of [NiFe]-hydrogenases has been defined that appear to have a great impact in the global hydrogen cycle. This so-called group 5 [NiFe]-hydrogenase is widespread in soil-living actinobacteria and can oxidize molecular hydrogen at atmospheric levels, which suggests a high affinity of the enzyme toward H2. Here, we provide a biochemical characterization of a group 5 hydrogenase from the betaproteobacterium Ralstonia eutropha H16. The hydrogenase was designated an actinobacterial hydrogenase (AH) and is catalytically active, as shown by the in vivo H2 uptake and by activity staining in native gels. However, the enzyme does not sustain autotrophic growth on H2. The AH was purified to homogeneity by affinity chromatography and consists of two subunits with molecular masses of 65 and 37 kDa. Among the electron acceptors tested, nitroblue tetrazolium chloride was reduced by the AH at highest rates. At 30°C and pH 8, the specific activity of the enzyme was 0.3 ?mol of H2 per min and mg of protein. However, an unexpectedly high Michaelis constant (Km) for H2 of 3.6 ± 0.5 ?M was determined, which is in contrast to the previously proposed low Km of group 5 hydrogenases and makes atmospheric H2 uptake by R. eutropha most unlikely. Amperometric activity measurements revealed that the AH maintains full H2 oxidation activity even at atmospheric oxygen concentrations, showing that the enzyme is insensitive toward O2. PMID:23793632

  17. Flow-FISH analysis and isolation of clostridial strains in an anaerobic semi-solid bio-hydrogen producing system by hydrogenase gene target.

    PubMed

    Jen, Chang Jui; Chou, Chia-Hung; Hsu, Ping-Chi; Yu, Sian-Jhong; Chen, Wei-En; Lay, Jiunn-Jyi; Huang, Chieh-Chen; Wen, Fu-Shyan

    2007-04-01

    By using hydrogenase gene-targeted polymerase chain reaction (PCR) and reverse transcriptase PCR (RT-PCR), the predominant clostridial hydrogenase that may have contributed to biohydrogen production in an anaerobic semi-solid fermentation system has been monitored. The results revealed that a Clostridium pasteurianum-like hydrogenase gene sequence can be detected by both PCR and RT-PCR and suggested that the bacterial strain possessing this specific hydrogenase gene was dominant in hydrogenase activity and population. Whereas another Clostridium saccharobutylicum-like hydrogenase gene can be detected only by RT-PCR and suggest that the bacterial strain possessing this specific hydrogenase gene may be less dominant in population. In this study, hydrogenase gene-targeted fluorescence in situ hybridization (FISH) and flow cytometry analysis confirmed that only 6.6% of the total eubacterial cells in a hydrogen-producing culture were detected to express the C. saccharobutylicum-like hydrogenase, whereas the eubacteria that expressed the C. pasteurianum-like hydrogenase was 25.6%. A clostridial strain M1 possessing the identical nucleotide sequences of the C. saccharobutylicum-like hydrogenase gene was then isolated and identified as Clostridium butyricum based on 16S rRNA sequence. Comparing to the original inoculum with mixed microflora, either using C. butyricum M1 as the only inoculum or co-culturing with a Bacillus thermoamylovorans isolate will guarantee an effective and even better production of hydrogen from brewery yeast waste. PMID:17277963

  18. Hydrogen Formation and Its Regulation in Ruminococcus albus: Involvement of an Electron-Bifurcating [FeFe]-Hydrogenase, of a Non-Electron-Bifurcating [FeFe]-Hydrogenase, and of a Putative Hydrogen-Sensing [FeFe]-Hydrogenase

    PubMed Central

    Zheng, Yanning; Kahnt, Jörg; Kwon, In Hyuk; Mackie, Roderick I.

    2014-01-01

    Ruminococcus albus 7 has played a key role in the development of the concept of interspecies hydrogen transfer. The rumen bacterium ferments glucose to 1.3 acetate, 0.7 ethanol, 2 CO2, and 2.6 H2 when growing in batch culture and to 2 acetate, 2 CO2, and 4 H2 when growing in continuous culture in syntrophic association with H2-consuming microorganisms that keep the H2 partial pressure low. The organism uses NAD+ and ferredoxin for glucose oxidation to acetyl coenzyme A (acetyl-CoA) and CO2, NADH for the reduction of acetyl-CoA to ethanol, and NADH and reduced ferredoxin for the reduction of protons to H2. Of all the enzymes involved, only the enzyme catalyzing the formation of H2 from NADH remained unknown. Here, we report that R. albus 7 grown in batch culture on glucose contained, besides a ferredoxin-dependent [FeFe]-hydrogenase (HydA2), a ferredoxin- and NAD-dependent electron-bifurcating [FeFe]-hydrogenase (HydABC) that couples the endergonic formation of H2 from NADH to the exergonic formation of H2 from reduced ferredoxin. Interestingly, hydA2 is adjacent to the hydS gene, which is predicted to encode an [FeFe]-hydrogenase with a C-terminal PAS domain. We showed that hydS and hydA2 are part of a larger transcriptional unit also harboring putative genes for a bifunctional acetaldehyde/ethanol dehydrogenase (Aad), serine/threonine protein kinase, serine/threonine protein phosphatase, and a redox-sensing transcriptional repressor. Since HydA2 and Aad are required only when R. albus grows at high H2 partial pressures, HydS could be a H2-sensing [FeFe]-hydrogenase involved in the regulation of their biosynthesis. PMID:25157086

  19. Hydrogen Production by a Hyperthermophilic Membrane-Bound Hydrogenase in Soluble Nanolipoprotein Particles

    SciTech Connect

    Baker, S E; Hopkins, R C; Blanchette, C; Walsworth, V; Sumbad, R; Fischer, N; Kuhn, E; Coleman, M; Chromy, B; Letant, S; Hoeprich, P; Adams, M W; Henderson, P T

    2008-10-22

    Hydrogenases constitute a promising class of enzymes for ex vivo hydrogen production. Implementation of such applications is currently hindered by oxygen sensitivity and, in the case of membrane-bound hydrogenases (MBH), poor water solubility. Nanolipoprotein particles (NLPs), formed from apolipoproteins and phospholipids, offer a novel means to incorporate MBH into in a well-defined water-soluble matrix that maintains the enzymatic activity and is amenable to incorporation into more complex architectures. We report the synthesis, hydrogen-evolving activity and physical characterization of the first MBH-NLP assembly. This may ultimately lead to the development of biomimetic hydrogen production devices.

  20. Mutational analysis of the hyc-operon determining the relationship between hydrogenase-3 and NADH pathway in Enterobacter aerogenes.

    PubMed

    Pi, Jian; Jawed, Muhammad; Wang, Jun; Xu, Li; Yan, Yunjun

    2016-01-01

    In this study, the hydrogenase-3 gene cluster (hycDEFGH) was isolated and identified from Enterobacter aerogenes CCTCC AB91102. All gene products were highly homologous to the reported bacterial hydrogenase-3 (Hyd-3) proteins. The genes hycE, hycF, hycG encoding the subunits of hydrogenase-3 were targeted for genetic knockout to inhibit the FHL hydrogen production pathway via the Red recombination system, generating three mutant strains AB91102-E (?hycE), AB91102-F (?hycF) and AB91102-G (?hycG). Deletion of the three genes affected the integrity of hydrogenase-3. The hydrogen production experiments with the mutant strains showed that no hydrogen was detected compared with the wild type (0.886mol/mol glucose), demonstrating that knocking out any of the three genes could inhibit NADH hydrogen production pathway. Meanwhile, the metabolites of the mutant strains were significantly changed in comparison with the wild type, indicating corresponding changes in metabolic flux by mutation. Additionally, the activity of NADH-mediated hydrogenase was found to be nil in the mutant strains. The chemostat experiments showed that the NADH/NAD(+) ratio of the mutant strains increased nearly 1.4-fold compared with the wild type. The NADH-mediated hydrogenase activity and NADH/NAD(+) ratio analysis both suggested that NADH pathway required the involvement of the electron transport chain of hydrogenase-3. PMID:26672442

  1. Powerful fermentative hydrogen evolution of photosynthate in the cyanobacterium Lyngbya aestuarii BL J mediated by a bidirectional hydrogenase

    PubMed Central

    Kothari, Ankita; Parameswaran, Prathap; Garcia-Pichel, Ferran

    2014-01-01

    Cyanobacteria are considered good models for biohydrogen production because they are relatively simple organisms with a demonstrable ability to generate H2 under certain physiological conditions. However, most produce only little H2, revert readily to H2 consumption, and suffer from hydrogenase sensitivity to O2. Strains of the cyanobacteria Lyngbya aestuarii and Microcoleus chthonoplastes obtained from marine intertidal cyanobacterial mats were recently found to display much better H2 production potential. Because of their ecological origin in environments that become quickly anoxic in the dark, we hypothesized that this differential ability may have evolved to serve a role in the fermentation of the photosynthate. Here we show that, when forced to ferment internal substrate, these cyanobacteria display desirable characteristics of physiological H2 production. Among them, the strain L. aestuarii BL J had the fastest specific rates and attained the highest H2 concentrations during fermentation of photosynthate, which proceeded via a mixed acid fermentation pathway to yield acetate, ethanol, lactate, H2, CO2, and pyruvate. Contrary to expectations, the H2 yield per mole of glucose was only average compared to that of other cyanobacteria. Thermodynamic analyses point to the use of electron donors more electronegative than NAD(P)H in Lyngbya hydrogenases as the basis for its strong H2 production ability. In any event, the high specific rates and H2 concentrations coupled with the lack of reversibility of the enzyme, at the expense of internal, photosynthetically generated reductants, makes L. aestuarii BL J and/or its enzymes, a potentially feasible platform for large-scale H2 production. PMID:25540642

  2. The Uptake Hydrogenase in the Unicellular Diazotrophic Cyanobacterium Cyanothece sp. Strain PCC 7822 Protects Nitrogenase from Oxygen Toxicity

    PubMed Central

    Zhang, Xiaohui; Sherman, Debra M.

    2014-01-01

    Cyanothece sp. strain PCC 7822 is a unicellular, diazotrophic cyanobacterium that can produce large quantities of H2 when grown diazotrophically. This strain is also capable of genetic manipulations and can represent a good model for improving H2 production from cyanobacteria. To this end, a knockout mutation was made in the hupL gene (?hupL), and we determined how this would affect the amount of H2 produced. The ?hupL mutant demonstrated virtually no nitrogenase activity or H2 production when grown under N2-fixing conditions. To ensure that this mutation only affected the hupL gene, a complementation strain was constructed readily with wild-type properties; this indicated that the original insertion was only in hupL. The mutant had no uptake hydrogenase activity but had increased bidirectional hydrogenase (Hox) activity. Western blotting and immunocytochemistry under the electron microscope indicated that the mutant had neither HupL nor NifHDK, although the nif genes were transcribed. Interestingly, biochemical analysis demonstrated that both HupL and NifH could be membrane associated. The results indicated that the nif genes were transcribed but that NifHDK was either not translated or was translated but rapidly degraded. We hypothesized that the Nif proteins were made but were unusually susceptible to O2 damage. Thus, we grew the mutant cells under anaerobic conditions and found that they grew well under N2-fixing conditions. We conclude that in unicellular diazotrophs, like Cyanothece sp. strain PCC 7822, the HupLS complex helps remove oxygen from the nitrogenase, and that this is a more important function than merely oxidizing the H2 produced by the nitrogenase. PMID:24317398

  3. Vibrational spectroscopic characterization of the phosphate mineral barbosalite FeFe23+()2( - Implications for the molecular structure

    NASA Astrophysics Data System (ADS)

    Frost, Ray L.; Xi, Yunfei; López, Andrés; Scholz, Ricardo; Lana, Cristiano de Carvalho; Souza, Bárbara Firmino e.

    2013-11-01

    Natural single-crystal specimens of barbosalite from Brazil, with general formula FeFe23+()2( were investigated by Raman and infrared spectroscopy. The mineral occurs as secondary products in granitic pegmatites. The Raman spectrum of barbosalite is characterized by bands at 1020, 1033 and 1044 cm-1 cm-1, assigned to ?1 symmetric stretching mode of the HOPO33- and PO43- units. Raman bands at around 1067, 1083 and 1138 cm-1 are attributed to both the HOP and PO antisymmetric stretching vibrations. The set of Raman bands observed at 575, 589 and 606 cm-1 are assigned to the ?4 out of plane bending modes of the PO4 and H2PO4 units. Raman bands at 439, 461, 475 and 503 cm-1 are attributed to the ?2 PO4 and H2PO4 bending modes. Strong Raman bands observed at 312, 346 cm-1 with shoulder bands at 361, 381 and 398 cm-1 are assigned to FeO stretching vibrations. No bands which are attributable to water vibrations were found. Vibrational spectroscopy enables aspects of the molecular structure of barbosalite to be assessed.

  4. Disclosure of key stereoelectronic factors for efficient H2 binding and cleavage in the active site of [NiFe]-hydrogenases.

    PubMed

    Bruschi, Maurizio; Tiberti, Matteo; Guerra, Alessandro; De Gioia, Luca

    2014-02-01

    A comparative analysis of a series of DFT models of [NiFe]-hydrogenases, ranging from minimal NiFe clusters to very large systems including both the first and second coordination sphere of the bimetallic cofactor, was carried out with the aim of unraveling which stereoelectronic properties of the active site of [NiFe]-hydrogenases are crucial for efficient H2 binding and cleavage. H2 binding to the Ni-SIa redox state is energetically favored (by 4.0 kcal mol(-1)) only when H2 binds to Ni, the NiFe metal cluster is in a low spin state, and the Ni cysteine ligands have a peculiar seesaw coordination geometry, which in the enzyme is stabilized by the protein environment. The influence of the Ni coordination geometry on the H2 binding affinity was then quantitatively evaluated and rationalized analyzing frontier molecular orbitals and populations. Several plausible reaction pathways leading to H2 cleavage were also studied. It turned out that a two-step pathway, where H2 cleavage takes place on the Ni-SIa redox state of the enzyme, is characterized by very low reaction barriers and favorable reaction energies. More importantly, the seesaw coordination geometry of Ni was found to be a key feature for facile H2 cleavage. The discovery of the crucial influence of the Ni coordination geometry on H2 binding and activation in the active site of [NiFe]-hydrogenases could be exploited in the design of novel biomimetic synthetic catalysts. PMID:24392667

  5. Hydrogenase activity of mineral-associated and suspended populations of Desulfovibrio Desulfuricans Essex 6

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The interactions between sulfate-reducing microorganisms and iron oxides influence a number of important redox-sensitive biogeochemical processes including the formation of iron sulfides. Enzymes, such as hydrogenase which catalyze the reversible oxidation of molecular hydrogen, are known to mediate...

  6. Lyophilization protects [FeFe]-hydrogenases against O2-induced H-cluster degradation.

    PubMed

    Noth, Jens; Kositzki, Ramona; Klein, Kathrin; Winkler, Martin; Haumann, Michael; Happe, Thomas

    2015-01-01

    Nature has developed an impressive repertoire of metal-based enzymes that perform complex chemical reactions under moderate conditions. Catalysts that produce molecular hydrogen (H2) are particularly promising for renewable energy applications. Unfortunately, natural and chemical H2-catalysts are often irreversibly degraded by molecular oxygen (O2). Here we present a straightforward procedure based on freeze-drying (lyophilization), that turns [FeFe]-hydrogenases, which are excellent H2-producers, but typically extremely O2-sensitive in solution, into enzymes that are fully resistant against O2. Complete dryness protects and conserves both, the [FeFe]-hydrogenase proteins and their inorganic active-site cofactor (H-cluster), when exposed to 100% O2 for days. The full H2-formation capacity is restored after solvation of the lyophilized enzymes. However, even minimal moisturizing re-establishes O2-sensitivity. The dry [FeFe]-hydrogenase material is superior also for advanced spectroscopic investigations on the H-cluster reaction mechanism. Our method provides a convenient way for long-term storage and impacts on potential biotechnological hydrogen production applications of hydrogenase enzymes. PMID:26364994

  7. Metabolic control of Clostridium thermocellum via inhibition of hydrogenase activity and the glucose transport rate

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Clostridium thermocellum has the ability to catabolize cellulosic biomass into ethanol, but acetic acid, lactic acid, carbon dioxide, and hydrogen gas (H2) are also produced. The effect of hydrogenase inhibitors (H2, carbon monoxide (CO) and methyl viologen) on product selectivity was investigated....

  8. Carbon Nitride-TiO2 Hybrid Modified with Hydrogenase for Visible Light Driven Hydrogen Production

    E-print Network

    Caputo, Christine A.; Wang, Lidong; Beranek, Radim; Reisner, Erwin

    2015-06-29

    A system consisting of a [NiFeSe]-hydrogenase (H2ase) grafted on the surface of a TiO2 nanoparticle modified with polyheptazine carbon nitride polymer, melon (CNx) is reported. This semi biological assembly shows a turnover number (TON) of more than...

  9. Wiring of Photosystem II to Hydrogenase for Photoelectrochemical Water-splitting

    E-print Network

    Mersch, Dirk; Lee, Chong-Yong; Zhang, Jenny Zhenqi; Brinkert, Katharina; Fontecilla-Camps, Juan C.; Rutherford, A. William; Reisner, Erwin

    2015-06-05

    for understanding the process itself. Here, we employ a semi-artificial approach to study photo-biological water-splitting via a pathway unavailable to nature: the direct coupling of the water-oxidation enzyme, Photosystem II, to the H2 evolving enzyme, hydrogenase...

  10. BIOTECHNOLOGICALLY RELEVANT ENZYMES AND PROTEINS Protein engineering of hydrogenase 3 to enhance

    E-print Network

    Wood, Thomas K.

    -Verlag 2008 Abstract The large subunit (HycE, 569 amino acids) of Escherichia coli hydrogenase 3 produces yield from formate compared to wild-type HycE. Deoxyribonucleic acid shuffling using the three most on formate due to a 74-amino acid carboxy-terminal truncation. Satu- ration mutagenesis at T366 of HycE also

  11. Designed Surface Residue Substitutions in [NiFe] Hydrogenase that Improve Electron Transfer Characteristics

    PubMed Central

    Yonemoto, Isaac T.; Smith, Hamilton O.; Weyman, Philip D.

    2015-01-01

    Photobiological hydrogen production is an attractive, carbon-neutral means to convert solar energy to hydrogen. We build on previous research improving the Alteromonas macleodii “Deep Ecotype” [NiFe] hydrogenase, and report progress towards creating an artificial electron transfer pathway to supply the hydrogenase with electrons necessary for hydrogen production. Ferredoxin is the first soluble electron transfer mediator to receive high-energy electrons from photosystem I, and bears an electron with sufficient potential to efficiently reduce protons. Thus, we engineered a hydrogenase-ferredoxin fusion that also contained several other modifications. In addition to the C-terminal ferredoxin fusion, we truncated the C-terminus of the hydrogenase small subunit, identified as the available terminus closer to the electron transfer region. We also neutralized an anionic patch surrounding the interface Fe-S cluster to improve transfer kinetics with the negatively charged ferredoxin. Initial screening showed the enzyme tolerated both truncation and charge neutralization on the small subunit ferredoxin-binding face. While the enzyme activity was relatively unchanged using the substrate methyl viologen, we observed a marked improvement from both the ferredoxin fusion and surface modification using only dithionite as an electron donor. Combining ferredoxin fusion and surface charge modification showed progressively improved activity in an in vitro assay with purified enzyme. PMID:25603181

  12. Lyophilization protects [FeFe]-hydrogenases against O2-induced H-cluster degradation

    PubMed Central

    Noth, Jens; Kositzki, Ramona; Klein, Kathrin; Winkler, Martin; Haumann, Michael; Happe, Thomas

    2015-01-01

    Nature has developed an impressive repertoire of metal-based enzymes that perform complex chemical reactions under moderate conditions. Catalysts that produce molecular hydrogen (H2) are particularly promising for renewable energy applications. Unfortunately, natural and chemical H2-catalysts are often irreversibly degraded by molecular oxygen (O2). Here we present a straightforward procedure based on freeze-drying (lyophilization), that turns [FeFe]-hydrogenases, which are excellent H2-producers, but typically extremely O2-sensitive in solution, into enzymes that are fully resistant against O2. Complete dryness protects and conserves both, the [FeFe]-hydrogenase proteins and their inorganic active-site cofactor (H-cluster), when exposed to 100% O2 for days. The full H2-formation capacity is restored after solvation of the lyophilized enzymes. However, even minimal moisturizing re-establishes O2-sensitivity. The dry [FeFe]-hydrogenase material is superior also for advanced spectroscopic investigations on the H-cluster reaction mechanism. Our method provides a convenient way for long-term storage and impacts on potential biotechnological hydrogen production applications of hydrogenase enzymes. PMID:26364994

  13. Molecular and immunological comparison of membrane-bound, H2-oxidizing hydrogenases of Bradyrhizobium japonicum, Alcaligenes eutrophus, Alcaligenes latus, and Azotobacter vinelandii.

    PubMed

    Arp, D J; McCollum, L C; Seefeldt, L C

    1985-07-01

    The membrane-bound hydrogenases of Bradyrhizobium japonicum, Alcaligenes eutrophus, Alcaligenes latus, and Azotobacter vinelandii were purified extensively and compared. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of each hydrogenase revealed two prominent protein bands, one near 60 kilodaltons and the other near 30 kilodaltons. The migration distances during nondenaturing polyacrylamide gel electrophoresis were similar for all except A. vinelandii hydrogenase, which migrated further than the other three. The amino acid composition of each hydrogenase was determined, revealing substantial similarity among these enzymes. This was confirmed by calculation of S delta Q values, which ranged from 8.0 to 26.7 S delta Q units. S delta Q is defined as sigma j(Xi,j-Xk,j)2, where i and k identify the proteins compared and Xj is the content (residues per 100) of a given amino acid of type j. The hydrogenases of this study were also compared with an enzyme-linked immunosorbent assay. Antibody raised against B. japonicum hydrogenase cross-reacted with all four hydrogenases, but to various degrees and in the order B. japonicum greater than A. latus greater than A. eutrophus greater than A. vinelandii. Antibody raised against A. eutrophus hydrogenase also cross-reacted with all four hydrogenases, following the pattern of cross-reaction A. eutrophus greater than A. latus = B. japonicum greater than A. vinelandii. Antibody raised against B. japonicum hydrogenase inhibited B. japonicum hydrogenase activity to a greater extent than the A. eutrophus and A. latus activities; no inhibition of A. vinelandii hydrogenase activity was detected. The results of these experiments indicated remarkable homology of the hydrogenases from these four microorganisms. PMID:4008438

  14. Distribution of Hydrogenase Genes in Desulfovibrio spp. and Their Use in Identification of Species from the Oil Field Environment

    PubMed Central

    Voordouw, Gerrit; Niviere, Vincent; Ferris, F. Grant; Fedorak, Phillip M.; Westlake, Donald W. S.

    1990-01-01

    The distribution of genes for [Fe], [NiFe], and [NiFeSe] hydrogenases was determined for 22 Desulfovibrio species. The genes for [NiFe] hydrogenase were present in all species, whereas those for the [Fe] and [NiFeSe] hydrogenases had a more limited distribution. Sulfate-reducing bacteria from 16S rRNA groups other than the genus Desulfovibrio (R. Devereux, M. Delaney, F. Widdel, and D. A. Stahl, J. Bacteriol. 171:6689-6695, 1989) did not react with the [NiFe] hydrogenase gene probe, which could be used to identify different Desulfovibrio species in oil field samples following growth on lactate-sulfate medium. Images PMID:16348376

  15. Photosynthetic electron partitioning between [FeFe]-hydrogenase and ferredoxin:NADP+-oxidoreductase (FNR) enzymes in vitro

    E-print Network

    Yacoby, Iftach

    Photosynthetic water splitting, coupled to hydrogenase-catalyzed hydrogen production, is considered a promising clean, renewable source of energy. It is widely accepted that the oxygen sensitivity of hydrogen production, ...

  16. A Redox Hydrogel Protects the O2 -Sensitive [FeFe]-Hydrogenase from Chlamydomonas reinhardtii from Oxidative Damage.

    PubMed

    Oughli, Alaa Alsheikh; Conzuelo, Felipe; Winkler, Martin; Happe, Thomas; Lubitz, Wolfgang; Schuhmann, Wolfgang; Rüdiger, Olaf; Plumeré, Nicolas

    2015-10-12

    The integration of sensitive catalysts in redox matrices opens up the possibility for their protection from deactivating molecules such as O2 . [FeFe]-hydrogenases are enzymes catalyzing H2 oxidation/production which are irreversibly deactivated by O2 . Therefore, their use under aerobic conditions has never been achieved. Integration of such hydrogenases in viologen-modified hydrogel films allows the enzyme to maintain catalytic current for H2 oxidation in the presence of O2 , demonstrating a protection mechanism independent of reactivation processes. Within the hydrogel, electrons from the hydrogenase-catalyzed H2 oxidation are shuttled to the hydrogel-solution interface for O2 reduction. Hence, the harmful O2 molecules do not reach the hydrogenase. We illustrate the potential applications of this protection concept with a biofuel cell under H2 /O2 mixed feed. PMID:26073322

  17. Heterologous expression and maturation of an NADP-dependent [NiFe]-hydrogenase: a key enzyme in biofuel production.

    PubMed

    Sun, Junsong; Hopkins, Robert C; Jenney, Francis E; McTernan, Patrick M; Adams, Michael W W

    2010-01-01

    Hydrogen gas is a major biofuel and is metabolized by a wide range of microorganisms. Microbial hydrogen production is catalyzed by hydrogenase, an extremely complex, air-sensitive enzyme that utilizes a binuclear nickel-iron [NiFe] catalytic site. Production and engineering of recombinant [NiFe]-hydrogenases in a genetically-tractable organism, as with metalloprotein complexes in general, has met with limited success due to the elaborate maturation process that is required, primarily in the absence of oxygen, to assemble the catalytic center and functional enzyme. We report here the successful production in Escherichia coli of the recombinant form of a cytoplasmic, NADP-dependent hydrogenase from Pyrococcus furiosus, an anaerobic hyperthermophile. This was achieved using novel expression vectors for the co-expression of thirteen P. furiosus genes (four structural genes encoding the hydrogenase and nine encoding maturation proteins). Remarkably, the native E. coli maturation machinery will also generate a functional hydrogenase when provided with only the genes encoding the hydrogenase subunits and a single protease from P. furiosus. Another novel feature is that their expression was induced by anaerobic conditions, whereby E. coli was grown aerobically and production of recombinant hydrogenase was achieved by simply changing the gas feed from air to an inert gas (N2). The recombinant enzyme was purified and shown to be functionally similar to the native enzyme purified from P. furiosus. The methodology to generate this key hydrogen-producing enzyme has dramatic implications for the production of hydrogen and NADPH as vehicles for energy storage and transport, for engineering hydrogenase to optimize production and catalysis, as well as for the general production of complex, oxygen-sensitive metalloproteins. PMID:20463892

  18. Electrochemical kinetic investigations of the reactions of [FeFe]-hydrogenases with carbon monoxide and oxygen: comparing the importance of gas tunnels and active-site electronic/redox effects.

    PubMed

    Goldet, Gabrielle; Brandmayr, Caterina; Stripp, Sven T; Happe, Thomas; Cavazza, Christine; Fontecilla-Camps, Juan C; Armstrong, Fraser A

    2009-10-21

    A major obstacle for future biohydrogen production is the oxygen sensitivity of [FeFe]-hydrogenases, the highly active catalysts produced by bacteria and green algae. The reactions of three representative [FeFe]-hydrogenases with O(2) have been studied by protein film electrochemistry under conditions of both H(2) oxidation and H(2) production, using CO as a complementary probe. The hydrogenases are DdHydAB and CaHydA from the bacteria Desulfovibrio desulfuricans and Clostridium acetobutylicum , and CrHydA1 from the green alga Chlamydomonas reinhardtii . Rates of inactivation depend on the redox state of the active site 'H-cluster' and on transport through the protein to reach the pocket in which the H-cluster is housed. In all cases CO reacts much faster than O(2). In the model proposed, CaHydA shows the most sluggish gas transport and hence little dependence of inactivation rate on H-cluster state, whereas DdHydAB shows a large dependence on H-cluster state and the least effective barrier to gas transport. All three enzymes show a similar rate of reactivation from CO inhibition, which increases upon illumination: the rate-determining step is thus assigned to cleavage of the labile Fe-CO bond, a reaction likely to be intrinsic to the atomic and electronic state of the H-cluster and less sensitive to the surrounding protein. PMID:19824734

  19. From core/shell to hollow Fe/?-Fe2O3 nanoparticles: evolution of the magnetic behavior

    NASA Astrophysics Data System (ADS)

    Nemati, Z.; Khurshid, H.; Alonso, J.; Phan, M. H.; Mukherjee, P.; Srikanth, H.

    2015-10-01

    High quality Fe/?-Fe2O3 core/shell, core/void/shell, and hollow nanoparticles with two different sizes of 8 and 12 nm were synthesized, and the effect of morphology, surface and finite-size effects on their magnetic properties including the exchange bias (EB) effect were systematically investigated. We find a general trend for both systems that as the morphology changes from core/shell to core/void/shell, the magnetization of the system decays and inter-particle interactions become weaker, while the effective anisotropy and the EB effect increase. The changes are more drastic when the nanoparticles become completely hollow. Noticeably, the morphological change from core/shell to hollow increases the mean blocking temperature for the 12 nm particles but decreases for the 8 nm particles. The low-temperature magnetic behavior of the 12 nm particles changes from a collective super-spin-glass system mediated by dipolar interactions for the core/shell nanoparticles to a frustrated cluster glass-like state for the shell nanograins in the hollow morphology. On the other hand for the 8 nm nanoparticles core/shell and hollow particles the magnetic behavior is more similar, and a conventional spin glass-like transition is obtained at low temperatures. In the case of the hollow nanoparticles, the coupling between the inner and outer spin layers in the shell gives rise to an enhanced EB effect, which increases with increasing shell thickness. This indicates that the morphology of the shell plays a crucial role in this kind of exchange-biased systems.

  20. Hydrogenase of the hyperthermophile Pyrococcus furiosus is an elemental sulfur reductase or sulfhydrogenase: Evidence for a sulfur-reducing hydrogenase ancestor

    SciTech Connect

    Ma, K.; Adams, M.W.W. ); Schicho, R.N. ); Kelly, R.M. )

    1993-06-01

    Microorganisms growing near and above 100[degrees]C have recently been discovered near shallow and deep sea hydrothermal vents. Most are obligately dependent upon the reduction of elemental sulfur (S[sup 0]) to hydrogen sulfide (H[sub 2]S) for optimal growth, even though S[sup 0] reduction readily occurs abiotically at their growth temperatures. The sulfur reductase activity of the anaerobic archaeon Pyrococcus furiosus, which grows optimally at 100[degrees]C by a metabolism that produces H[sub 2]S if S[sup 0] is present, was found in the cytoplasm. It was purified anaerobically and was shown to be identical to the hydrogenase that had been previously purified from this organism. Both S[sup 0] and polysulfide served as substrates for H[sub 2]S production, and the S[sub 0] reduction activity but not the H[sub 2]-oxidation activity was enhanced by the redox protein rubredoxin. The H[sub 2]-oxidizing and S[sup 0]-reduction activities of the enzyme also showed different responses to pH, temperature, and inhibitors. This bifunctional [open quotes]sulfhydrogenase[close quotes] enzyme can, therefore, dispose of the excess reductant generated during fermentation using either protons or polysulfides as the electron acceptor. In addition, purified hydrogenases from both hyperthermophilic and mesophilic representatives of the archaeal and bacterial domains were shown to reduce S[sup 0] to H[sub 2]S. It is suggested that the function of some form of ancestral hydrogenase was S[sup 0] reduction rather than, or in addition, to the reduction of protons. 33 refs., 4 figs., 2 tabs.

  1. Reversible Electrocatalytic Production and Oxidation of Hydrogen at Low Overpotentials by a Functional Hydrogenase Mimic

    SciTech Connect

    Smith, Stuart E.; Yang, Jenny Y.; DuBois, Daniel L.; Bullock, Morris

    2012-03-26

    A new bis(diphosphine) nickel(II) complex, [Ni(PPh2NR2)2](BF4)2, 1, (R = CH2CH2OCH3) is described. A {Delta}G{sup o} of 0.84 kcal/mol{sup -1} for hydrogen addition for this complex was calculated from the experimentally determined equilibrium constant. This complex displays reversible electrocatalytic activity for hydrogen production and oxidation at low overpotentials, a characteristic most commonly associated with hydrogenase enzymes.

  2. Diversity in hydrogen evolution from bidirectional hydrogenases in cyanobacteria from terrestrial, freshwater and marine intertidal environments.

    PubMed

    Kothari, Ankita; Potrafka, Ruth; Garcia-Pichel, Ferran

    2012-11-30

    We characterized a set of 36 strains of cyanobacteria isolated from terrestrial, freshwater and marine intertidal settings to probe their potential to produce hydrogen from excess reductant, in the hope of finding novel strains with improved traits for biohydrogen production. The set was diverse with respect to origin, morphology, taxonomy and phylogeny. We found that about one half of the strains could produce hydrogen from hydrogenases in standard assays, a trait that corresponded invariably with the presence of homologues of the gene hoxH, coding for subunit H in the bidirectional Ni-Fe hydrogenase. Strains from freshwater and intertidal settings had a high incidence of hydrogen producing, hoxH containing strains, but all terrestrial isolates were negative for both. While specific rates of hydrogen production varied among strains, some novel strains displayed rates several fold higher than those previously reported. We detected two different patterns in hydrogen production. Pattern 1, corresponding to that previously known in Synechocystis PCC 6803, encompassed strains whose hydrogenase system produced hydrogen only temporarily to revert to hydrogen consumption within a short time and after reaching moderate hydrogen concentrations. Cyanobacteria displaying pattern 2, in the genera Lyngbya and Microcoleus, tended to have higher rates, did not reverse the direction of the reaction and reached much higher concentrations of hydrogen at steady state, making them of interest as potential platforms for biohydrogen production. PMID:22771887

  3. Molecular characterization and transcriptional analysis of the putative hydrogenase gene of Clostridium acetobutylicum ATCC 824.

    PubMed Central

    Gorwa, M F; Croux, C; Soucaille, P

    1996-01-01

    A 2.8-kbp DNA region of Clostridium acetobutylicum ATCC 824 containing the putative hydrogenase gene (hydA) was cloned and sequenced. The 1,745-bp hydA encodes a 64,415-Da protein and presents strong identity with the [Fe] hydrogenase genes of Desulfovibrio and Clostridium species. The level of the putative hydA mRNA was high in cells from an acidogenic or an alcohologenic phosphate-limited continuous culture, while it was comparatively very low in cells from a solventogenic phosphate-limited continuous culture. These results were in agreement with the hydrogenase protein level, indicating that expression of hydA is regulated at the transcriptional level. Primer extension analysis identified a major transcriptional start site 90 bp upstream of the hydA start codon. The position of a putative rho-independent transcription terminator immediately downstream of the termination codon is in agreement with the size of the hydA transcript (1.9 kb) determined by Northern (RNA) blot experiments and confirms that the gene is transcribed as a monocistronic operon. Two truncated open reading frames (ORFs) were identified downstream and upstream of hydA and in opposite directions. The amino acid sequence deduced from ORF2 presents strong identity with ortho phosphoribosyl transferases involved in pyrimidine synthesis. The amino acid sequence deduced from ORF3 presents no significant similarity to any sequence in various available databases. PMID:8626337

  4. [NiFe] Hydrogenase from Alteromonas macleodii with Unusual Stability in the Presence of Oxygen and High Temperature ? †

    PubMed Central

    Vargas, Walter A.; Weyman, Philip D.; Tong, Yingkai; Smith, Hamilton O.; Xu, Qing

    2011-01-01

    Hydrogenases are enzymes involved in the bioproduction of hydrogen, a clean alternative energy source whose combustion generates water as the only end product. In this article we identified and characterized a [NiFe] hydrogenase from the marine bacterium Alteromonas macleodii “deep ecotype” with unusual stability toward oxygen and high temperature. The A. macleodii hydrogenase (HynSL) can catalyze both H2 evolution and H2 uptake reactions. HynSL was expressed in A. macleodii under aerobic conditions and reached the maximum activity when the cells entered the late exponential phase. The higher level of hydrogenase activity was accompanied by a greater abundance of the HynSL protein in the late-log or stationary phase. The addition of nickel to the growth medium significantly enhanced the hydrogenase activity. Ni treatment affected the level of the protein, but not the mRNA, indicating that the effect of Ni was exerted at the posttranscriptional level. Hydrogenase activity was distributed ?30% in the membrane fraction and ?70% in the cytoplasmic fraction. Thus, HynSL appears to be loosely membrane-bound. Partially purified A. macleodii hydrogenase demonstrated extraordinary stability. It retained 84% of its activity after exposure to 80°C for 2 h. After exposure to air for 45 days at 4°C, it retained nearly 100% of its activity when assayed under anaerobic conditions. Its catalytic activity in the presence of O2 was evaluated by the hydrogen-deuterium (H-D) exchange assay. In 1% O2, 20.4% of its H-D exchange activity was retained. The great stability of HynSL makes it a potential candidate for biotechnological applications. PMID:21257809

  5. A soil actinobacterium scavenges atmospheric H2 using two membrane-associated, oxygen-dependent [NiFe] hydrogenases

    PubMed Central

    Greening, Chris; Berney, Michael; Hards, Kiel; Cook, Gregory M.; Conrad, Ralf

    2014-01-01

    In the Earth’s lower atmosphere, H2 is maintained at trace concentrations (0.53 ppmv/0.40 nM) and rapidly turned over (lifetime ? 2.1 y?1). It is thought that soil microbes, likely actinomycetes, serve as the main global sink for tropospheric H2. However, no study has ever unambiguously proven that a hydrogenase can oxidize this trace gas. In this work, we demonstrate, by using genetic dissection and sensitive GC measurements, that the soil actinomycete Mycobacterium smegmatis mc2155 constitutively oxidizes subtropospheric concentrations of H2. We show that two membrane-associated, oxygen-dependent [NiFe] hydrogenases mediate this process. Hydrogenase-1 (Hyd1) (MSMEG_2262-2263) is well-adapted to rapidly oxidize H2 at a range of concentrations [Vmax(app) = 12 nmol?g?dw?1?min?1; Km(app) = 180 nM; threshold = 130 pM in the ?hyd23 (Hyd1 only) strain], whereas Hyd2 (MSMEG_2719-2720) catalyzes a slower-acting, higher-affinity process [Vmax(app) = 2.5 nmol?g?dw?1?min?1; Km(app) = 50 nM; threshold = 50 pM in the ?hyd13 (Hyd2 only) strain]. These observations strongly support previous studies that have linked group 5 [NiFe] hydrogenases (e.g., Hyd2) to the oxidation of tropospheric H2 in soil ecosystems. We further reveal that group 2a [NiFe] hydrogenases (e.g., Hyd1) can contribute to this process. Hydrogenase expression and activity increases in carbon-limited cells, suggesting that scavenging of trace H2 helps to sustain dormancy. Distinct physiological roles for Hyd1 and Hyd2 during the adaptation to this condition are proposed. Soil organisms harboring high-affinity hydrogenases may be especially competitive, given that they harness a highly dependable fuel source in otherwise unstable environments. PMID:24591586

  6. Diphenylene iodonium as an inhibitor for the hydrogenase complex of Rhodobacter capsulatus. Evidence for two distinct electron donor sites.

    PubMed

    Magnani, P; Doussiere, J; Lissolo, T

    2000-07-20

    The photosynthetic bacterium Rhodobacter capsulatus synthesises a membrane-bound [NiFe] hydrogenase encoded by the H2 uptake hydrogenase (hup)SLC structural operon. The hupS and hupL genes encode the small and large subunits of hydrogenase, respectively; hupC encodes a membrane electron carrier protein which may be considered as the third subunit of the uptake hydrogenase. In Wolinella succinogenes, the hydC gene, homologous to hupC, has been shown to encode a low potential cytochrome b which mediates electron transfer from H2 to the quinone pool of the bacterial membrane. In whole cells of R. capsulatus or intact membrane preparation of the wild type strain B10, methylene blue but not benzyl viologen can be used as acceptor of the electrons donated by H2 to hydrogenase; on the other hand, membranes of B10 treated with Triton X-100 or whole cells of a HupC- mutant exhibit both benzyl viologen and methylene blue reductase activities. We report the effect of diphenylene iodonium (Ph2I), a known inhibitor of mitochondrial complex I and of various monooxygenases on R. capsulatus hydrogenase activity. With H2 as electron donor, Ph2I inhibited partially the methylene blue reductase activity in an uncompetitive manner, and totally benzyl viologen reductase activity in a competitive manner. Furthermore, with benzyl viologen as electron acceptor, Ph2I increased dramatically the observed lagtime for dye reduction. These results suggest that two different sites exist on the electron donor side of the membrane-bound [NiFe] hydrogenase of R. capsulatus, both located on the small subunit. A low redox potential site which reduces benzyl viologen, binds Ph2I and could be located on the distal [Fe4S4] cluster. A higher redox potential site which can reduce methylene blue in vitro could be connected to the high potential [Fe3S4] cluster and freely accessible from the periplasm. PMID:10924909

  7. [NiFe]-hydrogenases revisited: nickel-carboxamido bond formation in a variant with accrued O2-tolerance and a tentative re-interpretation of Ni-SI states.

    PubMed

    Volbeda, Anne; Martin, Lydie; Liebgott, Pierre-Pol; De Lacey, Antonio L; Fontecilla-Camps, Juan C

    2015-04-01

    [NiFe]-hydrogenases are well-studied enzymes capable of oxidizing molecular hydrogen and reducing protons. EPR and FTIR spectroscopic studies have shown that these enzymes can be isolated in several redox states that include paramagnetic oxidized inactive Ni-A and Ni-B species and a reduced Ni-C form. The latter and the diamagnetic respectively more oxidized Ni-SI and more reduced Ni-R forms are generally thought to be involved in the catalytic cycle of [NiFe]-hydrogenases. With the exception of Ni-SI, these different stable states have been well characterized. Here, based on the crystal structure of a partially reduced Desulfovibrio fructosovorans (Df) enzyme and data from the literature we propose that at least one of the Ni-SI sub-states contains an unexpected combination of hydride and sulfenic acid moieties. We have also determined the structure of the less oxygen-sensitive Df [NiFe]-hydrogenase V74C mutant and found that more than half of the active site nickel occupies a novel position, called Ni'. In this new position, the metal ion is coordinated by two cysteine thiolates, a bridging species modeled as SH(-) and a main chain carboxamido N atom. The Ni' coordination is similar to the one found in Ni superoxide dismutase, an enzyme that operates at significantly more positive potentials than [NiFe]-hydrogenases. We propose that the oxygen-tolerance of the V74C variant results from a high potential stabilization of a Ni'(iii) species induced by the change in the metal ion coordination sphere. We also propose that transient Ni'(iii) species can rapidly attract successive electrons from the Fe4S4 proximal cluster accelerating the reduction of oxygen to water and hydroxide. The naturally occurring oxygen-tolerant [NiFe]-hydrogenases have an unusual proximal cluster that has been shown to be exceptionally plastic and capable of undergoing two successive one-electron oxidations. This double oxidation is modulated by the migration of one of the iron atoms in the cluster to the main chain where, as Fe(iii), it forms a bond with a carboxamido N ligand. Like in the Df V74C variant the electrons from the proximal cluster help reducing O2 to H2O and OH(-). In conclusion, in both cases a metal-carboxamido bond may explain, at least partially, the observed oxygen tolerance. PMID:25780984

  8. Halotolerant and Resistant to High pH Hydrogenase from Haloalkaliphilic Sulfate-Reducing Bacterium Desulfonatronum thiodismutans

    NASA Technical Reports Server (NTRS)

    Detkova, Ekaterina N.; Pikuta, Elena V.; Hoover, Richard B.

    2004-01-01

    Hydrogenase is the key enzyme of energetic metabolism in cells, it catalyzing the converse reaction of hydrogen oxidation and responsible for consumption and excretion of hydrogen in bacteria. Hydrogenases are proteins containing either Nickel and Iron, or the only Iron in theirs active center. Hydrogenases have been found in many microorganisms, such as Methanogenic, acetogenic, nitrogen-fixing, photosynthetic and sulfate-reducing bacteria that could utilize the hydrogen as energy source or use it as electron sink. Hydrogenases are subject for wide physiological, biochemical, physicochemical and genetic studies due to theirs abilities produce the molecular hydrogen as alternative source of pure energy. Notwithstanding on enough large quantity of works that deal with intracellular and extrasellular enzymes of halophilic bacteria, the data about hydrogenases and theirs functions of salts practically are absent. The study of hydrogenase in cell-free extracts of extremely halophilic eubacterium Acetohalobium mabaticum showed dramatic increasing activity of the enzyme at high concentrations of NaCl and KCI (close to saturated solution). Here we present the data of free-cells extracted hydrogenase from new haloalkaliphilic sulfate-reducing bacterium Desulfonatronum thiodismutans, which grow on highly miniralized carbonate-bicarbonate medium in salinity range 1 to 7 % and at pH 7.8 - 10.5. Studied enzyme was active in Concentration range from 0 to 4.3 M NaCl with optimum at 1.0 M NaCl. At 1.0 M NaCl the enzyme activity was increased on 20 %, but with changing concentration from 2.1 M to 3.4 M the activity decreased and was kept on constant level. NaHCO3 inhibited hydrogenase activity on more then 30 %. The maximum of enzyme activity was observed at pH 9.5 with limits 7.5 and 11.5 that practically equal to pH optimum of bacterial growth. Therefore the hydrogenase of Desulfanatronum thiodismutans is tolerant to high concentrations of sodium salts and it also resistant to high pH that make it the unique subject for different biochemical research and detects the possibility for biotechnological application.

  9. Metabolic control of Clostridium thermocellum via inhibition of hydrogenase activity and the glucose transport rate.

    PubMed

    Li, Hsin-Fen; Knutson, Barbara L; Nokes, Sue E; Lynn, Bert C; Flythe, Michael D

    2012-02-01

    Clostridium thermocellum has the ability to catabolize cellulosic biomass into ethanol, but acetic acid, lactic acid, carbon dioxide, and hydrogen gas (H(2)) are also produced. The effect of hydrogenase inhibitors (H(2), carbon monoxide (CO), and methyl viologen) on product selectivity was investigated. The anticipated effect of these hydrogenase inhibitors was to decrease acetate production. However, shifts to ethanol and lactate production are also observed as a function of cultivation conditions. When the sparge gas of cellobiose-limited chemostat cultures was switched from N(2) to H(2), acetate declined, and ethanol production increased 350%. In resting cell suspensions, lactate increased when H(2) or CO was the inhibitor or when the cells were held at elevated hyperbaric pressure (6.8 atm). In contrast, methyl-viologen-treated resting cells produced twice as much ethanol as the other treatments. The relationship of chemostat physiology to methyl viologen inhibition was revealed by glucose transport experiments, in which methyl viologen decreased the rate of glucose transport by 90%. C. thermocellum produces NAD(+) from NADH by H(2), lactate, and ethanol production. When the hydrogenases were inhibited, the latter two products increased. However, excess substrate availability causes fructose 1,6-diphosphate, the glycolytic intermediate that triggers lactate production, to increase. Compensatory ethanol production was observed when the chemostat fluid dilution rate or methyl viologen decreased substrate transport. This research highlights the complex effects of high concentrations of dissolved gases in fermentation, which are increasingly envisioned in microbial applications of H(2) production for the conversion of synthetic gases to chemicals. PMID:22218768

  10. Molecular detection of the clostridia in an anaerobic biohydrogen fermentation system by hydrogenase mRNA-targeted reverse transcription-PCR.

    PubMed

    Chang, Jui-Jen; Chen, Wei-En; Shih, Shiou-Yun; Yu, Sian-Jhong; Lay, Jiunn-Jyi; Wen, Fu-Shyan; Huang, Chieh-Chen

    2006-05-01

    Molecular biological approaches were developed to monitor the potential biohydrogen-producing clostridia in an anaerobic semisolid fermentation system that used brewery yeast waste as the fermentation substrate. The denaturing gradient gel electrophoresis with 16S rDNA gene-targeted polymerase chain reaction (PCR) analysis was employed to confirm the existence of clostridia in the system. Remarkably, reproducible nucleotide sequences of clostridia were obtained from different hydrogen production stages by using hydrogenase gene-targeted reverse transcription (RT)-PCR. These RNA-based information suggested that the predominant hydrogen-producing strains possess either a specific Clostridium pasteurianum-like or a specific Clostridium saccharobutylicum-like hydrogenase sequence. Comparison of the hydrogenase gene-targeted sequence profiles between PCR and RT-PCR revealed that the specific C. pasteurianum-like hydrogenase harboring bacterial strains were dominant in both mRNA and bacterial population level. On the other hand, the specific C. saccharobutylicum-like hydrogenase harboring strains expressed high level of hydrogenase mRNA but may not be dominant in population. Furthermore, quantitative real-time RT-PCR analysis showed the expression pattern of the clostridial hydrogenase mRNA and may serve as an activity index for the system. PMID:16217655

  11. Fast and efficient molecular electrocatalysts for H2 production: Using hydrogenase enzymes as guides

    SciTech Connect

    Yang, Jenny Y.; Bullock, R. Morris; Rakowski DuBois, Mary; DuBois, Daniel L.

    2011-01-15

    Hydrogen generation using solar energy will require the development of efficient electrocatalysts for proton reduction. This article discusses the important role that proton movement plays in hydrogenase enzymes and potentials devices for solar generation. Studies of hydrogenase enzymes provide many import design principles for the development of simpler molecular catalysts. These principles are illustrated with examples from the literature and from the authors’ laboratories. In particular, pendant bases incorporated in the second coordination sphere of catalytic molecules play a number of important roles that are crucial to efficient catalysis. These include acting as relays to move protons between the metal center and solution, promoting intra- and inter-molecular proton transfer reactions, coupling proton and electron transfer reactions, assisting heterolytic cleavage of hydrogen, and stabilizing critical reaction intermediates. The importance of controlling proton movement on the molecular scale underscores the importance of a similar degree of control in devices designed for the solar production of hydrogen or any fuel generation process involving multiple electrons and protons. This material is based upon work supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences.

  12. How oxygen reacts with oxygen-tolerant respiratory [NiFe]-hydrogenases

    PubMed Central

    Wulff, Philip; Day, Christopher C.; Sargent, Frank; Armstrong, Fraser A.

    2014-01-01

    An oxygen-tolerant respiratory [NiFe]-hydrogenase is proven to be a four-electron hydrogen/oxygen oxidoreductase, catalyzing the reaction 2 H2 + O2 = 2 H2O, equivalent to hydrogen combustion, over a sustained period without inactivating. At least 86% of the H2O produced by Escherichia coli hydrogenase-1 exposed to a mixture of 90% H2 and 10% O2 is accounted for by a direct four-electron pathway, whereas up to 14% arises from slower side reactions proceeding via superoxide and hydrogen peroxide. The direct pathway is assigned to O2 reduction at the [NiFe] active site, whereas the side reactions are an unavoidable consequence of the presence of low-potential relay centers that release electrons derived from H2 oxidation. The oxidase activity is too slow to be useful in removing O2 from the bacterial periplasm; instead, the four-electron reduction of molecular oxygen to harmless water ensures that the active site survives to catalyze sustained hydrogen oxidation. PMID:24715724

  13. Electron transfer activation of a second water channel for proton transport in [FeFe]-hydrogenase

    SciTech Connect

    Sode, Olaseni; Voth, Gregory A.

    2014-12-14

    Hydrogenase enzymes are important because they can reversibly catalyze the production of molecular hydrogen. Proton transport mechanisms have been previously studied in residue pathways that lead to the active site of the enzyme via residues Cys299 and Ser319. The importance of this pathway and these residues has been previously exhibited through site-specific mutations, which were shown to interrupt the enzyme activity. It has been shown recently that a separate water channel (WC2) is coupled with electron transport to the active site of the [FeFe]-hydrogenase. The water-mediated proton transport mechanisms of the enzyme in different electronic states have been studied using the multistate empirical valence bond reactive molecular dynamics method, in order to understand any role WC2 may have in facilitating the residue pathway in bringing an additional proton to the enzyme active site. In a single electronic state A{sup 2?}, a water wire was formed through which protons can be transported with a low free energy barrier. The remaining electronic states were shown, however, to be highly unfavorable to proton transport in WC2. A double amino acid substitution is predicted to obstruct proton transport in electronic state A{sup 2-} by closing a cavity that could otherwise fill with water near the proximal Fe of the active site.

  14. Hydride bridge in [NiFe]-hydrogenase observed by nuclear resonance vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Ogata, Hideaki; Krämer, Tobias; Wang, Hongxin; Schilter, David; Pelmenschikov, Vladimir; van Gastel, Maurice; Neese, Frank; Rauchfuss, Thomas B.; Gee, Leland B.; Scott, Aubrey D.; Yoda, Yoshitaka; Tanaka, Yoshihito; Lubitz, Wolfgang; Cramer, Stephen P.

    2015-08-01

    The metabolism of many anaerobes relies on [NiFe]-hydrogenases, whose characterization when bound to substrates has proven non-trivial. Presented here is direct evidence for a hydride bridge in the active site of the 57Fe-labelled fully reduced Ni-R form of Desulfovibrio vulgaris Miyazaki F [NiFe]-hydrogenase. A unique `wagging' mode involving H- motion perpendicular to the Ni(?-H)57Fe plane was studied using 57Fe-specific nuclear resonance vibrational spectroscopy and density functional theory (DFT) calculations. On Ni(?-D)57Fe deuteride substitution, this wagging causes a characteristic perturbation of Fe-CO/CN bands. Spectra have been interpreted by comparison with Ni(?-H/D)57Fe enzyme mimics [(dppe)Ni(?-pdt)(?-H/D)57Fe(CO)3]+ and DFT calculations, which collectively indicate a low-spin Ni(II)(?-H)Fe(II) core for Ni-R, with H- binding Ni more tightly than Fe. The present methodology is also relevant to characterizing Fe-H moieties in other important natural and synthetic catalysts.

  15. Artificial hydrogenases: biohybrid and supramolecular systems for catalytic hydrogen production or uptake.

    PubMed

    Caserta, Giorgio; Roy, Souvik; Atta, Mohamed; Artero, Vincent; Fontecave, Marc

    2015-04-01

    There is an urgent need for cheap, abundant and efficient catalysts as an alternative to platinum for hydrogen production and oxidation in (photo)electrolyzers and fuel cells. Hydrogenases are attractive solutions. These enzymes use exclusively nickel and iron in their active sites and function with high catalytic rates at the thermodynamic equilibrium. As an alternative, a number of biomimetic and bioinspired catalysts for H2 production and/or uptake, based on Ni, Fe and Co, have been developed and shown to display encouraging performances. In this review we discuss specifically recent approaches aiming at incorporating these compounds within oligomeric and polymeric hosts. The latter are most often biological compounds (peptides, proteins, polysaccharides, etc.) but we also discuss non-biological scaffolds (synthetic polymers, Metal-organic-Frameworks, etc.) which can provide the appropriate environment to tune the activity and stability of the synthetic catalysts. These supramolecular catalytic systems thus define a class of original compounds so-called artificial hydrogenases. PMID:25553541

  16. How the structure of the large subunit controls function in an oxygen-tolerant [NiFe]-hydrogenase

    PubMed Central

    Bowman, Lisa; Flanagan, Lindsey; Fyfe, Paul K.; Parkin, Alison; Hunter, William N.; Sargent, Frank

    2014-01-01

    Salmonella enterica is an opportunistic pathogen that produces a [NiFe]-hydrogenase under aerobic conditions. In the present study, genetic engineering approaches were used to facilitate isolation of this enzyme, termed Hyd-5. The crystal structure was determined to a resolution of 3.2 Å and the hydro-genase was observed to comprise associated large and small subunits. The structure indicated that His229 from the large subunit was close to the proximal [4Fe–3S] cluster in the small subunit. In addition, His229 was observed to lie close to a buried glutamic acid (Glu73), which is conserved in oxygen-tolerant hydrogenases. His229 and Glu73 of the Hyd-5 large subunit were found to be important in both hydrogen oxidation activity and the oxygen-tolerance mechanism. Substitution of His229 or Glu73 with alanine led to a loss in the ability of Hyd-5 to oxidize hydrogen in air. Furthermore, the H229A variant was found to have lost the overpotential requirement for activity that is always observed with oxygen-tolerant [NiFe]-hydrogenases. It is possible that His229 has a role in stabilizing the super-oxidized form of the proximal cluster in the presence of oxygen, and it is proposed that Glu73could play a supporting role in fine-tuning the chemistry of His229 to enable this function. PMID:24428762

  17. Amphiphilic polymeric micelles as microreactors: improving the photocatalytic hydrogen production of the [FeFe]-hydrogenase mimic in water.

    PubMed

    Wang, Feng; Wen, Min; Feng, Ke; Liang, Wen-Jing; Li, Xu-Bing; Chen, Bin; Tung, Chen-Ho; Wu, Li-Zhu

    2016-01-11

    An amphiphilic polymeric micelle is utilized as a microreactor to load a hydrophobic [FeFe]-hydrogenase mimic in water. The local concentration enhancement and strong interaction between the mimic and the photosensitizer as well as the water-mediated fast proton migration caused by the microreactor improve photocatalytic hydrogen production remarkably in water. PMID:26442776

  18. Expression of Shewanella oneidensis MR-1 [FeFe]-Hydrogenase Genes in Anabaena sp. Strain PCC 7120

    PubMed Central

    Gärtner, Katrin; Lechno-Yossef, Sigal; Cornish, Adam J.; Wolk, C. Peter

    2012-01-01

    H2 generated from renewable resources holds promise as an environmentally innocuous fuel that releases only energy and water when consumed. In biotechnology, photoautotrophic oxygenic diazotrophs could produce H2 from water and sunlight using the cells' endogenous nitrogenases. However, nitrogenases have low turnover numbers and require large amounts of ATP. [FeFe]-hydrogenases found in other organisms can have 1,000-fold higher turnover numbers and no specific requirement for ATP but are very O2 sensitive. Certain filamentous cyanobacteria protect nitrogenase from O2 by sequestering the enzyme within internally micro-oxic, differentiated cells called heterocysts. We heterologously expressed the [FeFe]-hydrogenase operon from Shewanella oneidensis MR-1 in Anabaena sp. strain PCC 7120 using the heterocyst-specific promoter PhetN. Active [FeFe]-hydrogenase was detected in and could be purified from aerobically grown Anabaena sp. strain PCC 7120, but only when the organism was grown under nitrate-depleted conditions that elicited heterocyst formation. These results suggest that the heterocysts protected the [FeFe]-hydrogenase against inactivation by O2. PMID:23023750

  19. The Bidirectional NiFe-hydrogenase in Synechocystis sp. PCC 6803 Is Reduced by Flavodoxin and Ferredoxin and Is Essential under Mixotrophic, Nitrate-limiting Conditions*

    PubMed Central

    Gutekunst, Kirstin; Chen, Xi; Schreiber, Karoline; Kaspar, Ursula; Makam, Srinivas; Appel, Jens

    2014-01-01

    Cyanobacteria are able to use solar energy for the production of hydrogen. It is generally accepted that cyanobacterial NiFe-hydrogenases are reduced by NAD(P)H. This is in conflict with thermodynamic considerations, as the midpoint potentials of NAD(P)H do not suffice to support the measured hydrogen production under physiological conditions. We show that flavodoxin and ferredoxin directly reduce the bidirectional NiFe-hydrogenase of Synechocystis sp. PCC 6803 in vitro. A merodiploid ferredoxin-NADP reductase mutant produced correspondingly more photohydrogen. We furthermore found that the hydrogenase receives its electrons via pyruvate:flavodoxin/ferredoxin oxidoreductase (PFOR)-flavodoxin/ferredoxin under fermentative conditions, enabling the cells to gain ATP. These results strongly support that the bidirectional NiFe-hydrogenases in cyanobacteria function as electron sinks for low potential electrons from photosystem I and as a redox balancing device under fermentative conditions. However, the selective advantage of this enzyme is not known. No strong phenotype of mutants lacking the hydrogenase has been found. Because bidirectional hydrogenases are widespread in aquatic nutrient-rich environments that are capable of triggering phytoplankton blooms, we mimicked those conditions by growing cells in the presence of increased amounts of dissolved organic carbon and dissolved organic nitrogen. Under these conditions the hydrogenase was found to be essential. As these conditions close the two most important sinks for reduced flavodoxin/ferredoxin (CO2-fixation and nitrate reduction), this discovery further substantiates the connection between flavodoxin/ferredoxin and the NiFe-hydrogenase. PMID:24311779

  20. Comparison of N2 Fixation and Yields in Cajanus cajan between Hydrogenase-Positive and Hydrogenase-Negative Rhizobia by In Situ Acetylene Reduction Assays and Direct 15N Partitioning 1

    PubMed Central

    La Favre, Jeffrey S.; Focht, Dennis D.

    1983-01-01

    Pigeon peas [Cajanus cajan (L.) Millsp.] were grown in soil columns containing 15N-enriched organic matter. Seasonal N2 fixation activity was determined by periodically assaying plants for reduction of C2H2. N2 fixation rose sharply from the first assay period at 51 days after planting to a peak of activity between floral initiation and fruit set. N2 fixation (acetylene reduction) activity dropped concomitantly with pod maturation but recovered after pod harvests. Analysis of 15N content of plant shoots revealed that approximately 91 to 94% of plant N was derived from N2 fixation. The effect of inoculation with hydrogenase-positive and hydrogenase-negative rhizobia was examined. Pigeon peas inoculated with strain P132 (hydrogenase-positive) yielded significantly more total shoot N than other inoculated or uninoculated treatments. However, two other hydrogenase-positive strains did not yield significantly more total shoot N than a hydrogenase-negative strain. The extent of nodulation by inoculum strains compared to indigenous rhizobia was determined by typing nodules according to intrinsic antibiotic resistance of the inoculum strains. The inoculum strains were detected in almost all typed nodules of inoculated plants. Gas samples were taken from soil columns several times during the growth cycle of the plants. H2 was never detected, even in columns containing pigeon peas inoculated with hydrogenase-negative rhizobia. This was attributed to H2 consumption by soil bacteria. Estimation of N2 fixation by acetylene reduction activity was closest to the direct 15N method when ethylene concentrations in the gas headspace (between the column lid and soil surface) were extrapolated to include the soil pore space as opposed solely to measurement in the headspace. There was an 8-fold difference between the two acetylene reduction assay methods of estimation. Based on a planting density of 15,000 plants per hectare, the direct 15N fixation rates ranged from 67 (noninoculated) to 134 kilograms per hectare, while grain yields ranged from 540 to 825 kilograms per hectare. Grain yields were not increased with N fertilizer. PMID:16663148

  1. Photocatalytic Hydrogen Production using Polymeric Carbon Nitride with a Hydrogenase and a Bioinspired Synthetic Ni Catalyst**

    PubMed Central

    Caputo, Christine A; Gross, Manuela A; Lau, Vincent W; Cavazza, Christine; Lotsch, Bettina V; Reisner, Erwin

    2014-01-01

    Solar-light-driven H2 production in water with a [NiFeSe]-hydrogenase (H2ase) and a bioinspired synthetic nickel catalyst (NiP) in combination with a heptazine carbon nitride polymer, melon (CNx), is reported. The semibiological and purely synthetic systems show catalytic activity during solar light irradiation with turnover numbers (TONs) of more than 50?000?mol?H2?(mol?H2ase)?1 and approximately 155?mol?H2?(mol?NiP)?1 in redox-mediator-free aqueous solution at pH?6 and 4.5, respectively. Both systems maintained a reduced photoactivity under UV-free solar light irradiation (?>420?nm). PMID:25205168

  2. Photocatalytic Hydrogen Production using Polymeric Carbon Nitride with a Hydrogenase and a Bioinspired Synthetic Ni Catalyst**

    PubMed Central

    Caputo, Christine A; Gross, Manuela A; Lau, Vincent W; Cavazza, Christine; Lotsch, Bettina V; Reisner, Erwin

    2014-01-01

    Solar-light-driven H2 production in water with a [NiFeSe]-hydrogenase (H2ase) and a bioinspired synthetic nickel catalyst (NiP) in combination with a heptazine carbon nitride polymer, melon (CNx), is reported. The semibiological and purely synthetic systems show catalytic activity during solar light irradiation with turnover numbers (TONs) of more than 50 000 mol H2 (mol H2ase)?1 and approximately 155 mol H2 (mol NiP)?1 in redox-mediator-free aqueous solution at pH 6 and 4.5, respectively. Both systems maintained a reduced photoactivity under UV-free solar light irradiation (?>420 nm). PMID:26300567

  3. Aerobic Damage to [FeFe]-Hydrogenases: Activation Barriers for the Chemical Attachment of O2**

    PubMed Central

    Kubas, Adam; De?Sancho, David; Best, Robert B; Blumberger, Jochen

    2014-01-01

    [FeFe]-hydrogenases are the best natural hydrogen-producing enzymes but their biotechnological exploitation is hampered by their extreme oxygen sensitivity. The free energy profile for the chemical attachment of O2 to the enzyme active site was investigated by using a range-separated density functional re-parametrized to reproduce high-level ab?initio data. An activation free-energy barrier of 13?kcal?mol?1 was obtained for chemical bond formation between the di-iron active site and O2, a value in good agreement with experimental inactivation rates. The oxygen binding can be viewed as an inner-sphere electron-transfer process that is strongly influenced by Coulombic interactions with the proximal cubane cluster and the protein environment. The implications of these results for future mutation studies with the aim of increasing the oxygen tolerance of this enzyme are discussed. PMID:24615978

  4. Orientation-Controlled Electrocatalytic Efficiency of an Adsorbed Oxygen-Tolerant Hydrogenase

    PubMed Central

    Zerball, Maximilian; Horch, Marius; Millo, Diego; Fritsch, Johannes; Lenz, Oliver; von Klitzing, Regine; Hildebrandt, Peter; Fischer, Anna; Mroginski, Maria Andrea; Zebger, Ingo

    2015-01-01

    Protein immobilization on electrodes is a key concept in exploiting enzymatic processes for bioelectronic devices. For optimum performance, an in-depth understanding of the enzyme-surface interactions is required. Here, we introduce an integral approach of experimental and theoretical methods that provides detailed insights into the adsorption of an oxygen-tolerant [NiFe] hydrogenase on a biocompatible gold electrode. Using atomic force microscopy, ellipsometry, surface-enhanced IR spectroscopy, and protein film voltammetry, we explore enzyme coverage, integrity, and activity, thereby probing both structure and catalytic H2 conversion of the enzyme. Electrocatalytic efficiencies can be correlated with the mode of protein adsorption on the electrode as estimated theoretically by molecular dynamics simulations. Our results reveal that pre-activation at low potentials results in increased current densities, which can be rationalized in terms of a potential-induced re-orientation of the immobilized enzyme. PMID:26580976

  5. Cloning and nucleotide sequences of the genes for the subunits of NAD-reducing hydrogenase of Alcaligenes eutrophus H16.

    PubMed Central

    Tran-Betcke, A; Warnecke, U; Böcker, C; Zaborosch, C; Friedrich, B

    1990-01-01

    The genes hoxF, -U, -Y, and -H which encode the four subunit polypeptides alpha, gamma, delta, and beta of the NAD-reducing hydrogenase (HoxS) of Alcaligenes eutrophus H16, were cloned, expressed in Pseudomonas facilis, and sequenced. On the basis of the nucleotide sequence, the predicted amino acid sequences, and the N-terminal amino acid sequences, it was concluded that the structural genes are tightly linked and presumably organized as an operon, denoted hoxS. Two pairs of -24 and -12 consensus sequences resembling RpoN-activatable promoters lie upstream of hoxF, the first of the four genes. Primer extension experiments indicate that the second promoter is responsible for hoxS transcription. hoxF and hoxU code for the flavin-containing dimer (alpha and gamma subunits) of HoxS which exhibits NADH:oxidoreductase activity. A putative flavin-binding region is discussed. The 26.0-kilodalton (kDa) gamma subunit contains two cysteine clusters which may participate in the coordination of two [4F3-4S]centers. The genes hoxY and hoxH code for the small 22.9-kDa delta subunit and the nickel-containing 54.8-kDa beta subunit, respectively, of the hydrogenase dimer of HoxS. The latter dimer exhibits several conserved regions found in all nickel-containing hydrogenases. The roles of these regions in coordinating iron and nickel are discussed. Although the deduced amino acid sequences of the delta and beta subunits share some conserved regions with the corresponding polypeptides of other [NiFe] hydrogenases, the overall amino acid homology is marginal. Nevertheless, significant sequence homology (35%) to the corresponding polypeptides of the soluble methylviologen-reducing hydrogenase of Methanobacterium thermoautotrophicum was found. Unlike the small subunits of the membrane-bound and soluble periplasmic hydrogenases, the HoxS protein does not appear to be synthesized with an N-terminal leader peptide. Images PMID:2188945

  6. The importance of iron in the biosynthesis and assembly of [NiFe]-hydrogenases.

    PubMed

    Pinske, Constanze; Sawers, R Gary

    2014-03-01

    [NiFe]-hydrogenases (Hyd) are redox-active metalloenzymes that catalyze the reversible oxidation of molecular hydrogen to protons and electrons. These enzymes are frequently heterodimeric and have a unique bimetallic active site in their catalytic large subunit and possess a complement of iron sulfur (Fe-S) clusters for electron transfer in the small subunit. Depending on environmental and metabolic requirements, the Fe-S cluster relay shows considerable variation among the Hyd, even employing high potential [4Fe-3S] clusters for improved oxygen tolerance. The general iron sulfur cluster (Isc) machinery is required for small subunit maturation, possibly providing standard [4Fe-4S], which are then modified as required in situ. The [NiFe] cofactor in the active site also has an iron ion to which one CO and two CN- diatomic ligands are attached. Specific accessory proteins synthesize these ligands and insert the cofactor into the apo-hydrogenase large subunit. Carbamoyl phosphate is the precursor of the CN- ligands, and recent experimental evidence suggests that endogenously generated CO2 might be one precursor of CO. Recent advances also indicate how the machineries responsible for cofactor generation obtain iron. Several transport systems for iron into bacterial cells exist; however, in Escherichia coli, it is mainly the ferrous iron transporter Feo and the ferric-citrate siderphore system Fec that are involved in delivering the metal for Hyd biosynthesis. Genetic analyses have provided evidence for the existence of key checkpoints during cofactor biosynthesis and enzyme assembly that ensure correct spatiotemporal maturation of these modular oxidoreductases. PMID:25372742

  7. Photosensitivity of the Ni-A state of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F with visible light

    SciTech Connect

    Osuka, Hisao; Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma-shi, Nara 630-0192 ; Shomura, Yasuhito; Komori, Hirofumi; Shibata, Naoki; Nagao, Satoshi; Higuchi, Yoshiki; CREST, JST, Gobancho, Chiyoda-ku, Tokyo 102-0076 ; Hirota, Shun; CREST, JST, Gobancho, Chiyoda-ku, Tokyo 102-0076

    2013-01-04

    Highlights: Black-Right-Pointing-Pointer Ni-A state of [NiFe] hydrogenase showed light sensitivity. Black-Right-Pointing-Pointer New FT-IR bands were observed with light irradiation of the Ni-A state. Black-Right-Pointing-Pointer EPR g-values of the Ni-A state shifted upon light irradiation. Black-Right-Pointing-Pointer The light-induced state converted back to the Ni-A state under the dark condition. -- Abstract: [NiFe] hydrogenase catalyzes reversible oxidation of molecular hydrogen. Its active site is constructed of a hetero dinuclear Ni-Fe complex, and the oxidation state of the Ni ion changes according to the redox state of the enzyme. We found that the Ni-A state (an inactive unready, oxidized state) of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F (DvMF) is light sensitive and forms a new state (Ni-AL) with irradiation of visible light. The Fourier transform infrared (FT-IR) bands at 1956, 2084 and 2094 cm{sup -1} of the Ni-A state shifted to 1971, 2086 and 2098 cm{sup -1} in the Ni-AL state. The g-values of g{sub x} = 2.30, g{sub y} = 2.23 and g{sub z} = 2.01 for the signals in the electron paramagnetic resonance (EPR) spectrum of the Ni-A state at room temperature varied for -0.009, +0.012 and +0.010, respectively, upon light irradiation. The light-induced Ni-AL state converted back immediately to the Ni-A state under dark condition at room temperature. These results show that the coordination structure of the Fe site of the Ni-A state of [NiFe] hydrogenase is perturbed significantly by light irradiation with relatively small coordination change at the Ni site.

  8. Molecular Dynamics Study of the Proposed Proton Transport Pathways in [FeFe]-Hydrogenase

    SciTech Connect

    Ginovska-Pangovska, Bojana; Ho, Ming-Hsun; Linehan, John C.; Cheng, Yuhui; Dupuis, Michel; Raugei, Simone; Shaw, Wendy J.

    2014-01-15

    Possible proton channels in Clostridium pasteurianum [FeFe]-hydrogenase were investigated with molecular dynamics simulations. This study was undertaken to discern proposed channels, compare their properties, evaluate the functional channel, and to provide insight into the features of an active proton channel. Our simulations suggest that protons are not transported through water wires. Instead, a five-residue motif (E282, S319, E279, HOH, C299) was found to be the likely channel, consistent with experimental observations. This channel connects the surface of the enzyme and the di-thiomethylamine bridge of the catalytic H-cluster, permitting the transport of protons. The channel was found to have a persistent hydrogen bonded core (residues E279 to S319), with less persistent hydrogen bonds at the ends of the channel. The hydrogen bond occupancy in this network was found to be sensitive to the protonation state of the residues in the channel, with different protonation states enhancing or stabilizing hydrogen bonding in different regions of the network. Single site mutations to non-hydrogen bonding residues break the hydrogen bonding network at that residue, consistent with experimental observations showing catalyst inactivation. In many cases, these mutations alter the hydrogen bonding in other regions of the channel which may be equally important in catalytic failure. A correlation between the protein dynamics near the proton channel and the redox partner binding regions was also found as a function of protonation state. The likely mechanism of proton movement in [FeFe]-hydrogenases is discussed based on the structural analysis presented here. This work was funded by the DOE Office of Science Early Career Research Program through the Office of Basic Energy Sciences. Computational resources were provided at W. R. Wiley Environmental Molecular Science Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research located at Pacific Northwest National Laboratory, and a portion of the research was performed using PNNL Institutional Computing at Pacific Northwest National Laboratory. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

  9. Light-Driven Hydrogen Production by Hydrogenases and a Ru-Complex inside a Nanoporous Glass Plate under Aerobic External Conditions.

    PubMed

    Noji, Tomoyasu; Kondo, Masaharu; Jin, Tetsuro; Yazawa, Tetsuo; Osuka, Hisao; Higuchi, Yoshiki; Nango, Mamoru; Itoh, Shigeru; Dewa, Takehisa

    2014-07-17

    Hydrogenases are powerful catalysts for light-driven H2 production using a combination of photosensitizers. However, except oxygen-tolerant hydrogenases, they are immediately deactivated under aerobic conditions. We report a light-driven H2 evolution system that works stably even under aerobic conditions. A [NiFe]-hydrogenase from Desulfovibrio vulgaris Miyazaki F was immobilized inside nanoporous glass plates (PGPs) with a pore diameter of 50 nm together with a ruthenium complex and methyl viologen as a photosensitizer and an electron mediator, respectively. After immersion of PGP into the medium containing the catalytic components, an anaerobic environment automatically established inside the nanopores even under aerobic external conditions upon irradiation with solar-simulated light; this system constantly evolved H2 with an efficiency of 3.7 ?mol H2 m(-2) s(-1). The PGP system proposed in this work represents a promising first step toward the development of an O2-tolerant solar energy conversion system. PMID:26277806

  10. Synthesis of nickel-iron hydrogenase in Cupriavidus metallidurans is controlled by metal-dependent silencing and un-silencing of genomic islands.

    PubMed

    Herzberg, Martin; Schüttau, Marcel; Reimers, Matthias; Große, Cornelia; Hans-Günther-Schlegel; Nies, Dietrich H

    2015-04-01

    Cupriavidus metallidurans CH34 is able to grow autotrophically as a hydrogen-oxidizing bacterium and produces nickel-dependent hydrogenases, even under heterotrophic conditions. Loss of its two native plasmids resulted in inability of the resulting strain AE104 to synthesize the hydrogenases and to grow autotrophically in phosphate-poor, Tris-buffered mineral salts medium (TMM). Three of eleven previously identified catabolic genomic islands (CMGIs; Van Houdt et al., 2009), two of which harbor the genes for the membrane-bound (CMGI-2) and the soluble hydrogenase (CMGI-3), were silenced in strain AE104 when cultivated in phosphate-poor TMM, explaining its inability to produce hydrogenases. Production of the soluble hydrogenase from the aut region 1 of CMGI-3, and concomitant autotrophic growth, was recovered when the gene for the zinc importer ZupT was deleted in strain AE104. The transcriptome of the ?zupT mutant exhibited two up-regulated gene regions compared to its parent strain AE104. Expression of the genes in the aut region 1 increased independently of the presence of added zinc. A second gene region was expressed only under metal starvation conditions. This region encoded a TonB-dependent outer membrane protein, a putative metal chaperone plus paralogs of essential zinc-dependent proteins, indicating the presence of a zinc allocation pathway in C. metallidurans. Thus, expression of the genes for the soluble hydrogenase and the Calvin cycle enzymes on aut region 1 of CMGI-3 of C. metallidurans is under global control and needs efficient ZupT-dependent zinc allocation for a regulatory role, which might be discrimination of nickel. PMID:25720835

  11. Electronic reorganization triggered by electron transfer: the intervalence charge transfer of a Fe³?/Fe²? bimetallic complex.

    PubMed

    Domingo, Alex; Angeli, Celestino; de Graaf, Coen; Robert, Vincent

    2015-04-30

    The key role of the molecular orbitals in describing electron transfer processes is put in evidence for the intervalence charge transfer (IVCT) of a synthetic nonheme binuclear mixed-valence Fe(3+)/Fe(2+) compound. The electronic reorganization induced by the IVCT can be quantified by controlling the adaptation of the molecular orbitals to the charge transfer process. We evaluate the transition energy and its polarization effects on the molecular orbitals by means of ab initio calculations. The resulting energetic profile of the IVCT shows strong similarities to the Marcus' model, suggesting a response behaviour of the ensemble of electrons analogue to that of the solvent. We quantify the extent of the electronic reorganization induced by the IVCT process to be 11.74 eV, a very large effect that induces the crossing of states reducing the total energy of the transfer to 0.89 eV. PMID:25739890

  12. Cloning and sequencing of the genes encoding the large and small subunits of the periplasmic (NiFeSe) hydrogenase of Desulfovibrio baculatus

    SciTech Connect

    Menon, N.K.; Peck, H.D. Jr.; Le Gall, J.; Przybyla, A.E.

    1987-12-01

    The genes coding for the large and small subunits of the periplasmic hydrogenase from Desulfovibrio baculatus have been cloned and sequenced. The genes are arranged in an operon with the small subunit gene preceding the large subunit gene. The small subunit gene codes for a 32 amino acid leader sequence supporting the periplasmic localization of the protein, however no ferredoxin-like or other characteristic iron-sulfur coordination sites were observed. The periplasmic hydrogenases from D. baculatus (an NiFeSe protein) and D. vulgaris (an Fe protein) exhibit no homology suggesting that they are structurally different, unrelated entities.

  13. Overproduction of the membrane-bound [NiFe]-hydrogenase in Thermococcus kodakarensis and its effect on hydrogen production

    PubMed Central

    Kanai, Tamotsu; Simons, Jan-Robert; Tsukamoto, Ryohei; Nakajima, Akihito; Omori, Yoshiyuki; Matsuoka, Ryoji; Beppu, Haruki; Imanaka, Tadayuki; Atomi, Haruyuki

    2015-01-01

    The hyperthermophilic archaeon Thermococcus kodakarensis can utilize sugars or pyruvate for growth. In the absence of elemental sulfur, the electrons via oxidation of these substrates are accepted by protons, generating molecular hydrogen (H2). The hydrogenase responsible for this reaction is a membrane-bound [NiFe]-hydrogenase (Mbh). In this study, we have examined several possibilities to increase the protein levels of Mbh in T. kodakarensis by genetic engineering. Highest levels of intracellular Mbh levels were achieved when the promoter of the entire mbh operon (TK2080-TK2093) was exchanged to a strong constitutive promoter from the glutamate dehydrogenase gene (TK1431) (strain MHG1). When MHG1 was cultivated under continuous culture conditions using pyruvate-based medium, a nearly 25% higher specific hydrogen production rate (SHPR) of 35.3 mmol H2 g-dcw?1 h?1 was observed at a dilution rate of 0.31 h?1. We also combined mbh overexpression using an even stronger constitutive promoter from the cell surface glycoprotein gene (TK0895) with disruption of the genes encoding the cytosolic hydrogenase (Hyh) and an alanine aminotransferase (AlaAT), both of which are involved in hydrogen consumption (strain MAH1). At a dilution rate of 0.30 h?1, the SHPR was 36.2 mmol H2 g-dcw?1 h?1, corresponding to a 28% increase compared to that of the host T. kodakarensis strain. Increasing the dilution rate to 0.83 h?1 or 1.07 h?1 resulted in a SHPR of 120 mmol H2 g-dcw?1 h?1, which is one of the highest production rates observed in microbial fermentation. PMID:26379632

  14. On the active sites of the [NiFe] hydrogenase from Desulfovibrio gigas. Mössbauer and redox-titration studies.

    PubMed

    Huynh, B H; Patil, D S; Moura, I; Teixeira, M; Moura, J J; DerVartanian, D V; Czechowski, M H; Prickril, B C; Peck, H D; LeGall, J

    1987-01-15

    The [NiFe] hydrogenase isolated from Desulfovibrio gigas was poised at different redox potentials and studied by Mössbauer spectroscopy. The data firmly establish that this hydrogenase contains four prosthetic groups: one nickel center, one [3Fe-xS], and two [4Fe-4S] clusters. In the native enzyme, both the nickel and the [3Fe-xS] cluster are EPR-active. At low temperature (4.2 K), the [3Fe-xS] cluster exhibits a paramagnetic Mössbauer spectrum typical for oxidized [3Fe-xS] clusters. At higher temperatures (greater than 20 K), the paramagnetic spectrum collapses into a quadrupole doublet with parameters magnitude of delta EQ magnitude of = 0.7 +/- 0.06 mm/s and delta = 0.36 +/- 0.06 mm/s, typical of high-spin Fe(III). The observed isomer shift is slightly larger than those observed for the three-iron clusters in D. gigas ferredoxin II (Huynh, B. H., Moura, J. J. G., Moura, I., Kent, T. A., LeGall, J., Xavier, A. V., and Münck, E. (1980) J. Biol. Chem. 255, 3242-3244) and in Azotobacter vinelandii ferredoxin I (Emptage, M. H., Kent, T. A., Huynh, B. H., Rawlings, J., Orme-Johnson, W. H., and Münck, E. (1980) J. Biol. Chem. 255, 1793-1796) and may indicate a different iron coordination environment. When D. gigas hydrogenase is poised at potentials lower than -80 mV (versus normal hydrogen electrode), the [3Fe-xS] cluster is reduced and becomes EPR-silent. The Mössbauer data indicate that the reduced [3Fe-xS] cluster remains intact, i.e. it does not interconvert into a [4Fe-4S] cluster. Also, the electronic properties of the reduced [3Fe-xS] cluster suggest that it is magnetically isolated from the other paramagnetic centers. PMID:3027068

  15. Unraveling the role of the protein environment for [FeFe]-hydrogenase: a new application of coarse-graining.

    PubMed

    McCullagh, Martin; Voth, Gregory A

    2013-04-18

    Hydrogenase enzymes are natural biocatalysts that might be harnessed to reduce the cost of hydrogen gas production. [FeFe]-hydrogenases are the most effective of three such enzymes at catalyzing H(+) reduction. In this study, we develop and apply a novel combination of all-atom molecular dynamics and coarse-grained (CG) analysis to characterize two important steps of the catalytic cycle of [FeFe]-hydrogenase. The first is the electron transport through FeS clusters to the active site. We use a Marcus formulation to compute the free energy and the reorganization energy of three electron transport steps and decompose these values into contributions from the CG protein sites and the solvent. The three-step transport process is found to be downhill with relative free energies of -11.7 for the first step, -14.8 for the second step, and -17.1 kcal/mol for the third step. The electron-transport process is also found to activate a water channel suggesting a coupled mechanism for proton and electron transport to the active site. The channel opening is orchestrated by three CG sites located in the active-site domain of the protein with one of the sites also contributing a strong attractive electrostatic potential (ESP) to help shuttle protons to the active site. Overall, our CG analysis points to a concerted mechanism of electron and proton delivery to the active site in these proteins thus providing important insight for the development of biomimetic devices. PMID:23484958

  16. Rubredoxin-related Maturation Factor Guarantees Metal Cofactor Integrity during Aerobic Biosynthesis of Membrane-bound [NiFe] Hydrogenase*

    PubMed Central

    Fritsch, Johannes; Siebert, Elisabeth; Priebe, Jacqueline; Zebger, Ingo; Lendzian, Friedhelm; Teutloff, Christian; Friedrich, Bärbel; Lenz, Oliver

    2014-01-01

    The membrane-bound [NiFe] hydrogenase (MBH) supports growth of Ralstonia eutropha H16 with H2 as the sole energy source. The enzyme undergoes a complex biosynthesis process that proceeds during cell growth even at ambient O2 levels and involves 14 specific maturation proteins. One of these is a rubredoxin-like protein, which is essential for biosynthesis of active MBH at high oxygen concentrations but dispensable under microaerobic growth conditions. To obtain insights into the function of HoxR, we investigated the MBH protein purified from the cytoplasmic membrane of hoxR mutant cells. Compared with wild-type MBH, the mutant enzyme displayed severely decreased hydrogenase activity. Electron paramagnetic resonance and infrared spectroscopic analyses revealed features resembling those of O2-sensitive [NiFe] hydrogenases and/or oxidatively damaged protein. The catalytic center resided partially in an inactive Niu-A-like state, and the electron transfer chain consisting of three different Fe-S clusters showed marked alterations compared with wild-type enzyme. Purification of HoxR protein from its original host, R. eutropha, revealed only low protein amounts. Therefore, recombinant HoxR protein was isolated from Escherichia coli. Unlike common rubredoxins, the HoxR protein was colorless, rather unstable, and essentially metal-free. Conversion of the atypical iron-binding motif into a canonical one through genetic engineering led to a stable reddish rubredoxin. Remarkably, the modified HoxR protein did not support MBH-dependent growth at high O2. Analysis of MBH-associated protein complexes points toward a specific interaction of HoxR with the Fe-S cluster-bearing small subunit. This supports the previously made notion that HoxR avoids oxidative damage of the metal centers of the MBH, in particular the unprecedented Cys6[4Fe-3S] cluster. PMID:24448806

  17. Crystallization and preliminary X-ray diffraction analysis of membrane-bound respiratory [NiFe] hydrogenase from Hydrogenovibrio marinus.

    PubMed

    Shomura, Yasuhito; Hagiya, Keisuke; Yoon, Ki-Seok; Nishihara, Hirofumi; Higuchi, Yoshiki

    2011-07-01

    Membrane-bound respiratory [NiFe] hydrogenase is an H2-uptake enzyme found in the periplasmic space of bacteria that plays a crucial role in energy-conservation processes. The heterodimeric unit of the enzyme from Hydrogenovibrio marinus was purified to homogeneity using chromatographic procedures. Crystals were grown using the sitting-drop vapour-diffusion method at room temperature. Preliminary crystallographic analysis revealed that the crystals belonged to space group P2(1), with unit-cell parameters a=75.72, b=116.59, c=113.40?Å, ?=91.3°, indicating that two heterodimers were present in the asymmetric unit. PMID:21795805

  18. Hybrid [FeFe]-hydrogenases with modified active sites show remarkable residual enzymatic activity.

    PubMed

    Siebel, Judith F; Adamska-Venkatesh, Agnieszka; Weber, Katharina; Rumpel, Sigrun; Reijerse, Edward; Lubitz, Wolfgang

    2015-02-24

    [FeFe]-hydrogenases are to date the only enzymes for which it has been demonstrated that the native inorganic binuclear cofactor of the active site Fe2(adt)(CO)3(CN)2 (adt = azadithiolate = [S-CH2-NH-CH2-S](2-)) can be synthesized on the laboratory bench and subsequently inserted into the unmaturated enzyme to yield fully functional holo-enzyme (Berggren, G. et al. (2013) Nature 499, 66-70; Esselborn, J. et al. (2013) Nat. Chem. Biol. 9, 607-610). In the current study, we exploit this procedure to introduce non-native cofactors into the enzyme. Mimics of the binuclear subcluster with a modified bridging dithiolate ligand (thiodithiolate, N-methylazadithiolate, dimethyl-azadithiolate) and three variants containing only one CN(-) ligand were inserted into the active site of the enzyme. We investigated the activity of these variants for hydrogen oxidation as well as proton reduction and their structural accommodation within the active site was analyzed using Fourier transform infrared spectroscopy. Interestingly, the monocyanide variant with the azadithiolate bridge showed ?50% of the native enzyme activity. This would suggest that the CN(-) ligands are not essential for catalytic activity, but rather serve to anchor the binuclear subsite inside the protein pocket through hydrogen bonding. The inserted artificial cofactors with a propanedithiolate and an N-methylazadithiolate bridge as well as their monocyanide variants also showed residual activity. However, these activities were less than 1% of the native enzyme. Our findings indicate that even small changes in the dithiolate bridge of the binuclear subsite lead to a rather strong decrease of the catalytic activity. We conclude that both the Brønsted base function and the conformational flexibility of the native azadithiolate amine moiety are essential for the high catalytic activity of the native enzyme. PMID:25633077

  19. Crystal structures of hydrogenase maturation protein HypE in the Apo and ATP-bound forms.

    PubMed

    Shomura, Yasuhito; Komori, Hirofumi; Miyabe, Natsuko; Tomiyama, Masamitsu; Shibata, Naoki; Higuchi, Yoshiki

    2007-09-28

    The hydrogenase maturation protein HypE serves an essential function in the biosynthesis of the nitrile group, which is subsequently coordinated to Fe as CN(-) ligands in [Ni-Fe] hydrogenase. Here, we present the crystal structures of HypE from Desulfovibrio vulgaris Hildenborough in the presence and in the absence of ATP at a resolution of 2.0 A and 2.6 A, respectively. Comparison of the apo structure with the ATP-bound structure reveals that binding ATP causes an induced-fit movement of the N-terminal portion, but does not entail an overall structural change. The residue Cys341 at the C terminus, whose thiol group is supposed to be carbamoylated before the nitrile group synthesis, is completely buried within the protein and is located in the vicinity of the gamma-phosphate group of the bound ATP. This suggests that the catalytic reaction occurs in this configuration but that a conformational change is required for the carbamoylation of Cys341. A glutamate residue is found close to the thiol group as well, which is suggestive of deprotonation of the carbamoyl group at the beginning of the reactions. PMID:17706667

  20. Radioassay for Hydrogenase Activity in Viable Cells and Documentation of Aerobic Hydrogen-Consuming Bacteria Living in Extreme Environments

    PubMed Central

    Schink, Bernhard; Lupton, F. S.; Zeikus, J. G.

    1983-01-01

    An isotopic tracer assay based on the hydrogenase-dependent formation of tritiated water from tritium gas was developed for in life analysis of microbial hydrogen transformation. This method allowed detection of bacterial hydrogen metabolism in pure cultures or in natural samples obtained from aquatic ecosystems. A differentiation between chemical-biological and aerobic-anaerobic hydrogen metabolism was established by variation of the experimental incubation temperature or by addition of selective inhibitors. Hydrogenase activity was shown to be proportional to the consumption or production of hydrogen by cultures of Desulfovibrio vulgaris, Clostridium pasteurianum, and Methanosarcina barkeri. This method was applied, in connection with measurements of free hydrogen and most-probable-number enumerations, in aerobic natural source waters to establish the activity and document the ecology of hydrogen-consuming bacteria in extreme acid, thermal, or saline environments. The utility of the assay is based in part on the ability to quantify bacterial hydrogen transformation at natural hydrogen partial pressures, without the use of artificial electron acceptors. PMID:16346288

  1. Observation of the Fe—CN and Fe—CO Vibrations in the Active Site of [NiFe] Hydrogenase by Nuclear Resonance Vibrational Spectroscopy**

    PubMed Central

    Kamali, Saeed; Wang, Hongxin; Mitra, Devrani; Ogata, Hideaki; Manor, Brian C.; Rauchfuss, Thomas B.; Byrne, Deborah; Bonnefoy, Violaine; Jenney, Francis E.; Adams, Michael W. W.; Yoda, Yoshitaka; Alp, Ercan; Zhao, Jiyong; Cramer, Stephen P.

    2012-01-01

    Nuclear inelastic scattering of 57Fe labeled [NiFe] hydrogenase is shown to give information on different states of the enzyme. It was thus possible to detect and assign Fe–CO and Fe–CN bending and stretching vibrations of the active site outside the spectral range of the Fe–S cluster normal modes. PMID:23136119

  2. Reversible oxygen-tolerant hydrogenase carried by free-living N2-fixing bacteria isolated from the rhizospheres of rice, maize, and wheat

    PubMed Central

    Roumagnac, Philippe; Richaud, Pierre; Barakat, Mohamed; Ortet, Philippe; Roncato, Marie-Anne; Heulin, Thierry; Peltier, Gilles; Achouak, Wafa; Cournac, Laurent

    2012-01-01

    Hydrogen production by microorganisms is often described as a promising sustainable and clean energy source, but still faces several obstacles, which prevent practical application. Among them, oxygen sensitivity of hydrogenases represents one of the major limitations hampering the biotechnological implementation of photobiological production processes. Here, we describe a hierarchical biodiversity-based approach, including a chemochromic screening of hydrogenase activity of hundreds of bacterial strains collected from several ecosystems, followed by mass spectrometry measurements of hydrogenase activity of a selection of the H2-oxidizing bacterial strains identified during the screen. In all, 131 of 1266 strains, isolated from cereal rhizospheres and basins containing irradiating waste, were scored as H2-oxidizing bacteria, including Pseudomonas sp., Serratia sp., Stenotrophomonas sp., Enterobacter sp., Rahnella sp., Burkholderia sp., and Ralstonia sp. isolates. Four free-living N2-fixing bacteria harbored a high and oxygen-tolerant hydrogenase activity, which was not fully inhibited within entire cells up to 150–250 ?mol/L O2 concentration or within soluble protein extracts up to 25–30 ?mol/L. The only hydrogenase-related genes that we could reveal in these strains were of the hyc type (subunits of formate hydrogenlyase complex). The four free-living N2-fixing bacteria were closely related to Enterobacter radicincitans based on the sequences of four genes (16S rRNA, rpoB, hsp60, and hycE genes). These results should bring interesting prospects for microbial biohydrogen production and might have ecophysiological significance for bacterial adaptation to the oxic–anoxic interfaces in the rhizosphere. PMID:23233392

  3. Purification and Characterization of the [NiFe]-Hydrogenase of Shewanella oneidensis MR-1 ?

    PubMed Central

    Shi, Liang; Belchik, Sara M.; Plymale, Andrew E.; Heald, Steve; Dohnalkova, Alice C.; Sybirna, Kateryna; Bottin, Hervé; Squier, Thomas C.; Zachara, John M.; Fredrickson, James K.

    2011-01-01

    Shewanella oneidensis MR-1 possesses a periplasmic [NiFe]-hydrogenase (MR-1 [NiFe]-H2ase) that has been implicated in H2 production and oxidation as well as technetium [Tc(VII)] reduction. To characterize the roles of MR-1 [NiFe]-H2ase in these proposed reactions, the genes encoding both subunits of MR-1 [NiFe]-H2ase were cloned and then expressed in an MR-1 mutant without hyaB and hydA genes. Expression of recombinant MR-1 [NiFe]-H2ase in trans restored the mutant's ability to produce H2 at 37% of that for the wild type. Following purification, MR-1 [NiFe]-H2ase coupled H2 oxidation to reduction of Tc(VII)O4? and methyl viologen. Change of the buffers used affected MR-1 [NiFe]-H2ase-mediated reduction of Tc(VII)O4? but not methyl viologen. Under the conditions tested, all Tc(VII)O4? used was reduced in Tris buffer, while in HEPES buffer, only 20% of Tc(VII)O4? was reduced. The reduced products were soluble in Tris buffer but insoluble in HEPES buffer. Transmission electron microscopy analysis revealed that Tc precipitates reduced in HEPES buffer were aggregates of crystallites with diameters of ?5 nm. Measurements with X-ray absorption near-edge spectroscopy revealed that the reduction products were a mixture of Tc(IV) and Tc(V) in Tris buffer but only Tc(IV) in HEPES buffer. Measurements with extended X-ray adsorption fine structure showed that while the Tc bonding environment in Tris buffer could not be determined, the Tc(IV) product in HEPES buffer was very similar to Tc(IV)O2·nH2O, which was also the product of Tc(VII)O4? reduction by MR-1 cells. These results shows for the first time that MR-1 [NiFe]-H2ase catalyzes Tc(VII)O4? reduction directly by coupling to H2 oxidation. PMID:21724888

  4. Purification and Characterization of [NiFe]-Hydrogenase of Shewanella oneidensis MR-1

    SciTech Connect

    Shi, Liang; Belchik, Sara M.; Plymale, Andrew E.; Heald, Steve M.; Dohnalkova, Alice; Sybirna, Kateryna; Bottin, Herve; Squier, Thomas C.; Zachara, John M.; Fredrickson, Jim K.

    2011-08-02

    The ?-proteobacterium Shewanella oneidensis MR-1 possesses a periplasmic [NiFe]-hydrogenase (MR-1 [NiFe]-H2ase) that was implicated in both H2 production and oxidation as well as technetium [Tc(VII)] reduction. To characterize the roles of MR-1 [NiFe]-H2ase in these proposed reactions, the genes encoding both subunits of MR-1 [NiFe]-H2ase were cloned into a protein expression vector. The resulting plasmid was transformed into a MR-1 mutant deficient in H2 formation. Expression of MR-1 [NiFe]-H2ase in trans restored the mutant’s ability to produce H2 at 37% of that for wild type. Following expression, MR-1 [NiFe]-H2ase was purified to near homogeneity. The purified MR-1 [NiFe]-H2ase could couple H2 oxidation to reduction of Tc(VII) and methyl viologen directly. Change of the buffers used affected MR-1 [NiFe]-H2ase-mediated Tc(VII) but not methyl viologen reductions. Under the conditions tested, Tc(VII) reduction was complete in Tris buffer but not in HEPES buffer. The reduced Tc(IV) was soluble in Tris buffer but insoluble in HEPES buffer. Transmission electron microscopy analysis revealed that Tc(IV) precipitates formed in HEPES buffer were packed with crystallites. Although X-ray absorption near-edge spectroscopy measurements confirmed that the reduction products found in both buffers were Tc(IV), extended X-ray adsorption fine-structure measurements revealed that these products were very different. While the product in Tris buffer could not be determined, the Tc(IV) product in HEPES buffer was very similar to Tc(IV)O2•nH2O. These results shows for the first time that MR-1 [NiFe]-H2ase is a bidirectional enzyme that catalyzes both H2 formation and oxidation as well as Tc(VII) reduction directly by coupling H2 oxidation.

  5. Explorations of iron-iron hydrogenase active site models by experiment and theory 

    E-print Network

    Tye, Jesse Wayne

    2009-05-15

    to form a 3c-2eâ Fe-H-Fe bond, while Et+ reacts to form a new C-S bond. The instability of a bridging ethyl complex is attributed to the inability of the ethyl group, in contrast to a hydride, to form a stable 3c-2eâ bond with the two iron centers. Gas-phase...

  6. Protonation of Nickel–Iron Hydrogenase Models Proceeds after Isomerization at Nickel

    PubMed Central

    2015-01-01

    Theory and experiment indicate that the protonation of reduced NiFe dithiolates proceeds via a previously undetected isomer with enhanced basicity. In particular, it is proposed that protonation of (OC)3Fe(pdt)Ni(dppe) (1; pdt2– = –S(CH2)3S–; dppe = Ph2P(CH2)2PPh2) occurs at the Fe site of the two-electron mixed-valence Fe(0)Ni(II) species, not the Fe(I)-Ni(I) bond for the homovalence isomer of 1. The new pathway, which may have implications for protonation of other complexes and clusters, was uncovered through studies on the homologous series L(OC)2Fe(pdt)M(dppe), where M = Ni, Pd (2), and Pt (3) and L = CO, PCy3. Similar to 1, complexes 2 and 3 undergo both protonation and 1e– oxidation to afford well-characterized hydrides ([2H]+ and [3H]+) and mixed-valence derivatives ([2]+ and [3]+), respectively. Whereas the Pd site is tetrahedral in 2, the Pt site is square-planar in 3, indicating that this complex is best described as Fe(0)Pt(II). In view of the results on 2 and 3, the potential energy surface of 1 was reinvestigated with density functional theory. These calculations revealed the existence of an energetically accessible and more basic Fe(0)Ni(II) isomer with a square-planar Ni site. PMID:25094041

  7. Intact functional fourteen-subunit respiratory membrane-bound [NiFe]-hydrogenase complex of the hyperthermophilic archaeon Pyrococcus furiosus.

    PubMed

    McTernan, Patrick M; Chandrayan, Sanjeev K; Wu, Chang-Hao; Vaccaro, Brian J; Lancaster, W Andrew; Yang, Qingyuan; Fu, Dax; Hura, Greg L; Tainer, John A; Adams, Michael W W

    2014-07-11

    The archaeon Pyrococcus furiosus grows optimally at 100 °C by converting carbohydrates to acetate, CO2, and H2, obtaining energy from a respiratory membrane-bound hydrogenase (MBH). This conserves energy by coupling H2 production to oxidation of reduced ferredoxin with generation of a sodium ion gradient. MBH is encoded by a 14-gene operon with both hydrogenase and Na(+)/H(+) antiporter modules. Herein a His-tagged MBH was expressed in P. furiosus and the detergent-solubilized complex purified under anaerobic conditions by affinity chromatography. Purified MBH contains all 14 subunits by electrophoretic analysis (13 subunits were also identified by mass spectrometry) and had a measured iron:nickel ratio of 15:1, resembling the predicted value of 13:1. The as-purified enzyme exhibited a rhombic EPR signal characteristic of the ready nickel-boron state. The purified and membrane-bound forms of MBH both preferentially evolved H2 with the physiological donor (reduced ferredoxin) as well as with standard dyes. The O2 sensitivities of the two forms were similar (half-lives of ? 15 h in air), but the purified enzyme was more thermolabile (half-lives at 90 °C of 1 and 25 h, respectively). Structural analysis of purified MBH by small angle x-ray scattering indicated a Z-shaped structure with a mass of 310 kDa, resembling the predicted value (298 kDa). The angle x-ray scattering analyses reinforce and extend the conserved sequence relationships of group 4 enzymes and complex I (NADH quinone oxidoreductase). This is the first report on the properties of a solubilized form of an intact respiratory MBH complex that is proposed to evolve H2 and pump Na(+) ions. PMID:24860091

  8. [FeFe]-Hydrogenase Abundance and Diversity along a Vertical Redox Gradient in Great Salt Lake, USA

    PubMed Central

    Boyd, Eric S.; Hamilton, Trinity L.; Swanson, Kevin D.; Howells, Alta E.; Baxter, Bonnie K.; Meuser, Jonathan E.; Posewitz, Matthew C.; Peters, John W.

    2014-01-01

    The use of [FeFe]-hydrogenase enzymes for the biotechnological production of H2 or other reduced products has been limited by their sensitivity to oxygen (O2). Here, we apply a PCR-directed approach to determine the distribution, abundance, and diversity of hydA gene fragments along co-varying salinity and O2 gradients in a vertical water column of Great Salt Lake (GSL), UT. The distribution of hydA was constrained to water column transects that had high salt and relatively low O2 concentrations. Recovered HydA deduced amino acid sequences were enriched in hydrophilic amino acids relative to HydA from less saline environments. In addition, they harbored interesting variations in the amino acid environment of the complex H-cluster metalloenzyme active site and putative gas transfer channels that may be important for both H2 transfer and O2 susceptibility. A phylogenetic framework was created to infer the accessory cluster composition and quaternary structure of recovered HydA protein sequences based on phylogenetic relationships and the gene contexts of known complete HydA sequences. Numerous recovered HydA are predicted to harbor multiple N- and C-terminal accessory iron-sulfur cluster binding domains and are likely to exist as multisubunit complexes. This study indicates an important role for [FeFe]-hydrogenases in the functioning of the GSL ecosystem and provides new target genes and variants for use in identifying O2 tolerant enzymes for biotechnological applications. PMID:25464382

  9. Investigations on the role of proton-coupled electron transfer in hydrogen activation by [FeFe]-hydrogenase.

    PubMed

    Mulder, David W; Ratzloff, Michael W; Bruschi, Maurizio; Greco, Claudio; Koonce, Evangeline; Peters, John W; King, Paul W

    2014-10-29

    Proton-coupled electron transfer (PCET) is a fundamental process at the core of oxidation-reduction reactions for energy conversion. The [FeFe]-hydrogenases catalyze the reversible activation of molecular H2 through a unique metallocofactor, the H-cluster, which is finely tuned by the surrounding protein environment to undergo fast PCET transitions. The correlation of electronic and structural transitions at the H-cluster with proton-transfer (PT) steps has not been well-resolved experimentally. Here, we explore how modification of the conserved PT network via a Cys ? Ser substitution at position 169 proximal to the H-cluster of Chlamydomonas reinhardtii [FeFe]-hydrogenase (CrHydA1) affects the H-cluster using electron paramagnetic resonance (EPR) and Fourier transform infrared (FTIR) spectroscopy. Despite a substantial decrease in catalytic activity, the EPR and FTIR spectra reveal different H-cluster catalytic states under reducing and oxidizing conditions. Under H2 or sodium dithionite reductive treatments, the EPR spectra show signals that are consistent with a reduced [4Fe-4S]H(+) subcluster. The FTIR spectra showed upshifts of ?CO modes to energies that are consistent with an increase in oxidation state of the [2Fe]H subcluster, which was corroborated by DFT analysis. In contrast to the case for wild-type CrHydA1, spectra associated with Hred and Hsred states are less populated in the Cys ? Ser variant, demonstrating that the exchange of -SH with -OH alters how the H-cluster equilibrates among different reduced states of the catalytic cycle under steady-state conditions. PMID:25286239

  10. Direct Comparison of the Performance of a Bio-inspired Synthetic Nickel Catalyst and a [NiFe]-Hydrogenase, Both Covalently Attached to Electrodes.

    PubMed

    Rodriguez-Maciá, Patricia; Dutta, Arnab; Lubitz, Wolfgang; Shaw, Wendy J; Rüdiger, Olaf

    2015-10-12

    The active site of hydrogenases has been a source of inspiration for the development of molecular catalysts. However, direct comparisons between molecular catalysts and enzymes have not been possible because different techniques are used to evaluate both types of catalysts, minimizing our ability to determine how far we have come in mimicking the enzymatic performance. The catalytic properties of the [Ni(P(Cy) 2 N(Gly) 2 )2 ](2+) complex with the [NiFe]-hydrogenase from Desulfovibrio vulgaris immobilized on a functionalized electrode were compared under identical conditions. At pH?7, the enzyme shows higher activity and lower overpotential with better stability, while at low pH, the molecular catalyst outperforms the enzyme in all respects. This is the first direct comparison of enzymes and molecular complexes, enabling a unique understanding of the benefits and detriments of both systems, and advancing our understanding of the utilization of these bio-inspired complexes in fuel cells. PMID:26140506

  11. Crystallization and preliminary X-ray crystallographic analysis of the [NiFe]-hydrogenase maturation factor HypF1 from Ralstonia eutropha H16

    PubMed Central

    Winter, Gordon; Dökel, Simon; Jones, Anne K.; Scheerer, Patrick; Krauss, Norbert; Höhne, Wolfgang; Friedrich, Bärbel

    2010-01-01

    The hydrogenase maturation factor HypF1 is a truncated but functional version of the HypF protein. HypF is known to be involved in the supply of the CN? ligands of the active site of [NiFe]-hydrogenases, utilizing carbamoyl phosphate as a substrate. The first crystallization and preliminary X-ray studies of HypF1 from Ralstonia eutropha H16 are reported here. Crystals of HypF1 (394 amino acids, 40.7?kDa) were obtained by the sitting-drop vapour-diffusion technique using sodium formate as a precipitant. The crystals belonged to space group I222, with unit-cell parameters a = 79.7, b = 91.6, c = 107.2?Å. Complete X-ray diffraction data sets were collected at 100?K from native crystals and from a platinum derivative to a maximum resolution of 1.65?Å. PMID:20383020

  12. Nuclear resonance vibrational spectroscopy reveals the FeS cluster composition and active site vibrational properties of an O2-tolerant NAD+-reducing [NiFe] hydrogenase

    DOE PAGESBeta

    Lauterbach, Lars; Wang, Hongxin; Horch, Marius; Gee, Leland B.; Yoda, Yoshitaka; Tanaka, Yoshihito; Zebger, Ingo; Lenz, Oliver; Cramer, Stephen P.

    2014-10-30

    Hydrogenases are complex metalloenzymes that catalyze the reversible splitting of molecular hydrogen into protons and electrons essentially without overpotential. The NAD+-reducing soluble hydrogenase (SH) from Ralstonia eutropha is capable of H2 conversion even in the presence of usually toxic dioxygen. The molecular details of the underlying reactions are largely unknown, mainly because of limited knowledge of the structure and function of the various metal cofactors present in the enzyme. Here, all iron-containing cofactors of the SH were investigated by 57Fe specific nuclear resonance vibrational spectroscopy (NRVS). Our data provide experimental evidence for one [2Fe2S] center and four [4Fe4S] clusters, whichmore »is consistent with the amino acid sequence composition. Only the [2Fe2S] cluster and one of the four [4Fe4S] clusters were reduced upon incubation of the SH with NADH. This finding explains the discrepancy between the large number of FeS clusters and the small amount of FeS cluster-related signals as detected by electron paramagnetic resonance spectroscopic analysis of several NAD+-reducing hydrogenases. For the first time, Fe–CO and Fe–CN modes derived from the [NiFe] active site could be distinguished by NRVS through selective 13C labeling of the CO ligand. This strategy also revealed the molecular coordinates that dominate the individual Fe–CO modes. The present approach explores the complex vibrational signature of the Fe–S clusters and the hydrogenase active site, thereby showing that NRVS represents a powerful tool for the elucidation of complex biocatalysts containing multiple cofactors.« less

  13. Electronic structure of the unique [4Fe-3S] cluster in O2-tolerant hydrogenases characterized by 57Fe Mössbauer and EPR spectroscopy

    PubMed Central

    Pandelia, Maria-Eirini; Bykov, Dmytro; Izsak, Robert; Infossi, Pascale; Giudici-Orticoni, Marie-Thérèse; Bill, Eckhard; Neese, Frank; Lubitz, Wolfgang

    2013-01-01

    Iron–sulfur clusters are ubiquitous electron transfer cofactors in hydrogenases. Their types and redox properties are important for H2 catalysis, but, recently, their role in a protection mechanism against oxidative inactivation has also been recognized for a [4Fe-3S] cluster in O2-tolerant group 1 [NiFe] hydrogenases. This cluster, which is uniquely coordinated by six cysteines, is situated in the proximity of the catalytic [NiFe] site and exhibits unusual redox versatility. The [4Fe-3S] cluster in hydrogenase (Hase) I from Aquifex aeolicus performs two redox transitions within a very small potential range, forming a superoxidized state above +200 mV vs. standard hydrogen electrode (SHE). Crystallographic data has revealed that this state is stabilized by the coordination of one of the iron atoms to a backbone nitrogen. Thus, the proximal [4Fe-3S] cluster undergoes redox-dependent changes to serve multiple purposes beyond classical electron transfer. In this paper, we present field-dependent 57Fe-Mössbauer and EPR data for Hase I, which, in conjunction with spectroscopically calibrated density functional theory (DFT) calculations, reveal the distribution of Fe valences and spin-coupling schemes for the iron–sulfur clusters. The data demonstrate that the electronic structure of the [4Fe-3S] core in its three oxidation states closely resembles that of corresponding conventional [4Fe-4S] cubanes, albeit with distinct differences for some individual iron sites. The medial and distal iron–sulfur clusters have similar electronic properties as the corresponding cofactors in standard hydrogenases, although their redox potentials are higher. PMID:23267108

  14. Nuclear resonance vibrational spectroscopy reveals the FeS cluster composition and active site vibrational properties of an O2-tolerant NAD+-reducing [NiFe] hydrogenase

    PubMed Central

    Lauterbach, Lars; Wang, Hongxin; Horch, Marius; Gee, Leland B.; Yoda, Yoshitaka; Tanaka, Yoshihito; Zebger, Ingo; Lenz, Oliver; Cramer, Stephen P.

    2015-01-01

    Hydrogenases are complex metalloenzymes that catalyze the reversible splitting of molecular hydrogen into protons and electrons essentially without overpotential. The NAD+-reducing soluble hydrogenase (SH) from Ralstonia eutropha is capable of H2 conversion even in the presence of usually toxic dioxygen. The molecular details of the underlying reactions are largely unknown, mainly because of limited knowledge of the structure and function the various metal cofactors present in the enzyme. Here all iron-containing cofactors of the SH were investigated by 57Fe specific nuclear resonance vibrational spectroscopy (NRVS). Our data provide experimental evidence for one [2Fe2S] center and four [4Fe4S] clusters, which is consistent with amino acid sequence composition. Only the [2Fe2S] cluster and one of the four [4Fe4S] clusters were reduced upon incubation of the SH with NADH. This finding explains the discrepancy between the large number of FeS clusters and the small amount of FeS cluster-related signals as detected by electron paramagnetic resonance spectroscopic analysis of several NAD+-reducing hydrogenases. For the first time, Fe-CO and Fe-CN modes derived from the [NiFe] active site could be distinguished by NRVS through selective 13C labeling of the CO ligand. This strategy also revealed the molecular coordinates that dominate the individual Fe-CO modes. The present approach explores the complex vibrational signature of the Fe-S clusters and the hydrogenase active site, thereby showing that NRVS represents a powerful tool for the elucidation of complex biocatalysts containing multiple cofactors. PMID:25678951

  15. Crystallization and preliminary X-ray crystallographic studies of the [NiFe] hydrogenase maturation proteins HypC and HypD

    SciTech Connect

    Watanabe, Satoshi; Matsumi, Rie; Atomi, Haruyuki; Imanaka, Tadayuki; Miki, Kunio

    2007-06-01

    The [NiFe] hydrogenase maturation proteins HypC and HypD were purified and crystallized. Crystals of HypC and HypD suitable for data collection diffracted to 1.80 and 2.07 Å resolution, respectively. HypC and HypD proteins are required for the insertion of the Fe atom with diatomic ligands into the large subunit of [NiFe] hydrogenases, an important step in the maturation process of this type of hydrogenase. The crystallization and preliminary crystallographic analysis of HypC and HypD from Thermococcus kodakaraensis KOD1 are reported. Crystals of HypC grew in two different forms. Monoclinic crystals of HypC in space group C2 with unit-cell parameters a = 78.2, b = 59.1, c = 54.0 Å, ? = 109.0° were obtained using PEG 4000 and ammonium sulfate or sodium bromide as precipitants. They diffracted X-rays to 1.8 Å resolution and were suitable for structure determination. Crystals of HypD were also obtained in two different forms. The monoclinic crystals obtained using PEG 4000 and magnesium chloride diffracted X-rays to beyond 2.1 Å resolution, despite growing as clusters. They belong to space group P2{sub 1}, with unit-cell parameters a = 42.3, b = 118.4, c = 81.2 Å, ? = 100.9°, and are suitable for data collection.

  16. Identification of an Isothiocyanate on the HypEF Complex Suggests a Route for Efficient Cyanyl–Group Channeling during [NiFe]–Hydrogenase Cofactor Generation

    PubMed Central

    Stripp, Sven T.; Lindenstrauss, Ute; Sawers, R. Gary; Soboh, Basem

    2015-01-01

    [NiFe]–hydrogenases catalyze uptake and evolution of H2 in a wide range of microorganisms. The enzyme is characterized by an inorganic nickel/ iron cofactor, the latter of which carries carbon monoxide and cyanide ligands. In vivo generation of these ligands requires a number of auxiliary proteins, the so–called Hyp family. Initially, HypF binds and activates the precursor metabolite carbamoyl phosphate. HypF catalyzes removal of phosphate and transfers the carbamate group to HypE. In an ATP–dependent condensation reaction, the C–terminal cysteinyl residue of HypE is modified to what has been interpreted as thiocyanate. This group is the direct precursor of the cyanide ligands of the [NiFe]–hydrogenase active site cofactor. We present a FT–IR analysis of HypE and HypF as isolated from E. coli. We follow the HypF–catalyzed cyanation of HypE in vitro and screen for the influence of carbamoyl phosphate and ATP. To elucidate on the differences between HypE and the HypEF complex, spectro–electrochemistry was used to map the vibrational Stark effect of naturally cyanated HypE. The IR signature of HypE could ultimately be assigned to isothiocyanate (–N=C=S) rather than thiocyanate (–S–C?N). This has important implications for cyanyl–group channeling during [NiFe]–hydrogenase cofactor generation. PMID:26186649

  17. Electrochemical and Infrared Spectroscopic Studies Provide Insight into Reactions of the NiFe Regulatory Hydrogenase from Ralstonia eutropha with O2 and CO.

    PubMed

    Ash, Philip A; Liu, Juan; Coutard, Nathan; Heidary, Nina; Horch, Marius; Gudim, Ingvild; Simler, Thomas; Zebger, Ingo; Lenz, Oliver; Vincent, Kylie A

    2015-10-29

    The regulatory hydrogenase (RH) from Ralstonia eutropha acts as the H2-sensing unit of a two-component system that regulates biosynthesis of the energy conserving hydrogenases of the organism according to the availability of H2. The H2 oxidation activity, which was so far determined in vitro with artificial electron acceptors, has been considered to be insensitive to O2 and CO. It is assumed that bulky isoleucine and phenylalanine amino acid residues close to the NiFe active site "gate" gas access, preventing molecules larger than H2 interacting with the active site. We have carried out sensitive electrochemical measurements to demonstrate that O2 is in fact an inhibitor of H2 oxidation by the RH, and that both H(+) reduction and H2 oxidation are inhibited by CO. Furthermore, we have demonstrated that the inhibitory effect of O2 arises due to interaction of O2 with the active site. Using protein film infrared electrochemistry (PFIRE) under H2 oxidation conditions, in conjunction with solution infrared measurements, we have identified previously unreported oxidized inactive and catalytically active reduced states of the RH active site. These findings suggest that the RH has a rich active site chemistry similar to that of other NiFe hydrogenases. PMID:26115011

  18. Computational studies of the H-cluster of Fe-only hydrogenases: geometric, electronic, and magnetic properties and their dependence on the [Fe4S4] cubane.

    PubMed

    Fiedler, Adam T; Brunold, Thomas C

    2005-12-12

    The active sites of Fe-only hydrogenases (FeHases) feature an unusual polynuclear iron-sulfur cluster, known as the H-cluster, that consists of a [Fe4S4] cubane linked to a di-iron subunit (the [2Fe]H component) via a bridging cysteine ligand (SCys). While previous computational studies of FeHases employed H-cluster models that only included the [2Fe]H component, we have utilized density functional theory (DFT), in conjunction with the broken-symmetry (BS) approach, to explore the geometric, electronic, and magnetic properties of the entire H-cluster. These calculations have allowed us to evaluate, for the first time, the influence of the [Fe4S4] cubane on the [2Fe]H component of the H-cluster in its active (Hox) and CO-inhibited (Hox-CO) states, both of which are paramagnetic (S=1/2). Our results reveal that the presence of the cubane tunes both the position and the donor strength of the SCys ligand, which, in turn, modulates the internal geometric and electronic structures of the [2Fe]H subcluster. Importantly, the BS methodology provides an accurate description of the exchange interactions within the H-cluster, permitting insight into the electronic origin of the changes in magnetic properties observed experimentally upon conversion of Hox to Hox-CO. Specifically, while the unpaired spin density in the Hox state is localized on the distal Fe center, in the Hox-CO state, it is delocalized over the [2Fe]H component, such that the proximal Fe center acquires significant spin density (where distal and proximal refer to the positions of the Fe centers relative to the cubane). To validate our H-cluster models on the basis of experimental data, two DFT-based approaches and the semiempirical INDO/S method have been employed to compute electron paramagnetic resonance parameters for the H-cluster states. While most computations yield reasonably accurate g values and ligand hyperfine coupling constants (i.e., A values) for the Hox and Hox-CO states, they fail to reproduce the isotropic 57Fe A tensors found experimentally. Finally, extension of the computational methodology employed successfully for the Hox and Hox-CO states to the metastable Hoxphoto state, generated by irradiation of the Hox-CO state at cryogenic temperatures, has allowed us to discriminate between proposed structural models for this species. PMID:16323916

  19. Bis[1,2-bis-(eth-oxy-carbon-yl)ethene-1,2-dithiol-ato-?(2) S,S']bis-(?(5)-penta-methyl-cyclo-penta-dien-yl)tetra-?3-sulfido-diiron(IV)diiron(III)(3 Fe-Fe).

    PubMed

    Ito, Shohei; Hisamichi, Nozomu; Takase, Tsugiko; Inomata, Shinji

    2013-04-01

    The title compound, [Fe4(C10H15)2(C8H10O4S2)2S4], contains a twisted Fe4S4 cubane-like core. A twofold rotation axis passes through the Fe4S4 core, completing the coordination of the four Fe atoms with two penta-methyl-cyclo-penta-dienyl ligands and two chelating dithiol-ate ligands. There are three short Fe-Fe and three long Fe?Fe contacts in the Fe4S4 core, suggesting bonding and non-bonding inter-actions, respectively. The Fe-S bonds in the Fe4S4 core range from 2.1523?(5) to 2.2667?(6)?Å and are somewhat longer than the Fe-S bonds involving the dithiol-ate ligand. PMID:23633986

  20. Fractionation of Sulfur Isotopes by Desulfovibrio vulgaris Mutants Lacking Periplasmic Hydrogenases or the Type I Tetraheme Cytochrome c3

    NASA Astrophysics Data System (ADS)

    Sim, M.; Ono, S.; Bosak, T.

    2012-12-01

    A large fraction of anaerobic mineralization of organic compounds relies on microbial sulfate reduction. Sulfur isotope fractionation by these microbes has been widely used to trace the biogeochemical cycling of sulfur and carbon, but intracellular mechanisms behind the wide range of fractionations observed in nature and cultures are not fully understood. In this study, we investigated the influence of electron transport chain components on the fractionation of sulfur isotopes by culturing Desulfovibrio vulgaris Hildenborough mutants lacking hydrogenases or type I tetraheme cytochrome c3 (Tp1-c3). The mutants were grown both in batch and continuous cultures. All tested mutants grew on lactate or pyruvate as the sole carbon and energy sources, generating sulfide. Mutants lacking cytoplasmic and periplasmic hydrogenases exhibited similar growth physiologies and sulfur isotope fractionations to their parent strains. On the other hand, a mutant lacking Tp1-c3 (?cycA) fractionated the 34S/32S ratio more than the wild type, evolving H2 in the headspace and exhibiting a lower specific respiration rate. In the presence of high concentrations of pyruvate, the growth of ?cycA relied largely on fermentation rather than sulfate reduction, even when sulfate was abundant, producing the largest sulfur isotope effect observed in this study. Differences between sulfur isotope fractionation by ?cycA and the wild type highlight the effect of electron transfer chains on the magnitude of sulfur isotope fractionation. Because Tp1-c3 is known to exclusively shuttle electrons from periplasmic hydrogenases to transmembrane complexes, electron transfers in the absence of Tp1-c3 should bypass the periplasmic hydrogen cycling, and the loss of reducing equivalents in the form of H2 can impair the flow of electrons from organic acids to sulfur, increasing isotope fractionation. Larger fractionation by ?cycA can inform interpretations of sulfur isotope data at an environmental scale as well, because intracellular concentrations of electron transport components can be altered by environmental factors such as iron availability. Simultaneous sulfate reduction and fermentation, and their corresponding sulfur isotope effects, also generate a hypothesis that links sulfur isotope fractionation to the cellular energy budget. Theoretically, the largest fractionation during microbial sulfate reduction occurs when the backward fluxes equal the forward fluxes in sulfate reduction pathway. However, when the generation of ATP depends exclusively on sulfate respiration, a minimum respiration rate is required to fulfill the maintenance energy requirement. In contrast, when sulfate reduction occurs simultaneously with fermentation, the latter process may contribute toward maintenance energy, enabling slower and more reversible sulfate reduction, and leading to larger fractionation. Given that many sulfate-reducing microbes are also facultative fermenters, fermentation by sulfate reducing microbes in natural habitats and sulfur isotope signatures produced by such communities deserve further exploration.

  1. Solar powered biohydrogen production requires specific localization of the hydrogenase† †Electronic supplementary information (ESI) available: Supplementary Fig. 1–12 and supplementary Table 1. See DOI: 10.1039/c4ee02502d Click here for additional data file.

    PubMed Central

    Burroughs, Nigel J.; Boehm, Marko; Eckert, Carrie; Mastroianni, Giulia; Spence, Edward M.; Yu, Jianfeng; Nixon, Peter J.; Appel, Jens; Mullineaux, Conrad W.

    2014-01-01

    Cyanobacteria contain a bidirectional [NiFe] hydrogenase which transiently produces hydrogen upon exposure of anoxic cells to light, potentially acting as a “valve” releasing excess electrons from the electron transport chain. However, its interaction with the photosynthetic electron transport chain remains unclear. By GFP-tagging the HoxF diaphorase subunit we show that the hydrogenase is thylakoid associated, comprising a population dispersed uniformly through the thylakoids and a subpopulation localized to discrete puncta in the distal thylakoid. Thylakoid localisation of both the HoxH and HoxY hydrogenase subunits is confirmed by immunogold electron microscopy. The diaphorase HoxE subunit is essential for recruitment to the dispersed thylakoid population, potentially anchoring the hydrogenase to the membrane, but aggregation to puncta occurs through a distinct HoxE-independent mechanism. Membrane association does not require NDH-1. Localization is dynamic on a scale of minutes, with anoxia and high light inducing a significant redistribution between these populations in favour of puncta. Since HoxE is essential for access to its electron donor, electron supply to the hydrogenase depends on a physiologically controlled localization, potentially offering a new avenue to enhance photosynthetic hydrogen production by exploiting localization/aggregation signals. PMID:26339289

  2. Control of the transition between Ni-C and Ni-SI(a) states by the redox state of the proximal Fe-S cluster in the catalytic cycle of [NiFe] hydrogenase.

    PubMed

    Tai, Hulin; Nishikawa, Koji; Suzuki, Masayuki; Higuchi, Yoshiki; Hirota, Shun

    2014-12-01

    [NiFe] hydrogenase catalyzes the reversible cleavage of H2. The electrons produced by the H2 cleavage pass through three Fe-S clusters in [NiFe] hydrogenase to its redox partner. It has been reported that the Ni-SI(a), Ni-C, and Ni-R states of [NiFe] hydrogenase are involved in the catalytic cycle, although the mechanism and regulation of the transition between the Ni-C and Ni-SI(a) states remain unrevealed. In this study, the FT-IR spectra under light irradiation at 138-198?K show that the Ni-L state of [NiFe] hydrogenase is an intermediate between the transition of the Ni-C and Ni-SI(a) states. The transition of the Ni-C state to the Ni-SI(a) state occurred when the proximal [Fe4S4]p(2+/+) cluster was oxidized, but not when it was reduced. These results show that the catalytic cycle of [NiFe] hydrogenase is controlled by the redox state of its [Fe4S4]p(2+/+) cluster, which may function as a gate for the electron flow from the NiFe active site to the redox partner. PMID:25297065

  3. Structure of [NiFe] hydrogenase maturation protein HypE from Escherichia coli and its interaction with HypF.

    PubMed

    Rangarajan, Erumbi S; Asinas, Abdalin; Proteau, Ariane; Munger, Christine; Baardsnes, Jason; Iannuzzi, Pietro; Matte, Allan; Cygler, Miroslaw

    2008-02-01

    Hydrogenases are enzymes involved in hydrogen metabolism, utilizing H2 as an electron source. [NiFe] hydrogenases are heterodimeric Fe-S proteins, with a large subunit containing the reaction center involving Fe and Ni metal ions and a small subunit containing one or more Fe-S clusters. Maturation of the [NiFe] hydrogenase involves assembly of nonproteinaceous ligands on the large subunit by accessory proteins encoded by the hyp operon. HypE is an essential accessory protein and participates in the synthesis of two cyano groups found in the large subunit. We report the crystal structure of Escherichia coli HypE at 2.0-A resolution. HypE exhibits a fold similar to that of PurM and ThiL and forms dimers. The C-terminal catalytically essential Cys336 is internalized at the dimer interface between the N- and C-terminal domains. A mechanism for dehydration of the thiocarbamate to the thiocyanate is proposed, involving Asp83 and Glu272. The interactions of HypE and HypF were characterized in detail by surface plasmon resonance and isothermal titration calorimetry, revealing a Kd (dissociation constant) of approximately 400 nM. The stoichiometry and molecular weights of the complex were verified by size exclusion chromatography and gel scanning densitometry. These experiments reveal that HypE and HypF associate to form a stoichiometric, hetero-oligomeric complex predominantly consisting of a [EF]2 heterotetramer which exists in a dynamic equilibrium with the EF heterodimer. The surface plasmon resonance results indicate that a conformational change occurs upon heterodimerization which facilitates formation of a productive complex as part of the carbamate transfer reaction. PMID:18065529

  4. Structure of [NiFe] Hydrogenase Maturation Protein HypE from Escherichia coli and its Interaction with HypF

    SciTech Connect

    Rangarajan,E.; Asinas, A.; Proteau, A.; Munger, C.; Baardsnes, j.; Iannuzzi, P.; Matte, A.; Cygler, m.

    2008-01-01

    Hydrogenases are enzymes involved in hydrogen metabolism, utilizing H2 as an electron source. [NiFe] hydrogenases are heterodimeric Fe-S proteins, with a large subunit containing the reaction center involving Fe and Ni metal ions and a small subunit containing one or more Fe-S clusters. Maturation of the [NiFe] hydrogenase involves assembly of nonproteinaceous ligands on the large subunit by accessory proteins encoded by the hyp operon. HypE is an essential accessory protein and participates in the synthesis of two cyano groups found in the large subunit. We report the crystal structure of Escherichia coli HypE at 2.0- Angstroms resolution. HypE exhibits a fold similar to that of PurM and ThiL and forms dimers. The C-terminal catalytically essential Cys336 is internalized at the dimer interface between the N- and C-terminal domains. A mechanism for dehydration of the thiocarbamate to the thiocyanate is proposed, involving Asp83 and Glu272. The interactions of HypE and HypF were characterized in detail by surface plasmon resonance and isothermal titration calorimetry, revealing a Kd (dissociation constant) of {approx}400 nM. The stoichiometry and molecular weights of the complex were verified by size exclusion chromatography and gel scanning densitometry. These experiments reveal that HypE and HypF associate to form a stoichiometric, hetero-oligomeric complex predominantly consisting of a [EF]2 heterotetramer which exists in a dynamic equilibrium with the EF heterodimer. The surface plasmon resonance results indicate that a conformational change occurs upon heterodimerization which facilitates formation of a productive complex as part of the carbamate transfer reaction.

  5. Expression of Uptake Hydrogenase and Molybdenum Nitrogenase in Rhodobacter capsulatus Is Coregulated by the RegB-RegA Two-Component Regulatory System

    PubMed Central

    Elsen, Sylvie; Dischert, Wanda; Colbeau, Annette; Bauer, Carl E.

    2000-01-01

    Purple photosynthetic bacteria are capable of generating cellular energy from several sources, including photosynthesis, respiration, and H2 oxidation. Under nutrient-limiting conditions, cellular energy can be used to assimilate carbon and nitrogen. This study provides the first evidence of a molecular link for the coregulation of nitrogenase and hydrogenase biosynthesis in an anoxygenic photosynthetic bacterium. We demonstrated that molybdenum nitrogenase biosynthesis is under the control of the RegB-RegA two-component regulatory system in Rhodobacter capsulatus. Footprint analyses and in vivo transcription studies showed that RegA indirectly activates nitrogenase synthesis by binding to and activating the expression of nifA2, which encodes one of the two functional copies of the nif-specific transcriptional activator, NifA. Expression of nifA2 but not nifA1 is reduced in the reg mutants up to eightfold under derepressing conditions and is also reduced under repressing conditions. Thus, although NtrC is absolutely required for nifA2 expression, RegA acts as a coactivator of nifA2. We also demonstrated that in reg mutants, [NiFe]hydrogenase synthesis and activity are increased up to sixfold. RegA binds to the promoter of the hydrogenase gene operon and therefore directly represses its expression. Thus, the RegB-RegA system controls such diverse processes as energy-generating photosynthesis and H2 oxidation, as well as the energy-demanding processes of N2 fixation and CO2 assimilation. PMID:10781552

  6. Reduction of unusual iron-sulfur clusters in the H2-sensing regulatory Ni-Fe hydrogenase from Ralstonia eutropha H16.

    PubMed

    Buhrke, Thorsten; Löscher, Simone; Lenz, Oliver; Schlodder, Eberhard; Zebger, Ingo; Andersen, Lars K; Hildebrandt, Peter; Meyer-Klaucke, Wolfram; Dau, Holger; Friedrich, Bärbel; Haumann, Michael

    2005-05-20

    The regulatory Ni-Fe hydrogenase (RH) from Ralstonia eutropha functions as a hydrogen sensor. The RH consists of the large subunit HoxC housing the Ni-Fe active site and the small subunit HoxB containing Fe-S clusters. The heterolytic cleavage of H(2) at the Ni-Fe active site leads to the EPR-detectable Ni-C state of the protein. For the first time, the simultaneous but EPR-invisible reduction of Fe-S clusters during Ni-C state formation was demonstrated by changes in the UV-visible absorption spectrum as well as by shifts of the iron K-edge from x-ray absorption spectroscopy in the wild-type double dimeric RH(WT) [HoxBC](2) and in a monodimeric derivative designated RH(stop) lacking the C-terminal 55 amino acids of HoxB. According to the analysis of iron EXAFS spectra, the Fe-S clusters of HoxB pronouncedly differ from the three Fe-S clusters in the small subunits of crystallized standard Ni-Fe hydrogenases. Each HoxBC unit of RH(WT) seems to harbor two [2Fe-2S] clusters in addition to a 4Fe species, which may be a [4Fe-3S-3O] cluster. The additional 4Fe-cluster was absent in RH(stop). Reduction of Fe-S clusters in the hydrogen sensor RH may be a first step in the signal transduction chain, which involves complex formation between [HoxBC](2) and tetrameric HoxJ protein, leading to the expression of the energy converting Ni-Fe hydrogenases in R. eutropha. PMID:15764814

  7. Structural studies of the carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F: suggestion for the initial activation site for dihydrogen.

    PubMed

    Ogata, Hideaki; Mizoguchi, Yasutaka; Mizuno, Nobuhiro; Miki, Kunio; Adachi, Shin-ichi; Yasuoka, Noritake; Yagi, Tatsuhiko; Yamauchi, Osamu; Hirota, Shun; Higuchi, Yoshiki

    2002-10-01

    The carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F has been characterized by X-ray crystallography and absorption and resonance Raman spectroscopy. Nine crystal structures of the [NiFe]hydrogenase in the CO-bound and CO-liberated forms were determined at 1.2-1.4 A resolution. The exogenously added CO was assigned to be bound to the Ni atom at the Ni-Fe active site. The CO was not replaced with H(2) in the dark at 100 K, but was liberated by illumination with a strong white light. The Ni-C distances and Ni-C-O angles were about 1.77 A and 160 degrees, respectively, except for one case (1.72 A and 135 degrees ), in which an additional electron density peak between the CO and Sgamma(Cys546) was recognized. Distinct changes were observed in the electron density distribution of the Ni and Sgamma(Cys546) atoms between the CO-bound and CO-liberated structures for all the crystals tested. The novel structural features found near the Ni and Sgamma(Cys546) atoms suggest that these two atoms at the Ni-Fe active site play a role during the initial H(2)-binding process. Anaerobic addition of CO to dithionite-reduced [NiFe]hydrogenase led to a new absorption band at about 470 nm ( approximately 3000 M(-1)cm(-1)). Resonance Raman spectra (excitation at 476.5 nm) of the CO complex revealed CO-isotope-sensitive bands at 375/393 and 430 cm(-1) (368 and 413 cm(-1) for (13)C(18)O). The frequencies and relative intensities of the CO-related Raman bands indicated that the exogenous CO is bound to the Ni atom with a bent Ni-C-O structure in solution, in agreement with the refined structure determined by X-ray crystallography. PMID:12296727

  8. Impact of membrane-associated hydrogenases on the F?F?-ATPase in Escherichia coli during glycerol and mixed carbon fermentation: ATPase activity and its inhibition by N,N'-dicyclohexylcarbodiimide in the mutants lacking hydrogenases.

    PubMed

    Blbulyan, Syuzanna; Trchounian, Armen

    2015-08-01

    Escherichia coli is able to ferment glycerol and to produce molecular hydrogen (H2) by four membrane-associated hydrogenases (Hyd) changing activity in response to different conditions. In this study, overall ATPase activity of glycerol alone and mixed carbon sources (glucose and glycerol) fermented E. coli wild type and different Hyd mutants and its inhibition by N,N'-dicyclohexylcarbodiimide (DCCD) were first investigated. ATPase activity was higher in glycerol fermented wild type cells at pH 7.5 compared to pH 6.5 and pH 5.5; DCCD inhibited markedly ATPase activity at pH 7.5. The ATPase activity at pH 7.5, compared with wild type, was lower in selC and less in hypF single mutants, suppressed in hyaB hybC selC triple mutant. Moreover, total ATPase activity of mixed carbon fermented wild type cells was maximal at pH 7.5 and lowered at pH 5.5. The ATPase activities of hypF and hyaB hybC selC mutants were higher at pH 5.5, compared with wild type; DCCD inhibited markedly ATPase activity of hypF mutant. These results demonstrate that in E. coli during glycerol fermentation the membrane proton-translocating FOF1-ATPase has major input in overall ATPase activity and alkaline pH is more optimal for the FOF1-ATPase operation. Hyd-1 and Hyd-2 are required for the FOF1-ATPase activity upon anaerobic fermentation of glycerol. The impact of Hyd-1 and Hyd-2 on the FOF1-ATPase is more obvious during mixed carbon fermentation at slightly acidic pH. PMID:26049001

  9. Characterization of Photochemical Processes for H2 Production by CdS Nanorod-[FeFe] Hydrogenase Complexes

    SciTech Connect

    Brown, K. A.; Wilker, M. B.; Boehm, M.; Dukovic, G.; King, P. W.

    2012-03-28

    We have developed complexes of CdS nanorods capped with 3-mercaptopropionic acid (MPA) and Clostridium acetobutylicum [FeFe]-hydrogenase I (CaI) that photocatalyze reduction of H{sup +} to H{sub 2} at a CaI turnover frequency of 380-900 s{sup -1} and photon conversion efficiencies of up to 20% under illumination at 405 nm. In this paper, we focus on the compositional and mechanistic aspects of CdS:CaI complexes that control the photochemical conversion of solar energy into H{sub 2}. Self-assembly of CdS with CaI was driven by electrostatics, demonstrated as the inhibition of ferredoxin-mediated H{sub 2} evolution by CaI. Production of H{sub 2} by CdS:CaI was observed only under illumination and only in the presence of a sacrificial donor. We explored the effects of the CdS:CaI molar ratio, sacrificial donor concentration, and light intensity on photocatalytic H{sub 2} production, which were interpreted on the basis of contributions to electron transfer, hole transfer, or rate of photon absorption, respectively. Each parameter was found to have pronounced effects on the CdS:CaI photocatalytic activity. Specifically, we found that under 405 nm light at an intensity equivalent to total AM 1.5 solar flux, H{sub 2} production was limited by the rate of photon absorption ({approx}1 ms{sup -1}) and not by the turnover of CaI. Complexes were capable of H{sub 2} production for up to 4 h with a total turnover number of 106 before photocatalytic activity was lost. This loss correlated with inactivation of CaI, resulting from the photo-oxidation of the CdS capping ligand MPA.

  10. Synthetic analogues of [Fe4S4(Cys)3(His)] in hydrogenases and [Fe4S4(Cys)4] in HiPIP derived from all-ferric [Fe4S4{N(SiMe3)2}4].

    PubMed

    Ohki, Yasuhiro; Tanifuji, Kazuki; Yamada, Norihiro; Imada, Motosuke; Tajima, Tomoyuki; Tatsumi, Kazuyuki

    2011-08-01

    The all-ferric [Fe(4)S(4)](4+) cluster [Fe(4)S(4){N(SiMe(3))(2)}(4)] 1 and its one-electron reduced form [1](-) serve as convenient precursors for the synthesis of 31-site differentiated [Fe(4)S(4)] clusters and high-potential iron-sulfur protein (HiPIP) model clusters. The reaction of 1 with four equivalents (equiv) of the bulky thiol HSDmp (Dmp = 2,6-(mesityl)(2)C(6)H(3), mesityl = 2,4,6-Me(3)C(6)H(2)) followed by treatment with tetrahydrofuran (THF) resulted in the isolation of [Fe(4)S(4)(SDmp)(3)(THF)(3)] 2. Cluster 2 contains an octahedral iron atom with three THF ligands, and its Fe(S)(3)(O)(3) coordination environment is relevant to that in the active site of substrate-bound aconitase. An analogous reaction of [1](-) with four equiv of HSDmp gave [Fe(4)S(4)(SDmp)(4)](-) 3, which models the oxidized form of HiPIP. The THF ligands in 2 can be replaced by tetramethyl-imidazole (Me(4)Im) to give [Fe(4)S(4)(SDmp)(3)(Me(4)Im)] 4 modeling the [Fe(4)S(4)(Cys)(3)(His)] cluster in hydrogenases, and its one-electron reduced form [4](-) was synthesized from the reaction of 3 with Me(4)Im. The reversible redox couple between 3 and [3](-) was observed at E(1/2) = -820 mV vs. Ag/Ag(+), and the corresponding reversible couple for 4 and [4](-) is positively shifted by +440 mV. The cyclic voltammogram of 3 also exhibited a reversible oxidation couple, which indicates generation of the all-ferric [Fe(4)S(4)](4+) cluster, [Fe(4)S(4)(SDmp)(4)]. PMID:21768339

  11. Hydrogen bioelectrooxidation on gold nanoparticle-based electrodes modified by Aquifex aeolicus hydrogenase: Application to hydrogen/oxygen enzymatic biofuel cells.

    PubMed

    Monsalve, Karen; Roger, Magali; Gutierrez-Sanchez, Cristina; Ilbert, Marianne; Nitsche, Serge; Byrne-Kodjabachian, Deborah; Marchi, Valérie; Lojou, Elisabeth

    2015-12-01

    For the first time, gold nanoparticle-based electrodes have been used as platforms for efficient immobilization of the [NiFe] hydrogenase from the hyperthermophilic bacterium Aquifex aeolicus. AuNPs were characterized by electronic microscopy, dynamic light scattering and UV-Vis spectroscopy. Two sizes around 20.0±5.3 nm and 37.2±4.3 nm nm were synthesized. After thiol-based functionalization, the AuNPs were proved to allow direct H2 oxidation over a large range of temperatures. A high current density up to 1.85±0.15 mA·cm(-2) was reached at the smallest AuNPs, which is 170 times higher than the one recorded at the bare gold electrode. The catalytic current was especially studied as a function of the AuNP size and amount, and procedure for deposition. A synergetic effect between the AuNP porous deposit and the increase surface area was shown. Compared to previously used nanomaterials such as carbon nanofibers, the covalent grafting of the enzyme on the thiol-modified gold nanoparticles was shown to enhance the stability of the hydrogenase. This bioanode was finally coupled to a biocathode where BOD from Myrothecium verrucaria was immobilized on AuNP-based film. The performance of the so-mounted H2/O2 biofuel cell was evaluated, and a power density of 0.25 mW·cm(-2) was recorded. PMID:25960259

  12. A strenuous experimental journey searching for spectroscopic evidence of a bridging nickel-iron-hydride in [NiFe] hydrogenase.

    PubMed

    Wang, Hongxin; Yoda, Yoshitaka; Ogata, Hideaki; Tanaka, Yoshihito; Lubitz, Wolfgang

    2015-11-01

    Direct spectroscopic evidence for a hydride bridge in the Ni-R form of [NiFe] hydrogenase has been obtained using iron-specific nuclear resonance vibrational spectroscopy (NRVS). The Ni-H-Fe wag mode at 675?cm(-1) is the first spectroscopic evidence for a bridging hydride in Ni-R as well as the first iron-hydride-related NRVS feature observed for a biological system. Although density function theory (DFT) calculation assisted the determination of the Ni-R structure, it did not predict the Ni-H-Fe wag mode at ?675?cm(-1) before NRVS. Instead, the observed Ni-H-Fe mode provided a critical reference for the DFT calculations. While the overall science about Ni-R is presented and discussed elsewhere, this article focuses on the long and strenuous experimental journey to search for and experimentally identify the Ni-H-Fe wag mode in a Ni-R sample. As a methodology, the results presented here will go beyond Ni-R and hydrogenase research and will also be of interest to other scientists who use synchrotron radiation for measuring dilute samples or weak spectroscopic features. PMID:26524296

  13. Contributions of the [NiFe]- and [FeFe]-hydrogenase to H2 production in Shewanella oneidensis MR-1 as revealed by isotope ratio analysis of evolved H2

    SciTech Connect

    Kreuzer, Helen W.; Hill, Eric A.; Moran, James J.; Bartholomew, Rachel A.; Hui, Yang; Hegg, Eric L.

    2014-03-01

    Shewanella oneidensis MR-1 encodes both a [NiFe]- and an [FeFe]-hydrogenase. While the output of these proteins has been characterized in mutant strains expressing only one of the enzymes, the contribution of each to H2 synthesis in the wild-type organism is not clear. Here we use stable isotope analysis of H2 in the culture headspace, along with transcription data and measurements of the concentrations of gases in the headspace, to characterize H2 production in the wild-type strain. After most of the O2 in the headspace had been consumed, H2 was produced and then consumed by the bidirectional [NiFe]-hydrogenase. Once the cultures were completely anaerobic, a new burst of H2 synthesis catalyzed by both enzymes took place. Our data is consistent with the hypothesis that at this point in the culture cycle, a pool of electrons is shunted toward both hydrogenases in the wild-type organism, but that in the absence of one of the hydrogenases, the flux is redirected to the available enzyme. To our knowledge, this is the first use of stable isotope analysis of a metabolic product to elucidate substrate flux through two alternative enzymes in the same cellular system.

  14. Genome Data Mining and Soil Survey for the Novel Group 5 [NiFe]-Hydrogenase To Explore the Diversity and Ecological Importance of Presumptive High-Affinity H2-Oxidizing Bacteria ?†

    PubMed Central

    Constant, Philippe; Chowdhury, Soumitra Paul; Hesse, Laura; Pratscher, Jennifer; Conrad, Ralf

    2011-01-01

    Streptomyces soil isolates exhibiting the unique ability to oxidize atmospheric H2 possess genes specifying a putative high-affinity [NiFe]-hydrogenase. This study was undertaken to explore the taxonomic diversity and the ecological importance of this novel functional group. We propose to designate the genes encoding the small and large subunits of the putative high-affinity hydrogenase hhyS and hhyL, respectively. Genome data mining revealed that the hhyL gene is unevenly distributed in the phyla Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria. The hhyL gene sequences comprised a phylogenetically distinct group, namely, the group 5 [NiFe]-hydrogenase genes. The presumptive high-affinity H2-oxidizing bacteria constituting group 5 were shown to possess a hydrogenase gene cluster, including the genes encoding auxiliary and structural components of the enzyme and four additional open reading frames (ORFs) of unknown function. A soil survey confirmed that both high-affinity H2 oxidation activity and the hhyL gene are ubiquitous. A quantitative PCR assay revealed that soil contained 106 to 108 hhyL gene copies g (dry weight)?1. Assuming one hhyL gene copy per genome, the abundance of presumptive high-affinity H2-oxidizing bacteria was higher than the maximal population size for which maintenance energy requirements would be fully supplied through the H2 oxidation activity measured in soil. Our data indicate that the abundance of the hhyL gene should not be taken as a reliable proxy for the uptake of atmospheric H2 by soil, because high-affinity H2 oxidation is a facultatively mixotrophic metabolism, and microorganisms harboring a nonfunctional group 5 [NiFe]-hydrogenase may occur. PMID:21742924

  15. NADP-Specific Electron-Bifurcating [FeFe]-Hydrogenase in a Functional Complex with Formate Dehydrogenase in Clostridium autoethanogenum Grown on CO

    PubMed Central

    Wang, Shuning; Huang, Haiyan; Kahnt, Jörg; Mueller, Alexander P.; Köpke, Michael

    2013-01-01

    Flavin-based electron bifurcation is a recently discovered mechanism of coupling endergonic to exergonic redox reactions in the cytoplasm of anaerobic bacteria and archaea. Among the five electron-bifurcating enzyme complexes characterized to date, one is a heteromeric ferredoxin- and NAD-dependent [FeFe]-hydrogenase. We report here a novel electron-bifurcating [FeFe]-hydrogenase that is NADP rather than NAD specific and forms a complex with a formate dehydrogenase. The complex was found in high concentrations (6% of the cytoplasmic proteins) in the acetogenic Clostridium autoethanogenum autotrophically grown on CO, which was fermented to acetate, ethanol, and 2,3-butanediol. The purified complex was composed of seven different subunits. As predicted from the sequence of the encoding clustered genes (fdhA/hytA-E) and from chemical analyses, the 78.8-kDa subunit (FdhA) is a selenocysteine- and tungsten-containing formate dehydrogenase, the 65.5-kDa subunit (HytB) is an iron-sulfur flavin mononucleotide protein harboring the NADP binding site, the 51.4-kDa subunit (HytA) is the [FeFe]-hydrogenase proper, and the 18.1-kDa (HytC), 28.6-kDa (HytD), 19.9-kDa (HytE1), and 20.1-kDa (HytE2) subunits are iron-sulfur proteins. The complex catalyzed both the reversible coupled reduction of ferredoxin and NADP+ with H2 or formate and the reversible formation of H2 and CO2 from formate. We propose the complex to have two functions in vivo, namely, to normally catalyze CO2 reduction to formate with NADPH and reduced ferredoxin in the Wood-Ljungdahl pathway and to catalyze H2 formation from NADPH and reduced ferredoxin when these redox mediators get too reduced during unbalanced growth of C. autoethanogenum on CO (E0? = ?520 mV). PMID:23893107

  16. Bis[1,2-bis-(meth-oxy-carbon-yl)ethene-1,2-dithiol-ato-?(2) S,S']bis-(?(5)-penta-methyl-cyclo-penta-dien-yl)tetra-?3-sulfido-tetra-iron(4 Fe-Fe) hexa-fluoridophosphate.

    PubMed

    Inomata, Shinji; Ito, Shohei; Takase, Tsugiko

    2013-04-01

    The asymmetric unit of the title compound, [Fe4(C6H6O4S2)2(C10H15)2S4]PF6, contains two different complex cations and two PF6 (-) anions. The two complex cations have similar conformations with the butterfly-like Fe4S4 core surrounded by two penta-methyl-cyclo-penta-dienyl ligands and the S atoms of two dithiol-ate ligands. In each Fe4S4 core, there are four short Fe-Fe and two long Fe?Fe contacts, suggesting bonding and non-bonding inter-actions, respectively. The Fe-S distances range from 2.1287?(13) to 2.2706?(16)?Å for one and from 2.1233?(13) to 2.2650?(16)?Å for the other Fe4S4 core. The Fe-S distances involving the dithiol-ate ligands are in a more narrow range [2.1764?(16)-2.1874?(13)?Å for one and 2.1743?(14)-2.1779?(16)?Å for the other cation]. There are no significant inter-actions between cations and anions. PMID:23634019

  17. Designing interfaces of hydrogenase-nanomaterial hybrids for efficient solar conversion.

    PubMed

    King, Paul W

    2013-01-01

    The direct conversion of sunlight into biofuels is an intriguing alternative to a continued reliance on fossil fuels. Natural photosynthesis has long been investigated both as a potential solution, and as a model for utilizing solar energy to drive a water-to-fuel cycle. The molecules and organizational structure provide a template to inspire the design of efficient molecular systems for photocatalysis. A clear design strategy is the coordination of molecular interactions that match kinetic rates and energetic levels to control the direction and flow of energy from light harvesting to catalysis. Energy transduction and electron-transfer reactions occur through interfaces formed between complexes of donor-acceptor molecules. Although the structures of several of the key biological complexes have been solved, detailed descriptions of many electron-transfer complexes are lacking, which presents a challenge to designing and engineering biomolecular systems for solar conversion. Alternatively, it is possible to couple the catalytic power of biological enzymes to light harvesting by semiconductor nanomaterials. In these molecules, surface chemistry and structure can be designed using ligands. The passivation effect of the ligand can also dramatically affect the photophysical properties of the semiconductor, and energetics of external charge-transfer. The length, degree of bond saturation (aromaticity), and solvent exposed functional groups of ligands can be manipulated to further tune the interface to control molecular assembly, and complex stability in photocatalytic hybrids. The results of this research show how ligand selection is critical to designing molecular interfaces that promote efficient self-assembly, charge-transfer and photocatalysis. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems. PMID:23541891

  18. Hydrogen production at high Faradaic efficiency by a bio-electrode based on TiO2 adsorption of a new [FeFe]-hydrogenase from Clostridium perfringens.

    PubMed

    Morra, Simone; Valetti, Francesca; Sarasso, Veronica; Castrignanò, Silvia; Sadeghi, Sheila J; Gilardi, Gianfranco

    2015-12-01

    The [FeFe]-hydrogenase CpHydA from Clostridium perfringens was immobilized by adsorption on anatase TiO2 electrodes for clean hydrogen production. The immobilized enzyme proved to perform direct electron transfer to and from the electrode surface and catalyses both H2 oxidation (H2 uptake) and H2 production (H2 evolution) with a current density for H2 evolution of about 2 mA cm(-1). The TiO2/CpHydA bioelectrode remained active for several days upon storage and when a reducing potential was set, H2 evolution occurred with a mean Faradaic efficiency of 98%. The high turnover frequency of H2 production and the tight coupling of electron transfer, resulting in a Faradaic efficiency close to 100%, support the exploitation of the novel TiO2/CpHydA stationary electrode as a powerful device for H2 production. PMID:26278509

  19. Transcriptional regulation of genes encoding the selenium-free [NiFe]-hydrogenases in the archaeon Methanococcus voltae involves positive and negative control elements.

    PubMed Central

    Noll, I; Müller, S; Klein, A

    1999-01-01

    Methanococcus voltae harbors genetic information for two pairs of homologous [NiFe]-hydrogenases. Two of the enzymes contain selenocysteine, while the other two gene groups encode apparent isoenzymes that carry cysteinyl residues in the homologous positions. The genes coding for the selenium-free enzymes, frc and vhc, are expressed only under selenium limitation. They are transcribed out of a common intergenic region. A series of deletions made in the intergenic region localized a common negative regulatory element for the vhc and frc promoters as well as two activator elements that are specific for each of the two transcription units. Repeated sequences, partially overlapping the frc promoter, were also detected. Mutations in these repeated heptanucleotide sequences led to a weak induction of a reporter gene under the control of the frc promoters in the presence of selenium. This result suggests that the heptamer repeats contribute to the negative regulation of the frc transcription unit. PMID:10430564

  20. Physiology and bioenergetics of [NiFe]-hydrogenase 2-catalyzed H2-consuming and H2-producing reactions in Escherichia coli.

    PubMed

    Pinske, Constanze; Jaroschinsky, Monique; Linek, Sabine; Kelly, Ciarán L; Sargent, Frank; Sawers, R Gary

    2015-01-01

    Escherichia coli uptake hydrogenase 2 (Hyd-2) catalyzes the reversible oxidation of H2 to protons and electrons. Hyd-2 synthesis is strongly upregulated during growth on glycerol or on glycerol-fumarate. Membrane-associated Hyd-2 is an unusual heterotetrameric [NiFe]-hydrogenase that lacks a typical cytochrome b membrane anchor subunit, which transfers electrons to the quinone pool. Instead, Hyd-2 has an additional electron transfer subunit, termed HybA, with four predicted iron-sulfur clusters. Here, we examined the physiological role of the HybA subunit. During respiratory growth with glycerol and fumarate, Hyd-2 used menaquinone/demethylmenaquinone (MQ/DMQ) to couple hydrogen oxidation to fumarate reduction. HybA was essential for electron transfer from Hyd-2 to MQ/DMQ. H2 evolution catalyzed by Hyd-2 during fermentation of glycerol in the presence of Casamino Acids or in a fumarate reductase-negative strain growing with glycerol-fumarate was also shown to be dependent on both HybA and MQ/DMQ. The uncoupler carbonyl cyanide m-chlorophenylhydrazone (CCCP) inhibited Hyd-2-dependent H2 evolution from glycerol, indicating the requirement for a proton gradient. In contrast, CCCP failed to inhibit H2-coupled fumarate reduction. Although a Hyd-2 enzyme lacking HybA could not catalyze Hyd-2-dependent H2 oxidation or H2 evolution in whole cells, reversible H2-dependent reduction of viologen dyes still occurred. Finally, hydrogen-dependent dye reduction by Hyd-2 was reversibly inhibited in extracts derived from cells grown in H2 evolution mode. Our findings suggest that Hyd-2 switches between H2-consuming and H2-producing modes in response to the redox status of the quinone pool. Hyd-2-dependent H2 evolution from glycerol requires reverse electron transport. PMID:25368299

  1. Structural Basis for the Reaction Mechanism of S-Carbamoylation of HypE by HypF in the Maturation of [NiFe]-Hydrogenases*

    PubMed Central

    Shomura, Yasuhito; Higuchi, Yoshiki

    2012-01-01

    As a remarkable structural feature of hydrogenase active sites, [NiFe]-hydrogenases harbor one carbonyl and two cyano ligands, where HypE and HypF are involved in the biosynthesis of the nitrile group as a precursor of the cyano groups. HypF catalyzes S-carbamoylation of the C-terminal cysteine of HypE via three steps using carbamoylphosphate and ATP, producing two unstable intermediates: carbamate and carbamoyladenylate. Although the crystal structures of intact HypE homodimers and partial HypF have been reported, it remains unclear how the consecutive reactions occur without the loss of unstable intermediates during the proposed reaction scheme. Here we report the crystal structures of full-length HypF both alone and in complex with HypE at resolutions of 2.0 and 2.6 ?, respectively. Three catalytic sites of the structures of the HypF nucleotide- and phosphate-bound forms have been identified, with each site connected via channels inside the protein. This finding suggests that the first two consecutive reactions occur without the release of carbamate or carbamoyladenylate from the enzyme. The structure of HypF in complex with HypE revealed that HypF can associate with HypE without disturbing its homodimeric interaction and that the binding manner allows the C-terminal Cys-351 of HypE to access the S-carbamoylation active site in HypF, suggesting that the third step can also proceed without the release of carbamoyladenylate. A comparison of the structure of HypF with the recently reported structures of O-carbamoyltransferase revealed different reaction mechanisms for carbamoyladenylate synthesis and a similar reaction mechanism for carbamoyltransfer to produce the carbamoyl-HypE molecule. PMID:22740694

  2. Structural basis for the reaction mechanism of S-carbamoylation of HypE by HypF in the maturation of [NiFe]-hydrogenases.

    PubMed

    Shomura, Yasuhito; Higuchi, Yoshiki

    2012-08-17

    As a remarkable structural feature of hydrogenase active sites, [NiFe]-hydrogenases harbor one carbonyl and two cyano ligands, where HypE and HypF are involved in the biosynthesis of the nitrile group as a precursor of the cyano groups. HypF catalyzes S-carbamoylation of the C-terminal cysteine of HypE via three steps using carbamoylphosphate and ATP, producing two unstable intermediates: carbamate and carbamoyladenylate. Although the crystal structures of intact HypE homodimers and partial HypF have been reported, it remains unclear how the consecutive reactions occur without the loss of unstable intermediates during the proposed reaction scheme. Here we report the crystal structures of full-length HypF both alone and in complex with HypE at resolutions of 2.0 and 2.6 ?, respectively. Three catalytic sites of the structures of the HypF nucleotide- and phosphate-bound forms have been identified, with each site connected via channels inside the protein. This finding suggests that the first two consecutive reactions occur without the release of carbamate or carbamoyladenylate from the enzyme. The structure of HypF in complex with HypE revealed that HypF can associate with HypE without disturbing its homodimeric interaction and that the binding manner allows the C-terminal Cys-351 of HypE to access the S-carbamoylation active site in HypF, suggesting that the third step can also proceed without the release of carbamoyladenylate. A comparison of the structure of HypF with the recently reported structures of O-carbamoyltransferase revealed different reaction mechanisms for carbamoyladenylate synthesis and a similar reaction mechanism for carbamoyltransfer to produce the carbamoyl-HypE molecule. PMID:22740694

  3. Structural basis for a [4Fe-3S] cluster in the oxygen-tolerant membrane-bound [NiFe]-hydrogenase.

    PubMed

    Shomura, Yasuhito; Yoon, Ki-Seok; Nishihara, Hirofumi; Higuchi, Yoshiki

    2011-11-10

    Membrane-bound respiratory [NiFe]-hydrogenase (MBH), a H(2)-uptake enzyme found in the periplasmic space of bacteria, catalyses the oxidation of dihydrogen: H(2)???2H(+)?+?2e(-) (ref. 1). In contrast to the well-studied O(2)-sensitive [NiFe]-hydrogenases (referred to as the standard enzymes), MBH has an O(2)-tolerant H(2) oxidation activity; however, the mechanism of O(2) tolerance is unclear. Here we report the crystal structures of Hydrogenovibrio marinus MBH in three different redox conditions at resolutions between 1.18 and 1.32?Å. We find that the proximal iron-sulphur (Fe-S) cluster of MBH has a [4Fe-3S] structure coordinated by six cysteine residues--in contrast to the [4Fe-4S] cubane structure coordinated by four cysteine residues found in the proximal Fe-S cluster of the standard enzymes--and that an amide nitrogen of the polypeptide backbone is deprotonated and additionally coordinates the cluster when chemically oxidized, thus stabilizing the superoxidized state of the cluster. The structure of MBH is very similar to that of the O(2)-sensitive standard enzymes except for the proximal Fe-S cluster. Our results give a reasonable explanation why the O(2) tolerance of MBH is attributable to the unique proximal Fe-S cluster; we propose that the cluster is not only a component of the electron transfer for the catalytic cycle, but that it also donates two electrons and one proton crucial for the appropriate reduction of O(2) in preventing the formation of an unready, inactive state of the enzyme. PMID:22002607

  4. Structural basis of a Ni acquisition cycle for [NiFe] hydrogenase by Ni-metallochaperone HypA and its enhancer

    PubMed Central

    Watanabe, Satoshi; Kawashima, Takumi; Nishitani, Yuichi; Kanai, Tamotsu; Wada, Takehiko; Inaba, Kenji; Atomi, Haruyuki; Imanaka, Tadayuki; Miki, Kunio

    2015-01-01

    The Ni atom at the catalytic center of [NiFe] hydrogenases is incorporated by a Ni-metallochaperone, HypA, and a GTPase/ATPase, HypB. We report the crystal structures of the transient complex formed between HypA and ATPase-type HypB (HypBAT) with Ni ions. Transient association between HypA and HypBAT is controlled by the ATP hydrolysis cycle of HypBAT, which is accelerated by HypA. Only the ATP-bound form of HypBAT can interact with HypA and induces drastic conformational changes of HypA. Consequently, upon complex formation, a conserved His residue of HypA comes close to the N-terminal conserved motif of HypA and forms a Ni-binding site, to which a Ni ion is bound with a nearly square-planar geometry. The Ni binding site in the HypABAT complex has a nanomolar affinity (Kd = 7 nM), which is in contrast to the micromolar affinity (Kd = 4 µM) observed with the isolated HypA. The ATP hydrolysis and Ni binding cause conformational changes of HypBAT, affecting its association with HypA. These findings indicate that HypA and HypBAT constitute an ATP-dependent Ni acquisition cycle for [NiFe]-hydrogenase maturation, wherein HypBAT functions as a metallochaperone enhancer and considerably increases the Ni-binding affinity of HypA. PMID:26056269

  5. X-ray crystallographic and EPR spectroscopic analysis of HydG, a maturase in [FeFe]-hydrogenase H-cluster assembly

    PubMed Central

    Dinis, Pedro; Suess, Daniel L. M.; Fox, Stephen J.; Harmer, Jenny E.; Driesener, Rebecca C.; De La Paz, Liliana; Swartz, James R.; Essex, Jonathan W.; Britt, R. David; Roach, Peter L.

    2015-01-01

    Hydrogenases use complex metal cofactors to catalyze the reversible formation of hydrogen. In [FeFe]-hydrogenases, the H-cluster cofactor includes a diiron subcluster containing azadithiolate, three CO, and two CN? ligands. During the assembly of the H cluster, the radical S-adenosyl methionine (SAM) enzyme HydG lyses the substrate tyrosine to yield the diatomic ligands. These diatomic products form an enzyme-bound Fe(CO)x(CN)y synthon that serves as a precursor for eventual H-cluster assembly. To further elucidate the mechanism of this complex reaction, we report the crystal structure and EPR analysis of HydG. At one end of the HydG (??)8 triosephosphate isomerase (TIM) barrel, a canonical [4Fe-4S] cluster binds SAM in close proximity to the proposed tyrosine binding site. At the opposite end of the active-site cavity, the structure reveals the auxiliary Fe-S cluster in two states: one monomer contains a [4Fe-5S] cluster, and the other monomer contains a [5Fe-5S] cluster consisting of a [4Fe-4S] cubane bridged by a ?2-sulfide ion to a mononuclear Fe2+ center. This fifth iron is held in place by a single highly conserved protein-derived ligand: histidine 265. EPR analysis confirms the presence of the [5Fe-5S] cluster, which on incubation with cyanide, undergoes loss of the labile iron to yield a [4Fe-4S] cluster. We hypothesize that the labile iron of the [5Fe-5S] cluster is the site of Fe(CO)x(CN)y synthon formation and that the limited bonding between this iron and HydG may facilitate transfer of the intact synthon to its cognate acceptor for subsequent H-cluster assembly. PMID:25605932

  6. Relationship between Ni(II) and Zn(II) Coordination and Nucleotide Binding by the Helicobacter pylori [NiFe]-Hydrogenase and Urease Maturation Factor HypB*

    PubMed Central

    Sydor, Andrew M.; Lebrette, Hugo; Ariyakumaran, Rishikesh; Cavazza, Christine; Zamble, Deborah B.

    2014-01-01

    The pathogen Helicobacter pylori requires two nickel-containing enzymes, urease and [NiFe]-hydrogenase, for efficient colonization of the human gastric mucosa. These enzymes possess complex metallocenters that are assembled by teams of proteins in multistep pathways. One essential accessory protein is the GTPase HypB, which is required for Ni(II) delivery to [NiFe]-hydrogenase and participates in urease maturation. Ni(II) or Zn(II) binding to a site embedded in the GTPase domain of HypB modulates the enzymatic activity, suggesting a mechanism of regulation. In this study, biochemical and structural analyses of H. pylori HypB (HpHypB) revealed an intricate link between nucleotide and metal binding. HpHypB nickel coordination, stoichiometry, and affinity were modulated by GTP and GDP, an effect not observed for zinc, and biochemical evidence suggests that His-107 coordination to nickel toggles on and off in a nucleotide-dependent manner. These results are consistent with the crystal structure of HpHypB loaded with Ni(II), GDP, and Pi, which reveals a nickel site distinct from that of zinc-loaded Methanocaldococcus jannaschii HypB as well as subtle changes to the protein structure. Furthermore, Cys-142, a metal ligand from the Switch II GTPase motif, was identified as a key component of the signal transduction between metal binding and the enzymatic activity. Finally, potassium accelerated the enzymatic activity of HpHypB but had no effect on the other biochemical properties of the protein. Altogether, this molecular level information about HpHypB provides insight into its cellular function and illuminates a possible mechanism of metal ion discrimination. PMID:24338018

  7. Effect of Secondary Interactions on the Fundamental Properties of Small Molecule Models of the Diiron Hydrogenase Active Site 

    E-print Network

    Singleton, Michael Lee

    2012-02-14

    mixed-valent FeIFeII complexes. An X-ray crystal structure of one of these complexes, (?-SCH2C(CH3)2CH2S-)[Fe(CO)2PMe3]2PF6 shows both a semi-bridging carbonyl and an open site similar to the 2-Fe subsite in the Hox state of the enzyme active site...

  8. A reversible proton relay process mediated by hydrogen-bonding interactions in [FeFe]hydrogenase modeling.

    PubMed

    Chu, Kai-Ti; Liu, Yu-Chiao; Huang, Yi-Lan; Hsu, Cheng-Huey; Lee, Gene-Hsiang; Chiang, Ming-Hsi

    2015-07-27

    A reversible and temperature-dependent proton-relay process is demonstrated for a Fe2 complex possessing a terminal thiolate in the presence of nitrogen-based acids. The terminal sulfur site (S(t) ) of the complex forms a hydrogen-bond interaction with N,N-dimethylanilinium acid at 183?K. The Fe2 core, instead, is protonated to generate a bridging hydride at 298?K. Reversibility is observed for the tautomerization between the hydrogen-bonded pair and the Fe-hydride species. X-ray structural analysis of the hydrogen-bonded species at 193?K reveals a short N(H)???S(t) contact. Employment of pyridinium acid also results in similar behavior, with reversible proton-hydride interconversion. DFT investigation of the proton-transfer pathways indicates that the pKa value of the hydrogen-bonded species is enhanced by 3.2 pKa units when the temperature is decreased from 298?K to 183?K. PMID:26118674

  9. Borane-Protected Cyanides as Surrogates of H-Bonded Cyanides in [FeFe]-Hydrogenase Active Site Models

    PubMed Central

    Manor, Brian C.; Ringenberg, Mark R.; Rauchfuss, Thomas B.

    2015-01-01

    Triarylborane Lewis acids bind [Fe2(pdt)-(CO)4(CN)2]2? (pdt2? = 1,3-propanedithiolate) and [Fe2(adt)(CO)4(CN)2]2? [3]2? (adt2? = 1,3-azadithiolate, HN(CH2S?)2) to give the 2:1 adducts [Fe2(xdt)-(CO)4(CNBAr3)2]2?. Attempts to prepare the 1:1 adducts [1(BAr3)]2? (Ar = Ph, C6F5) were unsuccessful, but related 1:1 adducts were obtained using the bulky borane B(C6F4-o-C6F5)3 (BArF*3). By virtue of the N-protection by the borane, salts of [Fe2(pdt)(CO)4(CNBAr3)2]2? sustain protonation to give hydrides that are stable (in contrast to [H1]?). The hydrides [H1(BAr3)2]? are 2.5–5 pKa units more acidic than the parent [H1]?. The adducts [1(BAr3)2]2? oxidize quasi-reversibly around ?0.3 V versus Fc0/+ in contrast to ca. ?0.8 V observed for the [1]2?/? couple. A simplified synthesis of [1]2?, [3]2?, and [Fe2(pdt)(CO)5(CN)]? ([2]?) was developed, entailing reaction of the diiron hexacarbonyl complexes with KCN in MeCN. PMID:24992155

  10. Multiple-Timescale Photoreactivity of a Model Compound Related to the Active Site of [FeFe]-Hydrogenase

    E-print Network

    Strathclyde, University of

    Versity of East Anglia, Norwich NR4 7TJ, U.K., Max Born Institut fuer Nichtlineare Optik and Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany, and Department of Chemistry, UniVersity College London

  11. Nuclear resonance vibrational spectroscopy reveals the FeS cluster composition and active site vibrational properties of an O2-tolerant NAD+-reducing [NiFe] hydrogenase

    SciTech Connect

    Lauterbach, Lars; Wang, Hongxin; Horch, Marius; Gee, Leland B.; Yoda, Yoshitaka; Tanaka, Yoshihito; Zebger, Ingo; Lenz, Oliver; Cramer, Stephen P.

    2014-10-30

    Hydrogenases are complex metalloenzymes that catalyze the reversible splitting of molecular hydrogen into protons and electrons essentially without overpotential. The NAD+-reducing soluble hydrogenase (SH) from Ralstonia eutropha is capable of H2 conversion even in the presence of usually toxic dioxygen. The molecular details of the underlying reactions are largely unknown, mainly because of limited knowledge of the structure and function of the various metal cofactors present in the enzyme. Here, all iron-containing cofactors of the SH were investigated by 57Fe specific nuclear resonance vibrational spectroscopy (NRVS). Our data provide experimental evidence for one [2Fe2S] center and four [4Fe4S] clusters, which is consistent with the amino acid sequence composition. Only the [2Fe2S] cluster and one of the four [4Fe4S] clusters were reduced upon incubation of the SH with NADH. This finding explains the discrepancy between the large number of FeS clusters and the small amount of FeS cluster-related signals as detected by electron paramagnetic resonance spectroscopic analysis of several NAD+-reducing hydrogenases. For the first time, Fe–CO and Fe–CN modes derived from the [NiFe] active site could be distinguished by NRVS through selective 13C labeling of the CO ligand. This strategy also revealed the molecular coordinates that dominate the individual Fe–CO modes. The present approach explores the complex vibrational signature of the Fe–S clusters and the hydrogenase active site, thereby showing that NRVS represents a powerful tool for the elucidation of complex biocatalysts containing multiple cofactors.

  12. An Innovative Cloning Platform Enables Large-Scale Production and Maturation of an Oxygen-Tolerant [NiFe]-Hydrogenase from Cupriavidus necator in Escherichia coli

    PubMed Central

    Schiffels, Johannes; Pinkenburg, Olaf; Schelden, Maximilian; Aboulnaga, El-Hussiny A. A.; Baumann, Marcus E. M.; Selmer, Thorsten

    2013-01-01

    Expression of multiple heterologous genes in a dedicated host is a prerequisite for approaches in synthetic biology, spanning from the production of recombinant multiprotein complexes to the transfer of tailor-made metabolic pathways. Such attempts are often exacerbated, due in most cases to a lack of proper directional, robust and readily accessible genetic tools. Here, we introduce an innovative system for cloning and expression of multiple genes in Escherichia coli BL21 (DE3). Using the novel methodology, genes are equipped with individual promoters and terminators and subsequently assembled. The resulting multiple gene cassettes may either be placed in one vector or alternatively distributed among a set of compatible plasmids. We demonstrate the effectiveness of the developed tool by production and maturation of the NAD+reducing soluble [NiFe]-hydrogenase (SH) from Cupriavidus necator H16 (formerly Ralstonia eutropha H16) in E. coli BL21Star™ (DE3). The SH (encoded in hoxFUYHI) was successfully matured by co-expression of a dedicated set of auxiliary genes, comprising seven hyp genes (hypC1D1E1A2B2F2X) along with hoxW, which encodes a specific endopeptidase. Deletion of genes involved in SH maturation reduced maturation efficiency substantially. Further addition of hoxN1, encoding a high-affinity nickel permease from C. necator, considerably increased maturation efficiency in E. coli. Carefully balanced growth conditions enabled hydrogenase production at high cell-densities, scoring mg·(Liter culture)?1 yields of purified functional SH. Specific activities of up to 7.2±1.15 U·mg?1 were obtained in cell-free extracts, which is in the range of the highest activities ever determined in C. necator extracts. The recombinant enzyme was isolated in equal purity and stability as previously achieved with the native form, yielding ultrapure preparations with anaerobic specific activities of up to 230 U·mg?1. Owing to the combinatorial power exhibited by the presented cloning platform, the system might represent an important step towards new routes in synthetic biology. PMID:23861944

  13. Polarized potential and electrode materials implication on electro-fermentative di-hydrogen production: Microbial assemblages and hydrogenase gene copy variation.

    PubMed

    Arunasri, Kotakonda; Annie Modestra, J; Yeruva, Dileep Kumar; Vamshi Krishna, K; Venkata Mohan, S

    2016-01-01

    This study examined the changes in microbial diversity in response to different electrode materials viz., stainless steel mesh (SS) and graphite plate as anodes in two microbial electrolysis cell (MEC) each poised at 0.2V, 0.4V, 0.6V and 0.8V. Changes in microbiota prior to and after pretreatment along with microbiota enriched in response to various poised potentials with SS and graphite are monitored by 16S rRNA gene based DGGE profiling. Significant shifts in microbial community were noticed at all these experimental conditions. Correspondingly, the level of hydrogenase belonging to genera Bacillus, Pseudomonas, Rhodopseudomonas and Clostridium was studied by quantitative real time PCR (RT-PCR) at various applied potentials. DGGE based 16S rRNA gene profiling revealed enriched members belonging to phylum Firmicutes predominantly present at 0.8V in both MECs contributing to high hydrogen production. This study first time explored the growth behavior of mixed consortia in response to poised potentials and electrode materials. PMID:26556403

  14. Investigating the Role of the Outer-Coordination Sphere in [Ni(PPh2NPh-R2)2]2+ Hydrogenase Mimics

    SciTech Connect

    Jain, Avijita; Reback, Matthew L.; Lindstrom, Mary L.; Thogerson, Colleen E.; Helm, Monte L.; Appel, Aaron M.; Shaw, Wendy J.

    2012-06-18

    A series of dipeptide nickel complexes with the general formula, [Ni(PPh2NNNA-amino acid/ester2)2](BF4)2, have been synthesized and characterized (P2N2= 1,5-diaza-3,7-diphosphacyclooctane, amino acid/esters = glutamic acid, alanine, lysine, and aspartic acid). Each of these complexes is an efficient electrocatalyst for H2 production. The contribution of the outer-coordination sphere, specifically the impact of sterics, the ability to protonate and the pKa of amino acid side chain on the hydrogen production activity of these complexes, was investigated. The rates of all of the catalysts ranged over an order of magnitude. The amino acid containing complexes display 2-3 times higher rates of hydrogen production than the corresponding ester complexes, suggesting the significance of protonated species (side chains/backbone of amino acids) in the outer-coordination sphere. The largest had the fastest rates suggesting that catalytic activity is not hindered by sterics. However, the shapes of catalytic waves are indicative of hindered electron transfer and may suggest a competing mechanism for catalysis than that observed for the unsubstituted parent complex. These studies demonstrate the significant contribution that the outer-coordination sphere can have in tuning the catalytic activity of small molecule hydrogenase mimics.

  15. Hydrogen Photoproduction by Immobilized N2-Fixing Cyanobacteria: Understanding the Role of the Uptake Hydrogenase in the Long-Term Process

    PubMed Central

    Kosourov, Sergey; Leino, Hannu; Murukesan, Gayathri; Lynch, Fiona; Sivonen, Kaarina; Tsygankov, Anatoly A.; Aro, Eva-Mari

    2014-01-01

    We have investigated two approaches to enhance and extend H2 photoproduction yields in heterocystous, N2-fixing cyanobacteria entrapped in thin alginate films. In the first approach, periodic CO2 supplementation was provided to alginate-entrapped, N-deprived cells. N deprivation led to the inhibition of photosynthetic activity in vegetative cells and the attenuation of H2 production over time. Our results demonstrated that alginate-entrapped ?hupL cells were considerably more sensitive to high light intensity, N deficiency, and imbalances in C/N ratios than wild-type cells. In the second approach, Anabaena strain PCC 7120, its ?hupL mutant, and Calothrix strain 336/3 films were supplemented with N2 by periodic treatments of air, or air plus CO2. These treatments restored the photosynthetic activity of the cells and led to a high level of H2 production in Calothrix 336/3 and ?hupL cells (except for the treatment air plus CO2) but not in the Anabaena PCC 7120 strain (for which H2 yields did not change after air treatments). The highest H2 yield was obtained by the air treatment of ?hupL cells. Notably, the supplementation of CO2 under an air atmosphere led to prominent symptoms of N deficiency in the ?hupL strain but not in the wild-type strain. We propose that uptake hydrogenase activity in heterocystous cyanobacteria not only supports nitrogenase activity by removing excess O2 from heterocysts but also indirectly protects the photosynthetic apparatus of vegetative cells from photoinhibition, especially under stressful conditions that cause an imbalance in the C/N ratio in cells. PMID:25015894

  16. Pd(II)-Directed Encapsulation of Hydrogenase within the Layer-by-Layer Multilayers of Carbon Nanotube Polyelectrolyte Used as a Heterogeneous Catalyst for Oxidation of Hydrogen.

    PubMed

    Liu, Jiang; Zorin, Nikolay A; Chen, Meng; Qian, Dong-Jin

    2015-06-16

    A metal-directed assembling approach has been developed to encapsulate hydrogenase (H2ase) within a layer-by-layer (LBL) multilayer of carbon nanotube polyelectrolyte (MWNT-PVPMe), which showed efficient biocatalytic oxidation of H2 gas. The MWNT-PVPMe was prepared via a diazonium process and addition reactions with poly(4-vinylpyridine) (PVP) and methyl iodide (MeI). The covalently attached polymers and organic substituents in the polyelectrolyte comprised 60-70% of the total weight. The polyelectrolyte was then used as a substrate for H2ase binding to produce MWNT-PVPMe@H2ase bionanocomposites. X-ray photoelectron spectra revealed that the bionanocomposites included the elements of Br, S, C, N, O, I, Fe, and Ni, which confirmed that they were composed of MWNT-PVPMe and H2ase. Field emission transmission electron microscope images revealed that the H2ase was adsorbed on the surface of MWNT-PVPMe with the domains ranging from 20 to 40 nm. Further, with the use of the bionanocomposites as nanolinkers and Na2PdCl4 as connectors, the (Pd/MWNT-PVPMe@H2ase)n multilayers were constructed on the quartz and gold substrate surfaces by the Pd(II)-directed LBL assembling technique. Finally, the as-prepared LBL multilayers were used as heterogeneous catalysts for hydrogen oxidation with methyl viologen (MV(2+)) as an electron carrier. The dynamic processes for the reversible color change between blue-colored MV(+) and colorless MV(2+) (catalyzed by the LBL multilayers) were video recorded, which confirmed that the H2ase encapsulated within the present LBL multilayers was of much stronger stability and higher biocatalytic activity of H2 oxidation resulting in potential applications for the development of H2 biosensors and fuel cells. PMID:26010012

  17. Probing the Solvent Accessibility of the [4Fe-4S] Cluster of the Hydrogenase Maturation Protein HydF from Thermotoga neapolitana by HYSCORE and 3p-ESEEM.

    PubMed

    Albertini, Marco; Berto, Paola; Vallese, Francesca; Di Valentin, Marilena; Costantini, Paola; Carbonera, Donatella

    2015-10-29

    The catalytic site of [FeFe]-hydrogenase, the "H-cluster", composed of a [4Fe-4S] unit connected by a cysteinyl residue to a [2Fe] center coordinated by three CO, two CN(-), and a bridging dithiolate, is assembled in a complex maturation pathway, at present not fully characterized, involving three conserved proteins, HydG, HydE, and HydF. HydF is a complex enzyme, which is thought to act as a scaffold and carrier for the [2Fe] subunit of the H-cluster. This maturase protein contains itself a [4Fe-4S] cluster binding site, with three conserved cysteine residues and a noncysteinyl fourth ligand. In this work, we have exploited 3p-ESEEM and HYSCORE spectroscopies to get insight into the structure and the chemical environment of the [4Fe-4S] cluster of HydF from the hyperthermophilic organism Thermotoga neapolitana. The nature of the fourth ligand and the solvent accessibility of the active site comprising the [4Fe-4S] cluster are discussed on the basis of the spectroscopic results obtained upon H/D exchange. We propose that the noncysteinyl ligated Fe atom of the [4Fe-4S] cluster is the site where the [2Fe] subcluster precursor is anchored and finally processed to be delivered to the hydrogenase (HydA). PMID:25978307

  18. Electronic Structure and Chemistry of Iron-Based Metal Oxide Nanostructured Materials: A NEXAFS Investigation of BiFeO3, Bi2Fe4O9, ?-Fe2O3, ?-Fe2O3, and Fe/Fe3O4

    SciTech Connect

    Park,T.; Sambasivan, S.; Fischer, D.; Yoon, W.; Misewich, J.; Wong, S.

    2008-01-01

    We present a systematic and detailed near edge X-ray absorption fine structure (NEXAFS) experimental investigation of the electronic structure and chemistry of iron-based metal oxide nanostructured (FeMONS) materials including BiFeO3, Bi2Fe4O9, a-Fe2O3, ?-Fe2O3, and Fe/Fe3O4. Correlations of the electronic structure and structural chemistry of these intriguing nanomaterials are presented, ranging from the nano to the bulk scale. In this work, variations in the shape, position, and intensity of the O K-edge and Fe L-edge NEXAFS spectra have been analyzed in terms of electronic structure and surface chemistry of the FeMONS materials as compared with that of the bulk. We hypothesize that surface imperfection and surface strain anisotropies in nanoparticles induce distortion and site inequivalency of the oxygen Oh sites around the Fe ion located close to the surface, resulting in an increase in the degree of multiplicity as well as in nonstoichiometric effects in FeMONS materials.

  19. Binding of Iron(III) to Organic Soils: Exafs Spectroscopy And Chemical Equilibrium Modeling

    SciTech Connect

    Gustafsson, J.P.; Persson, I.; Kleja, D.B.; Schaik, J.W.J.van

    2007-07-09

    The complexation of iron(III) to soil organic matter is important for the binding of trace metals in natural environments because of competition effects. In this study, we used extended X-ray absorption fine structure (EXAFS) spectroscopy to characterize the binding mode for iron(III) in two soil samples from organic mor layers, one of which was also treated with iron(III). In most cases the EXAFS spectra had three significant contributions, inner-core Fe-O/N interactions at about 2.02(2) angstroms, Fe-C interactions in the second scattering shell at 3.00(4) angstroms, and a mean Fe-Fe distance at 3.37(3) angstroms. One untreated sample showed features typical for iron (hydr)oxides; however, after treatment of iron(III) the EXAFS spectrum was dominated by organically complexed iron. The presence of a Fe-Fe distance in all samples showed that the major part of the organically complexed iron was hydrolyzed, most likely in a mixture of complexes with an inner core of (O{sub 5}Fe){sub 2}O and (O{sub 5}Fe){sub 3}O. These results were used to constrain a model for metal-humic complexation, the Stockholm Humic Model (SHM). The model was able to describe iron(III) binding very well at low pH considering only one dimeric iron(III)-humic complex. The competition effect on trace metals was also well described.

  20. A computational library for multiscale modeling of material failure

    NASA Astrophysics Data System (ADS)

    Talebi, Hossein; Silani, Mohammad; Bordas, Stéphane P. A.; Kerfriden, Pierre; Rabczuk, Timon

    2014-05-01

    We present an open-source software framework called PERMIX for multiscale modeling and simulation of fracture in solids. The framework is an object oriented open-source effort written primarily in Fortran 2003 standard with Fortran/C++ interfaces to a number of other libraries such as LAMMPS, ABAQUS, LS-DYNA and GMSH. Fracture on the continuum level is modeled by the extended finite element method (XFEM). Using several novel or state of the art methods, the piece software handles semi-concurrent multiscale methods as well as concurrent multiscale methods for fracture, coupling two continuum domains or atomistic domains to continuum domains, respectively. The efficiency of our open-source software is shown through several simulations including a 3D crack modeling in clay nanocomposites, a semi-concurrent FE-FE coupling, a 3D Arlequin multiscale example and an MD-XFEM coupling for dynamic crack propagation.

  1. Resonance Raman Spectroscopic Analysis of the [NiFe] Active Site and the Proximal [4Fe-3S] Cluster of an O2-Tolerant Membrane-Bound Hydrogenase in the Crystalline State.

    PubMed

    Siebert, Elisabeth; Rippers, Yvonne; Frielingsdorf, Stefan; Fritsch, Johannes; Schmidt, Andrea; Kalms, Jacqueline; Katz, Sagie; Lenz, Oliver; Scheerer, Patrick; Paasche, Lars; Pelmenschikov, Vladimir; Kuhlmann, Uwe; Mroginski, Maria Andrea; Zebger, Ingo; Hildebrandt, Peter

    2015-10-29

    We have applied resonance Raman (RR) spectroscopy on single protein crystals of the O2-tolerant membrane-bound [NiFe] hydrogenase (MBH from Ralstonia eutropha) which catalyzes the splitting of H2 into protons and electrons. RR spectra taken from 65 MBH samples in different redox states were analyzed in terms of the respective component spectra of the active site and the unprecedented proximal [4Fe-3S] cluster using a combination of statistical methods and global fitting procedures. These component spectra of the individual cofactors were compared with calculated spectra obtained by quantum mechanics/molecular mechanics (QM/MM) methods. Thus, the recently discovered hydroxyl-coordination of one iron in the [4Fe-3S] cluster was confirmed. Infrared (IR) microscopy of oxidized MBH crystals revealed the [NiFe] active site to be in the Nir-B [Ni(III)] and Nir-S [Ni(II)] states, whereas RR measurements of these crystals uncovered the Nia-S [Ni(II)] state as the main spectral component, suggesting its in situ formation via photodissociation of the assumed bridging hydroxyl or water ligand. On the basis of QM/MM calculations, individual band frequencies could be correlated with structural parameters for the Nia-S state as well as for the Ni-L state, which is formed upon photodissociation of the bridging hydride of H2-reduced active site states. PMID:26201814

  2. The effect of a C298D mutation in CaHydA [FeFe]-hydrogenase: Insights into the protein-metal cluster interaction by EPR and FTIR spectroscopic investigation.

    PubMed

    Morra, Simone; Maurelli, Sara; Chiesa, Mario; Mulder, David W; Ratzloff, Michael W; Giamello, Elio; King, Paul W; Gilardi, Gianfranco; Valetti, Francesca

    2016-01-01

    A conserved cysteine located in the signature motif of the catalytic center (H-cluster) of [FeFe]-hydrogenases functions in proton transfer. This residue corresponds to C298 in Clostridium acetobutylicum CaHydA. Despite the chemical and structural difference, the mutant C298D retains fast catalytic activity, while replacement with any other amino acid causes significant activity loss. Given the proximity of C298 to the H-cluster, the effect of the C298D mutation on the catalytic center was studied by continuous wave (CW) and pulse electron paramagnetic resonance (EPR) and by Fourier transform infrared (FTIR) spectroscopies. Comparison of the C298D mutant with the wild type CaHydA by CW and pulse EPR showed that the electronic structure of the center is not altered. FTIR spectroscopy confirmed that absorption peak values observed in the mutant are virtually identical to those observed in the wild type, indicating that the H-cluster is not generally affected by the mutation. Significant differences were observed only in the inhibited state Hox-CO: the vibrational modes assigned to the COexo and Fed-CO in this state are shifted to lower values in C298D, suggesting different interaction of these ligands with the protein moiety when C298 is changed to D298. More relevant to the catalytic cycle, the redox equilibrium between the Hox and Hred states is modified by the mutation, causing a prevalence of the oxidized state. This work highlights how the interactions between the protein environment and the H-cluster, a dynamic closely interconnected system, can be engineered and studied in the perspective of designing bio-inspired catalysts and mimics. PMID:26482707

  3. Fe-Mn alloys: A mixed-bond spin-1/2 Ising model version

    NASA Astrophysics Data System (ADS)

    Freitas, A. S.; de Albuquerque, Douglas F.; Moreno, N. O.

    2014-06-01

    In this work, we apply the mixed-bond spin-1/2 Ising model to study the magnetic properties of Fe-Mn alloys in the ? phase by employing the effective field theory (EFT). Here, we suggest a new approach to the ferromagnetic coupling between nearest neighbours Fe-Fe that depends on the ratio between the Mn-Mn coupling and the Fe-Mn coupling and of second power of the Mn concentration q in contrast to linear dependence considered in the other articles. Also, we propose a new probability distribution for binary alloys with mixed-bonds based on the distribution for ternary alloys and we obtain a very good agreement for all considered values of q in T-q plane, in particular for q>0.11.

  4. Modelling the Thermal History of Asteroid 4 Vesta

    NASA Technical Reports Server (NTRS)

    Solano, James M.; Kiefer, W. S.; Mittlefehldt, D. W.

    2012-01-01

    The asteroid 4 Vesta is widely thought to be the source of the HED (Howardite, Eucrite and Diogenite) meteorites, with this link supported by spectroscopic and dynamical studies. The availability of the HED meteorites for study and the new data being gained from the Dawn mission provides an excellent opportunity to investigate Vesta s history. In this study, modelling of Vesta has been undertaken to investigate its evolution from an unconsolidated chondritic body to a differentiated body with an iron core. In contrast to previous modelling, both heat and mass transfer are considered as coupled processes. This work draws on models of melt segregation in terrestrial environments to inform the evolution of Vesta into the differentiated body observed today. In order for a core to form in this body, a separation of the metallic iron from the silicates must take place. Temperatures in excess of the solidus temperatures for the Fe-FeS system and the silicates are therefore required. Thermal modelling has shown accretion before 2Myr leads to temperatures in excess of the silicate solidus.

  5. MetREx: a protein design approach for the exploration of sequence-reactivity relationships in metalloenzymes.

    PubMed

    Stiebritz, Martin T

    2015-03-30

    Metalloenzymes represent a particular challenge for any rational (re)design approach because the modeling of reaction events at their metallic cofactors requires time-consuming quantum mechanical calculations, which cannot easily be reconciled with the fast, knowledge-based approaches commonly applied in protein design studies. Here, an approach for the exploration of sequence-reactivity relationships in metalloenzymes is presented (MetREx) that consists of force field-based screening of mutants that lie energetically between a wild-type sequence and the global minimum energy conformation and which should, therefore, be compatible with a given protein fold. Mutant candidates are subsequently evaluated with a fast and approximate quantum mechanical/molecular mechanical-like procedure that models the influence of the protein environment on the active site by taking partial charges and van der Waals repulsions into account. The feasibility of the procedure is demonstrated for the active site of [FeFe] hydrogenase from Desulfovibrio desulfuricans. The method described allows for the identification of mutants with altered properties, such as inhibitor-coordination energies, and the understanding of the robustness of enzymatic reaction steps with respect to variations in sequence space. PMID:25649465

  6. Iron-sulfur clusters—new features in enzymes and synthetic models

    NASA Astrophysics Data System (ADS)

    Bill, Eckhard

    2012-03-01

    Mössbauer spectroscopy is very important for the characterization of iron sulfur clusters in biological and synthetic molecules. The electric and magnetic hyperfine parameters obtained for 57Fe provide valuable information about the electronic structure of the different iron sites occurring in Fe:S clusters. Although known since more than four decades, research in this field is very active, revealing unexpected functions, structures and redox states. In this overview, new aspects of double exchange and vibronic coupling in a structurally well-characterized two-iron model compound are discussed, the electronic structure of extremely reduced clusters with all iron in ferrous or even in iron(I) state is elucidated, and an exciting new type of cubane cluster occurring in oxygen-insensitive hydrogenases is presented. The latter cluster involves structural changes during function and it supports more than one redox transition, which may be essential for oxygen protection of the enzymes.

  7. A Tale of Two Gases: Isotope Effects Associated with the Enzymatic Production of H2 and N2O

    NASA Astrophysics Data System (ADS)

    Yang, H.; Gandhi, H.; Kreuzer, H. W.; Moran, J.; Hill, E. A.; McQuarters, A.; Lehnert, N.; Ostrom, N. E.; Hegg, E. L.

    2014-12-01

    Stable isotopes can provide considerable insight into enzymatic mechanisms and fluxes in various biological processes. In our studies, we used stable isotopes to characterize both enzyme-catalyzed H2 and N2O production. H2 is a potential alternative clean energy source and also a key metabolite in many microbial communities. Biological H2 production is generally catalyzed by hydrogenases, enzymes that combine protons and electrons to produce H2 under anaerobic conditions. In our study, H isotopes and fractionation factors (?) were used to characterize two types of hydrogenases: [FeFe]- and [NiFe]-hydrogenases. Due to differences in the active site, the ? associated with H2 production for [FeFe]- and [NiFe]-hydrogenases separated into two distinct clusters (?FeFe > ?NiFe). The calculated kinetic isotope effects indicate that hydrogenase-catalyzed H2 production has a preference for light isotopes, consistent with the relative bond strengths of O-H and H-H bonds. Interestingly, the isotope effects associated with H2 consumption and H2-H2O exchange reactions were also characterized, but in this case no specific difference was observed between the different enzymes. N2O is a potent greenhouse gas with a global warming potential 300 times that of CO2, and the concentration of N2O is currently increasing at a rate of ~0.25% per year. Thus far, bacterial and fungal denitrification processes have been identified as two of the major sources of biologically generated N2O. In this study, we measured the ?15N, ?18O, ?15N? (central N atom in N2O), and ?15N? (terminal N atom in N2O) of N2O generated by purified fungal P450 nitric oxide reductase (P450nor) from Histoplasma capsulatum. We observed normal isotope effects for ?18O and ?15N?, and inverse isotope effects for bulk ?15N (the average of N? and N?) and ?15N?. The observed isotope effects have been used in conjunction with DFT calculations to provide important insight into the mechanism of P450nor. Similar experiments were performed with bacterial nitric oxide reductase from Paracoccus denitrificans (cNOR). In this case both N? and N? exhibited inverse isotope effects, while O had a normal isotope effect. Together, these data highlight the utility in using stable isotopes as both tracers and mechanistic probes when studying metabolic processes.

  8. Shock compression of Fe-FeS mixture up to 204 GPa

    NASA Astrophysics Data System (ADS)

    Huang, Haijun; Wu, Shijie; Hu, Xiaojun; Wang, Qingsong; Wang, Xiang; Fei, Yingwei

    2013-02-01

    AbstractUsing a two-stage light gas gun, we obtained new shock wave Hugoniot data for an iron-sulfur alloy (Fe-11.8wt%S) over the pressure range of 94-204 GPa. A least-squares fit to the Hugoniot data yields a linear relationship between shock velocity DS and particle velocity u, DS (km/s) =3.60(0.14) +1.57(0.05) u. The measured Hugoniot data for Fe-11.8wt%S agree well with the calculated results based on the thermodynamic parameters of Fe and FeS using the additive law. By comparing the calculated densities along the adiabatic core temperature with the PREM density profile, an iron core with 10 wt.% sulfur (S) provides the best solution for the composition of the Earth's outer core.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/22117026','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/22117026"><span id="translatedtitle">Structure and magnetic properties of irradiated <span class="hlt">Fe-Fe</span> oxide core-shell nanoclusters</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>McCloy, John S.; Jiang Weilin; Sundararajan, Jennifer A.; Qiang, You; Burks, Edward; Liu Kai</p> <p>2013-04-19</p> <p>A cluster deposition method was used to produce a film of loosely aggregated particles of Fe-Fe{sub 3}O{sub 4} coreshell nanoclusters with an 8 nm iron core size and 2 nm oxide shell thickness. The film of particles on a silicon substrate was irradiated with 5.5 MeV Si{sup 2+} ions to a fluence of 10{sup 16} cm{sup -2} near room temperature, and computer simulations based on the SRIM (Stopping and Range of Ions in Matter) code show that the implanted Si species stops near the filmsubstrate interface. The ion irradiation creates a structural change in the film with corresponding chemical and magnetic changes. X-ray diffraction shows that the core size and chemistry stay the same but the shell becomes FeO that grows to a thickness of 17 nm. Helium ion microscopy shows that the previously separate particles have densified into a nearly continuous film. Major loop magnetic hysteresis measurements show a decrease in saturation magnetization that we attribute to the presence of the antiferromagnetic (AFM) FeO shell. First-order reversal curve measurements on the irradiated film performed with a vibrating sample magnetometer show that the AFM shell prevents the particles from interacting magnetically, leading to low coercivity from the iron core and little bias field from the core interactions. These results, and others reported previously on different compositions (Fe{sub 3}O{sub 4} or FeO+Fe{sub 3}N nanoclusters), show that the ion irradiation behavior of nanocluster films such as these depends strongly on the initial nanostructure and chemistry.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3869222','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3869222"><span id="translatedtitle">Spin relaxation in antiferromagnetic <span class="hlt">Fe–Fe</span> dimers slowed down by anisotropic DyIII ions</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Klöwer, Frederik; Lan, Yanhua; Clérac, Rodolphe; Wolny, Juliusz A; Schünemann, Volker; Anson, Christopher E</p> <p>2013-01-01</p> <p>Summary By using Mössbauer spectroscopy in combination with susceptibility measurements it was possible to identify the supertransferred hyperfine field through the oxygen bridges between DyIII and FeIII in a {Fe4Dy2} coordination cluster. The presence of the dysprosium ions provides enough magnetic anisotropy to “block” the hyperfine field that is experienced by the iron nuclei. This has resulted in magnetic spectra with internal hyperfine fields of the iron nuclei of about 23 T. The set of data permitted us to conclude that the direction of the anisotropy in lanthanide nanosize molecular clusters is associated with the single ion and crystal field contributions and 57Fe Mössbauer spectroscopy may be informative with regard to the the anisotropy not only of the studied isotope, but also of elements interacting with this isotope. PMID:24367750</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.er.usgs.gov/publication/70015588','USGSPUBS'); return false;" href="http://pubs.er.usgs.gov/publication/70015588"><span id="translatedtitle">Cluster molecular orbital description of the electronic structures of mixed-valence iron oxides and silicates</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Sherman, David M.</p> <p>1986-01-01</p> <p>A molecular orbital description, based on spin-unrestricted X??-scattered wave calculations, is given for the electronic structures of mixed valence iron oxides and silicates. The cluster calculations show that electron hopping and optical intervalence charge-transger result from weak <span class="hlt">FeFe</span> bonding across shared edges of FeO6 coordination polyhedra. In agreement with Zener's double exchange <span class="hlt">model</span>, <span class="hlt">FeFe</span> bonding is found to stabilize ferromagnetic coupling between Fe2+ and Fe3+ cations. ?? 1986.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/doepatents/biblio/894277','DOE-PATENT-XML'); return false;" href="http://www.osti.gov/doepatents/biblio/894277"><span id="translatedtitle">Hydrogen Production Using <span class="hlt">Hydrogenase</span>-Containing Oxygenic Photosynthetic Organisms</span></a></p> <p><a target="_blank" href="http://www.osti.gov/doepatents">DOEpatents</a></p> <p>Melis, A.; Zhang, L.; Benemann, J. R.; Forestier, M.; Ghirardi, M.; Seibert, M.</p> <p>2006-01-24</p> <p>A reversible physiological process provides for the temporal separation of oxygen evolution and hydrogen production in a microorganism, which includes the steps of growing a culture of the microorganism in medium under illuminated conditions to accumulate an endogenous substrate, depleting from the medium a nutrient selected from the group consisting of sulfur, iron, and/or manganese, sealing the culture from atmospheric oxygen, incubating the culture in light whereby a rate of light-induced oxygen production is equal to or less than a rate of respiration, and collecting an evolved gas. The process is particularly useful to accomplish a sustained photobiological hydrogen gas production in cultures of microorganisms, such as Chlamydomonas reinhardtii.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/doepatents/biblio/1175631','DOE-PATENT-XML'); return false;" href="http://www.osti.gov/doepatents/biblio/1175631"><span id="translatedtitle">Hydrogen production using <span class="hlt">hydrogenase</span>-containing oxygenic photosynthetic organisms</span></a></p> <p><a target="_blank" href="http://www.osti.gov/doepatents">DOEpatents</a></p> <p>Melis, Anastasios; Zhang, Liping; Benemann, John R.; Forestier, Marc; Ghirardi, Maria; Seibert, Michael</p> <p>2006-01-24</p> <p>A reversible physiological process provides for the temporal separation of oxygen evolution and hydrogen production in a microorganism, which includes the steps of growing a culture of the microorganism in medium under illuminated conditions to accumulate an endogenous substrate, depleting from the medium a nutrient selected from the group consisting of sulfur, iron, and/or manganese, sealing the culture from atmospheric oxygen, incubating the culture in light whereby a rate of light-induced oxygen production is equal to or less than a rate of respiration, and collecting an evolved gas. The process is particularly useful to accomplish a sustained photobiological hydrogen gas production in cultures of microorganisms, such as Chlamydomonas reinhardtii.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/1068602','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/1068602"><span id="translatedtitle">Survey of <span class="hlt">Hydrogenase</span> Activity in Algae: Final Report</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Brand, J. J.</p> <p>1982-04-01</p> <p>The capacity for hydrogen gas production was examined in nearly 100 strains of Eukaryotic algae. Each strain was assessed for rate of H2 production in darkness, at compensating light intensity and at saturating Tight intensity. Maximum H2 yield on illumination and sensitivity to molecular oxygen were also measured.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/19530077','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/19530077"><span id="translatedtitle">An electron-flow <span class="hlt">model</span> can predict complex redox reactions in mixed-culture fermentative bioH2: microbial ecology evidence.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Lee, Hyung-Sool; Krajmalinik-Brown, Rosa; Zhang, Husen; Rittmann, Bruce E</p> <p>2009-11-01</p> <p>We developed the first <span class="hlt">model</span> for predicting community structure in mixed-culture fermentative biohydrogen production using electron flows and NADH2 balances. A key assumption of the <span class="hlt">model</span> is that H2 is produced only via the pyruvate decarboxylation-ferredoxin-<span class="hlt">hydrogenase</span> pathway, which is commonly the case for fermentation by Clostridium and Ethanoligenens species. We experimentally tested the <span class="hlt">model</span> using clone libraries to gauge community structures with mixed cultures in which we did not pre-select for specific bacterial groups, such as spore-formers. For experiments having final pHs 3.5 and 4.0, where H2 yield and soluble end-product distribution were distinctly different, we established stoichiometric reactions for each condition by using experimentally determined electron equivalent balances. The error in electron balancing was only 3% at final pH 3.5, in which butyrate and acetate were dominant organic products and the H2 yield was 2.1 mol H2/mol glucose. Clone-library analysis showed that clones affiliated with Clostridium sp. BL-22 and Clostridium sp. HPB-16 were dominant at final pH 3.5. For final pH 4.0, the H2 yield was 0.9 mol H2/mol glucose, ethanol, and acetate were the dominant organic products, and the electron balance error was 13%. The significant error indicates that a second pathway for H2 generation was active. The most abundant clones were affiliated with Klebsiella pneumoniae, which uses the formate-cleavage pathway for H2 production. Thus, the clone-library analyses confirmed that the <span class="hlt">model</span> predictions for when the pyruvate decarboxylation-ferredoxin-<span class="hlt">hydrogenase</span> pathway was (final pH 3.5) or was not (final pH 4.0) dominant. With the electron-flow <span class="hlt">model</span>, we can easily assess the main mechanisms for H2 formation and the dominant H2-producing bacteria in mixed-culture fermentative bioH2. PMID:19530077</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/5694589','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/5694589"><span id="translatedtitle">Geochemical <span class="hlt">modeling</span> of low melt-fraction anatexis in a peraluminous system: The Pena Negra complex (central Spain)</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Bea, F. )</p> <p>1991-07-01</p> <p>A study was made of the chemical fractionation associated with four cases of anatectic segregation of low melt-fraction cordieritic granites from migmatized meta-greywackes. The aims of the study were to (1) reveal the fractionation patterns of major and trace elements, (2) compare the major element chemistry of leucogranites and the quantitative behavior of source minerals during anatexis - inferred by mass-balance adjustment - with available experimental data for peraluminous systems, and (3) discuss the behavior of trace elements in crustal melting by comparing the chemically determined composition of leucogranites with the results of three fractionation <span class="hlt">models</span>. Two of these assume a perfect diffusive behavior of trace elements within residual solids, but they use a different set of distribution coefficients. The third assumes a perfect nondiffusive behavior. In relation to their source rocks, the leucogranites are strongly depleted in Li, Transition Elements, and Light Rare Earth Elements, but enriched in K{sub 2}O, SiO{sub 2}, and Ba. Mass balance analysis using the Anatexis Mixing <span class="hlt">Model</span> shows that the chemistry of cordierite leucogranites is compatible with its having originated by closed-system, water-undersaturated anatexis on previously migmatized meta-greywackes, leaving a residue enriched in cordierite plus biotite and exhausted in K-feldspar. Biotite melts congruently unless important amounts of sillimanite were also present in the source. Compared with experimental metals obtained from sources with the same chemical composition but with a different femic mineralogy (biotite + sillimanite, instead of cordierite + biotite), the Pena Negra leucogranites are richer in K{sub 2}O and MgO with a lower <span class="hlt">Fe/(Fe</span> + Mg) ratio. The differences in magnesium are believed to result from the changes in the mineral assemblage of the source rocks.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://oaktrust.library.tamu.edu//handle/1969.1/150039','EPRINT'); return false;" href="http://oaktrust.library.tamu.edu//handle/1969.1/150039"><span id="translatedtitle">The Soils of Texas. </span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Carter, W. T. (William Thomas)</p> <p>1931-01-01</p> <p>The unique active site of [FeFe]-<span class="hlt">hydrogenase</span> has inspired over 300 small molecule <span class="hlt">models</span> derived from the classical organometallic complex, (?-SRS-)[Fe(CO)3]2. However, no <span class="hlt">model</span> complex has yet reproduced the hydrogen ...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/1091462','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/1091462"><span id="translatedtitle">Ion irradiation of <span class="hlt">Fe-Fe</span> oxide core-shell nanocluster films: Effect of interface on stability of magnetic properties</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>McCloy, John S.; Jiang, Weilin; Droubay, Timothy C.; Varga, Tamas; Kovarik, Libor; Sundararajan, Jennifer A.; Kaur, Maninder; Qiang, You; Burks, Edward; Liu, Kai</p> <p>2013-08-23</p> <p>A cluster deposition method was used to produce films of loosely aggregated nanoclusters (NC) of Fe core-Fe3O4 shell or fully oxidized Fe3O4. Films of these NC on Si(100) or MgO(100)/Fe3O4(100) were irradiated to 1016 Si2+/cm2 near room temperature using an ion accelerator. Ion irradiation creates structural change in the NC film with corresponding chemical and magnetic changes which depend on the initial oxidation state of the cluster. Films were characterized using magnetometry (hysteresis, first order reversal curves), microscopy (transmission electron, helium ion), and x-ray diffraction. In all cases, the particle sizes increased due to ion irradiation, and when a core of Fe is present, irradiation reduces the oxide shells to lower valent Fe species. These results show that ion irradiated behavior of the nanocluster films depends strongly on the initial nanostructure and chemistry, but in general saturation magnetization decreases slightly.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/22218100','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/22218100"><span id="translatedtitle">Ion irradiation of <span class="hlt">Fe-Fe</span> oxide core-shell nanocluster films: Effect of interface on stability of magnetic properties</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>McCloy, John S.; Jiang, Weilin; Droubay, Timothy C.; Varga, Tamas; Kovarik, Libor; Sundararajan, Jennifer A.; Kaur, Maninder; Qiang, You; Burks, Edward C.; Liu, Kai</p> <p>2013-08-28</p> <p>A cluster deposition method was used to produce films of loosely aggregated nanoclusters (NCs) of Fe core-Fe{sub 3}O{sub 4} shell or fully oxidized Fe{sub 3}O{sub 4}. Films of these NC on Si(100) or MgO(100)/Fe{sub 3}O{sub 4}(100) were irradiated to 10{sup 16} Si{sup 2+}/cm{sup 2} near room temperature using an ion accelerator. Ion irradiation creates structural change in the NC film with corresponding chemical and magnetic changes which depend on the initial oxidation state of the cluster. Films were characterized using magnetometry (hysteresis, first order reversal curves), microscopy (transmission electron, helium ion), and x-ray diffraction. In all cases, the particle sizes increased due to ion irradiation, and when a core of Fe is present, irradiation reduces the oxide shells to lower valent Fe species. These results show that ion irradiated behavior of the NC films depends strongly on the initial nanostructure and chemistry, but in general saturation magnetization decreases slightly.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/1051787','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/1051787"><span id="translatedtitle">Toward a rigorous network of protein-protein interactions of the <span class="hlt">model</span> sulfate reducer Desulfovibrio vulgaris Hildenborough</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Chhabra, S.R.; Joachimiak, M.P.; Petzold, C.J.; Zane, G.M.; Price, M.N.; Gaucher, S.; Reveco, S.A.; Fok, V.; Johanson, A.R.; Batth, T.S.; Singer, M.; Chandonia, J.M.; Joyner, D.; Hazen, T.C.; Arkin, A.P.; Wall, J.D.; Singh, A.K.; Keasling, J.D.</p> <p>2011-05-01</p> <p>Protein–protein interactions offer an insight into cellular processes beyond what may be obtained by the quantitative functional genomics tools of proteomics and transcriptomics. The aforementioned tools have been extensively applied to study E. coli and other aerobes and more recently to study the stress response behavior of Desulfovibrio 5 vulgaris Hildenborough, a <span class="hlt">model</span> anaerobe and sulfate reducer. In this paper we present the first attempt to identify protein-protein interactions in an obligate anaerobic bacterium. We used suicide vector-assisted chromosomal modification of 12 open reading frames encoded by this sulfate reducer to append an eight amino acid affinity tag to the carboxy-terminus of the chosen proteins. Three biological replicates of the 10 ‘pulled-down’ proteins were separated and analyzed using liquid chromatography-mass spectrometry. Replicate agreement ranged between 35% and 69%. An interaction network among 12 bait and 90 prey proteins was reconstructed based on 134 bait-prey interactions computationally identified to be of high confidence. We discuss the biological significance of several unique metabolic features of D. vulgaris revealed by this protein-protein interaction data 15 and protein modifications that were observed. These include the distinct role of the putative carbon monoxide-induced <span class="hlt">hydrogenase</span>, unique electron transfer routes associated with different oxidoreductases, and the possible role of methylation in regulating sulfate reduction.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_11");'>11</a></li> <li><a href="#" onclick='return showDiv("page_12");'>12</a></li> <li class="active"><span>13</span></li> <li><a href="#" onclick='return showDiv("page_14");'>14</a></li> <li><a href="#" onclick='return showDiv("page_15");'>15</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_13 --> <div id="page_14" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_12");'>12</a></li> <li><a href="#" onclick='return showDiv("page_13");'>13</a></li> <li class="active"><span>14</span></li> <li><a href="#" onclick='return showDiv("page_15");'>15</a></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="261"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/1214968','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/1214968"><span id="translatedtitle">Hydrogen Production by Water Biophotolysis</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Ghirardi, Maria L.; King, Paul W.; Mulder, David W.; Eckert, Carrie; Dubini, Alexandra; Maness, Pin-Ching; Yu, Jianping</p> <p>2014-01-22</p> <p>The use of microalgae for production of hydrogen gas from water photolysis has been studied for many years, but its commercialization is still limited by multiple challenges. Most of the barriers to commercialization are attributed to the existence of biological regulatory mechanisms that, under anaerobic conditions, quench the absorbed light energy, down-regulate linear electron transfer, inactivate the H2-producing enzyme, and compete for electrons with the <span class="hlt">hydrogenase</span>. Consequently, the conversion efficiency of absorbed photons into H2 is significantly lower than its estimated potential of 12–13 %. However, extensive research continues towards addressing these barriers by either trying to understand and circumvent intracellular regulatory mechanisms at the enzyme and metabolic level or by developing biological systems that achieve prolonged H2 production albeit under lower than 12–13 % solar conversion efficiency. This chapter describes the metabolic pathways involved in biological H2 photoproduction from water photolysis, the attributes of the two <span class="hlt">hydrogenases</span>, [<span class="hlt">FeFe</span>] and [NiFe], that catalyze biological H2 production, and highlights research related to addressing the barriers described above. These highlights include: (a) recent advances in improving our understanding of the O2 inactivation mechanism in different classes of <span class="hlt">hydrogenases</span>; (b) progress made in preventing competitive pathways from diverting electrons from H2 photoproduction; and (c) new developments in bypassing the non-dissipated proton gradient from down-regulating photosynthetic electron transfer. As an example of a major success story, we mention the generation of truncated-antenna mutants in Chlamydomonas and Synechocystis that address the inherent low-light saturation of photosynthesis. In addition, we highlight the rationale and progress towards coupling biological <span class="hlt">hydrogenases</span> to non-biological, photochemical charge-separation as a means to bypass the barriers of photobiological systems.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4257681','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4257681"><span id="translatedtitle">Genome Annotation Provides Insight into Carbon Monoxide and Hydrogen Metabolism in Rubrivivax gelatinosus</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Wawrousek, Karen; Noble, Scott; Korlach, Jonas; Chen, Jin; Eckert, Carrie; Yu, Jianping; Maness, Pin-Ching</p> <p>2014-01-01</p> <p>We report here the sequencing and analysis of the genome of the purple non-sulfur photosynthetic bacterium Rubrivivax gelatinosus CBS. This microbe is a <span class="hlt">model</span> for studies of its carboxydotrophic life style under anaerobic condition, based on its ability to utilize carbon monoxide (CO) as the sole carbon substrate and water as the electron acceptor, yielding CO2 and H2 as the end products. The CO-oxidation reaction is known to be catalyzed by two enzyme complexes, the CO dehydrogenase and <span class="hlt">hydrogenase</span>. As expected, analysis of the genome of Rx. gelatinosus CBS reveals the presence of genes encoding both enzyme complexes. The CO-oxidation reaction is CO-inducible, which is consistent with the presence of two putative CO-sensing transcription factors in its genome. Genome analysis also reveals the presence of two additional <span class="hlt">hydrogenases</span>, an uptake <span class="hlt">hydrogenase</span> that liberates the electrons in H2 in support of cell growth, and a regulatory <span class="hlt">hydrogenase</span> that senses H2 and relays the signal to a two-component system that ultimately controls synthesis of the uptake <span class="hlt">hydrogenase</span>. The genome also contains two sets of <span class="hlt">hydrogenase</span> maturation genes which are known to assemble the catalytic metallocluster of the <span class="hlt">hydrogenase</span> NiFe active site. Collectively, the genome sequence and analysis information reveals the blueprint of an intricate network of signal transduction pathways and its underlying regulation that enables Rx. gelatinosus CBS to thrive on CO or H2 in support of cell growth. PMID:25479613</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1284704','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1284704"><span id="translatedtitle"><span class="hlt">Modeling</span> <span class="hlt">modeling</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Killeen, P R</p> <p>1999-01-01</p> <p><span class="hlt">Models</span> are tools; they need to fit both the hand and the task. Presence or absence of a feature such as a pacemaker or a cascade is not in itself good. Or bad. Criteria for <span class="hlt">model</span> evaluation involve benefit-cost ratios, with the numerator a function of the range of phenomena explained, goodness of fit, consistency with other nearby <span class="hlt">models</span>, and intangibles such as beauty. The denominator is a function of complexity, the number of phenomena that must be ignored, and the effort necessary to incorporate the <span class="hlt">model</span> into one's parlance. Neither part of the ratio can yet be evaluated for MTS, whose authors provide some cogent challenges to SET. PMID:10220934</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4287179','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4287179"><span id="translatedtitle">Genome sequence of the <span class="hlt">model</span> sulfate reducer Desulfovibrio gigas: a comparative analysis within the Desulfovibrio genus*</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Morais-Silva, Fabio O; Rezende, Antonio Mauro; Pimentel, Catarina; Santos, Catia I; Clemente, Carla; Varela–Raposo, Ana; Resende, Daniela M; da Silva, Sofia M; de Oliveira, Luciana Márcia; Matos, Marcia; Costa, Daniela A; Flores, Orfeu; Ruiz, Jerónimo C; Rodrigues-Pousada, Claudina</p> <p>2014-01-01</p> <p>Desulfovibrio gigas is a <span class="hlt">model</span> organism of sulfate-reducing bacteria of which energy metabolism and stress response have been extensively studied. The complete genomic context of this organism was however, not yet available. The sequencing of the D. gigas genome provides insights into the integrated network of energy conserving complexes and structures present in this bacterium. Comparison with genomes of other Desulfovibrio spp. reveals the presence of two different CRISPR/Cas systems in D. gigas. Phylogenetic analysis using conserved protein sequences (encoded by rpoB and gyrB) indicates two main groups of Desulfovibrio spp, being D. gigas more closely related to D. vulgaris and D. desulfuricans strains. Gene duplications were found such as those encoding fumarate reductase, formate dehydrogenase, and superoxide dismutase. Complexes not yet described within Desulfovibrio genus were identified: Mnh complex, a v-type ATP-synthase as well as genes encoding the MinCDE system that could be responsible for the larger size of D. gigas when compared to other members of the genus. A low number of <span class="hlt">hydrogenases</span> and the absence of the codh/acs and pfl genes, both present in D. vulgaris strains, indicate that intermediate cycling mechanisms may contribute substantially less to the energy gain in D. gigas compared to other Desulfovibrio spp. This might be compensated by the presence of other unique genomic arrangements of complexes such as the Rnf and the Hdr/Flox, or by the presence of NAD(P)H related complexes, like the Nuo, NfnAB or Mnh. PMID:25055974</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/1024072','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/1024072"><span id="translatedtitle">A Synthetic Nickel Electrocatalyst With a Turnover Frequency Above 100,000 s-1 for H2 Production</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Helm, Monte L.; Stewart, Michael P.; Bullock, R. Morris; Rakowski DuBois, Mary; DuBois, Daniel L.</p> <p>2011-08-12</p> <p>Increased worldwide energy demand will require greater use of carbon-neutral sustainable energy sources. The intermittent nature of solar and wind power requires storage of energy, so electrocatalysts that convert electrical energy to chemical bonds in fuels are needed. Platinum is an excellent catalyst, but it is of low abundance and high cost. <span class="hlt">Hydrogenase</span> enzymes in Nature catalyze the evolution of H2 and use earth-abundant metals such as nickel and iron. We report that a synthetic nickel catalyst, [Ni(7PPh2NPh)2](BF4)2, (7PPh2NPh = 1,3,6-triphenyl-1-aza-3,6-diphosphacycloheptane) catalyzes the production of H2 using [(DMF)H]+OTf as the proton source, with turnover frequencies of 31,000 s-1 in dry acetonitrile and 108,000 s-1 in the presence of H2O (1.2 M), at a potential of -1.13 V (vs. the ferrocenium/ferrocene couple). These turnover frequencies exceed those reported for the [<span class="hlt">FeFe</span>] <span class="hlt">hydrogenase</span> enzyme by more than an order of magnitude, and are the fastest reported for any molecular catalyst for H2 production. This material is based upon work supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2006AstL...32..495Z','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2006AstL...32..495Z"><span id="translatedtitle"><span class="hlt">Models</span>, figures, and gravitational moments of Jupiter's satellites Io and Europa</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Zharkov, V. N.; Karamurzov, B. S.</p> <p>2006-07-01</p> <p>Two types of trial three-layer <span class="hlt">models</span> have been constructed for the satellites Io and Europa. In the <span class="hlt">models</span> of the first type (Io1 and E1), the cores are assumed to consist of eutectic <span class="hlt">Fe-FeS</span> melt with the densities ? 1 = 5.15 g cm-3 (Io1) and 5.2 g cm-3 (E1). In the <span class="hlt">models</span> of the second type (Io3 and E3), the cores consist of FeS with an admixture of nickel and have the density ? 1 = 4.6 g cm-3. The approach used here differs from that used previously both in chosen <span class="hlt">model</span> chemical composition of these satellites and in boundary conditions imposed on the <span class="hlt">models</span>. The most important question to be answered by <span class="hlt">modeling</span> the internal structure of the Galilean satellites is that of the condensate composition at the formation epoch of Jupiter's system. Jupiter's core and the Galilean satellites were formed from the condensate. Ganymede and Callisto were formed fairly far from Jupiter in zones with temperatures below the water condensation temperature, water was entirely incorporated into their bodies, and their <span class="hlt">modeling</span> showed the mass ratio of the icy (I) component to the rock (R) component in them to be I/R ˜ 1. The R composition must be clarified by <span class="hlt">modeling</span> Io and Europa. The <span class="hlt">models</span> of the second type (Io3 and E3), in which the satellite cores consist of FeS, yield 25.2 (Io3) and 22.8 (E3) for the core masses (in weight %). In discussing the R composition, we note that, theoretically, the material of which the FeS+Ni core can consist in the R accounts for ˜25.4% of the satellite mass. In this case, such an important parameter as the mantle silicate iron saturation is Fe# = 0.265. The Io3 and E3 <span class="hlt">models</span> agree well with this theoretical prediction. The <span class="hlt">models</span> of the first and second types differ markedly in core radius; thus, in principle, the R composition in the formation zone of Jupiter's system can be clarified by geophysical studies. Another problem studied here is that of the error made in <span class="hlt">modeling</span> Io and Europa using the Radau-Darvin formula when passing from the Love number k 2 to the nondimensional polar moment of inertia bar C. For Io, the Radau-Darvin formula underestimates the true value of bar C by one and a half units in the third decimal digit. For Europa, this effect is approximately a factor of 3 smaller, which roughly corresponds to a ratio of the small parameters for the satellites under consideration ? Io/? Europa ˜ 3.4. In <span class="hlt">modeling</span> the internal structure of the satellites, the core radius depends strongly on both the mean moment of inertia I* and k 2. Therefore, the above discrepancy in bar C for Io is appreciable.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/953511','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/953511"><span id="translatedtitle">Insights Into the P-To-Q Conversion in the Catalytic Cycle of Methane Monooxygenase From a Synthetic <span class="hlt">Model</span> System</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Xue, G.; Fiedler, A.T.; Martinho, M.; Munck, E.; Que, L.; Jr.</p> <p>2009-05-28</p> <p>For the catalytic cycle of soluble methane monooxygenase (sMMO), it has been proposed that cleavage of the O-O bond in the ({mu}-peroxo)diiron(III) intermediate P gives rise to the diiron(IV) intermediate Q with an Fe{sub 2}({mu}-O){sub 2} diamond core, which oxidizes methane to methanol. As a <span class="hlt">model</span> for this conversion, ({mu}-oxo) diiron(III) complex 1 ([Fe{sup III}{sub 2}({mu}-O)({mu}-O{sub 2}H{sub 3})(L){sub 2}]{sup 3+}, L = tris(3,5-dimethyl-4-methoxypyridyl-2-methyl)amine) has been treated consecutively with one eq of H{sub 2}O{sub 2} and one eq of HClO{sub 4} to form 3 ([Fe{sup IV}{sub 2}({mu}-O){sub 2}(L){sub 2}]{sup 4+}). In the course of this reaction a new species, 2, can be observed before the protonation step; 2 gives rise to a cationic peak cluster by ESI-MS at m/z 1,399, corresponding to the [Fe{sub 2}O{sub 3}L{sub 2}H](OTf){sub 2}{sup +} ion in which 1 oxygen atom derives from 1 and the other two originate from H{sub 2}O{sub 2}. Moessbauer studies of 2 reveal the presence of two distinct, exchange coupled iron(IV) centers, and EXAFS fits indicate a short Fe-O bond at 1.66 {angstrom} and an <span class="hlt">Fe-Fe</span> distance of 3.32 {angstrom}. Taken together, the spectroscopic data point to an HO-Fe{sup IV}-O-Fe{sup IV} = O core for 2. Protonation of 2 results in the loss of H{sub 2}O and the formation of 3. Isotope labeling experiments show that the [Fe{sup IV}{sub 2}({mu}-O){sub 2}] core of 3 can incorporate both oxygen atoms from H{sub 2}O{sub 2}. The reactions described here serve as the only biomimetic precedent for the conversion of intermediates P to Q in the sMMO reaction cycle and shed light on how a peroxodiiron(III) unit can transform into an [Fe{sup IV}{sub 2}({mu}-O){sub 2}] core.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.dspace.cam.ac.uk/handle/1810/247464','EPRINT'); return false;" href="http://www.dspace.cam.ac.uk/handle/1810/247464"><span id="translatedtitle">Analysis of the cyanobacterial hydrogen photoproduction process via <span class="hlt">model</span> identification and process simulation</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Zhang, Dongda; Dechatiwongse, Pongsathorn; Del-Rio-Chanona, Ehecatl Antonio; Hellgardt, Klaus; Maitland, Geoffrey C.; Vassiliadis, Vassilios S.</p> <p>2015-02-02</p> <p>of sulphur, oxygen production rate is significantly reduced and even drops lower than algal respiration rate. Hence, oxygen produced by oxygenic photosynthesis is totally consumed by algae respira- tion and anaerobic conditions are achieved. In addition... by water through photosynthesis with the generation of oxygen. As the activity of <span class="hlt">hydrogenase</span> is completely inhibited by oxygen, C. reinhardtii can only produce hydrogen in anaerobic conditions (Antal et al., 2011). Different methods have been used...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://ntrs.nasa.gov/search.jsp?R=19930040727&hterms=element+iron&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D10%26Ntt%3Delement%2Biron','NASA-TRS'); return false;" href="http://ntrs.nasa.gov/search.jsp?R=19930040727&hterms=element+iron&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D10%26Ntt%3Delement%2Biron"><span id="translatedtitle">Experimental partitioning studies near the <span class="hlt">Fe-FeS</span> eutectic, with an emphasis on elements important to iron meteorite chronologies (Pb, Ag, Pd, and Tl)</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Jones, J. H.; Hart, S. R.; Benjamin, T. M.</p> <p>1993-01-01</p> <p>Partitioning coefficients for metal/sulfide liquid, troilite/sulfide liquid, and schreibersite/sulfide liquid were determined for Ag, Au, Mo, Ni, Pd, and Tl (using EMPA and proton-induced X-ray microprobe and ion microprobe analyses) in order to understand the chronometer systems of iron meteorites. In general, the obtained schreibersite/metal and troilite/metal partition coefficients for 'compatible' elements were quite similar to those inferred from natural assemblages, reinforcing an earlier made conclusion that there is a class of elements for which experimental troilite/metal and schreibersite/metal partition coefficients approximate those inferred from natural samples. The consistency between experimental and natural assemblages, however, was not observed for Ag, Pb, and Tl, indicating that the abundances of these elements determined in 'metal' and 'troilite' separates from iron meteorites are influenced by trace minerals that concentrate incompatible elements.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://carnegiedpb.stanford.edu/sites/dpb.carnegiescience.edu/files/Mus%20et%20al,%202007.pdf','EPRINT'); return false;" href="http://carnegiedpb.stanford.edu/sites/dpb.carnegiescience.edu/files/Mus%20et%20al,%202007.pdf"><span id="translatedtitle">Anaerobic Acclimation in Chlamydomonas reinhardtii ANOXIC GENE EXPRESSION, <span class="hlt">HYDROGENASE</span> INDUCTION, AND METABOLIC PATHWAYS*S</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p></p> <p></p> <p>of transcripts encoding proteins associ- ated with the production of H2, organic acids, and ethanol were observed, transhydrogenase, catalase, and several putative pro- teins of unknown function. Overall, this study uses</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.gso.uri.edu/dcsmith/page3/page19/assets/SoffientinoetalJMM.pdf','EPRINT'); return false;" href="http://www.gso.uri.edu/dcsmith/page3/page19/assets/SoffientinoetalJMM.pdf"><span id="translatedtitle">A versatile and sensitive tritium-based radioassay for measuring <span class="hlt">hydrogenase</span> activity in aquatic sediments</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Smith, David C.</p> <p></p> <p>for measuring HT specific activity based on liquid scintillation counting is also presented. Validation tests a fundamental role in the geochemical cycling of carbon and of many other biologically significant elements</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://oaktrust.library.tamu.edu//handle/1969.1/155459','EPRINT'); return false;" href="http://oaktrust.library.tamu.edu//handle/1969.1/155459"><span id="translatedtitle">Synthetic Analogues of the Diiron <span class="hlt">Hydrogenase</span> Enzyme Active Site and Possible Primordial H2-Producing Catalysts </span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Crouthers, Danielle Jerine</p> <p>2015-08-25</p> <p>Nature has developed enzymes that utilize the base metals, iron and nickel, in sulfur-rich environments, capable of performing the reversible interconversion of protons and electrons into hydrogen under mild conditions. ...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://carnegiedpb.stanford.edu/sites/dpb.carnegiescience.edu/files/DubiniJBC2009.pdf','EPRINT'); return false;" href="http://carnegiedpb.stanford.edu/sites/dpb.carnegiescience.edu/files/DubiniJBC2009.pdf"><span id="translatedtitle">Flexibility in Anaerobic Metabolism as Revealed in a Mutant of Chlamydomonas reinhardtii Lacking <span class="hlt">Hydrogenase</span> Activity</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p></p> <p></p> <p>fumarase and fumarate reductase, enzymes putatively required to convert malate to succinate. These results of the Tricarboxylic Acid Cycle with fermentation when the rate of respiratory O2 consumption exceeds the rate</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=201348','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=201348"><span id="translatedtitle">Classification of the uptake <span class="hlt">hydrogenase</span>-positive (Hup+) bean rhizobia as Rhizobium tropici.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>van Berkum, P; Navarro, R B; Vargas, A A</p> <p>1994-01-01</p> <p>Phenotypic and genetic characterization indicated that Hup+ bean rhizobial strains are type IIA and type IIB Rhizobium tropici. The Hup+ strain USDA 2840, which did not cluster with either of the two types of R. tropici in a restriction fragment length polymorphism analysis, had electrophoretic patterns of PCR products generated with primers for repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus sequences similar to those of three reference strains of R. tropici type IIA. The Hup+ strain USDA 2738, which clustered with the reference strain of R. tropici IIB in a restriction fragment length polymorphism analysis, had electrophoretic patterns of PCR products generated with primers for repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus sequences more closely resembling those of the reference strains of R. tropici type IIA than those of type IIB. DNA amplification with the Y1 and Y2 primers to generate a portion of the 16S rDNA operon was useful to distinguish R. tropici type IIA strains from other bean rhizobial strains. The phylogenetic position of the type IIA strain of R. tropici USDA 2840, determined from the partial 16S rDNA sequence, indicated a more distant relationship with the type IIB strain of R. tropici CIAT899 than with the as yet unnamed rhizobial species of Leucaena leucocephala, TAL 1145. Therefore, we suggest that it may be appropriate either to separate R. tropici types IIA and IIB into two different species or to identify TAL 1145 to the species level as a third type of R. tropici. Images PMID:8135515</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4139163','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4139163"><span id="translatedtitle">Paramagnetic Intermediates Generated by Radical S-Adenosylmethionine (SAM) Enzymes</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p></p> <p>2015-01-01</p> <p>Conspectus A [4Fe–4S]+ cluster reduces a bound S-adenosylmethionine (SAM) molecule, cleaving it into methionine and a 5?-deoxyadenosyl radical (5?-dA•). This step initiates the varied chemistry catalyzed by each of the so-called radical SAM enzymes. The strongly oxidizing 5?-dA• is quenched by abstracting a H-atom from a target species. In some cases, this species is an exogenous molecule of substrate, for example, l-tyrosine in the [<span class="hlt">FeFe</span>] <span class="hlt">hydrogenase</span> maturase, HydG. In other cases, the target is a proteinaceous residue as in all the glycyl radical forming enzymes. The generation of this initial radical species and the subsequent chemistry involving downstream radical intermediates is meticulously controlled by the enzyme so as to prevent unwanted reactions. But the manner in which this control is exerted is unknown. Electron paramagnetic resonance (EPR) spectroscopy has proven to be a valuable tool used to gain insight into these mechanisms. In this Account, we summarize efforts to trap such radical intermediates in radical SAM enzymes and highlight four examples in which EPR spectroscopic results have shed significant light on the corresponding mechanism. For lysine 2,3-aminomutase, nearly each possible intermediate, from an analogue of the initial 5?-dA• to the product radical l-?-lysine, has been explored. A paramagnetic intermediate observed in biotin synthase is shown to involve an auxiliary [FeS] cluster whose bridging sulfide is a co-substrate for the final step in the biosynthesis of vitamin B7. In HydG, the l-tyrosine substrate is converted in unprecedented fashion to a 4-oxidobenzyl radical on the way to generating CO and CN– ligands for the [<span class="hlt">FeFe</span>] cluster of <span class="hlt">hydrogenase</span>. And finally, EPR has confirmed a mechanistic proposal for the antibiotic resistance protein Cfr, which methylates the unactivated sp2-hybridized C8-carbon of an adenosine base of 23S ribosomal RNA. These four systems provide just a brief survey of the ever-growing set of radical SAM enzymes. The diverse chemistries catalyzed by these enzymes make them an intriguing target for continuing study, and EPR spectroscopy, in particular, seems ideally placed to contribute to our understanding. PMID:24991701</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2014sems.book..107L','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2014sems.book..107L"><span id="translatedtitle"><span class="hlt">Models</span>, Fiction, and Fictional <span class="hlt">Models</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Liu, Chuang</p> <p>2014-03-01</p> <p>The following sections are included: * Introduction * Why Most <span class="hlt">Models</span> in Science Are Not Fictional * Typically Fictional <span class="hlt">Models</span> in Science * <span class="hlt">Modeling</span> the Unobservable * Fictional <span class="hlt">Models</span> for the Unobservable? * References</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=metal&pg=4&id=EJ770219','ERIC'); return false;" href="http://eric.ed.gov/?q=metal&pg=4&id=EJ770219"><span id="translatedtitle">Synthesis, Purification, and Characterization of a [mu]-(1,3-Propanedithiolato)-Hexacarbonyldiiron</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Works, Carmen F.</p> <p>2007-01-01</p> <p>A project which exposes students to biologically important transition-metal chemistry is illustrated by taking an example of the iron-carbonyl compound, [mu]-(1,3-Propanedithiolaro)-hexa-carbonyldiiron as a structural <span class="hlt">model</span> for an iron-only <span class="hlt">hydro-genase</span>. The project provides the students with experience of Schlenk line techniques, purification,…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4374699','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4374699"><span id="translatedtitle">Genome-Guided Analysis of Physiological Capacities of Tepidanaerobacter acetatoxydans Provides Insights into Environmental Adaptations and Syntrophic Acetate Oxidation</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Niazi, Adnan; Bongcam-Rudloff, Erik; Schnürer, Anna</p> <p>2015-01-01</p> <p>This paper describes the genome-based analysis of Tepidanaerobacter acetatoxydans strain Re1, a syntrophic acetate-oxidising bacterium (SAOB). Principal issues such as environmental adaptations, metabolic capacities, and energy conserving systems have been investigated and the potential consequences for syntrophic acetate oxidation discussed. Briefly, in pure culture, T. acetatoxydans grows with different organic compounds and produces acetate as the main product. In a syntrophic consortium with a hydrogenotrophic methanogen, it can also reverse its metabolism and instead convert acetate to formate/H2 and CO2. It can only proceed if the product formed is continuously removed. This process generates a very small amount of energy that is scarcely enough for growth, which makes this particular syntrophy of special interest. As a crucial member of the biogas-producing community in ammonium-rich engineered AD processes, genomic features conferring ammonium resistance, bacterial defense, oxygen and temperature tolerance were found, as well as attributes related to biofilm formation and flocculation. It is likely that T. acetatoxydans can form an electrochemical gradient by putative electron-bifurcating Rnf complex and [<span class="hlt">Fe-Fe</span>] <span class="hlt">hydrogenases</span>, as observed in other acetogens. However, genomic deficiencies related to acetogenic metabolism and anaerobic respiration were discovered, such as the lack of formate dehydrogenase and F1F0 ATP synthase. This has potential consequences for the metabolic pathways used under SAO and non-SAO conditions. The two complete sets of bacteriophage genomes, which were found to be encoded in the genome, are also worthy of mention. PMID:25811859</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://kuscholarworks.ku.edu/handle/1808/10059','EPRINT'); return false;" href="http://kuscholarworks.ku.edu/handle/1808/10059"><span id="translatedtitle">Niche <span class="hlt">Modeling</span>: <span class="hlt">Model</span> Evaluation</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Peterson, A. Townsend</p> <p>2012-08-29</p> <p>Ecological niche <span class="hlt">modeling</span> has become a very popular tool in ecological and biogeographic studies across broad extents. The tool is used in hundreds of publications each year now, but some fundamental aspects of the approach ...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=conceptual+AND+modeling&pg=7&id=EJ605626','ERIC'); return false;" href="http://eric.ed.gov/?q=conceptual+AND+modeling&pg=7&id=EJ605626"><span id="translatedtitle">Mental <span class="hlt">Models</span>, Conceptual <span class="hlt">Models</span>, and <span class="hlt">Modelling</span>.</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Greca, Ileana Maria; Moreira, Marco Antonio</p> <p>2000-01-01</p> <p>Reviews science education research into representations constructed by students in their interactions with the world, its phenomena, and artefacts. Features discussions of mental <span class="hlt">models</span>, conceptual <span class="hlt">models</span>, and the activity of <span class="hlt">modeling</span>. (Contains 30 references.) (Author/WRM)</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_12");'>12</a></li> <li><a href="#" onclick='return showDiv("page_13");'>13</a></li> <li class="active"><span>14</span></li> <li><a href="#" onclick='return showDiv("page_15");'>15</a></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_14 --> <div id="page_15" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_13");'>13</a></li> <li><a href="#" onclick='return showDiv("page_14");'>14</a></li> <li class="active"><span>15</span></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="281"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.math.tamu.edu/~rowell/RowellQCSem.pdf','EPRINT'); return false;" href="http://www.math.tamu.edu/~rowell/RowellQCSem.pdf"><span id="translatedtitle">Quantum Circuit <span class="hlt">Model</span> Topological <span class="hlt">Model</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Rowell, Eric C.</p> <p></p> <p>Quantum Circuit <span class="hlt">Model</span> Topological <span class="hlt">Model</span> Comparison of <span class="hlt">Models</span> Topological Quantum Computation Eric Rowell Texas A&M University October 2010 Eric Rowell Topological Quantum Computation #12;Quantum Circuit <span class="hlt">Model</span> Topological <span class="hlt">Model</span> Comparison of <span class="hlt">Models</span> Outline 1 Quantum Circuit <span class="hlt">Model</span> Gates, Circuits</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=137225&keyword=Human+AND+body+AND+still+AND+Evolving&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=43018595&CFTOKEN=49530955','EPA-EIMS'); return false;" href="http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=137225&keyword=Human+AND+body+AND+still+AND+Evolving&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=43018595&CFTOKEN=49530955"><span id="translatedtitle"><span class="hlt">MODEL</span> DEVELOPMENT - DOSE <span class="hlt">MODELS</span></span></a></p> <p><a target="_blank" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p></p> <p></p> <p><span class="hlt">Model</span> Development<br><br>Humans are exposed to mixtures of chemicals from multiple pathways and routes. These exposures may result from a single event or may accumulate over time if multiple exposure events occur. The traditional approach of assessing risk from a single chemica...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://ntrs.nasa.gov/search.jsp?R=19860023426&hterms=guthrie+test&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D10%26Ntt%3Dguthrie%2Btest','NASA-TRS'); return false;" href="http://ntrs.nasa.gov/search.jsp?R=19860023426&hterms=guthrie+test&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D10%26Ntt%3Dguthrie%2Btest"><span id="translatedtitle">Assessment <span class="hlt">models</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Pyle, J. A.; Butler, D. M.; Cariolle, D.; Garcia, R. R.; Grose, W. L.; Guthrie, P. D.; Ko, M.; Owens, A. J.; Plumb, R. A.; Prather, M. J.</p> <p>1985-01-01</p> <p>The types of <span class="hlt">models</span> used in assessment of possible chemical perturbations to the stratosphere are reviewed. The statue of one and two dimensional <span class="hlt">models</span> are discussed. The problem of <span class="hlt">model</span> validation is covered before the status of photochemical <span class="hlt">modeling</span> efforts is discussed. A hierarchy of tests for photochemical <span class="hlt">models</span> is presented.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=drafting+AND+effect&pg=3&id=EJ178879','ERIC'); return false;" href="http://eric.ed.gov/?q=drafting+AND+effect&pg=3&id=EJ178879"><span id="translatedtitle">Architectural <span class="hlt">Models</span></span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Levenson, Harold E.; Hurni, Andre</p> <p>1978-01-01</p> <p>Suggests building <span class="hlt">models</span> as a way to reinforce and enhance related subjects such as architectural drafting, structural carpentry, etc., and discusses time, materials, scales, tools or equipment needed, how to achieve realistic special effects, and the types of projects that can be built (<span class="hlt">model</span> of complete building, a panoramic <span class="hlt">model</span>, and <span class="hlt">model</span>…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://dspace.mit.edu/handle/1721.1/80786','EPRINT'); return false;" href="http://dspace.mit.edu/handle/1721.1/80786"><span id="translatedtitle">Fractionation of sulfur isotopes by Desulfovibrio vulgaris mutants lacking <span class="hlt">hydrogenases</span> or type I tetraheme cytochrome c[subscript 3</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Sim, Min Sub</p> <p></p> <p>The sulfur isotope effect produced by sulfate reducing microbes is commonly used to trace biogeochemical cycles of sulfur and carbon in aquatic and sedimentary environments. To test the contribution of intracellular coupling ...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.scs.uiuc.edu/rauchfus/refs/JACS_NH.pdf','EPRINT'); return false;" href="http://www.scs.uiuc.edu/rauchfus/refs/JACS_NH.pdf"><span id="translatedtitle">Iron Carbonyl Sulfides, Formaldehyde, and Amines Condense To Give the Proposed Azadithiolate Cofactor of the Fe-Only <span class="hlt">Hydrogenases</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Rauchfuss, Thomas B.</p> <p></p> <p>and the oxidation of dihydrogen, depending on the particular enzyme and its location in the cell.1 The ironIron Carbonyl Sulfides, Formaldehyde, and Amines Condense To Give the Proposed Azadithiolate to room temperature. The efficiency of the process can be tested by thin-layer chromatography on silica</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/1177288','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/1177288"><span id="translatedtitle">Systems Level Approaches to Understanding and Manipulating Heterocyst Differentiation in Nostoc Punctiforme: Sites of <span class="hlt">Hydrogenase</span> and Nitrogenase Synthesis and Activity</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Meeks, John C.</p> <p>2015-04-02</p> <p>Heterocysts are specialized cells that establish a physiologically low oxygen concentration; they function as the sites of oxygen-sensitive nitrogen fixation and hydrogen metabolism in certain filamentous cyanobacteria. They are present at a frequency of less than 10% of the cells and singly in a nonrandom spacing pattern in the filaments. The extent of differential gene expression during heterocyst differentiation was defined by DNA microarray analysis in wild type and mutant cultures of Nostoc punctiforme. The results in wild-type cultures identified two groups of genes; approximately 440 that are unique to heterocyst formation and function, and 500 that respond positively and negatively to the transient stress of nitrogen starvation. Nitrogen fixation is initiated within 24 h after induction, but the cultures require another 24 h before growth is reinitiated. Microarray analyses were conducted on strains with altered expression of three genes that regulate the presence and spacing of heterocysts in the filaments; loss of function or over expression of these genes increases the heterocyst frequency 2 to 3 fold compared to the wild-type. Mutations in the genes hetR and hetF result in the inability to differentiate heterocysts, whereas over expression of each gene individually yields multiple contiguous heterocysts at sites in the filaments; they are positive regulatory elements. Mutation of the gene patN results in an increase in heterocysts frequency, but, in this case, the heterocysts are singly spaced in the filaments with a decrease in the number of vegetative cells in the interval between heterocysts; this is a negative regulatory element. However, over expression of patN resulted in the wild-type heterocyst frequency and spacing pattern. Microarray results indicated HetR and HetF influence the transcription of a common set of about 395 genes, as well as about 350 genes unique to each protein. HetR is known to be a transcriptional regulator and HetF is predicted to be a protease, perhaps operating thorough stability of HetR; thus, the influence of HetF on transcription of a unique set of genes was unanticipated. These two proteins are also found in non-heterocyst-forming filamentous cyanobacteria and the results have implications on their other physiological role(s). The PatN protein is unique to heterocyst-forming cyanobacteria. Cytological analysis indicated PatN is present in only one of the two daughter cells following division, but is present in both cell less than 8 h after division. Microarray analysis indicated only five genes were differentially transcribed in the patN mutant compared to the wild type; three up-regulated genes that are known to influence heterocyst differentiation and two down-regulated genes that have an unassigned function. Mutational analyses indicted the two down-regulated genes do not have a distinct role in heterocyst differentiation. Thus, PatN only indirectly impacts transcription. These databases provide lists of differentially transcribed genes involved in nitrogen starvation and cellular differentiation that can be mined for detailed genetic analysis of the regulation of heterocyst formation and function for subsequent photo-biohydrogen production.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4497599','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4497599"><span id="translatedtitle">[FeFe]?<span class="hlt">Hydrogenase</span>: Protonation of {2Fe3S} Systems and Formation of Super-reduced Hydride States**</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Jablonskyt?, Aušra; Wright, Joseph A; Fairhurst, Shirley A; Webster, Lee R; Pickett, Christopher J</p> <p>2014-01-01</p> <p>The synthesis and crystallographic characterization of a complex possessing a well-defined {2Fe3S(?-H)}?core gives access to a paramagnetic bridging hydride with retention of the core geometry. Chemistry of this 35-electron species within the confines of a thin-layer FTIR spectro-electrochemistry cell provides evidence for a unprecedented super-reduced FeI(?-H)FeI intermediate. PMID:25079249</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=2808&keyword=momentum&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=41056291&CFTOKEN=64764134','EPA-EIMS'); return false;" href="http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=2808&keyword=momentum&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=41056291&CFTOKEN=64764134"><span id="translatedtitle"><span class="hlt">MODELS</span> - 3</span></a></p> <p><a target="_blank" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p></p> <p></p> <p><span class="hlt">Models</span>-3 is a third generation air quality <span class="hlt">modeling</span> system that contains a variety of tools to perform research and analysis of critical environmental questions and problems. These tools provide regulatory analysts and scientists with quicker results, greater scientific accuracy ...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=151530&keyword=Identifying+AND+bacteria&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=50671610&CFTOKEN=18397589','EPA-EIMS'); return false;" href="http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=151530&keyword=Identifying+AND+bacteria&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=50671610&CFTOKEN=18397589"><span id="translatedtitle">ENTRAINMENT <span class="hlt">MODELS</span></span></a></p> <p><a target="_blank" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p></p> <p></p> <p>This presentation presented information on entrainment <span class="hlt">models</span>. Entrainment <span class="hlt">models</span> use entrainment hypotheses to express the continuity equation. The advantage is that plume boundaries are known. A major disadvantage is that the problems that can be solved are rather simple. The ...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/19870016585','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/19870016585"><span id="translatedtitle">Turbulence <span class="hlt">modeling</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Rubesin, Morris W.</p> <p>1987-01-01</p> <p>Recent developments at several levels of statistical turbulence <span class="hlt">modeling</span> applicable to aerodynamics are briefly surveyed. Emphasis is on examples of <span class="hlt">model</span> improvements for transonic, two-dimensional flows. Experience with the development of these improved <span class="hlt">models</span> is cited to suggest methods of accelerating the <span class="hlt">modeling</span> process necessary to keep abreast of the rapid movement of computational fluid dynamics into the computation of complex three-dimensional flows.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=240424&keyword=trade+AND+policy&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=48160678&CFTOKEN=19884750','EPA-EIMS'); return false;" href="http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=240424&keyword=trade+AND+policy&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=48160678&CFTOKEN=19884750"><span id="translatedtitle">Phoenix <span class="hlt">model</span></span></a></p> <p><a target="_blank" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p></p> <p></p> <p>Phoenix (formerly referred to as the Second Generation <span class="hlt">Model</span> or SGM) is a global general equilibrium <span class="hlt">model</span> designed to analyze energy-economy-climate related questions and policy implications in the medium- to long-term. This <span class="hlt">model</span> disaggregates the global economy into 26 industr...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/245226','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/245226"><span id="translatedtitle">Dispersion <span class="hlt">modeling</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Sadar, A.J.</p> <p>1993-03-01</p> <p>Mathematical <span class="hlt">modeling</span> of air pollution dispersion has been performed for many years to estimate the impact of source emissions on air quality. EPA provides guidance on choosing appropriate computer <span class="hlt">models</span>, such as COMPLEX I for regulator applications. The agency says several <span class="hlt">models</span> are suitable for predicting air quality impacts for most situations.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=Two+AND+photon&pg=2&id=EJ020652','ERIC'); return false;" href="http://eric.ed.gov/?q=Two+AND+photon&pg=2&id=EJ020652"><span id="translatedtitle">Radiation <span class="hlt">Models</span></span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>James, W. G. G.</p> <p>1970-01-01</p> <p>Discusses the historical development of both the wave and the corpuscular photon <span class="hlt">model</span> of light. Suggests that students should be informed that the two <span class="hlt">models</span> are complementary and that each <span class="hlt">model</span> successfully describes a wide range of radiation phenomena. Cites 19 references which might be of interest to physics teachers and students. (LC)</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2013HESSD..1010535B','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2013HESSD..1010535B"><span id="translatedtitle">Hydrological <span class="hlt">models</span> are mediating <span class="hlt">models</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Babel, L. V.; Karssenberg, D.</p> <p>2013-08-01</p> <p>Despite the increasing role of <span class="hlt">models</span> in hydrological research and decision-making processes, only few accounts of the nature and function of <span class="hlt">models</span> exist in hydrology. Earlier considerations have traditionally been conducted while making a clear distinction between physically-based and conceptual <span class="hlt">models</span>. A new philosophical account, primarily based on the fields of physics and economics, transcends classes of <span class="hlt">models</span> and scientific disciplines by considering <span class="hlt">models</span> as "mediators" between theory and observations. The core of this approach lies in identifying <span class="hlt">models</span> as (1) being only partially dependent on theory and observations, (2) integrating non-deductive elements in their construction, and (3) carrying the role of instruments of scientific enquiry about both theory and the world. The applicability of this approach to hydrology is evaluated in the present article. Three widely used hydrological <span class="hlt">models</span>, each showing a different degree of apparent physicality, are confronted to the main characteristics of the "mediating <span class="hlt">models</span>" concept. We argue that irrespective of their kind, hydrological <span class="hlt">models</span> depend on both theory and observations, rather than merely on one of these two domains. Their construction is additionally involving a large number of miscellaneous, external ingredients, such as past experiences, <span class="hlt">model</span> objectives, knowledge and preferences of the <span class="hlt">modeller</span>, as well as hardware and software resources. We show that hydrological <span class="hlt">models</span> convey the role of instruments in scientific practice by mediating between theory and the world. It results from these considerations that the traditional distinction between physically-based and conceptual <span class="hlt">models</span> is necessarily too simplistic and refers at best to the stage at which theory and observations are steering <span class="hlt">model</span> construction. The large variety of ingredients involved in <span class="hlt">model</span> construction would deserve closer attention, for being rarely explicitly presented in peer-reviewed literature. We believe that devoting more importance to identifying and communicating on the many factors involved in <span class="hlt">model</span> development might increase transparency of <span class="hlt">model</span> building.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://ntrs.nasa.gov/search.jsp?R=20000024740&hterms=chlorofluorocarbon&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D30%26Ntt%3Dchlorofluorocarbon','NASA-TRS'); return false;" href="http://ntrs.nasa.gov/search.jsp?R=20000024740&hterms=chlorofluorocarbon&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D30%26Ntt%3Dchlorofluorocarbon"><span id="translatedtitle"><span class="hlt">Model</span> Experiments and <span class="hlt">Model</span> Descriptions</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Jackman, Charles H.; Ko, Malcolm K. W.; Weisenstein, Debra; Scott, Courtney J.; Shia, Run-Lie; Rodriguez, Jose; Sze, N. D.; Vohralik, Peter; Randeniya, Lakshman; Plumb, Ian</p> <p>1999-01-01</p> <p>The Second Workshop on Stratospheric <span class="hlt">Models</span> and Measurements Workshop (M&M II) is the continuation of the effort previously started in the first Workshop (M&M I, Prather and Remsberg [1993]) held in 1992. As originally stated, the aim of M&M is to provide a foundation for establishing the credibility of stratospheric <span class="hlt">models</span> used in environmental assessments of the ozone response to chlorofluorocarbons, aircraft emissions, and other climate-chemistry interactions. To accomplish this, a set of measurements of the present day atmosphere was selected. The intent was that successful simulations of the set of measurements should become the prerequisite for the acceptance of these <span class="hlt">models</span> as having a reliable prediction for future ozone behavior. This section is divided into two: <span class="hlt">model</span> experiment and <span class="hlt">model</span> descriptions. In the <span class="hlt">model</span> experiment, participant were given the charge to design a number of experiments that would use observations to test whether <span class="hlt">models</span> are using the correct mechanisms to simulate the distributions of ozone and other trace gases in the atmosphere. The purpose is closely tied to the needs to reduce the uncertainties in the <span class="hlt">model</span> predicted responses of stratospheric ozone to perturbations. The specifications for the experiments were sent out to the <span class="hlt">modeling</span> community in June 1997. Twenty eight <span class="hlt">modeling</span> groups responded to the requests for input. The first part of this section discusses the different <span class="hlt">modeling</span> group, along with the experiments performed. Part two of this section, gives brief descriptions of each <span class="hlt">model</span> as provided by the individual <span class="hlt">modeling</span> groups.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2014AGUFMIN43B3684Y','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2014AGUFMIN43B3684Y"><span id="translatedtitle"><span class="hlt">Model</span> Reduction in Groundwater <span class="hlt">Modeling</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Yeh, W. W. G.</p> <p>2014-12-01</p> <p><span class="hlt">Model</span> reduction has been shown to be a very effective method for reducing the computational burden of large-scale simulations. <span class="hlt">Model</span> reduction techniques preserve much of the physical knowledge of the system and primarily seek to remove components from the <span class="hlt">model</span> that do not provide significant information of interest. Proper Orthogonal Decomposition (POD) is a <span class="hlt">model</span> reduction technique by which a system of ordinary equations is projected onto a much smaller subspace in such a way that the span of the subspace is equal to the span of the original full <span class="hlt">model</span> space. Basically, the POD technique selects a small number of orthonormal basis functions (principal components) that span the spatial variability of the solutions. In this way the state variable (head) is approximated by a linear combination of these basis functions and, using a Galerkin projection, the dimension of the problem is significantly reduced. It has been shown that for a highly discritized <span class="hlt">model</span>, the reduced <span class="hlt">model</span> can be two to three orders of magnitude smaller than the original <span class="hlt">model</span> and runs 1,000 faster. More importantly, the reduced <span class="hlt">model</span> captures the dominating characteristics of the full <span class="hlt">model</span> and produces sufficiently accurate solutions. One of the major tasks in the development of the reduced <span class="hlt">model</span> is the selection of snapshots which are used to determine the dominant eigenvectors. This paper discusses ways to optimize the snapshot selection. Additionally, the paper also discusses applications of the reduced <span class="hlt">model</span> to parameter estimation, Monte Carlo simulation and experimental design in groundwater <span class="hlt">modeling</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/6245971','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/6245971"><span id="translatedtitle">ICRF <span class="hlt">modelling</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Phillips, C.K.</p> <p>1985-12-01</p> <p>This lecture provides a survey of the methods used to <span class="hlt">model</span> fast magnetosonic wave coupling, propagation, and absorption in tokamaks. The validity and limitations of three distinct types of <span class="hlt">modelling</span> codes, which will be contrasted, include discrete <span class="hlt">models</span> which utilize ray tracing techniques, approximate continuous field <span class="hlt">models</span> based on a parabolic approximation of the wave equation, and full field <span class="hlt">models</span> derived using finite difference techniques. Inclusion of mode conversion effects in these <span class="hlt">models</span> and modification of the minority distribution function will also be discussed. The lecture will conclude with a presentation of time-dependent global transport simulations of ICRF-heated tokamak discharges obtained in conjunction with the ICRF <span class="hlt">modelling</span> codes. 52 refs., 15 figs.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/828102','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/828102"><span id="translatedtitle">Ventilation <span class="hlt">Model</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>H. Yang</p> <p>1999-11-04</p> <p>The purpose of this analysis and <span class="hlt">model</span> report (AMR) for the Ventilation <span class="hlt">Model</span> is to analyze the effects of pre-closure continuous ventilation in the Engineered Barrier System (EBS) emplacement drifts and provide heat removal data to support EBS design. It will also provide input data (initial conditions, and time varying boundary conditions) for the EBS post-closure performance assessment and the EBS Water Distribution and Removal Process <span class="hlt">Model</span>. The objective of the analysis is to develop, describe, and apply calculation methods and <span class="hlt">models</span> that can be used to predict thermal conditions within emplacement drifts under forced ventilation during the pre-closure period. The scope of this analysis includes: (1) Provide a general description of effects and heat transfer process of emplacement drift ventilation. (2) Develop a <span class="hlt">modeling</span> approach to simulate the impacts of pre-closure ventilation on the thermal conditions in emplacement drifts. (3) Identify and document inputs to be used for <span class="hlt">modeling</span> emplacement ventilation. (4) Perform calculations of temperatures and heat removal in the emplacement drift. (5) Address general considerations of the effect of water/moisture removal by ventilation on the repository thermal conditions. The numerical <span class="hlt">modeling</span> in this document will be limited to heat-only <span class="hlt">modeling</span> and calculations. Only a preliminary assessment of the heat/moisture ventilation effects and <span class="hlt">modeling</span> method will be performed in this revision. <span class="hlt">Modeling</span> of moisture effects on heat removal and emplacement drift temperature may be performed in the future.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20120013440','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20120013440"><span id="translatedtitle">Climate <span class="hlt">Models</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Druyan, Leonard M.</p> <p>2012-01-01</p> <p>Climate <span class="hlt">models</span> is a very broad topic, so a single volume can only offer a small sampling of relevant research activities. This volume of 14 chapters includes descriptions of a variety of <span class="hlt">modeling</span> studies for a variety of geographic regions by an international roster of authors. The climate research community generally uses the rubric climate <span class="hlt">models</span> to refer to organized sets of computer instructions that produce simulations of climate evolution. The code is based on physical relationships that describe the shared variability of meteorological parameters such as temperature, humidity, precipitation rate, circulation, radiation fluxes, etc. Three-dimensional climate <span class="hlt">models</span> are integrated over time in order to compute the temporal and spatial variations of these parameters. <span class="hlt">Model</span> domains can be global or regional and the horizontal and vertical resolutions of the computational grid vary from <span class="hlt">model</span> to <span class="hlt">model</span>. Considering the entire climate system requires accounting for interactions between solar insolation, atmospheric, oceanic and continental processes, the latter including land hydrology and vegetation. <span class="hlt">Model</span> simulations may concentrate on one or more of these components, but the most sophisticated <span class="hlt">models</span> will estimate the mutual interactions of all of these environments. Advances in computer technology have prompted investments in more complex <span class="hlt">model</span> configurations that consider more phenomena interactions than were possible with yesterday s computers. However, not every attempt to add to the computational layers is rewarded by better <span class="hlt">model</span> performance. Extensive research is required to test and document any advantages gained by greater sophistication in <span class="hlt">model</span> formulation. One purpose for publishing climate <span class="hlt">model</span> research results is to present purported advances for evaluation by the scientific community.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_13");'>13</a></li> <li><a href="#" onclick='return showDiv("page_14");'>14</a></li> <li class="active"><span>15</span></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_15 --> <div id="page_16" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_14");'>14</a></li> <li><a href="#" onclick='return showDiv("page_15");'>15</a></li> <li class="active"><span>16</span></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="301"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/821313','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/821313"><span id="translatedtitle">Measurement and Calculation of Electrochemical Potentials in Hydrogenated High Temperature Water, including an Evaluation of the Yttria-Stabilized Zirconia/Iron-Iron Oxide (<span class="hlt">Fe/Fe</span>3O4) Probe as Reference Electrode</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Steven A. Attanasio; David S. Morton; Mark A. Ando</p> <p>2001-10-22</p> <p>The importance of knowing the electrochemical corrosion potential (ECP, also referred to as E{sub con}) of nickel-base alloys in hydrogenated water is related to the need to understand the effects of dissolved (i.e., aqueous) hydrogen concentration ([H{sub 2}]) on primary water stress corrosion cracking (PWSCC). Also, the use of a reference electrode (RE) can improve test quality by heightening the ability to detect instances of out-of-specification or unexpected chemistry. Three methods are used to measure and calculate the ECP of nickel-based alloys in hydrogenated water containing {approx} 1 to 150 scc/kg H{sub 2} (0.1 to 13.6 ppm H{sub 2}) at 260 to 360 C. The three methods are referred to as the specimen/component method, the platinum (Pt) method, and the yttria-stabilized zirconia/iron-iron oxide (YSZ/Fe-Fe{sub 3}O{sub 4}) RE method. The specimen/component method relies upon the assumption that the specimen or component behaves as a hydrogen electrode, and its E{sub corr} is calculated using the Nernst equation. The present work shows that this method is valid for aqueous H{sub 2} levels {ge} {approx} 5 to 10 scc/kg H{sub 2}. The Pt method uses a voltage measurement between the specimen or component and a Pt electrode, with the Pt assumed to behave as a hydrogen electrode; this method is valid as long as the aqueous H{sub 2}level is known. The YSZ/Fe-Fe{sub 3}O{sub 4}, which represents a relatively new approach for measuring E{sub corr} in this environment, can be used even if the aqueous H{sub 2} level is unknown. The electrochemical performance of the YSZ/Fe-Fe{sub 3}O{sub 4} probe supports its viability as a RE for use in high temperature hydrogenated water. Recent design modifications incorporating a teflon sealant have improved the durability of this RE (however, some of the REs do still fail prematurely due to water in-leakage). The Pt method is judged to represent the best overall approach, though there are cases where the other methods are superior. For example, the specimen/component method provides the simplest approach for calculating the E{sub corr} of plant components, and the YSZ/Fe-Fe{sub 3}O{sub 4} RE method provides the best approach if the H{sub 2} level is unknown, or in off-nominal chemistry conditions. The present paper describes the use of these methods to determine the ECP of a specimen or component versus the ECP of the nickel/nickel oxide (Ni/NiO) phase transition, which is important since prior work has shown that this parameter (ECP-ECP{sub Ni/NiO}) can be used to assess aqueous H{sub 2} effects on PWSCC.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25370904','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25370904"><span id="translatedtitle">Effects of an intensive hog farming operation on groundwater in east Mediterranean (II): a study on K?, Na?, Cl ?, PO?³?-P, Ca²?, Mg²?, <span class="hlt">Fe³?/Fe</span>²?, Mn²?, Cu²?, Zn²? and Ni²?.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Michalopoulos, Charalampos; Tzamtzis, Nikolaos; Liodakis, Stylianos</p> <p>2014-12-01</p> <p>The application of treated animal wastewater generated in concentrated animal feeding operations on surface soil (within farm borders) leads to degradation of groundwater. Effects of an intensive hog farming operation, located at a Mediterranean limestone soil coastal area, on groundwater were investigated. Treated animal wastewater was discharged on a small plot (~10.8 ha) with a geologic fault. Samples were taken from seven groundwater monitoring wells close to the farm. A significant increase of K(+), Na(+), Cl(-), PO4 (3-)-P, Ca(2+) and Mg(2+) concentrations was found in monitoring wells which are affected by the subsurface flow of groundwater. Concentrations of Fe(3+)/Fe(2+), Mn(2+), Cu(2+), Zn(2+) and Ni(2+) in all groundwater monitoring wells were extremely low. During the winter, significant increases in concentrations of K(+) and PO4 (3-)-P were noted and attributed to high precipitation, which assisted in the leaching of K and P to groundwater. PMID:25370904</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20010068934','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20010068934"><span id="translatedtitle">Cloud <span class="hlt">Modeling</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Tao, Wei-Kuo; Moncrieff, Mitchell; Einaud, Franco (Technical Monitor)</p> <p>2001-01-01</p> <p>Numerical cloud <span class="hlt">models</span> have been developed and applied extensively to study cloud-scale and mesoscale processes during the past four decades. The distinctive aspect of these cloud <span class="hlt">models</span> is their ability to treat explicitly (or resolve) cloud-scale dynamics. This requires the cloud <span class="hlt">models</span> to be formulated from the non-hydrostatic equations of motion that explicitly include the vertical acceleration terms since the vertical and horizontal scales of convection are similar. Such <span class="hlt">models</span> are also necessary in order to allow gravity waves, such as those triggered by clouds, to be resolved explicitly. In contrast, the hydrostatic approximation, usually applied in global or regional <span class="hlt">models</span>, does allow the presence of gravity waves. In addition, the availability of exponentially increasing computer capabilities has resulted in time integrations increasing from hours to days, domain grids boxes (points) increasing from less than 2000 to more than 2,500,000 grid points with 500 to 1000 m resolution, and 3-D <span class="hlt">models</span> becoming increasingly prevalent. The cloud resolving <span class="hlt">model</span> is now at a stage where it can provide reasonably accurate statistical information of the sub-grid, cloud-resolving processes poorly parameterized in climate <span class="hlt">models</span> and numerical prediction <span class="hlt">models</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/837038','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/837038"><span id="translatedtitle">Ventilation <span class="hlt">Model</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>V. Chipman</p> <p>2002-10-05</p> <p>The purpose of the Ventilation <span class="hlt">Model</span> is to simulate the heat transfer processes in and around waste emplacement drifts during periods of forced ventilation. The <span class="hlt">model</span> evaluates the effects of emplacement drift ventilation on the thermal conditions in the emplacement drifts and surrounding rock mass, and calculates the heat removal by ventilation as a measure of the viability of ventilation to delay the onset of peak repository temperature and reduce its magnitude. The heat removal by ventilation is temporally and spatially dependent, and is expressed as the fraction of heat carried away by the ventilation air compared to the fraction of heat produced by radionuclide decay. One minus the heat removal is called the wall heat fraction, or the remaining amount of heat that is transferred via conduction to the surrounding rock mass. Downstream <span class="hlt">models</span>, such as the ''Multiscale Thermohydrologic <span class="hlt">Model</span>'' (BSC 2001), use the wall heat fractions as outputted from the Ventilation <span class="hlt">Model</span> to initialize their post-closure analyses. The Ventilation <span class="hlt">Model</span> report was initially developed to analyze the effects of preclosure continuous ventilation in the Engineered Barrier System (EBS) emplacement drifts, and to provide heat removal data to support EBS design. Revision 00 of the Ventilation <span class="hlt">Model</span> included documentation of the <span class="hlt">modeling</span> results from the ANSYS-based heat transfer <span class="hlt">model</span>. The purposes of Revision 01 of the Ventilation <span class="hlt">Model</span> are: (1) To validate the conceptual <span class="hlt">model</span> for preclosure ventilation of emplacement drifts and verify its numerical application in accordance with new procedural requirements as outlined in AP-SIII-10Q, <span class="hlt">Models</span> (Section 7.0). (2) To satisfy technical issues posed in KTI agreement RDTME 3.14 (Reamer and Williams 2001a). Specifically to demonstrate, with respect to the ANSYS ventilation <span class="hlt">model</span>, the adequacy of the discretization (Section 6.2.3.1), and the downstream applicability of the <span class="hlt">model</span> results (i.e. wall heat fractions) to initialize post-closure thermal <span class="hlt">models</span> (Section 6.6). (3) To satisfy the remainder of KTI agreement TEF 2.07 (Reamer and Williams 2001b). Specifically to provide the results of post-test ANSYS <span class="hlt">modeling</span> of the Atlas Facility forced convection tests (Section 7.1.2). This portion of the <span class="hlt">model</span> report also serves as a validation exercise per AP-SIII.10Q, <span class="hlt">Models</span>, for the ANSYS ventilation <span class="hlt">model</span>. (4) To further satisfy KTI agreements RDTME 3.01 and 3.14 (Reamer and Williams 2001a) by providing the source documentation referred to in the KTI Letter Report, ''Effect of Forced Ventilation on Thermal-Hydrologic Conditions in the Engineered Barrier System and Near Field Environment'' (Williams 2002). Specifically to provide the results of the MULTIFLUX <span class="hlt">model</span> which simulates the coupled processes of heat and mass transfer in and around waste emplacement drifts during periods of forced ventilation. This portion of the <span class="hlt">model</span> report is presented as an Alternative Conceptual <span class="hlt">Model</span> with a numerical application, and also provides corroborative results used for <span class="hlt">model</span> validation purposes (Section 6.3 and 6.4).</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/878658','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/878658"><span id="translatedtitle"><span class="hlt">Model</span> Selection for Geostatistical <span class="hlt">Models</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Hoeting, Jennifer A.; Davis, Richard A.; Merton, Andrew A.; Thompson, Sandra E.</p> <p>2006-02-01</p> <p>We consider the problem of <span class="hlt">model</span> selection for geospatial data. Spatial correlation is typically ignored in the selection of explanatory variables and this can influence <span class="hlt">model</span> selection results. For example, the inclusion or exclusion of particular explanatory variables may not be apparent when spatial correlation is ignored. To address this problem, we consider the Akaike Information Criterion (AIC) as applied to a geostatistical <span class="hlt">model</span>. We offer a heuristic derivation of the AIC in this context and provide simulation results that show that using AIC for a geostatistical <span class="hlt">model</span> is superior to the often used approach of ignoring spatial correlation in the selection of explanatory variables. These ideas are further demonstrated via a <span class="hlt">model</span> for lizard abundance. We also employ the principle of minimum description length (MDL) to variable selection for the geostatistical <span class="hlt">model</span>. The effect of sampling design on the selection of explanatory covariates is also explored.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=star&pg=3&id=EJ1046112','ERIC'); return false;" href="http://eric.ed.gov/?q=star&pg=3&id=EJ1046112"><span id="translatedtitle"><span class="hlt">Modeling</span> Sunspots</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Oh, Phil Seok; Oh, Sung Jin</p> <p>2013-01-01</p> <p><span class="hlt">Modeling</span> in science has been studied by education researchers for decades and is now being applied broadly in school. It is among the scientific practices featured in the "Next Generation Science Standards" ("NGSS") (Achieve Inc. 2013). This article describes <span class="hlt">modeling</span> activities in an extracurricular science club in a high…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://files.eric.ed.gov/fulltext/ED024022.pdf','ERIC'); return false;" href="http://files.eric.ed.gov/fulltext/ED024022.pdf"><span id="translatedtitle">Phonological <span class="hlt">Models</span>.</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Ballard, W.L.</p> <p>1968-01-01</p> <p>The article discusses <span class="hlt">models</span> of synchronic and diachronic phonology and suggests changes in them. The basic generative <span class="hlt">model</span> of phonology is outlined with the author's reinterpretations. The systematic phonemic level is questioned in terms of its unreality with respect to linguistic performance and its lack of validity with respect to historical…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/19950020245','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/19950020245"><span id="translatedtitle">Turbulence <span class="hlt">modeling</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Bardina, Jorge E.</p> <p>1995-01-01</p> <p>The objective of this work is to develop, verify, and incorporate the baseline two-equation turbulence <span class="hlt">models</span> which account for the effects of compressibility into the three-dimensional Reynolds averaged Navier-Stokes (RANS) code and to provide documented descriptions of the <span class="hlt">models</span> and their numerical procedures so that they can be implemented into 3-D CFD codes for engineering applications.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=air+AND+pollutants&pg=4&id=EJ222510','ERIC'); return false;" href="http://eric.ed.gov/?q=air+AND+pollutants&pg=4&id=EJ222510"><span id="translatedtitle">Dispersion <span class="hlt">Modeling</span>.</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Budiansky, Stephen</p> <p>1980-01-01</p> <p>This article discusses the need for more accurate and complete input data and field verification of the various <span class="hlt">models</span> of air pollutant dispension. Consideration should be given to changing the form of air quality standards based on enhanced dispersion <span class="hlt">modeling</span> techniques. (Author/RE)</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/931637','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/931637"><span id="translatedtitle"><span class="hlt">Model</span> Execution</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Perumalla, Kalyan S</p> <p>2007-01-01</p> <p>A computer software-based <span class="hlt">model</span> is typically designed to produce a trace of system evolution over time. The actual process of computing the <span class="hlt">model</span> state and producing the state values as the simulation time is advanced is called <span class="hlt">model</span> execution. <span class="hlt">Models</span> could be designed with a specific execution technique in mind, or could be generally amenable to multiple different execution techniques. Two popular methods that are used to execute <span class="hlt">models</span> are: time-stepped method and discrete-event method. Each of these methods could in turn be executed either sequentially (on a single processor), or in parallel (using multiple processors concurrently). In this chapter, we describe the time-stepped and discrete event execution methods and outline some of the common approaches to their sequential and parallel execution. Execution concepts common to the methods are described followed by implementation details of the methods.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/1062195','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/1062195"><span id="translatedtitle">OSPREY <span class="hlt">Model</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Veronica J. Rutledge</p> <p>2013-01-01</p> <p>The absence of industrial scale nuclear fuel reprocessing in the U.S. has precluded the necessary driver for developing the advanced simulation capability now prevalent in so many other countries. Thus, it is essential to <span class="hlt">model</span> complex series of unit operations to simulate, understand, and predict inherent transient behavior and feedback loops. A capability of accurately simulating the dynamic behavior of advanced fuel cycle separation processes will provide substantial cost savings and many technical benefits. The specific fuel cycle separation process discussed in this report is the off-gas treatment system. The off-gas separation consists of a series of scrubbers and adsorption beds to capture constituents of interest. Dynamic <span class="hlt">models</span> are being developed to simulate each unit operation involved so each unit operation can be used as a stand-alone <span class="hlt">model</span> and in series with multiple others. Currently, an adsorption <span class="hlt">model</span> has been developed within Multi-physics Object Oriented Simulation Environment (MOOSE) developed at the Idaho National Laboratory (INL). Off-gas Separation and REcoverY (OSPREY) <span class="hlt">models</span> the adsorption of off-gas constituents for dispersed plug flow in a packed bed under non-isothermal and non-isobaric conditions. Inputs to the <span class="hlt">model</span> include gas, sorbent, and column properties, equilibrium and kinetic data, and inlet conditions. The simulation outputs component concentrations along the column length as a function of time from which breakthrough data is obtained. The breakthrough data can be used to determine bed capacity, which in turn can be used to size columns. It also outputs temperature along the column length as a function of time and pressure drop along the column length. Experimental data and parameters were input into the adsorption <span class="hlt">model</span> to develop <span class="hlt">models</span> specific for krypton adsorption. The same can be done for iodine, xenon, and tritium. The <span class="hlt">model</span> will be validated with experimental breakthrough curves. Customers will be given access to OSPREY to used and evaluate the <span class="hlt">model</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/1811477','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/1811477"><span id="translatedtitle">Phenomenological <span class="hlt">models</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Braby, L A</p> <p>1991-01-01</p> <p>The biological effects of ionizing radiation exposure are the result of a complex sequence of physical, chemical, biochemical, and physiological interactions which are modified by characteristics of the radiation, the timing of its administration, the chemical and physical environment, and the nature of the biological system. However, it is generally agreed that the health effects in animals originate from changes in individual cells, or possibly small groups of cells, and that these cellular changes are initiated by ionizations and excitations produced by the passage of charged particles through the cells. One way to begin a search for an understanding of health effects of radiation is through the development of phenomenological <span class="hlt">models</span> of the response. Many <span class="hlt">models</span> have been presented and tested in the slowly evolving process of characterizing cellular response. Different phenomena (LET dependence, dose rate effect, oxygen effect etc.) and different end points (cell survival, aberration formation, transformation, etc.) have been observed, and no single <span class="hlt">model</span> has been developed to cover all of them. Instead, a range of <span class="hlt">models</span> covering different end points and phenomena have developed in parallel. Many of these <span class="hlt">models</span> employ similar assumptions about some underlying processes while differing about the nature of others. An attempt is made to organize many of the <span class="hlt">models</span> into groups with similar features and to compare the consequences of those features with the actual experimental observations. It is assumed that by showing that some assumptions are inconsistent with experimental observations, the job of devising and testing mechanistic <span class="hlt">models</span> can be simplified. PMID:1811477</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/474433','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/474433"><span id="translatedtitle">Modular <span class="hlt">Modeling</span> System <span class="hlt">Model</span> Builder</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>McKim, C.S.; Matthews, M.T.</p> <p>1996-12-31</p> <p>The latest release of the Modular <span class="hlt">Modeling</span> System (MMS) <span class="hlt">Model</span> Builder adds still more time-saving features to an already powerful MMS dynamic-simulation tool set. The <span class="hlt">Model</span> Builder takes advantage of 32-bit architecture within the Microsoft Windows 95/NT{trademark} Operating Systems to better integrate a mature library of power-plant components. In addition, the MMS Library of components can now be modified and extended with a new tool named MMS CompGen{trademark}. The MMS <span class="hlt">Model</span> Builder allows the user to quickly build a graphical schematic representation for a plant by selecting from a library of predefined power plant components to dynamically simulate their operation. In addition, each component has a calculation subroutine stored in a dynamic-link library (DLL), which facilitates the determination of a steady-state condition and performance of routine calculations for the component. These calculations, termed auto-parameterization, help avoid repetitive and often tedious hand calculations for <span class="hlt">model</span> initialization. In striving to meet the needs for large <span class="hlt">models</span> and increase user productivity, the MMS <span class="hlt">Model</span> Builder has been completely revamped to make power plant <span class="hlt">model</span> creation and maintainability easier and more efficient.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=199951&keyword=PHP&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=56083972&CFTOKEN=68596417','EPA-EIMS'); return false;" href="http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=199951&keyword=PHP&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=56083972&CFTOKEN=68596417"><span id="translatedtitle">Energy <span class="hlt">Models</span></span></a></p> <p><a target="_blank" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p></p> <p></p> <p>Energy <span class="hlt">models</span> characterize the energy system, its evolution, and its interactions with the broader economy. The energy system consists of primary resources, including both fossil fuels and renewables; power plants, refineries, and other technologies to process and convert these r...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/1047128','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/1047128"><span id="translatedtitle">Programming <span class="hlt">models</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Daniel, David J; Mc Pherson, Allen; Thorp, John R; Barrett, Richard; Clay, Robert; De Supinski, Bronis; Dube, Evi; Heroux, Mike; Janssen, Curtis; Langer, Steve; Laros, Jim</p> <p>2011-01-14</p> <p>A programming <span class="hlt">model</span> is a set of software technologies that support the expression of algorithms and provide applications with an abstract representation of the capabilities of the underlying hardware architecture. The primary goals are productivity, portability and performance.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/10124827','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/10124827"><span id="translatedtitle">Mechanistic <span class="hlt">models</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Curtis, S.B.</p> <p>1990-09-01</p> <p>Several <span class="hlt">models</span> and theories are reviewed that incorporate the idea of radiation-induced lesions (repairable and/or irreparable) that can be related to molecular lesions in the DNA molecule. Usually the DNA double-strand or chromatin break is suggested as the critical lesion. In the <span class="hlt">models</span>, the shoulder on the low-LET survival curve is hypothesized as being due to one (or more) of the following three mechanisms: (1) ``interaction`` of lesions produced by statistically independent particle tracks; (2) nonlinear (i.e., linear-quadratic) increase in the yield of initial lesions, and (3) saturation of repair processes at high dose. Comparisons are made between the various approaches. Several significant advances in <span class="hlt">model</span> development are discussed; in particular, a description of the matrix formulation of the Markov versions of the RMR and LPL <span class="hlt">models</span> is given. The more advanced theories have incorporated statistical fluctuations in various aspects of the energy-loss and lesion-formation process. An important direction is the inclusion of physical and chemical processes into the formulations by incorporating relevant track structure theory (Monte Carlo track simulations) and chemical reactions of radiation-induced radicals. At the biological end, identification of repair genes and how they operate as well as a better understanding of how DNA misjoinings lead to lethal chromosome aberrations are needed for appropriate inclusion into the theories. More effort is necessary to <span class="hlt">model</span> the complex end point of radiation-induced carcinogenesis.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/5679976','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/5679976"><span id="translatedtitle">Mechanistic <span class="hlt">models</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Curtis, S.B.</p> <p>1990-09-01</p> <p>Several <span class="hlt">models</span> and theories are reviewed that incorporate the idea of radiation-induced lesions (repairable and/or irreparable) that can be related to molecular lesions in the DNA molecule. Usually the DNA double-strand or chromatin break is suggested as the critical lesion. In the <span class="hlt">models</span>, the shoulder on the low-LET survival curve is hypothesized as being due to one (or more) of the following three mechanisms: (1) interaction'' of lesions produced by statistically independent particle tracks; (2) nonlinear (i.e., linear-quadratic) increase in the yield of initial lesions, and (3) saturation of repair processes at high dose. Comparisons are made between the various approaches. Several significant advances in <span class="hlt">model</span> development are discussed; in particular, a description of the matrix formulation of the Markov versions of the RMR and LPL <span class="hlt">models</span> is given. The more advanced theories have incorporated statistical fluctuations in various aspects of the energy-loss and lesion-formation process. An important direction is the inclusion of physical and chemical processes into the formulations by incorporating relevant track structure theory (Monte Carlo track simulations) and chemical reactions of radiation-induced radicals. At the biological end, identification of repair genes and how they operate as well as a better understanding of how DNA misjoinings lead to lethal chromosome aberrations are needed for appropriate inclusion into the theories. More effort is necessary to <span class="hlt">model</span> the complex end point of radiation-induced carcinogenesis.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/19920001089','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/19920001089"><span id="translatedtitle"><span class="hlt">Modeling</span> reality</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Denning, Peter J.</p> <p>1990-01-01</p> <p>Although powerful computers have allowed complex physical and manmade hardware systems to be <span class="hlt">modeled</span> successfully, we have encountered persistent problems with the reliability of computer <span class="hlt">models</span> for systems involving human learning, human action, and human organizations. This is not a misfortune; unlike physical and manmade systems, human systems do not operate under a fixed set of laws. The rules governing the actions allowable in the system can be changed without warning at any moment, and can evolve over time. That the governing laws are inherently unpredictable raises serious questions about the reliability of <span class="hlt">models</span> when applied to human situations. In these domains, computers are better used, not for prediction and planning, but for aiding humans. Examples are systems that help humans speculate about possible futures, offer advice about possible actions in a domain, systems that gather information from the networks, and systems that track and support work flows in organizations.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/6525424','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/6525424"><span id="translatedtitle">Supernova <span class="hlt">models</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Woosley, S.E.; Weaver, T.A.</p> <p>1980-01-01</p> <p>Recent progress in understanding the observed properties of Type I supernovae as a consequence of the thermonuclear detonation of white dwarf stars and the ensuing decay of the /sup 56/Ni produced therein is reviewed. Within the context of this <span class="hlt">model</span> for Type I explosions and the 1978 <span class="hlt">model</span> for Type II explosions, the expected nucleosynthesis and gamma-line spectra from both kinds of supernovae are presented. Finally, a qualitatively new approach to the problem of massive star death and Type II supernovae based upon a combination of rotation and thermonuclear burning is discussed.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://bcp.phys.strath.ac.uk/wp-content/uploads/2011/03/NTH-PCCP-CO-CN.pdf','EPRINT'); return false;" href="http://bcp.phys.strath.ac.uk/wp-content/uploads/2011/03/NTH-PCCP-CO-CN.pdf"><span id="translatedtitle">This journal is c the Owner Societies 2011 Phys. Chem. Chem. Phys., 2011, 13, 1029510305 10295 Cite this: Phys. Chem. Chem. Phys., 2011, 13, 1029510305</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Strathclyde, University of</p> <p></p> <p>,c Christopher J. Pickettb and Neil T. Hunt*a Received 2nd March 2011, Accepted 30th March 2011 DOI: 10.1039/c1cp of the active site of the [FeFe]-<span class="hlt">hydrogenase</span> enzyme, have been examined via ultrafast 2D-IR spectroscopy <span class="hlt">model</span> systems based upon the iron­sulfur cluster architecture of the enzyme active site are also able</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_14");'>14</a></li> <li><a href="#" onclick='return showDiv("page_15");'>15</a></li> <li class="active"><span>16</span></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_16 --> <div id="page_17" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_15");'>15</a></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li class="active"><span>17</span></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="321"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=density+AND+water&pg=4&id=EJ758568','ERIC'); return false;" href="http://eric.ed.gov/?q=density+AND+water&pg=4&id=EJ758568"><span id="translatedtitle"><span class="hlt">Modeling</span> Convection</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Ebert, James R.; Elliott, Nancy A.; Hurteau, Laura; Schulz, Amanda</p> <p>2004-01-01</p> <p>Students must understand the fundamental process of convection before they can grasp a wide variety of Earth processes, many of which may seem abstract because of the scales on which they operate. Presentation of a very visual, concrete <span class="hlt">model</span> prior to instruction on these topics may facilitate students' understanding of processes that are largely…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=216023&keyword=K-T+AND+boundary&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=39492952&CFTOKEN=78884198','EPA-EIMS'); return false;" href="http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=216023&keyword=K-T+AND+boundary&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=39492952&CFTOKEN=78884198"><span id="translatedtitle">Atmospheric <span class="hlt">Modeling</span></span></a></p> <p><a target="_blank" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p></p> <p></p> <p>Although air quality <span class="hlt">models</span> have been applied historically to address issues specific to ambient air quality standards (i.e., one criteria pollutant at a time) or welfare (e.g.. acid deposition or visibility impairment). they are inherently multipollutant based. Therefore. in pri...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2009chil.book..121B','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2009chil.book..121B"><span id="translatedtitle">Situation <span class="hlt">Modeling</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Brdiczka, Oliver; Crowley, James L.; Cu?ín, Jan; Kleindienst, Jan</p> <p></p> <p>CHIL services are intended to anticipate the needs of their users. An important step toward this is to <span class="hlt">model</span> and understand human behavior. Human activity can be sensed and recognized (as described in Chapter 11). However, a higher-level representation of human actions and human relationships (social context) is necessary to effectively describe human behavior and detect human needs.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=muscle&pg=2&id=EJ780578','ERIC'); return false;" href="http://eric.ed.gov/?q=muscle&pg=2&id=EJ780578"><span id="translatedtitle"><span class="hlt">Modeling</span> Muscles</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Goodwyn, Lauren; Salm, Sarah</p> <p>2007-01-01</p> <p>Teaching the anatomy of the muscle system to high school students can be challenging. Students often learn about muscle anatomy by memorizing information from textbooks or by observing plastic, inflexible <span class="hlt">models</span>. Although these mediums help students learn about muscle placement, the mediums do not facilitate understanding regarding integration of…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=235875&keyword=Kalman&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=48055530&CFTOKEN=58609306','EPA-EIMS'); return false;" href="http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=235875&keyword=Kalman&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=48055530&CFTOKEN=58609306"><span id="translatedtitle">Ensemble <span class="hlt">Models</span></span></a></p> <p><a target="_blank" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p></p> <p></p> <p>Ensemble forecasting has been used for operational numerical weather prediction in the United States and Europe since the early 1990s. An ensemble of weather or climate forecasts is used to characterize the two main sources of uncertainty in computer <span class="hlt">models</span> of physical systems: ...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/840122','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/840122"><span id="translatedtitle">Criticality <span class="hlt">Model</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>A. Alsaed</p> <p>2004-09-14</p> <p>The ''Disposal Criticality Analysis Methodology Topical Report'' (YMP 2003) presents the methodology for evaluating potential criticality situations in the monitored geologic repository. As stated in the referenced Topical Report, the detailed methodology for performing the disposal criticality analyses will be documented in <span class="hlt">model</span> reports. Many of the <span class="hlt">models</span> developed in support of the Topical Report differ from the definition of <span class="hlt">models</span> as given in the Office of Civilian Radioactive Waste Management procedure AP-SIII.10Q, ''<span class="hlt">Models</span>'', in that they are procedural, rather than mathematical. These <span class="hlt">model</span> reports document the detailed methodology necessary to implement the approach presented in the Disposal Criticality Analysis Methodology Topical Report and provide calculations utilizing the methodology. Thus, the governing procedure for this type of report is AP-3.12Q, ''Design Calculations and Analyses''. The ''Criticality <span class="hlt">Model</span>'' is of this latter type, providing a process evaluating the criticality potential of in-package and external configurations. The purpose of this analysis is to layout the process for calculating the criticality potential for various in-package and external configurations and to calculate lower-bound tolerance limit (LBTL) values and determine range of applicability (ROA) parameters. The LBTL calculations and the ROA determinations are performed using selected benchmark experiments that are applicable to various waste forms and various in-package and external configurations. The waste forms considered in this calculation are pressurized water reactor (PWR), boiling water reactor (BWR), Fast Flux Test Facility (FFTF), Training Research Isotope General Atomic (TRIGA), Enrico Fermi, Shippingport pressurized water reactor, Shippingport light water breeder reactor (LWBR), N-Reactor, Melt and Dilute, and Fort Saint Vrain Reactor spent nuclear fuel (SNF). The scope of this analysis is to document the criticality computational method. The criticality computational method will be used for evaluating the criticality potential of configurations of fissionable materials (in-package and external to the waste package) within the repository at Yucca Mountain, Nevada for all waste packages/waste forms. The criticality computational method is also applicable to preclosure configurations. The criticality computational method is a component of the methodology presented in ''Disposal Criticality Analysis Methodology Topical Report'' (YMP 2003). How the criticality computational method fits in the overall disposal criticality analysis methodology is illustrated in Figure 1 (YMP 2003, Figure 3). This calculation will not provide direct input to the total system performance assessment for license application. It is to be used as necessary to determine the criticality potential of configuration classes as determined by the configuration probability analysis of the configuration generator <span class="hlt">model</span> (BSC 2003a).</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=heritage+AND+science&id=EJ664885','ERIC'); return false;" href="http://eric.ed.gov/?q=heritage+AND+science&id=EJ664885"><span id="translatedtitle"><span class="hlt">Models</span>, Part V: Composition <span class="hlt">Models</span>.</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Callison, Daniel</p> <p>2003-01-01</p> <p>Describes four <span class="hlt">models</span>: The Authoring Cycle, a whole language approach that reflects the inquiry process; I-Search, an approach to research that uses the power of student interests; Cultural Celebration, using local heritage topics; and Science Lab Report, for the composition of a lab report. (LRW)</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2007AIPC..965..213H','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2007AIPC..965..213H"><span id="translatedtitle">Fibre <span class="hlt">Models</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Herrmann, H. J.; Kun, F.</p> <p>2007-12-01</p> <p>Fibre <span class="hlt">models</span> have been introduced as simple <span class="hlt">models</span> to describe failure. They are based on the probability distribution of broken fibres. The load redistribution after a fibre yields can be global or local and the first case can often be solved analytically. We will present an interpolation between these the local and the global case and apply it to experimental situations like the compression of granular packings. Introducing viscoelastic fibres allows to describe the creep of wood. It is even possible to deal analytically with a gradual degradation of fibres and consider damage as well as healing. In this way Basquin's law of fatigue can be reproduced and new universalities concerning the histograms of bursts and waiting times can be uncovered.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/1178934','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/1178934"><span id="translatedtitle">Protein Scaffolding for Small Molecule Catalysts</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Baker, David</p> <p>2014-09-14</p> <p>We aim to design hybrid catalysts for energy production and storage that combine the high specificity, affinity, and tunability of proteins with the potent chemical reactivities of small organometallic molecules. The widely used Rosetta and RosettaDesign methodologies will be extended to <span class="hlt">model</span> novel protein / small molecule catalysts in which one or many small molecule active centers are supported and coordinated by protein scaffolding. The promise of such hybrid molecular systems will be demonstrated with the nickel-phosphine <span class="hlt">hydrogenase</span> of DuBois et. al.We will enhance the <span class="hlt">hydrogenase</span> activity of the catalyst by designing protein scaffolds that incorporate proton relays and systematically modulate the local environment of the catalyticcenter. In collaboration with DuBois and Shaw, the designs will be experimentally synthesized and characterized.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/19960000035','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/19960000035"><span id="translatedtitle"><span class="hlt">Model</span> checking</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Dill, David L.</p> <p>1995-01-01</p> <p>Automatic formal verification methods for finite-state systems, also known as <span class="hlt">model</span>-checking, successfully reduce labor costs since they are mostly automatic. <span class="hlt">Model</span> checkers explicitly or implicitly enumerate the reachable state space of a system, whose behavior is described implicitly, perhaps by a program or a collection of finite automata. Simple properties, such as mutual exclusion or absence of deadlock, can be checked by inspecting individual states. More complex properties, such as lack of starvation, require search for cycles in the state graph with particular properties. Specifications to be checked may consist of built-in properties, such as deadlock or 'unspecified receptions' of messages, another program or implicit description, to be compared with a simulation, bisimulation, or language inclusion relation, or an assertion in one of several temporal logics. Finite-state verification tools are beginning to have a significant impact in commercial designs. There are many success stories of verification tools finding bugs in protocols or hardware controllers. In some cases, these tools have been incorporated into design methodology. Research in finite-state verification has been advancing rapidly, and is showing no signs of slowing down. Recent results include probabilistic algorithms for verification, exploitation of symmetry and independent events, and the use symbolic representations for Boolean functions and systems of linear inequalities. One of the most exciting areas for further research is the combination of <span class="hlt">model</span>-checking with theorem-proving methods.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/875627','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/875627"><span id="translatedtitle"><span class="hlt">Modeling</span> biomembranes.</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Plimpton, Steven James; Heffernan, Julieanne; Sasaki, Darryl Yoshio; Frischknecht, Amalie Lucile; Stevens, Mark Jackson; Frink, Laura J. Douglas</p> <p>2005-11-01</p> <p>Understanding the properties and behavior of biomembranes is fundamental to many biological processes and technologies. Microdomains in biomembranes or ''lipid rafts'' are now known to be an integral part of cell signaling, vesicle formation, fusion processes, protein trafficking, and viral and toxin infection processes. Understanding how microdomains form, how they depend on membrane constituents, and how they act not only has biological implications, but also will impact Sandia's effort in development of membranes that structurally adapt to their environment in a controlled manner. To provide such understanding, we created physically-based <span class="hlt">models</span> of biomembranes. Molecular dynamics (MD) simulations and classical density functional theory (DFT) calculations using these <span class="hlt">models</span> were applied to phenomena such as microdomain formation, membrane fusion, pattern formation, and protein insertion. Because lipid dynamics and self-organization in membranes occur on length and time scales beyond atomistic MD, we used coarse-grained <span class="hlt">models</span> of double tail lipid molecules that spontaneously self-assemble into bilayers. DFT provided equilibrium information on membrane structure. Experimental work was performed to further help elucidate the fundamental membrane organization principles.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/1999JChEd..76..871H','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/1999JChEd..76..871H"><span id="translatedtitle">Molecular <span class="hlt">Modeling</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Holmes, Jon L.</p> <p>1999-06-01</p> <p>Molecular <span class="hlt">modeling</span> has trickled down from the realm of pharmaceutical and research laboratories into the realm of undergraduate chemistry instruction. It has opened avenues for the visualization of chemical concepts that previously were difficult or impossible to convey. I am sure that many of you have developed exercises using the various molecular <span class="hlt">modeling</span> tools. It is the desire of this Journal to become an avenue for you to share these exercises among your colleagues. It is to this end that Ron Starkey has agreed to edit such a column and to publish not only the description of such exercises, but also the software documents they use. The WWW is the obvious medium to distribute this combination and so accepted submissions will appear online as a feature of JCE Internet. <img src="Images/jun99p871_1.gif" width=211 heighth=164 align=right> Typical molecular <span class="hlt">modeling</span> exercise: finding conformation energies. Molecular <span class="hlt">Modeling</span> Exercises and Experiments is the latest feature column of JCE Internet, joining Conceptual Questions and Challenge Problems, Hal's Picks, and Mathcad in the Chemistry Curriculum. JCE Internet continues to seek submissions in these areas of interest and submissions of general interest. If you have developed materials and would like to submit them, please see our Guide to Submissions for more information. The Chemical Education Resource Shelf, Equipment Buyers Guide, and WWW Site Review would also like to hear about chemistry textbooks and software, equipment, and WWW sites, respectively. Please consult JCE Internet Features to learn more about these resources at JCE Online. Email Announcements Would you like to be informed by email when the latest issue of the Journal is available online? when a new JCE Software title is shipping? when a new JCE Internet article has been published or is available for Open Review? when your subscription is about to expire? A new feature of JCE Online makes this possible. Visit our Guestbook to learn how. When you submit the form on this page, which includes your email address, you may choose to receive an email notice about a Journal event that interests you. Currently such events include availability of the latest issue of the Journal at JCE Online, expiration of your Journal subscription, shipment of a new JCE Software issue, publication of a new JCE Internet article or its availability for Open Review, and other announcements from the Journal. You may choose any number of these options independently. <img src="Images/jun99p871_2.gif" width=213 heighth=226 align=right> JCE Online Guestbook. Your Privacy JCE Online promises to you that we will not use the information that you provide in our Guestbook for anything other than our own internal information. We will not provide this information to third parties. We will use the information you provide only in our effort to help make the JCE serve you better. You only need to provide your email address to take advantage of this service; the other information you provide is optional. Molecular <span class="hlt">Modeling</span> Exercises and Experiments: Mission Statement We are seeking in this JCE Internet feature column to publish molecular <span class="hlt">modeling</span> exercises and experiments that have been used successfully in undergraduate instruction. The exercises will be published here on JCE Internet. An abstract of published submissions will appear in print in the Journal of Chemical Education. Acceptable exercises could be used in either a chemistry laboratory or a chemistry computer laboratory. The exercise could cover any area of chemistry, but should be limited to undergraduate instructional applications. We envision that most of the exercises/experiments will utilize one of the popular instructional molecular <span class="hlt">modeling</span> software programs (e.g. HyperChem, Spartan, CAChe, PC <span class="hlt">Model</span>). Exercises that are specific to a particular <span class="hlt">modeling</span> program are acceptable, but those usable with any <span class="hlt">modeling</span> program are preferred. Ideally the exercises/experiments will be of the type where the "correct"answer is not obvious so </p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1693259','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1693259"><span id="translatedtitle">Biomimetic <span class="hlt">modelling</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Vincent, Julian F V</p> <p>2003-01-01</p> <p>Biomimetics is seen as a path from biology to engineering. The only path from engineering to biology in current use is the application of engineering concepts and <span class="hlt">models</span> to biological systems. However, there is another pathway: the verification of biological mechanisms by manufacture, leading to an iterative process between biology and engineering in which the new understanding that the engineering implementation of a biological system can bring is fed back into biology, allowing a more complete and certain understanding and the possibility of further revelations for application in engineering. This is a pathway as yet unformalized, and one that offers the possibility that engineers can also be scientists. PMID:14561351</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.er.usgs.gov/publication/70006394','USGSPUBS'); return false;" href="http://pubs.er.usgs.gov/publication/70006394"><span id="translatedtitle"><span class="hlt">Modeling</span> uncertainty: quicksand for water temperature <span class="hlt">modeling</span></span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Bartholow, John M.</p> <p>2003-01-01</p> <p>Uncertainty has been a hot topic relative to science generally, and <span class="hlt">modeling</span> specifically. <span class="hlt">Modeling</span> uncertainty comes in various forms: measured data, limited <span class="hlt">model</span> domain, <span class="hlt">model</span> parameter estimation, <span class="hlt">model</span> structure, sensitivity to inputs, <span class="hlt">modelers</span> themselves, and users of the results. This paper will address important components of uncertainty in <span class="hlt">modeling</span> water temperatures, and discuss several areas that need attention as the <span class="hlt">modeling</span> community grapples with how to incorporate uncertainty into <span class="hlt">modeling</span> without getting stuck in the quicksand that prevents constructive contributions to policy making. The material, and in particular the reference, are meant to supplement the presentation given at this conference.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ces.clemson.edu/~petersj/CurrentPapers/MSSeminar-2008.pdf','EPRINT'); return false;" href="http://www.ces.clemson.edu/~petersj/CurrentPapers/MSSeminar-2008.pdf"><span id="translatedtitle">Analysis Meets <span class="hlt">Modeling</span> Analysis Meets <span class="hlt">Modeling</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Peterson, James K</p> <p></p> <p>on directed graphs of computational objects (DGs) Simple sigmoidal neurons Integrate and fire neurons Hodgkin Of Computational Nodes Implementation: Abstract Neuron Circuits 5 West Nile Virus <span class="hlt">Models</span> <span class="hlt">Model</span> Setup <span class="hlt">Model</span> DynamicsAnalysis Meets <span class="hlt">Modeling</span> Analysis Meets <span class="hlt">Modeling</span> The Intersection of Mathematics, Computing</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=simple+AND+machines&pg=2&id=EJ916642','ERIC'); return false;" href="http://eric.ed.gov/?q=simple+AND+machines&pg=2&id=EJ916642"><span id="translatedtitle">Pre-<span class="hlt">Modeling</span> Ensures Accurate Solid <span class="hlt">Models</span></span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Gow, George</p> <p>2010-01-01</p> <p>Successful solid <span class="hlt">modeling</span> requires a well-organized design tree. The design tree is a list of all the object's features and the sequential order in which they are <span class="hlt">modeled</span>. The solid-<span class="hlt">modeling</span> process is faster and less prone to <span class="hlt">modeling</span> errors when the design tree is a simple and geometrically logical definition of the <span class="hlt">modeled</span> object. Few high…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/3972791','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/3972791"><span id="translatedtitle">Iron-sulfur cluster in aconitase. Crystallographic evidence for a three-iron center.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Robbins, A H; Stout, C D</p> <p>1985-02-25</p> <p>Native x-ray diffraction data from single crystals of inactive aconitase from pig heart (Mr 80,000) have been collected on oscillation films to 2.7 A. Analysis shows that significant measurements of the anomalous scattering signal from the Fe-S cluster in the enzyme are available in the film data. The 5.0-A resolution anomalous difference Patterson function contains vectors for one Fe-S cluster (one aconitase molecule) per asymmetric unit in space group P2(1)2(1)2 with a = 173.6, b = 72.0, and c = 72.7 A. At 2.7-A resolution, the vector map is best interpreted by three Fe sites separated from each other by less than 3 A. The single-crystal diffraction data thus confirm the presence of a 3Fe center in the inactive form of aconitase. Furthermore, the data provide crystallographic evidence that 3Fe clusters exhibit structural heterogeneity. The <span class="hlt">Fe-Fe</span> vectors cannot be interpreted in terms of 4-A distances as observed for the [3Fe-3S] cluster in Azotobacter ferrodoxin (Ghosh, D., O'Donnell, S., Furey, W., Robbins, A. H., and Stout, C. D. (1982) J. Mol. Biol. 158, 73-109). The results are therefore in agreement with a [3Fe-4S] cluster having 2.7-A <span class="hlt">Fe-Fe</span> distances (Beinert, H., Emptage, M. H., Dreyer, J.-L., Scott, R. A., Hahn, J. E., Hodgson, K. O., and Thomson, A. J. (1983) Proc. Natl. Acad. Sci. U. S. A. 80, 393-396). However, the data do not unambiguously discriminate between this <span class="hlt">model</span> and other 3Fe clusters having short <span class="hlt">Fe-Fe</span> distances. PMID:3972791</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.era.lib.ed.ac.uk/handle/1842/1223','EPRINT'); return false;" href="http://www.era.lib.ed.ac.uk/handle/1842/1223"><span id="translatedtitle"><span class="hlt">Modelling</span> intonational structure using hidden markov <span class="hlt">models</span>. </span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Wright, Helen; Taylor, Paul A</p> <p>1997-01-01</p> <p>A method is introduced for using hidden Markov <span class="hlt">models</span> (HMMs) to <span class="hlt">model</span> intonational structure. HMMs are probabilistic and can capture the variability in structure which previous finite state network <span class="hlt">models</span> lack. We show ...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://wwwhome.math.utwente.nl/~phdtwcol/Archive/Presentations/14January_Presentation_of_Sid_Visser.pdf','EPRINT'); return false;" href="http://wwwhome.math.utwente.nl/~phdtwcol/Archive/Presentations/14January_Presentation_of_Sid_Visser.pdf"><span id="translatedtitle">Introduction Detailed <span class="hlt">model</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Al Hanbali, Ahmad</p> <p></p> <p>Background Definition of problem Different <span class="hlt">models</span> Meso-scale Population Analysis Comparison Conclusions SidIntroduction Detailed <span class="hlt">model</span> Population <span class="hlt">model</span> Comparison and conclusion <span class="hlt">Modeling</span> the Neocortex with Meso-scale <span class="hlt">Models</span> and Population <span class="hlt">Models</span> Sid Visser January 14, 2010 Sid Visser <span class="hlt">Modeling</span> the Neocortex</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www-rohan.sdsu.edu/~vadim/mayolewis.pdf','EPRINT'); return false;" href="http://www-rohan.sdsu.edu/~vadim/mayolewis.pdf"><span id="translatedtitle">Chemistry Old <span class="hlt">Models</span> New <span class="hlt">Models</span> The Mayo-Lewis Copolymerization <span class="hlt">Model</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Ponomarenko, Vadim</p> <p></p> <p>Chemistry Old <span class="hlt">Models</span> New <span class="hlt">Models</span> The Mayo-Lewis Copolymerization <span class="hlt">Model</span> Vadim Ponomarenko Department://www-rohan.sdsu.edu/vadim/mayolewis.pdf #12;Chemistry Old <span class="hlt">Models</span> New <span class="hlt">Models</span> Outline Chemistry Old <span class="hlt">Models</span> New <span class="hlt">Models</span> #12;Chemistry Old <span class="hlt">Models</span> New <span class="hlt">Models</span> Outline Chemistry Old <span class="hlt">Models</span> New <span class="hlt">Models</span> #12;Chemistry Old <span class="hlt">Models</span> New <span class="hlt">Models</span> Basics</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_15");'>15</a></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li class="active"><span>17</span></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_17 --> <div id="page_18" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li class="active"><span>18</span></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="341"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.shihada.com/S15-337/papers/Notes%204d.pdf','EPRINT'); return false;" href="http://www.shihada.com/S15-337/papers/Notes%204d.pdf"><span id="translatedtitle">Analytic <span class="hlt">Modeling</span> Birth-Death <span class="hlt">Model</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Shihada, Basem</p> <p></p> <p>Analytic <span class="hlt">Modeling</span> Birth-Death <span class="hlt">Model</span> 1 A Review -Random Variables · A variable representing on Exponential Distribution 11 Birth-Death <span class="hlt">Model</span> 12 #12;Birth-Death <span class="hlt">Model</span> · Queuing system with a single service State Dependent Arrival Rate 14 #12;State Dependent Service Rate 15 Definition of Birth-Death Process 16</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/1046069','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/1046069"><span id="translatedtitle">I&C <span class="hlt">Modeling</span> in SPAR <span class="hlt">Models</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>John A. Schroeder</p> <p>2012-06-01</p> <p>The Standardized Plant Analysis Risk (SPAR) <span class="hlt">models</span> for the U.S. commercial nuclear power plants currently have very limited instrumentation and control (I&C) <span class="hlt">modeling</span> [1]. Most of the I&C components in the operating plant SPAR <span class="hlt">models</span> are related to the reactor protection system. This was identified as a finding during the industry peer review of SPAR <span class="hlt">models</span>. While the Emergency Safeguard Features (ESF) actuation and control system was incorporated into the Peach Bottom Unit 2 SPAR <span class="hlt">model</span> in a recent effort [2], various approaches to expend resources for detailed I&C <span class="hlt">modeling</span> in other SPAR <span class="hlt">models</span> are investigated.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://cisnet.cancer.gov/profiles/','NCI'); return false;" href="http://cisnet.cancer.gov/profiles/"><span id="translatedtitle">CISNET: Standardized <span class="hlt">Model</span> Documents</span></a></p> <p><a target="_blank" href="http://www.cancer.gov">Cancer.gov</a></p> <p></p> <p></p> <p><span class="hlt">Modeling</span> is a complex endeavor, and often it is very difficult to reconcile results from different <span class="hlt">models</span>. To aid in this process of <span class="hlt">model</span> description and comparison, CISNET has developed and implemented standardized <span class="hlt">model</span> documentation. <span class="hlt">Model</span> profiles are standardized descriptions that facilitate the comparison of <span class="hlt">models</span> and their results. Users can read documentation about a single <span class="hlt">model</span> or read side-by-side descriptions that contrast how <span class="hlt">models</span> address different components of the process.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/1993aiaa.meetU....J','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/1993aiaa.meetU....J"><span id="translatedtitle">Comparisons of debris environment <span class="hlt">model</span> breakup <span class="hlt">models</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Jonas, F.; Yates, K.; Evans, R.</p> <p>1993-01-01</p> <p>This paper presents a comparison of current spacecraft breakup <span class="hlt">models</span> used in orbital (space) debris computational environment <span class="hlt">models</span>. The breakup <span class="hlt">models</span> to be compared come from the NASA EVOLVE (Evolutionary) <span class="hlt">model</span> long term debris <span class="hlt">model</span>, the IMPACT code developed by Aerospace Corp., and the Fragmentation Algorithms for Satellite Targets (FAST) developed by Kaman Sciences. The comparison will show the methodologies and results obtained for each <span class="hlt">model</span> such as mass versus fragment number distributions. Implications for debris cloud formation will be discussed in terms of the environments produced. No attempt is made to recommend any one <span class="hlt">model</span> over the other as each were designed and employed for specific purposes in the environment <span class="hlt">models</span> they are part of or contribute to. The comparisons are intended to provide researchers both quantitative and qualitative information on the <span class="hlt">models</span> for use in their own research activities.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/5371244','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/5371244"><span id="translatedtitle">A shock-metamorphic <span class="hlt">model</span> for silicate darkening and compositionally variable plagioclase in CK and ordinary chondrites</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Rubin, A.E. )</p> <p>1992-04-01</p> <p>Silicate darkening in ordinary chondrites (OC) is caused by tiny grains of metallic Fe-Ni and troilite occurring mainly within curvilinear trails that traverse silicate interiors and decorate or, in some cases, cut across silicate grain boundaries. Highly shocked OC tend to have greater degrees of silicate darkening than lightly shocked OC; this indicates that silicate darkening is probably a result of shock metamorphism. The low <span class="hlt">Fe-FeS</span> eutectic temperature (988C) renders metal and troilite susceptible to melting and mobilization during shock heating. Unshocked OC tend to have plagioclase with uniform compositions; shocked OC tend to have plagioclase with more variable (albeit still stoichiometric) compositions. The low impedance of plagioclase to shock compression makes it particularly susceptible to melting and mobilization; this is consistent with the molten appearance of plagioclase in highly shocked OC (e.g., Rose City and Paragould). CK chondrites also have compositionally variable plagioclase. The common association of silicate darkening with compositionally variable plagioclase is consistent with the hypothesis that both are products of shock metamorphism. Some CK and OC chondrites exhibit light shock effects in olivine that are consistent with equilibrium peak shock pressures that are too low to account for the silicate darkening or opaque shock veins in these meteorites. Therefore, the olivine in these chondrites may have been annealed after intense shock produced these effects. A few CK chondrites that contain olivine with undulose or mosaic extinction (e.g., LEW87009 and EET83311) may have been shocked again, after annealing.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2012AIPC.1479..414D','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2012AIPC.1479..414D"><span id="translatedtitle"><span class="hlt">Model</span> selection for logistic regression <span class="hlt">models</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Duller, Christine</p> <p>2012-09-01</p> <p><span class="hlt">Model</span> selection for logistic regression <span class="hlt">models</span> decides which of some given potential regressors have an effect and hence should be included in the final <span class="hlt">model</span>. The second interesting question is whether a certain factor is heterogeneous among some subsets, i.e. whether the <span class="hlt">model</span> should include a random intercept or not. In this paper these questions will be answered with classical as well as with Bayesian methods. The application show some results of recent research projects in medicine and business administration.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=bayesian+AND+prediction+AND+tool&id=EJ922103','ERIC'); return false;" href="http://eric.ed.gov/?q=bayesian+AND+prediction+AND+tool&id=EJ922103"><span id="translatedtitle">Multilevel <span class="hlt">Model</span> Prediction</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Frees, Edward W.; Kim, Jee-Seon</p> <p>2006-01-01</p> <p>Multilevel <span class="hlt">models</span> are proven tools in social research for <span class="hlt">modeling</span> complex, hierarchical systems. In multilevel <span class="hlt">modeling</span>, statistical inference is based largely on quantification of random variables. This paper distinguishes among three types of random variables in multilevel <span class="hlt">modeling--model</span> disturbances, random coefficients, and future response…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=atomic+AND+model&id=EJ621866','ERIC'); return false;" href="http://eric.ed.gov/?q=atomic+AND+model&id=EJ621866"><span id="translatedtitle">"Bohr's Atomic <span class="hlt">Model</span>."</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Willden, Jeff</p> <p>2001-01-01</p> <p>"Bohr's Atomic <span class="hlt">Model</span>" is a small interactive multimedia program that introduces the viewer to a simplified <span class="hlt">model</span> of the atom. This interactive simulation lets students build an atom using an atomic construction set. The underlying design methodology for "Bohr's Atomic <span class="hlt">Model</span>" is <span class="hlt">model</span>-centered instruction, which means the central <span class="hlt">model</span> of the…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://math.umons.ac.be/logic/sources/sonia_3.pdf','EPRINT'); return false;" href="http://math.umons.ac.be/logic/sources/sonia_3.pdf"><span id="translatedtitle"><span class="hlt">Model</span> Theory and Quantum</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Mons-Hainaut, Université de</p> <p></p> <p><span class="hlt">Model</span> Theory and Quantum Groups Sonia L'Innocente <span class="hlt">Model</span> Theory and Quantum Groups Sonia L'Innocente (University of Mons) <span class="hlt">Model</span> Theory and Quantum Groups 1 / 40 #12;<span class="hlt">Model</span> Theory and Quantum Groups Sonia L Theory and Quantum Groups 2 / 40 #12;<span class="hlt">Model</span> Theory and Quantum Groups Sonia L'Innocente Seminar's aim We</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.esf.edu/efb/limburg/EcoMod/Chapter5_Analytical_Solutions.pdf','EPRINT'); return false;" href="http://www.esf.edu/efb/limburg/EcoMod/Chapter5_Analytical_Solutions.pdf"><span id="translatedtitle"><span class="hlt">Model</span> solution State variable <span class="hlt">model</span>: differential equation</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Limburg, Karin E.</p> <p></p> <p>2/26/2014 1 <span class="hlt">Model</span> solution State variable <span class="hlt">model</span>: differential equation <span class="hlt">Models</span> a rate of change up the general solution to a differential equation in a book Solve for initial and boundary in repeating the theory on how to integrate a differential equation." Is anyone else wholly unsatisfied</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=232235','TEKTRAN'); return false;" href="http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=232235"><span id="translatedtitle"><span class="hlt">Modeling</span> transient rootzone salinity (SWS <span class="hlt">Model</span>)</span></a></p> <p><a target="_blank" href="http://www.ars.usda.gov/services/TekTran.htm">Technology Transfer Automated Retrieval System (TEKTRAN)</a></p> <p></p> <p></p> <p>The combined, water quality criteria for irrigation, water and ion processes in soils, and plant and soil response is sufficiently complex that adequate analysis requires computer <span class="hlt">models</span>. <span class="hlt">Models</span> for management are also needed but these <span class="hlt">models</span> must consider that the input requirements must be reasona...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.csc.lsu.edu/~kundu/soft-engg/3-libraryDFDiagram.pdf','EPRINT'); return false;" href="http://www.csc.lsu.edu/~kundu/soft-engg/3-libraryDFDiagram.pdf"><span id="translatedtitle">FINITE-STATE <span class="hlt">MODEL</span>, DATAFLOW <span class="hlt">MODEL</span>, ENTITY-RELATIONSHIP <span class="hlt">MODEL</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Kundu, Sukhamay</p> <p></p> <p>in the <span class="hlt">model</span> either. #12;3.5 ENTITY vs. AN ATTRIBUTE · An attribute stands only in the context of an entity in the new ER-<span class="hlt">model</span>? #12;3.6 EXERCISE 1. Table 10.1 in the text book lists the following ER <span class="hlt">modeling</span> con association between two or more entities Why can't we talk about relationship types and relationship val- ues</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.nwcouncil.org/media/5829/Appendix_F__Model_Conservation_Standards_.pdf','EPRINT'); return false;" href="http://www.nwcouncil.org/media/5829/Appendix_F__Model_Conservation_Standards_.pdf"><span id="translatedtitle"><span class="hlt">MODEL</span> CONSERVATION STANDARD INTRODUCTION</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p></p> <p></p> <p><span class="hlt">MODEL</span> CONSERVATION STANDARD INTRODUCTION As directed by the Northwest Power Act, the Council has designed <span class="hlt">model</span> conservation standards to produce all electricity savings that are cost believes the measures used to achieve the <span class="hlt">model</span> conservation standards should provide reliable savings</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=aircraft&pg=6&id=EJ152126','ERIC'); return false;" href="http://eric.ed.gov/?q=aircraft&pg=6&id=EJ152126"><span id="translatedtitle">Educating with Aircraft <span class="hlt">Models</span></span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Steele, Hobie</p> <p>1976-01-01</p> <p>Described is utilization of aircraft <span class="hlt">models</span>, <span class="hlt">model</span> aircraft clubs, and <span class="hlt">model</span> aircraft magazines to promote student interest in aerospace education. The addresses for clubs and magazines are included. (SL)</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/5801890','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/5801890"><span id="translatedtitle"><span class="hlt">Modeling</span> of geothermal systems</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Bodvarsson, G.S.; Pruess, K.; Lippmann, M.J.</p> <p>1985-03-01</p> <p>During the last decade the use of numerical <span class="hlt">modeling</span> for geothermal resource evaluation has grown significantly, and new <span class="hlt">modeling</span> approaches have been developed. In this paper we present a summary of the present status in numerical <span class="hlt">modeling</span> of geothermal systems, emphasizing recent developments. Different <span class="hlt">modeling</span> approaches are described and their applicability discussed. The various <span class="hlt">modeling</span> tasks, including natural-state, exploitation, injection, multi-component and subsidence <span class="hlt">modeling</span>, are illustrated with geothermal field examples. 99 refs., 14 figs.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/837107','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/837107"><span id="translatedtitle">Geologic Framework <span class="hlt">Model</span> Analysis <span class="hlt">Model</span> Report</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>R. Clayton</p> <p>2000-12-19</p> <p>The purpose of this report is to document the Geologic Framework <span class="hlt">Model</span> (GFM), Version 3.1 (GFM3.1) with regard to data input, <span class="hlt">modeling</span> methods, assumptions, uncertainties, limitations, and validation of the <span class="hlt">model</span> results, qualification status of the <span class="hlt">model</span>, and the differences between Version 3.1 and previous versions. The GFM represents a three-dimensional interpretation of the stratigraphy and structural features of the location of the potential Yucca Mountain radioactive waste repository. The GFM encompasses an area of 65 square miles (170 square kilometers) and a volume of 185 cubic miles (771 cubic kilometers). The boundaries of the GFM were chosen to encompass the most widely distributed set of exploratory boreholes (the Water Table or WT series) and to provide a geologic framework over the area of interest for hydrologic flow and radionuclide transport <span class="hlt">modeling</span> through the unsaturated zone (UZ). The depth of the <span class="hlt">model</span> is constrained by the inferred depth of the Tertiary-Paleozoic unconformity. The GFM was constructed from geologic map and borehole data. Additional information from measured stratigraphy sections, gravity profiles, and seismic profiles was also considered. This interim change notice (ICN) was prepared in accordance with the Technical Work Plan for the Integrated Site <span class="hlt">Model</span> Process <span class="hlt">Model</span> Report Revision 01 (CRWMS M&O 2000). The constraints, caveats, and limitations associated with this <span class="hlt">model</span> are discussed in the appropriate text sections that follow. The GFM is one component of the Integrated Site <span class="hlt">Model</span> (ISM) (Figure l), which has been developed to provide a consistent volumetric portrayal of the rock layers, rock properties, and mineralogy of the Yucca Mountain site. The ISM consists of three components: (1) Geologic Framework <span class="hlt">Model</span> (GFM); (2) Rock Properties <span class="hlt">Model</span> (RPM); and (3) Mineralogic <span class="hlt">Model</span> (MM). The ISM merges the detailed project stratigraphy into <span class="hlt">model</span> stratigraphic units that are most useful for the primary downstream <span class="hlt">models</span> and the repository design. These downstream <span class="hlt">models</span> include the hydrologic flow <span class="hlt">models</span> and the radionuclide transport <span class="hlt">models</span>. All the <span class="hlt">models</span> and the repository design, in turn, will be incorporated into the Total System Performance Assessment (TSPA) of the potential radioactive waste repository block and vicinity to determine the suitability of Yucca Mountain as a host for the repository. The interrelationship of the three components of the ISM and their interface with downstream uses are illustrated in Figure 2.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/10157123','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/10157123"><span id="translatedtitle">Generalized smooth <span class="hlt">models</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Glosup, J.</p> <p>1992-07-23</p> <p>The class of gene linear <span class="hlt">models</span> is extended to develop a class of nonparametric regression <span class="hlt">models</span> known as generalized smooth <span class="hlt">models</span>. The technique of local scoring is used to estimate a generalized smooth <span class="hlt">model</span> and the estimation procedure based on locally weighted regression is shown to produce local likelihood estimates. The asymptotically correct distribution of the deviance difference is derived and its use in comparing the fits of generalized linear <span class="hlt">models</span> and generalized smooth <span class="hlt">models</span> is illustrated. The relationship between generalized smooth <span class="hlt">models</span> and generalized additive <span class="hlt">models</span> is discussed, also.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/183906','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/183906"><span id="translatedtitle">Interfacing materials <span class="hlt">models</span> with fire field <span class="hlt">models</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Nicolette, V.F.; Tieszen, S.R.; Moya, J.L.</p> <p>1995-12-01</p> <p>For flame spread over solid materials, there has traditionally been a large technology gap between fundamental combustion research and the somewhat simplistic approaches used for practical, real-world applications. Recent advances in computational hardware and computational fluid dynamics (CFD)-based software have led to the development of fire field <span class="hlt">models</span>. These <span class="hlt">models</span>, when used in conjunction with material burning <span class="hlt">models</span>, have the potential to bridge the gap between research and application by implementing physics-based engineering <span class="hlt">models</span> in a transient, multi-dimensional tool. This paper discusses the coupling that is necessary between fire field <span class="hlt">models</span> and burning material <span class="hlt">models</span> for the simulation of solid material fires. Fire field <span class="hlt">models</span> are capable of providing detailed information about the local fire environment. This information serves as an input to the solid material combustion submodel, which subsequently calculates the impact of the fire environment on the material. The response of the solid material (in terms of thermal response, decomposition, charring, and off-gassing) is then fed back into the field <span class="hlt">model</span> as a source of mass, momentum and energy. The critical parameters which must be passed between the field <span class="hlt">model</span> and the material burning <span class="hlt">model</span> have been identified. Many computational issues must be addressed when developing such an interface. Some examples include the ability to track multiple fuels and species, local ignition criteria, and the need to use local grid refinement over the burning material of interest.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/7085594','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/7085594"><span id="translatedtitle">Core dimensions in the 3Fe cluster of Desulfovibrio gigas ferredoxin II by extended X-ray absorption fine structure spectroscopy.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Antonio, M R; Averill, B A; Moura, I; Moura, J J; Orme-Johnson, W H; Teo, B K; Xavier, A V</p> <p>1982-06-25</p> <p>We have obtained the iron K-edge extended X-ray adsorption fine structure spectra of the 3Fe ferredoxin II of Desulfovibrio gigas in the oxidized and reduced states. For both states, interpretation of the EXAFS data suggests that the Fe-S first shell coordination distance is near 2.25 A, in agreement with crystallographic studies of <span class="hlt">model</span> compounds and proteins containing 2Fe-2S and 4Fe-4S centers, as well as with a recent crystallographic study of Azotobacter vinelandii ferredoxin I (Ghosh, D., Furey, W., Jr., O'Donnell, S., and Stout, C. D. (1981) J. Biol. Chem. 256, 4185-4192). The apparent <span class="hlt">Fe-Fe</span> distance we obtain for the desulfovibrio protein (2.7 A) also agrees with similar distances seen in other Fe-S centers, except with the 3Fe cluster in the Azotobacter vinelandii ferredoxin I structure, for which an <span class="hlt">Fe-Fe</span> distance of 4.2 A was reported. We conclude that either the two 3Fe ferredoxins have substantially different core dimensions, a possibility apparently unique to 3Fe centers among known Fe-S systems in proteins, or that one (or more) of the structural studies is in substantial error. PMID:7085594</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/24881997','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/24881997"><span id="translatedtitle">Iron/iron oxide core/shell nanoparticles for magnetic targeting MRI and near-infrared photothermal therapy.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Zhou, Zhiguo; Sun, Yanan; Shen, Jinchao; Wei, Jie; Yu, Chao; Kong, Bin; Liu, Wei; Yang, Hong; Yang, Shiping; Wang, Wei</p> <p>2014-08-01</p> <p>The development of photothermal agents (PTAs) with good stability, low toxicity, highly targeting ability and photothermal conversion efficiency is an essential pre-requisite to near-infrared photothermal therapy (PTT) in vivo. Herein, we report the readily available PEGylated <span class="hlt">Fe@Fe</span>3O4 NPs, which possess triple functional properties in one entity - targeting, PTT, and imaging. Compared to Au nanorods, they exhibit comparable photothermal conversion efficiency (?20%), and much higher photothermal stability. They also show a high magnetization value and transverse relaxivity (?156 mm(-1) s(-1)), which should be applied for magnetic targeting MRI. With the Nd-Fe-B magnet (0.5 T) beside the tumour for 12 h on the xenograft HeLa tumour <span class="hlt">model</span>, PEGylated <span class="hlt">Fe@Fe</span>3O4 NPs exhibit an obvious accumulation. In tumour, the intensity of MRI signal is ? three folds and the increased temperature is ? two times than those without magnetic targeting, indicating the good magnetic targeting ability. Notably, the intrinsic high photothermal conversion efficiency and selective magnetic targeting effect of the NPs in tumour play synergistically in highly efficient ablation of cancer cells in vitro and in vivo. PMID:24881997</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li class="active"><span>18</span></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_18 --> <div id="page_19" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li class="active"><span>19</span></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="361"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015A%26A...584A..71R','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015A%26A...584A..71R"><span id="translatedtitle">Scaled <span class="hlt">models</span>, scaled frequencies, and <span class="hlt">model</span> fitting</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Roxburgh, Ian W.</p> <p>2015-12-01</p> <p>I show that given a <span class="hlt">model</span> star of mass M, radius R, and density profile ?(x) [x = r/R], there exists a two parameter family of <span class="hlt">models</span> with masses Mk, radii Rk, density profile ?k(x) = ??(x) and frequencies ?kn? = ?1/2?n?, where ?,Rk/RA are scaling factors. These <span class="hlt">models</span> have different internal structures, but all have the same value of separation ratios calculated at given radial orders n, and all exactly satisfy a frequency matching algorithm with an offset function determined as part of the fitting procedure. But they do not satisfy ratio matching at given frequencies nor phase shift matching. This illustrates that erroneous results may be obtained when <span class="hlt">model</span> fitting with ratios at given n values or frequency matching. I give examples from scaled <span class="hlt">models</span> and from non scaled evolutionary <span class="hlt">models</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/875317','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/875317"><span id="translatedtitle">ROCK PROPERTIES <span class="hlt">MODEL</span> ANALYSIS <span class="hlt">MODEL</span> REPORT</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Clinton Lum</p> <p>2002-02-04</p> <p>The purpose of this Analysis and <span class="hlt">Model</span> Report (AMR) is to document Rock Properties <span class="hlt">Model</span> (RPM) 3.1 with regard to input data, <span class="hlt">model</span> methods, assumptions, uncertainties and limitations of <span class="hlt">model</span> results, and qualification status of the <span class="hlt">model</span>. The report also documents the differences between the current and previous versions and validation of the <span class="hlt">model</span>. The rock properties <span class="hlt">models</span> are intended principally for use as input to numerical physical-process <span class="hlt">modeling</span>, such as of ground-water flow and/or radionuclide transport. The constraints, caveats, and limitations associated with this <span class="hlt">model</span> are discussed in the appropriate text sections that follow. This work was conducted in accordance with the following planning documents: WA-0344, ''3-D Rock Properties <span class="hlt">Modeling</span> for FY 1998'' (SNL 1997, WA-0358), ''3-D Rock Properties <span class="hlt">Modeling</span> for FY 1999'' (SNL 1999), and the technical development plan, Rock Properties <span class="hlt">Model</span> Version 3.1, (CRWMS M&O 1999c). The Interim Change Notice (ICNs), ICN 02 and ICN 03, of this AMR were prepared as part of activities being conducted under the Technical Work Plan, TWP-NBS-GS-000003, ''Technical Work Plan for the Integrated Site <span class="hlt">Model</span>, Process <span class="hlt">Model</span> Report, Revision 01'' (CRWMS M&O 2000b). The purpose of ICN 03 is to record changes in data input status due to data qualification and verification activities. These work plans describe the scope, objectives, tasks, methodology, and implementing procedures for <span class="hlt">model</span> construction. The constraints, caveats, and limitations associated with this <span class="hlt">model</span> are discussed in the appropriate text sections that follow. The work scope for this activity consists of the following: (1) Conversion of the input data (laboratory measured porosity data, x-ray diffraction mineralogy, petrophysical calculations of bound water, and petrophysical calculations of porosity) for each borehole into stratigraphic coordinates; (2) Re-sampling and merging of data sets; (3) Development of geostatistical simulations of porosity; (4) Generation of derivative property <span class="hlt">models</span> via linear coregionalization with porosity; (5) Post-processing of the simulated <span class="hlt">models</span> to impart desired secondary geologic attributes and to create summary and uncertainty <span class="hlt">models</span>; and (6) Conversion of the <span class="hlt">models</span> into real-world coordinates. The conversion to real world coordinates is performed as part of the integration of the RPM into the Integrated Site <span class="hlt">Model</span> (ISM) 3.1; this activity is not part of the current analysis. The ISM provides a consistent volumetric portrayal of the rock layers, rock properties, and mineralogy of the Yucca Mountain site and consists of three components: (1) Geologic Framework <span class="hlt">Model</span> (GFM); (2) RPM, which is the subject of this AMR; and (3) Mineralogic <span class="hlt">Model</span>. The interrelationship of the three components of the ISM and their interface with downstream uses are illustrated in Figure 1. Figure 2 shows the geographic boundaries of the RPM and other component <span class="hlt">models</span> of the ISM.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/828241','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/828241"><span id="translatedtitle">Biosphere <span class="hlt">Model</span> Report</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>M. A. Wasiolek</p> <p>2003-10-27</p> <p>The purpose of this report is to document the biosphere <span class="hlt">model</span>, the Environmental Radiation <span class="hlt">Model</span> for Yucca Mountain, Nevada (ERMYN), which describes radionuclide transport processes in the biosphere and associated human exposure that may arise as the result of radionuclide release from the geologic repository at Yucca Mountain. The biosphere <span class="hlt">model</span> is one of the process <span class="hlt">models</span> that support the Yucca Mountain Project (YMP) Total System Performance Assessment (TSPA) for the license application (LA), the TSPA-LA. The ERMYN <span class="hlt">model</span> provides the capability of performing human radiation dose assessments. This report documents the biosphere <span class="hlt">model</span>, which includes: (1) Describing the reference biosphere, human receptor, exposure scenarios, and primary radionuclides for each exposure scenario (Section 6.1); (2) Developing a biosphere conceptual <span class="hlt">model</span> using site-specific features, events, and processes (FEPs), the reference biosphere, the human receptor, and assumptions (Section 6.2 and Section 6.3); (3) Building a mathematical <span class="hlt">model</span> using the biosphere conceptual <span class="hlt">model</span> and published biosphere <span class="hlt">models</span> (Sections 6.4 and 6.5); (4) Summarizing input parameters for the mathematical <span class="hlt">model</span>, including the uncertainty associated with input values (Section 6.6); (5) Identifying improvements in the ERMYN <span class="hlt">model</span> compared with the <span class="hlt">model</span> used in previous biosphere <span class="hlt">modeling</span> (Section 6.7); (6) Constructing an ERMYN implementation tool (<span class="hlt">model</span>) based on the biosphere mathematical <span class="hlt">model</span> using GoldSim stochastic simulation software (Sections 6.8 and 6.9); (7) Verifying the ERMYN <span class="hlt">model</span> by comparing output from the software with hand calculations to ensure that the GoldSim implementation is correct (Section 6.10); and (8) Validating the ERMYN <span class="hlt">model</span> by corroborating it with published biosphere <span class="hlt">models</span>; comparing conceptual <span class="hlt">models</span>, mathematical <span class="hlt">models</span>, and numerical results (Section 7).</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/836512','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/836512"><span id="translatedtitle">Biosphere <span class="hlt">Model</span> Report</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>D. W. Wu</p> <p>2003-07-16</p> <p>The purpose of this report is to document the biosphere <span class="hlt">model</span>, the Environmental Radiation <span class="hlt">Model</span> for Yucca Mountain, Nevada (ERMYN), which describes radionuclide transport processes in the biosphere and associated human exposure that may arise as the result of radionuclide release from the geologic repository at Yucca Mountain. The biosphere <span class="hlt">model</span> is one of the process <span class="hlt">models</span> that support the Yucca Mountain Project (YMP) Total System Performance Assessment (TSPA) for the license application (LA), the TSPA-LA. The ERMYN <span class="hlt">model</span> provides the capability of performing human radiation dose assessments. This report documents the biosphere <span class="hlt">model</span>, which includes: (1) Describing the reference biosphere, human receptor, exposure scenarios, and primary radionuclides for each exposure scenario (Section 6.1); (2) Developing a biosphere conceptual <span class="hlt">model</span> using site-specific features, events, and processes (FEPs), the reference biosphere, the human receptor, and assumptions (Section 6.2 and Section 6.3); (3) Building a mathematical <span class="hlt">model</span> using the biosphere conceptual <span class="hlt">model</span> and published biosphere <span class="hlt">models</span> (Sections 6.4 and 6.5); (4) Summarizing input parameters for the mathematical <span class="hlt">model</span>, including the uncertainty associated with input values (Section 6.6); (5) Identifying improvements in the ERMYN <span class="hlt">model</span> compared with the <span class="hlt">model</span> used in previous biosphere <span class="hlt">modeling</span> (Section 6.7); (6) Constructing an ERMYN implementation tool (<span class="hlt">model</span>) based on the biosphere mathematical <span class="hlt">model</span> using GoldSim stochastic simulation software (Sections 6.8 and 6.9); (7) Verifying the ERMYN <span class="hlt">model</span> by comparing output from the software with hand calculations to ensure that the GoldSim implementation is correct (Section 6.10); and (8) Validating the ERMYN <span class="hlt">model</span> by corroborating it with published biosphere <span class="hlt">models</span>; comparing conceptual <span class="hlt">models</span>, mathematical <span class="hlt">models</span>, and numerical results (Section 7).</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=effects+AND+early+AND+death&pg=5&id=ED179142','ERIC'); return false;" href="http://eric.ed.gov/?q=effects+AND+early+AND+death&pg=5&id=ED179142"><span id="translatedtitle">The USC Faculty <span class="hlt">Model</span>.</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Linnell, Robert H.; Bottomley, Wayne N.</p> <p></p> <p>A description of the University of Southern California (USC) faculty <span class="hlt">model</span> and some of the results obtained from using the <span class="hlt">model</span> are presented. The <span class="hlt">model</span> traces faculty cohorts from 1974 to 1984, under given policies of hiring, tenure, promotion, and retirement. The <span class="hlt">model</span> takes into account resignations, deaths, anticipated enrollments, and costs.…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=depth+AND+map&pg=5&id=ED519318','ERIC'); return false;" href="http://eric.ed.gov/?q=depth+AND+map&pg=5&id=ED519318"><span id="translatedtitle">Generative <span class="hlt">Models</span> of Disfluency</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Miller, Timothy A.</p> <p>2010-01-01</p> <p>This thesis describes a generative <span class="hlt">model</span> for representing disfluent phenomena in human speech. This <span class="hlt">model</span> makes use of observed syntactic structure present in disfluent speech, and uses a right-corner transform on syntax trees to <span class="hlt">model</span> this structure in a very natural way. Specifically, the phenomenon of speech repair is <span class="hlt">modeled</span> by explicitly…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.levreyzin.com/presentations/IBM2010.pdf','EPRINT'); return false;" href="http://www.levreyzin.com/presentations/IBM2010.pdf"><span id="translatedtitle">Analog Circuits, Graphical <span class="hlt">Models</span>,</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Reyzin, Lev</p> <p></p> <p>AND OR AND G1 I1 G2 I2V [ACCW '06] 4 #12;+ Motivation for The <span class="hlt">Model</span> To <span class="hlt">model</span> gene regulatory networks as Boolean networks to represent gene expressions and disruptions Previous gene regulatory network <span class="hlt">model</span> be manipulated. Only the output is observable. Value Injection Query <span class="hlt">model</span> [AACW '06] Fully controllable. Only</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2010AIPC.1309..769R','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2010AIPC.1309..769R"><span id="translatedtitle">AIDS Epidemiological <span class="hlt">models</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Rahmani, Fouad Lazhar</p> <p>2010-11-01</p> <p>The aim of this paper is to present mathematical <span class="hlt">modelling</span> of the spread of infection in the context of the transmission of the human immunodeficiency virus (HIV) and the acquired immune deficiency syndrome (AIDS). These <span class="hlt">models</span> are based in part on the <span class="hlt">models</span> suggested in the field of th AIDS mathematical <span class="hlt">modelling</span> as reported by ISHAM [6].</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/1225898','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/1225898"><span id="translatedtitle">Biomass Scenario <span class="hlt">Model</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p></p> <p>2015-09-01</p> <p>The Biomass Scenario <span class="hlt">Model</span> (BSM) is a unique, carefully validated, state-of-the-art dynamic <span class="hlt">model</span> of the domestic biofuels supply chain which explicitly focuses on policy issues, their feasibility, and potential side effects. It integrates resource availability, physical/technological/economic constraints, behavior, and policy. The <span class="hlt">model</span> uses a system dynamics simulation (not optimization) to <span class="hlt">model</span> dynamic interactions across the supply chain.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/1991PhRvC..44.2230Z','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/1991PhRvC..44.2230Z"><span id="translatedtitle">Derivative scalar coupling <span class="hlt">model</span> versus ?-? <span class="hlt">model</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Zhang, Jian-Kang; Onley, D. S.</p> <p>1991-11-01</p> <p>The relativistic derivative scalar coupling <span class="hlt">model</span> of Zimanyi and Moszkowski, which is based on the original ?-? <span class="hlt">model</span>, is investigated both for infinite symmetric nuclear matter and finite spherical nuclei. We find that while this <span class="hlt">model</span> yields satisfactory compressibility in nuclear matter, and consequently gives good total binding energies for finite nuclei, it however fails to give the right spin-orbit interaction in finite nuclei. Calculated results are shown for 16O and compared to the ?-? <span class="hlt">model</span> and experimental data; the origin of the discrepancy is discussed.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/5412144','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/5412144"><span id="translatedtitle">Dynamic cable analysis <span class="hlt">models</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Palo, P.A.; Meggitt, D.J.; Nordell, W.J.</p> <p>1983-05-01</p> <p>This paper presents a summary of the development and validation of undersea cable dynamics computer <span class="hlt">models</span> by the Naval Civil Engineering Laboratory (NCEL) under the sponsorship of the Naval Facilities Engineering Command. These <span class="hlt">models</span> allow for the analysis of both small displacement (strumming) and large displacement (static and dynamic) deformations of arbitrarily configured cable structures. All of the large displacement <span class="hlt">models</span> described in this paper are available to the public. This paper does not emphasize the theoretical development of the <span class="hlt">models</span> (this information is available in other references) but emphasizes the various features of the <span class="hlt">models</span>, the comparisons between <span class="hlt">model</span> output and experimental data, and applications for which the <span class="hlt">models</span> have been used.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/795790','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/795790"><span id="translatedtitle">Calibrated Properties <span class="hlt">Model</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>C.F. Ahlers, H.H. Liu</p> <p>2001-12-18</p> <p>The purpose of this Analysis/<span class="hlt">Model</span> Report (AMR) is to document the Calibrated Properties <span class="hlt">Model</span> that provides calibrated parameter sets for unsaturated zone (UZ) flow and transport process <span class="hlt">models</span> for the Yucca Mountain Site Characterization Project (YMP). This work was performed in accordance with the AMR Development Plan for U0035 Calibrated Properties <span class="hlt">Model</span> REV00 (CRWMS M&O 1999c). These calibrated property sets include matrix and fracture parameters for the UZ Flow and Transport <span class="hlt">Model</span> (UZ <span class="hlt">Model</span>), drift seepage <span class="hlt">models</span>, drift-scale and mountain-scale coupled-processes <span class="hlt">models</span>, and Total System Performance Assessment (TSPA) <span class="hlt">models</span> as well as Performance Assessment (PA) and other participating national laboratories and government agencies. These process <span class="hlt">models</span> provide the necessary framework to test conceptual hypotheses of flow and transport at different scales and predict flow and transport behavior under a variety of climatic and thermal-loading conditions.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/837082','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/837082"><span id="translatedtitle">Calibrated Properties <span class="hlt">Model</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>C. Ahlers; H. Liu</p> <p>2000-03-12</p> <p>The purpose of this Analysis/<span class="hlt">Model</span> Report (AMR) is to document the Calibrated Properties <span class="hlt">Model</span> that provides calibrated parameter sets for unsaturated zone (UZ) flow and transport process <span class="hlt">models</span> for the Yucca Mountain Site Characterization Project (YMP). This work was performed in accordance with the ''AMR Development Plan for U0035 Calibrated Properties <span class="hlt">Model</span> REV00. These calibrated property sets include matrix and fracture parameters for the UZ Flow and Transport <span class="hlt">Model</span> (UZ <span class="hlt">Model</span>), drift seepage <span class="hlt">models</span>, drift-scale and mountain-scale coupled-processes <span class="hlt">models</span>, and Total System Performance Assessment (TSPA) <span class="hlt">models</span> as well as Performance Assessment (PA) and other participating national laboratories and government agencies. These process <span class="hlt">models</span> provide the necessary framework to test conceptual hypotheses of flow and transport at different scales and predict flow and transport behavior under a variety of climatic and thermal-loading conditions.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/20933288','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/20933288"><span id="translatedtitle">Stable <span class="hlt">models</span> of superacceleration</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Kaplinghat, Manoj; Rajaraman, Arvind</p> <p>2007-05-15</p> <p>We discuss an instability in a large class of <span class="hlt">models</span> where dark energy is coupled to matter. In these <span class="hlt">models</span> the mass of the scalar field is much larger than the expansion rate of the Universe. We find <span class="hlt">models</span> in which this instability is absent, and show that these <span class="hlt">models</span> generically predict an apparent equation of state for dark energy smaller than -1, i.e., superacceleration. These <span class="hlt">models</span> have no acausal behavior or ghosts.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://cisnet.cancer.gov/modeling/comparative.html','NCI'); return false;" href="http://cisnet.cancer.gov/modeling/comparative.html"><span id="translatedtitle">CISNET: Comparative <span class="hlt">Modeling</span></span></a></p> <p><a target="_blank" href="http://www.cancer.gov">Cancer.gov</a></p> <p></p> <p></p> <p>Independent <span class="hlt">modeling</span> efforts often yield disparate results that are difficult to reconcile. A comparative <span class="hlt">modeling</span> approach explores differences between <span class="hlt">models</span> in a systematic way. In joint collaborations, a set of common population inputs is shared across all <span class="hlt">models</span> (e.g., dissemination patterns of screening and treatment, mortality from non-cancer causes), and common sets of intermediate and final outputs are developed. Results are then compared across <span class="hlt">models</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://cisnet.cancer.gov/lung/','NCI'); return false;" href="http://cisnet.cancer.gov/lung/"><span id="translatedtitle">CISNET: Lung Cancer <span class="hlt">Modeling</span></span></a></p> <p><a target="_blank" href="http://www.cancer.gov">Cancer.gov</a></p> <p></p> <p></p> <p>The CISNET lung group was initiated in the second round of CISNET I and consists of five <span class="hlt">modeling</span> teams and two affiliate members. The groups' interests include areas such as tobacco control policies, screening, and genetic susceptibility. The <span class="hlt">models</span> incorporate the association between smoking and lung cancer in various ways, from epidemiologic <span class="hlt">models</span> to more mechanistic <span class="hlt">models</span>, including various versions of the two-stage clonal expansion <span class="hlt">model</span> of carcinogenesis.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.gpo.gov:80/fdsys/pkg/FR-2010-07-13/pdf/2010-17046.pdf','FEDREG'); return false;" href="http://www.gpo.gov:80/fdsys/pkg/FR-2010-07-13/pdf/2010-17046.pdf"><span id="translatedtitle">75 FR 39804 - Airworthiness Directives; The Boeing Company <span class="hlt">Model</span> 757 Airplanes, <span class="hlt">Model</span> 767 Airplanes, and <span class="hlt">Model</span>...</span></a></p> <p><a target="_blank" href="http://www.gpo.gov/fdsys/browse/collection.action?collectionCode=FR">Federal Register 2010, 2011, 2012, 2013, 2014</a></p> <p></p> <p>2010-07-13</p> <p>...Boeing Company <span class="hlt">Model</span> 757 Airplanes, <span class="hlt">Model</span> 767 Airplanes, and <span class="hlt">Model</span> 777-200 and -300...for certain <span class="hlt">Model</span> 757 airplanes, <span class="hlt">Model</span> 767 airplanes, and <span class="hlt">Model</span> 777-200 and -300...apply to certain <span class="hlt">Model</span> 757 airplanes, <span class="hlt">Model</span> 767 airplanes, and <span class="hlt">Model</span> 777-200 and...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=140670&keyword=turkey&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=46733652&CFTOKEN=73483317','EPA-EIMS'); return false;" href="http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=140670&keyword=turkey&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=46733652&CFTOKEN=73483317"><span id="translatedtitle">WASP TRANSPORT <span class="hlt">MODELING</span> AND WASP ECOLOGICAL <span class="hlt">MODELING</span></span></a></p> <p><a target="_blank" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p></p> <p></p> <p>A combination of lectures, demonstrations, and hands-on excercises will be used to introduce pollutant transport <span class="hlt">modeling</span> with the U.S. EPA's general water quality <span class="hlt">model</span>, WASP (Water Quality Analysis Simulation Program). WASP features include a user-friendly Windows-based interfa...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://jazz.physik.unibas.ch/~krusche/publications/quarkmod_review.pdf','EPRINT'); return false;" href="http://jazz.physik.unibas.ch/~krusche/publications/quarkmod_review.pdf"><span id="translatedtitle">14. Quark <span class="hlt">model</span> 1 14. QUARK <span class="hlt">MODEL</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Krusche, Bernd</p> <p></p> <p>14. Quark <span class="hlt">model</span> 1 14. QUARK <span class="hlt">MODEL</span> Revised December 2005 by C. Amsler (University of Z¨urich), T. DeGrand (University of Colorado, Boulder) and B. Krusche (University of Basel). 14.1. Quantum numbers of the quarks Quarks are strongly interacting fermions with spin 1/2 and, by convention, positive parity</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://jazz.physik.unibas.ch/~krusche/publications/quarkmod.pdf','EPRINT'); return false;" href="http://jazz.physik.unibas.ch/~krusche/publications/quarkmod.pdf"><span id="translatedtitle">1. Quark <span class="hlt">model</span> 1 1. QUARK <span class="hlt">MODEL</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Krusche, Bernd</p> <p></p> <p>1. Quark <span class="hlt">model</span> 1 1. QUARK <span class="hlt">MODEL</span> Revised December 2005 by C. Amsler (University of Z¨urich), T. DeGrand (University of Colorado, Boulder) and B. Krusche (University of Basel). 1.1. Quantum numbers of the quarks Quarks are strongly interacting fermions with spin 1/2 and, by convention, positive parity</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li class="active"><span>19</span></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_19 --> <div id="page_20" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li class="active"><span>20</span></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="381"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://ilab.usc.edu/rjpeters/pubs/2003_SFN_Poster.pdf','EPRINT'); return false;" href="http://ilab.usc.edu/rjpeters/pubs/2003_SFN_Poster.pdf"><span id="translatedtitle">3 Human vs. <span class="hlt">model</span> 2 Salience <span class="hlt">model</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Peters, Rob</p> <p></p> <p>· Collected new eye movement data -- different subjects -- different aerial images · Fitted the contour <span class="hlt">model</span> parameters to match these new data · Tested the fitted <span class="hlt">model</span> against the original data fixation cross -- 1. filter output connection kernel input output leak recurrent excitation modulation of inhibition oriented</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.mat.univie.ac.at/~herman/papers/modtheoc.ps.gz','EPRINT'); return false;" href="http://www.mat.univie.ac.at/~herman/papers/modtheoc.ps.gz"><span id="translatedtitle"><span class="hlt">MODELS</span> AND HISTORY OF <span class="hlt">MODELING</span> Hermann Schichl</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Schichl, Hermann</p> <p></p> <p>the Ancient Near East and with Ancient Greek. The recognizable <span class="hlt">models</span> werenumbers; counting ``writing <span class="hlt">models</span> played a role, already about 4.000 well known that 2.000 at three cultures (Babylon, Egypt, India of mathematics independently application. Thales brought knowledge from Egypt, predicted solar eclipse</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20000032457','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20000032457"><span id="translatedtitle">Trapped Radiation <span class="hlt">Model</span> Uncertainties: <span class="hlt">Model</span>-Data and <span class="hlt">Model-Model</span> Comparisons</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Armstrong, T. W.; Colborn, B. L.</p> <p>2000-01-01</p> <p>The standard AP8 and AE8 <span class="hlt">models</span> for predicting trapped proton and electron environments have been compared with several sets of flight data to evaluate <span class="hlt">model</span> uncertainties. <span class="hlt">Model</span> comparisons are made with flux and dose measurements made on various U.S. low-Earth orbit satellites (APEX, CRRES, DMSP, LDEF, NOAA) and Space Shuttle flights, on Russian satellites (Photon-8, Cosmos-1887, Cosmos-2044), and on the Russian Mir Space Station. This report gives the details of the <span class="hlt">model</span>-data comparisons-summary results in terms of empirical <span class="hlt">model</span> uncertainty factors that can be applied for spacecraft design applications are given in a combination report. The results of <span class="hlt">model-model</span> comparisons are also presented from standard AP8 and AE8 <span class="hlt">model</span> predictions compared with the European Space Agency versions of AP8 and AE8 and with Russian-trapped radiation <span class="hlt">models</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20000021429','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20000021429"><span id="translatedtitle">Trapped Radiation <span class="hlt">Model</span> Uncertainties: <span class="hlt">Model</span>-Data and <span class="hlt">Model-Model</span> Comparisons</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Armstrong, T. W.; Colborn, B. L.</p> <p>2000-01-01</p> <p>The standard AP8 and AE8 <span class="hlt">models</span> for predicting trapped proton and electron environments have been compared with several sets of flight data to evaluate <span class="hlt">model</span> uncertainties. <span class="hlt">Model</span> comparisons are made with flux and dose measurements made on various U.S. low-Earth orbit satellites (APEX, CRRES, DMSP. LDEF, NOAA) and Space Shuttle flights, on Russian satellites (Photon-8, Cosmos-1887, Cosmos-2044), and on the Russian Mir space station. This report gives the details of the <span class="hlt">model</span>-data comparisons -- summary results in terms of empirical <span class="hlt">model</span> uncertainty factors that can be applied for spacecraft design applications are given in a companion report. The results of <span class="hlt">model-model</span> comparisons are also presented from standard AP8 and AE8 <span class="hlt">model</span> predictions compared with the European Space Agency versions of AP8 and AE8 and with Russian trapped radiation <span class="hlt">models</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/894170','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/894170"><span id="translatedtitle"><span class="hlt">Model</span> Validation Status Review</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>E.L. Hardin</p> <p>2001-11-28</p> <p>The primary objective for the <span class="hlt">Model</span> Validation Status Review was to perform a one-time evaluation of <span class="hlt">model</span> validation associated with the analysis/<span class="hlt">model</span> reports (AMRs) containing <span class="hlt">model</span> input to total-system performance assessment (TSPA) for the Yucca Mountain site recommendation (SR). This review was performed in response to Corrective Action Request BSC-01-C-01 (Clark 2001, Krisha 2001) pursuant to Quality Assurance review findings of an adverse trend in <span class="hlt">model</span> validation deficiency. The review findings in this report provide the following information which defines the extent of <span class="hlt">model</span> validation deficiency and the corrective action needed: (1) AMRs that contain or support <span class="hlt">models</span> are identified, and conversely, for each <span class="hlt">model</span> the supporting documentation is identified. (2) The use for each <span class="hlt">model</span> is determined based on whether the output is used directly for TSPA-SR, or for screening (exclusion) of features, events, and processes (FEPs), and the nature of the <span class="hlt">model</span> output. (3) Two approaches are used to evaluate the extent to which the validation for each <span class="hlt">model</span> is compliant with AP-3.10Q (Analyses and <span class="hlt">Models</span>). The approaches differ in regard to whether <span class="hlt">model</span> validation is achieved within individual AMRs as originally intended, or whether <span class="hlt">model</span> validation could be readily achieved by incorporating information from other sources. (4) Recommendations are presented for changes to the AMRs, and additional <span class="hlt">model</span> development activities or data collection, that will remedy <span class="hlt">model</span> validation review findings, in support of licensing activities. The <span class="hlt">Model</span> Validation Status Review emphasized those AMRs that support TSPA-SR (CRWMS M&O 2000bl and 2000bm). A series of workshops and teleconferences was held to discuss and integrate the review findings. The review encompassed 125 AMRs (Table 1) plus certain other supporting documents and data needed to assess <span class="hlt">model</span> validity. The AMRs were grouped in 21 <span class="hlt">model</span> areas representing the <span class="hlt">modeling</span> of processes affecting the natural and engineered barriers, plus the TSPA <span class="hlt">model</span> itself Description of the <span class="hlt">model</span> areas is provided in Section 3, and the documents reviewed are described in Section 4. The responsible manager for the <span class="hlt">Model</span> Validation Status Review was the Chief Science Officer (CSO) for Bechtel-SAIC Co. (BSC). The team lead was assigned by the CSO. A total of 32 technical specialists were engaged to evaluate <span class="hlt">model</span> validation status in the 21 <span class="hlt">model</span> areas. The technical specialists were generally independent of the work reviewed, meeting technical qualifications as discussed in Section 5.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/24931159','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/24931159"><span id="translatedtitle">All <span class="hlt">models</span> are wrong.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Hickerson, Michael J</p> <p>2014-06-01</p> <p>As the field of phylogeography has continued to move in the <span class="hlt">model</span>-based direction, researchers continue struggling to construct useful <span class="hlt">models</span> for inference. These <span class="hlt">models</span> must be both simple enough to be tractable yet contain enough of the complexity of the natural world to make meaningful inference. Beyond constructing such <span class="hlt">models</span> for inference, researchers explore <span class="hlt">model</span> space and test competing <span class="hlt">models</span> with the data on hand, with the goal of improving the understanding of the natural world and the processes underlying natural biological communities. Approximate Bayesian computation (ABC) has increased in recent popularity as a tool for evaluating alternative historical demographic <span class="hlt">models</span> given population genetic samples. As a thorough demonstration, Pelletier & Carstens (2014) use ABC to test 143 phylogeographic submodels given geographically widespread genetic samples from the salamander species Plethodon idahoensis (Carstens et al. 2014) and, in so doing, demonstrate how the results of the ABC <span class="hlt">model</span> choice procedure are dependent on the <span class="hlt">model</span> set one chooses to evaluate. PMID:24931159</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.infosys.tuwien.ac.at/Staff/sd/papers/FMCO%202008%20C.%20Mayr.pdf','EPRINT'); return false;" href="http://www.infosys.tuwien.ac.at/Staff/sd/papers/FMCO%202008%20C.%20Mayr.pdf"><span id="translatedtitle">Reusable Architectural Decision <span class="hlt">Model</span> for <span class="hlt">Model</span> and Metadata Repositories</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Dustdar, Schahram</p> <p></p> <p>Reusable Architectural Decision <span class="hlt">Model</span> for <span class="hlt">Model</span> and Metadata Repositories Christine Mayr, Uwe Zdun, and Schahram Dustdar Distributed Systems Group Information System Institute Vienna University of Technology. <span class="hlt">Model</span> repositories support this trend by managing these <span class="hlt">model</span> artifacts. While setting up <span class="hlt">model</span></p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/5034719','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/5034719"><span id="translatedtitle">Energy-consumption <span class="hlt">modelling</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Reiter, E.R.</p> <p>1980-01-01</p> <p>A highly sophisticated and accurate approach is described to compute on an hourly or daily basis the energy consumption for space heating by individual buildings, urban sectors, and whole cities. The need for <span class="hlt">models</span> and specifically weather-sensitive <span class="hlt">models</span>, composite <span class="hlt">models</span>, and space-heating <span class="hlt">models</span> are discussed. Development of the Colorado State University <span class="hlt">Model</span>, based on heat-transfer equations and on a heuristic, adaptive, self-organizing computation learning approach, is described. Results of <span class="hlt">modeling</span> energy consumption by the city of Minneapolis and Cheyenne are given. Some data on energy consumption in individual buildings are included.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26024160','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26024160"><span id="translatedtitle">Holographic twin Higgs <span class="hlt">model</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Geller, Michael; Telem, Ofri</p> <p>2015-05-15</p> <p>We present the first realization of a "twin Higgs" <span class="hlt">model</span> as a holographic composite Higgs <span class="hlt">model</span>. Uniquely among composite Higgs <span class="hlt">models</span>, the Higgs potential is protected by a new standard <span class="hlt">model</span> (SM) singlet elementary "mirror" sector at the sigma <span class="hlt">model</span> scale f and not by the composite states at m_{KK}, naturally allowing for m_{KK} beyond the LHC reach. As a result, naturalness in our <span class="hlt">model</span> cannot be constrained by the LHC, but may be probed by precision Higgs measurements at future lepton colliders, and by direct searches for Kaluza-Klein excitations at a 100 TeV collider. PMID:26024160</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/1980STIN...8113499R','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/1980STIN...8113499R"><span id="translatedtitle">Energy-consumption <span class="hlt">modelling</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Reiter, E. R.</p> <p></p> <p>A sophisticated and accurate approach is described to compute on an hourly or daily basis the energy consumption for space heating by individual buildings, urban sectors, and whole cities. The need for <span class="hlt">models</span> and specifically weather-sensitive <span class="hlt">models</span>, composite <span class="hlt">models</span>, and space heating <span class="hlt">models</span> are discussed. Development of the Colorado State University <span class="hlt">Model</span>, based on heat transfer equations and on a heuristic, adaptive, self-organizing computation learning approach, is described. Results of <span class="hlt">modeling</span> energy consumption by the city of Minneapolis and Cheyenne are given. Some data on energy consumption in individual buildings are included.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/19870008659','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/19870008659"><span id="translatedtitle">Gear mesh compliance <span class="hlt">modeling</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Savage, M.; Caldwell, R. J.; Wisor, G. D.; Lewicki, D. G.</p> <p>1986-01-01</p> <p>A computer <span class="hlt">model</span> has been constructed to simulate the compliance and load sharing in a spur gear mesh. The <span class="hlt">model</span> adds the effect of rim deflections to previously developed state-of-the-art gear tooth deflection <span class="hlt">models</span>. The effects of deflections on mesh compliance and load sharing are examined. The <span class="hlt">model</span> can treat gear meshes composed to two external gears or an external gear driving an internal gear. The <span class="hlt">model</span> includes deflection contributions from the bending and shear in the teeth, the Hertzian contact deformations, and primary and secondary rotations of the gear rims. The <span class="hlt">model</span> shows that rimmed gears increase mesh compliance and, in some cases, improve load sharing.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://ntrs.nasa.gov/search.jsp?R=19870066148&hterms=rimmed&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D40%26Ntt%3Drimmed','NASA-TRS'); return false;" href="http://ntrs.nasa.gov/search.jsp?R=19870066148&hterms=rimmed&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D40%26Ntt%3Drimmed"><span id="translatedtitle">Gear mesh compliance <span class="hlt">modeling</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Savage, M.; Caldwell, R. J.; Wisor, G. D.; Lewicki, D. G.</p> <p>1987-01-01</p> <p>A computer <span class="hlt">model</span> has been constructed to simulate the compliance and load sharing in a spur gear mesh. The <span class="hlt">model</span> adds the effect of rim deflections to previously developed state-of-the-art gear tooth deflection <span class="hlt">models</span>. The effects of deflections on mesh compliance and load sharing are examined. The <span class="hlt">model</span> can treat gear meshes composed of two external gears or an external gear driving an internal gear. The <span class="hlt">model</span> includes deflection contributions from the bending and shear in the teeth, the Hertzian contact deformations, and primary and secondary rotations of the gear rims. The <span class="hlt">model</span> shows that rimmed gears increase mesh compliance and, in some cases, improve load sharing.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/19930009826','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/19930009826"><span id="translatedtitle"><span class="hlt">Modeling</span> the transition region</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Singer, Bart A.</p> <p>1993-01-01</p> <p>The current status of transition-region <span class="hlt">models</span> is reviewed in this report. To understand <span class="hlt">modeling</span> problems, various flow features that influence the transition process are discussed first. Then an overview of the different approaches to transition-region <span class="hlt">modeling</span> is given. This is followed by a detailed discussion of turbulence <span class="hlt">models</span> and the specific modifications that are needed to predict flows undergoing laminar-turbulent transition. Methods for determining the usefulness of the <span class="hlt">models</span> are presented, and an outlook for the future of transition-region <span class="hlt">modeling</span> is suggested.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2011PhDT.......212B','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2011PhDT.......212B"><span id="translatedtitle">High Pressure Melting of Iron with Nonmetals Sulfur, Carbon, Oxygen, and Hydrogen: Implications for Planetary Cores</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Buono, Antonio Salvatore</p> <p></p> <p>The earth's core consists of a solid metallic center surrounded by a liquid metallic outer layer. Understanding the compositions of the inner and outer cores allows us to better understand the dynamics of the earth's core, as well as the dynamics of the cores of other terrestrial planets and moons. The density and size of the earth's core indicate that it is approximately 90% metallic, predominantly iron, with about 10% light elements. Iron meteorites, believed to be the remnants of planetary cores, provide further constraints on the composition of the earth's core, indicating a composition of 86% iron, 4% nickel, and 10% light elements. Any potential candidate for the major light element core component must meet two criteria: first, it must have high cosmic abundances and second, it must be compatible with Fe. Given these two constraints there are five plausible elements that could be the major light element in the core: H, O, C, S, and Si. Of these five possible candidates this thesis focuses on S and C as well exploring the effect of minor amounts of O and H on the eutectic temperature in a <span class="hlt">Fe-FeS</span> core. We look at two specific aspects of the <span class="hlt">Fe-FeS</span> system: first, the shape of the liquidus as a function of pressure, second, a possible cause for the reported variations in the eutectic temperature, which draws on the effect of H and O. Finally we look at the effect of S and C on partitioning behavior of Ni, Pt, Re,Co, Os and W between cohenite and metallic liquid. We are interested in constraining the shape of the <span class="hlt">Fe-FeS</span> liquidus because as a planet with a S-enriched core cools, the thermal and compositional evolution of its core is constrained by this liquidus. In Chapter 1 I present an equation that allows for calculation of the temperature along the liquidus as a function of pressure and composition for Fe-rich compositions and pressures from 1 bar to 10 GPa. One particularly interesting feature of the Fe --rich side of the <span class="hlt">Fe-FeS</span> eutectic is the sigmoidal shape of the liquidus. This morphology indicates non-ideal liquid solution behavior and suggests the presence of a metastable solvus beneath the liquidus. An important consequence of such curved liquidi is that isobaric, uniform cooling requires substantial variations in the solidification rate of the core. Additionally, in bodies large enough for P variation within the core to be significant, solidification behavior is further complicated by the P dependence of the liquidus shape. Brett and Bell (1969) show that at 3 GPa, the liquidus curvature relaxes, implying that the liquid solution becomes more ideal. By 10 GPa, the liquidus approaches nearly ideal behavior (Chen et al., 2008b). However, at 14 GPa, the liquidus again assumes a sigmoidal curvature (Chen et al., 2008a; Chen et al., 2008b), suggesting a fundamental change in the thermodynamic behavior of the liquid. Chapter 1 of this thesis accounts for the observed complexity in the liquidus up to 10 GPa thus enabling more accurate <span class="hlt">modeling</span> of the evolution of the cores of small planets (Buono and Walker, 2011). Accurately knowing the eutectic temperature for the <span class="hlt">Fe-FeS</span> system is important because it places a minimum bound on the temperature of a S-enriched core that has a solid and liquid component which are in equilibrium. Unfortunately literature values for the 1 bar to 10 GPa eutectic temperature in the <span class="hlt">Fe-FeS</span> system are highly variable making the estimation of core temperature, an important geodynamic parameter, very difficult. In Chapter 2 we look at a possible cause of this observed variation by experimentally investigating the effects of H on the eutectic temperature in the <span class="hlt">Fe-FeS</span> system at 6 and 8 GPa. We find that H causes a decrease in the eutectic temperature (but that O does not) and that this decrease can explain some of the observed scatter in the available data. The effect of H on the eutectic temperature increases with increasing pressure (i.e. the eutectic temperature is more depressed at higher pressures), matching the trend reported for the <span class="hlt">Fe-FeS</span> system (Fei et al., 1997). Our work suggests </p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/24633955','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/24633955"><span id="translatedtitle">Antibody <span class="hlt">modeling</span> assessment II. Structures and <span class="hlt">models</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Teplyakov, Alexey; Luo, Jinquan; Obmolova, Galina; Malia, Thomas J; Sweet, Raymond; Stanfield, Robyn L; Kodangattil, Sreekumar; Almagro, Juan Carlos; Gilliland, Gary L</p> <p>2014-08-01</p> <p>To assess the state-of-the-art in antibody structure <span class="hlt">modeling</span>, a blinded study was conducted. Eleven unpublished Fab crystal structures were used as a benchmark to compare Fv <span class="hlt">models</span> generated by seven structure prediction methodologies. In the first round, each participant submitted three non-ranked complete Fv <span class="hlt">models</span> for each target. In the second round, CDR-H3 <span class="hlt">modeling</span> was performed in the context of the correct environment provided by the crystal structures with CDR-H3 removed. In this report we describe the reference structures and present our assessment of the <span class="hlt">models</span>. Some of the essential sources of errors in the predictions were traced to the selection of the structure template, both in terms of the CDR canonical structures and VL/VH packing. On top of this, the errors present in the Protein Data Bank structures were sometimes propagated in the current <span class="hlt">models</span>, which emphasized the need for the curated structural database devoid of errors. <span class="hlt">Modeling</span> non-canonical structures, including CDR-H3, remains the biggest challenge for antibody structure prediction. PMID:24633955</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/838328','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/838328"><span id="translatedtitle">Biosphere <span class="hlt">Model</span> Report</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>D.W. Wu; A.J. Smith</p> <p>2004-11-08</p> <p>The purpose of this report is to document the biosphere <span class="hlt">model</span>, the Environmental Radiation <span class="hlt">Model</span> for Yucca Mountain, Nevada (ERMYN), which describes radionuclide transport processes in the biosphere and associated human exposure that may arise as the result of radionuclide release from the geologic repository at Yucca Mountain. The biosphere <span class="hlt">model</span> is one of the process <span class="hlt">models</span> that support the Yucca Mountain Project (YMP) Total System Performance Assessment (TSPA) for the license application (LA), TSPA-LA. The ERMYN provides the capability of performing human radiation dose assessments. This report documents the biosphere <span class="hlt">model</span>, which includes: (1) Describing the reference biosphere, human receptor, exposure scenarios, and primary radionuclides for each exposure scenario (Section 6.1); (2) Developing a biosphere conceptual <span class="hlt">model</span> using site-specific features, events, and processes (FEPs) (Section 6.2), the reference biosphere (Section 6.1.1), the human receptor (Section 6.1.2), and approximations (Sections 6.3.1.4 and 6.3.2.4); (3) Building a mathematical <span class="hlt">model</span> using the biosphere conceptual <span class="hlt">model</span> (Section 6.3) and published biosphere <span class="hlt">models</span> (Sections 6.4 and 6.5); (4) Summarizing input parameters for the mathematical <span class="hlt">model</span>, including the uncertainty associated with input values (Section 6.6); (5) Identifying improvements in the ERMYN compared with the <span class="hlt">model</span> used in previous biosphere <span class="hlt">modeling</span> (Section 6.7); (6) Constructing an ERMYN implementation tool (<span class="hlt">model</span>) based on the biosphere mathematical <span class="hlt">model</span> using GoldSim stochastic simulation software (Sections 6.8 and 6.9); (7) Verifying the ERMYN by comparing output from the software with hand calculations to ensure that the GoldSim implementation is correct (Section 6.10); (8) Validating the ERMYN by corroborating it with published biosphere <span class="hlt">models</span>; comparing conceptual <span class="hlt">models</span>, mathematical <span class="hlt">models</span>, and numerical results (Section 7).</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20140002338','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20140002338"><span id="translatedtitle">Develop a <span class="hlt">Model</span> Component</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Ensey, Tyler S.</p> <p>2013-01-01</p> <p>During my internship at NASA, I was a <span class="hlt">model</span> developer for Ground Support Equipment (GSE). The purpose of a <span class="hlt">model</span> developer is to develop and unit test <span class="hlt">model</span> component libraries (fluid, electrical, gas, etc.). The <span class="hlt">models</span> are designed to simulate software for GSE (Ground Special Power, Crew Access Arm, Cryo, Fire and Leak Detection System, Environmental Control System (ECS), etc. .) before they are implemented into hardware. These <span class="hlt">models</span> support verifying local control and remote software for End-Item Software Under Test (SUT). The <span class="hlt">model</span> simulates the physical behavior (function, state, limits and 110) of each end-item and it's dependencies as defined in the Subsystem Interface Table, Software Requirements & Design Specification (SRDS), Ground Integrated Schematic (GIS), and System Mechanical Schematic.(SMS). The software of each specific <span class="hlt">model</span> component is simulated through MATLAB's Simulink program. The intensiv <span class="hlt">model</span> development life cycle is a.s follows: Identify source documents; identify <span class="hlt">model</span> scope; update schedule; preliminary design review; develop <span class="hlt">model</span> requirements; update <span class="hlt">model</span>.. scope; update schedule; detailed design review; create/modify library component; implement library components reference; implement subsystem components; develop a test script; run the test script; develop users guide; send <span class="hlt">model</span> out for peer review; the <span class="hlt">model</span> is sent out for verifictionlvalidation; if there is empirical data, a validation data package is generated; if there is not empirical data, a verification package is generated; the test results are then reviewed; and finally, the user. requests accreditation, and a statement of accreditation is prepared. Once each component <span class="hlt">model</span> is reviewed and approved, they are intertwined together into one integrated <span class="hlt">model</span>. This integrated <span class="hlt">model</span> is then tested itself, through a test script and autotest, so that it can be concluded that all <span class="hlt">models</span> work conjointly, for a single purpose. The component I was assigned, specifically, was a fluid component, a discrete pressure switch. The switch takes a fluid pressure input, and if the pressure is greater than a designated cutoff pressure, the switch would stop fluid flow.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://arxiv.org/pdf/1111.6362v2','EPRINT'); return false;" href="http://arxiv.org/pdf/1111.6362v2"><span id="translatedtitle"><span class="hlt">Modeling</span> error in Approximate Deconvolution <span class="hlt">Models</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Adrian Dunca; Roger Lewandowski</p> <p>2012-10-09</p> <p>We investigate the assymptotic behaviour of the <span class="hlt">modeling</span> error in approximate deconvolution <span class="hlt">model</span> in the 3D periodic case, when the order $N$ of deconvolution goes to $\\infty$. We consider successively the generalised Helmholz filters of order $p$ and the Gaussian filter. For Helmholz filters, we estimate the rate of convergence to zero thanks to energy budgets, Gronwall's Lemma and sharp inequalities about Fouriers coefficients of the residual stress. We next show why the same analysis does not allow to conclude convergence to zero of the error <span class="hlt">modeling</span> in the case of Gaussian filter, leaving open issues.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2009AGUSMIN32A..02S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2009AGUSMIN32A..02S"><span id="translatedtitle"><span class="hlt">Modeling</span> Guru: Knowledge Base for NASA <span class="hlt">Modelers</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Seablom, M. S.; Wojcik, G. S.; van Aartsen, B. H.</p> <p>2009-05-01</p> <p><span class="hlt">Modeling</span> Guru is an on-line knowledge-sharing resource for anyone involved with or interested in NASA's scientific <span class="hlt">models</span> or High End Computing (HEC) systems. Developed and maintained by the NASA's Software Integration and Visualization Office (SIVO) and the NASA Center for Computational Sciences (NCCS), <span class="hlt">Modeling</span> Guru's combined forums and knowledge base for research and collaboration is becoming a repository for the accumulated expertise of NASA's scientific <span class="hlt">modeling</span> and HEC communities. All NASA <span class="hlt">modelers</span> and associates are encouraged to participate and provide knowledge about the <span class="hlt">models</span> and systems so that other users may benefit from their experience. <span class="hlt">Modeling</span> Guru is divided into a hierarchy of communities, each with its own set forums and knowledge base documents. Current <span class="hlt">modeling</span> communities include those for space science, land and atmospheric dynamics, atmospheric chemistry, and oceanography. In addition, there are communities focused on NCCS systems, HEC tools and libraries, and programming and scripting languages. Anyone may view most of the content on <span class="hlt">Modeling</span> Guru (available at http://modelingguru.nasa.gov/), but you must log in to post messages and subscribe to community postings. The site offers a full range of "Web 2.0" features, including discussion forums, "wiki" document generation, document uploading, RSS feeds, search tools, blogs, email notification, and "breadcrumb" links. A discussion (a.k.a. forum "thread") is used to post comments, solicit feedback, or ask questions. If marked as a question, SIVO will monitor the thread, and normally respond within a day. Discussions can include embedded images, tables, and formatting through the use of the Rich Text Editor. Also, the user can add "Tags" to their thread to facilitate later searches. The "knowledge base" is comprised of documents that are used to capture and share expertise with others. The default "wiki" document lets users edit within the browser so others can easily collaborate on the same document, even allowing the author to select those who may edit and approve the document. To maintain knowledge integrity, all documents are moderated before they are visible to the public. <span class="hlt">Modeling</span> Guru, running on Clearspace by Jive Software, has been an active resource to the NASA <span class="hlt">modeling</span> and HEC communities for more than a year and currently has more than 100 active users. SIVO will soon install live instant messaging support, as well as a user-customizable homepage with social-networking features. In addition, SIVO plans to implement a large dataset/file storage capability so that users can quickly and easily exchange datasets and files with one another. Continued active community participation combined with periodic software updates and improved features will ensure that <span class="hlt">Modeling</span> Guru remains a vibrant, effective, easy-to-use tool for the NASA scientific community.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=information+AND+search&pg=2&id=EJ656113','ERIC'); return false;" href="http://eric.ed.gov/?q=information+AND+search&pg=2&id=EJ656113"><span id="translatedtitle"><span class="hlt">Models</span> (Part 1).</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Callison, Daniel</p> <p>2002-01-01</p> <p>Defines <span class="hlt">models</span> and describes information search <span class="hlt">models</span> that can be helpful to instructional media specialists in meeting users' abilities and information needs. Explains pathfinders and Kuhlthau's information search process, including the pre-writing information search process. (LRW)</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li class="active"><span>20</span></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_20 --> <div id="page_21" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li class="active"><span>21</span></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="401"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/1216573','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/1216573"><span id="translatedtitle"><span class="hlt">Modeling</span> EERE deployment programs</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Cort, K. A.; Hostick, D. J.; Belzer, D. B.; Livingston, O. V.</p> <p>2007-11-01</p> <p>The purpose of the project was to identify and characterize the <span class="hlt">modeling</span> of deployment programs within the EERE Technology Development (TD) programs, address possible improvements to the <span class="hlt">modeling</span> process, and note gaps in knowledge for future research.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=64093&keyword=laptop&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=48164249&CFTOKEN=54599086','EPA-EIMS'); return false;" href="http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=64093&keyword=laptop&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=48164249&CFTOKEN=54599086"><span id="translatedtitle">TMDL RUSLE <span class="hlt">MODEL</span></span></a></p> <p><a target="_blank" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p></p> <p></p> <p>We developed a simplified spreadsheet <span class="hlt">modeling</span> approach for characterizing and prioritizing sources of sediment loadings from watersheds in the United States. A simplified <span class="hlt">modeling</span> approach was developed to evaluate sediment loadings from watersheds and selected land segments. ...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://dspace.mit.edu/handle/1721.1/68072','EPRINT'); return false;" href="http://dspace.mit.edu/handle/1721.1/68072"><span id="translatedtitle">Aircraft collision <span class="hlt">models</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Endoh, Shinsuke</p> <p>1982-01-01</p> <p>Introduction: The threat of midair collisions is one of the most serious problems facing the air traffic control system and has been studied by many researchers. The gas <span class="hlt">model</span> is one of the <span class="hlt">models</span> which describe the expected ...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/10397850','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/10397850"><span id="translatedtitle">Protein solubility <span class="hlt">modeling</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Agena, S M; Pusey, M L; Bogle, I D</p> <p>1999-07-20</p> <p>A thermodynamic framework (UNIQUAC <span class="hlt">model</span> with temperature dependent parameters) is applied to <span class="hlt">model</span> the salt-induced protein crystallization equilibrium, i.e., protein solubility. The framework introduces a term for the solubility product describing protein transfer between the liquid and solid phase and a term for the solution behavior describing deviation from ideal solution. Protein solubility is <span class="hlt">modeled</span> as a function of salt concentration and temperature for a four-component system consisting of a protein, pseudo solvent (water and buffer), cation, and anion (salt). Two different systems, lysozyme with sodium chloride and concanavalin A with ammonium sulfate, are investigated. Comparison of the <span class="hlt">modeled</span> and experimental protein solubility data results in an average root mean square deviation of 5.8%, demonstrating that the <span class="hlt">model</span> closely follows the experimental behavior. <span class="hlt">Model</span> calculations and <span class="hlt">model</span> parameters are reviewed to examine the <span class="hlt">model</span> and protein crystallization process. PMID:10397850</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=48905&keyword=differential+AND+equation&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=52651630&CFTOKEN=91786387','EPA-EIMS'); return false;" href="http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=48905&keyword=differential+AND+equation&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=52651630&CFTOKEN=91786387"><span id="translatedtitle">PERSISTENCE IN <span class="hlt">MODEL</span> ECOSYSTEMS</span></a></p> <p><a target="_blank" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p></p> <p></p> <p>Mathematical <span class="hlt">models</span> aid in understanding environmental systems and in developing testable hypotheses relevant to the fate and ecological effects of toxic substances in such systems. Within the framework of microcosm or laboratory ecosystem <span class="hlt">modeling</span>, some differential equation mod...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/1231460-system-advisor-model','SCIGOV-ESTSC'); return false;" href="http://www.osti.gov/scitech/biblio/1231460-system-advisor-model"><span id="translatedtitle">System Advisor <span class="hlt">Model</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech/">Energy Science and Technology Software Center (ESTSC)</a></p> <p></p> <p>2010-03-01</p> <p>The System Advisor <span class="hlt">Model</span> (SAM) is a performance and economic <span class="hlt">model</span> designed to facilitate decision making for people involved in the renewable energy industry, ranging from project managers and engineers to incentive program designers, technology developers, and researchers.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015SPIE.9662E..3ON','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015SPIE.9662E..3ON"><span id="translatedtitle">Consistent <span class="hlt">model</span> driven architecture</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Niepostyn, Stanis?aw J.</p> <p>2015-09-01</p> <p>The goal of the MDA is to produce software systems from abstract <span class="hlt">models</span> in a way where human interaction is restricted to a minimum. These abstract <span class="hlt">models</span> are based on the UML language. However, the semantics of UML <span class="hlt">models</span> is defined in a natural language. Subsequently the verification of consistency of these diagrams is needed in order to identify errors in requirements at the early stage of the development process. The verification of consistency is difficult due to a semi-formal nature of UML diagrams. We propose automatic verification of consistency of the series of UML diagrams originating from abstract <span class="hlt">models</span> implemented with our consistency rules. This Consistent <span class="hlt">Model</span> Driven Architecture approach enables us to generate automatically complete workflow applications from consistent and complete <span class="hlt">models</span> developed from abstract <span class="hlt">models</span> (e.g. Business Context Diagram). Therefore, our method can be used to check practicability (feasibility) of software architecture <span class="hlt">models</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://ntrs.nasa.gov/search.jsp?R=20120010076&hterms=zoology&qs=N%3D0%26Ntk%3DAll%26Ntx%3Dmode%2Bmatchall%26Ntt%3Dzoology','NASA-TRS'); return false;" href="http://ntrs.nasa.gov/search.jsp?R=20120010076&hterms=zoology&qs=N%3D0%26Ntk%3DAll%26Ntx%3Dmode%2Bmatchall%26Ntt%3Dzoology"><span id="translatedtitle">Bounding Species Distribution <span class="hlt">Models</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Stohlgren, Thomas J.; Jarnevich, Cahterine S.; Morisette, Jeffrey T.; Esaias, Wayne E.</p> <p>2011-01-01</p> <p>Species distribution <span class="hlt">models</span> are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these <span class="hlt">models</span> with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" <span class="hlt">model</span> extrapolations. We relied on two commonly used <span class="hlt">modeling</span> approaches: classification and regression tree (CART) and maximum entropy (Maxent) <span class="hlt">models</span>, and we tested a simple alteration of the <span class="hlt">model</span> extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple <span class="hlt">models</span> of bounding, and the most conservative bounding of species distribution <span class="hlt">models</span>, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5): 642-647, 2011].</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.er.usgs.gov/publication/70036389','USGSPUBS'); return false;" href="http://pubs.er.usgs.gov/publication/70036389"><span id="translatedtitle">Bounding species distribution <span class="hlt">models</span></span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Stohlgren, T.J.; Jarnevich, C.S.; Esaias, W.E.; Morisette, J.T.</p> <p>2011-01-01</p> <p>Species distribution <span class="hlt">models</span> are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these <span class="hlt">models</span> with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" <span class="hlt">model</span> extrapolations. We relied on two commonly used <span class="hlt">modeling</span> approaches: classification and regression tree (CART) and maximum entropy (Maxent) <span class="hlt">models</span>, and we tested a simple alteration of the <span class="hlt">model</span> extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple <span class="hlt">models</span> of bounding, and the most conservative bounding of species distribution <span class="hlt">models</span>, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used. ?? 2011 Current Zoology.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://oaktrust.library.tamu.edu//handle/1969.1/5937','EPRINT'); return false;" href="http://oaktrust.library.tamu.edu//handle/1969.1/5937"><span id="translatedtitle">Volumetric particle <span class="hlt">modeling</span> </span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Dingle, Brent Michael</p> <p>2007-09-17</p> <p>This dissertation presents a robust method of <span class="hlt">modeling</span> objects and forces for computer animation. Within this method objects and forces are represented as particles. As in most <span class="hlt">modeling</span> systems, the movement of objects is ...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=15866&keyword=%28Ozone+AND+layer%29&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=55107236&CFTOKEN=59993309','EPA-EIMS'); return false;" href="http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=15866&keyword=%28Ozone+AND+layer%29&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=55107236&CFTOKEN=59993309"><span id="translatedtitle">METEOROLOGICAL AND TRANSPORT <span class="hlt">MODELING</span></span></a></p> <p><a target="_blank" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p></p> <p></p> <p>Advanced air quality simulation <span class="hlt">models</span>, such as CMAQ, as well as other transport and dispersion <span class="hlt">models</span>, require accurate and detailed meteorology fields. These meteorology fields include primary 3-dimensional dynamical and thermodynamical variables (e.g., winds, temperature, mo...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://dspace.mit.edu/handle/1721.1/32826','EPRINT'); return false;" href="http://dspace.mit.edu/handle/1721.1/32826"><span id="translatedtitle">Dahl friction <span class="hlt">modeling</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Chou, Danielle, 1981-</p> <p>2004-01-01</p> <p>The drive behind improved friction <span class="hlt">models</span> has been better prediction and control of dynamic systems. The earliest <span class="hlt">model</span> was of classical Coulomb friction; however, the discontinuity during force reversal of the Coulomb ...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/19720011551','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/19720011551"><span id="translatedtitle">Communication system <span class="hlt">modeling</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Holland, L. D.; Walsh, J. R., Jr.; Wetherington, R. D.</p> <p>1971-01-01</p> <p>This report presents the results of work on communications systems <span class="hlt">modeling</span> and covers three different areas of <span class="hlt">modeling</span>. The first of these deals with the <span class="hlt">modeling</span> of signals in communication systems in the frequency domain and the calculation of spectra for various modulations. These techniques are applied in determining the frequency spectra produced by a unified carrier system, the down-link portion of the Command and Communications System (CCS). The second <span class="hlt">modeling</span> area covers the <span class="hlt">modeling</span> of portions of a communication system on a block basis. A detailed analysis and <span class="hlt">modeling</span> effort based on control theory is presented along with its application to <span class="hlt">modeling</span> of the automatic frequency control system of an FM transmitter. A third topic discussed is a method for approximate <span class="hlt">modeling</span> of stiff systems using state variable techniques.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=72058&keyword=Lagoons&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=56084930&CFTOKEN=82981824','EPA-EIMS'); return false;" href="http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=72058&keyword=Lagoons&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=56084930&CFTOKEN=82981824"><span id="translatedtitle">SEDIMENT GEOCHEMICAL <span class="hlt">MODEL</span></span></a></p> <p><a target="_blank" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p></p> <p></p> <p>Until recently, sediment geochemical <span class="hlt">models</span> (diagenetic <span class="hlt">models</span>) have been only able to explain sedimentary flux and concentration profiles for a few simplified geochemical cycles (e.g., nitrogen, carbon and sulfur). However with advances in numerical methods, increased accuracy ...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://ntrs.nasa.gov/search.jsp?R=20040147352&hterms=anions+cations&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D60%26Ntt%3Danions%2Bcations','NASA-TRS'); return false;" href="http://ntrs.nasa.gov/search.jsp?R=20040147352&hterms=anions+cations&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D60%26Ntt%3Danions%2Bcations"><span id="translatedtitle">Protein solubility <span class="hlt">modeling</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Agena, S. M.; Pusey, M. L.; Bogle, I. D.</p> <p>1999-01-01</p> <p>A thermodynamic framework (UNIQUAC <span class="hlt">model</span> with temperature dependent parameters) is applied to <span class="hlt">model</span> the salt-induced protein crystallization equilibrium, i.e., protein solubility. The framework introduces a term for the solubility product describing protein transfer between the liquid and solid phase and a term for the solution behavior describing deviation from ideal solution. Protein solubility is <span class="hlt">modeled</span> as a function of salt concentration and temperature for a four-component system consisting of a protein, pseudo solvent (water and buffer), cation, and anion (salt). Two different systems, lysozyme with sodium chloride and concanavalin A with ammonium sulfate, are investigated. Comparison of the <span class="hlt">modeled</span> and experimental protein solubility data results in an average root mean square deviation of 5.8%, demonstrating that the <span class="hlt">model</span> closely follows the experimental behavior. <span class="hlt">Model</span> calculations and <span class="hlt">model</span> parameters are reviewed to examine the <span class="hlt">model</span> and protein crystallization process. Copyright 1999 John Wiley & Sons, Inc.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://dspace.mit.edu/handle/1721.1/74247','EPRINT'); return false;" href="http://dspace.mit.edu/handle/1721.1/74247"><span id="translatedtitle">Content <span class="hlt">models</span> with attitude</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Sauper, Christina Joan</p> <p></p> <p>We present a probabilistic topic <span class="hlt">model</span> for jointly identifying properties and attributes of social media review snippets. Our <span class="hlt">model</span> simultaneously learns a set of properties of a product and captures aggregate user sentiments ...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=RNA+AND+RNA&pg=6&id=EJ469627','ERIC'); return false;" href="http://eric.ed.gov/?q=RNA+AND+RNA&pg=6&id=EJ469627"><span id="translatedtitle">Of Molecules and <span class="hlt">Models</span>.</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Brinner, Bonnie</p> <p>1992-01-01</p> <p>Presents an activity in which <span class="hlt">models</span> help students visualize both the DNA process and transcription. After constructing DNA, RNA messenger, and RNA transfer molecules; students <span class="hlt">model</span> cells, protein synthesis, codons, and RNA movement. (MDH)</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://dspace.mit.edu/handle/1721.1/6716','EPRINT'); return false;" href="http://dspace.mit.edu/handle/1721.1/6716"><span id="translatedtitle">Light Field Morphable <span class="hlt">Models</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Christoudias, Chris Mario</p> <p>2003-04-18</p> <p>Statistical shape and texture appearance <span class="hlt">models</span> are powerful image representations, but previously had been restricted to 2D or simple 3D shapes. In this paper we present a novel 3D morphable <span class="hlt">model</span> based on image-based ...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://dspace.mit.edu/handle/1721.1/82635','EPRINT'); return false;" href="http://dspace.mit.edu/handle/1721.1/82635"><span id="translatedtitle">Quantile <span class="hlt">Models</span> with Endogeneity</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Chernozhukov, Victor V.</p> <p></p> <p>In this article, we review quantile <span class="hlt">models</span> with endogeneity. We focus on <span class="hlt">models</span> that achieve identification through the use of instrumental variables and discuss conditions under which partial and point identification are ...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://http.cs.berkeley.edu/~lazzaro/biblio/barochip-vlsi.pdf','EPRINT'); return false;" href="http://http.cs.berkeley.edu/~lazzaro/biblio/barochip-vlsi.pdf"><span id="translatedtitle">Silicon Baroreceptors: <span class="hlt">Modeling</span> Cardiovascular</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Lazzaro, John</p> <p></p> <p>Silicon Baroreceptors: <span class="hlt">Modeling</span> Cardiovascular Pressure Transduction in Analog VLSI John Lazzaro of the baroreceptors in the carotid vessel. Inspired by re- cent work in silicon <span class="hlt">models</span> of the cochlea [3</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li class="active"><span>21</span></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_21 --> <div id="page_22" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li class="active"><span>22</span></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="421"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://cisnet.cancer.gov/esophagus/','NCI'); return false;" href="http://cisnet.cancer.gov/esophagus/"><span id="translatedtitle">CISNET: Esophageal Cancer <span class="hlt">Modeling</span></span></a></p> <p><a target="_blank" href="http://www.cancer.gov">Cancer.gov</a></p> <p></p> <p></p> <p>The CISNET esophageal cancer group was formed in 2010 in the third round of CISNET funding with three distinct <span class="hlt">modeling</span> teams focused on collaboratively <span class="hlt">modeling</span> the incidence and mortality of esophageal adenocarcinoma (EAC) in the US population. The group’s work will include performing collaborative <span class="hlt">modeling</span> of the natural history <span class="hlt">models</span> of esophageal adenocarcinoma which will include precursor states such as Barrett’s esophagus and dysplasia that are calibrated to US SEER data.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2014JPhCS.490a2181T','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2014JPhCS.490a2181T"><span id="translatedtitle">Hierarchical Bass <span class="hlt">model</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Tashiro, Tohru</p> <p>2014-03-01</p> <p>We propose a new <span class="hlt">model</span> about diffusion of a product which includes a memory of how many adopters or advertisements a non-adopter met, where (non-)adopters mean people (not) possessing the product. This effect is lacking in the Bass <span class="hlt">model</span>. As an application, we utilize the <span class="hlt">model</span> to fit the iPod sales data, and so the better agreement is obtained than the Bass <span class="hlt">model</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20100040702','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20100040702"><span id="translatedtitle">Mathematical circulatory system <span class="hlt">model</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Lakin, William D. (Inventor); Stevens, Scott A. (Inventor)</p> <p>2010-01-01</p> <p>A system and method of <span class="hlt">modeling</span> a circulatory system including a regulatory mechanism parameter. In one embodiment, a regulatory mechanism parameter in a lumped parameter <span class="hlt">model</span> is represented as a logistic function. In another embodiment, the circulatory system <span class="hlt">model</span> includes a compliant vessel, the <span class="hlt">model</span> having a parameter representing a change in pressure due to contraction of smooth muscles of a wall of the vessel.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/19780015703','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/19780015703"><span id="translatedtitle">Soil moisture <span class="hlt">modeling</span> review</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Hildreth, W. W.</p> <p>1978-01-01</p> <p>A determination of the state of the art in soil moisture transport <span class="hlt">modeling</span> based on physical or physiological principles was made. It was found that soil moisture <span class="hlt">models</span> based on physical principles have been under development for more than 10 years. However, these <span class="hlt">models</span> were shown to represent infiltration and redistribution of soil moisture quite well. Evapotranspiration has not been as adequately incorporated into the <span class="hlt">models</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://kmrs.kaist.ac.kr/wp-content/uploads/2013/12/Xue-Cheng-Tai_part2-2012.08.pdf','EPRINT'); return false;" href="http://kmrs.kaist.ac.kr/wp-content/uploads/2013/12/Xue-Cheng-Tai_part2-2012.08.pdf"><span id="translatedtitle">Elementary <span class="hlt">models</span> Numerical Techniques</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Kim, Yong Jung</p> <p></p> <p>-Shah is reduced to the Potts <span class="hlt">model</span> choosing fi = |ci - u0|2. #12;The GAC (Geodesic active contour) <span class="hlt">model</span> Give an image u0, the GAC <span class="hlt">model</span> is trying to find a contour to minimize min g(| u|) + || g is an edge;Combining Mumford-Shah with GAC It is possible to combine these two popular <span class="hlt">models</span> together and it has been</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://dx.doi.org/10.1111/j.1745-6584.2012.00937.x','USGSPUBS'); return false;" href="http://dx.doi.org/10.1111/j.1745-6584.2012.00937.x"><span id="translatedtitle">Future of groundwater <span class="hlt">modeling</span></span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Langevin, Christian D.; Panday, Sorab</p> <p>2012-01-01</p> <p>With an increasing need to better manage water resources, the future of groundwater <span class="hlt">modeling</span> is bright and exciting. However, while the past can be described and the present is known, the future of groundwater <span class="hlt">modeling</span>, just like a groundwater <span class="hlt">model</span> result, is highly uncertain and any prediction is probably not going to be entirely representative. Thus we acknowledge this as we present our vision of where groundwater <span class="hlt">modeling</span> may be headed.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20150009574','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20150009574"><span id="translatedtitle">Nonlinear <span class="hlt">Modeling</span> by Assembling Piecewise Linear <span class="hlt">Models</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Yao, Weigang; Liou, Meng-Sing</p> <p>2013-01-01</p> <p>To preserve nonlinearity of a full order system over a parameters range of interest, we propose a simple <span class="hlt">modeling</span> approach by assembling a set of piecewise local solutions, including the first-order Taylor series terms expanded about some sampling states. The work by Rewienski and White inspired our use of piecewise linear local solutions. The assembly of these local approximations is accomplished by assigning nonlinear weights, through radial basis functions in this study. The efficacy of the proposed procedure is validated for a two-dimensional airfoil moving at different Mach numbers and pitching motions, under which the flow exhibits prominent nonlinear behaviors. All results confirm that our nonlinear <span class="hlt">model</span> is accurate and stable for predicting not only aerodynamic forces but also detailed flowfields. Moreover, the <span class="hlt">model</span> is robustness-accurate for inputs considerably different from the base trajectory in form and magnitude. This <span class="hlt">modeling</span> preserves nonlinearity of the problems considered in a rather simple and accurate manner.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20010032412','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20010032412"><span id="translatedtitle">Aerosol <span class="hlt">Modeling</span> for the Global <span class="hlt">Model</span> Initiative</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Weisenstein, Debra K.; Ko, Malcolm K. W.</p> <p>2001-01-01</p> <p>The goal of this project is to develop an aerosol module to be used within the framework of the Global <span class="hlt">Modeling</span> Initiative (GMI). The <span class="hlt">model</span> development work will be preformed jointly by the University of Michigan and AER, using existing aerosol <span class="hlt">models</span> at the two institutions as starting points. The GMI aerosol <span class="hlt">model</span> will be tested, evaluated against observations, and then applied to assessment of the effects of aircraft sulfur emissions as needed by the NASA Subsonic Assessment in 2001. The work includes the following tasks: 1. Implementation of the sulfur cycle within GMI, including sources, sinks, and aqueous conversion of sulfur. Aerosol modules will be added as they are developed and the GMI schedule permits. 2. Addition of aerosol types other than sulfate particles, including dust, soot, organic carbon, and black carbon. 3. Development of new and more efficient parameterizations for treating sulfate aerosol nucleation, condensation, and coagulation among different particle sizes and types.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015PrOce.134..190G','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015PrOce.134..190G"><span id="translatedtitle">Aggregation in ecosystem <span class="hlt">models</span> and <span class="hlt">model</span> stability</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Giricheva, Evgeniya</p> <p>2015-05-01</p> <p>Using a multimodal approach to research ecosystems improves usage of available information on an object. This study presents several <span class="hlt">models</span> of the Bering Sea ecosystem. The ecosystem is considered as a closed object, that is, the influence of the environment is not provided. We then add the links with the external medium in the <span class="hlt">models</span>. The <span class="hlt">models</span> differ in terms of the degree and method of grouping components. Our method is based on the differences in habitat and food source of groups, which allows us to determine the grouping of species with a greater effect on system dynamics. In particular, we determine whether benthic fish aggregation or pelagic fish aggregation can change the consumption structure of some groups of species, and consequently, the behavior of the entire <span class="hlt">model</span> system.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/1219272','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/1219272"><span id="translatedtitle"><span class="hlt">Modeling</span> EERE Deployment Programs</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Cort, K. A.; Hostick, D. J.; Belzer, D. B.; Livingston, O. V.</p> <p>2007-11-01</p> <p>This report compiles information and conclusions gathered as part of the “<span class="hlt">Modeling</span> EERE Deployment Programs” project. The purpose of the project was to identify and characterize the <span class="hlt">modeling</span> of deployment programs within the EERE Technology Development (TD) programs, address possible improvements to the <span class="hlt">modeling</span> process, and note gaps in knowledge in which future research is needed.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=193020','TEKTRAN'); return false;" href="http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=193020"><span id="translatedtitle">QUALITATIVE ECOLOGICAL <span class="hlt">MODELING</span></span></a></p> <p><a target="_blank" href="http://www.ars.usda.gov/services/TekTran.htm">Technology Transfer Automated Retrieval System (TEKTRAN)</a></p> <p></p> <p></p> <p>Students construct qualitative <span class="hlt">models</span> of an ecosystem and use the <span class="hlt">models</span> to evaluate the direct and indirect effects that may result from perturbations to the ecosystem. Qualitative <span class="hlt">modeling</span> is described for use in two procedures, each with different educational goals and student backgrounds in min...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://staff.science.uva.nl/~bloewe/2010-11-II/RFMFS-7.pdf','EPRINT'); return false;" href="http://staff.science.uva.nl/~bloewe/2010-11-II/RFMFS-7.pdf"><span id="translatedtitle">Reasoning and Formal <span class="hlt">Modelling</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Löwe, Benedikt</p> <p></p> <p>Reasoning and Formal <span class="hlt">Modelling</span> for Forensic Science Lecture 7 Prof. Dr. Benedikt L¨owe Reasoning and Formal <span class="hlt">Modelling</span> for Forensic Science Lecture 7 Prof. Dr. Benedikt L¨owe 2nd Semester 2010/11 #12;Reasoning and Formal <span class="hlt">Modelling</span> for Forensic Science Lecture 7 Prof. Dr. Benedikt L¨owe Reminder: logica</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=natural+AND+selection&id=EJ921632','ERIC'); return false;" href="http://eric.ed.gov/?q=natural+AND+selection&id=EJ921632"><span id="translatedtitle"><span class="hlt">Modeling</span> Natural Selection</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Bogiages, Christopher A.; Lotter, Christine</p> <p>2011-01-01</p> <p>In their research, scientists generate, test, and modify scientific <span class="hlt">models</span>. These <span class="hlt">models</span> can be shared with others and demonstrate a scientist's understanding of how the natural world works. Similarly, students can generate and modify <span class="hlt">models</span> to gain a better understanding of the content, process, and nature of science (Kenyon, Schwarz, and Hug…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/34289','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/34289"><span id="translatedtitle">IR DIAL performance <span class="hlt">modeling</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Sharlemann, E.T.</p> <p>1994-07-01</p> <p>We are developing a DIAL performance <span class="hlt">model</span> for CALIOPE at LLNL. The intent of the <span class="hlt">model</span> is to provide quick and interactive parameter sensitivity calculations with immediate graphical output. A brief overview of the features of the performance <span class="hlt">model</span> is given, along with an example of performance calculations for a non-CALIOPE application.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.fsl.orst.edu/clams/download/posters/boughton_stochPost.pdf','EPRINT'); return false;" href="http://www.fsl.orst.edu/clams/download/posters/boughton_stochPost.pdf"><span id="translatedtitle">Succession <span class="hlt">Model</span> Landscape Stochasticity</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p></p> <p></p> <p>100 1000 10000 patch sizes birth rate both Disturbance <span class="hlt">Model</span> Landscape Stochasticity Low Control High" accomplished by incrementing the patch birth rate (Control: s = a = 10) A simple <span class="hlt">model</span> of species viabilitySuccession <span class="hlt">Model</span> Landscape Stochasticity Low Control High Very High ThresholdMultiplier 0.1 1 10</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/4127','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/4127"><span id="translatedtitle">Crushed Salt Constitutive <span class="hlt">Model</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Callahan, G.D.</p> <p>1999-02-01</p> <p>The constitutive <span class="hlt">model</span> used to describe the deformation of crushed salt is presented in this report. Two mechanisms -- dislocation creep and grain boundary diffusional pressure solution -- are combined to form the basis for the constitutive <span class="hlt">model</span> governing the deformation of crushed salt. The constitutive <span class="hlt">model</span> is generalized to represent three-dimensional states of stress. Upon complete consolidation, the crushed-salt <span class="hlt">model</span> reproduces the Multimechanism Deformation (M-D) <span class="hlt">model</span> typically used for the Waste Isolation Pilot Plant (WIPP) host geological formation salt. New shear consolidation tests are combined with an existing database that includes hydrostatic consolidation and shear consolidation tests conducted on WIPP and southeastern New Mexico salt. Nonlinear least-squares <span class="hlt">model</span> fitting to the database produced two sets of material parameter values for the <span class="hlt">model</span> -- one for the shear consolidation tests and one for a combination of the shear and hydrostatic consolidation tests. Using the parameter values determined from the fitted database, the constitutive <span class="hlt">model</span> is validated against constant strain-rate tests. Shaft seal problems are analyzed to demonstrate <span class="hlt">model</span>-predicted consolidation of the shaft seal crushed-salt component. Based on the fitting statistics, the ability of the <span class="hlt">model</span> to predict the test data, and the ability of the <span class="hlt">model</span> to predict load paths and test data outside of the fitted database, the <span class="hlt">model</span> appears to capture the creep consolidation behavior of crushed salt reasonably well.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://ptolemy.eecs.berkeley.edu/publications/papers/02/ptIIdesign/design.pdf','EPRINT'); return false;" href="http://ptolemy.eecs.berkeley.edu/publications/papers/02/ptIIdesign/design.pdf"><span id="translatedtitle">HETEROGENEOUS <span class="hlt">MODELING</span> AND</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>California at Berkeley, University of</p> <p></p> <p>PTOLEMY II HETEROGENEOUS CONCURRENT <span class="hlt">MODELING</span> AND DESIGN IN JAVA Edited by: Christopher Hylands of California at Berkeley http://ptolemy.eecs.berkeley.edu Document Version 2.0.1 for use with Ptolemy II 2 Concurrent <span class="hlt">Modeling</span> and Design Contents Part 1: Using Ptolemy II 1. Introduction 1-1 1.1.<span class="hlt">Modeling</span> and Design</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=73724&keyword=Internet&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=53085938&CFTOKEN=88448373','EPA-EIMS'); return false;" href="http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=73724&keyword=Internet&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=53085938&CFTOKEN=88448373"><span id="translatedtitle">REGULATORY AIR QUALITY <span class="hlt">MODELS</span></span></a></p> <p><a target="_blank" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p></p> <p></p> <p>Appendix W to 40CFR Part 51 (Guideline on Air Quality <span class="hlt">Models</span>) specifies the <span class="hlt">models</span> to be used for purposes of permitting, PSD, and SIPs. Through a formal regulatory process this <span class="hlt">modeling</span> guidance is periodically updated to reflect current science. In the most recent action, thr...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=293579','TEKTRAN'); return false;" href="http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=293579"><span id="translatedtitle">Surface complexation <span class="hlt">modeling</span></span></a></p> <p><a target="_blank" href="http://www.ars.usda.gov/services/TekTran.htm">Technology Transfer Automated Retrieval System (TEKTRAN)</a></p> <p></p> <p></p> <p>Adsorption-desorption reactions are important processes that affect the transport of contaminants in the environment. Surface complexation <span class="hlt">models</span> are chemical <span class="hlt">models</span> that can account for the effects of variable chemical conditions, such as pH, on adsorption reactions. These <span class="hlt">models</span> define specific ...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://ccrod.cancer.gov/confluence/display/CCRJB6','NCI'); return false;" href="https://ccrod.cancer.gov/confluence/display/CCRJB6"><span id="translatedtitle">JB6 Mouse <span class="hlt">Model</span></span></a></p> <p><a target="_blank" href="http://www.cancer.gov">Cancer.gov</a></p> <p></p> <p></p> <p>JB6 Mouse <span class="hlt">Model</span> The mouse Balb/C JB6 <span class="hlt">model</span> (1) is the only well characterized <span class="hlt">model</span> of genetic variants for a neoplastic transformation response to tumor promoters. These cells are not differentially sensitive to tumor promoter induced mitogenesis or diff</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li class="active"><span>22</span></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_22 --> <div id="page_23" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li class="active"><span>23</span></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li><a href="#" onclick='return showDiv("page_25");'>25</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="441"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=83092&keyword=%28Kyoto+AND+Protocol%29&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=56081470&CFTOKEN=38144285','EPA-EIMS'); return false;" href="http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=83092&keyword=%28Kyoto+AND+Protocol%29&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=56081470&CFTOKEN=38144285"><span id="translatedtitle">SECOND GENERATION <span class="hlt">MODEL</span></span></a></p> <p><a target="_blank" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p></p> <p></p> <p>One of the environmental and economic <span class="hlt">models</span> that the U.S. EPA uses to assess climate change policies is the Second Generation <span class="hlt">Model</span> (SGM). SGM is a 13 region, 24 sector computable general equilibrium (CGE) <span class="hlt">model</span> of the world that can be used to estimate the domestic and intern...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2009TJSAI..24..241R','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2009TJSAI..24..241R"><span id="translatedtitle">Two Cognitive <span class="hlt">Modeling</span> Frontiers</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Ritter, Frank E.</p> <p></p> <p>This paper reviews three hybrid cognitive architectures (Soar, ACT-R, and CoJACK) and how they can support including <span class="hlt">models</span> of emotions. There remain problems creating <span class="hlt">models</span> in these architectures, which is a research and engineering problem. Thus, the term cognitive science engineering is introduced as an area that would support making <span class="hlt">models</span> easier to create, understand, and re-use.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=house+AND+construction&pg=5&id=EJ798518','ERIC'); return false;" href="http://eric.ed.gov/?q=house+AND+construction&pg=5&id=EJ798518"><span id="translatedtitle">A <span class="hlt">Model</span> Performance</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Thornton, Bradley D.; Smalley, Robert A.</p> <p>2008-01-01</p> <p>Building information <span class="hlt">modeling</span> (BIM) uses three-dimensional <span class="hlt">modeling</span> concepts, information technology and interoperable software to design, construct and operate a facility. However, BIM can be more than a tool for virtual <span class="hlt">modeling</span>--it can provide schools with a 3-D walkthrough of a project while it still is on the electronic drawing board. BIM can…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=products&pg=5&id=EJ943279','ERIC'); return false;" href="http://eric.ed.gov/?q=products&pg=5&id=EJ943279"><span id="translatedtitle"><span class="hlt">Models</span> for Products</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Speiser, Bob; Walter, Chuck</p> <p>2011-01-01</p> <p>This paper explores how <span class="hlt">models</span> can support productive thinking. For us a <span class="hlt">model</span> is a "thing", a tool to help make sense of something. We restrict attention to specific <span class="hlt">models</span> for whole-number multiplication, hence the wording of the title. They support evolving thinking in large measure through the ways their users redesign them. They assume new…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://arxiv.org/pdf/1212.6747v1','EPRINT'); return false;" href="http://arxiv.org/pdf/1212.6747v1"><span id="translatedtitle">A Holographic Energy <span class="hlt">Model</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>P. Huang; Yong-Chang Huang</p> <p>2012-12-30</p> <p>We suggest a holographic energy <span class="hlt">model</span> in which the energy coming from spatial curvature, matter and radiation can be obtained by using the particle horizon for the infrared cut-off. We show the consistency between the holographic dark-energy <span class="hlt">model</span> and the holographic energy <span class="hlt">model</span> proposed in this paper. Then, we give a holographic description of the universe.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=models+AND+young&id=EJ973522','ERIC'); return false;" href="http://eric.ed.gov/?q=models+AND+young&id=EJ973522"><span id="translatedtitle"><span class="hlt">Modeling</span> and Remodeling Writing</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Hayes, John R.</p> <p>2012-01-01</p> <p>In Section 1 of this article, the author discusses the succession of <span class="hlt">models</span> of adult writing that he and his colleagues have proposed from 1980 to the present. He notes the most important changes that differentiate earlier and later <span class="hlt">models</span> and discusses reasons for the changes. In Section 2, he describes his recent efforts to <span class="hlt">model</span> young…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=vig&id=EJ1036774','ERIC'); return false;" href="http://eric.ed.gov/?q=vig&id=EJ1036774"><span id="translatedtitle"><span class="hlt">Model</span> Breaking Points Conceptualized</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Vig, Rozy; Murray, Eileen; Star, Jon R.</p> <p>2014-01-01</p> <p>Current curriculum initiatives (e.g., National Governors Association Center for Best Practices and Council of Chief State School Officers 2010) advocate that <span class="hlt">models</span> be used in the mathematics classroom. However, despite their apparent promise, there comes a point when <span class="hlt">models</span> break, a point in the mathematical problem space where the <span class="hlt">model</span> cannot,…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://files.eric.ed.gov/fulltext/ED046512.pdf','ERIC'); return false;" href="http://files.eric.ed.gov/fulltext/ED046512.pdf"><span id="translatedtitle"><span class="hlt">Models</span>, Norms and Sharing.</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Harris, Mary B.</p> <p></p> <p>To investigate the effect of <span class="hlt">modeling</span> on altruism, 156 third and fifth grade children were exposed to a <span class="hlt">model</span> who either shared with them, gave to a charity, or refused to share. The test apparatus, identified as a game, consisted of a box with signal lights and a chute through which marbles were dispensed. Subjects and the <span class="hlt">model</span> played the game…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=rocketry&pg=3&id=EJ333506','ERIC'); return false;" href="http://eric.ed.gov/?q=rocketry&pg=3&id=EJ333506"><span id="translatedtitle"><span class="hlt">Model</span> Rockets and Microchips.</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Fitzsimmons, Charles P.</p> <p>1986-01-01</p> <p>Points out the instructional applications and program possibilities of a unit on <span class="hlt">model</span> rocketry. Describes the ways that microcomputers can assist in <span class="hlt">model</span> rocket design and in problem calculations. Provides a descriptive listing of <span class="hlt">model</span> rocket software for the Apple II microcomputer. (ML)</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://faculty.up.edu/kuhn/papers/EMI2012_Undrained.pdf','EPRINT'); return false;" href="http://faculty.up.edu/kuhn/papers/EMI2012_Undrained.pdf"><span id="translatedtitle"><span class="hlt">Model</span> definition DEM summary</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Kuhn, Matthew R.</p> <p></p> <p><span class="hlt">Model</span> definition DEM summary Simple-shear Simulating undrained loading of sand with the discrete University of Portland EMI 2012 Conference South Bend, Indiana June 18­20, 2012 National Science Foundation_Undrained.pdf #12;<span class="hlt">Model</span> definition DEM summary Simple-shear Nevada Sand Particles and contacts <span class="hlt">Model</span></p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=suspension+AND+bridges&id=EJ445008','ERIC'); return false;" href="http://eric.ed.gov/?q=suspension+AND+bridges&id=EJ445008"><span id="translatedtitle"><span class="hlt">Modelling</span> a Suspension Bridge.</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Rawlins, Phil</p> <p>1991-01-01</p> <p>The quadratic function can be <span class="hlt">modeled</span> in real life by a suspension bridge that supports a uniform weight. This activity uses concrete <span class="hlt">models</span> and computer generated graphs to discover the mathematical <span class="hlt">model</span> of the shape of the main cable of a suspension bridge. (MDH)</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=198002&keyword=computer&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=56086162&CFTOKEN=48605521','EPA-EIMS'); return false;" href="http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=198002&keyword=computer&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50&CFID=56086162&CFTOKEN=48605521"><span id="translatedtitle">Global Timber <span class="hlt">Model</span> (GTM)</span></a></p> <p><a target="_blank" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p></p> <p></p> <p>GTM is an economic <span class="hlt">model</span> capable of examining global forestry land-use, management, and trade responses to policies. In responding to a policy, the <span class="hlt">model</span> captures afforestation, forest management, and avoided deforestation behavior. The <span class="hlt">model</span> estimates harvests in industrial fore...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=climate+AND+energy&id=EJ1017691','ERIC'); return false;" href="http://eric.ed.gov/?q=climate+AND+energy&id=EJ1017691"><span id="translatedtitle"><span class="hlt">Modeling</span> Climate Dynamically</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Walsh, Jim; McGehee, Richard</p> <p>2013-01-01</p> <p>A dynamical systems approach to energy balance <span class="hlt">models</span> of climate is presented, focusing on low order, or conceptual, <span class="hlt">models</span>. Included are global average and latitude-dependent, surface temperature <span class="hlt">models</span>. The development and analysis of the differential equations and corresponding bifurcation diagrams provides a host of appropriate material for…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/838644','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/838644"><span id="translatedtitle">Rock Properties <span class="hlt">Model</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>C. Lum</p> <p>2004-09-16</p> <p>The purpose of this <span class="hlt">model</span> report is to document the Rock Properties <span class="hlt">Model</span> version 3.1 with regard to input data, <span class="hlt">model</span> methods, assumptions, uncertainties and limitations of <span class="hlt">model</span> results, and qualification status of the <span class="hlt">model</span>. The report also documents the differences between the current and previous versions and validation of the <span class="hlt">model</span>. The rock properties <span class="hlt">model</span> provides mean matrix and lithophysae porosity, and the cross-correlated mean bulk density as direct input to the ''Saturated Zone Flow and Transport <span class="hlt">Model</span> Abstraction'', MDL-NBS-HS-000021, REV 02 (BSC 2004 [DIRS 170042]). The constraints, caveats, and limitations associated with this <span class="hlt">model</span> are discussed in Section 6.6 and 8.2. <span class="hlt">Model</span> validation accomplished by corroboration with data not cited as direct input is discussed in Section 7. The revision of this <span class="hlt">model</span> report was performed as part of activities being conducted under the ''Technical Work Plan for: The Integrated Site <span class="hlt">Model</span>, Revision 05'' (BSC 2004 [DIRS 169635]). The purpose of this revision is to bring the report up to current procedural requirements and address the Regulatory Integration Team evaluation comments. The work plan describes the scope, objectives, tasks, methodology, and procedures for this process.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=herbert+AND+simon&id=EJ534069','ERIC'); return false;" href="http://eric.ed.gov/?q=herbert+AND+simon&id=EJ534069"><span id="translatedtitle">What Is a <span class="hlt">Model</span>?</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>McNamara, James F.</p> <p>1996-01-01</p> <p>Uses R.A. Ackoff's connotations to define "<span class="hlt">model</span>" as noun, adjective, and verb. Researchers should use various types of <span class="hlt">models</span> (iconic, analogue, or symbolic) for three purposes: to reveal reality, to explain the past and present, and to predict and control the future. Herbert Simon's process <span class="hlt">model</span> for administrative decision making has widespread…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=unified+AND+equation&pg=3&id=EJ622391','ERIC'); return false;" href="http://eric.ed.gov/?q=unified+AND+equation&pg=3&id=EJ622391"><span id="translatedtitle">Generalized Latent Trait <span class="hlt">Models</span>.</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Moustaki, Irini; Knott, Martin</p> <p>2000-01-01</p> <p>Discusses a general <span class="hlt">model</span> framework within which manifest variables with different distributions in the exponential family can be analyzed with a latent trait <span class="hlt">model</span>. Presents a unified maximum likelihood method for estimating the parameters of the generalized latent trait <span class="hlt">model</span> and discusses the scoring of individuals on the latent dimensions.…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=periodic+AND+table+AND+elements&pg=4&id=EJ406070','ERIC'); return false;" href="http://eric.ed.gov/?q=periodic+AND+table+AND+elements&pg=4&id=EJ406070"><span id="translatedtitle">A <span class="hlt">Model</span> Chemistry Class.</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Summerlin, Lee; Borgford, Christie</p> <p>1989-01-01</p> <p>Described is an activity which uses a 96-well reaction plate and soda straws to construct a <span class="hlt">model</span> of the periodic table of the elements. The <span class="hlt">model</span> illustrates the ionization energies of the various elements. Construction of the <span class="hlt">model</span> and related concepts are discussed. (CW)</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://oaktrust.library.tamu.edu//handle/1969.1/2372','EPRINT'); return false;" href="http://oaktrust.library.tamu.edu//handle/1969.1/2372"><span id="translatedtitle"><span class="hlt">Models</span> of scientific explanation </span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Sutton, Peter Andrew</p> <p>2005-08-29</p> <p>V EXPLANATION VS. INFERENCE?????????????.? 54 Jeffrey on Explanation and Inference??????????... 55 Salmon on Explanation and Inference???????.???. 66 v CHAPTER Page VI.... The Statistical Relevance <span class="hlt">Model</span> Hempel?s requirement of maximal specificity leads naturally into our next <span class="hlt">model</span>, which is Wesley Salmon's Statistical Relevance (S-R) <span class="hlt">model</span> of scientific explanation. Basically Salmon takes maximal specificity (as given...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.math.uni-leipzig.de/~frey/frey-mcneil-02a.pdf','EPRINT'); return false;" href="http://www.math.uni-leipzig.de/~frey/frey-mcneil-02a.pdf"><span id="translatedtitle">Dependence <span class="hlt">Modelling</span>, <span class="hlt">Model</span> Risk and <span class="hlt">Model</span> Calibration in <span class="hlt">Models</span> of Portfolio Credit Risk</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Frey, Rüdiger</p> <p></p> <p>as internal <span class="hlt">models</span> are nowadays used for capital adequacy purposes in market risk management calibration in credit risk <span class="hlt">models</span>. J.E.L. Subject Classification: G31, G11, C15 Keywords: Risk Management, Credit Risk, Dependence <span class="hlt">Modelling</span>, Copulas 1 Introduction A major cause of concern in managing the credit</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=194745','TEKTRAN'); return false;" href="http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=194745"><span id="translatedtitle">A GENERAL CROP <span class="hlt">MODEL</span></span></a></p> <p><a target="_blank" href="http://www.ars.usda.gov/services/TekTran.htm">Technology Transfer Automated Retrieval System (TEKTRAN)</a></p> <p></p> <p></p> <p>Agricultural and ecosystem simulation <span class="hlt">models</span> valuable for technology transfer require a realistic, process-oriented plant <span class="hlt">model</span> that can be easily applied to different crops, grasses, and woody species. The objective of this chapter was to describe a general plant <span class="hlt">model</span> that can be easily applied i...</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li class="active"><span>23</span></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li><a href="#" onclick='return showDiv("page_25");'>25</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_23 --> <div id="page_24" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li class="active"><span>24</span></li> <li><a href="#" onclick='return showDiv("page_25");'>25</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="461"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://stl.mie.utoronto.ca/publications/modelling.pdf','EPRINT'); return false;" href="http://stl.mie.utoronto.ca/publications/modelling.pdf"><span id="translatedtitle">Enterprise <span class="hlt">Modelling</span> Michael Gruninger</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Grüninger, Michael</p> <p></p> <p>Chapter 16 Enterprise <span class="hlt">Modelling</span> Michael Gruninger National Institute of Standards and Technology E-Mail: gruning@nist.gov Abstract: An enterprise <span class="hlt">model</span> is a computational representation of the structure or other enterprise. An enterprise <span class="hlt">model</span> can be both descriptive and definitional and it may cover both</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://files.eric.ed.gov/fulltext/EJ1054963.pdf','ERIC'); return false;" href="http://files.eric.ed.gov/fulltext/EJ1054963.pdf"><span id="translatedtitle">Modern Media Education <span class="hlt">Models</span></span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Fedorov, Alexander</p> <p>2011-01-01</p> <p>The author supposed that media education <span class="hlt">models</span> can be divided into the following groups: (1) educational-information <span class="hlt">models</span> (the study of the theory, history, language of media culture, etc.), based on the cultural, aesthetic, semiotic, socio-cultural theories of media education; (2) educational-ethical <span class="hlt">models</span> (the study of moral, religions,…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/6825186','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/6825186"><span id="translatedtitle">Solid Waste Projection <span class="hlt">Model</span>: <span class="hlt">Model</span> user's guide</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Stiles, D.L.; Crow, V.L.</p> <p>1990-08-01</p> <p>The Solid Waste Projection <span class="hlt">Model</span> (SWPM) system is an analytical tool developed by Pacific Northwest Laboratory (PNL) for Westinghouse Hanford company (WHC) specifically to address solid waste management issues at the Hanford Central Waste Complex (HCWC). This document, one of six documents supporting the SWPM system, contains a description of the system and instructions for preparing to use SWPM and operating Version 1 of the <span class="hlt">model</span>. 4 figs., 1 tab.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/23283665','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/23283665"><span id="translatedtitle"><span class="hlt">Modeling</span> physical growth using mixed effects <span class="hlt">models</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Johnson, William; Balakrishna, Nagalla; Griffiths, Paula L</p> <p>2013-01-01</p> <p>This article demonstrates the use of mixed effects <span class="hlt">models</span> for characterizing individual and sample average growth curves based on serial anthropometric data. These <span class="hlt">models</span> are advancement over conventional general linear regression because they effectively handle the hierarchical nature of serial growth data. Using body weight data on 70 infants in the Born in Bradford study, we demonstrate how a mixed effects <span class="hlt">model</span> provides a better fit than a conventional regression <span class="hlt">model</span>. Further, we demonstrate how mixed effects <span class="hlt">models</span> can be used to explore the influence of environmental factors on the sample average growth curve. Analyzing data from 183 infant boys (aged 3-15 months) from rural South India, we show how maternal education shapes infant growth patterns as early as within the first 6 months of life. The presented analyses highlight the utility of mixed effects <span class="hlt">models</span> for analyzing serial growth data because they allow researchers to simultaneously predict individual curves, estimate sample average curves, and investigate the effects of environmental exposure variables. PMID:23283665</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://sandraplancade.perso.math.cnrs.fr/SemStat.pdf','EPRINT'); return false;" href="http://sandraplancade.perso.math.cnrs.fr/SemStat.pdf"><span id="translatedtitle">Data and biological <span class="hlt">model</span> Linear <span class="hlt">model</span> with latent variable</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Nuel, Gregory</p> <p></p> <p>Data and biological <span class="hlt">model</span> Linear <span class="hlt">model</span> with latent variable Results on simulated data Latent for carcinogenesis. #12;Data and biological <span class="hlt">model</span> Linear <span class="hlt">model</span> with latent variable Results on simulated data on gene expression. Latent variable <span class="hlt">model</span> for carcinogenesis. #12;Data and biological <span class="hlt">model</span> Linear <span class="hlt">model</span></p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/21935986','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/21935986"><span id="translatedtitle">Antibody <span class="hlt">modeling</span> assessment.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Almagro, Juan C; Beavers, Mary Pat; Hernandez-Guzman, Francisco; Maier, Johannes; Shaulsky, Jodi; Butenhof, Kenneth; Labute, Paul; Thorsteinson, Nels; Kelly, Kenneth; Teplyakov, Alexey; Luo, Jinquan; Sweet, Raymond; Gilliland, Gary L</p> <p>2011-11-01</p> <p>A blinded study to assess the state of the art in three-dimensional structure <span class="hlt">modeling</span> of the variable region (Fv) of antibodies was conducted. Nine unpublished high-resolution x-ray Fab crystal structures covering a wide range of antigen-binding site conformations were used as benchmark to compare Fv <span class="hlt">models</span> generated by four structure prediction methodologies. The methodologies included two homology <span class="hlt">modeling</span> strategies independently developed by CCG (Chemical Computer Group) and Accerlys Inc, and two fully automated antibody <span class="hlt">modeling</span> servers: PIGS (Prediction of ImmunoGlobulin Structure), based on the canonical structure <span class="hlt">model</span>, and Rosetta Antibody <span class="hlt">Modeling</span>, based on homology <span class="hlt">modeling</span> and Rosetta structure prediction methodology. The benchmark structure sequences were submitted to Accelrys and CCG and a set of <span class="hlt">models</span> for each of the nine antibody structures were generated. PIGS and Rosetta <span class="hlt">models</span> were obtained using the default parameters of the servers. In most cases, we found good agreement between the <span class="hlt">models</span> and x-ray structures. The average rmsd (root mean square deviation) values calculated over the backbone atoms between the <span class="hlt">models</span> and structures were fairly consistent, around 1.2 Å. Average rmsd values of the framework and hypervariable loops with canonical structures (L1, L2, L3, H1, and H2) were close to 1.0 Å. H3 prediction yielded rmsd values around 3.0 Å for most of the <span class="hlt">models</span>. Quality assessment of the <span class="hlt">models</span> and the relative strengths and weaknesses of the methods are discussed. We hope this initiative will serve as a <span class="hlt">model</span> of scientific partnership and look forward to future antibody <span class="hlt">modeling</span> assessments. PMID:21935986</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3775400','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3775400"><span id="translatedtitle"><span class="hlt">Models</span> of Abnormal Scarring</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Seo, Bommie F.; Lee, Jun Yong; Jung, Sung-No</p> <p>2013-01-01</p> <p>Keloids and hypertrophic scars are thick, raised dermal scars, caused by derailing of the normal scarring process. Extensive research on such abnormal scarring has been done; however, these being refractory disorders specific to humans, it has been difficult to establish a universal animal <span class="hlt">model</span>. A wide variety of animal <span class="hlt">models</span> have been used. These include the athymic mouse, rats, rabbits, and pigs. Although these <span class="hlt">models</span> have provided valuable insight into abnormal scarring, there is currently still no ideal <span class="hlt">model</span>. This paper reviews the <span class="hlt">models</span> that have been developed. PMID:24078916</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/6861441','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/6861441"><span id="translatedtitle">CRAC2 <span class="hlt">model</span> description</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Ritchie, L.T.; Alpert, D.J.; Burke, R.P.; Johnson, J.D.; Ostmeyer, R.M.; Aldrich, D.C.; Blond, R.M.</p> <p>1984-03-01</p> <p>The CRAC2 computer code is a revised version of CRAC (Calculation of Reactor Accident Consequences) which was developed for the Reactor Safety Study. This document provides an overview of the CRAC2 code and a description of each of the <span class="hlt">models</span> used. Significant improvements incorporated into CRAC2 include an improved weather sequence sampling technique, a new evacuation <span class="hlt">model</span>, and new output capabilities. In addition, refinements have been made to the atmospheric transport and deposition <span class="hlt">model</span>. Details of the <span class="hlt">modeling</span> differences between CRAC2 and CRAC are emphasized in the <span class="hlt">model</span> descriptions.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/837081','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/837081"><span id="translatedtitle">UZ Colloid Transport <span class="hlt">Model</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>M. McGraw</p> <p>2000-04-13</p> <p>The UZ Colloid Transport <span class="hlt">model</span> development plan states that the objective of this Analysis/<span class="hlt">Model</span> Report (AMR) is to document the development of a <span class="hlt">model</span> for simulating unsaturated colloid transport. This objective includes the following: (1) use of a process level <span class="hlt">model</span> to evaluate the potential mechanisms for colloid transport at Yucca Mountain; (2) Provide ranges of parameters for significant colloid transport processes to Performance Assessment (PA) for the unsaturated zone (UZ); (3) Provide a basis for development of an abstracted <span class="hlt">model</span> for use in PA calculations.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2008capg.book...19M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2008capg.book...19M"><span id="translatedtitle">The FREZCHEM <span class="hlt">Model</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Marion, Giles M.; Kargel, Jeffrey S.</p> <p></p> <p>Implementation of the Pitzer approach is through the FREZCHEM (FREEZING CHEMISTRY) <span class="hlt">model</span>, which is at the core of this work. This <span class="hlt">model</span> was originally designed to simulate salt chemistries and freezing processes at low temperatures (-54 to 25°C) and 1 atm pressure. Over the years, this <span class="hlt">model</span> has been broadened to include more chemistries (from 16 to 58 solid phases), a broader temperature range for some chemistries (to 113°C), and incorporation of a pressure dependence (1 to 1000 bars) into the <span class="hlt">model</span>. Implementation, parameterization, validation, and limitations of the FREZCHEM <span class="hlt">model</span> are extensively discussed in Chapter 3.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2008AEdRv...7b.176F','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2008AEdRv...7b.176F"><span id="translatedtitle">The Milky Way <span class="hlt">Model</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Friedman, Robert Bryan</p> <p></p> <p>In this article, I describe constructing a scale <span class="hlt">model</span> of our galaxy—the Milky Way—and using this <span class="hlt">model</span> to teach modern astronomy. The Milky Way <span class="hlt">model</span> expands on concepts usually explored in the more common solar system <span class="hlt">model</span>. The Milky Way <span class="hlt">model</span> presents an opportunity to probe a broad array of physical processes and astrophysical systems, as well as multiple astronomical coordinate systems and far more expansive spatial scales. This exercise is kinetic, interactive, and designed to be done in large spaces (such as a gymnasium floor) with students at the middle school to high school levels.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4494395','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4494395"><span id="translatedtitle"><span class="hlt">Modelling</span> Farm Animal Welfare</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Collins, Lisa M.; Part, Chérie E.</p> <p>2013-01-01</p> <p>Simple Summary In this review paper we discuss the different <span class="hlt">modeling</span> techniques that have been used in animal welfare research to date. We look at what questions they have been used to answer, the advantages and pitfalls of the methods, and how future research can best use these approaches to answer some of the most important upcoming questions in farm animal welfare. Abstract The use of <span class="hlt">models</span> in the life sciences has greatly expanded in scope and advanced in technique in recent decades. However, the range, type and complexity of <span class="hlt">models</span> used in farm animal welfare is comparatively poor, despite the great scope for use of <span class="hlt">modeling</span> in this field of research. In this paper, we review the different <span class="hlt">modeling</span> approaches used in farm animal welfare science to date, discussing the types of questions they have been used to answer, the merits and problems associated with the method, and possible future applications of each technique. We find that the most frequently published types of <span class="hlt">model</span> used in farm animal welfare are conceptual and assessment <span class="hlt">models</span>; two types of <span class="hlt">model</span> that are frequently (though not exclusively) based on expert opinion. Simulation, optimization, scenario, and systems <span class="hlt">modeling</span> approaches are rarer in animal welfare, despite being commonly used in other related fields. Finally, common issues such as a lack of quantitative data to parameterize <span class="hlt">models</span>, and <span class="hlt">model</span> selection and validation are discussed throughout the review, with possible solutions and alternative approaches suggested. PMID:26487411</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.er.usgs.gov/publication/70048761','USGSPUBS'); return false;" href="http://pubs.er.usgs.gov/publication/70048761"><span id="translatedtitle">A <span class="hlt">model</span> of strength</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Johnson, Douglas H.; Cook, R.D.</p> <p>2013-01-01</p> <p>In her AAAS News & Notes piece "Can the Southwest manage its thirst?" (26 July, p. 362), K. Wren quotes Ajay Kalra, who advocates a particular method for predicting Colorado River streamflow "because it eschews complex physical climate <span class="hlt">models</span> for a statistical data-driven <span class="hlt">modeling</span> approach." A preference for data-driven <span class="hlt">models</span> may be appropriate in this individual situation, but it is not so generally, Data-driven <span class="hlt">models</span> often come with a warning against extrapolating beyond the range of the data used to develop the <span class="hlt">models</span>. When the future is like the past, data-driven <span class="hlt">models</span> can work well for prediction, but it is easy to over-<span class="hlt">model</span> local or transient phenomena, often leading to predictive inaccuracy (1). Mechanistic <span class="hlt">models</span> are built on established knowledge of the process that connects the response variables with the predictors, using information obtained outside of an extant data set. One may shy away from a mechanistic approach when the underlying process is judged to be too complicated, but good predictive <span class="hlt">models</span> can be constructed with statistical components that account for ingredients missing in the mechanistic analysis. <span class="hlt">Models</span> with sound mechanistic components are more generally applicable and robust than data-driven <span class="hlt">models</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/24868511','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/24868511"><span id="translatedtitle">Animal <span class="hlt">models</span> of atherosclerosis.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Kapourchali, Fatemeh Ramezani; Surendiran, Gangadaran; Chen, Li; Uitz, Elisabeth; Bahadori, Babak; Moghadasian, Mohammed H</p> <p>2014-05-16</p> <p>In this mini-review several commonly used animal <span class="hlt">models</span> of atherosclerosis have been discussed. Among them, emphasis has been made on mice, rabbits, pigs and non-human primates. Although these animal <span class="hlt">models</span> have played a significant role in our understanding of induction of atherosclerotic lesions, we still lack a reliable animal <span class="hlt">model</span> for regression of the disease. Researchers have reported several genetically modified and transgenic animal <span class="hlt">models</span> that replicate human atherosclerosis, however each of current animal <span class="hlt">models</span> have some limitations. Among these animal <span class="hlt">models</span>, the apolipoprotein (apo) E-knockout (KO) mice have been used extensively because they develop spontaneous atherosclerosis. Furthermore, atherosclerotic lesions developed in this <span class="hlt">model</span> depending on experimental design may resemble humans' stable and unstable atherosclerotic lesions. This mouse <span class="hlt">model</span> of hypercholesterolemia and atherosclerosis has been also used to investigate the impact of oxidative stress and inflammation on atherogenesis. Low density lipoprotein (LDL)-r-KO mice are a <span class="hlt">model</span> of human familial hypercholesterolemia. However, unlike apo E-KO mice, the LDL-r-KO mice do not develop spontaneous atherosclerosis. Both apo E-KO and LDL-r-KO mice have been employed to generate other relevant mouse <span class="hlt">models</span> of cardiovascular disease through breeding strategies. In addition to mice, rabbits have been used extensively particularly to understand the mechanisms of cholesterol-induced atherosclerosis. The present review paper details the characteristics of animal <span class="hlt">models</span> that are used in atherosclerosis research. PMID:24868511</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4023305','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4023305"><span id="translatedtitle">Animal <span class="hlt">models</span> of atherosclerosis</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Kapourchali, Fatemeh Ramezani; Surendiran, Gangadaran; Chen, Li; Uitz, Elisabeth; Bahadori, Babak; Moghadasian, Mohammed H</p> <p>2014-01-01</p> <p>In this mini-review several commonly used animal <span class="hlt">models</span> of atherosclerosis have been discussed. Among them, emphasis has been made on mice, rabbits, pigs and non-human primates. Although these animal <span class="hlt">models</span> have played a significant role in our understanding of induction of atherosclerotic lesions, we still lack a reliable animal <span class="hlt">model</span> for regression of the disease. Researchers have reported several genetically modified and transgenic animal <span class="hlt">models</span> that replicate human atherosclerosis, however each of current animal <span class="hlt">models</span> have some limitations. Among these animal <span class="hlt">models</span>, the apolipoprotein (apo) E-knockout (KO) mice have been used extensively because they develop spontaneous atherosclerosis. Furthermore, atherosclerotic lesions developed in this <span class="hlt">model</span> depending on experimental design may resemble humans’ stable and unstable atherosclerotic lesions. This mouse <span class="hlt">model</span> of hypercholesterolemia and atherosclerosis has been also used to investigate the impact of oxidative stress and inflammation on atherogenesis. Low density lipoprotein (LDL)-r-KO mice are a <span class="hlt">model</span> of human familial hypercholesterolemia. However, unlike apo E-KO mice, the LDL-r-KO mice do not develop spontaneous atherosclerosis. Both apo E-KO and LDL-r-KO mice have been employed to generate other relevant mouse <span class="hlt">models</span> of cardiovascular disease through breeding strategies. In addition to mice, rabbits have been used extensively particularly to understand the mechanisms of cholesterol-induced atherosclerosis. The present review paper details the characteristics of animal <span class="hlt">models</span> that are used in atherosclerosis research. PMID:24868511</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/837619','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/837619"><span id="translatedtitle">Calibrated Properties <span class="hlt">Model</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>T. Ghezzehej</p> <p>2004-10-04</p> <p>The purpose of this <span class="hlt">model</span> report is to document the calibrated properties <span class="hlt">model</span> that provides calibrated property sets for unsaturated zone (UZ) flow and transport process <span class="hlt">models</span> (UZ <span class="hlt">models</span>). The calibration of the property sets is performed through inverse <span class="hlt">modeling</span>. This work followed, and was planned in, ''Technical Work Plan (TWP) for: Unsaturated Zone Flow Analysis and <span class="hlt">Model</span> Report Integration'' (BSC 2004 [DIRS 169654], Sections 1.2.6 and 2.1.1.6). Direct inputs to this <span class="hlt">model</span> report were derived from the following upstream analysis and <span class="hlt">model</span> reports: ''Analysis of Hydrologic Properties Data'' (BSC 2004 [DIRS 170038]); ''Development of Numerical Grids for UZ Flow and Transport <span class="hlt">Modeling</span>'' (BSC 2004 [DIRS 169855]); ''Simulation of Net Infiltration for Present-Day and Potential Future Climates'' (BSC 2004 [DIRS 170007]); ''Geologic Framework <span class="hlt">Model</span>'' (GFM2000) (BSC 2004 [DIRS 170029]). Additionally, this <span class="hlt">model</span> report incorporates errata of the previous version and closure of the Key Technical Issue agreement TSPAI 3.26 (Section 6.2.2 and Appendix B), and it is revised for improved transparency.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20100033609','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20100033609"><span id="translatedtitle">TEAMS <span class="hlt">Model</span> Analyzer</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Tijidjian, Raffi P.</p> <p>2010-01-01</p> <p>The TEAMS <span class="hlt">model</span> analyzer is a supporting tool developed to work with <span class="hlt">models</span> created with TEAMS (Testability, Engineering, and Maintenance System), which was developed by QSI. In an effort to reduce the time spent in the manual process that each TEAMS <span class="hlt">modeler</span> must perform in the preparation of reporting for <span class="hlt">model</span> reviews, a new tool has been developed as an aid to <span class="hlt">models</span> developed in TEAMS. The software allows for the viewing, reporting, and checking of TEAMS <span class="hlt">models</span> that are checked into the TEAMS <span class="hlt">model</span> database. The software allows the user to selectively <span class="hlt">model</span> in a hierarchical tree outline view that displays the components, failure modes, and ports. The reporting features allow the user to quickly gather statistics about the <span class="hlt">model</span>, and generate an input/output report pertaining to all of the components. Rules can be automatically validated against the <span class="hlt">model</span>, with a report generated containing resulting inconsistencies. In addition to reducing manual effort, this software also provides an automated process framework for the Verification and Validation (V&V) effort that will follow development of these <span class="hlt">models</span>. The aid of such an automated tool would have a significant impact on the V&V process.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/942055','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/942055"><span id="translatedtitle">Foam process <span class="hlt">models</span>.</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Moffat, Harry K.; Noble, David R.; Baer, Thomas A.; Adolf, Douglas Brian; Rao, Rekha Ranjana; Mondy, Lisa Ann</p> <p>2008-09-01</p> <p>In this report, we summarize our work on developing a production level foam processing computational <span class="hlt">model</span> suitable for predicting the self-expansion of foam in complex geometries. The <span class="hlt">model</span> is based on a finite element representation of the equations of motion, with the movement of the free surface represented using the level set method, and has been implemented in SIERRA/ARIA. An empirically based time- and temperature-dependent density <span class="hlt">model</span> is used to encapsulate the complex physics of foam nucleation and growth in a numerically tractable <span class="hlt">model</span>. The change in density with time is at the heart of the foam self-expansion as it creates the motion of the foam. This continuum-level <span class="hlt">model</span> uses an homogenized description of foam, which does not include the gas explicitly. Results from the <span class="hlt">model</span> are compared to temperature-instrumented flow visualization experiments giving the location of the foam front as a function of time for our EFAR <span class="hlt">model</span> system.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://ntrs.nasa.gov/search.jsp?R=20080002263&hterms=scientific+community&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D30%26Ntt%3Dscientific%2Bcommunity','NASA-TRS'); return false;" href="http://ntrs.nasa.gov/search.jsp?R=20080002263&hterms=scientific+community&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D30%26Ntt%3Dscientific%2Bcommunity"><span id="translatedtitle">Toward Scientific Numerical <span class="hlt">Modeling</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Kleb, Bil</p> <p>2007-01-01</p> <p>Ultimately, scientific numerical <span class="hlt">models</span> need quantified output uncertainties so that <span class="hlt">modeling</span> can evolve to better match reality. Documenting <span class="hlt">model</span> input uncertainties and verifying that numerical <span class="hlt">models</span> are translated into code correctly, however, are necessary first steps toward that goal. Without known input parameter uncertainties, <span class="hlt">model</span> sensitivities are all one can determine, and without code verification, output uncertainties are simply not reliable. To address these two shortcomings, two proposals are offered: (1) an unobtrusive mechanism to document input parameter uncertainties in situ and (2) an adaptation of the Scientific Method to numerical <span class="hlt">model</span> development and deployment. Because these two steps require changes in the computational simulation community to bear fruit, they are presented in terms of the Beckhard-Harris-Gleicher change <span class="hlt">model</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://cds.cern.ch/record/977465/files/0608184.pdf','EPRINT'); return false;" href="http://cds.cern.ch/record/977465/files/0608184.pdf"><span id="translatedtitle">Cosmological <span class="hlt">model</span> selection</span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Liddle, A R; Parkinson, D; Liddle, Andrew R.; Mukherjee, Pia; Parkinson, David</p> <p>2006-01-01</p> <p><span class="hlt">Model</span> selection aims to determine which theoretical <span class="hlt">models</span> are most plausible given some data, without necessarily asking about the preferred values of the <span class="hlt">model</span> parameters. A common <span class="hlt">model</span> selection question is to ask when new data require introduction of an additional parameter, describing a newly-discovered physical effect. We review several <span class="hlt">model</span> selection statistics, and then focus on use of the Bayesian evidence, which implements the usual Bayesian analysis framework at the level of <span class="hlt">models</span> rather than parameters. We describe our CosmoNest code, which is the first computationally-efficient implementation of Bayesian <span class="hlt">model</span> selection in a cosmological context. We apply it to recent WMAP satellite data, examining the need for a perturbation spectral index differing from the scale-invariant (Harrison-Zel'dovich) case.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li class="active"><span>24</span></li> <li><a href="#" onclick='return showDiv("page_25");'>25</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_24 --> <div id="page_25" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li class="active"><span>25</span></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="481"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2010paoc.book...87H','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2010paoc.book...87H"><span id="translatedtitle">Multiscale <span class="hlt">Modeling</span>: A Review</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Horstemeyer, M. F.</p> <p></p> <p>This review of multiscale <span class="hlt">modeling</span> covers a brief history of various multiscale methodologies related to solid materials and the associated experimental influences, the various influence of multiscale <span class="hlt">modeling</span> on different disciplines, and some examples of multiscale <span class="hlt">modeling</span> in the design of structural components. Although computational multiscale <span class="hlt">modeling</span> methodologies have been developed in the late twentieth century, the fundamental notions of multiscale <span class="hlt">modeling</span> have been around since da Vinci studied different sizes of ropes. The recent rapid growth in multiscale <span class="hlt">modeling</span> is the result of the confluence of parallel computing power, experimental capabilities to characterize structure-property relations down to the atomic level, and theories that admit multiple length scales. The ubiquitous research that focus on multiscale <span class="hlt">modeling</span> has broached different disciplines (solid mechanics, fluid mechanics, materials science, physics, mathematics, biological, and chemistry), different regions of the world (most continents), and different length scales (from atoms to autos).</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/899287','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/899287"><span id="translatedtitle">Ventilation <span class="hlt">Model</span> Report</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>V. Chipman; J. Case</p> <p>2002-12-20</p> <p>The purpose of the Ventilation <span class="hlt">Model</span> is to simulate the heat transfer processes in and around waste emplacement drifts during periods of forced ventilation. The <span class="hlt">model</span> evaluates the effects of emplacement drift ventilation on the thermal conditions in the emplacement drifts and surrounding rock mass, and calculates the heat removal by ventilation as a measure of the viability of ventilation to delay the onset of peak repository temperature and reduce its magnitude. The heat removal by ventilation is temporally and spatially dependent, and is expressed as the fraction of heat carried away by the ventilation air compared to the fraction of heat produced by radionuclide decay. One minus the heat removal is called the wall heat fraction, or the remaining amount of heat that is transferred via conduction to the surrounding rock mass. Downstream <span class="hlt">models</span>, such as the ''Multiscale Thermohydrologic <span class="hlt">Model</span>'' (BSC 2001), use the wall heat fractions as outputted from the Ventilation <span class="hlt">Model</span> to initialize their post-closure analyses. The Ventilation <span class="hlt">Model</span> report was initially developed to analyze the effects of preclosure continuous ventilation in the Engineered Barrier System (EBS) emplacement drifts, and to provide heat removal data to support EBS design. Revision 00 of the Ventilation <span class="hlt">Model</span> included documentation of the <span class="hlt">modeling</span> results from the ANSYS-based heat transfer <span class="hlt">model</span>. Revision 01 ICN 01 included the results of the unqualified software code MULTIFLUX to assess the influence of moisture on the ventilation efficiency. The purposes of Revision 02 of the Ventilation <span class="hlt">Model</span> are: (1) To validate the conceptual <span class="hlt">model</span> for preclosure ventilation of emplacement drifts and verify its numerical application in accordance with new procedural requirements as outlined in AP-SIII-10Q, <span class="hlt">Models</span> (Section 7.0). (2) To satisfy technical issues posed in KTI agreement RDTME 3.14 (Reamer and Williams 2001a). Specifically to demonstrate, with respect to the ANSYS ventilation <span class="hlt">model</span>, the adequacy of the discretization (Section 6.2.3.1), and the downstream applicability of the <span class="hlt">model</span> results (i.e. wall heat fractions) to initialize post-closure thermal <span class="hlt">models</span> (Section 6.6). (3) To satisfy the remainder of KTI agreement TEF 2.07 (Reamer and Williams 2001b). Specifically to provide the results of post-test ANSYS <span class="hlt">modeling</span> of the Atlas Facility forced convection tests (Section 7.1.2). This portion of the <span class="hlt">model</span> report also serves as a validation exercise per AP-SIII.10Q, <span class="hlt">Models</span>, for the ANSYS ventilation <span class="hlt">model</span>. (4) To asses the impacts of moisture on the ventilation efficiency.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=pickles&pg=6&id=EJ736619','ERIC'); return false;" href="http://eric.ed.gov/?q=pickles&pg=6&id=EJ736619"><span id="translatedtitle">Generalized Multilevel Structural Equation <span class="hlt">Modeling</span></span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Rabe-Hesketh, Sophia; Skrondal, Anders; Pickles, Andrew</p> <p>2004-01-01</p> <p>A unifying framework for generalized multilevel structural equation <span class="hlt">modeling</span> is introduced. The <span class="hlt">models</span> in the framework, called generalized linear latent and mixed <span class="hlt">models</span> (GLLAMM), combine features of generalized linear mixed <span class="hlt">models</span> (GLMM) and structural equation <span class="hlt">models</span> (SEM) and consist of a response <span class="hlt">model</span> and a structural <span class="hlt">model</span> for the latent…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/945916','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/945916"><span id="translatedtitle">Constitutive <span class="hlt">models</span> in LAME.</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Hammerand, Daniel Carl; Scherzinger, William Mark</p> <p>2007-09-01</p> <p>The Library of Advanced Materials for Engineering (LAME) provides a common repository for constitutive <span class="hlt">models</span> that can be used in computational solid mechanics codes. A number of <span class="hlt">models</span> including both hypoelastic (rate) and hyperelastic (total strain) constitutive forms have been implemented in LAME. The structure and testing of LAME is described in Scherzinger and Hammerand ([3] and [4]). The purpose of the present report is to describe the material <span class="hlt">models</span> which have already been implemented into LAME. The descriptions are designed to give useful information to both analysts and code developers. Thus far, 33 non-ITAR/non-CRADA protected material <span class="hlt">models</span> have been incorporated. These include everything from the simple isotropic linear elastic <span class="hlt">models</span> to a number of elastic-plastic <span class="hlt">models</span> for metals to <span class="hlt">models</span> for honeycomb, foams, potting epoxies and rubber. A complete description of each <span class="hlt">model</span> is outside the scope of the current report. Rather, the aim here is to delineate the properties, state variables, functions, and methods for each <span class="hlt">model</span>. However, a brief description of some of the constitutive details is provided for a number of the material <span class="hlt">models</span>. Where appropriate, the SAND reports available for each <span class="hlt">model</span> have been cited. Many <span class="hlt">models</span> have state variable aliases for some or all of their state variables. These alias names can be used for outputting desired quantities. The state variable aliases available for results output have been listed in this report. However, not all <span class="hlt">models</span> use these aliases. For those <span class="hlt">models</span>, no state variable names are listed. Nevertheless, the number of state variables employed by each <span class="hlt">model</span> is always given. Currently, there are four possible functions for a material <span class="hlt">model</span>. This report lists which of these four methods are employed in each material <span class="hlt">model</span>. As far as analysts are concerned, this information is included only for the awareness purposes. The analyst can take confidence in the fact that <span class="hlt">model</span> has been properly implemented and the methods necessary for achieving accurate and efficient solutions have been incorporated. The most important method is the getStress function where the actual material <span class="hlt">model</span> evaluation takes place. Obviously, all material <span class="hlt">models</span> incorporate this function. The initialize function is included in most material <span class="hlt">models</span>. The initialize function is called once at the beginning of an analysis and its primary purpose is to initialize the material state variables associated with the <span class="hlt">model</span>. Many times, there is some information which can be set once per load step. For instance, we may have temperature dependent material properties in an analysis where temperature is prescribed. Instead of setting those parameters at each iteration in a time step, it is much more efficient to set them once per time step at the beginning of the step. These types of load step initializations are performed in the loadStepInit method. The final function used by many <span class="hlt">models</span> is the pcElasticModuli method which changes the moduli that are to be used by the elastic preconditioner in Adagio. The moduli for the elastic preconditioner are set during the initialization of Adagio. Sometimes, better convergence can be achieved by changing these moduli for the elastic preconditioner. For instance, it typically helps to modify the preconditioner when the material <span class="hlt">model</span> has temperature dependent moduli. For many material <span class="hlt">models</span>, it is not necessary to change the values of the moduli that are set initially in the code. Hence, those <span class="hlt">models</span> do not have pcElasticModuli functions. All four of these methods receive information from the matParams structure as described by Scherzinger and Hammerand.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/10158402','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/10158402"><span id="translatedtitle">Preliminary DIAL <span class="hlt">model</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Gentry, S.; Taylor, J.; Stephenson, D.</p> <p>1994-06-01</p> <p>A unique end-to-end LIDAR sensor <span class="hlt">model</span> has been developed supporting the concept development stage of the CALIOPE UV DIAL and UV laser-induced-fluorescence (LIF) efforts. The <span class="hlt">model</span> focuses on preserving the temporal and spectral nature of signals as they pass through the atmosphere, are collected by the optics, detected by the sensor, and processed by the sensor electronics and algorithms. This is done by developing accurate component sub-<span class="hlt">models</span> with realistic inputs and outputs, as well as internal noise sources and operating parameters. These sub-<span class="hlt">models</span> are then configured using data-flow diagrams to operate together to reflect the performance of the entire DIAL system. This <span class="hlt">modeling</span> philosophy allows the developer to have a realistic indication of the nature of signals throughout the system and to design components and processing in a realistic environment. Current component <span class="hlt">models</span> include atmospheric absorption and scattering losses, plume absorption and scattering losses, background, telescope and optical filter <span class="hlt">models</span>, PMT (photomultiplier tube) with realistic noise sources, amplifier operation and noise, A/D converter operation, noise and distortion, pulse averaging, and DIAL computation. Preliminary results of the <span class="hlt">model</span> will be presented indicating the expected <span class="hlt">model</span> operation depicting the October field test at the NTS spill test facility. Indications will be given concerning near-term upgrades to the <span class="hlt">model</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26487411','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26487411"><span id="translatedtitle"><span class="hlt">Modelling</span> Farm Animal Welfare.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Collins, Lisa M; Part, Chérie E</p> <p>2013-01-01</p> <p>The use of <span class="hlt">models</span> in the life sciences has greatly expanded in scope and advanced in technique in recent decades. However, the range, type and complexity of <span class="hlt">models</span> used in farm animal welfare is comparatively poor, despite the great scope for use of <span class="hlt">modeling</span> in this field of research. In this paper, we review the different <span class="hlt">modeling</span> approaches used in farm animal welfare science to date, discussing the types of questions they have been used to answer, the merits and problems associated with the method, and possible future applications of each technique. We find that the most frequently published types of <span class="hlt">model</span> used in farm animal welfare are conceptual and assessment <span class="hlt">models</span>; two types of <span class="hlt">model</span> that are frequently (though not exclusively) based on expert opinion. Simulation, optimization, scenario, and systems <span class="hlt">modeling</span> approaches are rarer in animal welfare, despite being commonly used in other related fields. Finally, common issues such as a lack of quantitative data to parameterize <span class="hlt">models</span>, and <span class="hlt">model</span> selection and validation are discussed throughout the review, with possible solutions and alternative approaches suggested. PMID:26487411</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20030093737','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20030093737"><span id="translatedtitle">The Earth System <span class="hlt">Model</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Schoeberl, Mark; Rood, Richard B.; Hildebrand, Peter; Raymond, Carol</p> <p>2003-01-01</p> <p>The Earth System <span class="hlt">Model</span> is the natural evolution of current climate <span class="hlt">models</span> and will be the ultimate embodiment of our geophysical understanding of the planet. These <span class="hlt">models</span> are constructed from components - atmosphere, ocean, ice, land, chemistry, solid earth, etc. <span class="hlt">models</span> and merged together through a coupling program which is responsible for the exchange of data from the components. Climate <span class="hlt">models</span> and future earth system <span class="hlt">models</span> will have standardized modules, and these standards are now being developed by the ESMF project funded by NASA. The Earth System <span class="hlt">Model</span> will have a variety of uses beyond climate prediction. The <span class="hlt">model</span> can be used to build climate data records making it the core of an assimilation system, and it can be used in OSSE experiments to evaluate. The computing and storage requirements for the ESM appear to be daunting. However, the Japanese ES theoretical computing capability is already within 20% of the minimum requirements needed for some 2010 climate <span class="hlt">model</span> applications. Thus it seems very possible that a focused effort to build an Earth System <span class="hlt">Model</span> will achieve succcss.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/6311070','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/6311070"><span id="translatedtitle">Geochemical <span class="hlt">modeling</span>: a review</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Jenne, E.A.</p> <p>1981-06-01</p> <p>Two general families of geochemical <span class="hlt">models</span> presently exist. The ion speciation-solubility group of geochemical <span class="hlt">models</span> contain submodels to first calculate a distribution of aqueous species and to secondly test the hypothesis that the water is near equilibrium with particular solid phases. These <span class="hlt">models</span> may or may not calculate the adsorption of dissolved constituents and simulate the dissolution and precipitation (mass transfer) of solid phases. Another family of geochemical <span class="hlt">models</span>, the reaction path <span class="hlt">models</span>, simulates the stepwise precipitation of solid phases as a result of reacting specified amounts of water and rock. Reaction path <span class="hlt">models</span> first perform an aqueous speciation of the dissolved constituents of the water, test solubility hypotheses, then perform the reaction path <span class="hlt">modeling</span>. Certain improvements in the present versions of these <span class="hlt">models</span> would enhance their value and usefulness to applications in nuclear-waste isolation, etc. Mass-transfer calculations of limited extent are certainly within the capabilities of state-of-the-art <span class="hlt">models</span>. However, the reaction path <span class="hlt">models</span> require an expansion of their thermodynamic data bases and systematic validation before they are generally accepted.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/2637154','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/2637154"><span id="translatedtitle">Risk <span class="hlt">modelling</span>: which <span class="hlt">models</span> to choose?</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Csicsaky, M J; Roller, M; Pott, F</p> <p>1989-01-01</p> <p>Using as examples excess lung cancer mortality in coke oven workers and lung tumor induction in rats by inhalation of diesel engine emissions or cadmium chloride aerosol, the maximum likelihood estimate and the upper limit of risk were determined using a set of conventional risk <span class="hlt">models</span>. The additional safety offered by going to the upper limit of the 95% confidence interval when deriving a unit risk value was found to be less than a factor of 5 in all but one case, and usually much less than 2. It is concluded that the selection of an adequate <span class="hlt">model</span> is the most critical step in risk assessment, and that an additional safety factor may be required to allow for a better protection of the public in case <span class="hlt">models</span> other than the most conservative ones come into use. PMID:2637154</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.er.usgs.gov/publication/70015294','USGSPUBS'); return false;" href="http://pubs.er.usgs.gov/publication/70015294"><span id="translatedtitle">Molecular orbital (SCF-X?-SW) theory of metal-metal charge transfer processes in minerals</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Sherman, David M.</p> <p>1987-01-01</p> <p>Electronic transitions between the <span class="hlt">Fe-Fe</span> bonding and <span class="hlt">Fe-Fe</span> antibonding orbitals results in the optically-induced intervalence charge transfer bands observed in the electronic spectra of mixed valence minerals. Such transitions are predicted to be polarized along the metal-metal bond direction, in agreement with experimental observations.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=fefe&id=EJ762663','ERIC'); return false;" href="http://eric.ed.gov/?q=fefe&id=EJ762663"><span id="translatedtitle">Private Sector/Educator Collaboration: Project Improves Financial, Economic Literacy of America's Youth</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Haynes, Deborah C.; Chinadle, Nicole</p> <p>2007-01-01</p> <p>The Family Economics and Financial Education Project (<span class="hlt">FEFE</span>) began in 2001 at Montana State University with an annual grant from Take Charge America, Inc., a credit counseling and debt management company headquartered in Phoenix, Arizona. <span class="hlt">FEFE</span>'s mission is to provide educators with curriculum materials and training to be effective teachers of…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://selab.netlab.uky.edu/homepage/publications/April%20Huffman%20Abran%20Dumke%20Journal%202005.pdf','EPRINT'); return false;" href="http://selab.netlab.uky.edu/homepage/publications/April%20Huffman%20Abran%20Dumke%20Journal%202005.pdf"><span id="translatedtitle">Software Maintenance Maturity <span class="hlt">Model</span> (SMmm The software maintenance process <span class="hlt">model</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/eprints/">E-print Network</a></p> <p>Hayes, Jane E.</p> <p></p> <p>Software Maintenance Maturity <span class="hlt">Model</span> (SMmm ): The software maintenance process <span class="hlt">model</span> Alain April1 improvements to the software maintenance standards and introducing a proposed maturity <span class="hlt">model</span> for daily software maintenance activities: Software Maintenance Maturity <span class="hlt">Model</span> (SMmm ). The software maintenance function suffers</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20070006516','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20070006516"><span id="translatedtitle">Radiation Environment <span class="hlt">Modeling</span> for Spacecraft Design: New <span class="hlt">Model</span> Developments</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Barth, Janet; Xapsos, Mike; Lauenstein, Jean-Marie; Ladbury, Ray</p> <p>2006-01-01</p> <p>A viewgraph presentation on various new space radiation environment <span class="hlt">models</span> for spacecraft design is described. The topics include: 1) The Space Radiatio Environment; 2) Effects of Space Environments on Systems; 3) Space Radiatio Environment <span class="hlt">Model</span> Use During Space Mission Development and Operations; 4) Space Radiation Hazards for Humans; 5) "Standard" Space Radiation Environment <span class="hlt">Models</span>; 6) Concerns about Standard <span class="hlt">Models</span>; 7) Inadequacies of Current <span class="hlt">Models</span>; 8) Development of New <span class="hlt">Models</span>; 9) New <span class="hlt">Model</span> Developments: Proton Belt <span class="hlt">Models</span>; 10) Coverage of New Proton <span class="hlt">Models</span>; 11) Comparison of TPM-1, PSB97, AP-8; 12) New <span class="hlt">Model</span> Developments: Electron Belt <span class="hlt">Models</span>; 13) Coverage of New Electron <span class="hlt">Models</span>; 14) Comparison of "Worst Case" POLE, CRESELE, and FLUMIC <span class="hlt">Models</span> with the AE-8 <span class="hlt">Model</span>; 15) New <span class="hlt">Model</span> Developments: Galactic Cosmic Ray <span class="hlt">Model</span>; 16) Comparison of NASA, MSU, CIT <span class="hlt">Models</span> with ACE Instrument Data; 17) New <span class="hlt">Model</span> Developmemts: Solar Proton <span class="hlt">Model</span>; 18) Comparison of ESP, JPL91, KIng/Stassinopoulos, and PSYCHIC <span class="hlt">Models</span>; 19) New <span class="hlt">Model</span> Developments: Solar Heavy Ion <span class="hlt">Model</span>; 20) Comparison of CREME96 to CREDO Measurements During 2000 and 2002; 21) PSYCHIC Heavy ion <span class="hlt">Model</span>; 22) <span class="hlt">Model</span> Standardization; 23) Working Group Meeting on New Standard Radiation Belt and Space Plasma <span class="hlt">Models</span>; and 24) Summary.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/19850021674','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/19850021674"><span id="translatedtitle">Outside users payload <span class="hlt">model</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p></p> <p>1985-01-01</p> <p>The outside users payload <span class="hlt">model</span> which is a continuation of documents and replaces and supersedes the July 1984 edition is presented. The time period covered by this <span class="hlt">model</span> is 1985 through 2000. The following sections are included: (1) definition of the scope of the <span class="hlt">model</span>; (2) discussion of the methodology used; (3) overview of total demand; (4) summary of the estimated market segmentation by launch vehicle; (5) summary of the estimated market segmentation by user type; (6) details of the STS market forecast; (7) summary of transponder trends; (8) <span class="hlt">model</span> overview by mission category; and (9) detailed mission <span class="hlt">models</span>. All known non-NASA, non-DOD reimbursable payloads forecast to be flown by non-Soviet-block countries are included in this <span class="hlt">model</span> with the exception of Spacelab payloads and small self contained payloads. Certain DOD-sponsored or cosponsored payloads are included if they are reimbursable launches.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/44909','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/44909"><span id="translatedtitle">Carcinogenesis <span class="hlt">models</span>: An overview</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Moolgavkar, S.H.</p> <p>1992-12-31</p> <p>Biologically based mathematical <span class="hlt">models</span> of carcinogenesis are not only an essential part of a rational approach to quantitative cancer risk assessment but also raise fundamental questions about the nature of the events leading to malignancy. In this paper two such <span class="hlt">models</span> are reviewed. The first is the multistage <span class="hlt">model</span> proposed by Armitage and Doll in the 1950s; most of the paper is devoted to a discussion of the two-mutation <span class="hlt">model</span> proposed by the author and his colleagues. This <span class="hlt">model</span> is a generalization of the idea of recessive oncogenesis proposed by Knudson and has been shown to be consistent with a large body of epidemiologic and experimental data. The usefulness of the <span class="hlt">model</span> is illustrated by analyzing a large experimental data set in which rats exposed to radon developed malignant lung tumors.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/5222322','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/5222322"><span id="translatedtitle"><span class="hlt">Models</span> for poloidal divertors</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Post, D.E.; Heifetz, D.; Petravic, M.</p> <p>1982-07-01</p> <p>Recent progress in <span class="hlt">models</span> for poloidal divertors has both helped to explain current divertor experiments and contributed significantly to design efforts for future large tokamak (INTOR, etc.) divertor systems. These <span class="hlt">models</span> range in sophistication from zero-dimensional treatments and dimensional analysis to two-dimensional <span class="hlt">models</span> for plasma and neutral particle transport which include a wide variety of atomic and molecular processes as well as detailed treatments of the plasma-wall interaction. This paper presents a brief review of some of these <span class="hlt">models</span>, describing the physics and approximations involved in each <span class="hlt">model</span>. We discuss the wide variety of physics necessary for a comprehensive description of poloidal divertors. To illustrate the progress in <span class="hlt">models</span> for poloidal divertors, we discuss some of our recent work as typical examples of the kinds of calculations being done.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://ntrs.nasa.gov/search.jsp?R=19820032405&hterms=climate+energy&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D20%26Ntt%3Dclimate%2Benergy','NASA-TRS'); return false;" href="http://ntrs.nasa.gov/search.jsp?R=19820032405&hterms=climate+energy&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D20%26Ntt%3Dclimate%2Benergy"><span id="translatedtitle">Energy balance climate <span class="hlt">models</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>North, G. R.; Cahalan, R. F.; Coakley, J. A., Jr.</p> <p>1981-01-01</p> <p>An introductory survey of the global energy balance climate <span class="hlt">models</span> is presented with an emphasis on analytical results. A sequence of increasingly complicated <span class="hlt">models</span> involving ice cap and radiative feedback processes are solved, and the solutions and parameter sensitivities are studied. The <span class="hlt">model</span> parameterizations are examined critically in light of many current uncertainties. A simple seasonal <span class="hlt">model</span> is used to study the effects of changes in orbital elements on the temperature field. A linear stability theorem and a complete nonlinear stability analysis for the <span class="hlt">models</span> are developed. Analytical solutions are also obtained for the linearized <span class="hlt">models</span> driven by stochastic forcing elements. In this context the relation between natural fluctuation statistics and climate sensitivity is stressed.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/19970016840','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/19970016840"><span id="translatedtitle">Probabilistic Mesomechanical Fatigue <span class="hlt">Model</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Tryon, Robert G.</p> <p>1997-01-01</p> <p>A probabilistic mesomechanical fatigue life <span class="hlt">model</span> is proposed to link the microstructural material heterogeneities to the statistical scatter in the macrostructural response. The macrostructure is <span class="hlt">modeled</span> as an ensemble of microelements. Cracks nucleation within the microelements and grow from the microelements to final fracture. Variations of the microelement properties are defined using statistical parameters. A micromechanical slip band decohesion <span class="hlt">model</span> is used to determine the crack nucleation life and size. A crack tip opening displacement <span class="hlt">model</span> is used to determine the small crack growth life and size. Paris law is used to determine the long crack growth life. The <span class="hlt">models</span> are combined in a Monte Carlo simulation to determine the statistical distribution of total fatigue life for the macrostructure. The <span class="hlt">modeled</span> response is compared to trends in experimental observations from the literature.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/19810011550','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/19810011550"><span id="translatedtitle">Extended frequency turbofan <span class="hlt">model</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Mason, J. R.; Park, J. W.; Jaekel, R. F.</p> <p>1980-01-01</p> <p>The fan <span class="hlt">model</span> was developed using two dimensional <span class="hlt">modeling</span> techniques to add dynamic radial coupling between the core stream and the bypass stream of the fan. When incorporated into a complete TF-30 engine simulation, the fan <span class="hlt">model</span> greatly improved compression system frequency response to planar inlet pressure disturbances up to 100 Hz. The improved simulation also matched engine stability limits at 15 Hz, whereas the one dimensional fan <span class="hlt">model</span> required twice the inlet pressure amplitude to stall the simulation. With verification of the two dimensional fan <span class="hlt">model</span>, this program formulated a high frequency F-100(3) engine simulation using row by row compression system characteristics. In addition to the F-100(3) remote splitter fan, the program modified the <span class="hlt">model</span> fan characteristics to simulate a proximate splitter version of the F-100(3) engine.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/567504','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/567504"><span id="translatedtitle">Solid <span class="hlt">model</span> design simplification</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Ames, A.L.; Rivera, J.J.; Webb, A.J.; Hensinger, D.M.</p> <p>1997-12-01</p> <p>This paper documents an investigation of approaches to improving the quality of Pro/Engineer-created solid <span class="hlt">model</span> data for use by downstream applications. The investigation identified a number of sources of problems caused by deficiencies in Pro/Engineer`s geometric engine, and developed prototype software capable of detecting many of these problems and guiding users towards simplified, useable <span class="hlt">models</span>. The prototype software was tested using Sandia production solid <span class="hlt">models</span>, and provided significant leverage in attacking the simplification problem.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li class="active"><span>25</span></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_25 --> <center> <div class="footer-extlink text-muted"><small>Some links on this page may take you to non-federal websites. Their policies may differ from this site.</small> </div> </center> <div id="footer-wrapper"> <div class="footer-content"> <div id="footerOSTI" class=""> <div class="row"> <div class="col-md-4 text-center col-md-push-4 footer-content-center"><small><a href="http://www.science.gov/disclaimer.html">Privacy and Security</a></small> <div class="visible-sm visible-xs push_footer"></div> </div> <div class="col-md-4 text-center col-md-pull-4 footer-content-left"> <img src="http://www.osti.gov/images/DOE_SC31.png" alt="U.S. Department of Energy" usemap="#doe" height="31" width="177"><map style="display:none;" name="doe" id="doe"><area shape="rect" coords="1,3,107,30" href="http://www.energy.gov" alt="U.S. Deparment of Energy"><area shape="rect" coords="114,3,165,30" href="http://www.science.energy.gov" alt="Office of Science"></map> <a ref="http://www.osti.gov" style="margin-left: 15px;"><img src="http://www.osti.gov/images/footerimages/ostigov53.png" alt="Office of Scientific and Technical Information" height="31" width="53"></a> <div class="visible-sm visible-xs push_footer"></div> </div> <div class="col-md-4 text-center footer-content-right"> <a href="http://www.osti.gov/nle"><img src="http://www.osti.gov/images/footerimages/NLElogo31.png" alt="National Library of Energy" height="31" width="79"></a> <a href="http://www.science.gov"><img src="http://www.osti.gov/images/footerimages/scigov77.png" alt="science.gov" height="31" width="98"></a> <a href="http://worldwidescience.org"><img src="http://www.osti.gov/images/footerimages/wws82.png" alt="WorldWideScience.org" height="31" width="90"></a> </div> </div> </div> </div> </div> <p><br></p> </div><!-- container --> </body> </html>